Documentation/Nightly/Developers/Tutorials/MigrationGuide/SlicerExtension

Slicer Extension updates

Slicer 5.0: ITKv4 to ITKv5

To remove support for ITKv4 and only support ITKv5. See Documentation/Nightly/Developers/Tutorials/MigrationGuide#Transition_from_ITK4_to_ITK5, it includes the following sections:

• Upgrading to ITKv5 or keep using ITKv4 GenerateThreadedData
• itkMultiThreader refactor
• SimpleFastMutexLock, FastMutexLock and MutexLock are deprecated

If completely removing support for ITKv4 and only supporting ITKv5 is not possible. It is possible to conditionally include the ITKv4 code.

For example:

#if ITK_VERSION_MAJOR >= 5
  itk::ITK_THREAD_RETURN_TYPE
#else
  ITK_THREAD_RETURN_TYPE
#endif

Example of commits:

• ResampleDTIlogEuclidean
  • ResampleDTIlogEuclidean@f779bf7 COMP: Use std::mutex instead of deprecated ITK implementation
  • ResampleDTIlogEuclidean@ed5093b BUG: ITKv5: Fix tests updating ITK filters to use ITKv5 dynamic multi-threading
• PETTumorSegmentation
  • PETTumorSegmentation PR#18 BUG: Add support for ITKv5 dynamic multithreader
  • PETTumorSegmentation PR#18 COMP: Support ITKv5 refactored threading models

Slicer 5.0: Python2 to Python3

Depending on the complexity of the extension, two approaches shall be considered:

• code base common to Slicer 4.10 and Slicer 5.0. This means backward compatibility with the latest release is maintained.
• specific branch for each Slicer version (e.g master-4.10 and master)

Example of commits

• Slicer r28079 STYLE: Update python classes to follow new-style
• MultiVolumeImporter@f9917b2 STYLE: Apply lib2to3.fixes.fix_idioms to support python3
• MultiVolumeImporter@3edd1bc ENH: Support for Python3
• ShapeVariationAnalyzer@4234377 STYLE: Update python scripts for python 3.x
• PETTumorSegmentation PR#18 BUG: Add support for Python 3

Step 1

Understanding the scope of changes needed to support Python 3 can be done by:

1. installing future package (see https://python-future.org/)

   Slicer_DIR=/path/to/Slicer-SuperBuild/Slicer-build
   ${Slicer_DIR}/../python-install/bin/PythonSlicer -m pip install future
   

2. applying all fixes

     for f in `find ./ -name "*.py"`; do \
       ${Slicer_DIR}/../python-install/bin/PythonSlicer \
         --launch futurize --nobackups --write $f; \
     done
   

   Alternatively the future package could be installed in a regular python environment and used from there.

     for f in `find ./ -name "*.py"`; do \
       futurize --nobackups --write $f; \
     done
   

This first step will apply the following transformations:

lib2to3.fixes.fix_apply
lib2to3.fixes.fix_dict
lib2to3.fixes.fix_except
lib2to3.fixes.fix_exec
lib2to3.fixes.fix_exitfunc
lib2to3.fixes.fix_filter
lib2to3.fixes.fix_funcattrs
lib2to3.fixes.fix_getcwdu
lib2to3.fixes.fix_has_key
lib2to3.fixes.fix_input
lib2to3.fixes.fix_intern
lib2to3.fixes.fix_isinstance
lib2to3.fixes.fix_itertools
lib2to3.fixes.fix_itertools_imports
lib2to3.fixes.fix_long
lib2to3.fixes.fix_map
lib2to3.fixes.fix_methodattrs
lib2to3.fixes.fix_ne
lib2to3.fixes.fix_next
lib2to3.fixes.fix_nonzero
lib2to3.fixes.fix_numliterals
lib2to3.fixes.fix_operator
lib2to3.fixes.fix_paren
lib2to3.fixes.fix_raw_input
lib2to3.fixes.fix_reduce
lib2to3.fixes.fix_renamesSlicer migration guide describes how to update the code. See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/SlicerExtension#Slicer_5.0:_Python2_to_Python3
lib2to3.fixes.fix_repr
lib2to3.fixes.fix_standarderror
lib2to3.fixes.fix_sys_exc
lib2to3.fixes.fix_throw
lib2to3.fixes.fix_tuple_params
lib2to3.fixes.fix_types
lib2to3.fixes.fix_xreadlines
lib2to3.fixes.fix_zip
libfuturize.fixes.fix_absolute_import
libfuturize.fixes.fix_basestring
libfuturize.fixes.fix_cmp
libfuturize.fixes.fix_division_safe
libfuturize.fixes.fix_execfile
libfuturize.fixes.fix_future_builtins
libfuturize.fixes.fix_future_standard_library
libfuturize.fixes.fix_future_standard_library_urllib
libfuturize.fixes.fix_metaclass
libfuturize.fixes.fix_next_call
libfuturize.fixes.fix_object
libfuturize.fixes.fix_print_with_import
libfuturize.fixes.fix_raise
libfuturize.fixes.fix_unicode_keep_u
libfuturize.fixes.fix_xrange_with_import
libpasteurize.fixes.fix_newstyle

