diff options
272 files changed, 28275 insertions, 6745 deletions
diff --git a/README.md b/README.md new file mode 100644 index 0000000..ec86136 --- /dev/null +++ b/README.md @@ -0,0 +1,82 @@ +# The ASTRA Toolbox + +The ASTRA Toolbox is a MATLAB toolbox of high-performance GPU primitives for 2D and 3D tomography. + +We support 2D parallel and fan beam geometries, and 3D parallel and cone beam. All of them have highly flexible source/detector positioning. + +A large number of 2D and 3D algorithms are available, including FBP, SIRT, SART, CGLS. + +The basic forward and backward projection operations are GPU-accelerated, and directly callable from MATLAB to enable building new algorithms. + + + +## Documentation / samples + +See the matlab code samples in samples/ and on http://sf.net/projects/astra-toolbox . + + +## Installation instructions + +### Windows, binary + +Add the mex and tools subdirectories to your matlab path. + +### Linux, from source + +Requirements: g++, boost, CUDA (driver+toolkit), matlab + +``` +cd build/linux +./configure --with-cuda=/usr/local/cuda \ + --with-matlab=/usr/local/MATLAB/R2012a \ + --prefix=/usr/local/astra +make +make install +``` +Add /usr/local/astra/lib to your LD_LIBRARY_PATH. +Add /usr/local/astra/matlab and its subdirectories (tools, mex) + to your matlab path. + + +NB: Each matlab version only supports a specific range of g++ versions. +Despite this, if you have a newer g++ and if you get errors related to missing +GLIBCXX_3.4.xx symbols, it is often possible to work around this requirement +by deleting the version of libstdc++ supplied by matlab in +MATLAB_PATH/bin/glnx86 or MATLAB_PATH/bin/glnxa64 (at your own risk). + + +### Windows, from source using Visual Studio 2008 + +Requirements: Visual Studio 2008, boost, CUDA (driver+toolkit), matlab. +Note that a .zip with all required (and precompiled) boost files is + available from our website. + +Set the environment variable MATLAB_ROOT to your matlab install location. +Open astra_vc08.sln in Visual Studio. +Select the appropriate solution configuration. + (typically Release_CUDA|win32 or Release_CUDA|x64) +Build the solution. +Install by copying AstraCuda32.dll or AstraCuda64.dll from bin/ and + all .mexw32 or .mexw64 files from bin/Release_CUDA or bin/Debug_CUDA + and the entire matlab/tools directory to a directory to be added to + your matlab path. + + +## References + +If you use parallel beam GPU code for your research, we would appreciate it if you would refer to the following paper: + +W. J. Palenstijn, K J. Batenburg, and J. Sijbers, "Performance improvements for iterative electron tomography reconstruction using graphics processing units (GPUs)", Journal of Structural Biology, vol. 176, issue 2, pp. 250-253, 2011. + +## License + +The ASTRA Toolbox is open source under the GPLv3 license. + +## Contact + +email: astra@uantwerpen.be +website: http://sf.net/projects/astra-toolbox + +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + http://visielab.uantwerpen.be/ and http://www.cwi.nl/
\ No newline at end of file diff --git a/astra_vc08.sln b/astra_vc09.sln index 60f2e25..9b93a0f 100644 --- a/astra_vc08.sln +++ b/astra_vc09.sln @@ -1,215 +1,221 @@ -
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+ /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\darthelper3d.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\fdk.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\par3d_bp.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\par3d_fp.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\sirt3d.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + <File + RelativePath=".\cuda\3d\util3d.cu" + > + <FileConfiguration + Name="Debug|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Debug|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|Win32" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + <FileConfiguration + Name="Release|x64" + ExcludedFromBuild="true" + > + <Tool + Name="Cudart Build Rule" + /> + </FileConfiguration> + </File> + </Filter> + </Filter> + </Files> + <Globals> + </Globals> +</VisualStudioProject> diff --git a/astra_vc11.sln b/astra_vc11.sln index 784fe7a..2832eab 100644 --- a/astra_vc11.sln +++ b/astra_vc11.sln @@ -4,20 +4,49 @@ Microsoft Visual Studio Solution File, Format Version 12.00 Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_vc11", "astra_vc11.vcxproj", "{BE9F1326-527C-4284-AE2C-D1E25D539CEA}" EndProject Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "astra_mex", "astra_mex", "{5E99A109-374E-4102-BE9B-99BA1FA8AA30}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex", "matlab\mex\astra_mex_vc11.vcxproj", "{3FDA35E0-0D54-4663-A3E6-5ABA96F32221}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_algorithm", "matlab\mex\astra_mex_algorithm_vc11.vcxproj", "{056BF7A9-294D-487C-8CC3-BE629077CA94}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_data2d", "matlab\mex\astra_mex_data2d_vc11.vcxproj", "{E4092269-B19C-46F7-A84E-4F146CC70E44}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_data3d", "matlab\mex\astra_mex_data3d_vc11.vcxproj", "{0BEC029B-0929-4BF9-BD8B-9C9806A52065}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_matrix", "matlab\mex\astra_mex_matrix_vc11.vcxproj", "{9D041710-2119-4230-BCF2-5FBE753FDE49}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_projector", "matlab\mex\astra_mex_projector_vc11.vcxproj", "{4DD6056F-8EEE-4C9A-B2A9-923F01A32E97}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_projector3d", "matlab\mex\astra_mex_projector3d_vc11.vcxproj", "{F94CCD79-AA11-42DF-AC8A-6C9D2238A883}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection +EndProject +Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "astra_mex_log", "matlab\mex\astra_mex_log_vc11.vcxproj", "{03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}" + ProjectSection(ProjectDependencies) = postProject + {BE9F1326-527C-4284-AE2C-D1E25D539CEA} = {BE9F1326-527C-4284-AE2C-D1E25D539CEA} + EndProjectSection EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution @@ -31,10 +60,10 @@ Global Release|x64 = Release|x64 EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution - {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|Win32.ActiveCfg = Debug|Win32 - {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|Win32.Build.0 = Debug|Win32 - {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|x64.ActiveCfg = Debug|x64 - {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|x64.Build.0 = Debug|x64 + {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|Win32.ActiveCfg = Debug_CUDA|Win32 + {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|Win32.Build.0 = Debug_CUDA|Win32 + {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|x64.ActiveCfg = Debug_CUDA|x64 + {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug_CUDA|x64.Build.0 = Debug_CUDA|x64 {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug|Win32.ActiveCfg = Debug|Win32 {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug|Win32.Build.0 = Debug|Win32 {BE9F1326-527C-4284-AE2C-D1E25D539CEA}.Debug|x64.ActiveCfg = Debug|x64 @@ -159,6 +188,22 @@ Global {F94CCD79-AA11-42DF-AC8A-6C9D2238A883}.Release|Win32.Build.0 = Release|Win32 {F94CCD79-AA11-42DF-AC8A-6C9D2238A883}.Release|x64.ActiveCfg = Release|x64 {F94CCD79-AA11-42DF-AC8A-6C9D2238A883}.Release|x64.Build.0 = Release|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug_CUDA|Win32.ActiveCfg = Debug_CUDA|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug_CUDA|Win32.Build.0 = Debug_CUDA|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug_CUDA|x64.ActiveCfg = Debug_CUDA|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug_CUDA|x64.Build.0 = Debug_CUDA|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug|Win32.ActiveCfg = Debug|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug|Win32.Build.0 = Debug|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug|x64.ActiveCfg = Debug|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Debug|x64.Build.0 = Debug|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release_CUDA|Win32.ActiveCfg = Release_CUDA|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release_CUDA|Win32.Build.0 = Release_CUDA|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release_CUDA|x64.ActiveCfg = Release_CUDA|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release_CUDA|x64.Build.0 = Release_CUDA|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|Win32.ActiveCfg = Release|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|Win32.Build.0 = Release|Win32 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|x64.ActiveCfg = Release|x64 + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E}.Release|x64.Build.0 = Release|x64 EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE @@ -171,5 +216,6 @@ Global {9D041710-2119-4230-BCF2-5FBE753FDE49} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} {4DD6056F-8EEE-4C9A-B2A9-923F01A32E97} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} {F94CCD79-AA11-42DF-AC8A-6C9D2238A883} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} + {03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E} = {5E99A109-374E-4102-BE9B-99BA1FA8AA30} EndGlobalSection EndGlobal diff --git a/astra_vc11.vcxproj b/astra_vc11.vcxproj index d0a52e0..bc11b23 100644 --- a/astra_vc11.vcxproj +++ b/astra_vc11.vcxproj @@ -1,6 +1,14 @@ <?xml version="1.0" encoding="utf-8"?> <Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003"> <ItemGroup Label="ProjectConfigurations"> + <ProjectConfiguration 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Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\cone_fp.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\darthelper3d.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\fdk.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\par3d_bp.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\par3d_fp.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\sirt3d.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> + <CudaCompile Include="cuda\3d\util3d.cu"> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">true</ExcludedFromBuild> + <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release|x64'">true</ExcludedFromBuild> + </CudaCompile> </ItemGroup> <ItemGroup> <None Include="include\astra\DataProjectorPolicies.inl" /> <None Include="include\astra\FanFlatBeamLineKernelProjector2D.inl" /> <None Include="include\astra\FanFlatBeamStripKernelProjector2D.inl" /> <None Include="include\astra\ParallelBeamBlobKernelProjector2D.inl" /> - <None Include="include\astra\ParallelBeamLinearKernelProjector2D.inl" /> <None Include="include\astra\ParallelBeamLineKernelProjector2D.inl" /> + <None Include="include\astra\ParallelBeamLinearKernelProjector2D.inl" /> <None Include="include\astra\ParallelBeamStripKernelProjector2D.inl" /> <None Include="include\astra\SparseMatrixProjector2D.inl" /> </ItemGroup> diff --git a/astra_vc11.vcxproj.filters b/astra_vc11.vcxproj.filters index 404f34e..a597962 100644 --- a/astra_vc11.vcxproj.filters +++ b/astra_vc11.vcxproj.filters @@ -4,76 +4,76 @@ <CudaCompile Include="cuda\2d\algo.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\algo3d.cu"> + <CudaCompile Include="cuda\2d\arith.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\arith.cu"> + <CudaCompile Include="cuda\2d\astra.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\arith3d.cu"> + <CudaCompile Include="cuda\2d\cgls.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\astra.cu"> + <CudaCompile Include="cuda\2d\darthelper.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\astra3d.cu"> + <CudaCompile Include="cuda\2d\em.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\cgls.cu"> + <CudaCompile Include="cuda\2d\fan_bp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\cgls3d.cu"> + <CudaCompile Include="cuda\2d\fan_fp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\cone_bp.cu"> + <CudaCompile Include="cuda\2d\fft.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\cone_fp.cu"> + <CudaCompile Include="cuda\2d\par_bp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\darthelper.cu"> + <CudaCompile Include="cuda\2d\par_fp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\darthelper3d.cu"> + <CudaCompile Include="cuda\2d\sart.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\em.cu"> + <CudaCompile Include="cuda\2d\sirt.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\fan_bp.cu"> + <CudaCompile Include="cuda\2d\util.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\fan_fp.cu"> + <CudaCompile Include="cuda\3d\algo3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\fdk.cu"> + <CudaCompile Include="cuda\3d\arith3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\fft.cu"> + <CudaCompile Include="cuda\3d\astra3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\par3d_bp.cu"> + <CudaCompile Include="cuda\3d\cgls3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\par3d_fp.cu"> + <CudaCompile Include="cuda\3d\cone_bp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\par_bp.cu"> + <CudaCompile Include="cuda\3d\cone_fp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\par_fp.cu"> + <CudaCompile Include="cuda\3d\darthelper3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\sart.cu"> + <CudaCompile Include="cuda\3d\fdk.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\sirt.cu"> + <CudaCompile Include="cuda\3d\par3d_bp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\3d\sirt3d.cu"> + <CudaCompile Include="cuda\3d\par3d_fp.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> - <CudaCompile Include="cuda\2d\util.cu"> + <CudaCompile Include="cuda\3d\sirt3d.cu"> <Filter>CUDA\cuda source</Filter> </CudaCompile> <CudaCompile Include="cuda\3d\util3d.cu"> @@ -162,7 +162,7 @@ <ClCompile Include="src\Globals.cpp"> <Filter>Global & Other\source</Filter> </ClCompile> - <ClCompile Include="src\Logger.cpp"> + <ClCompile Include="src\Logging.cpp"> <Filter>Global & Other\source</Filter> </ClCompile> <ClCompile Include="src\PlatformDepSystemCode.cpp"> @@ -189,6 +189,9 @@ <ClCompile Include="src\FanFlatVecProjectionGeometry2D.cpp"> <Filter>Geometries\source</Filter> </ClCompile> + <ClCompile Include="src\GeometryUtil3D.cpp"> + <Filter>Geometries\source</Filter> + </ClCompile> <ClCompile Include="src\ParallelProjectionGeometry2D.cpp"> <Filter>Geometries\source</Filter> </ClCompile> @@ -329,7 +332,10 @@ <ClInclude Include="include\astra\CglsAlgorithm.h"> <Filter>Algorithms\headers</Filter> </ClInclude> - <ClInclude Include="include\astra\DartAlgorithm.h"> + <ClInclude Include="include\astra\CudaBackProjectionAlgorithm.h"> + <Filter>Algorithms\headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaBackProjectionAlgorithm3D.h"> <Filter>Algorithms\headers</Filter> </ClInclude> <ClInclude Include="include\astra\FilteredBackProjectionAlgorithm.h"> @@ -389,6 +395,9 @@ <ClInclude Include="include\astra\AstraObjectManager.h"> <Filter>Global & Other\headers</Filter> </ClInclude> + <ClInclude Include="include\astra\clog.h"> + <Filter>Global & Other\headers</Filter> + </ClInclude> <ClInclude Include="include\astra\Config.h"> <Filter>Global & Other\headers</Filter> </ClInclude> @@ -398,7 +407,7 @@ <ClInclude Include="include\astra\Globals.h"> <Filter>Global & Other\headers</Filter> </ClInclude> - <ClInclude Include="include\astra\Logger.h"> + <ClInclude Include="include\astra\Logging.h"> <Filter>Global & Other\headers</Filter> </ClInclude> <ClInclude Include="include\astra\PlatformDepSystemCode.h"> @@ -410,6 +419,9 @@ <ClInclude Include="include\astra\TypeList.h"> <Filter>Global & Other\headers</Filter> </ClInclude> + <ClInclude Include="include\astra\Utilities.h"> + <Filter>Global & Other\headers</Filter> + </ClInclude> <ClInclude Include="include\astra\Vector3D.h"> <Filter>Global & Other\headers</Filter> </ClInclude> @@ -431,6 +443,12 @@ <ClInclude Include="include\astra\FanFlatVecProjectionGeometry2D.h"> <Filter>Geometries\headers</Filter> </ClInclude> + <ClInclude Include="include\astra\GeometryUtil2D.h"> + <Filter>Geometries\headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\GeometryUtil3D.h"> + <Filter>Geometries\headers</Filter> + </ClInclude> <ClInclude Include="include\astra\ParallelProjectionGeometry2D.h"> <Filter>Geometries\headers</Filter> </ClInclude> @@ -491,46 +509,79 @@ <ClInclude Include="include\astra\SparseMatrixProjector2D.h"> <Filter>Projectors\headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\algo.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaCglsAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\algo3d.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaCglsAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\arith.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaDartMaskAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\arith3d.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaDartMaskAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\astra.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaDartSmoothingAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\astra3d.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaDartSmoothingAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\cgls.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaDataOperationAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\cgls3d.h"> - <Filter>CUDA\cuda headers</Filter> + <ClInclude Include="include\astra\CudaEMAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\cone_bp.h"> + <ClInclude Include="include\astra\CudaFDKAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaFilteredBackProjectionAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaForwardProjectionAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaForwardProjectionAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaProjector2D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaProjector3D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaReconstructionAlgorithm2D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaRoiSelectAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaSartAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaSirtAlgorithm.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="include\astra\CudaSirtAlgorithm3D.h"> + <Filter>CUDA\astra headers</Filter> + </ClInclude> + <ClInclude Include="cuda\2d\algo.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\cone_fp.h"> + <ClInclude Include="cuda\2d\arith.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\darthelper.h"> + <ClInclude Include="cuda\2d\astra.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\darthelper3d.h"> + <ClInclude Include="cuda\2d\cgls.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\2d\dims.h"> + <ClInclude Include="cuda\2d\darthelper.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\dims3d.h"> + <ClInclude Include="cuda\2d\dims.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> <ClInclude Include="cuda\2d\em.h"> @@ -545,18 +596,9 @@ <ClInclude Include="cuda\2d\fbp_filters.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\fdk.h"> - <Filter>CUDA\cuda headers</Filter> - </ClInclude> <ClInclude Include="cuda\2d\fft.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\par3d_bp.h"> - <Filter>CUDA\cuda headers</Filter> - </ClInclude> - <ClInclude Include="cuda\3d\par3d_fp.h"> - <Filter>CUDA\cuda headers</Filter> - </ClInclude> <ClInclude Include="cuda\2d\par_bp.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> @@ -569,74 +611,44 @@ <ClInclude Include="cuda\2d\sirt.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="cuda\3d\sirt3d.h"> - <Filter>CUDA\cuda headers</Filter> - </ClInclude> <ClInclude Include="cuda\2d\util.h"> <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaBackProjectionAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaBackProjectionAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaCglsAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaCglsAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaDartMaskAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaDartMaskAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaDartSmoothingAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaDartSmoothingAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaDataOperationAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> - </ClInclude> - <ClInclude Include="include\astra\CudaEMAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\algo3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaFDKAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\arith3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaFilteredBackProjectionAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\astra3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaForwardProjectionAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\cgls3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaForwardProjectionAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\cone_bp.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaProjector2D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\cone_fp.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaProjector3D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\darthelper3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaReconstructionAlgorithm2D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\dims3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaRoiSelectAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\fdk.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaSartAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\par3d_bp.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaSirtAlgorithm.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\par3d_fp.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> - <ClInclude Include="include\astra\CudaSirtAlgorithm3D.h"> - <Filter>CUDA\astra headers</Filter> + <ClInclude Include="cuda\3d\sirt3d.h"> + <Filter>CUDA\cuda headers</Filter> </ClInclude> <ClInclude Include="cuda\3d\util3d.h"> <Filter>CUDA\cuda headers</Filter> diff --git a/build/linux/Makefile.in b/build/linux/Makefile.in index a7ac1f2..0dfa15a 100644 --- a/build/linux/Makefile.in +++ b/build/linux/Makefile.in @@ -1,5 +1,8 @@ cuda=@HAVECUDA@ matlab=@HAVEMATLAB@ +python=@HAVEPYTHON@ +boostutf=@HAVEBOOSTUTF@ + MATLAB_ROOT=@MATLAB_ROOT@ @@ -9,6 +12,10 @@ ifeq ($(matlab),yes) TARGETS+=mex endif +ifeq ($(python),yes) +TARGETS+=py +endif + all: $(TARGETS) prefix=@prefix@ @@ -19,12 +26,15 @@ VPATH=../.. CPPFLAGS=@SAVED_CPPFLAGS@ CXXFLAGS=@SAVED_CXXFLAGS@ LDFLAGS=@SAVED_LDFLAGS@ +LIBS=@SAVED_LIBS@ CPPFLAGS+=-I../.. -I../../include -I../../lib/include/rapidxml CXXFLAGS+=-g -O3 -Wall -Wshadow -LIBS=-lpthread -lrt +LIBS+=-lpthread LDFLAGS+=-g +CPPFLAGS+=@CPPFLAGS_OS@ + ifeq ($(cuda),yes) CPPFLAGS += @CPPFLAGS_CUDA@ -DASTRA_CUDA NVCCFLAGS = @NVCCFLAGS@ @CPPFLAGS_CUDA@ -I../.. -I../../include -DASTRA_CUDA @@ -39,9 +49,19 @@ CXXFLAGS+=-fopenmp LDFLAGS+=-fopenmp endif +ifeq ($(python),yes) +PYCPPFLAGS = ${CPPFLAGS} +PYCPPFLAGS += -I../include +PYLDFLAGS = ${LDFLAGS} +PYLDFLAGS += -L../build/linux/.libs +PYTHON = @PYTHON@ +endif + BOOST_CPPFLAGS= BOOST_LDFLAGS= +BOOSTUTF_LIBS=@LIBS_BOOSTUTF@ + CPPFLAGS+=$(BOOST_CPPFLAGS) LDFLAGS+=$(BOOST_LDFLAGS) @@ -53,7 +73,7 @@ LD=@CXX@ SHELL=@SHELL@ ifeq ($(matlab),yes) -MEXFLAGS = -cxx +MEXFLAGS = -cxx MEXLDFLAGS='$$LDFLAGS $(LDFLAGS)' MEXLIBS = -L.libs -lut MEXSUFFIX = @MEXSUFFIX@ @@ -101,8 +121,9 @@ BASE_OBJECTS=\ src/Float32VolumeData3DMemory.lo \ src/ForwardProjectionAlgorithm.lo \ src/Fourier.lo \ + src/GeometryUtil3D.lo \ src/Globals.lo \ - src/Logger.lo \ + src/Logging.lo \ src/ParallelBeamBlobKernelProjector2D.lo \ src/ParallelBeamLinearKernelProjector2D.lo \ src/ParallelBeamLineKernelProjector2D.lo \ @@ -200,6 +221,7 @@ TEST_OBJECTS=\ MATLAB_CXX_OBJECTS=\ matlab/mex/mexHelpFunctions.o \ matlab/mex/mexCopyDataHelpFunctions.o \ + matlab/mex/mexInitFunctions.o \ matlab/mex/mexDataManagerHelpFunctions.o MATLAB_MEX=\ @@ -209,6 +231,7 @@ MATLAB_MEX=\ matlab/mex/astra_mex_matrix_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_projector_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_projector3d_c.$(MEXSUFFIX) \ + matlab/mex/astra_mex_log_c.$(MEXSUFFIX) \ matlab/mex/astra_mex_data3d_c.$(MEXSUFFIX) @@ -225,6 +248,14 @@ mex: $(MATLAB_MEX) $(MEX) LDFLAGS=$(MEXLDFLAGS) $(MEXFLAGS) $(LIBS) $(MEXLIBS) -lastra -output $* $*.o $(MATLAB_CXX_OBJECTS) endif +ifeq ($(python),yes) +py: libastra.la + cd ../../python; CPPFLAGS="${PYCPPFLAGS}" LDFLAGS="${PYLDFLAGS}" $(PYTHON) builder.py install \ + --install-base=./finalbuild --install-headers=./finalbuild --install-purelib=./finalbuild \ + --install-platlib=./finalbuild --install-scripts=./finalbuild --install-data=./finalbuild +endif + + libastra.la: $(ALL_OBJECTS) ./libtool --mode=link --tag=CXX $(LD) -rpath $(LIBDIR) -o $@ $(LDFLAGS) $(LIBS) $+ @@ -264,11 +295,16 @@ ifeq ($(cuda),yes) @rm -f $(*F).linkinfo endif +ifeq ($(boostutf),yes) test.bin: $(ALL_OBJECTS) $(TEST_OBJECTS) - ./libtool --mode=link $(LD) -o $@ $(LDFLAGS) $(LIBS) $+ -lboost_unit_test_framework + ./libtool --mode=link $(LD) -o $@ $(LDFLAGS) $+ $(LIBS) $(BOOSTUTF_LIBS) test: test.bin ./test.bin +else +test: + @echo "Tests have been disabled by configure" +endif clean: rm -f $(MATLAB_MEX) libastra.la @@ -277,6 +313,10 @@ clean: rm -f $(addsuffix /*.d,$(DEPDIRS)) rm -f $(addsuffix /*,$(LIBDIRS)) rm -f $(TEST_OBJECTS) test.bin + rm -fr ../../python/finalbuild/ + rm -fr ../../python/build/ + rm -f ../../python/astra/*.cpp + rm -f ../../python/astra/*.c distclean: clean rm -f config.guess config.sub ltmain.sh libtool install-sh @@ -285,7 +325,7 @@ distclean: clean rm -rf autom4te.cache rm -f configure Makefile -install: install-libraries install-matlab +install: install-libraries install-matlab install-python install-libraries: libastra.la ./install-sh -m 755 -d @libdir@ @@ -305,6 +345,23 @@ else install-matlab: endif +ifeq ($(python),yes) +# TODO: This install location doesn't work well for /usr or /usr/local +install-python: py + ./install-sh -m 755 -d @prefix@/python + ./install-sh -m 755 -d @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/astra/*.so @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/astra/*.py @prefix@/python/astra + ./install-sh -m 644 ../../python/finalbuild/*.egg-info @prefix@/python/ + @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" + @echo "To use ASTRA in Python, add @prefix@/python/ to your PYTHONPATH" + @echo "and @libdir@ to your LD_LIBRARY_PATH." + @echo "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" +# TODO: docs +else +install-python: +endif + Makefile: Makefile.in config.status CONFIG_HEADERS= CONFIG_LINKS= CONFIG_FILES=$@ $(SHELL) ./config.status diff --git a/build/linux/acinclude.m4 b/build/linux/acinclude.m4 index 4ff9e4b..e4b6de7 100644 --- a/build/linux/acinclude.m4 +++ b/build/linux/acinclude.m4 @@ -60,10 +60,28 @@ AC_DEFUN([ASTRA_RUN_STOREOUTPUT],[{ test $ac_status = 0; }]) -dnl ASTRA_RUN(command) -AC_DEFUN([ASTRA_RUN],[ASTRA_RUN_STOREOUTPUT($1,/dev/null)]) +dnl ASTRA_RUN_LOGOUTPUT(command) +AC_DEFUN([ASTRA_RUN_LOGOUTPUT],[{ + AS_ECHO(["$as_me:${as_lineno-$LINENO}: $1"]) >&AS_MESSAGE_LOG_FD + ( $1 ) >&AS_MESSAGE_LOG_FD 2>&1 + ac_status=$? + AS_ECHO(["$as_me:${as_lineno-$LINENO}: \$? = $ac_status"]) >&AS_MESSAGE_LOG_FD + test $ac_status = 0; + }]) +dnl ASTRA_TRY_PYTHON(code, action-if-ok, action-if-not-ok) +AC_DEFUN([ASTRA_TRY_PYTHON],[ +cat >conftest.py <<_ACEOF +$1 +_ACEOF +ASTRA_RUN_LOGOUTPUT($PYTHON conftest.py) +AS_IF([test $? = 0],[$2],[ + AS_ECHO(["$as_me: failed program was:"]) >&AS_MESSAGE_LOG_FD + sed 's/^/| /' conftest.py >&AS_MESSAGE_LOG_FD + $3]) +]) + dnl ASTRA_CHECK_NVCC(variable-to-set,cppflags-to-set) AC_DEFUN([ASTRA_CHECK_NVCC],[ @@ -79,9 +97,9 @@ ASTRA_RUN_STOREOUTPUT([$NVCC -c -o conftest.o conftest.cu $$2],conftest.nvcc.out $1="no" # Check if hack for gcc 4.4 helps if grep -q __builtin_stdarg_start conftest.nvcc.out; then + AS_ECHO(["$as_me:${as_lineno-$LINENO}: Trying CUDA hack for gcc 4.4"]) >&AS_MESSAGE_LOG_FD NVCC_OPT="-Xcompiler -D__builtin_stdarg_start=__builtin_va_start" - - ASTRA_RUN([$NVCC -c -o conftest.o conftest.cu $$2 $NVCC_OPT]) && { + ASTRA_RUN_LOGOUTPUT([$NVCC -c -o conftest.o conftest.cu $$2 $NVCC_OPT]) && { $1="yes" $2="$$2 $NVCC_OPT" } @@ -94,6 +112,7 @@ fi rm -f conftest.cu conftest.o conftest.nvcc.out ]) + dnl ASTRA_FIND_NVCC_ARCHS(archs-to-try,cppflags-to-extend,output-list) dnl Architectures should be of the form 10,20,30,35, dnl and should be in order. The last accepted one will be used for PTX output. diff --git a/build/linux/autogen.sh b/build/linux/autogen.sh index c856793..544fdeb 100755 --- a/build/linux/autogen.sh +++ b/build/linux/autogen.sh @@ -12,9 +12,12 @@ if test $? -ne 0; then exit 1 fi -libtoolize --install --force > /dev/null 2>&1 +case `uname` in Darwin*) LIBTOOLIZEBIN=glibtoolize ;; + *) LIBTOOLIZEBIN=libtoolize ;; esac + +$LIBTOOLIZEBIN --install --force > /dev/null 2>&1 if test $? -ne 0; then - libtoolize --force + $LIBTOOLIZEBIN --force if test $? -ne 0; then echo "Error running libtoolize" exit 1 diff --git a/build/linux/configure.ac b/build/linux/configure.ac index f99c4d3..d9e1f1a 100644 --- a/build/linux/configure.ac +++ b/build/linux/configure.ac @@ -1,26 +1,26 @@ dnl ----------------------------------------------------------------------- dnl Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp dnl 2014-2015, CWI, Amsterdam -dnl +dnl dnl Contact: astra@uantwerpen.be dnl Website: http://sf.net/projects/astra-toolbox -dnl +dnl dnl This file is part of the ASTRA Toolbox. -dnl -dnl +dnl +dnl dnl The ASTRA Toolbox is free software: you can redistribute it and/or modify dnl it under the terms of the GNU General Public License as published by dnl the Free Software Foundation, either version 3 of the License, or dnl (at your option) any later version. -dnl +dnl dnl The ASTRA Toolbox is distributed in the hope that it will be useful, dnl but WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the dnl GNU General Public License for more details. -dnl +dnl dnl You should have received a copy of the GNU General Public License dnl along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. -dnl +dnl dnl ----------------------------------------------------------------------- dnl $Id$ @@ -31,6 +31,7 @@ LT_INIT([disable-static]) SAVED_CPPFLAGS="$CPPFLAGS" SAVED_CXXFLAGS="$CXXFLAGS" SAVED_LDFLAGS="$LDFLAGS" +SAVED_LIBS="$LIBS" AC_CANONICAL_BUILD AC_CANONICAL_HOST @@ -52,61 +53,70 @@ AC_CHECK_HEADER(iostream, , AC_MSG_ERROR([No working c++ compiler found])) AC_MSG_CHECKING([for boost-unit-test-framework]) ASTRA_CHECK_BOOST_UNIT_TEST_FRAMEWORK(-lboost_unit_test_framework-mt, BOOSTUTF=yes_mt, BOOSTUTF=no) +HAVEBOOSTUTF=no if test x$BOOSTUTF = xno; then ASTRA_CHECK_BOOST_UNIT_TEST_FRAMEWORK(-lboost_unit_test_framework, BOOSTUTF=yes, BOOSTUTF=no) - if test x$BOOSTTHREAD = xno; then + if test x$BOOSTUTF = xno; then AC_MSG_RESULT(no) - AC_MSG_ERROR([No boost-unit-test-framework library found]) else AC_MSG_RESULT([yes, libboost_unit_test_framework]) LIBS_BOOSTUTF="-lboost_unit_test_framework" + HAVEBOOSTUTF=yes fi else AC_MSG_RESULT([yes, libboost_unit_test_framework-mt]) LIBS_BOOSTUTF="-lboost_unit_test_framework-mt" + HAVEBOOSTUTF=yes fi -# TODO: do something with the result +AC_SUBST(HAVEBOOSTUTF) +AC_SUBST(LIBS_BOOSTUTF) + +BOOSTok=yes +AC_CHECK_HEADER([boost/lexical_cast.hpp],[],[BOOSTok=no],[]) +AC_CHECK_HEADER([boost/any.hpp],[],[BOOSTok=no],[]) +dnl AC_CHECK_HEADER([boost/thread.hpp],[],[BOOSTok=no],[]) +dnl AC_CHECK_HEADER([boost/bind.hpp],[],[BOOSTok=no],[]) +AC_CHECK_HEADER([boost/static_assert.hpp],[],[BOOSTok=no],[]) +AC_CHECK_HEADER([boost/throw_exception.hpp],[],[BOOSTok=no],[]) + +if test x$BOOSTok = xno; then + AC_MSG_ERROR([boost not found]) +fi # nvcc, cuda AC_ARG_WITH(cuda, [[ --with-cuda=path path of CUDA SDK (optional)]],,) -NVCC_PATH=$PATH -if test x"$with_cuda" != x; then - NVCC_PATH="$with_cuda/bin:$NVCC_PATH" +if test x"$with_cuda" != xno; then + NVCC_PATH=$PATH + if test x"$with_cuda" != x -a x"$with_cuda" != xyes; then + NVCC_PATH="$with_cuda/bin:$NVCC_PATH" + fi + AC_PATH_PROG([NVCC], [nvcc], [no], [$NVCC_PATH]) +else + NVCC=no fi -AC_PATH_PROG([NVCC], [nvcc], [no], [$NVCC_PATH]) -# TODO: do something with the result HAVECUDA=no if test x"$NVCC" != xno; then HAVECUDA=yes BACKUP_CUDA_LDFLAGS="$LDFLAGS" - if test x"$with_cuda" != x; then - LDFLAGS_CUDA="-L$with_cuda/lib" + if test x"$with_cuda" != x -a x"$with_cuda" != xyes; then + case $host_cpu in + x86_64) + LDFLAGS_CUDA="-L$with_cuda/lib64" + ;; + *) + LDFLAGS_CUDA="-L$with_cuda/lib" + ;; + esac CPPFLAGS_CUDA="-I$with_cuda/include" LDFLAGS="$LDFLAGS $LDFLAGS_CUDA" fi AC_CHECK_LIB(cudart,cudaMalloc, ,HAVECUDA=no) AC_CHECK_LIB(cufft,cufftPlan1d, ,HAVECUDA=no) - if test x"$HAVECUDA" = xno; then - # try lib64 instead of lib - - HAVECUDA=yes - LDFLAGS="$BACKUP_CUDA_LDFLAGS" - - # prevent cached values from being used - unset ac_cv_lib_cudart_cudaMalloc - unset ac_cv_lib_cufft_cufftPlan1d - - LDFLAGS_CUDA="-L$with_cuda/lib64" - LDFLAGS="$LDFLAGS $LDFLAGS_CUDA" - AC_CHECK_LIB(cudart,cudaMalloc, ,HAVECUDA=no) - AC_CHECK_LIB(cufft,cufftPlan1d, ,HAVECUDA=no) - fi - LDFLAGS="$BACKUP_CUDA_LDFLAGS" unset BACKUP_CUDA_LDFLAGS # TODO: check for cuda headers? @@ -115,11 +125,11 @@ if test x"$NVCC" != xno; then fi NVCCFLAGS="" -AC_MSG_CHECKING([if nvcc works]) if test x"$HAVECUDA" = xyes; then + AC_MSG_CHECKING([if nvcc works]) ASTRA_CHECK_NVCC(HAVECUDA,NVCCFLAGS) + AC_MSG_RESULT($HAVECUDA) fi -AC_MSG_RESULT($HAVECUDA) AC_ARG_WITH(cuda_compute, [[ --with-cuda-compute=archs comma separated list of CUDA compute models (optional)]],,) if test x"$HAVECUDA" = xyes; then @@ -154,7 +164,7 @@ if test x"$with_matlab" != x; then AC_SUBST(MEX) MATLAB_ROOT="$with_matlab" AC_SUBST(MATLAB_ROOT) - + # TODO: maybe catch mex warnings ASTRA_CHECK_MEX_SUFFIX([mexa64 mexglx mexmaci64 mexmaci],[MEXSUFFIX]) if test x$MEXSUFFIX = x; then AC_MSG_FAILURE([Unable to determine matlab mex suffix]) @@ -166,6 +176,67 @@ fi AC_SUBST(HAVEMATLAB) +# python + +AC_ARG_WITH(python, [[ --with-python=path path of Python binary (optional)]],,) + +HAVEPYTHON=no +if test x"$with_python" != x -a x"$with_python" != xno; then + if test x"$with_python" = xyes; then + PYTHON=python + else + PYTHON="$with_python" + fi + AC_MSG_CHECKING(for python) + ASTRA_RUN_LOGOUTPUT(echo 'import sys' | $PYTHON -) + if test $? -ne 0; then + AC_MSG_ERROR(Python binary not found)] + fi + AC_MSG_RESULT([$PYTHON]) + HAVEPYTHON=yes + AC_SUBST(PYTHON) + AC_MSG_CHECKING(for numpy module) + ASTRA_TRY_PYTHON([import numpy],,HAVEPYTHON=no) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) + AC_MSG_ERROR(You need the numpy module to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(yes) + AC_MSG_CHECKING(for Cython module) + ASTRA_TRY_PYTHON([ +import Cython +from distutils.version import LooseVersion +assert(LooseVersion(Cython.__version__)>=LooseVersion("0.13")) +],,HAVEPYTHON=no) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) + AC_MSG_ERROR(You need the Cython module (version >=0.13) to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(yes) + AC_MSG_CHECKING(for six module) + ASTRA_TRY_PYTHON([import six]) + if test x$HAVEPYTHON = xno; then + AC_MSG_RESULT(no) + AC_MSG_ERROR(You need the six module to use the ASTRA toolbox in Python) + fi + AC_MSG_RESULT(yes) +fi + +AC_SUBST(HAVEPYTHON) + +#OS specific setup +AC_CANONICAL_HOST +case $host_os in + darwin* ) + CPPFLAGS_OS="-stdlib=libstdc++ -mmacosx-version-min=10.6" + ;; + *) + CPPFLAGS_OS="" + ;; +esac + +AC_SUBST(CPPFLAGS_OS) + # TODO: @@ -179,7 +250,15 @@ AC_SUBST(HAVEMATLAB) AC_SUBST(SAVED_CPPFLAGS) AC_SUBST(SAVED_CXXFLAGS) AC_SUBST(SAVED_LDFLAGS) - - +AC_SUBST(SAVED_LIBS) AC_CONFIG_FILES([Makefile]) AC_OUTPUT + +echo +echo "Summary of ASTRA Toolbox build options:" +echo " CUDA : $HAVECUDA" +echo " Matlab : $HAVEMATLAB" +echo " Python : $HAVEPYTHON" +echo +echo " prefix : $prefix" +echo diff --git a/build/msvc/gen.py b/build/msvc/gen.py new file mode 100644 index 0000000..9f5e367 --- /dev/null +++ b/build/msvc/gen.py @@ -0,0 +1,1127 @@ +from __future__ import print_function +import sys +import os + +vcppguid = "8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942" # C++ project +siguid = "2150E333-8FDC-42A3-9474-1A3956D46DE8" # project group + +# to generate a new uuid: +# +# import uuid +# uuid.uuid4().__str__().upper() + +def create_mex_project(name, uuid11, uuid09): + return { "type": vcppguid, "name": name, "file11": "matlab\\mex\\" + name + "_vc11.vcxproj", "file09": "matlab\\mex\\" + name + "_vc09.vcproj", "uuid11": uuid11, "uuid09": uuid09, "files": [] } + +P_astra = { "type": vcppguid, "name": "astra_vc11", "file11": "astra_vc11.vcxproj", "file09": "astra_vc09.vcproj", "uuid11": "BE9F1326-527C-4284-AE2C-D1E25D539CEA", "uuid09": "12926444-6723-46A8-B388-12E65E0577FA" } + +P0 = create_mex_project("astra_mex", "3FDA35E0-0D54-4663-A3E6-5ABA96F32221", "3FDA35E0-0D54-4663-A3E6-5ABA96F32221") + +P1 = create_mex_project("astra_mex_algorithm", "056BF7A9-294D-487C-8CC3-BE629077CA94", "056BF7A9-294D-487C-8CC3-BE629077CA94") +P2 = create_mex_project("astra_mex_data2d", "E4092269-B19C-46F7-A84E-4F146CC70E44", "E4092269-B19C-46F7-A84E-4F146CC70E44") +P3 = create_mex_project("astra_mex_data3d", "0BEC029B-0929-4BF9-BD8B-9C9806A52065", "0BEC029B-0929-4BF9-BD8B-9C9806A52065") +P4 = create_mex_project("astra_mex_matrix", "9D041710-2119-4230-BCF2-5FBE753FDE49", "9D041710-2119-4230-BCF2-5FBE753FDE49") +P5 = create_mex_project("astra_mex_projector", "4DD6056F-8EEE-4C9A-B2A9-923F01A32E97", "4DD6056F-8EEE-4C9A-B2A9-923F01A32E97") +P6 = create_mex_project("astra_mex_projector3d", "F94CCD79-AA11-42DF-AC8A-6C9D2238A883", "F94CCD79-AA11-42DF-AC8A-6C9D2238A883") +P7 = create_mex_project("astra_mex_log", "03B833F5-4FD6-4FBE-AAF4-E3305CD56D2E", "CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8") + +F_astra_mex = { "type": siguid, + "name": "astra_mex", + "file11": "astra_mex", + "file09": "astra_mex", + "uuid11": "5E99A109-374E-4102-BE9B-99BA1FA8AA30", + "uuid09": "33EF0AC5-B475-40BF-BAE5-67075B204D10", + "entries": [ P0, P1, P2, P3, P4, P5, P6, P7 ] } + + +P0["files"] = [ +"astra_mex_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P1["files"] = [ +"astra_mex_algorithm_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P2["files"] = [ +"astra_mex_data2d_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexCopyDataHelpFunctions.cpp", +"mexCopyDataHelpFunctions.h", +"mexDataManagerHelpFunctions.cpp", +"mexDataManagerHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P3["files"] = [ +"astra_mex_data3d_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexCopyDataHelpFunctions.cpp", +"mexCopyDataHelpFunctions.h", +"mexDataManagerHelpFunctions.cpp", +"mexDataManagerHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P4["files"] = [ +"astra_mex_matrix_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P5["files"] = [ +"astra_mex_projector_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P6["files"] = [ +"astra_mex_projector3d_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] +P7["files"] = [ +"astra_mex_log_c.cpp", +"mexHelpFunctions.cpp", +"mexHelpFunctions.h", +"mexInitFunctions.cpp", +"mexInitFunctions.h", +] + + + +P_astra["filter_names"] = [ +"Algorithms", +"Data Structures", +"Projectors", +"CUDA", +"Global & Other", +"Geometries", +"Algorithms\\headers", +"Algorithms\\source", +"Data Structures\\headers", +"Data Structures\\source", +"Global & Other\\headers", +"Global & Other\\source", +"Geometries\\headers", +"Geometries\\source", +"Projectors\\headers", +"Projectors\\inline", +"Projectors\\source", +"CUDA\\astra headers", +"CUDA\\astra source", +"CUDA\\cuda headers", +"CUDA\\cuda source", +] +P_astra["filters"] = {} +P_astra["filters"]["Algorithms"] = [ "262b0d17-774a-4cb1-b51a-b358d2d02791" ] +P_astra["filters"]["Data Structures"] = [ "76d6d672-670b-4454-b3ab-10dc8f9b8710" ] +P_astra["filters"]["Projectors"] = [ "77a581a9-60da-4265-97c0-80cdf97408c0" ] +P_astra["filters"]["CUDA"] = [ "c1af0e56-5fcc-4e75-b5db-88eeb4148185" ] +P_astra["filters"]["Global & Other"] = [ "72fbe846-10ef-4c52-88df-13bd66c4cbfc" ] +P_astra["filters"]["Geometries"] = [ "7ef37c12-c98c-4dd6-938d-12f49279eae0" ] +P_astra["filters"]["CUDA\\cuda source"] = [ +"04a878ed-77b4-4525-9bc2-38ccd65282c5", +"cuda\\2d\\algo.cu", +"cuda\\2d\\arith.cu", +"cuda\\2d\\astra.cu", +"cuda\\2d\\cgls.cu", +"cuda\\2d\\darthelper.cu", +"cuda\\2d\\em.cu", +"cuda\\2d\\fan_bp.cu", +"cuda\\2d\\fan_fp.cu", +"cuda\\2d\\fft.cu", +"cuda\\2d\\par_bp.cu", +"cuda\\2d\\par_fp.cu", +"cuda\\2d\\sart.cu", +"cuda\\2d\\sirt.cu", +"cuda\\2d\\util.cu", +"cuda\\3d\\algo3d.cu", +"cuda\\3d\\arith3d.cu", +"cuda\\3d\\astra3d.cu", +"cuda\\3d\\cgls3d.cu", +"cuda\\3d\\cone_bp.cu", +"cuda\\3d\\cone_fp.cu", +"cuda\\3d\\darthelper3d.cu", +"cuda\\3d\\fdk.cu", +"cuda\\3d\\par3d_bp.cu", +"cuda\\3d\\par3d_fp.cu", +"cuda\\3d\\sirt3d.cu", +"cuda\\3d\\util3d.cu", +] +P_astra["filters"]["Algorithms\\source"] = [ +"9df653ab-26c3-4bec-92a2-3dda22fda761", +"src\\Algorithm.cpp", +"src\\ArtAlgorithm.cpp", +"src\\AsyncAlgorithm.cpp", +"src\\BackProjectionAlgorithm.cpp", +"src\\CglsAlgorithm.cpp", +"src\\FilteredBackProjectionAlgorithm.cpp", +"src\\ForwardProjectionAlgorithm.cpp", +"src\\ReconstructionAlgorithm2D.cpp", +"src\\ReconstructionAlgorithm3D.cpp", +"src\\SartAlgorithm.cpp", +"src\\SirtAlgorithm.cpp", +] +P_astra["filters"]["Data Structures\\source"] = [ +"95346487-8185-487b-a794-3e7fb5fcbd4c", +"src\\Float32Data.cpp", +"src\\Float32Data2D.cpp", +"src\\Float32Data3D.cpp", +"src\\Float32Data3DMemory.cpp", +"src\\Float32ProjectionData2D.cpp", +"src\\Float32ProjectionData3D.cpp", +"src\\Float32ProjectionData3DMemory.cpp", +"src\\Float32VolumeData2D.cpp", +"src\\Float32VolumeData3D.cpp", +"src\\Float32VolumeData3DMemory.cpp", +"src\\SparseMatrix.cpp", +] +P_astra["filters"]["Global & Other\\source"] = [ +"1546cb47-7e5b-42c2-b695-ef172024c14b", +"src\\AstraObjectFactory.cpp", +"src\\AstraObjectManager.cpp", +"src\\Config.cpp", +"src\\Fourier.cpp", +"src\\Globals.cpp", +"src\\Logging.cpp", +"src\\PlatformDepSystemCode.cpp", +"src\\Utilities.cpp", +"src\\XMLDocument.cpp", +"src\\XMLNode.cpp", +] +P_astra["filters"]["Geometries\\source"] = [ +"dc27bff7-4256-4311-a131-47612a44af20", +"src\\ConeProjectionGeometry3D.cpp", +"src\\ConeVecProjectionGeometry3D.cpp", +"src\\FanFlatProjectionGeometry2D.cpp", +"src\\FanFlatVecProjectionGeometry2D.cpp", +"src\\GeometryUtil3D.cpp", +"src\\ParallelProjectionGeometry2D.cpp", +"src\\ParallelProjectionGeometry3D.cpp", +"src\\ParallelVecProjectionGeometry3D.cpp", +"src\\ProjectionGeometry2D.cpp", +"src\\ProjectionGeometry3D.cpp", +"src\\SparseMatrixProjectionGeometry2D.cpp", +"src\\VolumeGeometry2D.cpp", +"src\\VolumeGeometry3D.cpp", +] +P_astra["filters"]["Projectors\\source"] = [ +"2d60e3c8-7874-4cee-b139-991ac15e811d", +"src\\DataProjector.cpp", +"src\\DataProjectorPolicies.cpp", +"src\\FanFlatBeamLineKernelProjector2D.cpp", +"src\\FanFlatBeamStripKernelProjector2D.cpp", +"src\\ParallelBeamBlobKernelProjector2D.cpp", +"src\\ParallelBeamLinearKernelProjector2D.cpp", +"src\\ParallelBeamLineKernelProjector2D.cpp", +"src\\ParallelBeamStripKernelProjector2D.cpp", +"src\\Projector2D.cpp", +"src\\Projector3D.cpp", +"src\\SparseMatrixProjector2D.cpp", +] +P_astra["filters"]["CUDA\\astra source"] = [ +"bbef012e-598a-456f-90d8-416bdcb4221c", +"src\\CudaBackProjectionAlgorithm.cpp", +"src\\CudaBackProjectionAlgorithm3D.cpp", +"src\\CudaCglsAlgorithm.cpp", +"src\\CudaCglsAlgorithm3D.cpp", +"src\\CudaDartMaskAlgorithm.cpp", +"src\\CudaDartMaskAlgorithm3D.cpp", +"src\\CudaDartSmoothingAlgorithm.cpp", +"src\\CudaDartSmoothingAlgorithm3D.cpp", +"src\\CudaDataOperationAlgorithm.cpp", +"src\\CudaEMAlgorithm.cpp", +"src\\CudaFDKAlgorithm3D.cpp", +"src\\CudaFilteredBackProjectionAlgorithm.cpp", +"src\\CudaForwardProjectionAlgorithm.cpp", +"src\\CudaForwardProjectionAlgorithm3D.cpp", +"src\\CudaProjector2D.cpp", +"src\\CudaProjector3D.cpp", +"src\\CudaReconstructionAlgorithm2D.cpp", +"src\\CudaRoiSelectAlgorithm.cpp", +"src\\CudaSartAlgorithm.cpp", +"src\\CudaSirtAlgorithm.cpp", +"src\\CudaSirtAlgorithm3D.cpp", +] +P_astra["filters"]["CUDA\\cuda headers"] = [ +"4e17872e-db7d-41bc-9760-fad1c253b583", +"cuda\\2d\\algo.h", +"cuda\\2d\\arith.h", +"cuda\\2d\\astra.h", +"cuda\\2d\\cgls.h", +"cuda\\2d\\darthelper.h", +"cuda\\2d\\dims.h", +"cuda\\2d\\em.h", +"cuda\\2d\\fan_bp.h", +"cuda\\2d\\fan_fp.h", +"cuda\\2d\\fbp_filters.h", +"cuda\\2d\\fft.h", +"cuda\\2d\\par_bp.h", +"cuda\\2d\\par_fp.h", +"cuda\\2d\\sart.h", +"cuda\\2d\\sirt.h", +"cuda\\2d\\util.h", +"cuda\\3d\\algo3d.h", +"cuda\\3d\\arith3d.h", +"cuda\\3d\\astra3d.h", +"cuda\\3d\\cgls3d.h", +"cuda\\3d\\cone_bp.h", +"cuda\\3d\\cone_fp.h", +"cuda\\3d\\darthelper3d.h", +"cuda\\3d\\dims3d.h", +"cuda\\3d\\fdk.h", +"cuda\\3d\\par3d_bp.h", +"cuda\\3d\\par3d_fp.h", +"cuda\\3d\\sirt3d.h", +"cuda\\3d\\util3d.h", +] +P_astra["filters"]["Algorithms\\headers"] = [ +"a76ffd6d-3895-4365-b27e-fc9a72f2ed75", +"include\\astra\\Algorithm.h", +"include\\astra\\AlgorithmTypelist.h", +"include\\astra\\ArtAlgorithm.h", +"include\\astra\\AsyncAlgorithm.h", +"include\\astra\\BackProjectionAlgorithm.h", +"include\\astra\\CglsAlgorithm.h", +"include\\astra\\CudaBackProjectionAlgorithm.h", +"include\\astra\\CudaBackProjectionAlgorithm3D.h", +"include\\astra\\FilteredBackProjectionAlgorithm.h", +"include\\astra\\ForwardProjectionAlgorithm.h", +"include\\astra\\ReconstructionAlgorithm2D.h", +"include\\astra\\ReconstructionAlgorithm3D.h", +"include\\astra\\SartAlgorithm.h", +"include\\astra\\SirtAlgorithm.h", +] +P_astra["filters"]["Data Structures\\headers"] = [ +"444c44b0-6454-483a-be26-7cb9c8ab0b98", +"include\\astra\\Float32Data.h", +"include\\astra\\Float32Data2D.h", +"include\\astra\\Float32Data3D.h", +"include\\astra\\Float32Data3DMemory.h", +"include\\astra\\Float32ProjectionData2D.h", +"include\\astra\\Float32ProjectionData3D.h", +"include\\astra\\Float32ProjectionData3DMemory.h", +"include\\astra\\Float32VolumeData2D.h", +"include\\astra\\Float32VolumeData3D.h", +"include\\astra\\Float32VolumeData3DMemory.h", +"include\\astra\\SparseMatrix.h", +] +P_astra["filters"]["Global & Other\\headers"] = [ +"1c52efc8-a77e-4c72-b9be-f6429a87e6d7", +"include\\astra\\AstraObjectFactory.h", +"include\\astra\\AstraObjectManager.h", +"include\\astra\\clog.h", +"include\\astra\\Config.h", +"include\\astra\\Fourier.h", +"include\\astra\\Globals.h", +"include\\astra\\Logging.h", +"include\\astra\\PlatformDepSystemCode.h", +"include\\astra\\Singleton.h", +"include\\astra\\TypeList.h", +"include\\astra\\Utilities.h", +"include\\astra\\Vector3D.h", +"include\\astra\\XMLDocument.h", +"include\\astra\\XMLNode.h", +] +P_astra["filters"]["Geometries\\headers"] = [ +"eddb31ba-0db7-4ab1-a490-36623aaf8901", +"include\\astra\\ConeProjectionGeometry3D.h", +"include\\astra\\ConeVecProjectionGeometry3D.h", +"include\\astra\\FanFlatProjectionGeometry2D.h", +"include\\astra\\FanFlatVecProjectionGeometry2D.h", +"include\\astra\\GeometryUtil2D.h", +"include\\astra\\GeometryUtil3D.h", +"include\\astra\\ParallelProjectionGeometry2D.h", +"include\\astra\\ParallelProjectionGeometry3D.h", +"include\\astra\\ParallelVecProjectionGeometry3D.h", +"include\\astra\\ProjectionGeometry2D.h", +"include\\astra\\ProjectionGeometry3D.h", +"include\\astra\\SparseMatrixProjectionGeometry2D.h", +"include\\astra\\VolumeGeometry2D.h", +"include\\astra\\VolumeGeometry3D.h", +] +P_astra["filters"]["Projectors\\headers"] = [ +"91ae2cfd-6b45-46eb-ad99-2f16e5ce4b1e", +"include\\astra\\DataProjector.h", +"include\\astra\\DataProjectorPolicies.h", +"include\\astra\\FanFlatBeamLineKernelProjector2D.h", +"include\\astra\\FanFlatBeamStripKernelProjector2D.h", +"include\\astra\\ParallelBeamBlobKernelProjector2D.h", +"include\\astra\\ParallelBeamLinearKernelProjector2D.h", +"include\\astra\\ParallelBeamLineKernelProjector2D.h", +"include\\astra\\ParallelBeamStripKernelProjector2D.h", +"include\\astra\\Projector2D.h", +"include\\astra\\Projector3D.h", +"include\\astra\\ProjectorTypelist.h", +"include\\astra\\SparseMatrixProjector2D.h", +] +P_astra["filters"]["CUDA\\astra headers"] = [ +"bd4e1f94-2f56-4db6-b946-20c29d65a351", +"include\\astra\\CudaCglsAlgorithm.h", +"include\\astra\\CudaCglsAlgorithm3D.h", +"include\\astra\\CudaDartMaskAlgorithm.h", +"include\\astra\\CudaDartMaskAlgorithm3D.h", +"include\\astra\\CudaDartSmoothingAlgorithm.h", +"include\\astra\\CudaDartSmoothingAlgorithm3D.h", +"include\\astra\\CudaDataOperationAlgorithm.h", +"include\\astra\\CudaEMAlgorithm.h", +"include\\astra\\CudaFDKAlgorithm3D.h", +"include\\astra\\CudaFilteredBackProjectionAlgorithm.h", +"include\\astra\\CudaForwardProjectionAlgorithm.h", +"include\\astra\\CudaForwardProjectionAlgorithm3D.h", +"include\\astra\\CudaProjector2D.h", +"include\\astra\\CudaProjector3D.h", +"include\\astra\\CudaReconstructionAlgorithm2D.h", +"include\\astra\\CudaRoiSelectAlgorithm.h", +"include\\astra\\CudaSartAlgorithm.h", +"include\\astra\\CudaSirtAlgorithm.h", +"include\\astra\\CudaSirtAlgorithm3D.h", + +] +P_astra["filters"]["Projectors\\inline"] = [ +"0daffd63-ba49-4a5f-8d7a-5322e0e74f22", +"include\\astra\\DataProjectorPolicies.inl", +"include\\astra\\FanFlatBeamLineKernelProjector2D.inl", +"include\\astra\\FanFlatBeamStripKernelProjector2D.inl", +"include\\astra\\ParallelBeamBlobKernelProjector2D.inl", +"include\\astra\\ParallelBeamLinearKernelProjector2D.inl", +"include\\astra\\ParallelBeamLineKernelProjector2D.inl", +"include\\astra\\ParallelBeamStripKernelProjector2D.inl", +"include\\astra\\SparseMatrixProjector2D.inl", +] + +P_astra["files"] = [] +for f in P_astra["filters"]: + P_astra["files"].extend(P_astra["filters"][f][1:]) +P_astra["files"].sort() + +projects = [ P_astra, F_astra_mex, P0, P1, P2, P3, P4, P5, P6, P7 ] + +bom = "\xef\xbb\xbf" + +class Configuration: + def __init__(self, debug, cuda, x64): + self.debug = debug + self.cuda = cuda + self.x64 = x64 + def type(self): + if self.debug: + return "Debug" + else: + return "Release" + def config(self): + n = self.type() + if self.cuda: + n += "_CUDA" + return n + def platform(self): + if self.x64: + n = "x64" + else: + n = "Win32" + return n + def name(self): + n = self.config() + n += "|" + n += self.platform() + return n + def target(self): + n = "Astra" + if self.cuda: + n += "Cuda" + if self.x64: + n += "64" + else: + n += "32" + if self.debug: + n += "D" + return n + + + +configs = [ Configuration(a,b,c) for a in [ True, False ] for b in [ True, False ] for c in [ False, True ] ] + +def write_sln(version): + main_project = P_astra + if version == 9: + F = open("astra_vc09.sln", "w") + elif version == 11: + F = open("astra_vc11.sln", "w") + else: + assert(False) + print(bom, file=F) + if version == 9: + print("Microsoft Visual Studio Solution File, Format Version 10.00", file=F) + print("# Visual Studio 2008", file=F) + uuid = "uuid09" + file_ = "file09" + elif version == 11: + print("Microsoft Visual Studio Solution File, Format Version 12.00", file=F) + print("# Visual Studio 2012", file=F) + uuid = "uuid11" + file_ = "file11" + for p in projects: + s = '''Project("{%s}") = "%s", "%s", "{%s}"''' % (p["type"], p["name"], p[file_], p[uuid]) + print(s, file=F) + if "mex" in p["name"]: + print("\tProjectSection(ProjectDependencies) = postProject", file=F) + print("\t\t{%s} = {%s}" % (main_project[uuid], main_project[uuid]), file=F) + print("\tEndProjectSection", file=F) + print("EndProject", file=F) + print("Global", file=F) + print("\tGlobalSection(SolutionConfigurationPlatforms) = preSolution", file=F) + for c in configs: + print("\t\t" + c.name() + " = " + c.name(), file=F) + print("\tEndGlobalSection", file=F) + print("\tGlobalSection(ProjectConfigurationPlatforms) = postSolution", file=F) + for p in projects: + if "entries" in p: + continue + for c in configs: + print("\t\t{" + p[uuid] + "}." + c.name() + ".ActiveCfg = " + c.name(), file=F) + print("\t\t{" + p[uuid] + "}." + c.name() + ".Build.0 = " + c.name(), file=F) + print("\tEndGlobalSection", file=F) + print("\tGlobalSection(SolutionProperties) = preSolution", file=F) + print("\t\tHideSolutionNode = FALSE", file=F) + print("\tEndGlobalSection", file=F) + print("\tGlobalSection(NestedProjects) = preSolution", file=F) + for p in projects: + if "entries" not in p: + continue + for e in p["entries"]: + print("\t\t{" + e[uuid] + "} = {" + p[uuid] + "}", file=F) + print("\tEndGlobalSection", file=F) + print("EndGlobal", file=F) + F.close() + +def write_project11_start(P, F): + print(bom + '<?xml version="1.0" encoding="utf-8"?>', file=F) + print('<Project DefaultTargets="Build" ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">', file=F) + print(' <ItemGroup Label="ProjectConfigurations">', file=F) + for c in configs: + print(' <ProjectConfiguration Include="' + c.name() + '">', file=F) + print(' <Configuration>' + c.config() + '</Configuration>', file=F) + print(' <Platform>' + c.platform() + '</Platform>', file=F) + print(' </ProjectConfiguration>', file=F) + print(' </ItemGroup>', file=F) + print(' <PropertyGroup Label="Globals">', file=F) + if 'mex' in P["name"]: + print(' <ProjectName>' + P["name"] + '</ProjectName>', file=F) + print(' <ProjectGuid>{' + P["uuid11"] + '}</ProjectGuid>', file=F) + if 'mex' in P["name"]: + print(' <RootNamespace>astraMatlab</RootNamespace>', file=F) + else: + print(' <RootNamespace>' + P["name"] + '</RootNamespace>', file=F) + print(' </PropertyGroup>', file=F) + print(' <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />', file=F) + for c in configs: + print(''' <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='%s'" Label="Configuration">''' % (c.name(), ), file=F) + print(' <ConfigurationType>DynamicLibrary</ConfigurationType>', file=F) + if 'mex' not in P["name"]: + if c.debug: + print(' <UseDebugLibraries>true</UseDebugLibraries>', file=F) + else: + print(' <UseDebugLibraries>false</UseDebugLibraries>', file=F) + print(' <PlatformToolset>v110</PlatformToolset>', file=F) + if 'mex' not in P["name"]: + if not c.debug: + print(' <WholeProgramOptimization>true</WholeProgramOptimization>', file=F) + print(' <CharacterSet>MultiByte</CharacterSet>', file=F) + print(' </PropertyGroup>', file=F) + print(' <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />', file=F) + print(' <ImportGroup Label="ExtensionSettings">', file=F) + if "mex" not in P["name"]: + print(' <Import Project="$(VCTargetsPath)\BuildCustomizations\CUDA 5.5.props" />', file=F) + print(' </ImportGroup>', file=F) + for c in configs: + print(''' <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='%s'">''' % (c.name(), ), file=F) + print(''' <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />''', file=F) + print(''' </ImportGroup>''', file=F) + print(' <PropertyGroup Label="UserMacros" />', file=F) + +def write_project11_end(P, F): + l = [ f for f in P["files"] if len(f) > 4 and f[-4:] == ".cpp" ] + if l: + print(' <ItemGroup>', file=F) + for f in l: + if ("cuda" in f) or ("Cuda" in f): + print(' <ClCompile Include="' + f + '">', file=F) + for c in configs: + if not c.cuda: + print(''' <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='%s'">true</ExcludedFromBuild>''' % (c.name(), ), file=F) + print(' </ClCompile>', file=F) + else: + print(' <ClCompile Include="' + f + '" />', file=F) + print(' </ItemGroup>', file=F) + l = [ f for f in P["files"] if len(f) > 2 and f[-2:] == ".h" ] + if l: + print(' <ItemGroup>', file=F) + for f in l: + print(' <ClInclude Include="' + f + '" />', file=F) + print(' </ItemGroup>', file=F) + l = [ f for f in P["files"] if len(f) > 3 and f[-3:] == ".cu" ] + if l: + print(' <ItemGroup>', file=F) + for f in l: + print(' <CudaCompile Include="' + f + '">', file=F) + for c in configs: + if not c.cuda: + print(''' <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='%s'">true</ExcludedFromBuild>''' % (c.name(), ), file=F) + print(' </CudaCompile>', file=F) + print(' </ItemGroup>', file=F) + l = [ f for f in P["files"] if len(f) > 4 and f[-4:] == ".inl" ] + if l: + print(' <ItemGroup>', file=F) + for f in l: + print(' <None Include="' + f + '" />', file=F) + print(' </ItemGroup>', file=F) + print(' <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />', file=F) + print(' <ImportGroup Label="ExtensionTargets">', file=F) + if "mex" not in P["name"]: + print(' <Import Project="$(VCTargetsPath)\BuildCustomizations\CUDA 5.5.targets" />', file=F) + print(' </ImportGroup>', file=F) + print('</Project>', end="", file=F) + + +def write_main_project11(): + P = P_astra; + F = open(P["file11"], "w") + write_project11_start(P, F) + for c in configs: + print(''' <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='%s'">''' % (c.name(), ), file=F) + if c.cuda: + print(' <IncludePath>$(CUDA_INC_PATH);$(IncludePath)</IncludePath>', file=F) + print(' <LibraryPath>$(CUDA_LIB_PATH);$(LibraryPath)</LibraryPath>', file=F) + print(' <OutDir>$(SolutionDir)bin\\$(Platform)\\' + c.config() + '\\</OutDir>', file=F) + print(' <IntDir>$(OutDir)obj\\</IntDir>', file=F) + print(' <TargetExt>.dll</TargetExt>', file=F) + print(' <TargetName>' + c.target() + '</TargetName>', file=F) + print(' <GenerateManifest>true</GenerateManifest>', file=F) + print(' </PropertyGroup>', file=F) + for c in configs: + print(''' <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='%s'">''' % (c.name(), ), file=F) + print(' <ClCompile>', file=F) + if c.debug: + print(' <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>', file=F) + else: + print(' <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>', file=F) + print(' <WarningLevel>Level3</WarningLevel>', file=F) + print(' <AdditionalIncludeDirectories>lib\include;include\;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>', file=F) + print(' <OpenMPSupport>true</OpenMPSupport>', file=F) + if not c.x64: # /arch:SSE2 is implicit on x64 + print(' <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>', file=F) + if c.debug: + print(' <Optimization>Disabled</Optimization>', file=F) + else: + print(' <Optimization>MaxSpeed</Optimization>', file=F) + print(' <FunctionLevelLinking>true</FunctionLevelLinking>', file=F) + print(' <IntrinsicFunctions>true</IntrinsicFunctions>', file=F) + print(' <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>', file=F) + print(' <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>', file=F) + d=' <PreprocessorDefinitions>' + if c.cuda: + d+="ASTRA_CUDA;" + d+="__SSE2__;" + d+="DLL_EXPORTS;_CRT_SECURE_NO_WARNINGS;" + d+='%(PreprocessorDefinitions)</PreprocessorDefinitions>' + print(d, file=F) + print(' <MultiProcessorCompilation>true</MultiProcessorCompilation>', file=F) + print(' <SDLCheck>true</SDLCheck>', file=F) + print(' </ClCompile>', file=F) + print(' <Link>', file=F) + print(' <GenerateDebugInformation>true</GenerateDebugInformation>', file=F) + if not c.debug: + print(' <EnableCOMDATFolding>true</EnableCOMDATFolding>', file=F) + print(' <OptimizeReferences>true</OptimizeReferences>', file=F) + print(' <OutputFile>bin\\' + c.platform() + '\\' + c.config() + '\\' + c.target() + '.dll</OutputFile>', file=F) + if c.cuda: + print(' <AdditionalDependencies>cudart.lib;cufft.lib;%(AdditionalDependencies)</AdditionalDependencies>', file=F) + l = ' <AdditionalLibraryDirectories>'; + if c.x64: + l += 'lib\\x64' + else: + l += 'lib\\win32' + l += ';%(AdditionalLibraryDirectories)' + if c.cuda: + l += ';$(CudaToolkitLibDir)' + l += '</AdditionalLibraryDirectories>' + print(l, file=F) + print(' </Link>', file=F) + if c.cuda: + print(' <CudaCompile>', file=F) + if c.x64: + print(' <TargetMachinePlatform>64</TargetMachinePlatform>', file=F) + else: + print(' <TargetMachinePlatform>32</TargetMachinePlatform>', file=F) + print(' <GenerateLineInfo>true</GenerateLineInfo>', file=F) + print(' <CodeGeneration>compute_20,sm_20;compute_30,sm_30;compute_30,sm_35;compute_30,compute_30</CodeGeneration>', file=F) + print(' </CudaCompile>', file=F) + print(' </ItemDefinitionGroup>', file=F) + write_project11_end(P, F) + F.close() + +def write_mex_project11(P): + F = open("matlab/mex/" + P["name"] + "_vc11.vcxproj", "w") + write_project11_start(P, F) + print(' <PropertyGroup>', file=F) + print(' <_ProjectFileVersion>11.0.60610.1</_ProjectFileVersion>', file=F) + print(' </PropertyGroup>', file=F) + for c in configs: + print(''' <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='%s'">''' % (c.name(), ), file=F) + print(' <OutDir>$(SolutionDir)bin\\$(Platform)\\$(Configuration)\\</OutDir>', file=F) + print(' <IntDir>$(OutDir)obj\\$(ProjectName)\\</IntDir>', file=F) + print(' <TargetName>$(ProjectName)_c</TargetName>', file=F) + if c.x64: + print(' <TargetExt>.mexw64</TargetExt>', file=F) + else: + print(' <TargetExt>.mexw32</TargetExt>', file=F) + print(' </PropertyGroup>', file=F) + for c in configs: + print(''' <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='%s'">''' % (c.name(), ), file=F) + print(' <ClCompile>', file=F) + if c.debug: + print(' <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>', file=F) + else: + print(' <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>', file=F) +# print(' <WarningLevel>Level3</WarningLevel>', file=F) + #print(' <AdditionalIncludeDirectories>$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>', file=F) + # FIXME: This CUDA_PATH shouldn't be necessary + print(' <AdditionalIncludeDirectories>$(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>', file=F) + print(' <OpenMPSupport>true</OpenMPSupport>', file=F) + if not c.x64: # /arch:SSE2 is implicit on x64 + print(' <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>', file=F) + if c.debug: + print(' <Optimization>Disabled</Optimization>', file=F) + else: + print(' <Optimization>MaxSpeed</Optimization>', file=F) +# print(' <FunctionLevelLinking>true</FunctionLevelLinking>', file=F) +# print(' <IntrinsicFunctions>true</IntrinsicFunctions>', file=F) +# print(' <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>', file=F) +# print(' <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>', file=F) + d=' <PreprocessorDefinitions>' + if c.cuda: + d+="ASTRA_CUDA;" + d+="__SSE2__;" +# d+="DLL_EXPORTS;_CRT_SECURE_NO_WARNINGS;" + d+='%(PreprocessorDefinitions)</PreprocessorDefinitions>' + print(d, file=F) + print(' <MultiProcessorCompilation>true</MultiProcessorCompilation>', file=F) +# print(' <SDLCheck>true</SDLCheck>', file=F) +# if c.debug: +# <DebugInformationFormat>EditAndContinue</DebugInformationFormat> ?? + print(' </ClCompile>', file=F) + print(' <Link>', file=F) +# if not c.debug: +# print(' <EnableCOMDATFolding>true</EnableCOMDATFolding>', file=F) +# print(' <OptimizeReferences>true</OptimizeReferences>', file=F) + if c.x64: + print(' <OutputFile>$(OutDir)$(ProjectName)_c.mexw64</OutputFile>', file=F) + else: + print(' <OutputFile>$(OutDir)$(ProjectName)_c.mexw32</OutputFile>', file=F) + print(' <AdditionalDependencies>%s.lib;libmex.lib;libmx.lib;libut.lib;%%(AdditionalDependencies)</AdditionalDependencies>' % (c.target(), ), file=F) + l = ' <AdditionalLibraryDirectories>'; + if c.x64: + l += '..\\..\\lib\\x64\\;..\\..\\bin\\x64\\' + else: + l += '..\\..\\lib\\win32\\;..\\..\\bin\\win32\\' + l += c.config() + if c.x64: + l += ';$(MATLAB_ROOT)\extern\lib\win64\microsoft' + else: + l += ';$(MATLAB_ROOT)\extern\lib\win32\microsoft' + l += ';%(AdditionalLibraryDirectories)' + l += '</AdditionalLibraryDirectories>' + print(l, file=F) + print(' <ModuleDefinitionFile>mex.def</ModuleDefinitionFile>', file=F) + print(' <GenerateDebugInformation>true</GenerateDebugInformation>', file=F) + print(' </Link>', file=F) + print(' </ItemDefinitionGroup>', file=F) + write_project11_end(P, F) + F.close() + +def write_main_filters11(): + P = P_astra + F = open(P["name"] + ".vcxproj.filters", "w") + print(bom + '<?xml version="1.0" encoding="utf-8"?>', file=F) + print('<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">', file=F) + print(' <ItemGroup>', file=F) + for Filter in P_astra["filter_names"]: + L = P_astra["filters"][Filter][1:] + l = [ f for f in L if len(f) > 3 and f[-3:] == ".cu" ] + for f in l: + print(' <CudaCompile Include="' + f + '">', file=F) + print(' <Filter>' + Filter + '</Filter>', file=F) + print(' </CudaCompile>', file=F) + print(' </ItemGroup>', file=F) + print(' <ItemGroup>', file=F) + for Filter in P_astra["filter_names"]: + L = P_astra["filters"][Filter][1:] + l = [ f for f in L if len(f) > 4 and f[-4:] == ".cpp" ] + for f in l: + print(' <ClCompile Include="' + f + '">', file=F) + print(' <Filter>' + Filter + '</Filter>', file=F) + print(' </ClCompile>', file=F) + print(' </ItemGroup>', file=F) + print(' <ItemGroup>', file=F) + for Filter in P_astra["filter_names"]: + L = P_astra["filters"][Filter][1:] + l = [ f for f in L if len(f) > 2 and f[-2:] == ".h" ] + for f in l: + print(' <ClInclude Include="' + f + '">', file=F) + print(' <Filter>' + Filter + '</Filter>', file=F) + print(' </ClInclude>', file=F) + print(' </ItemGroup>', file=F) + print(' <ItemGroup>', file=F) + for Filter in P_astra["filter_names"]: + L = P_astra["filters"][Filter][1:] + l = [ f for f in L if len(f) > 4 and f[-4:] == ".inl" ] + for f in l: + print(' <None Include="' + f + '">', file=F) + print(' <Filter>' + Filter + '</Filter>', file=F) + print(' </None>', file=F) + print(' </ItemGroup>', file=F) + print(' <ItemGroup>', file=F) + for f in P["filter_names"]: + print(' <Filter Include="' + f + '">', file=F) + print(' <UniqueIdentifier>{' + P["filters"][f][0] + '}</UniqueIdentifier>', file=F) + print(' </Filter>', file=F) + print(' </ItemGroup>', file=F) + print('</Project>', end="", file=F) + F.close() + +def write_project09_start(P, F): + print('<?xml version="1.0" encoding="Windows-1252"?>', file=F) + print('<VisualStudioProject', file=F) + print('\tProjectType="Visual C++"', file=F) + print('\tVersion="9.00"', file=F) + if "mex" in P["name"]: + print('\tName="%s"' % (P["name"], ), file=F) + print('\tProjectGUID="{%s}"' % (P["uuid09"],), file=F) + if "mex" in P["name"]: + print('\tRootNamespace="astraMatlab"', file=F) + else: + print('\tRootNamespace="astra"', file=F) + print('\tTargetFrameworkVersion="131072"', file=F) + print('\t>', file=F) + print(r''' <Platforms> + <Platform + Name="Win32" + /> + <Platform + Name="x64" + /> + </Platforms>''', file=F) + +def write_project09_unused_tools(F): + print(r''' <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + />''', file=F) + + +def write_main_project09(): + P = P_astra; + F = open(P["file09"], "w") + write_project09_start(P, F) + print(r''' <ToolFiles> + <DefaultToolFile + FileName="NvCudaRuntimeApi.v5.5.rules" + /> + </ToolFiles>''', file=F) + print('\t<Configurations>', file=F) + for c in configs: + print('\t\t<Configuration', file=F) + print('\t\t\tName="%s"' % (c.name(), ), file=F) + print('\t\t\tOutputDirectory="$(SolutionDir)bin\$(PlatformName)\%s"' % (c.config(), ), file=F) + print(r''' IntermediateDirectory="$(OutDir)/obj" + ConfigurationType="2" + >''', file=F) + write_project09_unused_tools(F) + print('\t\t\t<Tool', file=F) + print('\t\t\t\tName="VCCLCompilerTool"', file=F) + if c.cuda: + print('\t\t\t\tAdditionalIncludeDirectories=""$(CUDA_INC_PATH)";lib\\include;include"', file=F) + print('\t\t\t\tPreprocessorDefinitions="ASTRA_CUDA;DLL_EXPORTS;__SSE2__"', file=F) + else: + print('\t\t\t\tAdditionalIncludeDirectories="lib\\include;include"', file=F) + print('\t\t\t\tPreprocessorDefinitions="DLL_EXPORTS;__SSE2__"', file=F) + if c.debug: + print(r''' Optimization="0" + InlineFunctionExpansion="0" + FavorSizeOrSpeed="0" + EnableFiberSafeOptimizations="false" + WholeProgramOptimization="false" + RuntimeLibrary="3"''', file=F) + else: + print(r''' Optimization="3" + InlineFunctionExpansion="2" + FavorSizeOrSpeed="1" + RuntimeLibrary="2"''', file=F) + if not c.x64: # /arch:SSE2 is implicit on x64 + print('\t\t\t\tEnableEnhancedInstructionSet="2"', file=F) # SSE2 + print('\t\t\t\tOpenMP="true"', file=F) + print('\t\t\t\tAdditionalOptions="/MP"', file=F) # build with multiple processes + print('\t\t\t/>', file=F) + print('\t\t\t<Tool', file=F) + print('\t\t\t\tName="VCLinkerTool"', file=F) + if c.cuda: + print('\t\t\t\tAdditionalDependencies="cudart.lib cufft.lib"', file=F) + print('\t\t\t\tOutputFile="bin\\%s\\%s.dll"' % (c.platform(), c.target()), file=F) + if c.cuda: + print('\t\t\t\tAdditionalLibraryDirectories="".\\lib\\%s";"$(CUDA_LIB_PATH)""' % (c.platform(), ), file=F) + else: + print('\t\t\t\tAdditionalLibraryDirectories="".\\lib\\%s""' % (c.platform(), ), file=F) + print('\t\t\t\tGenerateManifest="true"', file=F) + print('\t\t\t\tModuleDefinitionFile=""', file=F) + if c.debug: + print('\t\t\t\tGenerateDebugInformation="true"', file=F) + if c.x64: + print('\t\t\t\tTargetMachine="17"', file=F) # x64 + else: + print('\t\t\t\tTargetMachine="1"', file=F) # x86 + print('\t\t\t/>', file=F) + print('\t\t\t<Tool', file=F) + print('\t\t\t\tName="Cudart Build Rule"', file=F) + print('\t\t\t\tArch1="20"', file=F) + print('\t\t\t\tArch2="30"', file=F) + print('\t\t\t\tArch3="35"', file=F) + if c.x64: + print('\t\t\t\tTargetMachinePlatform="1"', file=F) # x64 + else: + print('\t\t\t\tTargetMachinePlatform="0"', file=F) # x86 + if c.debug: + print('\t\t\t\tRuntime="3"', file=F) # MDD + else: + print('\t\t\t\tRuntime="2"', file=F) # MD + if c.cuda: + print('\t\t\t\tDefines="-DASTRA_CUDA -DDLL_EXPORTS"', file=F) + else: # This 'else' doesn't make much sense + print('\t\t\t\tDefines="-DDLL_EXPORTS"', file=F) + # TODO!!! + print('\t\t\t/>', file=F) + print('\t\t</Configuration>', file=F) + print('\t</Configurations>', file=F) + print('\t<References>', file=F) + print('\t</References>', file=F) + print('\t<Files>', file=F) + print(r''' <Filter + Name="Resource Files" + Filter="rc;ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe;resx;tiff;tif;png;wav" + UniqueIdentifier="{67DA6AB6-F800-4c08-8B7A-83BB121AAD01}" + > + <File + RelativePath=".\src\astra.def" + > + </File> + </Filter>''', file=F) + curgroup = None + for Filter in P["filter_names"]: + if "\\" not in Filter: + continue + # TODO + [ group, subgroup ] = Filter.split("\\") + if group != curgroup: + if curgroup != None: + print('\t\t</Filter>', file=F) + print('\t\t<Filter', file=F) + print('\t\t\tName="%s"' % (group, ), file=F) + print('\t\t\t>', file=F) + curgroup = group + print('\t\t\t<Filter', file=F) + print('\t\t\t\tName="%s"' % (subgroup, ), file=F) + print('\t\t\t\t>', file=F) + for f in P["filters"][Filter][1:]: + print('\t\t\t\t<File', file=F) + print('\t\t\t\t\tRelativePath=".\\%s"' % (f, ), file=F) + print('\t\t\t\t\t>', file=F) + if (("Cuda" in f) or ("cuda" in f)) and not (f[-2:] == ".h"): + for c in configs: + if not c.cuda: + print('\t\t\t\t\t<FileConfiguration', file=F) + print('\t\t\t\t\t\tName="%s"' % (c.name(), ), file=F) + print('\t\t\t\t\t\tExcludedFromBuild="true"', file=F) + print('\t\t\t\t\t\t>', file=F) + print('\t\t\t\t\t\t<Tool', file=F) + if len(f) > 3 and f[-3:] == ".cu": + print('\t\t\t\t\t\t\tName="Cudart Build Rule"', file=F) + else: + print('\t\t\t\t\t\t\tName="VCCLCompilerTool"', file=F) + print('\t\t\t\t\t\t/>', file=F) + print('\t\t\t\t\t</FileConfiguration>', file=F) + print('\t\t\t\t</File>', file=F) + print('\t\t\t</Filter>', file=F) + print('\t\t</Filter>', file=F) + print('\t</Files>', file=F) + print('\t<Globals>', file=F) + print('\t</Globals>', file=F) + print('</VisualStudioProject>', file=F) + F.close() + +def write_mex_project09(P): + F = open("matlab/mex/" + P["name"] + "_vc09.vcproj", "w") + write_project09_start(P, F) + print('\t<ToolFiles>', file=F) + print('\t</ToolFiles>', file=F) + print('\t<Configurations>', file=F) + for c in configs: + print('\t\t<Configuration', file=F) + print('\t\t\tName="%s"' % (c.name(), ), file=F) + print('\t\t\tOutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)"', file=F) + print(r''' IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + >''', file=F) + write_project09_unused_tools(F) + print('\t\t\t<Tool', file=F) + print('\t\t\t\tName="VCCLCompilerTool"', file=F) + if c.cuda: + print('\t\t\t\tAdditionalIncludeDirectories="$(MATLAB_ROOT)\\extern\\include\\;"$(CUDA_INC_PATH)";..\\..\\lib\\include;..\\..\\include"', file=F) + print('\t\t\t\tPreprocessorDefinitions="ASTRA_CUDA;__SSE2__"', file=F) + else: + print('\t\t\t\tAdditionalIncludeDirectories="$(MATLAB_ROOT)\\extern\\include\\;..\\..\\lib\\include;..\\..\\include"', file=F) + print('\t\t\t\tPreprocessorDefinitions="__SSE2__"', file=F) + if c.debug: + print(r''' Optimization="0" + RuntimeLibrary="3"''', file=F) + else: + print(r''' Optimization="2" + RuntimeLibrary="2"''', file=F) + if not c.x64: # /arch:SSE2 is implicit on x64 + print('\t\t\t\tEnableEnhancedInstructionSet="2"', file=F) # SSE2 + print('\t\t\t\tOpenMP="true"', file=F) + print('\t\t\t\tAdditionalOptions="/MP"', file=F) # build with multiple processes + print('\t\t\t/>', file=F) + print('\t\t\t<Tool', file=F) + print('\t\t\t\tName="VCLinkerTool"', file=F) + print('\t\t\t\tAdditionalDependencies="%s.lib libmex.lib libmx.lib libut.lib"' % (c.target(), ), file=F) + if c.x64: + print('\t\t\t\tOutputFile="$(OutDir)\\$(ProjectName)_c.mexw64"', file=F) + else: + print('\t\t\t\tOutputFile="$(OutDir)\\$(ProjectName)_c.mexw32"', file=F) + if c.x64: + print('\t\t\t\tAdditionalLibraryDirectories="..\\..\\bin\\x64;$(MATLAB_ROOT)\\extern\\lib\\win64\\microsoft;..\\..\\lib\\x64"', file=F) + else: + print('\t\t\t\tAdditionalLibraryDirectories="..\\..\\bin\\win32;$(MATLAB_ROOT)\\extern\\lib\\win32\\microsoft;..\\..\\lib\\win32"', file=F) + print('\t\t\t\tModuleDefinitionFile="mex.def"', file=F) + if c.debug: + print('\t\t\t\tGenerateDebugInformation="true"', file=F) + else: + print('\t\t\t\tGenerateDebugInformation="false"', file=F) + if c.x64: + print('\t\t\t\tTargetMachine="17"', file=F) # x64 + else: + print('\t\t\t\tTargetMachine="1"', file=F) # x86 + print('\t\t\t/>', file=F) + print('\t\t</Configuration>', file=F) + print('\t</Configurations>', file=F) + print('\t<References>', file=F) + print('\t</References>', file=F) + print('\t<Files>', file=F) + for f in P["files"]: + print('\t\t<File', file=F) + print('\t\t\tRelativePath=".