Add cil

.travis.yml

@@ -29,15 +29,27 @@ matrix:
  include:
  # linux g{cc,++}-6 py{27,3}
  - os: linux
-   python: 3
+   python: 3.6
+   # -boost +fftw3 +hdf5 +ace +cil
+   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON -DBUILD_CIL=ON -DSIRF_TAG=origin/add_to_sirf_classes -DCCPi-Framework_TAG=origin/finite_diff_for_sirf" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
+ - os: linux
+   python: 2.7
+   # -boost +fftw3 +hdf5 +ace +cil
+   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON -DBUILD_CIL=ON -DSIRF_TAG=origin/add_to_sirf_classes -DCCPi-Framework_TAG=origin/finite_diff_for_sirf" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=2
+ - os: linux
+   python: 2.7
+   # -boost +fftw3 +hdf5 +ace +cil_lite
+   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON -DBUILD_CIL_LITE=ON -DSIRF_TAG=origin/add_to_sirf_classes -DCCPi-Framework_TAG=origin/finite_diff_for_sirf" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=2
+ - os: linux
+   python: 3.6
    # -boost +fftw3 +hdf5 +ace
    env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
  - os: linux
    python: 2.7
    # -boost +fftw3 +hdf5 +siemens_to_ismrmrd +swig +ace
    env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON -DBUILD_siemens_to_ismrmrd=ON -DUSE_SYSTEM_SWIG=ON -DUSE_SYSTEM_ACE=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=2
  - os: linux
-   python: 3
+   python: 3.6
    # +DEVEL -boost -hdf5 -fftw3 +ace +siemens_to_ismrmrd
    env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_ACE=ON -DBUILD_siemens_to_ismrmrd=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
  - os: linux
@@ -50,7 +62,7 @@ matrix:
  #   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
  # - os: osx
  #   # +boost +fftw3 -hdf5 -swig
- #   python: 3
+ #   python: 3.6
  #   env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=OFF" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=3
  # - os: osx
  #   python: 2.7
@@ -62,7 +74,7 @@ matrix:
  #   env: EXTRA_BUILD_FLAGS="-DDEVEL_BUILD=ON -DUSE_SYSTEM_Boost=ON -DUSE_SYSTEM_FFTW3=OFF -DUSE_SYSTEM_HDF5=OFF -DUSE_SYSTEM_SWIG=ON" MATRIX_EVAL="CC=gcc CXX=g++" PYMVER=2
  # itk
  - os: linux
-   python: 3
+   python: 3.6
    # -boost +itk +fftw3 +hdf5
    env: EXTRA_BUILD_FLAGS="-DUSE_SYSTEM_Boost=OFF -DUSE_ITK=ON -DUSE_SYSTEM_FFTW3=ON -DUSE_SYSTEM_HDF5=ON" MATRIX_EVAL="CC=gcc-6 CXX=g++-6" PYMVER=3
  # - os: osx
@@ -120,6 +132,12 @@ addons:
   - libxslt-dev
   - libace-dev
   # - root-system-bin
+  # dependencies for ASTRA toolbox
+  - autotools-dev
+  - automake
+  - autogen
+  - autoconf
+  - libtool
 
