COMP: Fix missing header build error for mac/linux

See merge request !14

Fix build error "use of undefined type" in
macOS and Linux due to the missing header.

ENH: Read/write color properties of components and seg transform

See merge request !13

Handle overlapping segments in a segmentation node
when exporting to SMTK format. All segments
within a segmentation if exported to a single labelmap,
will overwrite each other.
Preserve the overlapping segments, by exporting them
to separate labelmaps.
Use of `vtkMRMLSegmentationNode::CollapseBinaryLabelmaps(false)`
ensures that minimal number of labelmaps are generated when
this separation occurs.

Read/write color property between MRML nodes and respective SMTK components.

Copy origin, spacing, and orientation matrix of MRML segmentation
nodes to SMTK image. This was not done previously, causing spatial
mismatch of segmentation image with extracted geometries.

Read/Write colors, names, and orientation of segmentations
correctly. Each segmentation will be saved as a vtkImageData labelmap,
which implies that segments are mutually exclusive. Overlapping
segments will overwrite each other. To preserve overlapping
segments, user must create separate segmentation nodes in Slicer.

COMP: Fix slicer testsuite

See merge request !12

ENH: Add reading of aeva.smtk files

See merge request !11

Basic reading capability of volumes labelmaps and models
will ignore UUIDs in the smtk source file
Includes tests for reading an empty scene and a scene with one
- model
- labelmap
- volume

COMP: Update aeva-session to fix windows packaging

See merge request !10

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 aeva-session changes:

$ git shortlog 32736ae..3ee30f7 --no-merges
Jean-Christophe Fillion-Robin (1):
      COMP: Fix session/aeva icons install rule using relative path for DESTINATION

Fix macOS packaging ensuring MOAB is built & installed with full RPATH

See merge request !9

List of MOAB changes:

$ git shortlog e4d480898..3861e5dcc
Jean-Christophe Fillion-Robin (1):
      COMP: Support configuring the project with custom CMAKE_INSTALL_NAME_DIR value

Since the original repository hosted add on bitbucket (See [1])
contains large files in its history (> 100Mb), a regular branch
based of the tag 5.3.1 couldn't be created and pushed. The following
error was reported:

  [...]
  git checkout -b aevaSlicer-5.3.1-2021-11-12-65880ffe8 5.3.1
  git push origin aevaSlicer-5.3.1-2021-11-12-65880ffe8
  [...]
  remote: error: Trace: 35e6858490cd58269e32186cf671d7814fdfec6bb76c375b0e7822d461d9d0b1
  remote: error: See http://git.io/iEPt8g for more information.
  remote: error: File MeshFiles/unittest/io/rtttest2.rtt is 155.82 MB; this exceeds GitHub's file size limit of 100.00 MB
  remote: error: GH001: Large files detected. You may want to try Git Large File Storage - https://git-lfs.github.com.
  To github.com:KitwareMedical/MOAB.git
   ! [remote rejected]     aevaSlicer-5.3.1-2021-11-12-65880ffe8 -> aevaSlicer-5.3.1-2021-11-12-65880ffe8 (pre-receive hook declined)


Instead a new base commit was created using the following commands
adapted from [2]

```
git clone git@github.com:KitwareMedical/MOAB.git
cd MOAB
git remote add upstream git@bitbucket.org:fathomteam/moab.git
git fetch upstream

# 65880ffe8 corresponds to the commit associated with tag 5.3.1
# See https://bitbucket.org/fathomteam/moab/commits/65880ffe8

echo 'Base commit with tree from 65880ffe8 (Merged in release/version5.3.1)' | git commit-tree 65880ffe8^{tree}
e4d480898a1f0045e764508b81b3f9d6441b0603

git checkout -b aevaSlicer-5.3.1-2021-11-12-65880ffe8 e4d480898a1f0045e764508b81b3f9d6441b0603

git push origin aevaSlicer-5.3.1-2021-11-12-65880ffe8
```

