BUG: Update BRAINSTools to include fixes for BRAINSFit and BRAINSResample.
This commit fixes a regression introduced
by InsightSoftwareConsortium/ITK@d1e9fe2 (BUG: Ensure Transform IO
factories are registered once.) and integrated in r24836 (ENH: Update
ITKv4 to v4.9.0 release branch).
Following this ITK commit, the ITKIO transform libraries are build as
shared and dynamic_cast can NOT be used with templated classes that are
instantiated in a translation unit different than the one where they are
defined. It will work only if the classes are explicitly instantiated
and exported.
To workaround the issue, code that was relying on dynamic_cast is updated
to (1) ensure the objects are of the right type doing string comparison
and (2) then use static_cast instead of dynamic_cast.
This patch fixes the following EMSegment test (internally using
BRAINSFit) when compiled using gcc 4.4.3 and executed on Ubuntu 10.04:
EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_float_very_small
EMSegCL_Task_BRAINS_MRIHumanBrain_scalartype_uint_very_small
EMSegCL_Task_HumanEye_BRAINS_small
EMSegCL_Task_MRIHumanBrain_BRAINS_small
EMSegCL_Task_MRIHumanBrainExp_BRAINS_small
EMSegCL_Task_MRIHumanBrainFullParcellation_BRAINS_small
EMSegCL_Task_MRIHumanBrainParcellation_BRAINS_small
EMSegCL_Task_NonHumanPrimate_BRAINS_small
It fixes runtime error like the following:
//-----------------
Read ITK transform from file: /tmp/EMSegmentCommandLine/EMS282744605229D1c.h5
HACK: 0 VersorRigid3DTransform
Caught an ITK exception:
itk::ExceptionObject (0x18ef450)
Location: "unknown"
File: /path/to/Slicer-0-build/BRAINSTools/BRAINSCommonLib/GenericTransformImage.cxx
Line: 346
Description: itk::ERROR: Error in type conversion
//-----------------
Complete list of BRAINSTools updates:
$ git shortlog c658c75..e257e62 --no-merges
Alexander Leinoff (18):
DOC: Updates build instructions for OS X
COMP: Updates ITK dependency and Removes Python from build system
COMP: Allows Top-level cmake options to be passed down to BRAINSTools
COMP: Fixes data dependency for BRAINSCommonLib test
COMP: Fixes build errors on debain8
COMP: Fixes some CMake dependency issues with the FindVTKUtil module
COMP: Fixes Unused parameter warning on Linux in BRAINSCut
COMP: Fixes sign compare warning on linux
BUG: Fix failing BCD tests by adjusting image compare tolerences
BUG: Fixes failing test BCDTest_rescaleIntensity
BUG: Adds multiple baselines to BCD tests
BUG: Adds new baseline fcsv files so BCD tests pass on ubuntu
BUG: Fixes BCDTest_rescaleIntensity on Debian
BUG: Adds baseline for chk_BCDTest_ForcePCPoint
ENH: Updates compareTwoCVSFiels.py.in to work with python3
BUG: Adds null check to string assignment in BRAINSMeasureSurface.cxx
BUG: Fixes ctest dependencies for BRAINSTransformConvert
BUG: TBB should only be requested when building BRAINSABC
Ali Ghayoor (18):
ENH: Added two more tests to gtract
ENH: Remove most calls to EncapsulateMetaData in GTRACT
ENH: Compute seedsPerVoxel for UKF in DWI pipeline
BUG: Fixed a bug in DWI pipeline tractography workflow
BUG: now ANTs returns composite transform not as a list
BUG: import necessary module from python
BUG: Added proper python module inside the function
BUG: Unnecessary computation of ListOfClassStatistics
ENH: Convert a 4D image to a series of 3D images
ENH: Change internal pixel type to float
ENH: Increased dilate size in AtlasToSubject registration
ENH: run multiresolution AtlasToSubject SyN registration
ENH: NO atlasToSubject registration if transform filename exist
ENH: Make sure there are anough samples for KNN training
ENH: A samrter way to set the feature space values of KNN
ENH: Generate pure plugs mask and its incorporation in BABC
DOC: Added more detailed explanations for atlasVolume flag in BCD
ENH: A confusing print statement was modified for BABC
Csaba Pinter (1):
STYLE: Reconcile orphan module categories for DWICleanup and LabelStatistics
Hans J. Johnson (68):
BUG: Update path change for neuromorphometric data.
BUG: activate_this is not available in anaconda.
ENH: New version of NIPYPE ants interface
STYLE: Fixed spelling error.
BUG: Failure multi-modal BABC is run without a T2
BUG: Need to verify that dependant submodules are specified.
BUG: Indexing for MALF was off
ENH: Update ITK, ANTs
BUG: Now that ANTs composite transform is not a list, fix code
ENH: Improve cluster performance tuning.
BUG: Revised MALF indexing to work both for single and multi-modal cases.
ENH: Prepare code base for Python version 3
ENH: Stage 2 futurize
BUG: Remove incorrect use of relative import from non-package
ENH: Improve fall through with sentinal values
COMP: Fixe linkage failures with ITK changes
COMP: Fix new linkage issues with ITK
BUG: Force string from path
BUG: BrainStem cleanup bug when non-identity image was used.
BUG: MALF_SNAPSHOT_WRITER fails on non-identity images
ENH: Zeropad output images for easier sorting.
COMP: Remove shadow typedef warning.
BUG: Incorrect library specification
STYLE: Remove errant xcode build files.
