diff --git a/Wrapping/Common/mitk_swig_common.i b/Wrapping/Common/mitk_swig_common.i
index cdcbc58efa..42cf0b1f73 100644
--- a/Wrapping/Common/mitk_swig_common.i
+++ b/Wrapping/Common/mitk_swig_common.i
@@ -1,37 +1,37 @@
// Ignore common warnings:
// 302 : Redefinition of Macro, usually not a problem
// 362 : Operator= is ignored. Can't help it.
// 503 : Can't wrap operator of type "*" unless renamed to a valid identifier, no problem as operator not needed.
// 509 : Overloaded function ignored. Usually not a problem, as overloaded functions shouldn't give different results.
// 511 : Can't use keyword arguments with overloaded functions
#pragma SWIG nowarn=302,362,503,509,511
-// Splitted the information about the addition files into sub-files:
+// Split the information about the additional files into sub-files:
%naturalvar;
// Includes of STD-Files goes in here
%include <mitk_swig_std.i>
// Include c++ code in this file. It is basically a c++-header wrapped in the commands so it is included in the std-file
%include <mitk_swig_cpp_include.i>
// SWIG-Macro definition goes in here, for example SWIG_ADD_MITK_CLASS
%include <mitk_swig_macros.i>
// information about classes that are going to be wrapped are in here:
%include <mitk_swig_classes.i>
//
// How to wrap a new class:
// ------------------------------------
// (1. Add the c++ include file to mitk_swig_cpp_include.i
// If the class is in a new module, make sure that this module is added as dependency in cmake )
// This step should no longer be necessary as the corresponding header is now included by
// the SWIG_ADD_MITK_CLASS macro.
// 2. Add the class definition in mitk_swig_classes.i
// If the definition of the class needs new macros, for example because it is not in the core
// and has a new Export-Macro, be sure to define this macro first.
// If the class inherit from mitk::BaseData use the SWIG_ADD_MITK_CLASS macro, as it defines
// some redundante code.
//
std::vector<std::size_t> mitk::GetImageSize(mitk::Image::Pointer image);
\ No newline at end of file
diff --git a/Wrapping/Common/mitk_swig_macros.i b/Wrapping/Common/mitk_swig_macros.i
index f3f8c589a5..1d8c746414 100644
--- a/Wrapping/Common/mitk_swig_macros.i
+++ b/Wrapping/Common/mitk_swig_macros.i
@@ -1,232 +1,232 @@
//
// This file contains macros for swig.
//
//
// MITKSWIG_ADD_HEADERFILE includes a header-file into SWIG
//
%define MITKSWIG_ADD_HEADERFILE( classinclude )
// Include the given header, where the class definition is found
%include < ## classinclude ## >
// Include the include file in the generated cpp file
%{
#include < ## classinclude ## >
%}
%enddef
//
// MITKSWIG_ADD_CLASS is a helper macro in order to do
// all important stuff in order to wrap an existing
// class
//
%define MITKSWIG_ADD_CLASS(classname, classinclude, nspace)
MITKSWIG_ADD_HEADERFILE( classinclude )
// Using class name in order to remove ambigiouties
%{
typedef nspace ## :: ## classname classname ## ;
using nspace ## :: ## classname ;
%}
using nspace ##:: ## classname ;
// Typedef is necessary to overcome ambigiouties resulting in the fact that SWIG
// ignores namespaces. This can lead to some problems with templates.
typedef nspace ## :: ## classname classname ## ;
%enddef
//
// MITKSWIG_AUTOMATED_CASTING is a helper macro in order to
-// provide a convinience interface for up/downcasting of
+// provide a convenience interface for up/downcasting of
// classes
//
%define MITKSWIG_AUTOMATED_CASTING(classname, classinclude, nspace)
// Define a conversion method to convert from and to types
%template(ConvertTo ## classname) ConvertTo< nspace ##:: ## classname ## >;
// This extend is necessary to have the automatic cast methods available
%extend itk::SmartPointer< nspace ## :: ## classname ## ::Self> {
%pythoncode %{
def _GetListOfValidItems(self):
return [str(k) for k in self.GetClassHierarchy() if str(k) in convertion_list.keys() ]
%}
%pythoncode %{
def __getattr__(self, item):
if type(item)==str:
if (len(item) > 9) and ('ConvertTo' in item):
searchString=item[9:]
if searchString in self._GetListOfValidItems():
def func_t():
return convertion_list[searchString](self)
return func_t
%}
%pythoncode %{
def __dir__(self):
return super().__dir__() + ['ConvertTo'+k for k in self._GetListOfValidItems()]
%}
}
%extend std::vector< nspace ## :: ## classname *>::value_type {
%pythoncode %{
def _GetListOfValidItems(self):
return [str(k) for k in self.GetClassHierarchy() if str(k) in convertion_list.keys() ]
%}
%pythoncode %{
def __getattr__(self, item):
if type(item)==str:
if (len(item) > 9) and ('ConvertTo' in item):
searchString=item[9:]
if searchString in self._GetListOfValidItems():
def func_t():
return convertion_list[searchString](self)
return func_t
%}
%pythoncode %{
def __dir__(self):
return super().__dir__() + ['ConvertTo'+k for k in self._GetListOfValidItems()]
%}
}
%pythoncode %{
convertion_list['classname'] = ConvertTo ## classname
%}
%enddef
//
// MITKSWIG_SMARTPOINTERVECTOR : Wrapper for Vectors of Smartpointer-Classes
//
%define MITKSWIG_SMARTPOINTERVECTOR(classname, classinclude, nspace)
// Initianziation of std. vectors containing pointers to these classes. This allows to use
// vectors of these types as target language arrays.
%template(Vector ## classname ## Pointer) std::vector< nspace ## :: ## classname ## ::Pointer >;
%template(Vector ## classname) std::vector< nspace ## :: ## classname ## ::Self *>;
%enddef
//
// MITKSWIG_POINTERVECTOR : Wrapper for Vectors of Classes
//
%define MITKSWIG_POINTERVECTOR(classname, classinclude, nspace)
// Initianziation of std. vectors containing pointers to these classes. This allows to use
// vectors of these types as target language arrays.
%template(Vector ## classname ## Pointer) std::vector< nspace ## :: ## classname * >;
%template(Vector ## classname) std::vector< nspace ## :: ## classname >;
%enddef
//
// MITKSWIG_MITKSMARTPOINTER_INITIALIZATION : Wrapper for Vectors of Smartpointer-Classes
//
%define MITKSWIG_MITKSMARTPOINTER_INITIALIZATION(classname, classinclude, nspace)
// Declaring that this class is a smart-pointer class, in order to handle
// online upcasting where necessary (for example python)
%feature("smartptr", noblock=1) nspace ##:: ## classname { itk::SmartPointer<nspace ## :: ## classname ## ::Self> }
%enddef
//
// MITKSWIG_MITKSMARTPOINTER_TEMPLATE : Wrapper for Vectors of Smartpointer-Classes
//
%define MITKSWIG_MITKSMARTPOINTER_TEMPLATE(classname, classinclude, nspace)
// Defining the Smartpointer, allows easy access in target language
%template(classname ## Pointer) itk::SmartPointer<nspace ## :: ## classname ## ::Self>;
%enddef
//
// SWIG_ADD_MITK_CLASS is a helper macro in order to do
// all important stuff before an mitk::Class is included.
// Requires the name of the class as it is in c++ as classname
// and the include file, in which the class is defined.
// It is assumed that the class is somehow inherited from
// mitk::BaseData, and supports smartpointers.
//
%define SWIG_ADD_MITK_CLASS_VECTORFREE(classname, classinclude, nspace)
%include < ## classinclude ## >
MITKSWIG_MITKSMARTPOINTER_INITIALIZATION(classname, classinclude, nspace)
MITKSWIG_ADD_CLASS( classname, classinclude, nspace )
class nspace ## :: ## classname ## ;
class nspace ## :: ## classname ## ::Pointer;
MITKSWIG_MITKSMARTPOINTER_TEMPLATE(classname, classinclude, nspace)
MITKSWIG_AUTOMATED_CASTING(classname, classinclude, nspace)
%enddef
//
// SWIG_ADD_MITK_CLASS is a helper macro in order to do
// all important stuff before an mitk::Class is included.
