ENH: Update ITK from v4.13 to v5.0rc1, Update BRAINSTools and SimpleITK #1096
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This was referenced Mar 6, 2019
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@phcerdan Thanks for pushing this forward. It is long overdue. |
dzenanz
approved these changes
Mar 6, 2019
Modules/CLI/ExpertAutomatedRegistration/ExpertAutomatedRegistration.cxx
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Thanks 👍 I suggest to move the update of CMake version into its own Pr that will integrate asap. The Here is a suggested commit message: |
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Should SimpleITK be also updated at the same time ? |
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I think that SimpleITK build against both ITKv4 and ITKv5. If so, it does not have to be updated. @blowekamp is that correct? |
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CMake update of internal projects moved new PR: #1097 |
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SimpleITK v1.1 will not work against ITKv5. It will need to be updated to v1.2.0 release. ( Note: there is also [this patch ] (SimpleITK/SimpleITK@88f9e7b) on the SimpleITK release brach which addresses some build issues with the latest XCode which should be included too. ) |
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Thanks @blowekamp! I am testing with SimpleITK OFF for now. But will use v1.2.0 release plus the patch. By the way, your link contained a spurious: |
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In addition of the suggested commit message update, consider adding @sjh26 as a co-author too: |
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Hey @dzenanz, @jcfr are the two commits on top of BRAINSTools here: https://github.com/Slicer/BRAINSTools/commits/slicer-2017-12-09-v4.7.1-b045970 planned to be merged upstream? |
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They have already. See BRAINSia/BRAINSTools@a9045b9 and BRAINSia/BRAINSTools@a1e7fab Next time, we will make sure to label the commit in the fork with |
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Since you will be moving to the latest ITK, and don't need to provide option to build against ITK 4.x, you might as well move to the latest version of BRAINSTools. @hjmjohnson what do you think? |
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@dzenanz Thanks for the review 👍
That is the plan. @phcerdan will push an updated branch shortly 🚀 |
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Created branches in Slicer for ITK, BRAINSTools and SimpleITK ITK: updated to rc01 + 1DCMTK patch |
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FYI: I'll do my best to make any changes to BRAINSTools that are necessary. |
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The rational behind creating branches in the Slicer forks is to avoid full rebuild when applying changes that are being reviewed in the upstream project. Indeed, changing GIT_REPOSITORY causes the source tree to be removed and cloned again, whereas updating GIT_TAG lead to an update. |
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Testing locally: "D:\T\Pablo\S-R\ITK-build\Modules\Compatibility\Deprecated\src\ITKDeprecated.vcxproj" (default target) (32) ->
(Link target) ->
10>itkConditionVariable.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) const itk::ConditionVariable::`vftable'" (__imp_??_7ConditionVariable@itk@@6B@) referenced in function "protected: __cdecl itk::ConditionVariable::ConditionVariable(void)" (??0ConditionVariable@itk@@IEAA@XZ) [D:\T\Pablo\S-R\ITK-build\Modules\Compatibility\Deprecated\src\ITKDeprecated.vcxproj] [D:\T\Pablo\S-R\ITK.vcxproj]
10>itkMutexLock.obj : error LNK2001: unresolved external symbol "public: virtual char const * __cdecl itk::SimpleMutexLock::GetNameOfClass(void)" (?GetNameOfClass@SimpleMutexLock@itk@@UEAAPEBDXZ) [D:\T\Pablo\S-R\ITK-build\Modules\Compatibility\Deprecated\src\ITKDeprecated.vcxproj] [D:\T\Pablo\S-R\ITK.vcxproj]
10>itkMutexLock.obj : error LNK2019: unresolved external symbol "__declspec(dllimport) const itk::SimpleMutexLock::`vftable'" (__imp_??_7SimpleMutexLock@itk@@6B@) referenced in function "public: __cdecl itk::SimpleMutexLock::SimpleMutexLock(void)" (??0SimpleMutexLock@itk@@QEAA@XZ) [D:\T\Pablo\S-R\ITK-build\Modules\Compatibility\Deprecated\src\ITKDeprecated.vcxproj] [D:\T\Pablo\S-R\ITK.vcxproj]
