Merge pull request #60 from vais-ral/cmaking

Cmaking

32 files changed, 483 insertions, 141 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 6d931ee..06e9c78 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -22,7 +22,7 @@ set (RGL_VERSION_MAJOR 1)
 set (RGL_VERSION_MINOR 0)
 
 set (CIL_VERSION_MAJOR 0)
-set (CIL_VERSION_MINOR 9)
+set (CIL_VERSION_MINOR 10)
 set (CIL_VERSION_PATCH 1)
 
 set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
@@ -30,5 +30,27 @@ set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}
 # set the Python variables for the Conda environment
 #include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
 
+option (BUILD_MATLAB_WRAPPER "Build Matlab Wrappers" OFF)
+option (BUILD_PYTHON_WRAPPER "Build Python Wrappers" ON)
+option (CONDA_BUILD "Conda Build" OFF)
+option (BUILD_CUDA "Build the CUDA modules" ON)
+
+set(MATLAB_DEST_DIR "" CACHE PATH "Directory of the Matlab wrappers")
+if (MATLAB_DEST_DIR)
+set(MATLAB_DEST "${MATLAB_DEST_DIR}")
+else() 
+set(MATLAB_DEST "${CMAKE_INSTALL_PREFIX}/matlab")
+endif()
+message(STATUS "Matlab wrappers will be installed in " ${MATLAB_DEST})
+
+set(PYTHON_DEST_DIR "" CACHE PATH "Directory of the Matlab wrappers")
+if (PYTHON_DEST_DIR)
+ set(PYTHON_DEST "${PYTHON_DEST_DIR}")
+else() 
+ set(PYTHON_DEST "${CMAKE_INSTALL_PREFIX}/python")
+endif()
+message(STATUS "Python wrappers will be installed in " ${PYTHON_DEST})
+
+
 add_subdirectory(Core)
 add_subdirectory(Wrappers)
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index e596da9..ca6879a 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -1,12 +1,12 @@
 #   Copyright 2018 Edoardo Pasca
-cmake_minimum_required (VERSION 3.0)
+#cmake_minimum_required (VERSION 3.0)
 
-project(RGL)
+project(RGL_core)
 #https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
 
 # 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 ${CIL_VERSION}")
@@ -18,12 +18,19 @@ if (OPENMP_FOUND)
     set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
     set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
     set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+   set (CMAKE_SHARED_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+   set (CMAKE_STATIC_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_STATIC_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+   
 endif()
 
 ## Build the regularisers package as a library
 message("Creating Regularisers as a shared library")
 
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
+message("CMAKE_C_FLAGS ${CMAKE_C_FLAGS}")
+message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")
+message("CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS}")
+message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}")
 
 set(CMAKE_BUILD_TYPE "Release")
 
@@ -94,36 +101,48 @@ message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
 	)
 endif()
 
+
+
 # GPU Regularisers
+if (BUILD_CUDA)
+    find_package(CUDA)
+    if (CUDA_FOUND)
+      set(CUDA_NVCC_FLAGS "-Xcompiler -fPIC -shared -D_FORCE_INLINES")
+      message("CUDA FLAGS ${CUDA_NVCC_FLAGS}")
+      CUDA_ADD_LIBRARY(cilregcuda SHARED
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_ROF_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_FGP_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_SB_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/LLT_ROF_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TGV_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/dTV_FGP_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/NonlDiff_GPU_core.cu
+        ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/Diffus_4thO_GPU_core.cu
+      )
+      if (UNIX)
+        message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
+        install(TARGETS cilregcuda
+        LIBRARY DESTINATION lib
+        CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
+        )
+      elseif(WIN32)
+        message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
+        install(TARGETS cilregcuda
+        RUNTIME DESTINATION bin
+        ARCHIVE DESTINATION lib
+        CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
+        )
+      endif()
+    else()
+      message("CUDA NOT FOUND")
+    endif()
+endif()
 
