Merge branch 'master' of https://github.com/vais-ral/CCPi-Regularisation-Toolkit

Conflicts:
	build/jenkins-build.sh

13 files changed, 45 insertions, 26 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 550b896..b95107a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -25,7 +25,10 @@ set (CIL_VERSION_MAJOR 0)
 set (CIL_VERSION_MINOR 10)
 set (CIL_VERSION_PATCH 2)
 
-set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+# get CIL_VERSION from environment variable and set it in cmake
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+message(STATUS "CIL_VERSION set to " ${CIL_VERSION})
 
 # set the Python variables for the Conda environment
 #include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index d92db82..b3c0dfb 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -6,7 +6,7 @@ project(RGL_core)
 
 # The version number.
 
-#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
 
 # conda orchestrated build
 message("CIL_VERSION ${CIL_VERSION}")
diff --git a/Core/regularisers_CPU/TGV_core.c b/Core/regularisers_CPU/TGV_core.c
index edd77b2..477e909 100644
--- a/Core/regularisers_CPU/TGV_core.c
+++ b/Core/regularisers_CPU/TGV_core.c
@@ -100,6 +100,9 @@ float TGV_main(float *U0, float *U, float lambda, float alpha1, float alpha0, in
             newU(V1, V1_old, (long)(dimX), (long)(dimY));
             newU(V2, V2_old, (long)(dimX), (long)(dimY));
         } /*end of iterations*/
+    /*freeing*/
+    free(P1);free(P2);free(Q1);free(Q2);free(Q3);free(U_old);
+    free(V1);free(V2);free(V1_old);free(V2_old);
 	return *U;
 }
 
diff --git a/Core/regularisers_GPU/PatchSelect_GPU_core.cu b/Core/regularisers_GPU/PatchSelect_GPU_core.cu
index d173124..98c8488 100644
--- a/Core/regularisers_GPU/PatchSelect_GPU_core.cu
+++ b/Core/regularisers_GPU/PatchSelect_GPU_core.cu
@@ -449,10 +449,12 @@ extern "C" int PatchSelect_GPU_main(float *A, unsigned short *H_i, unsigned shor
     checkCudaErrors(cudaMemcpy(H_j, H_j_d, N*M*NumNeighb*sizeof(unsigned short),cudaMemcpyDeviceToHost) );  
     checkCudaErrors(cudaMemcpy(Weights, Weights_d, N*M*NumNeighb*sizeof(float),cudaMemcpyDeviceToHost) );   
     
+    
     cudaFree(Ad); 
     cudaFree(H_i_d); 
     cudaFree(H_j_d);    
-    cudaFree(Weights_d);    
+    cudaFree(Weights_d);
     cudaFree(Eucl_Vec_d);
+    cudaDeviceReset();
     return 0;
 }
diff --git a/Core/regularisers_GPU/TV_FGP_GPU_core.h b/Core/regularisers_GPU/TV_FGP_GPU_core.h
index b28cdf3..bf13508 100755
--- a/Core/regularisers_GPU/TV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/TV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _TV_FGP_GPU_
 #define _TV_FGP_GPU_
 
-extern "C" int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Core/regularisers_GPU/TV_SB_GPU_core.h b/Core/regularisers_GPU/TV_SB_GPU_core.h
index d44ab77..901b90f 100755
--- a/Core/regularisers_GPU/TV_SB_GPU_core.h
+++ b/Core/regularisers_GPU/TV_SB_GPU_core.h
@@ -1,10 +1,10 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _SB_TV_GPU_
 #define _SB_TV_GPU_
 
-extern "C" int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+
+extern "C" CCPI_EXPORT int TV_SB_GPU_main(float *Input, float *Output, float mu, int iter, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Core/regularisers_GPU/dTV_FGP_GPU_core.h b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
index 9020b1a..f9281e8 100644
--- a/Core/regularisers_GPU/dTV_FGP_GPU_core.h
+++ b/Core/regularisers_GPU/dTV_FGP_GPU_core.h
@@ -1,10 +1,9 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <memory.h>
-
 #ifndef _dTV_FGP_GPU_
 #define _dTV_FGP_GPU_
 
-extern "C" int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+#include "CCPiDefines.h"
+#include <memory.h>
+
+extern "C" CCPI_EXPORT int dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iter, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
 
