Bump SlicerSMTK extension sha to include new features regarding
reading and writing of node properties such as names and colors
assigned to models and segments.

Updates to SlicerSMTK:

$ git shortlog 7fa1a1c..5995b54 --no-merges
Shreeraj Jadhav (4):
      ENH: Read/write color properties of components and seg transform
      TEST: Add and update unit tests for segmentation import/export and properties
      ENH: Preserve overlapping segments when exporting SMTK
      COMP: Fix missing header build error for mac/linux

This corresponds to the identifier that should be used during the macos
code signing process.

Update version number of latest release.
Use the new version numbering decided for aeva (YY.MM)
Currently not possible to use leading zeroes in the MAJOR/MINOR
versions (hence the 22.8 in place of 22.08).

Bump SlicerSMTK to include the new
SMTK file reader module.

$ git shortlog --no-merges 949b4ee..7fa1a1c
Harald Scheirich (2):
      ENH: Add reading of aeva.smtk files
      COMP: Fix slicer testsuite

Create a .gitlab folder for issue templates (.gitlab/issue_templates)
and add a release template to it. This will be a checklist that
should be followed/updated during every release milestone for
aevaSlicer and related extensions / modules.

Co-authored-by: Jean-Christophe Fillion-Robin <jcfr@kitware.com>

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

Considering the time required to finalize the integration of SlicerSMTK, the
previous 2.4.0 and 2.5.0 releases were skipped. To match aevaCMB release cycle,
this commit updates to 2.6.0.

This commit fixes a regression introduced in session@17820588 (Always
show 3D widgets even if Qt controls are hidden.) ensuring installing the
project succeeds on platform where CMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION
is ON.

List of SlicerSMTK changes:

$ git shortlog e763625..949b4ee --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update aeva-session to fix windows packaging

This commit ensures MOAB library in either build and install trees
have RPATH with full paths.

List of SlicerSMTK changes:

$ git shortlog 4f2ab68..e763625 --no-merges
Jean-Christophe Fillion-Robin (3):
      COMP: Fix macOS packaging ensuring MOAB is built & installed with full RPATH
      COMP: Update MOAB external project to fetch source from KitwareMedical fork
      COMP: Update MOAB to fix macOS fixup by accepting custom CMAKE_INSTALL_NAME_DIR value

List of SlicerSMTK changes:

$ git shortlog 45f3c6636..4f2ab68b9 --no-merges
Shreeraj Jadhav (1):
      ENH: Add cxx test cases for testing smtk export

Co-authored-by: Shreeraj Jadhav <shreeraj.jadhav@kitware.com>

This commit fixes memory leaks (see below) reported when building
the project with the option Slicer_USE_VTK_DEBUG_LEAKS set to ON.

The following leaks were reported by vtkDebugLeaks:

    vtkDebugLeaks has detected LEAKS!
    Class "vtkIntArray" has 2 instances still around.
    Class "vtkInformation" has 4 instances still around.
    Class "vtkInformationVector" has 2 instances still around.
    Class "class vtkBuffer<int>" has 2 instances still around.
    Class "vtkInformationDoubleVectorValue" has 2 instances still around.

See commit session@423cbedd (BUG: Fix memory leaks in Session::offsetGlobalIds)

List of SlicerSMTK changes:

$ git shortlog 448b957..45f3c66 --no-merges
Shreeraj Jadhav (1):
      BUG: Update SMTK and aeva-session to fix memory leaks

Co-authored-by: Shreeraj Jadhav <shreeraj.jadhav@kitware.com>

This commit ensures libraries associated with external projects in either
build and install trees have RPATH with full paths.

List of SlicerSMTK changes:

$ git shortlog 7ca3830..448b957 --no-merges
Jean-Christophe Fillion-Robin (10):
      COMP: Update MOAB external project to disable build of unused mbmerge tool
      COMP: Fix macOS packaging ensuring Netgen is built & installed with full RPATH
      COMP: Fix macOS packaging disabling explicit install of Netgen/MOAB/smtk/aeva-session
      COMP: Remove obsolete setting of <proj>_INSTALL_*_DIR vars from external projects
      COMP: Remove CMAKE_INSTALL_LIBDIR hard-coded value from external projects
      COMP: Ensure macOS fix-up script can looking up and copy external project libraries
      COMP: Fix macOS packaging ensuring aeva-session is built & installed with full RPATH
      COMP: Fix inner project configuration error updating aeva-session_DIR
      COMP: Ensure boost libraries are bundled in macOS package
      COMP: Fix bundling of Netgen and aeva-session libraries

This commit fixes the launcher settings to ensure both the application
and/or tests can be executed.