-find_package(CUDA)
-if (CUDA_FOUND)
-  set(CUDA_NVCC_FLAGS "-Xcompiler -fPIC -shared -D_FORCE_INLINES")
-  message("CUDA FLAGS ${CUDA_NVCC_FLAGS}")
-  CUDA_ADD_LIBRARY(cilregcuda SHARED
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_ROF_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_FGP_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_SB_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/LLT_ROF_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TGV_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/dTV_FGP_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/NonlDiff_GPU_core.cu
-	${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/Diffus_4thO_GPU_core.cu
-  )
-  if (UNIX)
-    message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
-    install(TARGETS cilregcuda
-	LIBRARY DESTINATION lib
-	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
-	)
-  elseif(WIN32)
-    message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
-    install(TARGETS cilregcuda
-	RUNTIME DESTINATION bin
-	ARCHIVE DESTINATION lib
-	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
-	)
+if (${BUILD_MATLAB_WRAPPER})
+  if (WIN32)
+        install(TARGETS cilreg DESTINATION ${MATLAB_DEST})
+        if (CUDA_FOUND)
+            install(TARGETS cilregcuda DESTINATION ${MATLAB_DEST})
+        endif()
   endif()
-else()
-  message("CUDA NOT FOUND")
-endif()
+endif()
\ No newline at end of file
diff --git a/Readme.md b/Readme.md
index f88f3e1..fb3fdc8 100644
--- a/Readme.md
+++ b/Readme.md
@@ -35,27 +35,62 @@
 
 ## Installation:
 
-### Python binaries
+The package comes as a CMake project so you will need CMake to install it. After checking out the repository to a directory, i.e. `CCPi-Regularisation-Toolkit`, create a build directory. Additional flags to CMake will allow you to create the Matlab wrapper and/or the Python wrapper and the CUDA regularisers. In the following example I will write a line to build both wrappers and CUDA.
+
+```bash
+git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git
+mkdir build
+cd build
+cmake ../CCPi-Regularisation-Toolkit -DCONDA_BUILD=OFF -DBUILD_MATLAB_WRAPPER=ON -DBUILD_PYTHON_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=<your favourite install directory>
+make install
+```
+
+The library may be used directly from C/C++ as it is compiled as a shared library. Check-out the include files in `Core`. We provide wrappers in Python and Matlab.
+
+### Python
+#### Python binaries
 Python binaries are distributed via the [ccpi](https://anaconda.org/ccpi/ccpi-regulariser) conda channel. Currently we produce packages for Linux64, Python 2.7, 3.5 and 3.6, NumPy 1.12 and 1.13.
 
 ```
 conda install ccpi-regulariser -c ccpi -c conda-forge
 ```
 
