133 files changed, 259 insertions, 154 deletions

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..62c8935
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+.idea/
\ No newline at end of file
diff --git a/CMakeLists.txt b/CMakeLists.txt
index b95107a..043f13c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -46,7 +46,7 @@ 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")
+set(PYTHON_DEST_DIR "" CACHE PATH "Directory of the Python wrappers")
 if (PYTHON_DEST_DIR)
  set(PYTHON_DEST "${PYTHON_DEST_DIR}")
 else() 
@@ -55,5 +55,5 @@ endif()
 message(STATUS "Python wrappers will be installed in " ${PYTHON_DEST})
 
 
-add_subdirectory(Core)
-add_subdirectory(Wrappers)
+#add_subdirectory(src/Core)
+add_subdirectory(src)
diff --git a/Readme.md b/Readme.md
index aeefffd..92b4273 100644
--- a/Readme.md
+++ b/Readme.md
@@ -9,15 +9,15 @@
 **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.** 
 
 <div align="center">
-  <img src="docs/images/probl.png" height="225"><br>  
+  <img src="demos/images/probl.png" height="225"><br>  
 </div>
 
 <div align="center">
-  <img src="docs/images/reg_penalties.jpg" height="450"><br>  
+  <img src="demos/images/reg_penalties.jpg" height="450"><br>  
 </div>
 
 <div align="center">
-  <img src="docs/images/TV_vs_NLTV.jpg" height="300"><br>  
+  <img src="demos/images/TV_vs_NLTV.jpg" height="300"><br>  
 </div>
 
 ## Prerequisites: 
@@ -50,13 +50,29 @@
 
 ## Installation:
 
-The package comes as a [CMake](https://cmake.org) project so you will need CMake (v.>=3) to configure it. Additionally you will need a C compiler, `make` (on linux) and CUDA SDK where available. The toolkit may be used directly from C/C++ as it is compiled as a shared library (check-out the include files in `Core` for this). We provide wrappers for Python and Matlab.
+The package comes as a [CMake](https://cmake.org) project
+and additional wrappers for Python and Matlab.
 
+To install precompiled binaries, you need `conda` and install from `ccpi` channel using :
+```
+conda install ccpi-regulariser -c ccpi -c conda-forge
+```
+
+In order to compile C/C++ sources and additional wrappers from source code for numpy 1.12 and python 3.6, the recommended way is:
+```
+git clone https://github.com/vais-ral/CCPi-Regularisation-Toolkit
+cd CCPi-Regularisation-Toolkit
+export CCPI_BUILD_ARGS="--numpy 1.12 --python 3.6"
+build/jenkins-build.sh
+```
+this will install `conda build` environment and compiles C/C++ and Python wrappers and performs basic tests for environment with python 3.6 and numpy 1.12.
+
+### CMake
+If you want to build directly using cmake, install CMake (v.>=3) to configure it. Additionally you will need a C compiler, `make` (on linux) and CUDA SDK where available. The toolkit may be used directly from C/C++ as it is compiled as a shared library (check-out the include files in `Core` for this) 
 1. Clone this repository to a directory, i.e. `CCPi-Regularisation-Toolkit`, 
 2. create a build directory. 
 3. Issue `cmake` to configure (or `cmake-gui`, or `ccmake`, or `cmake3`). Use additional flags to fine tune the configuration. 
 
-### CMake flags
 Flags used during configuration
 
 | CMake flag | type | meaning |
@@ -94,7 +110,7 @@ conda install ccpi-regulariser -c ccpi -c conda-forge
 #### Python (conda-build)
 ```
 	export CIL_VERSION=19.02
-	conda build Wrappers/Python/conda-recipe --numpy 1.12 --python 3.5 
+	conda build 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
@@ -167,8 +183,7 @@ addpath(/path/to/library);
 
 ### Applications:
 
-* [Regularised FISTA iterative reconstruction algorithm for X-ray tomographic reconstruction with highly inaccurate measurements (MATLAB/Python code)](https://github.com/dkazanc/FISTA-tomo)
-* [Regularised ADMM iterative reconstruction algorithm for X-ray tomographic reconstruction (MATLAB code)](https://github.com/dkazanc/ADMM-tomo)
+* [A library of tomographic reconstruction methods: direct and model-based iterative (MATLAB/Python code)](https://github.com/dkazanc/TomoRec)
 * [Joint image reconstruction method with correlative multi-channel prior for X-ray spectral computed tomography (MATLAB code)](https://github.com/dkazanc/multi-channel-X-ray-CT)
 
 ### License:
diff --git a/Wrappers/Python/conda-recipe/build.sh b/Wrappers/Python/conda-recipe/build.sh
deleted file mode 100644
index 39c0f2c..0000000
--- a/Wrappers/Python/conda-recipe/build.sh
+++ /dev/null
@@ -1,17 +0,0 @@
-
-mkdir "$SRC_DIR/ccpi"
-cp -rv "$RECIPE_DIR/../.." "$SRC_DIR/ccpi"
-cp -rv "$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
-
-
-make install
-
-#$PYTHON setup-regularisers.py build_ext
-#$PYTHON setup-regularisers.py install
-
-
diff --git a/CMake/FindAnacondaEnvironment.cmake b/build/FindAnacondaEnvironment.cmake
index 6475128..6475128 100644
--- a/CMake/FindAnacondaEnvironment.cmake
+++ b/build/FindAnacondaEnvironment.cmake
diff --git a/build/build-install.sh b/build/build-install.sh
new file mode 100755
index 0000000..def66a4
--- /dev/null
+++ b/build/build-install.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+export CCPI_BUILD_ARGS="--numpy 1.12 --python 3.6"
+bash <(curl -L https://raw.githubusercontent.com/vais-ral/CCPi-VirtualMachine/master/scripts/jenkins-build.sh)
+conda install -y ccpi-regulariser --use-local --force
\ No newline at end of file
diff --git a/run.sh b/build/run.sh
index 332d660..332d660 100644
--- a/run.sh
+++ b/build/run.sh
diff --git a/Wrappers/Python/demos/SoftwareX_supp/Demo_RealData_Recon_SX.py b/demos/SoftwareX_supp/Demo_RealData_Recon_SX.py
