Conda

SuperBuild.cmake

@@ -407,5 +407,56 @@ else ()
   file(CREATE_LINK ${SyneRBI_INSTALL}/bin/env_sirf.csh ${SyneRBI_INSTALL}/bin/env_ccppetmr.csh SYMBOLIC)
 endif()
 
+# Install python packages via pip and setup.py
+if(PYTHONINTERP_FOUND)
+  set(PYTHON_SETUP_PKGS "sirf" CACHE INTERNAL "list of provided python packages")
+
+  # alias sirf.p* -> p* for backward-compatibility
+  function(python_pkg_alias PY_PKG_NEW PY_PKG_OLD)
+    list(APPEND PYTHON_SETUP_PKGS ${PY_PKG_NEW})
+    set(PYTHON_SETUP_PKGS "${PYTHON_SETUP_PKGS}" PARENT_SCOPE)
+    set(SETUP_PY_INIT_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/__init__.py.in")
+    set(SETUP_PY_INIT "${PYTHON_DEST}/${PY_PKG_NEW}/__init__.py")
+    configure_file("${SETUP_PY_INIT_IN}" "${SETUP_PY_INIT}")
+    # message(STATUS "setup.py:${SETUP_PY_INIT}")
+    message(STATUS "setup.py:${PY_PKG_NEW}<-${PY_PKG_OLD}")
+  endfunction(python_pkg_alias)
+  python_pkg_alias(pGadgetron "sirf.pGadgetron")
+  python_pkg_alias(pSTIR "sirf.pSTIR")
+  python_pkg_alias(pUtilities "sirf.pUtilities")
+  python_pkg_alias(pygadgetron "sirf.pygadgetron")
+  python_pkg_alias(pystir "sirf.pystir")
+  python_pkg_alias(pyiutilities "sirf.pyiutilities")
+  # convert to python CSV tuple for setup.py configure_file
+  string(REPLACE ";" "', '" PYTHON_SETUP_PKGS_CSV "${PYTHON_SETUP_PKGS}")
+  set(PYTHON_SETUP_PKGS_CSV "'${PYTHON_SETUP_PKGS_CSV}'")
+  # message(STATUS "setup.py:pacakges:${PYTHON_SETUP_PKGS_CSV}")
+
+  # Create setup.py
+  set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild/setup.py.in")
+  set(SETUP_PY "${PYTHON_DEST}/setup.py")
+  set(SETUP_PY_INIT "${PYTHON_DEST}/sirf/__init__.py")
+  message(STATUS "setup.py:${SETUP_PY}")
+  configure_file("${SETUP_PY_IN}" "${SETUP_PY}")
+
+  # python setup.py build
+  add_custom_command(OUTPUT "${SETUP_PY_INIT}"
+    COMMAND "${CMAKE_COMMAND}" -E make_directory "${PYTHON_DEST}/sirf"
+    COMMAND "${CMAKE_COMMAND}" -E touch "${SETUP_PY_INIT}"
+    COMMAND "${PYTHON_EXECUTABLE}" setup.py build
+    DEPENDS "${SETUP_PY_IN}"
+    WORKING_DIRECTORY "${PYTHON_DEST}")
+
+  add_custom_target(pybuild_sirf ALL DEPENDS ${SETUP_PY_INIT})
+
+  if (NOT CONDA_BUILD)
+    # python setup.py install
+    install(CODE "execute_process(COMMAND\n\
+      \"${PYTHON_EXECUTABLE}\" setup.py install\n\
+      WORKING_DIRECTORY \"${PYTHON_DEST}\")")
+  endif()
+endif(PYTHONINTERP_FOUND)
+
+
 # add tests
 enable_testing()

SuperBuild/External_Boost.cmake

@@ -43,7 +43,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
   mark_as_superbuild(Boost_NO_SYSTEM_PATHS)
 
   ### --- Project specific additions here
-  set(Boost_Install_Dir ${SUPERBUILD_INSTALL_DIR})
+  set(${proj}_Install_Dir ${SUPERBUILD_INSTALL_DIR})
   set(Boost_Configure_Script ${CMAKE_CURRENT_LIST_DIR}/External_Boost_configureboost.cmake)
   set(Boost_Build_Script ${CMAKE_CURRENT_LIST_DIR}/External_Boost_buildboost.cmake)
 

