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

8 files changed, 307 insertions, 0 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..cbe2fec
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,14 @@
+#   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
new file mode 100644
index 0000000..3eb4158
--- /dev/null
+++ b/src/Python/CMakeLists.txt
@@ -0,0 +1,59 @@
+#   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.
+
+message("CIL VERSION " ${CIL_VERSION})
+
+# variables that are set by conda
+
+#PREFIX=C:\Apps\Miniconda2\envs\cil\Library
+#LIBRARY_INC=C:\\Apps\\Miniconda2\\envs\\cil\\Library\\include
+
+set (NUMPY_VERSION 1.12)
+#set (PYTHON_VERSION 3.5)
+
+#https://groups.google.com/a/continuum.io/forum/#!topic/anaconda/R9gWjl09UFs
+set (CONDA_ENVIRONMENT "cil")
+set (CONDA_ENVIRONMENT_PATH "C:\\Apps\\Miniconda2\\envs\\${CONDA_ENVIRONMENT}" CACHE PATH "env dir")
+
+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})
+findPythonPackagesPath()
+message("PYTHON_PACKAGES_FOUND " ${PYTHON_PACKAGES_PATH})
+
+# copy the Pyhon files of the package
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/ccpi/imaging/)
+file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/ccpi/__init__.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/ccpi)
+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)
+	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()
+
+
diff --git a/src/Python/FindAnacondaEnvironment.cmake b/src/Python/FindAnacondaEnvironment.cmake
new file mode 100644
index 0000000..3abb5d1
--- /dev/null
+++ b/src/Python/FindAnacondaEnvironment.cmake
@@ -0,0 +1,166 @@
+#   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)
+	
+	file(TO_CMAKE_PATH ${env}/python.exe PYTHON_EXECUTABLE)
+	
+	message("Found " ${PYTHON_EXECUTABLE})
+	####### FROM FindPythonInterpr ########
+	# determine python version string
+	if(PYTHON_EXECUTABLE)
+		execute_process(COMMAND "${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})
+
+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)
+### https://openlab.ncl.ac.uk/gitlab/john.shearer/clappertracker/raw/549885e5decd37f7b23e9c1fd39e86f207156795/src/3rdparty/opencv/cmake/OpenCVDetectPython.cmake
+###
+if(CMAKE_HOST_UNIX)
+      execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "from distutils.sysconfig import *; print get_python_lib()"
+                      RESULT_VARIABLE PYTHON_CVPY_PROCESS
+                      OUTPUT_VARIABLE PYTHON_STD_PACKAGES_PATH
+                      OUTPUT_STRIP_TRAILING_WHITESPACE)
+      if("${PYTHON_STD_PACKAGES_PATH}" MATCHES "site-packages")
+        set(_PYTHON_PACKAGES_PATH "python${PYTHON_VERSION_MAJOR_MINOR}/site-packages")
+      else() #debian based assumed, install to the dist-packages.
+        set(_PYTHON_PACKAGES_PATH "python${PYTHON_VERSION_MAJOR_MINOR}/dist-packages")
+      endif()
+      if(EXISTS "${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}/${PYTHON_PACKAGES_PATH}")
+        set(_PYTHON_PACKAGES_PATH "lib${LIB_SUFFIX}/${_PYTHON_PACKAGES_PATH}")
+      else()
+        set(_PYTHON_PACKAGES_PATH "lib/${_PYTHON_PACKAGES_PATH}")
+      endif()
+    elseif(CMAKE_HOST_WIN32)
+      get_filename_component(PYTHON_PATH "${PYTHON_EXECUTABLE}" PATH)
+      file(TO_CMAKE_PATH "${PYTHON_PATH}" PYTHON_PATH)
+      if(NOT EXISTS "${PYTHON_PATH}/Lib/site-packages")
+        unset(PYTHON_PATH)
+        get_filename_component(PYTHON_PATH "[HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${PYTHON_VERSION_MAJOR_MINOR}\\InstallPath]" ABSOLUTE)
+        if(NOT PYTHON_PATH)
+           get_filename_component(PYTHON_PATH "[HKEY_CURRENT_USER\\SOFTWARE\\Python\\PythonCore\\${PYTHON_VERSION_MAJOR_MINOR}\\InstallPath]" ABSOLUTE)
+        endif()
+        file(TO_CMAKE_PATH "${PYTHON_PATH}" PYTHON_PATH)
+      endif()
+      set(_PYTHON_PACKAGES_PATH "${PYTHON_PATH}/Lib/site-packages")
+    endif()
+    SET(PYTHON_PACKAGES_PATH "${_PYTHON_PACKAGES_PATH}" PARENT_SCOPE)
+
+endfunction()
+
+
diff --git a/src/Python/compile.bat.in b/src/Python/compile.bat.in
new file mode 100644
index 0000000..d4ddc92
--- /dev/null
+++ b/src/Python/compile.bat.in
@@ -0,0 +1,4 @@
+set CIL_VERSION=@CIL_VERSION@
+
+activate @CONDA_ENVIRONMENT@
+conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi
\ No newline at end of file
diff --git a/src/Python/compile.sh.in b/src/Python/compile.sh.in
new file mode 100644
index 0000000..dd29973
--- /dev/null
+++ b/src/Python/compile.sh.in
@@ -0,0 +1,6 @@
+#!/bin/sh
+
+export CIL_VERSION=@CIL_VERSION@
+module load python/anaconda
+source activate @CONDA_ENVIRONMENT@
+conda build conda-recipe --python=@PYTHON_VERSION_MAJOR@.@PYTHON_VERSION_MINOR@ --numpy=@NUMPY_VERSION@ -c ccpi
\ No newline at end of file
diff --git a/src/Python/conda-recipe/bld.bat b/src/Python/conda-recipe/bld.bat
new file mode 100644
index 0000000..69491de
--- /dev/null
+++ b/src/Python/conda-recipe/bld.bat
@@ -0,0 +1,14 @@
+IF NOT DEFINED CIL_VERSION (
+ECHO CIL_VERSION Not Defined.
+exit 1
+)
+
+mkdir "%SRC_DIR%\ccpi"
+xcopy /e "%RECIPE_DIR%\..\.." "%SRC_DIR%\ccpi"
+
+cd %SRC_DIR%\ccpi\Python
+
+%PYTHON% setup.py build_ext
+if errorlevel 1 exit 1
+%PYTHON% setup.py install
+if errorlevel 1 exit 1
diff --git a/src/Python/conda-recipe/build.sh b/src/Python/conda-recipe/build.sh
new file mode 100644
index 0000000..855047f
--- /dev/null
+++ b/src/Python/conda-recipe/build.sh
@@ -0,0 +1,14 @@
+
+if [ -z "$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
new file mode 100644
index 0000000..c5b7a89
--- /dev/null
+++ b/src/Python/conda-recipe/meta.yaml
@@ -0,0 +1,30 @@
+package:
+  name: ccpi-fista
+  version: {{ environ['CIL_VERSION'] }}
+
+
+build:
+  preserve_egg_dir: False
+  script_env:
+    - CIL_VERSION   
+#  number: 0
+  
+requirements:
+  build:
+    - python
+    - numpy
+    - setuptools
+    - boost ==1.64
+    - boost-cpp ==1.64
+    - cython
+
+  run:
+    - python
+    - numpy
+    - boost ==1.64
+
+	
+about:
+  home: http://www.ccpi.ac.uk
+  license:  BSD license
+  summary: 'CCPi Core Imaging Library Quantification Toolbox'