index 01491d9..01491d9 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/Demo_RealData_Recon_SX.py
+++ b/demos/SoftwareX_supp/Demo_RealData_Recon_SX.py
diff --git a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_ParOptimis_SX.py b/demos/SoftwareX_supp/Demo_SimulData_ParOptimis_SX.py
index 59ffc0e..59ffc0e 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_ParOptimis_SX.py
+++ b/demos/SoftwareX_supp/Demo_SimulData_ParOptimis_SX.py
diff --git a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_Recon_SX.py b/demos/SoftwareX_supp/Demo_SimulData_Recon_SX.py
index 93b0cef..93b0cef 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_Recon_SX.py
+++ b/demos/SoftwareX_supp/Demo_SimulData_Recon_SX.py
diff --git a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_SX.py b/demos/SoftwareX_supp/Demo_SimulData_SX.py
index cdf4325..cdf4325 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/Demo_SimulData_SX.py
+++ b/demos/SoftwareX_supp/Demo_SimulData_SX.py
diff --git a/Wrappers/Python/demos/SoftwareX_supp/Readme.md b/demos/SoftwareX_supp/Readme.md
index 54e83f1..54e83f1 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/Readme.md
+++ b/demos/SoftwareX_supp/Readme.md
diff --git a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_rofllt.h5 b/demos/SoftwareX_supp/optim_param/Optim_admm_rofllt.h5
index 63bc4fd..63bc4fd 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_rofllt.h5
+++ b/demos/SoftwareX_supp/optim_param/Optim_admm_rofllt.h5
diff --git a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_sbtv.h5 b/demos/SoftwareX_supp/optim_param/Optim_admm_sbtv.h5
index 03c0c14..03c0c14 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_sbtv.h5
+++ b/demos/SoftwareX_supp/optim_param/Optim_admm_sbtv.h5
diff --git a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_tgv.h5 b/demos/SoftwareX_supp/optim_param/Optim_admm_tgv.h5
index 056d915..056d915 100644
--- a/Wrappers/Python/demos/SoftwareX_supp/optim_param/Optim_admm_tgv.h5
+++ b/demos/SoftwareX_supp/optim_param/Optim_admm_tgv.h5
diff --git a/data/SinoInpaint.mat b/demos/data/SinoInpaint.mat
index d748fb4..d748fb4 100644
--- a/data/SinoInpaint.mat
+++ b/demos/data/SinoInpaint.mat
diff --git a/Wrappers/Python/conda-recipe/lena_gray_512.tif b/demos/data/lena_gray_512.tif
index f80cafc..f80cafc 100644
--- a/Wrappers/Python/conda-recipe/lena_gray_512.tif
+++ b/demos/data/lena_gray_512.tif
diff --git a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m b/demos/demoMatlab_3Ddenoise.m
index ac8e1ba..cf2c88a 100644
--- a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
+++ b/demos/demoMatlab_3Ddenoise.m
@@ -1,8 +1,8 @@
 % Volume (3D) denoising demo using CCPi-RGL
 clear; close all
-Path1 = sprintf(['..' filesep 'mex_compile' filesep 'installed'], 1i);
-Path2 = sprintf(['..' filesep '..' filesep '..' filesep 'data' filesep], 1i);
-Path3 = sprintf(['..' filesep 'supp'], 1i);
+Path1 = sprintf(['..' filesep 'src' filesep 'Matlab' filesep 'mex_compile' filesep 'installed'], 1i);
+Path2 = sprintf(['data' filesep], 1i);
+Path3 = sprintf(['..' filesep 'src' filesep 'Matlab' filesep 'supp'], 1i);
 addpath(Path1);
 addpath(Path2);
 addpath(Path3);
diff --git a/Wrappers/Matlab/demos/demoMatlab_denoise.m b/demos/demoMatlab_denoise.m
index 7e041c6..5e92ee1 100644
--- a/Wrappers/Matlab/demos/demoMatlab_denoise.m
+++ b/demos/demoMatlab_denoise.m
@@ -2,11 +2,11 @@
 clear; close all
 fsep = '/';
 
-Path1 = sprintf(['..' fsep 'mex_compile' fsep 'installed'], 1i);
-Path2 = sprintf(['..' fsep '..' fsep '..' fsep 'data' fsep], 1i);
-Path3 = sprintf(['..' fsep 'supp'], 1i);
-addpath(Path1); 
-addpath(Path2); 
+Path1 = sprintf(['..' fsep 'src' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
+Path2 = sprintf([ data' fsep], 1i);
+Path3 = sprintf(['..' filesep 'src' filesep 'Matlab' filesep 'supp'], 1i);
+addpath(Path1);
+addpath(Path2);
 addpath(Path3);
 
 Im = double(imread('lena_gray_512.tif'))/255;  % loading image
diff --git a/Wrappers/Matlab/demos/demoMatlab_inpaint.m b/demos/demoMatlab_inpaint.m
index 66f9c15..a85f2b9 100644
--- a/Wrappers/Matlab/demos/demoMatlab_inpaint.m
+++ b/demos/demoMatlab_inpaint.m
@@ -1,7 +1,7 @@
 % Image (2D) inpainting demo using CCPi-RGL
 clear; close all
-Path1 = sprintf(['..' filesep 'mex_compile' filesep 'installed'], 1i);
-Path2 = sprintf(['..' filesep '..' filesep '..' filesep 'data' filesep], 1i);
+Path1 = sprintf(['..' filesep 'src' filesep 'Matlab' filesep 'mex_compile' filesep 'installed'], 1i);
+Path2 = sprintf(['data' filesep], 1i);
 addpath(Path1);
 addpath(Path2);
 
diff --git a/Wrappers/Python/demos/demo_cpu_inpainters.py b/demos/demo_cpu_inpainters.py
index c61ea50..2e6ccf2 100644
--- a/Wrappers/Python/demos/demo_cpu_inpainters.py
+++ b/demos/demo_cpu_inpainters.py
@@ -29,7 +29,7 @@ def printParametersToString(pars):
 ###############################################################################
 
 # read sinogram and the mask
-filename = os.path.join(".." , ".." , ".." , "data" ,"SinoInpaint.mat")
+filename = os.path.join("data" ,"SinoInpaint.mat")
 sino = io.loadmat(filename)
 sino_full = sino.get('Sinogram')
 Mask = sino.get('Mask')
diff --git a/Wrappers/Python/demos/demo_cpu_regularisers.py b/demos/demo_cpu_regularisers.py
index b8dadf5..d34607a 100644
--- a/Wrappers/Python/demos/demo_cpu_regularisers.py
+++ b/demos/demo_cpu_regularisers.py
@@ -31,7 +31,7 @@ def printParametersToString(pars):
         return txt
 ###############################################################################