// Requires the name of the class as it is in c++ as classname
// and the include file, in which the class is defined.
// It is assumed that the class is somehow inherited from
// mitk::BaseData, and supports smartpointers.
//
%define SWIG_ADD_MITK_CLASS(classname, classinclude, nspace)
%include < ## classinclude ## >
MITKSWIG_MITKSMARTPOINTER_INITIALIZATION(classname, classinclude, nspace)
MITKSWIG_ADD_CLASS( classname, classinclude, nspace )
class nspace ## :: ## classname ## ;
class nspace ## :: ## classname ## ::Pointer;
// It is important to first define the Vectors and
// then define the Smartpointer. Otherwise a SWIG-bug ...
MITKSWIG_SMARTPOINTERVECTOR(classname, classinclude, nspace)
MITKSWIG_MITKSMARTPOINTER_TEMPLATE(classname, classinclude, nspace)
MITKSWIG_AUTOMATED_CASTING(classname, classinclude, nspace)
%enddef
//
// SWIG_ADD_NONOBJECT_CLASS is a helper macro in order to do
// all important stuff before an mitk::Class is included.
// Requires the name of the class as it is in c++ as classname
// and the include file, in which the class is defined.
// It is assumed that the class is somehow inherited from
// mitk::BaseData, and supports smartpointers.
//
%define SWIG_ADD_NONOBJECT_CLASS(classname, classinclude, nspace)
%include < ## classinclude ## >
MITKSWIG_ADD_CLASS( classname, classinclude, nspace )
// Typedef is necessary to overcome ambigiouties resulting in the fact that SWIG
// ignores namespaces. This can lead to some problems with templates.
typedef nspace ## :: ## classname classname ## ;
class nspace ## :: ## classname ## ;
MITKSWIG_POINTERVECTOR(classname, classinclude, nspace)
%enddef
//
// SWIG_ADD_NONOBJECT_CLASS is a helper macro in order to do
// all important stuff before an mitk::Class is included.
// Requires the name of the class as it is in c++ as classname
// and the include file, in which the class is defined.
// It is assumed that the class is somehow inherited from
// mitk::BaseData, and supports smartpointers.
//
%define SWIG_ADD_NONOBJECT_NOVECTOR_CLASS(classname, classinclude, nspace)
%include < ## classinclude ## >
MITKSWIG_ADD_CLASS( classname, classinclude, nspace )
// Typedef is necessary to overcome ambigiouties resulting in the fact that SWIG
// ignores namespaces. This can lead to some problems with templates.
typedef nspace ## :: ## classname classname ## ;
// Initianziation of std. vectors containing pointers to these classes. This allows to use
// vectors of these types as target language arrays.
%template(Vector ## classname ## Pointer) std::vector< nspace ## :: ## classname * >;
%enddef
diff --git a/Wrapping/Python/CMakeLists.txt b/Wrapping/Python/CMakeLists.txt
index 260623b192..cca64accd3 100644
--- a/Wrapping/Python/CMakeLists.txt
+++ b/Wrapping/Python/CMakeLists.txt
@@ -1,77 +1,77 @@
-# Version 2.8.1 is the minium requirement for this script.
+# Version 2.8.1 is the minimum requirement for this script.
# this is lower than the general minimum requirement.
#cmake_minimum_required ( VERSION 2.8.1 FATAL_ERROR )
include(mitkTargetLinkLibrariesWithDynamicLookup)
project( MITK_Python )
set(CMAKE_SHARED_LINKER_FLAGS "" CACHE INTERNAL "" FORCE)
set(CMAKE_MODULE_LINKER_FLAGS "" CACHE INTERNAL "" FORCE)
mitk_check_dynamic_lookup(MODULE
SHARED
MITK_UNDEFINED_SYMBOLS_ALLOWED
)
#
# Find the necessary libraries etc..
#
if ( MITK_UNDEFINED_SYMBOLS_ALLOWED )
set( _QUIET_LIBRARY "QUIET" )
else()
set( _QUIET_LIBRARY "REQUIRED" )
endif()
find_package ( PythonInterp REQUIRED )
find_package ( PythonLibs ${_QUIET_LIBRARY} )
include_directories ( ${CMAKE_CURRENT_SOURCE_DIR} )
#
# Options
#
option ( MITK_PYTHON_THREADS "Enable threaded python usage by unlocking the GIL." ON )
mark_as_advanced( MITK_PYTHON_THREADS )
option ( MITK_PYTHON_EGG "Add building of python eggs to the dist target." OFF )
mark_as_advanced( MITK_PYTHON_EGG )
option ( MITK_PYTHON_WHEEL "Add building of python wheels to the dist target." ON )
mark_as_advanced( MITK_PYTHON_WHEEL )
# Prepare the SWIG-File, i.e. especially add necessary include folders
mitkSwigPrepareFiles(pyMITK MITK.i "MitkCore;MitkCLCore;MitkCLUtilities;ITKCommon;MitkMatchPointRegistration;MitkSegmentation;MitkMultilabel;MitkDICOM;MitkDICOMImageIO;MitkRT")
# Add additional SWIG Parameters
# These parameters depend on the target language
set(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_GLOBAL_FLAGS} -features autodoc=1 -keyword )
if( MITK_PYTHON_THREADS )
set(CMAKE_SWIG_FLAGS ${CMAKE_SWIG_FLAGS} -threads)
endif()
set(CMAKE_SWIG_OUTDIR ${CMAKE_CURRENT_BINARY_DIR})
# Create the actual SWIG project
swig_add_module(pyMITK python MITK.i )
mitkSwigAddLibraryDependencies(pyMITK "MitkCore;MitkCLCore;MitkCLUtilities;ITKCommon;MitkMatchPointRegistration;MitkSegmentation;MitkMultilabel;MitkDICOM;MitkDICOMImageIO;MitkRT")
mitk_target_link_libraries_with_dynamic_lookup(${SWIG_MODULE_pyMITK_REAL_NAME} ${PYTHON_LIBRARIES})
if(DEFINED SKBUILD)
message(WARNING "SKBuild exists")
# Currently this installation
install(FILES
${CMAKE_CURRENT_BINARY_DIR}/pyMITK.py
${CMAKE_CURRENT_SOURCE_DIR}/Packaging/__init__.py
# ${MITK_DOC_FILES}
DESTINATION pyMITK
COMPONENT Runtime
)
install(TARGETS ${SWIG_MODULE_pyMITK_REAL_NAME}
RUNTIME DESTINATION pyMITK
LIBRARY DESTINATION pyMITK
COMPONENT Runtime
)
else()
message(WARNING "SKBuild missing")
include(LegacyPackaging.cmake)
endif()
diff --git a/Wrapping/Python/LegacyPackaging.cmake b/Wrapping/Python/LegacyPackaging.cmake
index 41ff58f18e..f50a11f74e 100644
--- a/Wrapping/Python/LegacyPackaging.cmake
+++ b/Wrapping/Python/LegacyPackaging.cmake
@@ -1,113 +1,113 @@
if ( MITK_DOC_FILES )
# create a python list for the import documents to include in
# packaging
# specially handle the first element
list( GET MITK_DOC_FILES 0 d )
file(TO_NATIVE_PATH "${d}" d )
set( MITK_DOC_FILES_AS_LIST "[r'${d}'")
set( _doc_list "${MITK_DOC_FILES}" )
list( REMOVE_AT _doc_list 0 )
foreach( d ${_doc_list} )
file(TO_NATIVE_PATH "${d}" d )
set( MITK_DOC_FILES_AS_LIST "${MITK_DOC_FILES_AS_LIST},r'${d}'")
endforeach()
set( MITK_DOC_FILES_AS_LIST "${MITK_DOC_FILES_AS_LIST}]")
endif()