 before_install:
 # Set C and C++ compiler etc using trick from
@@ -207,6 +225,17 @@ before_install:
 - $PY_EXE -m pip install --user -U pip setuptools wheel
 # ensure python bin dir exists (and coverage dependencies installed)
 - $PY_EXE -m pip install --user -U nose codecov coveralls
+# additional python deps
+- $PY_EXE -m pip install --user -U Cython  # first install Cython separately
+- $PY_EXE -m pip install --user -U numpy
+- |
+   if [[ "$EXTRA_BUILD_FLAGS" == *"-DBUILD_CIL=ON"* ]]; then
+     $PY_EXE -m pip install --user -U scipy h5py Pillow wget
+   fi
+- |
+   if [[ "$EXTRA_BUILD_FLAGS" == *"-DBUILD_CIL_LITE=ON"* ]]; then
+     $PY_EXE -m pip install --user -U scipy h5py Pillow wget
+   fi
 # for counting clones, excluding ours
 - |
    if [[ -n "$GITHUB_API_TOKEN" ]]; then
@@ -236,6 +265,8 @@ install:
 - |
    if [[ -n "$DOCKER_BUILD" ]]; then
      cd docker
+     [[ -n "$GROUPS" ]] || export GROUPS=$(id -g)
+     [[ -n "$UID" ]] || export UID=$(id -u)
      export DCC="docker-compose -p "travis_${TRAVIS_JOB_NUMBER/./_}" -f $PWD/docker-compose.yml"
      [[ "$DOCKER_BUILD" == *"DEVEL"* ]] && export DCC="$DCC -f $PWD/docker-compose.devel.yml"
      [[ "$DOCKER_BUILD" == *"SERVICE"* ]] && export DCC="$DCC -f $PWD/docker-compose.srv.yml"
@@ -247,20 +278,22 @@ install:
        # rebuild base image (using above docker cache)
        # and sirf image (with travis' ccache)
        rm -rf devel/.ccache
-       if [[ -n "$DOCKER_RECREATE_CCACHE" ]]; then
+       if [[ -n "$DOCKER_RECREATE_CCACHE" || ! -d ~/.ccache ]]; then
          mkdir devel/.ccache
          sudo rm -rf ~/.ccache
        else
+         sudo chown -R $USER:$(id -g) ~/.ccache
          mv ~/.ccache devel/
        fi
+       rm .dockerignore  # TODO: remove this line
        $DCC build --pull core
        # don't count the extra clone we're about to do
        # TODO: Do we need this? Is docker a distinct cloner from travis?
        # cloners_count_decrement
        $DCC build sirf
        # extract updated ccache
-       sudo rm -rf devel/.ccache/*
-       $DCC run --rm sirf /bin/bash -c 'sudo cp -a /opt/ccache/* /devel/.ccache/'
+       # sudo rm -rf devel/.ccache/*
+       $DCC run --rm sirf /bin/bash -c 'sudo rm -rf /devel/.ccache/* && sudo cp -a /opt/ccache/* /devel/.ccache/'
        # replace travis' ccache with the built images's
        mv devel/.ccache ~
      )

CMake/FindCython.cmake

@@ -0,0 +1,50 @@
+# code adapted from 
+# https://github.com/symengine/symengine.py/blob/master/cmake/FindCython.cmake
+# MIT License https://github.com/symengine/symengine.py/blob/master/LICENSE
+# 16/11/18
+#
+# Cython
+#
+
+# This finds the "cython" executable in your PATH, and then in some standard
+# paths:
+SET(CYTHON_EXECUTABLE cython CACHE STRING "Cython executable name")
+SET(CYTHON_FLAGS --cplus --fast-fail)
+
+SET(Cython_FOUND FALSE)
+IF (CYTHON_EXECUTABLE)
+    # Try to run Cython, to make sure it works:
+    execute_process(
+        COMMAND ${CYTHON_EXECUTABLE} "--version"
+        RESULT_VARIABLE CYTHON_RESULT
+        OUTPUT_QUIET
+        ERROR_QUIET
+        )
+    if (CYTHON_RESULT EQUAL 0)
+        # Only if cython exits with the return code 0, we know that all is ok:
+        SET(Cython_FOUND TRUE)
+        SET(Cython_Compilation_Failed FALSE)
+    else (CYTHON_RESULT EQUAL 0)
+        SET(Cython_Compilation_Failed TRUE)
+    endif (CYTHON_RESULT EQUAL 0)
+ENDIF (CYTHON_EXECUTABLE)
+
+
+IF (Cython_FOUND)
+	IF (NOT Cython_FIND_QUIETLY)
+		MESSAGE(STATUS "Found CYTHON: ${CYTHON_EXECUTABLE}")
+	ENDIF (NOT Cython_FIND_QUIETLY)
+ELSE (Cython_FOUND)
+	IF (Cython_FIND_REQUIRED)
+        if(Cython_Compilation_Failed)
+            MESSAGE(STATUS "Found CYTHON: ${CYTHON_EXECUTABLE}")
+			# On Win the testing of Cython does not return any accessible value, so the test is not carried out. Fresh Cython install was tested and works.
+			IF(NOT MSVC)
+				MESSAGE(FATAL_ERROR "Your Cython version is too old. Please upgrade Cython.")
+			ENDIF(NOT MSVC)
+        else(Cython_Compilation_Failed)
+            MESSAGE(FATAL_ERROR "Could not find Cython. Please install Cython.")
+        endif(Cython_Compilation_Failed)
+	ENDIF (Cython_FIND_REQUIRED)
+ENDIF (Cython_FOUND)
+

