During the past few days, while testing the recent updates associated with Slicer build system, I ended updating some extensions.
List of extension that will be fixed shortly
-
Eigen3
- missing packageupload: We will probably extend the extension description file to include support for
skip_packageupload 1
- missing packageupload: We will probably extend the extension description file to include support for
List of extension fixed: Waiting integration and review of proposed Pull Requests by maintainers
Yes, for these extensions … the work has been done.
Please, consider reviewing and integrating these PRs during this week. We would like to have as much extensions as possible available for an upcoming release. (to be announced)
If you would prefer not to maintain your extension, let us know and we will remove it from the extension build system.
-
CBC_3D_I2MConversion - See fdrakopo/CBC3D_I2M_Conversion_SlicerExtension#1
- Fix build error caused by use of ITK ivar.
- Fix sign-compare warnings
- Fix undefined itkFactoryRegistration link error
-
MarginCalculator
- Repository converted to Git: https://github.com/jcfr/MarginCalculator
- Patches available at https://github.com/jcfr/MarginCalculator/compare/add-vtk7-and-qt5-support
-
PBNRR_SlicerExtension
- Fix undefined itkFactoryRegistration link error. See fdrakopo/PBNRR_SlicerExtension#1
-
RSSExtension - See gaoyi/RSSExtension#9
- Transition to VTK6 API
- Update to use
vtkMRMLLabelMapVolumeNode
- Add support for Qt5
List of extensions failing to configure or build: Action required by maintainer
-
DTI-Reg:
- TODO: Fix problem with boost (extension is attempting to build boost internally)
-
FacetedVisualizer
- Fix error
fatal error C1083: Cannot open include file: 'vtk_sqlite3.h'
- Fix error
-
FiberViewerLight
- The extension still requires work to compile using Qt5 and VTK8
-
MABMIS
- Fix build error updating code to use
itkInverseDisplacementFieldImageFilter
instead ofitkInverseDeformationFieldImageFilter
. This filteritkInverseDeformationFieldImageFilter
is deprecated and available only when building ITK withITKV3_COMPATIBILITY
set to 1 and this
is NOT the case anymore in Slicer.
- Fix build error updating code to use
-
SegmentationAidedRegistration (see gaoyi/SegmentationAidedRegistration#7)
- see below
LASegmenter
- see below
-
ErodeDilateLabel (see tokjun/ErodeDilateLabel#2)
- see below
LASegmenter
- see below
List of extensions expected to fail to configure or build: No actions required
-
DTIAtlasFiberAnalyzer
- Failure expected - look like the build system was updated to require Qt5
List of extension fixed and updated
-
SlicerOpenCV
- numpy issue should be addressed by
https://github.com/Slicer/Slicer/pull/786Merged
- numpy issue should be addressed by
-
ModelClip
PR j-lin/ModelClip#3Merged. Repository transfer to https://github.com/Ting-Jia/ModelClip- Fix build error adding support for VTK >= 6 and Qt5
-
LightWeightRobotIGT
PR SNRLab/LightWeightRobotIGT#1Merged- Fix configure and build, add support for Qt5
-
boost:
PR Slicer/ExtensionsIndex#1457- Merged- Remove unused and failing extension
-
CarreraSlice
PR ikolesov/CarreraSlice#9- Merged- Simplify build system and update extension to support VTK8
-
DCMQI
- Fix warnings
QIICR/dcmqi#299- Merged - cmake: Fix forcebuild step
QIICR/dcmqi#300- Merged - Fix setting of cxx standard
QIICR/dcmqi#298- Merged
- Fix warnings
-
DTIPrep
PR NIRALUser/DTIPrep#45- Merged- Remove dependency on ITKv3Compatibility
- Build against BRAINSTools, ITKv4 and SlicerExecutionModel provided by Slicer
- Updated Slicer to allow extension reusing BRAINSCommonLib. See r26331
-
Eigen:
PR Slicer/ExtensionsIndex#1455- Merged- Rename build time extension Eigen to Eigen3, and update to the latest version to add modern CMake support. Target
Eigen3::Eigen
should now be used to build against Eigen.