-### Python (conda-build)
+#### Python (conda-build)
 ```
-	export CIL_VERSION=0.10.0
-	conda build recipes/regularisers --numpy 1.12 --python 3.5 
-	conda install cil_regulariser=${CIL_VERSION} --use-local --force
-	cd Wrappers/Python
-	conda build conda-recipe --numpy 1.12 --python 3.5 --no-test
+	export CIL_VERSION=0.10.1
+	conda build Wrappers/Python/conda-recipe --numpy 1.12 --python 3.5 
 	conda install ccpi-regulariser=${CIL_VERSION} --use-local --force
 	cd demos/
 	python demo_cpu_regularisers.py # to run CPU demo
 	python demo_gpu_regularisers.py # to run GPU demo
 ```
+
+#### Python build
+
+If Python is not picked by CMake you can provide the additional flag to CMake `-DPYTHON_EXECUTABLE=/path/to/python/executable`.
+
 ### Matlab
+
+If Matlab is not picked by CMake, you could add `-DMatlab_ROOT_DIR=<Matlab directory>`. 
+
+#### Linux
+Because you've installed the modules in `<your favourite install directory>` you need to instruct Matlab to look in those directories:
+
+```bash 
+
+PATH="/path/to/mex/:$PATH" LD_LIBRARY_PATH="/path/to/library:$LD_LIBRARY_PATH" matlab
+```
+By default `/path/to/mex` is `${CMAKE_INSTALL_PREFIX}/bin` and `/path/to/library/` is `${CMAKE_INSTALL_PREFIX}/lib`
+
+#### Windows
+On Windows the `dll` and the mex modules must reside in the same directory. It is sufficient to add the directory at the beginning of the m-file.
+```matlab
+addpath(/path/to/library);
+```
+
+#### Legacy Matlab installation
 ```
+	
 	cd /Wrappers/Matlab/mex_compile
 	compileCPU_mex.m % to compile CPU modules
 	compileGPU_mex.m % to compile GPU modules (see instructions in the file)
diff --git a/Wrappers/CMakeLists.txt b/Wrappers/CMakeLists.txt
index cbe2fec..bdcb8f4 100644
--- a/Wrappers/CMakeLists.txt
+++ b/Wrappers/CMakeLists.txt
@@ -11,4 +11,9 @@
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
-add_subdirectory(Python)
\ No newline at end of file
+if (BUILD_MATLAB_WRAPPER)
+    add_subdirectory(Matlab)
+endif()
+if (BUILD_PYTHON_WRAPPER)
+    add_subdirectory(Python)
+endif()
\ No newline at end of file
diff --git a/Wrappers/Matlab/CMakeLists.txt b/Wrappers/Matlab/CMakeLists.txt
new file mode 100755
index 0000000..0c26148
--- /dev/null
+++ b/Wrappers/Matlab/CMakeLists.txt
@@ -0,0 +1,147 @@
+project(regulariserMatlab)

+

+

+find_package(Matlab REQUIRED COMPONENTS MAIN_PROGRAM MX_LIBRARY ENG_LIBRARY )

+

+

+

+#C:\Users\ofn77899\Documents\Projects\CCPi\GitHub\CCPi-FISTA_Reconstruction\Core\regularisers_CPU

+# matlab_add_mex(

+    # NAME CPU_ROF

+    # SRC 

+      # ${CMAKE_SOURCE_DIR}/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c

+    # LINK_TO cilreg ${Matlab_LIBRARIES}

+    # )

+    

+# target_include_directories(CPU_ROF 

+   # PUBLIC ${CMAKE_SOURCE_DIR}/Core/regularisers_CPU

+   # ${CMAKE_SOURCE_DIR}/Core/regularisers_GPU

+   # ${CMAKE_SOURCE_DIR}/Core/inpainters_CPU

+   # ${CMAKE_SOURCE_DIR}/Core/

+   # ${MATLAB_INCLUDE_DIR})

+   

+   # matlab_add_mex(

+    # NAME CPU_TNV

+    # SRC 

+      # ${CMAKE_SOURCE_DIR}/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c 

+    # LINK_TO cilreg ${Matlab_LIBRARIES}

+    # )

+    

+# target_include_directories(CPU_TNV 

+   # PUBLIC ${CMAKE_SOURCE_DIR}/Core/regularisers_CPU

+   # ${CMAKE_SOURCE_DIR}/Core/regularisers_GPU

+   # ${CMAKE_SOURCE_DIR}/Core/inpainters_CPU

+   # ${CMAKE_SOURCE_DIR}/Core/

+   # ${MATLAB_INCLUDE_DIR})

+   

+#set (CPU_MEX_FILES "regularisers_CPU/TNV.c;regularisers_CPU/ROF_TV.c")

+#set (MEX_TARGETS "CPU_TNV;CPU_ROF")

+#list(APPEND MEX_TARGETS "CPU_TNV")

+#list(APPEND MEX_TARGETS "CPU_ROF")

+

+file(GLOB CPU_MEX_FILES

+    "${CMAKE_SOURCE_DIR}/Wrappers/Matlab/mex_compile/regularisers_CPU/*.c"

+    #"${CMAKE_SOURCE_DIR}/Wrappers/Matlab/mex_compile/regularisers_GPU/*.c"

+)

+

+#message("CPU_MEX_FILES " ${CPU_MEX_FILES})

+

+list(LENGTH CPU_MEX_FILES num)

+

+

+MATH(EXPR num "${num}-1")

+#set(num "-1")

+message("found ${num} files")

+

+foreach(tgt RANGE 0 ${num})

+  message("number " ${tgt})

+  list(LENGTH CPU_MEX_FILES num2)

+  message("the list is ${num2}")

+  #list(GET CPU_TARGETS ${tgt} current_target)

+  list(GET CPU_MEX_FILES ${tgt} current_file_name)

+  get_filename_component(current_file ${current_file_name} NAME)

+  string(REGEX MATCH "(.+).c" match ${current_file})

+  if (NOT ${match} EQUAL "" )

+  set (current_target ${CMAKE_MATCH_1})

+  endif()

+  message("matlab_add_mex target " ${current_file} " and " ${current_target})

+  matlab_add_mex(

+    NAME ${current_target}

+    SRC 

+      ${current_file_name} 

