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

40 files changed, 0 insertions, 7518 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
deleted file mode 100644
index cbe2fec..0000000
--- a/src/CMakeLists.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-#   Copyright 2017 Edoardo Pasca
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   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
diff --git a/src/Python/CMakeLists.txt b/src/Python/CMakeLists.txt
deleted file mode 100644
index 506159a..0000000
--- a/src/Python/CMakeLists.txt
+++ /dev/null
@@ -1,183 +0,0 @@
-#   Copyright 2017 Edoardo Pasca
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   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.
-
-# variables that must be set for conda compilation
-
-#PREFIX=C:\Apps\Miniconda2\envs\cil\Library
-#LIBRARY_INC=C:\\Apps\\Miniconda2\\envs\\cil\\Library\\include
-set (NUMPY_VERSION 1.12)
-
-## Tries to parse the output of conda env list to determine the current
-## active conda environment
-message ("Trying to determine your active conda environment...")
-execute_process(COMMAND "conda" "env" "list"
-					OUTPUT_VARIABLE _CONDA_ENVS
-					RESULT_VARIABLE _CONDA_RESULT
-					ERROR_VARIABLE _CONDA_ERR)
-			if(NOT _CONDA_RESULT)
-				string(REPLACE "\n" ";" ENV_LIST ${_CONDA_ENVS})
-				foreach(line ${ENV_LIST})
-				  string(REGEX MATCHALL "(.+)[*](.+)" match ${line})
-				  if (NOT ${match} EQUAL "")
-				    #message("MATCHED " ${CMAKE_MATCH_0})
-					#message("MATCHED " ${CMAKE_MATCH_1})
-					#message("MATCHED " ${CMAKE_MATCH_2})
-					string(STRIP ${CMAKE_MATCH_1} CONDA_ENVIRONMENT)
-					string(STRIP ${CMAKE_MATCH_2} CONDA_ENVIRONMENT_PATH)   
-				  endif()
-				endforeach()
-			else()
-				message(FATAL_ERROR "ERROR with conda command " ${_CONDA_ERR})
-			endif()
-
-if (${CONDA_ENVIRONMENT} AND ${CONDA_ENVIRONMENT_PATH})
-  message (FATAL_ERROR "CONDA NOT FOUND")
-else()
-  message("**********************************************************")
-  message("Using current conda environmnet " ${CONDA_ENVIRONMENT})
-  message("Using current conda environmnet path " ${CONDA_ENVIRONMENT_PATH})
-endif()
-
-message("CIL VERSION " ${CIL_VERSION})
-
-# set the Python variables for the Conda environment
-include(FindAnacondaEnvironment.cmake)
-findPythonForAnacondaEnvironment(${CONDA_ENVIRONMENT_PATH})
-
-message("Python found " ${PYTHON_VERSION_STRING})
-message("Python found Major " ${PYTHON_VERSION_MAJOR})
-message("Python found Minor " ${PYTHON_VERSION_MINOR})
-
-findPythonPackagesPath()
-message("PYTHON_PACKAGES_FOUND " ${PYTHON_PACKAGES_PATH})
-
-## CACHE SOME VARIABLES ##
-set (CONDA_ENVIRONMENT ${CONDA_ENVIRONMENT} CACHE INTERNAL "active conda environment" FORCE)
-set (CONDA_ENVIRONMENT_PATH ${CONDA_ENVIRONMENT_PATH} CACHE INTERNAL "active conda environment" FORCE)
-
-set (PYTHON_VERSION_STRING ${PYTHON_VERSION_STRING} CACHE INTERNAL "conda environment Python version string" FORCE)
-set (PYTHON_VERSION_MAJOR ${PYTHON_VERSION_MAJOR} CACHE INTERNAL "conda environment Python version major" FORCE)
-set (PYTHON_VERSION_MINOR ${PYTHON_VERSION_MINOR} CACHE INTERNAL "conda environment Python version minor" FORCE)
-set (PYTHON_VERSION_PATCH ${PYTHON_VERSION_PATCH} CACHE INTERNAL "conda environment Python version patch" FORCE)
-set (PYTHON_PACKAGES_PATH ${PYTHON_PACKAGES_PATH} CACHE INTERNAL "conda environment Python packages path" FORCE)
-
-if (WIN32)
-  #set (CONDA_ENVIRONMENT_PATH "C:\\Apps\\Miniconda2\\envs\\${CONDA_ENVIRONMENT}" CACHE PATH "Main environment directory")
-  set (CONDA_ENVIRONMENT_PREFIX "${CONDA_ENVIRONMENT_PATH}\\Library" CACHE PATH "env dir")
-  set (CONDA_ENVIRONMENT_LIBRARY_INC "${CONDA_ENVIRONMENT_PREFIX}\\include" CACHE PATH "env dir")
-elseif (UNIX)
-  #set (CONDA_ENVIRONMENT_PATH "/apps/anaconda/2.4/envs/${CONDA_ENVIRONMENT}" CACHE PATH "Main environment directory")
-  set (CONDA_ENVIRONMENT_PREFIX "${CONDA_ENVIRONMENT_PATH}/lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}" CACHE PATH "env dir")
-  set (CONDA_ENVIRONMENT_LIBRARY_INC "${CONDA_ENVIRONMENT_PREFIX}/include" CACHE PATH "env dir")
-endif()
-
-######### CONFIGURE REGULARIZER PACKAGE #############
-
-# copy the Pyhon files of the package regularizer
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging/)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi)
-# regularizers
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/imaging/Regularizer.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging)
-
-# Copy and configure the relative conda build and recipes
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup.py)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/meta.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe)
-
-if (WIN32)
-	
-  file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/) 
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile.bat)
-
-elseif(UNIX)
-  
-  message ("We are on UNIX")
-  file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/conda-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/conda-recipe/)
-  # assumes we will use bash
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile.sh)
-
-endif()
-
-########## CONFIGURE FISTA RECONSTRUCTOR PACKAGE
-# fista reconstructor
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/FISTAReconstructor.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/DeviceModel.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/reconstruction/AstraDevice.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi/reconstruction)
-
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/setup-fista.py.in ${CMAKE_CURRENT_BINARY_DIR}/setup-fista.py)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe)
-file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/meta.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe)
-
-if (WIN32)
-
-  file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/bld.bat DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe/)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile-fista.bat.in ${CMAKE_CURRENT_BINARY_DIR}/compile-fista.bat)
-
-elseif(UNIX)
-  message ("We are on UNIX")
-  file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/fista-recipe/build.sh DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/fista-recipe/)
-  # assumes we will use bash
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/compile-fista.sh.in ${CMAKE_CURRENT_BINARY_DIR}/compile-fista.sh)
-endif()
-
-#############################  TARGETS
-
-##########################  REGULARIZER PACKAGE ###############################
-
-# runs cmake on the build tree to update the code from source
-add_custom_target(update_code 
-		COMMAND ${CMAKE_COMMAND} 
-		ARGS ${CMAKE_SOURCE_DIR}
-		WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-		) 
-
-
-add_custom_target(fista
-		COMMAND bash
-		compile-fista.sh
-		WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-		DEPENDS ${update_code}
-		)
-
-add_custom_target(regularizers
-		COMMAND bash
-		compile.sh
-		WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-		DEPENDS update_code
-		)
-
-add_custom_target(install-fista
-		COMMAND ${CONDA_EXECUTABLE}
-		install --force --use-local ccpi-fista=${CIL_VERSION} -c ccpi -c conda-forge
-		WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-		)
-
-add_custom_target(install-regularizers
-		COMMAND ${CONDA_EXECUTABLE}
-		install --force --use-local ccpi-regularizers=${CIL_VERSION} -c ccpi -c conda-forge
-		WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-		)
-### add tests
-
-#add_executable(RegularizersTest )
-#find_package(tiff)
-#if (TIFF_FOUND)
-#  message("LibTIFF Found")
-#  message("TIFF_INCLUDE_DIR " ${TIFF_INCLUDE_DIR})
-#  message("TIFF_LIBRARIES" ${TIFF_LIBRARIES})
-#else()
-#  message("LibTIFF not found")
-#endif()
diff --git a/src/Python/FindAnacondaEnvironment.cmake b/src/Python/FindAnacondaEnvironment.cmake
deleted file mode 100644
index 6475128..0000000
--- a/src/Python/FindAnacondaEnvironment.cmake
+++ /dev/null
@@ -1,154 +0,0 @@
-#   Copyright 2017 Edoardo Pasca
-#
-#   Licensed under the Apache License, Version 2.0 (the "License");
-#   you may not use this file except in compliance with the License.
-#   You may obtain a copy of the License at
-#
-#       http://www.apache.org/licenses/LICENSE-2.0
-#
-#   Unless required by applicable law or agreed to in writing, software
-#   distributed under the License is distributed on an "AS IS" BASIS,
-#   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.
-
-# #.rst:
-# FindAnacondaEnvironment
-# --------------
-#
-# Find Python executable and library for a specific Anaconda environment
-#
-# This module finds the Python interpreter for a specific Anaconda enviroment, 
-# if installed and determines where the include files and libraries are.  
-# This code sets the following variables:
-#
-# ::
-#   PYTHONINTERP_FOUND         - if the Python interpret has been found
-#   PYTHON_EXECUTABLE          - the Python interpret found
-#   PYTHON_LIBRARY             - path to the python library
-#   PYTHON_INCLUDE_PATH        - path to where Python.h is found (deprecated)
-#   PYTHON_INCLUDE_DIRS        - path to where Python.h is found
-#   PYTHONLIBS_VERSION_STRING  - version of the Python libs found (since CMake 2.8.8)
-#   PYTHON_VERSION_MAJOR       - major Python version
-#   PYTHON_VERSION_MINOR       - minor Python version
-#   PYTHON_VERSION_PATCH       - patch Python version
-
-
-
-function (findPythonForAnacondaEnvironment env)
-	if (WIN32)
-	  file(TO_CMAKE_PATH ${env}/python.exe PYTHON_EXECUTABLE)
-        elseif (UNIX)
-  	  file(TO_CMAKE_PATH ${env}/bin/python PYTHON_EXECUTABLE)
-	endif()
-
-	
-	message("findPythonForAnacondaEnvironment Found Python Executable" ${PYTHON_EXECUTABLE})
-	####### FROM FindPythonInterpr ########
-	# determine python version string
-	if(PYTHON_EXECUTABLE)
-		execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c
-								"import sys; sys.stdout.write(';'.join([str(x) for x in sys.version_info[:3]]))"
-						OUTPUT_VARIABLE _VERSION
-						RESULT_VARIABLE _PYTHON_VERSION_RESULT
-						ERROR_QUIET)
-		if(NOT _PYTHON_VERSION_RESULT)
-			string(REPLACE ";" "." _PYTHON_VERSION_STRING "${_VERSION}")
-			list(GET _VERSION 0 _PYTHON_VERSION_MAJOR)
-			list(GET _VERSION 1 _PYTHON_VERSION_MINOR)
-			list(GET _VERSION 2 _PYTHON_VERSION_PATCH)
-			if(PYTHON_VERSION_PATCH EQUAL 0)
-				# it's called "Python 2.7", not "2.7.0"
-				string(REGEX REPLACE "\\.0$" "" _PYTHON_VERSION_STRING "${PYTHON_VERSION_STRING}")
-			endif()
-		else()
-			# sys.version predates sys.version_info, so use that
-			execute_process(COMMAND "${PYTHON_EXECUTABLE}" -c "import sys; sys.stdout.write(sys.version)"
-							OUTPUT_VARIABLE _VERSION
-							RESULT_VARIABLE _PYTHON_VERSION_RESULT
-							ERROR_QUIET)
-			if(NOT _PYTHON_VERSION_RESULT)
-				string(REGEX REPLACE " .*" "" _PYTHON_VERSION_STRING "${_VERSION}")
-				string(REGEX REPLACE "^([0-9]+)\\.[0-9]+.*" "\\1" _PYTHON_VERSION_MAJOR "${PYTHON_VERSION_STRING}")
-				string(REGEX REPLACE "^[0-9]+\\.([0-9])+.*" "\\1" _PYTHON_VERSION_MINOR "${PYTHON_VERSION_STRING}")
-				if(PYTHON_VERSION_STRING MATCHES "^[0-9]+\\.[0-9]+\\.([0-9]+)")
-					set(PYTHON_VERSION_PATCH "${CMAKE_MATCH_1}")
-				else()
-					set(PYTHON_VERSION_PATCH "0")
-				endif()
-			else()
-				# sys.version was first documented for Python 1.5, so assume
-				# this is older.
-				set(PYTHON_VERSION_STRING "1.4" PARENT_SCOPE)
-				set(PYTHON_VERSION_MAJOR "1" PARENT_SCOPE)
-				set(PYTHON_VERSION_MINOR "4" PARENT_SCOPE)
-				set(PYTHON_VERSION_PATCH "0" PARENT_SCOPE)
-			endif()
-		endif()
-		unset(_PYTHON_VERSION_RESULT)
-		unset(_VERSION)
-	endif()
-	###############################################
-	
-	set (PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE} PARENT_SCOPE)
-	set (PYTHONINTERP_FOUND "ON" PARENT_SCOPE)
-	set (PYTHON_VERSION_STRING ${_PYTHON_VERSION_STRING} PARENT_SCOPE)
-	set (PYTHON_VERSION_MAJOR ${_PYTHON_VERSION_MAJOR} PARENT_SCOPE)
-	set (PYTHON_VERSION_MINOR ${_PYTHON_VERSION_MINOR} PARENT_SCOPE)
-	set (PYTHON_VERSION_PATCH ${_PYTHON_VERSION_PATCH} PARENT_SCOPE)
-	message("My version found " ${PYTHON_VERSION_STRING})
-	## find conda executable
-	if (WIN32)
-	  set (CONDA_EXECUTABLE ${env}/Script/conda PARENT_SCOPE)
-	elseif(UNIX)
-	  set (CONDA_EXECUTABLE ${env}/bin/conda PARENT_SCOPE)
-	endif()
-endfunction()
-
-
-
-set(Python_ADDITIONAL_VERSIONS 3.5)
-
-find_package(PythonInterp)
-if (PYTHONINTERP_FOUND)
-  
-  message("Found interpret " ${PYTHON_EXECUTABLE})
-  message("Python Library " ${PYTHON_LIBRARY})
-  message("Python Include Dir " ${PYTHON_INCLUDE_DIR})
-  message("Python Include Path " ${PYTHON_INCLUDE_PATH})
-  
-  foreach(pv ${PYTHON_VERSION_STRING})
-    message("Found interpret " ${pv})
-  endforeach()
-endif()
-
-
-
-find_package(PythonLibs)
-if (PYTHONLIB_FOUND) 
-  message("Found PythonLibs PYTHON_LIBRARIES " ${PYTHON_LIBRARIES})
-  message("Found PythonLibs PYTHON_INCLUDE_PATH " ${PYTHON_INCLUDE_PATH})
-  message("Found PythonLibs PYTHON_INCLUDE_DIRS " ${PYTHON_INCLUDE_DIRS})
-  message("Found PythonLibs PYTHONLIBS_VERSION_STRING " ${PYTHONLIBS_VERSION_STRING}  )
-else()
-  message("No PythonLibs Found")  
-endif()
-
-
-
-
-function(findPythonPackagesPath)
-   execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import *; print (get_python_lib())"
-                      RESULT_VARIABLE PYTHON_CVPY_PROCESS
-                      OUTPUT_VARIABLE PYTHON_STD_PACKAGES_PATH
-                      OUTPUT_STRIP_TRAILING_WHITESPACE)
-   #message("STD_PACKAGES " ${PYTHON_STD_PACKAGES_PATH})
-   if("${PYTHON_STD_PACKAGES_PATH}" MATCHES "site-packages")
-        set(_PYTHON_PACKAGES_PATH "python${PYTHON_VERSION_MAJOR_MINOR}/site-packages")
-   endif()
-
-    SET(PYTHON_PACKAGES_PATH "${PYTHON_STD_PACKAGES_PATH}" PARENT_SCOPE)
-
-endfunction()
-
-
diff --git a/src/Python/Matlab2Python_utils.cpp b/src/Python/Matlab2Python_utils.cpp
deleted file mode 100644
index ee76bc7..0000000
--- a/src/Python/Matlab2Python_utils.cpp
+++ /dev/null
@@ -1,276 +0,0 @@
-/*
-This work is part of the Core Imaging Library developed by
-Visual Analytics and Imaging System Group of the Science Technology
-Facilities Council, STFC
-
-Copyright 2017 Daniil Kazanteev
-Copyright 2017 Srikanth Nagella, Edoardo Pasca
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-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.
-*/
-
-#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
-
-#include <iostream>
-#include <cmath>
-
-#include <boost/python.hpp>
-#include <boost/python/numpy.hpp>
-#include "boost/tuple/tuple.hpp"
-
-#if defined(_WIN32) || defined(_WIN32) || defined(__WIN32__) || defined(_WIN64)
-#include <windows.h>
-// this trick only if compiler is MSVC
-__if_not_exists(uint8_t) { typedef __int8 uint8_t; }
-__if_not_exists(uint16_t) { typedef __int8 uint16_t; }
-#endif
-
-namespace bp = boost::python;
-namespace np = boost::python::numpy;
-
-/*! in the Matlab implementation this is called as
-void mexFunction(
-int nlhs, mxArray *plhs[],
-int nrhs, const mxArray *prhs[])
-where:
-prhs Array of pointers to the INPUT mxArrays
-nrhs int number of INPUT mxArrays
-
-nlhs Array of pointers to the OUTPUT mxArrays
-plhs int number of OUTPUT mxArrays
-
-***********************************************************
-	
-***********************************************************
-double mxGetScalar(const mxArray *pm);
-args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray.
-Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray.	In C, mxGetScalar returns a double.
-***********************************************************
-char *mxArrayToString(const mxArray *array_ptr);
-args: array_ptr Pointer to mxCHAR array.
-Returns: C-style string. Returns NULL on failure. Possible reasons for failure include out of memory and specifying an array that is not an mxCHAR array.
-Description: Call mxArrayToString to copy the character data of an mxCHAR array into a C-style string.
-***********************************************************
-mxClassID mxGetClassID(const mxArray *pm);
-args: pm Pointer to an mxArray
-Returns: Numeric identifier of the class (category) of the mxArray that pm points to.For user-defined types,
-mxGetClassId returns a unique value identifying the class of the array contents.
-Use mxIsClass to determine whether an array is of a specific user-defined type.
-
-mxClassID Value	  MATLAB Type   MEX Type	 C Primitive Type
-mxINT8_CLASS 	  int8	        int8_T	     char, byte
-mxUINT8_CLASS	  uint8	        uint8_T	     unsigned char, byte
-mxINT16_CLASS	  int16	        int16_T	     short
-mxUINT16_CLASS	  uint16	    uint16_T	 unsigned short
-mxINT32_CLASS	  int32	        int32_T	     int
-mxUINT32_CLASS	  uint32	    uint32_T	 unsigned int
-mxINT64_CLASS	  int64	        int64_T	     long long
-mxUINT64_CLASS	  uint64	    uint64_T 	 unsigned long long
-mxSINGLE_CLASS	  single	    float	     float
-mxDOUBLE_CLASS	  double	    double	     double
-
-****************************************************************
-double *mxGetPr(const mxArray *pm);
-args: pm Pointer to an mxArray of type double
-Returns: Pointer to the first element of the real data. Returns NULL in C (0 in Fortran) if there is no real data.
-****************************************************************
-mxArray *mxCreateNumericArray(mwSize ndim, const mwSize *dims,
-mxClassID classid, mxComplexity ComplexFlag);
-args: ndimNumber of dimensions. If you specify a value for ndim that is less than 2, mxCreateNumericArray automatically sets the number of dimensions to 2.
-dims Dimensions array. Each element in the dimensions array contains the size of the array in that dimension.
-For example, in C, setting dims[0] to 5 and dims[1] to 7 establishes a 5-by-7 mxArray. Usually there are ndim elements in the dims array.
-classid Identifier for the class of the array, which determines the way the numerical data is represented in memory.
-For example, specifying mxINT16_CLASS in C causes each piece of numerical data in the mxArray to be represented as a 16-bit signed integer.
-ComplexFlag  If the mxArray you are creating is to contain imaginary data, set ComplexFlag to mxCOMPLEX in C (1 in Fortran). Otherwise, set ComplexFlag to mxREAL in C (0 in Fortran).
-Returns: Pointer to the created mxArray, if successful. If unsuccessful in a standalone (non-MEX file) application, returns NULL in C (0 in Fortran).
-If unsuccessful in a MEX file, the MEX file terminates and returns control to the MATLAB prompt. The function is unsuccessful when there is not
-enough free heap space to create the mxArray.
-*/
-
-void mexErrMessageText(char* text) {
-	std::cerr << text << std::endl;
-}
-
-/*
-double mxGetScalar(const mxArray *pm);
-args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray.
-Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray.	In C, mxGetScalar returns a double.
-*/
-
-template<typename T>
-double mxGetScalar(const np::ndarray plh) {
-	return (double)bp::extract<T>(plh[0]);
-}
-
-
-
-template<typename T>
-T * mxGetData(const np::ndarray pm) {
-    //args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray.
-	//Returns: Pointer to the value of the first real(nonimaginary) element of the mxArray.In C, mxGetScalar returns a double.
-	/*Access the numpy array pointer:
-	char * get_data() const;
-	Returns:	Array’s raw data pointer as a char
-	Note:	This returns char so stride math works properly on it.User will have to reinterpret_cast it.
-	probably this would work.
-	A = reinterpret_cast<float *>(prhs[0]);
-	*/
-	//return reinterpret_cast<T *>(prhs[0]);
-}
-
-template<typename T>
-np::ndarray zeros(int dims , int * dim_array, T el) {
-	bp::tuple shape;
-	if (dims == 3)
-		shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]);
-	else if (dims == 2)
-		shape = bp::make_tuple(dim_array[0], dim_array[1]);
-	np::dtype dtype = np::dtype::get_builtin<T>();
-	np::ndarray zz = np::zeros(shape, dtype);
-	return zz;
-}
-
-
-bp::list mexFunction( np::ndarray input ) {
-	int number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-
-	/**************************************************************************/
-	np::ndarray zz = zeros(3, dim_array, (int)0);
-	np::ndarray fzz = zeros(3, dim_array, (float)0);
-	/**************************************************************************/
-	
-	int * A = reinterpret_cast<int *>( input.get_data() );
-	int * B = reinterpret_cast<int *>( zz.get_data() );
-	float * C = reinterpret_cast<float *>(fzz.get_data());
-
-	//Copy data and cast
-	for (int i = 0; i < dim_array[0]; i++) {
-		for (int j = 0; j < dim_array[1]; j++) {
-			for (int k = 0; k < dim_array[2]; k++) {
-				int index = k + dim_array[2] * j + dim_array[2] * dim_array[1] * i;
-				int val = (*(A + index));
-				float fval = sqrt((float)val);
-				std::memcpy(B + index , &val, sizeof(int));
-				std::memcpy(C + index , &fval, sizeof(float));
-			}
-		}
-	}
-
-
-	bp::list result;
-
-	result.append<int>(number_of_dims);
-	result.append<int>(dim_array[0]);
-	result.append<int>(dim_array[1]);
-	result.append<int>(dim_array[2]);
-	result.append<np::ndarray>(zz);
-	result.append<np::ndarray>(fzz);
-
-	//result.append<bp::tuple>(tup);
-	return result;
-
-}
-bp::list doSomething(np::ndarray input, PyObject *pyobj , PyObject *pyobj2) {
-
-	boost::python::object output(boost::python::handle<>(boost::python::borrowed(pyobj)));
-	int isOutput = !(output == boost::python::api::object());
-
-	boost::python::object calculate(boost::python::handle<>(boost::python::borrowed(pyobj2)));
-	int isCalculate = !(calculate == boost::python::api::object());
-
-	int number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-
-	/**************************************************************************/
-	np::ndarray zz = zeros(3, dim_array, (int)0);
-	np::ndarray fzz = zeros(3, dim_array, (float)0);
-	/**************************************************************************/
-
-	int * A = reinterpret_cast<int *>(input.get_data());
-	int * B = reinterpret_cast<int *>(zz.get_data());
-	float * C = reinterpret_cast<float *>(fzz.get_data());
-
-	//Copy data and cast
-	for (int i = 0; i < dim_array[0]; i++) {
-		for (int j = 0; j < dim_array[1]; j++) {
-			for (int k = 0; k < dim_array[2]; k++) {
-				int index = k + dim_array[2] * j + dim_array[2] * dim_array[1] * i;
-				int val = (*(A + index));
-				float fval = sqrt((float)val);
-				std::memcpy(B + index, &val, sizeof(int));
-				std::memcpy(C + index, &fval, sizeof(float));
-				// if the PyObj is not None evaluate the function 
-				if (isOutput)	
-					output(fval);
-				if (isCalculate) {
-					float nfval = (float)bp::extract<float>(calculate(val));
-					if (isOutput)
-						output(nfval);
-					std::memcpy(C + index, &nfval, sizeof(float));
-				}
-			}
-		}
-	}
-
-
-	bp::list result;
-
-	result.append<int>(number_of_dims);
-	result.append<int>(dim_array[0]);
-	result.append<int>(dim_array[1]);
-	result.append<int>(dim_array[2]);
-	result.append<np::ndarray>(zz);
-	result.append<np::ndarray>(fzz);
-
-	//result.append<bp::tuple>(tup);
-	return result;
-
-}
-
-
-BOOST_PYTHON_MODULE(prova)
-{
-	np::initialize();
-
-	//To specify that this module is a package
-	bp::object package = bp::scope();
-	package.attr("__path__") = "prova";
-
-	np::dtype dt1 = np::dtype::get_builtin<uint8_t>();
-	np::dtype dt2 = np::dtype::get_builtin<uint16_t>();
-	
-	//import_array();
-	//numpy_boost_python_register_type<float, 1>();
-	//numpy_boost_python_register_type<float, 2>();
-	//numpy_boost_python_register_type<float, 3>();
-	//numpy_boost_python_register_type<double, 3>();
-	def("mexFunction", mexFunction);
-	def("doSomething", doSomething);
-}
diff --git a/src/Python/Regularizer.py b/src/Python/Regularizer.py
deleted file mode 100644
index 15dbbb4..0000000
--- a/src/Python/Regularizer.py
+++ /dev/null
@@ -1,322 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Aug  8 14:26:00 2017
-
-@author: ofn77899
-"""
-
-import regularizers
-import numpy as np
-from enum import Enum
-import timeit
-
-class Regularizer():
-    '''Class to handle regularizer algorithms to be used during reconstruction
-    
-    Currently 5 CPU (OMP) regularization algorithms are available:
-        
-    1) SplitBregman_TV
-    2) FGP_TV
-    3) LLT_model
-    4) PatchBased_Regul
-    5) TGV_PD
-    
-    Usage:
-        the regularizer can be invoked as object or as static method
-        Depending on the actual regularizer the input parameter may vary, and 
-        a different default setting is defined.
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-
-        out = reg(input=u0, regularization_parameter=10., number_of_iterations=30,
-          tolerance_constant=1e-4, 
-          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-
-        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10.,
-          number_of_iterations=30, tolerance_constant=1e-4, 
-          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-        
-        A number of optional parameters can be passed or skipped
-        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
-
-    '''
-    class Algorithm(Enum):
-        SplitBregman_TV = regularizers.SplitBregman_TV
-        FGP_TV = regularizers.FGP_TV
-        LLT_model = regularizers.LLT_model
-        PatchBased_Regul = regularizers.PatchBased_Regul
-        TGV_PD = regularizers.TGV_PD
-    # Algorithm
-    
-    class TotalVariationPenalty(Enum):
-        isotropic = 0
-        l1 = 1
-    # TotalVariationPenalty
-        
-    def __init__(self , algorithm, debug = True):
-        self.setAlgorithm ( algorithm )
-        self.debug = debug
-    # __init__
-    
-    def setAlgorithm(self, algorithm):
-        self.algorithm = algorithm
-        self.pars = self.getDefaultParsForAlgorithm(algorithm)
-    # setAlgorithm
-        
-    def getDefaultParsForAlgorithm(self, algorithm):
-        pars = dict()
-        
-        if algorithm == Regularizer.Algorithm.SplitBregman_TV :
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['number_of_iterations'] = 35
-            pars['tolerance_constant'] = 0.0001
-            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
-            
-        elif algorithm == Regularizer.Algorithm.FGP_TV :
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['number_of_iterations'] = 50
-            pars['tolerance_constant'] = 0.001
-            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
-            
-        elif algorithm == Regularizer.Algorithm.LLT_model:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['time_step'] = None
-            pars['number_of_iterations'] = None
-            pars['tolerance_constant'] = None
-            pars['restrictive_Z_smoothing'] = 0
-            
-        elif algorithm == Regularizer.Algorithm.PatchBased_Regul:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['searching_window_ratio'] = None
-            pars['similarity_window_ratio'] = None
-            pars['PB_filtering_parameter'] = None
-            pars['regularization_parameter'] = None
-            
-        elif algorithm == Regularizer.Algorithm.TGV_PD:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['first_order_term'] = None
-            pars['second_order_term'] = None
-            pars['number_of_iterations'] = None
-            pars['regularization_parameter'] = None
-            
-        else:
-            raise Exception('Unknown regularizer algorithm')
-            
-        return pars
-    # parsForAlgorithm
-    
-    def setParameter(self, **kwargs):
-        '''set named parameter for the regularization engine
-        
-        raises Exception if the named parameter is not recognized
-        Typical usage is:
-            
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        reg.setParameter(input=u0)    
-        reg.setParameter(regularization_parameter=10.)
-        
-        it can be also used as
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        reg.setParameter(input=u0 , regularization_parameter=10.)
-        '''
-        
-        for key , value in kwargs.items():
-            if key in self.pars.keys():
-                self.pars[key] = value
-            else:
-                raise Exception('Wrong parameter {0} for regularizer algorithm'.format(key))
-    # setParameter
-	
-    def getParameter(self, **kwargs):
-        ret = {}
-        for key , value in kwargs.items():
-            if key in self.pars.keys():
-                ret[key] = self.pars[key]
-        else:
-            raise Exception('Wrong parameter {0} for regularizer algorithm'.format(key))
-    # setParameter
-	
-        
-    def __call__(self, input = None, regularization_parameter = None, **kwargs):
-        '''Actual call for the regularizer. 
-        
-        One can either set the regularization parameters first and then call the
-        algorithm or set the regularization parameter during the call (as 
-        is done in the static methods). 