# Step 1:
# Do initial configuration of setup.py with variable a available
# at configuration time.
set(MITK_BINARY_MODULE "@MITK_BINARY_MODULE@")
set(MITK_RUNTIME_PATH "@MITK_RUNTIME_PATH@")
set(PYTHON_LIB_DEPENDENCIES "@PYTHON_LIB_DEPENDENCIES@")
set(TMP_MITK_BINARY_MODULE "@MITK_BINARY_MODULE@" )
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/Packaging/setup.py.in"
"${CMAKE_CURRENT_BINARY_DIR}/Packaging/setup.py.in" )
set(MITK_BINARY_MODULE)
# Step 2:
# Do file configuration during compilation with generator expressions
mitkFunctionGetLibrarySearchPaths(MITK_RUNTIME_PATH release)
add_custom_command(TARGET ${SWIG_MODULE_pyMITK_REAL_NAME}
POST_BUILD
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
COMMAND ${CMAKE_COMMAND}
"-DMITK_BINARY_MODULE=$<TARGET_FILE_NAME:${SWIG_MODULE_pyMITK_REAL_NAME}>"
"-DMITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY=${MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY}"
"-\"DMITK_RUNTIME_PATH=${MITK_RUNTIME_PATH}\""
"-DCONFIGUREBUILDTIME_filename=${CMAKE_CURRENT_BINARY_DIR}/Packaging/setup.py.in"
"-DCONFIGUREBUILDTIME_out_filename=${CMAKE_CURRENT_BINARY_DIR}/Packaging/setup.py"
-P "${MITK_SOURCE_DIR}/CMake/mitkSWIGConfigurePythonfileBuildtime.cmake"
COMMENT "Generating setup.py..."
)
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/Packaging/__init__.py"
"${CMAKE_CURRENT_BINARY_DIR}/__init__.py"
COPYONLY )
# Hopefully being able to turn this option on at some point in future.
option(MITK_PYTHON_USE_VIRTUALENV "Create a Python Virtual Environment for testing." OFF)
mark_as_advanced(MITK_PYTHON_USE_VIRTUALENV)
set(VIRTUAL_PYTHON_EXECUTABLE ${PYTHON_EXECUTABLE})
if (MITK_PYTHON_USE_VIRTUALENV)
# Executable to setup a new Python virtual environment
find_package( PythonVirtualEnv REQUIRED )
sitk_enforce_forbid_downloads( MITK_PYTHON_USE_VIRTUALENV )
if (MITK_PYTHON_WHEEL AND PYTHON_VIRTUALENV_VERSION_STRING VERSION_LESS "13")
- message(SEND_ERROR "In sufficient version of virutalenv for \
+ message(SEND_ERROR "In sufficient version of virtualenv for \
building wheels. Require virtualenv>=13.0.")
endif()
#
# Setup Python Virtual Environment for testing and packaging
#
set( PythonVirtualenvHome "${${CMAKE_PROJECT_NAME}_BINARY_DIR}/Testing/Installation/PythonVirtualenv" )
# virtualenv places the python executable in different
# locations. Also note than on windows installations where python is
# installed only for a single user the may be a missing dll issue.
if( WIN32 )
set( VIRTUAL_PYTHON_EXECUTABLE
"${PythonVirtualenvHome}/Scripts/python")
else( )
set( VIRTUAL_PYTHON_EXECUTABLE "${PythonVirtualenvHome}/bin/python" )
endif()
set(MITK_PYTHON_TEST_EXECUTABLE "${VIRTUAL_PYTHON_EXECUTABLE}"
CACHE INTERNAL "Python executable for testing." FORCE )
# configure a scripts which creates the virtualenv and installs numpy
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/PythonVirtualEnvInstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/PythonVirtualEnvInstall.cmake"
@ONLY )
set( PythonVirtualEnv_ALL "" )
if ( BUILD_TESTING )
set( PythonVirtualEnv_ALL "ALL" )
endif()
add_custom_target( PythonVirtualEnv ${PythonVirtualEnv_ALL}
DEPENDS "${VIRTUAL_PYTHON_EXECUTABLE}"
SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/PythonVirtualEnvInstall.cmake.in )
add_custom_command( OUTPUT "${VIRTUAL_PYTHON_EXECUTABLE}"
COMMAND ${CMAKE_COMMAND} -P "${CMAKE_CURRENT_BINARY_DIR}/PythonVirtualEnvInstall.cmake"
DEPENDS
"${SWIG_MODULE_pyMITK_REAL_NAME}"
"${CMAKE_CURRENT_BINARY_DIR}/PythonVirtualEnvInstall.cmake"
- COMMENT "Creating python virtual enviroment..."
+ COMMENT "Creating python virtual environment..."
)
endif()
# Packaging for distribution
add_subdirectory(dist)
diff --git a/Wrapping/Python/MITK.i b/Wrapping/Python/MITK.i
index f7a188f7ed..83649ee83b 100644
--- a/Wrapping/Python/MITK.i
+++ b/Wrapping/Python/MITK.i
@@ -1,167 +1,167 @@
%module pyMITK
%include <mitk_swig_common.i>
%{
#include "mitkNumpyArrayConversion.cxx"
%}
// Numpy array conversion support
%native(_GetMemoryViewFromImage) PyObject *mitk_GetMemoryViewFromImage( PyObject *self, PyObject *args );
%native(_SetImageFromArray) PyObject *mitk_SetImageFromArray( PyObject *(self), PyObject *args );
%pythoncode %{
HAVE_NUMPY = True
try:
import numpy
except ImportError:
HAVE_NUMPY = False
def _get_numpy_dtype( mitkImage ):
"""Given a MITK image, returns the numpy.dtype which describes the data"""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# this is a mapping from MITK's pixel id to numpy's dtype
_mitk_np = {ComponentTypeUInt8:numpy.uint8,
ComponentTypeUInt16:numpy.uint16,
ComponentTypeUInt32:numpy.uint32,
ComponentTypeInt8:numpy.int8,
ComponentTypeInt16:numpy.int16,
ComponentTypeInt32:numpy.int32,
ComponentTypeFloat:numpy.float32,
ComponentTypeDouble:numpy.float64,
}
return _mitk_np[ mitkImage.GetPixelType().GetComponentType() ]
def _get_mitk_pixelid(numpy_array_type):
"""Returns a MITK PixelID given a numpy array."""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# This is a Mapping from numpy array types to sitks pixel types.
_np_mitk = {numpy.character:ComponentTypeUInt8,
numpy.uint8:ComponentTypeUInt8,
numpy.uint16:ComponentTypeUInt16,
numpy.uint32:ComponentTypeUInt32,
numpy.int8:ComponentTypeInt8,
numpy.int16:ComponentTypeInt16,
numpy.int32:ComponentTypeInt32,
numpy.float32:ComponentTypeFloat,
numpy.float64:ComponentTypeDouble,
}
try:
return _np_mitk[numpy_array_type.dtype]
except KeyError:
for key in _np_mitk:
if numpy.issubdtype(numpy_array_type.dtype, key):
return _np_mitk[key]
raise TypeError('dtype: {0} is not supported.'.format(numpy_array_type.dtype))
def _get_sitk_vector_pixelid(numpy_array_type):
- """Returns a MITK vecotr PixelID given a numpy array."""
+ """Returns a MITK vector PixelID given a numpy array."""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
# This is a Mapping from numpy array types to sitks pixel types.
_np_sitk = {numpy.character:sitkVectorUInt8,
numpy.uint8:sitkVectorUInt8,
numpy.uint16:sitkVectorUInt16,
numpy.uint32:sitkVectorUInt32,
numpy.uint64:sitkVectorUInt64,
numpy.int8:sitkVectorInt8,
numpy.int16:sitkVectorInt16,
numpy.int32:sitkVectorInt32,
numpy.int64:sitkVectorInt64,
numpy.float32:sitkVectorFloat32,
numpy.float64:sitkVectorFloat64,
}
try:
return _np_sitk[numpy_array_type.dtype]
except KeyError:
for key in _np_sitk:
if numpy.issubdtype(numpy_array_type.dtype, key):
return _np_sitk[key]
raise TypeError('dtype: {0} is not supported.'.format(numpy_array_type.dtype))
# MITK <-> Numpy Array conversion support.
#http://www.nickdarnell.com/swig-casting-revisited/
def GetArrayViewFromImage(image):
"""Get a NumPy ndarray view of a MITK Image.
Returns a Numpy ndarray object as a "view" of the MITK's Image buffer. This reduces pixel buffer copies, but requires that the MITK image object is kept around while the buffer is being used.