expect these two:

lib2to3.fixes.fix_idioms
lib2to3.fixes.fix_ws_comma

If the number of changes is large, you should consider applying each fixes independently.

Step 2

Not all changes applied automatically should be integrated. Most of the changes introducing imports from the future python package can simply be removed or removed after making use of try/except or check of sys.version_info[0].

• Systematic conversion of keys, values or items from dictionaries do not need to be systematically converted from dict_keys/dict_values/dict_items to list. For example, this Slicer r28077 reverted some of the automatic changes applied by the future CLI.

• Unless python classes implement the object functions next and __unicode__ specific to Python 2, nothing specific should be done and from builtins import object can be removed. Automatic removal of imports can also be automated doing:

 for f in `find ./ -name "*.py"`; do \
   sed -i '/from builtins import object/ d' $f; \
 done

• Unless there are performances issue associated with using range in Python 2, the from builtins import range can be removed:

 for f in `find ./ -name "*.py"`; do \
   sed -i '/from builtins import range/ d' $f; \
 done

• If there are performance issue with using range in Python 2, the following could also be done:

 import sys
 if sys.version_info[0] == 2:
   range = xrange

• Use of aliases can also be avoided by removing

 from future import standard_library
 standard_library.install_aliases()

and instead doing something like this:

 try:
   import queue
 except ImportError:
   import Queue as queue

For a complete list aliases, see https://python-future.org/reference.html#module-future.standard_library

• Use of old_div() function can generally be avoided by using int()

Step 3

The lib2to3.fixes.fix_idioms transformation should explicitly be applied:

  for f in `find ./ -name "*.py"`; do \
    ${Slicer_DIR}/../python-install/bin/PythonSlicer \
      --launch futurize -f lib2to3.fixes.fix_idioms --nobackups --write $f; \
  done

Slicer 5.0: Python2 to Python3 (EditorEffect imports)

Import of Editor classes should be updated. For example, see r28122.

Before:

import EditorLib
from EditorLib.EditOptions import HelpButton
from EditorLib.EditOptions import EditOptions
from EditorLib import EditUtil

class TemplateKeyEffectOptions(EditorLib.LabelEffectOptions):
  [...]

After:

import EditorLib
from EditorLib import EditOptions, HelpButton
from EditorLib import EditUtil
from EditorLib import LabelEffectOptions, LabelEffectTool, LabelEffectLogic, LabelEffect

class TemplateKeyEffectOptions(LabelEffectOptions):
  [...]

Slicer 4.9: Explicit include of ExternalProject module not needed anymore

Following r26984, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) ensure the ExternalProject CMake module is included.

Note that ExternalProjectDependency CMake module is also included.

Slicer 4.9: Explicit passing of CMAKE_OSX_* variables not needed anymore

Following r26983, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) initializes CMAKE_OSX_* variables and ensures the variables CMAKE_OSX_ARCHITECTURES, CMAKE_OSX_SYSROOT and CMAKE_OSX_DEPLOYMENT_TARGET are passed to all external projects when configuring SuperBuild based extension.

Slicer 4.9: Explicit initialization of CMAKE_BUILD_TYPE not needed anymore

Following r26978, calling find_package(Slicer REQUIRED) and include(${Slicer_USE_FILE}) initializes CMAKE_BUILD_TYPE and ensures the variables CMAKE_BUILD_TYPE and CMAKE_CONFIGURATION_TYPES are passed to all external projects when configuring SuperBuild based extension.

The module SlicerInitializeBuildType is automatically included in UseSlicer CMake module.

Slicer 4.9: Subversion not required anymore

Following r27060, Subversion is not required anymore.

