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Update Slicer and adopt SlicerCustomAppTemplate v2 #40
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This commit fixes the following error: [...] -- -------------------------------------------------- -- Configuring SlicerSALT application library: qSlicerSALTApp -- -------------------------------------------------- -- Setting SlicerSALT DESCRIPTION_SUMMARY to 'Customized version of slicer for SlicerSALT' -- Setting SlicerSALT DESCRIPTION_FILE to '/path/to/SlicerSALT-Release/Slicer/README.txt' CMake Error at /path/to/SlicerSALT-Release/Slicer/CMake/SlicerMacroBuildApplication.cmake:330 (message): LICENSE_FILE is mandatory Call Stack (most recent call first): /path/to/SlicerSALT/Applications/App/CMakeLists.txt:156 (slicerMacroBuildApplication) [...]
…e v2 Co-authored-by: Laura Pascal <[email protected]> * Add support Qt5 (and implicitly for the VTK OpenGL2 backend). Note that since ShapePopulationViewer still require Qt4, we can not require Qt5 yet. * Transition from a 3-level superbuild to a 2-level one by checking out the source of Slicer at configure time. * Update to the most recent version of Slicer, ShapePopulationViewer, ShapeRegressionExtension, SPHARM-PDM and Sequences. See below for detailed list of changes. Note: Since the hash originally associated with ShapeRegressionExtension was invalid at the time of this commit, the original hash was deduced from the change date associated with file External_ShapeRegressionExtension.cmake kitware/ShapeRegressionExtension@27e42c4 was considered to list the changes instead of the invalid kitware/ShapeRegressionExtension@a78faad. * Simplify Application/App/Main.cxx using preInitializeApplication and postInitializeApplication functions provided by qSlicerApplicationHelper. * Update SPHARM-PDM, ShapePopulationViewer and ShapeRegressionExtension external project to pass CXX standard option to support building with Qt5 and C++11 * Remove Modules/HomeModule entry from DefaultSettings and instead set CMake option Slicer_DEFAULT_HOME_MODULE * Set Slicer_DEFAULT_FAVORITE_MODULES option and remove Editor module from the list. // ------------------------------------------------------------------------ List of ShapePopulationViewer changes: $ git shortlog NIRALUser/ShapePopulationViewer@5888b0e..NIRALUser/ShapePopulationViewer@a3c6dc0 --no-merges Nina Tubau (10): README: Fix rendering of section headers on GitHub README: Add hyperlink for License file README: Add "Build instructions" section README: Fix typo README: Specify link to file from repository using recommended convention Rename license file to follow GitHub best practices COMP: Simplify configuration of CLI output and install directories COMP: Fix usage as a Slicer extension from a build directory COMP: Simplify build system removing obsolete code related to VTK 5 or 6 COMP: Update minimum required CMake version to match Slicer requirements // ------------------------------------------------------------------------ List of ShapeRegressionExtension changes: $ git shortlog kitware/[email protected]/ShapeRegressionExtension@d8b11ae --no-merges Laura Pascal (12): STYLE: Adding some descriptions for each module BUG: RegressionComputation module - Shape4D is not launched if there is not at least two input shapes ENH: Update of the shape4D used in RegressionComputation module PERF: RegressionComputation module - Modification of the data for the test of shape4D STYLE: Update README.md STYLE: Adding of a License file BUG: RegressionComputation module - Allow the users to specify decimal numbers (instead of only integers) for the input parameter sigma w STYLE: Modification of the user interfaces of the both modules ENH: RegressionComputation module - Adding default values to some parameters ENH: Regression's time point range is set by default to the min and max of the range of the observations ENH: RegressionComputation module - Implementation of the close scene function ENH: RegressionComputation module - Sort alphabetically the input shapes in the table // ------------------------------------------------------------------------ List of Sequences changes: $ git shortlog c867c67..d8f0189 --no-merges Sunderlandkyl (1): Add Qt5 plugin support // ------------------------------------------------------------------------ List of Slicer changes: $ agirault (9): ENH: Add option for popup vertical alignment