"""
if not HAVE_NUMPY:
raise ImportError('NumPy not available.')
dtype = _get_numpy_dtype( image )
shape = GetImageSize(image);
if image.GetPixelType().GetNumberOfComponents() > 1:
shape = ( image.GetPixelType().GetNumberOfComponents(), ) + shape
imageMemoryView = _pyMITK._GetMemoryViewFromImage(image)
arrayView = numpy.asarray(imageMemoryView).view(dtype = dtype)
arrayView.shape = shape[::-1]
return arrayView
def GetArrayFromImage(image):
"""Get a NumPy ndarray from a MITK Image.
This is a deep copy of the image buffer and is completely safe and without potential side effects.
"""
# TODO: If the image is already not unique then a second copy may be made before the numpy copy is done.
arrayView = GetArrayViewFromImage(image)
# perform deep copy of the image buffer
return numpy.array(arrayView, copy=True)
def GetImageFromArray( arr, isVector=False):
"""Get a MITK Image from a numpy array. If isVector is True, then a 3D array will be treated as a 2D vector image, otherwise it will be treated as a 3D image"""
if not HAVE_NUMPY:
raise ImportError('Numpy not available.')
z = numpy.asarray( arr )
assert z.ndim in ( 2, 3, 4 ), \
"Only arrays of 2, 3 or 4 dimensions are supported."
id = _get_mitk_pixelid( z )
#img = Image_New()
if ( z.ndim == 3 and isVector ) or (z.ndim == 4):
pixelType=MakePixelTypeFromTypeID(id, z.shape[-1])
newShape=VectorUInt32(z.shape[-2::-1])
img = MakeImage(pixelType, newShape)
#img.Initialize(pixelType, z.ndim - 1, z.shape[-2::-1])
elif z.ndim in ( 2, 3 ):
pixelType=MakePixelTypeFromTypeID(id, 1)
newShape=VectorUInt32(z.shape[::-1])
img = MakeImage(pixelType, newShape)
#img.Initialize(pixelType, z.ndim, z.shape[::-1])
_pyMITK._SetImageFromArray( z.tostring(), img )
return img
%}
diff --git a/Wrapping/Python/PackageUtility/imagefiles/imagefiles/install-gcc.sh b/Wrapping/Python/PackageUtility/imagefiles/imagefiles/install-gcc.sh
index b36458f281..6d095a83db 100755
--- a/Wrapping/Python/PackageUtility/imagefiles/imagefiles/install-gcc.sh
+++ b/Wrapping/Python/PackageUtility/imagefiles/imagefiles/install-gcc.sh
@@ -1,680 +1,680 @@
#!/bin/bash
#
# Date: 2015-09-29
#
# This downloads, builds and installs the gcc-4.9.3 compiler and boost
# 1.58. It handles the dependent packages like gmp-6.0.0a, mpfr-3.1.3,
# mpc-1.0.2, ppl-1.1, cloog-0.18.0 and binutils-2.24.
#
# To install gcc-4.9.3 in ~/tmp/gcc-4.9.3/rtf/bin you would run this
# script as follows:
#
# % # Install in ~/tmp/gcc-4.9.3/rtf/bin
# % bld.sh ~/tmp/gcc-4.9.3 2>&1 | tee bld.log
#
# If you do not specify a directory, then it will install in the
# current directory which means that following command will also
# install in ~/tmp/gcc-4.9.3/rtf/bin:
#
# % # Install in ~/tmp/gcc-4.9.3/rtf/bin
# % mkdir -p ~/tmp/gcc-4.9.3
# % cd ~/tmp/gcc-4.9.3
# % bld.sh 2>&1 | tee bld.log
#
# This script creates 4 subdirectories:
#
# Directory Description
# ========= ==================================================
# archives This is where the package archives are downloaded.
# src This is where the package source is located.
# bld This is where the packages are built from source.
# rtf This is where the packages are installed.
#
# When the build is complete you can safely remove the archives, bld
# and src directory trees to save disk space.
#
# Copyright (C) 2014 Joe Linoff
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# ================================================================
# Trim a string, remove internal spaces, convert to lower case.
# ================================================================
function get-platform-trim {
local s=$(echo "$1" | tr -d '[ \t]' | tr 'A-Z' 'a-z')
echo $s
}
# ================================================================
# Get the platform root name.
# ================================================================
function get-platform-root
{
if which uname >/dev/null 2>&1 ; then
# Greg Moeller reported that the original code didn't
# work because the -o option is not available on solaris.
# I modified the script to correctly identify that
# case and recover by using the -s option.
if uname -o >/dev/null 2>&1 ; then
# Linux distro
uname -o | tr 'A-Z' 'a-z'
elif uname -s >/dev/null 2>&1 ; then
# Solaris variant
uname -s | tr 'A-Z' 'a-z'
else
- echo "unkown"
+ echo "unknown"
fi
else
- echo "unkown"
+ echo "unknown"
fi
}
# ================================================================
# Get the platform identifier.
#
# The format of the output is:
# <plat>-<dist>-<ver>-<arch>
# ^ ^ ^ ^
# | | | +----- architecture: x86_64, i86pc, etc.
# | | +----------- version: 5.5, 6.4, 10.9, etc.
# | +------------------ distribution: centos, rhel, nexenta, darwin
# +------------------------- platform: linux, sunos, macos
#
# ================================================================
function get-platform
{
local plat=$(get-platform-root)
case "$plat" in
"gnu/linux")
d=$(get-platform-trim "$(lsb_release -i)" | awk -F: '{print $2;}')
r=$(get-platform-trim "$(lsb_release -r)" | awk -F: '{print $2;}')
m=$(get-platform-trim "$(uname -m)")
if [[ "$d" == "redhatenterprise"* ]] ; then
# Need a little help for Red Hat because
# they don't make the minor version obvious.
d="rhel_${d:16}" # keep the tail (e.g., es or client)
x=$(get-platform-trim "$(lsb_release -c)" | \
awk -F: '{print $2;}' | \
sed -e 's/[^0-9]//g')
r="$r.$x"
fi
echo "linux-$d-$r-$m"
;;
"cygwin")
x=$(get-platform-trim "$(uname)")
echo "linux-$x"
;;
"sunos")
d=$(get-platform-trim "$(uname -v)")
r=$(get-platform-trim "$(uname -r)")
m=$(get-platform-trim "$(uname -m)")
echo "sunos-$d-$r-$m"
;;
"darwin")
d=$(get-platform-trim "$(uname -s)")
r=$(get-platform-trim "$(uname -r)")
m=$(get-platform-trim "$(uname -m)")
echo "macos-$d-$r-$m"
;;
"unknown")
echo "unk-unk-unk-unk"
;;
*)
echo "$plat-unk-unk-unk"
;;
esac
}
# ================================================================
# Command header
# Usage : docmd_hdr $ar $*
# Example: docmd_hdr $ar <args>
# ================================================================
function docmd_hdr {
local ar=$1
shift
local cmd=($*)
echo
echo " # ================================================================"
if [[ "$ar" != "" ]] ; then
echo " # Archive: $ar"
fi
echo " # PWD: "$(pwd)
echo " # CMD: "${cmd[@]}
echo " # ================================================================"
}
# ================================================================
# Execute command with decorations and status testing.
# Usage : docmd $ar <cmd>
# Example: docmd $ar ls -l
# ================================================================
function docmd {
docmd_hdr $*
shift
local cmd=($*)
${cmd[@]}
local st=$?