Slicer 4.9: Support EP_GIT_PROTOCOL and use of ExternalProject_SetIfNotDefined for setting GIT_REPOSITORY, GIT_TAG and alike

Following r26957, extension may use the following convention to define GIT_REPOSITORY and GIT_TAG, this allows developer to override the value before the first configuration by setting the corresponding environment variable, or by explicitly configuring the project with that variable.

The option EP_GIT_PROTOCOL is also already set in ExternalProjectDependency module included by Slicer and its value is updated based on the <SUPERBUILD_TOPLEVEL_PROJECT>_USE_GIT_PROTOCOL option.

  ExternalProject_SetIfNotDefined(
    ${CMAKE_PROJECT_NAME}_${proj}_GIT_REPOSITORY
    "${EP_GIT_PROTOCOL}://github.com/jcfr/shape4D.git"
    QUIET
    )

  ExternalProject_SetIfNotDefined(
    ${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG
    "12fef84ca2a56feffc59d8159bdadd2ce4a4138e" # slicersalt-2018-01-22-c74c766a4c
    QUIET
    )

See:

• https://cmake-artichoke.readthedocs.io/en/latest/ExternalProjectDependency.html#variable:EP_GIT_PROTOCOL
• https://cmake-artichoke.readthedocs.io/en/latest/ExternalProjectDependency.html#function:ExternalProject_SetIfNotDefined

Slicer 4.9: Use ExternalProject_AlwaysConfigure to force reconfigure of inner project

Following r26551, the function ExternalProject_AlwaysConfigure may be used to ensure the inner project is always reconfigured.

Using the `BUILD_ALWAYS` option supported by ExternalProject_Add will not have the intended effect.

See https://cmake-artichoke.readthedocs.io/en/latest/ExternalProjectDependency.html#function:ExternalProject_AlwaysConfigure

Slicer 4.9: Specifying external projects to install in SuperBuild extension

Following r27267 and r27232, the following should be used to ensure the extension can also be bundled into a Slicer custom application. When bundled, the variable ${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS is then used to update the application's list of project to install.

#-----------------------------------------------------------------------------
set(EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS)
#list(APPEND EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS "${Foo_DIR};Foo;RuntimeLibraries;/")
set(${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS "${EXTENSION_CPACK_INSTALL_CMAKE_PROJECTS}" CACHE STRING "List of external projects to install" FORCE)

#-----------------------------------------------------------------------------
list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${CMAKE_BINARY_DIR};${EXTENSION_NAME};ALL;/")
list(APPEND CPACK_INSTALL_CMAKE_PROJECTS "${${EXTENSION_NAME}_CPACK_INSTALL_CMAKE_PROJECTS}")
include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})

Slicer 4.9: Generating (Extension)Config.cmake

Initially introduced in r25944, and later improved in r25991, including ${Slicer_EXTENSION_GENERATE_CONFIG} ensure a config is generated and allow an extension to import targets from another extension by using find_package(ExtensionName REQUIRED).

[...]

include(${Slicer_EXTENSION_GENERATE_CONFIG})
include(${Slicer_EXTENSION_CPACK})

Slicer 4.9: Initializing <projectName>_BUILD_SLICER_EXTENSION option: Standalone vs Slicer extension build

The following snippet allows to automatically initialize <projectName>_BUILD_SLICER_EXTENSION to ON if Slicer_DIR is defined.

#-----------------------------------------------------------------------------
# Standalone vs Slicer extension option
#-----------------------------------------------------------------------------

# This option should be named after the project name, it corresponds to the
# option set to ON when the project is build by the Slicer Extension build
# system.

set(_default OFF)
set(_reason "${PROJECT_NAME}_BUILD_SLICER_EXTENSION is ON")
if(NOT DEFINED ${PROJECT_NAME}_BUILD_SLICER_EXTENSION AND DEFINED Slicer_DIR)
  set(_default ON)
  set(_reason "Slicer_DIR is SET")
endif()

option(${PROJECT_NAME}_BUILD_SLICER_EXTENSION "Build as a Slicer Extension" ${_default})

set(_msg "Checking if building as a Slicer extension")
message(STATUS ${_msg})
if(${PROJECT_NAME}_BUILD_SLICER_EXTENSION)
  message(STATUS "${_msg} - yes (${_reason})")
else()
  message(STATUS "${_msg} - no (${PROJECT_NAME}_BUILD_SLICER_EXTENSION is OFF)")
endif()
mark_as_superbuild(${PROJECT_NAME}_BUILD_SLICER_EXTENSION:BOOL)