10>D:\T\Pablo\S-R\ITK-build\bin\Release\ITKDeprecated-5.0.dll : fatal error LNK1120: 3 unresolved externals [D:\T\Pablo\S-R\ITK-build\Modules\Compatibility\Deprecated\src\ITKDeprecated.vcxproj] [D:\T\Pablo\S-R\ITK.vcxproj]MacOS: |
For reference:
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As I am trying to incorporate newer versions of TBB to accelerate some processing, I choose to use 10.11 as the base deployment target. |
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From the TBB Changelog file:
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Makes sense. We will most likely target 10.11 as well. To get an idea of the user base, I also setup a poll. When you have a chance, would appreciate your input: |
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To help extension developers transition their code base, a migration guide is also available on the wiki. See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/ITK4-to-ITK5 This commit implements the following changes - Compatibility with refactor of threading models in ITK: Fix compilation using ProcessingThreader class instead of PlatformMultiThreader. ITKv5 reorganized the multi-threading capabilities of ITK into a more modular organization and naming to support several modern parallelism paradigms. Note that these changes allow Slicer to compile with ITKv5, but does not take advantage of any enhancement supporting new threading models. ProcessingThreader is still the old-renamed PlatformMultiThreader. These changes were originally associated with PR Slicer/Slicer#1057 - Fix compilation issue related to ComputeJacobianWithRespectToPosition parameter mismatch. ITKv5 change the argument of some transform functions from JacobianType to JacobianPositionType. This fixes the new signatures. These changes were originally associated with PR Slicer/Slicer#1055 List of BRAINSTools changes: ``` git shortlog --no-merges b045970..ac4dafaa ``` ``` Alexander Leinoff (1): COMP: Allow cmake generation on OSX without XCode David Ellis (2): ENH: Adds logismosb interfaces and workflows ENH: Nipype recon-all workflow added Hans J. Johnson (196): ENH: Prefer to build everything as static to avoid libary dependancies. ENH: Force the NO_MODULE for RTK. ENH: Resyncronized with Slicer packages. ENH: Update Opencv ENH: Propagate CXX settings to all sub-projects ENH: ITK Intermediate update. STYLE: Name ITKv5 as target name for dependancies ENH: Turn off ITK_LEGACY to prep for ITKv5 ENH: Update ANTS,RTK and SlicerExecutionModel checkout tags COMP: Set VTK version identifier. ENH: Updated VTK with C++11 override instrumentation. BUG: UseImageSpacing should be defaulted to On ENH: Add github templates for PR and ISSUES COMP: Disable floating point exceptions checking BUG: New ITK enhanced random needs consistency in test. ENH: Set random number generated to historical ITK values COMP: Make tests pass BUG: Fix incorrect DATA{} syntax. ENH: Fix pre-mature exit when writing debug image STYLE: Minor code organization ENH: Setting min cmake version number. STYLE: Remove CMake-language block-end command arguments STYLE: Convert CMake-language commands to lower case COMP: Use recommended const interfaces ENH: Explicitly use parameters instead of defaults. ENH: Instrument to identify test failures COMP: Link to correct version of zlib COMP: Use C++11 nullptr directly COMP: Identify null pointer assignments COMP: Use C++11 override directly STYLE: Setting override for overriden member functions. BUG: Missing data dependancies for test suite COMP: Remove compiler warnings from cnpy COMP: BRAINSSurfaceTools are not compiling currently. COMP: Remove outdated policies for CMP0017. STYLE: Use override statements for C++11 ENH: Change to https from git download. ENH: Set BRAINSABC to always build. COMP: Update to new version of tbb ENH: Use C++ headers instead of C headers. COMP: Missing dependancy on ITKv5 ENH: Setting deployment target to 10.9 for mac ENH: Put BRAINSSuperResolution code together. COMP: Attempt to build BRAINSTools for redistribution. STYLE: Push parts of codebase into an ARCHIVE dir BUG: Provide mechanism to move some modules to the ARCHIVAL status. COMP: Remove outdated cmake policy behavior ENH: Move old programs to an archive directory COMP: Remove shadowed typedefs by using explit namespaces ENH: Move BRAINSTalairach to the ARCHIVE Directory. ENH: Move BRAINSRefacer to the archive directory. ENH: Set ARHIVE project