echo "STATUS = $st"
if (( $st != 0 )) ; then
exit $st;
fi
}
# ================================================================
# Report an error and exit.
# Usage : doerr <line1> [<line2> .. <line(n)>]
# Example: doerr "line 1 msg"
# Example: doerr "line 1 msg" "line 2 msg"
# ================================================================
function doerr {
local prefix="ERROR: "
for ln in "$@" ; do
echo "${prefix}${ln}"
prefix=" "
done
exit 1
}
# ================================================================
# Extract archive information.
# Usage : ard=( $(extract-ar-info $ar) )
# Example: ard=( $(extract-ar-info $ar) )
# fn=${ard[1]}
# ext=${ard[2]}
# d=${ard[3]}
# ================================================================
function extract-ar-info {
local ar=$1
local fn=$(basename $ar)
local ext=$(echo $fn | awk -F. '{print $NF}')
local d=${fn%.*tar.$ext}
echo $ar
echo $fn
echo $ext
echo $d
}
# ================================================================
# Print a banner for a new section.
# Usage : banner STEP $ar
# Example: banner "DOWNLOAD" $ar
# Example: banner "BUILD" $ar
# ================================================================
function banner {
local step=$1
local ard=( $(extract-ar-info $2) )
local ar=${ard[0]}
local fn=${ard[1]}
local ext=${ard[2]}
local d=${ard[3]}
echo
echo '# ================================================================'
echo "# Step : $step"
echo "# Archive: $ar"
echo "# File : $fn"
echo "# Ext : $ext"
echo "# Dir : $d"
echo '# ================================================================'
}
# ================================================================
# Make a set of directories
# Usage : mkdirs <dir1> [<dir2> .. <dir(n)>]
# Example: mkdirs foo bar spam spam/foo/bar
# ================================================================
function mkdirs {
local ds=($*)
#echo "mkdirs"
for d in ${ds[@]} ; do
#echo " testing $d"
if [ ! -d $d ] ; then
#echo " creating $d"
mkdir -p $d
fi
done
}
# ================================================================
# Check the current platform to see if it is in the tested list,
# if it isn't, then issue a warning.
# It doesn't work on CentOS 5.x.
# It doesn't work on Mac OS X 10.9 (Maverick) but is close.
# ================================================================
function check-platform
{
local plat=$(get-platform)
local tested_plats=(
'linux-centos-6.4-x86_64')
local plat_found=0
echo "PLATFORM: $plat"
for tested_plat in ${tested_plats[@]} ; do
if [[ "$plat" == "$tested_plat" ]] ; then
plat_found=1
break
fi
done
if (( $plat_found == 0 )) ; then
echo "WARNING: This platform ($plat) has not been tested."
fi
}
# ================================================================
# my-readlink <dir>
# Some platforms (like darwin) do not support "readlink -f".
# This function checks to see if readlink -f is available,
# if it isn't then it uses a more POSIX compliant approach.
# ================================================================
function my-readlink
{
# First make sure that the command works.
readlink -f "$1" 1>/dev/null 2>/dev/null
local st=$?
if (( $st )) ; then
# If readlink didn't work then this may be a platform
# like Mac OS X.
local abspath="$(cd $(dirname .); pwd)"
else
local abspath=$(readlink -f "$1" 2>/dev/null)
fi
echo "$abspath"
}
# ================================================================
# DATA
# ================================================================
# List of archives
# The order is important.
ARS=(
http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz
https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2
http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.bz2
http://www.multiprecision.org/mpc/download/mpc-1.0.2.tar.gz
http://bugseng.com/products/ppl/download/ftp/releases/1.1/ppl-1.1.tar.bz2
http://www.bastoul.net/cloog/pages/download/cloog-0.18.1.tar.gz
http://ftp.gnu.org/gnu/gcc/gcc-4.9.4/gcc-4.9.4.tar.bz2
http://ftp.gnu.org/gnu/binutils/binutils-2.24.tar.bz2
#http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.bz2
#
# Why glibc is disabled (for now).
#
# glibc does not work on CentOS because the versions of the shared
- # libraries we are building are not compatiable with installed
+ # libraries we are building are not compatible with installed
# shared libraries.
#
# This is the run-time error: ELF file OS ABI invalid that I see
# when I try to run binaries compiled with the local glibc-2.15.
#
# Note that the oldest supported ABI for glibc-2.15 is 2.2. The
# CentOS 5.5 ABI is 0.
# http://ftp.gnu.org/gnu/glibc/glibc-2.15.tar.bz2
)
# ================================================================
# MAIN
# ================================================================
umask 0
check-platform
# Read the command line argument, if it exists.
ROOTDIR=$(my-readlink .)
if (( $# == 1 )) ; then
ROOTDIR=$(my-readlink $1)
elif (( $# > 1 )) ; then
doerr "too many command line arguments ($#), only zero or one is allowed" "foo"
fi
# Setup the directories.
ARDIR="/tmp/archives"
RTFDIR="$ROOTDIR"
SRCDIR="/tmp/src"
BLDDIR="/tmp/bld"
TSTDIR="/tmp/LOCAL-TEST"
export PATH="${RTFDIR}/bin:${PATH}"
export LD_LIBRARY_PATH="${RTFDIR}/lib:${RTFDIR}/lib64:${LD_LIBRARY_PATH}"
echo
echo "# ================================================================"
echo '# Version : gcc-4.9.3 2015-08-15'
echo "# RootDir : $ROOTDIR"
echo "# ArchiveDir : $ARDIR"
echo "# RtfDir : $RTFDIR"
echo "# SrcDir : $SRCDIR"
echo "# BldDir : $BLDDIR"
echo "# TstDir : $TSTDIR"
echo "# Gcc : "$(which gcc)
echo "# GccVersion : "$(gcc --version | head -1)
echo "# Hostname : "$(hostname)
echo "# O/S : "$(uname -s -r -v -m)
echo "# Date : "$(date)
echo "# Platform : "$(get-platform)
echo "# ================================================================"
mkdirs $ARDIR $RTFDIR $SRCDIR $BLDDIR
# ================================================================
# Download
# ================================================================
#for ar in ${ARS[@]} ; do
# banner 'DOWNLOAD' $ar
# ard=( $(extract-ar-info $ar) )
# fn=${ard[1]}
# ext=${ard[2]}
# d=${ard[3]}
# if [ -f "${ARDIR}/$fn" ] ; then
# echo "skipping $fn"
# else
# # get
# docmd $ar wget $ar -O "${ARDIR}/$fn"
# fi
#done
# ================================================================
# Extract
# ================================================================
for ar in ${ARS[@]} ; do
banner 'EXTRACT' $ar
ard=( $(extract-ar-info $ar) )
fn=${ard[1]}
ext=${ard[2]}
d=${ard[3]}
sd="$SRCDIR/$d"
if [ -d $sd ] ; then
echo "skipping $fn"
else
# unpack
pushd $SRCDIR
case "$ext" in
"bz2")
docmd $ar tar jxf ${ARDIR}/$fn
;;
"gz")
docmd $ar tar zxf ${ARDIR}/$fn
;;
"tar")
docmd $ar tar xf ${ARDIR}/$fn
;;
*)
doerr "unrecognized extension: $ext" "Can't continue."
;;
esac
popd
if [ ! -d $sd ] ; then
# Some archives (like gcc-g++) overlay. We create a dummy
# directory to avoid extracting them every time.
mkdir -p $sd
fi
fi
# special hack for gmp-6.0.0a
if [[ $d == "gmp-6.0.0a" ]] ; then
if [ ! -f $sd/configure ] ; then
sdn="$SRCDIR/gmp-6.0.0"
echo "fixing $sdn --> $sd"
docmd $sd rm -rf $sd
docmd $sd ln -s $sdn $sd
fi
fi
done
# ================================================================
# Build
# ================================================================
for ar in ${ARS[@]} ; do
banner 'BUILD' $ar
ard=( $(extract-ar-info $ar) )
fn=${ard[1]}
ext=${ard[2]}
d=${ard[3]}
sd="$SRCDIR/$d"
bd="$BLDDIR/$d"
if [ -d $bd ] ; then
echo "skipping $sd"
else
# Build
regex='^gcc-g\+\+.*'
if [[ $fn =~ $regex ]] ; then
# Don't build/configure the gcc-g++ package explicitly because
# it is part of the regular gcc package.
echo "skipping $sd"
# Dummy
continue
fi
# Set the CONF_ARGS
plat=$(get-platform)
run_conf=1
run_boost_bootstrap=0
case "$d" in
binutils-*)