with subjectHierarchyComboBox ENH: Disable selections of parent items with filters ENH: Do not hide popup when no item was selected ENH: Implement qMRMLSubjectHierarchyComboBox::clearSelection BUG: Update combobox label on SubjectHierarchyItemModifiedEvent ENH: Expand subject hierarchy combobox horizontally ENH: Fix treeview popup width in subject hierarchy combobox BUG: Fix subject hierarchy treeview popup height ENH: Display placeholder label when subject hierarchy treeview is empty cpinter (2): ENH: Allow excluding views from main layout management ENH: Added accessor functions to layout manager and factory ihnorton (3): ENH: add MeanDiffusivity calculation to DTMathematics COMP: don't exclude Qt as system library when packaging COMP: ensure copied items writable in cpack staging dir jcfr (214): ENH: Begin 4.9.0 development STYLE: Update slicer/release/midasdata.py to support python 3 COMP: Update CTK to support building using C++98 BUG: Update MultiVolumeImporter to fix DICOM settings panel error with Qt5 COMP: Update CTK to fix remaining c++98 build errors ENH: ScreenCapture: Allow setting of max number of frame to capture. BUG: ExtensionWizard: Fix contribution of extensions for a specific target BUG: ExtensionWizard: Include name of target in pull request title ENH: Update VTK8 to include OpenVR and ExternalModule improvements COMP: Fix NUMPY rebuild error ensuring patch are re-applied if needed BUG: Update VTKv8 to include OpenVR and VTKChart fixes STYLE: Remove debug stmt inadvertently integrated to SlicerCheckSourceTree.cmake COMP: Fix build with Slicer_USE_PYTHONQT set to OFF STYLE: Simplify python external project re-using variable Slicer_TCL_DIR BUG: GenerateProjectDesc: Improve robustness getting source directory COMP: qSlicerModuleFactoryManager: Fix build without cli or scripted support enabled STYLE: BuildSystem: Improve status messages in SlicerMacroBuildApplication STYLE: Ensure Qt version is displayed when configuring using Qt5 STYLE: Facilitate maintenance of external projects improving consistency STYLE: Simplify top-level CMakeLists introducing SlicerApplicationOptions STYLE: Set Slicer_APPLICATIONS_DIR in SlicerApplicationOptions STYLE: Document variables in Superbuild.cmake STYLE: SlicerCPack: Facilitate reading re-organizing code STYLE: SlicerCPack: Set CPACK_PACKAGE_NAME using application name property STYLE: BuildSystem: Explicitly set all app metadata in application CMakeLists STYLE: BuildSystem: Set lib/include/share/libexec dir using main project name ENH: BuildSystem: Generalize SlicerVersion module COMP: SlicerApplicationOptions: Only mark as advanced cache variables ENH: BuildSystem: Introduce Slicer_BUILD_QT_DESIGNER_PLUGINS option BUG: Fix initialization of module displayable managers ENH: BuildSystem: Add support for building with/without selected modules BUG: Ensure core displayable managers are registered and available COMP: Update vtkMacroKitPythonWrap to detect first degree cyclic dependencies COMP: Support building with DICOM support disabled COMP: Update CTK to ensure it is reconfigured on Git SHA update on windows COMP: Update CTK to fix macOS build error due to use of "nullptr" COMP: Fix application of NUMPY patches when using multi-config build system BUG: Fix Annotations module tests registering displayable manager COMP: Extension packaging: Fail configuration if expected variable is not set ENH: Update ExternalProjectDependency based on commontk/Artichoke@0437a6d ENH: Update VTKv8 BUG: Update BRAINSTools to include fix for FSLToNrrd mode. See 4463 COMP: Update python to improve heuristic checking if patches should be re-applied BUG: Update CLI UI generator to avoid super-wide boxes for long paths ENH: Update to VTKv9 to include VTK OpenVR fix ENH: Open solution file when "Slicer --VisualStudio" is used ENH: Propagate CMAKE_CONFIGURATION_TYPES to all external projects BUG: Update CTK to prevent crash in ctkVTKVolumePropertyWidget COMP: Update CTK build to respect Slicer_BUILD_QT_DESIGNER_PLUGINS option COMP: Fix -Woverloaded-virtual warning in FreeSurfer/vtkFSLookupTable.h STYLE: Additional external project consistency fixes COMP: Fix unused variable warning in qSlicerIOOptionsWidget.cxx COMP: SlicerCPack: Ensure install directory is set based on main app name ENH: Support customization of SlicerApp metadata through CMake options COMP: SlicerMacroPythonTesting: Fix typo in CMake variable