List of SlicerSMTK changes:

$ git shortlog d4e76dd..7ca3830 --no-merges
Shreeraj Jadhav (1):
      COMP: Fix library paths for build tree launcher settings

List of SlicerSMTK changes:

$ git shortlog 3dd5b07..d4e76dd --no-merges
Shreeraj Jadhav (1):
      BUG: Copy direction cosines to exported image data

Copy direction cosines (DirectionMatrix) from vtkMRMLVolumeNode to the
extracted vtkImageData before exporting. This is in concurrence with other
grid related metadata such as origin and spacing, that need to be copied
before exporting vtkImageData.

Refer to discussion here [1] for the necessity to do this.
[1] https://github.com/Slicer/Slicer/blob/d010e8c075a9a66ce21a38ed549a20296ab7669d/Libs/MRML/Core/vtkMRMLVolumeNode.h#L17

List of SlicerSMTK changes:

$ git shortlog 00ea9ec9d..3dd5b071c --no-merges
Shreeraj Jadhav (3):
      COMP: Update SMTK to support finding build tree & modern compiler
      COMP: Update aeva-session to fix building without ParaView support.
      COMP: Update include paths for session headers

This commit was adapted from KitwareMedical/SlicerCustomAppTemplate@3fc867700

Co-authored-by: Shreeraj Jadhav <shreeraj.jadhav@kitware.com>

GitHub has disabled the unauthenticated git protocol by default
See https://github.blog/2021-09-01-improving-git-protocol-security-github



List of changes:

$ git shortlog f4a3456..4e505b1 --no-merges
Jean-Christophe Fillion-Robin (1):
      [Backport PR-11] COMP: Update tetgen & cleaver external project to fix git source checkout

Co-authored-by: Shreeraj Jadhav <shreeraj.jadhav@kitware.com>

Co-authored-by: Shreeraj Jadhav <shreeraj.jadhav@kitware.com>

Shreeraj Jadhav authored 3 years ago and Shreeraj Jadhav committed 3 years ago

Force standardLightPalette from Slicer-core as initialization value.
The app style assumes a single palette rather than providing light
and dark alternatives. Hence, there is an inherent assumption that
its always light mode.

Given the implementation of qSlicerStyle::standardPalette [1],
the mentioned issue is specific to Windows.
[1] https://github.com/Slicer/Slicer/blob/d14f18f386f83943d6717cedb5d18f1ce423cada/Base/QTGUI/qSlicerStyle.cxx#L195

This is a quick fix for improving usability of list widgets in the
application, which shows alternating black and white rows with
(unreadable) blue text over black background.

Addresses issue #9

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

List of SlicerSMTK changes:

$ git shortlog 89691cd42..00ea9ec9d --no-merges
Shreeraj Jadhav (15):
      COMP: Fix install rule for Boost windows shared libraries
      ENH: Update FileWrite to use subdirectory for individual components
      STYLE: Streamline usage refactoring SMTKFileWriter API
      STYLE: Faciliate reuse relocating export functions to vtkSlicerSMTKFileWriterLogic
      ENH: Change output file extension to .aeva.smtk
      ENH: Apply transform hardening to MRML nodes
      COMP: Ensure aeva-session is installed in "lib" subdirectory on Linux
      COMP: Fix packaging of boost libraries
      COMP: Use official git repo for session and smtk
      STYLE: Re-order headers and update comments in vtkSlicerSMTKFileWriterLogic
      STYLE: Add LICENSE file and update license headers
      STYLE: Add a README file with aeva's logo image.
      BUG: Update smtk to fix exception related to std::regex
      COMP: Ensure smtk is installed in "lib" subdirectory on Linux
      BUG: Update aeva-session to support saving image with relative path

List of Slicer changes:

$ git shortlog cc7b094af..2ac1657b80 --no-merges
Shreeraj Jadhav (3):
      ENH: refactor transform hardening as static function
      COMP: fix for Unix: add CMAKE_INSTALL_LIBDIR to launcher settings
      ENH: rebase to VTK version used by CMB/Paraview