 #%%
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join( "data" ,"lena_gray_512.tif")
 
 # read image
 Im = plt.imread(filename)
diff --git a/Wrappers/Python/demos/demo_cpu_regularisers3D.py b/demos/demo_cpu_regularisers3D.py
index df8af27..fd6c545 100644
--- a/Wrappers/Python/demos/demo_cpu_regularisers3D.py
+++ b/demos/demo_cpu_regularisers3D.py
@@ -30,7 +30,7 @@ def printParametersToString(pars):
         return txt
 ###############################################################################
 #%%
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join( "data" ,"lena_gray_512.tif")
 
 # read image
 Im = plt.imread(filename)
diff --git a/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py b/demos/demo_cpu_vs_gpu_regularisers.py
index 6c4ab5e..e1eb91f 100644
--- a/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py
+++ b/demos/demo_cpu_vs_gpu_regularisers.py
@@ -31,7 +31,7 @@ def printParametersToString(pars):
         return txt
 ###############################################################################
 
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join("data" ,"lena_gray_512.tif")
 
 # read image
 Im = plt.imread(filename)                     
diff --git a/Wrappers/Python/demos/demo_gpu_regularisers.py b/demos/demo_gpu_regularisers.py
index 54a1c14..89bb948 100644
--- a/Wrappers/Python/demos/demo_gpu_regularisers.py
+++ b/demos/demo_gpu_regularisers.py
@@ -31,7 +31,7 @@ def printParametersToString(pars):
         return txt
 ###############################################################################
 #%%
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join( "data" ,"lena_gray_512.tif")
 
 # read image
 Im = plt.imread(filename)                     
diff --git a/Wrappers/Python/demos/demo_gpu_regularisers3D.py b/demos/demo_gpu_regularisers3D.py
index d50c08e..be16921 100644
--- a/Wrappers/Python/demos/demo_gpu_regularisers3D.py
+++ b/demos/demo_gpu_regularisers3D.py
@@ -30,7 +30,7 @@ def printParametersToString(pars):
         return txt
 ###############################################################################
 #%%
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join( "data" ,"lena_gray_512.tif")
 
 # read image
 Im = plt.imread(filename)                     
@@ -70,7 +70,7 @@ del Im2
 
 slices = 20
 
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+filename = os.path.join( "data" ,"lena_gray_512.tif")
 Im = plt.imread(filename)
 Im = np.asarray(Im, dtype='float32')
 
diff --git a/docs/images/TV_vs_NLTV.jpg b/demos/images/TV_vs_NLTV.jpg
index e976512..e976512 100644
--- a/docs/images/TV_vs_NLTV.jpg
+++ b/demos/images/TV_vs_NLTV.jpg
diff --git a/docs/images/probl.pdf b/demos/images/probl.pdf
index 6a06021..6a06021 100644
--- a/docs/images/probl.pdf
+++ b/demos/images/probl.pdf
diff --git a/docs/images/probl.png b/demos/images/probl.png
index af0e852..af0e852 100644
--- a/docs/images/probl.png
+++ b/demos/images/probl.png
diff --git a/docs/images/reg_penalties.jpg b/demos/images/reg_penalties.jpg
index 923d5c4..923d5c4 100644
--- a/docs/images/reg_penalties.jpg
+++ b/demos/images/reg_penalties.jpg
diff --git a/Wrappers/Matlab/mex_compile/installed/MEXed_files_location.txt b/demos/qualitymetrics.py
index e69de29..e69de29 100644
--- a/Wrappers/Matlab/mex_compile/installed/MEXed_files_location.txt
+++ b/demos/qualitymetrics.py
diff --git a/docs/installation.txt b/docs/installation.txt
deleted file mode 100644
index f6db38c..0000000
--- a/docs/installation.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-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/Wrappers/Python/conda-recipe/bld.bat b/recipe/bld.bat
index 6c84355..6c84355 100644
--- a/Wrappers/Python/conda-recipe/bld.bat
+++ b/recipe/bld.bat
diff --git a/recipe/build.sh b/recipe/build.sh
new file mode 100644
index 0000000..a156193
--- /dev/null
+++ b/recipe/build.sh
@@ -0,0 +1,18 @@
+
+#mkdir "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/Matlab" "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/Python" "$SRC_DIR/ccpi"
+#cp -rv "$RECIPE_DIR/../src/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
+
+
+make install
+
+#$PYTHON setup-regularisers.py build_ext
+#$PYTHON setup-regularisers.py install
+
+
diff --git a/Wrappers/Python/conda-recipe/conda_build_config.yaml b/recipe/conda_build_config.yaml
index fbe82dc..fbe82dc 100644
--- a/Wrappers/Python/conda-recipe/conda_build_config.yaml
+++ b/recipe/conda_build_config.yaml
diff --git a/Wrappers/Python/conda-recipe/meta.yaml b/recipe/meta.yaml
index 7435b2b..6f36906 100644
--- a/Wrappers/Python/conda-recipe/meta.yaml
+++ b/recipe/meta.yaml
@@ -10,9 +10,12 @@ build:
   
 test:
   files:
-    - lena_gray_512.tif
+    - ../test/lena_gray_512.tif
   requires:
-    - pillow=4.1.1
+    - pillow
+    - pillow=4.1.1 # [win]
+#  command:
+#    - unittest -d discover .... ../test
 
 requirements:
   build:
diff --git a/Wrappers/Python/conda-recipe/run_test.py b/recipe/run_test.py
index 21f3216..f551616 100755
--- a/Wrappers/Python/conda-recipe/run_test.py
+++ b/recipe/run_test.py
@@ -815,5 +815,7 @@ class TestRegularisers(unittest.TestCase):
 

         self.assertLess(abs(rms_fgp-rms_fgp_exp) , tolerance)

 

+

+

 if __name__ == '__main__':

     unittest.main()

diff --git a/recipes/regularisers/bld.bat b/recipes/regularisers/bld.bat
deleted file mode 100644
index 43a5286..0000000
--- a/recipes/regularisers/bld.bat
+++ /dev/null
@@ -1,21 +0,0 @@
-IF NOT DEFINED CIL_VERSION (
-ECHO CIL_VERSION Not Defined.