COMP: Avoid symbol clash detecting brew install of Qt. COMP: Fix Slicer extension VTK wrapping ensuring availability of hierarchy files COMP: Update python external project to ensure it is built in release ENH: BuildSystem: Refactor adding CMake modules to initialize build/release types ENH: BuildSystem: Introduce Slicer_BUILD_DOCUMENTATION option STYLE: Update Extension Build System to use SlicerInitializeBuildType COMP: Extension build system: Do not recursively collect description files COMP: Fix "install_tree_cleanup" python-GitPython build step error COMP: Update CTK external project to ensure Python wrapping option are passed ENH: Update OpenIGTLinkIF ENH: Update BRAINSTools COMP: Fix build reverting OpenIGTLinkIF ENH: BuildSystem: Consolidate handling of remote module/extension directories STYLE: Improve comment in top-level CMakeLists COMP: BuildSystem: Exclude remote modules if dependent options are OFF STYLE: Remove unused and obsolete ROI core module STYLE: vtkMRMLVolumeRenderingDM: Remove commented includes STYLE: vtkMRMLSegmentationStorageNode: Fix include order and remove duplicate BUG: Update BRAINSTools to integrate Nifti-related fixes BUG: Fix Qt5 implementation of qSlicerCoreApplication::defaultScenePath() BUG: DICOMDetailsBase: Fix promptForDatabaseDirectory implementation for Qt5 COMP: ExternalProjectForNonCMakeProject: Fix ExternalProject_Execute ENH: ExternalProjectForNonCMakeProject: Support disabling file capture COMP: Fix setting of Slicer_SUPERBUILD_DIR for Slicer Custom application COMP: Update VisualStudioProject launcher option to always open Slicer.sln BUG: Ensure user site-packages are not imported by PythonQt COMP: ExternalProjectForNonCMakeProject: Only re-use CMAKE_(C|CXX)_FLAGS_INIT COMP: Prevent CDash false positive configuring CTestCustom in extension build dir COMP: Fix setting of EXTERNAL_PROJECT_DIR COMP: Improve support for <projectName>_USE_GIT_PROTOCOL option ENH: Update CTK to include python console fix COMP: CTestCustom: Update warning exceptions ENH: Update VTK COMP: Update CTK to fix compilation error when using Qt4 and C++98 COMP: Fix macOS CMP0009 warning in SlicerCPackBundleFixup CMake module COMP: CTestCustom: Remove obsolete Numpy warning exceptions COMP: CTestCustom: De-duplicate handling of python "UserWarning" exceptions COMP: CTestCustom: Add Lua, PythonQtConversion and vtkkwiml warning exceptions COMP: CTestCustom: Generalize warning exception associated with LNK4221 COMP: CTestCustom: Generalize warning exception for "warn_unused_result" COMP: CTestCustom: Remove exception associated with Qt 4.6.2 COMP: CTestCustom: Update list of Qt warning exceptions based on VTK COMP: CTestCustom: Update exception list to ignore Python windows warnings COMP: Update VTKv7 to fix build error COMP: Update vtkFSLookupTable to support changes integrated in previous commit COMP: Update VTK project removing support for Slicer_VTK_VERSION_MAJOR=8 COMP: Fix unused variable warnings COMP: Fix in sign-compare warning in vtkITKTransformConverter COMP: Update CTK to fix DICOM/Widgets unused-variable warnings COMP: CTestCustom: Add warning exception for related to dangerous tmp functions ENH: Update vtkMRMLScene API adding "IsNodeClassRegistered" function STYLE: qSlicerSceneWriter: Remove unused variable BUG: Prevent crash when saving MRML scene with SceneView module disabled. STYLE: Update VTK external project removing obsolete Tcl options BUG: Fix import of vtk modules when building against VTKv9 and Qt5 COMP: Fix macOS CMP0011 warning in SlicerExtensionCPackBundleFixup CMake module ENH: add qSlicerExtensionsManagerModel::retrieveExtensionMetadataByName ENH: update DMRIInstall helper extension STYLE: Remove CMake-language block-end command arguments STYLE: Convert CMake-language commands to lower case ENH: Update VTKv9 BUG: Update qRestAPI to fix Qt5 support COMP: Fix invalid operand build error in qSlicerSettingsStylesPanel COMP: Fixing generation when using VTK9 BUG: Fix import of vtk modules when built with Qt5 and VTK9 COMP: Update OpenSSL external project to use version 1.0.2n on UNIX ENH: Set default for Slicer_USE_OpenIGTLink option to OFF ENH: Add Restore Tab to the extension manager widget ENH: Update SlicerExecutionModel STYLE: Update qRestAPI to include license file COMP: Use C++11 ITK_DELETED_FUNCTION directly STYLE: Update DataStore version to include License file STYLE: Update CompareVolumes