\\%s"' % (f, ), file=F) + print('\t\t\t>', file=F) + print('\t\t</File>', file=F) + print('\t</Files>', file=F) + print('\t<Globals>', file=F) + print('\t</Globals>', file=F) + print('</VisualStudioProject>', file=F) + + + +if (len(sys.argv) != 2) or (sys.argv[1] not in ["vc09", "vc11", "all"]): + print("Usage: python gen.py [vc09|vc11|all]", file=sys.stderr) + sys.exit(1) + + + +try: + open("../../src/AstraObjectManager.cpp", "r") +except IOError: + print("Run gen.py from the build/msvc directory", file=sys.stderr) + sys.exit(1) + +# Change directory to main dir +os.chdir("../..") + +if sys.argv[1] in ["vc11", "all"]: + # HACK + P_astra["name"] = "astra_vc11" + write_sln(11) + write_main_project11() + write_main_filters11() + write_mex_project11(P0) + write_mex_project11(P1) + write_mex_project11(P2) + write_mex_project11(P3) + write_mex_project11(P4) + write_mex_project11(P5) + write_mex_project11(P6) + write_mex_project11(P7) + +if sys.argv[1] in ["vc09", "all"]: + # HACK + P_astra["name"] = "astra" + + write_sln(9) + write_main_project09() + write_mex_project09(P0) + write_mex_project09(P1) + write_mex_project09(P2) + write_mex_project09(P3) + write_mex_project09(P4) + write_mex_project09(P5) + write_mex_project09(P6) + write_mex_project09(P7) diff --git a/cuda/2d/astra.cu b/cuda/2d/astra.cu index d7ddc26..2f72db0 100644 --- a/cuda/2d/astra.cu +++ b/cuda/2d/astra.cu @@ -42,7 +42,12 @@ $Id$ #include <fstream> #include <cuda.h> -#include "../../include/astra/Logger.h" +#include "../../include/astra/VolumeGeometry2D.h" +#include "../../include/astra/ParallelProjectionGeometry2D.h" +#include "../../include/astra/FanFlatProjectionGeometry2D.h" +#include "../../include/astra/FanFlatVecProjectionGeometry2D.h" + +#include "../../include/astra/Logging.h" // For fan beam FBP weighting #include "../3d/fdk.h" @@ -64,6 +69,7 @@ public: SDimensions dims; float* angles; float* TOffsets; + astraCUDA::SFanProjection* fanProjections; float fOriginSourceDistance; float fOriginDetectorDistance; @@ -90,6 +96,8 @@ AstraFBP::AstraFBP() pData = new AstraFBP_internal(); pData->angles = 0; + pData->fanProjections = 0; + pData->TOffsets = 0; pData->D_sinoData = 0; pData->D_volumeData = 0; @@ -113,6 +121,9 @@ AstraFBP::~AstraFBP() delete[] pData->TOffsets; pData->TOffsets = 0; + delete[] pData->fanProjections; + pData->fanProjections = 0; + cudaFree(pData->D_sinoData); pData->D_sinoData = 0; @@ -169,6 +180,7 @@ bool AstraFBP::setProjectionGeometry(unsigned int iProjAngles, bool AstraFBP::setFanGeometry(unsigned int iProjAngles, unsigned int iProjDets, + const astraCUDA::SFanProjection *fanProjs, const float* pfAngles, float fOriginSourceDistance, float fOriginDetectorDistance, @@ -182,6 +194,9 @@ bool AstraFBP::setFanGeometry(unsigned int iProjAngles, pData->fOriginSourceDistance = fOriginSourceDistance; pData->fOriginDetectorDistance = fOriginDetectorDistance; + pData->fanProjections = new astraCUDA::SFanProjection[iProjAngles]; + memcpy(pData->fanProjections, fanProjs, iProjAngles * sizeof(fanProjs[0])); + pData->bFanBeam = true; pData->bShortScan = bShortScan; @@ -310,7 +325,7 @@ bool AstraFBP::run() // Call FDK_PreWeight to handle fan beam geometry. We treat // this as a cone beam setup of a single slice: - // TODO: TOffsets... + // TODO: TOffsets affects this preweighting... // We create a fake cudaPitchedPtr cudaPitchedPtr tmp; @@ -354,29 +369,7 @@ bool AstraFBP::run() } if (pData->bFanBeam) { - // TODO: TOffsets? - // TODO: Remove this code duplication with CudaReconstructionAlgorithm - SFanProjection* projs; - projs = new SFanProjection[pData->dims.iProjAngles]; - - float fSrcX0 = 0.0f; - float fSrcY0 = -pData->fOriginSourceDistance / pData->fPixelSize; - float fDetUX0 = pData->dims.fDetScale; - float fDetUY0 = 0.0f; - float fDetSX0 = pData->dims.iProjDets * fDetUX0 / -2.0f; - float fDetSY0 = pData->fOriginDetectorDistance / pData->fPixelSize; - -#define ROTATE0(name,i,alpha) do { projs[i].f##name##X = f##name##X0 * cos(alpha) - f##name##Y0 * sin(alpha); projs[i].f##name##Y = f##name##X0 * sin(alpha) + f##name##Y0 * cos(alpha); } while(0) - for (unsigned int i = 0; i < pData->dims.iProjAngles; ++i) { - ROTATE0(Src, i, pData->angles[i]); - ROTATE0(DetS, i, pData->angles[i]); - ROTATE0(DetU, i, pData->angles[i]); - } - -#undef ROTATE0 - ok = FanBP_FBPWeighted(pData->D_volumeData, pData->volumePitch, pData->D_sinoData, pData->sinoPitch, pData->dims, projs); - - delete[] projs; + ok = FanBP_FBPWeighted(pData->D_volumeData, pData->volumePitch, pData->D_sinoData, pData->sinoPitch, pData->dims, pData->fanProjections); } else { ok = BP(pData->D_volumeData, pData->volumePitch, pData->D_sinoData, pData->sinoPitch, pData->dims, pData->angles, pData->TOffsets); @@ -546,7 +539,7 @@ bool AstraFBP::setFilter(E_FBPFILTER _eFilter, const float * _pfHostFilter /* = int iMaxFilterIndex = iStartFilterIndex + iUsedFilterWidth; int iFilterShiftSize = _iFilterWidth / 2; - + for(int iDetectorIndex = iStartFilterIndex; iDetectorIndex < iMaxFilterIndex; iDetectorIndex++) { int iFFTInFilterIndex = (iDetectorIndex + iFFTRealDetCount - iFilterShiftSize) % iFFTRealDetCount; @@ -571,7 +564,7 @@ bool AstraFBP::setFilter(E_FBPFILTER _eFilter, const float * _pfHostFilter /* = } default: { - fprintf(stderr, "AstraFBP::setFilter: Unknown filter type requested"); + ASTRA_ERROR("AstraFBP::setFilter: Unknown filter type requested"); delete [] pHostFilter; return false; } @@ -628,7 +621,7 @@ bool astraCudaFP(const float* pfVolume, float* pfSinogram, unsigned int iProjAngles, unsigned int iProjDets, const float *pfAngles, const float *pfOffsets, float fDetSize, unsigned int iDetSuperSampling, - int iGPUIndex) + float fOutputScale, int iGPUIndex) { SDimensions dims; @@ -687,7 +680,7 @@ bool astraCudaFP(const float* pfVolume, float* pfSinogram, } zeroProjectionData(D_sinoData, sinoPitch, dims); - ok = FP(D_volumeData, volumePitch, D_sinoData, sinoPitch, dims, pfAngles, pfOffsets, 1.0f); + ok = FP(D_volumeData, volumePitch, D_sinoData, sinoPitch, dims, pfAngles, pfOffsets, fOutputScale); if (!ok) { cudaFree(D_volumeData); cudaFree(D_sinoData); @@ -711,19 +704,18 @@ bool astraCudaFP(const float* pfVolume, float* pfSinogram, bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, unsigned int iVolWidth, unsigned int iVolHeight, unsigned int iProjAngles, unsigned int iProjDets, - const float *pfAngles, float fOriginSourceDistance, - float fOriginDetectorDistance, float fPixelSize, - float fDetSize, - unsigned int iDetSuperSampling, + const SFanProjection *pAngles, + unsigned int iDetSuperSampling, float fOutputScale, int iGPUIndex) { SDimensions dims; - if (iProjAngles == 0 || iProjDets == 0 || pfAngles == 0) + if (iProjAngles == 0 || iProjDets == 0 || pAngles == 0) return false; dims.iProjAngles = iProjAngles; dims.iProjDets = iProjDets; + dims.fDetScale = 1.0f; // TODO? if (iDetSuperSampling == 0) return false; @@ -774,27 +766,7 @@ bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, zeroProjectionData(D_sinoData, sinoPitch, dims); - // TODO: Turn this geometry conversion into a util function - SFanProjection* projs = new SFanProjection[dims.iProjAngles]; - - float fSrcX0 = 0.0f; - float fSrcY0 = -fOriginSourceDistance / fPixelSize; - float fDetUX0 = fDetSize / fPixelSize; - float fDetUY0 = 0.0f; - float fDetSX0 = dims.iProjDets * fDetUX0 / -2.0f; - float fDetSY0 = fOriginDetectorDistance / fPixelSize; - -#define ROTATE0(name,i,alpha) do { projs[i].f##name##X = f##name##X0 * cos(alpha) - f##name##Y0 * sin(alpha); projs[i].f##name##Y = f##name##X0 * sin(alpha) + f##name##Y0 * cos(alpha); } while(0) - for (int i = 0; i < dims.iProjAngles; ++i) { - ROTATE0(Src, i, pfAngles[i]); - ROTATE0(DetS, i, pfAngles[i]); - ROTATE0(DetU, i, pfAngles[i]); - } - -#undef ROTATE0 - - ok = FanFP(D_volumeData, volumePitch, D_sinoData, sinoPitch, dims, projs, 1.0f); - delete[] projs; + ok = FanFP(D_volumeData, volumePitch, D_sinoData, sinoPitch, dims, pAngles, fOutputScale); if (!ok) { cudaFree(D_volumeData); @@ -819,94 +791,205 @@ bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, } -bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, - unsigned int iVolWidth, unsigned int iVolHeight, - unsigned int iProjAngles, unsigned int iProjDets, - const SFanProjection *pAngles, - unsigned int iDetSuperSampling, - int iGPUIndex) +bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CParallelProjectionGeometry2D* pProjGeom, + float*& detectorOffsets, float*& projectionAngles, + float& detSize, float& outputScale) { - SDimensions dims; + assert(pVolGeom); + assert(pProjGeom); + assert(pProjGeom->getProjectionAngles()); - if (iProjAngles == 0 || iProjDets == 0 || pAngles == 0) - return false; + const float EPS = 0.00001f; - dims.iProjAngles = iProjAngles; - dims.iProjDets = iProjDets; - dims.fDetScale = 1.0f; // TODO? + int nth = pProjGeom->getProjectionAngleCount(); - if (iDetSuperSampling == 0) + // Check if pixels are square + if (abs(pVolGeom->getPixelLengthX() - pVolGeom->getPixelLengthY()) > EPS) return false; - dims.iRaysPerDet = iDetSuperSampling; - - if (iVolWidth <= 0 || iVolHeight <= 0) - return false; - dims.iVolWidth = iVolWidth; - dims.iVolHeight = iVolHeight; + // Scale volume pixels to 1x1 + detSize = pProjGeom->getDetectorWidth() / pVolGeom->getPixelLengthX(); - if (iGPUIndex != -1) { - cudaSetDevice(iGPUIndex); - cudaError_t err = cudaGetLastError(); + // Copy angles + float *angles = new float[nth]; + for (int i = 0; i < nth; ++i) + angles[i] = pProjGeom->getProjectionAngles()[i]; + projectionAngles = angles; - // Ignore errors caused by calling cudaSetDevice multiple times - if (err != cudaSuccess && err != cudaErrorSetOnActiveProcess) - return false; + // Check if we need to translate + bool offCenter = false; + if (abs(pVolGeom->getWindowMinX() + pVolGeom->getWindowMaxX()) > EPS || + abs(pVolGeom->getWindowMinY() + pVolGeom->getWindowMaxY()) > EPS) + { + offCenter = true; } - bool ok; + // If there are existing detector offsets, or if we need to translate, + // we need to return offsets + if (pProjGeom->getExtraDetectorOffset() || offCenter) + { + float* offset = new float[nth]; + + if (pProjGeom->getExtraDetectorOffset()) { + for (int i = 0; i < nth; ++i) + offset[i] = pProjGeom->getExtraDetectorOffset()[i]; + } else { + for (int i = 0; i < nth; ++i) + offset[i] = 0.0f; + } - float* D_volumeData; - unsigned int volumePitch; + if (offCenter) { + float dx = (pVolGeom->getWindowMinX() + pVolGeom->getWindowMaxX()) / 2; + float dy = (pVolGeom->getWindowMinY() + pVolGeom->getWindowMaxY()) / 2; - ok = allocateVolumeData(D_volumeData, volumePitch, dims); - if (!ok) - return false; + // CHECKME: Is d in pixels or in units? - float* D_sinoData; - unsigned int sinoPitch; + for (int i = 0; i < nth; ++i) { + float d = dx * cos(angles[i]) + dy * sin(angles[i]); + offset[i] += d; + } + } - ok = allocateProjectionData(D_sinoData, sinoPitch, dims); - if (!ok) { - cudaFree(D_volumeData); - return false; + // CHECKME: Order of scaling and translation + + // Scale volume pixels to 1x1 + for (int i = 0; i < nth; ++i) { + //offset[i] /= pVolGeom->getPixelLengthX(); + //offset[i] *= detSize; + } + + + detectorOffsets = offset; + } else { + detectorOffsets = 0; } - ok = copyVolumeToDevice(pfVolume, dims.iVolWidth, - dims, - D_volumeData, volumePitch); - if (!ok) { - cudaFree(D_volumeData); - cudaFree(D_sinoData); - return false; + outputScale = pVolGeom->getPixelLengthX(); + outputScale *= outputScale; + + return true; +} + +static void convertAstraGeometry_internal(const CVolumeGeometry2D* pVolGeom, + unsigned int iProjectionAngleCount, + astraCUDA::SFanProjection*& pProjs, + float& outputScale) +{ + // Translate + float dx = (pVolGeom->getWindowMinX() + pVolGeom->getWindowMaxX()) / 2; + float dy = (pVolGeom->getWindowMinY() + pVolGeom->getWindowMaxY()) / 2; + + for (int i = 0; i < iProjectionAngleCount; ++i) { + pProjs[i].fSrcX -= dx; + pProjs[i].fSrcY -= dy; + pProjs[i].fDetSX -= dx; + pProjs[i].fDetSY -= dy; } - zeroProjectionData(D_sinoData, sinoPitch, dims); + // CHECKME: Order of scaling and translation - ok = FanFP(D_volumeData, volumePitch, D_sinoData, sinoPitch, dims, pAngles, 1.0f); + // Scale + float factor = 1.0f / pVolGeom->getPixelLengthX(); + for (int i = 0; i < iProjectionAngleCount; ++i) { + pProjs[i].fSrcX *= factor; + pProjs[i].fSrcY *= factor; + pProjs[i].fDetSX *= factor; + pProjs[i].fDetSY *= factor; + pProjs[i].fDetUX *= factor; + pProjs[i].fDetUY *= factor; - if (!ok) { - cudaFree(D_volumeData); - cudaFree(D_sinoData); - return false; } - ok = copySinogramFromDevice(pfSinogram, dims.iProjDets, - dims, - D_sinoData, sinoPitch); - if (!ok) { - cudaFree(D_volumeData); - cudaFree(D_sinoData); + // CHECKME: Check factor + outputScale = pVolGeom->getPixelLengthX(); +// outputScale *= outputScale; +} + + +bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CFanFlatProjectionGeometry2D* pProjGeom, + astraCUDA::SFanProjection*& pProjs, + float& outputScale) +{ + assert(pVolGeom); + assert(pProjGeom); + assert(pProjGeom->getProjectionAngles()); + + const float EPS = 0.00001f; + + int nth = pProjGeom->getProjectionAngleCount(); + + // Check if pixels are square + if (abs(pVolGeom->getPixelLengthX() - pVolGeom->getPixelLengthY()) > EPS) return false; + + // TODO: Deprecate this. +// if (pProjGeom->getExtraDetectorOffset()) +// return false; + + + float fOriginSourceDistance = pProjGeom->getOriginSourceDistance(); + float fOriginDetectorDistance = pProjGeom->getOriginDetectorDistance(); + float fDetSize = pProjGeom->getDetectorWidth(); + const float *pfAngles = pProjGeom->getProjectionAngles(); + + pProjs = new SFanProjection[nth]; + + float fSrcX0 = 0.0f; + float fSrcY0 = -fOriginSourceDistance; + float fDetUX0 = fDetSize; + float fDetUY0 = 0.0f; + float fDetSX0 = pProjGeom->getDetectorCount() * fDetUX0 / -2.0f; + float fDetSY0 = fOriginDetectorDistance; + +#define ROTATE0(name,i,alpha) do { pProjs[i].f##name##X = f##name##X0 * cos(alpha) - f##name##Y0 * sin(alpha); pProjs[i].f##name##Y = f##name##X0 * sin(alpha) + f##name##Y0 * cos(alpha); } while(0) + for (int i = 0; i < nth; ++i) { + ROTATE0(Src, i, pfAngles[i]); + ROTATE0(DetS, i, pfAngles[i]); + ROTATE0(DetU, i, pfAngles[i]); } - cudaFree(D_volumeData); - cudaFree(D_sinoData); +#undef ROTATE0 + + convertAstraGeometry_internal(pVolGeom, nth, pProjs, outputScale); return true; } +bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CFanFlatVecProjectionGeometry2D* pProjGeom, + astraCUDA::SFanProjection*& pProjs, + float& outputScale) +{ + assert(pVolGeom); + assert(pProjGeom); + assert(pProjGeom->getProjectionVectors()); + + const float EPS = 0.00001f; + + int nx = pVolGeom->getGridColCount(); + int ny = pVolGeom->getGridRowCount(); + int nth = pProjGeom->getProjectionAngleCount(); + + // Check if pixels are square + if (abs(pVolGeom->getPixelLengthX() - pVolGeom->getPixelLengthY()) > EPS) + return false; + + pProjs = new SFanProjection[nth]; + + // Copy vectors + for (int i = 0; i < nth; ++i) + pProjs[i] = pProjGeom->getProjectionVectors()[i]; + + convertAstraGeometry_internal(pVolGeom, nth, pProjs, outputScale); + + return true; +} + + + } diff --git a/cuda/2d/astra.h b/cuda/2d/astra.h index 474f99a..617883b 100644 --- a/cuda/2d/astra.h +++ b/cuda/2d/astra.h @@ -42,6 +42,11 @@ enum Cuda2DProjectionKernel { ker2d_default = 0 }; +class CParallelProjectionGeometry2D; +class CFanFlatProjectionGeometry2D; +class CFanFlatVecProjectionGeometry2D; +class CVolumeGeometry2D; + class AstraFBP_internal; class _AstraExport AstraFBP { @@ -73,9 +78,10 @@ public: // fDetSize indicates the size of a detector pixel compared to a // volume pixel edge. // - // pfAngles will only be read from during this call. + // pfAngles, fanProjs will only be read from during this call. bool setFanGeometry(unsigned int iProjAngles, unsigned int iProjDets, + const astraCUDA::SFanProjection *fanProjs, const float *pfAngles, float fOriginSourceDistance, float fOriginDetectorDistance, @@ -195,24 +201,31 @@ _AstraExport bool astraCudaFP(const float* pfVolume, float* pfSinogram, unsigned int iProjAngles, unsigned int iProjDets, const float *pfAngles, const float *pfOffsets, float fDetSize = 1.0f, unsigned int iDetSuperSampling = 1, - int iGPUIndex = 0); - -// Do a single forward projection, fan beam -_AstraExport bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, - unsigned int iVolWidth, unsigned int iVolHeight, - unsigned int iProjAngles, unsigned int iProjDets, - const float *pfAngles, float fOriginSourceDistance, - float fOriginDetectorDistance, float fPixelSize = 1.0f, - float fDetSize = 1.0f, - unsigned int iDetSuperSampling = 1, - int iGPUIndex = 0); + float fOutputScale = 1.0f, int iGPUIndex = 0); _AstraExport bool astraCudaFanFP(const float* pfVolume, float* pfSinogram, unsigned int iVolWidth, unsigned int iVolHeight, unsigned int iProjAngles, unsigned int iProjDets, const SFanProjection *pAngles, unsigned int iDetSuperSampling = 1, - int iGPUIndex = 0); + float fOutputScale = 1.0f, int iGPUIndex = 0); + + +_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CParallelProjectionGeometry2D* pProjGeom, + float*& pfDetectorOffsets, float*& pfProjectionAngles, + float& fDetSize, float& fOutputScale); + +_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CFanFlatProjectionGeometry2D* pProjGeom, + astraCUDA::SFanProjection*& pProjs, + float& outputScale); + +_AstraExport bool convertAstraGeometry(const CVolumeGeometry2D* pVolGeom, + const CFanFlatVecProjectionGeometry2D* pProjGeom, + astraCUDA::SFanProjection*& pProjs, + float& outputScale); + } #endif diff --git a/cuda/2d/dims.h b/cuda/2d/dims.h index 37bfa66..e870da5 100644 --- a/cuda/2d/dims.h +++ b/cuda/2d/dims.h @@ -29,18 +29,12 @@ $Id$ #ifndef _CUDA_DIMS_H #define _CUDA_DIMS_H -namespace astraCUDA { +#include "astra/GeometryUtil2D.h" -struct SFanProjection { - // the source - float fSrcX, fSrcY; - // the start of the (linear) detector - float fDetSX, fDetSY; +namespace astraCUDA { - // the length of a single detector pixel - float fDetUX, fDetUY; -}; +using astra::SFanProjection; struct SDimensions { diff --git a/cuda/2d/fft.cu b/cuda/2d/fft.cu index d105e29..2bfd493 100644 --- a/cuda/2d/fft.cu +++ b/cuda/2d/fft.cu @@ -34,7 +34,7 @@ $Id$ #include <cuda.h> #include <fstream> -#include "../../include/astra/Logger.h" +#include "../../include/astra/Logging.h" using namespace astra; @@ -43,25 +43,22 @@ using namespace astra; #define CHECK_ERROR(errorMessage) do { \ cudaError_t err = cudaThreadSynchronize(); \ if( cudaSuccess != err) { \ - fprintf(stderr, "Cuda error: %s in file '%s' in line %i : %s.\n", \ - errorMessage, __FILE__, __LINE__, cudaGetErrorString( err) );\ - CLogger::writeTerminalCUDAError(__FILE__, __LINE__, cudaGetErrorString( err)); \ + ASTRA_ERROR("Cuda error %s : %s", \ + errorMessage,cudaGetErrorString( err)); \ exit(EXIT_FAILURE); \ } } while (0) #define SAFE_CALL( call) do { \ cudaError err = call; \ if( cudaSuccess != err) { \ - fprintf(stderr, "Cuda error in file '%s' in line %i : %s.\n", \ - __FILE__, __LINE__, cudaGetErrorString( err) ); \ - CLogger::writeTerminalCUDAError(__FILE__, __LINE__, cudaGetErrorString( err)); \ + ASTRA_ERROR("Cuda error: %s ", \ + cudaGetErrorString( err)); \ exit(EXIT_FAILURE); \ } \ err = cudaThreadSynchronize(); \ if( cudaSuccess != err) { \ - fprintf(stderr, "Cuda error in file '%s' in line %i : %s.\n", \ - __FILE__, __LINE__, cudaGetErrorString( err) ); \ - CLogger::writeTerminalCUDAError(__FILE__, __LINE__, cudaGetErrorString( err)); \ + ASTRA_ERROR("Cuda error: %s : ", \ + cudaGetErrorString( err)); \ exit(EXIT_FAILURE); \ } } while (0) @@ -140,7 +137,7 @@ static bool invokeCudaFFT(int _iProjectionCount, int _iDetectorCount, result = cufftPlan1d(&plan, _iDetectorCount, CUFFT_R2C, _iProjectionCount); if(result != CUFFT_SUCCESS) { - std::cerr << "Failed to plan 1d r2c fft" << std::endl; + ASTRA_ERROR("Failed to plan 1d r2c fft"); return false; } @@ -149,7 +146,7 @@ static bool invokeCudaFFT(int _iProjectionCount, int _iDetectorCount, if(result != CUFFT_SUCCESS) { - std::cerr << "Failed to exec 1d r2c fft" << std::endl; + ASTRA_ERROR("Failed to exec 1d r2c fft"); return false; } @@ -166,18 +163,18 @@ static bool invokeCudaIFFT(int _iProjectionCount, int _iDetectorCount, result = cufftPlan1d(&plan, _iDetectorCount, CUFFT_C2R, _iProjectionCount); if(result != CUFFT_SUCCESS) { - std::cerr << "Failed to plan 1d c2r fft" << std::endl; + ASTRA_ERROR("Failed to plan 1d c2r fft"); return false; } // todo: why do we have to get rid of the const qualifier? result = cufftExecC2R(plan, (cufftComplex *)_pDevSourceComplex, - (cufftReal *)_pfDevTarget); + (cufftReal *)_pfDevTarget); cufftDestroy(plan); if(result != CUFFT_SUCCESS) { - std::cerr << "Failed to exec 1d c2r fft" << std::endl; + ASTRA_ERROR("Failed to exec 1d c2r fft"); return false; } @@ -257,7 +254,7 @@ bool runCudaIFFT(int _iProjectionCount, const cufftComplex* _pDevSourceComplex, } rescaleInverseFourier(_iProjectionCount, _iFFTRealDetectorCount, - pfDevRealFFTTarget); + pfDevRealFFTTarget); SAFE_CALL(cudaMemset(_pfRealTarget, 0, sizeof(float) * _iProjectionCount * _iTargetPitch)); @@ -460,7 +457,7 @@ void genFilter(E_FBPFILTER _eFilter, float _fD, int _iProjectionCount, const float fA1 = 0.48f; const float fA2 = 0.38f; float fNMinusOne = (float)(_iFFTFourierDetectorCount) - 1.0f; - + for(int iDetectorIndex = 1; iDetectorIndex < _iFFTFourierDetectorCount; iDetectorIndex++) { float fSmallN = (float)iDetectorIndex; @@ -633,7 +630,7 @@ void genFilter(E_FBPFILTER _eFilter, float _fD, int _iProjectionCount, } default: { - std::cerr << "Cannot serve requested filter" << std::endl; + ASTRA_ERROR("Cannot serve requested filter"); } } @@ -746,7 +743,7 @@ void testCudaFFT() { for(int iDetectorIndex = 0; iDetectorIndex < iDetectorCount; iDetectorIndex++) { -// int +// int // pfHostProj[iIndex] = (float)rand() / (float)RAND_MAX; } @@ -767,13 +764,13 @@ void testCudaFFT() result = cufftPlan1d(&plan, iDetectorCount, CUFFT_R2C, iProjectionCount); if(result != CUFFT_SUCCESS) { - cerr << "Failed to plan 1d r2c fft" << endl; + ASTRA_ERROR("Failed to plan 1d r2c fft"); } result = cufftExecR2C(plan, pfDevProj, pDevFourProj); if(result != CUFFT_SUCCESS) { - cerr << "Failed to exec 1d r2c fft" << endl; + ASTRA_ERROR("Failed to exec 1d r2c fft"); } cufftDestroy(plan); @@ -787,7 +784,7 @@ void testCudaFFT() float * pfHostFourProjImaginary = new float[iTotalElementCount]; convertComplexToRealImg(pHostFourProj, iTotalElementCount, pfHostFourProjReal, pfHostFourProjImaginary); - + writeToMatlabFile("proj_four_real.mat", pfHostFourProjReal, iProjectionCount, iDetectorCount); writeToMatlabFile("proj_four_imaginary.mat", pfHostFourProjImaginary, iProjectionCount, iDetectorCount); @@ -797,13 +794,13 @@ void testCudaFFT() result = cufftPlan1d(&plan, iDetectorCount, CUFFT_C2R, iProjectionCount); if(result != CUFFT_SUCCESS) { - cerr << "Failed to plan 1d c2r fft" << endl; + ASTRA_ERROR("Failed to plan 1d c2r fft"); } result = cufftExecC2R(plan, pDevFourProj, pfDevInFourProj); if(result != CUFFT_SUCCESS) { - cerr << "Failed to exec 1d c2r fft" << endl; + ASTRA_ERROR("Failed to exec 1d c2r fft"); } cufftDestroy(plan); diff --git a/cuda/2d/util.cu b/cuda/2d/util.cu index 81e368f..a4f8f3e 100644 --- a/cuda/2d/util.cu +++ b/cuda/2d/util.cu @@ -30,6 +30,8 @@ $Id$ #include <cassert> #include "util.h" +#include "../../include/astra/Logging.h" + namespace astraCUDA { bool copyVolumeToDevice(const float* in_data, unsigned int in_pitch, @@ -91,7 +93,7 @@ bool allocateVolume(float*& ptr, unsigned int width, unsigned int height, unsign cudaError_t ret = cudaMallocPitch((void**)&ptr, &p, sizeof(float)*width, height); if (ret != cudaSuccess) { reportCudaError(ret); - fprintf(stderr, "Failed to allocate %dx%d GPU buffer\n", width, height); + ASTRA_ERROR("Failed to allocate %dx%d GPU buffer", width, height); return false; } @@ -259,7 +261,7 @@ bool cudaTextForceKernelsCompletion() cudaError_t returnedCudaError = cudaThreadSynchronize(); if(returnedCudaError != cudaSuccess) { - fprintf(stderr, "Failed to force completion of cuda kernels: %d: %s.\n", returnedCudaError, cudaGetErrorString(returnedCudaError)); + ASTRA_ERROR("Failed to force completion of cuda kernels: %d: %s.", returnedCudaError, cudaGetErrorString(returnedCudaError)); return false; } @@ -269,7 +271,7 @@ bool cudaTextForceKernelsCompletion() void reportCudaError(cudaError_t err) { if(err != cudaSuccess) - fprintf(stderr, "CUDA error %d: %s.\n", err, cudaGetErrorString(err)); + ASTRA_ERROR("CUDA error %d: %s.", err, cudaGetErrorString(err)); } diff --git a/cuda/3d/cone_bp.cu b/cuda/3d/cone_bp.cu index 18ee4b7..5648d6f 100644 --- a/cuda/3d/cone_bp.cu +++ b/cuda/3d/cone_bp.cu @@ -47,27 +47,16 @@ static texture3D gT_coneProjTexture; namespace astraCUDA3d { -static const unsigned int g_volBlockZ = 16; +#define ZSIZE 6 +static const unsigned int g_volBlockZ = ZSIZE; -static const unsigned int g_anglesPerBlock = 64; -static const unsigned int g_volBlockX = 32; -static const unsigned int g_volBlockY = 16; +static const unsigned int g_anglesPerBlock = 32; +static const unsigned int g_volBlockX = 16; +static const unsigned int g_volBlockY = 32; static const unsigned g_MaxAngles = 1024; -__constant__ float gC_Cux[g_MaxAngles]; -__constant__ float gC_Cuy[g_MaxAngles]; -__constant__ float gC_Cuz[g_MaxAngles]; -__constant__ float gC_Cuc[g_MaxAngles]; -__constant__ float gC_Cvx[g_MaxAngles]; -__constant__ float gC_Cvy[g_MaxAngles]; -__constant__ float gC_Cvz[g_MaxAngles]; -__constant__ float gC_Cvc[g_MaxAngles]; -__constant__ float gC_Cdx[g_MaxAngles]; -__constant__ float gC_Cdy[g_MaxAngles]; -__constant__ float gC_Cdz[g_MaxAngles]; -__constant__ float gC_Cdc[g_MaxAngles]; - +__constant__ float gC_C[12*g_MaxAngles]; bool bindProjDataTexture(const cudaArray* array) { @@ -87,7 +76,9 @@ bool bindProjDataTexture(const cudaArray* array) } -__global__ void dev_cone_BP(void* D_volData, unsigned int volPitch, int startAngle, int angleOffset, const SDimensions3D dims) +//__launch_bounds__(32*16, 4) +__global__ void dev_cone_BP(void* D_volData, unsigned int volPitch, int startAngle, + int angleOffset, const astraCUDA3d::SDimensions3D dims) { float* volData = (float*)D_volData; @@ -99,11 +90,9 @@ __global__ void dev_cone_BP(void* D_volData, unsigned int volPitch, int startAng // y = rel y // blockIdx: x = x + y - // y = z + // y = z - // TO TRY: precompute part of detector intersection formulas in shared mem? - // TO TRY: inner loop over z, gather ray values in shared mem const int X = blockIdx.x % ((dims.iVolX+g_volBlockX-1)/g_volBlockX) * g_volBlockX + threadIdx.x; const int Y = blockIdx.x / ((dims.iVolX+g_volBlockX-1)/g_volBlockX) * g_volBlockY + threadIdx.y; @@ -114,51 +103,54 @@ __global__ void dev_cone_BP(void* D_volData, unsigned int volPitch, int startAng return; const int startZ = blockIdx.y * g_volBlockZ; - int endZ = startZ + g_volBlockZ; - if (endZ > dims.iVolZ) - endZ = dims.iVolZ; + const float fX = X - 0.5f*dims.iVolX + 0.5f; + const float fY = Y - 0.5f*dims.iVolY + 0.5f; + const float fZ = startZ - 0.5f*dims.iVolZ + 0.5f; - float fX = X - 0.5f*dims.iVolX + 0.5f; - float fY = Y - 0.5f*dims.iVolY + 0.5f; - float fZ = startZ - 0.5f*dims.iVolZ + 0.5f; + float Z[ZSIZE]; + for(int i=0; i < ZSIZE; i++) + Z[i] = 0.0f; - for (int Z = startZ; Z < endZ; ++Z, fZ += 1.0f) - { - float fVal = 0.0f; + { float fAngle = startAngle + angleOffset + 0.5f; for (int angle = startAngle; angle < endAngle; ++angle, fAngle += 1.0f) { + float4 fCu = make_float4(gC_C[12*angle+0], gC_C[12*angle+1], gC_C[12*angle+2], gC_C[12*angle+3]); + float4 fCv = make_float4(gC_C[12*angle+4], gC_C[12*angle+5], gC_C[12*angle+6], gC_C[12*angle+7]); + float4 fCd = make_float4(gC_C[12*angle+8], gC_C[12*angle+9], gC_C[12*angle+10], gC_C[12*angle+11]); + + float fUNum = fCu.w + fX * fCu.x + fY * fCu.y + fZ * fCu.z; + float fVNum = fCv.w + fX * fCv.x + fY * fCv.y + fZ * fCv.z; + float fDen = fCd.w + fX * fCd.x + fY * fCd.y + fZ * fCd.z; + + float fU,fV, fr; + + for (int idx = 0; idx < ZSIZE; idx++) + { + fr = __fdividef(1.0f, fDen); + fU = fUNum * fr; + fV = fVNum * fr; + float fVal = tex3D(gT_coneProjTexture, fU, fAngle, fV); + Z[idx] += fVal; // fr*fr*fVal; + + fUNum += fCu.z; + fVNum += fCv.z; + fDen += fCd.z; + } + } + } - const float fCux = gC_Cux[angle]; - const float fCuy = gC_Cuy[angle]; - const float fCuz = gC_Cuz[angle]; - const float fCuc = gC_Cuc[angle]; - const float fCvx = gC_Cvx[angle]; - const float fCvy = gC_Cvy[angle]; - const float fCvz = gC_Cvz[angle]; - const float fCvc = gC_Cvc[angle]; - const float fCdx = gC_Cdx[angle]; - const float fCdy = gC_Cdy[angle]; - const float fCdz = gC_Cdz[angle]; - const float fCdc = gC_Cdc[angle]; - - const float fUNum = fCuc + fX * fCux + fY * fCuy + fZ * fCuz; - const float fVNum = fCvc + fX * fCvx + fY * fCvy + fZ * fCvz; - const float fDen = fCdc + fX * fCdx + fY * fCdy + fZ * fCdz; - - const float fU = fUNum / fDen; - const float fV = fVNum / fDen; - - fVal += tex3D(gT_coneProjTexture, fU, fAngle, fV); + int endZ = ZSIZE; + if (endZ > dims.iVolZ - startZ) + endZ = dims.iVolZ - startZ; - } + for(int i=0; i < endZ; i++) + volData[((startZ+i)*dims.iVolY+Y)*volPitch+X] += Z[i]; +} //End kernel - volData[(Z*dims.iVolY+Y)*volPitch+X] += fVal; - } -} // supersampling version __global__ void dev_cone_BP_SS(void* D_volData, unsigned int volPitch, int startAngle, int angleOffset, const SDimensions3D dims) @@ -206,18 +198,18 @@ __global__ void dev_cone_BP_SS(void* D_volData, unsigned int volPitch, int start for (int angle = startAngle; angle < endAngle; ++angle, fAngle += 1.0f) { - const float fCux = gC_Cux[angle]; - const float fCuy = gC_Cuy[angle]; - const float fCuz = gC_Cuz[angle]; - const float fCuc = gC_Cuc[angle]; - const float fCvx = gC_Cvx[angle]; - const float fCvy = gC_Cvy[angle]; - const float fCvz = gC_Cvz[angle]; - const float fCvc = gC_Cvc[angle]; - const float fCdx = gC_Cdx[angle]; - const float fCdy = gC_Cdy[angle]; - const float fCdz = gC_Cdz[angle]; - const float fCdc = gC_Cdc[angle]; + const float fCux = gC_C[12*angle+0]; + const float fCuy = gC_C[12*angle+1]; + const float fCuz = gC_C[12*angle+2]; + const float fCuc = gC_C[12*angle+3]; + const float fCvx = gC_C[12*angle+4]; + const float fCvy = gC_C[12*angle+5]; + const float fCvz = gC_C[12*angle+6]; + const float fCvc = gC_C[12*angle+7]; + const float fCdx = gC_C[12*angle+8]; + const float fCdy = gC_C[12*angle+9]; + const float fCdz = gC_C[12*angle+10]; + const float fCdc = gC_C[12*angle+11]; float fXs = fX; for (int iSubX = 0; iSubX < dims.iRaysPerVoxelDim; ++iSubX) { @@ -233,7 +225,7 @@ __global__ void dev_cone_BP_SS(void* D_volData, unsigned int volPitch, int start const float fU = fUNum / fDen; const float fV = fVNum / fDen; - fVal += tex3D(gT_coneProjTexture, fU, fAngle, fV); + fVal += tex3D(gT_coneProjTexture, fU, fV, fAngle); fZs += fSubStep; } @@ -246,7 +238,6 @@ __global__ void dev_cone_BP_SS(void* D_volData, unsigned int volPitch, int start volData[(Z*dims.iVolY+Y)*volPitch+X] += fVal / (dims.iRaysPerVoxelDim*dims.iRaysPerVoxelDim*dims.iRaysPerVoxelDim); } - } @@ -262,35 +253,37 @@ bool ConeBP_Array(cudaPitchedPtr D_volumeData, angleCount = dims.iProjAngles - th; // transfer angles to constant memory - float* tmp = new float[angleCount]; + float* tmp = new float[12*angleCount]; // NB: We increment angles at the end of the loop body. -#define TRANSFER_TO_CONSTANT(expr,name) do { for (unsigned int i = 0; i < angleCount; ++i) tmp[i] = (expr) ; cudaMemcpyToSymbol(gC_##name, tmp, angleCount*sizeof(float), 0, cudaMemcpyHostToDevice); } while (0) - TRANSFER_TO_CONSTANT( (angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetVY - (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetVZ , Cux ); - TRANSFER_TO_CONSTANT( (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetVZ -(angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetVX , Cuy ); - TRANSFER_TO_CONSTANT( (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetVX - (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetVY , Cuz ); - TRANSFER_TO_CONSTANT( (angles[i].fDetSY*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVY)*angles[i].fSrcX - (angles[i].fDetSX*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVX)*angles[i].fSrcY + (angles[i].fDetSX*angles[i].fDetVY - angles[i].fDetSY*angles[i].fDetVX)*angles[i].fSrcZ , Cuc ); +#define TRANSFER_TO_CONSTANT(expr,name) do { for (unsigned int i = 0; i < angleCount; ++i) tmp[12*i+name] = (expr) ; } while (0) - TRANSFER_TO_CONSTANT( (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetUZ-(angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetUY, Cvx ); - TRANSFER_TO_CONSTANT( (angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetUX - (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetUZ , Cvy ); - TRANSFER_TO_CONSTANT((angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetUY-(angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetUX , Cvz ); - TRANSFER_TO_CONSTANT( -(angles[i].fDetSY*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUY)*angles[i].fSrcX + (angles[i].fDetSX*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUX)*angles[i].fSrcY - (angles[i].fDetSX*angles[i].fDetUY - angles[i].fDetSY*angles[i].fDetUX)*angles[i].fSrcZ , Cvc ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetVY - (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetVZ , 0 ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetVZ -(angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetVX , 1 ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetVX - (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetVY , 2 ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSY*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVY)*angles[i].fSrcX - (angles[i].fDetSX*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVX)*angles[i].fSrcY + (angles[i].fDetSX*angles[i].fDetVY - angles[i].fDetSY*angles[i].fDetVX)*angles[i].fSrcZ , 3 ); - TRANSFER_TO_CONSTANT( angles[i].fDetUY*angles[i].fDetVZ - angles[i].fDetUZ*angles[i].fDetVY , Cdx ); - TRANSFER_TO_CONSTANT( angles[i].fDetUZ*angles[i].fDetVX - angles[i].fDetUX*angles[i].fDetVZ , Cdy ); - TRANSFER_TO_CONSTANT( angles[i].fDetUX*angles[i].fDetVY - angles[i].fDetUY*angles[i].fDetVX , Cdz ); - TRANSFER_TO_CONSTANT( -angles[i].fSrcX * (angles[i].fDetUY*angles[i].fDetVZ - angles[i].fDetUZ*angles[i].fDetVY) - angles[i].fSrcY * (angles[i].fDetUZ*angles[i].fDetVX - angles[i].fDetUX*angles[i].fDetVZ) - angles[i].fSrcZ * (angles[i].fDetUX*angles[i].fDetVY - angles[i].fDetUY*angles[i].fDetVX) , Cdc ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetUZ-(angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetUY, 4 ); + TRANSFER_TO_CONSTANT( (angles[i].fDetSZ - angles[i].fSrcZ)*angles[i].fDetUX - (angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetUZ , 5 ); + TRANSFER_TO_CONSTANT((angles[i].fDetSX - angles[i].fSrcX)*angles[i].fDetUY-(angles[i].fDetSY - angles[i].fSrcY)*angles[i].fDetUX , 6 ); + TRANSFER_TO_CONSTANT( -(angles[i].fDetSY*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUY)*angles[i].fSrcX + (angles[i].fDetSX*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUX)*angles[i].fSrcY - (angles[i].fDetSX*angles[i].fDetUY - angles[i].fDetSY*angles[i].fDetUX)*angles[i].fSrcZ , 7 ); + + TRANSFER_TO_CONSTANT( angles[i].fDetUY*angles[i].fDetVZ - angles[i].fDetUZ*angles[i].fDetVY , 8 ); + TRANSFER_TO_CONSTANT( angles[i].fDetUZ*angles[i].fDetVX - angles[i].fDetUX*angles[i].fDetVZ , 9 ); + TRANSFER_TO_CONSTANT( angles[i].fDetUX*angles[i].fDetVY - angles[i].fDetUY*angles[i].fDetVX , 10 ); + TRANSFER_TO_CONSTANT( -angles[i].fSrcX * (angles[i].fDetUY*angles[i].fDetVZ - angles[i].fDetUZ*angles[i].fDetVY) - angles[i].fSrcY * (angles[i].fDetUZ*angles[i].fDetVX - angles[i].fDetUX*angles[i].fDetVZ) - angles[i].fSrcZ * (angles[i].fDetUX*angles[i].fDetVY - angles[i].fDetUY*angles[i].fDetVX) , 11 ); #undef TRANSFER_TO_CONSTANT + cudaMemcpyToSymbol(gC_C, tmp, angleCount*12*sizeof(float), 0, cudaMemcpyHostToDevice); delete[] tmp; dim3 dimBlock(g_volBlockX, g_volBlockY); - dim3 dimGrid(((dims.iVolX+g_volBlockX-1)/g_volBlockX)*((dims.iVolY+g_volBlockY-1)/g_volBlockY), (dims.iVolZ+g_volBlockZ-1)/g_volBlockZ); + dim3 dimGrid(((dims.iVolX/1+g_volBlockX-1)/(g_volBlockX))*((dims.iVolY/1+1*g_volBlockY-1)/(1*g_volBlockY)), (dims.iVolZ+g_volBlockZ-1)/g_volBlockZ); // timeval t; // tic(t); @@ -336,14 +329,15 @@ bool ConeBP(cudaPitchedPtr D_volumeData, #ifdef STANDALONE int main() { - SDimensions3D dims; - dims.iVolX = 256; - dims.iVolY = 256; - dims.iVolZ = 256; - dims.iProjAngles = 180; + astraCUDA3d::SDimensions3D dims; + dims.iVolX = 512; + dims.iVolY = 512; + dims.iVolZ = 512; + dims.iProjAngles = 496; dims.iProjU = 512; dims.iProjV = 512; - dims.iRaysPerDet = 1; + dims.iRaysPerDetDim = 1; + dims.iRaysPerVoxelDim = 1; cudaExtent extentV; extentV.width = dims.iVolX*sizeof(float); @@ -364,6 +358,7 @@ int main() cudaMalloc3D(&projData, extentP); cudaMemset3D(projData, 0, extentP); +#if 0 float* slice = new float[256*256]; cudaPitchedPtr ptr; ptr.ptr = slice; @@ -397,10 +392,11 @@ int main() } #endif } +#endif - SConeProjection angle[180]; - angle[0].fSrcX = -1536; + astraCUDA3d::SConeProjection angle[512]; + angle[0].fSrcX = -5120; angle[0].fSrcY = 0; angle[0].fSrcZ = 0; @@ -417,16 +413,18 @@ int main() angle[0].fDetVZ = 1; #define ROTATE0(name,i,alpha) do { angle[i].f##name##X = angle[0].f##name##X * cos(alpha) - angle[0].f##name##Y * sin(alpha); angle[i].f##name##Y = angle[0].f##name##X * sin(alpha) + angle[0].f##name##Y * cos(alpha); } while(0) - for (int i = 1; i < 180; ++i) { + for (int i = 1; i < 512; ++i) { angle[i] = angle[0]; - ROTATE0(Src, i, i*2*M_PI/180); - ROTATE0(DetS, i, i*2*M_PI/180); - ROTATE0(DetU, i, i*2*M_PI/180); - ROTATE0(DetV, i, i*2*M_PI/180); + ROTATE0(Src, i, i*2*M_PI/512); + ROTATE0(DetS, i, i*2*M_PI/512); + ROTATE0(DetU, i, i*2*M_PI/512); + ROTATE0(DetV, i, i*2*M_PI/512); } #undef ROTATE0 +#if 0 astraCUDA3d::ConeFP(volData, projData, dims, angle, 1.0f); +#endif #if 0 float* bufs = new float[180*512]; @@ -452,6 +450,7 @@ int main() saveImage(fname, 512, 512, bufp); } #endif +#if 0 for (unsigned int i = 0; i < 256*256; ++i) slice[i] = 0.0f; for (unsigned int i = 0; i < 256; ++i) { @@ -472,6 +471,7 @@ int main() p.kind = cudaMemcpyHostToDevice; cudaMemcpy3D(&p); } +#endif astraCUDA3d::ConeBP(volData, projData, dims, angle); #if 0 diff --git a/cuda/3d/dims3d.h b/cuda/3d/dims3d.h index de2a0d0..5437a85 100644 --- a/cuda/3d/dims3d.h +++ b/cuda/3d/dims3d.h @@ -29,37 +29,7 @@ $Id$ #ifndef _CUDA_CONE_DIMS_H #define _CUDA_CONE_DIMS_H -namespace astra { - -struct SConeProjection { - // the source - double fSrcX, fSrcY, fSrcZ; - - // the origin ("bottom left") of the (flat-panel) detector - double fDetSX, fDetSY, fDetSZ; - - // the U-edge of a detector pixel - double fDetUX, fDetUY, fDetUZ; - - // the V-edge of a detector pixel - double fDetVX, fDetVY, fDetVZ; -}; - -struct SPar3DProjection { - // the ray direction - double fRayX, fRayY, fRayZ; - - // the origin ("bottom left") of the (flat-panel) detector - double fDetSX, fDetSY, fDetSZ; - - // the U-edge of a detector pixel - double fDetUX, fDetUY, fDetUZ; - - // the V-edge of a detector pixel - double fDetVX, fDetVY, fDetVZ; -}; - -} +#include "astra/GeometryUtil3D.h" namespace astraCUDA3d { diff --git a/cuda/3d/par3d_bp.cu b/cuda/3d/par3d_bp.cu index 8b9dac1..0c33280 100644 --- a/cuda/3d/par3d_bp.cu +++ b/cuda/3d/par3d_bp.cu @@ -47,22 +47,16 @@ static texture3D gT_par3DProjTexture; namespace astraCUDA3d { -static const unsigned int g_volBlockZ = 16; +#define ZSIZE 6 +static const unsigned int g_volBlockZ = ZSIZE; -static const unsigned int g_anglesPerBlock = 64; -static const unsigned int g_volBlockX = 32; -static const unsigned int g_volBlockY = 16; +static const unsigned int g_anglesPerBlock = 32; +static const unsigned int g_volBlockX = 16; +static const unsigned int g_volBlockY = 32; static const unsigned g_MaxAngles = 1024; -__constant__ float gC_Cux[g_MaxAngles]; -__constant__ float gC_Cuy[g_MaxAngles]; -__constant__ float gC_Cuz[g_MaxAngles]; -__constant__ float gC_Cuc[g_MaxAngles]; -__constant__ float gC_Cvx[g_MaxAngles]; -__constant__ float gC_Cvy[g_MaxAngles]; -__constant__ float gC_Cvz[g_MaxAngles]; -__constant__ float gC_Cvc[g_MaxAngles]; +__constant__ float gC_C[8*g_MaxAngles]; static bool bindProjDataTexture(const cudaArray* array) @@ -95,12 +89,9 @@ __global__ void dev_par3D_BP(void* D_volData, unsigned int volPitch, int startAn // y = rel y // blockIdx: x = x + y - // y = z + // y = z - // TO TRY: precompute part of detector intersection formulas in shared mem? - // TO TRY: inner loop over z, gather ray values in shared mem - const int X = blockIdx.x % ((dims.iVolX+g_volBlockX-1)/g_volBlockX) * g_volBlockX + threadIdx.x; const int Y = blockIdx.x / ((dims.iVolX+g_volBlockX-1)/g_volBlockX) * g_volBlockY + threadIdx.y; @@ -110,42 +101,45 @@ __global__ void dev_par3D_BP(void* D_volData, unsigned int volPitch, int startAn return; const int startZ = blockIdx.y * g_volBlockZ; - int endZ = startZ + g_volBlockZ; - if (endZ > dims.iVolZ) - endZ = dims.iVolZ; float fX = X - 0.5f*dims.iVolX + 0.5f; float fY = Y - 0.5f*dims.iVolY + 0.5f; float fZ = startZ - 0.5f*dims.iVolZ + 0.5f; - for (int Z = startZ; Z < endZ; ++Z, fZ += 1.0f) - { + float Z[ZSIZE]; + for(int i=0; i < ZSIZE; i++) + Z[i] = 0.0f; - float fVal = 0.0f; + { float fAngle = startAngle + angleOffset + 0.5f; for (int angle = startAngle; angle < endAngle; ++angle, fAngle += 1.0f) { - const float fCux = gC_Cux[angle]; - const float fCuy = gC_Cuy[angle]; - const float fCuz = gC_Cuz[angle]; - const float fCuc = gC_Cuc[angle]; - const float fCvx = gC_Cvx[angle]; - const float fCvy = gC_Cvy[angle]; - const float fCvz = gC_Cvz[angle]; - const float fCvc = gC_Cvc[angle]; + float4 fCu = make_float4(gC_C[8*angle+0], gC_C[8*angle+1], gC_C[8*angle+2], gC_C[8*angle+3]); + float4 fCv = make_float4(gC_C[8*angle+4], gC_C[8*angle+5], gC_C[8*angle+6], gC_C[8*angle+7]); - const float fU = fCuc + fX * fCux + fY * fCuy + fZ * fCuz; - const float fV = fCvc + fX * fCvx + fY * fCvy + fZ * fCvz; + float fU = fCu.w + fX * fCu.x + fY * fCu.y + fZ * fCu.z; + float fV = fCv.w + fX * fCv.x + fY * fCv.y + fZ * fCv.z; - fVal += tex3D(gT_par3DProjTexture, fU, fAngle, fV); + for (int idx = 0; idx < ZSIZE; ++idx) { - } + float fVal = tex3D(gT_par3DProjTexture, fU, fAngle, fV); + Z[idx] += fVal; + + fU += fCu.z; + fV += fCv.z; + } - volData[(Z*dims.iVolY+Y)*volPitch+X] += fVal; + } } + int endZ = ZSIZE; + if (endZ > dims.iVolZ - startZ) + endZ = dims.iVolZ - startZ; + + for(int i=0; i < endZ; i++) + volData[((startZ+i)*dims.iVolY+Y)*volPitch+X] += Z[i]; } // supersampling version @@ -194,14 +188,14 @@ __global__ void dev_par3D_BP_SS(void* D_volData, unsigned int volPitch, int star for (int angle = startAngle; angle < endAngle; ++angle, fAngle += 1.0f) { - const float fCux = gC_Cux[angle]; - const float fCuy = gC_Cuy[angle]; - const float fCuz = gC_Cuz[angle]; - const float fCuc = gC_Cuc[angle]; - const float fCvx = gC_Cvx[angle]; - const float fCvy = gC_Cvy[angle]; - const float fCvz = gC_Cvz[angle]; - const float fCvc = gC_Cvc[angle]; + const float fCux = gC_C[8*angle+0]; + const float fCuy = gC_C[8*angle+1]; + const float fCuz = gC_C[8*angle+2]; + const float fCuc = gC_C[8*angle+3]; + const float fCvx = gC_C[8*angle+4]; + const float fCvy = gC_C[8*angle+5]; + const float fCvz = gC_C[8*angle+6]; + const float fCvc = gC_C[8*angle+7]; float fXs = fX; for (int iSubX = 0; iSubX < dims.iRaysPerVoxelDim; ++iSubX) { @@ -240,26 +234,30 @@ bool Par3DBP_Array(cudaPitchedPtr D_volumeData, angleCount = dims.iProjAngles - th; // transfer angles to constant memory - float* tmp = new float[dims.iProjAngles]; + float* tmp = new float[8*dims.iProjAngles]; // NB: We increment angles at the end of the loop body. -#define TRANSFER_TO_CONSTANT(expr,name) do { for (unsigned int i = 0; i < angleCount; ++i) tmp[i] = (expr) ; cudaMemcpyToSymbol(gC_##name, tmp, angleCount*sizeof(float), 0, cudaMemcpyHostToDevice); } while (0) + + // TODO: Use functions from dims3d.cu for this: + +#define TRANSFER_TO_CONSTANT(expr,name) do { for (unsigned int i = 0; i < angleCount; ++i) tmp[8*i + name] = (expr) ; } while (0) #define DENOM (angles[i].fRayX*angles[i].fDetUY*angles[i].fDetVZ - angles[i].fRayX*angles[i].fDetUZ*angles[i].fDetVY - angles[i].fRayY*angles[i].fDetUX*angles[i].fDetVZ + angles[i].fRayY*angles[i].fDetUZ*angles[i].fDetVX + angles[i].fRayZ*angles[i].fDetUX*angles[i].fDetVY - angles[i].fRayZ*angles[i].fDetUY*angles[i].fDetVX) - TRANSFER_TO_CONSTANT( ( - (angles[i].fRayY*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVY)) / DENOM , Cux ); - TRANSFER_TO_CONSTANT( ( (angles[i].fRayX*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVX)) / DENOM , Cuy ); - TRANSFER_TO_CONSTANT( (- (angles[i].fRayX*angles[i].fDetVY - angles[i].fRayY*angles[i].fDetVX) ) / DENOM , Cuz ); - TRANSFER_TO_CONSTANT( (-(angles[i].fDetSY*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVY)*angles[i].fRayX + (angles[i].fRayY*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVY)*angles[i].fDetSX - (angles[i].fRayY*angles[i].fDetSZ - angles[i].fRayZ*angles[i].fDetSY)*angles[i].fDetVX) / DENOM , Cuc ); + TRANSFER_TO_CONSTANT( ( - (angles[i].fRayY*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVY)) / DENOM , 0 ); + TRANSFER_TO_CONSTANT( ( (angles[i].fRayX*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVX)) / DENOM , 1 ); + TRANSFER_TO_CONSTANT( (- (angles[i].fRayX*angles[i].fDetVY - angles[i].fRayY*angles[i].fDetVX) ) / DENOM , 2 ); + TRANSFER_TO_CONSTANT( (-(angles[i].fDetSY*angles[i].fDetVZ - angles[i].fDetSZ*angles[i].fDetVY)*angles[i].fRayX + (angles[i].fRayY*angles[i].fDetVZ - angles[i].fRayZ*angles[i].fDetVY)*angles[i].fDetSX - (angles[i].fRayY*angles[i].fDetSZ - angles[i].fRayZ*angles[i].fDetSY)*angles[i].fDetVX) / DENOM , 3 ); - TRANSFER_TO_CONSTANT( ((angles[i].fRayY*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUY) ) / DENOM , Cvx ); - TRANSFER_TO_CONSTANT( (- (angles[i].fRayX*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUX) ) / DENOM , Cvy ); - TRANSFER_TO_CONSTANT( ((angles[i].fRayX*angles[i].fDetUY - angles[i].fRayY*angles[i].fDetUX) ) / DENOM , Cvz ); - TRANSFER_TO_CONSTANT( ((angles[i].fDetSY*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUY)*angles[i].fRayX - (angles[i].fRayY*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUY)*angles[i].fDetSX + (angles[i].fRayY*angles[i].fDetSZ - angles[i].fRayZ*angles[i].fDetSY)*angles[i].fDetUX ) / DENOM , Cvc ); + TRANSFER_TO_CONSTANT( ((angles[i].fRayY*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUY) ) / DENOM , 4 ); + TRANSFER_TO_CONSTANT( (- (angles[i].fRayX*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUX) ) / DENOM , 5 ); + TRANSFER_TO_CONSTANT( ((angles[i].fRayX*angles[i].fDetUY - angles[i].fRayY*angles[i].fDetUX) ) / DENOM , 6 ); + TRANSFER_TO_CONSTANT( ((angles[i].fDetSY*angles[i].fDetUZ - angles[i].fDetSZ*angles[i].fDetUY)*angles[i].fRayX - (angles[i].fRayY*angles[i].fDetUZ - angles[i].fRayZ*angles[i].fDetUY)*angles[i].fDetSX + (angles[i].fRayY*angles[i].fDetSZ - angles[i].fRayZ*angles[i].fDetSY)*angles[i].fDetUX ) / DENOM , 7 ); #undef TRANSFER_TO_CONSTANT #undef DENOM + cudaMemcpyToSymbol(gC_C, tmp, angleCount*8*sizeof(float), 0, cudaMemcpyHostToDevice); delete[] tmp; diff --git a/cuda/3d/util3d.cu b/cuda/3d/util3d.cu index d85a928..537ed69 100644 --- a/cuda/3d/util3d.cu +++ b/cuda/3d/util3d.cu @@ -31,6 +31,8 @@ $Id$ #include "util3d.h" #include "../2d/util.h" +#include "../../include/astra/Logging.h" + namespace astraCUDA3d { @@ -46,7 +48,7 @@ cudaPitchedPtr allocateVolumeData(const SDimensions3D& dims) cudaError err = cudaMalloc3D(&volData, extentV); if (err != cudaSuccess) { astraCUDA::reportCudaError(err); - fprintf(stderr, "Failed to allocate %dx%dx%d GPU buffer\n", dims.iVolX, dims.iVolY, dims.iVolZ); + ASTRA_ERROR("Failed to allocate %dx%dx%d GPU buffer", dims.iVolX, dims.iVolY, dims.iVolZ); volData.ptr = 0; // TODO: return 0 somehow? } @@ -65,7 +67,7 @@ cudaPitchedPtr allocateProjectionData(const SDimensions3D& dims) cudaError err = cudaMalloc3D(&projData, extentP); if (err != cudaSuccess) { astraCUDA::reportCudaError(err); - fprintf(stderr, "Failed to allocate %dx%dx%d GPU buffer\n", dims.iProjU, dims.iProjAngles, dims.iProjV); + ASTRA_ERROR("Failed to allocate %dx%dx%d GPU buffer", dims.iProjU, dims.iProjAngles, dims.iProjV); projData.ptr = 0; // TODO: return 0 somehow? } @@ -303,7 +305,7 @@ cudaArray* allocateVolumeArray(const SDimensions3D& dims) cudaError err = cudaMalloc3DArray(&cuArray, &channelDesc, extentA); if (err != cudaSuccess) { astraCUDA::reportCudaError(err); - fprintf(stderr, "Failed to allocate %dx%dx%d GPU array\n", dims.iVolX, dims.iVolY, dims.iVolZ); + ASTRA_ERROR("Failed to allocate %dx%dx%d GPU array", dims.iVolX, dims.iVolY, dims.iVolZ); return 0; } @@ -321,7 +323,7 @@ cudaArray* allocateProjectionArray(const SDimensions3D& dims) if (err != cudaSuccess) { astraCUDA::reportCudaError(err); - fprintf(stderr, "Failed to allocate %dx%dx%d GPU array\n", dims.iProjU, dims.iProjAngles, dims.iProjV); + ASTRA_ERROR("Failed to allocate %dx%dx%d GPU array", dims.iProjU, dims.iProjAngles, dims.iProjV); return 0; } @@ -397,7 +399,7 @@ bool cudaTextForceKernelsCompletion() cudaError_t returnedCudaError = cudaThreadSynchronize(); if(returnedCudaError != cudaSuccess) { - fprintf(stderr, "Failed to force completion of cuda kernels: %d: %s.\n", returnedCudaError, cudaGetErrorString(returnedCudaError)); + ASTRA_ERROR("Failed to force completion of cuda kernels: %d: %s.", returnedCudaError, cudaGetErrorString(returnedCudaError)); return false; } diff --git a/include/astra/AsyncAlgorithm.h b/include/astra/AsyncAlgorithm.h index 2d5d31e..a3157fc 100644 --- a/include/astra/AsyncAlgorithm.h +++ b/include/astra/AsyncAlgorithm.h @@ -32,14 +32,12 @@ $Id$ #include "Config.h" #include "Algorithm.h" -#ifdef __linux__ -#define USE_PTHREADS +#ifdef USE_PTHREADS #include <pthread.h> #else #include <boost/thread.hpp> #endif - namespace astra { /** @@ -75,10 +73,6 @@ public: */ virtual void run(int _iNrIterations = 0); - /** Wait for thread to complete and delete thread. - */ - virtual void timedJoin(int _milliseconds); - /** Return pointer to the wrapped algorithm. */ CAlgorithm* getWrappedAlgorithm() { return m_pAlg; } diff --git a/include/astra/ConeProjectionGeometry3D.h b/include/astra/ConeProjectionGeometry3D.h index 9ef5fc0..00e72ce 100644 --- a/include/astra/ConeProjectionGeometry3D.h +++ b/include/astra/ConeProjectionGeometry3D.h @@ -40,8 +40,8 @@ namespace astra * \par XML Configuration * \astra_xml_item{DetectorRowCount, int, Number of detectors for each projection.} * \astra_xml_item{DetectorColCount, int, Number of detectors for each projection.} - * \astra_xml_item{DetectorWidth, float, Width of each detector.} - * \astra_xml_item{DetectorHeight, float, Width of each detector.} + * \astra_xml_item{DetectorSpacingX, float, Width of each detector.} + * \astra_xml_item{DetectorSpacingY, float, Width of each detector.} * \astra_xml_item{ProjectionAngles, vector of float, projection angles in radians.} * \astra_xml_item{DistanceOriginDetector, float, Distance between the center of rotation and the detectorarray.} * \astra_xml_item{DistanceOriginSource, float, Distance between the center of rotation the the x-ray source.} @@ -51,8 +51,8 @@ namespace astra * proj_geom = astra_struct('cone');\n * proj_geom.DetectorRowCount = 512;\n * proj_geom.DetectorColCount = 512;\n - * proj_geom.DetectorWidth = 1.0;\n - * proj_geom.DetectorHeight = 1.0;\n + * proj_geom.DetectorSpacingX = 1.0;\n + * proj_geom.DetectorSpacingY = 1.0;\n * proj_geom.ProjectionAngles = linspace(0,pi,100);\n * proj_geom.DistanceOriginDetector = 10000;\n * proj_geom.DistanceOriginSource = 10000;\n @@ -148,6 +148,12 @@ public: */ virtual bool isEqual(const CProjectionGeometry3D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * * @param _sType geometry type to compare to. @@ -155,12 +161,6 @@ public: */ virtual bool isOfType(const std::string& _sType) const; - /** Turn this object into an XML object. - * - * @param _sNode The XML object to fill. - */ - virtual void toXML(XMLNode* _sNode) const; - /** Returns the distance from the origin of the coordinate system to the source. * * @return Distance from the origin of the coordinate system to the source @@ -185,6 +185,11 @@ public: * Returns a vector giving the projection direction for a projection and detector index */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; + + virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const; + }; // Returns the distance from the origin of the coordinate system to the source. diff --git a/include/astra/ConeVecProjectionGeometry3D.h b/include/astra/ConeVecProjectionGeometry3D.h index 75ffa12..71e8010 100644 --- a/include/astra/ConeVecProjectionGeometry3D.h +++ b/include/astra/ConeVecProjectionGeometry3D.h @@ -30,7 +30,7 @@ $Id$ #define _INC_ASTRA_CONEVECPROJECTIONGEOMETRY3D #include "ProjectionGeometry3D.h" -#include "../cuda/3d/dims3d.h" +#include "GeometryUtil3D.h" namespace astra { @@ -56,7 +56,7 @@ namespace astra * to a single projection, and consists of: * ( srcX, srcY, srcZ, dX, dY, dZ, uX, uY, uZ, vX, vY, vZ ) * src: the ray source - * d : the corner of the detector + * d : the centre of the detector plane * u : the vector from detector pixel (0,0) to (0,1) * v : the vector from detector pixel (0,0) to (1,0) */ @@ -128,6 +128,12 @@ public: */ virtual bool isEqual(const CProjectionGeometry3D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * * @param _sType geometry type to compare to. @@ -135,18 +141,16 @@ public: */ virtual bool isOfType(const std::string& _sType) const; - /** Turn this object into an XML object. - * - * @param _sNode The XML object to fill. - */ - virtual void toXML(XMLNode* _sNode) const; - /** * Returns a vector giving the projection direction for a projection and detector index */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; const SConeProjection* getProjectionVectors() const { return m_pProjectionAngles; } + + virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const; }; } // namespace astra diff --git a/include/astra/Config.h b/include/astra/Config.h index 647462b..9893c90 100644 --- a/include/astra/Config.h +++ b/include/astra/Config.h @@ -31,6 +31,7 @@ $Id$ #include "Globals.h" #include "XMLNode.h" +#include "XMLDocument.h" #include <set> @@ -46,6 +47,8 @@ struct _AstraExport Config { Config(XMLNode* _self); ~Config(); + void initialize(std::string rootname); + XMLNode* self; XMLNode* global; }; diff --git a/include/astra/FanFlatProjectionGeometry2D.h b/include/astra/FanFlatProjectionGeometry2D.h index 8f22c35..180fe68 100644 --- a/include/astra/FanFlatProjectionGeometry2D.h +++ b/include/astra/FanFlatProjectionGeometry2D.h @@ -140,6 +140,12 @@ public: */ virtual bool isOfType(const std::string& _sType); + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Return true if this geometry instance is the same as the one specified. * * @return true if this geometry instance is the same as the one specified. diff --git a/include/astra/FanFlatVecProjectionGeometry2D.h b/include/astra/FanFlatVecProjectionGeometry2D.h index 85c994f..d93de79 100644 --- a/include/astra/FanFlatVecProjectionGeometry2D.h +++ b/include/astra/FanFlatVecProjectionGeometry2D.h @@ -30,13 +30,10 @@ $Id$ #define _INC_ASTRA_FANFLATVECPROJECTIONGEOMETRY2D #include "ProjectionGeometry2D.h" -#include "../cuda/2d/dims.h" +#include "GeometryUtil2D.h" #include <cmath> -// FIXME: Avoid using -using astraCUDA::SFanProjection; - namespace astra { @@ -53,6 +50,14 @@ namespace astra * proj_geom.DetectorCount = 512;\n * proj_geom.Vectors = V;\n * } + * + * \par Vectors + * Vectors is a matrix containing the actual geometry. Each row corresponds + * to a single projection, and consists of: + * ( srcX, srcY, srcZ, dX, dY uX, uY) + * src: the ray source + * d : the centre of the detector array + * u : the vector from detector 0 to detector 1 */ class _AstraExport CFanFlatVecProjectionGeometry2D : public CProjectionGeometry2D { @@ -126,6 +131,13 @@ public: */ virtual bool isEqual(CProjectionGeometry2D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + + /** Get the value for t and theta, based upon the row and column index. * * @param _iRow row index diff --git a/src/Logger.cpp b/include/astra/GeometryUtil2D.h index 148e18c..d4ee92e 100644 --- a/src/Logger.cpp +++ b/include/astra/GeometryUtil2D.h @@ -26,52 +26,22 @@ along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. $Id$ */ -#include <astra/Logger.h> +#ifndef _INC_ASTRA_GEOMETRYUTIL2D +#define _INC_ASTRA_GEOMETRYUTIL2D -using namespace astra; +namespace astra { -const char * g_loggerFileName = "astra_logger.txt"; +struct SFanProjection { + // the source + float fSrcX, fSrcY; -void CLogger::_assureIsInitialized() -{ - if(!m_bInitialized) - { - m_pOutFile = fopen(g_loggerFileName, "r"); - if(m_pOutFile != NULL) - { - // file exists, users wants to log - fclose(m_pOutFile); - m_pOutFile = fopen(g_loggerFileName, "w"); - } + // the start of the (linear) detector + float fDetSX, fDetSY; - m_bInitialized = true; - } -} - -void CLogger::writeLine(const char * _text) -{ - _assureIsInitialized(); - - if(m_pOutFile != NULL) - { - fprintf(m_pOutFile, "%s\n", _text); - fflush(m_pOutFile); - } -} - -void CLogger::writeTerminalCUDAError(const char * _fileName, int _iLine, const char * _errString) -{ - char buffer[256]; - - sprintf(buffer, "Cuda error in file '%s' in line %i : %s.", _fileName, _iLine, _errString); - - writeLine(buffer); -} + // the length of a single detector pixel + float fDetUX, fDetUY; +}; -CLogger::CLogger() -{ - ; } -FILE * CLogger::m_pOutFile = NULL; -bool CLogger::m_bInitialized = false; +#endif diff --git a/include/astra/GeometryUtil3D.h b/include/astra/GeometryUtil3D.h new file mode 100644 index 0000000..698372e --- /dev/null +++ b/include/astra/GeometryUtil3D.h @@ -0,0 +1,73 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_ASTRA_GEOMETRYUTIL3D +#define _INC_ASTRA_GEOMETRYUTIL3D + +namespace astra { + +struct SConeProjection { + // the source + double fSrcX, fSrcY, fSrcZ; + + // the origin ("bottom left") of the (flat-panel) detector + double fDetSX, fDetSY, fDetSZ; + + // the U-edge of a detector pixel + double fDetUX, fDetUY, fDetUZ; + + // the V-edge of a detector pixel + double fDetVX, fDetVY, fDetVZ; +}; + +struct SPar3DProjection { + // the ray direction + double fRayX, fRayY, fRayZ; + + // the origin ("bottom left") of the (flat-panel) detector + double fDetSX, fDetSY, fDetSZ; + + // the U-edge of a detector pixel + double fDetUX, fDetUY, fDetUZ; + + // the V-edge of a detector pixel + double fDetVX, fDetVY, fDetVZ; +}; + +void computeBP_UV_Coeffs(const SPar3DProjection& proj, + double &fUX, double &fUY, double &fUZ, double &fUC, + double &fVX, double &fVY, double &fVZ, double &fVC); + +void computeBP_UV_Coeffs(const SConeProjection& proj, + double &fUX, double &fUY, double &fUZ, double &fUC, + double &fVX, double &fVY, double &fVZ, double &fVC, + double &fDX, double &fDY, double &fDZ, double &fDC); + +} + +#endif diff --git a/include/astra/Globals.h b/include/astra/Globals.h index fdeaa23..9c8ddfb 100644 --- a/include/astra/Globals.h +++ b/include/astra/Globals.h @@ -306,4 +306,11 @@ _AstraExport inline bool cudaEnabled() { return false; } #endif +//---------------------------------------------------------------------------------------- +// use pthreads on Linux and OSX +#if defined(__linux__) || defined(__MACH__) +#define USE_PTHREADS +#endif + + #endif diff --git a/include/astra/Logger.h b/include/astra/Logger.h deleted file mode 100644 index 34fd364..0000000 --- a/include/astra/Logger.h +++ /dev/null @@ -1,72 +0,0 @@ -/* ------------------------------------------------------------------------ -Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp - 2014-2015, CWI, Amsterdam - -Contact: astra@uantwerpen.be -Website: http://sf.net/projects/astra-toolbox - -This file is part of the ASTRA Toolbox. - - -The ASTRA Toolbox is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -The ASTRA Toolbox is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. - ------------------------------------------------------------------------ -$Id$ -*/ - -#ifndef _INC_ASTRA_LOGGER -#define _INC_ASTRA_LOGGER - -#include <cstdio> - -namespace astra -{ - -/** - * This is the first stab at a decent logger. If the file "astra_logger.txt", it will be replaced - * with the text sent to this logger. If the file doesn't exist when the app starts, nothing is written. - */ -class CLogger -{ - static std::FILE * m_pOutFile; - static bool m_bInitialized; - - static void _assureIsInitialized(); - - CLogger(); - -public: - - /** - * Writes a line to the log file (newline is added). Ignored if logging is turned off. - * - * @param _text char pointer to text in line - */ - static void writeLine(const char * _text); - - /** - * Formats and writes a CUDA error to the log file. Ignored if logging is turned off. - * - * @param _fileName filename where error occurred (typically __FILE__) - * @param _line line in file (typically __LINE__) - * @param _errString string describing the error, can be output of cudaGetErrorString - */ - static void writeTerminalCUDAError(const char * _fileName, int _iLine, const char * _errString); -}; - -} - -#endif /* _INC_ASTRA_LOGGER */ - diff --git a/include/astra/Logging.h b/include/astra/Logging.h new file mode 100644 index 0000000..8e19ea4 --- /dev/null +++ b/include/astra/Logging.h @@ -0,0 +1,159 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +#ifndef _INC_ASTRA_LOGGING +#define _INC_ASTRA_LOGGING + +#include "astra/Globals.h" + +#define ASTRA_DEBUG(...) astra::CLogger::debug(__FILE__,__LINE__, __VA_ARGS__) +#define ASTRA_INFO(...) astra::CLogger::info(__FILE__,__LINE__, __VA_ARGS__) +#define ASTRA_WARN(...) astra::CLogger::warn(__FILE__,__LINE__, __VA_ARGS__) +#define ASTRA_ERROR(...) astra::CLogger::error(__FILE__,__LINE__, __VA_ARGS__) + +namespace astra +{ + +enum log_level { + LOG_DEBUG, + LOG_INFO, + LOG_WARN, + LOG_ERROR +}; + +class _AstraExport CLogger +{ + CLogger(); + ~CLogger(); + static bool m_bEnabledFile; + static bool m_bEnabledScreen; + static bool m_bFileProvided; + static bool m_bInitialized; + static void _assureIsInitialized(); + static void _setLevel(int id, log_level m_eLevel); + +public: + + /** + * Writes a line to the log file (newline is added). Ignored if logging is turned off. + * + * @param sfile + * The name of the source file making this log call (e.g. __FILE__). + * + * @param sline + * The line number of the call in the source code (e.g. __LINE__). + * + * @param id + * The id of the logger to write to. + * + * @param fmt + * The format string for the message (printf formatting). + * + * @param ... + * Any additional format arguments. + */ + static void debug(const char *sfile, int sline, const char *fmt, ...); + static void info(const char *sfile, int sline, const char *fmt, ...); + static void warn(const char *sfile, int sline, const char *fmt, ...); + static void error(const char *sfile, int sline, const char *fmt, ...); + + /** + * Sets the file to log to, with logging level. + * + * @param filename + * File to log to. + * + * @param m_eLevel + * Logging level (LOG_DEBUG, LOG_WARN, LOG_INFO, LOG_ERROR). + * + */ + static void setOutputFile(const char *filename, log_level m_eLevel); + + /** + * Sets the screen to log to, with logging level. + * + * @param screen_fd + * Screen file descriptor (1 for stdout, 2 for stderr) + * + * @param m_eLevel + * Logging level (LOG_DEBUG, LOG_WARN, LOG_INFO, LOG_ERROR). + * + */ + static void setOutputScreen(int fd, log_level m_eLevel); + + /** + * Set the format string for log messages. Here are the substitutions you may + * use: + * + * %f: Source file name generating the log call. + * %n: Source line number where the log call was made. + * %m: The message text sent to the logger (after printf formatting). + * %d: The current date, formatted using the logger's date format. + * %t: The current time, formatted using the logger's time format. + * %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR"). + * %%: A literal percent sign. + * + * The default format string is "%d %t %f(%n): %l: %m\n". + * + * @param fmt + * The new format string, which must be less than 256 bytes. + * You probably will want to end this with a newline (\n). + * + */ + static void setFormatFile(const char *fmt); + static void setFormatScreen(const char *fmt); + + + /** + * Enable logging. + * + */ + static void enable(); + static void enableScreen(); + static void enableFile(); + + /** + * Disable logging. + * + */ + static void disable(); + static void disableScreen(); + static void disableFile(); + + /** + * Set callback function for logging to screen. + * @return whether callback was set succesfully. + * + */ + static bool setCallbackScreen(void (*cb)(const char *msg, size_t len)); + +}; + +} + +#endif /* _INC_ASTRA_LOGGING */ diff --git a/include/astra/ParallelProjectionGeometry2D.h b/include/astra/ParallelProjectionGeometry2D.h index ed9d228..2f7d36f 100644 --- a/include/astra/ParallelProjectionGeometry2D.h +++ b/include/astra/ParallelProjectionGeometry2D.h @@ -136,6 +136,12 @@ public: */ virtual bool isOfType(const std::string& _sType); + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** * Returns a vector describing the direction of a ray belonging to a certain detector, * the direction is the same for all detectors in one projection diff --git a/include/astra/ParallelProjectionGeometry3D.h b/include/astra/ParallelProjectionGeometry3D.h index 9d61daa..72401e5 100644 --- a/include/astra/ParallelProjectionGeometry3D.h +++ b/include/astra/ParallelProjectionGeometry3D.h @@ -41,8 +41,8 @@ namespace astra * \par XML Configuration * \astra_xml_item{DetectorRowCount, int, Number of detectors for each projection.} * \astra_xml_item{DetectorColCount, int, Number of detectors for each projection.} - * \astra_xml_item{DetectorWidth, float, Width of each detector.} - * \astra_xml_item{DetectorHeight, float, Width of each detector.} + * \astra_xml_item{DetectorSpacingX, float, Width of each detector.} + * \astra_xml_item{DetectorSpacingY, float, Width of each detector.} * \astra_xml_item{ProjectionAngles, vector of float, projection angles in radians.} * * \par MATLAB example @@ -50,8 +50,8 @@ namespace astra * proj_geom = astra_struct('parallel');\n * proj_geom.DetectorRowCount = 512;\n * proj_geom.DetectorColCount = 512;\n - * proj_geom.DetectorWidth = 1.0;\n - * proj_geom.DetectorHeight = 1.0;\n + * proj_geom.DetectorSpacingX = 1.0;\n + * proj_geom.DetectorSpacingY = 1.0;\n * proj_geom.ProjectionAngles = linspace(0,pi,100);\n * } */ @@ -129,6 +129,12 @@ public: */ virtual bool isEqual(const CProjectionGeometry3D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * * @param _sType geometry type to compare to. @@ -136,17 +142,15 @@ public: */ virtual bool isOfType(const std::string& _sType) const; - /** Turn this object into an XML object. - * - * @param _sNode The XML object to fill. - */ - virtual void toXML(XMLNode* _sNode) const; - /** * Returns a vector giving the projection direction for a projection and detector index */ virtual CVector3D getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const; + virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const; + /** * Creates (= allocates) a 2D projection geometry used when projecting one slice using a 2D projector * diff --git a/include/astra/ParallelVecProjectionGeometry3D.h b/include/astra/ParallelVecProjectionGeometry3D.h index 12365a1..59238c8 100644 --- a/include/astra/ParallelVecProjectionGeometry3D.h +++ b/include/astra/ParallelVecProjectionGeometry3D.h @@ -30,7 +30,7 @@ $Id$ #define _INC_ASTRA_PARALLELVECPROJECTIONGEOMETRY3D #include "ProjectionGeometry3D.h" -#include "../cuda/3d/dims3d.h" +#include "GeometryUtil3D.h" namespace astra { @@ -55,7 +55,7 @@ namespace astra * to a single projection, and consists of: * ( rayX, rayY, rayZ, dX, dY, dZ, uX, uY, uZ, vX, vY, vZ ) * ray: the ray direction - * d : the corner of the detector + * d : the centre of the detector plane * u : the vector from detector pixel (0,0) to (0,1) * v : the vector from detector pixel (0,0) to (1,0) */ @@ -128,6 +128,12 @@ public: */ virtual bool isEqual(const CProjectionGeometry3D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * * @param _sType geometry type to compare to. @@ -135,12 +141,6 @@ public: */ virtual bool isOfType(const std::string& _sType) const; - /** Turn this object into an XML object. - * - * @param _sNode The XML object to fill. - */ - virtual void toXML(XMLNode* _sNode) const; - /** * Returns a vector giving the projection direction for a projection and detector index */ @@ -149,7 +149,9 @@ public: const SPar3DProjection* getProjectionVectors() const { return m_pProjectionAngles; } - + virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const; }; } // namespace astra diff --git a/include/astra/ProjectionGeometry2D.h b/include/astra/ProjectionGeometry2D.h index 303ca0a..b8324e2 100644 --- a/include/astra/ProjectionGeometry2D.h +++ b/include/astra/ProjectionGeometry2D.h @@ -157,6 +157,12 @@ public: */ virtual bool isEqual(CProjectionGeometry2D*) const = 0; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const = 0; + /** Get the number of projection angles. * * @return Number of projection angles diff --git a/include/astra/ProjectionGeometry3D.h b/include/astra/ProjectionGeometry3D.h index 6bc9368..19ac3ab 100644 --- a/include/astra/ProjectionGeometry3D.h +++ b/include/astra/ProjectionGeometry3D.h @@ -187,6 +187,12 @@ public: */ virtual bool isEqual(const CProjectionGeometry3D *) const = 0; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const = 0; + /** Get the number of projections. * * @return Number of projections @@ -298,10 +304,23 @@ public: * * @param _iIndex the index of the detector. * @param _iAngleIndex output: index of angle - * @param _iDetectorIndex output: index of dectecor + * @param _iDetectorIndex output: index of detector */ virtual void indexToAngleDetectorIndex(int _iIndex, int& _iAngleIndex, int& _iDetectorIndex) const; + /** Project a point onto the detector. The 3D point coordinates + * are in units. The output fU,fV are the (unrounded) indices of the + * detector column and row. + * This may fall outside of the actual detector. + * + * @param fX,fY,fZ coordinates of the point to project + * @param iAngleIndex the index of the angle to use + * @param fU,fV the projected point. + */ + virtual void projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const = 0; + /** Returns true if the type of geometry defined in this class is the one specified in _sType. * * @param _sType geometry type to compare to. @@ -309,12 +328,6 @@ public: */ virtual bool isOfType(const std::string& _sType) const = 0; - /** Turn this object into an XML object. - * - * @param _sNode The XML object to fill. - */ - virtual void toXML(XMLNode* _sNode) const = 0; - /** * Returns a vector giving the projection direction for a projection and detector index */ diff --git a/include/astra/Projector3D.h b/include/astra/Projector3D.h index e1f0646..1ef1ba7 100644 --- a/include/astra/Projector3D.h +++ b/include/astra/Projector3D.h @@ -34,13 +34,13 @@ $Id$ #include "Globals.h" #include "Config.h" -#include "ProjectionGeometry3D.h" -#include "VolumeGeometry3D.h" namespace astra { class CSparseMatrix; +class CProjectionGeometry3D; +class CVolumeGeometry3D; /** This is a base interface class for a three-dimensional projector. Each subclass should at least diff --git a/include/astra/SparseMatrixProjectionGeometry2D.h b/include/astra/SparseMatrixProjectionGeometry2D.h index 36964be..d56f95e 100644 --- a/include/astra/SparseMatrixProjectionGeometry2D.h +++ b/include/astra/SparseMatrixProjectionGeometry2D.h @@ -103,7 +103,6 @@ public: * @param _pMatrix Pointer to a CSparseMatrix. The caller is responsible for keeping this matrix valid until it is no longer required. * @return initialization successful? */ - bool setMatrix(CSparseMatrix* _pMatrix); /** Get a pointer to the associated sparse matrix. @@ -128,6 +127,13 @@ public: */ virtual bool isOfType(const std::string& _sType); + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + + /** * Returns a vector describing the direction of a ray belonging to a certain detector * diff --git a/include/astra/VolumeGeometry2D.h b/include/astra/VolumeGeometry2D.h index fa0528d..28703d5 100644 --- a/include/astra/VolumeGeometry2D.h +++ b/include/astra/VolumeGeometry2D.h @@ -205,6 +205,12 @@ public: */ virtual bool isEqual(CVolumeGeometry2D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Get the number of columns in the volume grid. * * @return Number of columns in the volume grid. diff --git a/include/astra/VolumeGeometry3D.h b/include/astra/VolumeGeometry3D.h index d5c8fff..ff94844 100644 --- a/include/astra/VolumeGeometry3D.h +++ b/include/astra/VolumeGeometry3D.h @@ -246,6 +246,12 @@ public: */ virtual bool isEqual(const CVolumeGeometry3D*) const; + /** Get all settings in a Config object. + * + * @return Configuration Object. + */ + virtual Config* getConfiguration() const; + /** Get the number of columns in the volume grid. * * @return Number of columns in the volume grid. diff --git a/include/astra/XMLDocument.h b/include/astra/XMLDocument.h index c6f1b9a..869e1a3 100644 --- a/include/astra/XMLDocument.h +++ b/include/astra/XMLDocument.h @@ -86,6 +86,9 @@ public: */ void saveToFile(string sFilename); + /** convert and XML DOM tree to a string + */ + std::string toString(); private: diff --git a/include/astra/clog.h b/include/astra/clog.h new file mode 100644 index 0000000..6ffb660 --- /dev/null +++ b/include/astra/clog.h @@ -0,0 +1,693 @@ +/* clog: Extremely simple logger for C. + * + * Features: + * - Implemented purely as a single header file. + * - Create multiple loggers. + * - Four log levels (debug, info, warn, error). + * - Custom formats. + * - Fast. + * + * Dependencies: + * - Should conform to C89, C++98 (but requires vsnprintf, unfortunately). + * - POSIX environment. + * + * USAGE: + * + * Include this header in any file that wishes to write to logger(s). In + * exactly one file (per executable), define CLOG_MAIN first (e.g. in your + * main .c file). + * + * #define CLOG_MAIN + * #include "clog.h" + * + * This will define the actual objects that all the other units will use. + * + * Loggers are identified by integers (0 - 15). It's expected that you'll + * create meaningful constants and then refer to the loggers as such. + * + * Example: + * + * const int MY_LOGGER = 0; + * + * int main() { + * int r; + * r = clog_init_path(MY_LOGGER, "my_log.txt"); + * if (r != 0) { + * fprintf(stderr, "Logger initialization failed.\n"); + * return 1; + * } + * clog_info(CLOG(MY_LOGGER), "Hello, world!"); + * clog_free(MY_LOGGER); + * return 0; + * } + * + * The CLOG macro used in the call to clog_info is a helper that passes the + * __FILE__ and __LINE__ parameters for you, so you don't have to type them + * every time. (It could be prettier with variadic macros, but that requires + * C99 or C++11 to be standards compliant.) + * + * Errors encountered by clog will be printed to stderr. You can suppress + * these by defining a macro called CLOG_SILENT before including clog.h. + * + * License: Do whatever you want. It would be nice if you contribute + * improvements as pull requests here: + * + * https://github.com/mmueller/clog + * + * Copyright 2013 Mike Mueller <mike@subfocal.net>. + * + * As is; no warranty is provided; use at your own risk. + */ + +#ifndef __CLOG_H__ +#define __CLOG_H__ + +#include <sys/types.h> +#include <sys/stat.h> +#include <errno.h> +#include <fcntl.h> +#include <stdarg.h> +#include <stdlib.h> +#include <stdio.h> +#include <string.h> +#include <time.h> +#ifndef _MSC_VER +#include <unistd.h> +#else +#define WIN32_LEAN_AND_MEAN +#include <windows.h> +#include <io.h> +#define open _open +#define close _close +#define write _write +#define snprintf _snprintf +#endif + +/* Number of loggers that can be defined. */ +#define CLOG_MAX_LOGGERS 16 + +/* Format strings cannot be longer than this. */ +#define CLOG_FORMAT_LENGTH 256 + +/* Formatted times and dates should be less than this length. If they are not, + * they will not appear in the log. */ +#define CLOG_DATETIME_LENGTH 256 + +/* Default format strings. */ +#define CLOG_DEFAULT_FORMAT "%d %t %f(%n): %l: %m\n" +#define CLOG_DEFAULT_DATE_FORMAT "%Y-%m-%d" +#define CLOG_DEFAULT_TIME_FORMAT "%H:%M:%S" + +#ifdef __cplusplus +extern "C" { +#endif + +enum clog_level { + CLOG_DEBUG, + CLOG_INFO, + CLOG_WARN, + CLOG_ERROR +}; + +struct clog; + +/** + * Create a new logger writing to the given file path. The file will always + * be opened in append mode. + * + * @param id + * A constant integer between 0 and 15 that uniquely identifies this logger. + * + * @param path + * Path to the file where log messages will be written. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_init_path(int id, const char *const path); + +/** + * Create a new logger writing to a file descriptor. + * + * @param id + * A constant integer between 0 and 15 that uniquely identifies this logger. + * + * @param fd + * The file descriptor where log messages will be written. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_init_fd(int id, int fd); + +/** + * Destroy (clean up) a logger. You should do this at the end of execution, + * or when you are done using the logger. + * + * @param id + * The id of the logger to destroy. + */ +void clog_free(int id); + +#define CLOG(id) __FILE__, __LINE__, id + +/** + * Log functions (one per level). Call these to write messages to the log + * file. The first three arguments can be replaced with a call to the CLOG + * macro defined above, e.g.: + * + * clog_debug(CLOG(MY_LOGGER_ID), "This is a log message."); + * + * @param sfile + * The name of the source file making this log call (e.g. __FILE__). + * + * @param sline + * The line number of the call in the source code (e.g. __LINE__). + * + * @param id + * The id of the logger to write to. + * + * @param fmt + * The format string for the message (printf formatting). + * + * @param ... + * Any additional format arguments. + */ +void clog_debug(const char *sfile, int sline, int id, const char *fmt, va_list ap); +void clog_info(const char *sfile, int sline, int id, const char *fmt, va_list ap); +void clog_warn(const char *sfile, int sline, int id, const char *fmt, va_list ap); +void clog_error(const char *sfile, int sline, int id, const char *fmt, va_list ap); + +/** + * Set the minimum level of messages that should be written to the log. + * Messages below this level will not be written. By default, loggers are + * created with level == CLOG_DEBUG. + * + * @param id + * The identifier of the logger. + * + * @param level + * The new minimum log level. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_level(int id, enum clog_level level); + +/** + * Set the format string used for times. See strftime(3) for how this string + * should be defined. The default format string is CLOG_DEFAULT_TIME_FORMAT. + * + * @param fmt + * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_time_fmt(int id, const char *fmt); + +/** + * Set the format string used for dates. See strftime(3) for how this string + * should be defined. The default format string is CLOG_DEFAULT_DATE_FORMAT. + * + * @param fmt + * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_date_fmt(int id, const char *fmt); + +/** + * Set the format string for log messages. Here are the substitutions you may + * use: + * + * %f: Source file name generating the log call. + * %n: Source line number where the log call was made. + * %m: The message text sent to the logger (after printf formatting). + * %d: The current date, formatted using the logger's date format. + * %t: The current time, formatted using the logger's time format. + * %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR"). + * %%: A literal percent sign. + * + * The default format string is CLOG_DEFAULT_FORMAT. + * + * @param fmt + * The new format string, which must be less than CLOG_FORMAT_LENGTH bytes. + * You probably will want to end this with a newline (\n). + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_fmt(int id, const char *fmt); + +/** + * Set the callback function. + * + * @param cb + * The new callback function. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_cb(int id, void (*cb)(const char *msg, size_t len)); + +/** + * Set the file descriptor. + * + * @param id + * The identifier of the logger. + * + * @param fd + * The new file descriptor. + * + * @return + * Zero on success, non-zero on failure. + */ +int clog_set_fd(int id, int fd); + + +/* + * No need to read below this point. + */ + +/** + * The C logger structure. + */ +struct clog { + + /* The current level of this logger. Messages below it will be dropped. */ + enum clog_level level; + + /* The file being written. */ + int fd; + + /* The format specifier. */ + char fmt[CLOG_FORMAT_LENGTH]; + + /* Date format */ + char date_fmt[CLOG_FORMAT_LENGTH]; + + /* Time format */ + char time_fmt[CLOG_FORMAT_LENGTH]; + + /* Tracks whether the fd needs to be closed eventually. */ + int opened; + + /* Callback function for each log message. */ + void (*cb)(const char *msg, size_t len); +}; + +void _clog_err(const char *fmt, ...); + +#ifdef CLOG_MAIN +struct clog *_clog_loggers[CLOG_MAX_LOGGERS] = { 0 }; +#else +extern struct clog *_clog_loggers[CLOG_MAX_LOGGERS]; +#endif + +#ifdef CLOG_MAIN + +const char *const CLOG_LEVEL_NAMES[] = { + "Debug", + "Info", + "Warning", + "Error", +}; + +int +clog_init_path(int id, const char *const path) +{ + int fd = open(path, O_CREAT | O_WRONLY | O_APPEND, 0666); + if (fd == -1) { + _clog_err("Unable to open %s: %s\n", path, strerror(errno)); + return 1; + } + if (clog_init_fd(id, fd)) { + close(fd); + return 1; + } + _clog_loggers[id]->opened = 1; + return 0; +} + +int +clog_init_fd(int id, int fd) +{ + struct clog *logger; + + if (_clog_loggers[id] != NULL) { + _clog_err("Logger %d already initialized.\n", id); + return 1; + } + + logger = (struct clog *) malloc(sizeof(struct clog)); + if (logger == NULL) { + _clog_err("Failed to allocate logger: %s\n", strerror(errno)); + return 1; + } + + logger->level = CLOG_DEBUG; + logger->fd = fd; + logger->opened = 0; + strcpy(logger->fmt, CLOG_DEFAULT_FORMAT); + strcpy(logger->date_fmt, CLOG_DEFAULT_DATE_FORMAT); + strcpy(logger->time_fmt, CLOG_DEFAULT_TIME_FORMAT); + logger->cb = NULL; + + _clog_loggers[id] = logger; + return 0; +} + +void +clog_free(int id) +{ + if (_clog_loggers[id]) { + if (_clog_loggers[id]->opened) { + close(_clog_loggers[id]->fd); + } + free(_clog_loggers[id]); + _clog_loggers[id]=NULL; + } +} + +int +clog_set_level(int id, enum clog_level level) +{ + if (_clog_loggers[id] == NULL) { + return 1; + } + if ((unsigned) level > CLOG_ERROR) { + return 1; + } + _clog_loggers[id]->level = level; + return 0; +} + +int +clog_set_fd(int id, int fd) +{ + if (_clog_loggers[id] == NULL) { + return 1; + } + _clog_loggers[id]->fd = fd; + return 0; +} + +int +clog_set_time_fmt(int id, const char *fmt) +{ + struct clog *logger = _clog_loggers[id]; + if (logger == NULL) { + _clog_err("clog_set_time_fmt: No such logger: %d\n", id); + return 1; + } + if (strlen(fmt) >= CLOG_FORMAT_LENGTH) { + _clog_err("clog_set_time_fmt: Format specifier too long.\n"); + return 1; + } + strcpy(logger->time_fmt, fmt); + return 0; +} + +int +clog_set_date_fmt(int id, const char *fmt) +{ + struct clog *logger = _clog_loggers[id]; + if (logger == NULL) { + _clog_err("clog_set_date_fmt: No such logger: %d\n", id); + return 1; + } + if (strlen(fmt) >= CLOG_FORMAT_LENGTH) { + _clog_err("clog_set_date_fmt: Format specifier too long.\n"); + return 1; + } + strcpy(logger->date_fmt, fmt); + return 0; +} + +int +clog_set_fmt(int id, const char *fmt) +{ + struct clog *logger = _clog_loggers[id]; + if (logger == NULL) { + _clog_err("clog_set_fmt: No such logger: %d\n", id); + return 1; + } + if (strlen(fmt) >= CLOG_FORMAT_LENGTH) { + _clog_err("clog_set_fmt: Format specifier too long.\n"); + return 1; + } + strcpy(logger->fmt, fmt); + return 0; +} + +int +clog_set_cb(int id, void (*cb)(const char *msg, size_t len)) +{ + struct clog *logger = _clog_loggers[id]; + if (logger == NULL) { + _clog_err("clog_set_cb: No such logger: %d\n", id); + return 1; + } + logger->cb = cb; + return 0; +} + +/* Internal functions */ + +size_t +_clog_append_str(char **dst, char *orig_buf, const char *src, size_t cur_size) +{ + size_t new_size = cur_size; + + while (strlen(*dst) + strlen(src) >= new_size) { + new_size *= 2; + } + if (new_size != cur_size) { + if (*dst == orig_buf) { + *dst = (char *) malloc(new_size); + strcpy(*dst, orig_buf); + } else { + *dst = (char *) realloc(*dst, new_size); + } + } + + strcat(*dst, src); + return new_size; +} + +size_t +_clog_append_int(char **dst, char *orig_buf, long int d, size_t cur_size) +{ + char buf[40]; /* Enough for 128-bit decimal */ + if (snprintf(buf, 40, "%ld", d) >= 40) { + return cur_size; + } + return _clog_append_str(dst, orig_buf, buf, cur_size); +} + +size_t +_clog_append_time(char **dst, char *orig_buf, struct tm *lt, + const char *fmt, size_t cur_size) +{ + char buf[CLOG_DATETIME_LENGTH]; + size_t result = strftime(buf, CLOG_DATETIME_LENGTH, fmt, lt); + + if (result > 0) { + return _clog_append_str(dst, orig_buf, buf, cur_size); + } + + return cur_size; +} + +const char * +_clog_basename(const char *path) +{ + const char *slash = strrchr(path, '/'); + if (slash) { + path = slash + 1; + } +#ifdef _WIN32 + slash = strrchr(path, '\\'); + if (slash) { + path = slash + 1; + } +#endif + return path; +} + +char * +_clog_format(const struct clog *logger, char buf[], size_t buf_size, + const char *sfile, int sline, const char *level, + const char *message) +{ + size_t cur_size = buf_size; + char *result = buf; + enum { NORMAL, SUBST } state = NORMAL; + size_t fmtlen = strlen(logger->fmt); + size_t i; + time_t t = time(NULL); + struct tm *lt = localtime(&t); + + sfile = _clog_basename(sfile); + result[0] = 0; + for (i = 0; i < fmtlen; ++i) { + if (state == NORMAL) { + if (logger->fmt[i] == '%') { + state = SUBST; + } else { + char str[2] = { 0 }; + str[0] = logger->fmt[i]; + cur_size = _clog_append_str(&result, buf, str, cur_size); + } + } else { + switch (logger->fmt[i]) { + case '%': + cur_size = _clog_append_str(&result, buf, "%", cur_size); + break; + case 't': + cur_size = _clog_append_time(&result, buf, lt, + logger->time_fmt, cur_size); + break; + case 'd': + cur_size = _clog_append_time(&result, buf, lt, + logger->date_fmt, cur_size); + break; + case 'l': + cur_size = _clog_append_str(&result, buf, level, cur_size); + break; + case 'n': + cur_size = _clog_append_int(&result, buf, sline, cur_size); + break; + case 'f': + cur_size = _clog_append_str(&result, buf, sfile, cur_size); + break; + case 'm': + cur_size = _clog_append_str(&result, buf, message, + cur_size); + break; + } + state = NORMAL; + } + } + + return result; +} + +void +_clog_log(const char *sfile, int sline, enum clog_level level, + int id, const char *fmt, va_list ap) +{ + /* For speed: Use a stack buffer until message exceeds 4096, then switch + * to dynamically allocated. This should greatly reduce the number of + * memory allocations (and subsequent fragmentation). */ + char buf[4096]; + size_t buf_size = 4096; + char *dynbuf = buf; + char *message; + int result; + struct clog *logger = _clog_loggers[id]; + + if (!logger) { + _clog_err("No such logger: %d\n", id); + return; + } + + if (level < logger->level) { + return; + } + + /* Format the message text with the argument list. */ + result = vsnprintf(dynbuf, buf_size, fmt, ap); + if ((size_t) result >= buf_size) { + buf_size = result + 1; + dynbuf = (char *) malloc(buf_size); + result = vsnprintf(dynbuf, buf_size, fmt, ap); + if ((size_t) result >= buf_size) { + /* Formatting failed -- too large */ + _clog_err("Formatting failed (1).\n"); + free(dynbuf); + return; + } + } + + /* Format according to log format and write to log */ + { + char message_buf[4096]; + message = _clog_format(logger, message_buf, 4096, sfile, sline, + CLOG_LEVEL_NAMES[level], dynbuf); + if (!message) { + _clog_err("Formatting failed (2).