+            #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/FGP_TV_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/SB_TV_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/TGV_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/Diffusion_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/Diffus4th_order_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/LLT_ROF_core.c

+            #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/ROF_TV_core.c

+            #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/FGP_dTV_core.c

+            #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/TNV_core.c

+            #${CMAKE_SOURCE_DIR}/Core/regularisers_CPU/utils.c

+	    #${CMAKE_SOURCE_DIR}/Core/inpainters_CPU/Diffusion_Inpaint_core.c

+	    #${CMAKE_SOURCE_DIR}/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.c

+    LINK_TO cilreg ${Matlab_LIBRARIES}

+    )

+    

+target_include_directories(${current_target}

+   PUBLIC ${CMAKE_SOURCE_DIR}/Core/regularisers_CPU

+   ${CMAKE_SOURCE_DIR}/Core/regularisers_GPU

+   ${CMAKE_SOURCE_DIR}/Core/inpainters_CPU

+   ${CMAKE_SOURCE_DIR}/Core/

+   ${MATLAB_INCLUDE_DIR})

+   set_property(TARGET ${current_target} PROPERTY C_STANDARD 99)

+   list(APPEND CPU_MEX_TARGETS ${current_target})

+   INSTALL(TARGETS ${current_target} DESTINATION "${MATLAB_DEST}")

+endforeach()

+   

+add_custom_target(MatlabWrapper DEPENDS ${CPU_MEX_TARGETS})

+

+if (BUILD_CUDA)

+    find_package(CUDA)

+    if (CUDA_FOUND)

+      file(GLOB GPU_MEX_FILES

+        "${CMAKE_SOURCE_DIR}/Wrappers/Matlab/mex_compile/regularisers_GPU/*.cpp"

+      )

+

+      list(LENGTH GPU_MEX_FILES num)

+message("number of GPU files  " ${num})

+

+      MATH(EXPR num "${num}-1")

+    #set(num "-1")

+

+      foreach(tgt RANGE ${num})

+        message("number " ${tgt})

+  list(LENGTH GPU_MEX_FILES num2)

+  message("the list is ${num2}")

+  #list(GET CPU_TARGETS ${tgt} current_target)

+  list(GET GPU_MEX_FILES ${tgt} current_file_name)

+  get_filename_component(current_file ${current_file_name} NAME)

+  string(REGEX MATCH "(.+).c" match ${current_file})

+  if (NOT ${match} EQUAL "" )

+  set (current_target ${CMAKE_MATCH_1})

+  endif()

+  message("matlab_add_mex target " ${current_file} " and " ${current_target})

+        message("matlab_add_mex " ${current_target})

+        matlab_add_mex(

+          NAME ${current_target}

+          SRC 

+            ${current_file_name} 

+          LINK_TO cilregcuda ${Matlab_LIBRARIES}

+          )

+        

+        target_include_directories(${current_target}

+        PUBLIC ${CMAKE_SOURCE_DIR}/Core/regularisers_CPU

+               ${CMAKE_SOURCE_DIR}/Core/regularisers_GPU

+               ${CMAKE_SOURCE_DIR}/Core/inpainters_CPU

+               ${CMAKE_SOURCE_DIR}/Core/

+               ${MATLAB_INCLUDE_DIR})

+       

+        list(APPEND GPU_MEX_TARGETS ${current_target})

+        INSTALL(TARGETS ${current_target} DESTINATION "${MATLAB_DEST}")

+      endforeach()

+       

+      add_custom_target(MatlabWrapperGPU DEPENDS ${GPU_MEX_TARGETS})

+      

+    endif()

+endif()

diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
index 81c0600..66ea9be 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
@@ -42,8 +42,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iter_numb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
     float *Input, *Output=NULL, lambda, tau, sigma;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
index aae1cb7..642362f 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
@@ -44,8 +44,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch, nonneg;
-    const int  *dim_array;
+    int number_of_dims, iter, methTV, printswitch, nonneg;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
     float *Input, *Output=NULL, lambda, epsil;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
index bb868c7..1a0c070 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
@@ -49,9 +49,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch, nonneg;
-    const int  *dim_array;
-    const int  *dim_array2;
+    int number_of_dims, iter, methTV, printswitch, nonneg;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    const mwSize *dim_array2;    
     float *Input, *InputRef, *Output=NULL, lambda, epsil, eta;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
index 81b717d..ab45446 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
@@ -46,8 +46,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iterationsNumb, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iterationsNumb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;    