# Binutils will not compile with strict error
# checking on so I disabled -Werror by setting
# --disable-werror.
CONF_ARGS=(
--disable-cloog-version-check
--disable-ppl-version-check
--disable-werror
--enable-cloog-backend=isl
--enable-lto
--enable-libssp
--enable-gold
--prefix=${RTFDIR}
--with-cloog=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mlgmp=${RTFDIR}
--with-mpc=${RTFDIR}
--with-mpfr=${RTFDIR}
--with-ppl=${RTFDIR}
CC=${RTFDIR}/bin/gcc
CXX=${RTFDIR}/bin/g++
)
;;
boost_*)
# The boost configuration scheme requires
# that the build occur in the source directory.
run_conf=0
run_boost_bootstrap=1
CONF_ARGS=(
--prefix=${RTFDIR}
--with-python=python2.7
)
;;
cloog-*)
GMPDIR=$(ls -1d ${BLDDIR}/gmp-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp-builddir=${GMPDIR}
--with-gmp=build
)
;;
gcc-*)
# We are using a newer version of CLooG (0.18.0).
# I have also made stack protection available
# (similar to DEP in windows).
CONF_ARGS=(
--disable-cloog-version-check
--disable-ppl-version-check
--enable-cloog-backend=isl
--enable-gold
--enable-languages='c,c++'
--enable-lto
--enable-libssp
--prefix=${RTFDIR}
--with-cloog=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mlgmp=${RTFDIR}
--with-mpc=${RTFDIR}
--with-mpfr=${RTFDIR}
--with-ppl=${RTFDIR}
)
macplats=("macos-darwin-13.0.0-x86_64" "macos-darwin-13.1.0-x86_64")
for macplat in ${macplats[@]} ; do
if [[ "$plat" == "$macplat" ]] ; then
# Special handling for Mac OS X 10.9.
# Fix the bad reference to CFBase.h in
# src/gcc-4.9.3/libsanitizer/asan/asan_malloc_mac.cc
src="$sd/libsanitizer/asan/asan_malloc_mac.cc"
if [ -f $src ] ; then
if [ ! -f $src.orig ] ; then
cp $src $src.orig
cat $src.orig |\
sed -e 's@#include <CoreFoundation/CFBase.h>@//#include <CoreFoundation/CFBase.h>@' >$src
fi
fi
fi
done
;;
glibc-*)
CONF_ARGS=(
--enable-static-nss=no
--prefix=${RTFDIR}
--with-binutils=${RTFDIR}
--with-elf
CC=${RTFDIR}/bin/gcc
CXX=${RTFDIR}/bin/g++
)
;;
gmp-*)
CONF_ARGS=(
--enable-cxx
--prefix=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
;;
libiconv-*)
CONF_ARGS=(
--prefix=${RTFDIR}
)
;;
mpc-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mpfr=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
;;
mpfr-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
)
;;
ppl-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
# Cygwin does not implement long double so I cheated.
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
# We need a special fix for the pax archive prompt.
# Change the configure code.
if [ ! -f "$sd/configure.orig" ] ; then
# Fix the configure code so that it does not use 'pax -r'.
# The problem with 'pax -r' is that it expects a "." input
# from stdin which breaks the flow.
cp $sd/configure{,.orig}
sed -e "s/am__untar='pax -r'/am__untar='tar -xf' #am__untar='pax -r'/" \
$sd/configure.orig >$sd/configure
fi
# We need to make a special fix here
src="$sd/src/mp_std_bits.defs.hh"
if [ -f $src ] ; then
if [ ! -f $src.orig ] ; then
if ! grep -q '__GNU_MP_VERSION' $src ; then
cp $src $src.orig
cat $src.orig | \
awk \
'{ \
if($1=="namespace" && $2 == "std") { \
printf("// Automatically patched by bld.sh for gcc-4.9.3.\n"); \
printf("#define tininess_before tinyness_before\n"); \
printf("#if __GNU_MP_VERSION < 5 || (__GNU_MP_VERSION == 5 && __GNU_MP_VERSION_MINOR < 1)\n");
} \
print $0; \
if($1 == "}" && $2=="//" && $3=="namespace") { \
printf("#endif // #if __GNU_MP_VERSION < 5 || (__GNU_MP_VERSION == 5 && __GNU_MP_VERSION_MINOR < 1)\n");
} \
}' >$src
fi
fi
fi
;;
*)
doerr "unrecognized package: $d"
;;
esac
mkdir -p $bd
pushd $bd
if (( $run_conf )) ; then
docmd $ar $sd/configure --help
docmd $ar $sd/configure ${CONF_ARGS[@]}
docmd $ar make
docmd $ar make install
fi
if (( $run_boost_bootstrap )) ; then
pushd $sd
docmd $ar which g++
docmd $ar gcc --version
docmd $ar $sd/bootstrap.sh --help
docmd $ar $sd/bootstrap.sh ${CONF_ARGS[@]}
docmd $ar ./b2 --help
docmd $ar ./b2 --clean
docmd $ar ./b2 --reconfigure
docmd $ar ./b2 -a -d+2 --build-dir $bd
docmd $ar ./b2 -d+2 --build-dir $bd install
docmd $ar ./b2 install
popd
fi
# Redo the tests if anything changed.
if [ -d $TSTDIR ] ; then
rm -rf $TSTDIR
fi
popd
fi
done
diff --git a/Wrapping/Python/PackageUtility/imagefiles/install-gcc.sh b/Wrapping/Python/PackageUtility/imagefiles/install-gcc.sh
index b36458f281..6d095a83db 100755
--- a/Wrapping/Python/PackageUtility/imagefiles/install-gcc.sh
+++ b/Wrapping/Python/PackageUtility/imagefiles/install-gcc.sh
@@ -1,680 +1,680 @@
#!/bin/bash
#
# Date: 2015-09-29
#
# This downloads, builds and installs the gcc-4.9.3 compiler and boost
# 1.58. It handles the dependent packages like gmp-6.0.0a, mpfr-3.1.3,
# mpc-1.0.2, ppl-1.1, cloog-0.18.0 and binutils-2.24.
#
# To install gcc-4.9.3 in ~/tmp/gcc-4.9.3/rtf/bin you would run this
# script as follows:
#
# % # Install in ~/tmp/gcc-4.9.3/rtf/bin
# % bld.sh ~/tmp/gcc-4.9.3 2>&1 | tee bld.log
#
# If you do not specify a directory, then it will install in the
# current directory which means that following command will also
# install in ~/tmp/gcc-4.9.3/rtf/bin:
#
# % # Install in ~/tmp/gcc-4.9.3/rtf/bin
# % mkdir -p ~/tmp/gcc-4.9.3
# % cd ~/tmp/gcc-4.9.3
# % bld.sh 2>&1 | tee bld.log
#
# This script creates 4 subdirectories:
#
# Directory Description
# ========= ==================================================
# archives This is where the package archives are downloaded.
# src This is where the package source is located.
# bld This is where the packages are built from source.
# rtf This is where the packages are installed.
#
# When the build is complete you can safely remove the archives, bld
# and src directory trees to save disk space.
#
# Copyright (C) 2014 Joe Linoff
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without limitation the rights to use, copy, modify, merge,
# publish, distribute, sublicense, and/or sell copies of the Software,
# and to permit persons to whom the Software is furnished to do so,
# subject to the following conditions:
#
# The above copyright notice and this permission notice shall be
# included in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
# ================================================================
# Trim a string, remove internal spaces, convert to lower case.
# ================================================================
function get-platform-trim {
local s=$(echo "$1" | tr -d '[ \t]' | tr 'A-Z' 'a-z')
echo $s
}
# ================================================================
# Get the platform root name.
# ================================================================
function get-platform-root
{
if which uname >/dev/null 2>&1 ; then
# Greg Moeller reported that the original code didn't
# work because the -o option is not available on solaris.
# I modified the script to correctly identify that
# case and recover by using the -s option.
if uname -o >/dev/null 2>&1 ; then
# Linux distro
uname -o | tr 'A-Z' 'a-z'
elif uname -s >/dev/null 2>&1 ; then
# Solaris variant
uname -s | tr 'A-Z' 'a-z'
else
- echo "unkown"
+ echo "unknown"
fi
else
- echo "unkown"
+ echo "unknown"