-        '''
-        
-        if kwargs is not None:
-            for key, value in kwargs.items():
-                #print("{0} = {1}".format(key, value))                        
-                self.pars[key] = value
-                    
-        if input is not None: 
-            self.pars['input'] = input
-        if regularization_parameter is not None:
-            self.pars['regularization_parameter'] = regularization_parameter
-            
-        if self.debug:
-            print ("--------------------------------------------------")
-            for key, value in self.pars.items():
-                if key== 'algorithm' :
-                    print("{0} = {1}".format(key, value.__name__))
-                elif key == 'input':
-                    print("{0} = {1}".format(key, np.shape(value)))
-                else:
-                    print("{0} = {1}".format(key, value))
-        
-            
-        if None in self.pars:
-                raise Exception("Not all parameters have been provided")
-        
-        input = self.pars['input']
-        regularization_parameter = self.pars['regularization_parameter']
-        if self.algorithm == Regularizer.Algorithm.SplitBregman_TV :
-            return self.algorithm(input, regularization_parameter,
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['TV_penalty'].value )    
-        elif self.algorithm == Regularizer.Algorithm.FGP_TV :
-            return self.algorithm(input, regularization_parameter,
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['TV_penalty'].value )
-        elif self.algorithm == Regularizer.Algorithm.LLT_model :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            return self.algorithm(input, 
-                              regularization_parameter,
-                              self.pars['time_step'] , 
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['restrictive_Z_smoothing'] )
-        elif self.algorithm == Regularizer.Algorithm.PatchBased_Regul :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            return self.algorithm(input, regularization_parameter,
-                                  self.pars['searching_window_ratio'] , 
-                                  self.pars['similarity_window_ratio'] , 
-                                  self.pars['PB_filtering_parameter'])
-        elif self.algorithm == Regularizer.Algorithm.TGV_PD :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            if len(np.shape(input)) == 2:
-                return self.algorithm(input, regularization_parameter,
-                                  self.pars['first_order_term'] , 
-                                  self.pars['second_order_term'] , 
-                                  self.pars['number_of_iterations'])
-            elif len(np.shape(input)) == 3:
-                #assuming it's 3D
-                # run independent calls on each slice
-                out3d = input.copy()
-                for i in range(np.shape(input)[2]):
-                    out = self.algorithm(input, regularization_parameter,
-                                 self.pars['first_order_term'] , 
-                                 self.pars['second_order_term'] , 
-                                 self.pars['number_of_iterations'])
-                    # copy the result in the 3D image
-                    out3d.T[i] = out[0].copy()
-                # append the rest of the info that the algorithm returns
-                output = [out3d]
-                for i in range(1,len(out)):
-                    output.append(out[i])
-                return output
-                
-                
-            
-            
-        
-    # __call__
-    
-    @staticmethod
-    def SplitBregman_TV(input, regularization_parameter , **kwargs):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        out = list( reg(input, regularization_parameter, **kwargs) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-        
-    @staticmethod
-    def FGP_TV(input, regularization_parameter , **kwargs):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-        out = list( reg(input, regularization_parameter, **kwargs) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def LLT_model(input, regularization_parameter , time_step, number_of_iterations,
-                  tolerance_constant, restrictive_Z_smoothing=0):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.LLT_model)
-        out = list( reg(input, regularization_parameter, time_step=time_step, 
-                        number_of_iterations=number_of_iterations,
-                        tolerance_constant=tolerance_constant, 
-                        restrictive_Z_smoothing=restrictive_Z_smoothing) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def PatchBased_Regul(input, regularization_parameter,
-                        searching_window_ratio, 
-                        similarity_window_ratio,
-                        PB_filtering_parameter):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.PatchBased_Regul)   
-        out = list( reg(input, 
-                        regularization_parameter,
-                        searching_window_ratio=searching_window_ratio, 
-                        similarity_window_ratio=similarity_window_ratio,
-                        PB_filtering_parameter=PB_filtering_parameter )
-            )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def TGV_PD(input, regularization_parameter , first_order_term, 
-               second_order_term, number_of_iterations):
-        start_time = timeit.default_timer()
-        
-        reg = Regularizer(Regularizer.Algorithm.TGV_PD)
-        out = list( reg(input, regularization_parameter, 
-                        first_order_term=first_order_term, 
-                        second_order_term=second_order_term,
-                        number_of_iterations=number_of_iterations) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        
-        return out
-    
-    def printParametersToString(self):
-        txt = r''
-        for key, value in self.pars.items():
-            if key== 'algorithm' :
-                txt += "{0} = {1}".format(key, value.__name__)
-            elif key == 'input':
-                txt += "{0} = {1}".format(key, np.shape(value))
-            else:
-                txt += "{0} = {1}".format(key, value)
-            txt += '\n'
-        return txt
-        
diff --git a/src/Python/ccpi/__init__.py b/src/Python/ccpi/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/src/Python/ccpi/__init__.py
+++ /dev/null
diff --git a/src/Python/ccpi/imaging/Regularizer.py b/src/Python/ccpi/imaging/Regularizer.py
deleted file mode 100644
index 23799d6..0000000
--- a/src/Python/ccpi/imaging/Regularizer.py
+++ /dev/null
@@ -1,334 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Aug  8 14:26:00 2017
-
-@author: ofn77899
-"""
-
-from ccpi.imaging import cpu_regularizers
-import numpy as np
-from enum import Enum
-import timeit
-
-class Regularizer():
-    '''Class to handle regularizer algorithms to be used during reconstruction
-    
-    Currently 5 CPU (OMP) regularization algorithms are available:
-        
-    1) SplitBregman_TV
-    2) FGP_TV
-    3) LLT_model
-    4) PatchBased_Regul
-    5) TGV_PD
-    
-    Usage:
-        the regularizer can be invoked as object or as static method
-        Depending on the actual regularizer the input parameter may vary, and 
-        a different default setting is defined.
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-
-        out = reg(input=u0, regularization_parameter=10., number_of_iterations=30,
-          tolerance_constant=1e-4, 
-          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-
-        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10.,
-          number_of_iterations=30, tolerance_constant=1e-4, 
-          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-        
-        A number of optional parameters can be passed or skipped
-        out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
-
-    '''
-    class Algorithm(Enum):
-        SplitBregman_TV = cpu_regularizers.SplitBregman_TV
-        FGP_TV = cpu_regularizers.FGP_TV
-        LLT_model = cpu_regularizers.LLT_model
-        PatchBased_Regul = cpu_regularizers.PatchBased_Regul
-        TGV_PD = cpu_regularizers.TGV_PD
-    # Algorithm
-    
-    class TotalVariationPenalty(Enum):
-        isotropic = 0
-        l1 = 1
-    # TotalVariationPenalty
-        
-    def __init__(self , algorithm, debug = True):
-        self.setAlgorithm ( algorithm )
-        self.debug = debug
-    # __init__
-    
-    def setAlgorithm(self, algorithm):
-        self.algorithm = algorithm
-        self.pars = self.getDefaultParsForAlgorithm(algorithm)
-    # setAlgorithm
-        
-    def getDefaultParsForAlgorithm(self, algorithm):
-        pars = dict()
-        
-        if algorithm == Regularizer.Algorithm.SplitBregman_TV :
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['number_of_iterations'] = 35
-            pars['tolerance_constant'] = 0.0001
-            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
-            
-        elif algorithm == Regularizer.Algorithm.FGP_TV :
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['number_of_iterations'] = 50
-            pars['tolerance_constant'] = 0.001
-            pars['TV_penalty'] = Regularizer.TotalVariationPenalty.isotropic
-            
-        elif algorithm == Regularizer.Algorithm.LLT_model:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['regularization_parameter'] = None
-            pars['time_step'] = None
-            pars['number_of_iterations'] = None
-            pars['tolerance_constant'] = None
-            pars['restrictive_Z_smoothing'] = 0
-            
-        elif algorithm == Regularizer.Algorithm.PatchBased_Regul:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['searching_window_ratio'] = None
-            pars['similarity_window_ratio'] = None
-            pars['PB_filtering_parameter'] = None
-            pars['regularization_parameter'] = None
-            
-        elif algorithm == Regularizer.Algorithm.TGV_PD:
-            pars['algorithm'] = algorithm
-            pars['input'] = None
-            pars['first_order_term'] = None
-            pars['second_order_term'] = None
-            pars['number_of_iterations'] = None
-            pars['regularization_parameter'] = None
-            
-        else:
-            raise Exception('Unknown regularizer algorithm')
-
-        self.acceptedInputKeywords = pars.keys()
-            
-        return pars
-    # parsForAlgorithm
-    
-    def setParameter(self, **kwargs):
-        '''set named parameter for the regularization engine
-        
-        raises Exception if the named parameter is not recognized
-        Typical usage is:
-            
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        reg.setParameter(input=u0)    
-        reg.setParameter(regularization_parameter=10.)
-        
-        it can be also used as
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        reg.setParameter(input=u0 , regularization_parameter=10.)
-        '''
-        
-        for key , value in kwargs.items():
-            if key in self.pars.keys():
-                self.pars[key] = value
-            else:
-                raise Exception('Wrong parameter {0} for regularizer algorithm'.format(key))
-    # setParameter
-	
-    def getParameter(self, key):
-        if type(key) is str:
-            if key in self.acceptedInputKeywords:
-                return self.pars[key]
-            else:
-                raise Exception('Unrecongnised parameter: {0} '.format(key) )
-        elif type(key) is list:
-            outpars = []
-            for k in key:
-                outpars.append(self.getParameter(k))
-            return outpars
-        else:
-            raise Exception('Unhandled input {0}' .format(str(type(key))))
-        # getParameter
-	
-        
-    def __call__(self, input = None, regularization_parameter = None,
-                 output_all = False, **kwargs):
-        '''Actual call for the regularizer. 
-        
-        One can either set the regularization parameters first and then call the
-        algorithm or set the regularization parameter during the call (as 
-        is done in the static methods). 
-        '''
-        
-        if kwargs is not None:
-            for key, value in kwargs.items():
-                #print("{0} = {1}".format(key, value))                        
-                self.pars[key] = value
-                    
-        if input is not None: 
-            self.pars['input'] = input
-        if regularization_parameter is not None:
-            self.pars['regularization_parameter'] = regularization_parameter
-            
-        if self.debug:
-            print ("--------------------------------------------------")
-            for key, value in self.pars.items():
-                if key== 'algorithm' :
-                    print("{0} = {1}".format(key, value.__name__))
-                elif key == 'input':
-                    print("{0} = {1}".format(key, np.shape(value)))
-                else:
-                    print("{0} = {1}".format(key, value))
-        
-            
-        if None in self.pars:
-                raise Exception("Not all parameters have been provided")
-        
-        input = self.pars['input']
-        regularization_parameter = self.pars['regularization_parameter']
-        if self.algorithm == Regularizer.Algorithm.SplitBregman_TV :
-            ret = self.algorithm(input, regularization_parameter,
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['TV_penalty'].value )    
-        elif self.algorithm == Regularizer.Algorithm.FGP_TV :
-            ret = self.algorithm(input, regularization_parameter,
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['TV_penalty'].value )
-        elif self.algorithm == Regularizer.Algorithm.LLT_model :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            ret = self.algorithm(input, 
-                              regularization_parameter,
-                              self.pars['time_step'] , 
-                              self.pars['number_of_iterations'],
-                              self.pars['tolerance_constant'],
-                              self.pars['restrictive_Z_smoothing'] )
-        elif self.algorithm == Regularizer.Algorithm.PatchBased_Regul :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            ret = self.algorithm(input, regularization_parameter,
-                                  self.pars['searching_window_ratio'] , 
-                                  self.pars['similarity_window_ratio'] , 
-                                  self.pars['PB_filtering_parameter'])
-        elif self.algorithm == Regularizer.Algorithm.TGV_PD :
-            #LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher)
-            # no default
-            if len(np.shape(input)) == 2:
-                ret = self.algorithm(input, regularization_parameter,
-                                  self.pars['first_order_term'] , 
-                                  self.pars['second_order_term'] , 
-                                  self.pars['number_of_iterations'])
-            elif len(np.shape(input)) == 3:
-                #assuming it's 3D
-                # run independent calls on each slice
-                out3d = input.copy()
-                for i in range(np.shape(input)[0]):
-                    out = self.algorithm(input[i], regularization_parameter,
-                                 self.pars['first_order_term'] , 
-                                 self.pars['second_order_term'] , 
-                                 self.pars['number_of_iterations'])
-                    # copy the result in the 3D image
-                    out3d[i] = out[0].copy()
-                # append the rest of the info that the algorithm returns
-                output = [out3d]
-                for i in range(1,len(out)):
-                    output.append(out[i])
-                ret = output
-                
-                
-            
-        if output_all:
-            return ret
-        else:
-            return ret[0]
-        
-    # __call__
-    
-    @staticmethod
-    def SplitBregman_TV(input, regularization_parameter , **kwargs):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-        out = list( reg(input, regularization_parameter, **kwargs) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-        
-    @staticmethod
-    def FGP_TV(input, regularization_parameter , **kwargs):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-        out = list( reg(input, regularization_parameter, **kwargs) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def LLT_model(input, regularization_parameter , time_step, number_of_iterations,
-                  tolerance_constant, restrictive_Z_smoothing=0):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.LLT_model)
-        out = list( reg(input, regularization_parameter, time_step=time_step, 
-                        number_of_iterations=number_of_iterations,
-                        tolerance_constant=tolerance_constant, 
-                        restrictive_Z_smoothing=restrictive_Z_smoothing) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def PatchBased_Regul(input, regularization_parameter,
-                        searching_window_ratio, 
-                        similarity_window_ratio,
-                        PB_filtering_parameter):
-        start_time = timeit.default_timer()
-        reg = Regularizer(Regularizer.Algorithm.PatchBased_Regul)   
-        out = list( reg(input, 
-                        regularization_parameter,
-                        searching_window_ratio=searching_window_ratio, 
-                        similarity_window_ratio=similarity_window_ratio,
-                        PB_filtering_parameter=PB_filtering_parameter )
-            )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        return out
-    
-    @staticmethod
-    def TGV_PD(input, regularization_parameter , first_order_term, 
-               second_order_term, number_of_iterations):
-        start_time = timeit.default_timer()
-        
-        reg = Regularizer(Regularizer.Algorithm.TGV_PD)
-        out = list( reg(input, regularization_parameter, 
-                        first_order_term=first_order_term, 
-                        second_order_term=second_order_term,
-                        number_of_iterations=number_of_iterations) )
-        out.append(reg.pars)
-        txt = reg.printParametersToString()
-        txt += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
-        out.append(txt)
-        
-        return out
-    
-    def printParametersToString(self):
-        txt = r''
-        for key, value in self.pars.items():
-            if key== 'algorithm' :
-                txt += "{0} = {1}".format(key, value.__name__)
-            elif key == 'input':
-                txt += "{0} = {1}".format(key, np.shape(value))
-            else:
-                txt += "{0} = {1}".format(key, value)
-            txt += '\n'
-        return txt
-        
diff --git a/src/Python/ccpi/imaging/__init__.py b/src/Python/ccpi/imaging/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/src/Python/ccpi/imaging/__init__.py
+++ /dev/null
diff --git a/src/Python/ccpi/reconstruction/AstraDevice.py b/src/Python/ccpi/reconstruction/AstraDevice.py
deleted file mode 100644
index 57435f8..0000000
--- a/src/Python/ccpi/reconstruction/AstraDevice.py
+++ /dev/null
@@ -1,95 +0,0 @@
-import astra
-from ccpi.reconstruction.DeviceModel import DeviceModel
-import numpy
-
-class AstraDevice(DeviceModel):
-    '''Concrete class for Astra Device'''
-
-    def __init__(self,
-                 device_type,
-                 data_aquisition_geometry,
-                 reconstructed_volume_geometry):
-        
-        super(AstraDevice, self).__init__(device_type,
-                                          data_aquisition_geometry,
-                                          reconstructed_volume_geometry)
-
-        self.type = device_type
-        self.proj_geom = astra.creators.create_proj_geom(
-            device_type,
-            self.acquisition_data_geometry['detectorSpacingX'],
-            self.acquisition_data_geometry['detectorSpacingY'],
-            self.acquisition_data_geometry['cameraX'],
-            self.acquisition_data_geometry['cameraY'],
-            self.acquisition_data_geometry['angles'],
-            )
-        
-        self.vol_geom = astra.creators.create_vol_geom(
-            self.reconstructed_volume_geometry['X'],
-            self.reconstructed_volume_geometry['Y'],
-            self.reconstructed_volume_geometry['Z']
-            )
-        
-    def doForwardProject(self, volume):
-        '''Forward projects the volume according to the device geometry
-
-Uses Astra-toolbox
-'''
-              
-        try:
-            sino_id, y = astra.creators.create_sino3d_gpu(
-                volume, self.proj_geom, self.vol_geom)
-            astra.matlab.data3d('delete', sino_id)
-            return y
-        except Exception as e:
-            print(e)
-            print("Value Error: ", self.proj_geom, self.vol_geom)
-
-    def doBackwardProject(self, projections):
-        '''Backward projects the projections according to the device geometry
-
-Uses Astra-toolbox
-'''
-        idx, volume = \
-               astra.creators.create_backprojection3d_gpu(
-                   projections,
-                   self.proj_geom,
-                   self.vol_geom)
-        
-        astra.matlab.data3d('delete', idx)
-        return volume
-    
-    def createReducedDevice(self, proj_par={'cameraY' : 1} , vol_par={'Z':1}):
-        '''Create a new device based on the current device by changing some parameter
-
-VERY RISKY'''
-        acquisition_data_geometry = self.acquisition_data_geometry.copy()
-        for k,v in proj_par.items():
-            if k in acquisition_data_geometry.keys():
-                acquisition_data_geometry[k] = v
-        proj_geom =  [ 
-            acquisition_data_geometry['cameraX'],
-            acquisition_data_geometry['cameraY'],
-            acquisition_data_geometry['detectorSpacingX'],
-            acquisition_data_geometry['detectorSpacingY'],
-            acquisition_data_geometry['angles']
-            ]
-
-        reconstructed_volume_geometry = self.reconstructed_volume_geometry.copy()
-        for k,v in vol_par.items():
-            if k in reconstructed_volume_geometry.keys():
-                reconstructed_volume_geometry[k] = v
-        
-        vol_geom = [
-            reconstructed_volume_geometry['X'],
-            reconstructed_volume_geometry['Y'],
-            reconstructed_volume_geometry['Z']
-            ]
-        return AstraDevice(self.type, proj_geom, vol_geom)
-        
-
-        
-if __name__=="main":
-    a = AstraDevice()
-
-
diff --git a/src/Python/ccpi/reconstruction/DeviceModel.py b/src/Python/ccpi/reconstruction/DeviceModel.py
deleted file mode 100644
index eeb9a34..0000000
--- a/src/Python/ccpi/reconstruction/DeviceModel.py
+++ /dev/null
@@ -1,63 +0,0 @@
-from abc import ABCMeta, abstractmethod
-from enum import Enum
-
-class DeviceModel(metaclass=ABCMeta):
-    '''Abstract class that defines the device for projection and backprojection
-
-This class defines the methods that must be implemented by concrete classes.
-
-    '''
-    
-    class DeviceType(Enum):
-        '''Type of device
-PARALLEL BEAM
-PARALLEL BEAM 3D
-CONE BEAM
-HELICAL'''
-        
-        PARALLEL = 'parallel'
-        PARALLEL3D = 'parallel3d'
-        CONE_BEAM = 'cone-beam'
-        HELICAL = 'helical'
-        
-    def __init__(self,
-                 device_type,
-                 data_aquisition_geometry,
-                 reconstructed_volume_geometry):
-        '''Initializes the class
-
-Mandatory parameters are:
-device_type from DeviceType Enum
-data_acquisition_geometry: tuple (camera_X, camera_Y, detectorSpacingX,
-                                  detectorSpacingY, angles)
-reconstructed_volume_geometry: tuple (dimX,dimY,dimZ)
-'''
-        self.device_geometry = device_type
-        self.acquisition_data_geometry = {
-            'cameraX':           data_aquisition_geometry[0],
-            'cameraY':           data_aquisition_geometry[1],
-            'detectorSpacingX' : data_aquisition_geometry[2],
-            'detectorSpacingY' : data_aquisition_geometry[3],
-            'angles' :           data_aquisition_geometry[4],}
-        self.reconstructed_volume_geometry = {
-            'X': reconstructed_volume_geometry[0] ,
-            'Y': reconstructed_volume_geometry[1] ,
-            'Z': reconstructed_volume_geometry[2] }
-
-    @abstractmethod
-    def doForwardProject(self, volume):
-        '''Forward projects the volume according to the device geometry'''
-        return NotImplemented
-
-    
-    @abstractmethod
-    def doBackwardProject(self, projections):
-        '''Backward projects the projections according to the device geometry'''
-        return NotImplemented
-
-    @abstractmethod
-    def createReducedDevice(self):
-        '''Create a Device to do forward/backward projections on 2D slices'''
-        return NotImplemented
-    
-
diff --git a/src/Python/ccpi/reconstruction/FISTAReconstructor.py b/src/Python/ccpi/reconstruction/FISTAReconstructor.py
deleted file mode 100644
index e40ad24..0000000
--- a/src/Python/ccpi/reconstruction/FISTAReconstructor.py
+++ /dev/null
@@ -1,882 +0,0 @@
-# -*- coding: utf-8 -*-
-###############################################################################
-#This work is part of the Core Imaging Library developed by
-#Visual Analytics and Imaging System Group of the Science Technology
-#Facilities Council, STFC
-#
-#Copyright 2017 Edoardo Pasca, Srikanth Nagella
-#Copyright 2017 Daniil Kazantsev
-#
-#Licensed under the Apache License, Version 2.0 (the "License");
-#you may not use this file except in compliance with the License.
-#You may obtain a copy of the License at
-#http://www.apache.org/licenses/LICENSE-2.0
-#Unless required by applicable law or agreed to in writing, software
-#distributed under the License is distributed on an "AS IS" BASIS,
-#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.
-###############################################################################
-
-
-
-import numpy
-#from ccpi.reconstruction.parallelbeam import alg
-
-#from ccpi.imaging.Regularizer import Regularizer
-from enum import Enum
-
-import astra
-from ccpi.reconstruction.AstraDevice import AstraDevice
-
-   
-    
-class FISTAReconstructor():
-    '''FISTA-based reconstruction algorithm using ASTRA-toolbox
-    
-    '''
-    # <<<< FISTA-based reconstruction algorithm using ASTRA-toolbox >>>>
-    # ___Input___:
-    # params.[] file:
-    #       - .proj_geom (geometry of the projector) [required]
-    #       - .vol_geom (geometry of the reconstructed object) [required]
-    #       - .sino (vectorized in 2D or 3D sinogram) [required]
-    #       - .iterFISTA (iterations for the main loop, default 40)
-    #       - .L_const (Lipschitz constant, default Power method)                                                                                                    )
-    #       - .X_ideal (ideal image, if given)
-    #       - .weights (statisitcal weights, size of the sinogram)
-    #       - .ROI (Region-of-interest, only if X_ideal is given)
-    #       - .initialize (a 'warm start' using SIRT method from ASTRA)
-    #----------------Regularization choices------------------------
-    #       - .Regul_Lambda_FGPTV (FGP-TV regularization parameter)
-    #       - .Regul_Lambda_SBTV (SplitBregman-TV regularization parameter)
-    #       - .Regul_Lambda_TVLLT (Higher order SB-LLT regularization parameter)
-    #       - .Regul_tol (tolerance to terminate regul iterations, default 1.0e-04)
-    #       - .Regul_Iterations (iterations for the selected penalty, default 25)
-    #       - .Regul_tauLLT (time step parameter for LLT term)
-    #       - .Ring_LambdaR_L1 (regularization parameter for L1-ring minimization, if lambdaR_L1 > 0 then switch on ring removal)
-    #       - .Ring_Alpha (larger values can accelerate convergence but check stability, default 1)
-    #----------------Visualization parameters------------------------
-    #       - .show (visualize reconstruction 1/0, (0 default))
-    #       - .maxvalplot (maximum value to use for imshow[0 maxvalplot])
-    #       - .slice (for 3D volumes - slice number to imshow)
-    # ___Output___:
-    # 1. X - reconstructed image/volume
-    # 2. output - a structure with
-    #    - .Resid_error - residual error (if X_ideal is given)
-    #    - .objective: value of the objective function
-    #    - .L_const: Lipshitz constant to avoid recalculations
-    
-    # References:
-    # 1. "A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse
-    # Problems" by A. Beck and M Teboulle
-    # 2. "Ring artifacts correction in compressed sensing..." by P. Paleo
-    # 3. "A novel tomographic reconstruction method based on the robust
-    # Student's t function for suppressing data outliers" D. Kazantsev et.al.
-    # D. Kazantsev, 2016-17
-    def __init__(self, projector_geometry,
-                 output_geometry,
-                 input_sinogram,
-                 device, 
-                 **kwargs):
-        # handle parmeters:
-        # obligatory parameters
-        self.pars = dict()
-        self.pars['projector_geometry'] = projector_geometry # proj_geom
-        self.pars['output_geometry'] = output_geometry       # vol_geom
-        self.pars['input_sinogram'] = input_sinogram         # sino
-        sliceZ, nangles, detectors = numpy.shape(input_sinogram)
-        self.pars['detectors'] = detectors
-        self.pars['number_of_angles'] = nangles
-        self.pars['SlicesZ'] = sliceZ
-        self.pars['output_volume'] = None
-        self.pars['device_model'] = device
-
-        self.use_device = True
-        
-        print (self.pars)
-        # handle optional input parameters (at instantiation)
-        
-        # Accepted input keywords
-        kw = (
-              # mandatory fields
-              'projector_geometry',
-              'output_geometry',
-              'input_sinogram',
-              'detectors',
-              'number_of_angles',
-              'SlicesZ',
-              # optional fields
-              'number_of_iterations', 
-              'Lipschitz_constant' , 
-              'ideal_image' ,
-              'weights' , 
-              'region_of_interest' , 
-              'initialize' , 
-              'regularizer' , 
-              'ring_lambda_R_L1',
-              'ring_alpha',
-              'subsets',
-              'output_volume',
-              'os_subsets',
-              'os_indices',
-              'os_bins',
-              'device_model',
-              'reduced_device_model')
-        self.acceptedInputKeywords = list(kw)
-        
-        # handle keyworded parameters
-        if kwargs is not None:
-            for key, value in kwargs.items():
-                if key in kw:
-                    #print("{0} = {1}".format(key, value))                        
-                    self.pars[key] = value
-                    
-        # set the default values for the parameters if not set
-        if 'number_of_iterations' in kwargs.keys():
-            self.pars['number_of_iterations'] = kwargs['number_of_iterations']
-        else:
-            self.pars['number_of_iterations'] = 40
-        if 'weights' in kwargs.keys():
-            self.pars['weights'] = kwargs['weights']
-        else:
-            self.pars['weights'] = \
-                                 numpy.ones(numpy.shape(
-                                     self.pars['input_sinogram']))
-        if 'Lipschitz_constant' in kwargs.keys():
-            self.pars['Lipschitz_constant'] = kwargs['Lipschitz_constant']
-        else:
-            self.pars['Lipschitz_constant'] = None
-        
-        if not 'ideal_image' in kwargs.keys():
-            self.pars['ideal_image'] = None
-        
-        if not 'region_of_interest'in kwargs.keys() :
-            if self.pars['ideal_image'] == None:
-                self.pars['region_of_interest'] = None
-            else:
-                ## nonzero if the image is larger than m
-                fsm = numpy.frompyfunc(lambda x,m: 1 if x>m else 0, 2,1)
-                
-                self.pars['region_of_interest'] = fsm(self.pars['ideal_image'], 0)
-                
-        # the regularizer must be a correctly instantiated object    
-        if not 'regularizer' in kwargs.keys() :
-            self.pars['regularizer'] = None
-
-        #RING REMOVAL
-        if not 'ring_lambda_R_L1' in kwargs.keys():
-            self.pars['ring_lambda_R_L1'] = 0
-        if not 'ring_alpha' in kwargs.keys():
-            self.pars['ring_alpha'] = 1
-
-        # ORDERED SUBSET
-        if not 'subsets' in kwargs.keys():
-            self.pars['subsets'] = 0
-        else:
-            self.createOrderedSubsets()
-
-        if not 'initialize' in kwargs.keys():
-            self.pars['initialize'] = False
-
-        reduced_device = device.createReducedDevice()
-        self.setParameter(reduced_device_model=reduced_device)
-
-        
-                
-    def setParameter(self, **kwargs):
-        '''set named parameter for the reconstructor engine
-        
-        raises Exception if the named parameter is not recognized
-        
-        '''
-        for key , value in kwargs.items():
-            if key in self.acceptedInputKeywords:
-                self.pars[key] = value
-            else:
-                raise Exception('Wrong parameter {0} for '.format(key) +
-                                'reconstructor')
-    # setParameter
-
-    def getParameter(self, key):
-        if type(key) is str:
-            if key in self.acceptedInputKeywords:
-                return self.pars[key]
-            else:
-                raise Exception('Unrecongnised parameter: {0} '.format(key) )
-        elif type(key) is list:
-            outpars = []
-            for k in key:
-                outpars.append(self.getParameter(k))
-            return outpars
-        else:
-            raise Exception('Unhandled input {0}' .format(str(type(key))))
-            
-    
-    def calculateLipschitzConstantWithPowerMethod(self):
-        ''' using Power method (PM) to establish L constant'''
-        
-        N = self.pars['output_geometry']['GridColCount']
-        proj_geom = self.pars['projector_geometry']
-        vol_geom = self.pars['output_geometry']
-        weights = self.pars['weights']
-        SlicesZ = self.pars['SlicesZ']
-        
-            
-                               
-        if (proj_geom['type'] == 'parallel') or \
-           (proj_geom['type'] == 'parallel3d'):
-            #% for parallel geometry we can do just one slice
-            #print('Calculating Lipshitz constant for parallel beam geometry...')
-            niter = 5;# % number of iteration for the PM
-            #N = params.vol_geom.GridColCount;
-            #x1 = rand(N,N,1);
-            x1 = numpy.random.rand(1,N,N)
-            #sqweight = sqrt(weights(:,:,1));
-            sqweight = numpy.sqrt(weights[0:1,:,:])
-            proj_geomT = proj_geom.copy();
-            proj_geomT['DetectorRowCount'] = 1;
-            vol_geomT = vol_geom.copy();
-            vol_geomT['GridSliceCount'] = 1;
-            
-            #[sino_id, y] = astra_create_sino3d_cuda(x1, proj_geomT, vol_geomT);
-            
-            
-            for i in range(niter):
-            #        [id,x1] = astra_create_backprojection3d_cuda(sqweight.*y, proj_geomT, vol_geomT);
-            #            s = norm(x1(:));
-            #            x1 = x1/s;
-            #            [sino_id, y] = astra_create_sino3d_cuda(x1, proj_geomT, vol_geomT);
-            #            y = sqweight.*y;
-            #            astra_mex_data3d('delete', sino_id);
-            #            astra_mex_data3d('delete', id);
-                #print ("iteration {0}".format(i))
-                                
-                sino_id, y = astra.creators.create_sino3d_gpu(x1,
-                                                          proj_geomT,
-                                                          vol_geomT)
-                
-                y = (sqweight * y).copy() # element wise multiplication
-                
-                #b=fig.add_subplot(2,1,2)
-                #imgplot = plt.imshow(x1[0])
-                #plt.show()
-                
-                #astra_mex_data3d('delete', sino_id);
-                astra.matlab.data3d('delete', sino_id)
-                del x1
-                    
-                idx,x1 = astra.creators.create_backprojection3d_gpu((sqweight*y).copy(), 
-                                                                    proj_geomT,
-                                                                    vol_geomT)
-                del y
-                
-                                                                    
-                s = numpy.linalg.norm(x1)
-                ### this line?
-                x1 = (x1/s).copy();
-                
-            #        ### this line?
-            #        sino_id, y = astra.creators.create_sino3d_gpu(x1, 
-            #                                                      proj_geomT, 
-            #                                                      vol_geomT);
-            #        y = sqweight * y;
-                astra.matlab.data3d('delete', sino_id);
-                astra.matlab.data3d('delete', idx)
-                print ("iteration {0} s= {1}".format(i,s))
-                
-            #end
-            del proj_geomT
-            del vol_geomT
-            #plt.show()
-        else:
-            #% divergen beam geometry
-            print('Calculating Lipshitz constant for divergen beam geometry...')
-            niter = 8; #% number of iteration for PM
-            x1 = numpy.random.rand(SlicesZ , N , N);
-            #sqweight = sqrt(weights);
-            sqweight = numpy.sqrt(weights[0])
-            
-            sino_id, y = astra.creators.create_sino3d_gpu(x1, proj_geom, vol_geom);
-            y = sqweight*y;
-            #astra_mex_data3d('delete', sino_id);
-            astra.matlab.data3d('delete', sino_id);
-            
-            for i in range(niter):
-                #[id,x1] = astra_create_backprojection3d_cuda(sqweight.*y, proj_geom, vol_geom);
-                idx,x1 = astra.creators.create_backprojection3d_gpu(sqweight*y, 
-                                                                    proj_geom, 
-                                                                    vol_geom)
-                s = numpy.linalg.norm(x1)
-                ### this line?
-                x1 = x1/s;
-                ### this line?
