2017 Winter Project Week/Support for volumetric meshes

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  Projects List

Previous works

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  FEMesh in Slicer 3

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  Cleaver Extensio

Results

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  Volumetric Mesh

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  Volumetric Mesh (gif)

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  Models module display widget (gif)

Key Investigators

• Alexis Girault (Kitware, Inc.)
• Curtis Lisle (KnowledgeVis, LLC)
• Steve Pieper (Isomics, Inc.)

Project Description

Objective	Approach and Plan	Progress/Results	Next steps/Future work
From top priority to possible future work: Being able to visualize, load and save volumetric meshes Improving clipped visualization of models (surface models or volumetric meshes) and facilitate the display of the point data (active scalars). Being able to create volumetric meshes from label maps (or segmentation?) and possibly edit them	Initial discussions needed with Curtis and Steve based on existing work: IA FEMesh from Slicer 3, BodyCentricCubicMesh and MeshCompression modules, and the CleaverExtension. Some parts of the IA FEMesh module were prototyped in early Slicer 4 (Curtis). Probably investigate the creation of a MRML node similar to Models (possibly create a hierarchy between both?) that would wrap a vtkUnstructuredGrid in order to visualize, load and save the meshes. Investigate best way to adapt previous Slicer-based volumetric work that allowed for creation and edition (bullet point 1) to work with the new architecture put in place within Slicer 4 (bullet point 2).	Can Read & Write Unstructured Grid mesh (vtk or vtu) Fix bug in vtk reader to retrieve all point data and cell data. vtkMRMLModelNode now holds a "mesh", either a polydata (surface mesh) or an unstructured grid (volumetric mesh) vtkMRMLDisplayNode had a major clean up to consolidate scalar range options (scalarRangeFlag and autoScalarRange). Other clean up made to retrieve the look-up table for specific nodes only holding color transfer functions (ex: vtkMRMLProceduralColorNode). DisplayableManager updated for 3D to allow cutting through volumetric mesh. SliceDisplableManager updated for 2D Slices to be able to use same display properties than 3D view. qMRMLModelDisplayNodeWidget updated to simplify scalar range mode selection, adapt number of decimals and single step for manual selection of the range based on the magnitude of the current values. Threshold displayed mesh by scalar values. Display information about the model type (surface or volumetric) for the user to be able to distinct it in the module widget. WIP branch on github: https://github.com/Slicer/Slicer/compare/master...agirault:volumetric-mesh-support	Clean up and consolidate qSlicerModelsModuleWidget (display properties, representations, wireframe, clipping... just move options around to make it more usable) Add clipping option to smoothen the cut (using vtkClipDataSet vs vtkExtractGeometry) Add support to pass through CLI (SlicerCLILogic) Test with more cases, like fiber bundles etc... (changes could have a lot of impacts because there were changes to vtkMRMLDisplayNode and vtkMRMLModelNode. Make sure the updated API stays backward compatible).

Background and References

• IA_FEMesh (Slicer 3) : https://www.slicer.org/wiki/Modules:IA_FEMesh-Documentation-3.6
• BodyCentricCubicMesh module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/BodyCentricCubicMesh
• MeshCompression module : https://www.slicer.org/wiki/Documentation/Nightly/Modules/MeshCompression
• CleaverExtenstion : https://www.slicer.org/wiki/Documentation/Nightly/Extensions/CleaverExtension
• vtkUnstructuredGrid : http://www.vtk.org/doc/nightly/html/classvtkUnstructuredGrid.html