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>

List of SlicerSMTK changes:

$ git shortlog 2588510..89691cd --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Add support for packaging Boost libraries on Linux and Windows

List of Slicer changes:

$ git shortlog 2ca69b8786..cc7b094af4 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update VTK/VTK-m to ensure vtk-m/diy library are packaged on linux

List of Slicer changes:

$ git shortlog cd71b377b5..2ca69b8786 --no-merges
Jean-Christophe Fillion-Robin (3):
      COMP: Update VTK external project to use KitwareMedical/VTK fork
      COMP: Update VTK/VTK-m to fix vtk-m library packaging rules
      COMP: Update VTK/VTK-m to fix vtk-m/diy library packaging rules

List of SlicerSMTK changes:

$ git shortlog bfdcb52..2588510 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update smtk and Netgen to reference KitwareMedical fork

This commit also updates NetGenSurfaceRemesher to remove the custom
commands and install rules associated Netgen libraries. These have been
obsoleted by the external project improvements associated with the
SlicerSMTK udpates described below.


List of SlicerSMTK changes:

$ git shortlog 808d66220..bfdcb52fe --no-merges
Jean-Christophe Fillion-Robin (3):
      COMP: Define build tree launcher settings to ensure shared libraries can be loaded
      COMP: Update Netgen and fix installation of associated libraries
      COMP: Update smtk to fix cloning from GitHub when git lfs is enabled locally

Shreeraj Jadhav (1):
      COMP: Add Netgen, smtk, moab, aeva-session to cpack

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

List of SlicerSMTK changes:

$ git shortlog 793cae1adb..808d66220 --no-merges
Shreeraj Jadhav (4):
      BUG: Copy spacing and origin info
      CHORE: Remove leftover couts and commented code
      ENH: Write vtkMRMLSegmentationNode nodes
      BUG: Skip hidden nodes when exporting

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

List of SlicerSMTK changes:

$ git shortlog b9728cf10..793cae1ad --no-merges
Shreeraj Jadhav (4):
      COMP: Add install step for aeva-session
      COMP: Find Netgen before aeva-session for nglib
      COMP: fix TBB_DIR not-found error for smtk and aeva-session
      COMP: Bump sha for aeva-session

List of aeva-session changes:

$ git shortlog 187c707..2e1c36534 --no-merges
Shreeraj Jadhav (2):
      COMP: fix unspecified deps VTK eigen, AcceleratorsVTKmFilters
      COMP: Update vtk-netgen git repo/tag

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

Remove ngcore (netgen core module) related cmake script
as ngcore is not used, not needed for linking.

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

List of changes:

$ git shortlog 55233baac..cd71b377b --no-merges
Shreeraj Jadhav (1):
      COMP: integrate vtk-m with FindTBB.cmake fix

List of changes:

$ git shortlog 5b83897db..55233baac --no-merges
Andras Lasso (9):
      DOC: Fix method saveGUIState/restoreGUIState methods documentation
      DOC: Improve description of model editing using Segment Editor
      DOC: Add model editing use case description to Models module documentation
      BUG: Fix vtkMRMLAnnotationStorageNodeTest1
      DOC: Describe limitation of volume rendering not supporting warping transforms
      ENH: Allow setting node type display name for abstract node classes
      BUG: Fix setting of noneDisplay text in qMRMLNodeComboBox
      DOC: Add note on adaptive quality limitations for GPU volume rendering
      ENH: Simplify custom markups registration and clean up code

Aymeric Chataigner (1):
      ENH: Center "Save before exit?" window on main window

Csaba Pinter (2):
      BUG: Update SH combobox title to no selection after scene close
      BUG: Fix selection restoration issue in SH tree view

Ebrahim Ebrahim (7):
      BUG: Fix check that a QFileInfo is empty
      STYLE: Rename checkbox member variable
      STYLE: Fix typo in warning message
      BUG: Fix uninitialized variable bug.
      STYLE: Remove class that was not being used
      ENH: Add export functionality and export module
      BUG: Make storage nodes return fail on write with error messages

Fernando Bordignon (1):
      DOC: Fix docs for dataframeFromMarkups

James Butler (4):
      DOC: Update link to Slicer Stable CDash
      DOC: Update link for extensions catalog
      DOC: Update Slicer CDash links to https
      ENH: Create node type display name for GUI usage

