gems and gemsbindings itk5 migration #7
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Freesurfer CentOS9 build now support ITK5.4. This commit includes the ITK5 migration related to gems and gemsbindings. See ITK v5 Migration Guide for details (https://github.com/InsightSoftwareConsortium/ITK/blob/master/Documentation/docs/migration_guides/itk_5_migration_guide.md). 1. Enhancements in nullptr behavior in ITKv5 provide more clear type checking and respect the nullptr identifier. The 'long 0' value known as NULL causes an ambiguity for overload compilations of the ITKv5 smartpointers. To be backwards compatible with pre C++11 compilers use the ITK_NULLPTR designation, otherwise replace NULL and 0 initialization of itk::SmartPointer with nullptr. 2. Since ITK 5.0, ITK_THREAD_RETURN_TYPE is now in the itk:: namespace, and ITK_THREAD_RETURN_VALUE is named itk::ITK_THREAD_RETURN_DEFAULT_VALUE 3. replace SimpleFastMutexLock with std::mutex, and #include "itkSimpleFastMutexLock.h" with #include <mutex> 4. For ITK_VERSION_MAJOR >= 5, use itk::MultiThreaderBase::SetGlobalDefaultNumberOfThreads()/GetGlobalDefaultNumberOfThreads() instead of itk::MultiThreader::SetGlobalDefaultNumberOfThreads()/GetGlobalDefaultNumberOfThreads() 5. Adapt to new multi-threading naming convention. Specifically: Change MultiThreader::ThreadInfoStruct to MultiThreaderBase::WorkUnitInfo Change (threadInfo)->ThreadID to (threadInfo)->WorkUnitID Change (threadInfo)->NumberOfThreads to (threadInfo)->NumberOfWorkUnits 6. For filter multi-threading, a new signature has been introduced: void DynamicThreadedGenerateData( const OutputRegionType& threadRegion ). By default, this new signature is invoked instead of the classic void ThreadedGenerateData( const OutputRegionType& threadRegion, ThreadIdType threadId ). To temporarily obtain the old behavior (classic signature invoked by default), set ITKV4_COMPATIBILITY to ON in ITK's CMake configuration. To permanently have your filter use the classic threading model, invoke this->DynamicMultiThreadingOff(); in the filter constructor. invoke 'this->DynamicMultiThreadingOff();' in the following likelihoodImageFilters to use the clasic signature ThreadedGenerateData(): kvlGMMLikelihoodImageFilter, kvlDSWbetaMMLikelihoodImageFilter, kvlFrobMMLikelihoodImageFilter, and kvlWMMLikelihoodImageFilter. 7. include "itkMacro.h" instead of "itkExceptionObject.h" for ITK_VERSION_MAJOR >= 5
Change library search order - search ZLIB_LIBRARIES before ITK_LIBRARIES. We compile with -DITK_USE_SYSTEM_ZLIB to use system installed zlib library. This should fix "Multiple defines" linking error.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.