VMTK SlicerExtension Multiprocessing

Support
1

Hi,

I have a python pipeline that utilizes several functions, such as ExtractCenterline and ClipVessel, from the SlicerExtension-VMTK (GitHub - vmtk/SlicerExtension-VMTK) for analyzing vessel segmentation. Since I need to process each segment in the segmentation, I am interested in using multiprocessing to speed up the analysis.

I’ve tried using SlicerParallelProcessing (GitHub - pieper/SlicerParallelProcessing: Slicer modules for running subprocesses to operate on data in parallel), but it doesn’t seem to work, possibly due to the presence of vtkMRMLNode in SlicerExtension-VMTK.

Is there any suggestion or other method to implement multiprocessing in this context?
BTW, I am working with SlicerJupyter and the Slicer 5.6 environment.

Thank you so much!

Best,
Tracy

2

By default the SlicerParallelProcessing just launches PythonSlicer which is the same python shell as Slicer but without the modules or extensions.

You should be able to create a subshell that has all the paths defined so that VMTK logic libraries are included and can be used. Perhaps lauchConsoleProcess, but I haven’t tried.

3

Hi Pieper,

Thanks for your advice.

I’m encountering an issue (which I believe is related to the environment) when trying to use launchConsoleProcess.

Here is the command

command = [
‘PythonSlicer’, ‘test_script.py’, # The Python interpreter and the script name
‘–segmentationName’, ‘segment_merge.nii.gz’,
‘–segmentName’, ‘Segment_1’,
‘–centerlineName’, ‘test’,
‘–point’, ‘145.66666666666666, 315.3333333333333, 301.6666666666667’ # Second 3D coordinate
]

process = slicer.util.launchConsoleProcess(command)
slicer.util.logProcessOutput(process)

When I use ‘python3’ as the executable, I get the error:
ModuleNotFoundError: No module named numpy
Additionally, all the SlicerExtension-VMTK modules seem to be missing.

On the other hand, if I use ‘PythonSlicer’, I encounter this error:
FileNotFoundError: [Errno 2] No such file or directory: ‘PythonSlicer’

Do you have any suggestions for resolving these issues?
If you need any further information, please let me know.
Thanks a lot.

Best,
Tracy

4

Try launchConsoleProcess(["PythonSlicer"], useStartupEnvironment=False)

5

Thanks for quick reply.

However, I face some other error (vtkMRMLNode)
Please refer to the attached image.

image
image1239×529 87.5 KB

Here is my function if useful
def centerline_extraction(segmentationName, segmentName, centerlineName, points=None):

segmentationNode = slicer.util.getNode(segmentationName)
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(segmentName)

# Init the VMTK ExtracCenterline class
extractLogic = ExtractCenterline.ExtractCenterlineLogic()

# Preprocess the surface
inputSurfacePolyData = extractLogic.polyDataFromNode(segmentationNode, segmentID)
targetNumberOfPoints = 5000.0
decimationAggressiveness = 3.5
subdivideInputSurface = False
preprocessedPolyData = extractLogic.preprocess(inputSurfacePolyData, targetNumberOfPoints, decimationAggressiveness, subdivideInputSurface)

endPointsMarkupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", "Centerline endpoints")
if not np.any(points):
    # Auto-detect the endpoints      
    networkPolyData = extractLogic.extractNetwork(preprocessedPolyData, endPointsMarkupsNode)
    startPointPosition=None
    endpointPositions = extractLogic.getEndPoints(networkPolyData, startPointPosition)
    endPointsMarkupsNode.RemoveAllMarkups()
    for position in endpointPositions:
      endPointsMarkupsNode.AddControlPoint(vtk.vtkVector3d(position))

else:
    assert points.shape[1] == 3
    # Self define start and end points
    endPointsMarkupsNode.RemoveAllMarkups()
    for p in points:
        endPointsMarkupsNode.AddControlPoint(vtk.vtkVector3d(p))
    
        #endPointsMarkupsNode.AddControlPoint(vtk.vtkVector3d(points[-1]))

# Extract the centerline
curveName = centerlineName+"Curve"
modelName = centerlineName+"Model"

centerlineCurveNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsCurveNode", curveName)

centerlinePolyData, voronoiDiagramPolyData = extractLogic.extractCenterline(preprocessedPolyData, endPointsMarkupsNode)
centerlinePropertiesTableNode = None
extractLogic.createCurveTreeFromCenterline(centerlinePolyData, centerlineCurveNode, centerlinePropertiesTableNode)

centerlineModelNode = slicer.modules.models.logic().AddModel(centerlinePolyData)
centerlineModelNode.SetName(modelName)

return centerlineCurveNode, centerlineModelNode
6

PythonSlicer is more just a python shell and not a full instance of Slicer. Maybe for what you want you can use Slicer --no-main-window. Since it runs the application you’ll need to explicitly exit() when you are done processing.

7

Dear Steve Pieper,
My writing is not belong to this conversation. Could you kindly review and approve my post request? I am new to the community and currently seeking assistance. Thank you for your time and understanding.