diff options
Diffstat (limited to 'python')
| -rw-r--r-- | python/astra/__init__.py | 1 | ||||
| -rw-r--r-- | python/astra/creators.py | 2 | ||||
| -rw-r--r-- | python/astra/plugins/__init__.py | 29 | ||||
| -rw-r--r-- | python/astra/plugins/cgls.py | 99 | ||||
| -rw-r--r-- | python/astra/plugins/sirt.py | 90 | ||||
| -rw-r--r-- | python/builder.py | 98 | ||||
| -rw-r--r-- | python/conda/build.sh | 12 | ||||
| -rw-r--r-- | python/conda/libastra/build.sh | 28 | ||||
| -rw-r--r-- | python/conda/libastra/meta.yaml | 10 | ||||
| -rw-r--r-- | python/conda/meta.yaml | 13 |
10 files changed, 309 insertions, 73 deletions
diff --git a/python/astra/__init__.py b/python/astra/__init__.py index 515d9a2..f4f5fe8 100644 --- a/python/astra/__init__.py +++ b/python/astra/__init__.py @@ -35,6 +35,7 @@ from . import projector from . import projector3d from . import matrix from . import plugin +from . import plugins from . import log from .optomo import OpTomo diff --git a/python/astra/creators.py b/python/astra/creators.py index 18504ea..7009884 100644 --- a/python/astra/creators.py +++ b/python/astra/creators.py @@ -535,7 +535,7 @@ def create_reconstruction(rec_type, proj_id, sinogram, iterations=1, use_mask='n def create_projector(proj_type, proj_geom, vol_geom): - """Create a 2D projector. + """Create a 2D or 3D projector. :param proj_type: Projector type, such as ``'line'``, ``'linear'``, ... :type proj_type: :class:`string` diff --git a/python/astra/plugins/__init__.py b/python/astra/plugins/__init__.py new file mode 100644 index 0000000..71e9b64 --- /dev/null +++ b/python/astra/plugins/__init__.py @@ -0,0 +1,29 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, 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/>. +# +# ----------------------------------------------------------------------- + + +from .sirt import SIRTPlugin +from .cgls import CGLSPlugin + diff --git a/python/astra/plugins/cgls.py b/python/astra/plugins/cgls.py new file mode 100644 index 0000000..2f4970b --- /dev/null +++ b/python/astra/plugins/cgls.py @@ -0,0 +1,99 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, 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/>. +# +# ----------------------------------------------------------------------- + + +import astra +import numpy as np +import six + +class CGLSPlugin(astra.plugin.base): + """CGLS.""" + + astra_name = "CGLS-PLUGIN" + + def initialize(self,cfg): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + + try: + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + self.data_mod = astra.data2d + except Exception: + v = astra.data3d.get_shared(self.vid) + s = astra.data3d.get_shared(self.sid) + self.data_mod = astra.data3d + + def run(self, its): + v = self.data_mod.get_shared(self.vid) + s = self.data_mod.get_shared(self.sid) + z = np.zeros(v.shape, dtype=np.float32) + p = np.zeros(v.shape, dtype=np.float32) + r = np.zeros(s.shape, dtype=np.float32) + w = np.zeros(s.shape, dtype=np.float32) + W = self.W + + # r = s - W*v + W.FP(v, out=w) + r[:] = s + r -= w + + # p = W'*r + W.BP(r, out=p) + + # gamma = <p,p> + gamma = np.dot(p.ravel(), p.ravel()) + + for i in range(its): + # w = W * p + W.FP(p, out=w) + + # alpha = gamma / <w,w> + alpha = gamma / np.dot(w.ravel(), w.ravel()) + + # v += alpha * p + z[:] = p + z *= alpha + v += z + + # r -= alpha * w + w *= -alpha; + r += w + + # z = W' * r + W.BP(r, out=z) + + # beta = <z,z> / gamma + newgamma = np.dot(z.ravel(), z.ravel()) + beta = newgamma / gamma + + # gamma = <z,z> + gamma = newgamma + + # p = z + beta * p + p *= beta + p += z + diff --git a/python/astra/plugins/sirt.py b/python/astra/plugins/sirt.py new file mode 100644 index 0000000..a0f1230 --- /dev/null +++ b/python/astra/plugins/sirt.py @@ -0,0 +1,90 @@ +# ----------------------------------------------------------------------- +# Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp +# 2013-2016, 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/>. +# +# ----------------------------------------------------------------------- + + +import