kitware / slicersalt

An open-source, free comprehensive software that will allow biomedical scientists to precisely locate shape changes in their imaging studies. This software called Slicer Shape AnaLysis Toolbox (SlicerSALT), will enhance the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.

SlicerSALT

SlicerSALT is an open-source, free comprehensive software that will allow biomedical scientists to precisely locate shape changes in their imaging studies.

This software called Slicer Shape AnaLysis Toolbox (SlicerSALT), will enhance the intuitiveness and ease of use for such studies, as well as allow researchers to find shape changes with higher statistical power. Altogether this constitutes a crucial resource for the imaging field that will enable many and important new findings in biomedical imaging studies.

Maintainers

• Contributing
• Building

Resources

To learn more about SlicerSALT and Slicer, check out the following resources.

• https://salt.slicer.org/
• https://slicer.readthedocs.io/

License

This software is licensed under the terms of the BSD 3-Clause.

slicersalt's Issues

Statistics function

Hello,
I heard you are working on new statistical function.
Is there any timeline or plan for that?
I'd rather postpone to using older t-test for 1-2 months if it will be implemented soon.

Change the Slicer tag to more recent version

As of September-14-2017, changing the Slicer tag to a latest gives:

• Bug fixes
• VTK8 addition
• enabled Qt5 (Although this still is in testing phase)
• Python3 (this is also in testing)

However, the tag change would also mean that there might be changes for the extensions. Even if Qt5 is not added to the extensions, they would need changes necessary for VTK8.

BUG: Update splash screen

Change splash screen to reflect new affiliations

Fix macOS build

See https://open.cdash.org/viewBuildError.php?buildid=5533395

RigidAlignment doesn't find SlicerExecutionModel

DMRI error on start up

Traceback (most recent call last):
File "/work/Projects/slicerSALT/SlicerSALT-0.1.0-c988d2d-linux-amd64/lib/Slicer-4.7/qt-scripted-modules/DMRIInstall.py", line 33, in init
model = slicer.app.extensionsManagerModel()
AttributeError: qSlicerApplication has no attribute named 'extensionsManagerModel'

Update external projects to latest commits

• ShapePopulationViewer: Update when this PR is merged: NIRALUser/ShapePopulationViewer#30. Done in #40
• Update Sequences. Done in #40
• Update Slicer. Done in #40, after Slicer updated CTK and backported VTKv9 patch in 04917a6ce74

Enable rigid alignment

Enable rigid alignment modules from slicer and add them to data importer for allowing cohort alignment.

Update the Logo in the README and the Splash screen.

MFSDA extension

We need this PR accepted DCBIA-OrthoLab/MFSDA_Python#1
Add into SlicerSALT build system

Missing Fortran_COMPILER_ID

In linux dashboard and locally reproduced.

-- Looking up any Fortran compiler - Fortran_COMPILER-NOTFOUND
CMake Error at /work/Sw/CMake/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find Fortran (missing: Fortran_COMPILER_ID)
Call Stack (most recent call first):
  /work/Sw/CMake/cmake-3.11.4-Linux-x86_64/share/cmake-3.11/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/CMake/FindFortran.cmake:621 (find_package_handle_standard_args)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/GROUPS/SuperBuild/External_LAPACK.cmake:155 (find_package)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/slicersources-src/CMake/ExternalProjectDependency.cmake:852 (include)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/slicersources-src/CMake/ExternalProjectDependency.cmake:916 (ExternalProject_Include_Dependencies)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/slicersources-src/SuperBuild.cmake:414 (ExternalProject_Include_Dependencies)
  /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/slicersources-src/CMakeLists.txt:717 (include)


-- Configuring incomplete, errors occurred!
See also "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/CMakeFiles/CMakeOutput.log".
See also "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/CMakeFiles/CMakeError.log".

ENH enable KWStyle as a git hook.