-                #[sino_id, y] = astra_create_sino3d_gpu(x1, proj_geom, vol_geom);
-                sino_id, y = astra.creators.create_sino3d_gpu(x1, 
-                                                              proj_geom, 
-                                                              vol_geom);
-                
-                y = sqweight*y;
-                #astra_mex_data3d('delete', sino_id);
-                #astra_mex_data3d('delete', id);
-                astra.matlab.data3d('delete', sino_id);
-                astra.matlab.data3d('delete', idx);
-            #end
-            #clear x1
-            del x1
-
-        
-        return s
-    
-    
-    def setRegularizer(self, regularizer):
-        if regularizer is not None:
-            self.pars['regularizer'] = regularizer
-        
-
-    def initialize(self):
-        # convenience variable storage
-        proj_geom = self.pars['projector_geometry']
-        vol_geom = self.pars['output_geometry']
-        sino = self.pars['input_sinogram']
-        
-        # a 'warm start' with SIRT method
-        # Create a data object for the reconstruction
-        rec_id = astra.matlab.data3d('create', '-vol',
-                                    vol_geom);
-        
-        #sinogram_id = astra_mex_data3d('create', '-proj3d', proj_geom, sino);
-        sinogram_id = astra.matlab.data3d('create', '-proj3d',
-                                          proj_geom,
-                                          sino)
-
-        sirt_config = astra.astra_dict('SIRT3D_CUDA')
-        sirt_config['ReconstructionDataId' ] = rec_id
-        sirt_config['ProjectionDataId'] = sinogram_id
-
-        sirt = astra.algorithm.create(sirt_config)
-        astra.algorithm.run(sirt, iterations=35)
-        X = astra.matlab.data3d('get', rec_id)
-
-        # clean up memory
-        astra.matlab.data3d('delete', rec_id)
-        astra.matlab.data3d('delete', sinogram_id)
-        astra.algorithm.delete(sirt)
-
-        
-
-        return X
-
-    def createOrderedSubsets(self, subsets=None):
-        if subsets is None:
-            try:
-                subsets = self.getParameter('subsets')
-            except Exception():
-                subsets = 0
-            #return subsets
-        else:
-            self.setParameter(subsets=subsets)
-            
-
-        angles = self.getParameter('projector_geometry')['ProjectionAngles'] 
-        
-        #binEdges = numpy.linspace(angles.min(),
-        #                          angles.max(),
-        #                          subsets + 1)
-        binsDiscr, binEdges = numpy.histogram(angles, bins=subsets)
-        # get rearranged subset indices
-        IndicesReorg = numpy.zeros((numpy.shape(angles)), dtype=numpy.int32)
-        counterM = 0
-        for ii in range(binsDiscr.max()):
-            counter = 0
-            for jj in range(subsets):
-                curr_index = ii + jj  + counter
-                #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM))
-                if binsDiscr[jj] > ii:
-                    if (counterM < numpy.size(IndicesReorg)):
-                        IndicesReorg[counterM] = curr_index
-                    counterM = counterM + 1
-                    
-                counter = counter + binsDiscr[jj] - 1    
-                
-        # store the OS in parameters
-        self.setParameter(os_subsets=subsets,
-                          os_bins=binsDiscr,
-                          os_indices=IndicesReorg)
-            
-
-    def prepareForIteration(self):
-        print ("FISTA Reconstructor: prepare for iteration")
-        
-        self.residual_error = numpy.zeros((self.pars['number_of_iterations']))
-        self.objective = numpy.zeros((self.pars['number_of_iterations']))
-
-        #2D array (for 3D data) of sparse "ring" 
-        detectors, nangles, sliceZ  = numpy.shape(self.pars['input_sinogram'])
-        self.r = numpy.zeros((detectors, sliceZ), dtype=numpy.float)
-        # another ring variable
-        self.r_x = self.r.copy()
-
-        self.residual = numpy.zeros(numpy.shape(self.pars['input_sinogram']))
-        
-        if self.getParameter('Lipschitz_constant') is None:
-            self.pars['Lipschitz_constant'] = \
-                            self.calculateLipschitzConstantWithPowerMethod()
-        # errors vector (if the ground truth is given)
-        self.Resid_error = numpy.zeros((self.getParameter('number_of_iterations')));
-        # objective function values vector
-        self.objective = numpy.zeros((self.getParameter('number_of_iterations')));      
-        
-
-    # prepareForIteration
-
-    def iterate (self, Xin=None):
-        if self.getParameter('subsets') == 0:
-            return self.iterateStandard(Xin)
-        else:
-            return self.iterateOrderedSubsets(Xin)
-        
-    def iterateStandard(self, Xin=None):
-        print ("FISTA Reconstructor: iterate")
-        
-        if Xin is None:    
-            if self.getParameter('initialize'):
-                X = self.initialize()
-            else:
-                N = vol_geom['GridColCount']
-                X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
-        else:
-            # copy by reference
-            X = Xin
-        # store the output volume in the parameters
-        self.setParameter(output_volume=X)
-        X_t = X.copy()
-        # convenience variable storage
-        proj_geom , vol_geom, sino , \
-          SlicesZ , ring_lambda_R_L1 , weights = \
-                            self.getParameter([ 'projector_geometry' ,
-                                                'output_geometry',
-                                                'input_sinogram',
-                                                'SlicesZ' ,
-                                                'ring_lambda_R_L1',
-                                                'weights'])
-                   
-        t = 1
-
-        device = self.getParameter('device_model')
-        reduced_device = self.getParameter('reduced_device_model')
-        
-        for i in range(self.getParameter('number_of_iterations')):
-            print("iteration", i)
-            X_old = X.copy()
-            t_old = t
-            r_old = self.r.copy()
-            pg = self.getParameter('projector_geometry')['type']
-            if pg == 'parallel' or \
-               pg == 'fanflat' or \
-               pg == 'fanflat_vec':
-                # if the geometry is parallel use slice-by-slice
-                # projection-backprojection routine
-                #sino_updt = zeros(size(sino),'single');
-                
-                if self.use_device :
-                    self.sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
-                    
-                    for kkk in range(SlicesZ):
-                        self.sino_updt[kkk] = \
-                            reduced_device.doForwardProject( X_t[kkk:kkk+1] )
-                else:
-                    proj_geomT = proj_geom.copy()
-                    proj_geomT['DetectorRowCount'] = 1
-                    vol_geomT = vol_geom.copy()
-                    vol_geomT['GridSliceCount'] = 1;
-                    self.sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
-                    for kkk in range(SlicesZ):
-                        sino_id, self.sino_updt[kkk] = \
-                                 astra.creators.create_sino3d_gpu(
-                                     X_t[kkk:kkk+1], proj_geomT, vol_geomT)
-                        astra.matlab.data3d('delete', sino_id)
-            else:
-                # for divergent 3D geometry (watch the GPU memory overflow in
-                # ASTRA versions < 1.8)
-                #[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
-                
-                if self.use_device:
-                    self.sino_updt = device.doForwardProject(X_t)
-                else:
-                    sino_id, self.sino_updt = astra.creators.create_sino3d_gpu(
-                        X_t, proj_geom, vol_geom)
-                    astra.matlab.data3d('delete', sino_id)
-
-
-            ## RING REMOVAL
-            if ring_lambda_R_L1 != 0:
-                self.ringRemoval(i)
-            else:
-                self.residual = weights * (self.sino_updt - sino)
-                self.objective[i] = 0.5 * numpy.linalg.norm(self.residual)
-                #objective(i) = 0.5*norm(residual(:)); % for the objective function output
-            ## Projection/Backprojection Routine
-            X, X_t = self.projectionBackprojection(X, X_t)
-            
-            ## REGULARIZATION
-            Y = self.regularize(X)
-            X = Y.copy()
-            ## Update Loop
-            X , X_t, t = self.updateLoop(i, X, X_old, r_old, t, t_old)
-
-            print ("t" , t)
-            print ("X min {0} max {1}".format(X_t.min(),X_t.max()))
-            self.setParameter(output_volume=X)
-        return X
-    ## iterate
-    
-    def ringRemoval(self, i):
-        print ("FISTA Reconstructor: ring removal")
-        residual = self.residual
-        lambdaR_L1 , alpha_ring , weights , L_const , sino= \
-                   self.getParameter(['ring_lambda_R_L1',
-                                      'ring_alpha' , 'weights',
-                                      'Lipschitz_constant',
-                                      'input_sinogram'])
-        r_x = self.r_x
-        sino_updt = self.sino_updt
-        
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(self.getParameter('input_sinogram'))
-        if lambdaR_L1 > 0 :
-             for kkk in range(anglesNumb):
-                 
-                 residual[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                       ((sino_updt[:,kkk,:]).squeeze() - \
-                                        (sino[:,kkk,:]).squeeze() -\
-                                        (alpha_ring * r_x)
-                                        )
-             vec = residual.sum(axis = 1)
-             #if SlicesZ > 1:
-             #    vec = vec[:,1,:].squeeze()
-             self.r = (r_x - (1./L_const) * vec).copy()
-             self.objective[i] = (0.5 * (residual ** 2).sum())
-
-    def projectionBackprojection(self, X, X_t):
-        print ("FISTA Reconstructor: projection-backprojection routine")
-        
-        # a few useful variables
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(self.getParameter('input_sinogram'))
-        residual = self.residual
-        proj_geom , vol_geom , L_const = \
-                  self.getParameter(['projector_geometry' ,
-                                                  'output_geometry',
-                                                  'Lipschitz_constant'])
-        
-        device, reduced_device = self.getParameter(['device_model',
-                                                    'reduced_device_model'])
-        
-        if self.getParameter('projector_geometry')['type'] == 'parallel' or \
-           self.getParameter('projector_geometry')['type'] == 'fanflat' or \
-           self.getParameter('projector_geometry')['type'] == 'fanflat_vec':
-            # if the geometry is parallel use slice-by-slice
-            # projection-backprojection routine
-            #sino_updt = zeros(size(sino),'single');
-            x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32)
-                
-            if self.use_device:
-                proj_geomT = proj_geom.copy()
-                proj_geomT['DetectorRowCount'] = 1
-                vol_geomT = vol_geom.copy()
-                vol_geomT['GridSliceCount'] = 1;
-                
-                for kkk in range(SlicesZ):
-                    
-                    x_id, x_temp[kkk] = \
-                             astra.creators.create_backprojection3d_gpu(
-                                 residual[kkk:kkk+1],
-                                 proj_geomT, vol_geomT)
-                    astra.matlab.data3d('delete', x_id)
-            else:
-                for kkk in range(SliceZ):
-                    x_temp[kkk] = \
-                        reduced_device.doBackwardProject(residual[kkk:kkk+1])
-        else:
-            if self.use_device:
-                x_id, x_temp = \
-                  astra.creators.create_backprojection3d_gpu(
-                      residual, proj_geom, vol_geom)
-                astra.matlab.data3d('delete', x_id)
-            else:
-                x_temp = \
-                    device.doBackwardProject(residual)
-                       
-
-        X = X_t - (1/L_const) * x_temp
-        #astra.matlab.data3d('delete', sino_id)
-        return (X , X_t)
-        
-
-    def regularize(self, X , output_all=False):
-        #print ("FISTA Reconstructor: regularize")
-        
-        regularizer = self.getParameter('regularizer')
-        if regularizer is not None:
-            return regularizer(input=X,
-                               output_all=output_all)
-        else:
-            return X
-
-    def updateLoop(self, i, X, X_old, r_old, t, t_old):
-        print ("FISTA Reconstructor: update loop")
-        lambdaR_L1 = self.getParameter('ring_lambda_R_L1')
-            
-        t = (1 + numpy.sqrt(1 + 4 * t**2))/2
-        X_t = X + (((t_old -1)/t) * (X - X_old))
-
-        if lambdaR_L1 > 0:
-            self.r = numpy.max(
-                numpy.abs(self.r) - lambdaR_L1 , 0) * \
-                numpy.sign(self.r)
-            self.r_x = self.r + \
-                             (((t_old-1)/t) * (self.r - r_old))
-
-        if self.getParameter('region_of_interest') is None:
-            string = 'Iteration Number {0} | Objective {1} \n'
-            print (string.format( i, self.objective[i]))
-        else:
-            ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                    'ideal_image')
-            
-            Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-            string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-            print (string.format(i,Resid_error[i], self.objective[i]))
-        return (X , X_t, t)
-
-    def iterateOrderedSubsets(self, Xin=None):
-        print ("FISTA Reconstructor: Ordered Subsets iterate")
-        
-        if Xin is None:    
-            if self.getParameter('initialize'):
-                X = self.initialize()
-            else:
-                N = vol_geom['GridColCount']
-                X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
-        else:
-            # copy by reference
-            X = Xin
-        # store the output volume in the parameters
-        self.setParameter(output_volume=X)
-        X_t = X.copy()
-
-        # some useful constants
-        proj_geom ,    vol_geom, sino , \
-          SlicesZ,     weights , alpha_ring ,\
-          lambdaR_L1 , L_const , iterFISTA         = self.getParameter(
-            ['projector_geometry' , 'output_geometry', 'input_sinogram',
-             'SlicesZ' ,            'weights',         'ring_alpha' ,
-             'ring_lambda_R_L1',    'Lipschitz_constant',
-             'number_of_iterations'])
-
-            
-        # errors vector (if the ground truth is given)
-        Resid_error = numpy.zeros((iterFISTA));
-        # objective function values vector
-        #objective = numpy.zeros((iterFISTA));
-        objective = self.objective
-
-          
-        t = 1
-
-        ## additional for 
-        proj_geomSUB = proj_geom.copy()
-        self.residual2 = numpy.zeros(numpy.shape(sino))
-        residual2 = self.residual2
-        sino_updt_FULL = self.residual.copy()
-        r_x = self.r.copy()
-
-        print ("starting iterations")
-        ##    % Outer FISTA iterations loop
-        for i in range(self.getParameter('number_of_iterations')):
-            # With OS approach it becomes trickier to correlate independent
-            # subsets, hence additional work is required one solution is to
-            # work with a full sinogram at times
-
-            r_old = self.r.copy()
-            t_old = t
-            SlicesZ, anglesNumb, Detectors = \
-                        numpy.shape(self.getParameter('input_sinogram'))        ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
-            if (i > 1 and lambdaR_L1 > 0) :
-                for kkk in range(anglesNumb):
-                     
-                     residual2[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                           ((sino_updt_FULL[:,kkk,:]).squeeze() - \
-                                            (sino[:,kkk,:]).squeeze() -\
-                                            (alpha_ring * r_x)
-                                            )
-                
-                vec = self.residual.sum(axis = 1)
-                #if SlicesZ > 1:
-                #    vec = vec[:,1,:] # 1 or 0?
-                r_x = self.r_x
-                # update ring variable
-                self.r = (r_x - (1./L_const) * vec).copy()
-
-            # subset loop
-            counterInd = 1
-            geometry_type = self.getParameter('projector_geometry')['type']
-            angles = self.getParameter('projector_geometry')['ProjectionAngles']
-
-            for ss in range(self.getParameter('subsets')):
-                #print ("Subset {0}".format(ss))
-                X_old = X.copy()
-                t_old = t
-                
-                # the number of projections per subset
-                numProjSub = self.getParameter('os_bins')[ss]
-                CurrSubIndices = self.getParameter('os_indices')\
-                                 [counterInd:counterInd+numProjSub]
-                #print ("Len CurrSubIndices {0}".format(numProjSub))
-                mask = numpy.zeros(numpy.shape(angles), dtype=bool)
-                #cc = 0
-                for j in range(len(CurrSubIndices)):
-                    mask[int(CurrSubIndices[j])] = True
-                proj_geomSUB['ProjectionAngles'] = angles[mask]
-                
-                if self.use_device:
-                    device = self.getParameter('device_model')\
-                             .createReducedDevice(
-                                 proj_par={'angles':angles[mask]},
-                                 vol_par={})
-        
-                shape = list(numpy.shape(self.getParameter('input_sinogram')))
-                shape[1] = numProjSub
-                sino_updt_Sub = numpy.zeros(shape)
-                if geometry_type == 'parallel' or \
-                   geometry_type == 'fanflat' or \
-                   geometry_type == 'fanflat_vec' :
-
-                    for kkk in range(SlicesZ):
-                        if self.use_device:
-                            sinoT = device.doForwardProject(X_t[kkk:kkk+1])
-                        else:
-                            sino_id, sinoT = astra.creators.create_sino3d_gpu (
-                                X_t[kkk:kkk+1] , proj_geomSUB, vol_geom)
-                            astra.matlab.data3d('delete', sino_id)
-                        sino_updt_Sub[kkk] = sinoT.T.copy()
-                        
-                else:
-                    # for 3D geometry (watch the GPU memory overflow in
-                    # ASTRA < 1.8)
-                    if self.use_device:
-                        sino_updt_Sub = device.doForwardProject(X_t)
-                        
-                    else:
-                        sino_id, sino_updt_Sub = \
-                             astra.creators.create_sino3d_gpu (X_t, proj_geomSUB, vol_geom)
-                        
-                        astra.matlab.data3d('delete', sino_id)
-        
-                #print ("shape(sino_updt_Sub)",numpy.shape(sino_updt_Sub))
-                if lambdaR_L1 > 0 :
-                    ## RING REMOVAL
-                    #print ("ring removal")
-                    residualSub , sino_updt_Sub, sino_updt_FULL = \
-                        self.ringRemovalOrderedSubsets(ss,
-                                                       counterInd,
-                                                       sino_updt_Sub,
-                                                       sino_updt_FULL)
-                else:
-                    #PWLS model
-                    #print ("PWLS model")
-                    residualSub = weights[:,CurrSubIndices,:] * \
-                                  ( sino_updt_Sub - \
-                                    sino[:,CurrSubIndices,:].squeeze() )
-                    objective[i] = 0.5 * numpy.linalg.norm(residualSub)
-
-                # projection/backprojection routine
-                if geometry_type == 'parallel' or \
-                   geometry_type == 'fanflat' or \
-                   geometry_type == 'fanflat_vec' :
-                    # if geometry is 2D use slice-by-slice projection-backprojection
-                    # routine
-                    x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
-                    for kkk in range(SlicesZ):
-                        if self.use_device:
-                            x_temp[kkk] = device.doBackwardProject(
-                                residualSub[kkk:kkk+1])
-                        else:
-                            x_id, x_temp[kkk] = \
-                                     astra.creators.create_backprojection3d_gpu(
-                                         residualSub[kkk:kkk+1],
-                                         proj_geomSUB, vol_geom)
-                            astra.matlab.data3d('delete', x_id)
-                        
-                else:
-                    if self.use_device:
-                        x_temp = device.doBackwardProject(
-                            residualSub)
-                    else:
-                        x_id, x_temp = \
-                          astra.creators.create_backprojection3d_gpu(
-                              residualSub, proj_geomSUB, vol_geom)
-
-                        astra.matlab.data3d('delete', x_id)
-                
-                X = X_t - (1/L_const) * x_temp
-                
-                ## REGULARIZATION
-                X = self.regularize(X)
-                
-                ## Update subset Loop
-                t = (1 + numpy.sqrt(1 + 4 * t**2))/2
-                X_t = X + (((t_old -1)/t) * (X - X_old))
-            # FINAL
-            ## update iteration loop
-            if lambdaR_L1 > 0:
-                self.r = numpy.max(
-                    numpy.abs(self.r) - lambdaR_L1 , 0) * \
-                    numpy.sign(self.r)
-                self.r_x = self.r + \
-                                 (((t_old-1)/t) * (self.r - r_old))
-
-            if self.getParameter('region_of_interest') is None:
-                string = 'Iteration Number {0} | Objective {1} \n'
-                print (string.format( i, self.objective[i]))
-            else:
-                ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                        'ideal_image')
-                
-                Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-                string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-                print (string.format(i,Resid_error[i], self.objective[i]))    
-            print("X min {0} max {1}".format(X.min(),X.max()))
-            self.setParameter(output_volume=X)
-            counterInd = counterInd + numProjSub
-
-        return X
-    
-    def ringRemovalOrderedSubsets(self, ss,counterInd,
-                                  sino_updt_Sub, sino_updt_FULL):
-        residual = self.residual
-        r_x = self.r_x
-        weights , alpha_ring , sino = \
-                self.getParameter( ['weights', 'ring_alpha', 'input_sinogram'])
-        numProjSub = self.getParameter('os_bins')[ss]
-        CurrSubIndices = self.getParameter('os_indices')\
-                         [counterInd:counterInd+numProjSub]
-
-        shape = list(numpy.shape(self.getParameter('input_sinogram')))
-        shape[1] = numProjSub
-            
-        residualSub = numpy.zeros(shape)
-
-        for kkk in range(numProjSub):
-            #print ("ring removal indC ... {0}".format(kkk))
-            indC = int(CurrSubIndices[kkk])
-            residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
-                (sino_updt_Sub[:,kkk,:].squeeze() - \
-                sino[:,indC,:].squeeze() - alpha_ring * r_x)
-            # filling the full sinogram
-            sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
-
-        return (residualSub , sino_updt_Sub, sino_updt_FULL)
-
-
diff --git a/src/Python/ccpi/reconstruction/Reconstructor.py b/src/Python/ccpi/reconstruction/Reconstructor.py
deleted file mode 100644
index ba67327..0000000
--- a/src/Python/ccpi/reconstruction/Reconstructor.py
+++ /dev/null
@@ -1,598 +0,0 @@
-# -*- coding: utf-8 -*-
-###############################################################################
-#This work is part of the Core Imaging Library developed by
-#Visual Analytics and Imaging System Group of the Science Technology
-#Facilities Council, STFC
-#
-#Copyright 2017 Edoardo Pasca, Srikanth Nagella
-#Copyright 2017 Daniil Kazantsev
-#
-#Licensed under the Apache License, Version 2.0 (the "License");
-#you may not use this file except in compliance with the License.
-#You may obtain a copy of the License at
-#http://www.apache.org/licenses/LICENSE-2.0
-#Unless required by applicable law or agreed to in writing, software
-#distributed under the License is distributed on an "AS IS" BASIS,
-#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.
-###############################################################################
-
-
-
-import numpy
-import h5py
-from ccpi.reconstruction.parallelbeam import alg
-
-from Regularizer import Regularizer
-from enum import Enum
-
-import astra
-
-
-class Reconstructor:
-    
-    class Algorithm(Enum):
-        CGLS = alg.cgls
-        CGLS_CONV = alg.cgls_conv
-        SIRT = alg.sirt
-        MLEM = alg.mlem
-        CGLS_TICHONOV = alg.cgls_tikhonov
-        CGLS_TVREG = alg.cgls_TVreg
-        FISTA = 'fista'
-        
-    def __init__(self, algorithm = None, projection_data = None,
-                 angles = None, center_of_rotation = None , 
-                 flat_field = None, dark_field = None, 
-                 iterations = None, resolution = None, isLogScale = False, threads = None, 
-                 normalized_projection = None):
-    
-        self.pars = dict()
-        self.pars['algorithm'] = algorithm
-        self.pars['projection_data'] = projection_data
-        self.pars['normalized_projection'] = normalized_projection
-        self.pars['angles'] = angles
-        self.pars['center_of_rotation'] = numpy.double(center_of_rotation)
-        self.pars['flat_field'] = flat_field
-        self.pars['iterations'] = iterations
-        self.pars['dark_field'] = dark_field
-        self.pars['resolution'] = resolution
-        self.pars['isLogScale'] = isLogScale
-        self.pars['threads'] = threads
-        if (iterations != None):
-            self.pars['iterationValues'] = numpy.zeros((iterations)) 
-        
-        if projection_data != None and dark_field != None and flat_field != None:
-            norm = self.normalize(projection_data, dark_field, flat_field, 0.1)
-            self.pars['normalized_projection'] = norm
-            
-    
-    def setPars(self, parameters):
-        keys = ['algorithm','projection_data' ,'normalized_projection', \
-                'angles' , 'center_of_rotation' , 'flat_field', \
-                'iterations','dark_field' , 'resolution', 'isLogScale' , \
-                'threads' , 'iterationValues', 'regularize']
-        
-        for k in keys:
-            if k not in parameters.keys():
-                self.pars[k] = None
-            else:
-                self.pars[k] = parameters[k]
-                
-        
-    def sanityCheck(self):
-        projection_data = self.pars['projection_data']
-        dark_field = self.pars['dark_field']
-        flat_field = self.pars['flat_field']
-        angles = self.pars['angles']
-        
-        if projection_data != None and dark_field != None and \
-            angles != None and flat_field != None:
-            data_shape =  numpy.shape(projection_data)
-            angle_shape = numpy.shape(angles)
-            
-            if angle_shape[0] != data_shape[0]:
-                #raise Exception('Projections and angles dimensions do not match: %d vs %d' % \
-                #                (angle_shape[0] , data_shape[0]) )
-                return (False , 'Projections and angles dimensions do not match: %d vs %d' % \
-                                (angle_shape[0] , data_shape[0]) )
-            
-            if data_shape[1:] != numpy.shape(flat_field):
-                #raise Exception('Projection and flat field dimensions do not match')
-                return (False , 'Projection and flat field dimensions do not match')
-            if data_shape[1:] != numpy.shape(dark_field):
-                #raise Exception('Projection and dark field dimensions do not match')
-                return (False , 'Projection and dark field dimensions do not match')
-            
-            return (True , '' )
-        elif self.pars['normalized_projection'] != None:
-            data_shape =  numpy.shape(self.pars['normalized_projection'])
-            angle_shape = numpy.shape(angles)
-            
-            if angle_shape[0] != data_shape[0]:
-                #raise Exception('Projections and angles dimensions do not match: %d vs %d' % \
-                #                (angle_shape[0] , data_shape[0]) )
-                return (False , 'Projections and angles dimensions do not match: %d vs %d' % \
-                                (angle_shape[0] , data_shape[0]) )
-            else:
-                return (True , '' )
-        else:
-            return (False , 'Not enough data')
-            
-    def reconstruct(self, parameters = None):
-        if parameters != None:
-            self.setPars(parameters)
-        
-        go , reason = self.sanityCheck()
-        if go:
-            return self._reconstruct()
-        else:
-            raise Exception(reason)
-            
-            
-    def _reconstruct(self, parameters=None):
-        if parameters!=None:
-            self.setPars(parameters)
-        parameters = self.pars
-        
-        if parameters['algorithm'] != None and \
-           parameters['normalized_projection'] != None and \
-           parameters['angles'] != None and \
-           parameters['center_of_rotation'] != None and \
-           parameters['iterations'] != None and \
-           parameters['resolution'] != None and\
-           parameters['threads'] != None and\
-           parameters['isLogScale'] != None:
-               
-               
-           if parameters['algorithm'] in (Reconstructor.Algorithm.CGLS,
-                        Reconstructor.Algorithm.MLEM, Reconstructor.Algorithm.SIRT):
-               #store parameters
-               self.pars = parameters
-               result = parameters['algorithm'](
-                           parameters['normalized_projection'] ,
-                           parameters['angles'],
-                           parameters['center_of_rotation'],
-                           parameters['resolution'],
-                           parameters['iterations'],
-                           parameters['threads'] ,
-                           parameters['isLogScale']
-                           )
-               return result
-           elif parameters['algorithm'] in (Reconstructor.Algorithm.CGLS_CONV,
-                          Reconstructor.Algorithm.CGLS_TICHONOV, 
-                          Reconstructor.Algorithm.CGLS_TVREG) :
-               self.pars = parameters
-               result = parameters['algorithm'](
-                           parameters['normalized_projection'] ,
-                           parameters['angles'],
-                           parameters['center_of_rotation'],
-                           parameters['resolution'],
-                           parameters['iterations'],
-                           parameters['threads'] ,
-                           parameters['regularize'],
-                           numpy.zeros((parameters['iterations'])),
-                           parameters['isLogScale']
-                           )
-               
-           elif parameters['algorithm'] == Reconstructor.Algorithm.FISTA:
-               pass
-             
-        else:
-           if parameters['projection_data'] != None and \
-                     parameters['dark_field'] != None and \
-                     parameters['flat_field'] != None:
-               norm = self.normalize(parameters['projection_data'],
-                                   parameters['dark_field'], 
-                                   parameters['flat_field'], 0.1)
-               self.pars['normalized_projection'] = norm
-               return self._reconstruct(parameters)
-              
-                
-                
-    def _normalize(self, projection, dark, flat, def_val=0):
-        a = (projection - dark)
-        b = (flat-dark)
-        with numpy.errstate(divide='ignore', invalid='ignore'):
-            c = numpy.true_divide( a, b )
-            c[ ~ numpy.isfinite( c )] = def_val  # set to not zero if 0/0 
-        return c
-    
-    def normalize(self, projections, dark, flat, def_val=0):
-        norm = [self._normalize(projection, dark, flat, def_val) for projection in projections]
-        return numpy.asarray (norm, dtype=numpy.float32)
-        
-    
-    
-class FISTA():
-    '''FISTA-based reconstruction algorithm using ASTRA-toolbox
-    
-    '''
-    # <<<< FISTA-based reconstruction algorithm using ASTRA-toolbox >>>>
-    # ___Input___:
-    # params.[] file:
-    #       - .proj_geom (geometry of the projector) [required]
-    #       - .vol_geom (geometry of the reconstructed object) [required]
-    #       - .sino (vectorized in 2D or 3D sinogram) [required]
-    #       - .iterFISTA (iterations for the main loop, default 40)
-    #       - .L_const (Lipschitz constant, default Power method)                                                                                                    )
-    #       - .X_ideal (ideal image, if given)
-    #       - .weights (statisitcal weights, size of the sinogram)
-    #       - .ROI (Region-of-interest, only if X_ideal is given)
-    #       - .initialize (a 'warm start' using SIRT method from ASTRA)
-    #----------------Regularization choices------------------------
-    #       - .Regul_Lambda_FGPTV (FGP-TV regularization parameter)
-    #       - .Regul_Lambda_SBTV (SplitBregman-TV regularization parameter)
-    #       - .Regul_Lambda_TVLLT (Higher order SB-LLT regularization parameter)
-    #       - .Regul_tol (tolerance to terminate regul iterations, default 1.0e-04)
-    #       - .Regul_Iterations (iterations for the selected penalty, default 25)
-    #       - .Regul_tauLLT (time step parameter for LLT term)
-    #       - .Ring_LambdaR_L1 (regularization parameter for L1-ring minimization, if lambdaR_L1 > 0 then switch on ring removal)
-    #       - .Ring_Alpha (larger values can accelerate convergence but check stability, default 1)
-    #----------------Visualization parameters------------------------
-    #       - .show (visualize reconstruction 1/0, (0 default))
-    #       - .maxvalplot (maximum value to use for imshow[0 maxvalplot])
-    #       - .slice (for 3D volumes - slice number to imshow)
-    # ___Output___:
-    # 1. X - reconstructed image/volume
-    # 2. output - a structure with
-    #    - .Resid_error - residual error (if X_ideal is given)
-    #    - .objective: value of the objective function
-    #    - .L_const: Lipshitz constant to avoid recalculations
-    
-    # References:
-    # 1. "A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse
-    # Problems" by A. Beck and M Teboulle
-    # 2. "Ring artifacts correction in compressed sensing..." by P. Paleo
-    # 3. "A novel tomographic reconstruction method based on the robust
-    # Student's t function for suppressing data outliers" D. Kazantsev et.al.
-    # D. Kazantsev, 2016-17
-    def __init__(self, projector_geometry, output_geometry, input_sinogram, **kwargs):
-        self.params = dict()
-        self.params['projector_geometry'] = projector_geometry
-        self.params['output_geometry'] = output_geometry
-        self.params['input_sinogram'] = input_sinogram
-        detectors, nangles, sliceZ = numpy.shape(input_sinogram)
-        self.params['detectors'] = detectors
-        self.params['number_og_angles'] = nangles
-        self.params['SlicesZ'] = sliceZ
-        
-        # Accepted input keywords
-        kw = ('number_of_iterations', 'Lipschitz_constant' , 'ideal_image' ,
-              'weights' , 'region_of_interest' , 'initialize' , 
-              'regularizer' , 
-              'ring_lambda_R_L1',
-              'ring_alpha')
-        
-        # handle keyworded parameters
-        if kwargs is not None:
-            for key, value in kwargs.items():
-                if key in kw:
-                    #print("{0} = {1}".format(key, value))                        
-                    self.pars[key] = value
-                    
-        # set the default values for the parameters if not set
-        if 'number_of_iterations' in kwargs.keys():
-            self.pars['number_of_iterations'] = kwargs['number_of_iterations']
-        else:
-            self.pars['number_of_iterations'] = 40
-        if 'weights' in kwargs.keys():
-            self.pars['weights'] = kwargs['weights']
-        else:
-            self.pars['weights'] = numpy.ones(numpy.shape(self.params['input_sinogram']))
-        if 'Lipschitz_constant' in kwargs.keys():
-            self.pars['Lipschitz_constant'] = kwargs['Lipschitz_constant']
-        else:
-            self.pars['Lipschitz_constant'] = self.calculateLipschitzConstantWithPowerMethod()
-        
-        if not self.pars['ideal_image'] in kwargs.keys():
-            self.pars['ideal_image'] = None
-        
-        if not self.pars['region_of_interest'] :
-            if self.pars['ideal_image'] == None:
-                pass
-            else:
-                self.pars['region_of_interest'] = numpy.nonzero(self.pars['ideal_image']>0.0)
-            
-        if not self.pars['regularizer'] :
-            self.pars['regularizer'] = None
-        else:
-            # the regularizer must be a correctly instantiated object
-            if not self.pars['ring_lambda_R_L1']:
-                self.pars['ring_lambda_R_L1'] = 0
-            if not self.pars['ring_alpha']:
-                self.pars['ring_alpha'] = 1
-        
-            
-            
-        
-    def calculateLipschitzConstantWithPowerMethod(self):
-        ''' using Power method (PM) to establish L constant'''
-        
-        #N = params.vol_geom.GridColCount
-        N = self.pars['output_geometry'].GridColCount
-        proj_geom = self.params['projector_geometry']
-        vol_geom = self.params['output_geometry']
-        weights = self.pars['weights']
-        SlicesZ = self.pars['SlicesZ']
-        
-        if (proj_geom['type'] == 'parallel') or (proj_geom['type'] == 'parallel3d'):
-            #% for parallel geometry we can do just one slice
-            #fprintf('%s \n', 'Calculating Lipshitz constant for parallel beam geometry...');
-            niter = 15;# % number of iteration for the PM
-            #N = params.vol_geom.GridColCount;
-            #x1 = rand(N,N,1);
-            x1 = numpy.random.rand(1,N,N)
-            #sqweight = sqrt(weights(:,:,1));
-            sqweight = numpy.sqrt(weights.T[0])
-            proj_geomT = proj_geom.copy();
-            proj_geomT.DetectorRowCount = 1;
-            vol_geomT = vol_geom.copy();
-            vol_geomT['GridSliceCount'] = 1;
-            
-            
-            for i in range(niter):
-                if i == 0:
-                    #[sino_id, y] = astra_create_sino3d_cuda(x1, proj_geomT, vol_geomT);
-                    sino_id, y = astra.creators.create_sino3d_gpu(x1, proj_geomT, vol_geomT);
-                    y = sqweight * y # element wise multiplication
-                    #astra_mex_data3d('delete', sino_id);
-                    astra.matlab.data3d('delete', sino_id)
-                    
-                idx,x1 = astra.creators.create_backprojection3d_gpu(sqweight*y, proj_geomT, vol_geomT);
-                s = numpy.linalg.norm(x1)
-                ### this line?