[1] https://bitbucket.org/fathomteam/moab/
[2] https://www.gloomycorner.com/pushing-partial-commits-to-remote-in-git/

ENH: Add cxx test cases for testing smtk export

See merge request !5

Add Cxx testing for vtkSlicerSMTKFileWriterLogic.
Tests include exporting into smtk format:
1) Empty scene
2) poly data mrml node
2) Image data mrml node
2) segmentation mrml node

BUG: Update SMTK and aeva-session to fix memory leaks

See merge request !8

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

This commit is intended to fix memory leaks reported when building
the project with the option Slicer_USE_VTK_DEBUG_LEAKS set to ON,
in aevaSlicer's superbuild.

List of aeva-session changes:
$ git shortlog 54ed002..32736ae7 --no-merges
Aron Helser (5):
      Fix export of an imported vtk volume mesh to .med
      Add the option to imprint scalar values from mesh to volume.
      Add scalarName and maxDist inputs to scalar imprint.
      In operators, use a tree view to input reference items.
      Always show 3D widgets even if Qt controls are hidden.

David Thompson (3):
      Track changes to SMTK.
      Bump CI images.
      Use the new API to fetch managers from the ParaView wrapper.

Robert O'Bara (2):
      BUG: Fixing Aeva Session Install
      ENH: Improved the UI (and Specification) for EditFreeFormAttribute Op

Shreeraj Jadhav (2):
      BUG: Fix memory leaks in Session::offsetGlobalIds
      COMP: Fix build error missing vtkShepardMethod header

List of SMTK changes:
$ git shortlog 01cab6b..2d69614 --no-merges
Aron Helser (9):
      Fix python tracing of component rename - create op with manager
      Bump ci base to pick up pybind11 update
      Remove ImportPythonOperation from test to help non-python builds.
      Bump ci tarballs for Mac, to catch up to win/linux
      Improve python tracing of Import operations
      Switch to QPointer for ref item data, avoid a segfault on exit.
      Add a setting to allow 3D widgets to show when their Qt gui hides.
      Fix how images are supplied by the source - restore the multiblock
      Make PyOperations execute on the main thread by default.

David Thompson (17):
      Add methods to `resource::Metadata` that accept `common::Managers`.
      Split the attribute-system python bindings...
      Invoke `smtk::resource::Metadata::write()` properly.
      Document graph-node initializers.
      Add `make()` methods to the `smtk::common::Factory`.
      Enable pybind11, opencascade in SMTK's CI images.
      Fix dereference of uninitialized weak pointer.
      Validate nodes as they are added to a graph resource.
      Fix warnings from g++ 11.2.1.
      Graph-resource fixes.
      Add a missing release note.
      Fix warnings.
      Turn on `-Wall -Wextra` flags for CI gcc builds.
      Expose graph traits object as passed by subclass.
      Add dependencies on present but previously un-indexed docs.
      Bump CI images to catch pybind11 fix and occt for CI.
      Add a contract test for the opencascade-session plugin.

Robert O'Bara (3):
      ENH: Added the ability to process solid cells in SMTK Reps
      ENH: Extended properties to include sets of ints
      ENH: Added the ability to hide pqSMTKAttributeItemWidget's labels

Ryan Krattiger (7):
      Graph: Enable inverse arc relationships
      Removed noexcept from weak reference T& conversion
      Release notes updated.
      Fix lint errors
      Add public class scope to test nodes.
      Fix template deduction in Inverse Arc test
      Fix string int conversion in test.

Shreeraj Jadhav (1):
      COMP: Fix missing VTK dependencies for vtkApplyTransforms

Fix macOS packaging ensuring libraries associated with external projects in either build and install trees have RPATH with full paths.

See merge request !7

This commit ensures both the IMPORTED_LOCATION and IMPORTED_SONAME
target properties match for Netgen & aeva-session targets exported
in <proj>Targets.cmake.

By having a valid path associated with IMPORTED_SONAME, the library
linking against either Netgen & aeva-session targets will list correct
entries in the output of otool. This ensures the fixup process can
properly locate and copy the relevant libraries into the package.

