Added conda recipe for FISTA

removed dangling files

9 files changed, 3 insertions, 326 deletions

diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt
deleted file mode 100644
index 92baf2c..0000000
--- a/Wrappers/Python/CMakeLists.txt
+++ /dev/null
@@ -1,195 +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
-cmake_minimum_required (VERSION 3.0)
-
-project(FISTA)
-#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
-
-# The version number.
-set (FISTA_VERSION_MAJOR 1)
-set (FISTA_VERSION_MINOR 0)
-
-set (CIL_VERSION_MAJOR 0)
-set (CIL_VERSION_MINOR 9)
-set (CIL_VERSION_PATCH 1)
-
-set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
-
-#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 " ${CIL_VERSION})
-
-findPythonForAnacondaEnvironment(${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/Wrappers/Python/ccpi/reconstruction/Reconstructor.py b/Wrappers/Python/ccpi/reconstruction/Reconstructor.py
index ba67327..2ad8a44 100644
--- a/Wrappers/Python/ccpi/reconstruction/Reconstructor.py
+++ b/Wrappers/Python/ccpi/reconstruction/Reconstructor.py
@@ -351,7 +351,7 @@ class FISTA():
             #end
             del proj_geomT
             del vol_geomT
-        else
+        else:
             #% divergen beam geometry
             #fprintf('%s \n', 'Calculating Lipshitz constant for divergen beam geometry...');
             niter = 8; #% number of iteration for PM
@@ -391,7 +391,7 @@ class FISTA():
     
     
     def setRegularizer(self, regularizer):
-        if regularizer
+        #if regularizer
         self.pars['regularizer'] = regularizer
         
     
diff --git a/Wrappers/Python/compile-fista.bat.in b/Wrappers/Python/compile-fista.bat.in
deleted file mode 100644
index b1db686..0000000
--- a/Wrappers/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/Wrappers/Python/compile-fista.sh.in b/Wrappers/Python/compile-fista.sh.in
deleted file mode 100644
index 267f014..0000000
--- a/Wrappers/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/Wrappers/Python/compile.bat.in b/Wrappers/Python/compile.bat.in
deleted file mode 100644
index e5342ed..0000000
--- a/Wrappers/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/Wrappers/Python/compile.sh.in b/Wrappers/Python/compile.sh.in
deleted file mode 100644
index 93fdba2..0000000
--- a/Wrappers/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/Wrappers/Python/fista-recipe/meta.yaml b/Wrappers/Python/fista-recipe/meta.yaml
index 265541f..4e5cba6 100644
--- a/Wrappers/Python/fista-recipe/meta.yaml
+++ b/Wrappers/Python/fista-recipe/meta.yaml
@@ -19,7 +19,7 @@ requirements:
     - python
     - numpy
     #- astra-toolbox
-    - ccpi-regularizers
+    - ccpi-regularizer
 
 
 	
diff --git a/Wrappers/Python/setup-fista.py.in b/Wrappers/Python/setup-fista.py.in
deleted file mode 100644
index c5c9f4d..0000000
--- a/Wrappers/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/Wrappers/Python/setup.py.in b/Wrappers/Python/setup.py.in
deleted file mode 100644
index 12e8af1..0000000
--- a/Wrappers/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'},
-)
-
-