-                x1 = x1/s;
-                ### this line?
-                sino_id, y = astra_create_sino3d_cuda(x1, proj_geomT, vol_geomT);
-                y = sqweight*y;
-                astra.matlab.data3d('delete', sino_id);
-                astra.matlab.data3d('delete', idx);
-            #end
-            del proj_geomT
-            del vol_geomT
-        else
-            #% divergen beam geometry
-            #fprintf('%s \n', 'Calculating Lipshitz constant for divergen beam geometry...');
-            niter = 8; #% number of iteration for PM
-            x1 = numpy.random.rand(SlicesZ , N , N);
-            #sqweight = sqrt(weights);
-            sqweight = numpy.sqrt(weights.T[0])
-            
-            sino_id, y = astra.creators.create_sino3d_gpu(x1, proj_geom, vol_geom);
-            y = sqweight*y;
-            #astra_mex_data3d('delete', sino_id);
-            astra.matlab.data3d('delete', sino_id);
-            
-            for i in range(niter):
-                #[id,x1] = astra_create_backprojection3d_cuda(sqweight.*y, proj_geom, vol_geom);
-                idx,x1 = astra.creators.create_backprojection3d_gpu(sqweight*y, 
-                                                                    proj_geom, 
-                                                                    vol_geom)
-                s = numpy.linalg.norm(x1)
-                ### this line?
-                x1 = x1/s;
-                ### this line?
-                #[sino_id, y] = astra_create_sino3d_gpu(x1, proj_geom, vol_geom);
-                sino_id, y = astra.creators.create_sino3d_gpu(x1, 
-                                                              proj_geom, 
-                                                              vol_geom);
-                
-                y = sqweight*y;
-                #astra_mex_data3d('delete', sino_id);
-                #astra_mex_data3d('delete', id);
-                astra.matlab.data3d('delete', sino_id);
-                astra.matlab.data3d('delete', idx);
-            #end
-            #clear x1
-            del x1
-        
-        return s
-    
-    
-    def setRegularizer(self, regularizer):
-        if regularizer
-        self.pars['regularizer'] = regularizer
-        
-    
-    
-
-
-def getEntry(location):
-    for item in nx[location].keys():
-        print (item)
-
-
-print ("Loading Data")
-
-##fname = "D:\\Documents\\Dataset\\IMAT\\20170419_crabtomo\\crabtomo\\Sample\\IMAT00005153_crabstomo_Sample_000.tif"
-####ind = [i * 1049 for i in range(360)]
-#### use only 360 images
-##images = 200
-##ind = [int(i * 1049 / images) for i in range(images)]
-##stack_image = dxchange.reader.read_tiff_stack(fname, ind, digit=None, slc=None)
-
-#fname = "D:\\Documents\\Dataset\\CGLS\\24737_fd.nxs"
-fname = "C:\\Users\\ofn77899\\Documents\\CCPi\\CGLS\\24737_fd_2.nxs"
-nx = h5py.File(fname, "r")
-
-# the data are stored in a particular location in the hdf5
-for item in nx['entry1/tomo_entry/data'].keys():
-    print (item)
-
-data = nx.get('entry1/tomo_entry/data/rotation_angle')
-angles = numpy.zeros(data.shape)
-data.read_direct(angles)
-print (angles)
-# angles should be in degrees
-
-data = nx.get('entry1/tomo_entry/data/data')
-stack = numpy.zeros(data.shape)
-data.read_direct(stack)
-print (data.shape)
-
-print ("Data Loaded")
-
-
-# Normalize
-data = nx.get('entry1/tomo_entry/instrument/detector/image_key')
-itype = numpy.zeros(data.shape)
-data.read_direct(itype)
-# 2 is dark field
-darks = [stack[i] for i in range(len(itype)) if itype[i] == 2 ]
-dark = darks[0]
-for i in range(1, len(darks)):
-    dark += darks[i]
-dark = dark / len(darks)
-#dark[0][0] = dark[0][1]
-
-# 1 is flat field
-flats = [stack[i] for i in range(len(itype)) if itype[i] == 1 ]
-flat = flats[0]
-for i in range(1, len(flats)):
-    flat += flats[i]
-flat = flat / len(flats)
-#flat[0][0] = dark[0][1]
-
-
-# 0 is projection data
-proj = [stack[i] for i in range(len(itype)) if itype[i] == 0 ]
-angle_proj = [angles[i] for i in range(len(itype)) if itype[i] == 0 ]
-angle_proj = numpy.asarray (angle_proj)
-angle_proj = angle_proj.astype(numpy.float32)
-
-# normalized data are
-# norm = (projection - dark)/(flat-dark)
-
-def normalize(projection, dark, flat, def_val=0.1):
-    a = (projection - dark)
-    b = (flat-dark)
-    with numpy.errstate(divide='ignore', invalid='ignore'):
-        c = numpy.true_divide( a, b )
-        c[ ~ numpy.isfinite( c )] = def_val  # set to not zero if 0/0 
-    return c
-    
-
-norm = [normalize(projection, dark, flat) for projection in proj]
-norm = numpy.asarray (norm)
-norm = norm.astype(numpy.float32)
-
-#recon = Reconstructor(algorithm = Algorithm.CGLS, normalized_projection = norm,
-#                 angles = angle_proj, center_of_rotation = 86.2 , 
-#                 flat_field = flat, dark_field = dark, 
-#                 iterations = 15, resolution = 1, isLogScale = False, threads = 3)
-
-#recon = Reconstructor(algorithm = Reconstructor.Algorithm.CGLS, projection_data = proj,
-#                 angles = angle_proj, center_of_rotation = 86.2 , 
-#                 flat_field = flat, dark_field = dark, 
-#                 iterations = 15, resolution = 1, isLogScale = False, threads = 3)
-#img_cgls = recon.reconstruct()
-#
-#pars = dict()
-#pars['algorithm'] = Reconstructor.Algorithm.SIRT
-#pars['projection_data'] = proj
-#pars['angles'] = angle_proj
-#pars['center_of_rotation'] = numpy.double(86.2)
-#pars['flat_field'] = flat
-#pars['iterations'] = 15
-#pars['dark_field'] = dark
-#pars['resolution'] = 1
-#pars['isLogScale'] = False
-#pars['threads'] = 3
-#
-#img_sirt = recon.reconstruct(pars)
-#
-#recon.pars['algorithm'] = Reconstructor.Algorithm.MLEM
-#img_mlem = recon.reconstruct()
-
-############################################################
-############################################################
-#recon.pars['algorithm'] = Reconstructor.Algorithm.CGLS_CONV
-#recon.pars['regularize'] = numpy.double(0.1)
-#img_cgls_conv = recon.reconstruct()
-
-niterations = 15
-threads = 3
-
-img_cgls = alg.cgls(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads, False)
-img_mlem = alg.mlem(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads, False)
-img_sirt = alg.sirt(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads, False)
-
-iteration_values = numpy.zeros((niterations,))
-img_cgls_conv = alg.cgls_conv(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads,
-                              iteration_values, False)
-print ("iteration values %s" % str(iteration_values))
-
-iteration_values = numpy.zeros((niterations,))
-img_cgls_tikhonov = alg.cgls_tikhonov(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads,
-                                      numpy.double(1e-5), iteration_values , False)
-print ("iteration values %s" % str(iteration_values))
-iteration_values = numpy.zeros((niterations,))
-img_cgls_TVreg = alg.cgls_TVreg(norm, angle_proj, numpy.double(86.2), 1 , niterations, threads,
-                                      numpy.double(1e-5), iteration_values , False)
-print ("iteration values %s" % str(iteration_values))
-
-
-##numpy.save("cgls_recon.npy", img_data)
-import matplotlib.pyplot as plt
-fig, ax = plt.subplots(1,6,sharey=True)
-ax[0].imshow(img_cgls[80])
-ax[0].axis('off')  # clear x- and y-axes
-ax[1].imshow(img_sirt[80])
-ax[1].axis('off')  # clear x- and y-axes
-ax[2].imshow(img_mlem[80])
-ax[2].axis('off')  # clear x- and y-axesplt.show()
-ax[3].imshow(img_cgls_conv[80])
-ax[3].axis('off')  # clear x- and y-axesplt.show()
-ax[4].imshow(img_cgls_tikhonov[80])
-ax[4].axis('off')  # clear x- and y-axesplt.show()
-ax[5].imshow(img_cgls_TVreg[80])
-ax[5].axis('off')  # clear x- and y-axesplt.show()
-
-
-plt.show()
-
-#viewer = edo.CILViewer()
-#viewer.setInputAsNumpy(img_cgls2)
-#viewer.displaySliceActor(0)
-#viewer.startRenderLoop()
-
-import vtk
-
-def NumpyToVTKImageData(numpyarray):
-    if (len(numpy.shape(numpyarray)) == 3):
-        doubleImg = vtk.vtkImageData()
-        shape = numpy.shape(numpyarray)
-        doubleImg.SetDimensions(shape[0], shape[1], shape[2])
-        doubleImg.SetOrigin(0,0,0)
-        doubleImg.SetSpacing(1,1,1)
-        doubleImg.SetExtent(0, shape[0]-1, 0, shape[1]-1, 0, shape[2]-1)
-        #self.img3D.SetScalarType(vtk.VTK_UNSIGNED_SHORT, vtk.vtkInformation())
-        doubleImg.AllocateScalars(vtk.VTK_DOUBLE,1)
-        
-        for i in range(shape[0]):
-            for j in range(shape[1]):
-                for k in range(shape[2]):
-                    doubleImg.SetScalarComponentFromDouble(
-                        i,j,k,0, numpyarray[i][j][k])
-    #self.setInput3DData( numpy_support.numpy_to_vtk(numpyarray) )
-        # rescale to appropriate VTK_UNSIGNED_SHORT
-        stats = vtk.vtkImageAccumulate()
-        stats.SetInputData(doubleImg)
-        stats.Update()
-        iMin = stats.GetMin()[0]
-        iMax = stats.GetMax()[0]
-        scale = vtk.VTK_UNSIGNED_SHORT_MAX / (iMax - iMin)
-
-        shiftScaler = vtk.vtkImageShiftScale ()
-        shiftScaler.SetInputData(doubleImg)
-        shiftScaler.SetScale(scale)
-        shiftScaler.SetShift(iMin)
-        shiftScaler.SetOutputScalarType(vtk.VTK_UNSIGNED_SHORT)
-        shiftScaler.Update()
-        return shiftScaler.GetOutput()
-        
-#writer = vtk.vtkMetaImageWriter()
-#writer.SetFileName(alg + "_recon.mha")
-#writer.SetInputData(NumpyToVTKImageData(img_cgls2))
-#writer.Write()
diff --git a/src/Python/ccpi/reconstruction/__init__.py b/src/Python/ccpi/reconstruction/__init__.py
deleted file mode 100644
index e69de29..0000000
--- a/src/Python/ccpi/reconstruction/__init__.py
+++ /dev/null
diff --git a/src/Python/compile-fista.bat.in b/src/Python/compile-fista.bat.in
deleted file mode 100644
index b1db686..0000000
--- a/src/Python/compile-fista.bat.in
+++ /dev/null
@@ -1,7 +0,0 @@
-set CIL_VERSION=@CIL_VERSION@
-
-set PREFIX=@CONDA_ENVIRONMENT_PREFIX@
-set LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@
-
-REM activate @CONDA_ENVIRONMENT@
-conda build fista-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi -c conda-forge
diff --git a/src/Python/compile-fista.sh.in b/src/Python/compile-fista.sh.in
deleted file mode 100644
index 267f014..0000000
--- a/src/Python/compile-fista.sh.in
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/sh
-# compile within the right conda environment
-#module load python/anaconda
-#source activate @CONDA_ENVIRONMENT@
-
-export CIL_VERSION=@CIL_VERSION@
-export LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@
-
-conda build fista-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi
diff --git a/src/Python/compile.bat.in b/src/Python/compile.bat.in
deleted file mode 100644
index e5342ed..0000000
--- a/src/Python/compile.bat.in
+++ /dev/null
@@ -1,7 +0,0 @@
-set CIL_VERSION=@CIL_VERSION@
-
-set PREFIX=@CONDA_ENVIRONMENT_PREFIX@
-set LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@
-
-REM activate @CONDA_ENVIRONMENT@
-conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi -c conda-forge
\ No newline at end of file
diff --git a/src/Python/compile.sh.in b/src/Python/compile.sh.in
deleted file mode 100644
index 93fdba2..0000000
--- a/src/Python/compile.sh.in
+++ /dev/null
@@ -1,9 +0,0 @@
-#!/bin/sh
-# compile within the right conda environment
-#module load python/anaconda
-#source activate @CONDA_ENVIRONMENT@
-
-export CIL_VERSION=@CIL_VERSION@
-export LIBRARY_INC=@CONDA_ENVIRONMENT_LIBRARY_INC@
-
-conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi
diff --git a/src/Python/conda-recipe/bld.bat b/src/Python/conda-recipe/bld.bat
deleted file mode 100644
index 69491de..0000000
--- a/src/Python/conda-recipe/bld.bat
+++ /dev/null
@@ -1,14 +0,0 @@
-IF NOT DEFINED CIL_VERSION (
-ECHO CIL_VERSION Not Defined.
-exit 1
-)
-
-mkdir "%SRC_DIR%\ccpi"
-xcopy /e "%RECIPE_DIR%\..\.." "%SRC_DIR%\ccpi"
-
-cd %SRC_DIR%\ccpi\Python
-
-%PYTHON% setup.py build_ext
-if errorlevel 1 exit 1
-%PYTHON% setup.py install
-if errorlevel 1 exit 1
diff --git a/src/Python/conda-recipe/build.sh b/src/Python/conda-recipe/build.sh
deleted file mode 100644
index 855047f..0000000
--- a/src/Python/conda-recipe/build.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-
-if [ -z "$CIL_VERSION" ]; then
-    echo "Need to set CIL_VERSION"
-    exit 1
-fi  
-mkdir "$SRC_DIR/ccpi"
-cp -r "$RECIPE_DIR/../.." "$SRC_DIR/ccpi"
-
-cd $SRC_DIR/ccpi/Python
-
-$PYTHON setup.py build_ext
-$PYTHON setup.py install
-
-
diff --git a/src/Python/conda-recipe/meta.yaml b/src/Python/conda-recipe/meta.yaml
deleted file mode 100644
index 9ef9156..0000000
--- a/src/Python/conda-recipe/meta.yaml
+++ /dev/null
@@ -1,30 +0,0 @@
-package:
-  name: ccpi-regularizers
-  version: {{ environ['CIL_VERSION'] }}
-
-
-build:
-  preserve_egg_dir: False
-  script_env:
-    - CIL_VERSION   
-#  number: 0
-  
-requirements:
-  build:
-    - python
-    - numpy
-    - setuptools
-    - boost ==1.65
-    - boost-cpp ==1.65
-    - cython
-
-  run:
-    - python
-    - numpy
-    - boost ==1.64
-
-	
-about:
-  home: http://www.ccpi.ac.uk
-  license:  BSD license
-  summary: 'CCPi Core Imaging Library Quantification Toolbox'
diff --git a/src/Python/demo/demo_dendrites.py b/src/Python/demo/demo_dendrites.py
deleted file mode 100644
index f5dc845..0000000
--- a/src/Python/demo/demo_dendrites.py
+++ /dev/null
@@ -1,168 +0,0 @@
-
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-Based on DemoRD2.m
-"""
-
-import h5py
-import numpy
-
-from ccpi.reconstruction.FISTAReconstructor import FISTAReconstructor
-import astra
-import matplotlib.pyplot as plt
-from ccpi.imaging.Regularizer import Regularizer
-from ccpi.reconstruction.AstraDevice import AstraDevice
-from ccpi.reconstruction.DeviceModel import DeviceModel
-
-def RMSE(signal1, signal2):
-    '''RMSE Root Mean Squared Error'''
-    if numpy.shape(signal1) == numpy.shape(signal2):
-        err = (signal1 - signal2)
-        err = numpy.sum( err * err )/numpy.size(signal1);  # MSE
-        err = sqrt(err);                                   # RMSE
-        return err
-    else:
-        raise Exception('Input signals must have the same shape')
-  
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-Sino3D = numpy.asarray(nx.get('/Sino3D'), dtype="float32")
-Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32")
-angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles_rad'), dtype="float32")
-recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0]
-size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0]
-slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-
-Z_slices = 20
-det_row_count = Z_slices
-# next definition is just for consistency of naming
-det_col_count = size_det
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-image_size_x = recon_size
-image_size_y = recon_size
-image_size_z = Z_slices
-vol_geom = astra.creators.create_vol_geom( image_size_x,
-                                           image_size_y,
-                                           image_size_z)
-
-
-## Create a Acquisition Device Model
-## Must specify some parameters of the acquisition:
-
-astradevice = AstraDevice(
-                DeviceModel.DeviceType.PARALLEL3D.value,
-                [det_row_count , det_col_count ,
-                 detectorSpacingX, detectorSpacingY ,
-                 angles_rad
-                 ],
-                [ image_size_x, image_size_y, image_size_z ] )
-
-fistaRecon = FISTAReconstructor(proj_geom,
-                            vol_geom,
-                            Sino3D ,
-                            weights=Weights3D,
-                            device=astradevice,
-                            Lipschitz_constant = 767893952.0,
-                            subsets = 8)
-
-print("Reconstruction using FISTA-OS-PWLS without regularization...")
-fistaRecon.setParameter(number_of_iterations = 5)
-
-### adjust the regularization parameter
-##lc = fistaRecon.getParameter('Lipschitz_constant')
-##fistaRecon.getParameter('regularizer')\
-##             .setParameter(regularization_parameter=5e6/lc)
-fistaRecon.use_device = True
-if True:
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA-OS-PWLS.npy",X)
-
-## setup a regularizer algorithm
-regul = Regularizer(Regularizer.Algorithm.FGP_TV)
-regul.setParameter(regularization_parameter=5e6,
-                   number_of_iterations=50,
-                   tolerance_constant=1e-4,
-                   TV_penalty=Regularizer.TotalVariationPenalty.isotropic)
-if False:
-    # adjust the regularization parameter
-    lc = fistaRecon.getParameter('Lipschitz_constant')
-    regul.setParameter(regularization_parameter=5e6/lc)
-    fistaRecon.setParameter(regularizer=regul)
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA-OS-PWLS-TV.npy",X)
-
-if False:
-    # adjust the regularization parameter
-    lc = fistaRecon.getParameter('Lipschitz_constant')
-    regul.setParameter(regularization_parameter=5e6/lc)
-    fistaRecon.setParameter(regularizer=regul)
-    fistaRecon.setParameter(ring_lambda_R_L1=0.002, ring_alpha=21)
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA-OS-GH-TV.npy",X)
-
-if False:
-    # adjust the regularization parameter
-    lc = fistaRecon.getParameter('Lipschitz_constant')
-    regul.setParameter(
-        algorithm=Regularizer.Algorithm.TGV_PD,
-        regularization_parameter=0.5/lc,
-        number_of_iterations=5)
-    fistaRecon.setParameter(regularizer=regul)
-    fistaRecon.setParameter(ring_lambda_R_L1=0.002, ring_alpha=21)
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA-OS-GH-TGV.npy",X)
-    
-if False:
-    # adjust the regularization parameter
-    lc = fistaRecon.getParameter('Lipschitz_constant')
-    regul.setParameter(
-        algorithm=Regularizer.Algorithm.PatchBased_Regul,
-        regularization_parameter=3/lc,
-        searching_window_ratio=3,
-        similarity_window_ratio=1,
-        PB_filtering_parameter=0.04
-        
-        )
-    fistaRecon.setParameter(regularizer=regul)
-    fistaRecon.setParameter(ring_lambda_R_L1=0.002, ring_alpha=21)
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA-OS-CPU_PB.npy",X)
-
-if False:
-    fistaRecon = FISTAReconstructor(proj_geom,
-                            vol_geom,
-                            Sino3D ,
-                            weights=Weights3D,
-                            device=astradevice,
-                            Lipschitz_constant = 7.6792e8,
-                            number_of_iterations=50)
-
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("../test/X.npy"))
-    numpy.save("FISTA.npy",X)
diff --git a/src/Python/fista-recipe/build.sh b/src/Python/fista-recipe/build.sh
deleted file mode 100644
index e3f3552..0000000
--- a/src/Python/fista-recipe/build.sh
+++ /dev/null
@@ -1,10 +0,0 @@
-if [ -z "$CIL_VERSION" ]; then
-    echo "Need to set CIL_VERSION"
-    exit 1
-fi  
-mkdir "$SRC_DIR/ccpifista"
-cp -r "$RECIPE_DIR/.." "$SRC_DIR/ccpifista"
-
-cd $SRC_DIR/ccpifista
-
-$PYTHON setup-fista.py install
diff --git a/src/Python/fista-recipe/meta.yaml b/src/Python/fista-recipe/meta.yaml
deleted file mode 100644
index 265541f..0000000
--- a/src/Python/fista-recipe/meta.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-package:
-  name: ccpi-fista
-  version: {{ environ['CIL_VERSION'] }}
-
-
-build:
-  preserve_egg_dir: False
-  script_env:
-    - CIL_VERSION   
-#  number: 0
-  
-requirements:
-  build:
-    - python
-    - numpy
-    - setuptools
- 
-  run:
-    - python
-    - numpy
-    #- astra-toolbox
-    - ccpi-regularizers
-
-
-	
-about:
-  home: http://www.ccpi.ac.uk
-  license:  Apache v.2.0 license
-  summary: 'CCPi Core Imaging Library (Viewer)'
diff --git a/src/Python/fista_module.cpp b/src/Python/fista_module.cpp
deleted file mode 100644
index f3add76..0000000
--- a/src/Python/fista_module.cpp
+++ /dev/null
@@ -1,1047 +0,0 @@
-/*
-This work is part of the Core Imaging Library developed by
-Visual Analytics and Imaging System Group of the Science Technology
-Facilities Council, STFC
-
-Copyright 2017 Daniil Kazantsev
-Copyright 2017 Srikanth Nagella, Edoardo Pasca
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-http://www.apache.org/licenses/LICENSE-2.0
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-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.
-*/
-
-#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
-
-#include <iostream>
-#include <cmath>
-
-#include <boost/python.hpp>
-#include <boost/python/numpy.hpp>
-#include "boost/tuple/tuple.hpp"
-
-#include "SplitBregman_TV_core.h"
-#include "FGP_TV_core.h"
-#include "LLT_model_core.h"
-#include "PatchBased_Regul_core.h"
-#include "TGV_PD_core.h"
-#include "utils.h"
-
-
-
-#if defined(_WIN32) || defined(_WIN32) || defined(__WIN32__) || defined(_WIN64)
-#include <windows.h>
-// this trick only if compiler is MSVC
-__if_not_exists(uint8_t) { typedef __int8 uint8_t; }
-__if_not_exists(uint16_t) { typedef __int8 uint16_t; }
-#endif
-
-namespace bp = boost::python;
-namespace np = boost::python::numpy;
-
-/*! in the Matlab implementation this is called as
-void mexFunction(
-int nlhs, mxArray *plhs[],
-int nrhs, const mxArray *prhs[])
-where:
-prhs Array of pointers to the INPUT mxArrays
-nrhs int number of INPUT mxArrays
-
-nlhs Array of pointers to the OUTPUT mxArrays
-plhs int number of OUTPUT mxArrays
-
-***********************************************************
-
-***********************************************************
-double mxGetScalar(const mxArray *pm);
-args: pm Pointer to an mxArray; cannot be a cell mxArray, a structure mxArray, or an empty mxArray.
-Returns: Pointer to the value of the first real (nonimaginary) element of the mxArray.	In C, mxGetScalar returns a double.
-***********************************************************
-char *mxArrayToString(const mxArray *array_ptr);
-args: array_ptr Pointer to mxCHAR array.
-Returns: C-style string. Returns NULL on failure. Possible reasons for failure include out of memory and specifying an array that is not an mxCHAR array.
-Description: Call mxArrayToString to copy the character data of an mxCHAR array into a C-style string.
-***********************************************************
-mxClassID mxGetClassID(const mxArray *pm);
-args: pm Pointer to an mxArray
-Returns: Numeric identifier of the class (category) of the mxArray that pm points to.For user-defined types,
-mxGetClassId returns a unique value identifying the class of the array contents.
-Use mxIsClass to determine whether an array is of a specific user-defined type.
-
-mxClassID Value	  MATLAB Type   MEX Type	 C Primitive Type
-mxINT8_CLASS 	  int8	        int8_T	     char, byte
-mxUINT8_CLASS	  uint8	        uint8_T	     unsigned char, byte
-mxINT16_CLASS	  int16	        int16_T	     short
-mxUINT16_CLASS	  uint16	    uint16_T	 unsigned short
-mxINT32_CLASS	  int32	        int32_T	     int
-mxUINT32_CLASS	  uint32	    uint32_T	 unsigned int
-mxINT64_CLASS	  int64	        int64_T	     long long
-mxUINT64_CLASS	  uint64	    uint64_T 	 unsigned long long
-mxSINGLE_CLASS	  single	    float	     float
-mxDOUBLE_CLASS	  double	    double	     double
-
-****************************************************************
-double *mxGetPr(const mxArray *pm);
-args: pm Pointer to an mxArray of type double
-Returns: Pointer to the first element of the real data. Returns NULL in C (0 in Fortran) if there is no real data.
-****************************************************************
-mxArray *mxCreateNumericArray(mwSize ndim, const mwSize *dims,
-mxClassID classid, mxComplexity ComplexFlag);
-args: ndimNumber of dimensions. If you specify a value for ndim that is less than 2, mxCreateNumericArray automatically sets the number of dimensions to 2.
-dims Dimensions array. Each element in the dimensions array contains the size of the array in that dimension.
-For example, in C, setting dims[0] to 5 and dims[1] to 7 establishes a 5-by-7 mxArray. Usually there are ndim elements in the dims array.
-classid Identifier for the class of the array, which determines the way the numerical data is represented in memory.
-For example, specifying mxINT16_CLASS in C causes each piece of numerical data in the mxArray to be represented as a 16-bit signed integer.
-ComplexFlag  If the mxArray you are creating is to contain imaginary data, set ComplexFlag to mxCOMPLEX in C (1 in Fortran). Otherwise, set ComplexFlag to mxREAL in C (0 in Fortran).
-Returns: Pointer to the created mxArray, if successful. If unsuccessful in a standalone (non-MEX file) application, returns NULL in C (0 in Fortran).
-If unsuccessful in a MEX file, the MEX file terminates and returns control to the MATLAB prompt. The function is unsuccessful when there is not
-enough free heap space to create the mxArray.