astra +import numpy as np +import six + +class SIRTPlugin(astra.plugin.base): + """SIRT. + + Options: + + 'Relaxation': relaxation factor (optional) + 'MinConstraint': constrain values to at least this (optional) + 'MaxConstraint': constrain values to at most this (optional) + """ + + astra_name = "SIRT-PLUGIN" + + def initialize(self,cfg, Relaxation = 1, MinConstraint = None, MaxConstraint = None): + self.W = astra.OpTomo(cfg['ProjectorId']) + self.vid = cfg['ReconstructionDataId'] + self.sid = cfg['ProjectionDataId'] + self.min_constraint = MinConstraint + self.max_constraint = MaxConstraint + + try: + v = astra.data2d.get_shared(self.vid) + s = astra.data2d.get_shared(self.sid) + self.data_mod = astra.data2d + except Exception: + v = astra.data3d.get_shared(self.vid) + s = astra.data3d.get_shared(self.sid) + self.data_mod = astra.data3d + + self.R = self.W * np.ones(v.shape,dtype=np.float32).ravel(); + self.R[self.R < 0.000001] = np.Inf + self.R = 1 / self.R + self.R = self.R.reshape(s.shape) + + self.mrC = self.W.T * np.ones(s.shape,dtype=np.float32).ravel(); + self.mrC[self.mrC < 0.000001] = np.Inf + self.mrC = -Relaxation / self.mrC + self.mrC = self.mrC.reshape(v.shape) + + + def run(self, its): + v = self.data_mod.get_shared(self.vid) + s = self.data_mod.get_shared(self.sid) + tv = np.zeros(v.shape, dtype=np.float32) + ts = np.zeros(s.shape, dtype=np.float32) + W = self.W + mrC = self.mrC + R = self.R + for i in range(its): + W.FP(v,out=ts) + ts -= s + ts *= R # ts = R * (W*v - s) + + W.BP(ts,out=tv) + tv *= mrC + + v += tv # v = v - rel * C * W' * ts + + if self.min_constraint is not None or self.max_constraint is not None: + v.clip(min=self.min_constraint, max=self.max_constraint, out=v) + diff --git a/python/builder.py b/python/builder.py index dcd62d8..218b427 100644 --- a/python/builder.py +++ b/python/builder.py @@ -21,72 +21,72 @@ # 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/>. # -#----------------------------------------------------------------------- +# ----------------------------------------------------------------------- -import sys import os import numpy as np -from distutils.version import LooseVersion from distutils.core import setup -from distutils.extension import Extension +from pkg_resources import parse_version 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 -try: - if os.environ['CL'].find('/DASTRA_CUDA')!=-1: - usecuda=True -except KeyError: - pass +if parse_version(Cython.__version__) < parse_version('0.13'): + raise ImportError('Cython version should be at least 0.13') + +use_cuda = ('-DASTRA_CUDA' in os.environ.get('CPPFLAGS', '') or + '/DASTRA_CUDA' in os.environ.get('CL', '')) +self_path = os.path.dirname(os.path.abspath(__file__)) -cfgToWrite = 'DEF HAVE_CUDA=' + str(usecuda) + "\n" -cfgHasToBeUpdated = True +cfg_string = 'DEF HAVE_CUDA=' + str(use_cuda) + '\n' +update_cfg = True try: - cfg = open('astra/config.pxi','r') - cfgIn = cfg.read() - cfg.close() - if cfgIn==cfgToWrite: - cfgHasToBeUpdated = False + with open(os.path.join(self_path, 'astra', 'config.pxi'), 'r') as cfg: + cfg_fromfile = cfg.read() + if cfg_fromfile == cfg_string: + update_cfg = False except IOError: pass -if cfgHasToBeUpdated: - cfg = open('astra/config.pxi','w') - cfg.write(cfgToWrite) - cfg.close() +if update_cfg: + with open(os.path.join(self_path, 'astra', 'config.pxi'), 'w') as cfg: + cfg.write(cfg_string) + +pkgdata = {} +if os.environ.get('ASTRA_INSTALL_LIBRARY_AS_DATA', ''): + pkgdata['astra'] = [os.environ['ASTRA_INSTALL_LIBRARY_AS_DATA']] -cmdclass = { } -ext_modules = [ ] +cmdclass = {} +ext_modules = [] -ext_modules = cythonize("astra/*.pyx", language_level=2) -cmdclass = { 'build_ext': build_ext } +ext_modules = cythonize(os.path.join(self_path, 'astra', '*.pyx'), + language_level=2) +cmdclass = {'build_ext': build_ext} for m in ext_modules: - if m.name == 'astra.plugin_c': - m.sources.append('astra/src/PythonPluginAlgorithm.cpp') + if m.name == 