SuperBuild.cmake

@@ -167,6 +167,8 @@ option(BUILD_STIR "Build STIR" ON)
 option(BUILD_Gadgetron "Build Gadgetron" ${build_Gadgetron_default})
 option(BUILD_siemens_to_ismrmrd "Build siemens_to_ismrmrd" OFF)
 option(BUILD_petmr_rd_tools "Build petmr_rd_tools" OFF)
+option(BUILD_CIL "Build CCPi CIL Modules and ASTRA engine" OFF)
+option(BUILD_CIL_LITE "Build CCPi CIL Modules" OFF)
 option(BUILD_NIFTYREG "Build NIFTYREG" ON)
 
 option(BUILD_SIRF_Registration "Build SIRFS's registration functionality" ${BUILD_NIFTYREG})
@@ -214,6 +216,25 @@ if (BUILD_petmr_rd_tools)
   list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES petmr_rd_tools)
 endif()
 
+if ("${PYTHON_STRATEGY}" STREQUAL "CONDA")
+  set (BUILD_CIL OFF)
+endif()
+if (APPLE)
+  if (BUILD_CIL or BUILD_CIL_LITE)
+    message(FATAL_ERROR "CIL Modules are not tested on OSX and will be disabled")
+  else()
+    message(WARNING "CIL Modules are not tested on OSX and will be disabled")
+  endif()
+  set(BUILD_CIL OFF)
+  set(BUILD_CIL_LITE OFF)
+endif()
+if (BUILD_CIL)
+  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CCPi-Regularisation-Toolkit CCPi-Astra CCPi-Framework CCPi-FrameworkPlugins TomoPhantom)
+endif()
+if (BUILD_CIL_LITE)
+  list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES CCPi-Regularisation-Toolkit CCPi-Framework CCPi-FrameworkPlugins)
+endif()
+
 if (BUILD_SIRF_Registration)
   list(APPEND ${PRIMARY_PROJECT_NAME}_DEPENDENCIES NIFTYREG)
 endif()

SuperBuild/External_CCPi-Astra.cmake

@@ -0,0 +1,92 @@
+#========================================================================
+# Author: Edoardo Pasca
+# Copyright 2018-2019 STFC
+#
+# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
+#
+# 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.txt
+#
+# 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.
+#
+#=========================================================================
+
+#This needs to be unique globally
+set(proj CCPi-Astra)
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "CCPi-Framework;astra-toolbox")
+
+# Include dependent projects if any
+ExternalProject_Include_Dependencies(${proj} DEPENDS_VAR ${proj}_DEPENDENCIES)
+
+# Set external name (same as internal for now)
+set(externalProjName ${proj})
+
+set(${proj}_SOURCE_DIR "${SOURCE_ROOT_DIR}/${proj}" )
+set(${proj}_BINARY_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/build" )
+set(${proj}_DOWNLOAD_DIR "${SUPERBUILD_WORK_DIR}/downloads/${proj}" )
+set(${proj}_STAMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/stamp" )
+set(${proj}_TMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/tmp" )
+
+if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalProjName}}" ) )
+  message(STATUS "${__indent}Adding project ${proj}")
+
+  ### --- Project specific additions here
+  set(libcilreg_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+
+  #message(STATUS "HDF5_ROOT in External_SIRF: " ${HDF5_ROOT})
+  set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
+  set(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} ${SUPERBUILD_INSTALL_DIR})
+
+
+  message("${proj} URL " ${${proj}_URL}  ) 
+  message("${proj} TAG " ${${proj}_TAG}  ) 
+  # conda build should never get here
+  if("${PYTHON_STRATEGY}" STREQUAL "PYTHONPATH")
+    # in case of PYTHONPATH it is sufficient to copy the files to the 
+    # $PYTHONPATH directory
+    ExternalProject_Add(${proj}
+      ${${proj}_EP_ARGS}
+      GIT_REPOSITORY ${${proj}_URL}
+      GIT_TAG ${${proj}_TAG}
+      SOURCE_DIR ${${proj}_SOURCE_DIR}
+      BINARY_DIR ${${proj}_BINARY_DIR}
+      DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+      STAMP_DIR ${${proj}_STAMP_DIR}
+      TMP_DIR ${${proj}_TMP_DIR}
+      INSTALL_DIR ${libcilreg_Install_Dir}
+
+      CONFIGURE_COMMAND ""
+      BUILD_COMMAND ""
+      INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/Wrappers/Python/ccpi ${PYTHON_DEST}/ccpi
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${libcilreg_Install_Dir}
+      DEPENDS ${${proj}_DEPENDENCIES}
+    )
+
+  else()
+    # if SETUP_PY one can launch the conda build.sh script setting 
+    # the appropriate variables.
+    message(FATAL_ERROR "Only PYTHONPATH install method is currently supported")
+  endif()
+
+
+  set(${proj}_ROOT        ${${proj}_SOURCE_DIR})
+  set(${proj}_INCLUDE_DIR ${${proj}_SOURCE_DIR})
+
+else()
+  ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}"
+    SOURCE_DIR ${${proj}_SOURCE_DIR}
+    BINARY_DIR ${${proj}_BINARY_DIR}
+    DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+    STAMP_DIR ${${proj}_STAMP_DIR}
+    TMP_DIR ${${proj}_TMP_DIR}
+  )
+endif()