-exit 1
-)
-
-mkdir "%SRC_DIR%\build"
-ROBOCOPY /E "%RECIPE_DIR%\..\..\Core" "%SRC_DIR%\build"
-::ROBOCOPY /E "%RECIPE_DIR%\..\..\Wrappers\python\src" "%SRC_DIR%\build\module"
-cd "%SRC_DIR%\build"
-
-echo "we should be in %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"
-
-:: Build C library
-nmake install
-if errorlevel 1 exit 1
-
-:: Install step
diff --git a/recipes/regularisers/build.sh b/recipes/regularisers/build.sh
deleted file mode 100644
index eaa778e..0000000
--- a/recipes/regularisers/build.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#!/usr/bin/env bash
-
-echo build.sh CIL_VERSION: $CIL_VERSION
-#if [ -z "$CIL_VERSION" ]; then
-#    echo "Need to set CIL_VERSION"
-#    exit 1
-#fi  
-#export CIL_VERSION=0.9.1
-
-
-
-mkdir ${SRC_DIR}/build
-cp -rv ${RECIPE_DIR}/../../Core/ ${SRC_DIR}/build
-mkdir ${SRC_DIR}/build/build
-cd ${SRC_DIR}/build/build
-cmake -G "Unix Makefiles" -DLIBRARY_LIB="${CONDA_PREFIX}/lib" -DLIBRARY_INC="${CONDA_PREFIX}" -DCMAKE_INSTALL_PREFIX="${PREFIX}" ../Core
-
-make -j2 VERBOSE=1
-make install
diff --git a/recipes/regularisers/meta.yaml b/recipes/regularisers/meta.yaml
deleted file mode 100644
index 3ffcd1d..0000000
--- a/recipes/regularisers/meta.yaml
+++ /dev/null
@@ -1,27 +0,0 @@
-package:
-  name: cil_regulariser
-  version: {{ environ['CIL_VERSION'] }}
-
-
-build:
-  preserve_egg_dir: False
-  script_env: 
-    - CIL_VERSION
-
-requirements:
-  build:
-    - cmake >=3.1
-    - vc 14 # [win and py36] 
-    - vc 14 # [win and py35] 
-    - vc 9  # [win and py27]
-
-  run:
-    - vc 14 # [win and py36]
-    - vc 14 # [win and py35]
-    - vc 9  # [win and py27]
-
-
-about:
-  home: http://www.ccpi.ac.uk
-  license: Apache v2.0
-  summary: Regulariser package from CCPi
diff --git a/Wrappers/CMakeLists.txt b/src/CMakeLists.txt
index bdcb8f4..5fe1a57 100644
--- a/Wrappers/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -11,6 +11,7 @@
 #   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(Core)
 if (BUILD_MATLAB_WRAPPER)
     add_subdirectory(Matlab)
 endif()
diff --git a/Core/CCPiDefines.h b/src/Core/CCPiDefines.h
index d3038f9..d3038f9 100644
--- a/Core/CCPiDefines.h
+++ b/src/Core/CCPiDefines.h
diff --git a/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index b3c0dfb..b3c0dfb 100644
--- a/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
diff --git a/Core/inpainters_CPU/Diffusion_Inpaint_core.c b/src/Core/inpainters_CPU/Diffusion_Inpaint_core.c
index 08b168a..08b168a 100644
--- a/Core/inpainters_CPU/Diffusion_Inpaint_core.c
+++ b/src/Core/inpainters_CPU/Diffusion_Inpaint_core.c
diff --git a/Core/inpainters_CPU/Diffusion_Inpaint_core.h b/src/Core/inpainters_CPU/Diffusion_Inpaint_core.h
index a96fe79..a96fe79 100644
--- a/Core/inpainters_CPU/Diffusion_Inpaint_core.h
+++ b/src/Core/inpainters_CPU/Diffusion_Inpaint_core.h
diff --git a/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.c b/src/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.c
index b488ca4..b488ca4 100644
--- a/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.c
+++ b/src/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.c
diff --git a/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.h b/src/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.h
index 0f99ed4..0f99ed4 100644
--- a/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.h
+++ b/src/Core/inpainters_CPU/NonlocalMarching_Inpaint_core.h
diff --git a/Core/regularisers_CPU/Diffus4th_order_core.c b/src/Core/regularisers_CPU/Diffus4th_order_core.c
index 01f4f64..01f4f64 100644
--- a/Core/regularisers_CPU/Diffus4th_order_core.c
+++ b/src/Core/regularisers_CPU/Diffus4th_order_core.c
diff --git a/Core/regularisers_CPU/Diffus4th_order_core.h b/src/Core/regularisers_CPU/Diffus4th_order_core.h
index d81afcb..d81afcb 100644
--- a/Core/regularisers_CPU/Diffus4th_order_core.h
+++ b/src/Core/regularisers_CPU/Diffus4th_order_core.h
diff --git a/Core/regularisers_CPU/Diffusion_core.c b/src/Core/regularisers_CPU/Diffusion_core.c
index b765796..b765796 100644
--- a/Core/regularisers_CPU/Diffusion_core.c
+++ b/src/Core/regularisers_CPU/Diffusion_core.c
diff --git a/Core/regularisers_CPU/Diffusion_core.h b/src/Core/regularisers_CPU/Diffusion_core.h
index cc36dad..cc36dad 100644
--- a/Core/regularisers_CPU/Diffusion_core.h
+++ b/src/Core/regularisers_CPU/Diffusion_core.h
diff --git a/Core/regularisers_CPU/FGP_TV_core.c b/src/Core/regularisers_CPU/FGP_TV_core.c
index 68d58b7..68d58b7 100644
--- a/Core/regularisers_CPU/FGP_TV_core.c
+++ b/src/Core/regularisers_CPU/FGP_TV_core.c
diff --git a/Core/regularisers_CPU/FGP_TV_core.h b/src/Core/regularisers_CPU/FGP_TV_core.h
index 3418604..3418604 100644
--- a/Core/regularisers_CPU/FGP_TV_core.h
+++ b/src/Core/regularisers_CPU/FGP_TV_core.h
diff --git a/Core/regularisers_CPU/FGP_dTV_core.c b/src/Core/regularisers_CPU/FGP_dTV_core.c
index 17b75ff..17b75ff 100644
--- a/Core/regularisers_CPU/FGP_dTV_core.c
+++ b/src/Core/regularisers_CPU/FGP_dTV_core.c
diff --git a/Core/regularisers_CPU/FGP_dTV_core.h b/src/Core/regularisers_CPU/FGP_dTV_core.h
index 442dd30..442dd30 100644
--- a/Core/regularisers_CPU/FGP_dTV_core.h
+++ b/src/Core/regularisers_CPU/FGP_dTV_core.h
diff --git a/Core/regularisers_CPU/LLT_ROF_core.c b/src/Core/regularisers_CPU/LLT_ROF_core.c
index 8416a14..8416a14 100644
--- a/Core/regularisers_CPU/LLT_ROF_core.c
+++ b/src/Core/regularisers_CPU/LLT_ROF_core.c
diff --git a/Core/regularisers_CPU/LLT_ROF_core.h b/src/Core/regularisers_CPU/LLT_ROF_core.h
index 8e6591e..8e6591e 100644
--- a/Core/regularisers_CPU/LLT_ROF_core.h
+++ b/src/Core/regularisers_CPU/LLT_ROF_core.h
diff --git a/Core/regularisers_CPU/Nonlocal_TV_core.c b/src/Core/regularisers_CPU/Nonlocal_TV_core.c
index c4c9118..c4c9118 100644
--- a/Core/regularisers_CPU/Nonlocal_TV_core.c
+++ b/src/Core/regularisers_CPU/Nonlocal_TV_core.c
diff --git a/Core/regularisers_CPU/Nonlocal_TV_core.h b/src/Core/regularisers_CPU/Nonlocal_TV_core.h
index 6d55101..6d55101 100644
--- a/Core/regularisers_CPU/Nonlocal_TV_core.h
+++ b/src/Core/regularisers_CPU/Nonlocal_TV_core.h