'astra.plugin_c': + m.sources.append(os.path.join(self_path, 'astra', 'src', + 'PythonPluginAlgorithm.cpp')) -setup (name = 'PyASTRAToolbox', - version = '1.7.1', - description = 'Python interface to the ASTRA-Toolbox', - author='D.M. Pelt', - author_email='D.M.Pelt@cwi.nl', - url='http://sf.net/projects/astra-toolbox', - #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"], - ) +setup(name='astra-toolbox', + version='1.7.1', + description='Python interface to the ASTRA Toolbox', + author='D.M. Pelt', + author_email='D.M.Pelt@cwi.nl', + url='https://github.com/astra-toolbox/astra-toolbox', + # 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', 'astra.plugins'], + package_data=pkgdata, + requires=['numpy', 'scipy', 'six'], + ) diff --git a/python/conda/build.sh b/python/conda/build.sh index 13ae3f8..951fd88 100644 --- a/python/conda/build.sh +++ b/python/conda/build.sh @@ -1,8 +1,4 @@ -cd build/linux -./autogen.sh -./configure --with-python --with-cuda=$CUDA_ROOT --prefix=$PREFIX -if [ $MAKEOPTS == '<UNDEFINED>' ] - then - MAKEOPTS="" -fi -make $MAKEOPTS python-root-install
\ No newline at end of file +#!/bin/sh + +cd $SRC_DIR/python/ +CPPFLAGS="-DASTRA_CUDA -DASTRA_PYTHON $CPPFLAGS -I$SRC_DIR/ -I$SRC_DIR/include -I$CUDA_ROOT/include" CC=$CC python ./builder.py build install diff --git a/python/conda/libastra/build.sh b/python/conda/libastra/build.sh index e1d9700..5807697 100644 --- a/python/conda/libastra/build.sh +++ b/python/conda/libastra/build.sh @@ -1,15 +1,23 @@ -cd build/linux -./autogen.sh -./configure --with-cuda=$CUDA_ROOT --prefix=$PREFIX -if [ $MAKEOPTS == '<UNDEFINED>' ] - then - MAKEOPTS="" -fi -make $MAKEOPTS install-libraries +#!/bin/sh + +cd $SRC_DIR/build/linux + +$SRC_DIR/build/linux/autogen.sh + +# Add C++11 to compiler flags if nvcc supports it, mostly to work around a boost bug +NVCC=$CUDA_ROOT/bin/nvcc +echo "int main(){return 0;}" > $CONDA_PREFIX/test.cu +$NVCC $CONDA_PREFIX/test.cu -ccbin $CC --std=c++11 -o $CONDA_PREFIX/test.out > /dev/null && EXTRA_NVCCFLAGS="--std=c++11" || /bin/true +rm -f $CONDA_PREFIX/test.out + +$SRC_DIR/build/linux/configure --with-install-type=prefix --with-cuda=$CUDA_ROOT --prefix=$CONDA_PREFIX NVCCFLAGS="-ccbin $CC $EXTRA_NVCCFLAGS" CC=$CC CXX=$CXX CFLAGS="-I$CONDA_PREFIX/include/boost" CXXFLAGS="-I$CONDA_PREFIX/include/boost" + +make install-libraries + LIBPATH=lib if [ $ARCH == 64 ] then LIBPATH+=64 fi -cp -P $CUDA_ROOT/$LIBPATH/libcudart.so.* $PREFIX/lib -cp -P $CUDA_ROOT/$LIBPATH/libcufft.so.* $PREFIX/lib +cp -P $CUDA_ROOT/$LIBPATH/libcudart.so.* $CONDA_PREFIX/lib +cp -P $CUDA_ROOT/$LIBPATH/libcufft.so.* $CONDA_PREFIX/lib diff --git a/python/conda/libastra/meta.yaml b/python/conda/libastra/meta.yaml index 73fa0d7..7c92e04 100644 --- a/python/conda/libastra/meta.yaml +++ b/python/conda/libastra/meta.yaml @@ -4,13 +4,19 @@ package: source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - #git_tag: v1.7.1 # Change to 1.8 after release + git_rev: master # for testing + # git_tag: 1.8 # TODO: change to this for next release build: number: 0 script_env: + - CC + - CXX - CUDA_ROOT - - MAKEOPTS + +requirements: + build: + - boost about: home: http://www.astra-toolbox.com diff --git a/python/conda/meta.yaml b/python/conda/meta.yaml index e6a7f52..94ce12f 100644 --- a/python/conda/meta.yaml +++ b/python/conda/meta.yaml @@ -4,32 +4,39 @@ package: source: git_url: https://github.com/astra-toolbox/astra-toolbox.git - #git_tag: v1.7.1 # Change to 1.8 after release + git_rev: master # for testing + # git_tag: 1.8 # TODO: change to this for next release build: number: 0 script_env: + - CC - CUDA_ROOT - - MAKEOPTS test: imports: - astra + requires: + # To avoid large downloads just for testing after build phase + - nomkl # [not win] + requirements: build: - python - cython >=0.13 + - nomkl # [not win] - numpy - scipy - six + - libastra ==1.8b # TODO: change to release version run: - python - numpy - scipy - six - - libastra ==1.8b + - libastra ==1.8b # TODO: change to release version about: |