\n"); + if (dynbuf != buf) { + free(dynbuf); + } + return; + } + result = write(logger->fd, message, strlen(message)); + if (logger->cb) logger->cb(message,strlen(message)); + if (result == -1) { + _clog_err("Unable to write to log file: %s\n", strerror(errno)); + } + if (message != message_buf) { + free(message); + } + if (dynbuf != buf) { + free(dynbuf); + } +#ifndef _MSC_VER + fsync(logger->fd); +#else + HANDLE h = (HANDLE) _get_osfhandle(logger->fd); + if (h != INVALID_HANDLE_VALUE) { + // This call will fail on a console fd, but that's ok. + FlushFileBuffers(h); + } +#endif + } +} + +void +clog_debug(const char *sfile, int sline, int id, const char *fmt, va_list ap) +{ + _clog_log(sfile, sline, CLOG_DEBUG, id, fmt, ap); +} + +void +clog_info(const char *sfile, int sline, int id, const char *fmt, va_list ap) +{ + _clog_log(sfile, sline, CLOG_INFO, id, fmt, ap); +} + +void +clog_warn(const char *sfile, int sline, int id, const char *fmt, va_list ap) +{ + _clog_log(sfile, sline, CLOG_WARN, id, fmt, ap); +} + +void +clog_error(const char *sfile, int sline, int id, const char *fmt, va_list ap) +{ + _clog_log(sfile, sline, CLOG_ERROR, id, fmt, ap); +} + +void +_clog_err(const char *fmt, ...) +{ +#ifdef CLOG_SILENT + (void) fmt; +#else + va_list ap; + + va_start(ap, fmt); + vfprintf(stderr, fmt, ap); +#endif +} + +#endif /* CLOG_MAIN */ + +#ifdef __cplusplus +} /* extern "C" */ +#endif + +#endif /* __CLOG_H__ */ diff --git a/matlab/algorithms/DART/DARTalgorithm.m b/matlab/algorithms/DART/DARTalgorithm.m index f8c2ce7..fc707dd 100644 --- a/matlab/algorithms/DART/DARTalgorithm.m +++ b/matlab/algorithms/DART/DARTalgorithm.m @@ -1,21 +1,16 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox %-------------------------------------------------------------------------- classdef DARTalgorithm < matlab.mixin.Copyable - % Algorithm class for Discrete Algebraic Reconstruction Technique (DART). - % todo: reset() - % todo: fixed random seed - % todo: initialize from settings (?) - %---------------------------------------------------------------------- properties (GetAccess=public, SetAccess=public) @@ -78,7 +73,6 @@ classdef DARTalgorithm < matlab.mixin.Copyable error('invalid arguments') end end - %------------------------------------------------------------------ function D = deepcopy(this) @@ -100,7 +94,6 @@ classdef DARTalgorithm < matlab.mixin.Copyable % Initialize tomography part if ~this.tomography.initialized - this.tomography.sinogram = this.base.sinogram; this.tomography.proj_geom = this.base.proj_geom; this.tomography.initialize(); end @@ -110,7 +103,7 @@ classdef DARTalgorithm < matlab.mixin.Copyable this.V0 = this.base.V0; else this.output.pre_initial_iteration(this); - this.V0 = this.tomography.reconstruct2(this.base.sinogram, [], this.t0); + this.V0 = this.tomography.reconstruct(this.base.sinogram, this.t0); this.output.post_initial_iteration(this); end this.V = this.V0; @@ -163,7 +156,7 @@ classdef DARTalgorithm < matlab.mixin.Copyable this.R = this.base.sinogram - this.tomography.project(F); % ART update part - this.V = this.tomography.reconstruct2_mask(this.R, this.V, this.Mask, this.t); + this.V = this.tomography.reconstruct_mask(this.R, this.V, this.Mask, this.t); % blur this.V = this.smoothing.apply(this, this.V); diff --git a/matlab/algorithms/DART/IterativeTomography.m b/matlab/algorithms/DART/IterativeTomography.m new file mode 100644 index 0000000..3875e6b --- /dev/null +++ b/matlab/algorithms/DART/IterativeTomography.m @@ -0,0 +1,435 @@ +classdef IterativeTomography < matlab.mixin.Copyable + + % Algorithm class for 2D Iterative Tomography. + + %---------------------------------------------------------------------- + properties (SetAccess=public, GetAccess=public) + superresolution = 1; % SETTING: Volume upsampling factor. + proj_type = 'linear'; % SETTING: Projector type, only when gpu='no'. + method = 'SIRT_CUDA'; % SETTING: Iterative method (see ASTRA toolbox documentation). + gpu = 'yes'; % SETTING: Use gpu? {'yes', 'no'} + gpu_core = 0; % SETTING: Which gpu core to use? Only when gpu='yes'. + inner_circle = 'yes'; % SETTING: Do roi only? {'yes', 'no'} + image_size = []; % SETTING: Overwrite default reconstruction size. Only if no vol_geom is specified. + use_minc = 'no'; % SETTING: Use minimum constraint. {'no', 'yes'} + end + %---------------------------------------------------------------------- + properties (SetAccess=public, GetAccess=public) + proj_geom = []; % DATA: Projection geometry. + vol_geom = []; % DATA: Volume geometry. + end + %---------------------------------------------------------------------- + properties (SetAccess=private, GetAccess=public) + initialized = 0; % Is this object initialized? + end + %---------------------------------------------------------------------- + properties (SetAccess=protected, GetAccess=protected) + cfg_base = struct(); % PROTECTED: base configuration structure for the reconstruction algorithm. + proj_geom_sr = []; % PROTECTED: geometry of sinogram (with super-resolution) + proj_id = []; % PROTECTED: astra id of projector (when gpu='no') + proj_id_sr = []; % PROTECTED: astra id of super-resolution projector (when gpu='no') + end + %---------------------------------------------------------------------- + + methods (Access=public) + + %------------------------------------------------------------------ + function this = IterativeTomography(varargin) + % Constructor + % >> tomography = IterativeTomography(proj_geom); + % >> tomography = IterativeTomography(proj_geom, vol_geom); + + % Input: IterativeTomography(proj_geom) + if nargin == 1 + this.proj_geom = varargin{1}; + + % Input: IterativeTomography(proj_geom, vol_geom) + elseif nargin == 2 + this.proj_geom = varargin{1}; + this.vol_geom = varargin{2}; + end + end + + %------------------------------------------------------------------ + function delete(this) + % Destructor + % >> clear tomography; + if strcmp(this.gpu,'no') && numel(this.proj_id) > 0 + astra_mex_projector('delete', this.proj_id, this.proj_id_sr); + end + end + + %------------------------------------------------------------------ + function settings = getsettings(this) + % Returns a structure containing all settings of this object. + % >> settings = tomography.getsettings(); + settings.superresolution = this.superresolution; + settings.proj_type = this.proj_type; + settings.method = this.method; + settings.gpu = this.gpu; + settings.gpu_core = this.gpu_core; + settings.inner_circle = this.inner_circle; + settings.image_size = this.image_size; + settings.use_minc = this.use_minc; + end + + %------------------------------------------------------------------ + function ok = initialize(this) + % Initialize this object. Returns 1 if succesful. + % >> tomography.initialize(); + + % create projection geometry with super-resolution + if this.superresolution > 1 + this.proj_geom_sr = astra_geom_superresolution(this.proj_geom, this.superresolution); + else + this.proj_geom_sr = this.proj_geom; + end + + % if no volume geometry is specified by the user: create volume geometry + if numel(this.vol_geom) == 0 + if numel(this.image_size) < 2 + this.image_size(1) = this.proj_geom.DetectorCount; + this.image_size(2) = this.proj_geom.DetectorCount; + end + this.vol_geom = astra_create_vol_geom(this.image_size(1) * this.superresolution, this.image_size(2) * this.superresolution, ... + -this.image_size(1)/2, this.image_size(1)/2, -this.image_size(2)/2, this.image_size(2)/2); + else + this.image_size(1) = this.vol_geom.GridRowCount; + this.image_size(2) = this.vol_geom.GridColCount; + end + + % create projector + if strcmp(this.gpu,'no') + this.proj_id = astra_create_projector(this.proj_type, this.proj_geom, this.vol_geom); + this.proj_id_sr = astra_create_projector(this.proj_type, this.proj_geom_sr, this.vol_geom); + end + + % create reconstruction configuration + this.cfg_base = astra_struct(upper(this.method)); + if strcmp(this.gpu,'no') + this.cfg_base.ProjectorId = this.proj_id; + this.cfg_base.ProjectionGeometry = this.proj_geom; + this.cfg_base.ReconstructionGeometry = this.vol_geom; + end + this.cfg_base.option.DetectorSuperSampling = this.superresolution; + if strcmp(this.gpu,'yes') + this.cfg_base.option.GPUindex = this.gpu_core; + end + if this.use_minc + this.cfg_base.option.MinConstraint = 0; + end + + this.initialized = 1; + ok = this.initialized; + end + + %------------------------------------------------------------------ + function projections = project(this, volume) + % Compute forward projection. + % >> projections = tomography.project(volume); + + if ~this.initialized + this.initialize(); + end + + % project + projections = this.project_c(volume); + end + + %------------------------------------------------------------------ + function reconstruction = reconstruct(this, varargin) + % Compute reconstruction. + % Uses tomography.sinogram + % Initial solution (if available) should be stored in tomography.V + % >> reconstruction = tomography.reconstruct(projections, iterations); + % >> reconstruction = tomography.reconstruct(projections, volume0, iterations); + + if ~this.initialized + this.initialize(); + end + + if numel(varargin) == 2 + reconstruction = this.reconstruct_c(varargin{1}, [], [], varargin{2}); + elseif numel(varargin) == 3 + reconstruction = this.reconstruct_c(varargin{1}, varargin{2}, [], varargin{3}); + else + error('invalid parameter list') + end + + if strcmp(this.inner_circle,'yes') + reconstruction = this.selectROI(reconstruction); + end + end + + %------------------------------------------------------------------ + function reconstruction = reconstruct_mask(this, varargin) + % Compute reconstruction with mask. + % Uses tomography.sinogram + % Initial solution (if available) should be stored in tomography.V + % >> reconstruction = tomography.reconstructMask(projections, mask, iterations); + % >> reconstruction = tomography.reconstructMask(projections, volume0, mask, iterations); + + if ~this.initialized + this.initialize(); + end + + if numel(varargin) == 3 + reconstruction = this.reconstruct_c(varargin{1}, [], varargin{2}, varargin{3}); + elseif numel(varargin) == 4 + reconstruction = this.reconstruct_c(varargin{1}, varargin{2}, varargin{3}, varargin{4}); + else + error('invalid parameter list') + end + + if strcmp(this.inner_circle,'yes') + reconstruction = this.selectROI(reconstruction); + end + + end + %------------------------------------------------------------------ + + end + + %---------------------------------------------------------------------- + methods (Access = protected) + + %------------------------------------------------------------------ + % Protected function: create FP + function sinogram = project_c(this, volume) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % data is stored in astra memory + if numel(volume) == 1 + + if strcmp(this.gpu, 'yes') + sinogram_tmp = astra_create_sino_cuda(volume, this.proj_geom_sr, this.vol_geom, this.gpu_core); + else + sinogram_tmp = astra_create_sino(volume, this.proj_id); + end + + % sinogram downsampling + if this.superresolution > 1 + sinogram_data = astra_mex_data2d('get', sinogram_tmp); + astra_mex_data2d('delete', sinogram_tmp); + sinogram_data = downsample_sinogram(sinogram_data, this.superresolution); + sinogram = astra_mex_data2d('create','sino', this.proj_geom, sinogram_data); + else + sinogram = sinogram_tmp; + end + + % data is stored in matlab memory + else + + % 2D and 3D slice by slice + sinogram_tmp = zeros([astra_geom_size(this.proj_geom_sr), size(volume,3)]); + sinogram_tmp2 = zeros([astra_geom_size(this.proj_geom), size(volume,3)]); + for slice = 1:size(volume,3) + + if strcmp(this.gpu, 'yes') + [tmp_id, sinogram_tmp2(:,:,slice)] = astra_create_sino_sampling(volume(:,:,slice), this.proj_geom, this.vol_geom, this.gpu_core, this.superresolution); + astra_mex_data2d('delete', tmp_id); + else + [tmp_id, tmp] = astra_create_sino(volume(:,:,slice), this.proj_id_sr); + sinogram_tmp2(:,:,slice) = downsample_sinogram(tmp, this.superresolution) * (this.superresolution^2); + astra_mex_data2d('delete', tmp_id); + end + + end + + % sinogram downsampling + if strcmp(this.gpu, 'yes') + %sinogram = downsample_sinogram(sinogram_tmp, this.superresolution); + sinogram2 = sinogram_tmp2; + if strcmp(this.proj_geom.type,'fanflat_vec') || strcmp(this.proj_geom.type,'fanflat') + sinogram2 = sinogram2 / this.superresolution; + elseif strcmp(this.proj_geom.type,'parallel') + sinogram2 = sinogram2 / (this.superresolution * this.superresolution); + end + sinogram = sinogram2; + else + sinogram = sinogram_tmp2; + end + + end + + end + + %------------------------------------------------------------------ + % Protected function: reconstruct + function V = reconstruct_c(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % data is stored in astra memory + if numel(sinogram) == 1 + V = this.reconstruct_c_astra(sinogram, V0, mask, iterations); + + % data is stored in matlab memory + else + V = this.reconstruct_c_matlab(sinogram, V0, mask, iterations); + end + + end + + %------------------------------------------------------------------ + % Protected function: reconstruct (data in matlab) + function V = reconstruct_c_matlab(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % parse method + method2 = upper(this.method); + if strcmp(method2, 'SART') || strcmp(method2, 'SART_CUDA') + iterations = iterations * size(sinogram,1); + elseif strcmp(method2, 'ART') + iterations = iterations * numel(sinogram); + end + + % create data objects + V = zeros(this.vol_geom.GridRowCount, this.vol_geom.GridColCount, size(sinogram,3)); + reconstruction_id = astra_mex_data2d('create', '-vol', this.vol_geom); + sinogram_id = astra_mex_data2d('create', '-sino', this.proj_geom); + if numel(mask) > 0 + mask_id = astra_mex_data2d('create', '-vol', this.vol_geom); + end + + % algorithm configuration + cfg = this.cfg_base; + cfg.ProjectionDataId = sinogram_id; + cfg.ReconstructionDataId = reconstruction_id; + if numel(mask) > 0 + cfg.option.ReconstructionMaskId = mask_id; + end + alg_id = astra_mex_algorithm('create', cfg); + + % loop slices + for slice = 1:size(sinogram,3) + + % fetch slice of initial reconstruction + if numel(V0) > 0 + astra_mex_data2d('store', reconstruction_id, V0(:,:,slice)); + else + astra_mex_data2d('store', reconstruction_id, 0); + end + + % fetch slice of sinogram + astra_mex_data2d('store', sinogram_id, sinogram(:,:,slice)); + + % fecth slice of mask + if numel(mask) > 0 + astra_mex_data2d('store', mask_id, mask(:,:,slice)); + end + + % iterate + astra_mex_algorithm('iterate', alg_id, iterations); + + % fetch data + V(:,:,slice) = astra_mex_data2d('get', reconstruction_id); + + end + + % correct attenuation factors for super-resolution + if this.superresolution > 1 && strcmp(this.gpu,'yes') + if strcmp(this.proj_geom.type,'fanflat_vec') || strcmp(this.proj_geom.type,'fanflat') + if numel(mask) > 0 + V(mask > 0) = V(mask > 0) ./ this.superresolution; + else + V = V ./ this.superresolution; + end + end + end + + % garbage collection + astra_mex_algorithm('delete', alg_id); + astra_mex_data2d('delete', sinogram_id, reconstruction_id); + if numel(mask) > 0 + astra_mex_data2d('delete', mask_id); + end + + end + + %------------------------------------------------------------------ + % Protected function: reconstruct (data in astra) + function V = reconstruct_c_astra(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + if numel(V0) > 1 || numel(mask) > 1 || numel(sinogram) > 1 + error('Not all required data is stored in the astra memory'); + end + + if numel(V0) == 0 + V0 = astra_mex_data2d('create', '-vol', this.vol_geom, 0); + end + + % parse method + method2 = upper(this.method); + if strcmp(method2, 'SART') || strcmp(method2, 'SART_CUDA') + iterations = iterations * astra_geom_size(this.proj_geom, 1) + this.cfg_base.option.ProjectionOrder = 'random'; + elseif strcmp(method2, 'ART') + s = astra_geom_size(this.proj_geom); + iterations = iterations * s(1) * s(2); + end + + % algorithm configuration + cfg = this.cfg_base; + cfg.ProjectionDataId = sinogram; + cfg.ReconstructionDataId = V0; + if numel(mask) > 0 + cfg.option.ReconstructionMaskId = mask; + end + alg_id = astra_mex_algorithm('create', cfg); + + % iterate + astra_mex_algorithm('iterate', alg_id, iterations); + + % fetch data + V = V0; + + % correct attenuation factors for super-resolution + if this.superresolution > 1 + if strcmp(this.proj_geom.type,'fanflat_vec') || strcmp(this.proj_geom.type,'fanflat') + if numel(mask) > 0 + astra_data_op_masked('$1./s1', [V V], [this.superresolution this.superresolution], mask, this.gpu_core); + else + astra_data_op('$1./s1', [V V], [this.superresolution this.superresolution], this.gpu_core); + end + end + end + + % garbage collection + astra_mex_algorithm('delete', alg_id); + + end + + %------------------------------------------------------------------ + function V_out = selectROI(~, V_in) + + if numel(V_in) == 1 + cfg = astra_struct('RoiSelect_CUDA'); + cfg.DataId = V_in; + alg_id = astra_mex_algorithm('create',cfg); + astra_mex_algorithm('run', alg_id); + astra_mex_algorithm('delete', alg_id); + V_out = V_in; + else + V_out = ROIselectfull(V_in, min([size(V_in,1), size(V_in,2)])); + end + + end + %------------------------------------------------------------------ + + end + +end + diff --git a/matlab/algorithms/DART/IterativeTomography3D.m b/matlab/algorithms/DART/IterativeTomography3D.m new file mode 100644 index 0000000..29b963f --- /dev/null +++ b/matlab/algorithms/DART/IterativeTomography3D.m @@ -0,0 +1,405 @@ +classdef IterativeTomography3D < matlab.mixin.Copyable + + % Algorithm class for 3D Iterative Tomography. + + %---------------------------------------------------------------------- + properties (SetAccess=public, GetAccess=public) + superresolution = 1; % SETTING: Volume upsampling factor. + proj_type = 'linear'; % SETTING: Projector type, only when gpu='no'. + method = 'SIRT3D_CUDA'; % SETTING: Iterative method (see ASTRA toolbox documentation). + gpu = 'yes'; % SETTING: Use gpu? {'yes', 'no'} + gpu_core = 0; % SETTING: Which gpu core to use? Only when gpu='yes'. + inner_circle = 'yes'; % SETTING: Do roi only? {'yes', 'no'} + image_size = []; % SETTING: Overwrite default reconstruction size. Only if no vol_geom is specified. + use_minc = 'no'; % SETTING: Use minimum constraint. {'no', 'yes'} + maxc = +Inf; % SETTING: Maximum constraint. +Inf means off. + end + %---------------------------------------------------------------------- + properties (SetAccess=public, GetAccess=public) + sinogram = []; % DATA: Projection data. + proj_geom = []; % DATA: Projection geometry. + V = []; % DATA: Volume data. Also used to set initial estimate (optional). + vol_geom = []; % DATA: Volume geometry. + end + %---------------------------------------------------------------------- + properties (SetAccess=private, GetAccess=public) + initialized = 0; % Is this object initialized? + end + %---------------------------------------------------------------------- + properties (SetAccess=protected, GetAccess=protected) + proj_geom_sr = []; % PROTECTED: geometry of sinogram (with super-resolution) + proj_id = []; % PROTECTED: astra id of projector (when gpu='no') + proj_id_sr = []; % PROTECTED: astra id of super-resolution projector (when gpu='no') + cfg_base = struct(); % PROTECTED: base configuration structure for the reconstruction algorithm. + end + %---------------------------------------------------------------------- + + methods (Access=public) + + %------------------------------------------------------------------ + function this = IterativeTomography3D(varargin) + % Constructor + % >> tomography = IterativeTomography3D(proj_geom); + % >> tomography = IterativeTomography3D(proj_geom, vol_geom); + + % Input: IterativeTomography(proj_geom) + if nargin == 1 + this.proj_geom = varargin{1}; + + % Input: IterativeTomography(proj_geom, vol_geom) + elseif nargin == 2 + this.proj_geom = varargin{1}; + this.vol_geom = varargin{2}; + end + end + + %------------------------------------------------------------------ + function delete(this) + % Destructor + % >> clear tomography; + if strcmp(this.gpu,'no') && numel(this.proj_id) > 0 + astra_mex_projector('delete', this.proj_id, this.proj_id_sr); + end + end + + %------------------------------------------------------------------ + function settings = getsettings(this) + % Returns a structure containing all settings of this object. + % >> settings = tomography.getsettings(); + settings.superresolution = this.superresolution; + settings.proj_type = this.proj_type; + settings.method = this.method; + settings.gpu = this.gpu; + settings.gpu_core = this.gpu_core; + settings.inner_circle = this.inner_circle; + settings.image_size = this.image_size; + settings.use_minc = this.use_minc; + settings.maxc = this.maxc; + end + + %------------------------------------------------------------------ + function ok = initialize(this) + % Initialize this object. Returns 1 if succesful. + % >> tomography.initialize(); + +% % create projection geometry with super-resolution +% this.proj_geom_sr = astra_geom_superresolution(this.proj_geom, this.superresolution); + + % if no volume geometry is specified by the user: create volume geometry + if numel(this.vol_geom) == 0 + if numel(this.image_size) < 2 + this.image_size(1) = this.proj_geom.DetectorRowCount; + this.image_size(2) = this.proj_geom.DetectorColCount; + end + this.vol_geom = astra_create_vol_geom(this.proj_geom.DetectorColCount, this.proj_geom.DetectorColCount, this.proj_geom.DetectorRowCount); + else + this.image_size(1) = this.vol_geom.GridRowCount; + this.image_size(2) = this.vol_geom.GridColCount; + end + + % create projector + if strcmp(this.gpu, 'no') + this.proj_id = astra_create_projector(this.proj_type, this.proj_geom, this.vol_geom); + this.proj_id_sr = astra_create_projector(this.proj_type, this.proj_geom_sr, this.vol_geom); + end + + % create reconstruction configuration + this.cfg_base = astra_struct(upper(this.method)); + if strcmp(this.gpu,'no') + this.cfg_base.ProjectorId = this.proj_id; + this.cfg_base.ProjectionGeometry = this.proj_geom; + this.cfg_base.ReconstructionGeometry = this.vol_geom; + this.cfg_base.option.ProjectionOrder = 'random'; + end + this.cfg_base.option.DetectorSuperSampling = this.superresolution; + if strcmp(this.gpu,'yes') + this.cfg_base.option.GPUindex = this.gpu_core; + end + this.cfg_base.option.UseMinConstraint = this.use_minc; + if ~isinf(this.maxc) + this.cfg_base.option.UseMaxConstraint = 'yes'; + this.cfg_base.option.MaxConstraintValue = this.maxc; + end + + this.initialized = 1; + ok = this.initialized; + end + + %------------------------------------------------------------------ + function projections = project(this, volume) + % Compute forward projection. + % >> projections = tomography.project(volume); + + if ~this.initialized + this.initialize(); + end + + % project + projections = this.project_c(volume); + end + + %------------------------------------------------------------------ + function reconstruction = reconstruct(this, varargin) + % Compute reconstruction. + % Uses tomography.sinogram + % Initial solution (if available) should be stored in tomography.V + % >> reconstruction = tomography.reconstruct(projections, iterations); + % >> reconstruction = tomography.reconstruct(projections, volume0, iterations); + + if ~this.initialized + this.initialize(); + end + + if numel(varargin) == 2 + reconstruction = this.reconstruct_c(varargin{1}, [], [], varargin{2}); + elseif numel(varargin) == 3 + reconstruction = this.reconstruct_c(varargin{1}, varargin{2}, [], varargin{3}); + else + error('invalid parameter list') + end + + if strcmp(this.inner_circle,'yes') + reconstruction = this.selectROI(reconstruction); + end + end + + %------------------------------------------------------------------ + function reconstruction = reconstruct_mask(this, varargin) + % Compute reconstruction with mask. + % Uses tomography.sinogram + % Initial solution (if available) should be stored in tomography.V + % >> reconstruction = tomography.reconstructMask(projections, mask, iterations); + % >> reconstruction = tomography.reconstructMask(projections, volume0, mask, iterations); + + if ~this.initialized + this.initialize(); + end + + if numel(varargin) == 3 + reconstruction = this.reconstruct_c(varargin{1}, [], varargin{2}, varargin{3}); + elseif numel(varargin) == 4 + reconstruction = this.reconstruct_c(varargin{1}, varargin{2}, varargin{3}, varargin{4}); + else + error('invalid parameter list') + end + + if strcmp(this.inner_circle,'yes') + reconstruction = this.selectROI(reconstruction); + end + + end + %------------------------------------------------------------------ + + end + + %---------------------------------------------------------------------- + methods (Access = protected) + + %------------------------------------------------------------------ + % Protected function: create FP + function sinogram = project_c(this, volume) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % data is stored in astra memory + if numel(volume) == 1 + + if strcmp(this.gpu, 'yes') + sinogram_tmp = astra_create_sino_cuda(volume, this.proj_geom_sr, this.vol_geom, this.gpu_core); + else + sinogram_tmp = astra_create_sino(volume, this.proj_id); + end + + % sinogram downsampling + if this.superresolution > 1 + sinogram_data = astra_mex_data2d('get', sinogram_tmp); + astra_mex_data2d('delete', sinogram_tmp); + sinogram_data = downsample_sinogram(sinogram_data, this.superresolution); + sinogram = astra_mex_data2d('create', 'sino', this.proj_geom, sinogram_data); + else + sinogram = sinogram_tmp; + end + + % data is stored in matlab memory + else + [tmp_id, sinogram] = astra_create_sino3d_cuda(volume, this.proj_geom, this.vol_geom); + astra_mex_data3d('delete', tmp_id); + end + end + + %------------------------------------------------------------------ + % Protected function: reconstruct + function V = reconstruct_c(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % data is stored in astra memory + if numel(sinogram) == 1 + V = this.reconstruct_c_astra(sinogram, V0, mask, iterations); + + % data is stored in matlab memory + else + V = this.reconstruct_c_matlab(sinogram, V0, mask, iterations); + end + end + + %------------------------------------------------------------------ + % Protected function: reconstruct (data in matlab) + function V = reconstruct_c_matlab(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + % parse method + method2 = upper(this.method); + if strcmp(method2, 'SART') || strcmp(method2, 'SART_CUDA') + iterations = iterations * size(sinogram,1); + elseif strcmp(method2, 'ART') + iterations = iterations * numel(sinogram); + end + + % create data objects +% V = zeros(this.vol_geom.GridRowCount, this.vol_geom.GridColCount, size(sinogram,3)); + reconstruction_id = astra_mex_data3d('create', '-vol', this.vol_geom); + sinogram_id = astra_mex_data3d('create', '-proj3d', this.proj_geom); + if numel(mask) > 0 + mask_id = astra_mex_data3d('create', '-vol', this.vol_geom); + end + + % algorithm configuration + cfg = this.cfg_base; + cfg.ProjectionDataId = sinogram_id; + cfg.ReconstructionDataId = reconstruction_id; + if numel(mask) > 0 + cfg.option.ReconstructionMaskId = mask_id; + end + alg_id = astra_mex_algorithm('create', cfg); + +% % loop slices +% for slice = 1:size(sinogram,3) + + % fetch slice of initial reconstruction + if numel(V0) > 0 + astra_mex_data3d('store', reconstruction_id, V0); + else + astra_mex_data3d('store', reconstruction_id, 0); + end + + % fetch slice of sinogram + astra_mex_data3d('store', sinogram_id, sinogram); + + % fecth slice of mask + if numel(mask) > 0 + astra_mex_data3d('store', mask_id, mask); + end + + % iterate + astra_mex_algorithm('iterate', alg_id, iterations); + + % fetch data + V = astra_mex_data3d('get', reconstruction_id); + +% end + + % correct attenuation factors for super-resolution + if this.superresolution > 1 && strcmp(this.gpu,'yes') + if strcmp(this.proj_geom.type,'fanflat_vec') || strcmp(this.proj_geom.type,'fanflat') + if numel(mask) > 0 + V(mask > 0) = V(mask > 0) ./ this.superresolution; + else + V = V ./ this.superresolution; + end + end + end + + % garbage collection + astra_mex_algorithm('delete', alg_id); + astra_mex_data3d('delete', sinogram_id, reconstruction_id); + if numel(mask) > 0 + astra_mex_data3d('delete', mask_id); + end + + end + + %------------------------------------------------------------------ + % Protected function: reconstruct (data in astra) + function V = reconstruct_c_astra(this, sinogram, V0, mask, iterations) + + if this.initialized == 0 + error('IterativeTomography not initialized'); + end + + if numel(V0) > 1 || numel(mask) > 1 || numel(sinogram) > 1 + error('Not all required data is stored in the astra memory'); + end + + if numel(V0) == 0 + V0 = astra_mex_data2d('create', '-vol', this.vol_geom, 0); + end + + % parse method + method2 = upper(this.method); + if strcmp(method2, 'SART') || strcmp(method2, 'SART_CUDA') + iterations = iterations * astra_geom_size(this.proj_geom, 1); + elseif strcmp(method2, 'ART') + s = astra_geom_size(this.proj_geom); + iterations = iterations * s(1) * s(2); + end + + % algorithm configuration + cfg = this.cfg_base; + cfg.ProjectionDataId = sinogram; + cfg.ReconstructionDataId = V0; + if numel(mask) > 0 + cfg.option.ReconstructionMaskId = mask; + end + alg_id = astra_mex_algorithm('create', cfg); + + % iterate + astra_mex_algorithm('iterate', alg_id, iterations); + + % fetch data + V = V0; + + % correct attenuation factors for super-resolution + if this.superresolution > 1 + if strcmp(this.proj_geom.type,'fanflat_vec') || strcmp(this.proj_geom.type,'fanflat') + if numel(mask) > 0 + astra_data_op_masked('$1./s1', [V V], [this.superresolution this.superresolution], mask, this.gpu_core); + else + astra_data_op('$1./s1', [V V], [this.superresolution this.superresolution], this.gpu_core); + end + end + end + + % garbage collection + astra_mex_algorithm('delete', alg_id); + + end + + %------------------------------------------------------------------ + function V_out = selectROI(~, V_in) + + if numel(V_in) == 1 + cfg = astra_struct('RoiSelect_CUDA'); + cfg.DataId = V_in; + alg_id = astra_mex_algorithm('create',cfg); + astra_mex_algorithm('run', alg_id); + astra_mex_algorithm('delete', alg_id); + V_out = V_in; + else + V_out = ROIselectfull(V_in, min([size(V_in,1), size(V_in,2)])); + end + + end + %------------------------------------------------------------------ + + end + +end + diff --git a/matlab/algorithms/DART/Kernels.m b/matlab/algorithms/DART/Kernels.m index f91bf33..558f611 100644 --- a/matlab/algorithms/DART/Kernels.m +++ b/matlab/algorithms/DART/Kernels.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/MaskingDefault.m b/matlab/algorithms/DART/MaskingDefault.m index 1ecbacb..f91a6f5 100644 --- a/matlab/algorithms/DART/MaskingDefault.m +++ b/matlab/algorithms/DART/MaskingDefault.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/MaskingGPU.m b/matlab/algorithms/DART/MaskingGPU.m index dfbbd54..7d31aa8 100644 --- a/matlab/algorithms/DART/MaskingGPU.m +++ b/matlab/algorithms/DART/MaskingGPU.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/OutputDefault.m b/matlab/algorithms/DART/OutputDefault.m index 968261d..33e908b 100644 --- a/matlab/algorithms/DART/OutputDefault.m +++ b/matlab/algorithms/DART/OutputDefault.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/SegmentationDefault.m b/matlab/algorithms/DART/SegmentationDefault.m index 3b42740..98265c0 100644 --- a/matlab/algorithms/DART/SegmentationDefault.m +++ b/matlab/algorithms/DART/SegmentationDefault.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/SmoothingDefault.m b/matlab/algorithms/DART/SmoothingDefault.m index f89526e..1974fa1 100644 --- a/matlab/algorithms/DART/SmoothingDefault.m +++ b/matlab/algorithms/DART/SmoothingDefault.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/SmoothingGPU.m b/matlab/algorithms/DART/SmoothingGPU.m index 5a8fa48..1249e19 100644 --- a/matlab/algorithms/DART/SmoothingGPU.m +++ b/matlab/algorithms/DART/SmoothingGPU.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/StatisticsDefault.m b/matlab/algorithms/DART/StatisticsDefault.m index 31ead14..9d33256 100644 --- a/matlab/algorithms/DART/StatisticsDefault.m +++ b/matlab/algorithms/DART/StatisticsDefault.m @@ -1,8 +1,8 @@ %-------------------------------------------------------------------------- % This file is part of the ASTRA Toolbox % -% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp -% 2014-2015, CWI, Amsterdam +% Copyright: 2010-2014, iMinds-Vision Lab, University of Antwerp +% 2014, CWI, Amsterdam % License: Open Source under GPLv3 % Contact: astra@uantwerpen.be % Website: http://sf.net/projects/astra-toolbox diff --git a/matlab/algorithms/DART/examples/example1.m b/matlab/algorithms/DART/examples/example1.m index 9a836f8..cb02e0f 100644 --- a/matlab/algorithms/DART/examples/example1.m +++ b/matlab/algorithms/DART/examples/example1.m @@ -8,15 +8,11 @@ % Website: http://sf.net/projects/astra-toolbox %-------------------------------------------------------------------------- -clear all; - addpath('../'); -%% -% Example 1: 2D parallel beam, cuda -% +%% Example 1: 2D parallel beam, cuda -% Configuration +% configuration proj_count = 20; dart_iterations = 20; filename = 'cylinders.png'; @@ -26,26 +22,20 @@ rho = [0, 255]; tau = 128; gpu_core = 0; -% Load phantom +% load phantom I = imreadgs(filename); -% Create projection and volume geometries +% create projection and volume geometries det_count = size(I, 1); angles = linspace2(0, pi, proj_count); proj_geom = astra_create_proj_geom('parallel', 1, det_count, angles); -vol_geom = astra_create_vol_geom(det_count, det_count, 1); +vol_geom = astra_create_vol_geom(det_count, det_count); -% Create sinogram. +% create sinogram [sinogram_id, sinogram] = astra_create_sino_cuda(I, proj_geom, vol_geom); astra_mex_data2d('delete', sinogram_id); -%% % DART -% - -%base.sinogram = sinogram; -%base.proj_geom = proj_geom; - D = DARTalgorithm(sinogram, proj_geom); D.t0 = 100; D.t = 10; @@ -63,21 +53,19 @@ D.smoothing.gpu_core = gpu_core; D.masking.random = 0.1; D.masking.gpu_core = gpu_core; -D.output.directory = outdir; -D.output.pre = [prefix '_']; -D.output.save_images = 'no'; -D.output.save_results = {'stats', 'settings', 'S', 'V'}; -D.output.save_interval = dart_iterations; -D.output.verbose = 'yes'; +D.output.directory = outdir; +D.output.pre = [prefix '_']; +D.output.save_images = 'no'; +D.output.save_results = {'stats', 'settings', 'S', 'V'}; +D.output.save_interval = dart_iterations; +D.output.verbose = 'yes'; -D.statistics.proj_diff = 'no'; +D.statistics.proj_diff = 'no'; D.initialize(); D.iterate(dart_iterations); -%% -% Convert middle slice of final iteration to png. -% +% save the reconstruction and the segmentation to file imwritesc(D.S, [outdir '/' prefix '_S.png']); imwritesc(D.V, [outdir '/' prefix '_V.png']); diff --git a/matlab/algorithms/DART/examples/example2.m b/matlab/algorithms/DART/examples/example2.m index 7fe6988..89660a5 100644 --- a/matlab/algorithms/DART/examples/example2.m +++ b/matlab/algorithms/DART/examples/example2.m @@ -8,15 +8,11 @@ % Website: http://sf.net/projects/astra-toolbox %-------------------------------------------------------------------------- -clear all; - addpath('../'); -%% -% Example Z: 3D parallel beam, cuda -% +%% Example 2: 3D parallel beam, cuda -% Configuration +% configuration proj_count = 20; dart_iterations = 20; outdir = './'; @@ -25,50 +21,47 @@ rho = [0, 0.5, 1]; tau = [0.25, 0.75]; gpu_core = 0; -% Load phantom +% load phantom load('phantom3d'); -% Create projection and volume geometries +% create projection and volume geometries det_count = size(I, 1); slice_count = size(I,3); angles = linspace2(0, pi, proj_count); proj_geom = astra_create_proj_geom('parallel3d', 1, 1, slice_count, det_count, angles); vol_geom = astra_create_vol_geom(size(I)); -% Create sinogram +% create sinogram [sinogram_id, sinogram] = astra_create_sino3d_cuda(I, proj_geom, vol_geom); astra_mex_data3d('delete', sinogram_id); -%% % DART -% - D = DARTalgorithm(sinogram, proj_geom); D.t0 = 100; D.t = 10; D.tomography = IterativeTomography3D(); -D.tomography.method = 'SIRT3D_CUDA'; -D.tomography.gpu_core = gpu_core; -D.tomography.use_minc = 'yes'; +D.tomography.method = 'SIRT3D_CUDA'; +D.tomography.gpu_core = gpu_core; +D.tomography.use_minc = 'yes'; -D.segmentation.rho = rho; -D.segmentation.tau = tau; +D.segmentation.rho = rho; +D.segmentation.tau = tau; -D.smoothing.b = 0.1; -D.smoothing.full3d = 'yes'; -D.smoothing.gpu_core = gpu_core; +D.smoothing.b = 0.1; +D.smoothing.full3d = 'yes'; +D.smoothing.gpu_core = gpu_core; -D.masking.random = 0.1; -D.masking.conn = 4; -D.masking.gpu_core = gpu_core; +D.masking.random = 0.1; +D.masking.conn = 4; +D.masking.gpu_core = gpu_core; -D.output.directory = outdir; -D.output.pre = [prefix '_']; -D.output.save_images = 'no'; -D.output.save_results = {'stats', 'settings', 'S', 'V'}; -D.output.save_interval = dart_iterations; -D.output.verbose = 'yes'; +D.output.directory = outdir; +D.output.pre = [prefix '_']; +D.output.save_images = 'no'; +D.output.save_results = {'stats', 'settings', 'S', 'V'}; +D.output.save_interval = dart_iterations; +D.output.verbose = 'yes'; D.statistics.proj_diff = 'no'; @@ -76,8 +69,6 @@ D.initialize(); D.iterate(dart_iterations); -%% -% Convert output of final iteration to png. -% +% save the central slice of the reconstruction and the segmentation to file imwritesc(D.S(:,:,64), [outdir '/' prefix '_S_slice_64.png']); imwritesc(D.V(:,:,64), [outdir '/' prefix '_V_slice_64.png']); diff --git a/matlab/algorithms/DART/examples/example3.m b/matlab/algorithms/DART/examples/example3.m index 895630b..cc80b0f 100644 --- a/matlab/algorithms/DART/examples/example3.m +++ b/matlab/algorithms/DART/examples/example3.m @@ -8,15 +8,11 @@ % Website: http://sf.net/projects/astra-toolbox %-------------------------------------------------------------------------- -clear all; - addpath('../'); -%% -% Example 3: 3D cone beam, cuda -% +%% Example 3: 3D cone beam, cuda -% Configuration +% configuration proj_count = 20; dart_iterations = 20; outdir = './'; @@ -25,24 +21,21 @@ rho = [0, 0.5, 1]; tau = [0.25, 0.75]; gpu_core = 0; -% Load phantom +% load phantom load('phantom3d'); -% Create projection and volume geometries +% create projection and volume geometries det_count = size(I, 1); slice_count = size(I,3); angles = linspace2(0, pi, proj_count); proj_geom = astra_create_proj_geom('cone', 1, 1, slice_count, det_count, angles, 500, 0); vol_geom = astra_create_vol_geom(size(I)); -% Create sinogram +% create sinogram [sinogram_id, sinogram] = astra_create_sino3d_cuda(I, proj_geom, vol_geom); astra_mex_data3d('delete', sinogram_id); -%% % DART -% - D = DARTalgorithm(sinogram, proj_geom); D.t0 = 100; D.t = 10; @@ -76,8 +69,6 @@ D.initialize(); D.iterate(dart_iterations); -%% -% Convert output of final iteration to png. -% +% save the central slice of the reconstruction and the segmentation to file imwritesc(D.S(:,:,64), [outdir '/' prefix '_S_slice_64.png']); imwritesc(D.V(:,:,64), [outdir '/' prefix '_V_slice_64.png']); diff --git a/matlab/mex/astra_mex.cpp b/matlab/mex/astra_mex.cpp index 0eb5662..4bf42dd 100644 --- a/matlab/mex/astra_mex.cpp +++ b/matlab/mex/astra_mex.cpp @@ -28,6 +28,7 @@ $Id$ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include "astra/Globals.h" @@ -104,6 +105,8 @@ void mexFunction(int nlhs, mxArray* plhs[], return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == std::string("version")) { astra_mex_version(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_algorithm_c.cpp b/matlab/mex/astra_mex_algorithm_c.cpp index f719a6b..e4afa63 100644 --- a/matlab/mex/astra_mex_algorithm_c.cpp +++ b/matlab/mex/astra_mex_algorithm_c.cpp @@ -32,13 +32,15 @@ $Id$ */ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" +#include "astra/Globals.h" #define USE_MATLAB_UNDOCUMENTED #ifdef USE_MATLAB_UNDOCUMENTED extern "C" { bool utIsInterruptPending(); } -#ifdef __linux__ +#ifdef USE_PTHREADS #define USE_PTHREADS_CTRLC #include <pthread.h> #else @@ -49,7 +51,6 @@ extern "C" { bool utIsInterruptPending(); } -#include "astra/Globals.h" #include "astra/AstraObjectManager.h" #include "astra/AstraObjectFactory.h" @@ -78,26 +79,23 @@ void astra_mex_algorithm_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr } // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Algorithm", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("Algorithm", prhs[1]); - CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg.self->getAttribute("type")); + CAlgorithm* pAlg = CAlgorithmFactory::getSingleton().create(cfg->self->getAttribute("type")); if (!pAlg) { - delete xml; + delete cfg; mexErrMsgTxt("Unknown algorithm. \n"); return; } // create algorithm - if (!pAlg->initialize(cfg)) { - delete xml; + if (!pAlg->initialize(*cfg)) { + delete cfg; delete pAlg; mexErrMsgTxt("Algorithm not initialized. \n"); return; } - - delete xml; + delete cfg; // store algorithm int iIndex = CAlgorithmManager::getSingleton().store(pAlg); @@ -322,12 +320,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == "create") { astra_mex_algorithm_create(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_algorithm_vc08.vcproj b/matlab/mex/astra_mex_algorithm_vc09.vcproj index baa4c44..d5cebc0 100644 --- a/matlab/mex/astra_mex_algorithm_vc08.vcproj +++ b/matlab/mex/astra_mex_algorithm_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,16 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -85,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -108,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -123,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -152,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -175,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -191,16 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="false" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -221,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -244,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -260,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -289,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -312,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -329,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -359,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -380,16 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - BrowseInformation="1" - DebugInformationFormat="4" /> <Tool Name="VCManagedResourceCompilerTool" @@ -401,17 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -432,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -455,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -471,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -501,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -522,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool 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<ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClCompile> - <ClCompile Include="mexDataManagerHelpFunctions.cpp" /> + <ClCompile Include="mexInitFunctions.cpp" /> </ItemGroup> <ItemGroup> <ClInclude Include="mexHelpFunctions.h" /> - <ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClInclude> - <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/astra_mex_c.cpp b/matlab/mex/astra_mex_c.cpp index 2989b7a..4a331f5 100644 --- a/matlab/mex/astra_mex_c.cpp +++ b/matlab/mex/astra_mex_c.cpp @@ -33,6 +33,7 @@ $Id$ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include "astra/Globals.h" @@ -122,12 +123,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == std::string("version")) { astra_mex_version(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_data2d_c.cpp b/matlab/mex/astra_mex_data2d_c.cpp index b219179..9576896 100644 --- a/matlab/mex/astra_mex_data2d_c.cpp +++ b/matlab/mex/astra_mex_data2d_c.cpp @@ -32,6 +32,7 @@ $Id$ */ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include <list> @@ -98,10 +99,10 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra return; } - string sDataType = mex_util_get_string(prhs[1]); + string sDataType = mexToString(prhs[1]); CFloat32Data2D* pDataObject2D = NULL; - if (nrhs >= 4 && !(mex_is_scalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) { + if (nrhs >= 4 && !(mexIsScalar(prhs[3])|| mxIsDouble(prhs[3]) || mxIsLogical(prhs[3]) || mxIsSingle(prhs[3]) )) { mexErrMsgTxt("Data must be single, double or logical."); return; } @@ -116,23 +117,20 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]); - if (!xml) - return; - Config cfg; - cfg.self = xml->getRootNode(); + + Config* cfg = structToConfig("VolumeGeometry", prhs[2]); CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D(); - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If data is specified, check dimensions - if (nrhs >= 4 && !mex_is_scalar(prhs[3])) { + if (nrhs >= 4 && !mexIsScalar(prhs[3])) { if (pGeometry->getGridColCount() != mxGetN(prhs[3]) || pGeometry->getGridRowCount() != mxGetM(prhs[3])) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); - delete xml; + delete cfg; delete pGeometry; return; } @@ -140,21 +138,18 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra // Initialize data object pDataObject2D = new CFloat32VolumeData2D(pGeometry); delete pGeometry; - delete xml; + delete cfg; } else if (sDataType == "-sino") { // Read geometry if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]); - if (!xml) - return; - Config cfg; - cfg.self = xml->getRootNode(); + + Config* cfg = structToConfig("ProjectionGeometry", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'change_geometry' and Projector2D.cpp.) - std::string type = cfg.self->getAttribute("type"); + std::string type = cfg->self->getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); @@ -168,25 +163,25 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra } else { pGeometry = new CParallelProjectionGeometry2D(); } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If data is specified, check dimensions - if (nrhs >= 4 && !mex_is_scalar(prhs[3])) { + if (nrhs >= 4 && !mexIsScalar(prhs[3])) { if (pGeometry->getDetectorCount() != mxGetN(prhs[3]) || pGeometry->getProjectionAngleCount() != mxGetM(prhs[3])) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); delete pGeometry; - delete xml; + delete cfg; return; } } // Initialize data object pDataObject2D = new CFloat32ProjectionData2D(pGeometry); delete pGeometry; - delete xml; + delete cfg; } else { mexErrMsgTxt("Invalid datatype. Please specify '-vol' or '-sino'. \n"); @@ -210,7 +205,7 @@ void astra_mex_data2d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra // Store data if (nrhs >= 4) { // fill with scalar value - if (mex_is_scalar(prhs[3])) { + if (mexIsScalar(prhs[3])) { float32 fValue = (float32)mxGetScalar(prhs[3]); for (int i = 0; i < pDataObject2D->getSize(); ++i) { pDataObject2D->getData()[i] = fValue; @@ -294,7 +289,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* } int iDataID = (int)(mxGetScalar(prhs[1])); - if (!(mex_is_scalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) { + if (!(mexIsScalar(prhs[2]) || mxIsDouble(prhs[2]) || mxIsLogical(prhs[2]) || mxIsSingle(prhs[2]))) { mexErrMsgTxt("Data must be single, double or logical."); return; } @@ -312,7 +307,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* // step3: insert data // fill with scalar value - if (mex_is_scalar(prhs[2])) { + if (mexIsScalar(prhs[2])) { float32 fValue = (float32)mxGetScalar(prhs[2]); for (int i = 0; i < pDataObject->getSize(); ++i) { pDataObject->getData()[i] = fValue; @@ -373,7 +368,7 @@ void astra_mex_data2d_store(int nlhs, mxArray* plhs[], int nrhs, const mxArray* */ void astra_mex_data2d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { - // step1: input + // parse input if (nrhs < 2) { mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); return; @@ -384,7 +379,7 @@ void astra_mex_data2d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mx } int iDataID = (int)(mxGetScalar(prhs[1])); - // step2: get data object + // fetch data object CFloat32Data2D* pDataObject = astra::CData2DManager::getSingleton().get(iDataID); if (!pDataObject || !pDataObject->isInitialized()) { mexErrMsgTxt("Data object not found or not initialized properly.\n"); @@ -395,11 +390,11 @@ void astra_mex_data2d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mx if (1 <= nlhs) { if (pDataObject->getType() == CFloat32Data2D::PROJECTION) { CFloat32ProjectionData2D* pDataObject2 = dynamic_cast<CFloat32ProjectionData2D*>(pDataObject); - plhs[0] = createProjectionGeometryStruct(pDataObject2->getGeometry()); + plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration()); } else if (pDataObject->getType() == CFloat32Data2D::VOLUME) { CFloat32VolumeData2D* pDataObject2 = dynamic_cast<CFloat32VolumeData2D*>(pDataObject); - plhs[0] = createVolumeGeometryStruct(pDataObject2->getGeometry()); + plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration()); } } } @@ -440,12 +435,10 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML("ProjectionGeometry", prhs[2]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("ProjectionGeometry2D", prhs[2]); // FIXME: Change how the base class is created. (This is duplicated // in 'create' and Projector2D.cpp.) - std::string type = cfg.self->getAttribute("type"); + std::string type = cfg->self->getAttribute("type"); CProjectionGeometry2D* pGeometry; if (type == "sparse_matrix") { pGeometry = new CSparseMatrixProjectionGeometry2D(); @@ -459,24 +452,24 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const } else { pGeometry = new CParallelProjectionGeometry2D(); } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If data is specified, check dimensions if (pGeometry->getDetectorCount() != pSinogram->getDetectorCount() || pGeometry->getProjectionAngleCount() != pSinogram->getAngleCount()) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); delete pGeometry; - delete xml; + delete cfg; return; } // If ok, change geometry pSinogram->changeGeometry(pGeometry); delete pGeometry; - delete xml; + delete cfg; return; } @@ -490,27 +483,25 @@ void astra_mex_data2d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const if (!mxIsStruct(prhs[2])) { mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n"); } - XMLDocument* xml = struct2XML(string("VolumeGeometry"), prhs[2]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("VolumeGeometry2D", prhs[2]); CVolumeGeometry2D* pGeometry = new CVolumeGeometry2D(); - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If data is specified, check dimensions if (pGeometry->getGridColCount() != pVolume->getWidth() || pGeometry->getGridRowCount() != pVolume->getHeight()) { mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n"); - delete xml; + delete cfg; delete pGeometry; return; } // If ok, change geometry pVolume->changeGeometry(pGeometry); - delete xml; + delete cfg; delete pGeometry; } @@ -639,12 +630,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == std::string("get")) { astra_mex_data2d_get(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_data2d_vc08.vcproj b/matlab/mex/astra_mex_data2d_vc09.vcproj index 8f1fc13..2c8a63f 100644 --- a/matlab/mex/astra_mex_data2d_vc08.vcproj +++ b/matlab/mex/astra_mex_data2d_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,16 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories=""$(CUDA_INC_PATH)";$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - BrowseInformation="1" - DebugInformationFormat="4" /> <Tool Name="VCManagedResourceCompilerTool" @@ -399,17 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -430,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -453,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -469,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -499,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -520,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -538,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -568,6 +563,24 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> @@ -585,6 +598,30 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexCopyDataHelpFunctions.cpp" + > + </File> + <File + RelativePath=".\mexCopyDataHelpFunctions.h" + > + </File> + <File + RelativePath=".\mexDataManagerHelpFunctions.cpp" + > + </File> + <File + RelativePath=".\mexDataManagerHelpFunctions.h" + > + </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git a/matlab/mex/astra_mex_data2d_vc11.vcxproj b/matlab/mex/astra_mex_data2d_vc11.vcxproj index eb09332..636780a 100644 --- a/matlab/mex/astra_mex_data2d_vc11.vcxproj +++ b/matlab/mex/astra_mex_data2d_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - 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<AdditionalLibraryDirectories>..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> + <AdditionalDependencies>Astra64.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies)</AdditionalDependencies> + <AdditionalLibraryDirectories>..\..\lib\x64\;..\..\bin\x64\Release;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> <ModuleDefinitionFile>mex.def</ModuleDefinitionFile> - <TargetMachine>MachineX64</TargetMachine> + <GenerateDebugInformation>true</GenerateDebugInformation> </Link> </ItemDefinitionGroup> <ItemGroup> <ClCompile Include="astra_mex_data2d_c.cpp" /> <ClCompile Include="mexHelpFunctions.cpp" /> - <ClCompile Include="mexCopyDataHelpFunctions.cpp"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">false</ExcludedFromBuild> - </ClCompile> + <ClCompile Include="mexCopyDataHelpFunctions.cpp" /> <ClCompile Include="mexDataManagerHelpFunctions.cpp" /> + <ClCompile Include="mexInitFunctions.cpp" /> </ItemGroup> <ItemGroup> <ClInclude Include="mexHelpFunctions.h" /> - <ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">false</ExcludedFromBuild> - </ClInclude> + <ClInclude Include="mexCopyDataHelpFunctions.h" /> <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp index db81519..32b0ba7 100644 --- a/matlab/mex/astra_mex_data3d_c.cpp +++ b/matlab/mex/astra_mex_data3d_c.cpp @@ -32,6 +32,7 @@ $Id$ */ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include "mexCopyDataHelpFunctions.h" #include "mexDataManagerHelpFunctions.h" @@ -79,11 +80,11 @@ void astra_mex_data3d_create(int& nlhs, mxArray* plhs[], int& nrhs, const mxArra } if (data && !checkDataType(data)) { - mexErrMsgTxt("Data must be single or double."); + mexErrMsgTxt("Data must be single, double or logical."); return; } - const string sDataType = mex_util_get_string(prhs[1]); + const string sDataType = mexToString(prhs[1]); // step2: Allocate data CFloat32Data3DMemory* pDataObject3D = @@ -152,7 +153,7 @@ void astra_mex_data3d_link(int& nlhs, mxArray* plhs[], int& nrhs, const mxArray* return; } - string sDataType = mex_util_get_string(prhs[1]); + string sDataType = mexToString(prhs[1]); // step2: Allocate data CFloat32Data3DMemory* pDataObject3D = @@ -266,48 +267,46 @@ void astra_mex_data3d_dimensions(int nlhs, mxArray* plhs[], int nrhs, const mxAr } //----------------------------------------------------------------------------------------- -/** - * [geom] = astra_mex_data3d('geometry', id); +/** geom = astra_mex_data3d('get_geometry', id); + * + * Fetch the geometry of a 3d data object stored in the astra-library. + * id: identifier of the 3d data object as stored in the astra-library. + * geom: MATLAB-struct containing information about the used geometry. */ -void astra_mex_data3d_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +void astra_mex_data3d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { - //// Get input - //if (nrhs < 2) { - // mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); - // return; - //} - //int iDid = (int)(mxGetScalar(prhs[1])); - - //// Get data object - //CFloat32Data3D* pData = CData3DManager::getSingleton().get(iDid); - //if (!pData) { - // mexErrMsgTxt("DataObject not valid. \n"); - // return; - //} - - //// Projection Data - //if (pData->getType() == CFloat32Data3D::PROJECTION) { - // CFloat32ProjectionData3D* pData2 = dynamic_cast<CFloat32ProjectionData3D*>(pData); - // CProjectionGeometry3D* pProjGeom = pData2->getGeometry(); - // XMLDocument* config = pProjGeom->toXML(); - - // if (1 <= nlhs) { - // plhs[0] = XML2struct(config); - // } - //} - //// Volume Data - //else if (pData->getType() == CFloat32Data3D::VOLUME) { - //// CFloat32VolumeData3D* pData2 = dynamic_cast<CFloat32VolumeData3D*>(pData); - //// CVolumeGeometry2D* pVolGeom = pData2->getGeometry2D(iSliceNr); - //// if (1 <= nlhs) { - //// plhs[0] = createVolumeGeometryStruct(pVolGeom); - //// } - //} - //// Error - //else { - // mexErrMsgTxt("Type not valid. \n"); - // return; - //} + // parse input + if (nrhs < 2) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + if (!mxIsDouble(prhs[1])) { + mexErrMsgTxt("Identifier should be a scalar value. \n"); + return; + } + int iDataID = (int)(mxGetScalar(prhs[1])); + + // fetch data object + CFloat32Data3D* pDataObject = astra::CData3DManager::getSingleton().get(iDataID); + if (!pDataObject || !pDataObject->isInitialized()) { + mexErrMsgTxt("Data object not found or not initialized properly.\n"); + return; + } + + // create output + if (1 <= nlhs) { + if (pDataObject->getType() == CFloat32Data3D::PROJECTION) { + CFloat32ProjectionData3DMemory* pDataObject2 = dynamic_cast<CFloat32ProjectionData3DMemory*>(pDataObject); + plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration()); + + } + else if (pDataObject->getType() == CFloat32Data3D::VOLUME) { + CFloat32VolumeData3DMemory* pDataObject2 = dynamic_cast<CFloat32VolumeData3DMemory*>(pDataObject); + plhs[0] = configToStruct(pDataObject2->getGeometry()->getConfiguration()); + } + } + + } //----------------------------------------------------------------------------------------- @@ -367,12 +366,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // 3D data if (sMode == std::string("create")) { astra_mex_data3d_create(nlhs, plhs, nrhs, prhs); @@ -395,8 +396,8 @@ void mexFunction(int nlhs, mxArray* plhs[], astra_mex_data3d_info(nlhs, plhs, nrhs, prhs); } else if (sMode == std::string("dimensions")) { astra_mex_data3d_dimensions(nlhs, plhs, nrhs, prhs); - } else if (sMode == std::string("geometry")) { - astra_mex_data3d_geometry(nlhs, plhs, nrhs, prhs); + } else if (sMode == std::string("get_geometry")) { + astra_mex_data3d_get_geometry(nlhs, plhs, nrhs, prhs); } else { printHelp(); } diff --git a/matlab/mex/astra_mex_data3d_vc09.vcproj b/matlab/mex/astra_mex_data3d_vc09.vcproj new file mode 100644 index 0000000..fd861a3 --- /dev/null +++ b/matlab/mex/astra_mex_data3d_vc09.vcproj @@ -0,0 +1,628 @@ +<?xml version="1.0" encoding="Windows-1252"?> +<VisualStudioProject + ProjectType="Visual C++" + Version="9.00" + Name="astra_mex_data3d" + ProjectGUID="{0BEC029B-0929-4BF9-BD8B-9C9806A52065}" + RootNamespace="astraMatlab" + TargetFrameworkVersion="131072" + > + <Platforms> + <Platform + Name="Win32" + /> + <Platform + Name="x64" + /> + </Platforms> + <ToolFiles> + </ToolFiles> + <Configurations> + <Configuration + Name="Debug_CUDA|Win32" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> + </Configuration> + <Configuration + Name="Debug_CUDA|x64" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> + </Configuration> + <Configuration + Name="Debug|Win32" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> + </Configuration> + <Configuration + Name="Debug|x64" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> + </Configuration> + <Configuration + Name="Release_CUDA|Win32" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> + </Configuration> + <Configuration + Name="Release_CUDA|x64" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> + </Configuration> + <Configuration + Name="Release|Win32" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> + </Configuration> + <Configuration + Name="Release|x64" + OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" + IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" + ConfigurationType="2" + > + <Tool + Name="VCPreBuildEventTool" + /> + <Tool + Name="VCCustomBuildTool" + /> + <Tool + Name="VCXMLDataGeneratorTool" + /> + <Tool + Name="VCWebServiceProxyGeneratorTool" + /> + <Tool + Name="VCMIDLTool" + /> + <Tool + Name="VCManagedResourceCompilerTool" + /> + <Tool + Name="VCResourceCompilerTool" + /> + <Tool + Name="VCPreLinkEventTool" + /> + <Tool + Name="VCALinkTool" + /> + <Tool + Name="VCManifestTool" + /> + <Tool + Name="VCXDCMakeTool" + /> + <Tool + Name="VCBscMakeTool" + /> + <Tool + Name="VCFxCopTool" + /> + <Tool + Name="VCAppVerifierTool" + /> + <Tool + Name="VCPostBuildEventTool" + /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> + </Configuration> + </Configurations> + <References> + </References> + <Files> + <File + RelativePath=".\astra_mex_data3d_c.cpp" + > + </File> + <File + RelativePath=".\mexHelpFunctions.cpp" + > + </File> + <File + RelativePath=".\mexHelpFunctions.h" + > + </File> + <File + RelativePath=".\mexCopyDataHelpFunctions.cpp" + > + </File> + <File + RelativePath=".\mexCopyDataHelpFunctions.h" + > + </File> + <File + RelativePath=".\mexDataManagerHelpFunctions.cpp" + > + </File> + <File + RelativePath=".\mexDataManagerHelpFunctions.h" + > + </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> + </Files> + <Globals> + </Globals> +</VisualStudioProject> diff --git a/matlab/mex/astra_mex_data3d_vc11.vcxproj b/matlab/mex/astra_mex_data3d_vc11.vcxproj index 064a4a1..1c3c620 100644 --- a/matlab/mex/astra_mex_data3d_vc11.vcxproj +++ b/matlab/mex/astra_mex_data3d_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> - <ConfigurationType>DynamicLibrary</ConfigurationType> - <PlatformToolset>v110</PlatformToolset> - </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -60,7 +56,7 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -68,6 +64,10 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> @@ -75,223 +75,234 @@ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" /> <ImportGroup Label="ExtensionSettings"> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets"> + <ImportGroup 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+----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +/** \file astra_mex_log_c.cpp + * + * \brief Manages astra logging + */ +#include <mex.h> +#include "mexHelpFunctions.h" +#include "mexInitFunctions.h" + +#include "astra/Logging.h" + +using namespace std; +using namespace astra; +//----------------------------------------------------------------------------------------- +/** astra_mex_log('debug', file, line, message); + * + * Log a debug message. + * file: Originating file name + * line: Originating line number + * message: Log message. + */ +void astra_mex_log_debug(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 4) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string filename = mexToString(prhs[1]); + int linenumber = (int)mxGetScalar(prhs[2]); + string message = mexToString(prhs[3]); + astra::CLogger::debug(filename.c_str(),linenumber,message.c_str()); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('info', file, line, message); + * + * Log an info message. + * file: Originating file name + * line: Originating line number + * message: Log message. + */ +void astra_mex_log_info(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 4) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string filename = mexToString(prhs[1]); + int linenumber = (int)mxGetScalar(prhs[2]); + string message = mexToString(prhs[3]); + astra::CLogger::info(filename.c_str(),linenumber,message.c_str()); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('warn', file, line, message); + * + * Log a warning message. + * file: Originating file name + * line: Originating line number + * message: Log message. + */ +void astra_mex_log_warn(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 4) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string filename = mexToString(prhs[1]); + int linenumber = (int)mxGetScalar(prhs[2]); + string message = mexToString(prhs[3]); + astra::CLogger::warn(filename.c_str(),linenumber,message.c_str()); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('error', file, line, message); + * + * Log an error message. + * file: Originating file name + * line: Originating line number + * message: Log message. + */ +void astra_mex_log_error(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 4) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string filename = mexToString(prhs[1]); + int linenumber = (int)mxGetScalar(prhs[2]); + string message = mexToString(prhs[3]); + astra::CLogger::error(filename.c_str(),linenumber,message.c_str()); +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('enable', type); + * + * Enable logging. + * type: which output to enable ('all', 'file', 'screen') + */ +void astra_mex_log_enable(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 2) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string sType = mexToString(prhs[1]); + if(sType == "all"){ + astra::CLogger::enable(); + }else if(sType == "file"){ + astra::CLogger::enableFile(); + }else if(sType == "screen"){ + astra::CLogger::enableScreen(); + } else { + mexErrMsgTxt("Specify which output to enable ('all', 'file', or 'screen')"); + } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('disable', type); + * + * Disable logging. + * type: which output to disable ('all', 'file', 'screen') + */ +void astra_mex_log_disable(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 2) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string sType = mexToString(prhs[1]); + if(sType == "all"){ + astra::CLogger::disable(); + }else if(sType == "file"){ + astra::CLogger::disableFile(); + }else if(sType == "screen"){ + astra::CLogger::disableScreen(); + } else { + mexErrMsgTxt("Specify which output to disable ('all', 'file', or 'screen')"); + } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('format', type, fmt); + * + * Enable logging. + * type: which output to format ('file', 'screen') + * fmt: format string + * Here are the substitutions you may use: + * %f: Source file name generating the log call. + * %n: Source line number where the log call was made. + * %m: The message text sent to the logger (after printf formatting). + * %d: The current date, formatted using the logger's date format. + * %t: The current time, formatted using the logger's time format. + * %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR"). + * %%: A literal percent sign. + * The default format string is "%d %t %f(%n): %l: %m\n". + */ +void astra_mex_log_format(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 3) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string sType = mexToString(prhs[1]); + string sFormat = mexToString(prhs[2]); + if (!sFormat.empty()) + { + char lastChar = *sFormat.rbegin(); + if (lastChar!='\n'){ + sFormat += '\n'; + } + }else{ + sFormat += '\n'; + } + if(sType == "file"){ + astra::CLogger::setFormatFile(sFormat.c_str()); + }else if(sType == "screen"){ + astra::CLogger::setFormatScreen(sFormat.c_str()); + } else { + mexErrMsgTxt("Specify which output to format ('file' or 'screen')"); + } +} + +//----------------------------------------------------------------------------------------- +/** astra_mex_log('output', type, output, level); + * + * Set output file / output screen. + * type: which output to set ('file', 'screen') + * output: which output file / screen to use: + * 'file': filename + * 'screen': 'stdout' or 'stderr' + * level: logging level to use ('debug', 'info', 'warn', or 'error') + */ +void astra_mex_log_output(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +{ + if (nrhs < 4) { + mexErrMsgTxt("Not enough arguments. See the help document for a detailed argument list. \n"); + return; + } + string sType = mexToString(prhs[1]); + string sOutput = mexToString(prhs[2]); + string sLevel = mexToString(prhs[3]); + log_level eLevel; + if(sLevel == "debug"){ + eLevel = LOG_DEBUG; + }else if(sLevel == "info"){ + eLevel = LOG_INFO; + }else if(sLevel == "warn"){ + eLevel = LOG_WARN; + }else if(sLevel == "error"){ + eLevel = LOG_ERROR; + }else{ + mexErrMsgTxt("Specify which log level to use ('debug', 'info', 'warn', or 'error')"); + } + if(sType == "file"){ + astra::CLogger::setOutputFile(sOutput.c_str(),eLevel); + }else if(sType == "screen"){ + int fd; + if(sOutput == "stdout"){ + fd=1; + }else if(sOutput == "stderr"){ + fd=2; + }else{ + mexErrMsgTxt("Specify which screen to output to ('stdout' or 'stderr')"); + } + astra::CLogger::setOutputScreen(fd,eLevel); + } else { + mexErrMsgTxt("Specify which output to set ('file' or 'screen')"); + } +} + +//----------------------------------------------------------------------------------------- +static void printHelp() +{ + mexPrintf("Please specify a mode of operation.\n"); + mexPrintf("Valid modes: debug, info, warn, error, enable, disable, format, output\n"); +} + +//----------------------------------------------------------------------------------------- +/** + * ... = astra_mex_log(mode, ...); + */ +void mexFunction(int nlhs, mxArray* plhs[], + int nrhs, const mxArray* prhs[]) +{ + // INPUT: Mode + string sMode = ""; + if (1 <= nrhs) { + sMode = mexToString(prhs[0]); + } else { + printHelp(); + return; + } + + initASTRAMex(); + + // SWITCH (MODE) + if (sMode == "debug") { + astra_mex_log_debug(nlhs, plhs, nrhs, prhs); + }else if (sMode == "info") { + astra_mex_log_info(nlhs, plhs, nrhs, prhs); + }else if (sMode == "warn") { + astra_mex_log_warn(nlhs, plhs, nrhs, prhs); + }else if (sMode == "error") { + astra_mex_log_error(nlhs, plhs, nrhs, prhs); + }else if (sMode == "enable") { + astra_mex_log_enable(nlhs, plhs, nrhs, prhs); + }else if (sMode == "disable") { + astra_mex_log_disable(nlhs, plhs, nrhs, prhs); + }else if (sMode == "format") { + astra_mex_log_format(nlhs, plhs, nrhs, prhs); + }else if (sMode == "output") { + astra_mex_log_output(nlhs, plhs, nrhs, prhs); + } else { + printHelp(); + } + return; +} diff --git a/matlab/mex/astra_mex_data3d_vc08.vcproj b/matlab/mex/astra_mex_log_vc09.vcproj index 2e69c16..0e0d469 100644 --- a/matlab/mex/astra_mex_data3d_vc08.vcproj +++ b/matlab/mex/astra_mex_log_vc09.vcproj @@ -2,8 +2,8 @@ <VisualStudioProject ProjectType="Visual C++" Version="9.00" - Name="astra_mex_data3d" - ProjectGUID="{0BEC029B-0929-4BF9-BD8B-9C9806A52065}" + Name="astra_mex_log" + ProjectGUID="{CA2840B3-DA68-41B5-AC57-F5DFD20ED8F8}" RootNamespace="astraMatlab" TargetFrameworkVersion="131072" > @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,14 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -397,16 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -427,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -450,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -466,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -496,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -517,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -535,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -565,13 +563,31 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> </References> <Files> <File - RelativePath=".\astra_mex_data3d_c.cpp" + RelativePath=".\astra_mex_log_c.cpp" > </File> <File @@ -582,6 +598,14 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git 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<ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> + <PropertyGroup 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<OutputFile>$(OutDir)$(ProjectName)_c.mexw32</OutputFile> + <AdditionalDependencies>Astra32.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies)</AdditionalDependencies> + <AdditionalLibraryDirectories>..\..\lib\win32\;..\..\bin\win32\Release;$(MATLAB_ROOT)\extern\lib\win32\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> + <ModuleDefinitionFile>mex.def</ModuleDefinitionFile> + <GenerateDebugInformation>true</GenerateDebugInformation> + </Link> + </ItemDefinitionGroup> + <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'"> + <ClCompile> + <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary> + <AdditionalIncludeDirectories>$(MATLAB_ROOT)\extern\include\;$(CUDA_PATH)\include;..\..\lib\include;..\..\include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories> + <OpenMPSupport>true</OpenMPSupport> + <Optimization>MaxSpeed</Optimization> + <PreprocessorDefinitions>__SSE2__;%(PreprocessorDefinitions)</PreprocessorDefinitions> + <MultiProcessorCompilation>true</MultiProcessorCompilation> + </ClCompile> + <Link> + <OutputFile>$(OutDir)$(ProjectName)_c.mexw64</OutputFile> + <AdditionalDependencies>Astra64.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies)</AdditionalDependencies> + <AdditionalLibraryDirectories>..\..\lib\x64\;..\..\bin\x64\Release;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> + <ModuleDefinitionFile>mex.def</ModuleDefinitionFile> + <GenerateDebugInformation>true</GenerateDebugInformation> + </Link> + </ItemDefinitionGroup> + <ItemGroup> + <ClCompile Include="astra_mex_log_c.cpp" /> + <ClCompile Include="mexHelpFunctions.cpp" /> + <ClCompile Include="mexInitFunctions.cpp" /> + </ItemGroup> + <ItemGroup> + <ClInclude Include="mexHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> + </ItemGroup> + <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> + <ImportGroup Label="ExtensionTargets"> + </ImportGroup> +</Project>