to on if ARCHIVE builds choosen. ENH: Add old DicomSignature program to archive COMP: Fix building against new GDCM version. Update NOTICE ENH: Use file introspection to determine BVec file format ENH: Remove unnecessary manual read file type flag ENH: Add thicknes from spacing when converting from FSL to NRRD. ENH: use constant scale factor initialization BUG: ITK_VERSION_MAJOR version checking ENH: Remove redundant ExternalData.cmake that overrode CMake version. STYLE: Prefer constexpr for const numeric literals STYLE: Replace itkStaticConstMacro with static constexpr STYLE: Prefer constexpr for const numeric literals STYLE: Do not use itkGetStaticConstMacro in ITK ENH: Update to ITKv5 with using over typedefs. ENH: Update dependancies for BRAINSTools. COMP: Wrong name specified for target_properties. BUG: regex substitution failure for const COMP: Silence build warning about unused CMAKE_EXPORT_COMPILE_COMMANDS COMP: Cleanup build options for BRAINSTools ENH: Organized for project name setting. ENH: Improve CXX_STANDARDS checking logic ENH: Remove outdated ITKv3 configuration checking. ENH: Set GENERATECLP_USE_MD5 unconditionally. STYLE: Organize build default settings. ENH: Use explicit named mark_as_superbuild parameters. ENH: Add better debugging to version checking. ENH: Improve version settings for BRAINSTools ENH: Use MultiThreaderBase to get GlobalVariables. ENH: Provide new baseline for BRAINSFitTest_RigidRotGeomNoMasks ENH: Prevent constant changes as patches are added BUG: Prevent constant changes as patches are added ENH: Fixed tests failures due to incorrect testing environments ENH: Syncronized external superbuilds with Slicer. ENH: Convert BRAINSCut python to python 3 ENH: Convert all python code to python 3 conformance ENH: Version 5.0.0 of BRAINSTools ENH: Allow for compressed transform files. ENH: Reorganize python code to be compliant with Python3 modules BUG: New versions of ANTs have slightly different options BUG: Fix new nipype behavior of data sink with missing values. ENH: Consolodate duplicate functions ENH: Fix simple itk usage failure. STYLE: Update comments. BUG: Nipype needs OrderedDict for hash consistency ENH: Passing dict() or OrderedDict() through pipeline causes hashing issues BUG: Incorrect debugging option retained for None images ENH: Allow for possiblility of compiling with ITKv4 ENH: Update ITKv5 to version with UseCompression for transforms. ENH: Update to latest version of boost. BUG: Fix bug in mark_as_superbuild PROJECT->PROJECTS BUG: Error in caused mark_as_superbuild items to be missed ENH: Sync with slicer mark_as_superbuild options. ENH: Re-organize build option settings STYLE: Reviewed and cleaned up superbuild ENH: Updated static version string setting. COMP: Add quick -march=native compiler flag adding ENH: Remove unnecessary build code for superbuild. ENH: Syncronized with NAMICExternalProjects build. ENH: Propogate default /lib /bin directories to all projects BUG: Bad hash for scan3Mask1.nii.gz.md5. ENH: Unlink ITK from VTK GUI build. COMP: HD5 changed API for printing Errors. COMP: Remove unused variables. COMP: ITKv5 updates for JPEG2000. ENH: Updated packages for improved C++11. ENH: Add azure testing scripts. COMP: Fix KWStyle compilation fixes. BUG: Mismatch type for CovariantVector initialization. COMP: virtual designation is redundant with override designation. COMP: ITKv5 multi-threading model compatibility. COMP: ITKv5 uses std::mutex directly. COMP: Only configure inner BRAINSTools COMP: Fix function signature for override COMP: Future proof vnl_math_XXX function usage. COMP: Replace vcl_XXX items with std::XXX COMP: Remove unused variable. ENH: ITKv5 itkMultiThreader.h -> itkMultiThreaderBase.h STYLE: Replace itkStaticConstMacro with static constexpr STYLE: Use "typename" for template parameters STYLE: Prefer error checked std::sto[id] over ato[if] COMP: Prefer C++ headers to C99 headers. COMP: Use C++11 nullptr directly COMP: Use and move ITK_DISALLOW_COPY_AND_ASSIGN calls to public section. ENH: Update external packages C++11 compliance ENH: ITKv5 Threading Model changes needed for testing STYLE: Prefer C++11 type alias over typedef DOC: Add documentation for newer OS versions. ENH: Comment out tests that do not work due to missing data ENH: Disable building of BRAINSSurfaceTools COMP: Remove compiler warnings. COMP: Make VerifyInputInformation a const function (ITKv5) ENH: Update to 2019_U2 to