and LandmarkRegistration to include license file ENH: Generate license-<projectname>.txt file for each external projects BUG: Fix detection of Qt5 designer availability COMP: ExtractSkeleton: Fix build error reported on Linux BUG: Simplify and fix detection of Qt5 designer availability on macOS STYLE: Update SimpleFilters external project BUG: Update CTK to fix for "bad scalar range" ctkVTKHistogram error ENH: Update ExternalProjectDependency based on commontk/Artichoke@31b6ba4 ENH: Update ITKv4 to v4.13.0 COMP: Fix unused-variable warning in ExtractSkeleton cli COMP: Fix strict-overflow warning in ExtractSkeleton COMP: Fix build warnings ENH: Added Median to LabelMapStatistics COMP: Fix build error related to qSlicerSegmentationsReader COMP: Fix warning in qSlicerSegmentationsReader COMP: Fix remaining build error in qSlicerSegmentationsReader COMP: Update Swig external project to avoid race condition COMP: Update dashboard driver script making coverage part more robust BUG: ExtensionManager: Fix empty dialog on startup STYLE: Fix indent in qSlicerExtensionsInstallWidget BUG: Update ExtensionManagerModel to fix QWebChannel Qt5 warnings COMP: Attempt to fix macOS packaging error related to cocoa BUG: Update qSlicerExtensionsInstallWidget to fix QWebChannel Qt5 warnings COMP: Fix Qt4 build error related to qSlicerExtensionsInstallWidget STYLE: Remove unused code from Base/QTGUI/CMakeLists.txt BUG: Fix crash in Slicer Qt4 built adding virtual ctor to qSlicerWebWidgetPrivate STYLE: Remove deprecated function isRelease() from application API BUG: Fix extraction of module name from associated library name BUG: Update macOS fixup script to package QtWebEngineProcess.app BUG: Update ITK to fix gdcm "missing implementation" error on macOS BUG: Update ITKv4 to fix FloatingPointExceptions not supported error on macOS BUG: Fix CreateDICOMSeriesTest updating baseline due to ITK test driver improvements ENH: Update Slicer.crt BUG: Update ITKv4 to include improved fix for FloatingPointExceptions issue BUG: Improve QWebEngineView integration to fix crash on exit COMP: Fix vtkMRMLNode warnings ENH: Add median to Segmentation statistics module COMP: Support configuring Slicer with custom value for CMAKE_CXX_STANDARD COMP: Fix linux build error adding missing include in vtkMRMLPlotViewNode.cxx COMP: Fix macOS package ensuring PythonQt library "id" is the full path STYLE: Update CTestCustom adding more warning suppressions COMP: Fix dashboard submission escaping charachers in CTestCustom STYLE: Ensure ExternalProjectAddSource dependent module are included COMP: Update LibArchive to fix GCC7 build error COMP: BuildSystem: Update External_Swig.cmake to fix ninja build error COMP: Update DMCTK to version 3.6.3 and fix GCC 7 build error BUG: Update CTK to support depth peel of volumes (e.g model) with volume rendering COMP: Update ITKv4 to fix GCC7 build error on Ubuntu 17.04 with Qt4 COMP: Fix unused-variable, unused-function and sign-compare warnings COMP: Update EMSegment to fix GCC7 warnings BUG: Fix issues revealed by implicit-fallthrough warnings reported by GCC7 COMP: Fix implicit-fallthrough warnings reported by GCC7 ENH: Rename CDash project associated with "nightly release" to "SlicerPreview" BUG: Fix extension build system tests using "SlicerPreview" as CDash project name ENH: Add support for uploading extension package to a Girder based server STYLE: sitkUtils: Fix typo in warning message BUG: Fix upload of macOS extensions to the Girder-based extension manager server STYLE: Support disabling midas upload in SlicerExtensionPackageAndUploadTarget ENH: Update VTKv9 COMP: Fix reorder warnings in vtkMRMLCameraNode and vtkMRMLPlotSeriesNode COMP: Fix unused-function warning in qMRMLPlotSeriesPropertiesWidget.cxx ENH: Exclude ts extension from git hook line lengths check BUG: i18n: Update loadTranslations() to ensure all *.qm files can be found BUG: i18n: Ensure Slicer_BUILD_I18N_SUPPORT is propagated to inner build BUG: i18n: Support Qt5 requiring LinguistTools library ENH: i18n: Add more string translation in qSlicerAppMainWindow and qMRMLCaptureToolBar ENH: i18n: Add translation support for MRML/Widgets ENH: i18n: Add translation support for Loadable modules COMP: Qt5: Fix buildsystem regression ensuring QT_LIBRARIES is set properly COMP: Qt5: Fix buildsystem regression ensuring QT_LIBRARIES is set (part 2) ENH: Update CTK COMP: Support building