diff --git a/Core/regularisers_CPU/PatchSelect_core.c b/src/Core/regularisers_CPU/PatchSelect_core.c
index cf5cdc7..cf5cdc7 100644
--- a/Core/regularisers_CPU/PatchSelect_core.c
+++ b/src/Core/regularisers_CPU/PatchSelect_core.c
diff --git a/Core/regularisers_CPU/PatchSelect_core.h b/src/Core/regularisers_CPU/PatchSelect_core.h
index ddaa428..ddaa428 100644
--- a/Core/regularisers_CPU/PatchSelect_core.h
+++ b/src/Core/regularisers_CPU/PatchSelect_core.h
diff --git a/Core/regularisers_CPU/ROF_TV_core.c b/src/Core/regularisers_CPU/ROF_TV_core.c
index 1858442..1858442 100644
--- a/Core/regularisers_CPU/ROF_TV_core.c
+++ b/src/Core/regularisers_CPU/ROF_TV_core.c
diff --git a/Core/regularisers_CPU/ROF_TV_core.h b/src/Core/regularisers_CPU/ROF_TV_core.h
index 4e320e9..4e320e9 100644
--- a/Core/regularisers_CPU/ROF_TV_core.h
+++ b/src/Core/regularisers_CPU/ROF_TV_core.h
diff --git a/Core/regularisers_CPU/SB_TV_core.c b/src/Core/regularisers_CPU/SB_TV_core.c
index 769ea67..769ea67 100755
--- a/Core/regularisers_CPU/SB_TV_core.c
+++ b/src/Core/regularisers_CPU/SB_TV_core.c
diff --git a/Core/regularisers_CPU/SB_TV_core.h b/src/Core/regularisers_CPU/SB_TV_core.h
index 7485e3b..7485e3b 100644
--- a/Core/regularisers_CPU/SB_TV_core.h
+++ b/src/Core/regularisers_CPU/SB_TV_core.h
diff --git a/Core/regularisers_CPU/TGV_core.c b/src/Core/regularisers_CPU/TGV_core.c
index 136e0bd..136e0bd 100644
--- a/Core/regularisers_CPU/TGV_core.c
+++ b/src/Core/regularisers_CPU/TGV_core.c
diff --git a/Core/regularisers_CPU/TGV_core.h b/src/Core/regularisers_CPU/TGV_core.h
index 11b12c1..11b12c1 100644
--- a/Core/regularisers_CPU/TGV_core.h
+++ b/src/Core/regularisers_CPU/TGV_core.h
diff --git a/Core/regularisers_CPU/TNV_core.c b/src/Core/regularisers_CPU/TNV_core.c
index 753cc5f..753cc5f 100755
--- a/Core/regularisers_CPU/TNV_core.c
+++ b/src/Core/regularisers_CPU/TNV_core.c
diff --git a/Core/regularisers_CPU/TNV_core.h b/src/Core/regularisers_CPU/TNV_core.h
index aa050a4..aa050a4 100644
--- a/Core/regularisers_CPU/TNV_core.h
+++ b/src/Core/regularisers_CPU/TNV_core.h
diff --git a/Core/regularisers_CPU/utils.c b/src/Core/regularisers_CPU/utils.c
index 7a4e80b..7a4e80b 100644
--- a/Core/regularisers_CPU/utils.c
+++ b/src/Core/regularisers_CPU/utils.c
diff --git a/Core/regularisers_CPU/utils.h b/src/Core/regularisers_CPU/utils.h
index cfaf6d7..cfaf6d7 100644
--- a/Core/regularisers_CPU/utils.h
+++ b/src/Core/regularisers_CPU/utils.h
diff --git a/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu b/src/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu
index a4dbe70..a4dbe70 100644
--- a/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu
+++ b/src/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu
diff --git a/Core/regularisers_GPU/Diffus_4thO_GPU_core.h b/src/Core/regularisers_GPU/Diffus_4thO_GPU_core.h
index 77d5d79..77d5d79 100644
--- a/Core/regularisers_GPU/Diffus_4thO_GPU_core.h
+++ b/src/Core/regularisers_GPU/Diffus_4thO_GPU_core.h
diff --git a/Core/regularisers_GPU/LLT_ROF_GPU_core.cu b/src/Core/regularisers_GPU/LLT_ROF_GPU_core.cu
index 87871be..87871be 100644
--- a/Core/regularisers_GPU/LLT_ROF_GPU_core.cu
+++ b/src/Core/regularisers_GPU/LLT_ROF_GPU_core.cu
diff --git a/Core/regularisers_GPU/LLT_ROF_GPU_core.h b/src/Core/regularisers_GPU/LLT_ROF_GPU_core.h
index a6bfcc7..a6bfcc7 100644
--- a/Core/regularisers_GPU/LLT_ROF_GPU_core.h
+++ b/src/Core/regularisers_GPU/LLT_ROF_GPU_core.h
diff --git a/Core/regularisers_GPU/NonlDiff_GPU_core.cu b/src/Core/regularisers_GPU/NonlDiff_GPU_core.cu
index ff7ce4d..ff7ce4d 100644
--- a/Core/regularisers_GPU/NonlDiff_GPU_core.cu
+++ b/src/Core/regularisers_GPU/NonlDiff_GPU_core.cu
diff --git a/Core/regularisers_GPU/NonlDiff_GPU_core.h b/src/Core/regularisers_GPU/NonlDiff_GPU_core.h
index 5fe457e..5fe457e 100644
--- a/Core/regularisers_GPU/NonlDiff_GPU_core.h
+++ b/src/Core/regularisers_GPU/NonlDiff_GPU_core.h
diff --git a/Core/regularisers_GPU/PatchSelect_GPU_core.cu b/src/Core/regularisers_GPU/PatchSelect_GPU_core.cu
index 98c8488..98c8488 100644
--- a/Core/regularisers_GPU/PatchSelect_GPU_core.cu
+++ b/src/Core/regularisers_GPU/PatchSelect_GPU_core.cu
diff --git a/Core/regularisers_GPU/PatchSelect_GPU_core.h b/src/Core/regularisers_GPU/PatchSelect_GPU_core.h
index 8c124d3..8c124d3 100644
--- a/Core/regularisers_GPU/PatchSelect_GPU_core.h
+++ b/src/Core/regularisers_GPU/PatchSelect_GPU_core.h
diff --git a/Core/regularisers_GPU/TGV_GPU_core.cu b/src/Core/regularisers_GPU/TGV_GPU_core.cu
index 849219b..849219b 100644
--- a/Core/regularisers_GPU/TGV_GPU_core.cu
+++ b/src/Core/regularisers_GPU/TGV_GPU_core.cu
diff --git a/Core/regularisers_GPU/TGV_GPU_core.h b/src/Core/regularisers_GPU/TGV_GPU_core.h
index e8f9c6e..e8f9c6e 100644
--- a/Core/regularisers_GPU/TGV_GPU_core.h
+++ b/src/Core/regularisers_GPU/TGV_GPU_core.h
diff --git a/Core/regularisers_GPU/TV_FGP_GPU_core.cu b/src/Core/regularisers_GPU/TV_FGP_GPU_core.cu
index b371c5d..b371c5d 100755
--- a/Core/regularisers_GPU/TV_FGP_GPU_core.cu
+++ b/src/Core/regularisers_GPU/TV_FGP_GPU_core.cu
diff --git a/Core/regularisers_GPU/TV_FGP_GPU_core.h b/src/Core/regularisers_GPU/TV_FGP_GPU_core.h
index bf13508..bf13508 100755
--- a/Core/regularisers_GPU/TV_FGP_GPU_core.h
+++ b/src/Core/regularisers_GPU/TV_FGP_GPU_core.h
diff --git a/Core/regularisers_GPU/TV_ROF_GPU_core.cu b/src/Core/regularisers_GPU/TV_ROF_GPU_core.cu
index 76f5be9..76f5be9 100755
--- a/Core/regularisers_GPU/TV_ROF_GPU_core.cu
+++ b/src/Core/regularisers_GPU/TV_ROF_GPU_core.cu
diff --git a/Core/regularisers_GPU/TV_ROF_GPU_core.h b/src/Core/regularisers_GPU/TV_ROF_GPU_core.h
index 3a09296..3a09296 100755
--- a/Core/regularisers_GPU/TV_ROF_GPU_core.h
+++ b/src/Core/regularisers_GPU/TV_ROF_GPU_core.h
diff --git a/Core/regularisers_GPU/TV_SB_GPU_core.cu b/src/Core/regularisers_GPU/TV_SB_GPU_core.cu
index 1f494ee..1f494ee 100755
--- a/Core/regularisers_GPU/TV_SB_GPU_core.cu
+++ b/src/Core/regularisers_GPU/TV_SB_GPU_core.cu
diff --git a/Core/regularisers_GPU/TV_SB_GPU_core.h b/src/Core/regularisers_GPU/TV_SB_GPU_core.h
index 901b90f..901b90f 100755
--- a/Core/regularisers_GPU/TV_SB_GPU_core.h