Jean-Christophe Fillion-Robin (4):
      ENH: Rename CDash project name from "Slicer4" to "SlicerPreview"
      COMP: Fix warning in vtkMRMLMarkupsROINode removing extra semicolon
      COMP: Update VTK backporting vtkProbeLineFilter fix
      COMP: Update VTK removing FindTBB to expect VTK to be configured with TBB_DIR

Kyle Sunderland (4):
      ENH: Add vtkMRMLMarkupsDisplayNode interaction handle scale property
      ENH: Add InsideOut flag to markups ROI
      BUG: Update SurfaceToolbox to fix linking Dynamic Modeler logic
      BUG: Fix vtkMRMLMarkupsNode::GetCenterPositionWorld deprecation warning

Nathan (1):
      DOC: Update prerequisite to reflect CMake > 3.20.4 and < 3.21.1 is broken

Sara Rolfe (1):
      BUG: Fix registration of custom markups

Shreeraj Jadhav (2):
      COMP: Update SystemTools use anticipating update from VTK 9.0 to 9.1
      ENH: Update VTK9 from 9.0.20201111 to 9.1.20211022

* Ensure SlicerSMTK dependencies are processed by including
  SuperBuildPrerequisites.cmake that is setting SlicerSMTK_EXTERNAL_PROJECT_DEPENDENCIES

* Remove "Slicer_BUILD_Extension_SlicerSMTK" option because the extension
  provides Netgen external project that is required.

* Remove netgen external project obsoleted by the one provided by
  the SlicerSMTK extension.

List of SlicerSMTK changes:

$ git shortlog 36f8c27f9..b9728cf --no-merges
Jean-Christophe Fillion-Robin (13):
      COMP: Update SuperBuildPrerequisites setting VTK_MODULE_ENABLE_VTK_FiltersParallelDIY2
      COMP: Streamline custom app integration definine SlicerSMTK dependencies
      COMP: Fix MOAB external project build error on windows explicitly disabling Fortran
      STYLE: Re-factor setting of inner project dependencies to avoid list duplication
      STYLE: Update SuperBuildPrerequisites to more clearly organize VTK build options
      COMP: Remove vtkFiltersParallelDIY2 from smtk dependency
      COMP: Update Eigen project removing unneeded Boost dependency
      STYLE: Avoid confusion renaming variables associated with the Eigen project
      COMP: Avoid unexpected lookup of Eigen3 disabling package registry export
      COMP: Update Eigen project disabling tests
      COMP: Rename Eigen external project to Eigen3 to be consistent with project name
      COMP: Update MOAB to disable unused modules
      STYLE: Update SuperBuildPrerequisites to use more generic comments

Shreeraj Jadhav (2):
      ENH: Added Eigen3 as external proj
      Chore: Cleanup for removing leftover >>>>>

List of Slicer changes:

$ git shortlog a861766b6..5b83897db --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Update VTK backporting vtkProbeLineFilter fix

Shreeraj Jadhav (2):
      COMP: Update SystemTools use anticipating update from VTK 9.0 to 9.1
      ENH: Update VTK9 from 9.0.20201111 to 9.1.20211022

Shreeraj Jadhav authored 3 years ago and Jean-Christophe Fillion-Robin committed 3 years ago

List of changes:

$ git shortlog 160604769..a861766b6 --no-merges
Andras Lasso (16):
      ENH: Improve DICOMweb download speed
      BUG: Fix display properties of cloned markup nodes
      DOC: Fix typo in script repository gui.md
      BUG: Fix window/level presets in Volumes module
      COMP: Fix VTK_USE_FILE warning when building extensions
      DOC: Update "Capture 3D view into PNG file" script repository example
      DOC: Update bug report template
      PERF: Markups performance improvement
      BUG: Fix markup control point not appearing when application settings is old
      DOC: Add note to Windows build about errors caused by existing Python installations on the system
      DOC: Add example script for saving nodes in folders matching subject hierarchy
      ENH: Log stack trace of deprecated slicer.util functions
      ENH: Clean up markups node API
      DOC: Update markups.md to make the link to the JSON schema easier to find
      BUG: Fix "child widget is not accessible" warnings in Markups module
      BUG: Fix detection of errors during writing of meshes