Slicer-based custom app including Slicer as external project ENH: Update ExternalProjectDependency based on commontk/Artichoke@dff914a ENH: Simplify buildsystem using EP_GIT_PROTOCOL provided by ExternalProjectDependency BUG: Do instantiated any scripted plugins when python is disabled ENH: Speedup app startup time by lazily instantiating extension dialog COMP: Fix unused-var warning in qSlicerCoreApplication STYLE: Fix typo in DICOMScalarVolumePlugin docstring BUG: Update ITKv4 to address HD5 initialization issue and crash STYLE: Simplify Main.cxx introducing (pre|post)InitializeApplication function STYLE: Do not use template with preInitializeApplication() function STYLE: Refactor qSlicerSettingsStylesPanel introducting availableSlicerStyles ENH: Initialize application style using its name COMP: Fix loss of precision due to 64->32 bit typecast BUG: Initialize ivar to prevent crash on application shutdown STYLE: Update comment in SlicerApplicationOption CMake module BUG: Ensure python is not initialized if Slicer started with --disable-python johan.andruejol (7): BUG: Fix missing checkboxes in qMRMLCheckableNodeComboBox BUG: Fix slicer styles plugin for Qt5 BUG: Fix disappearing text in comboboxes ENH: Remove QCleanlooksStyle BUG: Fix Slicer style setting display BUG: Fix menu/groupboxes display misalignenents in Qt5 BUG: Fix high DPI display on windows with multiple screens lassoan (53): ENH: Multivolume import improvements ENH: Allow forced setting of working copy modification date BUG: Fixed memory leak in UtilTest ENH: Added convenience function for creating table node from numpy array COMP: Fixed build error on Windows ENH: Create user-specific temporary directory on unix systems BUG: Fix disappearing volume rendering ENH: Show wait cursor while loading data using Slicer file dialog BUG: Do not report error on exit if module registered using module factory ENH: Slicer util messageBox shows current actual application name ENH: Added support for volumetric meshes in ProbeVolumeWithModel module BUG: Fixed setting "Clear existing scene" default value in Scene load dialog COMP: Fixed location of generated MyExtensionCongfig.cmake file BUG: Fixed crash on scene close caused by annotation ROI node BUG: Fixed DICOM browser not visible for usernames having special characters ENH: Added slicer.util.arrayFromSegment helper function BUG: Fixed plotting using Y axis indices ENH: Set unique name for image acquisition transforms ENH: Improved ScreenCapture module looping options BUG: Fixed segmentation logic ExportAllSegmentsToModelHierarchy BUG: Update cli.py, fix to runSync method ENH: Do not reset view when Segmentation master node selected BUG: Added Latin1 encoding specification to saved MRML file ENH: Made DICOM loading of scalar volume more configurable ENH: Only compute histogram in Volumes module if needed ENH: Added MRBrain sample data set BUG: Fixed loading of sequences from multiple series BUG: Added null-pointer checks to prevent potential crashes BUG: Fixed loading of segment display properties from scene file BUG: Prevent MarkupsFiducialStorage saving if invalid coordinate system ENH: Improve reslicing performance ENH: Remove some usages of GUI text in logic ENH: Throw an exception if getNode() does not find a node BUG: Fixed centerline points computation in ExtractSkeleton module ENH: Reduce usage of slicer.util.getNode ENH: Updated LandmarkRegistration extension BUG: fixed error in DICOM examine ENH: Allow loading STL files as segmentation node ENH: Allow setting default slice composite node properties BUG: Plotting fixes ENH: Allow using not visible master view in ScreenCapture ENH: Added MRML node property macros ENH: Added Plots module BUG: Minor plot fixes COMP: Fixed build error in linux COMP: Fixed qSlicerPlotsSubjectHierarchyPlugins import error ENH: Improve vtkMRMLPlotSeriesNode SetColor API BUG: Use startupCompleted signal for module initialization STYLE: Improved slicer.util.array* method documentation ENH: Added option to specify custom plot axes range ENH: Add option to set column name in updateTableFromArray COMP: Fixed build error on Mac COMP: Report build error if vtkMRMLCopyVectorMacro argument is missing pieper (11): ENH: model DICOM acquisition geometry (addresses #4409) ENH: only issue one convergence warning for inverse transform ENH: update CTK version, fixes #4360 ENH: Update LandmarkRegiration (save grid