Download statistics for SlicerSALT

Must decide between girder hosting vs package manager

ENH: add a home module and acknowledgements

External_python-scipy: Fix windows link error

Based on the change of https://github.com/jcfr/SlicerSALT/commits/release-1.0, the windows build is getting further and fails with the following error:

"D:\D\S\SSALT-0-build\slicersources-build\python-scipy.vcxproj" (default target) (1) ->
(CustomBuild target) ->
  CUSTOMBUILD : error : Command "lib.exe build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcosqb.o build\t
emp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcosqf.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dco
sqi.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcost.o build\temp.win-amd64-2.7\scipy\fftpack\src\
dfftpack\dcosti.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dfftb.o build\temp.win-amd64-2.7\scipy\
fftpack\src\dfftpack\dfftb1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dfftf.o build\temp.win-amd6
4-2.7\scipy\fftpack\src\dfftpack\dfftf1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dffti.o build\t
emp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dffti1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsi
nqb.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsinqf.o build\temp.win-amd64-2.7\scipy\fftpack\src
\dfftpack\dsinqi.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsint.o build\temp.win-amd64-2.7\scipy
\fftpack\src\dfftpack\dsint1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsinti.o build\temp.win-am
d64-2.7\scipy\fftpack\src\dfftpack\zfftb.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zfftb1.o build
\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zfftf.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zf
ftf1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zffti.o build\temp.win-amd64-2.7\scipy\fftpack\src
\dfftpack\zffti1.o /OUT:build\temp.win-amd64-2.7\dfftpack.lib" failed with exit status 127 [D:\D\S\SSALT-0-bu
ild\slicersources-build\python-scipy.vcxproj]

GUI Clean-up: Hide all functionality from modules menu except from SlicerSALT

Hide all functionality from modules menu except from SlicerSALT's

FEAT: Add a data importer module.

DataImporter.py throws errors on startup

Traceback (most recent call last):
File "/work/Projects/slicerSALT/SlicerSALT-0.1.0-c988d2d-linux-amd64/lib/Slicer-4.7/qt-scripted-modules/DataImporter.py", line 260, in setup
self.logic = DataImporterLogic()
File "/work/Projects/slicerSALT/SlicerSALT-0.1.0-c988d2d-linux-amd64/lib/Slicer-4.7/qt-scripted-modules/DataImporter.py", line 44, in init
self.createSingleDisplaySegmentModelNode()
File "/work/Projects/slicerSALT/SlicerSALT-0.1.0-c988d2d-linux-amd64/lib/Slicer-4.7/qt-scripted-modules/DataImporter.py", line 51, in createSingleDisplaySegmentModelNode
if MRMLUtility.isMRMLNodeEmpty(self.singleDisplayedSegmentation, 'vtkMRMLModelNode'):
AttributeError: type object 'MRMLUtility' has no attribute 'isMRMLNodeEmpty'

ShapeEvaluator extension

For whenever @juanprietob and the NIRAL intern get to modify ShapeVariationAnalyzer

Question: How can I pass a CMake option to a external module?

For example, for Sequences

# Sequences
set(extension_name "Sequences")
set(${extension_name}_SOURCE_DIR "${CMAKE_BINARY_DIR}/${extension_name}")
FetchContent_Populate(${extension_name}
  SOURCE_DIR     ${${extension_name}_SOURCE_DIR}
  GIT_REPOSITORY ${EP_GIT_PROTOCOL}://github.com/SlicerRt/Sequences.git
  GIT_TAG        a4b32e822505373d34f250123421ac9485f3947c
  GIT_PROGRESS   1
  QUIET
)

If I set a Sequences option in SlicerSALT (see upstream repo CMakeLists.txt for the option)
option(SEQUENCES_ENABLE_EXPERIMENTAL_MODULES "Enable the building of work-in-progress, experimental modules." ON)

Sequences ignores that option, and it is built with that option turned OFF (the default in their CMakelists.txt)
This is just an example, I don't want to build EXPERIMENTAL_MODULES, but I would like to provide an option to disable SampleData (see: #50)

Thanks

FEAT: Add Shape Population Viewer to the build

GROUPS extension

This extension has been facing some challenges to build on Windows:

• We need to compile lapack in windows which requires specific compilers (fortran)

MSFDA tutorial

@juanprietob will send email to follow up

Update Slicer tag

data importer tutorial

https://github.com/slicersalt/slicersalt.github.io/blob/master/docs/GROUPS-Tutorial-July16_2018.pdf

S-rep extension

Add to the build system of SlicerSALT

Data importer module in packages is empty

Data importer module in packages is empty. This is most probably due to a naming conflict with the directory in SPHARM-PDM for CommonUtilities. The easiest solution to this is to probably rename the folder in SPHARM-PDM. But ideally, the code for CommonUtilities should live in a repository if their task is the same.