\ No newline at end of file diff --git a/matlab/mex/astra_mex_matrix_c.cpp b/matlab/mex/astra_mex_matrix_c.cpp index 016566a..aa31383 100644 --- a/matlab/mex/astra_mex_matrix_c.cpp +++ b/matlab/mex/astra_mex_matrix_c.cpp @@ -32,6 +32,7 @@ $Id$ */ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include <list> @@ -406,12 +407,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT0: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == std::string("get")) { astra_mex_matrix_get(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_matrix_vc08.vcproj b/matlab/mex/astra_mex_matrix_vc09.vcproj index 47509f6..3aa17a5 100644 --- a/matlab/mex/astra_mex_matrix_vc08.vcproj +++ b/matlab/mex/astra_mex_matrix_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,16 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories=""$(CUDA_INC_PATH)";$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - BrowseInformation="1" - DebugInformationFormat="4" /> <Tool Name="VCManagedResourceCompilerTool" @@ -399,17 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -430,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -453,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -469,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -499,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -520,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -538,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -568,6 +563,24 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> @@ -585,6 +598,14 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git a/matlab/mex/astra_mex_matrix_vc11.vcxproj b/matlab/mex/astra_mex_matrix_vc11.vcxproj index 12393bf..abf86a7 100644 --- a/matlab/mex/astra_mex_matrix_vc11.vcxproj +++ b/matlab/mex/astra_mex_matrix_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> - <ConfigurationType>DynamicLibrary</ConfigurationType> - <PlatformToolset>v110</PlatformToolset> - </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -60,7 +56,7 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - 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<ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClInclude> - <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/astra_mex_projector3d_c.cpp b/matlab/mex/astra_mex_projector3d_c.cpp index 25980f9..c3b547f 100644 --- a/matlab/mex/astra_mex_projector3d_c.cpp +++ b/matlab/mex/astra_mex_projector3d_c.cpp @@ -33,6 +33,7 @@ $Id$ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include "astra/Globals.h" @@ -65,16 +66,16 @@ void astra_mex_projector3d_create(int nlhs, mxArray* plhs[], int nrhs, const mxA } // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Projector3D", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("Projector3D", prhs[1]); // create algorithm - CProjector3D* pProj = CProjector3DFactory::getSingleton().create(cfg); + CProjector3D* pProj = CProjector3DFactory::getSingleton().create(*cfg); if (pProj == NULL) { + delete cfg; mexErrMsgTxt("Error creating Projector3D. \n"); return; } + delete cfg; // store projector int iIndex = CProjector3DManager::getSingleton().store(pProj); @@ -135,16 +136,16 @@ void astra_mex_projector3d_get_projection_geometry(int nlhs, mxArray* plhs[], in } // step3: get projection_geometry and turn it into a MATLAB struct - //if (1 <= nlhs) { - // plhs[0] = createProjectionGeometryStruct(pProjector->getProjectionGeometry()); - //} + if (1 <= nlhs) { + plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); + } } //----------------------------------------------------------------------------------------- /** * [recon_geom] = astra_mex_projector3d('get_volume_geometry', pid); */ -void astra_mex_projector3d_get_reconstruction_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) +void astra_mex_projector3d_get_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[]) { // step1: read input if (nrhs < 2) { @@ -161,9 +162,9 @@ void astra_mex_projector3d_get_reconstruction_geometry(int nlhs, mxArray* plhs[] } // step3: get projection_geometry and turn it into a MATLAB struct - //if (1 <= nlhs) { - // plhs[0] = createVolumeGeometryStruct(pProjector->getVolumeGeometry()); - //} + if (1 <= nlhs) { + plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); + } } //----------------------------------------------------------------------------------------- @@ -397,12 +398,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == "create") { astra_mex_projector3d_create(nlhs, plhs, nrhs, prhs); @@ -413,7 +416,7 @@ void mexFunction(int nlhs, mxArray* plhs[], } else if (sMode == "get_projection_geometry") { astra_mex_projector3d_get_projection_geometry(nlhs, plhs, nrhs, prhs); } else if (sMode == "get_volume_geometry") { - astra_mex_projector3d_get_reconstruction_geometry(nlhs, plhs, nrhs, prhs); + astra_mex_projector3d_get_volume_geometry(nlhs, plhs, nrhs, prhs); } else if (sMode == "weights_single_ray") { astra_mex_projector_weights_single_ray(nlhs, plhs, nrhs, prhs); //} else if (sMode == "weights_projection") { diff --git a/matlab/mex/astra_mex_projector3d_vc08.vcproj b/matlab/mex/astra_mex_projector3d_vc09.vcproj index bedc53b..b9464a2 100644 --- a/matlab/mex/astra_mex_projector3d_vc08.vcproj +++ b/matlab/mex/astra_mex_projector3d_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,14 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -397,16 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -427,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -450,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -466,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -496,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -517,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -535,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -565,6 +563,24 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> @@ -582,6 +598,14 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git a/matlab/mex/astra_mex_projector3d_vc11.vcxproj b/matlab/mex/astra_mex_projector3d_vc11.vcxproj index 7981806..42eb0f1 100644 --- a/matlab/mex/astra_mex_projector3d_vc11.vcxproj +++ b/matlab/mex/astra_mex_projector3d_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> - <ConfigurationType>DynamicLibrary</ConfigurationType> - <PlatformToolset>v110</PlatformToolset> - </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -60,7 +56,7 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -68,6 +64,10 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> @@ -75,210 +75,230 @@ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" /> <ImportGroup Label="ExtensionSettings"> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - 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<ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClInclude> - <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/astra_mex_projector_c.cpp b/matlab/mex/astra_mex_projector_c.cpp index de73f07..204ba8e 100644 --- a/matlab/mex/astra_mex_projector_c.cpp +++ b/matlab/mex/astra_mex_projector_c.cpp @@ -34,6 +34,7 @@ $Id$ #include <mex.h> #include "mexHelpFunctions.h" +#include "mexInitFunctions.h" #include "astra/AstraObjectManager.h" #include "astra/Projector2D.h" @@ -74,19 +75,16 @@ void astra_mex_projector_create(int nlhs, mxArray* plhs[], int nrhs, const mxArr // turn MATLAB struct to an XML-based Config object - XMLDocument* xml = struct2XML("Projector2D", prhs[1]); - Config cfg; - cfg.self = xml->getRootNode(); + Config* cfg = structToConfig("Projector2D", prhs[1]); // create algorithm - CProjector2D* pProj = CProjector2DFactory::getSingleton().create(cfg); + CProjector2D* pProj = CProjector2DFactory::getSingleton().create(*cfg); if (pProj == NULL) { - delete xml; + delete cfg; mexErrMsgTxt("Error creating projector. \n"); return; } - - delete xml; + delete cfg; // store projector iIndex = CProjector2DManager::getSingleton().store(pProj); @@ -162,7 +160,7 @@ void astra_mex_projector_projection_geometry(int nlhs, mxArray* plhs[], int nrhs // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = createProjectionGeometryStruct(pProjector->getProjectionGeometry()); + plhs[0] = configToStruct(pProjector->getProjectionGeometry()->getConfiguration()); } } @@ -191,7 +189,8 @@ void astra_mex_projector_volume_geometry(int nlhs, mxArray* plhs[], int nrhs, co // step3: get projection_geometry and turn it into a MATLAB struct if (1 <= nlhs) { - plhs[0] = createVolumeGeometryStruct(pProjector->getVolumeGeometry()); + plhs[0] = configToStruct(pProjector->getVolumeGeometry()->getConfiguration()); + } } @@ -472,12 +471,14 @@ void mexFunction(int nlhs, mxArray* plhs[], // INPUT: Mode string sMode = ""; if (1 <= nrhs) { - sMode = mex_util_get_string(prhs[0]); + sMode = mexToString(prhs[0]); } else { printHelp(); return; } + initASTRAMex(); + // SWITCH (MODE) if (sMode == "create") { astra_mex_projector_create(nlhs, plhs, nrhs, prhs); diff --git a/matlab/mex/astra_mex_projector_vc08.vcproj b/matlab/mex/astra_mex_projector_vc09.vcproj index 1380061..05c207f 100644 --- a/matlab/mex/astra_mex_projector_vc08.vcproj +++ b/matlab/mex/astra_mex_projector_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories=""$(MATLAB_ROOT)\extern\include\";"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,16 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - BrowseInformation="1" - DebugInformationFormat="4" /> <Tool Name="VCManagedResourceCompilerTool" @@ -399,17 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -430,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -453,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -469,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -499,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -520,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -538,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -568,6 +563,24 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> @@ -585,6 +598,14 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git a/matlab/mex/astra_mex_projector_vc11.vcxproj b/matlab/mex/astra_mex_projector_vc11.vcxproj index 3ab1806..e944949 100644 --- a/matlab/mex/astra_mex_projector_vc11.vcxproj +++ b/matlab/mex/astra_mex_projector_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> - <ConfigurationType>DynamicLibrary</ConfigurationType> - <PlatformToolset>v110</PlatformToolset> - </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -60,7 +56,7 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - 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<AdditionalLibraryDirectories>..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> + <AdditionalDependencies>Astra64.lib;libmex.lib;libmx.lib;libut.lib;%(AdditionalDependencies)</AdditionalDependencies> + <AdditionalLibraryDirectories>..\..\lib\x64\;..\..\bin\x64\Release;$(MATLAB_ROOT)\extern\lib\win64\microsoft;%(AdditionalLibraryDirectories)</AdditionalLibraryDirectories> <ModuleDefinitionFile>mex.def</ModuleDefinitionFile> - <TargetMachine>MachineX64</TargetMachine> + <GenerateDebugInformation>true</GenerateDebugInformation> </Link> </ItemDefinitionGroup> <ItemGroup> <ClCompile Include="astra_mex_projector_c.cpp" /> <ClCompile Include="mexHelpFunctions.cpp" /> - <ClCompile Include="mexCopyDataHelpFunctions.cpp"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClCompile> - <ClCompile Include="mexDataManagerHelpFunctions.cpp" /> + <ClCompile Include="mexInitFunctions.cpp" /> </ItemGroup> <ItemGroup> <ClInclude Include="mexHelpFunctions.h" /> - <ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClInclude> - <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/astra_mex_vc08.vcproj b/matlab/mex/astra_mex_vc09.vcproj index 58c1e0a..e4d7d07 100644 --- a/matlab/mex/astra_mex_vc08.vcproj +++ b/matlab/mex/astra_mex_vc09.vcproj @@ -19,7 +19,7 @@ </ToolFiles> <Configurations> <Configuration - Name="Release|Win32" + Name="Debug_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -40,12 +40,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -55,15 +49,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -84,9 +69,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release|x64" + Name="Debug_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -107,12 +111,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -122,15 +120,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -151,9 +140,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Release_CUDA|Win32" + Name="Debug|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -174,13 +181,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -190,15 +190,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -219,9 +210,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Release_CUDA|x64" + Name="Debug|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -242,13 +252,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="2" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\lib\include\cuda;..\..\include\;" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="2" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -258,15 +261,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -287,9 +281,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="0" + RuntimeLibrary="3" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="true" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug_CUDA|Win32" + Name="Release_CUDA|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -310,14 +322,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -327,16 +331,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -357,9 +351,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug_CUDA|x64" + Name="Release_CUDA|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -378,16 +391,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories=""$(CUDA_INC_PATH)";$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - PreprocessorDefinitions="ASTRA_CUDA" - RuntimeLibrary="3" - BrowseInformation="1" - DebugInformationFormat="4" /> <Tool Name="VCManagedResourceCompilerTool" @@ -399,17 +402,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="AstraCuda64D.lib libmex.lib libmx.lib libut.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -430,9 +422,27 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;"$(CUDA_INC_PATH)";..\..\lib\include;..\..\include" + PreprocessorDefinitions="ASTRA_CUDA;__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="AstraCuda64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> <Configuration - Name="Debug|Win32" + Name="Release|Win32" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -453,13 +463,6 @@ Name="VCMIDLTool" /> <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" - DebugInformationFormat="4" - /> - <Tool Name="VCManagedResourceCompilerTool" /> <Tool @@ -469,16 +472,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra32D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" - AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft" - ModuleDefinitionFile="mex.def" - GenerateDebugInformation="true" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -499,9 +492,28 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + EnableEnhancedInstructionSet="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra32.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw32" + AdditionalLibraryDirectories="..\..\bin\win32;$(MATLAB_ROOT)\extern\lib\win32\microsoft;..\..\lib\win32" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="1" + /> </Configuration> <Configuration - Name="Debug|x64" + Name="Release|x64" OutputDirectory="$(SolutionDir)bin\$(PlatformName)\$(ConfigurationName)" IntermediateDirectory="$(OutDir)\obj\$(ProjectName)" ConfigurationType="2" @@ -520,13 +532,6 @@ /> <Tool Name="VCMIDLTool" - TargetEnvironment="3" - /> - <Tool - Name="VCCLCompilerTool" - Optimization="0" - AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" - RuntimeLibrary="3" /> <Tool Name="VCManagedResourceCompilerTool" @@ -538,16 +543,6 @@ Name="VCPreLinkEventTool" /> <Tool - Name="VCLinkerTool" - AdditionalDependencies="Astra64D.lib libmex.lib libmx.lib" - OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" - AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft" - ModuleDefinitionFile="mex.def" - RandomizedBaseAddress="1" - DataExecutionPrevention="0" - TargetMachine="17" - /> - <Tool Name="VCALinkTool" /> <Tool @@ -568,6 +563,24 @@ <Tool Name="VCPostBuildEventTool" /> + <Tool + Name="VCCLCompilerTool" + AdditionalIncludeDirectories="$(MATLAB_ROOT)\extern\include\;..\..\lib\include;..\..\include" + PreprocessorDefinitions="__SSE2__" + Optimization="2" + RuntimeLibrary="2" + OpenMP="true" + AdditionalOptions="/MP" + /> + <Tool + Name="VCLinkerTool" + AdditionalDependencies="Astra64.lib libmex.lib libmx.lib libut.lib" + OutputFile="$(OutDir)\$(ProjectName)_c.mexw64" + AdditionalLibraryDirectories="..\..\bin\x64;$(MATLAB_ROOT)\extern\lib\win64\microsoft;..\..\lib\x64" + ModuleDefinitionFile="mex.def" + GenerateDebugInformation="false" + TargetMachine="17" + /> </Configuration> </Configurations> <References> @@ -585,6 +598,14 @@ RelativePath=".\mexHelpFunctions.h" > </File> + <File + RelativePath=".\mexInitFunctions.cpp" + > + </File> + <File + RelativePath=".\mexInitFunctions.h" + > + </File> </Files> <Globals> </Globals> diff --git a/matlab/mex/astra_mex_vc11.vcxproj b/matlab/mex/astra_mex_vc11.vcxproj index 2e6857c..f1324b4 100644 --- a/matlab/mex/astra_mex_vc11.vcxproj +++ b/matlab/mex/astra_mex_vc11.vcxproj @@ -40,19 +40,15 @@ <RootNamespace>astraMatlab</RootNamespace> </PropertyGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" /> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> - <ConfigurationType>DynamicLibrary</ConfigurationType> - <PlatformToolset>v110</PlatformToolset> - </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -60,7 +56,7 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="Configuration"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> @@ -68,6 +64,10 @@ <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> </PropertyGroup> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration"> + <ConfigurationType>DynamicLibrary</ConfigurationType> + <PlatformToolset>v110</PlatformToolset> + </PropertyGroup> <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration"> <ConfigurationType>DynamicLibrary</ConfigurationType> <PlatformToolset>v110</PlatformToolset> @@ -75,213 +75,230 @@ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" /> <ImportGroup Label="ExtensionSettings"> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> - <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets"> + <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|x64'"> <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" /> </ImportGroup> <PropertyGroup Label="UserMacros" /> <PropertyGroup> <_ProjectFileVersion>11.0.60610.1</_ProjectFileVersion> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'"> <OutDir>$(SolutionDir)bin\$(Platform)\$(Configuration)\</OutDir> <IntDir>$(OutDir)obj\$(ProjectName)\</IntDir> + <TargetName>$(ProjectName)_c</TargetName> + <TargetExt>.mexw32</TargetExt> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|x64'"> <OutDir>$(SolutionDir)bin\$(Platform)\$(Configuration)\</OutDir> <IntDir>$(OutDir)obj\$(ProjectName)\</IntDir> + <TargetName>$(ProjectName)_c</TargetName> + <TargetExt>.mexw64</TargetExt> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'"> <OutDir>$(SolutionDir)bin\$(Platform)\$(Configuration)\</OutDir> <IntDir>$(OutDir)obj\$(ProjectName)\</IntDir> + <TargetName>$(ProjectName)_c</TargetName> + <TargetExt>.mexw32</TargetExt> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'"> <OutDir>$(SolutionDir)bin\$(Platform)\$(Configuration)\</OutDir> <IntDir>$(OutDir)obj\$(ProjectName)\</IntDir> <TargetName>$(ProjectName)_c</TargetName> <TargetExt>.mexw64</TargetExt> </PropertyGroup> - <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug_CUDA|Win32'"> + <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|Win32'"> <OutDir>$(SolutionDir)bin\$(Platform)\$(Configuration)\</OutDir> <IntDir>$(OutDir)obj\$(ProjectName)\</IntDir> + <TargetName>$(ProjectName)_c</TargetName> + <TargetExt>.mexw32</TargetExt> </PropertyGroup> - 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<ClInclude Include="mexCopyDataHelpFunctions.h"> - <ExcludedFromBuild Condition="'$(Configuration)|$(Platform)'=='Release_CUDA|x64'">true</ExcludedFromBuild> - </ClInclude> - <ClInclude Include="mexDataManagerHelpFunctions.h" /> + <ClInclude Include="mexInitFunctions.h" /> </ItemGroup> <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" /> <ImportGroup Label="ExtensionTargets"> diff --git a/matlab/mex/mexCopyDataHelpFunctions.cpp b/matlab/mex/mexCopyDataHelpFunctions.cpp index bbcad30..80fb834 100644 --- a/matlab/mex/mexCopyDataHelpFunctions.cpp +++ b/matlab/mex/mexCopyDataHelpFunctions.cpp @@ -1,13 +1,13 @@ /* ----------------------------------------------------------------------- -Copyright 2013 iMinds-Vision Lab, University of Antwerp +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam -Contact: astra@ua.ac.be -Website: http://astra.ua.ac.be +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox +This file is part of the ASTRA Toolbox. -This file is part of the -All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). The ASTRA Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -40,7 +40,6 @@ $Id$ #if defined(__SSE2__) # include <emmintrin.h> - # define STORE_32F_64F_CORE8(in, out, count, base) \ {\ const __m128 inV0 = *((const __m128 *) &in[count + 0 + base]);\ @@ -108,6 +107,17 @@ $Id$ out[count + 7 + base] = in[count + 7 + base];\ } #endif +#define STORE_8F_32F_CORE8(in, out, count, base) \ + {\ + out[count + 0 + base] = (float)in[count + 0 + base];\ + out[count + 1 + base] = (float)in[count + 1 + base];\ + out[count + 2 + base] = (float)in[count + 2 + base];\ + out[count + 3 + base] = (float)in[count + 3 + base];\ + out[count + 4 + base] = (float)in[count + 4 + base];\ + out[count + 5 + base] = (float)in[count + 5 + base];\ + out[count + 6 + base] = (float)in[count + 6 + base];\ + out[count + 7 + base] = (float)in[count + 7 + base];\ + } const char * warnDataTypeNotSupported = "Data type not supported: nothing was copied"; @@ -118,6 +128,7 @@ _copyMexToCFloat32Array(const mxArray * const inArray, astra::float32 * const ou const long long block = 32; const long long totRoundedPixels = ROUND_DOWN(tot_size, block); + // Array of doubles if (mxIsDouble(inArray)) { const double * const pdMatlabData = mxGetPr(inArray); @@ -133,6 +144,8 @@ _copyMexToCFloat32Array(const mxArray * const inArray, astra::float32 * const ou out[count] = pdMatlabData[count]; } } + + // Array of floats else if (mxIsSingle(inArray)) { const float * const pfMatlabData = (const float *)mxGetData(inArray); @@ -148,6 +161,23 @@ _copyMexToCFloat32Array(const mxArray * const inArray, astra::float32 * const ou out[count] = pfMatlabData[count]; } } + + // Array of logicals + else if (mxIsLogical(inArray)) { + const mxLogical * const pfMatlabData = (const mxLogical *)mxGetLogicals(inArray); + +#pragma omp for nowait + for (long long count = 0; count < totRoundedPixels; count += block) { + STORE_8F_32F_CORE8(pfMatlabData, out, count, 0); + STORE_8F_32F_CORE8(pfMatlabData, out, count, 8); + STORE_8F_32F_CORE8(pfMatlabData, out, count, 16); + STORE_8F_32F_CORE8(pfMatlabData, out, count, 24); + } +#pragma omp for nowait + for (long long count = totRoundedPixels; count < tot_size; count++) { + out[count] = pfMatlabData[count]; + } + } else { #pragma omp single nowait mexWarnMsgIdAndTxt("ASTRA_MEX:wrong_datatype", warnDataTypeNotSupported); @@ -233,7 +263,7 @@ copyMexToCFloat32Array(const mxArray * const in, #pragma omp parallel { // fill with scalar value - if (mex_is_scalar(in)) { + if (mexIsScalar(in)) { astra::float32 fValue = 0.f; if (!mxIsEmpty(in)) { fValue = (astra::float32)mxGetScalar(in); diff --git a/matlab/mex/mexCopyDataHelpFunctions.h b/matlab/mex/mexCopyDataHelpFunctions.h index d0cf3c6..0853879 100644 --- a/matlab/mex/mexCopyDataHelpFunctions.h +++ b/matlab/mex/mexCopyDataHelpFunctions.h @@ -1,13 +1,13 @@ /* ----------------------------------------------------------------------- -Copyright 2013 iMinds-Vision Lab, University of Antwerp +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam -Contact: astra@ua.ac.be -Website: http://astra.ua.ac.be +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox +This file is part of the ASTRA Toolbox. -This file is part of the -All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). The ASTRA Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by diff --git a/matlab/mex/mexDataManagerHelpFunctions.cpp b/matlab/mex/mexDataManagerHelpFunctions.cpp index 2985a9d..d482428 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.cpp +++ b/matlab/mex/mexDataManagerHelpFunctions.cpp @@ -1,13 +1,13 @@ /* ----------------------------------------------------------------------- -Copyright 2013 iMinds-Vision Lab, University of Antwerp +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam -Contact: astra@ua.ac.be -Website: http://astra.ua.ac.be +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox +This file is part of the ASTRA Toolbox. -This file is part of the -All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). The ASTRA Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -105,7 +105,7 @@ checkID(const astra::int32 & id, astra::CFloat32Data3DMemory *& pDataObj) bool checkDataType(const mxArray * const in) { - return (mex_is_scalar(in) || mxIsDouble(in) || mxIsSingle(in)); + return (mexIsScalar(in) || mxIsDouble(in) || mxIsSingle(in) || mxIsLogical(in)); } //----------------------------------------------------------------------------------------- @@ -213,7 +213,7 @@ allocateDataObject(const std::string & sDataType, bool bUnshare = true; if (unshare) { - if (!mex_is_scalar(unshare)) + if (!mexIsScalar(unshare)) { mexErrMsgTxt("Argument 5 (read-only) must be scalar"); return NULL; @@ -225,7 +225,7 @@ allocateDataObject(const std::string & sDataType, mwIndex iZ = 0; if (zIndex) { - if (!mex_is_scalar(zIndex)) + if (!mexIsScalar(zIndex)) { mexErrMsgTxt("Argument 6 (Z) must be scalar"); return NULL; @@ -237,25 +237,19 @@ allocateDataObject(const std::string & sDataType, if (sDataType == "-vol") { // Read geometry - astra::XMLDocument* xml = struct2XML("VolumeGeometry", geometry); - if (!xml) { - return NULL; - } - astra::Config cfg; - cfg.self = xml->getRootNode(); - + astra::Config* cfg = structToConfig("VolumeGeometry3D", geometry); astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D(); - if (!pGeometry->initialize(cfg)) + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return NULL; } - delete xml; + delete cfg; // If data is specified, check dimensions - if (data && !mex_is_scalar(data)) + if (data && !mexIsScalar(data)) { if (! (zIndex ? checkDataSize(data, pGeometry, iZ) @@ -288,16 +282,10 @@ allocateDataObject(const std::string & sDataType, else if (sDataType == "-sino" || sDataType == "-proj3d" || sDataType == "-sinocone") { // Read geometry - astra::XMLDocument* xml = struct2XML("ProjectionGeometry", geometry); - if (!xml) { - return NULL; - } - astra::Config cfg; - cfg.self = xml->getRootNode(); - + astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry); // FIXME: Change how the base class is created. (This is duplicated - // in Projector2D.cpp.) - std::string type = cfg.self->getAttribute("type"); + // in Projector3D.cpp.) + std::string type = cfg->self->getAttribute("type"); astra::CProjectionGeometry3D* pGeometry = 0; if (type == "parallel3d") { pGeometry = new astra::CParallelProjectionGeometry3D(); @@ -312,16 +300,16 @@ allocateDataObject(const std::string & sDataType, return NULL; } - if (!pGeometry->initialize(cfg)) { + if (!pGeometry->initialize(*cfg)) { mexErrMsgTxt("Geometry class not initialized. \n"); delete pGeometry; - delete xml; + delete cfg; return NULL; } - delete xml; + delete cfg; // If data is specified, check dimensions - if (data && !mex_is_scalar(data)) + if (data && !mexIsScalar(data)) { if (! (zIndex ? checkDataSize(data, pGeometry, iZ) diff --git a/matlab/mex/mexDataManagerHelpFunctions.h b/matlab/mex/mexDataManagerHelpFunctions.h index 36b74d8..0614e05 100644 --- a/matlab/mex/mexDataManagerHelpFunctions.h +++ b/matlab/mex/mexDataManagerHelpFunctions.h @@ -1,13 +1,13 @@ /* ----------------------------------------------------------------------- -Copyright 2013 iMinds-Vision Lab, University of Antwerp +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam -Contact: astra@ua.ac.be -Website: http://astra.ua.ac.be +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox +This file is part of the ASTRA Toolbox. -This file is part of the -All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). The ASTRA Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by diff --git a/matlab/mex/mexHelpFunctions.cpp b/matlab/mex/mexHelpFunctions.cpp index e919dd9..c0ac711 100644 --- a/matlab/mex/mexHelpFunctions.cpp +++ b/matlab/mex/mexHelpFunctions.cpp @@ -32,9 +32,11 @@ $Id$ */ #include "mexHelpFunctions.h" -#include "astra/SparseMatrixProjectionGeometry2D.h" -#include "astra/FanFlatVecProjectionGeometry2D.h" -#include "astra/AstraObjectManager.h" +#include <algorithm> +#include <boost/lexical_cast.hpp> +#include <boost/algorithm/string.hpp> +#include <boost/algorithm/string/split.hpp> +#include <boost/algorithm/string/classification.hpp> using namespace std; using namespace astra; @@ -42,387 +44,148 @@ using namespace astra; //----------------------------------------------------------------------------------------- // get string from matlab -std::string mex_util_get_string(const mxArray* pInput) +string mexToString(const mxArray* pInput) { - if (!mxIsChar(pInput)) { - return ""; + // is string? + if (mxIsChar(pInput)) { + mwSize iLength = mxGetNumberOfElements(pInput) + 1; + char* buf = new char[iLength]; + mxGetString(pInput, buf, iLength); + std::string res = std::string(buf); + delete[] buf; + return res; } - mwSize iLength = mxGetNumberOfElements(pInput) + 1; - char* buf = new char[iLength]; - mxGetString(pInput, buf, iLength); - std::string res = std::string(buf); - delete[] buf; - return res; + + // is scalar? + if (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1) { + return boost::lexical_cast<string>(mxGetScalar(pInput)); + } + + return ""; } //----------------------------------------------------------------------------------------- -// is option -bool isOption(std::list<std::string> lOptions, std::string sOption) +// return true if the argument is a scalar +bool mexIsScalar(const mxArray* pInput) { - return std::find(lOptions.begin(), lOptions.end(), sOption) != lOptions.end(); + return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1); } //----------------------------------------------------------------------------------------- -// turn a matlab struct into a c++ map -std::map<std::string, mxArray*> parseStruct(const mxArray* pInput) +void get3DMatrixDims(const mxArray* x, mwSize *dims) { - std::map<std::string, mxArray*> res; - - // check type - if (!mxIsStruct(pInput)) { - mexErrMsgTxt("Input must be a struct."); - return res; + const mwSize* mdims = mxGetDimensions(x); + mwSize dimCount = mxGetNumberOfDimensions(x); + if (dimCount == 1) { + dims[0] = mdims[0]; + dims[1] = 1; + dims[2] = 1; + } else if (dimCount == 2) { + dims[0] = mdims[0]; + dims[1] = mdims[1]; + dims[2] = 1; + } else if (dimCount == 3) { + dims[0] = mdims[0]; + dims[1] = mdims[1]; + dims[2] = mdims[2]; + } else { + dims[0] = 0; + dims[1] = 0; + dims[2] = 0; } +} + + + + - // get field names - int nfields = mxGetNumberOfFields(pInput); - for (int i = 0; i < nfields; i++) { - std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i)); - res[sFieldName] = mxGetFieldByNumber(pInput,0,i); - } - return res; -} //----------------------------------------------------------------------------------------- -// turn a c++ map into a matlab struct -mxArray* buildStruct(std::map<std::string, mxArray*> mInput) +// turn an std vector<float32> object to an mxArray +mxArray* vectorToMxArray(std::vector<astra::float32> mInput) { - mwSize dims[2] = {1, 1}; - mxArray* res = mxCreateStructArray(2,dims,0,0); - - for (std::map<std::string, mxArray*>::iterator it = mInput.begin(); it != mInput.end(); it++) { - mxAddField(res, (*it).first.c_str()); - mxSetField(res, 0, (*it).first.c_str(), (*it).second); + mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL); + double* pdData = mxGetPr(res); + for (unsigned int i = 0; i < mInput.size(); i++) { + pdData[i] = mInput[i]; } return res; } //----------------------------------------------------------------------------------------- -// parse projection geometry data -astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray* prhs) +// turn a vector<vector<float32>> object to an mxArray +mxArray* vector2DToMxArray(std::vector<std::vector<astra::float32> > mInput) { - // parse struct - std::map<string, mxArray*> mStruct = parseStruct(prhs); - - // create projection geometry object - string type = mex_util_get_string(mStruct["type"]); - if (type == "parallel") { - - // detector_width - float32 fDetWidth = 1.0f; - mxArray* tmp = mStruct["detector_width"]; - if (tmp != NULL) { - fDetWidth = (float32)(mxGetScalar(tmp)); - } - - // detector_count - int iDetCount = 100; - tmp = mStruct["detector_count"]; - if (tmp != NULL) { - iDetCount = (int)(mxGetScalar(tmp)); - } - - // angles - float32* pfAngles; - int iAngleCount; - tmp = mStruct["projection_angles"]; - if (tmp != NULL) { - double* angleValues = mxGetPr(tmp); - iAngleCount = mxGetN(tmp) * mxGetM(tmp); - pfAngles = new float32[iAngleCount]; - for (int i = 0; i < iAngleCount; i++) { - pfAngles[i] = angleValues[i]; - } - } else { - mexErrMsgTxt("'angles' not specified, error."); - return NULL; - } - - // create projection geometry - return new astra::CParallelProjectionGeometry2D(iAngleCount, // number of projections - iDetCount, // number of detectors - fDetWidth, // width of the detectors - pfAngles); // angles array - } - - else if (type == "fanflat") { - - // detector_width - float32 fDetWidth = 1.0f; - mxArray* tmp = mStruct["detector_width"]; - if (tmp != NULL) { - fDetWidth = (float32)(mxGetScalar(tmp)); - } - - // detector_count - int iDetCount = 100; - tmp = mStruct["detector_count"]; - if (tmp != NULL) { - iDetCount = (int)(mxGetScalar(tmp)); - } - - // angles - float32* pfAngles; - int iAngleCount; - tmp = mStruct["projection_angles"]; - if (tmp != NULL) { - double* angleValues = mxGetPr(tmp); - iAngleCount = mxGetN(tmp) * mxGetM(tmp); - pfAngles = new float32[iAngleCount]; - for (int i = 0; i < iAngleCount; i++) { - pfAngles[i] = angleValues[i]; - } - } else { - mexErrMsgTxt("'angles' not specified, error."); - return NULL; - } - - // origin_source_dist - int iDistOriginSource = 100; - tmp = mStruct["origin_source_dist"]; - if (tmp != NULL) { - iDistOriginSource = (int)(mxGetScalar(tmp)); - } + unsigned int sizex = mInput.size(); + if (sizex == 0) return mxCreateString("empty"); + unsigned int sizey = mInput[0].size(); - // origin_det_dist - int iDistOriginDet = 100; - tmp = mStruct["origin_det_dist"]; - if (tmp != NULL) { - iDistOriginDet = (int)(mxGetScalar(tmp)); + mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL); + double* pdData = mxGetPr(res); + for (unsigned int i = 0; i < sizex; i++) { + for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) { + pdData[j*sizex+i] = mInput[i][j]; } - - // create projection geometry - return new astra::CFanFlatProjectionGeometry2D(iAngleCount, // number of projections - iDetCount, // number of detectors - fDetWidth, // width of the detectors - pfAngles, // angles array - iDistOriginSource, // distance origin source - iDistOriginDet); // distance origin detector - } - - else { - mexPrintf("Only parallel and fanflat projection geometry implemented."); - return NULL; } + return res; } //----------------------------------------------------------------------------------------- -// create projection geometry data -mxArray* createProjectionGeometryStruct(astra::CProjectionGeometry2D* _pProjGeom) +// turn a boost::any object to an mxArray +mxArray* anyToMxArray(boost::any _any) { - // temporary map to store the data for the MATLAB struct - std::map<std::string, mxArray*> mGeometryInfo; - - // detectorCount - mGeometryInfo["DetectorCount"] = mxCreateDoubleScalar(_pProjGeom->getDetectorCount()); - - if (!_pProjGeom->isOfType("fanflat_vec")) { - // detectorWidth - mGeometryInfo["DetectorWidth"] = mxCreateDoubleScalar(_pProjGeom->getDetectorWidth()); - - // pfProjectionAngles - mxArray* pAngles = mxCreateDoubleMatrix(1, _pProjGeom->getProjectionAngleCount(), mxREAL); - double* out = mxGetPr(pAngles); - for (int i = 0; i < _pProjGeom->getProjectionAngleCount(); i++) { - out[i] = _pProjGeom->getProjectionAngle(i); - } - mGeometryInfo["ProjectionAngles"] = pAngles; - } - else { - astra::CFanFlatVecProjectionGeometry2D* pVecGeom = dynamic_cast<astra::CFanFlatVecProjectionGeometry2D*>(_pProjGeom); - mxArray* pVectors = mxCreateDoubleMatrix(1, pVecGeom->getProjectionAngleCount()*6, mxREAL); - double* out = mxGetPr(pVectors); - int iDetCount = pVecGeom->getDetectorCount(); - for (int i = 0; i < pVecGeom->getProjectionAngleCount(); i++) { - const SFanProjection* p = &pVecGeom->getProjectionVectors()[i]; - out[6*i + 0] = p->fSrcX; - out[6*i + 1] = p->fSrcY; - out[6*i + 2] = p->fDetSX + 0.5f*iDetCount*p->fDetUX; - out[6*i + 3] = p->fDetSY + 0.5f*iDetCount*p->fDetUY; - out[6*i + 4] = p->fDetUX; - out[6*i + 5] = p->fDetUY; - } - mGeometryInfo["Vectors"] = pVectors; + if (_any.type() == typeid(std::string)) { + std::string str = boost::any_cast<std::string>(_any); + return mxCreateString(str.c_str()); } - - // parallel specific options - if (_pProjGeom->isOfType("parallel")) { - // type - mGeometryInfo["type"] = mxCreateString("parallel"); + if (_any.type() == typeid(int)) { + return mxCreateDoubleScalar(boost::any_cast<int>(_any)); } - // fanflat specific options - else if (_pProjGeom->isOfType("fanflat")) { - astra::CFanFlatProjectionGeometry2D* pFanFlatGeom = dynamic_cast<astra::CFanFlatProjectionGeometry2D*>(_pProjGeom); - // detectorCount - mGeometryInfo["DistanceOriginSource"] = mxCreateDoubleScalar(pFanFlatGeom->getOriginSourceDistance()); - // detectorWidth - mGeometryInfo["DistanceOriginDetector"] = mxCreateDoubleScalar(pFanFlatGeom->getOriginDetectorDistance()); - // type - mGeometryInfo["type"] = mxCreateString("fanflat"); + if (_any.type() == typeid(float32)) { + return mxCreateDoubleScalar(boost::any_cast<float32>(_any)); } - else if (_pProjGeom->isOfType("sparse_matrix")) { - astra::CSparseMatrixProjectionGeometry2D* pSparseMatrixGeom = dynamic_cast<astra::CSparseMatrixProjectionGeometry2D*>(_pProjGeom); - mGeometryInfo["type"] = mxCreateString("sparse_matrix"); - mGeometryInfo["MatrixID"] = mxCreateDoubleScalar(CMatrixManager::getSingleton().getIndex(pSparseMatrixGeom->getMatrix())); + if (_any.type() == typeid(std::vector<astra::float32>)) { + return vectorToMxArray(boost::any_cast<std::vector<float32> >(_any)); } - else if(_pProjGeom->isOfType("fanflat_vec")) { - mGeometryInfo["type"] = mxCreateString("fanflat_vec"); + if (_any.type() == typeid(std::vector<std::vector<astra::float32> >)) { + return vector2DToMxArray(boost::any_cast<std::vector<std::vector<float32> > >(_any)); } - - // build and return the MATLAB struct - return buildStruct(mGeometryInfo); + return NULL; } -//----------------------------------------------------------------------------------------- -// parse reconstruction geometry data -astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray* prhs) -{ - // parse struct - std::map<string, mxArray*> mStruct = parseStruct(prhs); - - std::map<string, mxArray*> mOptions = parseStruct(mStruct["option"]); - - // GridColCount - int iWindowColCount = 128; - mxArray* tmp = mStruct["GridColCount"]; - if (tmp != NULL) { - iWindowColCount = (int)(mxGetScalar(tmp)); - } - - // GridRowCount - int iWindowRowCount = 128; - tmp = mStruct["GridRowCount"]; - if (tmp != NULL) { - iWindowRowCount = (int)(mxGetScalar(tmp)); - } - // WindowMinX - float32 fWindowMinX = - iWindowColCount / 2; - tmp = mOptions["WindowMinX"]; - if (tmp != NULL) { - fWindowMinX = (float32)(mxGetScalar(tmp)); - } - - // WindowMaxX - float32 fWindowMaxX = iWindowColCount / 2; - tmp = mOptions["WindowMaxX"]; - if (tmp != NULL) { - fWindowMaxX = (float32)(mxGetScalar(tmp)); - } - - // WindowMinY - float32 fWindowMinY = - iWindowRowCount / 2; - tmp = mOptions["WindowMinY"]; - if (tmp != NULL) { - fWindowMinY = (float32)(mxGetScalar(tmp)); - } - - // WindowMaxX - float32 fWindowMaxY = iWindowRowCount / 2; - tmp = mOptions["WindowMaxY"]; - if (tmp != NULL) { - fWindowMaxY = (float32)(mxGetScalar(tmp)); - } - - // create and return reconstruction geometry - return new astra::CVolumeGeometry2D(iWindowColCount, iWindowRowCount, - fWindowMinX, fWindowMinY, - fWindowMaxX, fWindowMaxY); -} -//----------------------------------------------------------------------------------------- -// create reconstruction geometry data -mxArray* createVolumeGeometryStruct(astra::CVolumeGeometry2D* _pReconGeom) -{ - // temporary map to store the data for the MATLAB struct - std::map<std::string, mxArray*> mGeometryInfo; - // fill up map - mGeometryInfo["GridColCount"] = mxCreateDoubleScalar(_pReconGeom->getGridColCount()); - mGeometryInfo["GridRowCount"] = mxCreateDoubleScalar(_pReconGeom->getGridRowCount()); - std::map<std::string, mxArray*> mGeometryOptions; - mGeometryOptions["WindowMinX"] = mxCreateDoubleScalar(_pReconGeom->getWindowMinX()); - mGeometryOptions["WindowMaxX"] = mxCreateDoubleScalar(_pReconGeom->getWindowMaxX()); - mGeometryOptions["WindowMinY"] = mxCreateDoubleScalar(_pReconGeom->getWindowMinY()); - mGeometryOptions["WindowMaxY"] = mxCreateDoubleScalar(_pReconGeom->getWindowMaxY()); - mGeometryInfo["option"] = buildStruct(mGeometryOptions); - // build and return the MATLAB struct - return buildStruct(mGeometryInfo); -} //----------------------------------------------------------------------------------------- -string matlab2string(const mxArray* pField) +// turn a MATLAB struct into a Config object +Config* structToConfig(string rootname, const mxArray* pStruct) { - // is string? - if (mxIsChar(pField)) { - return mex_util_get_string(pField); - } - - // is scalar? - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { - return boost::lexical_cast<string>(mxGetScalar(pField)); + if (!mxIsStruct(pStruct)) { + mexErrMsgTxt("Input must be a struct."); + return NULL; } - return ""; -} - -//----------------------------------------------------------------------------------------- -// Options struct to xml node -bool readOptions(XMLNode* node, const mxArray* pOptionStruct) -{ - // loop all fields - int nfields = mxGetNumberOfFields(pOptionStruct); - for (int i = 0; i < nfields; i++) { - std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); - const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); - - if (node->hasOption(sFieldName)) { - mexErrMsgTxt("Duplicate option"); - return false; - } - - // string or scalar - if (mxIsChar(pField) || mex_is_scalar(pField)) { - string sValue = matlab2string(pField); - node->addOption(sFieldName, sValue); - } else - // numerical array - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { - if (!mxIsDouble(pField)) { - mexErrMsgTxt("Numeric input must be double."); - return false; - } + // create the document + Config* cfg = new Config(); + cfg->initialize(rootname); - XMLNode* listbase = node->addChildNode("Option"); - listbase->addAttribute("key", sFieldName); - listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); - double* pdValues = mxGetPr(pField); - int index = 0; - for (unsigned int row = 0; row < mxGetM(pField); row++) { - for (unsigned int col = 0; col < mxGetN(pField); col++) { - XMLNode* item = listbase->addChildNode("ListItem"); - item->addAttribute("index", index); - item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); - index++; - delete item; - } - } - delete listbase; - } else { - mexErrMsgTxt("Unsupported option type"); - return false; - } + // read the struct + bool ret = structToXMLNode(cfg->self, pStruct); + if (!ret) { + delete cfg; + mexErrMsgTxt("Error parsing struct."); + return NULL; } - return true; + return cfg; } //----------------------------------------------------------------------------------------- -// struct to xml node -bool readStruct(XMLNode* root, const mxArray* pStruct) +bool structToXMLNode(XMLNode* node, const mxArray* pStruct) { // loop all fields int nfields = mxGetNumberOfFields(pStruct); @@ -434,27 +197,27 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) // string if (mxIsChar(pField)) { - string sValue = matlab2string(pField); + string sValue = mexToString(pField); if (sFieldName == "type") { - root->addAttribute("type", sValue); + node->addAttribute("type", sValue); } else { - delete root->addChildNode(sFieldName, sValue); + delete node->addChildNode(sFieldName, sValue); } } // scalar - if (mex_is_scalar(pField)) { - string sValue = matlab2string(pField); - delete root->addChildNode(sFieldName, sValue); + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) == 1) { + string sValue = mexToString(pField); + delete node->addChildNode(sFieldName, sValue); } // numerical array - if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { if (!mxIsDouble(pField)) { mexErrMsgTxt("Numeric input must be double."); return false; } - XMLNode* listbase = root->addChildNode(sFieldName); + XMLNode* listbase = node->addChildNode(sFieldName); listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); double* pdValues = mxGetPr(pField); int index = 0; @@ -470,16 +233,15 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) delete listbase; } - // not castable to a single string - if (mxIsStruct(pField)) { + else if (mxIsStruct(pField)) { if (sFieldName == "options" || sFieldName == "option" || sFieldName == "Options" || sFieldName == "Option") { - bool ret = readOptions(root, pField); + bool ret = optionsToXMLNode(node, pField); if (!ret) return false; } else { - XMLNode* newNode = root->addChildNode(sFieldName); - bool ret = readStruct(newNode, pField); + XMLNode* newNode = node->addChildNode(sFieldName); + bool ret = structToXMLNode(newNode, pField); delete newNode; if (!ret) return false; @@ -490,109 +252,101 @@ bool readStruct(XMLNode* root, const mxArray* pStruct) return true; } +//----------------------------------------------------------------------------------------- +// Options struct to xml node +bool optionsToXMLNode(XMLNode* node, const mxArray* pOptionStruct) +{ + // loop all fields + int nfields = mxGetNumberOfFields(pOptionStruct); + for (int i = 0; i < nfields; i++) { + std::string sFieldName = std::string(mxGetFieldNameByNumber(pOptionStruct, i)); + const mxArray* pField = mxGetFieldByNumber(pOptionStruct, 0, i); + if (node->hasOption(sFieldName)) { + mexErrMsgTxt("Duplicate option"); + return false; + } + + // string or scalar + if (mxIsChar(pField) || mexIsScalar(pField)) { + string sValue = mexToString(pField); + node->addOption(sFieldName, sValue); + } + // numerical array + else if (mxIsNumeric(pField) && mxGetM(pField)*mxGetN(pField) > 1) { + if (!mxIsDouble(pField)) { + mexErrMsgTxt("Numeric input must be double."); + return false; + } + + XMLNode* listbase = node->addChildNode("Option"); + listbase->addAttribute("key", sFieldName); + listbase->addAttribute("listsize", mxGetM(pField)*mxGetN(pField)); + double* pdValues = mxGetPr(pField); + int index = 0; + for (unsigned int row = 0; row < mxGetM(pField); row++) { + for (unsigned int col = 0; col < mxGetN(pField); col++) { + XMLNode* item = listbase->addChildNode("ListItem"); + item->addAttribute("index", index); + item->addAttribute("value", pdValues[col*mxGetM(pField)+row]); + index++; + delete item; + } + } + delete listbase; + } else { + mexErrMsgTxt("Unsupported option type"); + return false; + } + } + return true; +} //----------------------------------------------------------------------------------------- -// turn a MATLAB struct into an XML Document -XMLDocument* struct2XML(string rootname, const mxArray* pStruct) +// turn a matlab struct into a c++ map +std::map<std::string, mxArray*> parseStruct(const mxArray* pInput) { - if (!mxIsStruct(pStruct)) { + std::map<std::string, mxArray*> res; + + // check type + if (!mxIsStruct(pInput)) { mexErrMsgTxt("Input must be a struct."); - return NULL; + return res; } - // create the document - XMLDocument* doc = XMLDocument::createDocument(rootname); - XMLNode* rootnode = doc->getRootNode(); + // get field names + int nfields = mxGetNumberOfFields(pInput); + for (int i = 0; i < nfields; i++) { + std::string sFieldName = std::string(mxGetFieldNameByNumber(pInput, i)); + res[sFieldName] = mxGetFieldByNumber(pInput,0,i); + } + return res; +} + + - // read the struct - bool ret = readStruct(rootnode, pStruct); - //doc->getRootNode()->print(); - delete rootnode; - if (!ret) { - delete doc; - doc = 0; - } - return doc; -} -//----------------------------------------------------------------------------------------- -// turn an std vector<float32> object to an mxArray -mxArray* vectorToMxArray(std::vector<astra::float32> mInput) -{ - mxArray* res = mxCreateDoubleMatrix(1, mInput.size(), mxREAL); - double* pdData = mxGetPr(res); - for (unsigned int i = 0; i < mInput.size(); i++) { - pdData[i] = mInput[i]; - } - return res; -} -//----------------------------------------------------------------------------------------- -// turn a vector<vector<float32>> object to an mxArray -mxArray* vector2DToMxArray(std::vector<std::vector<astra::float32> > mInput) -{ - unsigned int sizex = mInput.size(); - if (sizex == 0) return mxCreateString("empty"); - unsigned int sizey = mInput[0].size(); - mxArray* res = mxCreateDoubleMatrix(sizex, sizey, mxREAL); - double* pdData = mxGetPr(res); - for (unsigned int i = 0; i < sizex; i++) { - for (unsigned int j = 0; j < sizey && j < mInput[i].size(); j++) { - pdData[j*sizex+i] = mInput[i][j]; - } - } - return res; -} -//----------------------------------------------------------------------------------------- -// turn a boost::any object to an mxArray -mxArray* anyToMxArray(boost::any _any) -{ - if (_any.type() == typeid(std::string)) { - std::string str = boost::any_cast<std::string>(_any); - return mxCreateString(str.c_str()); - } - if (_any.type() == typeid(int)) { - return mxCreateDoubleScalar(boost::any_cast<int>(_any)); - } - if (_any.type() == typeid(float32)) { - return mxCreateDoubleScalar(boost::any_cast<float32>(_any)); - } - if (_any.type() == typeid(std::vector<astra::float32>)) { - return vectorToMxArray(boost::any_cast<std::vector<float32> >(_any)); - } - if (_any.type() == typeid(std::vector<std::vector<astra::float32> >)) { - return vector2DToMxArray(boost::any_cast<std::vector<std::vector<float32> > >(_any)); - } - return NULL; -} -//----------------------------------------------------------------------------------------- -// return true ig the argument is a scalar -bool mex_is_scalar(const mxArray* pInput) -{ - return (mxIsNumeric(pInput) && mxGetM(pInput)*mxGetN(pInput) == 1); -} //----------------------------------------------------------------------------------------- -mxArray* XML2struct(astra::XMLDocument* xml) +// turn a Config object into a MATLAB struct +mxArray* configToStruct(astra::Config* cfg) { - XMLNode* node = xml->getRootNode(); - mxArray* str = XMLNode2struct(xml->getRootNode()); - delete node; - return str; + return XMLNodeToStruct(cfg->self); } //----------------------------------------------------------------------------------------- -mxArray* XMLNode2struct(astra::XMLNode* node) +mxArray* XMLNodeToStruct(astra::XMLNode* node) { - std::map<std::string, mxArray*> mList; + std::map<std::string, mxArray*> mList; + std::map<std::string, mxArray*> mOptions; // type_attribute if (node->hasAttribute("type")) { @@ -602,41 +356,103 @@ mxArray* XMLNode2struct(astra::XMLNode* node) list<XMLNode*> nodes = node->getNodes(); for (list<XMLNode*>::iterator it = nodes.begin(); it != nodes.end(); it++) { XMLNode* subnode = (*it); - // list - if (subnode->hasAttribute("listsize")) { - cout << "lkmdsqldqsjkl" << endl; - cout << " " << node->getContentNumericalArray().size() << endl; - mList[subnode->getName()] = vectorToMxArray(node->getContentNumericalArray()); + + // option + if (subnode->getName() == "Option") { + mOptions[subnode->getAttribute("key")] = stringToMxArray(subnode->getAttribute("value")); } - // string + + // regular content else { - mList[subnode->getName()] = mxCreateString(subnode->getContent().c_str()); + mList[subnode->getName()] = stringToMxArray(subnode->getContent()); } delete subnode; } + if (mOptions.size() > 0) mList["options"] = buildStruct(mOptions); return buildStruct(mList); } -void get3DMatrixDims(const mxArray* x, mwSize *dims) +//----------------------------------------------------------------------------------------- +mxArray* stringToMxArray(std::string input) { - const mwSize* mdims = mxGetDimensions(x); - mwSize dimCount = mxGetNumberOfDimensions(x); - if (dimCount == 1) { - dims[0] = mdims[0]; - dims[1] = 1; - dims[2] = 1; - } else if (dimCount == 2) { - dims[0] = mdims[0]; - dims[1] = mdims[1]; - dims[2] = 1; - } else if (dimCount == 3) { - dims[0] = mdims[0]; - dims[1] = mdims[1]; - dims[2] = mdims[2]; - } else { - dims[0] = 0; - dims[1] = 0; - dims[2] = 0; + // matrix + if (input.find(';') != std::string::npos) { + + // split rows + std::vector<std::string> row_strings; + std::vector<std::string> col_strings; + boost::split(row_strings, input, boost::is_any_of(";")); + boost::split(col_strings, row_strings[0], boost::is_any_of(",")); + + // get dimensions + int rows = row_strings.size(); + int cols = col_strings.size(); + + // init matrix + mxArray* pMatrix = mxCreateDoubleMatrix(rows, cols, mxREAL); + double* out = mxGetPr(pMatrix); + + // loop elements + for (unsigned int row = 0; row < rows; row++) { + boost::split(col_strings, row_strings[row], boost::is_any_of(",")); + // check size + for (unsigned int col = 0; col < col_strings.size(); col++) { + out[col*rows + row] = boost::lexical_cast<float32>(col_strings[col]); + } + } + return pMatrix; } -} + + // vector + if (input.find(',') != std::string::npos) { + + // split + std::vector<std::string> items; + boost::split(items, input, boost::is_any_of(",")); + + // init matrix + mxArray* pVector = mxCreateDoubleMatrix(1, items.size(), mxREAL); + double* out = mxGetPr(pVector); + + // loop elements + for (unsigned int i = 0; i < items.size(); i++) { + out[i] = boost::lexical_cast<float32>(items[i]); + } + return pVector; + } + + // number + char* end; + double content = ::strtod(input.c_str(), &end); + bool isnumber = !*end; + if (isnumber) { + return mxCreateDoubleScalar(content); + } + + // string + return mxCreateString(input.c_str()); +} +//----------------------------------------------------------------------------------------- +// turn a c++ map into a matlab struct +mxArray* buildStruct(std::map<std::string, mxArray*> mInput) +{ + mwSize dims[2] = {1, 1}; + mxArray* res = mxCreateStructArray(2,dims,0,0); + + for (std::map<std::string, mxArray*>::iterator it = mInput.begin(); it != mInput.end(); it++) { + mxAddField(res, (*it).first.c_str()); + mxSetField(res, 0, (*it).first.c_str(), (*it).second); + } + return res; +} + + + + + + + + + + diff --git a/matlab/mex/mexHelpFunctions.h b/matlab/mex/mexHelpFunctions.h index 425b4ef..f9ffcf2 100644 --- a/matlab/mex/mexHelpFunctions.h +++ b/matlab/mex/mexHelpFunctions.h @@ -1,13 +1,13 @@ /* ----------------------------------------------------------------------- -Copyright 2012 iMinds-Vision Lab, University of Antwerp +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam -Contact: astra@ua.ac.be -Website: http://astra.ua.ac.be +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox +This file is part of the ASTRA Toolbox. -This file is part of the -All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). The ASTRA Toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -43,34 +43,31 @@ $Id$ #include "astra/Globals.h" #include "astra/Utilities.h" -#include "astra/ParallelProjectionGeometry2D.h" -#include "astra/FanFlatProjectionGeometry2D.h" -#include "astra/VolumeGeometry2D.h" - +#include "astra/Config.h" #include "astra/XMLDocument.h" #include "astra/XMLNode.h" -std::string mex_util_get_string(const mxArray* pInput); -bool isOption(std::list<std::string> lOptions, std::string sOption); - -bool mex_is_scalar(const mxArray* pInput); +// utility functions +string mexToString(const mxArray* pInput); +bool mexIsScalar(const mxArray* pInput); +void get3DMatrixDims(const mxArray* x, mwSize *dims); -std::map<std::string, mxArray*> parseStruct(const mxArray* pInput); -mxArray* buildStruct(std::map<std::string, mxArray*> mInput); +// convert boost::any into a MALTAB object mxArray* vectorToMxArray(std::vector<astra::float32> mInput); - mxArray* anyToMxArray(boost::any _any); -astra::CProjectionGeometry2D* parseProjectionGeometryStruct(const mxArray*); -mxArray* createProjectionGeometryStruct(astra::CProjectionGeometry2D*); -astra::CVolumeGeometry2D* parseVolumeGeometryStruct(const mxArray*); -mxArray* createVolumeGeometryStruct(astra::CVolumeGeometry2D* _pReconGeom); +// turn a MATLAB struct into a Config object +astra::Config* structToConfig(string rootname, const mxArray* pStruct); +bool structToXMLNode(astra::XMLNode* node, const mxArray* pStruct); +bool optionsToXMLNode(astra::XMLNode* node, const mxArray* pOptionStruct); +std::map<std::string, mxArray*> parseStruct(const mxArray* pInput); -astra::XMLDocument* struct2XML(string rootname, const mxArray* pStruct); +// turn a Config object into a MATLAB struct +mxArray* configToStruct(astra::Config* cfg); +mxArray* XMLNodeToStruct(astra::XMLNode* xml); +mxArray* stringToMxArray(std::string input); +mxArray* buildStruct(std::map<std::string, mxArray*> mInput); -mxArray* XML2struct(astra::XMLDocument* xml); -mxArray* XMLNode2struct(astra::XMLNode* xml); -void get3DMatrixDims(const mxArray* x, mwSize *dims); #endif diff --git a/matlab/mex/mexInitFunctions.cpp b/matlab/mex/mexInitFunctions.cpp new file mode 100644 index 0000000..d8a50d7 --- /dev/null +++ b/matlab/mex/mexInitFunctions.cpp @@ -0,0 +1,24 @@ +#include <mex.h> +#include "astra/Logging.h" + +bool mexIsInitialized=false; + +/** + * Callback to print log message to Matlab window. + * + */ +void logCallBack(const char *msg, size_t len){ + mexPrintf(msg); +} + +/** + * Initialize mex functions. + * + */ +void initASTRAMex(){ + if(mexIsInitialized) return; + if(!astra::CLogger::setCallbackScreen(&logCallBack)){ + mexErrMsgTxt("Error initializing mex functions."); + } + mexIsInitialized=true; +} diff --git a/matlab/mex/mexInitFunctions.h b/matlab/mex/mexInitFunctions.h new file mode 100644 index 0000000..f16e9c9 --- /dev/null +++ b/matlab/mex/mexInitFunctions.h @@ -0,0 +1,6 @@ +#ifndef _INC_ASTRA_MEX_INITFUNCTIONS +#define _INC_ASTRA_MEX_INITFUNCTIONS + +void initASTRAMex(); + +#endif
\ No newline at end of file diff --git a/matlab/tools/astra_mex_log.m b/matlab/tools/astra_mex_log.m new file mode 100644 index 0000000..28cfa18 --- /dev/null +++ b/matlab/tools/astra_mex_log.m @@ -0,0 +1,33 @@ +function [varargout] = astra_mex_log(varargin) +%------------------------------------------------------------------------ +% Reference page in Help browser +% <a href="matlab:docsearch('astra_mex_log' )">astra_mex_log</a>. +%------------------------------------------------------------------------ +%------------------------------------------------------------------------ +% This file is part of the ASTRA Toolbox +% +% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp +% 2014-2015, CWI, Amsterdam +% License: Open Source under GPLv3 +% Contact: astra@uantwerpen.be +% Website: http://sf.net/projects/astra-toolbox +%------------------------------------------------------------------------ +% $Id$ +if size(varargin,2)==2 && (strcmp(varargin{1},'debug') || strcmp(varargin{1},'info') || strcmp(varargin{1},'warn') || strcmp(varargin{1},'error')) + d = dbstack(1); + if size(d,1)==0 + astra_mex_log_c(varargin{1},'Unknown',0,varargin{2}) + else + astra_mex_log_c(varargin{1},d(1).file,d(1).line,varargin{2}) + end +else + if nargout == 0 + astra_mex_log_c(varargin{:}); + if exist('ans','var') + varargout{1} = ans; + end + else + varargout = cell(1,nargout); + [varargout{:}] = astra_mex_log_c(varargin{:}); + end +end
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Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. diff --git a/python/LICENSE b/python/LICENSE new file mode 120000 index 0000000..d24842f --- /dev/null +++ b/python/LICENSE @@ -0,0 +1 @@ +COPYING
\ No newline at end of file diff --git a/python/astra/ASTRAProjector.py b/python/astra/ASTRAProjector.py new file mode 100644 index 0000000..f282618 --- /dev/null +++ b/python/astra/ASTRAProjector.py @@ -0,0 +1,135 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import math +from . import creators as ac +from . import data2d + + +class ASTRAProjector2DTranspose(): + """Implements the ``proj.T`` functionality. + + Do not use directly, since it can be accessed as member ``.T`` of + an :class:`ASTRAProjector2D` object. + + """ + def __init__(self, parentProj): + self.parentProj = parentProj + + def __mul__(self, data): + return self.parentProj.backProject(data) + + +class ASTRAProjector2D(object): + """Helps with various common ASTRA Toolbox 2D operations. + + This class can perform several often used toolbox operations, such as: + + * Forward projecting + * Back projecting + * Reconstructing + + Note that this class has a some computational overhead, because it + copies a lot of data. If you use many repeated operations, directly + using the PyAstraToolbox methods directly is faster. + + You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance + ``proj`` of this class by an image results in a forward projection of the image, and multiplying + ``proj.T`` by a sinogram results in a backprojection of the sinogram:: + + proj = ASTRAProjector2D(...) + fp = proj*image + bp = proj.T*sinogram + + :param proj_geom: The projection geometry. + :type proj_geom: :class:`dict` + :param vol_geom: The volume geometry. + :type vol_geom: :class:`dict` + :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... + :type proj_type: :class:`string` + """ + + def __init__(self, proj_geom, vol_geom, proj_type): + self.vol_geom = vol_geom + self.recSize = vol_geom['GridColCount'] + self.angles = proj_geom['ProjectionAngles'] + self.nDet = proj_geom['DetectorCount'] + nexpow = int(pow(2, math.ceil(math.log(2 * self.nDet, 2)))) + self.filterSize = nexpow / 2 + 1 + self.nProj = self.angles.shape[0] + self.proj_geom = proj_geom + self.proj_id = ac.create_projector(proj_type, proj_geom, vol_geom) + self.T = ASTRAProjector2DTranspose(self) + + def backProject(self, data): + """Backproject a sinogram. + + :param data: The sinogram data or ID. + :type data: :class:`numpy.ndarray` or :class:`int` + :returns: :class:`numpy.ndarray` -- The backprojection. + + """ + vol_id, vol = ac.create_backprojection( + data, self.proj_id, returnData=True) + data2d.delete(vol_id) + return vol + + def forwardProject(self, data): + """Forward project an image. + + :param data: The image data or ID. + :type data: :class:`numpy.ndarray` or :class:`int` + :returns: :class:`numpy.ndarray` -- The forward projection. + + """ + sin_id, sino = ac.create_sino(data, self.proj_id, returnData=True) + data2d.delete(sin_id) + return sino + + def reconstruct(self, data, method, **kwargs): + """Reconstruct an image from a sinogram. + + :param data: The sinogram data or ID. + :type data: :class:`numpy.ndarray` or :class:`int` + :param method: Name of the reconstruction algorithm. + :type method: :class:`string` + :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`. + :returns: :class:`numpy.ndarray` -- The reconstruction. + + Example of a SIRT reconstruction using CUDA:: + + proj = ASTRAProjector2D(...) + rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000) + + """ + kwargs['returnData'] = True + rec_id, rec = ac.create_reconstruction( + method, self.proj_id, data, **kwargs) + data2d.delete(rec_id) + return rec + + def __mul__(self, data): + return self.forwardProject(data) diff --git a/python/astra/PyAlgorithmFactory.pxd b/python/astra/PyAlgorithmFactory.pxd new file mode 100644 index 0000000..256d7b2 --- /dev/null +++ b/python/astra/PyAlgorithmFactory.pxd @@ -0,0 +1,36 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra": + cdef cppclass CAlgorithmFactory: + CAlgorithmFactory() + CAlgorithm *create(string) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CAlgorithmFactory": + cdef CAlgorithmFactory* getSingletonPtr() diff --git a/python/astra/PyAlgorithmManager.pxd b/python/astra/PyAlgorithmManager.pxd new file mode 100644 index 0000000..a99a807 --- /dev/null +++ b/python/astra/PyAlgorithmManager.pxd @@ -0,0 +1,40 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CAlgorithmManager: + int store(CAlgorithm *) + CAlgorithm * get(int) + void remove(int) + void clear() + string info() + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CAlgorithmManager": + cdef CAlgorithmManager* getSingletonPtr() + diff --git a/python/astra/PyData2DManager.pxd b/python/astra/PyData2DManager.pxd new file mode 100644 index 0000000..db8ec84 --- /dev/null +++ b/python/astra/PyData2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData2DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data2D *) + CFloat32Data2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData2DManager": + cdef CData2DManager* getSingletonPtr() diff --git a/python/astra/PyData3DManager.pxd b/python/astra/PyData3DManager.pxd new file mode 100644 index 0000000..9264a82 --- /dev/null +++ b/python/astra/PyData3DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CData3DManager: + string info() + void clear() + void remove(int i) + int store(CFloat32Data3D *) + CFloat32Data3D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CData3DManager": + cdef CData3DManager* getSingletonPtr() diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd new file mode 100644 index 0000000..7df02c5 --- /dev/null +++ b/python/astra/PyIncludes.pxd @@ -0,0 +1,244 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp cimport bool +from libcpp.string cimport string +from .PyXMLDocument cimport XMLNode + +include "config.pxi" + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/Config.h" namespace "astra": + cdef cppclass Config: + Config() + void initialize(string rootname) + XMLNode *self + +cdef extern from "astra/VolumeGeometry2D.h" namespace "astra": + cdef cppclass CVolumeGeometry2D: + bool initialize(Config) + int getGridColCount() + int getGridRowCount() + int getGridTotCount() + float32 getWindowLengthX() + float32 getWindowLengthY() + float32 getWindowArea() + float32 getPixelLengthX() + float32 getPixelLengthY() + float32 getPixelArea() + float32 getWindowMinX() + float32 getWindowMinY() + float32 getWindowMaxX() + float32 getWindowMaxY() + Config* getConfiguration() + + +cdef extern from "astra/Float32VolumeData2D.h" namespace "astra": + cdef cppclass CFloat32VolumeData2D: + CFloat32VolumeData2D(CVolumeGeometry2D*) + CVolumeGeometry2D * getGeometry() + int getWidth() + int getHeight() + void changeGeometry(CVolumeGeometry2D*) + Config* getConfiguration() + + + +cdef extern from "astra/ProjectionGeometry2D.h" namespace "astra": + cdef cppclass CProjectionGeometry2D: + CProjectionGeometry2D() + bool initialize(Config) + int getDetectorCount() + int getProjectionAngleCount() + bool isOfType(string) + float32 getProjectionAngle(int) + float32 getDetectorWidth() + Config* getConfiguration() + +cdef extern from "astra/Float32Data2D.h" namespace "astra::CFloat32Data2D": + cdef enum TWOEDataType "astra::CFloat32Data2D::EDataType": + TWOPROJECTION "astra::CFloat32Data2D::PROJECTION" + TWOVOLUME "astra::CFloat32Data2D::VOLUME" + +cdef extern from "astra/Float32Data3D.h" namespace "astra::CFloat32Data3D": + cdef enum THREEEDataType "astra::CFloat32Data3D::EDataType": + THREEPROJECTION "astra::CFloat32Data3D::PROJECTION" + THREEVOLUME "astra::CFloat32Data3D::VOLUME" + + +cdef extern from "astra/Float32Data2D.h" namespace "astra": + cdef cppclass CFloat32Data2D: + bool isInitialized() + int getSize() + float32 *getData() + float32 **getData2D() + int getWidth() + int getHeight() + TWOEDataType getType() + + + + +cdef extern from "astra/SparseMatrixProjectionGeometry2D.h" namespace "astra": + cdef cppclass CSparseMatrixProjectionGeometry2D: + CSparseMatrixProjectionGeometry2D() + +cdef extern from "astra/FanFlatProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatProjectionGeometry2D: + CFanFlatProjectionGeometry2D() + +cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra": + cdef cppclass CFanFlatVecProjectionGeometry2D: + CFanFlatVecProjectionGeometry2D() + +cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry2D: + CParallelProjectionGeometry2D() + + +cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra": + cdef cppclass CFloat32ProjectionData2D: + CFloat32ProjectionData2D(CProjectionGeometry2D*) + CProjectionGeometry2D * getGeometry() + void changeGeometry(CProjectionGeometry2D*) + int getDetectorCount() + int getAngleCount() + +cdef extern from "astra/Algorithm.h" namespace "astra": + cdef cppclass CAlgorithm: + bool initialize(Config) + void run(int) + bool isInitialized() + +cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra": + cdef cppclass CReconstructionAlgorithm2D: + bool getResidualNorm(float32&) + +cdef extern from "astra/Projector2D.h" namespace "astra": + cdef cppclass CProjector2D: + bool isInitialized() + CProjectionGeometry2D* getProjectionGeometry() + CVolumeGeometry2D* getVolumeGeometry() + CSparseMatrix* getMatrix() + +cdef extern from "astra/Projector3D.h" namespace "astra": + cdef cppclass CProjector3D: + bool isInitialized() + CProjectionGeometry3D* getProjectionGeometry() + CVolumeGeometry3D* getVolumeGeometry() + +IF HAVE_CUDA==True: + cdef extern from "astra/CudaProjector3D.h" namespace "astra": + cdef cppclass CCudaProjector3D + + cdef extern from "astra/CudaProjector2D.h" namespace "astra": + cdef cppclass CCudaProjector2D + + +cdef extern from "astra/SparseMatrix.h" namespace "astra": + cdef cppclass CSparseMatrix: + CSparseMatrix(unsigned int,unsigned int,unsigned long) + unsigned int m_iWidth + unsigned int m_iHeight + unsigned long m_lSize + bool isInitialized() + float32* m_pfValues + unsigned int* m_piColIndices + unsigned long* m_plRowStarts + +cdef extern from "astra/Float32Data3DMemory.h" namespace "astra": + cdef cppclass CFloat32Data3DMemory: + CFloat32Data3DMemory() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() + float32 *getData() + float32 ***getData3D() + THREEEDataType getType() + + +cdef extern from "astra/VolumeGeometry3D.h" namespace "astra": + cdef cppclass CVolumeGeometry3D: + CVolumeGeometry3D() + bool initialize(Config) + Config * getConfiguration() + +cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra": + cdef cppclass CProjectionGeometry3D: + CProjectionGeometry3D() + bool initialize(Config) + Config * getConfiguration() + + +cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra": + cdef cppclass CFloat32VolumeData3DMemory: + CFloat32VolumeData3DMemory(CVolumeGeometry3D*) + CVolumeGeometry3D* getGeometry() + + +cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelProjectionGeometry3D: + CParallelProjectionGeometry3D() + +cdef extern from "astra/ParallelVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CParallelVecProjectionGeometry3D: + CParallelVecProjectionGeometry3D() + +cdef extern from "astra/ConeProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeProjectionGeometry3D: + CConeProjectionGeometry3D() + bool initialize(Config) + +cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra": + cdef cppclass CConeVecProjectionGeometry3D: + CConeVecProjectionGeometry3D() + +cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": + cdef cppclass CFloat32ProjectionData3DMemory: + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + CProjectionGeometry3D* getGeometry() + +cdef extern from "astra/Float32Data3D.h" namespace "astra": + cdef cppclass CFloat32Data3D: + CFloat32Data3D() + bool isInitialized() + int getSize() + int getWidth() + int getHeight() + int getDepth() + void updateStatistics() diff --git a/python/astra/PyMatrixManager.pxd b/python/astra/PyMatrixManager.pxd new file mode 100644 index 0000000..b2b84c4 --- /dev/null +++ b/python/astra/PyMatrixManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CMatrixManager: + string info() + void clear() + void remove(int i) + int store(CSparseMatrix *) + CSparseMatrix * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CMatrixManager": + cdef CMatrixManager* getSingletonPtr() diff --git a/python/astra/PyProjector2DFactory.pxd b/python/astra/PyProjector2DFactory.pxd new file mode 100644 index 0000000..3314544 --- /dev/null +++ b/python/astra/PyProjector2DFactory.pxd @@ -0,0 +1,35 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra": + cdef cppclass CProjector2DFactory: + CProjector2D *create(Config) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CProjector2DFactory": + cdef CProjector2DFactory* getSingletonPtr() diff --git a/python/astra/PyProjector2DManager.pxd b/python/astra/PyProjector2DManager.pxd new file mode 100644 index 0000000..92176ba --- /dev/null +++ b/python/astra/PyProjector2DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CProjector2DManager: + string info() + void clear() + void remove(int i) + int store(CProjector2D *) + CProjector2D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CProjector2DManager": + cdef CProjector2DManager* getSingletonPtr() diff --git a/python/astra/PyProjector3DFactory.pxd b/python/astra/PyProjector3DFactory.pxd new file mode 100644 index 0000000..bcbce94 --- /dev/null +++ b/python/astra/PyProjector3DFactory.pxd @@ -0,0 +1,35 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string +from libcpp cimport bool +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra": + cdef cppclass CProjector3DFactory: + CProjector3D *create(Config) + +cdef extern from "astra/AstraObjectFactory.h" namespace "astra::CProjector3DFactory": + cdef CProjector3DFactory* getSingletonPtr() diff --git a/python/astra/PyProjector3DManager.pxd b/python/astra/PyProjector3DManager.pxd new file mode 100644 index 0000000..b1eac6b --- /dev/null +++ b/python/astra/PyProjector3DManager.pxd @@ -0,0 +1,39 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +from .PyIncludes cimport * + +cdef extern from "astra/AstraObjectManager.h" namespace "astra": + cdef cppclass CProjector3DManager: + string info() + void clear() + void remove(int i) + int store(CProjector3D *) + CProjector3D * get(int i) + +cdef extern from "astra/AstraObjectManager.h" namespace "astra::CProjector3DManager": + cdef CProjector3DManager* getSingletonPtr() diff --git a/python/astra/PyXMLDocument.pxd b/python/astra/PyXMLDocument.pxd new file mode 100644 index 0000000..69781f1 --- /dev/null +++ b/python/astra/PyXMLDocument.pxd @@ -0,0 +1,65 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +from libcpp.string cimport string +from libcpp cimport bool +from libcpp.list cimport list +from libcpp.vector cimport vector + +cdef extern from "astra/Globals.h" namespace "astra": + ctypedef float float32 + ctypedef double float64 + ctypedef unsigned short int uint16 + ctypedef signed short int sint16 + ctypedef unsigned char uchar8 + ctypedef signed char schar8 + ctypedef int int32 + ctypedef short int int16 + +cdef extern from "astra/XMLNode.h" namespace "astra": + cdef cppclass XMLNode: + string getName() + XMLNode *addChildNode(string name) + XMLNode *addChildNode(string, string) + void addAttribute(string, string) + void addAttribute(string, float32) + void addOption(string, string) + bool hasOption(string) + string getAttribute(string) + list[XMLNode *] getNodes() + vector[float32] getContentNumericalArray() + string getContent() + bool hasAttribute(string) + +cdef extern from "astra/XMLDocument.h" namespace "astra": + cdef cppclass XMLDocument: + void saveToFile(string sFilename) + XMLNode *getRootNode() + +cdef extern from "astra/XMLDocument.h" namespace "astra::XMLDocument": + cdef XMLDocument *createDocument(string rootname) diff --git a/python/astra/__init__.py b/python/astra/__init__.py new file mode 100644 index 0000000..063dc16 --- /dev/null +++ b/python/astra/__init__.py @@ -0,0 +1,44 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import matlab as m +from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu +from .functions import data_op, add_noise_to_sino, clear, move_vol_geom +from .extrautils import clipCircle +from .ASTRAProjector import ASTRAProjector2D +from . import data2d +from . import astra +from . import data3d +from . import algorithm +from . import projector +from . import projector3d +from . import matrix +from . import log + +import os +try: + astra.set_gpu_index(int(os.environ['ASTRA_GPU_INDEX'])) +except KeyError: + pass diff --git a/python/astra/algorithm.py b/python/astra/algorithm.py new file mode 100644 index 0000000..46cfccc --- /dev/null +++ b/python/astra/algorithm.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from . import algorithm_c as a + +def create(config): + """Create algorithm object. + + :param config: Algorithm options. + :type config: :class:`dict` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return a.create(config) + +def run(i, iterations=1): + """Run an algorithm. + + :param i: ID of object. + :type i: :class:`int` + :param iterations: Number of iterations to run. + :type iterations: :class:`int` + + """ + return a.run(i,iterations) + +def get_res_norm(i): + """Get residual norm of algorithm. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`float` -- The residual norm. + + """ + + return a.get_res_norm(i) + +def delete(ids): + """Delete a matrix object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return a.delete(ids) + +def clear(): + """Clear all matrix objects.""" + return a.clear() + +def info(): + """Print info on matrix objects in memory.""" + return a.info() diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx new file mode 100644 index 0000000..966d3d7 --- /dev/null +++ b/python/astra/algorithm_c.pyx @@ -0,0 +1,104 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +# distutils: language = c++ +# distutils: libraries = astra + +import six +from .PyIncludes cimport * + +cimport PyAlgorithmManager +from .PyAlgorithmManager cimport CAlgorithmManager + +cimport PyAlgorithmFactory +from .PyAlgorithmFactory cimport CAlgorithmFactory + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CAlgorithmManager * manAlg = <CAlgorithmManager * >PyAlgorithmManager.getSingletonPtr() + +cdef extern from *: + CReconstructionAlgorithm2D * dynamic_cast_recAlg "dynamic_cast<CReconstructionAlgorithm2D*>" (CAlgorithm * ) except NULL + + +def create(config): + cdef Config * cfg = utils.dictToConfig(six.b('Algorithm'), config) + cdef CAlgorithm * alg + alg = PyAlgorithmFactory.getSingletonPtr().create(cfg.self.getAttribute(six.b('type'))) + if alg == NULL: + del cfg + raise Exception("Unknown algorithm.") + if not alg.initialize(cfg[0]): + del cfg + del alg + raise Exception("Algorithm not initialized.") + del cfg + return manAlg.store(alg) + +cdef CAlgorithm * getAlg(i) except NULL: + cdef CAlgorithm * alg = manAlg.get(i) + if alg == NULL: + raise Exception("Unknown algorithm.") + if not alg.isInitialized(): + raise Exception("Algorithm not initialized.") + return alg + + +def run(i, iterations=0): + cdef CAlgorithm * alg = getAlg(i) + alg.run(iterations) + + +def get_res_norm(i): + cdef CReconstructionAlgorithm2D * pAlg2D + cdef CAlgorithm * alg = getAlg(i) + cdef float32 res = 0.0 + pAlg2D = dynamic_cast_recAlg(alg) + if pAlg2D == NULL: + raise Exception("Operation not supported.") + if not pAlg2D.getResidualNorm(res): + raise Exception("Operation not supported.") + return res + + +def delete(ids): + try: + for i in ids: + manAlg.remove(i) + except TypeError: + manAlg.remove(ids) + + +def clear(): + manAlg.clear() + + +def info(): + six.print_(wrap_from_bytes(manAlg.info())) diff --git a/python/astra/astra.py b/python/astra/astra.py new file mode 100644 index 0000000..26b1ff0 --- /dev/null +++ b/python/astra/astra.py @@ -0,0 +1,58 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from . import astra_c as a + +def credits(): + """Print credits of the ASTRA Toolbox.""" + return a.credits() + + +def use_cuda(): + """Test if CUDA is enabled. + + :returns: :class:`bool` -- ``True`` if CUDA is enabled. + """ + return a.use_cuda() + + +def version(printToScreen=False): + """Check version of the ASTRA Toolbox. + + :param printToScreen: If ``True``, print version string. If ``False``, return version integer. + :type printToScreen: :class:`bool` + :returns: :class:`string` or :class:`int` -- The version string or integer. + + """ + return a.version(printToScreen) + +def set_gpu_index(idx): + """Set default GPU index to use. + + :param idx: GPU index + :type idx: :class:`int` + """ + a.set_gpu_index(idx) diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx new file mode 100644 index 0000000..342a214 --- /dev/null +++ b/python/astra/astra_c.pyx @@ -0,0 +1,79 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +include "config.pxi" +import six +from .utils import wrap_from_bytes + +from libcpp.string cimport string +from libcpp cimport bool +cdef extern from "astra/Globals.h" namespace "astra": + int getVersion() + string getVersionString() + bool cudaEnabled() + +IF HAVE_CUDA==True: + cdef extern from "../cuda/2d/darthelper.h" namespace "astraCUDA": + bool setGPUIndex(int) +ELSE: + def setGPUIndex(): + pass + +def credits(): + six.print_(""" +All Scale Tomographic Reconstruction Antwerp Toolbox (ASTRA-Toolbox) +was developed at the University of Antwerp by + * Prof. dr. Joost Batenburg + * Andrei Dabravolski + * Gert Merckx + * Willem Jan Palenstijn + * Tom Roelandts + * Prof. dr. Jan Sijbers + * dr. Wim van Aarle + * Sander van der Maar + * dr. Gert Van Gompel + +Python interface written by + * Daniel M. Pelt (CWI, Amsterdam)""") + + +def use_cuda(): + return cudaEnabled() + + +def version(printToScreen=False): + if printToScreen: + six.print_(wrap_from_bytes(getVersionString())) + else: + return getVersion() + +def set_gpu_index(idx): + if use_cuda()==True: + ret = setGPUIndex(idx) + if not ret: + six.print_("Failed to set GPU " + str(idx)) diff --git a/python/astra/creators.py b/python/astra/creators.py new file mode 100644 index 0000000..68bc8a2 --- /dev/null +++ b/python/astra/creators.py @@ -0,0 +1,543 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import six +import numpy as np +import math +from . import data2d +from . import data3d +from . import projector +from . import projector3d +from . import algorithm + +def astra_dict(intype): + """Creates a dict to use with the ASTRA Toolbox. + + :param intype: Type of the ASTRA object. + :type intype: :class:`string` + :returns: :class:`dict` -- An ASTRA dict of type ``intype``. + + """ + if intype == 'SIRT_CUDA2': + intype = 'SIRT_CUDA' + six.print_('SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.') + elif intype == 'FP_CUDA2': + intype = 'FP_CUDA' + six.print_('FP_CUDA2 has been deprecated. Use FP_CUDA instead.') + return {'type': intype} + +def create_vol_geom(*varargin): + """Create a volume geometry structure. + +This method can be called in a number of ways: + +``create_vol_geom(N)``: + :returns: A 2D volume geometry of size :math:`N \\times N`. + +``create_vol_geom((M, N))``: + :returns: A 2D volume geometry of size :math:`M \\times N`. + +``create_vol_geom(M, N)``: + :returns: A 2D volume geometry of size :math:`M \\times N`. + +``create_vol_geom(M, N, minx, maxx, miny, maxy)``: + :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`. + +``create_vol_geom((M, N, Z))``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. + +``create_vol_geom(M, N, Z)``: + :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`. + +""" + vol_geom = {'option': {}} + # astra_create_vol_geom(row_count) + if len(varargin) == 1 and isinstance(varargin[0], int) == 1: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[0] + vol_geom['option']['WindowMinX'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0] / 2. + # astra_create_vol_geom([row_count col_count]) + elif len(varargin) == 1 and len(varargin[0]) == 2: + vol_geom['GridRowCount'] = varargin[0][0] + vol_geom['GridColCount'] = varargin[0][1] + vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2. + # astra_create_vol_geom([row_count col_count slice_count]) + elif len(varargin) == 1 and len(varargin[0]) == 3: + vol_geom['GridRowCount'] = varargin[0][0] + vol_geom['GridColCount'] = varargin[0][1] + vol_geom['GridSliceCount'] = varargin[0][2] + vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2. + vol_geom['option']['WindowMinZ'] = -varargin[0][2] / 2. + vol_geom['option']['WindowMaxZ'] = varargin[0][2] / 2. + # astra_create_vol_geom(row_count, col_count) + elif len(varargin) == 2: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['option']['WindowMinX'] = -varargin[1] / 2. + vol_geom['option']['WindowMaxX'] = varargin[1] / 2. + vol_geom['option']['WindowMinY'] = -varargin[0] / 2. + vol_geom['option']['WindowMaxY'] = varargin[0] / 2. + # astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y) + elif len(varargin) == 6: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['option']['WindowMinX'] = varargin[2] + vol_geom['option']['WindowMaxX'] = varargin[3] + vol_geom['option']['WindowMinY'] = varargin[4] + vol_geom['option']['WindowMaxY'] = varargin[5] + # astra_create_vol_geom(row_count, col_count, slice_count) + elif len(varargin) == 3: + vol_geom['GridRowCount'] = varargin[0] + vol_geom['GridColCount'] = varargin[1] + vol_geom['GridSliceCount'] = varargin[2] + return vol_geom + + +def create_proj_geom(intype, *args): + """Create a projection geometry. + +This method can be called in a number of ways: + +``create_proj_geom('parallel', detector_spacing, det_count, angles)``: + +:param detector_spacing: Distance between two adjacent detector pixels. +:type detector_spacing: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + + +``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``: + +:param det_width: Size of a detector pixel. +:type det_width: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param source_origin: Position of the source. +:param source_det: Position of the detector +:returns: A fan-beam projection geometry. + +``create_proj_geom('fanflat_vec', det_count, V)``: + +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A fan-beam projection geometry. + +``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``: + +:param detector_spacing_*: Distance between two adjacent detector pixels. +:type detector_spacing_*: :class:`float` +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + +``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``: + +:param detector_spacing_*: Distance between two adjacent detector pixels. +:type detector_spacing_*: :class:`float` +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param source_origin: Distance between point source and origin. +:type source_origin: :class:`float` +:param source_det: Distance between the detector and origin. +:type source_det: :class:`float` +:returns: A cone-beam projection geometry. + +``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``: + +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A cone-beam projection geometry. + +``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``: + +:param det_row_count: Number of detector pixel rows. +:type det_row_count: :class:`int` +:param det_col_count: Number of detector pixel columns. +:type det_col_count: :class:`int` +:param V: Vector array. +:type V: :class:`numpy.ndarray` +:returns: A parallel projection geometry. + +``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``: + +:param det_width: Size of a detector pixel. +:type det_width: :class:`float` +:param det_count: Number of detector pixels. +:type det_count: :class:`int` +:param angles: Array of angles in radians. +:type angles: :class:`numpy.ndarray` +:param matrix_id: ID of the sparse matrix. +:type matrix_id: :class:`int` +:returns: A projection geometry based on a sparse matrix. + +""" + if intype == 'parallel': + if len(args) < 3: + raise Exception( + 'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)') + return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]} + elif intype == 'fanflat': + if len(args) < 5: + raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)') + return {'type': 'fanflat', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'DistanceOriginSource': args[3], 'DistanceOriginDetector': args[4]} + elif intype == 'fanflat_vec': + if len(args) < 2: + raise Exception('not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)') + if not args[1].shape[1] == 6: + raise Exception('V should be a Nx6 matrix, with N the number of projections') + return {'type':'fanflat_vec', 'DetectorCount':args[0], 'Vectors':args[1]} + elif intype == 'parallel3d': + if len(args) < 5: + raise Exception('not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)') + return {'type':'parallel3d', 'DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2], 'DetectorColCount':args[3],'ProjectionAngles':args[4]} + elif intype == 'cone': + if len(args) < 7: + raise Exception('not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)') + return {'type': 'cone','DetectorSpacingX':args[0], 'DetectorSpacingY':args[1], 'DetectorRowCount':args[2],'DetectorColCount':args[3],'ProjectionAngles':args[4],'DistanceOriginSource': args[5],'DistanceOriginDetector':args[6]} + elif intype == 'cone_vec': + if len(args) < 3: + raise Exception('not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)') + if not args[2].shape[1] == 12: + raise Exception('V should be a Nx12 matrix, with N the number of projections') + return {'type': 'cone_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]} + elif intype == 'parallel3d_vec': + if len(args) < 3: + raise Exception('not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)') + if not args[2].shape[1] == 12: + raise Exception('V should be a Nx12 matrix, with N the number of projections') + return {'type': 'parallel3d_vec','DetectorRowCount':args[0],'DetectorColCount':args[1],'Vectors':args[2]} + elif intype == 'sparse_matrix': + if len(args) < 4: + raise Exception( + 'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)') + return {'type': 'sparse_matrix', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2], 'MatrixID': args[3]} + else: + raise Exception('Error: unknown type ' + intype) + + +def create_backprojection(data, proj_id, returnData=True): + """Create a backprojection of a sinogram (2D). + +:param data: Sinogram data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_id: ID of the projector to use. +:type proj_id: :class:`int` +:param returnData: If False, only return the ID of the backprojection. +:type returnData: :class:`bool` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order. + +""" + proj_geom = projector.projection_geometry(proj_id) + vol_geom = projector.volume_geometry(proj_id) + if isinstance(data, np.ndarray): + sino_id = data2d.create('-sino', proj_geom, data) + else: + sino_id = data + vol_id = data2d.create('-vol', vol_geom, 0) + + if projector.is_cuda(proj_id): + algString = 'BP_CUDA' + else: + algString = 'BP' + + cfg = astra_dict(algString) + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = vol_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data2d.delete(sino_id) + + if returnData: + return vol_id, data2d.get(vol_id) + else: + return vol_id + +def create_backprojection3d_gpu(data, proj_geom, vol_geom, returnData=True): + """Create a backprojection of a sinogram (3D) using CUDA. + +:param data: Sinogram data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:param returnData: If False, only return the ID of the backprojection. +:type returnData: :class:`bool` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order. + +""" + if isinstance(data, np.ndarray): + sino_id = data3d.create('-sino', proj_geom, data) + else: + sino_id = data + + vol_id = data3d.create('-vol', vol_geom, 0) + + cfg = astra_dict('BP3D_CUDA') + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = vol_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data3d.delete(sino_id) + + if returnData: + return vol_id, data3d.get(vol_id) + else: + return vol_id + + +def create_sino(data, proj_id, returnData=True, gpuIndex=None): + """Create a forward projection of an image (2D). + + :param data: Image data or ID. + :type data: :class:`numpy.ndarray` or :class:`int` + :param proj_id: ID of the projector to use. + :type proj_id: :class:`int` + :param returnData: If False, only return the ID of the forward projection. + :type returnData: :class:`bool` + :param gpuIndex: Optional GPU index. + :type gpuIndex: :class:`int` + :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) + + If ``returnData=False``, returns the ID of the forward + projection. Otherwise, returns a tuple containing the ID of the + forward projection and the forward projection itself, in that + order. +""" + proj_geom = projector.projection_geometry(proj_id) + vol_geom = projector.volume_geometry(proj_id) + + if isinstance(data, np.ndarray): + volume_id = data2d.create('-vol', vol_geom, data) + else: + volume_id = data + sino_id = data2d.create('-sino', proj_geom, 0) + if projector.is_cuda(proj_id): + algString = 'FP_CUDA' + else: + algString = 'FP' + cfg = astra_dict(algString) + cfg['ProjectorId'] = proj_id + if gpuIndex is not None: + cfg['option'] = {'GPUindex': gpuIndex} + cfg['ProjectionDataId'] = sino_id + cfg['VolumeDataId'] = volume_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data2d.delete(volume_id) + if returnData: + return sino_id, data2d.get(sino_id) + else: + return sino_id + + + +def create_sino3d_gpu(data, proj_geom, vol_geom, returnData=True, gpuIndex=None): + """Create a forward projection of an image (3D). + +:param data: Image data or ID. +:type data: :class:`numpy.ndarray` or :class:`int` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:param returnData: If False, only return the ID of the forward projection. +:type returnData: :class:`bool` +:param gpuIndex: Optional GPU index. +:type gpuIndex: :class:`int` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order. + +""" + + if isinstance(data, np.ndarray): + volume_id = data3d.create('-vol', vol_geom, data) + else: + volume_id = data + sino_id = data3d.create('-sino', proj_geom, 0) + algString = 'FP3D_CUDA' + cfg = astra_dict(algString) + if not gpuIndex==None: + cfg['option']={'GPUindex':gpuIndex} + cfg['ProjectionDataId'] = sino_id + cfg['VolumeDataId'] = volume_id + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + if isinstance(data, np.ndarray): + data3d.delete(volume_id) + if returnData: + return sino_id, data3d.get(sino_id) + else: + return sino_id + + +def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='no', mask=np.array([]), use_minc='no', minc=0, use_maxc='no', maxc=255, returnData=True, filterType=None, filterData=None): + """Create a reconstruction of a sinogram (2D). + +:param rec_type: Name of the reconstruction algorithm. +:type rec_type: :class:`string` +:param proj_id: ID of the projector to use. +:type proj_id: :class:`int` +:param sinogram: Sinogram data or ID. +:type sinogram: :class:`numpy.ndarray` or :class:`int` +:param iterations: Number of iterations to run. +:type iterations: :class:`int` +:param use_mask: Whether to use a mask. +:type use_mask: ``'yes'`` or ``'no'`` +:param mask: Mask data or ID +:type mask: :class:`numpy.ndarray` or :class:`int` +:param use_minc: Whether to force a minimum value on the reconstruction pixels. +:type use_minc: ``'yes'`` or ``'no'`` +:param minc: Minimum value to use. +:type minc: :class:`float` +:param use_maxc: Whether to force a maximum value on the reconstruction pixels. +:type use_maxc: ``'yes'`` or ``'no'`` +:param maxc: Maximum value to use. +:type maxc: :class:`float` +:param returnData: If False, only return the ID of the reconstruction. +:type returnData: :class:`bool` +:param filterType: Which type of filter to use for filter-based methods. +:type filterType: :class:`string` +:param filterData: Optional filter data for filter-based methods. +:type filterData: :class:`numpy.ndarray` +:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order. + +""" + proj_geom = projector.projection_geometry(proj_id) + if isinstance(sinogram, np.ndarray): + sino_id = data2d.create('-sino', proj_geom, sinogram) + else: + sino_id = sinogram + vol_geom = projector.volume_geometry(proj_id) + recon_id = data2d.create('-vol', vol_geom, 0) + cfg = astra_dict(rec_type) + cfg['ProjectorId'] = proj_id + cfg['ProjectionDataId'] = sino_id + cfg['ReconstructionDataId'] = recon_id + cfg['options'] = {} + if use_mask == 'yes': + if isinstance(mask, np.ndarray): + mask_id = data2d.create('-vol', vol_geom, mask) + else: + mask_id = mask + cfg['options']['ReconstructionMaskId'] = mask_id + if not filterType == None: + cfg['FilterType'] = filterType + if not filterData == None: + if isinstance(filterData, np.ndarray): + nexpow = int( + pow(2, math.ceil(math.log(2 * proj_geom['DetectorCount'], 2)))) + filtSize = nexpow / 2 + 1 + filt_proj_geom = create_proj_geom( + 'parallel', 1.0, filtSize, proj_geom['ProjectionAngles']) + filt_id = data2d.create('-sino', filt_proj_geom, filterData) + else: + filt_id = filterData + cfg['FilterSinogramId'] = filt_id + cfg['options']['UseMinConstraint'] = use_minc + cfg['options']['MinConstraintValue'] = minc + cfg['options']['UseMaxConstraint'] = use_maxc + cfg['options']['MaxConstraintValue'] = maxc + cfg['options']['ProjectionOrder'] = 'random' + alg_id = algorithm.create(cfg) + algorithm.run(alg_id, iterations) + + algorithm.delete(alg_id) + + if isinstance(sinogram, np.ndarray): + data2d.delete(sino_id) + if use_mask == 'yes' and isinstance(mask, np.ndarray): + data2d.delete(mask_id) + if not filterData == None: + if isinstance(filterData, np.ndarray): + data2d.delete(filt_id) + if returnData: + return recon_id, data2d.get(recon_id) + else: + return recon_id + + +def create_projector(proj_type, proj_geom, vol_geom): + """Create a 2D projector. + +:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... +:type proj_type: :class:`string` +:param proj_geom: Projection geometry. +:type proj_geom: :class:`dict` +:param vol_geom: Volume geometry. +:type vol_geom: :class:`dict` +:returns: :class:`int` -- The ID of the projector. + +""" + if proj_type == 'blob': + raise Exception('Blob type not yet implemented') + cfg = astra_dict(proj_type) + cfg['ProjectionGeometry'] = proj_geom + cfg['VolumeGeometry'] = vol_geom + types3d = ['linear3d', 'linearcone', 'cuda3d'] + if proj_type in types3d: + return projector3d.create(cfg) + else: + return projector.create(cfg) diff --git a/python/astra/data2d.py b/python/astra/data2d.py new file mode 100644 index 0000000..8c4be03 --- /dev/null +++ b/python/astra/data2d.py @@ -0,0 +1,120 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import data2d_c as d + +def clear(): + """Clear all 2D data objects.""" + return d.clear() + +def delete(ids): + """Delete a 2D object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return d.delete(ids) + +def create(datatype, geometry, data=None): + """Create a 2D object. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Data to fill the constructed object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return d.create(datatype,geometry,data) + +def store(i, data): + """Fill existing 2D object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + + """ + return d.store(i, data) + +def get_geometry(i): + """Get the geometry of a 2D object. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`dict` -- The geometry of object with ID ``i``. + + """ + return d.get_geometry(i) + +def change_geometry(i, geom): + """Change the geometry of a 2D object. + + :param i: ID of object. + :type i: :class:`int` + :param geom: new geometry. + :type geom: :class:`dict` + + """ + return d.change_geometry(i, geom) + +def get(i): + """Get a 2D object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get(i) + +def get_shared(i): + """Get a 2D object with memory shared between the ASTRA toolbox and numpy array. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_shared(i) + + +def get_single(i): + """Get a 2D object in single precision. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_single(i) + +def info(): + """Print info on 2D objects in memory.""" + return d.info() diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx new file mode 100644 index 0000000..b9c105e --- /dev/null +++ b/python/astra/data2d_c.pyx @@ -0,0 +1,233 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six + +cimport cython +from cython cimport view + +cimport PyData2DManager +from .PyData2DManager cimport CData2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +import numpy as np + +cimport numpy as np +np.import_array() + + +from .PyIncludes cimport * +cimport utils +from .utils import wrap_from_bytes + +cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr() + +def clear(): + man2d.clear() + + +def delete(ids): + try: + for i in ids: + man2d.remove(i) + except TypeError: + man2d.remove(ids) + + +def create(datatype, geometry, data=None): + cdef Config *cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject2D + if datatype == '-vol': + cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg[0]): + del cfg + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry) + del cfg + del pGeometry + elif datatype == '-sino': + cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg[0]): + del cfg + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry) + del ppGeometry + del cfg + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.") + + if not pDataObject2D.isInitialized(): + del pDataObject2D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject2D, data) + + return man2d.store(pDataObject2D) + +cdef fillDataObject(CFloat32Data2D * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data2D * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data): + if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,::1] cView = <float[:data.shape[0],:data.shape[1]]> obj.getData2D()[0] + cView[:] = data + +cdef CFloat32Data2D * getObject(i) except NULL: + cdef CFloat32Data2D * pDataObject = man2d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i, data): + cdef CFloat32Data2D * pDataObject = getObject(i) + fillDataObject(pDataObject, data) + + +def get_geometry(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == TWOPROJECTION: + pDataObject2 = <CFloat32ProjectionData2D * >pDataObject + geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration()) + elif pDataObject.getType() == TWOVOLUME: + pDataObject3 = <CFloat32VolumeData2D * >pDataObject + geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration()) + else: + raise Exception("Not a known data object") + return geom + + +def change_geometry(i, geom): + cdef Config *cfg + cdef CVolumeGeometry2D * pGeometry + cdef CProjectionGeometry2D * ppGeometry + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef CFloat32ProjectionData2D * pDataObject2 + cdef CFloat32VolumeData2D * pDataObject3 + if pDataObject.getType() == TWOPROJECTION: + pDataObject2 = <CFloat32ProjectionData2D * >pDataObject + cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom) + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == 'sparse_matrix'): + ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D() + elif (tpe == 'fanflat'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D() + elif (tpe == 'fanflat_vec'): + ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D() + else: + ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D() + if not ppGeometry.initialize(cfg[0]): + del cfg + del ppGeometry + raise Exception('Geometry class not initialized.') + if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()): + del ppGeometry + del cfg + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + pDataObject2.changeGeometry(ppGeometry) + del ppGeometry + del cfg + elif pDataObject.getType() == TWOVOLUME: + pDataObject3 = <CFloat32VolumeData2D * >pDataObject + cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom) + pGeometry = new CVolumeGeometry2D() + if not pGeometry.initialize(cfg[0]): + del cfg + del pGeometry + raise Exception('Geometry class not initialized.') + if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()): + del cfg + del pGeometry + raise Exception( + 'The dimensions of the data do not match those specified in the geometry.') + pDataObject3.changeGeometry(pGeometry) + del cfg + del pGeometry + else: + raise Exception("Not a known data object") + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,::1] mView = outArr + cdef float [:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1]]> pDataObject.getData2D()[0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data2D * pDataObject = getObject(i) + cdef np.npy_intp shape[2] + shape[0] = <np.npy_intp> pDataObject.getHeight() + shape[1] = <np.npy_intp> pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,<void *>pDataObject.getData2D()[0]) + + +def get_single(i): + raise Exception("Not yet implemented") + + +def info(): + six.print_(wrap_from_bytes(man2d.info())) diff --git a/python/astra/data3d.py b/python/astra/data3d.py new file mode 100644 index 0000000..a2e9201 --- /dev/null +++ b/python/astra/data3d.py @@ -0,0 +1,118 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import data3d_c as d + +def create(datatype,geometry,data=None): + """Create a 3D object. + + :param datatype: Data object type, '-vol' or '-sino'. + :type datatype: :class:`string` + :param geometry: Volume or projection geometry. + :type geometry: :class:`dict` + :param data: Data to fill the constructed object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return d.create(datatype,geometry,data) + +def get(i): + """Get a 3D object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get(i) + +def get_shared(i): + """Get a 3D object with memory shared between the ASTRA toolbox and numpy array. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return d.get_shared(i) + +def get_single(i): + """Get a 3D object in single precision. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`numpy.ndarray` -- The object data. + + """ + return g.get_single(i) + +def store(i,data): + """Fill existing 3D object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with, either a scalar or array. + :type data: :class:`float` or :class:`numpy.ndarray` + + """ + return d.store(i,data) + +def get_geometry(i): + """Get the geometry of a 3D object. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`dict` -- The geometry of object with ID ``i``. + + """ + return d.get_geometry(i) + +def dimensions(i): + """Get dimensions of a 3D object. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`tuple` -- dimensions of object with ID ``i``. + + """ + return d.dimensions(i) + +def delete(ids): + """Delete a 2D object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return d.delete(ids) + +def clear(): + """Clear all 3D data objects.""" + return d.clear() + +def info(): + """Print info on 3D objects in memory.""" + return d.info() diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx new file mode 100644 index 0000000..4b069f7 --- /dev/null +++ b/python/astra/data3d_c.pyx @@ -0,0 +1,197 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six + +cimport cython + +cimport PyData3DManager +from .PyData3DManager cimport CData3DManager + +from .PyIncludes cimport * +import numpy as np + +cimport numpy as np +np.import_array() + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport utils +from .utils import wrap_from_bytes + +cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr() + +cdef extern from *: + CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL + +def create(datatype,geometry,data=None): + cdef Config *cfg + cdef CVolumeGeometry3D * pGeometry + cdef CProjectionGeometry3D * ppGeometry + cdef CFloat32Data3DMemory * pDataObject3D + cdef CConeProjectionGeometry3D* pppGeometry + if datatype == '-vol': + cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) + pGeometry = new CVolumeGeometry3D() + if not pGeometry.initialize(cfg[0]): + del cfg + del pGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry) + del cfg + del pGeometry + elif datatype == '-sino' or datatype == '-proj3d': + cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) + tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) + if (tpe == "parallel3d"): + ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D(); + elif (tpe == "parallel3d_vec"): + ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D(); + elif (tpe == "cone"): + ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D(); + elif (tpe == "cone_vec"): + ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D(); + else: + raise Exception("Invalid geometry type.") + + if not ppGeometry.initialize(cfg[0]): + del cfg + del ppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry) + del ppGeometry + del cfg + elif datatype == "-sinocone": + cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) + pppGeometry = new CConeProjectionGeometry3D() + if not pppGeometry.initialize(cfg[0]): + del cfg + del pppGeometry + raise Exception('Geometry class not initialized.') + pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry) + else: + raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.") + + if not pDataObject3D.isInitialized(): + del pDataObject3D + raise Exception("Couldn't initialize data object.") + + fillDataObject(pDataObject3D, data) + + pDataObject3D.updateStatistics() + + return man3d.store(<CFloat32Data3D*>pDataObject3D) + +def get_geometry(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + cdef CFloat32ProjectionData3DMemory * pDataObject2 + cdef CFloat32VolumeData3DMemory * pDataObject3 + if pDataObject.getType() == THREEPROJECTION: + pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject + geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration()) + elif pDataObject.getType() == THREEVOLUME: + pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject + geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration()) + else: + raise Exception("Not a known data object") + return geom + +cdef fillDataObject(CFloat32Data3DMemory * obj, data): + if data is None: + fillDataObjectScalar(obj, 0) + else: + if isinstance(data, np.ndarray): + fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) + else: + fillDataObjectScalar(obj, np.float32(data)) + +cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s): + cdef int i + for i in range(obj.getSize()): + obj.getData()[i] = s + +@cython.boundscheck(False) +@cython.wraparound(False) +cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data): + if (not data.shape[0] == obj.getDepth()) or (not data.shape[1] == obj.getHeight()) or (not data.shape[2] == obj.getWidth()): + raise Exception( + "The dimensions of the data do not match those specified in the geometry.") + cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData3D()[0][0] + cView[:] = data + +cdef CFloat32Data3D * getObject(i) except NULL: + cdef CFloat32Data3D * pDataObject = man3d.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + +@cython.boundscheck(False) +@cython.wraparound(False) +def get(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef float [:,:,::1] mView = outArr + cdef float [:,:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1],:outArr.shape[2]]> pDataObject.getData3D()[0][0] + mView[:] = cView + return outArr + +def get_shared(i): + cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i)) + outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') + cdef np.npy_intp shape[3] + shape[0] = <np.npy_intp> pDataObject.getDepth() + shape[1] = <np.npy_intp> pDataObject.getHeight() + shape[2] = <np.npy_intp> pDataObject.getWidth() + return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0]) + +def get_single(i): + raise Exception("Not yet implemented") + +def store(i,data): + cdef CFloat32Data3D * pDataObject = getObject(i) + fillDataObject(dynamic_cast_mem(pDataObject), data) + +def dimensions(i): + cdef CFloat32Data3D * pDataObject = getObject(i) + return (pDataObject.getWidth(),pDataObject.getHeight(),pDataObject.getDepth()) + +def delete(ids): + try: + for i in ids: + man3d.remove(i) + except TypeError: + man3d.remove(ids) + +def clear(): + man3d.clear() + +def info(): + six.print_(wrap_from_bytes(man3d.info())) diff --git a/python/astra/extrautils.pyx b/python/astra/extrautils.pyx new file mode 100644 index 0000000..998f5cb --- /dev/null +++ b/python/astra/extrautils.pyx @@ -0,0 +1,43 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +def clipCircle(img): + cdef int i,j + cdef double x2,y2,mid,bnd + cdef long sz,sz2 + sz = img.shape[0] + sz2 = sz*sz + bnd = sz2/4. + mid = (sz-1.)/2. + nDel=0 + for i in range(sz): + for j in range(sz): + x2 = (i-mid)*(i-mid) + y2 = (j-mid)*(j-mid) + if x2+y2>bnd: + img[i,j]=0 + nDel=nDel+1 + return nDel diff --git a/python/astra/functions.py b/python/astra/functions.py new file mode 100644 index 0000000..4025468 --- /dev/null +++ b/python/astra/functions.py @@ -0,0 +1,270 @@ +#----------------------------------------------------------------------- +# Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +# Author: Daniel M. Pelt +# Contact: D.M.Pelt@cwi.nl +# Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +# This file is part of the Python interface to the +# All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +# The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +# The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +"""Additional functions for PyAstraToolbox. + +.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl> + + +""" + +from . import creators as ac +import numpy as np +from six.moves import range + +from . import data2d +from . import data3d +from . import projector +from . import algorithm + + + +def clear(): + """Clears all used memory of the ASTRA Toolbox. + + .. note:: + This is irreversible. + + """ + data2d.clear() + data3d.clear() + projector.clear() + algorithm.clear() + + +def data_op(op, data, scalar, gpu_core, mask=None): + """Perform data operation on data. + + :param op: Operation to perform. + :param data: Data to perform operation on. + :param scalar: Scalar argument to data operation. + :param gpu_core: GPU core to perform operation on. + :param mask: Optional mask. + + """ + + cfg = ac.astra_dict('DataOperation_CUDA') + cfg['Operation'] = op + cfg['Scalar'] = scalar + cfg['DataId'] = data + if not mask == None: + cfg['MaskId'] = mask + cfg['option']['GPUindex'] = gpu_core + alg_id = algorithm.create(cfg) + algorithm.run(alg_id) + algorithm.delete(alg_id) + + +def add_noise_to_sino(sinogram_in, I0, seed=None): + """Adds Poisson noise to a sinogram. + + :param sinogram_in: Sinogram to add noise to. + :type sinogram_in: :class:`numpy.ndarray` + :param I0: Background intensity. Lower values lead to higher noise. + :type I0: :class:`float` + :returns: :class:`numpy.ndarray` -- the sinogram with added noise. + + """ + + if not seed==None: + curstate = np.random.get_state() + np.random.seed(seed) + + if isinstance(sinogram_in, np.ndarray): + sinogramRaw = sinogram_in + else: + sinogramRaw = data2d.get(sinogram_in) + max_sinogramRaw = sinogramRaw.max() + sinogramRawScaled = sinogramRaw / max_sinogramRaw + # to detector count + sinogramCT = I0 * np.exp(-sinogramRawScaled) + # add poison noise + sinogramCT_C = np.zeros_like(sinogramCT) + for i in range(sinogramCT_C.shape[0]): + for j in range(sinogramCT_C.shape[1]): + sinogramCT_C[i, j] = np.random.poisson(sinogramCT[i, j]) + # to density + sinogramCT_D = sinogramCT_C / I0 + sinogram_out = -max_sinogramRaw * np.log(sinogramCT_D) + + if not isinstance(sinogram_in, np.ndarray): + at.data2d.store(sinogram_in, sinogram_out) + + if not seed==None: + np.random.set_state(curstate) + + return sinogram_out + +def move_vol_geom(geom, pos, is_relative=False): + """Moves center of volume geometry to new position. + + :param geom: Input volume geometry + :type geom: :class:`dict` + :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0]) + :type pos: :class:`tuple` + :param is_relative: Whether new position is relative to the old position + :type is_relative: :class:`bool` + :returns: :class:`dict` -- Volume geometry with the new center + """ + + ret_geom = geom.copy() + ret_geom['option'] = geom['option'].copy() + + if not is_relative: + ret_geom['option']['WindowMinX'] = -geom['GridColCount']/2. + ret_geom['option']['WindowMaxX'] = geom['GridColCount']/2. + ret_geom['option']['WindowMinY'] = -geom['GridRowCount']/2. + ret_geom['option']['WindowMaxY'] = geom['GridRowCount']/2. + if len(pos)>2: + ret_geom['option']['WindowMinZ'] = -geom['GridSliceCount']/2. + ret_geom['option']['WindowMaxZ'] = geom['GridSliceCount']/2. + ret_geom['option']['WindowMinX'] += pos[0] + ret_geom['option']['WindowMaxX'] += pos[0] + ret_geom['option']['WindowMinY'] += pos[1] + ret_geom['option']['WindowMaxY'] += pos[1] + if len(pos)>2: + ret_geom['option']['WindowMinZ'] += pos[2] + ret_geom['option']['WindowMaxZ'] += pos[2] + return ret_geom + + +def geom_size(geom, dim=None): + """Returns the size of a volume or sinogram, based on the projection or volume geometry. + + :param geom: Geometry to calculate size from + :type geometry: :class:`dict` + :param dim: Optional axis index to return + :type dim: :class:`int` + """ + + if 'GridSliceCount' in geom: + # 3D Volume geometry? + s = (geom['GridSliceCount'], geom[ + 'GridRowCount'], geom['GridColCount']) + elif 'GridColCount' in geom: + # 2D Volume geometry? + s = (geom['GridRowCount'], geom['GridColCount']) + elif geom['type'] == 'parallel' or geom['type'] == 'fanflat': + s = (len(geom['ProjectionAngles']), geom['DetectorCount']) + elif geom['type'] == 'parallel3d' or geom['type'] == 'cone': + s = (geom['DetectorRowCount'], len( + geom['ProjectionAngles']), geom['DetectorColCount']) + elif geom['type'] == 'fanflat_vec': + s = (geom['Vectors'].shape[0], geom['DetectorCount']) + elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec': + s = (geom['DetectorRowCount'], geom[ + 'Vectors'].shape[0], geom['DetectorColCount']) + + if dim != None: + s = s[dim] + + return s + + +def geom_2vec(proj_geom): + """Returns a vector-based projection geometry from a basic projection geometry. + + :param proj_geom: Projection geometry to convert + :type proj_geom: :class:`dict` + """ + if proj_geom['type'] == 'fanflat': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 6)) + for i in range(len(angles)): + + # source + vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource'] + + # center of detector + vectors[i, 2] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 3] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector'] + + # vector from detector pixel 0 to 1 + vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth'] + vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth'] + proj_geom_out = ac.create_proj_geom( + 'fanflat_vec', proj_geom['DetectorCount'], vectors) + + elif proj_geom['type'] == 'cone': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 12)) + for i in range(len(angles)): + # source + vectors[i, 0] = np.sin(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 1] = -np.cos(angles[i]) * proj_geom['DistanceOriginSource'] + vectors[i, 2] = 0 + + # center of detector + vectors[i, 3] = -np.sin(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 4] = np.cos(angles[i]) * proj_geom['DistanceOriginDetector'] + vectors[i, 5] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i, 9] = 0 + vectors[i, 10] = 0 + vectors[i, 11] = proj_geom['DetectorSpacingY'] + + proj_geom_out = ac.create_proj_geom( + 'cone_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors) + + # PARALLEL + elif proj_geom['type'] == 'parallel3d': + angles = proj_geom['ProjectionAngles'] + vectors = np.zeros((len(angles), 12)) + for i in range(len(angles)): + + # ray direction + vectors[i, 0] = np.sin(angles[i]) + vectors[i, 1] = -np.cos(angles[i]) + vectors[i, 2] = 0 + + # center of detector + vectors[i, 3] = 0 + vectors[i, 4] = 0 + vectors[i, 5] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i, 6] = np.cos(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 7] = np.sin(angles[i]) * proj_geom['DetectorSpacingX'] + vectors[i, 8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i, 9] = 0 + vectors[i, 10] = 0 + vectors[i, 11] = proj_geom['DetectorSpacingY'] + + proj_geom_out = ac.create_proj_geom( + 'parallel3d_vec', proj_geom['DetectorRowCount'], proj_geom['DetectorColCount'], vectors) + + else: + raise ValueError( + 'No suitable vector geometry found for type: ' + proj_geom['type']) + return proj_geom_out diff --git a/python/astra/log.py b/python/astra/log.py new file mode 100644 index 0000000..3ec0df5 --- /dev/null +++ b/python/astra/log.py @@ -0,0 +1,153 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from . import log_c as l + +import inspect + +def debug(message): + """Log a debug message. + + :param message: Message to log. + :type message: :class:`string` + """ + prev_f = inspect.getframeinfo(inspect.currentframe().f_back) + l.log_debug(prev_f.filename,prev_f.lineno,message) + +def info(message): + """Log an info message. + + :param message: Message to log. + :type message: :class:`string` + """ + prev_f = inspect.getframeinfo(inspect.currentframe().f_back) + l.log_info(prev_f.filename,prev_f.lineno,message) + +def warn(message): + """Log a warning message. + + :param message: Message to log. + :type message: :class:`string` + """ + prev_f = inspect.getframeinfo(inspect.currentframe().f_back) + l.log_warn(prev_f.filename,prev_f.lineno,message) + +def error(message): + """Log an error message. + + :param message: Message to log. + :type message: :class:`string` + """ + prev_f = inspect.getframeinfo(inspect.currentframe().f_back) + l.log_error(prev_f.filename,prev_f.lineno,message) + +def enable(): + """Enable logging to screen and file.""" + l.log_enable() + +def enableScreen(): + """Enable logging to screen.""" + l.log_enableScreen() + +def enableFile(): + """Enable logging to file (note that a file has to be set).""" + l.log_enableFile() + +def disable(): + """Disable all logging.""" + l.log_disable() + +def disableScreen(): + """Disable logging to screen.""" + l.log_disableScreen() + +def disableFile(): + """Disable logging to file.""" + l.log_disableFile() + +def setFormatFile(fmt): + """Set the format string for log messages. Here are the substitutions you may use: + + %f: Source file name generating the log call. + %n: Source line number where the log call was made. + %m: The message text sent to the logger (after printf formatting). + %d: The current date, formatted using the logger's date format. + %t: The current time, formatted using the logger's time format. + %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR"). + %%: A literal percent sign. + + The default format string is "%d %t %f(%n): %l: %m\n". + + :param fmt: Format to use, end with "\n". + :type fmt: :class:`string` + """ + l.log_setFormatFile(fmt) + +def setFormatScreen(fmt): + """Set the format string for log messages. Here are the substitutions you may use: + + %f: Source file name generating the log call. + %n: Source line number where the log call was made. + %m: The message text sent to the logger (after printf formatting). + %d: The current date, formatted using the logger's date format. + %t: The current time, formatted using the logger's time format. + %l: The log level (one of "DEBUG", "INFO", "WARN", or "ERROR"). + %%: A literal percent sign. + + The default format string is "%d %t %f(%n): %l: %m\n". + + :param fmt: Format to use, end with "\n". + :type fmt: :class:`string` + """ + l.log_setFormatScreen(fmt) + +STDOUT=1 +STDERR=2 + +DEBUG=0 +INFO=1 +WARN=2 +ERROR=3 + +def setOutputScreen(fd, level): + """Set which screen to output to, and which level to use. + + :param fd: File descriptor of output screen (STDOUT or STDERR). + :type fd: :class:`int` + :param level: Logging level to use (DEBUG, INFO, WARN, or ERROR). + :type level: :class:`int` + """ + l.log_setOutputScreen(fd, level) + +def setOutputFile(filename, level): + """Set which file to output to, and which level to use. + + :param filename: File name of output file. + :type filename: :class:`string` + :param level: Logging level to use (DEBUG, INFO, WARN, or ERROR). + :type level: :class:`int` + """ + l.log_setOutputFile(filename, level)
\ No newline at end of file diff --git a/python/astra/log_c.pyx b/python/astra/log_c.pyx new file mode 100644 index 0000000..969cc06 --- /dev/null +++ b/python/astra/log_c.pyx @@ -0,0 +1,96 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six + +cdef extern from "astra/Logging.h" namespace "astra": + cdef enum log_level: + LOG_DEBUG + LOG_INFO + LOG_WARN + LOG_ERROR + +cdef extern from "astra/Logging.h" namespace "astra::CLogger": + void debug(const char *sfile, int sline, const char *fmt, ...) + void info(const char *sfile, int sline, const char *fmt, ...) + void warn(const char *sfile, int sline, const char *fmt, ...) + void error(const char *sfile, int sline, const char *fmt, ...) + void setOutputScreen(int fd, log_level m_eLevel) + void setOutputFile(const char *filename, log_level m_eLevel) + void enable() + void enableScreen() + void enableFile() + void disable() + void disableScreen() + void disableFile() + void setFormatFile(const char *fmt) + void setFormatScreen(const char *fmt) + +def log_debug(sfile, sline, message): + debug(six.b(sfile),sline,six.b(message)) + +def log_info(sfile, sline, message): + info(six.b(sfile),sline,six.b(message)) + +def log_warn(sfile, sline, message): + warn(six.b(sfile),sline,six.b(message)) + +def log_error(sfile, sline, message): + error(six.b(sfile),sline,six.b(message)) + +def log_enable(): + enable() + +def log_enableScreen(): + enableScreen() + +def log_enableFile(): + enableFile() + +def log_disable(): + disable() + +def log_disableScreen(): + disableScreen() + +def log_disableFile(): + disableFile() + +def log_setFormatFile(fmt): + setFormatFile(six.b(fmt)) + +def log_setFormatScreen(fmt): + setFormatScreen(six.b(fmt)) + +enumList = [LOG_DEBUG,LOG_INFO,LOG_WARN,LOG_ERROR] + +def log_setOutputScreen(fd, level): + setOutputScreen(fd, enumList[level]) + +def log_setOutputFile(filename, level): + setOutputFile(six.b(filename), enumList[level])
\ No newline at end of file diff --git a/python/astra/matlab.py b/python/astra/matlab.py new file mode 100644 index 0000000..83b345d --- /dev/null +++ b/python/astra/matlab.py @@ -0,0 +1,112 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +"""This module implements a MATLAB-like interface to the ASTRA Toolbox. + +Note that all functions are called with a :class:`string` as the first +argument, specifying the operation to perform. This un-pythonic way +is used to make transitioning from MATLAB code to Python code easier, as +the MATLAB interface uses the same type of method calling. + +After an initial ``import astra``, these functions can be accessed in the +``astra.m`` module. + +""" + +from . import astra_c +from . import data2d_c +from . import data3d_c +from . import projector_c +from . import algorithm_c +from . import matrix_c +import numpy as np + + +def astra(command, *args): + """MATLAB-like interface to the :mod:`astra.astra` module + + For example: + + ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled. + + """ + return getattr(astra_c, command)(*args) + + +def data2d(command, *args): + """MATLAB-like interface to the :mod:`astra.data2d` module + + For example: + + ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object. + + """ + return getattr(data2d_c, command)(*args) + + +def data3d(command, *args): + """MATLAB-like interface to the :mod:`astra.data3d` module + + For example: + + ``astra.m.data3d('get',i)`` -- Get 3D object data. + + """ + return getattr(data3d_c, command)(*args) + + +def projector(command, *args): + """MATLAB-like interface to the :mod:`astra.projector` module + + For example: + + ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry. + + """ + return getattr(projector_c, command)(*args) + + +def matrix(command, *args): + """MATLAB-like interface to the :mod:`astra.matrix` module + + For example: + + ``astra.m.matrix('delete',i)`` -- Delete a matrix. + + """ + return getattr(matrix_c, command)(*args) + + +def algorithm(command, *args): + """MATLAB-like interface to the :mod:`astra.algorithm` module + + For example: + + ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations. + + """ + if command == 'iterate': + command = 'run' + return getattr(algorithm_c, command)(*args) diff --git a/python/astra/matrix.py b/python/astra/matrix.py new file mode 100644 index 0000000..27e4823 --- /dev/null +++ b/python/astra/matrix.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import matrix_c as m + +def delete(ids): + """Delete a matrix object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return m.delete(ids) + +def clear(): + """Clear all matrix objects.""" + return m.clear() + +def create(data): + """Create matrix object with data. + + :param data: Data to fill the created object with. + :type data: :class:`scipy.sparse.csr_matrix` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return m.create(data) + + +def store(i,data): + """Fill existing matrix object with data. + + :param i: ID of object to fill. + :type i: :class:`int` + :param data: Data to fill the object with. + :type data: :class:`scipy.sparse.csr_matrix` + + """ + return m.store(i,data) + +def get_size(i): + """Get matrix dimensions. + + :param i: ID of object. + :type i: :class:`int` + :returns: :class:`tuple` -- matrix dimensions. + """ + return m.get_size(i) + +def get(i): + """Get a matrix object. + + :param i: ID of object to get. + :type i: :class:`int` + :returns: :class:`scipy.sparse.csr_matrix` -- The object data. + + """ + return m.get(i) + +def info(): + """Print info on matrix objects in memory.""" + return m.info() + + diff --git a/python/astra/matrix_c.pyx b/python/astra/matrix_c.pyx new file mode 100644 index 0000000..b0d8bc4 --- /dev/null +++ b/python/astra/matrix_c.pyx @@ -0,0 +1,116 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +from six.moves import range +import numpy as np +import scipy.sparse as ss + +from libcpp cimport bool + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager +from .PyIncludes cimport * +from .utils import wrap_from_bytes + +cdef CMatrixManager * manM = <CMatrixManager * >PyMatrixManager.getSingletonPtr() + + +def delete(ids): + try: + for i in ids: + manM.remove(i) + except TypeError: + manM.remove(ids) + +def clear(): + manM.clear() + +cdef int csr_matrix_to_astra(data,CSparseMatrix *mat) except -1: + if isinstance(data,ss.csr_matrix): + csrD = data + else: + csrD = data.tocsr() + if not mat.isInitialized(): + raise Exception("Couldn't initialize data object.") + if csrD.nnz > mat.m_lSize or csrD.shape[0] > mat.m_iHeight: + raise Exception("Matrix too large to store in this object.") + for i in range(len(csrD.indptr)): + mat.m_plRowStarts[i] = csrD.indptr[i] + for i in range(csrD.nnz): + mat.m_piColIndices[i] = csrD.indices[i] + mat.m_pfValues[i] = csrD.data[i] + +cdef astra_to_csr_matrix(CSparseMatrix *mat): + indptr = np.zeros(mat.m_iHeight+1,dtype=np.int) + indices = np.zeros(mat.m_plRowStarts[mat.m_iHeight],dtype=np.int) + data = np.zeros(mat.m_plRowStarts[mat.m_iHeight]) + for i in range(mat.m_iHeight+1): + indptr[i] = mat.m_plRowStarts[i] + for i in range(mat.m_plRowStarts[mat.m_iHeight]): + indices[i] = mat.m_piColIndices[i] + data[i] = mat.m_pfValues[i] + return ss.csr_matrix((data,indices,indptr),shape=(mat.m_iHeight,mat.m_iWidth)) + +def create(data): + cdef CSparseMatrix* pMatrix + pMatrix = new CSparseMatrix(data.shape[0], data.shape[1], data.nnz) + if not pMatrix.isInitialized(): + del pMatrix + raise Exception("Couldn't initialize data object.") + try: + csr_matrix_to_astra(data,pMatrix) + except: + del pMatrix + raise Exception("Failed to create data object.") + + return manM.store(pMatrix) + +cdef CSparseMatrix * getObject(i) except NULL: + cdef CSparseMatrix * pDataObject = manM.get(i) + if pDataObject == NULL: + raise Exception("Data object not found") + if not pDataObject.isInitialized(): + raise Exception("Data object not initialized properly.") + return pDataObject + + +def store(i,data): + cdef CSparseMatrix * pDataObject = getObject(i) + csr_matrix_to_astra(data,pDataObject) + +def get_size(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return (pDataObject.m_iHeight,pDataObject.m_iWidth) + +def get(i): + cdef CSparseMatrix * pDataObject = getObject(i) + return astra_to_csr_matrix(pDataObject) + +def info(): + six.print_(wrap_from_bytes(manM.info())) diff --git a/python/astra/projector.py b/python/astra/projector.py new file mode 100644 index 0000000..e370e5a --- /dev/null +++ b/python/astra/projector.py @@ -0,0 +1,110 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import projector_c as p + +def create(config): + """Create projector object. + + :param config: Projector options. + :type config: :class:`dict` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return p.create(config) + + +def delete(ids): + """Delete a projector object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return p.delete(ids) + + +def clear(): + """Clear all projector objects.""" + return p.clear() + + +def info(): + """Print info on projector objects in memory.""" + return p.info() + +def projection_geometry(i): + """Get projection geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- projection geometry + + """ + return p.projection_geometry(i) + + +def volume_geometry(i): + """Get volume geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- volume geometry + + """ + return p.volume_geometry(i) + + +def weights_single_ray(i, projection_index, detector_index): + return p.weights_single_ray(i, projection_index, detector_index) + + +def weights_projection(i, projection_index): + return p.weights_projection(i, projection_index) + + +def splat(i, row, col): + return p.splat(i, row, col) + +def is_cuda(i): + """Check whether a projector is a CUDA projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`bool` -- True if the projector is a CUDA projector. + + """ + return p.is_cuda(i) + + +def matrix(i): + """Get sparse matrix of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`int` -- ID of sparse matrix. + + """ + return p.matrix(i) diff --git a/python/astra/projector3d.py b/python/astra/projector3d.py new file mode 100644 index 0000000..d1086b9 --- /dev/null +++ b/python/astra/projector3d.py @@ -0,0 +1,100 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from . import projector3d_c as p + +def create(config): + """Create projector object. + + :param config: Projector options. + :type config: :class:`dict` + :returns: :class:`int` -- the ID of the constructed object. + + """ + return p.create(config) + + +def delete(ids): + """Delete a projector object. + + :param ids: ID or list of ID's to delete. + :type ids: :class:`int` or :class:`list` + + """ + return p.delete(ids) + + +def clear(): + """Clear all projector objects.""" + return p.clear() + + +def info(): + """Print info on projector objects in memory.""" + return p.info() + +def projection_geometry(i): + """Get projection geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- projection geometry + + """ + return p.projection_geometry(i) + + +def volume_geometry(i): + """Get volume geometry of a projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`dict` -- volume geometry + + """ + return p.volume_geometry(i) + + +def weights_single_ray(i, projection_index, detector_index): + return p.weights_single_ray(i, projection_index, detector_index) + + +def weights_projection(i, projection_index): + return p.weights_projection(i, projection_index) + + +def splat(i, row, col): + return p.splat(i, row, col) + + +def is_cuda(i): + """Check whether a projector is a CUDA projector. + + :param i: ID of projector. + :type i: :class:`int` + :returns: :class:`bool` -- True if the projector is a CUDA projector. + + """ + return p.is_cuda(i) diff --git a/python/astra/projector3d_c.pyx b/python/astra/projector3d_c.pyx new file mode 100644 index 0000000..8b978d7 --- /dev/null +++ b/python/astra/projector3d_c.pyx @@ -0,0 +1,119 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +from .PyIncludes cimport * + +cimport utils +from .utils import wrap_from_bytes + +cimport PyProjector3DFactory +from .PyProjector3DFactory cimport CProjector3DFactory + +cimport PyProjector3DManager +from .PyProjector3DManager cimport CProjector3DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cdef CProjector3DManager * manProj = <CProjector3DManager * >PyProjector3DManager.getSingletonPtr() + +include "config.pxi" + +IF HAVE_CUDA: + cdef extern from *: + CCudaProjector3D* dynamic_cast_cuda_projector "dynamic_cast<astra::CCudaProjector3D*>" (CProjector3D*) + + +def create(config): + cdef Config * cfg = utils.dictToConfig(six.b('Projector3D'), config) + cdef CProjector3D * proj + proj = PyProjector3DFactory.getSingletonPtr().create(cfg[0]) + if proj == NULL: + del cfg + raise Exception("Error creating Projector3D.") + del cfg + return manProj.store(proj) + + +def delete(ids): + try: + for i in ids: + manProj.remove(i) + except TypeError: + manProj.remove(ids) + + +def clear(): + manProj.clear() + + +def info(): + six.print_(wrap_from_bytes(manProj.info())) + +cdef CProjector3D * getObject(i) except NULL: + cdef CProjector3D * proj = manProj.get(i) + if proj == NULL: + raise Exception("Projector not initialized.") + if not proj.isInitialized(): + raise Exception("Projector not initialized.") + return proj + + +def projection_geometry(i): + cdef CProjector3D * proj = getObject(i) + return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + + +def volume_geometry(i): + cdef CProjector3D * proj = getObject(i) + return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + + +def weights_single_ray(i, projection_index, detector_index): + raise Exception("Not yet implemented") + + +def weights_projection(i, projection_index): + raise Exception("Not yet implemented") + + +def splat(i, row, col): + raise Exception("Not yet implemented") + +def is_cuda(i): + cdef CProjector3D * proj = getObject(i) + IF HAVE_CUDA==True: + cdef CCudaProjector3D * cudaproj = NULL + cudaproj = dynamic_cast_cuda_projector(proj) + if cudaproj==NULL: + return False + else: + return True + ELSE: + return False diff --git a/python/astra/projector_c.pyx b/python/astra/projector_c.pyx new file mode 100644 index 0000000..9aa868e --- /dev/null +++ b/python/astra/projector_c.pyx @@ -0,0 +1,134 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import six +from .PyIncludes cimport * + +cimport utils +from .utils import wrap_from_bytes + +cimport PyProjector2DFactory +from .PyProjector2DFactory cimport CProjector2DFactory + +cimport PyProjector2DManager +from .PyProjector2DManager cimport CProjector2DManager + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument + +cimport PyMatrixManager +from .PyMatrixManager cimport CMatrixManager + +cdef CProjector2DManager * manProj = <CProjector2DManager * >PyProjector2DManager.getSingletonPtr() +cdef CMatrixManager * manM = <CMatrixManager * >PyMatrixManager.getSingletonPtr() + +include "config.pxi" + +IF HAVE_CUDA: + cdef extern from *: + CCudaProjector2D* dynamic_cast_cuda_projector "dynamic_cast<astra::CCudaProjector2D*>" (CProjector2D*) + + +def create(config): + cdef Config * cfg = utils.dictToConfig(six.b('Projector2D'), config) + cdef CProjector2D * proj + proj = PyProjector2DFactory.getSingletonPtr().create(cfg[0]) + if proj == NULL: + del cfg + raise Exception("Error creating projector.") + del cfg + return manProj.store(proj) + + +def delete(ids): + try: + for i in ids: + manProj.remove(i) + except TypeError: + manProj.remove(ids) + + +def clear(): + manProj.clear() + + +def info(): + six.print_(wrap_from_bytes(manProj.info())) + +cdef CProjector2D * getObject(i) except NULL: + cdef CProjector2D * proj = manProj.get(i) + if proj == NULL: + raise Exception("Projector not initialized.") + if not proj.isInitialized(): + raise Exception("Projector not initialized.") + return proj + + +def projection_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.configToDict(proj.getProjectionGeometry().getConfiguration()) + + +def volume_geometry(i): + cdef CProjector2D * proj = getObject(i) + return utils.configToDict(proj.getVolumeGeometry().getConfiguration()) + + +def weights_single_ray(i, projection_index, detector_index): + raise Exception("Not yet implemented") + + +def weights_projection(i, projection_index): + raise Exception("Not yet implemented") + + +def splat(i, row, col): + raise Exception("Not yet implemented") + +def is_cuda(i): + cdef CProjector2D * proj = getObject(i) + IF HAVE_CUDA==True: + cdef CCudaProjector2D * cudaproj = NULL + cudaproj = dynamic_cast_cuda_projector(proj) + if cudaproj==NULL: + return False + else: + return True + ELSE: + return False + +def matrix(i): + cdef CProjector2D * proj = getObject(i) + cdef CSparseMatrix * mat = proj.getMatrix() + if mat == NULL: + del mat + raise Exception("Data object not found") + if not mat.isInitialized(): + del mat + raise Exception("Data object not initialized properly.") + return manM.store(mat) diff --git a/python/astra/utils.pxd b/python/astra/utils.pxd new file mode 100644 index 0000000..ca84836 --- /dev/null +++ b/python/astra/utils.pxd @@ -0,0 +1,35 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +from libcpp.string cimport string + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode + +from .PyIncludes cimport * + +cdef configToDict(Config *) +cdef Config * dictToConfig(string rootname, dc) diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx new file mode 100644 index 0000000..0439f1b --- /dev/null +++ b/python/astra/utils.pyx @@ -0,0 +1,236 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +# distutils: language = c++ +# distutils: libraries = astra + +import numpy as np +import six +from libcpp.string cimport string +from libcpp.list cimport list +from libcpp.vector cimport vector +from cython.operator cimport dereference as deref, preincrement as inc +from cpython.version cimport PY_MAJOR_VERSION + +cimport PyXMLDocument +from .PyXMLDocument cimport XMLDocument +from .PyXMLDocument cimport XMLNode +from .PyIncludes cimport * + + +cdef Config * dictToConfig(string rootname, dc): + cdef Config * cfg = new Config() + cfg.initialize(rootname) + try: + readDict(cfg.self, dc) + except Exception as e: + del cfg + six.print_(e.strerror) + return NULL + return cfg + +def convert_item(item): + if isinstance(item, six.string_types): + return item.encode('ascii') + + if type(item) is not dict: + return item + + out_dict = {} + for k in item: + out_dict[convert_item(k)] = convert_item(item[k]) + return out_dict + + +def wrap_to_bytes(value): + if isinstance(value, six.binary_type): + return value + s = str(value) + if PY_MAJOR_VERSION == 3: + s = s.encode('ascii') + return s + + +def wrap_from_bytes(value): + s = value + if PY_MAJOR_VERSION == 3: + s = s.decode('ascii') + return s + + +cdef void readDict(XMLNode * root, _dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + + dc = convert_item(_dc) + for item in dc: + val = dc[item] + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = root.addChildNode(item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + elif isinstance(val, dict): + if item == six.b('option') or item == six.b('options') or item == six.b('Option') or item == six.b('Options'): + readOptions(root, val) + else: + itm = root.addChildNode(item) + readDict(itm, val) + del itm + else: + if item == six.b('type'): + root.addAttribute(< string > six.b('type'), <string> wrap_to_bytes(val)) + else: + itm = root.addChildNode(item, wrap_to_bytes(val)) + del itm + +cdef void readOptions(XMLNode * node, dc): + cdef XMLNode * listbase + cdef XMLNode * itm + cdef int i + cdef int j + for item in dc: + val = dc[item] + if node.hasOption(item): + raise Exception('Duplicate Option: %s' % item) + if isinstance(val, np.ndarray): + if val.size == 0: + break + listbase = node.addChildNode(six.b('Option')) + listbase.addAttribute(< string > six.b('key'), < string > item) + listbase.addAttribute(< string > six.b('listsize'), < float32 > val.size) + index = 0 + if val.ndim == 2: + for i in range(val.shape[0]): + for j in range(val.shape[1]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute( < string > six.b('value'), < float32 > val[i, j]) + index += 1 + del itm + elif val.ndim == 1: + for i in range(val.shape[0]): + itm = listbase.addChildNode(six.b('ListItem')) + itm.addAttribute(< string > six.b('index'), < float32 > index) + itm.addAttribute(< string > six.b('value'), < float32 > val[i]) + index += 1 + del itm + else: + raise Exception("Only 1 or 2 dimensions are allowed") + del listbase + else: + node.addOption(item, wrap_to_bytes(val)) + +cdef configToDict(Config *cfg): + return XMLNode2dict(cfg.self) + +def castString3(input): + return input.decode('utf-8') + +def castString2(input): + return input + +if six.PY3: + castString = castString3 +else: + castString = castString2 + +def stringToPythonValue(inputIn): + input = castString(inputIn) + # matrix + if ';' in input: + row_strings = input.split(';') + col_strings = row_strings[0].split(',') + nRows = len(row_strings) + nCols = len(col_strings) + + out = np.empty((nRows,nCols)) + for ridx, row in enumerate(row_strings): + col_strings = row.split(',') + for cidx, col in enumerate(col_strings): + out[ridx,cidx] = float(col) + return out + + # vector + if ',' in input: + items = input.split(',') + out = np.empty(len(items)) + for idx,item in enumerate(items): + out[idx] = float(item) + return out + + try: + # integer + return int(input) + except ValueError: + try: + #float + return float(input) + except ValueError: + # string + return str(input) + + +cdef XMLNode2dict(XMLNode * node): + cdef XMLNode * subnode + cdef list[XMLNode * ] nodes + cdef list[XMLNode * ].iterator it + dct = {} + opts = {} + if node.hasAttribute(six.b('type')): + dct['type'] = castString(node.getAttribute(six.b('type'))) + nodes = node.getNodes() + it = nodes.begin() + while it != nodes.end(): + subnode = deref(it) + if castString(subnode.getName())=="Option": + opts[castString(subnode.getAttribute('key'))] = stringToPythonValue(subnode.getAttribute('value')) + else: + dct[castString(subnode.getName())] = stringToPythonValue(subnode.getContent()) + del subnode + inc(it) + if len(opts)>0: dct['options'] = opts + return dct diff --git a/python/builder.py b/python/builder.py new file mode 100644 index 0000000..cfdb7d1 --- /dev/null +++ b/python/builder.py @@ -0,0 +1,82 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- +import sys +import os +import numpy as np + +from distutils.version import LooseVersion +from distutils.core import setup +from distutils.extension import Extension + +from Cython.Distutils import build_ext +from Cython.Build import cythonize +import Cython +if LooseVersion(Cython.__version__)<LooseVersion('0.13'): raise ImportError("Cython version should be at least 0.13") +usecuda=False +try: + if os.environ['CPPFLAGS'].find('-DASTRA_CUDA')!=-1: + usecuda=True +except KeyError: + pass + +cfgToWrite = 'DEF HAVE_CUDA=' + str(usecuda) + "\n" +cfgHasToBeUpdated = True +try: + cfg = open('astra/config.pxi','r') + cfgIn = cfg.read() + cfg.close() + if cfgIn==cfgToWrite: + cfgHasToBeUpdated = False +except IOError: + pass + +if cfgHasToBeUpdated: + cfg = open('astra/config.pxi','w') + cfg.write(cfgToWrite) + cfg.close() + +cmdclass = { } +ext_modules = [ ] + +ext_modules = cythonize("astra/*.pyx", language_level=2) +cmdclass = { 'build_ext': build_ext } + +setup (name = 'PyASTRAToolbox', + version = '1.6', + description = 'Python interface to the ASTRA-Toolbox', + author='D.M. Pelt', + author_email='D.M.Pelt@cwi.nl', + url='http://dmpelt.github.io/pyastratoolbox/', + #ext_package='astra', + #ext_modules = cythonize(Extension("astra/*.pyx",extra_compile_args=extra_compile_args,extra_linker_args=extra_compile_args)), + license='GPLv3', + ext_modules = ext_modules, + include_dirs=[np.get_include()], + cmdclass = cmdclass, + #ext_modules = [Extension("astra","astra/astra.pyx")], + packages=['astra'], + requires=["numpy"], + ) diff --git a/python/doc b/python/doc new file mode 120000 index 0000000..3705b55 --- /dev/null +++ b/python/doc @@ -0,0 +1 @@ +docSRC/_build/html
\ No newline at end of file diff --git a/python/docSRC/ASTRAProjector.rst b/python/docSRC/ASTRAProjector.rst new file mode 100644 index 0000000..1c267e3 --- /dev/null +++ b/python/docSRC/ASTRAProjector.rst @@ -0,0 +1,8 @@ +Helper class: the :mod:`ASTRAProjector` module +============================================== + +.. automodule:: astra.ASTRAProjector + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/Makefile b/python/docSRC/Makefile new file mode 100644 index 0000000..a005bab --- /dev/null +++ b/python/docSRC/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = _build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) . + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. 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If you use many repeated operations, directly +using the PyAstraToolbox methods directly is faster.</p> +<p>You can use this class as an abstracted weight matrix <span class="math">\(W\)</span>: multiplying an instance +<tt class="docutils literal"><span class="pre">proj</span></tt> of this class by an image results in a forward projection of the image, and multiplying +<tt class="docutils literal"><span class="pre">proj.T</span></tt> by a sinogram results in a backprojection of the sinogram:</p> +<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span> +<span class="n">fp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">*</span><span class="n">image</span> +<span class="n">bp</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">T</span><span class="o">*</span><span class="n">sinogram</span> +</pre></div> +</div> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – The projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – The volume geometry.</li> +<li><strong>proj_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Projector type, such as <tt class="docutils literal"><span class="pre">'line'</span></tt>, <tt class="docutils literal"><span class="pre">'linear'</span></tt>, ...</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for calculations, when possible.</li> +</ul> +</td> +</tr> +</tbody> +</table> +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.backProject"> +<tt class="descname">backProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.backProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.backProject" title="Permalink to this definition">¶</a></dt> +<dd><p>Backproject a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The sinogram data or ID.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The backprojection.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.forwardProject"> +<tt class="descname">forwardProject</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.forwardProject"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.forwardProject" title="Permalink to this definition">¶</a></dt> +<dd><p>Forward project an image.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The image data or ID.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The forward projection.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="method"> +<dt id="astra.ASTRAProjector.ASTRAProjector2D.reconstruct"> +<tt class="descname">reconstruct</tt><big>(</big><em>data</em>, <em>method</em>, <em>**kwargs</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2D.reconstruct"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2D.reconstruct" title="Permalink to this definition">¶</a></dt> +<dd><p>Reconstruct an image from a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – The sinogram data or ID.</li> +<li><strong>method</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Name of the reconstruction algorithm.</li> +<li><strong>kwargs</strong> – Additional named parameters to pass to <a class="reference internal" href="creators.html#astra.creators.create_reconstruction" title="astra.creators.create_reconstruction"><tt class="xref py py-func docutils literal"><span class="pre">astra.creators.create_reconstruction()</span></tt></a>.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The reconstruction.</p> +</td> +</tr> +</tbody> +</table> +<p>Example of a SIRT reconstruction using CUDA:</p> +<div class="highlight-python"><div class="highlight"><pre><span class="n">proj</span> <span class="o">=</span> <span class="n">ASTRAProjector2D</span><span class="p">(</span><span class="o">...</span><span class="p">)</span> +<span class="n">rec</span> <span class="o">=</span> <span class="n">proj</span><span class="o">.</span><span class="n">reconstruct</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span><span class="s">'SIRT_CUDA'</span><span class="p">,</span><span class="n">iterations</span><span class="o">=</span><span class="mi">1000</span><span class="p">)</span> +</pre></div> +</div> +</dd></dl> + +</dd></dl> + +<dl class="class"> +<dt id="astra.ASTRAProjector.ASTRAProjector2DTranspose"> +<em class="property">class </em><tt class="descclassname">astra.ASTRAProjector.</tt><tt class="descname">ASTRAProjector2DTranspose</tt><big>(</big><em>parentProj</em><big>)</big><a class="reference internal" href="_modules/astra/ASTRAProjector.html#ASTRAProjector2DTranspose"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.ASTRAProjector.ASTRAProjector2DTranspose" title="Permalink to this definition">¶</a></dt> +<dd><p>Bases: <tt class="xref py py-class docutils literal"><span class="pre">builtins.object</span></tt></p> +<p>Implements the <tt class="docutils literal"><span class="pre">proj.T</span></tt> functionality.</p> +<p>Do not use directly, since it can be accessed as member <tt class="docutils literal"><span class="pre">.T</span></tt> of +an <a class="reference internal" href="#astra.ASTRAProjector.ASTRAProjector2D" title="astra.ASTRAProjector.ASTRAProjector2D"><tt class="xref py py-class docutils literal"><span class="pre">ASTRAProjector2D</span></tt></a> object.</p> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html new file mode 100644 index 0000000..08789f2 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/ASTRAProjector.html @@ -0,0 +1,243 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.ASTRAProjector — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.ASTRAProjector</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">import</span> <span class="nn">math</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">creators</span> <span class="k">as</span> <span class="n">ac</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> + + +<div class="viewcode-block" id="ASTRAProjector2DTranspose"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2DTranspose">[docs]</a><span class="k">class</span> <span class="nc">ASTRAProjector2DTranspose</span><span class="p">():</span> + <span class="sd">"""Implements the ``proj.T`` functionality.</span> + +<span class="sd"> Do not use directly, since it can be accessed as member ``.T`` of</span> +<span class="sd"> an :class:`ASTRAProjector2D` object.</span> + +<span class="sd"> """</span> + <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">parentProj</span><span class="p">):</span> + <span class="bp">self</span><span class="o">.</span><span class="n">parentProj</span> <span class="o">=</span> <span class="n">parentProj</span> + + <span class="k">def</span> <span class="nf">__mul__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">parentProj</span><span class="o">.</span><span class="n">backProject</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="ASTRAProjector2D"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D">[docs]</a><span class="k">class</span> <span class="nc">ASTRAProjector2D</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span> + <span class="sd">"""Helps with various common ASTRA Toolbox 2D operations.</span> + +<span class="sd"> This class can perform several often used toolbox operations, such as:</span> + +<span class="sd"> * Forward projecting</span> +<span class="sd"> * Back projecting</span> +<span class="sd"> * Reconstructing</span> + +<span class="sd"> Note that this class has a some computational overhead, because it</span> +<span class="sd"> copies a lot of data. If you use many repeated operations, directly</span> +<span class="sd"> using the PyAstraToolbox methods directly is faster.</span> + +<span class="sd"> You can use this class as an abstracted weight matrix :math:`W`: multiplying an instance</span> +<span class="sd"> ``proj`` of this class by an image results in a forward projection of the image, and multiplying</span> +<span class="sd"> ``proj.T`` by a sinogram results in a backprojection of the sinogram::</span> + +<span class="sd"> proj = ASTRAProjector2D(...)</span> +<span class="sd"> fp = proj*image</span> +<span class="sd"> bp = proj.T*sinogram</span> + +<span class="sd"> :param proj_geom: The projection geometry.</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> :param vol_geom: The volume geometry.</span> +<span class="sd"> :type vol_geom: :class:`dict`</span> +<span class="sd"> :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...</span> +<span class="sd"> :type proj_type: :class:`string`</span> +<span class="sd"> :param useCUDA: If ``True``, use CUDA for calculations, when possible.</span> +<span class="sd"> :type useCUDA: :class:`bool`</span> +<span class="sd"> """</span> + + <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">proj_type</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="bp">self</span><span class="o">.</span><span class="n">vol_geom</span> <span class="o">=</span> <span class="n">vol_geom</span> + <span class="bp">self</span><span class="o">.</span><span class="n">recSize</span> <span class="o">=</span> <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nDet</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">]</span> + <span class="n">nexpow</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="nb">pow</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="bp">self</span><span class="o">.</span><span class="n">nDet</span><span class="p">,</span> <span class="mi">2</span><span class="p">))))</span> + <span class="bp">self</span><span class="o">.</span><span class="n">filterSize</span> <span class="o">=</span> <span class="n">nexpow</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">+</span> <span class="mi">1</span> + <span class="bp">self</span><span class="o">.</span><span class="n">nProj</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">angles</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="bp">self</span><span class="o">.</span><span class="n">proj_geom</span> <span class="o">=</span> <span class="n">proj_geom</span> + <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_projector</span><span class="p">(</span><span class="n">proj_type</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">)</span> + <span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span> <span class="o">=</span> <span class="n">useCUDA</span> + <span class="bp">self</span><span class="o">.</span><span class="n">T</span> <span class="o">=</span> <span class="n">ASTRAProjector2DTranspose</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> + +<div class="viewcode-block" id="ASTRAProjector2D.backProject"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.backProject">[docs]</a> <span class="k">def</span> <span class="nf">backProject</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Backproject a sinogram.</span> + +<span class="sd"> :param data: The sinogram data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The backprojection.</span> + +<span class="sd"> """</span> + <span class="n">vol_id</span><span class="p">,</span> <span class="n">vol</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_backprojection</span><span class="p">(</span> + <span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">vol</span> +</div> +<div class="viewcode-block" id="ASTRAProjector2D.forwardProject"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.forwardProject">[docs]</a> <span class="k">def</span> <span class="nf">forwardProject</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Forward project an image.</span> + +<span class="sd"> :param data: The image data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The forward projection.</span> + +<span class="sd"> """</span> + <span class="n">sin_id</span><span class="p">,</span> <span class="n">sino</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_sino</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">useCUDA</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sin_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">sino</span> +</div> +<div class="viewcode-block" id="ASTRAProjector2D.reconstruct"><a class="viewcode-back" href="../../ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.reconstruct">[docs]</a> <span class="k">def</span> <span class="nf">reconstruct</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">method</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> + <span class="sd">"""Reconstruct an image from a sinogram.</span> + +<span class="sd"> :param data: The sinogram data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :param method: Name of the reconstruction algorithm.</span> +<span class="sd"> :type method: :class:`string`</span> +<span class="sd"> :param kwargs: Additional named parameters to pass to :func:`astra.creators.create_reconstruction`.</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The reconstruction.</span> + +<span class="sd"> Example of a SIRT reconstruction using CUDA::</span> + +<span class="sd"> proj = ASTRAProjector2D(...)</span> +<span class="sd"> rec = proj.reconstruct(sinogram,'SIRT_CUDA',iterations=1000)</span> + +<span class="sd"> """</span> + <span class="n">kwargs</span><span class="p">[</span><span class="s">'returnData'</span><span class="p">]</span> <span class="o">=</span> <span class="bp">True</span> + <span class="n">rec_id</span><span class="p">,</span> <span class="n">rec</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_reconstruction</span><span class="p">(</span> + <span class="n">method</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">proj_id</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">rec_id</span><span class="p">)</span> + <span class="k">return</span> <span class="n">rec</span> +</div> + <span class="k">def</span> <span class="nf">__mul__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">forwardProject</span><span class="p">(</span><span class="n">data</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/algorithm.html b/python/docSRC/_build/html/_modules/astra/algorithm.html new file mode 100644 index 0000000..39816fd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/algorithm.html @@ -0,0 +1,181 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.algorithm — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.algorithm</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm_c</span> <span class="k">as</span> <span class="n">a</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">config</span><span class="p">):</span> + <span class="sd">"""Create algorithm object.</span> +<span class="sd"> </span> +<span class="sd"> :param config: Algorithm options.</span> +<span class="sd"> :type config: :class:`dict`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">config</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="run"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.run">[docs]</a><span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">iterations</span><span class="o">=</span><span class="mi">1</span><span class="p">):</span> + <span class="sd">"""Run an algorithm.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param iterations: Number of iterations to run.</span> +<span class="sd"> :type iterations: :class:`int`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">iterations</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_res_norm"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.get_res_norm">[docs]</a><span class="k">def</span> <span class="nf">get_res_norm</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get residual norm of algorithm.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`float` -- The residual norm.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">get_res_norm</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all matrix objects."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../algorithm.html#astra.algorithm.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on matrix objects in memory."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/astra.html b/python/docSRC/_build/html/_modules/astra/astra.html new file mode 100644 index 0000000..53fac8e --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/astra.html @@ -0,0 +1,163 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.astra — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.astra</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">astra_c</span> <span class="k">as</span> <span class="n">a</span> + +<div class="viewcode-block" id="credits"><a class="viewcode-back" href="../../astra.html#astra.astra.credits">[docs]</a><span class="k">def</span> <span class="nf">credits</span><span class="p">():</span> + <span class="sd">"""Print credits of the ASTRA Toolbox."""</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">credits</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="use_cuda"><a class="viewcode-back" href="../../astra.html#astra.astra.use_cuda">[docs]</a><span class="k">def</span> <span class="nf">use_cuda</span><span class="p">():</span> + <span class="sd">"""Test if CUDA is enabled.</span> +<span class="sd"> </span> +<span class="sd"> :returns: :class:`bool` -- ``True`` if CUDA is enabled.</span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">use_cuda</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="version"><a class="viewcode-back" href="../../astra.html#astra.astra.version">[docs]</a><span class="k">def</span> <span class="nf">version</span><span class="p">(</span><span class="n">printToScreen</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="sd">"""Check version of the ASTRA Toolbox.</span> +<span class="sd"> </span> +<span class="sd"> :param printToScreen: If ``True``, print version string. If ``False``, return version integer.</span> +<span class="sd"> :type printToScreen: :class:`bool`</span> +<span class="sd"> :returns: :class:`string` or :class:`int` -- The version string or integer.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">a</span><span class="o">.</span><span class="n">version</span><span class="p">(</span><span class="n">printToScreen</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="set_gpu_index"><a class="viewcode-back" href="../../astra.html#astra.astra.set_gpu_index">[docs]</a><span class="k">def</span> <span class="nf">set_gpu_index</span><span class="p">(</span><span class="n">idx</span><span class="p">):</span> + <span class="sd">"""Set default GPU index to use.</span> +<span class="sd"> </span> +<span class="sd"> :param idx: GPU index</span> +<span class="sd"> :type idx: :class:`int`</span> +<span class="sd"> """</span> + <span class="n">a</span><span class="o">.</span><span class="n">set_gpu_index</span><span class="p">(</span><span class="n">idx</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/creators.html b/python/docSRC/_build/html/_modules/astra/creators.html new file mode 100644 index 0000000..c43978a --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/creators.html @@ -0,0 +1,668 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.creators — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.creators</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> + +<span class="kn">import</span> <span class="nn">six</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> +<span class="kn">import</span> <span class="nn">math</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm</span> + +<div class="viewcode-block" id="astra_dict"><a class="viewcode-back" href="../../creators.html#astra.creators.astra_dict">[docs]</a><span class="k">def</span> <span class="nf">astra_dict</span><span class="p">(</span><span class="n">intype</span><span class="p">):</span> + <span class="sd">"""Creates a dict to use with the ASTRA Toolbox.</span> +<span class="sd"> </span> +<span class="sd"> :param intype: Type of the ASTRA object.</span> +<span class="sd"> :type intype: :class:`string`</span> +<span class="sd"> :returns: :class:`dict` -- An ASTRA dict of type ``intype``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'SIRT_CUDA2'</span><span class="p">:</span> + <span class="n">intype</span> <span class="o">=</span> <span class="s">'SIRT_CUDA'</span> + <span class="n">six</span><span class="o">.</span><span class="n">print_</span><span class="p">(</span><span class="s">'SIRT_CUDA2 has been deprecated. Use SIRT_CUDA instead.'</span><span class="p">)</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'FP_CUDA2'</span><span class="p">:</span> + <span class="n">intype</span> <span class="o">=</span> <span class="s">'FP_CUDA'</span> + <span class="n">six</span><span class="o">.</span><span class="n">print_</span><span class="p">(</span><span class="s">'FP_CUDA2 has been deprecated. Use FP_CUDA instead.'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="n">intype</span><span class="p">}</span> +</div> +<div class="viewcode-block" id="create_vol_geom"><a class="viewcode-back" href="../../creators.html#astra.creators.create_vol_geom">[docs]</a><span class="k">def</span> <span class="nf">create_vol_geom</span><span class="p">(</span><span class="o">*</span><span class="n">varargin</span><span class="p">):</span> + <span class="sd">"""Create a volume geometry structure.</span> + +<span class="sd">This method can be called in a number of ways:</span> + +<span class="sd">``create_vol_geom(N)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`N \\times N`.</span> + +<span class="sd">``create_vol_geom((M, N))``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`.</span> + +<span class="sd">``create_vol_geom(M, N)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`.</span> + +<span class="sd">``create_vol_geom(M, N, minx, maxx, miny, maxy)``:</span> +<span class="sd"> :returns: A 2D volume geometry of size :math:`M \\times N`, windowed as :math:`minx \\leq x \\leq maxx` and :math:`miny \\leq y \\leq maxy`.</span> + +<span class="sd">``create_vol_geom((M, N, Z))``:</span> +<span class="sd"> :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.</span> + +<span class="sd">``create_vol_geom(M, N, Z)``:</span> +<span class="sd"> :returns: A 3D volume geometry of size :math:`M \\times N \\times Z`.</span> + +<span class="sd">"""</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="p">{</span><span class="s">'option'</span><span class="p">:</span> <span class="p">{}}</span> + <span class="c"># astra_create_vol_geom(row_count)</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">int</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom([row_count col_count])</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom([row_count col_count slice_count])</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom(row_count, col_count)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">2</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">/</span> <span class="mf">2.</span> + <span class="c"># astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> + <span class="c"># astra_create_vol_geom(row_count, col_count, slice_count)</span> + <span class="k">elif</span> <span class="nb">len</span><span class="p">(</span><span class="n">varargin</span><span class="p">)</span> <span class="o">==</span> <span class="mi">3</span><span class="p">:</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">vol_geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span> <span class="o">=</span> <span class="n">varargin</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="k">return</span> <span class="n">vol_geom</span> + +</div> +<div class="viewcode-block" id="create_proj_geom"><a class="viewcode-back" href="../../creators.html#astra.creators.create_proj_geom">[docs]</a><span class="k">def</span> <span class="nf">create_proj_geom</span><span class="p">(</span><span class="n">intype</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""Create a projection geometry.</span> + +<span class="sd">This method can be called in a number of ways:</span> + +<span class="sd">``create_proj_geom('parallel', detector_spacing, det_count, angles)``:</span> + +<span class="sd">:param detector_spacing: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + + +<span class="sd">``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, source_det)``:</span> + +<span class="sd">:param det_width: Size of a detector pixel.</span> +<span class="sd">:type det_width: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param source_origin: Position of the source.</span> +<span class="sd">:param source_det: Position of the detector</span> +<span class="sd">:returns: A fan-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('fanflat_vec', det_count, V)``:</span> + +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A fan-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('parallel3d', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)``:</span> + +<span class="sd">:param detector_spacing_*: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing_*: :class:`float`</span> +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + +<span class="sd">``create_proj_geom('cone', detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)``:</span> + +<span class="sd">:param detector_spacing_*: Distance between two adjacent detector pixels.</span> +<span class="sd">:type detector_spacing_*: :class:`float`</span> +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param source_origin: Distance between point source and origin.</span> +<span class="sd">:type source_origin: :class:`float`</span> +<span class="sd">:param source_det: Distance between the detector and origin.</span> +<span class="sd">:type source_det: :class:`float`</span> +<span class="sd">:returns: A cone-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('cone_vec', det_row_count, det_col_count, V)``:</span> + +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A cone-beam projection geometry.</span> + +<span class="sd">``create_proj_geom('parallel3d_vec', det_row_count, det_col_count, V)``:</span> + +<span class="sd">:param det_row_count: Number of detector pixel rows.</span> +<span class="sd">:type det_row_count: :class:`int`</span> +<span class="sd">:param det_col_count: Number of detector pixel columns.</span> +<span class="sd">:type det_col_count: :class:`int`</span> +<span class="sd">:param V: Vector array.</span> +<span class="sd">:type V: :class:`numpy.ndarray`</span> +<span class="sd">:returns: A parallel projection geometry.</span> + +<span class="sd">``create_proj_geom('sparse_matrix', det_width, det_count, angles, matrix_id)``:</span> + +<span class="sd">:param det_width: Size of a detector pixel.</span> +<span class="sd">:type det_width: :class:`float`</span> +<span class="sd">:param det_count: Number of detector pixels.</span> +<span class="sd">:type det_count: :class:`int`</span> +<span class="sd">:param angles: Array of angles in radians.</span> +<span class="sd">:type angles: :class:`numpy.ndarray`</span> +<span class="sd">:param matrix_id: ID of the sparse matrix.</span> +<span class="sd">:type matrix_id: :class:`int`</span> +<span class="sd">:returns: A projection geometry based on a sparse matrix.