transform) BUG: #4483 catch dicom exception from itk reading seg ENH: observers of undo/redo in legacy editor BUG: update EMSegment to fix modulewidget bug COMP: fix build with Extension manager off COMP: fix cmake version logic for mac qt4 builds BUG: update CTK for Qt5 PythonQt wrapping COMP: fix mac/linux build errors in plot test pinter (20): BUG: Fix crash ThresholdSlider in segmentEditor when changing volume BUG: qMRMLLayoutManager::plotWidget was returning a Table Widget instead of a Plot one BUG: Segment Editor masking options update when segment is renamed BUG: Fixed segmentation slice intersection update after transform change ENH: Added python utilities that download, unzip, import, and load DICOM data BUG: Added new launcher option for the simplified VisualStudio switch BUG: getLoadablesFromFileLists was expecting a list of tuples only BUG: Fixed new segment color after last segment has been removed ENH: Move edited segmentation to the study of the master volume BUG: Fixed using specified database in DICOMUtils function BUG: Fixed anatomical modifier parsing when loading DICOM SEG ENH: Hide background segment after Grow from seeds effect ENH: Added options in Data module to convert labelmap/model to segmentation ENH: Try to download sample data again after loading fails ENH: Separated dicom image sorter util into DICOMUtils BUG: Fixed logging issue in getSortedImageFiles DICOMUtil function BUG: Fixed error handling in slice sorter DICOM util BUG: Fixed read float MRML attribute macro BUG: Encode special characters for subject hierarchy item attributes ENH: Separated volume rendering preset combobox from module widget
@laurapascal @bpaniagua This is ready for review and integration. |
List of changes: $ git shortlog 9e1f57d..e36fa70 --no-merges jcfr (2): ENH: Remove support for building OpenIGTLink now available as an extension COMP: Update qMRMLPlotView to support compiling against Qt4
List of changes: $ git shortlog d8f0189..fda38a0 --no-merges Jean-Christophe Fillion-Robin (4): COMP: Fix -Wpointer-arith warnings COMP: Fix -Wsign-compare warnings COMP: Fix -Wunused-parameter warnings COMP: Fix -Wreorder warnings
Following Slicer r26972 (ENH: Remove support for building OpenIGTLink now available as an extension), the option is removed.
List of changes: $ git shortlog e36fa70..efcf194 --no-merges jcfr (13): BUG: Update MeasureStartupTimes script to properly detect module type BUG: Enable high-resolution screenshots of slice views BUG: Fix toolbuttons icon size with Qt5 ENH: Ensure CMAKE_MACOSX_RPATH is consistently pass to all external projects ENH: Update UseSlicer to use SlicerInitializeBuildType STYLE: Update External_JsonCpp removing unneeded explicit passing of CMAKE_BUILD_TYPE ENH: SlicerGenerateExtensionTemplates target: Support SuperBuild template ENH: Re-generate extension templates STYLE: Rename CMake module SlicerBlockSetCMakeOSXVariables to SlicerInitializeOSXVariables ENH: Update UseSlicer to ensure CMAKE_OSX_ vars are propagated in extension ENH: Update UseSlicer to conveniently include ExternalProject CMake module STYLE: Simplify and cleanup SuperBuild extension template ENH: Support calling qSlicerWebWidget::evalJS() from python
…h CMAKE_CACHE_ARGS
@jcfr Any more changes coming or is this ready for review? |
I suggest to move forward and integrate. |
There are currently conflicts with ShapePopulationViewer and Qt5/VTK 9, I'm working on a fix. |
Indeed, if i recall ShapePopulationViewer should be updated to support
Qt5/VTK9
…On Thu, Apr 19, 2018, 1:10 PM vicory ***@***.***> wrote:
There are currently conflicts with ShapePopulationViewer and Qt5/VTK 9,
I'm working on a fix.
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ShapePopulationViewer problems should be fixed, but I've discovered a new issue: the qMRML widgets are not showing up under qt.QUiLoader().availableWidgets(), causing scripted modules to not work properly. |
Is this specific to a platform ? Or reproducible on Linux, macOS and Windows ? |
I've only tested on Linux thus far. |
I am going to test this, it should be a priority. If we do not have to maintain backwards compatibility... better to get up-to-date with slicer master and go for qt5. |
Thank you, Pablo. After you test it let us know how it goes. |
One issue found, not sure if this is the expected behavior. If I want to pass settings to Slicer, I have to use SlicerSALT as a prefix, not Slicer.