fix TBB issues with mac min version compilations. ENH: Propagate MAC_OS_X_VERSION_MIN_REQUIRED to TBB build. ENH: Improve TBB versioning selection. COMP: Update new reference data after VXL ITKv5 updates. ENH: Updated BCD baselines for ITKv5 COMP: ITKv5 backward compatibility fixess. ENH: Update BRAINSFit baselines for ITKv5 ENH: Try to make random number generation consistent. ENH: Update ANTs and ITKv5 for more test coverage. ENH: Update data regression. COMP: Remove compiler warnings. ENH: Duplicate names for testing BUG: Failing test updated after visual review COMP: Cleanup compiler warnings. ENH: UPdate ITK to include vxl explicit instantiations. COMP: Remove deprecated SetUseFixedSampledPointSet COMP: SetNumberOfThreads -> SetNumberOfWorkUnits ENH: Update reference data to sha512 on new data source. ENH: Remove duplicate md5 signatures. BUG: Failed uploads fixed for sha512 COMP: Valgrind un-initialized memory reads STYLE: Prefer error checked std::sto[id] over ato[if] ENH: Adding an editor config for BRAINSTools. ENH: Add extra landmark Eye sanity checking for BCD. ENH: Add component testing for valid values to workflow running. STYLE: Remove trailing whitespace from files COMP: Add missing iostream header. STYLE: Remove unused file and directory ExternalSources. ENH: Fix dependency ordering for new project() syntax. ENH: Use range of new CMake features. ENH: Update to latest TBB build 2019_U3 for 10.14 compatibility. ENH: Update to latest version of packages ENH: Temporary ITK branch for dcmtk api compatibility. ENH: Add Travis pull request builds. ENH: Add helper file for configuring BRAINSTools for IDE. COMP: Errors with VTK TBB building in superbuild mode. STYLE: Fix naming of variables for DWIConverter class. ENH: Force clean ITKv5 building, remove legacy modes. ENH: ITKv5 const fix for duplicater image filter. ENH: ITKv5 fix for duplicater image filter. COMP: Allow building with C++ > 11 ENH: Fix failing CI .travis.yml syntax. ENH: Add diagnostics for failed TBB download. ENH: Test for extra long test times. COMP: Moved my.cdash.org only supports https now. ENH: The maximum cmake version is only for policies ENH: Fix backward compatibility with OpenCV4. COMP: Match types for loops. BUG: Python set inclusion syntax error fixed. ENH: The maximum cmake version is only for policies ENH: Update wts reference file to have comment line. ENH: Wts file has header line to be ignored. BUG: Simple ITK does not currently expose SetNumberOfWorkUnits Hui-Xie (6): COMP: change VTK min version ENH: Add support for r/w Dicom, FSL, Nrrd formats BUG: erase unnecessary cmake config BUG: erase unnecessary lib in CMake file ENH: add DWI file convert utility interfaces BUG: stat uses ITK KWSys wrapper interface Isaiah Norton (4): BUG: DWIConverter hard-coded transpose/FSLBy3Rows setting ENH: don't allow matching bvec and bval file names ENH: DWIConvert, Philips: also check supplement 49 b value field Bump ITK to v5b1 to resolve FFTW broken download Jean-Christophe Fillion-Robin (4): Add License file STYLE: Add Notice file ENH: Improve build targets organization in IDE that support folders ENH: Use a single data management target and support customizing its name Johan Andruejol (1): BUG: Add try/catch around BrainsFitHelper update Regina EY Kim (2): BUG: Add a missing header ENH: fix the probabilityMap RegistrationToSubject option azure-pipelines[bot] (1): Set up CI with Azure Pipelines ``` List of SimpleITK changes: ``` git shortlog --no-merges v1.1.0..dc5c1a1d ``` ``` ASVBPREAUBV github_user (1): Update DicomSeriesReadModifySeriesWrite.R Bradley Lowekamp (164): Bumping version to 1.2 for development Adding Python wheel downloads for v1.1.0 from SourceForge Fix template generator custom method with multiple parameters Add docs for set methods Add SetRegionOfInterest method Document conventions for Image Regions Add GetRegion method to LabelMap based statistics filters Correct RegionOfInterest doxygen from proper ITK class Adding wrapping for filters from remote LabelErodeDilate module Use named inputs for the paste image filter Adding wrapping for StochasticFractalDimensionImageFilter Add names inputs for FFTConvolutionImageFilter Update JSON python scripts to end files with newline Add ExternalData step to building Sphinx documentation Adding Readme for Sphinx images directory Adding Readme to white list of files Correct code-block indentation Add overflow and underflow count