-*/
-
-
-
-bp::list SplitBregman_TV(np::ndarray input, double d_mu, int iter, double d_epsil, int methTV) {
-	
-	// the result is in the following list
-	bp::list result;
-		
-	int number_of_dims, dimX, dimY, dimZ, ll, j, count;
-	//const int  *dim_array;
-	float *A, *U = NULL, *U_old = NULL, *Dx = NULL, *Dy = NULL, *Dz = NULL, *Bx = NULL, *By = NULL, *Bz = NULL, lambda, mu, epsil, re, re1, re_old;
-	
-	//number_of_dims = mxGetNumberOfDimensions(prhs[0]);
-	//dim_array = mxGetDimensions(prhs[0]);
-
-	number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-
-	// Parameter handling is be done in Python
-	///*Handling Matlab input data*/
-	//if ((nrhs < 2) || (nrhs > 5)) mexErrMsgTxt("At least 2 parameters is required: Image(2D/3D), Regularization parameter. The full list of parameters: Image(2D/3D), Regularization parameter, iterations number, tolerance, penalty type ('iso' or 'l1')");
-
-	///*Handling Matlab input data*/
-	//A = (float *)mxGetData(prhs[0]); /*noisy image (2D/3D) */
-	A = reinterpret_cast<float *>(input.get_data());
-
-	//mu = (float)mxGetScalar(prhs[1]); /* regularization parameter */
-	mu = (float)d_mu;
-
-	//iter = 35; /* default iterations number */
-	
-	//epsil = 0.0001; /* default tolerance constant */
-	epsil = (float)d_epsil;
-	//methTV = 0;  /* default isotropic TV penalty */
-	//if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5))  iter = (int)mxGetScalar(prhs[2]); /* iterations number */
-	//if ((nrhs == 4) || (nrhs == 5))  epsil = (float)mxGetScalar(prhs[3]); /* tolerance constant */
-	//if (nrhs == 5) {
-	//	char *penalty_type;
-	//	penalty_type = mxArrayToString(prhs[4]); /* choosing TV penalty: 'iso' or 'l1', 'iso' is the default */
-	//	if ((strcmp(penalty_type, "l1") != 0) && (strcmp(penalty_type, "iso") != 0)) mexErrMsgTxt("Choose TV type: 'iso' or 'l1',");
-	//	if (strcmp(penalty_type, "l1") == 0)  methTV = 1;  /* enable 'l1' penalty */
-	//	mxFree(penalty_type);
-	//}
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input image must be in a single precision"); }
-
-	lambda = 2.0f*mu;
-	count = 1;
-	re_old = 0.0f;
-	/*Handling Matlab output data*/
-	dimY = dim_array[0]; dimX = dim_array[1]; dimZ = dim_array[2];
-
-	if (number_of_dims == 2) {
-		dimZ = 1; /*2D case*/
-		//U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		//U_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		//Dx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		//Dy = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		//Bx = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		//By = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-		np::ndarray npU = np::zeros(shape, dtype);
-		np::ndarray npU_old = np::zeros(shape, dtype);
-		np::ndarray npDx = np::zeros(shape, dtype);
-		np::ndarray npDy = np::zeros(shape, dtype);
-		np::ndarray npBx = np::zeros(shape, dtype);
-		np::ndarray npBy = np::zeros(shape, dtype);
-
-		U = reinterpret_cast<float *>(npU.get_data());
-		U_old = reinterpret_cast<float *>(npU_old.get_data());
-		Dx = reinterpret_cast<float *>(npDx.get_data());
-		Dy = reinterpret_cast<float *>(npDy.get_data());
-		Bx = reinterpret_cast<float *>(npBx.get_data());
-		By = reinterpret_cast<float *>(npBy.get_data());
-
-
-
-		copyIm(A, U, dimX, dimY, dimZ); /*initialize */
-
-										/* begin outer SB iterations */
-		for (ll = 0; ll < iter; ll++) {
-
-			/*storing old values*/
-			copyIm(U, U_old, dimX, dimY, dimZ);
-
-			/*GS iteration */
-			gauss_seidel2D(U, A, Dx, Dy, Bx, By, dimX, dimY, lambda, mu);
-
-			if (methTV == 1)  updDxDy_shrinkAniso2D(U, Dx, Dy, Bx, By, dimX, dimY, lambda);
-			else updDxDy_shrinkIso2D(U, Dx, Dy, Bx, By, dimX, dimY, lambda);
-
-			updBxBy2D(U, Dx, Dy, Bx, By, dimX, dimY);
-
-			/* calculate norm to terminate earlier */
-			re = 0.0f; re1 = 0.0f;
-			for (j = 0; j < dimX*dimY*dimZ; j++)
-			{
-				re += pow(U_old[j] - U[j], 2);
-				re1 += pow(U_old[j], 2);
-			}
-			re = sqrt(re) / sqrt(re1);
-			if (re < epsil)  count++;
-			if (count > 4) break;
-
-			/* check that the residual norm is decreasing */
-			if (ll > 2) {
-				if (re > re_old) break;
-			}
-			re_old = re;
-			/*printf("%f %i %i \n", re, ll, count); */
-
-			/*copyIm(U_old, U, dimX, dimY, dimZ); */
-			
-		}
-		//printf("SB iterations stopped at iteration: %i\n", ll);
-		result.append<np::ndarray>(npU);
-		result.append<int>(ll);
-	}
-	if (number_of_dims == 3) {
-			/*U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			U_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			Dx = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			Dy = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			Dz = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			Bx = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			By = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-			Bz = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));*/
-			bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]);
-			np::dtype dtype = np::dtype::get_builtin<float>();
-
-			np::ndarray npU     = np::zeros(shape, dtype);
-			np::ndarray npU_old = np::zeros(shape, dtype);
-			np::ndarray npDx    = np::zeros(shape, dtype);
-			np::ndarray npDy    = np::zeros(shape, dtype);
-			np::ndarray npDz    = np::zeros(shape, dtype);
-			np::ndarray npBx    = np::zeros(shape, dtype);
-			np::ndarray npBy    = np::zeros(shape, dtype);
-			np::ndarray npBz    = np::zeros(shape, dtype);
-
-			U     = reinterpret_cast<float *>(npU.get_data());
-			U_old = reinterpret_cast<float *>(npU_old.get_data());
-			Dx    = reinterpret_cast<float *>(npDx.get_data());
-			Dy    = reinterpret_cast<float *>(npDy.get_data());
-			Dz    = reinterpret_cast<float *>(npDz.get_data());
-			Bx    = reinterpret_cast<float *>(npBx.get_data());
-			By    = reinterpret_cast<float *>(npBy.get_data());
-			Bz    = reinterpret_cast<float *>(npBz.get_data());
-
-			copyIm(A, U, dimX, dimY, dimZ); /*initialize */
-
-											/* begin outer SB iterations */
-			for (ll = 0; ll<iter; ll++) {
-
-				/*storing old values*/
-				copyIm(U, U_old, dimX, dimY, dimZ);
-
-				/*GS iteration */
-				gauss_seidel3D(U, A, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda, mu);
-
-				if (methTV == 1) updDxDyDz_shrinkAniso3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda);
-				else updDxDyDz_shrinkIso3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ, lambda);
-
-				updBxByBz3D(U, Dx, Dy, Dz, Bx, By, Bz, dimX, dimY, dimZ);
-
-				/* calculate norm to terminate earlier */
-				re = 0.0f; re1 = 0.0f;
-				for (j = 0; j<dimX*dimY*dimZ; j++)
-				{
-					re += pow(U[j] - U_old[j], 2);
-					re1 += pow(U[j], 2);
-				}
-				re = sqrt(re) / sqrt(re1);
-				if (re < epsil)  count++;
-				if (count > 4) break;
-
-				/* check that the residual norm is decreasing */
-				if (ll > 2) {
-					if (re > re_old) break;
-				}
-				/*printf("%f %i %i \n", re, ll, count); */
-				re_old = re;
-			}
-			//printf("SB iterations stopped at iteration: %i\n", ll);
-			result.append<np::ndarray>(npU);
-			result.append<int>(ll);
-		}
-	return result;
-
-	}
-
-
-
-bp::list FGP_TV(np::ndarray input, double d_mu, int iter, double d_epsil, int methTV) {
-
-	// the result is in the following list
-	bp::list result;
-
-	int number_of_dims, dimX, dimY, dimZ, ll, j, count;
-	float *A, *D = NULL, *D_old = NULL, *P1 = NULL, *P2 = NULL, *P3 = NULL, *P1_old = NULL, *P2_old = NULL, *P3_old = NULL, *R1 = NULL, *R2 = NULL, *R3 = NULL;
-	float lambda, tk, tkp1, re, re1, re_old, epsil, funcval;
-
-	//number_of_dims = mxGetNumberOfDimensions(prhs[0]);
-	//dim_array = mxGetDimensions(prhs[0]);
-
-	number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-	// Parameter handling is be done in Python
-	///*Handling Matlab input data*/
-	//if ((nrhs < 2) || (nrhs > 5)) mexErrMsgTxt("At least 2 parameters is required: Image(2D/3D), Regularization parameter. The full list of parameters: Image(2D/3D), Regularization parameter, iterations number, tolerance, penalty type ('iso' or 'l1')");
-
-	///*Handling Matlab input data*/
-	//A = (float *)mxGetData(prhs[0]); /*noisy image (2D/3D) */
-	A = reinterpret_cast<float *>(input.get_data());
-
-	//mu = (float)mxGetScalar(prhs[1]); /* regularization parameter */
-	lambda = (float)d_mu;
-
-	//iter = 35; /* default iterations number */
-
-	//epsil = 0.0001; /* default tolerance constant */
-	epsil = (float)d_epsil;
-	//methTV = 0;  /* default isotropic TV penalty */
-	//if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5))  iter = (int)mxGetScalar(prhs[2]); /* iterations number */
-	//if ((nrhs == 4) || (nrhs == 5))  epsil = (float)mxGetScalar(prhs[3]); /* tolerance constant */
-	//if (nrhs == 5) {
-	//	char *penalty_type;
-	//	penalty_type = mxArrayToString(prhs[4]); /* choosing TV penalty: 'iso' or 'l1', 'iso' is the default */
-	//	if ((strcmp(penalty_type, "l1") != 0) && (strcmp(penalty_type, "iso") != 0)) mexErrMsgTxt("Choose TV type: 'iso' or 'l1',");
-	//	if (strcmp(penalty_type, "l1") == 0)  methTV = 1;  /* enable 'l1' penalty */
-	//	mxFree(penalty_type);
-	//}
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input image must be in a single precision"); }
-
-	//plhs[1] = mxCreateNumericMatrix(1, 1, mxSINGLE_CLASS, mxREAL);
-	bp::tuple shape1 = bp::make_tuple(dim_array[0], dim_array[1]);
-	np::dtype dtype = np::dtype::get_builtin<float>();
-	np::ndarray out1 = np::zeros(shape1, dtype);
-	
-	//float *funcvalA = (float *)mxGetData(plhs[1]);
-	float * funcvalA = reinterpret_cast<float *>(out1.get_data());
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input image must be in a single precision"); }
-
-	/*Handling Matlab output data*/
-	dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
-
-	tk = 1.0f;
-	tkp1 = 1.0f;
-	count = 1;
-	re_old = 0.0f;
-
-	if (number_of_dims == 2) {
-		dimZ = 1; /*2D case*/
-		/*D = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		D_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		P1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		P2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		P1_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		P2_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		R1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		R2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));*/
-
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-
-		np::ndarray npD      = np::zeros(shape, dtype);
-		np::ndarray npD_old  = np::zeros(shape, dtype);
-		np::ndarray npP1     = np::zeros(shape, dtype);
-		np::ndarray npP2     = np::zeros(shape, dtype);
-		np::ndarray npP1_old = np::zeros(shape, dtype);
-		np::ndarray npP2_old = np::zeros(shape, dtype);
-		np::ndarray npR1     = np::zeros(shape, dtype);
-		np::ndarray npR2     = np::zeros(shape, dtype);
-
-		D      = reinterpret_cast<float *>(npD.get_data());
-		D_old  = reinterpret_cast<float *>(npD_old.get_data());
-		P1     = reinterpret_cast<float *>(npP1.get_data());
-		P2     = reinterpret_cast<float *>(npP2.get_data());
-		P1_old = reinterpret_cast<float *>(npP1_old.get_data());
-		P2_old = reinterpret_cast<float *>(npP2_old.get_data());
-		R1     = reinterpret_cast<float *>(npR1.get_data());
-		R2     = reinterpret_cast<float *>(npR2.get_data());
-
-		/* begin iterations */
-		for (ll = 0; ll<iter; ll++) {
-			/* computing the gradient of the objective function */
-			Obj_func2D(A, D, R1, R2, lambda, dimX, dimY);
-
-			/*Taking a step towards minus of the gradient*/
-			Grad_func2D(P1, P2, D, R1, R2, lambda, dimX, dimY);
-
-
-
-
-			/*updating R and t*/
-			tkp1 = (1.0f + sqrt(1.0f + 4.0f*tk*tk))*0.5f;
-			Rupd_func2D(P1, P1_old, P2, P2_old, R1, R2, tkp1, tk, dimX, dimY);
-
-			/* calculate norm */
-			re = 0.0f; re1 = 0.0f;
-			for (j = 0; j<dimX*dimY*dimZ; j++)
-			{
-				re += pow(D[j] - D_old[j], 2);
-				re1 += pow(D[j], 2);
-			}
-			re = sqrt(re) / sqrt(re1);
-			if (re < epsil)  count++;
-			if (count > 3) {
-				Obj_func2D(A, D, P1, P2, lambda, dimX, dimY);
-				funcval = 0.0f;
-				for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-				//funcvalA[0] = sqrt(funcval);
-				float fv = sqrt(funcval);
-				std::memcpy(funcvalA, &fv, sizeof(float));
-				break;
-			}
-
-			/* check that the residual norm is decreasing */
-			if (ll > 2) {
-				if (re > re_old) {
-					Obj_func2D(A, D, P1, P2, lambda, dimX, dimY);
-					funcval = 0.0f;
-					for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-					//funcvalA[0] = sqrt(funcval);
-					float fv = sqrt(funcval);
-					std::memcpy(funcvalA, &fv, sizeof(float));
-					break;
-				}
-			}
-			re_old = re;
-			/*printf("%f %i %i \n", re, ll, count); */
-
-			/*storing old values*/
-			copyIm(D, D_old, dimX, dimY, dimZ);
-			copyIm(P1, P1_old, dimX, dimY, dimZ);
-			copyIm(P2, P2_old, dimX, dimY, dimZ);
-			tk = tkp1;
-
-			/* calculating the objective function value */
-			if (ll == (iter - 1)) {
-				Obj_func2D(A, D, P1, P2, lambda, dimX, dimY);
-				funcval = 0.0f;
-				for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-				//funcvalA[0] = sqrt(funcval);
-				float fv = sqrt(funcval);
-				std::memcpy(funcvalA, &fv, sizeof(float));
-			}
-		}
-		//printf("FGP-TV iterations stopped at iteration %i with the function value %f \n", ll, funcvalA[0]);
-		result.append<np::ndarray>(npD);
-		result.append<np::ndarray>(out1);
-		result.append<int>(ll);
-	}
-	if (number_of_dims == 3) {
-		/*D = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		D_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P1 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P2 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P3 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P1_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P2_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		P3_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		R1 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		R2 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		R3 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));*/
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-		
-		np::ndarray npD      = np::zeros(shape, dtype);
-		np::ndarray npD_old  = np::zeros(shape, dtype);
-		np::ndarray npP1     = np::zeros(shape, dtype);
-		np::ndarray npP2     = np::zeros(shape, dtype);
-		np::ndarray npP3     = np::zeros(shape, dtype);
-		np::ndarray npP1_old = np::zeros(shape, dtype);
-		np::ndarray npP2_old = np::zeros(shape, dtype);
-		np::ndarray npP3_old = np::zeros(shape, dtype);
-		np::ndarray npR1     = np::zeros(shape, dtype);
-		np::ndarray npR2     = np::zeros(shape, dtype);
-		np::ndarray npR3     = np::zeros(shape, dtype);
-
-		D      = reinterpret_cast<float *>(npD.get_data());
-		D_old  = reinterpret_cast<float *>(npD_old.get_data());
-		P1     = reinterpret_cast<float *>(npP1.get_data());
-		P2     = reinterpret_cast<float *>(npP2.get_data());
-		P3     = reinterpret_cast<float *>(npP3.get_data());
-		P1_old = reinterpret_cast<float *>(npP1_old.get_data());
-		P2_old = reinterpret_cast<float *>(npP2_old.get_data());
-		P3_old = reinterpret_cast<float *>(npP3_old.get_data());
-		R1     = reinterpret_cast<float *>(npR1.get_data());
-		R2     = reinterpret_cast<float *>(npR2.get_data());
-		R3     = reinterpret_cast<float *>(npR3.get_data());
-		/* begin iterations */
-		for (ll = 0; ll<iter; ll++) {
-			/* computing the gradient of the objective function */
-			Obj_func3D(A, D, R1, R2, R3, lambda, dimX, dimY, dimZ);
-			/*Taking a step towards minus of the gradient*/
-			Grad_func3D(P1, P2, P3, D, R1, R2, R3, lambda, dimX, dimY, dimZ);
-
-			/* projection step */
-			Proj_func3D(P1, P2, P3, dimX, dimY, dimZ);
-
-			/*updating R and t*/
-			tkp1 = (1.0f + sqrt(1.0f + 4.0f*tk*tk))*0.5f;
-			Rupd_func3D(P1, P1_old, P2, P2_old, P3, P3_old, R1, R2, R3, tkp1, tk, dimX, dimY, dimZ);
-
-			/* calculate norm - stopping rules*/
-			re = 0.0f; re1 = 0.0f;
-			for (j = 0; j<dimX*dimY*dimZ; j++)
-			{
-				re += pow(D[j] - D_old[j], 2);
-				re1 += pow(D[j], 2);
-			}
-			re = sqrt(re) / sqrt(re1);
-			/* stop if the norm residual is less than the tolerance EPS */
-			if (re < epsil)  count++;
-			if (count > 3) {
-				Obj_func3D(A, D, P1, P2, P3, lambda, dimX, dimY, dimZ);
-				funcval = 0.0f;
-				for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-				//funcvalA[0] = sqrt(funcval);
-				float fv = sqrt(funcval);
-				std::memcpy(funcvalA, &fv, sizeof(float));
-				break;
-			}
-
-			/* check that the residual norm is decreasing */
-			if (ll > 2) {
-				if (re > re_old) {
-					Obj_func3D(A, D, P1, P2, P3, lambda, dimX, dimY, dimZ);
-					funcval = 0.0f;
-					for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-					//funcvalA[0] = sqrt(funcval);
-					float fv = sqrt(funcval);
-					std::memcpy(funcvalA, &fv, sizeof(float));
-					break;
-				}
-			}
-
-			re_old = re;
-			/*printf("%f %i %i \n", re, ll, count); */
-
-			/*storing old values*/
-			copyIm(D, D_old, dimX, dimY, dimZ);
-			copyIm(P1, P1_old, dimX, dimY, dimZ);
-			copyIm(P2, P2_old, dimX, dimY, dimZ);
-			copyIm(P3, P3_old, dimX, dimY, dimZ);
-			tk = tkp1;
-
-			if (ll == (iter - 1)) {
-				Obj_func3D(A, D, P1, P2, P3, lambda, dimX, dimY, dimZ);
-				funcval = 0.0f;
-				for (j = 0; j<dimX*dimY*dimZ; j++) funcval += pow(D[j], 2);
-				//funcvalA[0] = sqrt(funcval);
-				float fv = sqrt(funcval);
-				std::memcpy(funcvalA, &fv, sizeof(float));
-			}
-
-		}
-		//printf("FGP-TV iterations stopped at iteration %i with the function value %f \n", ll, funcvalA[0]);
-		result.append<np::ndarray>(npD);
-		result.append<np::ndarray>(out1);
-		result.append<int>(ll);
-	}
-
-	return result;
-}
-
-bp::list LLT_model(np::ndarray input, double d_lambda, double d_tau, int iter, double d_epsil, int switcher) {
-	// the result is in the following list
-	bp::list result;
-
-	int number_of_dims, dimX, dimY, dimZ, ll, j, count;
-	//const int  *dim_array;
-	float *U0, *U = NULL, *U_old = NULL, *D1 = NULL, *D2 = NULL, *D3 = NULL, lambda, tau, re, re1, epsil, re_old;
-	unsigned short *Map = NULL;
-
-	number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-
-	///*Handling Matlab input data*/
-	//U0 = (float *)mxGetData(prhs[0]); /*origanal noise image/volume*/
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input in single precision is required"); }
-	//lambda = (float)mxGetScalar(prhs[1]); /*regularization parameter*/
-	//tau = (float)mxGetScalar(prhs[2]); /* time-step */
-	//iter = (int)mxGetScalar(prhs[3]); /*iterations number*/
-	//epsil = (float)mxGetScalar(prhs[4]); /* tolerance constant */
-	//switcher = (int)mxGetScalar(prhs[5]); /*switch on (1) restrictive smoothing in Z dimension*/
-	
-	U0 = reinterpret_cast<float *>(input.get_data());
-	lambda = (float)d_lambda;
-	tau = (float)d_tau;
-	// iter is passed as parameter
-	epsil = (float)d_epsil;
-	// switcher is passed as parameter
-										  /*Handling Matlab output data*/
-	dimX = dim_array[0]; dimY = dim_array[1];  dimZ = 1;
-
-	if (number_of_dims == 2) {
-		/*2D case*/
-		/*U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		U_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		D1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		D2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));*/
-
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-
-		np::ndarray npU = np::zeros(shape, dtype);
-		np::ndarray npU_old = np::zeros(shape, dtype);
-		np::ndarray npD1 = np::zeros(shape, dtype);
-		np::ndarray npD2 = np::zeros(shape, dtype);
-		
-
-		U = reinterpret_cast<float *>(npU.get_data());
-		U_old = reinterpret_cast<float *>(npU_old.get_data());
-		D1 = reinterpret_cast<float *>(npD1.get_data());
-		D2 = reinterpret_cast<float *>(npD2.get_data());
-		
-		/*Copy U0 to U*/
-		copyIm(U0, U, dimX, dimY, dimZ);
-
-		count = 1;
-		re_old = 0.0f;
-
-		for (ll = 0; ll < iter; ll++) {
-
-			copyIm(U, U_old, dimX, dimY, dimZ);
-
-			/*estimate inner derrivatives */
-			der2D(U, D1, D2, dimX, dimY, dimZ);
-			/* calculate div^2 and update */
-			div_upd2D(U0, U, D1, D2, dimX, dimY, dimZ, lambda, tau);
-
-			/* calculate norm to terminate earlier */
-			re = 0.0f; re1 = 0.0f;
-			for (j = 0; j<dimX*dimY*dimZ; j++)
-			{
-				re += pow(U_old[j] - U[j], 2);
-				re1 += pow(U_old[j], 2);
-			}
-			re = sqrt(re) / sqrt(re1);
-			if (re < epsil)  count++;
-			if (count > 4) break;
-
-			/* check that the residual norm is decreasing */
-			if (ll > 2) {
-				if (re > re_old) break;
-			}
-			re_old = re;
-
-		} /*end of iterations*/
-		  //printf("HO iterations stopped at iteration: %i\n", ll);
-
-		result.append<np::ndarray>(npU);
-	}
-	else if (number_of_dims == 3) {
-		/*3D case*/
-		dimZ = dim_array[2];
-		/*U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		U_old = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		D1 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		D2 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		D3 = (float*)mxGetPr(mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
-		if (switcher != 0) {
-			Map = (unsigned short*)mxGetPr(plhs[1] = mxCreateNumericArray(3, dim_array, mxUINT16_CLASS, mxREAL));
-		}*/
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1], dim_array[2]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-
-		np::ndarray npU = np::zeros(shape, dtype);
-		np::ndarray npU_old = np::zeros(shape, dtype);
-		np::ndarray npD1 = np::zeros(shape, dtype);
-		np::ndarray npD2 = np::zeros(shape, dtype);
-		np::ndarray npD3 = np::zeros(shape, dtype);
-		np::ndarray npMap = np::zeros(shape, np::dtype::get_builtin<unsigned short>());
-		Map = reinterpret_cast<unsigned short *>(npMap.get_data());
-		if (switcher != 0) {
-			//Map = (unsigned short*)mxGetPr(plhs[1] = mxCreateNumericArray(3, dim_array, mxUINT16_CLASS, mxREAL));
-			
-			Map = reinterpret_cast<unsigned short *>(npMap.get_data());
-		}
-
-		U = reinterpret_cast<float *>(npU.get_data());
-		U_old = reinterpret_cast<float *>(npU_old.get_data());
-		D1 = reinterpret_cast<float *>(npD1.get_data());
-		D2 = reinterpret_cast<float *>(npD2.get_data());
-		D3 = reinterpret_cast<float *>(npD2.get_data());
-		
-		/*Copy U0 to U*/
-		copyIm(U0, U, dimX, dimY, dimZ);
-
-		count = 1;
-		re_old = 0.0f;
-	
-
-		if (switcher == 1) {
-			/* apply restrictive smoothing */
-			calcMap(U, Map, dimX, dimY, dimZ);
-			/*clear outliers */
-			cleanMap(Map, dimX, dimY, dimZ);
-		}
-		for (ll = 0; ll < iter; ll++) {
-
-			copyIm(U, U_old, dimX, dimY, dimZ);
-
-			/*estimate inner derrivatives */
-			der3D(U, D1, D2, D3, dimX, dimY, dimZ);
-			/* calculate div^2 and update */
-			div_upd3D(U0, U, D1, D2, D3, Map, switcher, dimX, dimY, dimZ, lambda, tau);
-
-			/* calculate norm to terminate earlier */
-			re = 0.0f; re1 = 0.0f;
-			for (j = 0; j<dimX*dimY*dimZ; j++)
-			{
-				re += pow(U_old[j] - U[j], 2);
-				re1 += pow(U_old[j], 2);
-			}
-			re = sqrt(re) / sqrt(re1);
-			if (re < epsil)  count++;
-			if (count > 4) break;
-
-			/* check that the residual norm is decreasing */
-			if (ll > 2) {
-				if (re > re_old) break;
-			}
-			re_old = re;
-
-		} /*end of iterations*/
-		//printf("HO iterations stopped at iteration: %i\n", ll);
-		result.append<np::ndarray>(npU);
-		if (switcher != 0) result.append<np::ndarray>(npMap);
-
-	}
-	return result;
-}
-
-
-bp::list PatchBased_Regul(np::ndarray input, double d_lambda, int SearchW_real, int SimilW,  double d_h) {
-	// the result is in the following list
-	bp::list result;
-
-	int N, M, Z, numdims, SearchW, /*SimilW, SearchW_real,*/ padXY, newsizeX, newsizeY, newsizeZ, switchpad_crop;
-	//const int  *dims;
-	float *A, *B = NULL, *Ap = NULL, *Bp = NULL, h, lambda;
-
-	numdims = input.get_nd();
-	int dims[3];
-
-	dims[0] = input.shape(0);
-	dims[1] = input.shape(1);
-	if (numdims == 2) {
-		dims[2] = -1;
-	}
-	else {
-		dims[2] = input.shape(2);
-	}
-	/*numdims = mxGetNumberOfDimensions(prhs[0]);
-	dims = mxGetDimensions(prhs[0]);*/
-
-	N = dims[0];
-	M = dims[1];
-	Z = dims[2];
-
-	//if ((numdims < 2) || (numdims > 3)) { mexErrMsgTxt("The input should be 2D image or 3D volume"); }
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input in single precision is required"); }
-
-	//if (nrhs != 5) mexErrMsgTxt("Five inputs reqired: Image(2D,3D), SearchW, SimilW, Threshold, Regularization parameter");
-
-	///*Handling inputs*/
-	//A = (float *)mxGetData(prhs[0]);    /* the image to regularize/filter */
-	A = reinterpret_cast<float *>(input.get_data());
-	//SearchW_real = (int)mxGetScalar(prhs[1]); /* the searching window ratio */
-	//SimilW = (int)mxGetScalar(prhs[2]);  /* the similarity window ratio */
-	//h = (float)mxGetScalar(prhs[3]);  /* parameter for the PB filtering function */
-	//lambda = (float)mxGetScalar(prhs[4]); /* regularization parameter */
-
-	//if (h <= 0) mexErrMsgTxt("Parmeter for the PB penalty function should be > 0");
-	//if (lambda <= 0) mexErrMsgTxt(" Regularization parmeter should be > 0");
-
-	lambda = (float)d_lambda;
-	h = (float)d_h;
-	SearchW = SearchW_real + 2 * SimilW;
-
-	/* SearchW_full = 2*SearchW + 1; */ /* the full searching window  size */
-										/* SimilW_full = 2*SimilW + 1;  */  /* the full similarity window  size */
-
-
-	padXY = SearchW + 2 * SimilW; /* padding sizes */
-	newsizeX = N + 2 * (padXY); /* the X size of the padded array */
-	newsizeY = M + 2 * (padXY); /* the Y size of the padded array */
-	newsizeZ = Z + 2 * (padXY); /* the Z size of the padded array */
-	int N_dims[] = { newsizeX, newsizeY, newsizeZ };
-	/******************************2D case ****************************/
-	if (numdims == 2) {
-		///*Handling output*/
-		//B = (float*)mxGetData(plhs[0] = mxCreateNumericMatrix(N, M, mxSINGLE_CLASS, mxREAL));
-		///*allocating memory for the padded arrays */
-		//Ap = (float*)mxGetData(mxCreateNumericMatrix(newsizeX, newsizeY, mxSINGLE_CLASS, mxREAL));
-		//Bp = (float*)mxGetData(mxCreateNumericMatrix(newsizeX, newsizeY, mxSINGLE_CLASS, mxREAL));
-		///**************************************************************************/
-
-		bp::tuple shape = bp::make_tuple(N, M);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-		np::ndarray npB = np::zeros(shape, dtype);
-
-		shape = bp::make_tuple(newsizeX, newsizeY);
-		np::ndarray npAp = np::zeros(shape, dtype);
-		np::ndarray npBp = np::zeros(shape, dtype);
-		B = reinterpret_cast<float *>(npB.get_data());
-		Ap = reinterpret_cast<float *>(npAp.get_data());
-		Bp = reinterpret_cast<float *>(npBp.get_data());		
-
-		/*Perform padding of image A to the size of [newsizeX * newsizeY] */
-		switchpad_crop = 0; /*padding*/
-		pad_crop(A, Ap, M, N, 0, newsizeY, newsizeX, 0, padXY, switchpad_crop);
-		
-		/* Do PB regularization with the padded array  */
-		PB_FUNC2D(Ap, Bp, newsizeY, newsizeX, padXY, SearchW, SimilW, (float)h, (float)lambda);
-		
-		switchpad_crop = 1; /*cropping*/
-		pad_crop(Bp, B, M, N, 0, newsizeY, newsizeX, 0, padXY, switchpad_crop);
-		
-		result.append<np::ndarray>(npB);
-	}
-	else
-	{
-		/******************************3D case ****************************/
-		///*Handling output*/
-		//B = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL));
-		///*allocating memory for the padded arrays */
-		//Ap = (float*)mxGetPr(mxCreateNumericArray(3, N_dims, mxSINGLE_CLASS, mxREAL));
-		//Bp = (float*)mxGetPr(mxCreateNumericArray(3, N_dims, mxSINGLE_CLASS, mxREAL));
-		/**************************************************************************/
-		bp::tuple shape = bp::make_tuple(dims[0], dims[1], dims[2]);
-		bp::tuple shape_AB = bp::make_tuple(N_dims[0], N_dims[1], N_dims[2]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-		np::ndarray npB = np::zeros(shape, dtype);
-		np::ndarray npAp = np::zeros(shape_AB, dtype);
-		np::ndarray npBp = np::zeros(shape_AB, dtype);
-		B = reinterpret_cast<float *>(npB.get_data());
-		Ap = reinterpret_cast<float *>(npAp.get_data());
-		Bp = reinterpret_cast<float *>(npBp.get_data());
-		/*Perform padding of image A to the size of [newsizeX * newsizeY * newsizeZ] */
-		switchpad_crop = 0; /*padding*/
-		pad_crop(A, Ap, M, N, Z, newsizeY, newsizeX, newsizeZ, padXY, switchpad_crop);
-
-		/* Do PB regularization with the padded array  */
-		PB_FUNC3D(Ap, Bp, newsizeY, newsizeX, newsizeZ, padXY, SearchW, SimilW, (float)h, (float)lambda);
-
-		switchpad_crop = 1; /*cropping*/
-		pad_crop(Bp, B, M, N, Z, newsizeY, newsizeX, newsizeZ, padXY, switchpad_crop);
-
-		result.append<np::ndarray>(npB);
-	} /*end else ndims*/
-
-	return result;
-}
-
-bp::list TGV_PD(np::ndarray input, double d_lambda, double d_alpha1, double d_alpha0, int iter) {
-	// the result is in the following list
-	bp::list result;
-	int number_of_dims, /*iter,*/ dimX, dimY, dimZ, ll;
-	//const int  *dim_array;
-	float *A, *U, *U_old, *P1, *P2, *Q1, *Q2, *Q3, *V1, *V1_old, *V2, *V2_old, lambda, L2, tau, sigma, alpha1, alpha0;
-
-	//number_of_dims = mxGetNumberOfDimensions(prhs[0]);
-	//dim_array = mxGetDimensions(prhs[0]);
-	number_of_dims = input.get_nd();
-	int dim_array[3];
-
-	dim_array[0] = input.shape(0);
-	dim_array[1] = input.shape(1);
-	if (number_of_dims == 2) {
-		dim_array[2] = -1;
-	}
-	else {
-		dim_array[2] = input.shape(2);
-	}
-	/*Handling Matlab input data*/
-	//A = (float *)mxGetData(prhs[0]); /*origanal noise image/volume*/
-	//if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) { mexErrMsgTxt("The input in single precision is required"); }
-	
-	A = reinterpret_cast<float *>(input.get_data());
-
-	//lambda = (float)mxGetScalar(prhs[1]); /*regularization parameter*/
-	//alpha1 = (float)mxGetScalar(prhs[2]); /*first-order term*/
-	//alpha0 = (float)mxGetScalar(prhs[3]); /*second-order term*/
-	//iter = (int)mxGetScalar(prhs[4]); /*iterations number*/
-	//if (nrhs != 5) mexErrMsgTxt("Five input parameters is reqired: Image(2D/3D), Regularization parameter, alpha1, alpha0, Iterations");
-	lambda = (float)d_lambda;
-	alpha1 = (float)d_alpha1;
-	alpha0 = (float)d_alpha0;
-
-	/*Handling Matlab output data*/
-	dimX = dim_array[0]; dimY = dim_array[1];
-
-	if (number_of_dims == 2) {
-		/*2D case*/
-		dimZ = 1;
-		bp::tuple shape = bp::make_tuple(dim_array[0], dim_array[1]);
-		np::dtype dtype = np::dtype::get_builtin<float>();
-
-		np::ndarray npU = np::zeros(shape, dtype);
-		np::ndarray npP1 = np::zeros(shape, dtype);
-		np::ndarray npP2 = np::zeros(shape, dtype);
-		np::ndarray npQ1 = np::zeros(shape, dtype);
-		np::ndarray npQ2 = np::zeros(shape, dtype);
-		np::ndarray npQ3 = np::zeros(shape, dtype);
-		np::ndarray npV1 = np::zeros(shape, dtype);
-		np::ndarray npV1_old = np::zeros(shape, dtype);
-		np::ndarray npV2 = np::zeros(shape, dtype);
-		np::ndarray npV2_old = np::zeros(shape, dtype);
-		np::ndarray npU_old = np::zeros(shape, dtype);
-
-		U = reinterpret_cast<float *>(npU.get_data());
-		U_old = reinterpret_cast<float *>(npU_old.get_data());
-		P1 = reinterpret_cast<float *>(npP1.get_data());
-		P2 = reinterpret_cast<float *>(npP2.get_data());
-		Q1 = reinterpret_cast<float *>(npQ1.get_data());
-		Q2 = reinterpret_cast<float *>(npQ2.get_data());
-		Q3 = reinterpret_cast<float *>(npQ3.get_data());
-		V1 = reinterpret_cast<float *>(npV1.get_data());
-		V1_old = reinterpret_cast<float *>(npV1_old.get_data());
-		V2 = reinterpret_cast<float *>(npV2.get_data());
-		V2_old = reinterpret_cast<float *>(npV2_old.get_data());
-		//U = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-
-		/*dual variables*/
-		/*P1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		P2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-
-		Q1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		Q2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		Q3 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-
-		U_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-
-		V1 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		V1_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		V2 = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
-		V2_old = (float*)mxGetPr(mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));*/
-		/*printf("%i \n", i);*/
-		L2 = 12.0; /*Lipshitz constant*/
-		tau = 1.0 / pow(L2, 0.5);
-		sigma = 1.0 / pow(L2, 0.5);
-
-		/*Copy A to U*/
-		copyIm(A, U, dimX, dimY, dimZ);
-		/* Here primal-dual iterations begin for 2D */
-		for (ll = 0; ll < iter; ll++) {
-
-			/* Calculate Dual Variable P */
-			DualP_2D(U, V1, V2, P1, P2, dimX, dimY, dimZ, sigma);
-
-			/*Projection onto convex set for P*/
-			ProjP_2D(P1, P2, dimX, dimY, dimZ, alpha1);
-
-			/* Calculate Dual Variable Q */
-			DualQ_2D(V1, V2, Q1, Q2, Q3, dimX, dimY, dimZ, sigma);
-
-			/*Projection onto convex set for Q*/
-			ProjQ_2D(Q1, Q2, Q3, dimX, dimY, dimZ, alpha0);
-
-			/*saving U into U_old*/
-			copyIm(U, U_old, dimX, dimY, dimZ);
-
-			/*adjoint operation  -> divergence and projection of P*/
-			DivProjP_2D(U, A, P1, P2, dimX, dimY, dimZ, lambda, tau);
-
-			/*get updated solution U*/
-			newU(U, U_old, dimX, dimY, dimZ);
-
-			/*saving V into V_old*/
-			copyIm(V1, V1_old, dimX, dimY, dimZ);
-			copyIm(V2, V2_old, dimX, dimY, dimZ);
-
-			/* upd V*/
-			UpdV_2D(V1, V2, P1, P2, Q1, Q2, Q3, dimX, dimY, dimZ, tau);
-
-			/*get new V*/
-			newU(V1, V1_old, dimX, dimY, dimZ);
-			newU(V2, V2_old, dimX, dimY, dimZ);
-		} /*end of iterations*/
-	
-		result.append<np::ndarray>(npU);
-	}
-	
-
-	
-	
-	return result;
-}
-
-BOOST_PYTHON_MODULE(cpu_regularizers)
-{
-	np::initialize();
-
-	//To specify that this module is a package
-	bp::object package = bp::scope();
-	package.attr("__path__") = "cpu_regularizers";
-
-	np::dtype dt1 = np::dtype::get_builtin<uint8_t>();
-	np::dtype dt2 = np::dtype::get_builtin<uint16_t>();
-
-	def("SplitBregman_TV", SplitBregman_TV);
-	def("FGP_TV", FGP_TV);
-	def("LLT_model", LLT_model);
-	def("PatchBased_Regul", PatchBased_Regul);
-	def("TGV_PD", TGV_PD);
-}
diff --git a/src/Python/setup-fista.py.in b/src/Python/setup-fista.py.in
deleted file mode 100644
index c5c9f4d..0000000
--- a/src/Python/setup-fista.py.in
+++ /dev/null
@@ -1,27 +0,0 @@
-from distutils.core import setup
-#from setuptools import setup, find_packages
-import os
-
-cil_version=os.environ['CIL_VERSION']
-if  cil_version == '':
-    print("Please set the environmental variable CIL_VERSION")
-    sys.exit(1)
-
-setup(
-    name="ccpi-fista",
-    version=cil_version,
-    packages=['ccpi','ccpi.reconstruction'],
-	install_requires=['numpy'],
-
-     zip_safe = False,
-
-    # metadata for upload to PyPI
-    author="Edoardo Pasca",
-    author_email="edo.paskino@gmail.com",
-    description='CCPi Core Imaging Library - FISTA Reconstructor module',
-    license="Apache v2.0",
-    keywords="tomography interative reconstruction",
-    url="http://www.ccpi.ac.uk",   # project home page, if any
-
-    # could also include long_description, download_url, classifiers, etc.