+++ b/src/Core/regularisers_GPU/TV_SB_GPU_core.h
diff --git a/Core/regularisers_GPU/dTV_FGP_GPU_core.cu b/src/Core/regularisers_GPU/dTV_FGP_GPU_core.cu
index 7503ec7..7503ec7 100644
--- a/Core/regularisers_GPU/dTV_FGP_GPU_core.cu
+++ b/src/Core/regularisers_GPU/dTV_FGP_GPU_core.cu
diff --git a/Core/regularisers_GPU/dTV_FGP_GPU_core.h b/src/Core/regularisers_GPU/dTV_FGP_GPU_core.h
index f9281e8..f9281e8 100644
--- a/Core/regularisers_GPU/dTV_FGP_GPU_core.h
+++ b/src/Core/regularisers_GPU/dTV_FGP_GPU_core.h
diff --git a/Core/regularisers_GPU/shared.h b/src/Core/regularisers_GPU/shared.h
index fe98cd6..fe98cd6 100644
--- a/Core/regularisers_GPU/shared.h
+++ b/src/Core/regularisers_GPU/shared.h
diff --git a/Wrappers/Matlab/CMakeLists.txt b/src/Matlab/CMakeLists.txt
index 0c26148..b97f845 100755
--- a/Wrappers/Matlab/CMakeLists.txt
+++ b/src/Matlab/CMakeLists.txt
@@ -9,7 +9,7 @@ find_package(Matlab REQUIRED COMPONENTS MAIN_PROGRAM MX_LIBRARY ENG_LIBRARY )
 # matlab_add_mex(

     # NAME CPU_ROF

     # SRC 

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

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

     # LINK_TO cilreg ${Matlab_LIBRARIES}

     # )

     

@@ -23,7 +23,7 @@ find_package(Matlab REQUIRED COMPONENTS MAIN_PROGRAM MX_LIBRARY ENG_LIBRARY )
    # matlab_add_mex(

     # NAME CPU_TNV

     # SRC 

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

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

     # LINK_TO cilreg ${Matlab_LIBRARIES}

     # )

     

@@ -40,8 +40,8 @@ find_package(Matlab REQUIRED COMPONENTS MAIN_PROGRAM MX_LIBRARY ENG_LIBRARY )
 #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"

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

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

 )

 

 #message("CPU_MEX_FILES " ${CPU_MEX_FILES})

@@ -101,7 +101,7 @@ if (BUILD_CUDA)
     find_package(CUDA)

     if (CUDA_FOUND)

       file(GLOB GPU_MEX_FILES

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

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

       )

 

       list(LENGTH GPU_MEX_FILES num)

diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m b/src/Matlab/mex_compile/compileCPU_mex_Linux.m
index 72a828e..72a828e 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
+++ b/src/Matlab/mex_compile/compileCPU_mex_Linux.m
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m b/src/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
index 6f7541c..6f7541c 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
+++ b/src/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
diff --git a/Wrappers/Matlab/mex_compile/compileGPU_mex.m b/src/Matlab/mex_compile/compileGPU_mex.m
index dd1475c..dd1475c 100644
--- a/Wrappers/Matlab/mex_compile/compileGPU_mex.m
+++ b/src/Matlab/mex_compile/compileGPU_mex.m
diff --git a/Wrappers/Python/ccpi/__init__.py b/src/Matlab/mex_compile/installed/MEXed_files_location.txt
index e69de29..e69de29 100644
--- a/Wrappers/Python/ccpi/__init__.py
+++ b/src/Matlab/mex_compile/installed/MEXed_files_location.txt
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c b/src/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
index 66ea9be..66ea9be 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c b/src/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
index 642362f..642362f 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/FGP_TV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c b/src/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
index 1a0c070..1a0c070 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/FGP_dTV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c b/src/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
index ab45446..ab45446 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c b/src/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
index ec35b8b..ec35b8b 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/NonlDiff.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c b/src/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
index 9833392..9833392 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/NonlDiff_Inp.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c b/src/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
index b3f2c98..b3f2c98 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/NonlocalMarching_Inpaint.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c b/src/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c
index 014c0a0..014c0a0 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/PatchSelect.c b/src/Matlab/mex_compile/regularisers_CPU/PatchSelect.c
index f942539..f942539 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/PatchSelect.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/PatchSelect.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c b/src/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
index 55ef2b1..55ef2b1 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/ROF_TV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c b/src/Matlab/mex_compile/regularisers_CPU/SB_TV.c
index 8636322..8636322 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/SB_TV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c b/src/Matlab/mex_compile/regularisers_CPU/TGV.c
index aa4eed4..aa4eed4 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TGV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/TGV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c b/src/Matlab/mex_compile/regularisers_CPU/TNV.c
index acea75d..acea75d 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TNV.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/TNV.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c b/src/Matlab/mex_compile/regularisers_CPU/TV_energy.c
index d457f46..d457f46 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_CPU/TV_energy.c
+++ b/src/Matlab/mex_compile/regularisers_CPU/TV_energy.c
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
index 0cc042b..0cc042b 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
index c174e75..c174e75 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/FGP_TV_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