to ShiftScaleImageFilter Adding wrapping for the BSplineDecompositionImageFilter Add interpolator enum for the BSplineResampleImageFunction Fix documentation for GetCoefficientImages method Adding test for resampling with the BSplineResampler iterpolator Add specification of ITK ImageIO used to read image Use return self macro Adding testing for setting ImageIO Adding baseline hash for LabelSetErode filter Update require CMake version to 3.10 Remove CMake version checks for version before required version Remove local CMake GTest module, use gtest_discover_tests Set pointer to null after deleting Correct interpolate for ruby bspline_resample test Only label unstable on apple systems Correct capitalization style for ruby enum Update SimpleITK Version in Sphinx Adding support for ImageBase types to ImageTypeToPixelIDValue Add a descriptive error message for image casting failure Add propagation of CMake job pool variables in Superbuild Remove deprecated midas3 from external download URLs Remove unused variable value Remove imported CMake ExternalData module Update referenced json Update name field and reference script used for doc fields Add doc for itk_module json field Adding R language to CircleCI testing Only add R dependencies for R job Adding R Unit tests when R is built as a project Add junit test formatting for python and R Make and use separate environment anchor Update documented CMake required version Add wrapping for Toboggan filter Update ITK superbuild version along ITK v41.3 release Make variables, functions, and structs local scope Add support for VectorImages to the Tile filter Specifying Toboggan output types as uint32_t for portability Just link the SimpleITK on Sourceforge, not the versioned sub-directory. Reduce CircleCI dependencies, and use system SWIG Correcting link to Java visual guide Improve doxygen documentation for the Image class Fix tense per code review Use standard find_package for ITK in SimpleITK Config Use modern CMake IN_LIST if operator Remove legacy BasicFiltersN loop code Correct variable name used to disable building documentation Update Superbuild ITK version along 4.13 release branch Set CircleCI to use Github for ITK repo Add wrapping for SLICImageFilter from SimpleITKFilters module Correct Github ITK repo in CircleCI CMake configuration Specify data root as SimpleITK root project Add BUILD_EXAMPLES option to standalone language builds Enable CircleCI testing of examples when language is built ENH: Support passing ITKV4_COMPATIBILITY to ITK superbuild Enable ITK_LEGACY_REMOVE to be overridden Explicitly specify stretch docker image add python 3.6 for testing Explicitly use python to invoke pip, print python version COMP: Lengthen GTest discovery timeout Adding Java build to CircleCI Add testing for Java stand-alone project No CI for languages on next branch Remove BUILD_DOCUMENTS CMake option Exclude files leading with a '.' from globs Add Update data link for R man documents Add TransformVector method to Transform class Update Superbuild ITK version to 4.13.1 This data file hash is neither used nor does it exit Update links for downloads in tarball generation Adding data links from ContentLinkSynchronization.sh execution If ITKv5 map number of threads to number of "Work Units" Add access to number of valid point used during registration Fix Python index test with empty comparison Fix recursive option with GetGDCMSeriesFileNames Adding Transform method to flatten composites transforms Add mirror of SimpleITK External Data repository Documentation tweaks Remove dimension limitations form GetImageFromNumpy Improve exception for unsupported Image size Use baseline images for testing Set the default CMake policy to 3.10 Adding request of IO region to ImageFileReader Adding testing for reading an extraction region Update ITK superbuild along 4.13 release branch Adding vector image support to Mean and Sum projection image filters Improve documentation for SetExtractSize Add new 5d test image Add IO extract direction matrix behavior documentation Add IO extraction test with 5d file Fix size shortening warning Remove uint64 to uint copy to avoid warnings Add Doxygen grouping to ImageReaderBase::Set/GetImageIO Create common method to create ImageIO by string name Fix indentation in ImageFileWriter Add SetImageIO method to ImageFileWriter Add option to set ImageIO to the series writer Add debugging information to ReadInformation