fi
}
# ================================================================
# Get the platform identifier.
#
# The format of the output is:
# <plat>-<dist>-<ver>-<arch>
# ^ ^ ^ ^
# | | | +----- architecture: x86_64, i86pc, etc.
# | | +----------- version: 5.5, 6.4, 10.9, etc.
# | +------------------ distribution: centos, rhel, nexenta, darwin
# +------------------------- platform: linux, sunos, macos
#
# ================================================================
function get-platform
{
local plat=$(get-platform-root)
case "$plat" in
"gnu/linux")
d=$(get-platform-trim "$(lsb_release -i)" | awk -F: '{print $2;}')
r=$(get-platform-trim "$(lsb_release -r)" | awk -F: '{print $2;}')
m=$(get-platform-trim "$(uname -m)")
if [[ "$d" == "redhatenterprise"* ]] ; then
# Need a little help for Red Hat because
# they don't make the minor version obvious.
d="rhel_${d:16}" # keep the tail (e.g., es or client)
x=$(get-platform-trim "$(lsb_release -c)" | \
awk -F: '{print $2;}' | \
sed -e 's/[^0-9]//g')
r="$r.$x"
fi
echo "linux-$d-$r-$m"
;;
"cygwin")
x=$(get-platform-trim "$(uname)")
echo "linux-$x"
;;
"sunos")
d=$(get-platform-trim "$(uname -v)")
r=$(get-platform-trim "$(uname -r)")
m=$(get-platform-trim "$(uname -m)")
echo "sunos-$d-$r-$m"
;;
"darwin")
d=$(get-platform-trim "$(uname -s)")
r=$(get-platform-trim "$(uname -r)")
m=$(get-platform-trim "$(uname -m)")
echo "macos-$d-$r-$m"
;;
"unknown")
echo "unk-unk-unk-unk"
;;
*)
echo "$plat-unk-unk-unk"
;;
esac
}
# ================================================================
# Command header
# Usage : docmd_hdr $ar $*
# Example: docmd_hdr $ar <args>
# ================================================================
function docmd_hdr {
local ar=$1
shift
local cmd=($*)
echo
echo " # ================================================================"
if [[ "$ar" != "" ]] ; then
echo " # Archive: $ar"
fi
echo " # PWD: "$(pwd)
echo " # CMD: "${cmd[@]}
echo " # ================================================================"
}
# ================================================================
# Execute command with decorations and status testing.
# Usage : docmd $ar <cmd>
# Example: docmd $ar ls -l
# ================================================================
function docmd {
docmd_hdr $*
shift
local cmd=($*)
${cmd[@]}
local st=$?
echo "STATUS = $st"
if (( $st != 0 )) ; then
exit $st;
fi
}
# ================================================================
# Report an error and exit.
# Usage : doerr <line1> [<line2> .. <line(n)>]
# Example: doerr "line 1 msg"
# Example: doerr "line 1 msg" "line 2 msg"
# ================================================================
function doerr {
local prefix="ERROR: "
for ln in "$@" ; do
echo "${prefix}${ln}"
prefix=" "
done
exit 1
}
# ================================================================
# Extract archive information.
# Usage : ard=( $(extract-ar-info $ar) )
# Example: ard=( $(extract-ar-info $ar) )
# fn=${ard[1]}
# ext=${ard[2]}
# d=${ard[3]}
# ================================================================
function extract-ar-info {
local ar=$1
local fn=$(basename $ar)
local ext=$(echo $fn | awk -F. '{print $NF}')
local d=${fn%.*tar.$ext}
echo $ar
echo $fn
echo $ext
echo $d
}
# ================================================================
# Print a banner for a new section.
# Usage : banner STEP $ar
# Example: banner "DOWNLOAD" $ar
# Example: banner "BUILD" $ar
# ================================================================
function banner {
local step=$1
local ard=( $(extract-ar-info $2) )
local ar=${ard[0]}
local fn=${ard[1]}
local ext=${ard[2]}
local d=${ard[3]}
echo
echo '# ================================================================'
echo "# Step : $step"
echo "# Archive: $ar"
echo "# File : $fn"
echo "# Ext : $ext"
echo "# Dir : $d"
echo '# ================================================================'
}
# ================================================================
# Make a set of directories
# Usage : mkdirs <dir1> [<dir2> .. <dir(n)>]
# Example: mkdirs foo bar spam spam/foo/bar
# ================================================================
function mkdirs {
local ds=($*)
#echo "mkdirs"
for d in ${ds[@]} ; do
#echo " testing $d"
if [ ! -d $d ] ; then
#echo " creating $d"
mkdir -p $d
fi
done
}
# ================================================================
# Check the current platform to see if it is in the tested list,
# if it isn't, then issue a warning.
# It doesn't work on CentOS 5.x.
# It doesn't work on Mac OS X 10.9 (Maverick) but is close.
# ================================================================
function check-platform
{
local plat=$(get-platform)
local tested_plats=(
'linux-centos-6.4-x86_64')
local plat_found=0
echo "PLATFORM: $plat"
for tested_plat in ${tested_plats[@]} ; do
if [[ "$plat" == "$tested_plat" ]] ; then
plat_found=1
break
fi
done
if (( $plat_found == 0 )) ; then
echo "WARNING: This platform ($plat) has not been tested."
fi
}
# ================================================================
# my-readlink <dir>
# Some platforms (like darwin) do not support "readlink -f".
# This function checks to see if readlink -f is available,
# if it isn't then it uses a more POSIX compliant approach.
# ================================================================
function my-readlink
{
# First make sure that the command works.
readlink -f "$1" 1>/dev/null 2>/dev/null
local st=$?
if (( $st )) ; then
# If readlink didn't work then this may be a platform
# like Mac OS X.
local abspath="$(cd $(dirname .); pwd)"
else
local abspath=$(readlink -f "$1" 2>/dev/null)
fi
echo "$abspath"
}
# ================================================================
# DATA
# ================================================================
# List of archives
# The order is important.
ARS=(
http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.14.tar.gz
https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2
http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.bz2
http://www.multiprecision.org/mpc/download/mpc-1.0.2.tar.gz
http://bugseng.com/products/ppl/download/ftp/releases/1.1/ppl-1.1.tar.bz2
http://www.bastoul.net/cloog/pages/download/cloog-0.18.1.tar.gz
http://ftp.gnu.org/gnu/gcc/gcc-4.9.4/gcc-4.9.4.tar.bz2
http://ftp.gnu.org/gnu/binutils/binutils-2.24.tar.bz2
#http://sourceforge.net/projects/boost/files/boost/1.58.0/boost_1_58_0.tar.bz2
#
# Why glibc is disabled (for now).
#
# glibc does not work on CentOS because the versions of the shared
- # libraries we are building are not compatiable with installed
+ # libraries we are building are not compatible with installed
# shared libraries.
#
# This is the run-time error: ELF file OS ABI invalid that I see
# when I try to run binaries compiled with the local glibc-2.15.
#
# Note that the oldest supported ABI for glibc-2.15 is 2.2. The
# CentOS 5.5 ABI is 0.
# http://ftp.gnu.org/gnu/glibc/glibc-2.15.tar.bz2
)
# ================================================================
# MAIN
# ================================================================
umask 0
check-platform
# Read the command line argument, if it exists.
ROOTDIR=$(my-readlink .)
if (( $# == 1 )) ; then
ROOTDIR=$(my-readlink $1)
elif (( $# > 1 )) ; then
doerr "too many command line arguments ($#), only zero or one is allowed" "foo"