 #endif 
diff --git a/Readme.md b/Readme.md
index cdf823d..1745b9e 100644
--- a/Readme.md
+++ b/Readme.md
@@ -1,3 +1,6 @@
+| Master | Development |
+|--------|-------------|
+| [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit/) | [![Build Status](https://anvil.softeng-support.ac.uk/jenkins/buildStatus/icon?job=CILsingle/CCPi-Regularisation-Toolkit-dev)](https://anvil.softeng-support.ac.uk/jenkins/job/CILsingle/job/CCPi-Regularisation-Toolkit-dev/) |
 # CCPi-Regularisation Toolkit (CCPi-RGL)
 
 **Iterative image reconstruction (IIR) methods normally require regularisation to stabilise the convergence and make the reconstruction problem (inverse problem) more well-posed. The CCPi-RGL software provides 2D/3D and multi-channel regularisation strategies to ensure better performance of IIR methods. The regularisation modules are well-suited to use with [splitting algorithms](https://en.wikipedia.org/wiki/Augmented_Lagrangian_method#Alternating_direction_method_of_multipliers), such as, [ADMM](https://github.com/dkazanc/ADMM-tomo) and [FISTA](https://github.com/dkazanc/FISTA-tomo). Furthermore, the toolkit can be used for simpler inversion tasks, such as, image denoising, inpaiting, deconvolution etc. The core modules are written in C-OMP and CUDA languages and wrappers for Matlab and Python are provided.** 
diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
index d86d0ea..c2ef855 100644
--- a/Wrappers/Python/CMakeLists.txt
+++ b/Wrappers/Python/CMakeLists.txt
@@ -9,7 +9,7 @@ project(regulariserPython)
 #set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
 
 # conda orchestrated build
-message("CIL_VERSION ${CIL_VERSION}")
+message("CIL_VERSION: ${CIL_VERSION}")
 #include (GenerateExportHeader)
 
 find_package(PythonInterp REQUIRED)
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
index eec7c2f..39c0f2c 100644
--- a/Wrappers/Python/conda-recipe/build.sh
+++ b/Wrappers/Python/conda-recipe/build.sh
@@ -5,6 +5,7 @@ cp -rv "$RECIPE_DIR/../../../Core" "$SRC_DIR/Core"
 
 cd $SRC_DIR
 ##cuda=off
+
 cmake -G "Unix Makefiles" $RECIPE_DIR/../../../ -DBUILD_PYTHON_WRAPPER=ON -DCONDA_BUILD=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE="Release" -DLIBRARY_LIB=$CONDA_PREFIX/lib -DLIBRARY_INC=$CONDA_PREFIX -DCMAKE_INSTALL_PREFIX=$PREFIX
 
 
diff --git a/Wrappers/Python/conda-recipe/conda_build_config.yaml b/Wrappers/Python/conda-recipe/conda_build_config.yaml
new file mode 100644
index 0000000..b7977f3
--- /dev/null
+++ b/Wrappers/Python/conda-recipe/conda_build_config.yaml
@@ -0,0 +1,7 @@
+python:
+  - 2.7 # [not win]
+  - 3.5
+  - 3.6
+numpy:
+  - 1.12
+  - 1.15
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index 808493e..9dd5544 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -1,22 +1,23 @@
 package:
   name: ccpi-regulariser
-  version: 0.10.3
-
-
+  version: {{CIL_VERSION}}
+  
 build:
   preserve_egg_dir: False
   number: 0
+  script_env:
+    - CIL_VERSION
   
 test:
   files:
     - lena_gray_512.tif
   requires:
-    - pillow
+    - pillow=4.1.1
 
 requirements:
   build:
     - python
-    - numpy x.x
+    - numpy {{ numpy }}
     - setuptools
     - cython
     - vc 14 # [win and py36] 
@@ -25,8 +26,9 @@ requirements:
     - cmake 
 
   run:
+    - {{ pin_compatible('numpy', max_pin='x.x') }}
     - python
-    - numpy x.x
+    - numpy
     - vc 14 # [win and py36] 
     - vc 14 # [win and py35] 
     - vc 9  # [win and py27]
diff --git a/recipes/regularisers/build.sh b/recipes/regularisers/build.sh
index 0b8bce2..eaa778e 100644
--- a/recipes/regularisers/build.sh
+++ b/recipes/regularisers/build.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-echo $CIL_VERSION
+echo build.sh CIL_VERSION: $CIL_VERSION
 #if [ -z "$CIL_VERSION" ]; then
 #    echo "Need to set CIL_VERSION"
 #    exit 1