Poor resolution of logo

Not sure if this is because of the logo itself, or a Slicer issue.

Windows package: CPACK_PACKAGE_EXECUTABLES reference wrong version

It could be caused by the fact the build tree wasn't started clean ...

Python module SequenceSampleData depends on disabled SampleData

Failed to instantiate module when launching SlicerSALT.

Traceback (most recent call last):
  File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/SequenceSampleData.py", line 33, in __init__
    import SampleData
ImportError: No module named SampleData
qSlicerPythonCppAPI::instantiateClass  - [ "SequenceSampleData" ] - Failed to instantiate scripted pythonqt class "SequenceSampleData" 0x7f4c51d834c8
Fail to instantiate module  "SequenceSampleData"

It is triggered from here.

We have explicitly disabled SampleData here

Add distance transform option to the Data Importer module

Solve DMRIInstall error upon starting SlicerSALT

BUG: Python errors on start

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOM.py", line 11, in <module>
    import DICOMLib
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/__init__.py", line 4, in <module>
    from DICOMWidgets import *
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 6, in <module>
    from packaging import version
ImportError: No module named packaging
loadSourceAsModule - Failed to load file "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOM.py"  as module "DICOM" ! 
Fail to instantiate module  "DICOM" 
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMScalarVolumePlugin.py", line 4, in <module>
    from DICOMLib import DICOMPlugin
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/__init__.py", line 4, in <module>
    from DICOMWidgets import *
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 6, in <module>
    from packaging import version
ImportError: No module named packaging
loadSourceAsModule - Failed to load file "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMScalarVolumePlugin.py"  as module "DICOMScalarVolumePlugin" ! 
Fail to instantiate module  "DICOMScalarVolumePlugin" 
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMSlicerDataBundlePlugin.py", line 3, in <module>
    from DICOMLib import DICOMPlugin
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/__init__.py", line 4, in <module>
    from DICOMWidgets import *
  File "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMLib/DICOMWidgets.py", line 6, in <module>
    from packaging import version
ImportError: No module named packaging
loadSourceAsModule - Failed to load file "/work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/qt-scripted-modules/DICOMSlicerDataBundlePlugin.py"  as module "DICOMSlicerDataBundlePlugin" ! 
Fail to instantiate module  "DICOMSlicerDataBundlePlugin" 
  Error(s):
    Failed to find python interpreter for CLI: /work/Projects/slicerSALT/slicerSALT-Dashboards/Nightly/SlicerSALT-0-build/Slicer-build/lib/SlicerSALT-4.9/cli-modules/PyCLIModule4Test.py
Fail to instantiate module  "PyCLI4Test" 
When loading module  "DICOMPatcher" , the dependency "DICOM" failed to be loaded. 
Object::connect: No such signal qSlicerGPUMemoryComboBox::currentTextChanged(QString)
Object::connect:  (sender name:   'GPUMemoryComboBox')
Object::connect:  (receiver name: 'qSlicerVolumeRenderingSettingsPanel')
Switch to module:  "Home" 

Setup automated upload of SlicerSalt packages on girder

Slicer build system only support uploading on Midas, it should be updated to support upload using a girder client.

Similarly to what was already done to support upload the extension to both Midas and slicer package manager.

Currently, Not all the functions are implemented, right?

I saw "shape population viewer is not installed" message, and can't find any stat-related functions.
They are still on developing, right?

Add some of MeshMath functionality to the Surface Toolbox

MeshMath: https://github.com/NIRALUser/SPHARM-PDM/blob/master/Modules/CLI/MetaMeshTools/MeshMath.cxx

Surface Toolbox: https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/SurfaceToolbox/SurfaceToolbox.py

Add sequences extension and create hooks into it.

Sequences extension can be used to play an animation of models with chosen color maps. Addition of this would be especially beneficial for the regression extension.

Test DataImporter

https://github.com/Kitware/SlicerSALT/blob/master/Modules/Scripted/ShapeAnalysisToolBox/DataImporter.py

• Remove CSV mode

• VTK case:

• Rename General VTK to something else that also handles label map images.
• Implement Import from Directory, handling label images, and vtk: mesh and surfaces. Plus any other sensible SlicerSALT file format.