fi
# Setup the directories.
ARDIR="/tmp/archives"
RTFDIR="$ROOTDIR"
SRCDIR="/tmp/src"
BLDDIR="/tmp/bld"
TSTDIR="/tmp/LOCAL-TEST"
export PATH="${RTFDIR}/bin:${PATH}"
export LD_LIBRARY_PATH="${RTFDIR}/lib:${RTFDIR}/lib64:${LD_LIBRARY_PATH}"
echo
echo "# ================================================================"
echo '# Version : gcc-4.9.3 2015-08-15'
echo "# RootDir : $ROOTDIR"
echo "# ArchiveDir : $ARDIR"
echo "# RtfDir : $RTFDIR"
echo "# SrcDir : $SRCDIR"
echo "# BldDir : $BLDDIR"
echo "# TstDir : $TSTDIR"
echo "# Gcc : "$(which gcc)
echo "# GccVersion : "$(gcc --version | head -1)
echo "# Hostname : "$(hostname)
echo "# O/S : "$(uname -s -r -v -m)
echo "# Date : "$(date)
echo "# Platform : "$(get-platform)
echo "# ================================================================"
mkdirs $ARDIR $RTFDIR $SRCDIR $BLDDIR
# ================================================================
# Download
# ================================================================
#for ar in ${ARS[@]} ; do
# banner 'DOWNLOAD' $ar
# ard=( $(extract-ar-info $ar) )
# fn=${ard[1]}
# ext=${ard[2]}
# d=${ard[3]}
# if [ -f "${ARDIR}/$fn" ] ; then
# echo "skipping $fn"
# else
# # get
# docmd $ar wget $ar -O "${ARDIR}/$fn"
# fi
#done
# ================================================================
# Extract
# ================================================================
for ar in ${ARS[@]} ; do
banner 'EXTRACT' $ar
ard=( $(extract-ar-info $ar) )
fn=${ard[1]}
ext=${ard[2]}
d=${ard[3]}
sd="$SRCDIR/$d"
if [ -d $sd ] ; then
echo "skipping $fn"
else
# unpack
pushd $SRCDIR
case "$ext" in
"bz2")
docmd $ar tar jxf ${ARDIR}/$fn
;;
"gz")
docmd $ar tar zxf ${ARDIR}/$fn
;;
"tar")
docmd $ar tar xf ${ARDIR}/$fn
;;
*)
doerr "unrecognized extension: $ext" "Can't continue."
;;
esac
popd
if [ ! -d $sd ] ; then
# Some archives (like gcc-g++) overlay. We create a dummy
# directory to avoid extracting them every time.
mkdir -p $sd
fi
fi
# special hack for gmp-6.0.0a
if [[ $d == "gmp-6.0.0a" ]] ; then
if [ ! -f $sd/configure ] ; then
sdn="$SRCDIR/gmp-6.0.0"
echo "fixing $sdn --> $sd"
docmd $sd rm -rf $sd
docmd $sd ln -s $sdn $sd
fi
fi
done
# ================================================================
# Build
# ================================================================
for ar in ${ARS[@]} ; do
banner 'BUILD' $ar
ard=( $(extract-ar-info $ar) )
fn=${ard[1]}
ext=${ard[2]}
d=${ard[3]}
sd="$SRCDIR/$d"
bd="$BLDDIR/$d"
if [ -d $bd ] ; then
echo "skipping $sd"
else
# Build
regex='^gcc-g\+\+.*'
if [[ $fn =~ $regex ]] ; then
# Don't build/configure the gcc-g++ package explicitly because
# it is part of the regular gcc package.
echo "skipping $sd"
# Dummy
continue
fi
# Set the CONF_ARGS
plat=$(get-platform)
run_conf=1
run_boost_bootstrap=0
case "$d" in
binutils-*)
# Binutils will not compile with strict error
# checking on so I disabled -Werror by setting
# --disable-werror.
CONF_ARGS=(
--disable-cloog-version-check
--disable-ppl-version-check
--disable-werror
--enable-cloog-backend=isl
--enable-lto
--enable-libssp
--enable-gold
--prefix=${RTFDIR}
--with-cloog=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mlgmp=${RTFDIR}
--with-mpc=${RTFDIR}
--with-mpfr=${RTFDIR}
--with-ppl=${RTFDIR}
CC=${RTFDIR}/bin/gcc
CXX=${RTFDIR}/bin/g++
)
;;
boost_*)
# The boost configuration scheme requires
# that the build occur in the source directory.
run_conf=0
run_boost_bootstrap=1
CONF_ARGS=(
--prefix=${RTFDIR}
--with-python=python2.7
)
;;
cloog-*)
GMPDIR=$(ls -1d ${BLDDIR}/gmp-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp-builddir=${GMPDIR}
--with-gmp=build
)
;;
gcc-*)
# We are using a newer version of CLooG (0.18.0).
# I have also made stack protection available
# (similar to DEP in windows).
CONF_ARGS=(
--disable-cloog-version-check
--disable-ppl-version-check
--enable-cloog-backend=isl
--enable-gold
--enable-languages='c,c++'
--enable-lto
--enable-libssp
--prefix=${RTFDIR}
--with-cloog=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mlgmp=${RTFDIR}
--with-mpc=${RTFDIR}
--with-mpfr=${RTFDIR}
--with-ppl=${RTFDIR}
)
macplats=("macos-darwin-13.0.0-x86_64" "macos-darwin-13.1.0-x86_64")
for macplat in ${macplats[@]} ; do
if [[ "$plat" == "$macplat" ]] ; then
# Special handling for Mac OS X 10.9.
# Fix the bad reference to CFBase.h in
# src/gcc-4.9.3/libsanitizer/asan/asan_malloc_mac.cc
src="$sd/libsanitizer/asan/asan_malloc_mac.cc"
if [ -f $src ] ; then
if [ ! -f $src.orig ] ; then
cp $src $src.orig
cat $src.orig |\
sed -e 's@#include <CoreFoundation/CFBase.h>@//#include <CoreFoundation/CFBase.h>@' >$src
fi
fi
fi
done
;;
glibc-*)
CONF_ARGS=(
--enable-static-nss=no
--prefix=${RTFDIR}
--with-binutils=${RTFDIR}
--with-elf
CC=${RTFDIR}/bin/gcc
CXX=${RTFDIR}/bin/g++
)
;;
gmp-*)
CONF_ARGS=(
--enable-cxx
--prefix=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
;;
libiconv-*)
CONF_ARGS=(
--prefix=${RTFDIR}
)
;;
mpc-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
--with-mpfr=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
;;
mpfr-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
)
;;
ppl-*)
CONF_ARGS=(
--prefix=${RTFDIR}
--with-gmp=${RTFDIR}
)
if [[ "$plat" == "linux-cygwin_nt-6.1-wow64" ]] ; then
# Cygwin does not implement long double so I cheated.
CONF_ARGS+=('--enable-static')
CONF_ARGS+=('--disable-shared')
fi
# We need a special fix for the pax archive prompt.
# Change the configure code.
if [ ! -f "$sd/configure.orig" ] ; then
# Fix the configure code so that it does not use 'pax -r'.
# The problem with 'pax -r' is that it expects a "." input
# from stdin which breaks the flow.
cp $sd/configure{,.orig}
sed -e "s/am__untar='pax -r'/am__untar='tar -xf' #am__untar='pax -r'/" \
$sd/configure.orig >$sd/configure
fi
# We need to make a special fix here
src="$sd/src/mp_std_bits.defs.hh"
if [ -f $src ] ; then
if [ ! -f $src.orig ] ; then
if ! grep -q '__GNU_MP_VERSION' $src ; then
cp $src $src.orig
cat $src.orig | \
awk \
'{ \
if($1=="namespace" && $2 == "std") { \
printf("// Automatically patched by bld.sh for gcc-4.9.3.\n"); \
printf("#define tininess_before tinyness_before\n"); \
printf("#if __GNU_MP_VERSION < 5 || (__GNU_MP_VERSION == 5 && __GNU_MP_VERSION_MINOR < 1)\n");
} \
print $0; \
if($1 == "}" && $2=="//" && $3=="namespace") { \
printf("#endif // #if __GNU_MP_VERSION < 5 || (__GNU_MP_VERSION == 5 && __GNU_MP_VERSION_MINOR < 1)\n");
} \
}' >$src
fi
fi
fi
;;
*)
doerr "unrecognized package: $d"
;;
esac
mkdir -p $bd
pushd $bd
if (( $run_conf )) ; then
docmd $ar $sd/configure --help
docmd $ar $sd/configure ${CONF_ARGS[@]}
docmd $ar make
docmd $ar make install
fi
if (( $run_boost_bootstrap )) ; then
pushd $sd
docmd $ar which g++
docmd $ar gcc --version
docmd $ar $sd/bootstrap.sh --help
docmd $ar $sd/bootstrap.sh ${CONF_ARGS[@]}
docmd $ar ./b2 --help
docmd $ar ./b2 --clean
docmd $ar ./b2 --reconfigure
docmd $ar ./b2 -a -d+2 --build-dir $bd
docmd $ar ./b2 -d+2 --build-dir $bd install
docmd $ar ./b2 install
popd
fi
# Redo the tests if anything changed.
if [ -d $TSTDIR ] ; then
rm -rf $TSTDIR
fi
popd
fi
done