     float *Input, *Output=NULL, lambdaROF, lambdaLLT, tau;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
index e05f5d4..ec35b8b 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
@@ -43,8 +43,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ, penaltytype;
-    const int  *dim_array;
+    int number_of_dims, iter_numb, penaltytype;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;   
+    
     float *Input, *Output=NULL, lambda, tau, sigma;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
index eaab4a7..9833392 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
@@ -45,9 +45,11 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ, penaltytype, i, inpaint_elements;
-    const int  *dim_array;
-    const int  *dim_array2;
+    int number_of_dims, iter_numb, penaltytype, i, inpaint_elements;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;   
+    const mwSize *dim_array2;   
+    
     float *Input, *Output=NULL, lambda, tau, sigma;
     unsigned char *Mask;
     
@@ -95,7 +97,7 @@ void mexFunction(
     }    
     
     inpaint_elements = 0;
-    for (i=0; i<dimY*dimX*dimZ; i++) if (Mask[i] == 1) inpaint_elements++;
+    for (i=0; i<(int)(dimY*dimX*dimZ); i++) if (Mask[i] == 1) inpaint_elements++;
     if (inpaint_elements == 0) mexErrMsgTxt("The mask is full of zeros, nothing to inpaint");        
     Diffusion_Inpaint_CPU_main(Input, Mask, Output, lambda, sigma, iter_numb, tau, penaltytype, dimX, dimY, dimZ);
 }
\ No newline at end of file
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
index 36cf05c..b3f2c98 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
@@ -42,9 +42,11 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, dimX, dimY, dimZ, iterations, SW_increment;
-    const int  *dim_array;
-    const int  *dim_array2;
+    int number_of_dims, iterations, SW_increment;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    const mwSize *dim_array2;
+    
     float *Input, *Output=NULL;
     unsigned char *Mask, *Mask_upd=NULL;
     
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
index 6b9e1ea..55ef2b1 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
@@ -1,3 +1,4 @@
+
 /*
  * This work is part of the Core Imaging Library developed by
  * Visual Analytics and Imaging System Group of the Science Technology
@@ -43,11 +44,12 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ;
-    const int  *dim_array;
-    float *Input, *Output=NULL, lambda, tau;
+    int number_of_dims, iter_numb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array_i;
+    float *Input, *Output=NULL, lambda, tau;    
     
-    dim_array = mxGetDimensions(prhs[0]);
+    dim_array_i = mxGetDimensions(prhs[0]);
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
     
     /*Handling Matlab input data*/
@@ -59,15 +61,17 @@ void mexFunction(
     if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
     if(nrhs != 4) mexErrMsgTxt("Four inputs reqired: Image(2D,3D), regularization parameter, iterations number,  marching step constant");
     /*Handling Matlab output data*/
-    dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+    dimX = dim_array_i[0]; dimY = dim_array_i[1]; dimZ = dim_array_i[2];        
     
     /* output arrays*/
     if (number_of_dims == 2) {
         dimZ = 1; /*2D case*/
         /* output image/volume */
-        Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));                        
+        Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array_i, mxSINGLE_CLASS, mxREAL));          
     }    
-    if (number_of_dims == 3) Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-    
+    if (number_of_dims == 3) {
+        Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array_i, mxSINGLE_CLASS, mxREAL));
+    }
+     
     TV_ROF_CPU_main(Input, Output, lambda, iter_numb, tau, dimX, dimY, dimZ);    
 }
\ No newline at end of file
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
index d284cac..8636322 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
@@ -42,8 +42,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch;
-    const int  *dim_array;
+    int number_of_dims, iter, methTV, printswitch;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, epsil;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c
index 9516869..5459bf5 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c
@@ -43,8 +43,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY;
-    const int  *dim_array;
+    int number_of_dims, iter;
+    mwSize dimX, dimY;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, alpha0, alpha1, L2;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c