-)
diff --git a/src/Python/setup.py b/src/Python/setup.py
deleted file mode 100644
index 154f979..0000000
--- a/src/Python/setup.py
+++ /dev/null
@@ -1,64 +0,0 @@
-#!/usr/bin/env python
-
-import setuptools
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-
-import os
-import sys
-import numpy
-import platform	
-
-cil_version=os.environ['CIL_VERSION']
-if  cil_version == '':
-    print("Please set the environmental variable CIL_VERSION")
-    sys.exit(1)
-
-library_include_path = ""
-library_lib_path = ""
-try:
-    library_include_path = os.environ['LIBRARY_INC']
-    library_lib_path = os.environ['LIBRARY_LIB']
-except:
-    library_include_path = os.environ['PREFIX']+'/include'
-    pass
-    
-extra_include_dirs = [numpy.get_include(), library_include_path]
-extra_library_dirs = [library_include_path+"/../lib", "C:\\Apps\\Miniconda2\\envs\\cil27\\Library\\lib"]
-extra_compile_args = ['-fopenmp','-O2', '-funsigned-char', '-Wall', '-std=c++0x']
-extra_libraries = []
-if platform.system() == 'Windows':
-    extra_compile_args[0:] = ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB' , '/openmp' ]   
-    extra_include_dirs += ["..\\..\\main_func\\regularizers_CPU\\","."]
-    if sys.version_info.major == 3 :   
-        extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64']
-    else:
-        extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64']
-else:
-    extra_include_dirs += ["../../main_func/regularizers_CPU","."]
-    if sys.version_info.major == 3:
-        extra_libraries += ['boost_python3', 'boost_numpy3','gomp']
-    else:
-        extra_libraries += ['boost_python', 'boost_numpy','gomp']
-
-setup(
-    name='ccpi',
-	description='CCPi Core Imaging Library - FISTA Reconstruction Module',
-	version=cil_version,
-    cmdclass = {'build_ext': build_ext},
-    ext_modules = [Extension("ccpi.imaging.cpu_regularizers",
-                             sources=["fista_module.cpp",
-                                      "../../main_func/regularizers_CPU/FGP_TV_core.c",
-                                      "../../main_func/regularizers_CPU/SplitBregman_TV_core.c",
-                                      "../../main_func/regularizers_CPU/LLT_model_core.c",
-                                      "../../main_func/regularizers_CPU/PatchBased_Regul_core.c",
-                                      "../../main_func/regularizers_CPU/TGV_PD_core.c",
-                                      "../../main_func/regularizers_CPU/utils.c"
-                                        ],
-                             include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries ), 
-    
-    ],
-	zip_safe = False,	
-	packages = {'ccpi','ccpi.fistareconstruction'},
-)
diff --git a/src/Python/setup.py.in b/src/Python/setup.py.in
deleted file mode 100644
index 12e8af1..0000000
--- a/src/Python/setup.py.in
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/usr/bin/env python
-
-import setuptools
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-
-import os
-import sys
-import numpy
-import platform	
-
-cil_version=@CIL_VERSION@
-
-library_include_path = ""
-library_lib_path = ""
-try:
-    library_include_path = os.environ['LIBRARY_INC']
-    library_lib_path = os.environ['LIBRARY_LIB']
-except:
-    library_include_path = os.environ['PREFIX']+'/include'
-    pass
-    
-extra_include_dirs = [numpy.get_include(), library_include_path]
-extra_library_dirs = [os.path.join(library_include_path, "..", "lib")]
-extra_compile_args = ['-fopenmp','-O2', '-funsigned-char', '-Wall', '-std=c++0x']
-extra_libraries = []
-extra_include_dirs += [os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU"),
-                       	   os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_GPU") , 
-						   "@CMAKE_CURRENT_SOURCE_DIR@"]
-						   
-if platform.system() == 'Windows':
-    extra_compile_args[0:] = ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB' , '/openmp' ]   
-    
-    if sys.version_info.major == 3 :   
-        extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64']
-    else:
-        extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64']
-else:
-    if sys.version_info.major == 3:
-        extra_libraries += ['boost_python3', 'boost_numpy3','gomp']
-    else:
-        extra_libraries += ['boost_python', 'boost_numpy','gomp']
-
-setup(
-    name='ccpi',
-	description='CCPi Core Imaging Library - Image Regularizers',
-	version=cil_version,
-    cmdclass = {'build_ext': build_ext},
-    ext_modules = [Extension("ccpi.imaging.cpu_regularizers",
-                             sources=[os.path.join("@CMAKE_CURRENT_SOURCE_DIR@" , "fista_module.cpp" ),
-                                      os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "FGP_TV_core.c"),
-									  os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "SplitBregman_TV_core.c"),
-									  os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "LLT_model_core.c"),
-									  os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "PatchBased_Regul_core.c"),
-									  os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "TGV_PD_core.c"),
-									  os.path.join("@CMAKE_SOURCE_DIR@" , "main_func" ,  "regularizers_CPU", "utils.c")
-                                        ],
-                             include_dirs=extra_include_dirs, 
-							 library_dirs=extra_library_dirs, 
-							 extra_compile_args=extra_compile_args, 
-							 libraries=extra_libraries ), 
-    
-    ],
-	zip_safe = False,	
-	packages = {'ccpi','ccpi.imaging'},
-)
-
-
diff --git a/src/Python/setup_test.py b/src/Python/setup_test.py
deleted file mode 100644
index 7c86175..0000000
--- a/src/Python/setup_test.py
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env python
-
-import setuptools
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-
-import os
-import sys
-import numpy
-import platform	
-
-cil_version=os.environ['CIL_VERSION']
-if  cil_version == '':
-    print("Please set the environmental variable CIL_VERSION")
-    sys.exit(1)
-
-library_include_path = ""
-library_lib_path = ""
-try:
-    library_include_path = os.environ['LIBRARY_INC']
-    library_lib_path = os.environ['LIBRARY_LIB']
-except:
-    library_include_path = os.environ['PREFIX']+'/include'
-    pass
-    
-extra_include_dirs = [numpy.get_include(), library_include_path]
-extra_library_dirs = [library_include_path+"/../lib", "C:\\Apps\\Miniconda2\\envs\\cil27\\Library\\lib"]
-extra_compile_args = ['-fopenmp','-O2', '-funsigned-char', '-Wall', '-std=c++0x']
-extra_libraries = []
-if platform.system() == 'Windows':
-    extra_compile_args[0:] = ['/DWIN32','/EHsc','/DBOOST_ALL_NO_LIB']   
-    #extra_include_dirs += ["..\\ContourTree\\", "..\\win32\\" , "..\\Core\\","."]
-    if sys.version_info.major == 3 :   
-        extra_libraries += ['boost_python3-vc140-mt-1_64', 'boost_numpy3-vc140-mt-1_64']
-    else:
-        extra_libraries += ['boost_python-vc90-mt-1_64', 'boost_numpy-vc90-mt-1_64']
-else:
-    #extra_include_dirs += ["../ContourTree/", "../Core/","."]
-    if sys.version_info.major == 3:
-        extra_libraries += ['boost_python3', 'boost_numpy3','gomp']
-    else:
-        extra_libraries += ['boost_python', 'boost_numpy','gomp']
-
-setup(
-    name='ccpi',
-	description='CCPi Core Imaging Library - FISTA Reconstruction Module',
-	version=cil_version,
-    cmdclass = {'build_ext': build_ext},
-    ext_modules = [Extension("prova",
-                             sources=[  "Matlab2Python_utils.cpp",
-                                        ],
-                             include_dirs=extra_include_dirs, library_dirs=extra_library_dirs, extra_compile_args=extra_compile_args, libraries=extra_libraries ), 
-    
-    ],
-	zip_safe = False,	
-	packages = {'ccpi','ccpi.reconstruction'},
-)
diff --git a/src/Python/test.py b/src/Python/test.py
deleted file mode 100644
index db47380..0000000
--- a/src/Python/test.py
+++ /dev/null
@@ -1,42 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Thu Aug  3 14:08:09 2017
-
-@author: ofn77899
-"""
-
-import prova
-import numpy as np
-
-a = np.asarray([i for i in range(1*2*3)])
-a = a.reshape([1,2,3])
-print (a)
-b = prova.mexFunction(a)
-#print (b)
-print (b[4].shape)
-print (b[4])
-print (b[5])
-
-def print_element(input):
-	print ("f: {0}".format(input))
-	
-prova.doSomething(a, print_element, None)
-
-c = []
-def append_to_list(input, shouldPrint=False):
-	c.append(input)
-	if shouldPrint:
-		print ("{0} appended to list {1}".format(input, c))
-
-def element_wise_algebra(input, shouldPrint=True):
-	ret = input - 7
-	if shouldPrint:
-		print ("element_wise {0}".format(ret))
-	return ret
-		
-prova.doSomething(a, append_to_list, None)
-#print ("this is c: {0}".format(c))
-
-b = prova.doSomething(a, None, element_wise_algebra)
-#print (a)
-print (b[5])
diff --git a/src/Python/test/astra_test.py b/src/Python/test/astra_test.py
deleted file mode 100644
index 42c375a..0000000
--- a/src/Python/test/astra_test.py
+++ /dev/null
@@ -1,85 +0,0 @@
-import astra
-import numpy
-import filefun
-
-
-# read in the same data as the DemoRD2
-angles = filefun.dlmread("DemoRD2/angles.csv")
-darks_ar = filefun.dlmread("DemoRD2/darks_ar.csv", separator=",")
-flats_ar = filefun.dlmread("DemoRD2/flats_ar.csv", separator=",")
-
-if True:
-    Sino3D = numpy.load("DemoRD2/Sino3D.npy")
-else:
-    sino = filefun.dlmread("DemoRD2/sino_01.csv", separator=",")
-    a = map (lambda x:x, numpy.shape(sino))
-    a.append(20)
-
-    Sino3D = numpy.zeros(tuple(a), dtype="float")
-
-    for i in range(1,numpy.shape(Sino3D)[2]+1):
-        print("Read file DemoRD2/sino_%02d.csv" % i)
-        sino = filefun.dlmread("DemoRD2/sino_%02d.csv" % i, separator=",")
-        Sino3D.T[i-1] = sino.T
-    
-Weights3D = numpy.asarray(Sino3D, dtype="float")
-
-##angles_rad = angles*(pi/180); % conversion to radians
-##size_det = size(data_raw3D,1); % detectors dim
-##angSize = size(data_raw3D, 2); % angles dim
-##slices_tot = size(data_raw3D, 3); % no of slices
-##recon_size = 950; % reconstruction size
-
-
-angles_rad = angles * numpy.pi /180.
-size_det, angSize, slices_tot = numpy.shape(Sino3D)
-size_det, angSize, slices_tot = [int(i) for i in numpy.shape(Sino3D)]
-recon_size = 950
-Z_slices = 3;
-det_row_count = Z_slices;
-
-#proj_geom = astra_create_proj_geom('parallel3d', 1, 1,
-# det_row_count, size_det, angles_rad);
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-proj_geom = astra.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            size_det,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-vol_geom = astra.create_vol_geom(recon_size,recon_size,Z_slices);
-
-sino = numpy.zeros((size_det, angSize, slices_tot), dtype="float")
-
-#weights = ones(size(sino));
-weights = numpy.ones(numpy.shape(sino))
-
-#####################################################################
-## PowerMethod for Lipschitz constant
-
-N = vol_geom['GridColCount']
-x1 = numpy.random.rand(1,N,N)
-#sqweight = sqrt(weights(:,:,1));
-sqweight = numpy.sqrt(weights.T[0]).T
-##proj_geomT = proj_geom;
-proj_geomT = proj_geom.copy()
-##proj_geomT.DetectorRowCount = 1;
-proj_geomT['DetectorRowCount'] = 1
-##vol_geomT = vol_geom;
-vol_geomT = vol_geom.copy()
-##vol_geomT.GridSliceCount = 1;
-vol_geomT['GridSliceCount'] = 1
-
-##[sino_id, y] = astra_create_sino3d_cuda(x1, proj_geomT, vol_geomT);
-
-#sino_id, y = astra.create_sino3d_gpu(x1, proj_geomT, vol_geomT);
-sino_id, y = astra.create_sino(x1, proj_geomT, vol_geomT);
-
-##y = sqweight.*y;
-##astra_mex_data3d('delete', sino_id);
-        
-
diff --git a/src/Python/test/create_phantom_projections.py b/src/Python/test/create_phantom_projections.py
deleted file mode 100644
index 20a9278..0000000
--- a/src/Python/test/create_phantom_projections.py
+++ /dev/null
@@ -1,49 +0,0 @@
-from ccpi.reconstruction.AstraDevice import AstraDevice
-from ccpi.reconstruction.DeviceModel import DeviceModel
-import h5py
-import numpy
-import matplotlib.pyplot as plt
-
-nx = h5py.File('phant3D_256.h5', "r")
-phantom = numpy.asarray(nx.get('/dataset1'))
-pX,pY,pZ = numpy.shape(phantom)
-
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nxa = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nxa['/'].keys()]
-print (entries)
-
-angles_rad = numpy.asarray(nxa.get('/angles_rad'), dtype="float32")
-
-
-device = AstraDevice(
-    DeviceModel.DeviceType.PARALLEL3D.value,
-    [ pX , pY , 1., 1., angles_rad],
-    [ pX, pY, pZ ] )
-
-
-proj = device.doForwardProject(phantom)
-stack = [proj[:,i,:] for i in range(len(angles_rad))]
-stack = numpy.asarray(stack)
-
-
-fig = plt.figure()
-a=fig.add_subplot(1,2,1)
-a.set_title('proj')
-imgplot = plt.imshow(proj[:,100,:])
-a=fig.add_subplot(1,2,2)
-a.set_title('stack')
-imgplot = plt.imshow(stack[100])
-plt.show()
-
-pf = h5py.File("phantom3D256_projections.h5" , "w")
-pf.create_dataset("/projections", data=stack)
-pf.create_dataset("/sinogram", data=proj)
-pf.create_dataset("/angles", data=angles_rad)
-pf.create_dataset("/reconstruction_volume" , data=numpy.asarray([pX, pY, pZ]))
-pf.create_dataset("/camera/size" , data=numpy.asarray([pX , pY ]))
-pf.create_dataset("/camera/spacing" , data=numpy.asarray([1.,1.]))
-pf.flush()
-pf.close()
diff --git a/src/Python/test/readhd5.py b/src/Python/test/readhd5.py
deleted file mode 100644
index eff6c43..0000000
--- a/src/Python/test/readhd5.py
+++ /dev/null
@@ -1,42 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-"""
-
-import h5py
-import numpy
-
-def getEntry(nx, location):
-    for item in nx[location].keys():
-        print (item)
-        
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-Sino3D = numpy.asarray(nx.get('/Sino3D'))
-Weights3D = numpy.asarray(nx.get('/Weights3D'))
-angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles_rad'))
-recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0]
-size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0]
-
-slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-
-#from ccpi.viewer.CILViewer2D import CILViewer2D
-#v = CILViewer2D()
-#v.setInputAsNumpy(Weights3D)
-#v.startRenderLoop()
-
-import matplotlib.pyplot as plt
-fig = plt.figure()
-
-a=fig.add_subplot(1,1,1)
-a.set_title('noise')
-imgplot = plt.imshow(Weights3D[0].T)
-plt.show()
diff --git a/src/Python/test/simple_astra_test.py b/src/Python/test/simple_astra_test.py
deleted file mode 100644
index 905eeea..0000000
--- a/src/Python/test/simple_astra_test.py
+++ /dev/null
@@ -1,25 +0,0 @@
-import astra
-import numpy
-
-detectorSpacingX = 1.0
-detectorSpacingY = 1.0
-det_row_count = 128
-det_col_count = 128
-
-angles_rad = numpy.asarray([i for i in range(360)], dtype=float) / 180. * numpy.pi
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-image_size_x = 64
-image_size_y = 64
-image_size_z = 32
-
-vol_geom = astra.creators.create_vol_geom(image_size_x,image_size_y,image_size_z)
-
-x1 = numpy.random.rand(image_size_z,image_size_y,image_size_x)
-sino_id, y = astra.creators.create_sino3d_gpu(x1, proj_geom, vol_geom)
diff --git a/src/Python/test/test_reconstructor-os.py b/src/Python/test/test_reconstructor-os.py
deleted file mode 100644
index 21b7ecd..0000000
--- a/src/Python/test/test_reconstructor-os.py
+++ /dev/null
@@ -1,403 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-Based on DemoRD2.m
-"""
-
-import h5py
-import numpy
-
-from ccpi.reconstruction.FISTAReconstructor import FISTAReconstructor
-import astra
-import matplotlib.pyplot as plt
-from ccpi.imaging.Regularizer import Regularizer
-from ccpi.reconstruction.AstraDevice import AstraDevice
-from ccpi.reconstruction.DeviceModel import DeviceModel
-
-def RMSE(signal1, signal2):
-    '''RMSE Root Mean Squared Error'''
-    if numpy.shape(signal1) == numpy.shape(signal2):
-        err = (signal1 - signal2)
-        err = numpy.sum( err * err )/numpy.size(signal1);  # MSE
-        err = sqrt(err);                                   # RMSE
-        return err
-    else:
-        raise Exception('Input signals must have the same shape')
-  
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-Sino3D = numpy.asarray(nx.get('/Sino3D'), dtype="float32")
-Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32")
-angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles_rad'), dtype="float32")
-recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0]
-size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0]
-slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-
-Z_slices = 20
-det_row_count = Z_slices
-# next definition is just for consistency of naming
-det_col_count = size_det
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-image_size_x = recon_size
-image_size_y = recon_size
-image_size_z = Z_slices
-vol_geom = astra.creators.create_vol_geom( image_size_x,
-                                           image_size_y,
-                                           image_size_z)
-
-## First pass the arguments to the FISTAReconstructor and test the
-## Lipschitz constant
-astradevice = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [proj_geom['DetectorRowCount'] ,
-                 proj_geom['DetectorColCount'] ,
-                 proj_geom['DetectorSpacingX'] ,
-                 proj_geom['DetectorSpacingY'] ,
-                 proj_geom['ProjectionAngles']
-                 ],
-                [
-                    vol_geom['GridColCount'],
-                    vol_geom['GridRowCount'], 
-                    vol_geom['GridSliceCount'] ] )
-fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                weights=Weights3D,
-                                device=astradevice)
-
-print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-fistaRecon.setParameter(number_of_iterations = 2)
-fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-fistaRecon.setParameter(ring_alpha = 21)
-fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-fistaRecon.setParameter(ring_lambda_R_L1 = 0)
-subsets = 8
-fistaRecon.setParameter(subsets=subsets)
-
-
-#reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-#reg.setParameter(regularization_parameter=0.005,
-#                          number_of_iterations=50)
-reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-reg.setParameter(regularization_parameter=5e6,
-                          tolerance_constant=0.0001,
-                          number_of_iterations=50)
-
-fistaRecon.setParameter(regularizer=reg)
-lc = fistaRecon.getParameter('Lipschitz_constant')
-reg.setParameter(regularization_parameter=5e6/lc)
-
-## Ordered subset
-if True:
-    subsets = 8
-    fistaRecon.setParameter(subsets=subsets)
-    fistaRecon.createOrderedSubsets()
-else:
-    angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    #binEdges = numpy.linspace(angles.min(),
-    #                          angles.max(),
-    #                          subsets + 1)
-    binsDiscr, binEdges = numpy.histogram(angles, bins=subsets)
-    # get rearranged subset indices
-    IndicesReorg = numpy.zeros((numpy.shape(angles)))
-    counterM = 0
-    for ii in range(binsDiscr.max()):
-        counter = 0
-        for jj in range(subsets):
-            curr_index = ii + jj  + counter
-            #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM))
-            if binsDiscr[jj] > ii:
-                if (counterM < numpy.size(IndicesReorg)):
-                    IndicesReorg[counterM] = curr_index
-                counterM = counterM + 1
-                
-            counter = counter + binsDiscr[jj] - 1
-
-
-if False:
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    print ("prepare for iteration")
-    fistaRecon.prepareForIteration()
-    
-    
-
-    print("initializing  ...")
-    if False:
-        # if X doesn't exist
-        #N = params.vol_geom.GridColCount
-        N = vol_geom['GridColCount']
-        print ("N " + str(N))
-        X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
-    else:
-        #X = fistaRecon.initialize()
-        X = numpy.load("X.npy")
-    
-    print (numpy.shape(X))
-    X_t = X.copy()
-    print ("initialized")
-    proj_geom , vol_geom, sino , \
-        SlicesZ, weights , alpha_ring = fistaRecon.getParameter(
-            ['projector_geometry' , 'output_geometry',
-             'input_sinogram', 'SlicesZ' ,  'weights', 'ring_alpha'])
-    lambdaR_L1 , alpha_ring , weights , L_const= \
-                       fistaRecon.getParameter(['ring_lambda_R_L1',
-                                               'ring_alpha' , 'weights',
-                                               'Lipschitz_constant'])
-
-    #fistaRecon.setParameter(number_of_iterations = 3)
-    iterFISTA = fistaRecon.getParameter('number_of_iterations')
-    # errors vector (if the ground truth is given)
-    Resid_error = numpy.zeros((iterFISTA));
-    # objective function values vector
-    objective = numpy.zeros((iterFISTA)); 
-
-      
-    t = 1
-    
-
-    ## additional for 
-    proj_geomSUB = proj_geom.copy()
-    fistaRecon.residual2 = numpy.zeros(numpy.shape(fistaRecon.pars['input_sinogram']))
-    residual2 = fistaRecon.residual2
-    sino_updt_FULL = fistaRecon.residual.copy()
-    r_x = fistaRecon.r.copy()
-    
-    print ("starting iterations")
-##    % Outer FISTA iterations loop
-    for i in range(fistaRecon.getParameter('number_of_iterations')):
-##        % With OS approach it becomes trickier to correlate independent subsets, hence additional work is required
-##        % one solution is to work with a full sinogram at times
-##        if ((i >= 3) && (lambdaR_L1 > 0))
-##            [sino_id2, sino_updt2] = astra_create_sino3d_cuda(X, proj_geom, vol_geom);
-##            astra_mex_data3d('delete', sino_id2);
-##        end
-        # With OS approach it becomes trickier to correlate independent subsets,
-        # hence additional work is required one solution is to work with a full
-        # sinogram at times
-
-        r_old = fistaRecon.r.copy()
-        t_old = t
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(fistaRecon.getParameter('input_sinogram'))        ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
-        if (i > 1 and lambdaR_L1 > 0) :
-            for kkk in range(anglesNumb):
-                 
-                 residual2[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                       ((sino_updt_FULL[:,kkk,:]).squeeze() - \
-                                        (sino[:,kkk,:]).squeeze() -\
-                                        (alpha_ring * r_x)
-                                        )
-            
-            vec = fistaRecon.residual.sum(axis = 1)
-            #if SlicesZ > 1:
-            #    vec = vec[:,1,:] # 1 or 0?
-            r_x = fistaRecon.r_x
-            # update ring variable
-            fistaRecon.r = (r_x - (1./L_const) * vec).copy() 
-
-        # subset loop
-        counterInd = 1
-        geometry_type = fistaRecon.getParameter('projector_geometry')['type']
-        angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    
-##        if geometry_type == 'parallel' or \
-##           geometry_type == 'fanflat' or \
-##           geometry_type == 'fanflat_vec' :
-##            
-##            for kkk in range(SlicesZ):
-##                sino_id, sinoT[kkk] = \
-##                         astra.creators.create_sino3d_gpu(
-##                             X_t[kkk:kkk+1], proj_geomSUB, vol_geom)
-##                sino_updt_Sub[kkk] = sinoT.T.copy()
-##                
-##        else:
-##            sino_id, sino_updt_Sub = \
-##                astra.creators.create_sino3d_gpu(X_t, proj_geomSUB, vol_geom)
-##        
-##        astra.matlab.data3d('delete', sino_id)
-  
-        for ss in range(fistaRecon.getParameter('subsets')):
-            print ("Subset {0}".format(ss))
-            X_old = X.copy()
-            t_old = t
-            
-            # the number of projections per subset
-            numProjSub = fistaRecon.getParameter('os_bins')[ss]
-            CurrSubIndices = fistaRecon.getParameter('os_indices')\
-                             [counterInd:counterInd+numProjSub]
-            #print ("Len CurrSubIndices {0}".format(numProjSub))
-            mask = numpy.zeros(numpy.shape(angles), dtype=bool)
-            cc = 0
-            for j in range(len(CurrSubIndices)):
-                mask[int(CurrSubIndices[j])] = True
-            proj_geomSUB['ProjectionAngles'] = angles[mask]
-
-            shape = list(numpy.shape(fistaRecon.getParameter('input_sinogram')))
-            shape[1] = numProjSub
-            sino_updt_Sub = numpy.zeros(shape)
-
-            if geometry_type == 'parallel' or \
-               geometry_type == 'fanflat' or \
-               geometry_type == 'fanflat_vec' :
-
-                for kkk in range(SlicesZ):
-                    sino_id, sinoT = astra.creators.create_sino3d_gpu (
-                        X_t[kkk:kkk+1] , proj_geomSUB, vol_geom)
-                    sino_updt_Sub[kkk] = sinoT.T.copy()
-                    
-            else:
-                # for 3D geometry (watch the GPU memory overflow in ASTRA < 1.8)
-                sino_id, sino_updt_Sub = \
-                     astra.creators.create_sino3d_gpu (X_t, proj_geomSUB, vol_geom)
-                
-            astra.matlab.data3d('delete', sino_id)
-                
-            
-
-
-            ## RING REMOVAL
-            residual = fistaRecon.residual
-            
-            
-            if lambdaR_L1 > 0 :
-                 print ("ring removal")
-                 residualSub = numpy.zeros(shape)
-    ##             for a chosen subset
-    ##                for kkk = 1:numProjSub
-    ##                    indC = CurrSubIndeces(kkk);
-    ##                    residualSub(:,kkk,:) =  squeeze(weights(:,indC,:)).*(squeeze(sino_updt_Sub(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
-    ##                    sino_updt_FULL(:,indC,:) = squeeze(sino_updt_Sub(:,kkk,:)); % filling the full sinogram
-    ##                end
-                 for kkk in range(numProjSub):
-                     #print ("ring removal indC ... {0}".format(kkk))
-                     indC = int(CurrSubIndices[kkk])
-                     residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
-                            (sino_updt_Sub[:,kkk,:].squeeze() - \
-                             sino[:,indC,:].squeeze() - alpha_ring * r_x)
-                     # filling the full sinogram
-                     sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
-
-            else:
-                #PWLS model
-                # I guess we need to use mask here instead
-                residualSub = weights[:,CurrSubIndices,:] * \
-                              ( sino_updt_Sub - sino[:,CurrSubIndices,:].squeeze() )
-                objective[i] = 0.5 * numpy.linalg.norm(residualSub)
-
-            if geometry_type == 'parallel' or \
-               geometry_type == 'fanflat' or \
-               geometry_type == 'fanflat_vec' :
-                # if geometry is 2D use slice-by-slice projection-backprojection
-                # routine
-                x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
-                for kkk in range(SlicesZ):
-                    
-                    x_id, x_temp[kkk] = \
-                             astra.creators.create_backprojection3d_gpu(
-                                 residualSub[kkk:kkk+1],
-                                 proj_geomSUB, vol_geom)
-                    
-            else:
-                x_id, x_temp = \
-                      astra.creators.create_backprojection3d_gpu(
-                          residualSub, proj_geomSUB, vol_geom)
-
-            astra.matlab.data3d('delete', x_id)
-            X = X_t - (1/L_const) * x_temp
-
-        
-
-        ## REGULARIZATION
-        ## SKIPPING FOR NOW
-        ## Should be simpli
-        # regularizer = fistaRecon.getParameter('regularizer')
-        # for slices:
-        # out = regularizer(input=X)
-        print ("regularizer")
-        reg = fistaRecon.getParameter('regularizer')
-        
-        X = reg(input=X,
-                output_all=False)
-
-
-        ## FINAL
-        print ("final")
-        lambdaR_L1 = fistaRecon.getParameter('ring_lambda_R_L1')
-        if lambdaR_L1 > 0:
-            fistaRecon.r = numpy.max(
-                numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \
-                numpy.sign(fistaRecon.r)
-            # updating r
-            r_x = fistaRecon.r + ((t_old-1)/t) * (fistaRecon.r - r_old)
-        
-
-        if fistaRecon.getParameter('region_of_interest') is None:
-            string = 'Iteration Number {0} | Objective {1} \n'
-            print (string.format( i, objective[i]))
-        else:
-            ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                    'ideal_image')
-            
-            Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-            string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-            print (string.format(i,Resid_error[i], objective[i]))
-
-    numpy.save("X_out_os.npy", X)
-
-else:
-    astradevice = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [proj_geom['DetectorRowCount'] ,
-                 proj_geom['DetectorColCount'] ,
-                 proj_geom['DetectorSpacingX'] ,
-                 proj_geom['DetectorSpacingY'] ,
-                 proj_geom['ProjectionAngles']
-                 ],
-                [
-                    vol_geom['GridColCount'],
-                    vol_geom['GridRowCount'], 
-                    vol_geom['GridSliceCount'] ] )
-    regul = Regularizer(Regularizer.Algorithm.FGP_TV)
-    regul.setParameter(regularization_parameter=5e6,
-                       number_of_iterations=50,
-                       tolerance_constant=1e-4,
-                       TV_penalty=Regularizer.TotalVariationPenalty.isotropic)
-
-    fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                weights=Weights3D,
-                                device=astradevice,
-                                regularizer = regul,
-                                subsets=8)
-
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    fistaRecon.setParameter(number_of_iterations = 2)
-    fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-    fistaRecon.setParameter(ring_alpha = 21)
-    fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-    #fistaRecon.setParameter(subsets=8)
-    
-    lc = fistaRecon.getParameter('Lipschitz_constant')
-    fistaRecon.getParameter('regularizer').setParameter(regularization_parameter=5e6/lc)
-    
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("X.npy"))
diff --git a/src/Python/test/test_reconstructor-os_phantom.py b/src/Python/test/test_reconstructor-os_phantom.py
deleted file mode 100644
index 01f1354..0000000
--- a/src/Python/test/test_reconstructor-os_phantom.py
+++ /dev/null
@@ -1,480 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-Based on DemoRD2.m
-"""
-
-import h5py
-import numpy
-
-from ccpi.reconstruction.FISTAReconstructor import FISTAReconstructor
-import astra
-import matplotlib.pyplot as plt
-from ccpi.imaging.Regularizer import Regularizer
-from ccpi.reconstruction.AstraDevice import AstraDevice
-from ccpi.reconstruction.DeviceModel import DeviceModel
-
-#from ccpi.viewer.CILViewer2D import *
-
-
-def RMSE(signal1, signal2):
-    '''RMSE Root Mean Squared Error'''
-    if numpy.shape(signal1) == numpy.shape(signal2):
-        err = (signal1 - signal2)
-        err = numpy.sum( err * err )/numpy.size(signal1);  # MSE
-        err = sqrt(err);                                   # RMSE
-        return err
-    else:
-        raise Exception('Input signals must have the same shape')
-
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/src/Python/test/phantom3D256_projections.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-projections = numpy.asarray(nx.get('/projections'), dtype="float32")
-#Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32")
-#angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles'), dtype="float32")
-angSize = numpy.size(angles_rad)
-image_size_x, image_size_y, image_size_z = \
-              numpy.asarray(nx.get('/reconstruction_volume'), dtype=int)
-det_col_count, det_row_count = \
-              numpy.asarray(nx.get('/camera/size'))
-#slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-detectorSpacingX, detectorSpacingY = numpy.asarray(nx.get('/camera/spacing'), dtype=int)
-
-Z_slices = 20
-#det_row_count = image_size_y
-# next definition is just for consistency of naming
-#det_col_count = image_size_x
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-##image_size_x = recon_size
-##image_size_y = recon_size
-##image_size_z = Z_slices
-vol_geom = astra.creators.create_vol_geom( image_size_x,
-                                           image_size_y,
-                                           image_size_z)
-
-## First pass the arguments to the FISTAReconstructor and test the
-## Lipschitz constant
-astradevice = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [proj_geom['DetectorRowCount'] ,
-                 proj_geom['DetectorColCount'] ,
-                 proj_geom['DetectorSpacingX'] ,
-                 proj_geom['DetectorSpacingY'] ,
-                 proj_geom['ProjectionAngles']
-                 ],
-                [
-                    vol_geom['GridColCount'],
-                    vol_geom['GridRowCount'], 
-                    vol_geom['GridSliceCount'] ] )
-## create the sinogram 
-Sino3D = numpy.transpose(projections, axes=[1,0,2])
-
-fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                #weights=Weights3D,
-                                device=astradevice)
-
-print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-fistaRecon.setParameter(number_of_iterations = 4)
-#fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-fistaRecon.setParameter(ring_alpha = 21)
-fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-#fistaRecon.setParameter(ring_lambda_R_L1 = 0)
-subsets = 8
-fistaRecon.setParameter(subsets=subsets)
-
-
-#reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-#reg.setParameter(regularization_parameter=0.005,
-#                          number_of_iterations=50)
-reg = Regularizer(Regularizer.Algorithm.FGP_TV)
-reg.setParameter(regularization_parameter=5e6,
-                          tolerance_constant=0.0001,
-                          number_of_iterations=50)
-
-#fistaRecon.setParameter(regularizer=reg)
-#lc = fistaRecon.getParameter('Lipschitz_constant')
-#reg.setParameter(regularization_parameter=5e6/lc)
-
-## Ordered subset
-if True:
-    #subsets = 8
-    fistaRecon.setParameter(subsets=subsets)
-    fistaRecon.createOrderedSubsets()
-else:
-    angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    #binEdges = numpy.linspace(angles.min(),
-    #                          angles.max(),
-    #                          subsets + 1)
-    binsDiscr, binEdges = numpy.histogram(angles, bins=subsets)
-    # get rearranged subset indices
-    IndicesReorg = numpy.zeros((numpy.shape(angles)))
-    counterM = 0
-    for ii in range(binsDiscr.max()):
-        counter = 0
-        for jj in range(subsets):
-            curr_index = ii + jj  + counter
-            #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM))
-            if binsDiscr[jj] > ii:
-                if (counterM < numpy.size(IndicesReorg)):
-                    IndicesReorg[counterM] = curr_index
-                counterM = counterM + 1
-                
-            counter = counter + binsDiscr[jj] - 1
-
-
-if True:
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    print ("prepare for iteration")
-    fistaRecon.prepareForIteration()
-    
-    
-
-    print("initializing  ...")