SuperBuild/External_GTest.cmake

@@ -62,6 +62,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
       if(${USE_SYSTEM_${externalProjName}})
         message(STATUS "USING the system ${externalProjName}, set GTEST_ROOT if needed.")
         find_package(${proj} ${${externalProjName}_REQUIRED_VERSION} REQUIRED)
+        get_filename_component(GTEST_ROOT ${GTEST_LIBRARIES} DIRECTORY)
     endif()
     ExternalProject_Add_Empty(${proj} DEPENDS "${${proj}_DEPENDENCIES}"
     ${${proj}_EP_ARGS_DIRS}

SuperBuild/External_ISMRMRD.cmake

@@ -56,6 +56,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
     endif()
   endif ()
 
+
   ExternalProject_Add(${proj}
     ${${proj}_EP_ARGS}
     ${${proj}_EP_ARGS_GIT}

SuperBuild/__init__.py.in

@@ -0,0 +1 @@
+from ${PY_PKG_OLD} import *

SuperBuild/setup.py.in

@@ -0,0 +1,40 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+try:
+    from setuptools import setup
+except ImportError:
+    from distutils.core import setup
+
+__author__ = "Casper da Costa-Luis <imaging@caspersci.uk.to>"
+__version__ = "1.0.0"
+
+
+setup(
+    name='sirf',
+    version=__version__,
+    description='CCP PET-MR SIRF',
+    license='Apache 2.0',
+    author='CCP PET-MR',
+    author_email='ccppetmr@stfc.ac.uk',
+    url='https://github.com/CCPPETMR/SIRF',
+    platforms=['any'],
+    package_data={'sirf': ['*.so']},
+    packages=[${PYTHON_SETUP_PKGS_CSV}],
+    long_description='',
+    classifiers=[
+        # Trove classifiers
+        # (https://pypi.python.org/pypi?%3Aaction=list_classifiers)
+        'Development Status :: 5 - Production/Stable',
+        'Programming Language :: Python :: 2',
+        'Programming Language :: Python :: 2.6',
+        'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.2',
+        'Programming Language :: Python :: 3.3',
+        'Programming Language :: Python :: 3.4',
+        'Programming Language :: Python :: 3.5',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7'
+    ],
+    keywords='image reconstruction pet mr medical imaging',
+)

conda-recipe/build.sh

@@ -0,0 +1,72 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  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.
+#
+#=========================================================================
+
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+cp -rv "$RECIPE_DIR/../" "$SRC_DIR/SIRF-SuperBuild"
+
+cd $SRC_DIR/build
+
+echo "$SRC_DIR/ccpi/Python"
+
+#site-packages ${SP_DIR}/sirf
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=a9170557c0f883934033700c1dd312a3a74611d6\
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
+    -DUSE_SYSTEM_SWIG=On \
+    -DUSE_SYSTEM_Boost=Off \
+    -DUSE_SYSTEM_Armadillo=On \
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=On \
+    -DUSE_SYSTEM_GTEST=On\
+    -DCONDA_BUILD=On
+
+make -j1
+cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+cd ${PREFIX}/python
+${PYTHON} setup.py install
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python

conda-recipe/meta.yaml

@@ -0,0 +1,60 @@
+package:
+  name: sirf
+#  version: {{ environ['SIRF_VERSION'] }}
+  version: 1.0.0
+
+
+build:
+  preserve_egg_dir: False
+#  number: 0
+
+requirements:
+  build:
+    #- boost ==1.64.0	
+    #- boost-cpp ==1.64.0 
+#    - boost
+#    - boost-cpp
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - libxml2
+    - psutil
+    - nose
+    - coverage
+    - fftw
+    - swig >=3
+    - libxslt
+    - armadillo
+    - gtest
+
+
+  run:
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+    - python 3.6 # [py36]
+    - python 2.7 # [py27]
+    #- boost-dev ==1.63
+    - numpy
+    - scipy
+    - matplotlib
+    - docopt
+    - h5py
+    - psutil
+    - fftw
+    - libgcc-ng
+    - libstdcxx-ng
+    - openblas
+    - armadillo
+    - gtest
+
+about:
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'