- Rename build time extension Eigen to Eigen3, and update to the latest version to add modern CMake support. Target
-
exStone
PR qimo601/exStone#1- Merged- Fix configure and build, add support for Qt5
-
FiberViewerLight -
See NIRALUser/FiberViewerLight#1- Merged- Fix build error using dedicated macro for building CLI: SEMMacroBuildCLI
- Fix build warnings
-
ImageMaker:
PR Slicer/ExtensionsIndex#1459- Merged- Fix undefined itkFactoryRegistration link error
-
LASegmenter
PR ljzhu/LASegmenter#5- Merged- Simplify build system.
issue ljzhu/LASegmenter#4 still need to be fixed by maintainer- Fix build error updating code to use
itkDisplacementFieldJacobianDeterminantFilter
instead ofitkMultiplyByConstantImageFilter
. The filteritkMultiplyByConstantImageFilter
is deprecated and available only when building ITK withITKV3_COMPATIBILITY
set to 1 and this is NOT the case anymore in Slicer.
-
LongitudinalPETCT
PR QIICR/LongitudinalPETCT#10- Merged- Fix build error
- Add support for Qt5
-
PortPlacement:
PR giogadi/PortPlacement#3: Fix and improve build system, PR Slicer/ExtensionsIndex#1460 and PR Slicer/ExtensionsIndex#1461- Merged- Switch to a Superbuild structure to download and build NLopt
- Update to use the latest version of Eigen
- Add support for Qt5
-
SlicerCIP (Chest_Imaging_Platform) - See
acil-bwh/SlicerCIP#21- Merged- Fix build errors and warnings
- Fix memory leaks
- Update Slicer to call cleanup function when script module are unloaded. See Slicer/Slicer#785
- Remove usage of factory methods like
vtkMRMLScene::GetNodesByClass
and useslicer.util.getNodesByClass
. While wrapping of these methods can be improved with VTK8 thanks to wrapper hint likeVTK_NEWINSTANCE
, let’s avoid using them in Slicer. See Slicer wiki /MemoryManagement#Python_scripts_and_scripted_modules and VTK wiki /Wrapping_hints#Hinting_with_attributes for more details. - Add support for Qt5
-
SkullStripper:
PR Slicer/SkullStripper#9, PR Slicer/ExtensionsIndex#1453- Merged- Fix undefined itkFactoryRegistration link error
-
XNATSlicer:
PR Slicer/ExtensionsIndex#1456- Merged- Update extensionsIndex to fix “reference is not a tree” error.
-
Extensions having
@rpath
-like packaging error are fixed by Slicer r26305:- ABC
- CarreraSlice
- ChangeTracker
- Cleaver
- CMFreg
- DCMQI - ~See also PR QIICR/dcmqi#295~ - PR integrated
- DSCMRIAnalysis
- DTIProcess
- IASEM
- IntensitySegmenter
- LAScarSegmenter
- MarkupsToModel
- PET-IndiC
- PETDICOMExtension
- PkModeling
- ScatteredTransform
- Sequences
- ShapeVariationAnalyzer
- SkullStripper
- SlicerProstate
- SlicerRT
- SliceTracker
- SobolevSegmenter
- SPHARM-PDM - See also PR NIRALUser/SPHARM-PDM#22
- T1Mapping
- UKFTractography
Extension candidates for adoption
-
GraphCutSegmentExtension - See DaphneCD/GraphCutSegmentExtension#1 - Candidate for Adoption. See Adopting GraphCutSegmentExtension extension?
- Fix compilation errors and CMake warnings
- Add support for Qt5
-
VirtualFractureReconstruction PR kfritscher/VirtualFractureReconstructionSlicerExtension#3 - Candidate for Adoption. See Adopting VirtualFractureReconstruction extension?
- Fix warnings, add support for Qt5
List of extension removed from the extension index:
- FinslerTractography:
-
TODO: Update to build against VTK7 / VTK8- Removed from the extension index in PR Slicer/ExtensionsIndex#1479
-