-    if True:
-        # if X doesn't exist
-        #N = params.vol_geom.GridColCount
-        N = vol_geom['GridColCount']
-        print ("N " + str(N))
-        X = numpy.asarray(numpy.ones((image_size_x,image_size_y,image_size_z)),
-                        dtype=numpy.float) * 0.001
-        X = numpy.asarray(numpy.zeros((image_size_x,image_size_y,image_size_z)),
-                        dtype=numpy.float) 
-    else:
-        #X = fistaRecon.initialize()
-        X = numpy.load("X.npy")
-    
-    print (numpy.shape(X))
-    X_t = X.copy()
-    print ("initialized")
-    proj_geom , vol_geom, sino , \
-        SlicesZ, weights , alpha_ring = fistaRecon.getParameter(
-            ['projector_geometry' , 'output_geometry',
-             'input_sinogram', 'SlicesZ' ,  'weights', 'ring_alpha'])
-    lambdaR_L1 , alpha_ring , weights , L_const= \
-                       fistaRecon.getParameter(['ring_lambda_R_L1',
-                                               'ring_alpha' , 'weights',
-                                               'Lipschitz_constant'])
-
-    #fistaRecon.setParameter(number_of_iterations = 3)
-    iterFISTA = fistaRecon.getParameter('number_of_iterations')
-    # errors vector (if the ground truth is given)
-    Resid_error = numpy.zeros((iterFISTA));
-    # objective function values vector
-    objective = numpy.zeros((iterFISTA)); 
-
-      
-    t = 1
-    
-
-    ## additional for 
-    proj_geomSUB = proj_geom.copy()
-    fistaRecon.residual2 = numpy.zeros(numpy.shape(fistaRecon.pars['input_sinogram']))
-    residual2 = fistaRecon.residual2
-    sino_updt_FULL = fistaRecon.residual.copy()
-    r_x = fistaRecon.r.copy()
-
-    results = []
-    print ("starting iterations")
-##    % Outer FISTA iterations loop
-    for i in range(fistaRecon.getParameter('number_of_iterations')):
-##        % With OS approach it becomes trickier to correlate independent subsets, hence additional work is required
-##        % one solution is to work with a full sinogram at times
-##        if ((i >= 3) && (lambdaR_L1 > 0))
-##            [sino_id2, sino_updt2] = astra_create_sino3d_cuda(X, proj_geom, vol_geom);
-##            astra_mex_data3d('delete', sino_id2);
-##        end
-        # With OS approach it becomes trickier to correlate independent subsets,
-        # hence additional work is required one solution is to work with a full
-        # sinogram at times
-
-        
-        #t_old = t
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(fistaRecon.getParameter('input_sinogram'))
-        ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
-        r_old = fistaRecon.r.copy()
-            
-        if (i > 1 and lambdaR_L1 > 0) :
-            for kkk in range(anglesNumb):
-                 
-                 residual2[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                       ((sino_updt_FULL[:,kkk,:]).squeeze() - \
-                                        (sino[:,kkk,:]).squeeze() -\
-                                        (alpha_ring * r_x)
-                                        )
-            #r_old = fistaRecon.r.copy()
-            vec = fistaRecon.residual.sum(axis = 1)
-            #if SlicesZ > 1:
-            #    vec = vec[:,1,:] # 1 or 0?
-            r_x = fistaRecon.r_x
-            # update ring variable
-            fistaRecon.r = (r_x - (1./L_const) * vec)
-
-        # subset loop
-        counterInd = 1
-        geometry_type = fistaRecon.getParameter('projector_geometry')['type']
-        angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    
-##        if geometry_type == 'parallel' or \
-##           geometry_type == 'fanflat' or \
-##           geometry_type == 'fanflat_vec' :
-##            
-##            for kkk in range(SlicesZ):
-##                sino_id, sinoT[kkk] = \
-##                         astra.creators.create_sino3d_gpu(
-##                             X_t[kkk:kkk+1], proj_geomSUB, vol_geom)
-##                sino_updt_Sub[kkk] = sinoT.T.copy()
-##                
-##        else:
-##            sino_id, sino_updt_Sub = \
-##                astra.creators.create_sino3d_gpu(X_t, proj_geomSUB, vol_geom)
-##        
-##        astra.matlab.data3d('delete', sino_id)
-  
-        for ss in range(fistaRecon.getParameter('subsets')):
-            print ("Subset {0}".format(ss))
-            X_old = X.copy()
-            t_old = t
-            print ("X[0][0][0] {0} t {1}".format(X[0][0][0], t))
-            
-            # the number of projections per subset
-            numProjSub = fistaRecon.getParameter('os_bins')[ss]
-            CurrSubIndices = fistaRecon.getParameter('os_indices')\
-                             [counterInd:counterInd+numProjSub]
-            shape = list(numpy.shape(fistaRecon.getParameter('input_sinogram')))
-            shape[1] = numProjSub
-            sino_updt_Sub = numpy.zeros(shape)
-            
-            #print ("Len CurrSubIndices {0}".format(numProjSub))
-            mask = numpy.zeros(numpy.shape(angles), dtype=bool)
-            cc = 0
-            for j in range(len(CurrSubIndices)):
-                mask[int(CurrSubIndices[j])] = True
-
-            ## this is a reduced device
-            rdev = fistaRecon.getParameter('device_model')\
-                   .createReducedDevice(proj_par={'angles' : angles[mask]},
-                                        vol_par={})
-            proj_geomSUB['ProjectionAngles'] = angles[mask]
-
-            
-
-            if geometry_type == 'parallel' or \
-               geometry_type == 'fanflat' or \
-               geometry_type == 'fanflat_vec' :
-
-                for kkk in range(SlicesZ):
-                    sino_id, sinoT = astra.creators.create_sino3d_gpu (
-                        X_t[kkk:kkk+1] , proj_geomSUB, vol_geom)
-                    sino_updt_Sub[kkk] = sinoT.T.copy()
-                    astra.matlab.data3d('delete', sino_id)
-            else:
-                # for 3D geometry (watch the GPU memory overflow in ASTRA < 1.8)
-                sino_id, sino_updt_Sub = \
-                     astra.creators.create_sino3d_gpu (X_t,
-                                                       proj_geomSUB,
-                                                       vol_geom)
-                
-                astra.matlab.data3d('delete', sino_id)
-                
-            
-
-
-            ## RING REMOVAL
-            residual = fistaRecon.residual
-            
-            
-            if lambdaR_L1 > 0 :
-                 print ("ring removal")
-                 residualSub = numpy.zeros(shape)
-    ##             for a chosen subset
-    ##                for kkk = 1:numProjSub
-    ##                    indC = CurrSubIndeces(kkk);
-    ##                    residualSub(:,kkk,:) =  squeeze(weights(:,indC,:)).*(squeeze(sino_updt_Sub(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
-    ##                    sino_updt_FULL(:,indC,:) = squeeze(sino_updt_Sub(:,kkk,:)); % filling the full sinogram
-    ##                end
-                 for kkk in range(numProjSub):
-                     #print ("ring removal indC ... {0}".format(kkk))
-                     indC = int(CurrSubIndices[kkk])
-                     residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
-                            (sino_updt_Sub[:,kkk,:].squeeze() - \
-                             sino[:,indC,:].squeeze() - alpha_ring * r_x)
-                     # filling the full sinogram
-                     sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
-
-            else:
-                #PWLS model
-                # I guess we need to use mask here instead
-                residualSub = weights[:,CurrSubIndices,:] * \
-                              ( sino_updt_Sub - \
-                                sino[:,CurrSubIndices,:].squeeze() )
-            # it seems that in the original code the following like is not
-            # calculated in the case of ring removal
-            objective[i] = 0.5 * numpy.linalg.norm(residualSub)
-
-            #backprojection
-            if geometry_type == 'parallel' or \
-               geometry_type == 'fanflat' or \
-               geometry_type == 'fanflat_vec' :
-                # if geometry is 2D use slice-by-slice projection-backprojection
-                # routine
-                x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
-                for kkk in range(SlicesZ):
-                    
-                    x_id, x_temp[kkk] = \
-                             astra.creators.create_backprojection3d_gpu(
-                                 residualSub[kkk:kkk+1],
-                                 proj_geomSUB, vol_geom)
-                    astra.matlab.data3d('delete', x_id)
-                    
-            else:
-                x_id, x_temp = \
-                      astra.creators.create_backprojection3d_gpu(
-                          residualSub, proj_geomSUB, vol_geom)
-
-                astra.matlab.data3d('delete', x_id)
-                
-            X = X_t - (1/L_const) * x_temp
-
-        
-
-            ## REGULARIZATION
-            ## SKIPPING FOR NOW
-            ## Should be simpli
-            # regularizer = fistaRecon.getParameter('regularizer')
-            # for slices:
-            # out = regularizer(input=X)
-            print ("regularizer")
-            reg = fistaRecon.getParameter('regularizer')
-
-            if reg is not None:
-                X = reg(input=X,
-                        output_all=False)
-
-            t = (1 + numpy.sqrt(1 + 4 * t **2))/2
-            X_t = X + (((t_old -1)/t) * (X-X_old))
-            counterInd = counterInd + numProjSub - 1
-        if i == 1:
-            r_old = fistaRecon.r.copy()
-            
-        ## FINAL
-        print ("final")
-        lambdaR_L1 = fistaRecon.getParameter('ring_lambda_R_L1')
-        if lambdaR_L1 > 0:
-            fistaRecon.r = numpy.max(
-                numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \
-                numpy.sign(fistaRecon.r)
-            # updating r
-            r_x = fistaRecon.r + ((t_old-1)/t) * (fistaRecon.r - r_old)
-        
-
-        if fistaRecon.getParameter('region_of_interest') is None:
-            string = 'Iteration Number {0} | Objective {1} \n'
-            print (string.format( i, objective[i]))
-        else:
-            ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                    'ideal_image')
-            
-            Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-            string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-            print (string.format(i,Resid_error[i], objective[i]))
-
-        results.append(X[10])
-    numpy.save("X_out_os.npy", X)
-
-else:
-    
-    
-    
-    astradevice = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [proj_geom['DetectorRowCount'] ,
-                 proj_geom['DetectorColCount'] ,
-                 proj_geom['DetectorSpacingX'] ,
-                 proj_geom['DetectorSpacingY'] ,
-                 proj_geom['ProjectionAngles']
-                 ],
-                [
-                    vol_geom['GridColCount'],
-                    vol_geom['GridRowCount'], 
-                    vol_geom['GridSliceCount'] ] )
-    regul = Regularizer(Regularizer.Algorithm.FGP_TV)
-    regul.setParameter(regularization_parameter=5e6,
-                       number_of_iterations=50,
-                       tolerance_constant=1e-4,
-                       TV_penalty=Regularizer.TotalVariationPenalty.isotropic)
-
-    fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                weights=Weights3D,
-                                device=astradevice,
-                                #regularizer = regul,
-                                subsets=8)
-
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    fistaRecon.setParameter(number_of_iterations = 1)
-    fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-    fistaRecon.setParameter(ring_alpha = 21)
-    fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-    #fistaRecon.setParameter(subsets=8)
-    
-    #lc = fistaRecon.getParameter('Lipschitz_constant')
-    #fistaRecon.getParameter('regularizer').setParameter(regularization_parameter=5e6/lc)
-    
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("X.npy"))
-    
-
-# plot
-fig = plt.figure()
-cols = 3
-
-## add the difference
-rd = []
-for i in range(1,len(results)):
-    rd.append(results[i-1])
-    rd.append(results[i])
-    rd.append(results[i] - results[i-1])
-
-rows = (lambda x: int(numpy.floor(x/cols) + 1) if x%cols != 0  else int(x/cols)) \
-       (len (rd))
-for i in range(len (results)):
-    a=fig.add_subplot(rows,cols,i+1)
-    imgplot = plt.imshow(results[i], vmin=0, vmax=1)
-    a.text(0.05, 0.95, "iteration {0}".format(i),
-               verticalalignment='top')
-##    i = i + 1
-##    a=fig.add_subplot(rows,cols,i+1)
-##    imgplot = plt.imshow(results[i], vmin=0, vmax=10)
-##    a.text(0.05, 0.95, "iteration {0}".format(i),
-##               verticalalignment='top')
-    
-##    a=fig.add_subplot(rows,cols,i+2)
-##    imgplot = plt.imshow(results[i]-results[i-1], vmin=0, vmax=10)
-##    a.text(0.05, 0.95, "difference {0}-{1}".format(i, i-1),
-##               verticalalignment='top')
-        
-        
-
-plt.show()
diff --git a/src/Python/test/test_reconstructor.py b/src/Python/test/test_reconstructor.py
deleted file mode 100644
index 40065e7..0000000
--- a/src/Python/test/test_reconstructor.py
+++ /dev/null
@@ -1,359 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-Based on DemoRD2.m
-"""
-
-import h5py
-import numpy
-
-from ccpi.reconstruction.FISTAReconstructor import FISTAReconstructor
-import astra
-import matplotlib.pyplot as plt
-from ccpi.imaging.Regularizer import Regularizer
-from ccpi.reconstruction.AstraDevice import AstraDevice
-from ccpi.reconstruction.DeviceModel import DeviceModel
-
-def RMSE(signal1, signal2):
-    '''RMSE Root Mean Squared Error'''
-    if numpy.shape(signal1) == numpy.shape(signal2):
-        err = (signal1 - signal2)
-        err = numpy.sum( err * err )/numpy.size(signal1);  # MSE
-        err = sqrt(err);                                   # RMSE
-        return err
-    else:
-        raise Exception('Input signals must have the same shape')
-
-def createAstraDevice(projector_geometry, output_geometry):
-    '''TODO remove'''
-    
-    device = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [projector_geometry['DetectorRowCount'] ,
-                 projector_geometry['DetectorColCount'] ,
-                 projector_geometry['DetectorSpacingX'] ,
-                 projector_geometry['DetectorSpacingY'] ,
-                 projector_geometry['ProjectionAngles']
-                 ],
-                [
-                    output_geometry['GridColCount'],
-                    output_geometry['GridRowCount'], 
-                    output_geometry['GridSliceCount'] ] )
-    return device
-
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-Sino3D = numpy.asarray(nx.get('/Sino3D'), dtype="float32")
-Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32")
-angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles_rad'), dtype="float32")
-recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0]
-size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0]
-slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-
-Z_slices = 20
-det_row_count = Z_slices
-# next definition is just for consistency of naming
-det_col_count = size_det
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-image_size_x = recon_size
-image_size_y = recon_size
-image_size_z = Z_slices
-vol_geom = astra.creators.create_vol_geom( image_size_x,
-                                           image_size_y,
-                                           image_size_z)
-
-## First pass the arguments to the FISTAReconstructor and test the
-## Lipschitz constant
-
-##fistaRecon = FISTAReconstructor(proj_geom,
-##                                vol_geom,
-##                                Sino3D ,
-##                                weights=Weights3D)
-##
-##print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-##fistaRecon.setParameter(number_of_iterations = 12)
-##fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-##fistaRecon.setParameter(ring_alpha = 21)
-##fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-##
-##reg = Regularizer(Regularizer.Algorithm.LLT_model)
-##reg.setParameter(regularization_parameter=25,
-##                          time_step=0.0003,
-##                          tolerance_constant=0.0001,
-##                          number_of_iterations=300)
-##fistaRecon.setParameter(regularizer=reg)
-
-## Ordered subset
-if False:
-    subsets = 16
-    angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    #binEdges = numpy.linspace(angles.min(),
-    #                          angles.max(),
-    #                          subsets + 1)
-    binsDiscr, binEdges = numpy.histogram(angles, bins=subsets)
-    # get rearranged subset indices
-    IndicesReorg = numpy.zeros((numpy.shape(angles)))
-    counterM = 0
-    for ii in range(binsDiscr.max()):
-        counter = 0
-        for jj in range(subsets):
-            curr_index = ii + jj  + counter
-            #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM))
-            if binsDiscr[jj] > ii:
-                if (counterM < numpy.size(IndicesReorg)):
-                    IndicesReorg[counterM] = curr_index
-                counterM = counterM + 1
-                
-            counter = counter + binsDiscr[jj] - 1
-
-
-if False:
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    print ("prepare for iteration")
-    fistaRecon.prepareForIteration()
-    
-    
-
-    print("initializing  ...")
-    if False:
-        # if X doesn't exist
-        #N = params.vol_geom.GridColCount
-        N = vol_geom['GridColCount']
-        print ("N " + str(N))
-        X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
-    else:
-        #X = fistaRecon.initialize()
-        X = numpy.load("X.npy")
-    
-    print (numpy.shape(X))
-    X_t = X.copy()
-    print ("initialized")
-    proj_geom , vol_geom, sino , \
-                      SlicesZ = fistaRecon.getParameter(['projector_geometry' ,
-                                                            'output_geometry',
-                                                            'input_sinogram',
-                                                         'SlicesZ'])
-
-    #fistaRecon.setParameter(number_of_iterations = 3)
-    iterFISTA = fistaRecon.getParameter('number_of_iterations')
-    # errors vector (if the ground truth is given)
-    Resid_error = numpy.zeros((iterFISTA));
-    # objective function values vector
-    objective = numpy.zeros((iterFISTA)); 
-
-      
-    t = 1
-
-
-    print ("starting iterations")
-##    % Outer FISTA iterations loop
-    for i in range(fistaRecon.getParameter('number_of_iterations')):
-        X_old = X.copy()
-        t_old = t
-        r_old = fistaRecon.r.copy()
-        if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec' :
-            # if the geometry is parallel use slice-by-slice
-            # projection-backprojection routine
-            #sino_updt = zeros(size(sino),'single');
-            proj_geomT = proj_geom.copy()
-            proj_geomT['DetectorRowCount'] = 1
-            vol_geomT = vol_geom.copy()
-            vol_geomT['GridSliceCount'] = 1;
-            sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
-            for kkk in range(SlicesZ):
-                sino_id, sino_updt[kkk] = \
-                         astra.creators.create_sino3d_gpu(
-                             X_t[kkk:kkk+1], proj_geom, vol_geom)
-                astra.matlab.data3d('delete', sino_id)
-        else:
-            # for divergent 3D geometry (watch the GPU memory overflow in
-            # ASTRA versions < 1.8)
-            #[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
-            sino_id, sino_updt = astra.creators.create_sino3d_gpu(
-                X_t, proj_geom, vol_geom)
-
-        ## RING REMOVAL
-        residual = fistaRecon.residual
-        lambdaR_L1 , alpha_ring , weights , L_const= \
-                   fistaRecon.getParameter(['ring_lambda_R_L1',
-                                           'ring_alpha' , 'weights',
-                                           'Lipschitz_constant'])
-        r_x = fistaRecon.r_x
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(fistaRecon.getParameter('input_sinogram'))
-        if lambdaR_L1 > 0 :
-             print ("ring removal")
-             for kkk in range(anglesNumb):
-                 
-                 residual[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                       ((sino_updt[:,kkk,:]).squeeze() - \
-                                        (sino[:,kkk,:]).squeeze() -\
-                                        (alpha_ring * r_x)
-                                        )
-             vec = residual.sum(axis = 1)
-             #if SlicesZ > 1:
-             #    vec = vec[:,1,:].squeeze()
-             fistaRecon.r = (r_x - (1./L_const) * vec).copy()
-             objective[i] = (0.5 * (residual ** 2).sum())
-##            % the ring removal part (Group-Huber fidelity)
-##            for kkk = 1:anglesNumb
-##                residual(:,kkk,:) =  squeeze(weights(:,kkk,:)).*
-##                 (squeeze(sino_updt(:,kkk,:)) -
-##                 (squeeze(sino(:,kkk,:)) - alpha_ring.*r_x));
-##            end
-##            vec = sum(residual,2);
-##            if (SlicesZ > 1)
-##                vec = squeeze(vec(:,1,:));
-##            end
-##            r = r_x - (1./L_const).*vec;
-##            objective(i) = (0.5*sum(residual(:).^2)); % for the objective function output
-
-        
-
-        # Projection/Backprojection Routine
-        if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or\
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec':
-            x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32)
-            print ("Projection/Backprojection Routine")
-            for kkk in range(SlicesZ):
-                
-                x_id, x_temp[kkk] = \
-                         astra.creators.create_backprojection3d_gpu(
-                             residual[kkk:kkk+1],
-                             proj_geomT, vol_geomT)
-                astra.matlab.data3d('delete', x_id)
-        else:
-            x_id, x_temp = \
-                  astra.creators.create_backprojection3d_gpu(
-                      residual, proj_geom, vol_geom)            
-
-        X = X_t - (1/L_const) * x_temp
-        astra.matlab.data3d('delete', sino_id)
-        astra.matlab.data3d('delete', x_id)
-        
-
-        ## REGULARIZATION
-        ## SKIPPING FOR NOW
-        ## Should be simpli
-        # regularizer = fistaRecon.getParameter('regularizer')
-        # for slices:
-        # out = regularizer(input=X)
-        print ("skipping regularizer")
-
-
-        ## FINAL
-        print ("final")
-        lambdaR_L1 = fistaRecon.getParameter('ring_lambda_R_L1')
-        if lambdaR_L1 > 0:
-            fistaRecon.r = numpy.max(
-                numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \
-                numpy.sign(fistaRecon.r)
-        t = (1 + numpy.sqrt(1 + 4 * t**2))/2
-        X_t = X + (((t_old -1)/t) * (X - X_old))
-
-        if lambdaR_L1 > 0:
-            fistaRecon.r_x = fistaRecon.r + \
-                             (((t_old-1)/t) * (fistaRecon.r - r_old))
-
-        if fistaRecon.getParameter('region_of_interest') is None:
-            string = 'Iteration Number {0} | Objective {1} \n'
-            print (string.format( i, objective[i]))
-        else:
-            ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                    'ideal_image')
-            
-            Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-            string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-            print (string.format(i,Resid_error[i], objective[i]))
-            
-##        if (lambdaR_L1 > 0)
-##            r =  max(abs(r)-lambdaR_L1, 0).*sign(r); % soft-thresholding operator for ring vector
-##        end
-##        
-##        t = (1 + sqrt(1 + 4*t^2))/2; % updating t
-##        X_t = X + ((t_old-1)/t).*(X - X_old); % updating X
-##        
-##        if (lambdaR_L1 > 0)
-##            r_x = r + ((t_old-1)/t).*(r - r_old); % updating r
-##        end
-##        
-##        if (show == 1)
-##            figure(10); imshow(X(:,:,slice), [0 maxvalplot]);
-##            if (lambdaR_L1 > 0)
-##                figure(11); plot(r); title('Rings offset vector')
-##            end
-##            pause(0.01);
-##        end
-##        if (strcmp(X_ideal, 'none' ) == 0)
-##            Resid_error(i) = RMSE(X(ROI), X_ideal(ROI));
-##            fprintf('%s %i %s %s %.4f  %s %s %f \n', 'Iteration Number:', i, '|', 'Error RMSE:', Resid_error(i), '|', 'Objective:', objective(i));
-##        else
-##            fprintf('%s %i  %s %s %f \n', 'Iteration Number:', i, '|', 'Objective:', objective(i));
-##        end
-else:
-    
-    # create a device for forward/backprojection
-    #astradevice = createAstraDevice(proj_geom, vol_geom)
-    
-    astradevice = AstraDevice(DeviceModel.DeviceType.PARALLEL3D.value,
-                [proj_geom['DetectorRowCount'] ,
-                 proj_geom['DetectorColCount'] ,
-                 proj_geom['DetectorSpacingX'] ,
-                 proj_geom['DetectorSpacingY'] ,
-                 proj_geom['ProjectionAngles']
-                 ],
-                [
-                    vol_geom['GridColCount'],
-                    vol_geom['GridRowCount'], 
-                    vol_geom['GridSliceCount'] ] )
-
-    regul = Regularizer(Regularizer.Algorithm.FGP_TV)
-    regul.setParameter(regularization_parameter=5e6,
-                       number_of_iterations=50,
-                       tolerance_constant=1e-4,
-                       TV_penalty=Regularizer.TotalVariationPenalty.isotropic)
-    
-    fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                device = astradevice,
-                                weights=Weights3D,
-                                regularizer = regul
-                                )
-
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    fistaRecon.setParameter(number_of_iterations = 18)
-    fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-    fistaRecon.setParameter(ring_alpha = 21)
-    fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-
-    
-    
-    fistaRecon.prepareForIteration()
-    X = numpy.load("X.npy")
-
-    
-    X = fistaRecon.iterate(X)
-    #numpy.save("X_out.npy", X)
diff --git a/src/Python/test/test_regularizers.py b/src/Python/test/test_regularizers.py
deleted file mode 100644
index 27e4ed3..0000000
--- a/src/Python/test/test_regularizers.py
+++ /dev/null
@@ -1,412 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug  4 11:10:05 2017
-
-@author: ofn77899
-"""
-
-#from ccpi.viewer.CILViewer2D import Converter
-#import vtk
-
-import matplotlib.pyplot as plt
-import numpy as np
-import os    
-from enum import Enum
-import timeit
-#from PIL import Image
-#from Regularizer import Regularizer
-from ccpi.imaging.Regularizer import Regularizer
-
-###############################################################################
-#https://stackoverflow.com/questions/13875989/comparing-image-in-url-to-image-in-filesystem-in-python/13884956#13884956
-#NRMSE a normalization of the root of the mean squared error
-#NRMSE is simply 1 - [RMSE / (maxval - minval)]. Where maxval is the maximum
-# intensity from the two images being compared, and respectively the same for
-# minval. RMSE is given by the square root of MSE: 
-# sqrt[(sum(A - B) ** 2) / |A|],
-# where |A| means the number of elements in A. By doing this, the maximum value
-# given by RMSE is maxval.
-
-def nrmse(im1, im2):
-    a, b = im1.shape
-    rmse = np.sqrt(np.sum((im2 - im1) ** 2) / float(a * b))
-    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))
-###############################################################################
-
-###############################################################################
-#
-#  2D Regularizers
-#
-###############################################################################
-#Example:
-# figure;
-# Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\lena_gray_512.tif"
-filename = r"/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/data/lena_gray_512.tif"
-#filename = r'/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif'
-
-#reader = vtk.vtkTIFFReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-Im = plt.imread(filename)                     
-#Im = Image.open('/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif')/255
-#img.show()
-Im = np.asarray(Im, dtype='float32')
-
-
-
-
-#imgplot = plt.imshow(Im)
-perc = 0.05
-u0 = Im + (perc* np.random.normal(size=np.shape(Im)))
-# map the u0 u0->u0>0
-f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-u0 = f(u0).astype('float32')
-
-## plot 
-fig = plt.figure()
-#a=fig.add_subplot(3,3,1)
-#a.set_title('Original')
-#imgplot = plt.imshow(Im)
-
-a=fig.add_subplot(2,3,1)
-a.set_title('noise')
-imgplot = plt.imshow(u0,cmap="gray")
-
-reg_output = []
-##############################################################################
-# Call regularizer
-
-####################### SplitBregman_TV #####################################
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-use_object = True
-if use_object:
-    reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-    print (reg.pars)
-    reg.setParameter(input=u0)    
-    reg.setParameter(regularization_parameter=10.)
