IBBM networks and modules

[jessdtate]

IBBM/Bioelectricity/Forward_Problems/Dipole_Source/DipoleSourceExample.srn

• [ ] ShowAndEditDipoles #991
• [x] GenerateSinglePointProbeFromField (possible work around) #992

IBBM/Bioelectricity/Forward_Problems/rabbit_heart/bem_tank_forward.srn

• [ ] EditMeshBoundingBox (full functionality) #807

IBBM/Bioelectricity/Tissue_Modeling/Slab_Models/Display_PhiE_data.srn IBBM/Bioelectricity/Tissue_Stimulation/defib_fem_evaluate.srn (may want to skip)

• [x] InterfaceWithMatlab #927
• [x] Bundles (ReadBundle/GetFieldFromBundle)

IBBM/Bioelectricity/Inverse_Problems/dipole_localization/optimize_dipole.srn (This network is challenging and might be too hard to get done before the workshop)

• [x] GeneratePointSamplesFromField(OrWidget) #994
• [x] OptimizeDipole (this is the hard part) #997
• [x] SolveMinNormLeastSqSystem (only used with OptimizeDipole)
• [x] ReportColumnMatrixMisfit (only used with OptimizeDipole) #996
• [x] ConvertHexVolToTetVol
• [x] ShowFieldGlyphs #978

IBBM/Bioelectricity/Inverse_Problems/dipole_localization/dipole_forward.srn same as DipoleSourceExample.srn IBBM/Bioelectricity/Inverse_Problems/greensite.srn

• [x] InterfaceWithMatlab #927

IBBM/Bioelectricity/Inverse_Problems/wbp.srn

• [x] InterfaceWithMatlab #927
• [x] ShowString #530

IBBM/Numerical_Methods/Lab3/cube_simulation.srn

• [x] EditMeshBoundingBox #807
• [x] AddLinkedNodesToLinearSystem (kind of optional) #993

IBBM/Image_Processing/Lab3/Registration_Network.srn

• [x] RegisterWithCorrespondences #969

IBBM/Scientific_Visualization/Lab4/tensor_view.srn

• [x] ShowFieldGlyphs (tensors) #978
• [x] GetSliceFromStructuredFieldByIndices #995

IBBM/Scientific_Visualization/Lab4/view_fibers.srn

• [x] ShowFieldGlyphs (vectors) #978
• [x] GetSliceFromStructuredFieldByIndices #995

IBBM/Scientific_Visualization/Lab4/streamline.srn

• [x] Bundles(ReadBundle/GetFieldFromBundle)
• [x] GeneratePointSamplesFromField(OrWidget) #994

IBBM/Scientific_Visualization/Lab1/ibbm_lab_data/scirun/data_visualization.srn

• [x] ClipVolumeByIsovalue #922

IBBM/Scientific_Visualization/Lab2/IsosurfacingModule/Isosurfacing_Cube.srn

• [x] GenerateSinglePointProbeFromField (not really needed) #992

IBBM/Scientific_Visualization/Lab2/IsosurfacingModule/Isosurfacing_Hip.srn

• [x] ExtractIsosurfaces

ViewScene Features:

• [ ] widgets
• [x] turning objects on and off
• [x] clipping
• [ ] multiple windows/locking rotation together
• [x] glyphs
• [x] colormaps with text

[a-y-khan]

Thanks Jess! Are there any ViewScene features that you need?

[dcwhite]

Thanks for this great list!

[jessdtate]

we will show off as many features that we can get implemented. some of the viewscene features that are more important: widgets turning objects on and off clipping multiple windows/locking rotation together glyphs colormaps with text

should I add these to the original issue?

[jessdtate]

Also, some of these networks may not be worth getting working in time. We can discuss which ones would give us the most bang for buck.

[a-y-khan]

Yes please - having ViewScene features on the list will be helpful. Let's find a time to meet this week with @dcwhite, @cbrightsci.

[lizutah]

@moritzdannhauer - do you want to add some potential BrainStimulator demos and required modules to the list?

[moritzdannhauer]

Yes, some new ones, but I dont know if we can show off all of them in the demos since some of them might need some computation time. But maybe for a simplified model

• [ ] ElectrodeCoilSetup: I need some functionality from MarchingCube (Dan knows what I mean) #922
• [ ] InterfaceToCleaver2 (after Shankar fixed the bug): Talked to Brig about it today. Which features are needed?
• [ ] CreateElectrodeCoilPrototype (i am gonna implement that) - should not be too hard
• [ ] GenerateStreamLines (needs to become multi-threaded) (#888)
• [ ] For ECoG stimulation I am planning a module that computes a smooth convex hull of a segmentation (brain) - the collaborators in Freiburg will help me with it
• [ ] DBS capabilities: gonna talk to Chris about it

This is a long list and a lot of work. That is all I envision for BrainStimulator and of course not all of it needs to be ready for IBBM

[a-y-khan]

@moritzdannhauer @dcwhite is there a GitHub issue for required marching cube functionality? If not, someone please create it.

[dcwhite]

922

[dcwhite]

SCIRun 4 versions of the networks above can be found at https://github.com/SCIInstitute/SCIRun-Exchange/tree/master/IBBM2014

[jessdtate]

I realized I missed a module: GetSliceFromStructuredFieldByIndices for the tensor and fiber visualization

[dcwhite]

@jessdtate Here is last year's issue.