COMP: Remove compiler warnings
ENH: Update Superbuild packages.
ENH: Remove dependance on Boost.
COMP: Add ITK_OVERRIDE for ICCDEF
COMP: Improve compatibility with VTK 6.1
COMP: Remove compiler warning.
COMP: Fix VTK-6.3 compilation issues.
BUG: DCMTK APPs don't build with intel compiler.
ENH: Updated Superbuild for later C++11 support.
ENH: Newest version of ITK.
ENH: Updated ITKv4 for build.
COMP: make vcl_pow command non-ambiguous
BUG: Updated DCMTK requires new CMAKE settings
COMP: Remove unnecessary cmake config message.
ENH: Merged PREDICT logic for Freesurfer script wiht main tree.
ENH: Improve python 3 compatibility.
ENH: Update DCMTK, ITK and ANTs
ENH: TrackOn Freesurfer Processing.
COMP: Remove unnecessary typedef
COMP: Add ITK_OVERRIDE to functions
BUG: BCD post landmark ACPC to atlas only when atlas is from same subject.
ENH: Only allow QT 4.8 or higher.
ENH: VTK, ITK and ANTS Updated.
PERF: Do not use hyperthreads for ITK
ENH: Allow selecting C++11 from CMAKE_CXX_STANDARD
ENH: This is an initial implementation of tbb
BUG: Fix TBB propagations to BRAINSTools
ENH: Update BABC build only with C++11
PERF: Replace OPEN_MP with TBB
BUG: Need to ensure that TBB is respecting num threads specified.
STYLE: Modernize to C++11 style conformance
ENH: Update version of BRAINSTools to 4.6.0
ENH: Enable the new feature for BRAINSABC
BUG: Do not dereference a variable when checking for existance.
COMP: Remove unused programs unless BUILD_FOR_DASHBOARD is set
ENH: Improve logic checking for ANTs external tool
COMP: Make ANTs integration more robust.
COMP: Only require VTK when requested.
BUG: Incorrect block_range3d extents
ENH: Add grainsize explicitly for blocked_ranges
ENH: Parallelize preparation for KNN measurements
PERF: Prefer pass by const reference to pass by value
ENH: Instrument reductions with CompensatedSummationType
ENH: Instrument std::vector reductions with CompensatedSummationType
Isaiah Norton (4):
ENH: FSLToNrrd should default to transposed bvecs
ENH: refactor SiemensDWIConverter::ExtractDWIData
BUG: fix segfault when reading single-file dataset
ENH: SiemensDWI: add support for fallback to non-CSA diffusion tags
Jean-Christophe Fillion-Robin (17):
ENH: Allow testing to be optionally enabled in Slicer build.
BUG: Ensure IO factory are registered.
BUG: BRAINSResample: Fix tests removing usage of dynamic_cast with transform
BUG: BRAINSFitHelperTemplate: Add missing static_cast
STYLE: BRAINSResample: Remove now uneeded check.
STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
STYLE: BRAINSFit: Remove now uneeded check.
STYLE: Remove git merge conflict resolution artifacts
COMP: Update ITKVtkGlue requirements to fix build with default option.
BUG: BRAINSFitHelperTemplate: Add missing static_cast
STYLE: BRAINSResample: Remove now uneeded check.
STYLE: VTKITKVectorReader: Remove now unneeded itkFactoryRegistration code
BUG: BRAINSFit: Fix tests removing usage of dynamic_cast with transform
STYLE: BRAINSFit: Remove now uneeded check.
STYLE: Remove git merge conflict resolution artifacts
COMP: Update ITKVtkGlue requirements to fix build with default option.
Jessica Forbes (18):
ENH: Splits atlas list into lists with lengths of n_modality
ENH: Makes target_image into a list of list
ENH: Adds atlasSmallIslandCleanup.py for pipeline
ENH: Initial commit for WorkupAtlasDustCleanup.py
ENH: Moves import command inside the function
ENH: Sets inFN2/T2 input as optional/None if only T1 session
ENH: Sets the T2 file as an optional arg for the dust cleanup script
ENH: Removed unused BASE_DATA_GRABBER_DIR function parameter
ENH: Adds dust cleanup workflow to baseline.py after MALF
ENH: Specifies input params for dust cleaning workflow
ENH: Added option to not dilate in dust cleanup script
ENH: Includes new dilation arg for dust cleanup in pipeline
ENH: Adds suspicious dust cleaning node before other cleaning node
BUG: Sets includeList to str not int
ENH: Removes unused input arg in CreateDustCleanupWorkflow
ENH: Updates output naming schema for WorkupAtlasDustCleanup.py
ENH: Moves dustCleanup node within Malf after injectSurfaceCSFandVBIntoLabelMap
BUG: Fixes typo conflict left in CreateFreeSufereScripts.py
Regina Kim (20):
COMP: Remove Unused variable
WIP: Update interface for antsJointFusion
BUG: ants Joint Fusion requires search_radius option
ENH: Closes 0000221
BUG: outputs should be returned with fullpath
Update README.md
Update README.md
Update README.md
ENH: BRAINSTools AutoWorkup Tutorial
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
Update README.md
ENH: ITK version 4.9 Update
ENH: ANTs Version upgrade
ENH: ants Denoise for Auto Workup
BUG: Denoise interface fix
BUG: Resample T2 after BRAINSABC
git-svn-id: http://svn.slicer.org/Slicer4/trunk@24881 3bd1e089-480b-0410-8dfb-8563597acbee |