This is because |
@phcerdan Makes sense. From a usability stand point, it looks like we should always have the option starting with Would that help reduce confusion ? |
Replying to my own question. Answer is yes and the change will be added to Slicer shortly. |
Following Slicer r27286, option associated with Slicer core will all start with |
Awesome @jcfr, I agree that it will reduce confusion, thanks! |
Getting there! After using the latest SlicerCustomAppTemplate, and doing a merge of the generated template and this PR... it compiles! But, at running time, with python disabled, I get that the "internal" module: Errors: ./Slicer-build/SlicerSALT
Traceback (most recent call last):
File "<string>", line 7, in <module>
File "/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/Python/slicer/slicerqt.py", line 6, in <module>
import vtk
File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtk.py", line 12, in <module>
all_m = importlib.import_module('vtkmodules.all')
File "/usr/lib64/python2.7/importlib/__init__.py", line 37, in import_module
__import__(name)
File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/all.py", line 7, in <module>
from .vtkCommonKit import *
File "/home/user/Software/Slicer/buildSystemQtPython-RelWithDebInfo/VTKv9-build/lib/python2.7/site-packages/vtkmodules/vtkCommonKit.py", line 9, in <module>
from vtkCommonKitPython import *
ImportError: No module named vtkCommonKitPython
Traceback (most recent call last):
File "<string>", line 1, in <module>
NameError: name 'getSlicerRCFileName' is not defined
error: [/home/user/Software/Shape/SALT/buildRelWithDebInfo/Slicer-build/bin/./SlicerSALTApp-real] exit abnormally - Report the problem.
Disabling python:
|
Thanks for the late update ... Next week, could you report here the content of In a regular build directory, the VTK module is found here: In you case, I am assuming you built from a virtual environment ? can you locate that libraries ? I suspect that the launcher settings doesn't account for the path |
Spot on, it shouldn't, it makes no sense for my SALT installation (in folder For completion, your requested files,
I am using system python, but VTK still wraps python at build time, the
|
Next steps:
|
TODO: Add setAcknowledgmentsText to upstream SlicerAboutDialog WIP: Sequences module is disabled, and External_modules too.
`git shortlog --no-merges c890ed096d301ee7ea342..a4b32e822505373d3` Adam Rankin (1): Update vtkSlicerMetafileImporterLogic.cxx Andras Lasso (4): Keep using vtkNRRDReader/Writer in Slicer-4.8 ENH: Always set segmentation nrrd file vector axis to "list" kind Update README.md Added Crop volume sequence module Isaiah Norton (1): ENH: rename vtkNRRDReader, vtkNRRDWriter -> vtkTeemNRRD{R,W}
By explicitly including "ExternalProject" before using function like ExternalProject_Add, we ensure that local variables defined in the CMake module and needed to properly parse function arguments are available in the current scope. A fix has also been proposed to upstream CMake to ensure this type of error can easily be discovered. See https://gitlab.kitware.com/cmake/cmake/merge_requests/2281 Warnings and errors like the following are fixed by this commit: CMake Warning (dev) at /usr/share/cmake-3.11/Modules/ExternalProject.cmake:966 (message): value 'COMMAND' with no previous keyword in ExternalProject_Add_Step Call Stack (most recent call first): /usr/share/cmake-3.11/Modules/ExternalProject.cmake:2018 (_ep_parse_arguments) /usr/share/cmake-3.11/Modules/ExternalProject.cmake:2214 (ExternalProject_Add_Step) /usr/share/cmake-3.11/Modules/ExternalProject.cmake:3099 (_ep_add_mkdir_command) SuperBuild/SlicerPackageExtensions.cmake:185 (ExternalProject_Add) CMakeLists.txt:142 (include) This warning is for project developers. Use -Wno-dev to suppress it. CMake Error at /usr/share/cmake-3.11/Modules/ExternalProject.cmake:2525 (message): No download info given for 'SlicerPackageExtensions' and its source directory: /home/user/Software/Shape/SALT/buildRelWithDebInfo/SlicerPackageExtensions-prefix/src/SlicerPackageExtensions is not an existing non-empty directory. Please specify one of: * SOURCE_DIR with an existing non-empty directory * DOWNLOAD_COMMAND * URL * GIT_REPOSITORY * SVN_REPOSITORY * HG_REPOSITORY * CVS_REPOSITORY and CVS_MODULE Call Stack (most recent call first): /usr/share/cmake-3.11/Modules/ExternalProject.cmake:3100 (_ep_add_download_command) SuperBuild/SlicerPackageExtensions.cmake:185 (ExternalProject_Add) CMakeLists.txt:142 (include) Co-authored-by: Pablo Hernandez <[email protected]>