index 3f5a4b3..3f5a4b3 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/FGP_dTV_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
index e8da4ce..e8da4ce 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
index 1cd0cdc..1cd0cdc 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/NonlDiff_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
index bd01d55..bd01d55 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/ROF_TV_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
index 9d1328f..9d1328f 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp b/src/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
index 1173282..1173282 100644
--- a/Wrappers/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
+++ b/src/Matlab/mex_compile/regularisers_GPU/TGV_GPU.cpp
diff --git a/Wrappers/Matlab/supp/RMSE.m b/src/Matlab/supp/RMSE.m
index 002f776..002f776 100644
--- a/Wrappers/Matlab/supp/RMSE.m
+++ b/src/Matlab/supp/RMSE.m
diff --git a/Wrappers/Matlab/supp/my_red_yellowMAP.mat b/src/Matlab/supp/my_red_yellowMAP.mat
index c2a5b87..c2a5b87 100644
--- a/Wrappers/Matlab/supp/my_red_yellowMAP.mat
+++ b/src/Matlab/supp/my_red_yellowMAP.mat
diff --git a/Wrappers/Python/CMakeLists.txt b/src/Python/CMakeLists.txt
index c2ef855..ab95ecc 100644
--- a/Wrappers/Python/CMakeLists.txt
+++ b/src/Python/CMakeLists.txt
@@ -7,7 +7,7 @@ project(regulariserPython)
 # The version number.
 
 #set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
-
+message("Creating Python Wrapper")
 # conda orchestrated build
 message("CIL_VERSION: ${CIL_VERSION}")
 #include (GenerateExportHeader)
@@ -19,7 +19,7 @@ endif()
 
 	
 ## Build the regularisers package as a library
-message("Creating Regularisers as shared library")
+#TODO message("Creating Regularisers as shared library")
 
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
 
@@ -87,7 +87,7 @@ if (PYTHONINTERP_FOUND)
     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 (DEPS       "${CMAKE_BINARY_DIR}/src/Core/")
     set(OUTPUT      "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp")
 
     configure_file(${SETUP_PY_IN} ${SETUP_PY})
@@ -99,9 +99,9 @@ if (PYTHONINTERP_FOUND)
                        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=${CMAKE_BINARY_DIR}/Core
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} install
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
@@ -112,9 +112,9 @@ if (PYTHONINTERP_FOUND)
                        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}
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core/${CMAKE_BUILD_TYPE}
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
@@ -123,9 +123,9 @@ if (PYTHONINTERP_FOUND)
                        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=${CMAKE_BINARY_DIR}/Core
+                                                       PREFIX=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_INC=${CMAKE_SOURCE_DIR}/src/Core
+                                                       LIBRARY_LIB=${CMAKE_BINARY_DIR}/src/Core
                                                        ${PYTHON_EXECUTABLE} ${SETUP_PY} build_ext --inplace
                        COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
                        DEPENDS cilreg)
diff --git a/Wrappers/Python/ccpi/filters/__init__.py b/src/Python/__init__.py
index e69de29..e69de29 100644
--- a/Wrappers/Python/ccpi/filters/__init__.py
+++ b/src/Python/__init__.py
diff --git a/Wrappers/Python/ccpi/supp/__init__.py b/src/Python/ccpi/__init__.py
index e69de29..e69de29 100644
--- a/Wrappers/Python/ccpi/supp/__init__.py
+++ b/src/Python/ccpi/__init__.py
diff --git a/src/Python/ccpi/filters/__init__.py b/src/Python/ccpi/filters/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/src/Python/ccpi/filters/__init__.py
diff --git a/Wrappers/Python/ccpi/filters/regularisers.py b/src/Python/ccpi/filters/regularisers.py
index 588ea32..588ea32 100644
--- a/Wrappers/Python/ccpi/filters/regularisers.py
+++ b/src/Python/ccpi/filters/regularisers.py
diff --git a/src/Python/ccpi/supp/__init__.py b/src/Python/ccpi/supp/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/src/Python/ccpi/supp/__init__.py
diff --git a/Wrappers/Python/ccpi/supp/qualitymetrics.py b/src/Python/ccpi/supp/qualitymetrics.py
index f44d832..f44d832 100644
--- a/Wrappers/Python/ccpi/supp/qualitymetrics.py
+++ b/src/Python/ccpi/supp/qualitymetrics.py
diff --git a/Wrappers/Python/setup-regularisers.py.in b/src/Python/setup-regularisers.py.in
index 16fb380..82d9f9f 100644
--- a/Wrappers/Python/setup-regularisers.py.in
+++ b/src/Python/setup-regularisers.py.in
@@ -34,18 +34,18 @@ 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"),
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_FGP" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_ROF" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TV_SB" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "TGV" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "LLTROF" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "NDF" ) ,
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "dTV_FGP" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "DIFF4th" ) , 
-                       os.path.join(".." , ".." , "Core",  "regularisers_GPU" , "PatchSelect" ) ,
+extra_include_dirs += [os.path.join(".." , "Core"),
+                       os.path.join(".." , "Core",  "regularisers_CPU"),
+                       os.path.join(".." , "Core",  "inpainters_CPU"),
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_FGP" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_ROF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TV_SB" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "TGV" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "LLTROF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "NDF" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "dTV_FGP" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "DIFF4th" ) ,
+                       os.path.join(".." , "Core",  "regularisers_GPU" , "PatchSelect" ) ,
 						   "."]