Test public synthetic data here
And here (used in tests)

Current status:

fix dashboards

@jcfr suggests

• Linux - stays where it is (Bea will fix)
• Linux - slicer factory (JC and Pablo will set up)
• Mac - slicer factory (JC and Pablo will set up)
• Win - slicer factory (JC and Pablo will set up)

Error building python-scipy on Windows

CUSTOMBUILD : error : Command "lib.exe build\temp.win-amd64-2.7\scipy\fftpack\src\dfft
pack\dcosqb.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcosqf.o build\temp.wi
n-amd64-2.7\scipy\fftpack\src\dfftpack\dcosqi.o build\temp.win-amd64-2.7\scipy\fftpack\s
rc\dfftpack\dcost.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dcosti.o build\t
emp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dfftb.o build\temp.win-amd64-2.7\scipy\fftp
ack\src\dfftpack\dfftb1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dfftf.o bu
ild\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dfftf1.o build\temp.win-amd64-2.7\scip
y\fftpack\src\dfftpack\dffti.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dffti
1.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsinqb.o build\temp.win-amd64-2.
7\scipy\fftpack\src\dfftpack\dsinqf.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpac
k\dsinqi.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\dsint.o build\temp.win-am
d64-2.7\scipy\fftpack\src\dfftpack\dsint1.o build\temp.win-amd64-2.7\scipy\fftpack\src\d
fftpack\dsinti.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zfftb.o build\temp.
win-amd64-2.7\scipy\fftpack\src\dfftpack\zfftb1.o build\temp.win-amd64-2.7\scipy\fftpack
\src\dfftpack\zfftf.o build\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zfftf1.o build
\temp.win-amd64-2.7\scipy\fftpack\src\dfftpack\zffti.o build\temp.win-amd64-2.7\scipy\ff
tpack\src\dfftpack\zffti1.o /OUT:build\temp.win-amd64-2.7\dfftpack.lib" failed with exit
status 127 [C:\S\b\slicersources-build\python-scipy.vcxproj]

Update website with new tutorials

salt.slicer.org

Fix windows build error due to path too long

 C:\Program Files (x86)\MSBuild\Microsoft.Cpp\v4.0\V140\Microsoft.CppBuild.targets(312,5): error MSB3491: Could not write lines to file "x64\Release\vtkSlicerSkeletalRepresentationInitializerModuleLogicHierarchy\vtkSlice.273E9726.tlog\vtkSlicerSkeletalRepresentationInitializerModuleLogicHierarchy.lastbuildstate". The specified path, file name, or both are too long. The fully qualified file name must be less than 260 characters, and the directory name must be less than 248 characters. [D:\D\P\SSALT-0-build\Slicer-build\E\SlicerSkeletalRepresentation\SkeletalRepresentationInitializer\Logic\vtkSlicerSkeletalRepresentationInitializerModuleLogicHierarchy.vcxproj] [D:\D\P\SSALT-0-build\slicersources-build\Slicer.vcxproj

See https://open.cdash.org/viewBuildError.php?buildid=5532315

Add MeshToLabelMap to SlicerSALT

Mac executable problem

Solve problem on executables produced from packing cmake directives in mac

Add extra dashboard for linux

Add script for SALT based on current Slicer in https://github.com/Slicer/DashboardScripts

Error in ShapeRegressionExtension: multiple rules generate lib/SlicerSALT-4.9/qt-scripted-modules/Resources/Icons/ShapeRegressionExtension.png