@phcerdan Thanks for your help, this topic |
Thanks @jcfr, testing it, and hopefully, we can merge soon and start adding external projects. |
git shortlog --no-merges a3c6dc087a..deb14cdcae Jared Vicory (1): COMP: Add support for building with Qt5 and VTK9 Pablo Hernandez-Cerdan (3): STYLE: Run dos2unix to remove windows end of file STYLE: StripWhitespaces BUG: Missing QVTKInteractor header
It works but hitting #44
"Solved" using: |
Fixes Kitware#44 List of changes: $ git shortlog --no-merges d8b11ae..dbfbae5 Jean-Christophe Fillion-Robin (2): COMP: Deduplicate the icon and fix ninja build error COMP: Deduplicate RegressionUtilities python code and fix ninja build error
So that we can move forward with the integration, would be great to get one positive review. Packaging of all extensions work as expected. There only few minor issues that should be addressed afterward:
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List of changes: $ git shortlog 04917a6ce..c88b17d38 --no-merges jcfr (8): ENH: Update VTK to include vtkChartXY improvements ENH: Add single click selection in plot view COMP: Fix -Winconsistent-missing-override in vtkMRMLColorTableNode COMP: Fix -Winconsistent-missing-override in vtkMRMLPlotViewNode BUG: slicerMacroBuildApplication: Set correct executable path on macOS BUG: Ensure custom application version is used on macOS BUG: DataProbe: Fix logic hidding slice view corner annotations COMP: Fail early building script with PythonQt disabled lassoan (3): ENH: Move Editor module to Legacy category BUG: Fixed saving of vtkMRMLScriptedModuleNode parameters with special chars BUG: Fixed slice normal flipping by rotate to volume plane
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This really simplifies the infrastructure. Tested with the current enabled modules and extensions in linux and it works. We can solve the minor issues in other PRs
Thanks @phcerdan ✌️ 🍾 🎉 |
Jared Vicory (1): ENH: Rename files to fix Windows compilation issues Jean-Christophe Fillion-Robin (12): COMP: Refiner: Fix build error using nullptr COMP: Refiner: Fix build error using "std::abs" instead of "abs" COMP: Refiner: Fix unused-variable and unused-parameter warnings COMP: Refiner: Fix sign-compare warnings COMP: Refiner: Fix -Wmaybe-uninitialized warnings in vtkPolyData2ImageData COMP: Refiner: Use nullptr and override keywords COMP: Initializer: Fix unused-variable warning COMP: Refiner: Fix object name in UI file STYLE: Remove trailing whitespaces STYLE: Expand tabs into four spaces Merge pull request Kitware#29 from jcfr/cleanup-whitespaces Merge branch 'misc-tweaks' Zhiyuan (1): Add support for converting SALT srep to legacy sreps Zhiyuan Liu (20): Improve SkeletalRepresentationRefiner and SkeletalRepresentationVisualizer Merge pull request Kitware#27 from KitwareMedical/ENH_refinement-rebased STYLE: Remove redundant file COMP: C++11: Update source code to use nullptr STYLE: .gitgnore: Fix regex excluding QtCreator project file COMP: Refiner: Fix sign-compare and implicit conversion warnings ENH: Update module title, contributor list and acknowledgment ENH: Add support for saving initialized s-rep including fix connection of fold curve Merge pull request Kitware#30 from KitwareMedical/ENH_refinement-rebased-2 remove unused functions and variables; resolve some compile warnings Merge pull request Kitware#31 from ZhiyLiu/code_review new features and fix in initializer COMP: new feature (set the skeleton resolution) and fix in initializer COMP: update readme to include more instructions of using the refiner and initializer COMP: upload a screenshot to illustrate the result from the initializer COMP: add a picture to illustrate operations in this extension BUG: fix variable length of arrays to satisfy compiler in visusal studio Merge pull request Kitware#38 from ZhiyLiu/ENH_interpolate Reparametrize initial s-reps; Fix problems in the interpolation and refinement; Refine readme.md Merge branch 'master' into COMP_fix_refinement vicory (2): Merge pull request Kitware#40 from ZhiyLiu/COMP_fix_refinement Merge pull request Kitware#41 from vicory/compilation_fixes
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