Surface toolbox revamp

Development
#1

Hi Slicer developers,
cc: @pieper @lassoan @jcfr @styner

This week we plan to start a considerable effort to revamp the Surface Toolbox. The main idea is to port most of MeshMath’s functionality into it. We have created a lab’s page that details how we plan this effort to go.

If anybody has ideas or suggestions, please let us know!

Bea

4 Likes
rebuild the surface of skull bone
#2

@benwilson is making good progress and should have a pull request shortly :tada:

To move forward, considering we will be adding around ~20 CLIs, I was thinking to develop the SurfaceToolBox (and associated modules) in its own repository Slicer/Slicer-SurfaceToolBox that we would integrate in Slicer as a remote module like it is already done for SimpleFilters, LandmarkRegistration, …

What do you think ?

This would allow …

  • to easily enable/disable building of the surface toolbox within Slicer or Slicer custom application
  • to easily integrate the modules in any system compliant with the SlicerExecutionModel interface

To illustrate here is a repository I just created:

It was generated by extracting history using jcfr/dockgit-rocket-filter:

# Filter history
git clone git://github.com/Slicer/Slicer -b master Slicer-SurfaceToolBox
cd Slicer-SurfaceToolBox
git-rocket-filter --branch surfacetoolbox --keep Modules/Scripted/SurfaceToolbox

# publish extracted branch
git remote add SurfaceToolBox git@github.com:Slicer/Slicer-SurfaceToolBox.gi
git push SurfaceToolBox refs/heads/surfacetoolbox:master
#3

Sounds like a good idea to me - thanks @jcfr :+1:

#4

Thanks for the feedback.

  • Repository name changed to SlicerSurfaceToolbox
  • LICENSE, README.md and top-level CMakeLists.txt added
  • History filtered to have all modules at the root of the repo and to fix the the git message trailers so that both Co-authored-by and git-svn-id are recognized
#5

A post was split to a new topic: Convert mesh to engineering CAD software solid part

#6

Start with r28434, SurfaceToolbox is now integrated as a remote module whose sources are downloaded from https://github.com/Slicer/SlicerSurfaceToolbox

#7

Hi!

I was considering expanding the Connectivity option of the surface toolbox such, that not only the largest region is extracted, but to base the extraction on a volumetric threshold (I remember seeing a comment in the Python source code of the module in 4.10.2 regarding this). So I tried (in Python) to prototype something like this, without great success. Below is my prototype code.

input = slicer.mrmlScene.GetFirstNodeByName('Model')
surface = input.GetPolyDataConnection()

# get all regions
conn = vtk.vtkPolyDataConnectivityFilter()
conn.ScalarConnectivityOn()
conn.SetScalarRange(-1, 1)
conn.SetExtractionModeToAllRegions()
conn.SetInputConnection(surface)
conn.Update()

nrRegions = conn.GetNumberOfExtractedRegions()
sizes = conn.GetRegionSizes()

# now switch to extraction mode to process one after the other  
conn.SetExtractionModeToSpecifiedRegions()

fhf = vtk.vtkFillHolesFilter()
fhf.SetHoleSize(1000.0)
fhf.SetInputConnection(conn.GetOutputPort())

normals = vtk.vtkPolyDataNormals()
normals.ConsistencyOn();
normals.SplittingOff();
normals.SetInputConnection(fhf.GetOutputPort()) 

mass = vtk.vtkMassProperties()
mass.SetInputConnection(normals.GetOutputPort())

volumetricThreshold = 4000
volumes = []

# measure all cells
for id in range(0, nrRegions):
  if sizes.GetValue(id) > 5: # preselect, currently hardcoded
    conn.InitializeSpecifiedRegionList()
    conn.AddSpecifiedRegion(id)
    mass.Update()
    
    print(mass.GetVolume())
    volumes.append(mass.GetVolume())
  else:
    volumes.append(0)
    
fhf.RemoveAllInputConnections(0)      
  
# extract only those regions above the volumetricThreshold
conn.InitializeSpecifiedRegionList()
for id in range(0, nrRegions):
  if volumes[id] > volumetricThreshold:
    print(id)
    conn.AddSpecifiedRegion(id)

surface = conn.GetOutputPort()
input.SetPolyDataConnection(surface)
conn.Update()

Can someone tell me whether this goes into the right direction? In principle, it seems to do what it should (I believe, I have not rigorously tested it), but it is extremely slow (takes about 2 minutes for a CT-head). Is there a significant difference between Python implementation and C++? If we could get something like this running, it would be suited for expanding this module.

BTW: I did not see any difference in extraction when I manipulated the ScalarRange or turned FullScalarConnectivityOn().

#8

For segmentation problems like this, we normally use the Segment Editor:

  1. Use Threshold effect to specify intensity range you are interested in.
  2. Use Islands effect / Keep largest island method to keep the largest connected component.

You can continue with further processing or export directly to STL/OBJ file right from the Segment Editor.

1 Like