Connor Bowley (4):
      PERF: Increase rendering performance of markups
      PERF: Add fast WorldToDisplay to vtkMRMLInteractionEventData
      COMP: Compile with VTK updates to vtkWindow
      COMP: Fix build with VTK8

Csaba Pinter (1):
      STYLE: Fix indentation in Markups module widget

David Allemang (1):
      DOC: Add programmatic installation section to developer guide

Fernando (1):
      ENH: Add context managers for message and error display to slicer.util

James Butler (24):
      ENH: Add unset control point options as properties of Place widget
      BUG: Fix unset control point position options visible in default place widget
      BUG: Fix place control point button menu button always visible
      ENH: Move Annotations module to Legacy category
      ENH: Add deprecation warnings to deprecated Markups API methods
      ENH: Use non-deprecated markups API
      BUG: Fix null segment editor effect cursor icon overwriting mouse mode icon
      DOC: Remove Editor module documentation
      ENH: Remove Slicer3 Fiducial List classes
      ENH: Remove vtkSlicerGlyphSource2D
      DOC: Add retired modules page
      DOC: Move legacy modules to legacy category
      ENH: Move Label Statistics (BRAINS) to Legacy category
      DOC: Add warning message to top of deprecated modules
      DOC: Link to module pages explicitly with .md suffix
      ENH: Remove Label Statistics (BRAINS) module
      DOC: Remove Label Statistics from Legacy category
      DOC: Add build instructions for experimental VS2022 build
      DOC: Recommend Qt 5.15.2 in build instructions
      DOC: Fix unintended link in ResampleScalarVectorDWIVolme documentation
      ENH: Clean up qSlicerMarkupsModuleWidget to use appropriate Control Point terminology
      ENH: Use markup type internal name when display name not specified
      COMP: Update Landmark Registration
      ENH: Update FindVcvars for future MSVC versions

Jean-Christophe Fillion-Robin (17):
      COMP: Attempt to fix launching of designer in macOS package
      BUG: Fix memory leak related to JSON reading in vtkMRMLMarkupsJsonStorageNode
      STYLE: Remove svn references from extension description file
      ENH: Simplify build-system removing support for building extension from SVN
      COMP: Update CTK to fix QModelIndex::child() deprecation warnings
      ENH: Add saveGUIState/restoreGUIState to qSlicerMainWindow public API
      COMP: Fix CMake extension description tests
      COMP: Fix Qt 5.11 deprecation warning related to QFontMetrics::width
      COMP: Fix QTime::start(), QTime::elasped() deprecation warnings
      COMP: Fix QFlags deprecation warnings related to UnitAwareProperty
      COMP: Fix QFlags deprecation warnings related to Qt::ItemFlag
      COMP: Fix deprecation warnings related to use of Qt algorithmic functions
      COMP: Fix deprecation warnings related to use of QSet::toList()
      BUG: Ensure PythonSlicer loads extension settings
      DOC: Consistently reference the project or application using "Slicer"
      COMP: Add "CI" GitHub action workflow to replace CircleCI
      COMP: Improve "CI" GitHub Action workflow uploading package as artifact

Kyle Sunderland (12):
      BUG: Fix bad alloc error from sequence string validation on Linux
      COMP: Fix unknown escape sequence in vtkMRMLSequenceBrowserNode
      BUG: Fix Segment table update for Segmentation replay in Sequences
      BUG: Fix erase when using the selected segment as mask
      BUG: Unblock segment table signals when no Segmentation node is set
      ENH: Allow using markups ROI for specifying segment geometry
      ENH: Add additional plane modes to vtkMRMLMarkupsPlaneNode
      BUG: Fix Markups ROI visibility when all control points are removed
      ENH: Add ROI edge handles to slice views
      BUG: Fix intensity masking for Islands effect
      ENH: Improve Markups rotation handle appearance
      BUG: Prevent data probe from expanding horizontally

Rudolf Bumm (2):
      ENH: Add volume display preset selection to slice view right-click menu
      ENH: Add view reset and tilt lock actions to view context menu

Yi Gao (1):
      BUG: Fix slice intersection computation for nearly parallel slices

kerim371 (1):
      BUG: Fix camera translation in 3D views when camera is scaled

mikebind (1):
      DOC: Clarify "size" description in markups JSON schema (PR-6058)

Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com>