-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.18.0")
-- Found Subversion: /usr/bin/svn (found version "1.10.0")
-- Found PythonLibs: /usr/lib/libpython2.7.so (found version "2.7.15")
-- Trying to find DCMTK expecting DCMTKConfig.cmake
-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Found CURL: /usr/lib/libcurl.so (found version "7.61.0")
-- RapidJSON found. Headers: ./include/SlicerSALT-4.9
-- Trying to find DCMTK expecting DCMTKConfig.cmake
-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Found PythonLibs: /usr/lib/libpython2.7.so
-- Found PythonInterp: .virtualenvs/slicer/bin/python2.7 (found version "2.7.15")
-- Configuring ShapeRegressionExtension with Qt 5.11.1 (using modules: Core, Widgets, Multimedia, Network, OpenGL, PrintSupport, UiTools, Xml, XmlPatterns, Svg, Sql, WebEngine, WebEngineWidgets, WebChannel, )
-- Setting QT_PLUGINS_DIR: /usr/plugins
-- Setting QT_BINARY_DIR: /usr/bin
-- Checking EXTENSION_NAME variable
-- Checking EXTENSION_NAME variable - NOTDEFINED
-- Checking MODULE_NAME variable
-- Checking MODULE_NAME variable - NOTDEFINED
-- Checking PROJECT_NAME variable
-- Checking PROJECT_NAME variable - ShapeRegressionExtension
-- Setting EXTENSION_NAME ......................: ShapeRegressionExtension
-- Checking to see if CXX compiler accepts flag -Wno-deprecated
-- Checking to see if CXX compiler accepts flag -Wno-deprecated - Yes
-- Checking to see if CXX compiler accepts flag -features=no%anachronisms
-- Checking to see if CXX compiler accepts flag -features=no%anachronisms - No
-- Checking to see if CXX compiler accepts flag -fdiagnostics-show-option
-- Checking to see if CXX compiler accepts flag -fdiagnostics-show-option - yes
-- Checking to see if CXX compiler accepts flag -Wl,--no-undefined
-- Checking to see if CXX compiler accepts flag -Wl,--no-undefined - yes
-- Checking to see if CXX compiler accepts flag -fstack-protector-all
-- Checking to see if CXX compiler accepts flag -fstack-protector-all - yes
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - yes (because configuring ShapeRegressionExtension-build)
CMake Warning at Software/Slicer/Shape/build-experimental/slicersources-src/Extensions/CMake/SlicerBlockAdditionalLauncherSettings.cmake:48 (message):
  Dependent extension Sequences cannot be found by CMake find_package(),
  therefore paths variables cannot be imported from this extension.  The
  problem can be resolved by generating SequencesConfig.cmake by adding
  include(${Slicer_EXTENSION_GENERATE_CONFIG}) to the top-level
  CMakeLists.txt of the dependent exension.
Call Stack (most recent call first):
  Software/Slicer/Shape/build-experimental/Slicer-build/UseSlicer.cmake:279 (include)
  CMakeLists.txt:28 (include)