SuperBuild/External_CCPi-Framework.cmake

@@ -0,0 +1,102 @@
+#========================================================================
+# Author: Edoardo Pasca
+# Copyright 2018-2019 STFC
+#
+# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
+#
+# 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.txt
+#
+# 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.
+#
+#=========================================================================
+
+#This needs to be unique globally
+set(proj CCPi-Framework)
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "")
+
+# Include dependent projects if any
+ExternalProject_Include_Dependencies(${proj} DEPENDS_VAR ${proj}_DEPENDENCIES)
+
+# Set external name (same as internal for now)
+set(externalProjName ${proj})
+
+set(${proj}_SOURCE_DIR "${SOURCE_ROOT_DIR}/${proj}" )
+set(${proj}_BINARY_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/build" )
+set(${proj}_DOWNLOAD_DIR "${SUPERBUILD_WORK_DIR}/downloads/${proj}" )
+set(${proj}_STAMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/stamp" )
+set(${proj}_TMP_DIR "${SUPERBUILD_WORK_DIR}/builds/${proj}/tmp" )
+
+if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalProjName}}" ) )
+  message(STATUS "${__indent}Adding project ${proj}")
+
+  ### --- Project specific additions here
+  set(libcilreg_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+
+  set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${SUPERBUILD_INSTALL_DIR})
+  set(CMAKE_INCLUDE_PATH ${CMAKE_INCLUDE_PATH} ${SUPERBUILD_INSTALL_DIR})
+
+  message("${proj} URL " ${${proj}_URL}  ) 
+  message("${proj} TAG " ${${proj}_TAG}  ) 
+
+  # conda build should never get here
+  if("${PYTHON_STRATEGY}" STREQUAL "PYTHONPATH")
+    # in case of PYTHONPATH it is sufficient to copy the files to the 
+    # $PYTHONPATH directory
+    ExternalProject_Add(${proj}
+      ${${proj}_EP_ARGS}
+      GIT_REPOSITORY ${${proj}_URL}
+      GIT_TAG ${${proj}_TAG}
+      SOURCE_DIR ${${proj}_SOURCE_DIR}
+      BINARY_DIR ${${proj}_BINARY_DIR}
+      DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+      STAMP_DIR ${${proj}_STAMP_DIR}
+      TMP_DIR ${${proj}_TMP_DIR}
+      INSTALL_DIR ${libcilreg_Install_Dir}
+
+      CONFIGURE_COMMAND ""
+      BUILD_COMMAND ""
+      INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/Wrappers/Python/ccpi ${PYTHON_DEST}/ccpi && ${CMAKE_COMMAND} -E copy_directory ${${proj}_SOURCE_DIR}/Wrappers/Python/data ${SUPERBUILD_INSTALL_DIR}/share/ccpi/
+      CMAKE_ARGS
+        -DCMAKE_INSTALL_PREFIX=${libcilreg_Install_Dir}
+      DEPENDS ${${proj}_DEPENDENCIES}
+    )
+
+  else()
+    # if SETUP_PY one can launch the conda build.sh script setting 
+    # the appropriate variables.
+    message(FATAL_ERROR "Only PYTHONPATH install method is currently supported")
+  endif()
+
+
+  set(${proj}_ROOT        ${${proj}_SOURCE_DIR})
+  set(${proj}_INCLUDE_DIR ${${proj}_SOURCE_DIR})
+
+  add_test(NAME CIL_FRAMEWORK_TESTS_1
+           COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_Data*.py 
+           WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+  add_test(NAME CIL_FRAMEWORK_TESTS_2
+           COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_algor*.p 
+           WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+  add_test(NAME CIL_FRAMEWORK_TESTS_3
+           COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_run_*.py
+           WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
+
+  else()
+    ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}"
+      SOURCE_DIR ${${proj}_SOURCE_DIR}
+      BINARY_DIR ${${proj}_BINARY_DIR}
+      DOWNLOAD_DIR ${${proj}_DOWNLOAD_DIR}
+      STAMP_DIR ${${proj}_STAMP_DIR}
+      TMP_DIR ${${proj}_TMP_DIR}
+    )
+  endif()