-    # or 
-    # reg.setParameter(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-              #TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    plotme = reg() [0]
-    pars = reg.pars
-    textstr = reg.printParametersToString() 
-    
-    #out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-    #          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-
-else:
-    out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
-    pars = out2[2]
-    reg_output.append(out2)
-    plotme = reg_output[-1][0]
-    textstr = out2[-1]
-
-a=fig.add_subplot(2,3,2)
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(plotme,cmap="gray")
-
-###################### FGP_TV #########################################
-# u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.0005,
-                          number_of_iterations=50)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,3)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0])
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-###################### LLT_model #########################################
-# * u0 = Im + .03*randn(size(Im)); % adding noise
-# [Den] = LLT_model(single(u0), 10, 0.1, 1);
-#Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-#input, regularization_parameter , time_step, number_of_iterations,
-#                  tolerance_constant, restrictive_Z_smoothing=0
-out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-                          time_step=0.0003,
-                          tolerance_constant=0.0001,
-                          number_of_iterations=300)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,4)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-# ###################### PatchBased_Regul #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-
-out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-                       searching_window_ratio=3,
-                       similarity_window_ratio=1,
-                       PB_filtering_parameter=0.08)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,5)
-
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-# ###################### TGV_PD #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-                           first_order_term=1.3,
-                           second_order_term=1,
-                           number_of_iterations=550)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,6)
-
-
-textstr = out2[-1]
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-plt.show()
-
-################################################################################
-##
-##  3D Regularizers
-##
-################################################################################
-##Example:
-## figure;
-## Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-## u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Reconstruction\python\test\reconstruction_example.mha"
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Simpleflex\data\head.mha"
-#
-#reader = vtk.vtkMetaImageReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-##vtk returns 3D images, let's take just the one slice there is as 2D
-#Im = Converter.vtk2numpy(reader.GetOutput())
-#Im = Im.astype('float32')
-##imgplot = plt.imshow(Im)
-#perc = 0.05
-#u0 = Im + (perc* np.random.normal(size=np.shape(Im)))
-## map the u0 u0->u0>0
-#f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-#u0 = f(u0).astype('float32')
-#converter = Converter.numpy2vtkImporter(u0, reader.GetOutput().GetSpacing(),
-#                                        reader.GetOutput().GetOrigin())
-#converter.Update()
-#writer = vtk.vtkMetaImageWriter()
-#writer.SetInputData(converter.GetOutput())
-#writer.SetFileName(r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\noisy_head.mha")
-##writer.Write()
-#
-#
-### plot 
-#fig3D = plt.figure()
-##a=fig.add_subplot(3,3,1)
-##a.set_title('Original')
-##imgplot = plt.imshow(Im)
-#sliceNo = 32
-#
-#a=fig3D.add_subplot(2,3,1)
-#a.set_title('noise')
-#imgplot = plt.imshow(u0.T[sliceNo])
-#
-#reg_output3d = []
-#
-###############################################################################
-## Call regularizer
-#
-######################## SplitBregman_TV #####################################
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-#
-##out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-##          #tolerance_constant=1e-4, 
-##          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### FGP_TV #########################################
-## u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-#out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.005,
-#                          number_of_iterations=200)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### LLT_model #########################################
-## * u0 = Im + .03*randn(size(Im)); % adding noise
-## [Den] = LLT_model(single(u0), 10, 0.1, 1);
-##Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-##input, regularization_parameter , time_step, number_of_iterations,
-##                  tolerance_constant, restrictive_Z_smoothing=0
-#out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-#                          time_step=0.0003,
-#                          tolerance_constant=0.0001,
-#                          number_of_iterations=300)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### PatchBased_Regul #########################################
-## Quick 2D denoising example in Matlab:   
-##   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-##   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-##   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-#
-#out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-#                          searching_window_ratio=3,
-#                          similarity_window_ratio=1,
-#                          PB_filtering_parameter=0.08)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-
-###################### TGV_PD #########################################
-# Quick 2D denoising example in Matlab:   
-#   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-#   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-#   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-#out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-#                          first_order_term=1.3,
-#                          second_order_term=1,
-#                          number_of_iterations=550)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
diff --git a/src/Python/test/test_regularizers_3d.py b/src/Python/test/test_regularizers_3d.py
deleted file mode 100644
index 2d11a7e..0000000
--- a/src/Python/test/test_regularizers_3d.py
+++ /dev/null
@@ -1,425 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug  4 11:10:05 2017
-
-@author: ofn77899
-"""
-
-#from ccpi.viewer.CILViewer2D import Converter
-#import vtk
-
-import matplotlib.pyplot as plt
-import numpy as np
-import os    
-from enum import Enum
-import timeit
-#from PIL import Image
-#from Regularizer import Regularizer
-from ccpi.imaging.Regularizer import Regularizer
-
-###############################################################################
-#https://stackoverflow.com/questions/13875989/comparing-image-in-url-to-image-in-filesystem-in-python/13884956#13884956
-#NRMSE a normalization of the root of the mean squared error
-#NRMSE is simply 1 - [RMSE / (maxval - minval)]. Where maxval is the maximum
-# intensity from the two images being compared, and respectively the same for
-# minval. RMSE is given by the square root of MSE: 
-# sqrt[(sum(A - B) ** 2) / |A|],
-# where |A| means the number of elements in A. By doing this, the maximum value
-# given by RMSE is maxval.
-
-def nrmse(im1, im2):
-    a, b = im1.shape
-    rmse = np.sqrt(np.sum((im2 - im1) ** 2) / float(a * b))
-    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))
-###############################################################################
-
-###############################################################################
-#
-#  2D Regularizers
-#
-###############################################################################
-#Example:
-# figure;
-# Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\lena_gray_512.tif"
-filename = r"/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/data/lena_gray_512.tif"
-#filename = r'/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif'
-
-#reader = vtk.vtkTIFFReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-Im = plt.imread(filename)                     
-#Im = Image.open('/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif')/255
-#img.show()
-Im = np.asarray(Im, dtype='float32')
-
-# create a 3D image by stacking N of this images
-
-
-#imgplot = plt.imshow(Im)
-perc = 0.05
-u_n = Im + (perc* np.random.normal(size=np.shape(Im)))
-y,z = np.shape(u_n)
-u_n = np.reshape(u_n , (1,y,z))
-
-u0 = u_n.copy()
-for i in range (19):
-    u_n = Im + (perc* np.random.normal(size=np.shape(Im)))
-    u_n = np.reshape(u_n , (1,y,z))
-
-    u0 = np.vstack ( (u0, u_n) )
-
-# map the u0 u0->u0>0
-f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-u0 = f(u0).astype('float32')
-
-print ("Passed image shape {0}".format(np.shape(u0)))
-
-## plot 
-fig = plt.figure()
-#a=fig.add_subplot(3,3,1)
-#a.set_title('Original')
-#imgplot = plt.imshow(Im)
-sliceno = 10
-
-a=fig.add_subplot(2,3,1)
-a.set_title('noise')
-imgplot = plt.imshow(u0[sliceno],cmap="gray")
-
-reg_output = []
-##############################################################################
-# Call regularizer
-
-####################### SplitBregman_TV #####################################
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-use_object = True
-if use_object:
-    reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-    print (reg.pars)
-    reg.setParameter(input=u0)    
-    reg.setParameter(regularization_parameter=10.)
-    # or 
-    # reg.setParameter(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-              #TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    plotme = reg() [0]
-    pars = reg.pars
-    textstr = reg.printParametersToString() 
-    
-    #out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-    #          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-
-else:
-    out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
-    pars = out2[2]
-    reg_output.append(out2)
-    plotme = reg_output[-1][0]
-    textstr = out2[-1]
-
-a=fig.add_subplot(2,3,2)
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(plotme[sliceno],cmap="gray")
-
-###################### FGP_TV #########################################
-# u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.0005,
-                          number_of_iterations=50)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,3)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0][sliceno])
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0][sliceno],cmap="gray")
-
-###################### LLT_model #########################################
-# * u0 = Im + .03*randn(size(Im)); % adding noise
-# [Den] = LLT_model(single(u0), 10, 0.1, 1);
-#Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-#input, regularization_parameter , time_step, number_of_iterations,
-#                  tolerance_constant, restrictive_Z_smoothing=0
-out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-                          time_step=0.0003,
-                          tolerance_constant=0.0001,
-                          number_of_iterations=300)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,4)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0][sliceno],cmap="gray")
-
-
-# ###################### PatchBased_Regul #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-
-out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-                       searching_window_ratio=3,
-                       similarity_window_ratio=1,
-                       PB_filtering_parameter=0.08)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,5)
-
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0][sliceno],cmap="gray")
-
-
-# ###################### TGV_PD #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-                           first_order_term=1.3,
-                           second_order_term=1,
-                           number_of_iterations=550)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,6)
-
-
-textstr = out2[-1]
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0][sliceno],cmap="gray")
-
-
-plt.show()
-
-################################################################################
-##
-##  3D Regularizers
-##
-################################################################################
-##Example:
-## figure;
-## Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-## u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Reconstruction\python\test\reconstruction_example.mha"
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Simpleflex\data\head.mha"
-#
-#reader = vtk.vtkMetaImageReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-##vtk returns 3D images, let's take just the one slice there is as 2D
-#Im = Converter.vtk2numpy(reader.GetOutput())
-#Im = Im.astype('float32')
-##imgplot = plt.imshow(Im)
-#perc = 0.05
-#u0 = Im + (perc* np.random.normal(size=np.shape(Im)))
-## map the u0 u0->u0>0
-#f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-#u0 = f(u0).astype('float32')
-#converter = Converter.numpy2vtkImporter(u0, reader.GetOutput().GetSpacing(),
-#                                        reader.GetOutput().GetOrigin())
-#converter.Update()
-#writer = vtk.vtkMetaImageWriter()
-#writer.SetInputData(converter.GetOutput())
-#writer.SetFileName(r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\noisy_head.mha")
-##writer.Write()
-#
-#
-### plot 
-#fig3D = plt.figure()
-##a=fig.add_subplot(3,3,1)
-##a.set_title('Original')
-##imgplot = plt.imshow(Im)
-#sliceNo = 32
-#
-#a=fig3D.add_subplot(2,3,1)
-#a.set_title('noise')
-#imgplot = plt.imshow(u0.T[sliceNo])
-#
-#reg_output3d = []
-#
-###############################################################################
-## Call regularizer
-#
-######################## SplitBregman_TV #####################################
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-#
-##out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-##          #tolerance_constant=1e-4, 
-##          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### FGP_TV #########################################
-## u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-#out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.005,
-#                          number_of_iterations=200)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### LLT_model #########################################
-## * u0 = Im + .03*randn(size(Im)); % adding noise
-## [Den] = LLT_model(single(u0), 10, 0.1, 1);
-##Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-##input, regularization_parameter , time_step, number_of_iterations,
-##                  tolerance_constant, restrictive_Z_smoothing=0
-#out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-#                          time_step=0.0003,
-#                          tolerance_constant=0.0001,
-#                          number_of_iterations=300)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### PatchBased_Regul #########################################
-## Quick 2D denoising example in Matlab:   
-##   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-##   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-##   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-#
-#out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-#                          searching_window_ratio=3,
-#                          similarity_window_ratio=1,
-#                          PB_filtering_parameter=0.08)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-
-###################### TGV_PD #########################################
-# Quick 2D denoising example in Matlab:   
-#   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-#   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-#   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-#out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-#                          first_order_term=1.3,
-#                          second_order_term=1,
-#                          number_of_iterations=550)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
diff --git a/src/Python/test_reconstructor.py b/src/Python/test_reconstructor.py
deleted file mode 100644
index 07668ba..0000000
--- a/src/Python/test_reconstructor.py
+++ /dev/null
@@ -1,301 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Aug 23 16:34:49 2017
-
-@author: ofn77899
-Based on DemoRD2.m
-"""
-
-import h5py
-import numpy
-
-from ccpi.fista.FISTAReconstructor import FISTAReconstructor
-import astra
-import matplotlib.pyplot as plt
-
-def RMSE(signal1, signal2):
-    '''RMSE Root Mean Squared Error'''
-    if numpy.shape(signal1) == numpy.shape(signal2):
-        err = (signal1 - signal2)
-        err = numpy.sum( err * err )/numpy.size(signal1);  # MSE
-        err = sqrt(err);                                   # RMSE
-        return err
-    else:
-        raise Exception('Input signals must have the same shape')
-  
-filename = r'/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/demos/DendrData.h5'
-nx = h5py.File(filename, "r")
-#getEntry(nx, '/')
-# I have exported the entries as children of /
-entries = [entry for entry in nx['/'].keys()]
-print (entries)
-
-Sino3D = numpy.asarray(nx.get('/Sino3D'), dtype="float32")
-Weights3D = numpy.asarray(nx.get('/Weights3D'), dtype="float32")
-angSize = numpy.asarray(nx.get('/angSize'), dtype=int)[0]
-angles_rad = numpy.asarray(nx.get('/angles_rad'), dtype="float32")
-recon_size = numpy.asarray(nx.get('/recon_size'), dtype=int)[0]
-size_det = numpy.asarray(nx.get('/size_det'), dtype=int)[0]
-slices_tot = numpy.asarray(nx.get('/slices_tot'), dtype=int)[0]
-
-Z_slices = 20
-det_row_count = Z_slices
-# next definition is just for consistency of naming
-det_col_count = size_det
-
-detectorSpacingX = 1.0
-detectorSpacingY = detectorSpacingX
-
-
-proj_geom = astra.creators.create_proj_geom('parallel3d',
-                                            detectorSpacingX,
-                                            detectorSpacingY,
-                                            det_row_count,
-                                            det_col_count,
-                                            angles_rad)
-
-#vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices);
-image_size_x = recon_size
-image_size_y = recon_size
-image_size_z = Z_slices
-vol_geom = astra.creators.create_vol_geom( image_size_x,
-                                           image_size_y,
-                                           image_size_z)
-
-## First pass the arguments to the FISTAReconstructor and test the
-## Lipschitz constant
-
-fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                weights=Weights3D)
-
-print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-fistaRecon.setParameter(number_of_iterations = 12)
-fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-fistaRecon.setParameter(ring_alpha = 21)
-fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-
-## Ordered subset
-if False:
-    subsets = 16
-    angles = fistaRecon.getParameter('projector_geometry')['ProjectionAngles']
-    #binEdges = numpy.linspace(angles.min(),
-    #                          angles.max(),
-    #                          subsets + 1)
-    binsDiscr, binEdges = numpy.histogram(angles, bins=subsets)
-    # get rearranged subset indices
-    IndicesReorg = numpy.zeros((numpy.shape(angles)))
-    counterM = 0
-    for ii in range(binsDiscr.max()):
-        counter = 0
-        for jj in range(subsets):
-            curr_index = ii + jj  + counter
-            #print ("{0} {1} {2}".format(binsDiscr[jj] , ii, counterM))
-            if binsDiscr[jj] > ii:
-                if (counterM < numpy.size(IndicesReorg)):
-                    IndicesReorg[counterM] = curr_index
-                counterM = counterM + 1
-                
-            counter = counter + binsDiscr[jj] - 1
-
-
-if False:
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    print ("prepare for iteration")
-    fistaRecon.prepareForIteration()
-    
-    
-
-    print("initializing  ...")
-    if False:
-        # if X doesn't exist
-        #N = params.vol_geom.GridColCount
-        N = vol_geom['GridColCount']
-        print ("N " + str(N))
-        X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
-    else:
-        #X = fistaRecon.initialize()
-        X = numpy.load("X.npy")
-    
-    print (numpy.shape(X))
-    X_t = X.copy()
-    print ("initialized")
-    proj_geom , vol_geom, sino , \
-                      SlicesZ = fistaRecon.getParameter(['projector_geometry' ,
-                                                            'output_geometry',
-                                                            'input_sinogram',
-                                                         'SlicesZ'])
-
-    #fistaRecon.setParameter(number_of_iterations = 3)
-    iterFISTA = fistaRecon.getParameter('number_of_iterations')
-    # errors vector (if the ground truth is given)
-    Resid_error = numpy.zeros((iterFISTA));
-    # objective function values vector
-    objective = numpy.zeros((iterFISTA)); 
-
-      
-    t = 1
-
-
-    print ("starting iterations")
-##    % Outer FISTA iterations loop
-    for i in range(fistaRecon.getParameter('number_of_iterations')):
-        X_old = X.copy()
-        t_old = t
-        r_old = fistaRecon.r.copy()
-        if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec' :
-            # if the geometry is parallel use slice-by-slice
-            # projection-backprojection routine
-            #sino_updt = zeros(size(sino),'single');
-            proj_geomT = proj_geom.copy()
-            proj_geomT['DetectorRowCount'] = 1
-            vol_geomT = vol_geom.copy()
-            vol_geomT['GridSliceCount'] = 1;
-            sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
-            for kkk in range(SlicesZ):
-                sino_id, sino_updt[kkk] = \
-                         astra.creators.create_sino3d_gpu(
-                             X_t[kkk:kkk+1], proj_geom, vol_geom)
-                astra.matlab.data3d('delete', sino_id)
-        else:
-            # for divergent 3D geometry (watch the GPU memory overflow in
-            # ASTRA versions < 1.8)
-            #[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
-            sino_id, sino_updt = astra.creators.create_sino3d_gpu(
-                X_t, proj_geom, vol_geom)
-
-        ## RING REMOVAL
-        residual = fistaRecon.residual
-        lambdaR_L1 , alpha_ring , weights , L_const= \
-                   fistaRecon.getParameter(['ring_lambda_R_L1',
-                                           'ring_alpha' , 'weights',
-                                           'Lipschitz_constant'])
-        r_x = fistaRecon.r_x
-        SlicesZ, anglesNumb, Detectors = \
-                    numpy.shape(fistaRecon.getParameter('input_sinogram'))
-        if lambdaR_L1 > 0 :
-             print ("ring removal")
-             for kkk in range(anglesNumb):
-                 
-                 residual[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
-                                       ((sino_updt[:,kkk,:]).squeeze() - \
-                                        (sino[:,kkk,:]).squeeze() -\
-                                        (alpha_ring * r_x)
-                                        )
-             vec = residual.sum(axis = 1)
-             #if SlicesZ > 1:
-             #    vec = vec[:,1,:].squeeze()
-             fistaRecon.r = (r_x - (1./L_const) * vec).copy()
-             objective[i] = (0.5 * (residual ** 2).sum())
-##            % the ring removal part (Group-Huber fidelity)
-##            for kkk = 1:anglesNumb
-##                residual(:,kkk,:) =  squeeze(weights(:,kkk,:)).*
-##                 (squeeze(sino_updt(:,kkk,:)) -
-##                 (squeeze(sino(:,kkk,:)) - alpha_ring.*r_x));
-##            end
-##            vec = sum(residual,2);
-##            if (SlicesZ > 1)
-##                vec = squeeze(vec(:,1,:));
-##            end
-##            r = r_x - (1./L_const).*vec;
-##            objective(i) = (0.5*sum(residual(:).^2)); % for the objective function output
-
-        
-
-        # Projection/Backprojection Routine
-        if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or\
-           fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec':
-            x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32)
-            print ("Projection/Backprojection Routine")
-            for kkk in range(SlicesZ):
-                
-                x_id, x_temp[kkk] = \
-                         astra.creators.create_backprojection3d_gpu(
-                             residual[kkk:kkk+1],
-                             proj_geomT, vol_geomT)
-                astra.matlab.data3d('delete', x_id)
-        else:
-            x_id, x_temp = \
-                  astra.creators.create_backprojection3d_gpu(
-                      residual, proj_geom, vol_geom)            
-
-        X = X_t - (1/L_const) * x_temp
-        astra.matlab.data3d('delete', sino_id)
-        astra.matlab.data3d('delete', x_id)
-        
-
-        ## REGULARIZATION
-        ## SKIPPING FOR NOW
-        ## Should be simpli
-        # regularizer = fistaRecon.getParameter('regularizer')
-        # for slices:
-        # out = regularizer(input=X)
-        print ("skipping regularizer")
-
-
-        ## FINAL
-        print ("final")
-        lambdaR_L1 = fistaRecon.getParameter('ring_lambda_R_L1')
-        if lambdaR_L1 > 0:
-            fistaRecon.r = numpy.max(
-                numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \
-                numpy.sign(fistaRecon.r)
-        t = (1 + numpy.sqrt(1 + 4 * t**2))/2
-        X_t = X + (((t_old -1)/t) * (X - X_old))
-
-        if lambdaR_L1 > 0:
-            fistaRecon.r_x = fistaRecon.r + \
-                             (((t_old-1)/t) * (fistaRecon.r - r_old))
-
-        if fistaRecon.getParameter('region_of_interest') is None:
-            string = 'Iteration Number {0} | Objective {1} \n'
-            print (string.format( i, objective[i]))
-        else:
-            ROI , X_ideal = fistaRecon.getParameter('region_of_interest',
-                                                    'ideal_image')
-            
-            Resid_error[i] = RMSE(X*ROI, X_ideal*ROI)
-            string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
-            print (string.format(i,Resid_error[i], objective[i]))
-            
-##        if (lambdaR_L1 > 0)
-##            r =  max(abs(r)-lambdaR_L1, 0).*sign(r); % soft-thresholding operator for ring vector
-##        end
-##        
-##        t = (1 + sqrt(1 + 4*t^2))/2; % updating t
-##        X_t = X + ((t_old-1)/t).*(X - X_old); % updating X
-##        
-##        if (lambdaR_L1 > 0)
-##            r_x = r + ((t_old-1)/t).*(r - r_old); % updating r
-##        end
-##        
-##        if (show == 1)
-##            figure(10); imshow(X(:,:,slice), [0 maxvalplot]);
-##            if (lambdaR_L1 > 0)
-##                figure(11); plot(r); title('Rings offset vector')
-##            end
-##            pause(0.01);
-##        end
-##        if (strcmp(X_ideal, 'none' ) == 0)
-##            Resid_error(i) = RMSE(X(ROI), X_ideal(ROI));
-##            fprintf('%s %i %s %s %.4f  %s %s %f \n', 'Iteration Number:', i, '|', 'Error RMSE:', Resid_error(i), '|', 'Objective:', objective(i));
-##        else
-##            fprintf('%s %i  %s %s %f \n', 'Iteration Number:', i, '|', 'Objective:', objective(i));
-##        end
-else:
-    fistaRecon = FISTAReconstructor(proj_geom,
-                                vol_geom,
-                                Sino3D ,
-                                weights=Weights3D)
-
-    print ("Lipschitz Constant {0}".format(fistaRecon.pars['Lipschitz_constant']))
-    fistaRecon.setParameter(number_of_iterations = 12)
-    fistaRecon.setParameter(Lipschitz_constant = 767893952.0)
-    fistaRecon.setParameter(ring_alpha = 21)
-    fistaRecon.setParameter(ring_lambda_R_L1 = 0.002)
-    fistaRecon.prepareForIteration()
-    X = fistaRecon.iterate(numpy.load("X.npy"))
diff --git a/src/Python/test_regularizers.py b/src/Python/test_regularizers.py
deleted file mode 100644
index e76262c..0000000
--- a/src/Python/test_regularizers.py
+++ /dev/null
@@ -1,412 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Fri Aug  4 11:10:05 2017
-
-@author: ofn77899
-"""
-
-#from ccpi.viewer.CILViewer2D import Converter
-#import vtk
-
-import matplotlib.pyplot as plt
-import numpy as np
-import os    
-from enum import Enum
-import timeit
-#from PIL import Image
-#from Regularizer import Regularizer
-from ccpi.imaging.Regularizer import Regularizer
-
-###############################################################################
-#https://stackoverflow.com/questions/13875989/comparing-image-in-url-to-image-in-filesystem-in-python/13884956#13884956
-#NRMSE a normalization of the root of the mean squared error
-#NRMSE is simply 1 - [RMSE / (maxval - minval)]. Where maxval is the maximum
-# intensity from the two images being compared, and respectively the same for
-# minval. RMSE is given by the square root of MSE: 
-# sqrt[(sum(A - B) ** 2) / |A|],
-# where |A| means the number of elements in A. By doing this, the maximum value
-# given by RMSE is maxval.
-
-def nrmse(im1, im2):
-    a, b = im1.shape
-    rmse = np.sqrt(np.sum((im2 - im1) ** 2) / float(a * b))
-    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))
-###############################################################################
-
-###############################################################################
-#
-#  2D Regularizers
-#
-###############################################################################
-#Example:
-# figure;
-# Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\lena_gray_512.tif"
-filename = r"/home/ofn77899/Reconstruction/CCPi-FISTA_Reconstruction/data/lena_gray_512.tif"
-#filename = r'/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif'
-
-#reader = vtk.vtkTIFFReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-Im = plt.imread(filename)                     
-#Im = Image.open('/home/algol/Documents/Python/STD_test_images/lena_gray_512.tif')/255
-#img.show()
-Im = np.asarray(Im, dtype='float32')
-
-
-
-
-#imgplot = plt.imshow(Im)
-perc = 0.05
-u0 = Im + (perc* np.random.normal(size=np.shape(Im)))
-# map the u0 u0->u0>0
-f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-u0 = f(u0).astype('float32')
-
-## plot 
-fig = plt.figure()
-#a=fig.add_subplot(3,3,1)
-#a.set_title('Original')
-#imgplot = plt.imshow(Im)
-
-a=fig.add_subplot(2,3,1)
-a.set_title('noise')
-imgplot = plt.imshow(u0,cmap="gray")
-
-reg_output = []
-##############################################################################
-# Call regularizer
-
-####################### SplitBregman_TV #####################################
-# u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-
-use_object = True
-if use_object:
-    reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-    print (reg.pars)
-    reg.setParameter(input=u0)    
-    reg.setParameter(regularization_parameter=10.)
-    # or 
-    # reg.setParameter(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-              #TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    plotme = reg() [0]
-    pars = reg.pars
-    textstr = reg.printParametersToString() 
-    
-    #out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-              #tolerance_constant=1e-4, 
-    #          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-    
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-
-else:
-    out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10. )
-    pars = out2[2]
-    reg_output.append(out2)
-    plotme = reg_output[-1][0]
-    textstr = out2[-1]
-
-a=fig.add_subplot(2,3,2)
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(plotme,cmap="gray")
-
-###################### FGP_TV #########################################
-# u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.005,
-                          number_of_iterations=200)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,3)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0])
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-###################### LLT_model #########################################
-# * u0 = Im + .03*randn(size(Im)); % adding noise
-# [Den] = LLT_model(single(u0), 10, 0.1, 1);
-#Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-#input, regularization_parameter , time_step, number_of_iterations,
-#                  tolerance_constant, restrictive_Z_smoothing=0
-out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-                          time_step=0.0003,
-                          tolerance_constant=0.0001,
-                          number_of_iterations=300)
-pars = out2[-2]
-
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,4)
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-# ###################### PatchBased_Regul #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-
-out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-                       searching_window_ratio=3,
-                       similarity_window_ratio=1,
-                       PB_filtering_parameter=0.08)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,5)
-
-
-textstr = out2[-1]
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-        verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-# ###################### TGV_PD #########################################
-# # Quick 2D denoising example in Matlab:   
-# #   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-# #   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-# #   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-                           first_order_term=1.3,
-                           second_order_term=1,
-                           number_of_iterations=550)
-pars = out2[-2]
-reg_output.append(out2)
-
-a=fig.add_subplot(2,3,6)
-
-
-textstr = out2[-1]
-
-
-# these are matplotlib.patch.Patch properties
-props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-# place a text box in upper left in axes coords
-a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-         verticalalignment='top', bbox=props)
-imgplot = plt.imshow(reg_output[-1][0],cmap="gray")
-
-
-plt.show()
-
-################################################################################
-##
-##  3D Regularizers
-##
-################################################################################
-##Example:
-## figure;
-## Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-## u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Reconstruction\python\test\reconstruction_example.mha"
-#filename = r"C:\Users\ofn77899\Documents\GitHub\CCPi-Simpleflex\data\head.mha"
-#
-#reader = vtk.vtkMetaImageReader()
-#reader.SetFileName(os.path.normpath(filename))
-#reader.Update()
-##vtk returns 3D images, let's take just the one slice there is as 2D
-#Im = Converter.vtk2numpy(reader.GetOutput())
-#Im = Im.astype('float32')
-##imgplot = plt.imshow(Im)
-#perc = 0.05
-#u0 = Im + (perc* np.random.normal(size=np.shape(Im)))
-## map the u0 u0->u0>0
-#f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
-#u0 = f(u0).astype('float32')
-#converter = Converter.numpy2vtkImporter(u0, reader.GetOutput().GetSpacing(),
-#                                        reader.GetOutput().GetOrigin())
-#converter.Update()
-#writer = vtk.vtkMetaImageWriter()
-#writer.SetInputData(converter.GetOutput())
-#writer.SetFileName(r"C:\Users\ofn77899\Documents\GitHub\CCPi-FISTA_reconstruction\data\noisy_head.mha")
-##writer.Write()
-#
-#
-### plot 
-#fig3D = plt.figure()
-##a=fig.add_subplot(3,3,1)
-##a.set_title('Original')
-##imgplot = plt.imshow(Im)
-#sliceNo = 32
-#
-#a=fig3D.add_subplot(2,3,1)
-#a.set_title('noise')
-#imgplot = plt.imshow(u0.T[sliceNo])
-#
-#reg_output3d = []
-#
-###############################################################################
-## Call regularizer
-#
-######################## SplitBregman_TV #####################################
-## u = SplitBregman_TV(single(u0), 10, 30, 1e-04);
-#
-##reg = Regularizer(Regularizer.Algorithm.SplitBregman_TV)
-#
-##out = reg(input=u0, regularization_parameter=10., #number_of_iterations=30,
-##          #tolerance_constant=1e-4, 
-##          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#out2 = Regularizer.SplitBregman_TV(input=u0, regularization_parameter=10., number_of_iterations=30,
-#          tolerance_constant=1e-4, 
-#          TV_Penalty=Regularizer.TotalVariationPenalty.l1)
-#
-#
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### FGP_TV #########################################
-## u = FGP_TV(single(u0), 0.05, 100, 1e-04);
-#out2 = Regularizer.FGP_TV(input=u0, regularization_parameter=0.005,
-#                          number_of_iterations=200)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### LLT_model #########################################
-## * u0 = Im + .03*randn(size(Im)); % adding noise
-## [Den] = LLT_model(single(u0), 10, 0.1, 1);
-##Den = LLT_model(single(u0), 25, 0.0003, 300, 0.0001, 0); 
-##input, regularization_parameter , time_step, number_of_iterations,
-##                  tolerance_constant, restrictive_Z_smoothing=0
-#out2 = Regularizer.LLT_model(input=u0, regularization_parameter=25,
-#                          time_step=0.0003,
-#                          tolerance_constant=0.0001,
-#                          number_of_iterations=300)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-####################### PatchBased_Regul #########################################
-## Quick 2D denoising example in Matlab:   
-##   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-##   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-##   ImDen = PB_Regul_CPU(single(u0), 3, 1, 0.08, 0.05); 
-#
-#out2 = Regularizer.PatchBased_Regul(input=u0, regularization_parameter=0.05,
-#                          searching_window_ratio=3,
-#                          similarity_window_ratio=1,
-#                          PB_filtering_parameter=0.08)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])
-#
-
-###################### TGV_PD #########################################
-# Quick 2D denoising example in Matlab:   
-#   Im = double(imread('lena_gray_256.tif'))/255;  % loading image
-#   u0 = Im + .03*randn(size(Im)); u0(u0<0) = 0; % adding noise
-#   u = PrimalDual_TGV(single(u0), 0.02, 1.3, 1, 550);
-
-
-#out2 = Regularizer.TGV_PD(input=u0, regularization_parameter=0.05,
-#                          first_order_term=1.3,
-#                          second_order_term=1,
-#                          number_of_iterations=550)
-#pars = out2[-2]
-#reg_output3d.append(out2)
-#
-#a=fig3D.add_subplot(2,3,2)
-#
-#
-#textstr = out2[-1]
-#
-#
-## these are matplotlib.patch.Patch properties
-#props = dict(boxstyle='round', facecolor='wheat', alpha=0.5)
-## place a text box in upper left in axes coords
-#a.text(0.05, 0.95, textstr, transform=a.transAxes, fontsize=14,
-#        verticalalignment='top', bbox=props)
-#imgplot = plt.imshow(reg_output3d[-1][0].T[sliceNo])