conda/armadillo/build.sh

@@ -0,0 +1,72 @@
+#!/bin/bash
+#
+# Script to install/update the CCP-PETMR VM. It could also be used for any other system
+# but will currently change your .sirfrc. This is to be avoided later on.
+#
+# Author: Edoardo Pasca
+# Copyright 2016-2018 University College London
+# Copyright 2016-2018 Rutherford Appleton Laboratory STFC
+#
+# This is software developed for the Collaborative Computational
+# Project in Positron Emission Tomography and Magnetic Resonance imaging
+# (http://www.ccppetmr.ac.uk/).
+
+#  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.
+#
+#=========================================================================
+
+#if [ -z "$SIRF_VERSION" ]; then
+#    echo "Need to set SIRF_VERSION"
+#    exit 1
+#fi  
+
+mkdir "$SRC_DIR/build"
+mkdir "$SRC_DIR/SIRF-SuperBuild"
+cp -rv "$RECIPE_DIR/../../" "$SRC_DIR/SIRF-SuperBuild"
+
+cd $SRC_DIR/build
+
+
+#site-packages ${SP_DIR}/sirf
+cmake ../SIRF-SuperBuild \
+    -DCMAKE_INSTALL_PREFIX=${PREFIX} \
+    -DPYTHON_DEST_DIR=${PREFIX}/python\
+    -USIRF_URL \
+    -USIRF_TAG \
+    -DSIRF_TAG=v2.0.0\
+    -USTIR_URL \
+    -USTIR_TAG \
+    -UGadgetron_URL \
+    -UGadgetron_TAG \
+    -UISMRMRD_URL \
+    -UISMRMRD_TAG \
+    -DBUILD_GADGETRON=On \
+    -DUSE_SYSTEM_SWIG=Off \
+    -DUSE_SYSTEM_Boost=On \
+    -DUSE_SYSTEM_Armadillo=Off \
+    -DUSE_SYSTEM_FFTW3=On \
+    -DUSE_SYSTEM_HDF5=ON \
+    -DBUILD_siemens_to_ismrmrd=Off \
+    -DUSE_SYSTEM_GTest=Off\
+    -DCONDA_BUILD=On
+
+make  -j1 Armadillo
+
+#cp ${PREFIX}/share/gadgetron/config/gadgetron.xml.example ${PREFIX}/share/gadgetron/config/gadgetron.xml
+
+#cd ${PREFIX}/python
+#${PYTHON} setup.py install
+
+# add to 
+#echo "${PREFIX}/python" > ${PREFIX}
+#${PREFIX}/python

conda/armadillo/conda_build_config.yaml

@@ -0,0 +1,4 @@
+python:
+  - 2.7 
+numpy:
+  - 1.11

conda/armadillo/meta.yaml

@@ -0,0 +1,59 @@
+package:
+  name: armadillo
+  version: 7.800.0
+
+
+build:
+  preserve_egg_dir: False
+#  number: 0
+
+requirements:
+  build:
+    #- boost ==1.64.0	
+    - boost-cpp >=1.63.0 
+    - boost >=1.63
+#    - boost-cpp
+#    - python 3.6 # [py36]
+#    - python 2.7 # [py27]
+    - cmake >=3.1
+    - vc 14 # [win and py36] 
+    - vc 9  # [win and py27]
+#    - numpy
+#    - scipy
+#    - matplotlib
+#    - docopt
+    - h5py
+#    - libxml2
+    - psutil
+    - nose
+    - coverage
+    - fftw
+#    - swig >=3
+#    - libxslt
+#    - armadillo
+#    - gtest
+
+
+  run:
+    - boost >=1.63
+    - vc 14 # [win and py35]
+    - vc 9  # [win and py27]
+#    - python 3.6 # [py36]
+#    - python 2.7 # [py27]
+#    - numpy
+#    - scipy
+#    - matplotlib
+#    - docopt
+    - h5py
+    - psutil
+    - fftw
+    - libgcc-ng
+    - libstdcxx-ng
+    - openblas
+#    - armadillo
+#    - gtest
+
+about:
+  home: http://www.ccppetmr.ac.uk
+  license:  Apache 2.0 license
+  summary: 'Synergistic Image Reconstruction Framework'