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span> + <span class="s">'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'parallel'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, source_det)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'fanflat'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'DistanceOriginSource'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="s">'DistanceOriginDetector'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'fanflat_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">2</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(fanflat_vec, det_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">6</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx6 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span><span class="s">'fanflat_vec'</span><span class="p">,</span> <span class="s">'DetectorCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel3d'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">5</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(parallel3d, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span><span class="s">'parallel3d'</span><span class="p">,</span> <span class="s">'DetectorSpacingX'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorSpacingY'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="s">'ProjectionAngles'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">7</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(cone, detector_spacing_x, detector_spacing_y, det_row_count, det_col_count, angles, source_origin, source_det)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'cone'</span><span class="p">,</span><span class="s">'DetectorSpacingX'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorSpacingY'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="s">'ProjectionAngles'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">4</span><span class="p">],</span><span class="s">'DistanceOriginSource'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">5</span><span class="p">],</span><span class="s">'DistanceOriginDetector'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">6</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'cone_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(cone_vec, det_row_count, det_col_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">12</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx12 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'cone_vec'</span><span class="p">,</span><span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'parallel3d_vec'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">3</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'not enough variables: astra_create_proj_geom(parallel3d_vec, det_row_count, det_col_count, V)'</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="mi">12</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'V should be a Nx12 matrix, with N the number of projections'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'parallel3d_vec'</span><span class="p">,</span><span class="s">'DetectorRowCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="s">'DetectorColCount'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="s">'Vectors'</span><span class="p">:</span><span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">]}</span> + <span class="k">elif</span> <span class="n">intype</span> <span class="o">==</span> <span class="s">'sparse_matrix'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">args</span><span class="p">)</span> <span class="o"><</span> <span class="mi">4</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span> + <span class="s">'not enough variables: astra_create_proj_geom(sparse_matrix, det_width, det_count, angles, matrix_id)'</span><span class="p">)</span> + <span class="k">return</span> <span class="p">{</span><span class="s">'type'</span><span class="p">:</span> <span class="s">'sparse_matrix'</span><span class="p">,</span> <span class="s">'DetectorWidth'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="s">'DetectorCount'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="s">'ProjectionAngles'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">2</span><span class="p">],</span> <span class="s">'MatrixID'</span><span class="p">:</span> <span class="n">args</span><span class="p">[</span><span class="mi">3</span><span class="p">]}</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'Error: unknown type '</span> <span class="o">+</span> <span class="n">intype</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="create_backprojection"><a class="viewcode-back" href="../../creators.html#astra.creators.create_backprojection">[docs]</a><span class="k">def</span> <span class="nf">create_backprojection</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_id</span><span class="p">,</span> <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> + <span class="sd">"""Create a backprojection of a sinogram (2D).</span> + +<span class="sd">:param data: Sinogram data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_id: ID of the projector to use.</span> +<span class="sd">:type proj_id: :class:`int`</span> +<span class="sd">:param useCUDA: If ``True``, use CUDA for the calculation.</span> +<span class="sd">:type useCUDA: :class:`bool`</span> +<span class="sd">:param returnData: If False, only return the ID of the backprojection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</span> + +<span class="sd">"""</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">vol_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + + <span class="n">algString</span> <span class="o">=</span> <span class="s">'BP'</span> + <span class="k">if</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">algString</span> <span class="o">=</span> <span class="n">algString</span> <span class="o">+</span> <span class="s">'_CUDA'</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span> +</div> +<div class="viewcode-block" id="create_backprojection3d_gpu"><a class="viewcode-back" href="../../creators.html#astra.creators.create_backprojection3d_gpu">[docs]</a><span class="k">def</span> <span class="nf">create_backprojection3d_gpu</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> + <span class="sd">"""Create a backprojection of a sinogram (3D) using CUDA.</span> + +<span class="sd">:param data: Sinogram data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:param returnData: If False, only return the ID of the backprojection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data</span> + + <span class="n">vol_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="s">'BP3D_CUDA'</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span><span class="p">,</span> <span class="n">data3d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">vol_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">vol_id</span> + +</div> +<div class="viewcode-block" id="create_sino"><a class="viewcode-back" href="../../creators.html#astra.creators.create_sino">[docs]</a><span class="k">def</span> <span class="nf">create_sino</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_id</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">proj_geom</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">vol_geom</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> + <span class="n">useCUDA</span><span class="o">=</span><span class="bp">False</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">gpuIndex</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a forward projection of an image (2D).</span> + +<span class="sd"> :param data: Image data or ID.</span> +<span class="sd"> :type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd"> :param proj_id: ID of the projector to use.</span> +<span class="sd"> :type proj_id: :class:`int`</span> +<span class="sd"> :param proj_geom: Projection geometry.</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> :param vol_geom: Volume geometry.</span> +<span class="sd"> :type vol_geom: :class:`dict`</span> +<span class="sd"> :param useCUDA: If ``True``, use CUDA for the calculation.</span> +<span class="sd"> :type useCUDA: :class:`bool`</span> +<span class="sd"> :param returnData: If False, only return the ID of the forward projection.</span> +<span class="sd"> :type returnData: :class:`bool`</span> +<span class="sd"> :param gpuIndex: Optional GPU index.</span> +<span class="sd"> :type gpuIndex: :class:`int`</span> +<span class="sd"> :returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`)</span> + +<span class="sd"> If ``returnData=False``, returns the ID of the forward</span> +<span class="sd"> projection. Otherwise, returns a tuple containing the ID of the</span> +<span class="sd"> forward projection and the forward projection itself, in that</span> +<span class="sd"> order.</span> + +<span class="sd"> The geometry of setup is defined by ``proj_id`` or with</span> +<span class="sd"> ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then</span> +<span class="sd"> ``proj_geom`` and ``vol_geom`` must be None and vice versa.</span> +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">proj_id</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">elif</span> <span class="n">proj_geom</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span> <span class="ow">and</span> <span class="n">vol_geom</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="c"># We need more parameters to create projector.</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span> + <span class="sd">"""A ``proj_id`` is needed when CUDA is not used."""</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">"""The geometry setup is not defined.</span> +<span class="s"> The geometry of setup is defined by ``proj_id`` or with</span> +<span class="s"> ``proj_geom`` and ``vol_geom``. If ``proj_id`` is given, then</span> +<span class="s"> ``proj_geom`` and ``vol_geom`` must be None and vice versa."""</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">algString</span> <span class="o">=</span> <span class="s">'FP'</span> + <span class="k">if</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">algString</span> <span class="o">=</span> <span class="n">algString</span> <span class="o">+</span> <span class="s">'_CUDA'</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">useCUDA</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="k">if</span> <span class="n">gpuIndex</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span><span class="s">'GPUindex'</span><span class="p">:</span> <span class="n">gpuIndex</span><span class="p">}</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">volume_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">volume_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span> + + +</div> +<div class="viewcode-block" id="create_sino3d_gpu"><a class="viewcode-back" href="../../creators.html#astra.creators.create_sino3d_gpu">[docs]</a><span class="k">def</span> <span class="nf">create_sino3d_gpu</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">gpuIndex</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a forward projection of an image (3D).</span> + +<span class="sd">:param data: Image data or ID.</span> +<span class="sd">:type data: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:param returnData: If False, only return the ID of the forward projection.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:param gpuIndex: Optional GPU index.</span> +<span class="sd">:type gpuIndex: :class:`int`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.</span> + +<span class="sd">"""</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">volume_id</span> <span class="o">=</span> <span class="n">data</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data3d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">algString</span> <span class="o">=</span> <span class="s">'FP3D_CUDA'</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">algString</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">gpuIndex</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span><span class="o">=</span><span class="p">{</span><span class="s">'GPUindex'</span><span class="p">:</span><span class="n">gpuIndex</span><span class="p">}</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">volume_id</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">data</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">volume_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span><span class="p">,</span> <span class="n">data3d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">sino_id</span> + +</div> +<div class="viewcode-block" id="create_reconstruction"><a class="viewcode-back" href="../../creators.html#astra.creators.create_reconstruction">[docs]</a><span class="k">def</span> <span class="nf">create_reconstruction</span><span class="p">(</span><span class="n">rec_type</span><span class="p">,</span> <span class="n">proj_id</span><span class="p">,</span> <span class="n">sinogram</span><span class="p">,</span> <span class="n">iterations</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">use_mask</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([]),</span> <span class="n">use_minc</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">minc</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">use_maxc</span><span class="o">=</span><span class="s">'no'</span><span class="p">,</span> <span class="n">maxc</span><span class="o">=</span><span class="mi">255</span><span class="p">,</span> <span class="n">returnData</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">filterType</span><span class="o">=</span><span class="bp">None</span><span class="p">,</span> <span class="n">filterData</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a reconstruction of a sinogram (2D).</span> + +<span class="sd">:param rec_type: Name of the reconstruction algorithm.</span> +<span class="sd">:type rec_type: :class:`string`</span> +<span class="sd">:param proj_id: ID of the projector to use.</span> +<span class="sd">:type proj_id: :class:`int`</span> +<span class="sd">:param sinogram: Sinogram data or ID.</span> +<span class="sd">:type sinogram: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param iterations: Number of iterations to run.</span> +<span class="sd">:type iterations: :class:`int`</span> +<span class="sd">:param use_mask: Whether to use a mask.</span> +<span class="sd">:type use_mask: ``'yes'`` or ``'no'``</span> +<span class="sd">:param mask: Mask data or ID</span> +<span class="sd">:type mask: :class:`numpy.ndarray` or :class:`int`</span> +<span class="sd">:param use_minc: Whether to force a minimum value on the reconstruction pixels.</span> +<span class="sd">:type use_minc: ``'yes'`` or ``'no'``</span> +<span class="sd">:param minc: Minimum value to use.</span> +<span class="sd">:type minc: :class:`float`</span> +<span class="sd">:param use_maxc: Whether to force a maximum value on the reconstruction pixels.</span> +<span class="sd">:type use_maxc: ``'yes'`` or ``'no'``</span> +<span class="sd">:param maxc: Maximum value to use.</span> +<span class="sd">:type maxc: :class:`float`</span> +<span class="sd">:param returnData: If False, only return the ID of the reconstruction.</span> +<span class="sd">:type returnData: :class:`bool`</span> +<span class="sd">:param filterType: Which type of filter to use for filter-based methods.</span> +<span class="sd">:type filterType: :class:`string`</span> +<span class="sd">:param filterData: Optional filter data for filter-based methods.</span> +<span class="sd">:type filterData: :class:`numpy.ndarray`</span> +<span class="sd">:returns: :class:`int` or (:class:`int`, :class:`numpy.ndarray`) -- If ``returnData=False``, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.</span> + +<span class="sd">"""</span> + <span class="n">proj_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">sinogram</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sino_id</span> <span class="o">=</span> <span class="n">sinogram</span> + <span class="n">vol_geom</span> <span class="o">=</span> <span class="n">projector</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">proj_id</span><span class="p">)</span> + <span class="n">recon_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">rec_type</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="s">'CUDA'</span> <span class="ow">in</span> <span class="n">rec_type</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectorId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">sino_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ReconstructionDataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">recon_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span> + <span class="k">if</span> <span class="n">use_mask</span> <span class="o">==</span> <span class="s">'yes'</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">mask</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">mask_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-vol'</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">,</span> <span class="n">mask</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">mask_id</span> <span class="o">=</span> <span class="n">mask</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'ReconstructionMaskId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mask_id</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterType</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'FilterType'</span><span class="p">]</span> <span class="o">=</span> <span class="n">filterType</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterData</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filterData</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">nexpow</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span> + <span class="nb">pow</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="n">math</span><span class="o">.</span><span class="n">ceil</span><span class="p">(</span><span class="n">math</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">],</span> <span class="mi">2</span><span class="p">))))</span> + <span class="n">filtSize</span> <span class="o">=</span> <span class="n">nexpow</span> <span class="o">/</span> <span class="mi">2</span> <span class="o">+</span> <span class="mi">1</span> + <span class="n">filt_proj_geom</span> <span class="o">=</span> <span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'parallel'</span><span class="p">,</span> <span class="mf">1.0</span><span class="p">,</span> <span class="n">filtSize</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">])</span> + <span class="n">filt_id</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="s">'-sino'</span><span class="p">,</span> <span class="n">filt_proj_geom</span><span class="p">,</span> <span class="n">filterData</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">filt_id</span> <span class="o">=</span> <span class="n">filterData</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'FilterSinogramId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">filt_id</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'UseMinConstraint'</span><span class="p">]</span> <span class="o">=</span> <span class="n">use_minc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'MinConstraintValue'</span><span class="p">]</span> <span class="o">=</span> <span class="n">minc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'UseMaxConstraint'</span><span class="p">]</span> <span class="o">=</span> <span class="n">use_maxc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'MaxConstraintValue'</span><span class="p">]</span> <span class="o">=</span> <span class="n">maxc</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'options'</span><span class="p">][</span><span class="s">'ProjectionOrder'</span><span class="p">]</span> <span class="o">=</span> <span class="s">'random'</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">,</span> <span class="n">iterations</span><span class="p">)</span> + + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">sino_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">use_mask</span> <span class="o">==</span> <span class="s">'yes'</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">mask</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">mask_id</span><span class="p">)</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">filterData</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">filterData</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">filt_id</span><span class="p">)</span> + <span class="k">if</span> <span class="n">returnData</span><span class="p">:</span> + <span class="k">return</span> <span class="n">recon_id</span><span class="p">,</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">recon_id</span><span class="p">)</span> + <span class="k">else</span><span class="p">:</span> + <span class="k">return</span> <span class="n">recon_id</span> + +</div> +<div class="viewcode-block" id="create_projector"><a class="viewcode-back" href="../../creators.html#astra.creators.create_projector">[docs]</a><span class="k">def</span> <span class="nf">create_projector</span><span class="p">(</span><span class="n">proj_type</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">,</span> <span class="n">vol_geom</span><span class="p">):</span> + <span class="sd">"""Create a 2D projector.</span> + +<span class="sd">:param proj_type: Projector type, such as ``'line'``, ``'linear'``, ...</span> +<span class="sd">:type proj_type: :class:`string`</span> +<span class="sd">:param proj_geom: Projection geometry.</span> +<span class="sd">:type proj_geom: :class:`dict`</span> +<span class="sd">:param vol_geom: Volume geometry.</span> +<span class="sd">:type vol_geom: :class:`dict`</span> +<span class="sd">:returns: :class:`int` -- The ID of the projector.</span> + +<span class="sd">"""</span> + <span class="k">if</span> <span class="n">proj_type</span> <span class="o">==</span> <span class="s">'blob'</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s">'Blob type not yet implemented'</span><span class="p">)</span> + <span class="n">cfg</span> <span class="o">=</span> <span class="n">astra_dict</span><span class="p">(</span><span class="n">proj_type</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'ProjectionGeometry'</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'VolumeGeometry'</span><span class="p">]</span> <span class="o">=</span> <span class="n">vol_geom</span> + <span class="k">return</span> <span class="n">projector</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data2d.html b/python/docSRC/_build/html/_modules/astra/data2d.html new file mode 100644 index 0000000..d77cddd --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data2d.html @@ -0,0 +1,225 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.data2d — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.data2d</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d_c</span> <span class="k">as</span> <span class="n">d</span> + +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../data2d.html#astra.data2d.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all 2D data objects."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../data2d.html#astra.data2d.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../data2d.html#astra.data2d.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span> <span class="n">geometry</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param datatype: Data object type, '-vol' or '-sino'.</span> +<span class="sd"> :type datatype: :class:`string`</span> +<span class="sd"> :param geometry: Volume or projection geometry.</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param data: Data to fill the constructed object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../data2d.html#astra.data2d.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing 2D object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">data</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get_geometry"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_geometry">[docs]</a><span class="k">def</span> <span class="nf">get_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get the geometry of a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- The geometry of object with ID ``i``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="change_geometry"><a class="viewcode-back" href="../../data2d.html#astra.data2d.change_geometry">[docs]</a><span class="k">def</span> <span class="nf">change_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">geom</span><span class="p">):</span> + <span class="sd">"""Change the geometry of a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param geom: new geometry.</span> +<span class="sd"> :type geom: :class:`dict`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">change_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">geom</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_shared"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_shared">[docs]</a><span class="k">def</span> <span class="nf">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object with memory shared between the ASTRA toolbox and numpy array.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="get_single"><a class="viewcode-back" href="../../data2d.html#astra.data2d.get_single">[docs]</a><span class="k">def</span> <span class="nf">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 2D object in single precision.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../data2d.html#astra.data2d.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on 2D objects in memory."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/data3d.html b/python/docSRC/_build/html/_modules/astra/data3d.html new file mode 100644 index 0000000..674d6d1 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/data3d.html @@ -0,0 +1,213 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.data3d — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.data3d</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d_c</span> <span class="k">as</span> <span class="n">d</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../data3d.html#astra.data3d.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Create a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param datatype: Data object type, '-vol' or '-sino'.</span> +<span class="sd"> :type datatype: :class:`string`</span> +<span class="sd"> :param geometry: Volume or projection geometry.</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param data: Data to fill the constructed object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">datatype</span><span class="p">,</span><span class="n">geometry</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_shared"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get_shared">[docs]</a><span class="k">def</span> <span class="nf">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object with memory shared between the ASTRA toolbox and numpy array.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">get_shared</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_single"><a class="viewcode-back" href="../../data3d.html#astra.data3d.get_single">[docs]</a><span class="k">def</span> <span class="nf">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a 3D object in single precision.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">g</span><span class="o">.</span><span class="n">get_single</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../data3d.html#astra.data3d.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing 3D object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with, either a scalar or array.</span> +<span class="sd"> :type data: :class:`float` or :class:`numpy.ndarray`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="dimensions"><a class="viewcode-back" href="../../data3d.html#astra.data3d.dimensions">[docs]</a><span class="k">def</span> <span class="nf">dimensions</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get dimensions of a 3D object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`tuple` -- dimensions of object with ID ``i``.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">dimensions</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../data3d.html#astra.data3d.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../data3d.html#astra.data3d.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all 3D data objects."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../data3d.html#astra.data3d.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on 3D objects in memory."""</span> + <span class="k">return</span> <span class="n">d</span><span class="o">.</span><span class="n">info</span><span class="p">()</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/functions.html b/python/docSRC/_build/html/_modules/astra/functions.html new file mode 100644 index 0000000..336431f --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/functions.html @@ -0,0 +1,375 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.functions — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.functions</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c"># Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c"># Author: Daniel M. Pelt</span> +<span class="c"># Contact: D.M.Pelt@cwi.nl</span> +<span class="c"># Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c"># This file is part of the Python interface to the</span> +<span class="c"># All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c"># The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c"># it under the terms of the GNU General Public License as published by</span> +<span class="c"># the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c"># The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c"># GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c"># You should have received a copy of the GNU General Public License</span> +<span class="c"># along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="sd">"""Additional functions for PyAstraToolbox.</span> + +<span class="sd">.. moduleauthor:: Daniel M. Pelt <D.M.Pelt@cwi.nl></span> + + +<span class="sd">"""</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">creators</span> <span class="k">as</span> <span class="n">ac</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> +<span class="kn">from</span> <span class="nn">six.moves</span> <span class="kn">import</span> <span class="nb">range</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm</span> + + + +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../functions.html#astra.functions.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clears all used memory of the ASTRA Toolbox.</span> + +<span class="sd"> .. note::</span> +<span class="sd"> This is irreversible.</span> + +<span class="sd"> """</span> + <span class="n">data2d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">data3d</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">projector</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="data_op"><a class="viewcode-back" href="../../functions.html#astra.functions.data_op">[docs]</a><span class="k">def</span> <span class="nf">data_op</span><span class="p">(</span><span class="n">op</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">scalar</span><span class="p">,</span> <span class="n">gpu_core</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Perform data operation on data.</span> + +<span class="sd"> :param op: Operation to perform.</span> +<span class="sd"> :param data: Data to perform operation on.</span> +<span class="sd"> :param scalar: Scalar argument to data operation.</span> +<span class="sd"> :param gpu_core: GPU core to perform operation on.</span> +<span class="sd"> :param mask: Optional mask.</span> + +<span class="sd"> """</span> + + <span class="n">cfg</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">astra_dict</span><span class="p">(</span><span class="s">'DataOperation_CUDA'</span><span class="p">)</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'Operation'</span><span class="p">]</span> <span class="o">=</span> <span class="n">op</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'Scalar'</span><span class="p">]</span> <span class="o">=</span> <span class="n">scalar</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'DataId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">data</span> + <span class="k">if</span> <span class="ow">not</span> <span class="n">mask</span> <span class="o">==</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'MaskId'</span><span class="p">]</span> <span class="o">=</span> <span class="n">mask</span> + <span class="n">cfg</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'GPUindex'</span><span class="p">]</span> <span class="o">=</span> <span class="n">gpu_core</span> + <span class="n">alg_id</span> <span class="o">=</span> <span class="n">algorithm</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">cfg</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + <span class="n">algorithm</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">alg_id</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="add_noise_to_sino"><a class="viewcode-back" href="../../functions.html#astra.functions.add_noise_to_sino">[docs]</a><span class="k">def</span> <span class="nf">add_noise_to_sino</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">I0</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Adds Poisson noise to a sinogram.</span> + +<span class="sd"> :param sinogram_in: Sinogram to add noise to.</span> +<span class="sd"> :type sinogram_in: :class:`numpy.ndarray`</span> +<span class="sd"> :param I0: Background intensity. Lower values lead to higher noise.</span> +<span class="sd"> :type I0: :class:`float`</span> +<span class="sd"> :returns: :class:`numpy.ndarray` -- the sinogram with added noise.</span> + +<span class="sd"> """</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">seed</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">curstate</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">get_state</span><span class="p">()</span> + <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">seed</span><span class="p">(</span><span class="n">seed</span><span class="p">)</span> + + <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">sinogramRaw</span> <span class="o">=</span> <span class="n">sinogram_in</span> + <span class="k">else</span><span class="p">:</span> + <span class="n">sinogramRaw</span> <span class="o">=</span> <span class="n">data2d</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">)</span> + <span class="n">max_sinogramRaw</span> <span class="o">=</span> <span class="n">sinogramRaw</span><span class="o">.</span><span class="n">max</span><span class="p">()</span> + <span class="n">sinogramRawScaled</span> <span class="o">=</span> <span class="n">sinogramRaw</span> <span class="o">/</span> <span class="n">max_sinogramRaw</span> + <span class="c"># to detector count</span> + <span class="n">sinogramCT</span> <span class="o">=</span> <span class="n">I0</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="o">-</span><span class="n">sinogramRawScaled</span><span class="p">)</span> + <span class="c"># add poison noise</span> + <span class="n">sinogramCT_C</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros_like</span><span class="p">(</span><span class="n">sinogramCT</span><span class="p">)</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">sinogramCT_C</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]):</span> + <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">sinogramCT_C</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]):</span> + <span class="n">sinogramCT_C</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">poisson</span><span class="p">(</span><span class="n">sinogramCT</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">])</span> + <span class="c"># to density</span> + <span class="n">sinogramCT_D</span> <span class="o">=</span> <span class="n">sinogramCT_C</span> <span class="o">/</span> <span class="n">I0</span> + <span class="n">sinogram_out</span> <span class="o">=</span> <span class="o">-</span><span class="n">max_sinogramRaw</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">sinogramCT_D</span><span class="p">)</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">):</span> + <span class="n">at</span><span class="o">.</span><span class="n">data2d</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">sinogram_in</span><span class="p">,</span> <span class="n">sinogram_out</span><span class="p">)</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">seed</span><span class="o">==</span><span class="bp">None</span><span class="p">:</span> + <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">set_state</span><span class="p">(</span><span class="n">curstate</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">sinogram_out</span> +</div> +<div class="viewcode-block" id="move_vol_geom"><a class="viewcode-back" href="../../functions.html#astra.functions.move_vol_geom">[docs]</a><span class="k">def</span> <span class="nf">move_vol_geom</span><span class="p">(</span><span class="n">geom</span><span class="p">,</span> <span class="n">pos</span><span class="p">,</span> <span class="n">is_relative</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span> + <span class="sd">"""Moves center of volume geometry to new position.</span> + +<span class="sd"> :param geom: Input volume geometry</span> +<span class="sd"> :type geom: :class:`dict`</span> +<span class="sd"> :param pos: Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])</span> +<span class="sd"> :type pos: :class:`tuple`</span> +<span class="sd"> :param is_relative: Whether new position is relative to the old position</span> +<span class="sd"> :type is_relative: :class:`bool`</span> +<span class="sd"> :returns: :class:`dict` -- Volume geometry with the new center</span> +<span class="sd"> """</span> + + <span class="n">ret_geom</span> <span class="o">=</span> <span class="n">geom</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">]</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> + + <span class="k">if</span> <span class="ow">not</span> <span class="n">is_relative</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span><span class="o">></span><span class="mi">2</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">=</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">]</span><span class="o">/</span><span class="mf">2.</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinX'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxX'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinY'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxY'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> + <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">pos</span><span class="p">)</span><span class="o">></span><span class="mi">2</span><span class="p">:</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMinZ'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="n">ret_geom</span><span class="p">[</span><span class="s">'option'</span><span class="p">][</span><span class="s">'WindowMaxZ'</span><span class="p">]</span> <span class="o">+=</span> <span class="n">pos</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> + <span class="k">return</span> <span class="n">ret_geom</span> + +</div> +<div class="viewcode-block" id="geom_size"><a class="viewcode-back" href="../../functions.html#astra.functions.geom_size">[docs]</a><span class="k">def</span> <span class="nf">geom_size</span><span class="p">(</span><span class="n">geom</span><span class="p">,</span> <span class="n">dim</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span> + <span class="sd">"""Returns the size of a volume or sinogram, based on the projection or volume geometry.</span> + +<span class="sd"> :param geom: Geometry to calculate size from</span> +<span class="sd"> :type geometry: :class:`dict`</span> +<span class="sd"> :param dim: Optional axis index to return</span> +<span class="sd"> :type dim: :class:`int`</span> +<span class="sd"> """</span> + + <span class="k">if</span> <span class="s">'GridSliceCount'</span> <span class="ow">in</span> <span class="n">geom</span><span class="p">:</span> + <span class="c"># 3D Volume geometry?</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridSliceCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span> + <span class="s">'GridRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="s">'GridColCount'</span> <span class="ow">in</span> <span class="n">geom</span><span class="p">:</span> + <span class="c"># 2D Volume geometry?</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'GridRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'GridColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]),</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="nb">len</span><span class="p">(</span> + <span class="n">geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]),</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat_vec'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'Vectors'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">])</span> + <span class="k">elif</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d_vec'</span> <span class="ow">or</span> <span class="n">geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone_vec'</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="p">(</span><span class="n">geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span> + <span class="s">'Vectors'</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">])</span> + + <span class="k">if</span> <span class="n">dim</span> <span class="o">!=</span> <span class="bp">None</span><span class="p">:</span> + <span class="n">s</span> <span class="o">=</span> <span class="n">s</span><span class="p">[</span><span class="n">dim</span><span class="p">]</span> + + <span class="k">return</span> <span class="n">s</span> + +</div> +<div class="viewcode-block" id="geom_2vec"><a class="viewcode-back" href="../../functions.html#astra.functions.geom_2vec">[docs]</a><span class="k">def</span> <span class="nf">geom_2vec</span><span class="p">(</span><span class="n">proj_geom</span><span class="p">):</span> + <span class="sd">"""Returns a vector-based projection geometry from a basic projection geometry.</span> + +<span class="sd"> :param proj_geom: Projection geometry to convert</span> +<span class="sd"> :type proj_geom: :class:`dict`</span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'fanflat'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">6</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + + <span class="c"># source</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + + <span class="c"># vector from detector pixel 0 to 1</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorWidth'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorWidth'</span><span class="p">]</span> + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'fanflat_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="k">elif</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'cone'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">12</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + <span class="c"># source</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginSource'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DistanceOriginDetector'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (0,1)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (1,0)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingY'</span><span class="p">]</span> + + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'cone_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="c"># PARALLEL</span> + <span class="k">elif</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">]</span> <span class="o">==</span> <span class="s">'parallel3d'</span><span class="p">:</span> + <span class="n">angles</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'ProjectionAngles'</span><span class="p">]</span> + <span class="n">vectors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">),</span> <span class="mi">12</span><span class="p">))</span> + <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">angles</span><span class="p">)):</span> + + <span class="c"># ray direction</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># center of detector</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">4</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">5</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (0,1)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">6</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">cos</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">7</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sin</span><span class="p">(</span><span class="n">angles</span><span class="p">[</span><span class="n">i</span><span class="p">])</span> <span class="o">*</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingX'</span><span class="p">]</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">8</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + + <span class="c"># vector from detector pixel (0,0) to (1,0)</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">9</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">10</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span> + <span class="n">vectors</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="mi">11</span><span class="p">]</span> <span class="o">=</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorSpacingY'</span><span class="p">]</span> + + <span class="n">proj_geom_out</span> <span class="o">=</span> <span class="n">ac</span><span class="o">.</span><span class="n">create_proj_geom</span><span class="p">(</span> + <span class="s">'parallel3d_vec'</span><span class="p">,</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorRowCount'</span><span class="p">],</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'DetectorColCount'</span><span class="p">],</span> <span class="n">vectors</span><span class="p">)</span> + + <span class="k">else</span><span class="p">:</span> + <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span> + <span class="s">'No suitable vector geometry found for type: '</span> <span class="o">+</span> <span class="n">proj_geom</span><span class="p">[</span><span class="s">'type'</span><span class="p">])</span> + <span class="k">return</span> <span class="n">proj_geom_out</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p 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\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matlab.html b/python/docSRC/_build/html/_modules/astra/matlab.html new file mode 100644 index 0000000..b58ff06 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matlab.html @@ -0,0 +1,217 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.matlab — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.matlab</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="sd">"""This module implements a MATLAB-like interface to the ASTRA Toolbox.</span> + +<span class="sd">Note that all functions are called with a :class:`string` as the first</span> +<span class="sd">argument, specifying the operation to perform. This un-pythonic way</span> +<span class="sd">is used to make transitioning from MATLAB code to Python code easier, as</span> +<span class="sd">the MATLAB interface uses the same type of method calling.</span> + +<span class="sd">After an initial ``import astra``, these functions can be accessed in the</span> +<span class="sd">``astra.m`` module.</span> + +<span class="sd">"""</span> + +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">astra_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data2d_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">data3d_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">algorithm_c</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">matrix_c</span> +<span class="kn">import</span> <span class="nn">numpy</span> <span class="kn">as</span> <span class="nn">np</span> + + +<div class="viewcode-block" id="astra"><a class="viewcode-back" href="../../matlab.html#astra.matlab.astra">[docs]</a><span class="k">def</span> <span class="nf">astra</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.astra` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.astra('use_cuda')`` -- Check if CUDA is enabled.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">astra_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="data2d"><a class="viewcode-back" href="../../matlab.html#astra.matlab.data2d">[docs]</a><span class="k">def</span> <span class="nf">data2d</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.data2d` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.data2d('create',type,geometry,data)`` -- Create a 2D object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">data2d_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="data3d"><a class="viewcode-back" href="../../matlab.html#astra.matlab.data3d">[docs]</a><span class="k">def</span> <span class="nf">data3d</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.data3d` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.data3d('get',i)`` -- Get 3D object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">data3d_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="projector"><a class="viewcode-back" href="../../matlab.html#astra.matlab.projector">[docs]</a><span class="k">def</span> <span class="nf">projector</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.projector` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.projector('volume_geometry',i)`` -- Get volume geometry.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">projector_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="matrix"><a class="viewcode-back" href="../../matlab.html#astra.matlab.matrix">[docs]</a><span class="k">def</span> <span class="nf">matrix</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.matrix` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.matrix('delete',i)`` -- Delete a matrix.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">matrix_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="algorithm"><a class="viewcode-back" href="../../matlab.html#astra.matlab.algorithm">[docs]</a><span class="k">def</span> <span class="nf">algorithm</span><span class="p">(</span><span class="n">command</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">):</span> + <span class="sd">"""MATLAB-like interface to the :mod:`astra.algorithm` module</span> +<span class="sd"> </span> +<span class="sd"> For example:</span> +<span class="sd"> </span> +<span class="sd"> ``astra.m.algorithm('run',i,1000)`` -- Run an algorithm with 1000 iterations.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">if</span> <span class="n">command</span> <span class="o">==</span> <span class="s">'iterate'</span><span class="p">:</span> + <span class="n">command</span> <span class="o">=</span> <span class="s">'run'</span> + <span class="k">return</span> <span class="nb">getattr</span><span class="p">(</span><span class="n">algorithm_c</span><span class="p">,</span> <span class="n">command</span><span class="p">)(</span><span class="o">*</span><span class="n">args</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/matrix.html b/python/docSRC/_build/html/_modules/astra/matrix.html new file mode 100644 index 0000000..5f75455 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/matrix.html @@ -0,0 +1,191 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.matrix — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.matrix</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">matrix_c</span> <span class="k">as</span> <span class="n">m</span> + +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../matrix.html#astra.matrix.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../matrix.html#astra.matrix.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all matrix objects."""</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../matrix.html#astra.matrix.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Create matrix object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param data: Data to fill the created object with.</span> +<span class="sd"> :type data: :class:`scipy.sparse.csr_matrix`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">data</span><span class="p">)</span> + + </div> +<div class="viewcode-block" id="store"><a class="viewcode-back" href="../../matrix.html#astra.matrix.store">[docs]</a><span class="k">def</span> <span class="nf">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">):</span> + <span class="sd">"""Fill existing matrix object with data.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to fill.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :param data: Data to fill the object with.</span> +<span class="sd"> :type data: :class:`scipy.sparse.csr_matrix`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">store</span><span class="p">(</span><span class="n">i</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="get_size"><a class="viewcode-back" href="../../matrix.html#astra.matrix.get_size">[docs]</a><span class="k">def</span> <span class="nf">get_size</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get matrix dimensions.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`tuple` -- matrix dimensions.</span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">get_size</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + </div> +<div class="viewcode-block" id="get"><a class="viewcode-back" href="../../matrix.html#astra.matrix.get">[docs]</a><span class="k">def</span> <span class="nf">get</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get a matrix object.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of object to get.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`scipy.sparse.csr_matrix` -- The object data.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../matrix.html#astra.matrix.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on matrix objects in memory."""</span> + <span class="k">return</span> <span class="n">m</span><span class="o">.</span><span class="n">info</span><span class="p">()</span> + + </div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/astra/projector.html b/python/docSRC/_build/html/_modules/astra/projector.html new file mode 100644 index 0000000..5982b54 --- /dev/null +++ b/python/docSRC/_build/html/_modules/astra/projector.html @@ -0,0 +1,205 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>astra.projector — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../../_static/jquery.js"></script> + <script type="text/javascript" src="../../_static/underscore.js"></script> + <script type="text/javascript" src="../../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../../index.html" /> + <link rel="up" title="Module code" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" accesskey="U">Module code</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>Source code for astra.projector</h1><div class="highlight"><pre> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="c">#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam</span> +<span class="c">#</span> +<span class="c">#Author: Daniel M. Pelt</span> +<span class="c">#Contact: D.M.Pelt@cwi.nl</span> +<span class="c">#Website: http://dmpelt.github.io/pyastratoolbox/</span> +<span class="c">#</span> +<span class="c">#</span> +<span class="c">#This file is part of the Python interface to the</span> +<span class="c">#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify</span> +<span class="c">#it under the terms of the GNU General Public License as published by</span> +<span class="c">#the Free Software Foundation, either version 3 of the License, or</span> +<span class="c">#(at your option) any later version.</span> +<span class="c">#</span> +<span class="c">#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,</span> +<span class="c">#but WITHOUT ANY WARRANTY; without even the implied warranty of</span> +<span class="c">#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span> +<span class="c">#GNU General Public License for more details.</span> +<span class="c">#</span> +<span class="c">#You should have received a copy of the GNU General Public License</span> +<span class="c">#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.</span> +<span class="c">#</span> +<span class="c">#-----------------------------------------------------------------------</span> +<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">projector_c</span> <span class="k">as</span> <span class="n">p</span> + +<div class="viewcode-block" id="create"><a class="viewcode-back" href="../../projector.html#astra.projector.create">[docs]</a><span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="n">config</span><span class="p">):</span> + <span class="sd">"""Create projector object.</span> +<span class="sd"> </span> +<span class="sd"> :param config: Projector options.</span> +<span class="sd"> :type config: :class:`dict`</span> +<span class="sd"> :returns: :class:`int` -- the ID of the constructed object.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">config</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="delete"><a class="viewcode-back" href="../../projector.html#astra.projector.delete">[docs]</a><span class="k">def</span> <span class="nf">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">):</span> + <span class="sd">"""Delete a projector object.</span> +<span class="sd"> </span> +<span class="sd"> :param ids: ID or list of ID's to delete.</span> +<span class="sd"> :type ids: :class:`int` or :class:`list`</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">ids</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="clear"><a class="viewcode-back" href="../../projector.html#astra.projector.clear">[docs]</a><span class="k">def</span> <span class="nf">clear</span><span class="p">():</span> + <span class="sd">"""Clear all projector objects."""</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">clear</span><span class="p">()</span> + +</div> +<div class="viewcode-block" id="info"><a class="viewcode-back" href="../../projector.html#astra.projector.info">[docs]</a><span class="k">def</span> <span class="nf">info</span><span class="p">():</span> + <span class="sd">"""Print info on projector objects in memory."""</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">info</span><span class="p">()</span> +</div> +<div class="viewcode-block" id="projection_geometry"><a class="viewcode-back" href="../../projector.html#astra.projector.projection_geometry">[docs]</a><span class="k">def</span> <span class="nf">projection_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get projection geometry of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- projection geometry</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">projection_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="volume_geometry"><a class="viewcode-back" href="../../projector.html#astra.projector.volume_geometry">[docs]</a><span class="k">def</span> <span class="nf">volume_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get volume geometry of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`dict` -- volume geometry</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">volume_geometry</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="weights_single_ray"><a class="viewcode-back" href="../../projector.html#astra.projector.weights_single_ray">[docs]</a><span class="k">def</span> <span class="nf">weights_single_ray</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">,</span> <span class="n">detector_index</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">weights_single_ray</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">,</span> <span class="n">detector_index</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="weights_projection"><a class="viewcode-back" href="../../projector.html#astra.projector.weights_projection">[docs]</a><span class="k">def</span> <span class="nf">weights_projection</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">weights_projection</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">projection_index</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="splat"><a class="viewcode-back" href="../../projector.html#astra.projector.splat">[docs]</a><span class="k">def</span> <span class="nf">splat</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">row</span><span class="p">,</span> <span class="n">col</span><span class="p">):</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">splat</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">row</span><span class="p">,</span> <span class="n">col</span><span class="p">)</span> + +</div> +<div class="viewcode-block" id="matrix"><a class="viewcode-back" href="../../projector.html#astra.projector.matrix">[docs]</a><span class="k">def</span> <span class="nf">matrix</span><span class="p">(</span><span class="n">i</span><span class="p">):</span> + <span class="sd">"""Get sparse matrix of a projector.</span> +<span class="sd"> </span> +<span class="sd"> :param i: ID of projector.</span> +<span class="sd"> :type i: :class:`int`</span> +<span class="sd"> :returns: :class:`int` -- ID of sparse matrix.</span> +<span class="sd"> </span> +<span class="sd"> """</span> + <span class="k">return</span> <span class="n">p</span><span class="o">.</span><span class="n">matrix</span><span class="p">(</span><span class="n">i</span><span class="p">)</span></div> +</pre></div> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + <li><a href="../index.html" >Module code</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_modules/index.html b/python/docSRC/_build/html/_modules/index.html new file mode 100644 index 0000000..a844d93 --- /dev/null +++ b/python/docSRC/_build/html/_modules/index.html @@ -0,0 +1,112 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Overview: module code — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="../_static/default.css" type="text/css" /> + <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: '../', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="../_static/jquery.js"></script> + <script type="text/javascript" src="../_static/underscore.js"></script> + <script type="text/javascript" src="../_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="../index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <h1>All modules for which code is available</h1> +<ul><li><a href="astra/ASTRAProjector.html">astra.ASTRAProjector</a></li> +<li><a href="astra/algorithm.html">astra.algorithm</a></li> +<li><a href="astra/astra.html">astra.astra</a></li> +<li><a href="astra/creators.html">astra.creators</a></li> +<li><a href="astra/data2d.html">astra.data2d</a></li> +<li><a href="astra/data3d.html">astra.data3d</a></li> +<li><a href="astra/functions.html">astra.functions</a></li> +<li><a href="astra/matlab.html">astra.matlab</a></li> +<li><a href="astra/matrix.html">astra.matrix</a></li> +<li><a href="astra/projector.html">astra.projector</a></li> +</ul> + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="../search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="../genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="../py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="../index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/_sources/ASTRAProjector.txt b/python/docSRC/_build/html/_sources/ASTRAProjector.txt new file mode 100644 index 0000000..1c267e3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/ASTRAProjector.txt @@ -0,0 +1,8 @@ +Helper class: the :mod:`ASTRAProjector` module +============================================== + +.. automodule:: astra.ASTRAProjector + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/algorithm.txt b/python/docSRC/_build/html/_sources/algorithm.txt new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/_build/html/_sources/algorithm.txt @@ -0,0 +1,8 @@ +Algorithms: the :mod:`algorithm` module +======================================= + +.. automodule:: astra.algorithm + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/astra.txt b/python/docSRC/_build/html/_sources/astra.txt new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/_build/html/_sources/astra.txt @@ -0,0 +1,8 @@ +Additional ASTRA methods: the :mod:`astra` module +======================================================== + +.. automodule:: astra.astra + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/creators.txt b/python/docSRC/_build/html/_sources/creators.txt new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/_build/html/_sources/creators.txt @@ -0,0 +1,8 @@ +Creation of objects: the :mod:`creators` module +=============================================== + +.. automodule:: astra.creators + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/data2d.txt b/python/docSRC/_build/html/_sources/data2d.txt new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/_build/html/_sources/data2d.txt @@ -0,0 +1,8 @@ +2D data objects: the :mod:`data2d` module +========================================= + +.. automodule:: astra.data2d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/data3d.txt b/python/docSRC/_build/html/_sources/data3d.txt new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/_build/html/_sources/data3d.txt @@ -0,0 +1,8 @@ +3D data objects: the :mod:`data3d` module +========================================= + +.. automodule:: astra.data3d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/functions.txt b/python/docSRC/_build/html/_sources/functions.txt new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/_build/html/_sources/functions.txt @@ -0,0 +1,8 @@ +Additional functions: the :mod:`functions` module +================================================= + +.. automodule:: astra.functions + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/index.txt b/python/docSRC/_build/html/_sources/index.txt new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/_build/html/_sources/index.txt @@ -0,0 +1,34 @@ +.. .. documentation master file, created by + sphinx-quickstart on Wed Mar 13 16:36:32 2013. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to PyASTRAToolbox's documentation! +========================================== + +Contents: + +.. toctree:: + :maxdepth: 4 + + data2d + data3d + projector + algorithm + matrix + creators + functions + ASTRAProjector + matlab + astra +.. astra +.. builder + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/docSRC/_build/html/_sources/matlab.txt b/python/docSRC/_build/html/_sources/matlab.txt new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/_build/html/_sources/matlab.txt @@ -0,0 +1,8 @@ +MATLAB compatibility interface: the :mod:`matlab` module +======================================================== + +.. automodule:: astra.matlab + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/matrix.txt b/python/docSRC/_build/html/_sources/matrix.txt new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/_build/html/_sources/matrix.txt @@ -0,0 +1,8 @@ +Sparse matrices: the :mod:`matrix` module +========================================= + +.. automodule:: astra.matrix + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/_build/html/_sources/projector.txt b/python/docSRC/_build/html/_sources/projector.txt new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/_build/html/_sources/projector.txt @@ -0,0 +1,8 @@ +Projector object: the :mod:`projector` module 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+ + var c = "[^aeiou]"; // consonant + var v = "[aeiouy]"; // vowel + var C = c + "[^aeiouy]*"; // consonant sequence + var V = v + "[aeiou]*"; // vowel sequence + + var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0 + var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1 + var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1 + var s_v = "^(" + C + ")?" + v; // vowel in stem + + this.stemWord = function (w) { + var stem; + var suffix; + var firstch; + var origword = w; + + if (w.length < 3) + return w; + + var re; + var re2; + var re3; + var re4; + + firstch = w.substr(0,1); + if (firstch == "y") + w = firstch.toUpperCase() + w.substr(1); + + // Step 1a + re = /^(.+?)(ss|i)es$/; + re2 = /^(.+?)([^s])s$/; + + if (re.test(w)) + w = w.replace(re,"$1$2"); + else if (re2.test(w)) + w = w.replace(re2,"$1$2"); + + // Step 1b + re = /^(.+?)eed$/; + re2 = /^(.+?)(ed|ing)$/; + if (re.test(w)) { + var fp = re.exec(w); + re = new RegExp(mgr0); + if (re.test(fp[1])) { + re = /.$/; + w = w.replace(re,""); + } + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1]; + re2 = new RegExp(s_v); + if (re2.test(stem)) { + w = stem; + re2 = /(at|bl|iz)$/; + re3 = new RegExp("([^aeiouylsz])\\1$"); + re4 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re2.test(w)) + w = w + "e"; + else if (re3.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + else if (re4.test(w)) + w = w + "e"; + } + } + + // Step 1c + re = /^(.+?)y$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(s_v); + if (re.test(stem)) + w = stem + "i"; + } + + // Step 2 + re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step2list[suffix]; + } + + // Step 3 + re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + suffix = fp[2]; + re = new RegExp(mgr0); + if (re.test(stem)) + w = stem + step3list[suffix]; + } + + // Step 4 + re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/; + re2 = /^(.+?)(s|t)(ion)$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + if (re.test(stem)) + w = stem; + } + else if (re2.test(w)) { + var fp = re2.exec(w); + stem = fp[1] + fp[2]; + re2 = new RegExp(mgr1); + if (re2.test(stem)) + w = stem; + } + + // Step 5 + re = /^(.+?)e$/; + if (re.test(w)) { + var fp = re.exec(w); + stem = fp[1]; + re = new RegExp(mgr1); + re2 = new RegExp(meq1); + re3 = new RegExp("^" + C + v + "[^aeiouwxy]$"); + if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) + w = stem; + } + re = /ll$/; + re2 = new RegExp(mgr1); + if (re.test(w) && re2.test(w)) { + re = /.$/; + w = w.replace(re,""); + } + + // and turn initial Y back to y + if (firstch == "y") + w = firstch.toLowerCase() + w.substr(1); + return w; + } +} + + + +/** + * Simple result scoring code. + */ +var Scorer = { + // Implement the following function to further tweak the score for each result + // The function takes a result array [filename, title, anchor, descr, score] + // and returns the new score. + /* + score: function(result) { + return result[4]; + }, + */ + + // query matches the full name of an object + objNameMatch: 11, + // or matches in the last dotted part of the object name + objPartialMatch: 6, + // Additive scores depending on the priority of the object + objPrio: {0: 15, // used to be importantResults + 1: 5, // used to be objectResults + 2: -5}, // used to be unimportantResults + // Used when the priority is not in the mapping. + objPrioDefault: 0, + + // query found in title + title: 15, + // query found in terms + term: 5 +}; + + +/** + * Search Module + */ +var Search = { + + _index : null, + _queued_query : null, + _pulse_status : -1, + + init : function() { + var params = $.getQueryParameters(); + if (params.q) { + var query = params.q[0]; + $('input[name="q"]')[0].value = query; + this.performSearch(query); + } + }, + + loadIndex : function(url) { + $.ajax({type: "GET", url: url, data: null, + dataType: "script", cache: true, + complete: function(jqxhr, textstatus) { + if (textstatus != "success") { + document.getElementById("searchindexloader").src = url; + } + }}); + }, + + setIndex : function(index) { + var q; + this._index = index; + if ((q = this._queued_query) !== null) { + this._queued_query = null; + Search.query(q); + } + }, + + hasIndex : function() { + return this._index !== null; + }, + + deferQuery : function(query) { + this._queued_query = query; + }, + + stopPulse : function() { + this._pulse_status = 0; + }, + + startPulse : function() { + if (this._pulse_status >= 0) + return; + function pulse() { + var i; + Search._pulse_status = (Search._pulse_status + 1) % 4; + var dotString = ''; + for (i = 0; i < Search._pulse_status; i++) + dotString += '.'; + Search.dots.text(dotString); + if (Search._pulse_status > -1) + window.setTimeout(pulse, 500); + } + pulse(); + }, + + /** + * perform a search for something (or wait until index is loaded) + */ + performSearch : function(query) { + // create the required interface elements + this.out = $('#search-results'); + this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out); + this.dots = $('<span></span>').appendTo(this.title); + this.status = $('<p style="display: none"></p>').appendTo(this.out); + this.output = $('<ul class="search"/>').appendTo(this.out); + + $('#search-progress').text(_('Preparing search...')); + this.startPulse(); + + // index already loaded, the browser was quick! + if (this.hasIndex()) + this.query(query); + else + this.deferQuery(query); + }, + + /** + * execute search (requires search index to be loaded) + */ + query : function(query) { + var i; + var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"]; + + // stem the searchterms and add them to the correct list + var stemmer = new Stemmer(); + var searchterms = []; + var excluded = []; + var hlterms = []; + var tmp = query.split(/\s+/); + var objectterms = []; + for (i = 0; i < tmp.length; i++) { + if (tmp[i] !== "") { + objectterms.push(tmp[i].toLowerCase()); + } + + if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) || + tmp[i] === "") { + // skip this "word" + continue; + } + // stem the word + var word = stemmer.stemWord(tmp[i].toLowerCase()); + var toAppend; + // select the correct list + if (word[0] == '-') { + toAppend = excluded; + word = word.substr(1); + } + else { + toAppend = searchterms; + hlterms.push(tmp[i].toLowerCase()); + } + // only add if not already in the list + if (!$u.contains(toAppend, word)) + toAppend.push(word); + } + var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" ")); + + // console.debug('SEARCH: searching for:'); + // console.info('required: ', searchterms); + // console.info('excluded: ', excluded); + + // prepare search + var terms = this._index.terms; + var titleterms = this._index.titleterms; + + // array of [filename, title, anchor, descr, score] + var results = []; + $('#search-progress').empty(); + + // lookup as object + for (i = 0; i < objectterms.length; i++) { + var others = [].concat(objectterms.slice(0, i), + objectterms.slice(i+1, objectterms.length)); + results = results.concat(this.performObjectSearch(objectterms[i], others)); + } + + // lookup as search terms in fulltext + results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term)) + .concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title)); + + // let the scorer override scores with a custom scoring function + if (Scorer.score) { + for (i = 0; i < results.length; i++) + results[i][4] = Scorer.score(results[i]); + } + + // now sort the results by score (in opposite order of appearance, since the + // display function below uses pop() to retrieve items) and then + // alphabetically + results.sort(function(a, b) { + var left = a[4]; + var right = b[4]; + if (left > right) { + return 1; + } else if (left < right) { + return -1; + } else { + // same score: sort alphabetically + left = a[1].toLowerCase(); + right = b[1].toLowerCase(); + return (left > right) ? -1 : ((left < right) ? 1 : 0); + } + }); + + // for debugging + //Search.lastresults = results.slice(); // a copy + //console.info('search results:', Search.lastresults); + + // print the results + var resultCount = results.length; + function displayNextItem() { + // results left, load the summary and display it + if (results.length) { + var item = results.pop(); + var listItem = $('<li style="display:none"></li>'); + if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') { + // dirhtml builder + var dirname = item[0] + '/'; + if (dirname.match(/\/index\/$/)) { + dirname = dirname.substring(0, dirname.length-6); + } else if (dirname == 'index/') { + dirname = ''; + } + listItem.append($('<a/>').attr('href', + DOCUMENTATION_OPTIONS.URL_ROOT + dirname + + highlightstring + item[2]).html(item[1])); + } else { + // normal html builders + listItem.append($('<a/>').attr('href', + item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX + + highlightstring + item[2]).html(item[1])); + } + if (item[3]) { + listItem.append($('<span> (' + item[3] + ')</span>')); + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) { + $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt', + dataType: "text", + complete: function(jqxhr, textstatus) { + var data = jqxhr.responseText; + if (data !== '') { + listItem.append(Search.makeSearchSummary(data, searchterms, hlterms)); + } + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + }}); + } else { + // no source available, just display title + Search.output.append(listItem); + listItem.slideDown(5, function() { + displayNextItem(); + }); + } + } + // search finished, update title and status message + else { + Search.stopPulse(); 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Please make sure that all words are spelled correctly and that you\'ve selected enough categories.')); + else + Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount)); + Search.status.fadeIn(500); + } + } + displayNextItem(); + }, + + /** + * search for object names + */ + performObjectSearch : function(object, otherterms) { + var filenames = this._index.filenames; + var objects = this._index.objects; + var objnames = this._index.objnames; + var titles = this._index.titles; + + var i; + var results = []; + + for (var prefix in objects) { + for (var name in objects[prefix]) { + var fullname = (prefix ? prefix + '.' : '') + name; + if (fullname.toLowerCase().indexOf(object) > -1) { + var score = 0; + var parts = fullname.split('.'); + // check for different match types: exact matches of full name or + // "last name" (i.e. last dotted part) + if (fullname == object || parts[parts.length - 1] == object) { + score += Scorer.objNameMatch; + // matches in last name + } else if (parts[parts.length - 1].indexOf(object) > -1) { + score += Scorer.objPartialMatch; + } + var match = objects[prefix][name]; + var objname = objnames[match[1]][2]; + var title = titles[match[0]]; + // If more than one term searched for, we require other words to be + // found in the name/title/description + if (otherterms.length > 0) { + var haystack = (prefix + ' ' + name + ' ' + + objname + ' ' + title).toLowerCase(); + var allfound = true; + for (i = 0; i < otherterms.length; i++) { + if (haystack.indexOf(otherterms[i]) == -1) { + allfound = false; + break; + } + } + if (!allfound) { + continue; + } + } + var descr = objname + _(', in ') + title; + + var anchor = match[3]; + if (anchor === '') + anchor = fullname; + else if (anchor == '-') + anchor = objnames[match[1]][1] + '-' + fullname; + // add custom score for some objects according to scorer + if (Scorer.objPrio.hasOwnProperty(match[2])) { + score += Scorer.objPrio[match[2]]; + } else { + score += Scorer.objPrioDefault; + } + results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]); + } + } + } + + return results; + }, + + /** + * search for full-text terms in the index + */ + performTermsSearch : function(searchterms, excluded, terms, score) { + var filenames = this._index.filenames; + var titles = this._index.titles; + + var i, j, file, files; + var fileMap = {}; + var results = []; + + // perform the search on the required terms + for (i = 0; i < searchterms.length; i++) { + var word = searchterms[i]; + // no match but word was a required one + if ((files = terms[word]) === undefined) + break; + if (files.length === undefined) { + files = [files]; + } + // create the mapping + for (j = 0; j < files.length; j++) { + file = files[j]; + if (file in fileMap) + fileMap[file].push(word); + else + fileMap[file] = [word]; + } + } + + // now check if the files don't contain excluded terms + for (file in fileMap) { + var valid = true; + + // check if all requirements are matched + if (fileMap[file].length != searchterms.length) + continue; + + // ensure that none of the excluded terms is in the search result + for (i = 0; i < excluded.length; i++) { + if (terms[excluded[i]] == file || + $u.contains(terms[excluded[i]] || [], file)) { + valid = false; + break; + } + } + + // if we have still a valid result we can add it to the result list + if (valid) { + results.push([filenames[file], titles[file], '', null, score]); + } + } + return results; + }, + + /** + * helper function to return a node containing the + * search summary for a given text. keywords is a list + * of stemmed words, hlwords is the list of normal, unstemmed + * words. the first one is used to find the occurance, the + * latter for highlighting it. + */ + makeSearchSummary : function(text, keywords, hlwords) { + var textLower = text.toLowerCase(); + var start = 0; + $.each(keywords, function() { + var i = textLower.indexOf(this.toLowerCase()); + if (i > -1) + start = i; + }); + start = Math.max(start - 120, 0); + var excerpt = ((start > 0) ? 