Remove typename outside of template Add support for vector images to the clamp image filter Improve documentation of some RegistrationMethod methods. Add method to access the metric's sampling percentage. Add testing for GetMetricSamplingPercentagePerLevel method ITK superbuild version along the 4.13 release branch Address implicit conversion warnings from float to double Adding construction of BSpline transform from coefficient images Add testing of constructing BSpline Transform from images Add methods to transform class to get number of parameters Improve image registration per level documentation Add registration support for multi-resolution bspline transform Add unit testing of BSpline parameters Fix reassigning initial transform issue Adding testing of BSplineTransform registration in place Update the ITK superbuild version along release-4.13 ENH: Adding example of multi-resolution bspline registration Adding prose document to BSpline3 example Adding C++ BSpline3 example Add labels to docs referenced from BSpline3 Quote function name and remove extraneous prose fragment. Use the official ITK Github repo Restore needed storage option to increase default size Update manylinux to use CMake 3.11.4 Update manylinux openssl to 1.0.2q Create wheel even when tests fail Update JSON documentation from ITK release-4.13 Updating Java and Python docstrings from current build Updating ITK version with BSpline mesh parameter fix Add test for BSplineTransform copy on write Add multi-resolution BSpline registration test non-inplace Adding option to procedure ReadImage to specify the ImageIO Sort the json descriptions to maintain order Update Sphinx filter descriptions via script. Fix conversion warning Update the FAQ Fix up in wording in FAQ Update SwigDocStrings for Python and Java Update R documentation files Add missing parameter documentation to the ReadImage method Update from SwigDocUpdate.sh with latest changes Update R documentation archive Change broken quote to bash code block. Update R Rd document files with manual fix Applied correction to escape % in R documentation. Apply escape sequence to all occurrences of % Add isysroot as require flag in non-cmake superbuild projects Don't use CMAKE_OSX_SYSROOT is empty string Update ITK Superbuild version along 4.13 release branch Remove extraneous CMake message statement Adding Azure Pipelines configuration from master branch Dave Chen (11): Large refactor of GenerateDoc.py Ran JSONBeautify.py Ran new GenerateDoc.py on JSON files GenerateDoc.py fixed to handle Unicode input Added test of default ResampleImageFilter params Fixed wrong method. Missing '&' on Windows Fixed memory leak Improved testing of the ImageViewer class Modified test to improve code coverage Fix for hang in Show function on Windows David T. Chen (19): Fixed some formatting, adjusted a few other things. Use TextOutput for OutputWindow Fix string comparison bug ENH: Initial check-in of the ImageViewer class Use ImageViewer class Fix for ITK code style More code fixes Print more defaults it ToString Added SetGlobalDefaultDebugOn/Off methods Fix type warning on Windows Added 'command' param to SetApplication. Fix for Show w/o ImageJ or Fiji Improve test coverage for ImageViewer class. Removed ImageJ stuff from Installation doc Updated the building.rst doc A few small fixes Updated for Python 3 Re-run for SimpleITK v1.2rc1 Fix R documentation warning Jean-Christophe Fillion-Robin (2): circleci: Fix and simplify install of CMake circleci: Install scikit-ci-addons to ensure ctest_junit_formatter is available Kasper Marstal (2): ENH: Use return instead of raising StopIteration (PEP 479) ENH: Add empty image Python indexing test Richard Beare (25): Vignette update R package DESCRIPTION update moved methods import to namespace and referenced the dll Modified generation of namespace file R version check during configuration Installation of R from CRAN for circleci testing R package rules don't allow non standard file formats in the data directory. Add index entry to latex preamble of vignette Update formatting of license field in R DESCRIPTION file use Rd note section instead of usage as the latter requires R code Formulas processed to avoid breaking latex after conversion place holders in empty sections for procedural interface tidied up testing for missing fields importFrom for utils package in NAMESPACE file updated instructions for documentation Add as.image to