perklab / sliceropenanatomy Goto Github PK

Add feature to enable hierarchical organization of segments.

Design: vtkSegment::Tags can contain the grouping information: "hierarchy" tag would contain full path of the segment (e.g., "/brain/rhomboencephalon/metencephalon/cerebellum"). Tag name would identify hierarchy; there could be multiple tags that the user can choose from (e.g., spatial, functional, …)

Cross-reference:
https://issues.slicer.org/view.php?id=4402

• Populate hierarchy tag when imported from model hierarchy
  • Question: where to store information on a branch (name, color, visibility attribute)?
• Improve subject hierarchy infrastructure to support multi-level virtual branches
• Show segment hierarchy in the virtual tree

Reason: table view and segment selector widget make lots of populate calls (set opacities as well)

Solution: Below MRML level, so StartModify/EndModify cannot be used, but a simple flag may be used

We need to save segment hierarchy and terminology information for segmentations. Probably the best way to do it is to create a .json sidecar file. Format and content of this file is not yet specified.

Colors appear to be lighter, somewhat washed out in glTF viewers - see

https://discourse.slicer.org/t/open-anatomy-export-and-3dviewer-net-with-url/26726/12?u=lassoan

Transforms applied to modelNodes should not be ignored while exporting

Would it make sense to check the displayNode visibility of the to-be-exported nodes (i.e. not do it if the visibility is False)?

By not allocating the whole segmentation when saving or loading, but instead we stream the data, we can prevent memory overflow when allocating the huge 4D volume.

In order to label the existing atlases in Slicer properly, we need a way to assign standard terminologies to models in a hierarchy. Instead of fixing the current model hierarchy (which is quite buggy and that's part of the reason SH is not based on the original MRML scene model), we can achieve this within subject hierarchy:

• Add a new column for color
  • Proposed design: new function in abstract plugin which SH plugins can implement if makes sense to show one color (models, segments, fiducials, ?)
  • Add option to SH tree view to whitelist/blacklist plugins. This will be done with two QLists that, if not empty, will specify which plugins are used for populating the context menu
  • On double-click on color, the terminology selector will pop up, which sets the color and writes the terminology in the proper place (the relevant SH plugins would do this).
  • Add a remove button to terminology selector (in segments it's mandatory but in other nodes it's not)
• Add opacity SH plugin that has a slider in a sub-menu of the action (similarly to slice spacing in slice view controller)
• Add color information to folder items, allow them to override branch color

Is there a way to export markup points with the .ghlt models? We in the CAVFB (http://200.17.71.18/) would like to use this feature to add topographic descriptions to the bone models we present online.
Thanks in advance, best regards,

@rafael-vm

• Use Extension Wizard to create SlicerOpenAnatomy extension
• Extension has one loadable (C++) module called OpenAnatomyExporter
• Logic can export all the model nodes in the scene as obj files
• Write out glTF file for the exported obj files using JsonCPP. See an example here

It would be nice if planes could be exported as they usually used in surgical planning to mark surgical margins

It would contain models and volumes. Since 3D textures are not supported in gltf yet, we'll first work on models only. Volumes will be saved as nrrd.

Hierarchy information would be stored externally.

• Ask on VTK mailing list if anybody is working on gltf exporter already. Ask for comment on our choice of gltf toolkit (do they like it, is there any better suggestion). Send the email draft to Csaba and Andras before posting it to the mailing list.
• Create a VTK-based exporter (similar to OBJ exporter) - add it to https://github.com/PerkLab/SlicerOpenAnatomy/tree/master/OpenAnatomyExporter/Logic folder
• Add a test that sets up a simple rendering scene and writes it to gltf (similar to VTK\IO\Export\Testing\Cxx\TestOBJExporter.cxx)

The boxes models are not exported with reduction factor = 0.8 because they only have 24 points

Exporting...
Writing BoneReconstructionPlanner...
Writing Segmentation Models...
Model 1/35: Fibula
Model 2/35: decimatedFibula
Model 3/35: Mandible
Model 4/35: decimatedMandible
Writing Mandible reconstruction...
Writing Plane Cuts...
Writing Cut Bones...
Model 5/35: Fibula Segment 0A-0B
Model 6/35: Fibula Segment 1A-1B
Model 7/35: Fibula Segment 2A-2B
Model 8/35: Resected mandible
Writing Mandible2Fibula transforms...
Writing Bone Pieces Transforms...
Writing Transformed Fibula Pieces...
Model 9/35: Transformed Fibula Segment 0A-0B_4
Model 10/35: Transformed Fibula Segment 1A-1B_4
Model 11/35: Transformed Fibula Segment 2A-2B_4
Writing miterBoxes Models...
Model 12/35: miterBox0_A
  Warning: empty model, not exported.
Model 13/35: miterBox0_B
  Warning: empty model, not exported.
Model 14/35: miterBox1_A
  Warning: empty model, not exported.
Model 15/35: miterBox1_B
  Warning: empty model, not exported.
Model 16/35: miterBox2_A
  Warning: empty model, not exported.
Model 17/35: miterBox2_B
  Warning: empty model, not exported.
Writing biggerMiterBoxes Models...
Model 18/35: biggerMiterBox0_A
  Warning: empty model, not exported.
Model 19/35: biggerMiterBox0_B
  Warning: empty model, not exported.
Model 20/35: biggerMiterBox1_A
  Warning: empty model, not exported.
Model 21/35: biggerMiterBox1_B
  Warning: empty model, not exported.
Model 22/35: biggerMiterBox2_A
  Warning: empty model, not exported.
Model 23/35: biggerMiterBox2_B
  Warning: empty model, not exported.
Writing Fibula planes...
Writing Fibula Segments Lengths...
Writing Inverse mandible reconstruction...
Writing Inverse Plane Cuts...
Writing Inverse Append...
Writing Cut Mandible Pieces...
Model 24/35: Mandible Segment 0
Model 25/35: Mandible Segment 1
Model 26/35: Mandible Segment 2
Writing Full Mandibles...
Model 27/35: Mandible 0
Model 28/35: Mandible 1
Model 29/35: Mandible 2
Writing Transformed Mandible Pieces...
Model 30/35: Transformed Mandible Segment 0_4
Model 31/35: Transformed Mandible Segment 1_4
Model 32/35: Transformed Mandible Segment 2_4
Writing Transformed Full Mandible...
Model 33/35: Transformed Mandible 0_4
Model 34/35: Transformed Mandible 1_4
Model 35/35: Transformed Mandible 2_4
Writing Mandibular planes...
Writing file /home/BoneReconstructionPlanner.gltf...
Export successful.