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diff --git a/python/docSRC/_build/html/_static/up-pressed.png b/python/docSRC/_build/html/_static/up-pressed.png Binary files differnew file mode 100644 index 0000000..8bd587a --- /dev/null +++ b/python/docSRC/_build/html/_static/up-pressed.png diff --git a/python/docSRC/_build/html/_static/up.png b/python/docSRC/_build/html/_static/up.png Binary files differnew file mode 100644 index 0000000..b946256 --- /dev/null +++ b/python/docSRC/_build/html/_static/up.png diff --git a/python/docSRC/_build/html/_static/websupport.js b/python/docSRC/_build/html/_static/websupport.js new file mode 100644 index 0000000..71c0a13 --- /dev/null +++ b/python/docSRC/_build/html/_static/websupport.js @@ -0,0 +1,808 @@ +/* + * websupport.js + * ~~~~~~~~~~~~~ + * + * sphinx.websupport utilties for all documentation. + * + * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ + +(function($) { + $.fn.autogrow = function() { + return this.each(function() { + var textarea = this; + + $.fn.autogrow.resize(textarea); + + $(textarea) + .focus(function() { + textarea.interval = setInterval(function() { + $.fn.autogrow.resize(textarea); + }, 500); + }) + .blur(function() { + clearInterval(textarea.interval); + }); + }); + }; + + $.fn.autogrow.resize = function(textarea) { + var lineHeight = parseInt($(textarea).css('line-height'), 10); + var lines = textarea.value.split('\n'); + var columns = textarea.cols; + var lineCount = 0; + $.each(lines, function() { + lineCount += Math.ceil(this.length / columns) || 1; + }); + var height = lineHeight * (lineCount + 1); + $(textarea).css('height', height); + }; +})(jQuery); + +(function($) { + var comp, by; + + function init() { + initEvents(); + initComparator(); + } + + function initEvents() { + $('a.comment-close').live("click", function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }); + $('a.vote').live("click", function(event) { + event.preventDefault(); + handleVote($(this)); + }); + $('a.reply').live("click", function(event) { + event.preventDefault(); + openReply($(this).attr('id').substring(2)); + }); + $('a.close-reply').live("click", function(event) { + event.preventDefault(); + closeReply($(this).attr('id').substring(2)); + }); + $('a.sort-option').live("click", function(event) { + event.preventDefault(); + handleReSort($(this)); + }); + $('a.show-proposal').live("click", function(event) { + event.preventDefault(); + showProposal($(this).attr('id').substring(2)); + }); + $('a.hide-proposal').live("click", function(event) { + event.preventDefault(); + hideProposal($(this).attr('id').substring(2)); + }); + $('a.show-propose-change').live("click", function(event) { + event.preventDefault(); + showProposeChange($(this).attr('id').substring(2)); + }); + $('a.hide-propose-change').live("click", function(event) { + event.preventDefault(); + hideProposeChange($(this).attr('id').substring(2)); + }); + $('a.accept-comment').live("click", function(event) { + event.preventDefault(); + acceptComment($(this).attr('id').substring(2)); + }); + $('a.delete-comment').live("click", function(event) { + event.preventDefault(); + deleteComment($(this).attr('id').substring(2)); + }); + $('a.comment-markup').live("click", function(event) { + event.preventDefault(); + toggleCommentMarkupBox($(this).attr('id').substring(2)); + }); + } + + /** + * Set comp, which is a comparator function used for sorting and + * inserting comments into the list. + */ + function setComparator() { + // If the first three letters are "asc", sort in ascending order + // and remove the prefix. + if (by.substring(0,3) == 'asc') { + var i = by.substring(3); + comp = function(a, b) { return a[i] - b[i]; }; + } else { + // Otherwise sort in descending order. + comp = function(a, b) { return b[by] - a[by]; }; + } + + // Reset link styles and format the selected sort option. + $('a.sel').attr('href', '#').removeClass('sel'); + $('a.by' + by).removeAttr('href').addClass('sel'); + } + + /** + * Create a comp function. If the user has preferences stored in + * the sortBy cookie, use those, otherwise use the default. + */ + function initComparator() { + by = 'rating'; // Default to sort by rating. + // If the sortBy cookie is set, use that instead. + if (document.cookie.length > 0) { + var start = document.cookie.indexOf('sortBy='); + if (start != -1) { + start = start + 7; + var end = document.cookie.indexOf(";", start); + if (end == -1) { + end = document.cookie.length; + by = unescape(document.cookie.substring(start, end)); + } + } + } + setComparator(); + } + + /** + * Show a comment div. + */ + function show(id) { + $('#ao' + id).hide(); + $('#ah' + id).show(); + var context = $.extend({id: id}, opts); + var popup = $(renderTemplate(popupTemplate, context)).hide(); + popup.find('textarea[name="proposal"]').hide(); + popup.find('a.by' + by).addClass('sel'); + var form = popup.find('#cf' + id); + form.submit(function(event) { + event.preventDefault(); + addComment(form); + }); + $('#s' + id).after(popup); + popup.slideDown('fast', function() { + getComments(id); + }); + } + + /** + * Hide a comment div. + */ + function hide(id) { + $('#ah' + id).hide(); + $('#ao' + id).show(); + var div = $('#sc' + id); + div.slideUp('fast', function() { + div.remove(); + }); + } + + /** + * Perform an ajax request to get comments for a node + * and insert the comments into the comments tree. + */ + function getComments(id) { + $.ajax({ + type: 'GET', + url: opts.getCommentsURL, + data: {node: id}, + success: function(data, textStatus, request) { + var ul = $('#cl' + id); + var speed = 100; + $('#cf' + id) + .find('textarea[name="proposal"]') + .data('source', data.source); + + if (data.comments.length === 0) { + ul.html('<li>No comments yet.</li>'); + ul.data('empty', true); + } else { + // If there are comments, sort them and put them in the list. + var comments = sortComments(data.comments); + speed = data.comments.length * 100; + appendComments(comments, ul); + ul.data('empty', false); + } + $('#cn' + id).slideUp(speed + 200); + ul.slideDown(speed); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem retrieving the comments.'); + }, + dataType: 'json' + }); + } + + /** + * Add a comment via ajax and insert the comment into the comment tree. + */ + function addComment(form) { + var node_id = form.find('input[name="node"]').val(); + var parent_id = form.find('input[name="parent"]').val(); + var text = form.find('textarea[name="comment"]').val(); + var proposal = form.find('textarea[name="proposal"]').val(); + + if (text == '') { + showError('Please enter a comment.'); + return; + } + + // Disable the form that is being submitted. + form.find('textarea,input').attr('disabled', 'disabled'); + + // Send the comment to the server. + $.ajax({ + type: "POST", + url: opts.addCommentURL, + dataType: 'json', + data: { + node: node_id, + parent: parent_id, + text: text, + proposal: proposal + }, + success: function(data, textStatus, error) { + // Reset the form. + if (node_id) { + hideProposeChange(node_id); + } + form.find('textarea') + .val('') + .add(form.find('input')) + .removeAttr('disabled'); + var ul = $('#cl' + (node_id || parent_id)); + if (ul.data('empty')) { + $(ul).empty(); + ul.data('empty', false); + } + insertComment(data.comment); + var ao = $('#ao' + node_id); + ao.find('img').attr({'src': opts.commentBrightImage}); + if (node_id) { + // if this was a "root" comment, remove the commenting box + // (the user can get it back by reopening the comment popup) + $('#ca' + node_id).slideUp(); + } + }, + error: function(request, textStatus, error) { + form.find('textarea,input').removeAttr('disabled'); + showError('Oops, there was a problem adding the comment.'); + } + }); + } + + /** + * Recursively append comments to the main comment list and children + * lists, creating the comment tree. + */ + function appendComments(comments, ul) { + $.each(comments, function() { + var div = createCommentDiv(this); + ul.append($(document.createElement('li')).html(div)); + appendComments(this.children, div.find('ul.comment-children')); + // To avoid stagnating data, don't store the comments children in data. + this.children = null; + div.data('comment', this); + }); + } + + /** + * After adding a new comment, it must be inserted in the correct + * location in the comment tree. + */ + function insertComment(comment) { + var div = createCommentDiv(comment); + + // To avoid stagnating data, don't store the comments children in data. + comment.children = null; + div.data('comment', comment); + + var ul = $('#cl' + (comment.node || comment.parent)); + var siblings = getChildren(ul); + + var li = $(document.createElement('li')); + li.hide(); + + // Determine where in the parents children list to insert this comment. + for(i=0; i < siblings.length; i++) { + if (comp(comment, siblings[i]) <= 0) { + $('#cd' + siblings[i].id) + .parent() + .before(li.html(div)); + li.slideDown('fast'); + return; + } + } + + // If we get here, this comment rates lower than all the others, + // or it is the only comment in the list. + ul.append(li.html(div)); + li.slideDown('fast'); + } + + function acceptComment(id) { + $.ajax({ + type: 'POST', + url: opts.acceptCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + $('#cm' + id).fadeOut('fast'); + $('#cd' + id).removeClass('moderate'); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem accepting the comment.'); + } + }); + } + + function deleteComment(id) { + $.ajax({ + type: 'POST', + url: opts.deleteCommentURL, + data: {id: id}, + success: function(data, textStatus, request) { + var div = $('#cd' + id); + if (data == 'delete') { + // Moderator mode: remove the comment and all children immediately + div.slideUp('fast', function() { + div.remove(); + }); + return; + } + // User mode: only mark the comment as deleted + div + .find('span.user-id:first') + .text('[deleted]').end() + .find('div.comment-text:first') + .text('[deleted]').end() + .find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id + + ', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id) + .remove(); + var comment = div.data('comment'); + comment.username = '[deleted]'; + comment.text = '[deleted]'; + div.data('comment', comment); + }, + error: function(request, textStatus, error) { + showError('Oops, there was a problem deleting the comment.'); + } + }); + } + + function showProposal(id) { + $('#sp' + id).hide(); + $('#hp' + id).show(); + $('#pr' + id).slideDown('fast'); + } + + function hideProposal(id) { + $('#hp' + id).hide(); + $('#sp' + id).show(); + $('#pr' + id).slideUp('fast'); + } + + function showProposeChange(id) { + $('#pc' + id).hide(); + $('#hc' + id).show(); + var textarea = $('#pt' + id); + textarea.val(textarea.data('source')); + $.fn.autogrow.resize(textarea[0]); + textarea.slideDown('fast'); + } + + function hideProposeChange(id) { + $('#hc' + id).hide(); + $('#pc' + id).show(); + var textarea = $('#pt' + id); + textarea.val('').removeAttr('disabled'); + textarea.slideUp('fast'); + } + + function toggleCommentMarkupBox(id) { + $('#mb' + id).toggle(); + } + + /** Handle when the user clicks on a sort by link. */ + function handleReSort(link) { + var classes = link.attr('class').split(/\s+/); + for (var i=0; i<classes.length; i++) { + if (classes[i] != 'sort-option') { + by = classes[i].substring(2); + } + } + setComparator(); + // Save/update the sortBy cookie. + var expiration = new Date(); + expiration.setDate(expiration.getDate() + 365); + document.cookie= 'sortBy=' + escape(by) + + ';expires=' + expiration.toUTCString(); + $('ul.comment-ul').each(function(index, ul) { + var comments = getChildren($(ul), true); + comments = sortComments(comments); + appendComments(comments, $(ul).empty()); + }); + } + + /** + * Function to process a vote when a user clicks an arrow. + */ + function handleVote(link) { + if (!opts.voting) { + showError("You'll need to login to vote."); + return; + } + + var id = link.attr('id'); + if (!id) { + // Didn't click on one of the voting arrows. + return; + } + // If it is an unvote, the new vote value is 0, + // Otherwise it's 1 for an upvote, or -1 for a downvote. + var value = 0; + if (id.charAt(1) != 'u') { + value = id.charAt(0) == 'u' ? 1 : -1; + } + // The data to be sent to the server. + var d = { + comment_id: id.substring(2), + value: value + }; + + // Swap the vote and unvote links. + link.hide(); + $('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id) + .show(); + + // The div the comment is displayed in. + var div = $('div#cd' + d.comment_id); + var data = div.data('comment'); + + // If this is not an unvote, and the other vote arrow has + // already been pressed, unpress it. + if ((d.value !== 0) && (data.vote === d.value * -1)) { + $('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide(); + $('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show(); + } + + // Update the comments rating in the local data. + data.rating += (data.vote === 0) ? d.value : (d.value - data.vote); + data.vote = d.value; + div.data('comment', data); + + // Change the rating text. + div.find('.rating:first') + .text(data.rating + ' point' + (data.rating == 1 ? '' : 's')); + + // Send the vote information to the server. + $.ajax({ + type: "POST", + url: opts.processVoteURL, + data: d, + error: function(request, textStatus, error) { + showError('Oops, there was a problem casting that vote.'); + } + }); + } + + /** + * Open a reply form used to reply to an existing comment. + */ + function openReply(id) { + // Swap out the reply link for the hide link + $('#rl' + id).hide(); + $('#cr' + id).show(); + + // Add the reply li to the children ul. + var div = $(renderTemplate(replyTemplate, {id: id})).hide(); + $('#cl' + id) + .prepend(div) + // Setup the submit handler for the reply form. + .find('#rf' + id) + .submit(function(event) { + event.preventDefault(); + addComment($('#rf' + id)); + closeReply(id); + }) + .find('input[type=button]') + .click(function() { + closeReply(id); + }); + div.slideDown('fast', function() { + $('#rf' + id).find('textarea').focus(); + }); + } + + /** + * Close the reply form opened with openReply. + */ + function closeReply(id) { + // Remove the reply div from the DOM. + $('#rd' + id).slideUp('fast', function() { + $(this).remove(); + }); + + // Swap out the hide link for the reply link + $('#cr' + id).hide(); + $('#rl' + id).show(); + } + + /** + * Recursively sort a tree of comments using the comp comparator. + */ + function sortComments(comments) { + comments.sort(comp); + $.each(comments, function() { + this.children = sortComments(this.children); + }); + return comments; + } + + /** + * Get the children comments from a ul. If recursive is true, + * recursively include childrens' children. + */ + function getChildren(ul, recursive) { + var children = []; + ul.children().children("[id^='cd']") + .each(function() { + var comment = $(this).data('comment'); + if (recursive) + comment.children = getChildren($(this).find('#cl' + comment.id), true); + children.push(comment); + }); + return children; + } + + /** Create a div to display a comment in. */ + function createCommentDiv(comment) { + if (!comment.displayed && !opts.moderator) { + return $('<div class="moderate">Thank you! Your comment will show up ' + + 'once it is has been approved by a moderator.</div>'); + } + // Prettify the comment rating. + comment.pretty_rating = comment.rating + ' point' + + (comment.rating == 1 ? '' : 's'); + // Make a class (for displaying not yet moderated comments differently) + comment.css_class = comment.displayed ? '' : ' moderate'; + // Create a div for this comment. + var context = $.extend({}, opts, comment); + var div = $(renderTemplate(commentTemplate, context)); + + // If the user has voted on this comment, highlight the correct arrow. + if (comment.vote) { + var direction = (comment.vote == 1) ? 'u' : 'd'; + div.find('#' + direction + 'v' + comment.id).hide(); + div.find('#' + direction + 'u' + comment.id).show(); + } + + if (opts.moderator || comment.text != '[deleted]') { + div.find('a.reply').show(); + if (comment.proposal_diff) + div.find('#sp' + comment.id).show(); + if (opts.moderator && !comment.displayed) + div.find('#cm' + comment.id).show(); + if (opts.moderator || (opts.username == comment.username)) + div.find('#dc' + comment.id).show(); + } + return div; + } + + /** + * A simple template renderer. Placeholders such as <%id%> are replaced + * by context['id'] with items being escaped. Placeholders such as <#id#> + * are not escaped. + */ + function renderTemplate(template, context) { + var esc = $(document.createElement('div')); + + function handle(ph, escape) { + var cur = context; + $.each(ph.split('.'), function() { + cur = cur[this]; + }); + return escape ? esc.text(cur || "").html() : cur; + } + + return template.replace(/<([%#])([\w\.]*)\1>/g, function() { + return handle(arguments[2], arguments[1] == '%' ? true : false); + }); + } + + /** Flash an error message briefly. */ + function showError(message) { + $(document.createElement('div')).attr({'class': 'popup-error'}) + .append($(document.createElement('div')) + .attr({'class': 'error-message'}).text(message)) + .appendTo('body') + .fadeIn("slow") + .delay(2000) + .fadeOut("slow"); + } + + /** Add a link the user uses to open the comments popup. */ + $.fn.comment = function() { + return this.each(function() { + var id = $(this).attr('id').substring(1); + var count = COMMENT_METADATA[id]; + var title = count + ' comment' + (count == 1 ? '' : 's'); + var image = count > 0 ? opts.commentBrightImage : opts.commentImage; + var addcls = count == 0 ? ' nocomment' : ''; + $(this) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-open' + addcls, + id: 'ao' + id + }) + .append($(document.createElement('img')).attr({ + src: image, + alt: 'comment', + title: title + })) + .click(function(event) { + event.preventDefault(); + show($(this).attr('id').substring(2)); + }) + ) + .append( + $(document.createElement('a')).attr({ + href: '#', + 'class': 'sphinx-comment-close hidden', + id: 'ah' + id + }) + .append($(document.createElement('img')).attr({ + src: opts.closeCommentImage, + alt: 'close', + title: 'close' + })) + .click(function(event) { + event.preventDefault(); + hide($(this).attr('id').substring(2)); + }) + ); + }); + }; + + var opts = { + processVoteURL: '/_process_vote', + addCommentURL: '/_add_comment', + getCommentsURL: '/_get_comments', + acceptCommentURL: '/_accept_comment', + deleteCommentURL: '/_delete_comment', + commentImage: '/static/_static/comment.png', + closeCommentImage: 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xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Algorithms: the algorithm module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Sparse matrices: the matrix module" href="matrix.html" /> + <link rel="prev" title="Projector object: the projector module" href="projector.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="matrix.html" title="Sparse matrices: the matrix module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="projector.html" title="Projector object: the projector module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.algorithm"> +<span id="algorithms-the-algorithm-module"></span><h1>Algorithms: the <tt class="xref py py-mod docutils literal"><span class="pre">algorithm</span></tt> module<a class="headerlink" href="#module-astra.algorithm" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.algorithm.clear"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all matrix objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.create"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">create</tt><big>(</big><em>config</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create algorithm object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>config</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Algorithm options.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.delete"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.get_res_norm"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">get_res_norm</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#get_res_norm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.get_res_norm" title="Permalink to this definition">¶</a></dt> +<dd><p>Get residual norm of algorithm.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> – The residual norm.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.info"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on matrix objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.algorithm.run"> +<tt class="descclassname">astra.algorithm.</tt><tt class="descname">run</tt><big>(</big><em>i</em>, <em>iterations=1</em><big>)</big><a class="reference internal" href="_modules/astra/algorithm.html#run"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.algorithm.run" title="Permalink to this definition">¶</a></dt> +<dd><p>Run an algorithm.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</li> +<li><strong>iterations</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of iterations to run.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="projector.html" + title="previous chapter">Projector object: the <tt class="docutils literal"><span class="pre">projector</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="matrix.html" + title="next chapter">Sparse matrices: the <tt class="docutils literal"><span class="pre">matrix</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/algorithm.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" 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\ No newline at end of file diff --git a/python/docSRC/_build/html/astra.html b/python/docSRC/_build/html/astra.html new file mode 100644 index 0000000..42d68b8 --- /dev/null +++ b/python/docSRC/_build/html/astra.html @@ -0,0 +1,169 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Additional ASTRA methods: the astra module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.astra"> +<span id="additional-astra-methods-the-astra-module"></span><h1>Additional ASTRA methods: the <tt class="xref py py-mod docutils literal"><span class="pre">astra</span></tt> module<a class="headerlink" href="#module-astra.astra" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.astra.credits"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">credits</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/astra.html#credits"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.credits" title="Permalink to this definition">¶</a></dt> +<dd><p>Print credits of the ASTRA Toolbox.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.set_gpu_index"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">set_gpu_index</tt><big>(</big><em>idx</em><big>)</big><a class="reference internal" href="_modules/astra/astra.html#set_gpu_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.set_gpu_index" title="Permalink to this definition">¶</a></dt> +<dd><p>Set default GPU index to use.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>idx</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – GPU index</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.use_cuda"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">use_cuda</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/astra.html#use_cuda"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.use_cuda" title="Permalink to this definition">¶</a></dt> +<dd><p>Test if CUDA is enabled.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a> – <tt class="docutils literal"><span class="pre">True</span></tt> if CUDA is enabled.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.astra.version"> +<tt class="descclassname">astra.astra.</tt><tt class="descname">version</tt><big>(</big><em>printToScreen=False</em><big>)</big><a class="reference internal" href="_modules/astra/astra.html#version"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.astra.version" title="Permalink to this definition">¶</a></dt> +<dd><p>Check version of the ASTRA Toolbox.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>printToScreen</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, print version string. If <tt class="docutils literal"><span class="pre">False</span></tt>, return version integer.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">string</span></tt> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – The version string or integer.</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="matlab.html" + title="previous chapter">MATLAB compatibility interface: the <tt class="docutils literal"><span class="pre">matlab</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/astra.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="matlab.html" title="MATLAB compatibility interface: the matlab module" + >previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/creators.html b/python/docSRC/_build/html/creators.html new file mode 100644 index 0000000..2f29232 --- /dev/null +++ b/python/docSRC/_build/html/creators.html @@ -0,0 +1,520 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Creation of objects: the creators module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + 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href="matrix.html" title="Sparse matrices: the matrix module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.creators"> +<span id="creation-of-objects-the-creators-module"></span><h1>Creation of objects: the <tt class="xref py py-mod docutils literal"><span class="pre">creators</span></tt> module<a class="headerlink" href="#module-astra.creators" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.creators.astra_dict"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">astra_dict</tt><big>(</big><em>intype</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#astra_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.astra_dict" title="Permalink to this definition">¶</a></dt> +<dd><p>Creates a dict to use with the ASTRA Toolbox.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>intype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Type of the ASTRA object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – An ASTRA dict of type <tt class="docutils literal"><span class="pre">intype</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_backprojection"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_backprojection</tt><big>(</big><em>data</em>, <em>proj_id</em>, <em>useCUDA=False</em>, <em>returnData=True</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_backprojection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_backprojection" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a backprojection of a sinogram (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for the calculation.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the backprojection.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_backprojection3d_gpu"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_backprojection3d_gpu</tt><big>(</big><em>data</em>, <em>proj_geom</em>, <em>vol_geom</em>, <em>returnData=True</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_backprojection3d_gpu"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_backprojection3d_gpu" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a backprojection of a sinogram (3D) using CUDA.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the backprojection.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the backprojection. Otherwise, returns a tuple containing the ID of the backprojection and the backprojection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_proj_geom"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_proj_geom</tt><big>(</big><em>intype</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_proj_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_proj_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a projection geometry.</p> +<p>This method can be called in a number of ways:</p> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel',</span> <span class="pre">detector_spacing,</span> <span class="pre">det_count,</span> <span class="pre">angles)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('fanflat',</span> <span class="pre">det_width,</span> <span class="pre">det_count,</span> <span class="pre">angles,</span> <span class="pre">source_origin,</span> <span class="pre">source_det)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_width</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Size of a detector pixel.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>source_origin</strong> – Position of the source.</li> +<li><strong>source_det</strong> – Position of the detector</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A fan-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('fanflat_vec',</span> <span class="pre">det_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A fan-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel3d',</span> <span class="pre">detector_spacing_x,</span> <span class="pre">detector_spacing_y,</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">angles)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing_*</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('cone',</span> <span class="pre">detector_spacing_x,</span> <span class="pre">detector_spacing_y,</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">angles,</span> <span class="pre">source_origin,</span> <span class="pre">source_det)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>detector_spacing_*</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between two adjacent detector pixels.</li> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>source_origin</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between point source and origin.</li> +<li><strong>source_det</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Distance between the detector and origin.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A cone-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('cone_vec',</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A cone-beam projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('parallel3d_vec',</span> <span class="pre">det_row_count,</span> <span class="pre">det_col_count,</span> <span class="pre">V)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_row_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel rows.</li> +<li><strong>det_col_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixel columns.</li> +<li><strong>V</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Vector array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A parallel projection geometry.</p> +</td> +</tr> +</tbody> +</table> +<p><tt class="docutils literal"><span class="pre">create_proj_geom('sparse_matrix',</span> <span class="pre">det_width,</span> <span class="pre">det_count,</span> <span class="pre">angles,</span> <span class="pre">matrix_id)</span></tt>:</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>det_width</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Size of a detector pixel.</li> +<li><strong>det_count</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of detector pixels.</li> +<li><strong>angles</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Array of angles in radians.</li> +<li><strong>matrix_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the sparse matrix.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">A projection geometry based on a sparse matrix.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_projector"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_projector</tt><big>(</big><em>proj_type</em>, <em>proj_geom</em>, <em>vol_geom</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_projector"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_projector" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 2D projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>proj_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Projector type, such as <tt class="docutils literal"><span class="pre">'line'</span></tt>, <tt class="docutils literal"><span class="pre">'linear'</span></tt>, ...</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – The ID of the projector.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_reconstruction"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_reconstruction</tt><big>(</big><em>rec_type</em>, <em>proj_id</em>, <em>sinogram</em>, <em>iterations=1</em>, <em>use_mask='no'</em>, <em>mask=array([]</em>, <em>dtype=float64)</em>, <em>use_minc='no'</em>, <em>minc=0</em>, <em>use_maxc='no'</em>, <em>maxc=255</em>, <em>returnData=True</em>, <em>filterType=None</em>, <em>filterData=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_reconstruction"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_reconstruction" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a reconstruction of a sinogram (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>rec_type</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Name of the reconstruction algorithm.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>sinogram</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Sinogram data or ID.</li> +<li><strong>iterations</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Number of iterations to run.</li> +<li><strong>use_mask</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to use a mask.</li> +<li><strong>mask</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Mask data or ID</li> +<li><strong>use_minc</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to force a minimum value on the reconstruction pixels.</li> +<li><strong>minc</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Minimum value to use.</li> +<li><strong>use_maxc</strong> (<tt class="docutils literal"><span class="pre">'yes'</span></tt> or <tt class="docutils literal"><span class="pre">'no'</span></tt>) – Whether to force a maximum value on the reconstruction pixels.</li> +<li><strong>maxc</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Maximum value to use.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the reconstruction.</li> +<li><strong>filterType</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Which type of filter to use for filter-based methods.</li> +<li><strong>filterData</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Optional filter data for filter-based methods.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the reconstruction. Otherwise, returns a tuple containing the ID of the reconstruction and reconstruction itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_sino"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_sino</tt><big>(</big><em>data</em>, <em>proj_id=None</em>, <em>proj_geom=None</em>, <em>vol_geom=None</em>, <em>useCUDA=False</em>, <em>returnData=True</em>, <em>gpuIndex=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_sino"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_sino" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a forward projection of an image (2D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Image data or ID.</li> +<li><strong>proj_id</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of the projector to use.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>useCUDA</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If <tt class="docutils literal"><span class="pre">True</span></tt>, use CUDA for the calculation.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the forward projection.</li> +<li><strong>gpuIndex</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional GPU index.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>)</p> +</td> +</tr> +</tbody> +</table> +<p>If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the forward +projection. Otherwise, returns a tuple containing the ID of the +forward projection and the forward projection itself, in that +order.</p> +<p>The geometry of setup is defined by <tt class="docutils literal"><span class="pre">proj_id</span></tt> or with +<tt class="docutils literal"><span class="pre">proj_geom</span></tt> and <tt class="docutils literal"><span class="pre">vol_geom</span></tt>. If <tt class="docutils literal"><span class="pre">proj_id</span></tt> is given, then +<tt class="docutils literal"><span class="pre">proj_geom</span></tt> and <tt class="docutils literal"><span class="pre">vol_geom</span></tt> must be None and vice versa.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_sino3d_gpu"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_sino3d_gpu</tt><big>(</big><em>data</em>, <em>proj_geom</em>, <em>vol_geom</em>, <em>returnData=True</em>, <em>gpuIndex=None</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_sino3d_gpu"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_sino3d_gpu" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a forward projection of an image (3D).</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>data</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Image data or ID.</li> +<li><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry.</li> +<li><strong>vol_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume geometry.</li> +<li><strong>returnData</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – If False, only return the ID of the forward projection.</li> +<li><strong>gpuIndex</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional GPU index.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>, <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – If <tt class="docutils literal"><span class="pre">returnData=False</span></tt>, returns the ID of the forward projection. Otherwise, returns a tuple containing the ID of the forward projection and the forward projection itself, in that order.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.creators.create_vol_geom"> +<tt class="descclassname">astra.creators.</tt><tt class="descname">create_vol_geom</tt><big>(</big><em>*varargin</em><big>)</big><a class="reference internal" href="_modules/astra/creators.html#create_vol_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.creators.create_vol_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a volume geometry structure.</p> +<p>This method can be called in a number of ways:</p> +<dl class="docutils"> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(N)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(N \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom((M,</span> <span class="pre">N))</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N,</span> <span class="pre">minx,</span> <span class="pre">maxx,</span> <span class="pre">miny,</span> <span class="pre">maxy)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 2D volume geometry of size <span class="math">\(M \times N\)</span>, windowed as <span class="math">\(minx \leq x \leq maxx\)</span> and <span class="math">\(miny \leq y \leq maxy\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom((M,</span> <span class="pre">N,</span> <span class="pre">Z))</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 3D volume geometry of size <span class="math">\(M \times N \times Z\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +<dt><tt class="docutils literal"><span class="pre">create_vol_geom(M,</span> <span class="pre">N,</span> <span class="pre">Z)</span></tt>:</dt> +<dd><table class="first last docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">returns:</th><td class="field-body">A 3D volume geometry of size <span class="math">\(M \times N \times Z\)</span>.</td> +</tr> +</tbody> +</table> +</dd> +</dl> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/data2d.html b/python/docSRC/_build/html/data2d.html new file mode 100644 index 0000000..6b01d41 --- /dev/null +++ b/python/docSRC/_build/html/data2d.html @@ -0,0 +1,277 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>2D data objects: the data2d module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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PyASTRAToolbox’s documentation!" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.data2d"> +<span id="d-data-objects-the-data2d-module"></span><h1>2D data objects: the <tt class="xref py py-mod docutils literal"><span class="pre">data2d</span></tt> module<a class="headerlink" href="#module-astra.data2d" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.data2d.change_geometry"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">change_geometry</tt><big>(</big><em>i</em>, <em>geom</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#change_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.change_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Change the geometry of a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</li> +<li><strong>geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – new geometry.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.clear"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all 2D data objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.create"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">create</tt><big>(</big><em>datatype</em>, <em>geometry</em>, <em>data=None</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>datatype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Data object type, ‘-vol’ or ‘-sino’.</li> +<li><strong>geometry</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume or projection geometry.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the constructed object with, either a scalar or array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.delete"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_geometry"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get the geometry of a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – The geometry of object with ID <tt class="docutils literal"><span class="pre">i</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_shared"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_shared</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_shared"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_shared" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object with memory shared between the ASTRA toolbox and numpy array.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.get_single"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">get_single</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#get_single"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.get_single" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 2D object in single precision.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.info"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on 2D objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data2d.store"> +<tt class="descclassname">astra.data2d.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/data2d.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data2d.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing 2D object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the object with, either a scalar or array.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="index.html" + title="previous chapter">Welcome to PyASTRAToolbox’s documentation!</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="data3d.html" + title="next chapter">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/data2d.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p 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\ No newline at end of file diff --git a/python/docSRC/_build/html/data3d.html b/python/docSRC/_build/html/data3d.html new file mode 100644 index 0000000..926bd6e --- /dev/null +++ b/python/docSRC/_build/html/data3d.html @@ -0,0 +1,259 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>3D data objects: the data3d module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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objects: the data2d module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.data3d"> +<span id="d-data-objects-the-data3d-module"></span><h1>3D data objects: the <tt class="xref py py-mod docutils literal"><span class="pre">data3d</span></tt> module<a class="headerlink" href="#module-astra.data3d" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.data3d.clear"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all 3D data objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.create"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">create</tt><big>(</big><em>datatype</em>, <em>geometry</em>, <em>data=None</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>datatype</strong> (<tt class="xref py py-class docutils literal"><span class="pre">string</span></tt>) – Data object type, ‘-vol’ or ‘-sino’.</li> +<li><strong>geometry</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Volume or projection geometry.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the constructed object with, either a scalar or array.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.delete"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a 2D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.dimensions"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">dimensions</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#dimensions"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.dimensions" title="Permalink to this definition">¶</a></dt> +<dd><p>Get dimensions of a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt> – dimensions of object with ID <tt class="docutils literal"><span class="pre">i</span></tt>.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get_shared"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get_shared</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get_shared"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get_shared" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object with memory shared between the ASTRA toolbox and numpy array.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.get_single"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">get_single</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#get_single"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.get_single" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a 3D object in single precision.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.info"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on 3D objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.data3d.store"> +<tt class="descclassname">astra.data3d.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/data3d.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.data3d.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing 3D object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a> or <a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Data to fill the object with, either a scalar or array.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="data2d.html" + title="previous chapter">2D data objects: the <tt class="docutils literal"><span class="pre">data2d</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="projector.html" + title="next chapter">Projector object: the <tt class="docutils literal"><span 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\ No newline at end of file diff --git a/python/docSRC/_build/html/functions.html b/python/docSRC/_build/html/functions.html new file mode 100644 index 0000000..7ec397e --- /dev/null +++ b/python/docSRC/_build/html/functions.html @@ -0,0 +1,236 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Additional functions: the functions module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Helper class: the ASTRAProjector module" href="ASTRAProjector.html" /> + <link rel="prev" title="Creation of objects: the creators module" href="creators.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="creators.html" title="Creation of objects: the creators module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.functions"> +<span id="additional-functions-the-functions-module"></span><h1>Additional functions: the <tt class="xref py py-mod docutils literal"><span class="pre">functions</span></tt> module<a class="headerlink" href="#module-astra.functions" title="Permalink to this headline">¶</a></h1> +<p>Additional functions for PyAstraToolbox.</p> +<dl class="function"> +<dt id="astra.functions.add_noise_to_sino"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">add_noise_to_sino</tt><big>(</big><em>sinogram_in</em>, <em>I0</em>, <em>seed=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#add_noise_to_sino"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.add_noise_to_sino" title="Permalink to this definition">¶</a></dt> +<dd><p>Adds Poisson noise to a sinogram.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>sinogram_in</strong> (<a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a>) – Sinogram to add noise to.</li> +<li><strong>I0</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#float" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">float</span></tt></a>) – Background intensity. Lower values lead to higher noise.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.scipy.org/doc/numpy/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v1.9)"><tt class="xref py py-class docutils literal"><span class="pre">numpy.ndarray</span></tt></a> – the sinogram with added noise.</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.clear"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/functions.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clears all used memory of the ASTRA Toolbox.</p> +<div class="admonition note"> +<p class="first admonition-title">Note</p> +<p class="last">This is irreversible.</p> +</div> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.data_op"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">data_op</tt><big>(</big><em>op</em>, <em>data</em>, <em>scalar</em>, <em>gpu_core</em>, <em>mask=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#data_op"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.data_op" title="Permalink to this definition">¶</a></dt> +<dd><p>Perform data operation on data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>op</strong> – Operation to perform.</li> +<li><strong>data</strong> – Data to perform operation on.</li> +<li><strong>scalar</strong> – Scalar argument to data operation.</li> +<li><strong>gpu_core</strong> – GPU core to perform operation on.</li> +<li><strong>mask</strong> – Optional mask.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.geom_2vec"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">geom_2vec</tt><big>(</big><em>proj_geom</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#geom_2vec"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.geom_2vec" title="Permalink to this definition">¶</a></dt> +<dd><p>Returns a vector-based projection geometry from a basic projection geometry.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>proj_geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projection geometry to convert</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.geom_size"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">geom_size</tt><big>(</big><em>geom</em>, <em>dim=None</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#geom_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.geom_size" title="Permalink to this definition">¶</a></dt> +<dd><p>Returns the size of a volume or sinogram, based on the projection or volume geometry.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>geom</strong> – Geometry to calculate size from</li> +<li><strong>dim</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – Optional axis index to return</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.functions.move_vol_geom"> +<tt class="descclassname">astra.functions.</tt><tt class="descname">move_vol_geom</tt><big>(</big><em>geom</em>, <em>pos</em>, <em>is_relative=False</em><big>)</big><a class="reference internal" href="_modules/astra/functions.html#move_vol_geom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.functions.move_vol_geom" title="Permalink to this definition">¶</a></dt> +<dd><p>Moves center of volume geometry to new position.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>geom</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Input volume geometry</li> +<li><strong>pos</strong> (<tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt>) – Tuple (x,y[,z]) for new position, with the center of the image at (0,0[,0])</li> +<li><strong>is_relative</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">bool</span></tt></a>) – Whether new position is relative to the old position</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – Volume geometry with the new center</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="creators.html" + title="previous chapter">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="ASTRAProjector.html" + title="next chapter">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></p> + <h3>This Page</h3> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/genindex.html b/python/docSRC/_build/html/genindex.html new file mode 100644 index 0000000..3099bfa --- /dev/null +++ b/python/docSRC/_build/html/genindex.html @@ -0,0 +1,575 @@ + +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Index — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="#" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + +<h1 id="index">Index</h1> + +<div class="genindex-jumpbox"> + <a href="#A"><strong>A</strong></a> + | <a href="#B"><strong>B</strong></a> + | <a href="#C"><strong>C</strong></a> + | <a href="#D"><strong>D</strong></a> + | <a href="#F"><strong>F</strong></a> + | <a href="#G"><strong>G</strong></a> + | <a href="#I"><strong>I</strong></a> + | <a href="#M"><strong>M</strong></a> + | <a href="#P"><strong>P</strong></a> + | <a href="#R"><strong>R</strong></a> + | <a href="#S"><strong>S</strong></a> + | <a href="#U"><strong>U</strong></a> + | <a href="#V"><strong>V</strong></a> + | <a href="#W"><strong>W</strong></a> + +</div> +<h2 id="A">A</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.add_noise_to_sino">add_noise_to_sino() (in module astra.functions)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.algorithm">algorithm() (in module astra.matlab)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.astra">astra() (in module astra.matlab)</a> + </dt> + + + <dt><a href="algorithm.html#module-astra.algorithm">astra.algorithm (module)</a> + </dt> + + + <dt><a href="astra.html#module-astra.astra">astra.astra (module)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#module-astra.ASTRAProjector">astra.ASTRAProjector (module)</a> + </dt> + + + <dt><a href="creators.html#module-astra.creators">astra.creators (module)</a> + </dt> + + + <dt><a href="data2d.html#module-astra.data2d">astra.data2d (module)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data3d.html#module-astra.data3d">astra.data3d (module)</a> + </dt> + + + <dt><a href="functions.html#module-astra.functions">astra.functions (module)</a> + </dt> + + + <dt><a href="matlab.html#module-astra.matlab">astra.matlab (module)</a> + </dt> + + + <dt><a href="matrix.html#module-astra.matrix">astra.matrix (module)</a> + </dt> + + + <dt><a href="projector.html#module-astra.projector">astra.projector (module)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.astra_dict">astra_dict() (in module astra.creators)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D">ASTRAProjector2D (class in astra.ASTRAProjector)</a> + </dt> + + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2DTranspose">ASTRAProjector2DTranspose (class in astra.ASTRAProjector)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="B">B</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.backProject">backProject() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="C">C</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data2d.html#astra.data2d.change_geometry">change_geometry() (in module astra.data2d)</a> + </dt> + + + <dt><a href="algorithm.html#astra.algorithm.clear">clear() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.clear">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.clear">(in module astra.data3d)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.clear">(in module astra.functions)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.clear">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.clear">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="algorithm.html#astra.algorithm.create">create() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.create">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.create">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.create">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.create">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="creators.html#astra.creators.create_backprojection">create_backprojection() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_backprojection3d_gpu">create_backprojection3d_gpu() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_proj_geom">create_proj_geom() (in module astra.creators)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="creators.html#astra.creators.create_projector">create_projector() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_reconstruction">create_reconstruction() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_sino">create_sino() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_sino3d_gpu">create_sino3d_gpu() (in module astra.creators)</a> + </dt> + + + <dt><a href="creators.html#astra.creators.create_vol_geom">create_vol_geom() (in module astra.creators)</a> + </dt> + + + <dt><a href="astra.html#astra.astra.credits">credits() (in module astra.astra)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="D">D</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.data2d">data2d() (in module astra.matlab)</a> + </dt> + + + <dt><a href="matlab.html#astra.matlab.data3d">data3d() (in module astra.matlab)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.data_op">data_op() (in module astra.functions)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.delete">delete() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.delete">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.delete">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.delete">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.delete">(in module astra.projector)</a> + </dt> + + </dl></dd> + + <dt><a href="data3d.html#astra.data3d.dimensions">dimensions() (in module astra.data3d)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="F">F</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.forwardProject">forwardProject() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="G">G</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.geom_2vec">geom_2vec() (in module astra.functions)</a> + </dt> + + + <dt><a href="functions.html#astra.functions.geom_size">geom_size() (in module astra.functions)</a> + </dt> + + + <dt><a href="data2d.html#astra.data2d.get">get() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.get">(in module astra.matrix)</a> + </dt> + + </dl></dd> + + <dt><a href="data2d.html#astra.data2d.get_geometry">get_geometry() (in module astra.data2d)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.get_res_norm">get_res_norm() (in module astra.algorithm)</a> + </dt> + + + <dt><a href="data2d.html#astra.data2d.get_shared">get_shared() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get_shared">(in module astra.data3d)</a> + </dt> + + </dl></dd> + + <dt><a href="data2d.html#astra.data2d.get_single">get_single() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.get_single">(in module astra.data3d)</a> + </dt> + + </dl></dd> + + <dt><a href="matrix.html#astra.matrix.get_size">get_size() (in module astra.matrix)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="I">I</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.info">info() (in module astra.algorithm)</a> + </dt> + + <dd><dl> + + <dt><a href="data2d.html#astra.data2d.info">(in module astra.data2d)</a> + </dt> + + + <dt><a href="data3d.html#astra.data3d.info">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.info">(in module astra.matrix)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.info">(in module astra.projector)</a> + </dt> + + </dl></dd> + </dl></td> +</tr></table> + +<h2 id="M">M</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.matrix">matrix() (in module astra.matlab)</a> + </dt> + + <dd><dl> + + <dt><a href="projector.html#astra.projector.matrix">(in module astra.projector)</a> + </dt> + + </dl></dd> + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="functions.html#astra.functions.move_vol_geom">move_vol_geom() (in module astra.functions)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="P">P</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.projection_geometry">projection_geometry() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="matlab.html#astra.matlab.projector">projector() (in module astra.matlab)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="R">R</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="ASTRAProjector.html#astra.ASTRAProjector.ASTRAProjector2D.reconstruct">reconstruct() (astra.ASTRAProjector.ASTRAProjector2D method)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="algorithm.html#astra.algorithm.run">run() (in module astra.algorithm)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="S">S</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.set_gpu_index">set_gpu_index() (in module astra.astra)</a> + </dt> + + + <dt><a href="projector.html#astra.projector.splat">splat() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="data2d.html#astra.data2d.store">store() (in module astra.data2d)</a> + </dt> + + <dd><dl> + + <dt><a href="data3d.html#astra.data3d.store">(in module astra.data3d)</a> + </dt> + + + <dt><a href="matrix.html#astra.matrix.store">(in module astra.matrix)</a> + </dt> + + </dl></dd> + </dl></td> +</tr></table> + +<h2 id="U">U</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.use_cuda">use_cuda() (in module astra.astra)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="V">V</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="astra.html#astra.astra.version">version() (in module astra.astra)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.volume_geometry">volume_geometry() (in module astra.projector)</a> + </dt> + + </dl></td> +</tr></table> + +<h2 id="W">W</h2> +<table style="width: 100%" class="indextable genindextable"><tr> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.weights_projection">weights_projection() (in module astra.projector)</a> + </dt> + + </dl></td> + <td style="width: 33%" valign="top"><dl> + + <dt><a href="projector.html#astra.projector.weights_single_ray">weights_single_ray() (in module astra.projector)</a> + </dt> + + </dl></td> +</tr></table> + + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + + + +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/index.html b/python/docSRC/_build/html/index.html new file mode 100644 index 0000000..817e07f --- /dev/null +++ b/python/docSRC/_build/html/index.html @@ -0,0 +1,148 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Welcome to PyASTRAToolbox’s documentation! — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script 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<div class="body"> + + <div class="section" id="welcome-to-pyastratoolbox-s-documentation"> +<h1>Welcome to PyASTRAToolbox’s documentation!<a class="headerlink" href="#welcome-to-pyastratoolbox-s-documentation" title="Permalink to this headline">¶</a></h1> +<p>Contents:</p> +<div class="toctree-wrapper compound"> +<ul> +<li class="toctree-l1"><a class="reference internal" href="data2d.html">2D data objects: the <tt class="docutils literal"><span class="pre">data2d</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="data3d.html">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="projector.html">Projector object: the <tt class="docutils literal"><span class="pre">projector</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="algorithm.html">Algorithms: the <tt class="docutils literal"><span class="pre">algorithm</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="matrix.html">Sparse matrices: the <tt class="docutils literal"><span class="pre">matrix</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="creators.html">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="functions.html">Additional functions: the <tt class="docutils literal"><span class="pre">functions</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="ASTRAProjector.html">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="matlab.html">MATLAB compatibility interface: the <tt class="docutils literal"><span class="pre">matlab</span></tt> module</a></li> +<li class="toctree-l1"><a class="reference internal" href="astra.html">Additional ASTRA methods: the <tt class="docutils literal"><span class="pre">astra</span></tt> module</a></li> +</ul> +</div> +</div> +<div class="section" id="indices-and-tables"> +<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1> +<ul class="simple"> +<li><a class="reference internal" href="genindex.html"><em>Index</em></a></li> +<li><a class="reference internal" href="py-modindex.html"><em>Module Index</em></a></li> +<li><a class="reference internal" href="search.html"><em>Search Page</em></a></li> +</ul> +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h3><a href="#">Table Of Contents</a></h3> + <ul> +<li><a class="reference internal" href="#">Welcome to PyASTRAToolbox’s documentation!</a></li> +<li><a class="reference internal" href="#indices-and-tables">Indices and tables</a></li> +</ul> + 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\ No newline at end of file diff --git a/python/docSRC/_build/html/matlab.html b/python/docSRC/_build/html/matlab.html new file mode 100644 index 0000000..8b4bf31 --- /dev/null +++ b/python/docSRC/_build/html/matlab.html @@ -0,0 +1,184 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>MATLAB compatibility interface: the matlab module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Additional ASTRA methods: the astra module" href="astra.html" /> + <link rel="prev" title="Helper class: the ASTRAProjector module" href="ASTRAProjector.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="astra.html" title="Additional ASTRA methods: the astra module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.matlab"> +<span id="matlab-compatibility-interface-the-matlab-module"></span><h1>MATLAB compatibility interface: the <tt class="xref py py-mod docutils literal"><span class="pre">matlab</span></tt> module<a class="headerlink" href="#module-astra.matlab" title="Permalink to this headline">¶</a></h1> +<p>This module implements a MATLAB-like interface to the ASTRA Toolbox.</p> +<p>Note that all functions are called with a <tt class="xref py py-class docutils literal"><span class="pre">string</span></tt> as the first +argument, specifying the operation to perform. This un-pythonic way +is used to make transitioning from MATLAB code to Python code easier, as +the MATLAB interface uses the same type of method calling.</p> +<p>After an initial <tt class="docutils literal"><span class="pre">import</span> <span class="pre">astra</span></tt>, these functions can be accessed in the +<tt class="docutils literal"><span class="pre">astra.m</span></tt> module.</p> +<dl class="function"> +<dt id="astra.matlab.algorithm"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">algorithm</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#algorithm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.algorithm" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="algorithm.html#module-astra.algorithm" title="astra.algorithm"><tt class="xref py py-mod docutils literal"><span class="pre">astra.algorithm</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.algorithm('run',i,1000)</span></tt> – Run an algorithm with 1000 iterations.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.astra"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">astra</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#astra"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.astra" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="astra.html#module-astra.astra" title="astra.astra"><tt class="xref py py-mod docutils literal"><span class="pre">astra.astra</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.astra('use_cuda')</span></tt> – Check if CUDA is enabled.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.data2d"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">data2d</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#data2d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.data2d" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="data2d.html#module-astra.data2d" title="astra.data2d"><tt class="xref py py-mod docutils literal"><span class="pre">astra.data2d</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.data2d('create',type,geometry,data)</span></tt> – Create a 2D object.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.data3d"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">data3d</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#data3d"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.data3d" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="data3d.html#module-astra.data3d" title="astra.data3d"><tt class="xref py py-mod docutils literal"><span class="pre">astra.data3d</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.data3d('get',i)</span></tt> – Get 3D object data.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.matrix"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">matrix</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.matrix" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="matrix.html#module-astra.matrix" title="astra.matrix"><tt class="xref py py-mod docutils literal"><span class="pre">astra.matrix</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.matrix('delete',i)</span></tt> – Delete a matrix.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matlab.projector"> +<tt class="descclassname">astra.matlab.</tt><tt class="descname">projector</tt><big>(</big><em>command</em>, <em>*args</em><big>)</big><a class="reference internal" href="_modules/astra/matlab.html#projector"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matlab.projector" title="Permalink to this definition">¶</a></dt> +<dd><p>MATLAB-like interface to the <a class="reference internal" href="projector.html#module-astra.projector" title="astra.projector"><tt class="xref py py-mod docutils literal"><span class="pre">astra.projector</span></tt></a> module</p> +<p>For example:</p> +<p><tt class="docutils literal"><span class="pre">astra.m.projector('volume_geometry',i)</span></tt> – Get volume geometry.</p> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="ASTRAProjector.html" + title="previous chapter">Helper class: the <tt class="docutils literal"><span class="pre">ASTRAProjector</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="astra.html" + title="next chapter">Additional ASTRA methods: the <tt class="docutils literal"><span class="pre">astra</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/matlab.txt" + rel="nofollow">Show Source</a></li> + </ul> +<div id="searchbox" style="display: none"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <input type="text" name="q" /> + <input type="submit" value="Go" /> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> + <p class="searchtip" style="font-size: 90%"> + Enter search terms or a module, class or function name. + </p> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="astra.html" title="Additional ASTRA methods: the astra module" + >next</a> |</li> + <li class="right" > + <a href="ASTRAProjector.html" title="Helper class: the ASTRAProjector module" + >previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="footer"> + © Copyright 2013, Centrum Wiskunde & Informatica, Amsterdam. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3. + </div> +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> + + </body> +</html>