-- Setting EXTENSION_SOURCE_DIR ................: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension
-- Setting EXTENSION_SUPERBUILD_BINARY_DIR .....: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting MIDAS_PACKAGE_URL ...................: http://slicer.kitware.com/midas3
-- Setting MIDAS_PACKAGE_EMAIL .................: OBFUSCATED
-- Setting MIDAS_PACKAGE_API_KEY ...............: OBFUSCATED
-- Setting EXTENSION_SVNUSERNAME ...............: NOT DEFINED
-- Setting EXTENSION_SVNPASSWORD ...............: NOT DEFINED
-- Setting EXTENSION_DEPENDS ...................: Sequences
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting EXTENSION_HOMEPAGE ..................:
-- Setting EXTENSION_CONTRIBUTORS ..............: Laura Pascal (Kitware Inc.), Beatriz Paniagua (Kitware Inc.), James Fishb [...]
-- Setting EXTENSION_CATEGORY ..................: Shape Regression
-- Setting EXTENSION_ICONURL ...................:
-- Setting EXTENSION_DESCRIPTION ...............: Computation and visualization of time-regressed shapes in a collection of [...]
-- Setting EXTENSION_SCREENSHOTURLS ............:
-- Setting EXTENSION_ENABLED ...................: 1
-- Setting EXTENSION_STATUS ....................: Beta
-- Found Git: /usr/bin/git
-- RapidJSON found. Headers: ./include/SlicerSALT-4.9
-- Trying to find DCMTK expecting DCMTKConfig.cmake
-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Configuring ShapeRegressionExtension with Qt 5.11.1 (using modules: Core, Widgets, Multimedia, Network, OpenGL, PrintSupport, UiTools, Xml, XmlPatterns, Svg, Sql, WebEngine, WebEngineWidgets, WebChannel, )
-- Setting QT_PLUGINS_DIR: /usr/plugins
-- Setting QT_BINARY_DIR: /usr/bin
-- Checking EXTENSION_NAME variable
-- Checking EXTENSION_NAME variable - ShapeRegressionExtension
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - yes (because configuring ShapeRegressionExtension-build)
-- Setting EXTENSION_SOURCE_DIR ................: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension
-- Setting EXTENSION_SUPERBUILD_BINARY_DIR .....: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting MIDAS_PACKAGE_URL ...................: http://slicer.kitware.com/midas3
-- Setting MIDAS_PACKAGE_EMAIL .................: OBFUSCATED
-- Setting MIDAS_PACKAGE_API_KEY ...............: OBFUSCATED
-- Setting EXTENSION_SVNUSERNAME ...............: NOT DEFINED
-- Setting EXTENSION_SVNPASSWORD ...............: NOT DEFINED
-- Setting EXTENSION_DEPENDS ...................: Sequences
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting EXTENSION_HOMEPAGE ..................:
-- Setting EXTENSION_CONTRIBUTORS ..............: Laura Pascal (Kitware Inc.), Beatriz Paniagua (Kitware Inc.), James Fishb [...]
-- Setting EXTENSION_CATEGORY ..................: Shape Regression
-- Setting EXTENSION_ICONURL ...................:
-- Setting EXTENSION_DESCRIPTION ...............: Computation and visualization of time-regressed shapes in a collection of [...]
-- Setting EXTENSION_SCREENSHOTURLS ............:
-- Setting EXTENSION_ENABLED ...................: 1
-- Setting EXTENSION_STATUS ....................: Beta
-- Configuring Scripted module: RegressionComputation
-- RapidJSON found. Headers: ./include/SlicerSALT-4.9
-- Trying to find DCMTK expecting DCMTKConfig.cmake
-- Trying to find DCMTK expecting DCMTKConfig.cmake - ok
-- Configuring ShapeRegressionExtension with Qt 5.11.1 (using modules: Core, Widgets, Multimedia, Network, OpenGL, PrintSupport, UiTools, Xml, XmlPatterns, Svg, Sql, WebEngine, WebEngineWidgets, WebChannel, )
-- Setting QT_PLUGINS_DIR: /usr/plugins
-- Setting QT_BINARY_DIR: /usr/bin
-- Checking EXTENSION_NAME variable
-- Checking EXTENSION_NAME variable - ShapeRegressionExtension
-- Adding ConfigureAdditionalLauncherSettings target
-- Adding ConfigureAdditionalLauncherSettings target - yes (because configuring ShapeRegressionExtension-build)
-- Setting EXTENSION_SOURCE_DIR ................: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension
-- Setting EXTENSION_SUPERBUILD_BINARY_DIR .....: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting MIDAS_PACKAGE_URL ...................: http://slicer.kitware.com/midas3
-- Setting MIDAS_PACKAGE_EMAIL .................: OBFUSCATED
-- Setting MIDAS_PACKAGE_API_KEY ...............: OBFUSCATED
-- Setting EXTENSION_SVNUSERNAME ...............: NOT DEFINED
-- Setting EXTENSION_SVNPASSWORD ...............: NOT DEFINED
-- Setting EXTENSION_DEPENDS ...................: Sequences
-- Setting EXTENSION_BUILD_SUBDIRECTORY ........: ShapeRegressionExtension-build
-- Setting EXTENSION_HOMEPAGE ..................:
-- Setting EXTENSION_CONTRIBUTORS ..............: Laura Pascal (Kitware Inc.), Beatriz Paniagua (Kitware Inc.), James Fishb [...]
-- Setting EXTENSION_CATEGORY ..................: Shape Regression
-- Setting EXTENSION_ICONURL ...................:
-- Setting EXTENSION_DESCRIPTION ...............: Computation and visualization of time-regressed shapes in a collection of [...]
-- Setting EXTENSION_SCREENSHOTURLS ............:
-- Setting EXTENSION_ENABLED ...................: 1
-- Setting EXTENSION_STATUS ....................: Beta
-- Configuring Scripted module: RegressionVisualization
-- Extension description has been written to: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build/ShapeRegressionExtension-build/ShapeRegressionExtension.s4ext
-- Checking if extension type is SuperBuild
-- Checking if extension type is SuperBuild - true
-- Setting 'CTEST_MODEL' variable with default value 'Experimental'
-- Setting 'SLICER_EXTENSION_MANAGER_CLIENT_EXECUTABLE' variable with default value 'SLICER_EXTENSION_MANAGER_CLIENT_EXECUTABLE-NOTDEFINED'
-- Setting 'SLICER_EXTENSION_MANAGER_URL' variable with default value 'SLICER_EXTENSION_MANAGER_URL-NOTDEFINED'
-- Setting 'SLICER_EXTENSION_MANAGER_API_KEY' variable with default value 'OBFUSCATED'
-- Configuring done
-- Generating done
-- Build files have been written to: Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build/ShapeRegressionExtension-build
[13/16] Performing build step for 'ShapeRegressionExtension'
ninja: error: build.ninja:962: multiple rules generate lib/SlicerSALT-4.9/qt-scripted-modules/Resources/Icons/ShapeRegressionExtension.png [-w dupbuild=err]