index e0584c4..acea75d 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c
@@ -41,8 +41,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iter;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
     float *Input, *Output=NULL, lambda, epsil;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c
index f9eb2ce..d457f46 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c
@@ -36,8 +36,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, dimX, dimY, dimZ, type;
-    const int  *dim_array;
+    int number_of_dims, type;
+    
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
     float *Input, *Input0, lambda;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
index 0edc067..0cc042b 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
@@ -42,8 +42,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iter_numb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
     float *Input, *Output=NULL, lambda, tau, sigma;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
index 9ed9ae0..c174e75 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
@@ -43,8 +43,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch, nonneg;
-    const int  *dim_array;
+    int number_of_dims, iter, methTV, printswitch, nonneg;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, epsil;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
index 5b80616..3f5a4b3 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
@@ -47,9 +47,11 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch, nonneg;
-    const int  *dim_array;
-    const int  *dim_array2;
+    int number_of_dims, iter, methTV, printswitch, nonneg;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    const mwSize *dim_array2;
+    
     float *Input, *InputRef, *Output=NULL, lambda, epsil, eta;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
index 37563b0..e8da4ce 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
@@ -46,8 +46,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iterationsNumb, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iterationsNumb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambdaROF, lambdaLLT, tau;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
index bfba9ea..1cd0cdc 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
@@ -46,8 +46,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ, penaltytype;
-    const int  *dim_array;
+    int number_of_dims, iter_numb, penaltytype;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, tau, sigma;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
index f60ba7b..bd01d55 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
@@ -42,8 +42,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter_numb, dimX, dimY, dimZ;
-    const int  *dim_array;
+    int number_of_dims, iter_numb;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, tau;
     
     dim_array = mxGetDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
index 60847d9..9d1328f 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
@@ -42,8 +42,10 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch;
-    const int  *dim_array;
+    int number_of_dims, iter, methTV, printswitch;
+    mwSize dimX, dimY, dimZ;
+    const mwSize *dim_array;
+    
     float *Input, *Output=NULL, lambda, epsil;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
index 5a0df5b..edb551d 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
@@ -43,8 +43,9 @@ void mexFunction(
         int nrhs, const mxArray *prhs[])
         
 {
-    int number_of_dims, iter, dimX, dimY;
-    const int  *dim_array;
+    int number_of_dims, iter;
+    mwSize dimX, dimY;
+    const mwSize *dim_array;
     float *Input, *Output=NULL, lambda, alpha0, alpha1, L2;
     
     number_of_dims = mxGetNumberOfDimensions(prhs[0]);
diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
index fa1a30b..d86d0ea 100644
--- a/Wrappers/Python/CMakeLists.txt
+++ b/Wrappers/Python/CMakeLists.txt
@@ -6,7 +6,7 @@ project(regulariserPython)
 
 # 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}")
@@ -41,31 +41,101 @@ elseif(UNIX)
 endif()
 
 # GPU regularisers
-
-find_package(CUDA)
-if (CUDA_FOUND)
-  message("CUDA FOUND")
-  set (SETUP_GPU_WRAPPERS "extra_libraries += ['cilregcuda']\n\
+if (BUILD_CUDA)
+    find_package(CUDA)
+    if (CUDA_FOUND)
+      message("CUDA FOUND")
+      set (SETUP_GPU_WRAPPERS "extra_libraries += ['cilregcuda']\n\
 setup( \n\
-    name='ccpi', \n\
- 	description='CCPi Core Imaging Library - Image regularisers GPU',\n\
- 	version=cil_version,\n\
-    cmdclass = {'build_ext': build_ext},\n\
-    ext_modules = [Extension('ccpi.filters.gpu_regularisers',\n\
-                              sources=[ \n\