This commit fixes a regression introduced in 20352b4d (COMP: Remove
CMAKE_INSTALL_LIBDIR hard-coded value from external projects). It also
removes the hard-coded value user to set aeva-session_DIR.

Configuration error addressed by this commit is the following:

  CMake Error at /path/to/SlicerSMTK/CMakeLists.txt:41 (find_package):
    By not providing "Findaeva-session.cmake" in CMAKE_MODULE_PATH this project
    has asked CMake to find a package configuration file provided by
    "aeva-session", but CMake did not find one.

    Could not find a package configuration file provided by "aeva-session" with
    any of the following names:

      aeva-sessionConfig.cmake
      aeva-session-config.cmake

    Add the installation prefix of "aeva-session" to CMAKE_PREFIX_PATH or set
    "aeva-session_DIR" to a directory containing one of the above files.  If
    "aeva-session" provides a separate development package or SDK, be sure it

This commit improves the robustness of the build-system by updating
aeva-session and smtk external projects to use Slicer_INSTALL_THIRDPARTY_LIB_DIR
value instead of hard-coded value "lib".

This commit removes the setting of <proj>_INSTALL_RUNTIME_DIR and
<proj>_INSTALL_LIBRARY_DIR from external projects.

These variables were set due to their presence in the Slicer SuperBuild
extension template but they are no relevant anymore. Indeed, starting
with kitware/VTK@d75f5c0f7 [1] (vtkDirectories: remove unused file),
there are no occurrences in the VTK build-system and they are no used
in the other projects (aeva-session, MOAB, Netgen, nlohmann_json and smtk).

[1] https://github.com/Kitware/VTK/commit/d75f5c0f7

On macOS, this associated libraries will be copied into the package
during the fixup process (leveraging the full RPATH) and they should not
be installed.

List of Netgen changes:

$ git shortlog d06f2f4f..85fcab94 --no-merges
Jean-Christophe Fillion-Robin (1):
      [Backport PR-116] COMP: Support configuring project specifying custom CMAKE_MACOSX_RPATH value

This is a follow-up of 9bd56583 (COMP: Fix extension configuration and
build) where the MOAB external project was originally introduced.

The original list of options specified in External_MOAB.cmake was
was adapted from cmb/cmb-superbuild@359bc07a (moab: disable building
the tools). See [1]

[1] cmb/cmb-superbuild@359bc07a

COMP: Fix library paths for build tree launcher settings

See merge request !6

BUG: Copy direction cosines to exported image data

See merge request !4

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#L174

Addresses issue aeva#273

COMP: Update aeva-session and SMTK to fix build issues

See merge request !3

Fix a regression introduced in session@f333d62f
(cmake: install operation headers into the right subdir) [1]
where the installation path for aeva-session's operator
headers have changed due to introduction of `operators` subfolder.

[1] session@f333d62f

List of aeva-session changes:

  $ git shortlog 79f295a..54ed002 --no-merges
  David Thompson (2):
    Replace the old toolbar buttons with shiny new ones.
    Fix building aeva/session without ParaView support.

The commit cmb/smtk@53553deb (Add missing dependencies for vtk modules) [1] allows
to build client projects against a smtk build tree.

[1] cmb/smtk@53553deb

List of SMTK changes:

  $ git shortlog 669a575..01cab6b --no-merges
  Aron Helser (2):
    Add null-check to fix a crash in qtOperationTypeModel
    Fix typo in operator xml.

  Ben Boeckel (2):
    python: drop support for Python2
    python: add a release note about Pybind11-related changes

  David Thompson (2):
    Fix a superbuild (modelbuilder package) error.
    Fix error building graph resources w/ modern clang...

  Shreeraj Jadhav (2):
    Add missing dependencies for vtk modules
    COMP: Fix build of json(HelperFunction|Resource).cxx on AppleClang 11.0

Add SMTKFileWriter module  for exporting Slicer scene as .aeva.smtk file which can then be loaded into aevaCMB application.

See merge request !2