FAILED: ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
cd Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build/ShapeRegressionExtension-build && /usr/bin/cmake --build .
ninja: build stopped: subcommand failed.
FAILED: ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
cd Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-build && /usr/bin/cmake --build . && /usr/bin/cmake -E touch Software/Slicer/Shape/build-experimental/ShapeRegressionExtension-prefix/src/ShapeRegressionExtension-stamp/ShapeRegressionExtension-build
ninja: build stopped: subcommand failed.

Add shortcuts to module bar

We need to add shortcuts to module bar in the SlicerSALT program.

The things we should not add are crossed out in the snapshot above.

Add hooks to surface toolbox

Enable either surface toolbox, or create modules for doing surface processing.

This would be for things like: surface decimation, surface normal generation, etc.

Fix packaging of gfortran libraries on macOS

gfortran_osx-64 installed using conda (see https://conda.io/docs/user-guide/tasks/build-packages/compiler-tools.html) contain libraries already fixed up with @rpath, this is preventing a successful packaging by Slicer.

A python (or bash) script could be created to fix-up the installed libraries.

SPHARM-PDM Shape Population warning

Warning says - use the extension manager, but we have it disabled in SlicerSALT

About requiring LAPACK

Packaging LAPACK is a pain in windows, mainly because it requires a fortran compiler, which is only provided by MinGW or the intel compiler. Our best bet IMHO would be to use already compiled libraries and distribute them, however this is not recommended in general for testing, reproducibility, and security. If we go this way, we should create a recipe to create those binaries by our own first.

Even if we get lapack distributed, it will come with a generalistic, non-optimized blas library. There are commercial optimized blas libraries (AMD, intel) and open-blas. We should let the user link to these optimized libraries if they have any installed.
Other option is CLAPACK, which is an abandoned project using f2c in the fortran files to get c files. This is not optimized, nor getting bug updates. But it does not require a fortran compiler. I have tried to f2c in the modern codebase of lapack and it fails. SPHARM-PDM uses clapack, but... only once for solving a linear system, it can be workarounded.

Then I thought, if we are not providing a fast lapack, do we need lapack?
I started exploring in what SALT modules we are using lapack or clapack, and these are the results of my ongoing investigation:

• SPHARM-PDM: https://github.com/NIRALUser/SPHARM-PDM/blob/332d326b2b09fdffb60e98a676d6da89502783d1/Libraries/Shape/Algorithms/ParametricMeshToSPHARMSpatialObjectFilter.cxx
  Only used to solve a linear system, and with a comment complaining that VNL does not provide it.
  We can use other libraries for this. Or keep using CLAPACK. But no problem on this.
• GROUPS: https://github.com/NIRALUser/GROUPS/tree/master/SuperBuild
  Use of LAPACK function: ssyev_, provides External_LAPACK
  • MeshLib: https://github.com/NIRALUser/MeshLib/blob/master/CMakeLists.txt. No use of lapack.
  • RigidAlignment: https://github.com/NIRALUser/RigidAlignment . No use of lapack.
  • SurfRemesh: https://github.com/NIRALUser/SurfRemesh. No use of lapack.

Thanks @vicory @bpaniagua @jcfr