-                                      os.path.join('.' , 'src', 'gpu_regularisers.pyx' ),\n\
-                                        ],\n\
-                             include_dirs=extra_include_dirs, \n\
- 							 library_dirs=extra_library_dirs, \n\
- 							 extra_compile_args=extra_compile_args, \n\
- 							 libraries=extra_libraries ), \n\
-    ],\n\
- 	zip_safe = False,	\n\
- 	packages = {'ccpi','ccpi.filters'},\n\
-)")
-else()
-  message("CUDA NOT FOUND")
-  set(SETUP_GPU_WRAPPERS "#CUDA NOT FOUND")
+        name='ccpi', \n\
+        description='CCPi Core Imaging Library - Image regularisers GPU',\n\
+        version=cil_version,\n\
+        cmdclass = {'build_ext': build_ext},\n\
+        ext_modules = [Extension('ccpi.filters.gpu_regularisers',\n\
+                                  sources=[ \n\
+                                          os.path.join('.' , 'src', 'gpu_regularisers.pyx' ),\n\
+                                            ],\n\
+                                 include_dirs=extra_include_dirs, \n\
+                                 library_dirs=extra_library_dirs, \n\
+                                 extra_compile_args=extra_compile_args, \n\
+                                 libraries=extra_libraries ), \n\
+        ],\n\
+        zip_safe = False,	\n\
+        packages = {'ccpi','ccpi.filters'},\n\
+    )")
+    else()
+      message("CUDA NOT FOUND")
+      set(SETUP_GPU_WRAPPERS "#CUDA NOT FOUND")
+    endif()
+endif()
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/setup-regularisers.py.in" "${CMAKE_CURRENT_BINARY_DIR}/setup-regularisers.py")
+
+
+find_package(PythonInterp)
+find_package(PythonLibs)
+if (PYTHONINTERP_FOUND)
+  message(STATUS "Found PYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}")
+  message(STATUS "Python version ${PYTHON_VERSION_STRING}")
+endif()
+if (PYTHONLIBS_FOUND)
+  message(STATUS "Found PYTHON_INCLUDE_DIRS=${PYTHON_INCLUDE_DIRS}")
+  message(STATUS "Found PYTHON_LIBRARIES=${PYTHON_LIBRARIES}")
 endif()
 
-configure_file("setup-regularisers.py.in" "setup-regularisers.py")
+if (PYTHONINTERP_FOUND)
+    message("Python found " ${PYTHON_EXECUTABLE})
+    set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/setup-regularisers.py.in")
+    set(SETUP_PY    "${CMAKE_CURRENT_BINARY_DIR}/setup-regularisers.py")
+    #set(DEPS        "${CMAKE_CURRENT_SOURCE_DIR}/module/__init__.py")
+    set (DEPS       "${CMAKE_BINARY_DIR}/Core/")
+    set(OUTPUT      "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp")
+
+    configure_file(${SETUP_PY_IN} ${SETUP_PY})
+
+    message("Core binary dir " ${CMAKE_BINARY_DIR}/Core/${CMAKE_BUILD_TYPE})
+    
+    if (CONDA_BUILD)
+      add_custom_command(OUTPUT ${OUTPUT}
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
+                       COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core
+                                                       ${PYTHON_EXECUTABLE} ${SETUP_PY} install
+                       COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
+                       DEPENDS cilreg)
+
+    else()
+      if (WIN32)
+        add_custom_command(OUTPUT ${OUTPUT}
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
+                       COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core/${CMAKE_BUILD_TYPE}
+                                                       ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
+                       COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
+                       DEPENDS cilreg)
+      else()
+        add_custom_command(OUTPUT ${OUTPUT}
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/src ${CMAKE_CURRENT_BINARY_DIR}/src
+                       COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/ccpi ${CMAKE_CURRENT_BINARY_DIR}/ccpi
+                       COMMAND ${CMAKE_COMMAND} -E env CIL_VERSION=${CIL_VERSION}
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/Core 
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/Core
+                                                       ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
+                       COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
+                       DEPENDS cilreg)
+      endif()
+      install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi 
+              DESTINATION ${PYTHON_DEST})
+    endif()
+    
+    
+    add_custom_target(PythonWrapper ALL DEPENDS ${OUTPUT})
+
+    #install(CODE "execute_process(COMMAND ${PYTHON} ${SETUP_PY} install)")
+endif()
diff --git a/Wrappers/Python/conda-recipe/bld.bat b/Wrappers/Python/conda-recipe/bld.bat