index entry Add text to empty fields and allow additional sectiondef Modified creation of filenames of R documentation Add documentation file for S4 methods. Add replacement R functions. Add better support for R namespaces and documentation Fix: spurious bracket in script ENH: Improving formatting of DESCRIPTION file according to --as-cran checks Fix: C++11 style init causing problems with RTools(windows) c++ Modified functions exported by R package. Seungkyoon Bong (24): Updated tutorial link for SimpleITK Translated the common conventions page from the Doxygen Deleted the .rst change Added hyperlinks and inline markups for code Created a page with SimpleITK Filters Changed the HTML template of the documentation Added Relevant Resources and link to paper to index.rst Corrected LaTeX notation in Registration Overview Create image and transformation IO page Translate and Update Page for Eclipse Set Up Translate and Update Visual Studio Set Up Convert pngs to web-optimized jpgs Restore simpleitk_logo.png.md5 Translate N4BiasFieldCorrection R Example Create filter and slicing operator comparison Translate DemonsRegistration1 R Example Translate DemonsRegistration2 R Example Translate DicomSeriesFromArray R Example Translate ImageRegistrationMethodBSpline1-2 R Example Fix spelling error in N4BiasFieldCorrection Translate 2 ImageRegistrationMethod R Examples Translate ImageRegistrationMethod2-4 R Example Remove internal function in ImageRegistrationMethod1 Remove internal functions in DemonsRegistration1-2 Ziv Yaniv (18): Adding support for vector images in as.image conversion. Adding test to the patch (moving between R array 2 image 2 R array). Adding read the docs sphinx fundamental concepts documentation. Adding concepts of channels and resampling. Adding section on resampling and updating the images location. Adding reference to image md5 for download. Typo in example, comma instead of bar in the specification of Instance Number. ImageJ not found in expected location FAQ information. Updatind publication citation list. Adding the tutorials and course page to the documentation. Adding introductory information with respect to tutorials. Corrected backslash not visible in documentation of windows path. Renamed the example to reflect its content. Adding image viewing example. ENH: Adding new example illustrating new SimpleITK IO. ENH: separated the example in two based on code review. Upadated readme file to match our current state (rc1.2). Adding the SPIE course to the tutorials' list. ``` List of ITK changes: ``` ``` Co-authored-by: Pablo Hernandez-Cerdan <[email protected]> Co-authored-by: Hans Johnson <[email protected]> Co-authored-by: Sam Horvath <[email protected]> Co-authored-by: Jean-Christophe Fillion-Robin <[email protected]>
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Closing. This is superseded by Slicer/Slicer#1103 |
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To help extension developers transition their code base, a migration guide is also
available on the wiki.
See https://www.slicer.org/wiki/Documentation/Nightly/Developers/Tutorials/MigrationGuide/ITK4-to-ITK5
This commit implements the following changes
Compatibility with refactor of threading models in ITK: Fix compilation
using ProcessingThreader class instead of PlatformMultiThreader.
ITKv5 reorganized the multi-threading capabilities of ITK into a more modular organization
and naming to support several modern parallelism paradigms.
Note that these changes allow Slicer to compile with ITKv5, but does not take advantage
of any enhancement supporting new threading models. ProcessingThreader
is still the old-renamed PlatformMultiThreader.
These changes were originally associated with PR FastMarching crashes when applied to segment two different volumes in a row Slicer#1057
Fix compilation issue related to ComputeJacobianWithRespectToPosition parameter mismatch.
ITKv5 change the argument of some transform functions from JacobianType to JacobianPositionType.
This fixes the new signatures.
These changes were originally associated with PR about loading DTI dicom Siemens 3T images in Diffusion MR Slicer3 analysis Slicer#1055
List of BRAINSTools changes:
List of SimpleITK changes:
Co-authored-by: Pablo Hernandez-Cerdan [email protected]
Co-authored-by: Hans Johnson [email protected]
Co-authored-by: Sam Horvath [email protected]
Co-authored-by: Jean-Christophe Fillion-Robin [email protected]