\ No newline at end of file diff --git a/python/docSRC/_build/html/matrix.html b/python/docSRC/_build/html/matrix.html new file mode 100644 index 0000000..1df4c30 --- /dev/null +++ b/python/docSRC/_build/html/matrix.html @@ -0,0 +1,221 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Sparse matrices: the matrix module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Creation of objects: the creators module" href="creators.html" /> + <link rel="prev" title="Algorithms: the algorithm module" href="algorithm.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="creators.html" title="Creation of objects: the creators module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="algorithm.html" title="Algorithms: the algorithm module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.matrix"> +<span id="sparse-matrices-the-matrix-module"></span><h1>Sparse matrices: the <tt class="xref py py-mod docutils literal"><span class="pre">matrix</span></tt> module<a class="headerlink" href="#module-astra.matrix" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.matrix.clear"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all matrix objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.create"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">create</tt><big>(</big><em>data</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create matrix object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>data</strong> (<tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt>) – Data to fill the created object with.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.delete"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.get"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">get</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#get"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.get" title="Permalink to this definition">¶</a></dt> +<dd><p>Get a matrix object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to get.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt> – The object data.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.get_size"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">get_size</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#get_size"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.get_size" title="Permalink to this definition">¶</a></dt> +<dd><p>Get matrix dimensions.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><tt class="xref py py-class docutils literal"><span class="pre">tuple</span></tt> – matrix dimensions.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.info"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on matrix objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.matrix.store"> +<tt class="descclassname">astra.matrix.</tt><tt class="descname">store</tt><big>(</big><em>i</em>, <em>data</em><big>)</big><a class="reference internal" href="_modules/astra/matrix.html#store"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.matrix.store" title="Permalink to this definition">¶</a></dt> +<dd><p>Fill existing matrix object with data.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple"> +<li><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of object to fill.</li> +<li><strong>data</strong> (<tt class="xref py py-class docutils literal"><span class="pre">scipy.sparse.csr_matrix</span></tt>) – Data to fill the object with.</li> +</ul> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="algorithm.html" + title="previous chapter">Algorithms: the <tt class="docutils literal"><span class="pre">algorithm</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a href="creators.html" + title="next chapter">Creation of objects: the <tt class="docutils literal"><span class="pre">creators</span></tt> module</a></p> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a 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\ No newline at end of file diff --git a/python/docSRC/_build/html/objects.inv b/python/docSRC/_build/html/objects.inv Binary files differnew file mode 100644 index 0000000..54bab0b --- /dev/null +++ b/python/docSRC/_build/html/objects.inv diff --git a/python/docSRC/_build/html/projector.html b/python/docSRC/_build/html/projector.html new file mode 100644 index 0000000..9df5d0b --- /dev/null +++ b/python/docSRC/_build/html/projector.html @@ -0,0 +1,234 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Projector object: the projector module — PyASTRAToolbox 1.6 documentation</title> + + <link rel="stylesheet" href="_static/default.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '1.6', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="top" title="PyASTRAToolbox 1.6 documentation" href="index.html" /> + <link rel="next" title="Algorithms: the algorithm module" href="algorithm.html" /> + <link rel="prev" title="3D data objects: the data3d module" href="data3d.html" /> + </head> + <body> + <div class="related"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="algorithm.html" title="Algorithms: the algorithm module" + accesskey="N">next</a> |</li> + <li class="right" > + <a href="data3d.html" title="3D data objects: the data3d module" + accesskey="P">previous</a> |</li> + <li><a href="index.html">PyASTRAToolbox 1.6 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body"> + + <div class="section" id="module-astra.projector"> +<span id="projector-object-the-projector-module"></span><h1>Projector object: the <tt class="xref py py-mod docutils literal"><span class="pre">projector</span></tt> module<a class="headerlink" href="#module-astra.projector" title="Permalink to this headline">¶</a></h1> +<dl class="function"> +<dt id="astra.projector.clear"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">clear</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/projector.html#clear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.clear" title="Permalink to this definition">¶</a></dt> +<dd><p>Clear all projector objects.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.create"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">create</tt><big>(</big><em>config</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#create"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.create" title="Permalink to this definition">¶</a></dt> +<dd><p>Create projector object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>config</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a>) – Projector options.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – the ID of the constructed object.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.delete"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">delete</tt><big>(</big><em>ids</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#delete"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.delete" title="Permalink to this definition">¶</a></dt> +<dd><p>Delete a projector object.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>ids</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> or <a class="reference external" href="http://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">list</span></tt></a>) – ID or list of ID’s to delete.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.info"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">info</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/astra/projector.html#info"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.info" title="Permalink to this definition">¶</a></dt> +<dd><p>Print info on projector objects in memory.</p> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.matrix"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">matrix</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.matrix" title="Permalink to this definition">¶</a></dt> +<dd><p>Get sparse matrix of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a> – ID of sparse matrix.</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.projection_geometry"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">projection_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#projection_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.projection_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get projection geometry of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – projection geometry</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.splat"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">splat</tt><big>(</big><em>i</em>, <em>row</em>, <em>col</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#splat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.splat" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +<dl class="function"> +<dt id="astra.projector.volume_geometry"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">volume_geometry</tt><big>(</big><em>i</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#volume_geometry"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.volume_geometry" title="Permalink to this definition">¶</a></dt> +<dd><p>Get volume geometry of a projector.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>i</strong> (<a class="reference external" href="http://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">int</span></tt></a>) – ID of projector.</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><a class="reference external" href="http://docs.python.org/2.7/library/stdtypes.html#dict" title="(in Python v2.7)"><tt class="xref py py-class docutils literal"><span class="pre">dict</span></tt></a> – volume geometry</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="astra.projector.weights_projection"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">weights_projection</tt><big>(</big><em>i</em>, <em>projection_index</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#weights_projection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.weights_projection" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +<dl class="function"> +<dt id="astra.projector.weights_single_ray"> +<tt class="descclassname">astra.projector.</tt><tt class="descname">weights_single_ray</tt><big>(</big><em>i</em>, <em>projection_index</em>, <em>detector_index</em><big>)</big><a class="reference internal" href="_modules/astra/projector.html#weights_single_ray"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#astra.projector.weights_single_ray" title="Permalink to this definition">¶</a></dt> +<dd></dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="data3d.html" + title="previous chapter">3D data objects: the <tt class="docutils literal"><span class="pre">data3d</span></tt> module</a></p> + <h4>Next topic</h4> + <p class="topless"><a 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\ No newline at end of file diff --git a/python/docSRC/_build/html/searchindex.js b/python/docSRC/_build/html/searchindex.js new file mode 100644 index 0000000..cc69a68 --- /dev/null +++ b/python/docSRC/_build/html/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({objtypes:{"0":"py:module","1":"py:function","2":"py:method","3":"py:class"},objnames:{"0":["py","module","Python module"],"1":["py","function","Python function"],"2":["py","method","Python method"],"3":["py","class","Python 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\ No newline at end of file diff --git a/python/docSRC/_templates/layout.html b/python/docSRC/_templates/layout.html new file mode 100644 index 0000000..f30df11 --- /dev/null +++ b/python/docSRC/_templates/layout.html @@ -0,0 +1,15 @@ +{% extends "!layout.html" %} + +{% block footer %} +{{ super() }} +<script> + (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ + (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), + m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) + })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); + + ga('create', 'UA-40340335-1', 'dmpelt.github.io'); + ga('send', 'pageview'); + +</script> +{% endblock %} diff --git a/python/docSRC/algorithm.rst b/python/docSRC/algorithm.rst new file mode 100644 index 0000000..83752bd --- /dev/null +++ b/python/docSRC/algorithm.rst @@ -0,0 +1,8 @@ +Algorithms: the :mod:`algorithm` module +======================================= + +.. automodule:: astra.algorithm + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/astra.rst b/python/docSRC/astra.rst new file mode 100644 index 0000000..5d5fdf0 --- /dev/null +++ b/python/docSRC/astra.rst @@ -0,0 +1,8 @@ +Additional ASTRA methods: the :mod:`astra` module +======================================================== + +.. automodule:: astra.astra + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/conf.py b/python/docSRC/conf.py new file mode 100644 index 0000000..e54bbb8 --- /dev/null +++ b/python/docSRC/conf.py @@ -0,0 +1,287 @@ +# -*- coding: utf-8 -*- +# +# .. documentation build configuration file, created by +# sphinx-quickstart on Wed Mar 13 16:36:32 2013. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode','sphinx.ext.mathjax','sphinx.ext.intersphinx'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'PyASTRAToolbox' +copyright = u'2013, Centrum Wiskunde & Informatica, Amsterdam' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version = '1.6' +# The full version, including alpha/beta/rc tags. +release = '1.6' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = ['_build'] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +#add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'doc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', '.tex', u'.. Documentation', + u'Author', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', '', u'.. Documentation', + [u'Author'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', '', u'.. Documentation', + u'Author', '', 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' + + +# -- Options for Epub output --------------------------------------------------- + +# Bibliographic Dublin Core info. +epub_title = u'..' +epub_author = u'Author' +epub_publisher = u'Author' +epub_copyright = u'2013, Author' + +# The language of the text. It defaults to the language option +# or en if the language is not set. +#epub_language = '' + +# The scheme of the identifier. Typical schemes are ISBN or URL. +#epub_scheme = '' + +# The unique identifier of the text. This can be a ISBN number +# or the project homepage. +#epub_identifier = '' + +# A unique identification for the text. +#epub_uid = '' + +# A tuple containing the cover image and cover page html template filenames. +#epub_cover = () + +# HTML files that should be inserted before the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_pre_files = [] + +# HTML files shat should be inserted after the pages created by sphinx. +# The format is a list of tuples containing the path and title. +#epub_post_files = [] + +# A list of files that should not be packed into the epub file. +#epub_exclude_files = [] + +# The depth of the table of contents in toc.ncx. +#epub_tocdepth = 3 + +# Allow duplicate toc entries. +#epub_tocdup = True + +intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy':('http://docs.scipy.org/doc/numpy/',None)} diff --git a/python/docSRC/creators.rst b/python/docSRC/creators.rst new file mode 100644 index 0000000..d6249c3 --- /dev/null +++ b/python/docSRC/creators.rst @@ -0,0 +1,8 @@ +Creation of objects: the :mod:`creators` module +=============================================== + +.. automodule:: astra.creators + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/data2d.rst b/python/docSRC/data2d.rst new file mode 100644 index 0000000..342cbec --- /dev/null +++ b/python/docSRC/data2d.rst @@ -0,0 +1,8 @@ +2D data objects: the :mod:`data2d` module +========================================= + +.. automodule:: astra.data2d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/data3d.rst b/python/docSRC/data3d.rst new file mode 100644 index 0000000..5b7de23 --- /dev/null +++ b/python/docSRC/data3d.rst @@ -0,0 +1,8 @@ +3D data objects: the :mod:`data3d` module +========================================= + +.. automodule:: astra.data3d + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/functions.rst b/python/docSRC/functions.rst new file mode 100644 index 0000000..749eb27 --- /dev/null +++ b/python/docSRC/functions.rst @@ -0,0 +1,8 @@ +Additional functions: the :mod:`functions` module +================================================= + +.. automodule:: astra.functions + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/index.rst b/python/docSRC/index.rst new file mode 100644 index 0000000..8d17a4a --- /dev/null +++ b/python/docSRC/index.rst @@ -0,0 +1,34 @@ +.. .. documentation master file, created by + sphinx-quickstart on Wed Mar 13 16:36:32 2013. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to PyASTRAToolbox's documentation! +========================================== + +Contents: + +.. toctree:: + :maxdepth: 4 + + data2d + data3d + projector + algorithm + matrix + creators + functions + ASTRAProjector + matlab + astra +.. astra +.. builder + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff --git a/python/docSRC/make.bat b/python/docSRC/make.bat new file mode 100644 index 0000000..d70c604 --- /dev/null +++ b/python/docSRC/make.bat @@ -0,0 +1,190 @@ +@ECHO OFF + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set BUILDDIR=_build +set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% . +set I18NSPHINXOPTS=%SPHINXOPTS% . +if NOT "%PAPER%" == "" ( + set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS% + set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS% +) + +if "%1" == "" goto help + +if "%1" == "help" ( + :help + echo.Please use `make ^<target^>` where ^<target^> is one of + echo. html to make standalone HTML files + echo. dirhtml to make HTML files named index.html in directories + echo. singlehtml to make a single large HTML file + echo. pickle to make pickle files + echo. json to make JSON files + echo. htmlhelp to make HTML files and a HTML help project + echo. qthelp to make HTML files and a qthelp project + echo. devhelp to make HTML files and a Devhelp project + echo. epub to make an epub + echo. latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter + echo. text to make text files + echo. man to make manual pages + echo. texinfo to make Texinfo files + echo. gettext to make PO message catalogs + echo. changes to make an overview over all changed/added/deprecated items + echo. linkcheck to check all external links for integrity + echo. doctest to run all doctests embedded in the documentation if enabled + goto end +) + +if "%1" == "clean" ( + for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i + del /q /s %BUILDDIR%\* + goto end +) + +if "%1" == "html" ( + %SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/html. + goto end +) + +if "%1" == "dirhtml" ( + %SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml. + goto end +) + +if "%1" == "singlehtml" ( + %SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml. + goto end +) + +if "%1" == "pickle" ( + %SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the pickle files. + goto end +) + +if "%1" == "json" ( + %SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can process the JSON files. + goto end +) + +if "%1" == "htmlhelp" ( + %SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run HTML Help Workshop with the ^ +.hhp project file in %BUILDDIR%/htmlhelp. + goto end +) + +if "%1" == "qthelp" ( + %SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; now you can run "qcollectiongenerator" with the ^ +.qhcp project file in %BUILDDIR%/qthelp, like this: + echo.^> qcollectiongenerator %BUILDDIR%\qthelp\.qhcp + echo.To view the help file: + echo.^> assistant -collectionFile %BUILDDIR%\qthelp\.ghc + goto end +) + +if "%1" == "devhelp" ( + %SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. + goto end +) + +if "%1" == "epub" ( + %SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The epub file is in %BUILDDIR%/epub. + goto end +) + +if "%1" == "latex" ( + %SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex + if errorlevel 1 exit /b 1 + echo. + echo.Build finished; the LaTeX files are in %BUILDDIR%/latex. + goto end +) + +if "%1" == "text" ( + %SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The text files are in %BUILDDIR%/text. + goto end +) + +if "%1" == "man" ( + %SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The manual pages are in %BUILDDIR%/man. + goto end +) + +if "%1" == "texinfo" ( + %SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo. + goto end +) + +if "%1" == "gettext" ( + %SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale + if errorlevel 1 exit /b 1 + echo. + echo.Build finished. The message catalogs are in %BUILDDIR%/locale. + goto end +) + +if "%1" == "changes" ( + %SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes + if errorlevel 1 exit /b 1 + echo. + echo.The overview file is in %BUILDDIR%/changes. + goto end +) + +if "%1" == "linkcheck" ( + %SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck + if errorlevel 1 exit /b 1 + echo. + echo.Link check complete; look for any errors in the above output ^ +or in %BUILDDIR%/linkcheck/output.txt. + goto end +) + +if "%1" == "doctest" ( + %SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest + if errorlevel 1 exit /b 1 + echo. + echo.Testing of doctests in the sources finished, look at the ^ +results in %BUILDDIR%/doctest/output.txt. + goto end +) + +:end diff --git a/python/docSRC/matlab.rst b/python/docSRC/matlab.rst new file mode 100644 index 0000000..fb7033e --- /dev/null +++ b/python/docSRC/matlab.rst @@ -0,0 +1,8 @@ +MATLAB compatibility interface: the :mod:`matlab` module +======================================================== + +.. automodule:: astra.matlab + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/matrix.rst b/python/docSRC/matrix.rst new file mode 100644 index 0000000..6f11d8a --- /dev/null +++ b/python/docSRC/matrix.rst @@ -0,0 +1,8 @@ +Sparse matrices: the :mod:`matrix` module +========================================= + +.. automodule:: astra.matrix + :members: + :undoc-members: + :show-inheritance: + diff --git a/python/docSRC/projector.rst b/python/docSRC/projector.rst new file mode 100644 index 0000000..b0854e8 --- /dev/null +++ b/python/docSRC/projector.rst @@ -0,0 +1,8 @@ +Projector object: the :mod:`projector` module +============================================= + +.. automodule:: astra.projector + :members: + :undoc-members: + :show-inheritance: + diff --git a/samples/s001_sinogram_par2d.m b/samples/matlab/s001_sinogram_par2d.m index 4494e7b..4494e7b 100644 --- a/samples/s001_sinogram_par2d.m +++ b/samples/matlab/s001_sinogram_par2d.m diff --git a/samples/s002_data2d.m b/samples/matlab/s002_data2d.m index a91071f..a91071f 100644 --- a/samples/s002_data2d.m +++ b/samples/matlab/s002_data2d.m diff --git a/samples/s003_gpu_reconstruction.m b/samples/matlab/s003_gpu_reconstruction.m index efb5c68..efb5c68 100644 --- a/samples/s003_gpu_reconstruction.m +++ b/samples/matlab/s003_gpu_reconstruction.m diff --git a/samples/s004_cpu_reconstruction.m b/samples/matlab/s004_cpu_reconstruction.m index f25cd2b..f25cd2b 100644 --- a/samples/s004_cpu_reconstruction.m +++ b/samples/matlab/s004_cpu_reconstruction.m diff --git a/samples/s005_3d_geometry.m b/samples/matlab/s005_3d_geometry.m index 4b7360b..4b7360b 100644 --- a/samples/s005_3d_geometry.m +++ b/samples/matlab/s005_3d_geometry.m diff --git a/samples/s006_3d_data.m b/samples/matlab/s006_3d_data.m index 32d88cc..32d88cc 100644 --- a/samples/s006_3d_data.m +++ b/samples/matlab/s006_3d_data.m diff --git a/samples/s007_3d_reconstruction.m b/samples/matlab/s007_3d_reconstruction.m index fc9aca6..fc9aca6 100644 --- a/samples/s007_3d_reconstruction.m +++ b/samples/matlab/s007_3d_reconstruction.m diff --git a/samples/s008_gpu_selection.m b/samples/matlab/s008_gpu_selection.m index a9e152d..a9e152d 100644 --- a/samples/s008_gpu_selection.m +++ b/samples/matlab/s008_gpu_selection.m diff --git a/samples/s009_projection_matrix.m b/samples/matlab/s009_projection_matrix.m index efda0d2..efda0d2 100644 --- a/samples/s009_projection_matrix.m +++ b/samples/matlab/s009_projection_matrix.m diff --git a/samples/s010_supersampling.m b/samples/matlab/s010_supersampling.m index 80f6f56..80f6f56 100644 --- a/samples/s010_supersampling.m +++ b/samples/matlab/s010_supersampling.m diff --git a/samples/s011_object_info.m b/samples/matlab/s011_object_info.m index 61ecb83..61ecb83 100644 --- a/samples/s011_object_info.m +++ b/samples/matlab/s011_object_info.m diff --git a/samples/s012_masks.m b/samples/matlab/s012_masks.m index d3611a6..d3611a6 100644 --- a/samples/s012_masks.m +++ b/samples/matlab/s012_masks.m diff --git a/samples/s013_constraints.m b/samples/matlab/s013_constraints.m index d72195c..d72195c 100644 --- a/samples/s013_constraints.m +++ b/samples/matlab/s013_constraints.m diff --git a/samples/s014_FBP.m b/samples/matlab/s014_FBP.m index b73149c..b73149c 100644 --- a/samples/s014_FBP.m +++ b/samples/matlab/s014_FBP.m diff --git a/samples/s015_fp_bp.m b/samples/matlab/s015_fp_bp.m index 8cc417e..8cc417e 100644 --- a/samples/s015_fp_bp.m +++ b/samples/matlab/s015_fp_bp.m diff --git a/samples/s016_plots.m b/samples/matlab/s016_plots.m index 1455c6d..1455c6d 100644 --- a/samples/s016_plots.m +++ b/samples/matlab/s016_plots.m diff --git a/samples/python/phantom.mat b/samples/python/phantom.mat Binary files differnew file mode 100644 index 0000000..c465bbe --- /dev/null +++ b/samples/python/phantom.mat diff --git a/samples/python/s001_sinogram_par2d.py b/samples/python/s001_sinogram_par2d.py new file mode 100644 index 0000000..1d1b912 --- /dev/null +++ b/samples/python/s001_sinogram_par2d.py @@ -0,0 +1,60 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# Create a basic 256x256 square volume geometry +vol_geom = astra.create_vol_geom(256, 256) + +# Create a parallel beam geometry with 180 angles between 0 and pi, and +# 384 detector pixels of width 1. +# For more details on available geometries, see the online help of the +# function astra_create_proj_geom . +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# Load a 256x256 phantom image +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Create a sinogram using the GPU. +# Note that the first time the GPU is accessed, there may be a delay +# of up to 10 seconds for initialization. +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) +pylab.show() + + +# Free memory +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s002_data2d.py b/samples/python/s002_data2d.py new file mode 100644 index 0000000..35fb91f --- /dev/null +++ b/samples/python/s002_data2d.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) + +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + + +# Create volumes + +# initialized to zero +v0 = astra.data2d.create('-vol', vol_geom) + +# initialized to 3.0 +v1 = astra.data2d.create('-vol', vol_geom, 3.0) + +# initialized to a matrix. A may be a single, double or logical (0/1) array. +import scipy.io +A = scipy.io.loadmat('phantom.mat')['phantom256'] +v2 = astra.data2d.create('-vol', vol_geom, A) + + +# Projection data +s0 = astra.data2d.create('-sino', proj_geom) +# Initialization to a scalar or a matrix also works, exactly as with a volume. + + +# Update data + +# set to zero +astra.data2d.store(v0, 0) + +# set to a matrix +astra.data2d.store(v2, A) + + + +# Retrieve data + +R = astra.data2d.get(v2) +import pylab +pylab.gray() +pylab.imshow(R) +pylab.show() + + +# Free memory +astra.data2d.delete(v0) +astra.data2d.delete(v1) +astra.data2d.delete(v2) +astra.data2d.delete(s0) diff --git a/samples/python/s003_gpu_reconstruction.py b/samples/python/s003_gpu_reconstruction.py new file mode 100644 index 0000000..07b38ef --- /dev/null +++ b/samples/python/s003_gpu_reconstruction.py @@ -0,0 +1,75 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Available algorithms: +# SIRT_CUDA, SART_CUDA, EM_CUDA, FBP_CUDA (see the FBP sample) + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s004_cpu_reconstruction.py b/samples/python/s004_cpu_reconstruction.py new file mode 100644 index 0000000..8385cf8 --- /dev/null +++ b/samples/python/s004_cpu_reconstruction.py @@ -0,0 +1,81 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# For CPU-based algorithms, a "projector" object specifies the projection +# model used. In this case, we use the "strip" model. +proj_id = astra.create_projector('strip', proj_geom, vol_geom) + +# Create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the CPU +# The main difference with the configuration of a GPU algorithm is the +# extra ProjectorId setting. +cfg = astra.astra_dict('SIRT') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['ProjectorId'] = proj_id + +# Available algorithms: +# ART, SART, SIRT, CGLS, FBP + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 20 iterations of the algorithm +# This will have a runtime in the order of 10 seconds. +astra.algorithm.run(alg_id, 20) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s005_3d_geometry.py b/samples/python/s005_3d_geometry.py new file mode 100644 index 0000000..f43fc7e --- /dev/null +++ b/samples/python/s005_3d_geometry.py @@ -0,0 +1,114 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from six.moves import range +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(64, 64, 64) + + +# There are two main 3d projection geometry types: cone beam and parallel beam. +# Each has a regular variant, and a 'vec' variant. +# The 'vec' variants are completely free in the placement of source/detector, +# while the regular variants assume circular trajectories around the z-axis. + + +# ------------- +# Parallel beam +# ------------- + + +# Circular + +# Parameters: width of detector column, height of detector row, #rows, #columns +angles = np.linspace(0, 2*np.pi, 48, False) +proj_geom = astra.create_proj_geom('parallel3d', 1.0, 1.0, 32, 64, angles) + + +# Free + +# We generate the same geometry as the circular one above. +vectors = np.zeros((len(angles), 12)) +for i in range(len(angles)): + # ray direction + vectors[i,0] = np.sin(angles[i]) + vectors[i,1] = -np.cos(angles[i]) + vectors[i,2] = 0 + + # center of detector + vectors[i,3:6] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i,6] = np.cos(angles[i]) + vectors[i,7] = np.sin(angles[i]) + vectors[i,8] = 0; + + # vector from detector pixel (0,0) to (1,0) + vectors[i,9] = 0 + vectors[i,10] = 0 + vectors[i,11] = 1 + +# Parameters: #rows, #columns, vectors +proj_geom = astra.create_proj_geom('parallel3d_vec', 32, 64, vectors) + +# ---------- +# Cone beam +# ---------- + + +# Circular + +# Parameters: width of detector column, height of detector row, #rows, #columns, +# angles, distance source-origin, distance origin-detector +angles = np.linspace(0, 2*np.pi, 48, False) +proj_geom = astra.create_proj_geom('cone', 1.0, 1.0, 32, 64, angles, 1000, 0) + +# Free + +vectors = np.zeros((len(angles), 12)) +for i in range(len(angles)): + # source + vectors[i,0] = np.sin(angles[i]) * 1000 + vectors[i,1] = -np.cos(angles[i]) * 1000 + vectors[i,2] = 0 + + # center of detector + vectors[i,3:6] = 0 + + # vector from detector pixel (0,0) to (0,1) + vectors[i,6] = np.cos(angles[i]) + vectors[i,7] = np.sin(angles[i]) + vectors[i,8] = 0 + + # vector from detector pixel (0,0) to (1,0) + vectors[i,9] = 0 + vectors[i,10] = 0 + vectors[i,11] = 1 + +# Parameters: #rows, #columns, vectors +proj_geom = astra.create_proj_geom('cone_vec', 32, 64, vectors) + diff --git a/samples/python/s006_3d_data.py b/samples/python/s006_3d_data.py new file mode 100644 index 0000000..5178179 --- /dev/null +++ b/samples/python/s006_3d_data.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# Create a 3D volume geometry. +# Parameter order: rows, colums, slices (y, x, z) +vol_geom = astra.create_vol_geom(64, 48, 32) + + +# Create volumes + +# initialized to zero +v0 = astra.data3d.create('-vol', vol_geom) + +# initialized to 3.0 +v1 = astra.data3d.create('-vol', vol_geom, 3.0) + +# initialized to a matrix. A may be a single or double array. +# Coordinate order: slice, row, column (z, y, x) +A = np.zeros((32, 64, 48)) +v2 = astra.data3d.create('-vol', vol_geom, A) + + +# Projection data + +# 2 projection directions, along x and y axis resp. +V = np.array([[ 1,0,0, 0,0,0, 0,1,0, 0,0,1], + [0,1,0, 0,0,0, -1,0,0, 0,0,1]],dtype=np.float) +# 32 rows (v), 64 columns (u) +proj_geom = astra.create_proj_geom('parallel3d_vec', 32, 64, V) + +s0 = astra.data3d.create('-proj3d', proj_geom) + +# Initialization to a scalar or zero works exactly as with a volume. + +# Initialized to a matrix: +# Coordinate order: row (v), angle, column (u) +A = np.zeros((32, 2, 64)) +s1 = astra.data3d.create('-proj3d', proj_geom, A) + + +# Retrieve data: +R = astra.data3d.get(v1) + + +# Delete all created data objects +astra.data3d.delete(v0) +astra.data3d.delete(v1) +astra.data3d.delete(v2) +astra.data3d.delete(s0) +astra.data3d.delete(s1) diff --git a/samples/python/s007_3d_reconstruction.py b/samples/python/s007_3d_reconstruction.py new file mode 100644 index 0000000..40e9556 --- /dev/null +++ b/samples/python/s007_3d_reconstruction.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(128, 128, 128) + +angles = np.linspace(0, np.pi, 180,False) +proj_geom = astra.create_proj_geom('parallel3d', 1.0, 1.0, 128, 192, angles) + +# Create a simple hollow cube phantom +cube = np.zeros((128,128,128)) +cube[17:113,17:113,17:113] = 1 +cube[33:97,33:97,33:97] = 0 + +# Create projection data from this +proj_id, proj_data = astra.create_sino3d_gpu(cube, proj_geom, vol_geom) + +# Display a single projection image +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(proj_data[:,20,:]) + +# Create a data object for the reconstruction +rec_id = astra.data3d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT3D_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = proj_id + + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +# Note that this requires about 750MB of GPU memory, and has a runtime +# in the order of 10 seconds. +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data3d.get(rec_id) +pylab.figure(2) +pylab.imshow(rec[:,:,65]) +pylab.show() + + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data3d.delete(rec_id) +astra.data3d.delete(proj_id) diff --git a/samples/python/s008_gpu_selection.py b/samples/python/s008_gpu_selection.py new file mode 100644 index 0000000..a180802 --- /dev/null +++ b/samples/python/s008_gpu_selection.py @@ -0,0 +1,61 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + +# Create a sinogram from a phantom, using GPU #1. (The default is #0) +sinogram_id, sinogram = astra.create_sino(P, proj_id, gpuIndex=1) + + +# Set up the parameters for a reconstruction algorithm using the GPU +rec_id = astra.data2d.create('-vol', vol_geom) +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Use GPU #1 for the reconstruction. (The default is #0.) +cfg['option'] = {} +cfg['option']['GPUindex'] = 1 + +# Run 150 iterations of the algorithm +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id, 150) +rec = astra.data2d.get(rec_id) + + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s009_projection_matrix.py b/samples/python/s009_projection_matrix.py new file mode 100644 index 0000000..c4c4557 --- /dev/null +++ b/samples/python/s009_projection_matrix.py @@ -0,0 +1,65 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# For CPU-based algorithms, a "projector" object specifies the projection +# model used. In this case, we use the "line" model. +proj_id = astra.create_projector('line', proj_geom, vol_geom) + +# Generate the projection matrix for this projection model. +# This creates a matrix W where entry w_{i,j} corresponds to the +# contribution of volume element j to detector element i. +matrix_id = astra.projector.matrix(proj_id) + +# Get the projection matrix as a Scipy sparse matrix. +W = astra.matrix.get(matrix_id) + + +# Manually use this projection matrix to do a projection: +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +s = W.dot(P.flatten()) +s = np.reshape(s, (len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'])) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(s) +pylab.show() + +# Each row of the projection matrix corresponds to a detector element. +# Detector t for angle p is for row 1 + t + p*proj_geom.DetectorCount. +# Each column corresponds to a volume pixel. +# Pixel (x,y) corresponds to column 1 + x + y*vol_geom.GridColCount. + + +astra.projector.delete(proj_id) +astra.matrix.delete(matrix_id) diff --git a/samples/python/s010_supersampling.py b/samples/python/s010_supersampling.py new file mode 100644 index 0000000..1a337bc --- /dev/null +++ b/samples/python/s010_supersampling.py @@ -0,0 +1,85 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 3.0, 128, np.linspace(0,np.pi,180,False)) +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Because the astra.create_sino method does not have support for +# all possible algorithm options, we manually create a sinogram +phantom_id = astra.data2d.create('-vol', vol_geom, P) +sinogram_id = astra.data2d.create('-sino', proj_geom) +cfg = astra.astra_dict('FP_CUDA') +cfg['VolumeDataId'] = phantom_id +cfg['ProjectionDataId'] = sinogram_id + +# Set up 3 rays per detector element +cfg['option'] = {} +cfg['option']['DetectorSuperSampling'] = 3 + +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id) +astra.algorithm.delete(alg_id) +astra.data2d.delete(phantom_id) + +sinogram3 = astra.data2d.get(sinogram_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram3) + +# Create a reconstruction, also using supersampling +rec_id = astra.data2d.create('-vol', vol_geom) +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +# Set up 3 rays per detector element +cfg['option'] = {} +cfg['option']['DetectorSuperSampling'] = 3 + +# There is also an option for supersampling during the backprojection step. +# This should be used if your detector pixels are smaller than the voxels. + +# Set up 2 rays per image pixel dimension, for 4 rays total per image pixel. +# cfg['option']['PixelSuperSampling'] = 2 + + +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id, 150) +astra.algorithm.delete(alg_id) + +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + diff --git a/samples/python/s011_object_info.py b/samples/python/s011_object_info.py new file mode 100644 index 0000000..02f387a --- /dev/null +++ b/samples/python/s011_object_info.py @@ -0,0 +1,54 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra + +# Create two volume geometries +vol_geom1 = astra.create_vol_geom(256, 256) +vol_geom2 = astra.create_vol_geom(512, 256) + +# Create volumes +v0 = astra.data2d.create('-vol', vol_geom1) +v1 = astra.data2d.create('-vol', vol_geom2) +v2 = astra.data2d.create('-vol', vol_geom2) + +# Show the currently allocated volumes +astra.data2d.info() + + +astra.data2d.delete(v2) +astra.data2d.info() + +astra.data2d.clear() +astra.data2d.info() + + + +# The same clear and info command also work for other object types: +astra.algorithm.info() +astra.data3d.info() +astra.projector.info() +astra.matrix.info() diff --git a/samples/python/s012_masks.py b/samples/python/s012_masks.py new file mode 100644 index 0000000..0f667b0 --- /dev/null +++ b/samples/python/s012_masks.py @@ -0,0 +1,92 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + + +import astra +import numpy as np + +# In this example we will create a reconstruction in a circular region, +# instead of the usual rectangle. + +# This is done by placing a circular mask on the square reconstruction volume: + +c = np.linspace(-127.5,127.5,256) +x, y = np.meshgrid(c,c) +mask = np.array((x**2 + y**2 < 127.5**2),dtype=np.float) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(mask) + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,50,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +pylab.figure(2) +pylab.imshow(P) +pylab.figure(3) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Create a data object for the mask +mask_id = astra.data2d.create('-vol', vol_geom, mask) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['option'] = {} +cfg['option']['ReconstructionMaskId'] = mask_id + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) + +pylab.figure(4) +pylab.imshow(rec) + +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(mask_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s013_constraints.py b/samples/python/s013_constraints.py new file mode 100644 index 0000000..8b63d5e --- /dev/null +++ b/samples/python/s013_constraints.py @@ -0,0 +1,77 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +# In this example we will create a reconstruction constrained to +# greyvalues between 0 and 1 + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,50,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['option']={} +cfg['option']['MinConstraint'] = 0 +cfg['option']['MaxConstraint'] = 1 + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 150 iterations of the algorithm +astra.algorithm.run(alg_id, 150) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s014_FBP.py b/samples/python/s014_FBP.py new file mode 100644 index 0000000..2f8e388 --- /dev/null +++ b/samples/python/s014_FBP.py @@ -0,0 +1,76 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +import astra +import numpy as np + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# create configuration +cfg = astra.astra_dict('FBP_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id +cfg['FilterType'] = 'Ram-Lak' + +# possible values for FilterType: +# none, ram-lak, shepp-logan, cosine, hamming, hann, tukey, lanczos, +# triangular, gaussian, barlett-hann, blackman, nuttall, blackman-harris, +# blackman-nuttall, flat-top, kaiser, parzen + + +# Create and run the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) +astra.algorithm.run(alg_id) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) +pylab.show() + +# Clean up. Note that GPU memory is tied up in the algorithm object, +# and main RAM in the data objects. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/samples/python/s015_fp_bp.py b/samples/python/s015_fp_bp.py new file mode 100644 index 0000000..fa0bf86 --- /dev/null +++ b/samples/python/s015_fp_bp.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + + +# This example demonstrates using the FP and BP primitives with Matlab's lsqr +# solver. Calls to FP (astra.create_sino) and +# BP (astra.create_backprojection) are wrapped in a function astra_wrap, +# and a handle to this function is passed to lsqr. + +# Because in this case the inputs/outputs of FP and BP have to be vectors +# instead of images (matrices), the calls require reshaping to and from vectors. + +import astra +import numpy as np + +# FP/BP wrapper class +class astra_wrap(object): + def __init__(self,proj_geom,vol_geom): + self.proj_id = astra.create_projector('cuda',proj_geom,vol_geom) + self.shape = (proj_geom['DetectorCount']*len(proj_geom['ProjectionAngles']),vol_geom['GridColCount']*vol_geom['GridRowCount']) + self.dtype = np.float + + def matvec(self,v): + sid, s = astra.create_sino(np.reshape(v,(vol_geom['GridRowCount'],vol_geom['GridColCount'])),self.proj_id) + astra.data2d.delete(sid) + return s.flatten() + + def rmatvec(self,v): + bid, b = astra.create_backprojection(np.reshape(v,(len(proj_geom['ProjectionAngles']),proj_geom['DetectorCount'],)),self.proj_id) + astra.data2d.delete(bid) + return b.flatten() + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# Create a 256x256 phantom image +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] + +# Create a sinogram using the GPU. +proj_id = astra.create_projector('cuda',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id) + +# Reshape the sinogram into a vector +b = sinogram.flatten() + +# Call lsqr with ASTRA FP and BP +import scipy.sparse.linalg +wrapper = astra_wrap(proj_geom,vol_geom) +result = scipy.sparse.linalg.lsqr(wrapper,b,atol=1e-4,btol=1e-4,iter_lim=25) + +# Reshape the result into an image +Y = np.reshape(result[0],(vol_geom['GridRowCount'], vol_geom['GridColCount'])); + +import pylab +pylab.gray() +pylab.imshow(Y) +pylab.show() + +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) +astra.projector.delete(wrapper.proj_id) + diff --git a/samples/python/s016_plots.py b/samples/python/s016_plots.py new file mode 100644 index 0000000..cd4d98c --- /dev/null +++ b/samples/python/s016_plots.py @@ -0,0 +1,86 @@ +#----------------------------------------------------------------------- +#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam +# +#Author: Daniel M. Pelt +#Contact: D.M.Pelt@cwi.nl +#Website: http://dmpelt.github.io/pyastratoolbox/ +# +# +#This file is part of the Python interface to the +#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox"). +# +#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify +#it under the terms of the GNU General Public License as published by +#the Free Software Foundation, either version 3 of the License, or +#(at your option) any later version. +# +#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful, +#but WITHOUT ANY WARRANTY; without even the implied warranty of +#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +#GNU General Public License for more details. +# +#You should have received a copy of the GNU General Public License +#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. +# +#----------------------------------------------------------------------- + +from six.moves import range +import astra +import numpy as np + + +vol_geom = astra.create_vol_geom(256, 256) +proj_geom = astra.create_proj_geom('parallel', 1.0, 384, np.linspace(0,np.pi,180,False)) + +# As before, create a sinogram from a phantom +import scipy.io +P = scipy.io.loadmat('phantom.mat')['phantom256'] +proj_id = astra.create_projector('line',proj_geom,vol_geom) +sinogram_id, sinogram = astra.create_sino(P, proj_id,useCUDA=True) + +import pylab +pylab.gray() +pylab.figure(1) +pylab.imshow(P) +pylab.figure(2) +pylab.imshow(sinogram) + +# Create a data object for the reconstruction +rec_id = astra.data2d.create('-vol', vol_geom) + +# Set up the parameters for a reconstruction algorithm using the GPU +cfg = astra.astra_dict('SIRT_CUDA') +cfg['ReconstructionDataId'] = rec_id +cfg['ProjectionDataId'] = sinogram_id + +# Create the algorithm object from the configuration structure +alg_id = astra.algorithm.create(cfg) + +# Run 1500 iterations of the algorithm one at a time, keeping track of errors +nIters = 1500 +phantom_error = np.zeros(nIters) +residual_error = np.zeros(nIters) +for i in range(nIters): + # Run a single iteration + astra.algorithm.run(alg_id, 1) + residual_error[i] = astra.algorithm.get_res_norm(alg_id) + rec = astra.data2d.get(rec_id) + phantom_error[i] = np.sqrt(((rec - P)**2).sum()) + +# Get the result +rec = astra.data2d.get(rec_id) +pylab.figure(3) +pylab.imshow(rec) + +pylab.figure(4) +pylab.plot(residual_error) +pylab.figure(5) +pylab.plot(phantom_error) + +pylab.show() + +# Clean up. +astra.algorithm.delete(alg_id) +astra.data2d.delete(rec_id) +astra.data2d.delete(sinogram_id) +astra.projector.delete(proj_id) diff --git a/src/AsyncAlgorithm.cpp b/src/AsyncAlgorithm.cpp index fcc4dcb..b265f59 100644 --- a/src/AsyncAlgorithm.cpp +++ b/src/AsyncAlgorithm.cpp @@ -160,32 +160,6 @@ void CAsyncAlgorithm::runWrapped(int _iNrIterations) m_bDone = true; } -void CAsyncAlgorithm::timedJoin(int _milliseconds) -{ -#ifndef USE_PTHREADS - if (m_pThread) { - boost::posix_time::milliseconds rel(_milliseconds); - bool res = m_pThread->timed_join(rel); - if (res) { - delete m_pThread; - m_pThread = 0; - m_bThreadStarted = false; - } - } -#else - if (m_bThreadStarted) { - struct timespec abstime; - clock_gettime(CLOCK_REALTIME, &abstime); - abstime.tv_sec += _milliseconds / 1000; - abstime.tv_nsec += (_milliseconds % 1000) * 1000000L; - int err = pthread_timedjoin_np(m_thread, 0, &abstime); - if (err == 0) { - m_bThreadStarted = false; - } - } -#endif -} - void CAsyncAlgorithm::signalAbort() { if (m_pAlg) diff --git a/src/ConeProjectionGeometry3D.cpp b/src/ConeProjectionGeometry3D.cpp index ec64701..1976901 100644 --- a/src/ConeProjectionGeometry3D.cpp +++ b/src/ConeProjectionGeometry3D.cpp @@ -28,6 +28,8 @@ $Id$ #include "astra/ConeProjectionGeometry3D.h" +#include "astra/Logging.h" + #include <boost/lexical_cast.hpp> #include <cstring> @@ -186,17 +188,22 @@ bool CConeProjectionGeometry3D::isOfType(const std::string& _sType) const } //---------------------------------------------------------------------------------------- -void CConeProjectionGeometry3D::toXML(XMLNode* _sNode) const +// Get the configuration object +Config* CConeProjectionGeometry3D::getConfiguration() const { - _sNode->addAttribute("type", "cone"); - _sNode->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - _sNode->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - _sNode->addChildNode("DetectorRowCount", m_iDetectorRowCount); - _sNode->addChildNode("DetectorColCount", m_iDetectorColCount); - _sNode->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); - _sNode->addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); - _sNode->addChildNode("DistanceOriginSource", m_fOriginSourceDistance); + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry3D"); + cfg->self->addAttribute("type", "cone"); + cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self->addChildNode("DistanceOriginDetector", m_fOriginDetectorDistance); + cfg->self->addChildNode("DistanceOriginSource", m_fOriginSourceDistance); + cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + return cfg; } + //---------------------------------------------------------------------------------------- CVector3D CConeProjectionGeometry3D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const @@ -225,4 +232,36 @@ CVector3D CConeProjectionGeometry3D::getProjectionDirection(int _iProjectionInde return ret; } +void CConeProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + float alpha = m_pfProjectionAngles[iAngleIndex]; + + // Project point onto optical axis + + // Projector direction is (cos(alpha), sin(alpha)) + // Vector source->origin is (-sin(alpha), cos(alpha)) + + // Distance from source, projected on optical axis + float fD = -sin(alpha) * fX + cos(alpha) * fY + m_fOriginSourceDistance; + + // Scale fZ to detector plane + fV = detectorOffsetYToRowIndexFloat( (fZ * (m_fOriginSourceDistance + m_fOriginDetectorDistance)) / fD ); + + + // Orthogonal distance in XY-plane to optical axis + float fS = cos(alpha) * fX + sin(alpha) * fY; + + // Scale fS to detector plane + fU = detectorOffsetXToColIndexFloat( (fS * (m_fOriginSourceDistance + m_fOriginDetectorDistance)) / fD ); + + ASTRA_DEBUG("alpha: %f, D: %f, V: %f, S: %f, U: %f", alpha, fD, fV, fS, fU); + +} + + } // end namespace astra diff --git a/src/ConeVecProjectionGeometry3D.cpp b/src/ConeVecProjectionGeometry3D.cpp index 512b26c..9dc273d 100644 --- a/src/ConeVecProjectionGeometry3D.cpp +++ b/src/ConeVecProjectionGeometry3D.cpp @@ -198,18 +198,42 @@ bool CConeVecProjectionGeometry3D::isEqual(const CProjectionGeometry3D * _pGeom2 // is of type bool CConeVecProjectionGeometry3D::isOfType(const std::string& _sType) const { - return (_sType == "cone3d_vec"); + return (_sType == "cone_vec"); } //---------------------------------------------------------------------------------------- -void CConeVecProjectionGeometry3D::toXML(XMLNode* _sNode) const +// Get the configuration object +Config* CConeVecProjectionGeometry3D::getConfiguration() const { - _sNode->addAttribute("type","cone3d_vec"); - _sNode->addChildNode("DetectorRowCount", m_iDetectorRowCount); - _sNode->addChildNode("DetectorColCount", m_iDetectorColCount); - // TODO: - //_sNode->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry3D"); + + cfg->self->addAttribute("type", "cone_vec"); + cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + + std::string vectors = ""; + for (int i = 0; i < m_iProjectionAngleCount; ++i) { + SConeProjection& p = m_pProjectionAngles[i]; + vectors += boost::lexical_cast<string>(p.fSrcX) + ","; + vectors += boost::lexical_cast<string>(p.fSrcY) + ","; + vectors += boost::lexical_cast<string>(p.fSrcZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; + vectors += boost::lexical_cast<string>(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetUY) + ","; + vectors += boost::lexical_cast<string>(p.fDetUZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetVX) + ","; + vectors += boost::lexical_cast<string>(p.fDetVY) + ","; + vectors += boost::lexical_cast<string>(p.fDetVZ); + if (i < m_iProjectionAngleCount-1) vectors += ';'; + } + cfg->self->addChildNode("Vectors", vectors); + + return cfg; } +//---------------------------------------------------------------------------------------- CVector3D CConeVecProjectionGeometry3D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const { @@ -220,6 +244,26 @@ CVector3D CConeVecProjectionGeometry3D::getProjectionDirection(int _iProjectionI return CVector3D(p.fDetSX + (u+0.5)*p.fDetUX + (v+0.5)*p.fDetVX - p.fSrcX, p.fDetSY + (u+0.5)*p.fDetUY + (v+0.5)*p.fDetVY - p.fSrcY, p.fDetSZ + (u+0.5)*p.fDetUZ + (v+0.5)*p.fDetVZ - p.fSrcZ); } +void CConeVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + double fUX, fUY, fUZ, fUC; + double fVX, fVY, fVZ, fVC; + double fDX, fDY, fDZ, fDC; + + computeBP_UV_Coeffs(m_pProjectionAngles[iAngleIndex], + fUX, fUY, fUZ, fUC, fVX, fVY, fVZ, fVC, fDX, fDY, fDZ, fDC); + + // The -0.5f shifts from corner to center of detector pixels + double fD = fDX*fX + fDY*fY + fDZ*fZ + fDC; + fU = (fUX*fX + fUY*fY + fUZ*fZ + fUC) / fD - 0.5f; + fV = (fVX*fX + fVY*fY + fVZ*fZ + fVC) / fD - 0.5f; +} + //---------------------------------------------------------------------------------------- diff --git a/src/Config.cpp b/src/Config.cpp index 3a3cb53..d860638 100644 --- a/src/Config.cpp +++ b/src/Config.cpp @@ -37,6 +37,9 @@ $Id$ #include "astra/Projector2D.h" #include "astra/Projector3D.h" +#include "astra/Logging.h" +#include <sstream> + using namespace astra; using namespace std; @@ -54,12 +57,24 @@ Config::Config(XMLNode* _self) self = _self; } +//----------------------------------------------------------------------------- Config::~Config() { delete self; self = 0; } +//----------------------------------------------------------------------------- +void Config::initialize(std::string rootname) +{ + if (self == 0) { + XMLDocument* doc = XMLDocument::createDocument(rootname); + self = doc->getRootNode(); + } +} + + +//----------------------------------------------------------------------------- template <class T> ConfigStackCheck<T>::ConfigStackCheck(const char *_name, T* _obj, const Config& _cfg) : object(_obj), cfg(&_cfg), name(_name) @@ -132,7 +147,9 @@ bool ConfigStackCheck<T>::stopParsing() nodes.clear(); if (!errors.empty()) { - cout << "Warning: " << name << ": unused configuration options: " << errors << std::endl; + ostringstream os; + os << name << ": unused configuration options: " << errors; + ASTRA_WARN(os.str().c_str()); return false; } diff --git a/src/CudaFilteredBackProjectionAlgorithm.cpp b/src/CudaFilteredBackProjectionAlgorithm.cpp index 6593313..0badc20 100644 --- a/src/CudaFilteredBackProjectionAlgorithm.cpp +++ b/src/CudaFilteredBackProjectionAlgorithm.cpp @@ -32,8 +32,9 @@ $Id$ #include <cstring> #include "astra/AstraObjectManager.h" +#include "../cuda/2d/astra.h" -#include <astra/Logger.h> +#include "astra/Logging.h" using namespace std; using namespace astra; @@ -104,7 +105,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) } CC.markNodeParsed("FilterType"); ASTRA_DELETE(node); - + // filter node = _cfg.self->getSingleNode("FilterSinogramId"); if(node != NULL) @@ -167,7 +168,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) CC.markOptionParsed("ShortScan"); } - + m_pFBP = new AstraFBP; @@ -185,7 +186,7 @@ bool CCudaFilteredBackProjectionAlgorithm::initialize(CFloat32ProjectionData2D * { clear(); } - + // required classes m_pSinogram = _pSinogram; m_pReconstruction = _pReconstruction; @@ -241,28 +242,65 @@ void CCudaFilteredBackProjectionAlgorithm::run(int _iNrIterations /* = 0 */) bool ok = true; - // TODO: off-center geometry, non-square pixels + // TODO: non-square pixels? ok &= m_pFBP->setReconstructionGeometry(volgeom.getGridColCount(), volgeom.getGridRowCount(), volgeom.getPixelLengthX()); - // TODO: off-center geometry int iDetectorCount; if (parprojgeom) { + + float *offsets, *angles, detSize, outputScale; + + ok = convertAstraGeometry(&volgeom, parprojgeom, offsets, angles, detSize, outputScale); + + ok &= m_pFBP->setProjectionGeometry(parprojgeom->getProjectionAngleCount(), parprojgeom->getDetectorCount(), - parprojgeom->getProjectionAngles(), + angles, parprojgeom->getDetectorWidth()); iDetectorCount = parprojgeom->getDetectorCount(); + + // TODO: Are detSize and outputScale handled correctly? + + if (offsets) + ok &= m_pFBP->setTOffsets(offsets); + ASTRA_ASSERT(ok); + + delete[] offsets; + delete[] angles; + } else if (fanprojgeom) { + + astraCUDA::SFanProjection* projs; + float outputScale; + + // FIXME: Implement this, and clean up the interface to AstraFBP. + if (abs(volgeom.getWindowMinX() + volgeom.getWindowMaxX()) > 0.00001 * volgeom.getPixelLengthX()) { + // Off-center volume geometry isn't supported yet + ASTRA_ASSERT(false); + } + if (abs(volgeom.getWindowMinY() + volgeom.getWindowMaxY()) > 0.00001 * volgeom.getPixelLengthY()) { + // Off-center volume geometry isn't supported yet + ASTRA_ASSERT(false); + } + + ok = convertAstraGeometry(&volgeom, fanprojgeom, projs, outputScale); + + // CHECKME: outputScale? + ok &= m_pFBP->setFanGeometry(fanprojgeom->getProjectionAngleCount(), - fanprojgeom->getDetectorCount(), - fanprojgeom->getProjectionAngles(), - fanprojgeom->getOriginSourceDistance(), - fanprojgeom->getOriginDetectorDistance(), - fanprojgeom->getDetectorWidth(), - m_bShortScan); + fanprojgeom->getDetectorCount(), + projs, + fanprojgeom->getProjectionAngles(), + fanprojgeom->getOriginSourceDistance(), + fanprojgeom->getOriginDetectorDistance(), + + fanprojgeom->getDetectorWidth(), + m_bShortScan); iDetectorCount = fanprojgeom->getDetectorCount(); + + delete[] projs; } else { assert(false); } @@ -271,11 +309,6 @@ void CCudaFilteredBackProjectionAlgorithm::run(int _iNrIterations /* = 0 */) ASTRA_ASSERT(ok); - const float *pfTOffsets = m_pSinogram->getGeometry()->getExtraDetectorOffset(); - if (pfTOffsets) - ok &= m_pFBP->setTOffsets(pfTOffsets); - ASTRA_ASSERT(ok); - ok &= m_pFBP->init(m_iGPUIndex); ASTRA_ASSERT(ok); @@ -293,7 +326,7 @@ void CCudaFilteredBackProjectionAlgorithm::run(int _iNrIterations /* = 0 */) const CVolumeGeometry2D& volgeom = *m_pReconstruction->getGeometry(); ok &= m_pFBP->getReconstruction(m_pReconstruction->getData(), volgeom.getGridColCount()); - + ASTRA_ASSERT(ok); } @@ -302,7 +335,7 @@ bool CCudaFilteredBackProjectionAlgorithm::check() // check pointers ASTRA_CONFIG_CHECK(m_pSinogram, "FBP_CUDA", "Invalid Projection Data Object."); ASTRA_CONFIG_CHECK(m_pReconstruction, "FBP_CUDA", "Invalid Reconstruction Data Object."); - + if((m_eFilter == FILTER_PROJECTION) || (m_eFilter == FILTER_SINOGRAM) || (m_eFilter == FILTER_RPROJECTION) || (m_eFilter == FILTER_RSINOGRAM)) { ASTRA_CONFIG_CHECK(m_pfFilter, "FBP_CUDA", "Invalid filter pointer."); @@ -354,7 +387,7 @@ static bool stringCompareLowerCase(const char * _stringA, const char * _stringB) #else iCmpReturn = strcasecmp(_stringA, _stringB); #endif - + return (iCmpReturn == 0); } @@ -452,7 +485,7 @@ E_FBPFILTER CCudaFilteredBackProjectionAlgorithm::_convertStringToFilter(const c } else { - cerr << "Failed to convert \"" << _filterType << "\" into a filter." << endl; + ASTRA_ERROR("Failed to convert \"%s\" into a filter.",_filterType); } return output; diff --git a/src/CudaForwardProjectionAlgorithm.cpp b/src/CudaForwardProjectionAlgorithm.cpp index 4865887..95abb62 100644 --- a/src/CudaForwardProjectionAlgorithm.cpp +++ b/src/CudaForwardProjectionAlgorithm.cpp @@ -42,6 +42,8 @@ $Id$ #include "astra/FanFlatVecProjectionGeometry2D.h" #include "astra/CudaProjector2D.h" +#include "astra/Logging.h" + using namespace std; namespace astra { @@ -104,7 +106,7 @@ bool CCudaForwardProjectionAlgorithm::initialize(const Config& _cfg) id = boost::lexical_cast<int>(node->getContent()); CProjector2D *projector = CProjector2DManager::getSingleton().get(id); if (!dynamic_cast<CCudaProjector2D*>(projector)) { - cout << "Warning: non-CUDA Projector2D passed to FP_CUDA" << std::endl; + ASTRA_WARN("non-CUDA Projector2D passed to FP_CUDA"); } delete node; } @@ -214,52 +216,45 @@ void CCudaForwardProjectionAlgorithm::run(int) bool ok = false; if (parProjGeom) { + + float *offsets, *angles, detSize, outputScale; + ok = convertAstraGeometry(pVolGeom, parProjGeom, offsets, angles, detSize, outputScale); + + ASTRA_ASSERT(ok); // FIXME + + // FIXME: Output scaling + ok = astraCudaFP(m_pVolume->getDataConst(), m_pSinogram->getData(), pVolGeom->getGridColCount(), pVolGeom->getGridRowCount(), parProjGeom->getProjectionAngleCount(), parProjGeom->getDetectorCount(), - parProjGeom->getProjectionAngles(), - parProjGeom->getExtraDetectorOffset(), parProjGeom->getDetectorWidth() / pVolGeom->getPixelLengthX(), - m_iDetectorSuperSampling, m_iGPUIndex); + angles, offsets, detSize, + m_iDetectorSuperSampling, 1.0f * outputScale, m_iGPUIndex); - } else if (fanProjGeom) { + delete[] offsets; + delete[] angles; - ok = astraCudaFanFP(m_pVolume->getDataConst(), m_pSinogram->getData(), - pVolGeom->getGridColCount(), pVolGeom->getGridRowCount(), - fanProjGeom->getProjectionAngleCount(), - fanProjGeom->getDetectorCount(), - fanProjGeom->getProjectionAngles(), - fanProjGeom->getOriginSourceDistance(), - fanProjGeom->getOriginDetectorDistance(), - pVolGeom->getPixelLengthX(), - fanProjGeom->getDetectorWidth(), - m_iDetectorSuperSampling, m_iGPUIndex); - - } else if (fanVecProjGeom) { - - // Rescale projs to fPixelSize == 1 - float fPixelSize = pVolGeom->getPixelLengthX(); - const astraCUDA::SFanProjection* projs; - projs = fanVecProjGeom->getProjectionVectors(); - - astraCUDA::SFanProjection* scaledProjs = new astraCUDA::SFanProjection[fanVecProjGeom->getProjectionAngleCount()]; -#define SCALE(name,i,alpha) do { scaledProjs[i].f##name##X = projs[i].f##name##X * alpha; scaledProjs[i].f##name##Y = projs[i].f##name##Y * alpha; } while (0) - for (unsigned int i = 0; i < fanVecProjGeom->getProjectionAngleCount(); ++i) { - SCALE(Src,i,1.0f/fPixelSize); - SCALE(DetS,i,1.0f/fPixelSize); - SCALE(DetU,i,1.0f/fPixelSize); + } else if (fanProjGeom || fanVecProjGeom) { + + astraCUDA::SFanProjection* projs; + float outputScale; + + if (fanProjGeom) { + ok = convertAstraGeometry(pVolGeom, fanProjGeom, projs, outputScale); + } else { + ok = convertAstraGeometry(pVolGeom, fanVecProjGeom, projs, outputScale); } + ASTRA_ASSERT(ok); ok = astraCudaFanFP(m_pVolume->getDataConst(), m_pSinogram->getData(), pVolGeom->getGridColCount(), pVolGeom->getGridRowCount(), - fanVecProjGeom->getProjectionAngleCount(), - fanVecProjGeom->getDetectorCount(), - scaledProjs, - /* 1.0f / pVolGeom->getPixelLengthX(), */ - m_iDetectorSuperSampling, m_iGPUIndex); + m_pSinogram->getGeometry()->getProjectionAngleCount(), + m_pSinogram->getGeometry()->getDetectorCount(), + projs, + m_iDetectorSuperSampling, outputScale, m_iGPUIndex); - delete[] scaledProjs; + delete[] projs; } else { diff --git a/src/CudaForwardProjectionAlgorithm3D.cpp b/src/CudaForwardProjectionAlgorithm3D.cpp index 4ebecef..8e6bab5 100644 --- a/src/CudaForwardProjectionAlgorithm3D.cpp +++ b/src/CudaForwardProjectionAlgorithm3D.cpp @@ -40,6 +40,8 @@ $Id$ #include "astra/ParallelVecProjectionGeometry3D.h" #include "astra/ConeVecProjectionGeometry3D.h" +#include "astra/Logging.h" + #include "../cuda/3d/astra3d.h" using namespace std; @@ -251,6 +253,25 @@ void CCudaForwardProjectionAlgorithm3D::run(int) projKernel = projector->getProjectionKernel(); } +#if 0 + // Debugging code that gives the coordinates of the corners of the volume + // projected on the detector. + { + float fX[] = { volgeom.getWindowMinX(), volgeom.getWindowMaxX() }; + float fY[] = { volgeom.getWindowMinY(), volgeom.getWindowMaxY() }; + float fZ[] = { volgeom.getWindowMinZ(), volgeom.getWindowMaxZ() }; + + for (int a = 0; a < projgeom->getProjectionCount(); ++a) + for (int i = 0; i < 2; ++i) + for (int j = 0; j < 2; ++j) + for (int k = 0; k < 2; ++k) { + float fU, fV; + projgeom->projectPoint(fX[i], fY[j], fZ[k], a, fU, fV); + ASTRA_DEBUG("%3d %c1,%c1,%c1 -> %12f %12f", a, i ? ' ' : '-', j ? ' ' : '-', k ? ' ' : '-', fU, fV); + } + } +#endif + if (conegeom) { astraCudaConeFP(m_pVolume->getDataConst(), m_pProjections->getData(), volgeom.getGridColCount(), diff --git a/src/CudaProjector3D.cpp b/src/CudaProjector3D.cpp index f51433d..2f4c799 100644 --- a/src/CudaProjector3D.cpp +++ b/src/CudaProjector3D.cpp @@ -28,6 +28,9 @@ $Id$ #include "astra/CudaProjector3D.h" +#include "astra/VolumeGeometry3D.h" +#include "astra/ProjectionGeometry3D.h" + namespace astra { @@ -102,21 +105,7 @@ bool CCudaProjector3D::initialize(const Config& _cfg) return false; } - // TODO: These should go to the parent. - - // ProjectionGeometry - XMLNode* node = _cfg.self->getSingleNode("ProjectionGeometry"); - // TODO: Implement - ASTRA_DELETE(node); - CC.markNodeParsed("ProjectionGeometry"); - - // ReconstructionGeometry - node = _cfg.self->getSingleNode("VolumeGeometry"); - // TODO: Implement - ASTRA_DELETE(node); - CC.markNodeParsed("VolumeGeometry"); - - node = _cfg.self->getSingleNode("ProjectionKernel"); + XMLNode* node = _cfg.self->getSingleNode("ProjectionKernel"); m_projectionKernel = ker3d_default; if (node) { std::string sProjKernel = node->getContent(); diff --git a/src/CudaReconstructionAlgorithm2D.cpp b/src/CudaReconstructionAlgorithm2D.cpp index 1d66137..1c6b763 100644 --- a/src/CudaReconstructionAlgorithm2D.cpp +++ b/src/CudaReconstructionAlgorithm2D.cpp @@ -37,6 +37,8 @@ $Id$ #include "astra/FanFlatVecProjectionGeometry2D.h" #include "astra/CudaProjector2D.h" +#include "astra/Logging.h" + #include "../cuda/2d/algo.h" #include <ctime> @@ -176,7 +178,7 @@ bool CCudaReconstructionAlgorithm2D::initialize(const Config& _cfg) id = boost::lexical_cast<int>(node->getContent()); CProjector2D *projector = CProjector2DManager::getSingleton().get(id); if (!dynamic_cast<CCudaProjector2D*>(projector)) { - cout << "Warning: non-CUDA Projector2D passed" << std::endl; + ASTRA_WARN("non-CUDA Projector2D passed"); } delete node; } @@ -350,7 +352,7 @@ bool CCudaReconstructionAlgorithm2D::setupGeometry() const CVolumeGeometry2D& volgeom = *m_pReconstruction->getGeometry(); - // TODO: off-center geometry, non-square pixels + // TODO: non-square pixels? dims.iVolWidth = volgeom.getGridColCount(); dims.iVolHeight = volgeom.getGridRowCount(); float fPixelSize = volgeom.getPixelLengthX(); @@ -365,66 +367,42 @@ bool CCudaReconstructionAlgorithm2D::setupGeometry() if (parProjGeom) { + float *offsets, *angles, detSize, outputScale; + + ok = convertAstraGeometry(&volgeom, parProjGeom, offsets, angles, detSize, outputScale); + dims.iProjAngles = parProjGeom->getProjectionAngleCount(); dims.iProjDets = parProjGeom->getDetectorCount(); dims.fDetScale = parProjGeom->getDetectorWidth() / fPixelSize; ok = m_pAlgo->setGeometry(dims, parProjGeom->getProjectionAngles()); + ok &= m_pAlgo->setTOffsets(offsets); - } else if (fanProjGeom) { + // CHECKME: outputScale? detSize? - dims.iProjAngles = fanProjGeom->getProjectionAngleCount(); - dims.iProjDets = fanProjGeom->getDetectorCount(); - dims.fDetScale = fanProjGeom->getDetectorWidth() / fPixelSize; - float fOriginSourceDistance = fanProjGeom->getOriginSourceDistance(); - float fOriginDetectorDistance = fanProjGeom->getOriginDetectorDistance(); + delete[] offsets; + delete[] angles; - const float* angles = fanProjGeom->getProjectionAngles(); + } else if (fanProjGeom || fanVecProjGeom) { astraCUDA::SFanProjection* projs; - projs = new astraCUDA::SFanProjection[dims.iProjAngles]; - - float fSrcX0 = 0.0f; - float fSrcY0 = -fOriginSourceDistance / fPixelSize; - float fDetUX0 = dims.fDetScale; - float fDetUY0 = 0.0f; - float fDetSX0 = dims.iProjDets * fDetUX0 / -2.0f; - float fDetSY0 = fOriginDetectorDistance / fPixelSize; - -#define ROTATE0(name,i,alpha) do { projs[i].f##name##X = f##name##X0 * cos(alpha) - f##name##Y0 * sin(alpha); projs[i].f##name##Y = f##name##X0 * sin(alpha) + f##name##Y0 * cos(alpha); } while(0) - for (unsigned int i = 0; i < dims.iProjAngles; ++i) { - ROTATE0(Src, i, angles[i]); - ROTATE0(DetS, i, angles[i]); - ROTATE0(DetU, i, angles[i]); + float outputScale; + + if (fanProjGeom) { + ok = convertAstraGeometry(&volgeom, fanProjGeom, projs, outputScale); + } else { + ok = convertAstraGeometry(&volgeom, fanVecProjGeom, projs, outputScale); } -#undef ROTATE0 + dims.iProjAngles = m_pSinogram->getGeometry()->getProjectionAngleCount(); + dims.iProjDets = m_pSinogram->getGeometry()->getDetectorCount(); + dims.fDetScale = m_pSinogram->getGeometry()->getDetectorWidth() / fPixelSize; ok = m_pAlgo->setFanGeometry(dims, projs); - delete[] projs; - - } else if (fanVecProjGeom) { - - dims.iProjAngles = fanVecProjGeom->getProjectionAngleCount(); - dims.iProjDets = fanVecProjGeom->getDetectorCount(); - dims.fDetScale = fanVecProjGeom->getDetectorWidth() / fPixelSize; - const astraCUDA::SFanProjection* projs; - projs = fanVecProjGeom->getProjectionVectors(); + // CHECKME: outputScale? - // Rescale projs to fPixelSize == 1 - - astraCUDA::SFanProjection* scaledProjs = new astraCUDA::SFanProjection[dims.iProjAngles]; -#define SCALE(name,i,alpha) do { scaledProjs[i].f##name##X = projs[i].f##name##X * alpha; scaledProjs[i].f##name##Y = projs[i].f##name##Y * alpha; } while (0) - for (unsigned int i = 0; i < dims.iProjAngles; ++i) { - SCALE(Src,i,1.0f/fPixelSize); - SCALE(DetS,i,1.0f/fPixelSize); - SCALE(DetU,i,1.0f/fPixelSize); - } - - ok = m_pAlgo->setFanGeometry(dims, scaledProjs); - - delete[] scaledProjs; + delete[] projs; } else { @@ -441,11 +419,6 @@ bool CCudaReconstructionAlgorithm2D::setupGeometry() ok &= m_pAlgo->enableSinogramMask(); if (!ok) return false; - const float *pfTOffsets = m_pSinogram->getGeometry()->getExtraDetectorOffset(); - if (pfTOffsets) - ok &= m_pAlgo->setTOffsets(pfTOffsets); - if (!ok) return false; - ok &= m_pAlgo->init(); if (!ok) return false; diff --git a/src/FanFlatProjectionGeometry2D.cpp b/src/FanFlatProjectionGeometry2D.cpp index bfc7fa9..d757f18 100644 --- a/src/FanFlatProjectionGeometry2D.cpp +++ b/src/FanFlatProjectionGeometry2D.cpp @@ -204,6 +204,20 @@ CVector3D CFanFlatProjectionGeometry2D::getProjectionDirection(int _iProjectionI } //---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CFanFlatProjectionGeometry2D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry2D"); + cfg->self->addAttribute("type", "fanflat"); + cfg->self->addChildNode("DetectorCount", getDetectorCount()); + cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self->addChildNode("DistanceOriginSource", getOriginSourceDistance()); + cfg->self->addChildNode("DistanceOriginDetector", getOriginDetectorDistance()); + cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + return cfg; +} +//---------------------------------------------------------------------------------------- } // namespace astra diff --git a/src/FanFlatVecProjectionGeometry2D.cpp b/src/FanFlatVecProjectionGeometry2D.cpp index 77f9db7..9c7b596 100644 --- a/src/FanFlatVecProjectionGeometry2D.cpp +++ b/src/FanFlatVecProjectionGeometry2D.cpp @@ -194,7 +194,7 @@ bool CFanFlatVecProjectionGeometry2D::isEqual(CProjectionGeometry2D* _pGeom2) co // Is of type bool CFanFlatVecProjectionGeometry2D::isOfType(const std::string& _sType) { - return (_sType == "fanflat_vec"); + return (_sType == "fanflat_vec"); } //---------------------------------------------------------------------------------------- @@ -227,6 +227,28 @@ bool CFanFlatVecProjectionGeometry2D::_check() //---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CFanFlatVecProjectionGeometry2D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry2D"); + cfg->self->addAttribute("type", "fanflat_vec"); + cfg->self->addChildNode("DetectorCount", getDetectorCount()); + std::string vectors = ""; + for (int i = 0; i < m_iProjectionAngleCount; ++i) { + SFanProjection& p = m_pProjectionAngles[i]; + vectors += boost::lexical_cast<string>(p.fSrcX) + ","; + vectors += boost::lexical_cast<string>(p.fSrcY) + ","; + vectors += boost::lexical_cast<string>(p.fDetSX + 0.5f * m_iDetectorCount * p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetSY + 0.5f * m_iDetectorCount * p.fDetUY) + ","; + vectors += boost::lexical_cast<string>(p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetUY); + if (i < m_iProjectionAngleCount-1) vectors += ';'; + } + cfg->self->addChildNode("Vectors", vectors); + return cfg; +} +//---------------------------------------------------------------------------------------- } // namespace astra diff --git a/src/FilteredBackProjectionAlgorithm.cpp b/src/FilteredBackProjectionAlgorithm.cpp index 50cf939..4a8e5ac 100644 --- a/src/FilteredBackProjectionAlgorithm.cpp +++ b/src/FilteredBackProjectionAlgorithm.cpp @@ -39,6 +39,8 @@ $Id$ #include "astra/Fourier.h" #include "astra/DataProjector.h" +#include "astra/Logging.h" + using namespace std; namespace astra { @@ -133,7 +135,7 @@ bool CFilteredBackProjectionAlgorithm::initialize(const Config& _cfg) for (int i = 0; i < angleCount; i ++) { if (projectionIndex[i] > m_pProjector->getProjectionGeometry()->getProjectionAngleCount() -1 ) { - cout << "Invalid Projection Index" << endl; + ASTRA_ERROR("Invalid Projection Index"); return false; } else { int orgIndex = (int)projectionIndex[i]; diff --git a/src/GeometryUtil3D.cpp b/src/GeometryUtil3D.cpp new file mode 100644 index 0000000..52dd5a9 --- /dev/null +++ b/src/GeometryUtil3D.cpp @@ -0,0 +1,75 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +#include "astra/GeometryUtil3D.h" + +namespace astra { + +// (See declaration in header for (mathematical) description of these functions) + + +void computeBP_UV_Coeffs(const SPar3DProjection& proj, double &fUX, double &fUY, double &fUZ, double &fUC, + double &fVX, double &fVY, double &fVZ, double &fVC) +{ + double denom = (proj.fRayX*proj.fDetUY*proj.fDetVZ - proj.fRayX*proj.fDetUZ*proj.fDetVY - proj.fRayY*proj.fDetUX*proj.fDetVZ + proj.fRayY*proj.fDetUZ*proj.fDetVX + proj.fRayZ*proj.fDetUX*proj.fDetVY - proj.fRayZ*proj.fDetUY*proj.fDetVX); + + fUX = ( - (proj.fRayY*proj.fDetVZ - proj.fRayZ*proj.fDetVY)) / denom; + fUY = ( (proj.fRayX*proj.fDetVZ - proj.fRayZ*proj.fDetVX)) / denom; + fUZ = (- (proj.fRayX*proj.fDetVY - proj.fRayY*proj.fDetVX) ) / denom; + fUC = (-(proj.fDetSY*proj.fDetVZ - proj.fDetSZ*proj.fDetVY)*proj.fRayX + (proj.fRayY*proj.fDetVZ - proj.fRayZ*proj.fDetVY)*proj.fDetSX - (proj.fRayY*proj.fDetSZ - proj.fRayZ*proj.fDetSY)*proj.fDetVX) / denom; + + fVX = ((proj.fRayY*proj.fDetUZ - proj.fRayZ*proj.fDetUY) ) / denom; + fVY = (- (proj.fRayX*proj.fDetUZ - proj.fRayZ*proj.fDetUX) ) / denom; + fVZ = ((proj.fRayX*proj.fDetUY - proj.fRayY*proj.fDetUX) ) / denom; + fVC = ((proj.fDetSY*proj.fDetUZ - proj.fDetSZ*proj.fDetUY)*proj.fRayX - (proj.fRayY*proj.fDetUZ - proj.fRayZ*proj.fDetUY)*proj.fDetSX + (proj.fRayY*proj.fDetSZ - proj.fRayZ*proj.fDetSY)*proj.fDetUX ) / denom; +} + + + +void computeBP_UV_Coeffs(const SConeProjection& proj, double &fUX, double &fUY, double &fUZ, double &fUC, + double &fVX, double &fVY, double &fVZ, double &fVC, + double &fDX, double &fDY, double &fDZ, double &fDC) +{ + fUX = (proj.fDetSZ - proj.fSrcZ)*proj.fDetVY - (proj.fDetSY - proj.fSrcY)*proj.fDetVZ; + fUY = (proj.fDetSX - proj.fSrcX)*proj.fDetVZ -(proj.fDetSZ - proj.fSrcZ)*proj.fDetVX; + fUZ = (proj.fDetSY - proj.fSrcY)*proj.fDetVX - (proj.fDetSX - proj.fSrcX)*proj.fDetVY; + fUC = (proj.fDetSY*proj.fDetVZ - proj.fDetSZ*proj.fDetVY)*proj.fSrcX - (proj.fDetSX*proj.fDetVZ - proj.fDetSZ*proj.fDetVX)*proj.fSrcY + (proj.fDetSX*proj.fDetVY - proj.fDetSY*proj.fDetVX)*proj.fSrcZ; + + fVX = (proj.fDetSY - proj.fSrcY)*proj.fDetUZ-(proj.fDetSZ - proj.fSrcZ)*proj.fDetUY; + fVY = (proj.fDetSZ - proj.fSrcZ)*proj.fDetUX - (proj.fDetSX - proj.fSrcX)*proj.fDetUZ; + fVZ = (proj.fDetSX - proj.fSrcX)*proj.fDetUY-(proj.fDetSY - proj.fSrcY)*proj.fDetUX; + fVC = -(proj.fDetSY*proj.fDetUZ - proj.fDetSZ*proj.fDetUY)*proj.fSrcX + (proj.fDetSX*proj.fDetUZ - proj.fDetSZ*proj.fDetUX)*proj.fSrcY - (proj.fDetSX*proj.fDetUY - proj.fDetSY*proj.fDetUX)*proj.fSrcZ; + + fDX = proj.fDetUY*proj.fDetVZ - proj.fDetUZ*proj.fDetVY; + fDY = proj.fDetUZ*proj.fDetVX - proj.fDetUX*proj.fDetVZ; + fDZ = proj.fDetUX*proj.fDetVY - proj.fDetUY*proj.fDetVX; + fDC = -proj.fSrcX * (proj.fDetUY*proj.fDetVZ - proj.fDetUZ*proj.fDetVY) - proj.fSrcY * (proj.fDetUZ*proj.fDetVX - proj.fDetUX*proj.fDetVZ) - proj.fSrcZ * (proj.fDetUX*proj.fDetVY - proj.fDetUY*proj.fDetVX); +} + + +} diff --git a/src/Logging.cpp b/src/Logging.cpp new file mode 100644 index 0000000..8290ca0 --- /dev/null +++ b/src/Logging.cpp @@ -0,0 +1,184 @@ +/* +----------------------------------------------------------------------- +Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp + 2014-2015, CWI, Amsterdam + +Contact: astra@uantwerpen.be +Website: http://sf.net/projects/astra-toolbox + +This file is part of the ASTRA Toolbox. + + +The ASTRA Toolbox is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +The ASTRA Toolbox is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>. + +----------------------------------------------------------------------- +$Id$ +*/ + +#define CLOG_MAIN +#include <astra/clog.h> + +#include <astra/Logging.h> + +#include <cstdio> + +using namespace astra; + +void CLogger::enableScreen() +{ + m_bEnabledScreen = true; +} + +void CLogger::enableFile() +{ + m_bEnabledFile = true; +} + +void CLogger::enable() +{ + enableScreen(); + enableFile(); +} + +void CLogger::disableScreen() +{ + m_bEnabledScreen = false; +} + +void CLogger::disableFile() +{ + m_bEnabledFile = false; +} + +void CLogger::disable() +{ + disableScreen(); + disableFile(); +} + +void CLogger::debug(const char *sfile, int sline, const char *fmt, ...) +{ + _assureIsInitialized(); + va_list ap; + va_start(ap, fmt); + if(m_bEnabledScreen) clog_debug(sfile,sline,0,fmt,ap); + if(m_bEnabledFile && m_bFileProvided) clog_debug(sfile,sline,1,fmt,ap); +} + +void CLogger::info(const char *sfile, int sline, const char *fmt, ...) +{ + _assureIsInitialized(); + va_list ap; + va_start(ap, fmt); + if(m_bEnabledScreen) clog_info(sfile,sline,0,fmt,ap); + if(m_bEnabledFile && m_bFileProvided) clog_info(sfile,sline,1,fmt,ap); +} + +void CLogger::warn(const char *sfile, int sline, const char *fmt, ...) +{ + _assureIsInitialized(); + va_list ap; + va_start(ap, fmt); + if(m_bEnabledScreen) clog_warn(sfile,sline,0,fmt,ap); + if(m_bEnabledFile && m_bFileProvided) clog_warn(sfile,sline,1,fmt,ap); +} + +void CLogger::error(const char *sfile, int sline, const char *fmt, ...) +{ + _assureIsInitialized(); + va_list ap; + va_start(ap, fmt); + if(m_bEnabledScreen) clog_error(sfile,sline,0,fmt,ap); + if(m_bEnabledFile && m_bFileProvided) clog_error(sfile,sline,1,fmt,ap); +} + +void CLogger::_setLevel(int id, log_level m_eLevel) +{ + switch(m_eLevel){ + case LOG_DEBUG: + clog_set_level(id,CLOG_DEBUG); + break; + case LOG_INFO: + clog_set_level(id,CLOG_INFO); + break; + case LOG_WARN: + clog_set_level(id,CLOG_WARN); + break; + case LOG_ERROR: + clog_set_level(id,CLOG_ERROR); + break; + } +} + +void CLogger::setOutputScreen(int fd, log_level m_eLevel) +{ + _assureIsInitialized(); + if(fd==1||fd==2){ + clog_set_fd(0, fd); + }else{ + error(__FILE__,__LINE__,"Invalid file descriptor"); + } + _setLevel(0,m_eLevel); +} + +void CLogger::setOutputFile(const char *filename, log_level m_eLevel) +{ + if(m_bFileProvided){ + clog_free(1); + m_bFileProvided=false; + } + if(!clog_init_path(1,filename)){ + m_bFileProvided=true; + _setLevel(1,m_eLevel); + } +} + +void CLogger::_assureIsInitialized() +{ + if(!m_bInitialized) + { + clog_init_fd(0, 2); + clog_set_level(0, CLOG_INFO); + clog_set_fmt(0, "%l: %m\n"); + m_bInitialized = true; + } +} + +void CLogger::setFormatFile(const char *fmt) +{ + if(m_bFileProvided){ + clog_set_fmt(1,fmt); + }else{ + error(__FILE__,__LINE__,"No log file specified"); + } +} +void CLogger::setFormatScreen(const char *fmt) +{ + clog_set_fmt(0,fmt); +} + +CLogger::CLogger() +{ + ; +} + +bool CLogger::setCallbackScreen(void (*cb)(const char *msg, size_t len)){ + _assureIsInitialized(); + return clog_set_cb(0,cb)==0; +} + +bool CLogger::m_bEnabledScreen = true; +bool CLogger::m_bEnabledFile = true; +bool CLogger::m_bFileProvided = false; +bool CLogger::m_bInitialized = false; diff --git a/src/ParallelProjectionGeometry2D.cpp b/src/ParallelProjectionGeometry2D.cpp index 8f8faa4..cac8f30 100644 --- a/src/ParallelProjectionGeometry2D.cpp +++ b/src/ParallelProjectionGeometry2D.cpp @@ -27,6 +27,7 @@ $Id$ */ #include "astra/ParallelProjectionGeometry2D.h" +#include <boost/lexical_cast.hpp> #include <cstring> @@ -168,6 +169,19 @@ bool CParallelProjectionGeometry2D::isOfType(const std::string& _sType) { return (_sType == "parallel"); } + +//---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CParallelProjectionGeometry2D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry2D"); + cfg->self->addAttribute("type", "parallel"); + cfg->self->addChildNode("DetectorCount", getDetectorCount()); + cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + return cfg; +} //---------------------------------------------------------------------------------------- CVector3D CParallelProjectionGeometry2D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex /* = 0 */) diff --git a/src/ParallelProjectionGeometry3D.cpp b/src/ParallelProjectionGeometry3D.cpp index 104fc6e..eb200f9 100644 --- a/src/ParallelProjectionGeometry3D.cpp +++ b/src/ParallelProjectionGeometry3D.cpp @@ -27,6 +27,7 @@ $Id$ */ #include "astra/ParallelProjectionGeometry3D.h" +#include <boost/lexical_cast.hpp> #include <cstring> @@ -154,19 +155,24 @@ bool CParallelProjectionGeometry3D::isEqual(const CProjectionGeometry3D * _pGeom // is of type bool CParallelProjectionGeometry3D::isOfType(const std::string& _sType) const { - return (_sType == "parallel"); + return (_sType == "parallel3d"); } //---------------------------------------------------------------------------------------- -void CParallelProjectionGeometry3D::toXML(XMLNode* _sNode) const +// Get the configuration object +Config* CParallelProjectionGeometry3D::getConfiguration() const { - _sNode->addAttribute("type","parallel3d"); - _sNode->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); - _sNode->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); - _sNode->addChildNode("DetectorRowCount", m_iDetectorRowCount); - _sNode->addChildNode("DetectorColCount", m_iDetectorColCount); - _sNode->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry3D"); + cfg->self->addAttribute("type", "parallel3d"); + cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + cfg->self->addChildNode("DetectorSpacingX", m_fDetectorSpacingX); + cfg->self->addChildNode("DetectorSpacingY", m_fDetectorSpacingY); + cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + return cfg; } +//---------------------------------------------------------------------------------------- CVector3D CParallelProjectionGeometry3D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const { @@ -179,6 +185,22 @@ CVector3D CParallelProjectionGeometry3D::getProjectionDirection(int _iProjection return CVector3D(fDirX, fDirY, fDirZ); } +void CParallelProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + // V (detector row) + fV = detectorOffsetYToRowIndexFloat(fZ); + + // U (detector column) + float alpha = m_pfProjectionAngles[iAngleIndex]; + // projector direction is (cos(alpha), sin(alpha)) + fU = detectorOffsetXToColIndexFloat(cos(alpha) * fX + sin(alpha) * fY); +} + CParallelProjectionGeometry2D * CParallelProjectionGeometry3D::createProjectionGeometry2D() const { const float32 * pfProjectionAngles = getProjectionAngles(); //new float32[getProjectionCount()]; diff --git a/src/ParallelVecProjectionGeometry3D.cpp b/src/ParallelVecProjectionGeometry3D.cpp index c8071a6..dc325e9 100644 --- a/src/ParallelVecProjectionGeometry3D.cpp +++ b/src/ParallelVecProjectionGeometry3D.cpp @@ -202,14 +202,38 @@ bool CParallelVecProjectionGeometry3D::isOfType(const std::string& _sType) const } //---------------------------------------------------------------------------------------- -void CParallelVecProjectionGeometry3D::toXML(XMLNode* _sNode) const +// Get the configuration object +Config* CParallelVecProjectionGeometry3D::getConfiguration() const { - _sNode->addAttribute("type","parallel3d_vec"); - _sNode->addChildNode("DetectorRowCount", m_iDetectorRowCount); - _sNode->addChildNode("DetectorColCount", m_iDetectorColCount); - // TODO: - //_sNode->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry3D"); + + cfg->self->addAttribute("type", "parallel3d_vec"); + cfg->self->addChildNode("DetectorRowCount", m_iDetectorRowCount); + cfg->self->addChildNode("DetectorColCount", m_iDetectorColCount); + + std::string vectors = ""; + for (int i = 0; i < m_iProjectionAngleCount; ++i) { + SPar3DProjection& p = m_pProjectionAngles[i]; + vectors += boost::lexical_cast<string>(p.fRayX) + ","; + vectors += boost::lexical_cast<string>(p.fRayY) + ","; + vectors += boost::lexical_cast<string>(p.fRayZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetSX + 0.5f*m_iDetectorRowCount*p.fDetVX + 0.5f*m_iDetectorColCount*p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetSY + 0.5f*m_iDetectorRowCount*p.fDetVY + 0.5f*m_iDetectorColCount*p.fDetUY) + ","; + vectors += boost::lexical_cast<string>(p.fDetSZ + 0.5f*m_iDetectorRowCount*p.fDetVZ + 0.5f*m_iDetectorColCount*p.fDetUZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetUX) + ","; + vectors += boost::lexical_cast<string>(p.fDetUY) + ","; + vectors += boost::lexical_cast<string>(p.fDetUZ) + ","; + vectors += boost::lexical_cast<string>(p.fDetVX) + ","; + vectors += boost::lexical_cast<string>(p.fDetVY) + ","; + vectors += boost::lexical_cast<string>(p.fDetVZ); + if (i < m_iProjectionAngleCount-1) vectors += ';'; + } + cfg->self->addChildNode("Vectors", vectors); + + return cfg; } +//---------------------------------------------------------------------------------------- CVector3D CParallelVecProjectionGeometry3D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) const { @@ -218,6 +242,24 @@ CVector3D CParallelVecProjectionGeometry3D::getProjectionDirection(int _iProject return CVector3D(p.fRayX, p.fRayY, p.fRayZ); } +void CParallelVecProjectionGeometry3D::projectPoint(float32 fX, float32 fY, float32 fZ, + int iAngleIndex, + float32 &fU, float32 &fV) const +{ + ASTRA_ASSERT(iAngleIndex >= 0); + ASTRA_ASSERT(iAngleIndex < m_iProjectionAngleCount); + + double fUX, fUY, fUZ, fUC; + double fVX, fVY, fVZ, fVC; + + computeBP_UV_Coeffs(m_pProjectionAngles[iAngleIndex], + fUX, fUY, fUZ, fUC, fVX, fVY, fVZ, fVC); + + // The -0.5f shifts from corner to center of detector pixels + fU = (fUX*fX + fUY*fY + fUZ*fZ + fUC) - 0.5f; + fV = (fVX*fX + fVY*fY + fVZ*fZ + fVC) - 0.5f; + +} //---------------------------------------------------------------------------------------- diff --git a/src/Projector3D.cpp b/src/Projector3D.cpp index 0f5edb7..b546ee9 100644 --- a/src/Projector3D.cpp +++ b/src/Projector3D.cpp @@ -28,6 +28,12 @@ $Id$ #include "astra/Projector3D.h" +#include "astra/VolumeGeometry3D.h" +#include "astra/ParallelProjectionGeometry3D.h" +#include "astra/ParallelVecProjectionGeometry3D.h" +#include "astra/ConeProjectionGeometry3D.h" +#include "astra/ConeVecProjectionGeometry3D.h" + namespace astra { @@ -84,6 +90,37 @@ bool CProjector3D::_check() bool CProjector3D::initialize(const Config& _cfg) { assert(_cfg.self); + ConfigStackCheck<CProjector3D> CC("Projector3D", this, _cfg); + + XMLNode* node; + + node = _cfg.self->getSingleNode("ProjectionGeometry"); + ASTRA_CONFIG_CHECK(node, "Projector3D", "No ProjectionGeometry tag specified."); + std::string type = node->getAttribute("type"); + CProjectionGeometry3D* pProjGeometry = 0; + if (type == "parallel3d") { + pProjGeometry = new CParallelProjectionGeometry3D(); + } else if (type == "parallel3d_vec") { + pProjGeometry = new CParallelVecProjectionGeometry3D(); + } else if (type == "cone") { + pProjGeometry = new CConeProjectionGeometry3D(); + } else if (type == "cone_vec") { + pProjGeometry = new CConeVecProjectionGeometry3D(); + } else { + // Invalid geometry type + } + pProjGeometry->initialize(Config(node)); // this deletes node + m_pProjectionGeometry = pProjGeometry; + ASTRA_CONFIG_CHECK(m_pProjectionGeometry->isInitialized(), "Projector3D", "ProjectionGeometry not initialized."); + CC.markNodeParsed("ProjectionGeometry"); + + node = _cfg.self->getSingleNode("VolumeGeometry"); + ASTRA_CONFIG_CHECK(node, "Projector3D", "No VolumeGeometry tag specified."); + CVolumeGeometry3D* pVolGeometry = new CVolumeGeometry3D(); + pVolGeometry->initialize(Config(node)); // this deletes node + m_pVolumeGeometry = pVolGeometry; + ASTRA_CONFIG_CHECK(m_pVolumeGeometry->isInitialized(), "Projector2D", "VolumeGeometry not initialized."); + CC.markNodeParsed("VolumeGeometry"); return true; } diff --git a/src/ReconstructionAlgorithm3D.cpp b/src/ReconstructionAlgorithm3D.cpp index 0ce9777..13d069d 100644 --- a/src/ReconstructionAlgorithm3D.cpp +++ b/src/ReconstructionAlgorithm3D.cpp @@ -145,7 +145,6 @@ bool CReconstructionAlgorithm3D::initialize(const Config& _cfg) id = boost::lexical_cast<int>(_cfg.self->getOption("SinogramMaskId")); m_pSinogramMask = dynamic_cast<CFloat32ProjectionData3D*>(CData3DManager::getSingleton().get(id)); } - CC.markOptionParsed("SinogramMaskId"); // Constraints - NEW if (_cfg.self->hasOption("MinConstraint")) { diff --git a/src/SparseMatrixProjectionGeometry2D.cpp b/src/SparseMatrixProjectionGeometry2D.cpp index 7f14d9d..86357d2 100644 --- a/src/SparseMatrixProjectionGeometry2D.cpp +++ b/src/SparseMatrixProjectionGeometry2D.cpp @@ -189,7 +189,20 @@ bool CSparseMatrixProjectionGeometry2D::isOfType(const std::string& _sType) return (_sType == "sparse_matrix"); } //---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CSparseMatrixProjectionGeometry2D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("ProjectionGeometry2D"); + cfg->self->addAttribute("type", "sparse matrix"); + cfg->self->addChildNode("DetectorCount", getDetectorCount()); + cfg->self->addChildNode("DetectorWidth", getDetectorWidth()); + cfg->self->addChildNode("ProjectionAngles", m_pfProjectionAngles, m_iProjectionAngleCount); + cfg->self->addChildNode("MatrixID", CMatrixManager::getSingleton().getIndex(m_pMatrix)); + return cfg; +} +//---------------------------------------------------------------------------------------- CVector3D CSparseMatrixProjectionGeometry2D::getProjectionDirection(int _iProjectionIndex, int _iDetectorIndex) { CVector3D vOutput(0.0f, 0.0f, 0.0f); diff --git a/src/VolumeGeometry2D.cpp b/src/VolumeGeometry2D.cpp index 19aa905..d412914 100644 --- a/src/VolumeGeometry2D.cpp +++ b/src/VolumeGeometry2D.cpp @@ -152,7 +152,7 @@ CVolumeGeometry2D* CVolumeGeometry2D::clone() } //---------------------------------------------------------------------------------------- -// Initialization witha COnfig object +// Initialization witha Config object bool CVolumeGeometry2D::initialize(const Config& _cfg) { ASTRA_ASSERT(_cfg.self); @@ -277,6 +277,24 @@ bool CVolumeGeometry2D::isEqual(CVolumeGeometry2D* _pGeom2) const return true; } + +//---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CVolumeGeometry2D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("VolumeGeometry2D"); + + cfg->self->addChildNode("GridColCount", m_iGridColCount); + cfg->self->addChildNode("GridRowCount", m_iGridRowCount); + + cfg->self->addOption("WindowMinX", m_fWindowMinX); + cfg->self->addOption("WindowMaxX", m_fWindowMaxX); + cfg->self->addOption("WindowMinY", m_fWindowMinY); + cfg->self->addOption("WindowMaxY", m_fWindowMaxY); + + return cfg; +} //---------------------------------------------------------------------------------------- } // namespace astra diff --git a/src/VolumeGeometry3D.cpp b/src/VolumeGeometry3D.cpp index d7a93a9..66e6f0c 100644 --- a/src/VolumeGeometry3D.cpp +++ b/src/VolumeGeometry3D.cpp @@ -380,5 +380,28 @@ CVolumeGeometry2D * CVolumeGeometry3D::createVolumeGeometry2D() const } //---------------------------------------------------------------------------------------- +// Get the configuration object +Config* CVolumeGeometry3D::getConfiguration() const +{ + Config* cfg = new Config(); + cfg->initialize("VolumeGeometry3D"); + + cfg->self->addChildNode("GridColCount", m_iGridColCount); + cfg->self->addChildNode("GridRowCount", m_iGridRowCount); + cfg->self->addChildNode("GridSliceCount", m_iGridSliceCount); + + cfg->self->addOption("WindowMinX", m_fWindowMinX); + cfg->self->addOption("WindowMaxX", m_fWindowMaxX); + cfg->self->addOption("WindowMinY", m_fWindowMinY); + cfg->self->addOption("WindowMaxY", m_fWindowMaxY); + cfg->self->addOption("WindowMinZ", m_fWindowMinZ); + cfg->self->addOption("WindowMaxZ", m_fWindowMaxZ); + + return cfg; +} +//---------------------------------------------------------------------------------------- + + +//---------------------------------------------------------------------------------------- } // namespace astra diff --git a/src/XMLDocument.cpp b/src/XMLDocument.cpp index b39875b..406564f 100644 --- a/src/XMLDocument.cpp +++ b/src/XMLDocument.cpp @@ -109,4 +109,12 @@ void XMLDocument::saveToFile(string sFilename) } //----------------------------------------------------------------------------- +std::string XMLDocument::toString() +{ + std::stringstream ss; + ss << *fDOMDocument->first_node(); + return ss.str(); +} + +//----------------------------------------------------------------------------- diff --git a/src/XMLNode.cpp b/src/XMLNode.cpp index a5b6796..4b2bdf4 100644 --- a/src/XMLNode.cpp +++ b/src/XMLNode.cpp @@ -448,13 +448,11 @@ void XMLNode::setContent(float32 _fValue) // Set content - LIST void XMLNode::setContent(float32* pfList, int _iSize) { - addAttribute("listsize", _iSize); - for (int i = 0; i < _iSize; i++) { - XMLNode* item = addChildNode("ListItem"); - item->addAttribute("index", i); - item->addAttribute("value",pfList[i]); - delete item; + std::string str = (_iSize > 0) ? boost::lexical_cast<std::string>(pfList[0]) : ""; + for (int i = 1; i < _iSize; i++) { + str += "," + boost::lexical_cast<std::string>(pfList[i]); } + setContent(str); } //----------------------------------------------------------------------------- |