 
 if platform.system() == 'Windows':				   
diff --git a/Wrappers/Python/src/cpu_regularisers.pyx b/src/Python/src/cpu_regularisers.pyx
index 11a0617..11a0617 100644
--- a/Wrappers/Python/src/cpu_regularisers.pyx
+++ b/src/Python/src/cpu_regularisers.pyx
diff --git a/Wrappers/Python/src/gpu_regularisers.pyx b/src/Python/src/gpu_regularisers.pyx
index b52f669..b52f669 100644
--- a/Wrappers/Python/src/gpu_regularisers.pyx
+++ b/src/Python/src/gpu_regularisers.pyx
diff --git a/src/__init__.py b/src/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/src/__init__.py
diff --git a/data/lena_gray_512.tif b/test/lena_gray_512.tif
index f80cafc..f80cafc 100644
--- a/data/lena_gray_512.tif
+++ b/test/lena_gray_512.tif
diff --git a/test/test_CPU_regularisers.py b/test/test_CPU_regularisers.py
new file mode 100644
index 0000000..379b989
--- /dev/null
+++ b/test/test_CPU_regularisers.py
@@ -0,0 +1,119 @@
+import unittest
+import math
+import os
+import timeit
+import numpy as np
+from ccpi.filters.regularisers import FGP_TV, SB_TV, TGV, LLT_ROF, FGP_dTV, NDF, Diff4th, ROF_TV
+from testroutines import *
+
+###############################################################################
+
+class TestRegularisers(unittest.TestCase):
+
+    def getPars(self):
+        filename = os.path.join("lena_gray_512.tif")
+        plt = TiffReader()
+        # read image
+        Im = plt.imread(filename)
+        Im = np.asarray(Im, dtype='float32')
+        Im = Im / 255
+        perc = 0.05
+        u0 = Im + np.random.normal(loc=0,
+                                   scale=perc * Im,
+                                   size=np.shape(Im))
+        u_ref = Im + np.random.normal(loc=0,
+                                      scale=0.01 * Im,
+                                      size=np.shape(Im))
+        u0 = u0.astype('float32')
+        u_ref = u_ref.astype('float32')
+        return Im,u0,u_ref
+
+
+    def test_FGP_TV_CPU(self):
+        Im,input,ref = self.getPars()
+
+        fgp_cpu = FGP_TV(input,0.04,1200,1e-5,0,0,0,'cpu');
+
+        rms = rmse(Im, fgp_cpu)
+
+        self.assertAlmostEqual(rms,0.02,delta=0.01)
+
+    def test_TV_ROF_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        fgp_cpu = ROF_TV(input,0.04,1200,2e-5, 'cpu')
+
+        rms = rmse(Im, fgp_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms,0.02,delta=0.01)
+
+    def test_SB_TV_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = SB_TV(input,0.04,150,1e-5,0,0,'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms,0.02,delta=0.01)
+
+    def test_TGV_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = TGV(input,0.04,1.0,2.0,250,12,'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms,0.02,delta=0.01)
+
+    def test_LLT_ROF_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = LLT_ROF(input,0.04,0.01,1000,1e-4,'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms,0.02,delta=0.01)
+
+    def test_NDF_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = NDF(input, 0.06, 0.04,1000,0.025,1, 'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms, 0.02, delta=0.01)
+
+    def test_Diff4th_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = Diff4th(input, 3.5,0.02,500,0.001, 'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms, 0.02, delta=0.01)
+
+    def test_FGP_dTV_CPU(self):
+        # set parameters
+        Im, input,ref = self.getPars()
+        # call routine
+        sb_cpu = FGP_dTV(input,ref,0.04,1000,1e-7,0.2,0,0,0, 'cpu')
+
+        rms = rmse(Im, sb_cpu)
+
+        # now test that it generates some expected output
+        self.assertAlmostEqual(rms, 0.02, delta=0.01)
+
+if __name__ == '__main__':
+    unittest.main()
diff --git a/test/testroutines.py b/test/testroutines.py
new file mode 100644
index 0000000..8da5c5e
--- /dev/null
+++ b/test/testroutines.py
@@ -0,0 +1,37 @@
+import numpy as np
+from PIL import Image
+
+class TiffReader(object):
+    def imread(self, filename):
+        return np.asarray(Image.open(filename))
+
+
+###############################################################################
+def printParametersToString(pars):
+    txt = r''
+    for key, value in pars.items():
+        if key == 'algorithm':
+            txt += "{0} = {1}".format(key, value.__name__)
+        elif key == 'input':
+            txt += "{0} = {1}".format(key, np.shape(value))
+        elif key == 'refdata':
+            txt += "{0} = {1}".format(key, np.shape(value))
+        else:
+            txt += "{0} = {1}".format(key, value)
+        txt += '\n'
+    return txt
+
+
+def nrmse(im1, im2):
+    rmse = np.sqrt(np.sum((im2 - im1) ** 2) / float(im1.size))
+    max_val = max(np.max(im1), np.max(im2))
+    min_val = min(np.min(im1), np.min(im2))
+    return 1 - (rmse / (max_val - min_val))
+
+
+def rmse(im1, im2):
+    rmse = np.sqrt(np.sum((im1 - im2) ** 2) / float(im1.size))
+    return rmse
+
+
+###############################################################################