index e47f8d9..6c84355 100644
--- a/Wrappers/Python/conda-recipe/bld.bat
+++ b/Wrappers/Python/conda-recipe/bld.bat
@@ -6,12 +6,15 @@ exit 1
 mkdir "%SRC_DIR%\ccpi"
 ROBOCOPY /E "%RECIPE_DIR%\..\.." "%SRC_DIR%\ccpi"
 ROBOCOPY /E "%RECIPE_DIR%\..\..\..\Core" "%SRC_DIR%\Core"
-cd %SRC_DIR%\ccpi\Python
+::cd %SRC_DIR%\ccpi\Python
+cd %SRC_DIR%
 
 :: issue cmake to create setup.py
-cmake . 
+cmake -G "NMake Makefiles" %RECIPE_DIR%\..\..\..\ -DBUILD_PYTHON_WRAPPERS=ON -DCONDA_BUILD=ON -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE="Release" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" 
 
-%PYTHON% setup-regularisers.py build_ext
-if errorlevel 1 exit 1
-%PYTHON% setup-regularisers.py install
-if errorlevel 1 exit 1
+::%PYTHON% setup-regularisers.py build_ext
+::if errorlevel 1 exit 1
+::%PYTHON% setup-regularisers.py install
+::if errorlevel 1 exit 1
+nmake install
+if errorlevel 1 exit 1
\ No newline at end of file
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
index 8b05663..54bc8e2 100644
--- a/Wrappers/Python/conda-recipe/build.sh
+++ b/Wrappers/Python/conda-recipe/build.sh
@@ -1,19 +1,16 @@
 
-if [ -z "$CIL_VERSION" ]; then
-    echo "Need to set CIL_VERSION"
-    exit 1
-fi  
 mkdir "$SRC_DIR/ccpi"
 cp -rv "$RECIPE_DIR/../.." "$SRC_DIR/ccpi"
 cp -rv "$RECIPE_DIR/../../../Core" "$SRC_DIR/Core"
 
-cd $SRC_DIR/ccpi/Python
+cd $SRC_DIR
 
-echo "$SRC_DIR/ccpi/Python"
+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
 
-cmake . 
 
-$PYTHON setup-regularisers.py build_ext
-$PYTHON setup-regularisers.py install
+make install
+
+#$PYTHON setup-regularisers.py build_ext
+#$PYTHON setup-regularisers.py install
 
 
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/Wrappers/Python/conda-recipe/meta.yaml
index ca28bae..9286cc4 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/Wrappers/Python/conda-recipe/meta.yaml
@@ -1,12 +1,10 @@
 package:
   name: ccpi-regulariser
-  version: {{ environ['CIL_VERSION'] }}
+  version: 0.10.1
 
 
 build:
   preserve_egg_dir: False
-  script_env:
-    - CIL_VERSION   
 #  number: 0
   
 test:
@@ -21,7 +19,6 @@ requirements:
     - numpy x.x
     - setuptools
     - cython
-    - cil_regulariser =={{ environ['CIL_VERSION'] }}
     - vc 14 # [win and py36] 
     - vc 14 # [win and py35] 
     - vc 9  # [win and py27]
@@ -30,7 +27,6 @@ requirements:
   run:
     - python
     - numpy x.x
-    - cil_regulariser =={{ environ['CIL_VERSION'] }}
     - vc 14 # [win and py36] 
     - vc 14 # [win and py35] 
     - vc 9  # [win and py27]
diff --git a/Wrappers/Python/setup-regularisers.py.in b/Wrappers/Python/setup-regularisers.py.in
index 7108683..542dcb4 100644
--- a/Wrappers/Python/setup-regularisers.py.in
+++ b/Wrappers/Python/setup-regularisers.py.in
@@ -27,11 +27,13 @@ except:
 extra_include_dirs = [numpy.get_include(), library_include_path]
 #extra_library_dirs = [os.path.join(library_include_path, "..", "lib")]
 extra_compile_args = []
-extra_library_dirs = []
+extra_library_dirs = [library_lib_path]
 extra_compile_args = []
 extra_link_args = []
 extra_libraries = ['cilreg']
 
+print ("extra_library_dirs " , extra_library_dirs)
+
 extra_include_dirs += [os.path.join(".." , ".." , "Core"),
                        os.path.join(".." , ".." , "Core",  "regularisers_CPU"),
                        os.path.join(".." , ".." , "Core",  "inpainters_CPU"),
diff --git a/docs/installation.txt b/docs/installation.txt
new file mode 100644
index 0000000..f6db38c
--- /dev/null
+++ b/docs/installation.txt
@@ -0,0 +1,11 @@
+One can install CCPi-RGL toolkit using cmake:
+
+
+cmake ../CCPi-Regularisation-Toolkit/ -DBUILD_MATLAB_WRAPPERS=ON -DBUILD_PYTHON_WRAPPERS=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=install -DMatlab_ROOT_DIR=<Matlab directory> -DBUILD_CUDA=OFF
+
+make 
+
+make install 
+
+Running Matlab from Linux do:
+PATH="/path/to/mex/:$PATH" LD_LIBRARY_PATH="/path/to/library:$LD_LIBRARY_PATH" ./matlab -nosplash &
diff --git a/recipes/regularisers/bld.bat b/recipes/regularisers/bld.bat
index 6f2f7e7..43a5286 100644
--- a/recipes/regularisers/bld.bat
+++ b/recipes/regularisers/bld.bat
@@ -10,7 +10,7 @@ cd "%SRC_DIR%\build"
 
 echo "we should be in %SRC_DIR%\build"
 
-cmake -G "NMake Makefiles" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" "%SRC_DIR%\build"
+cmake -G "NMake Makefiles" "%RECIPE_DIR%\..\..\" -DLIBRARY_LIB="%CONDA_PREFIX%\lib" -DLIBRARY_INC="%CONDA_PREFIX%" -DCMAKE_INSTALL_PREFIX="%PREFIX%\Library" -DCONDA_BUILD=ON -DBUILD_WRAPPERS=OFF
 
 ::-DBOOST_LIBRARYDIR="%CONDA_PREFIX%\Library\lib" -DBOOST_INCLUDEDIR="%CONDA_PREFIX%\Library\include" -DBOOST_ROOT="%CONDA_PREFIX%\Library\lib"