Automatic centerline

It looks like the tests have not been updated since an earlier version of the module; the error message is correct that there is no run() method in ExtractCenterlineLogic. There is an extractCenterline() method which takes as inputs surfacePolyData, endPointsMarkupsNode, and a curveSamplingDistance. Here is what I think you need:

segmentationName = 'MySegmentationName' # replace with the name of your segmentation
segmentName = 'MySegmentName' # replace with the name of the segment you want to find the centerline of
segmentationNode = slicer.util.getNode(segmentationName)
segmentID = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(segmentName)

import ExtractCenterline
extractLogic = ExtractCenterline.ExtractCenterlineLogic()

# Preprocess the surface
inputSurfacePolyData = extractLogic.polyDataFromNode(segmentationNode, segmentID)
targetNumberOfPoints = 5000.0
decimationAggressiveness = 4 # I had to lower this to 3.5 in at least one case to get it to work, 4 is the default in the module
subdivideInputSurface = False
preprocessedPolyData = extractLogic.preprocess(inputSurfacePolyData, targetNumberOfPoints, decimationAggressiveness, subdivideInputSurface)

# Auto-detect the endpoints
endPointsMarkupsNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", "Centerline endpoints")
networkPolyData = extractLogic.extractNetwork(preprocessedPolyData, endPointsMarkupsNode)
endpointPositions = extractLogic.getEndPoints(networkPolyData, startPointPosition)
for position in endpointPositions:

# Extract the centerline
centerlineCurveNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsCurveNode", "Centerline curve")
centerlinePolyData, voronoiDiagramPolyData = extractLogic.extractCenterline(preprocessedPolyData, endPointsMarkupsNode)
centerlinePropertiesTableNode = None
extractLogic.createCurveTreeFromCenterline(centerlinePolyData, centerlineCurveNode, centerlinePropertiesTableNode)

After you run this, the centerline should be in centerlineCurveNode, and the auto-detected endpoints should be in endPointsMarkupsNode. I don’t know if the preprocessing step is strictly necessary (it seems like you may know more about the inner workings of VMTK than I do), but it seems recommended. To get this code snippet, I tried to pull the relevant lines out of a few functions in the ExtractCenterlineLogic class (SlicerExtension-VMTK/ at 3787ea4a300da28ec5f0824f0715f2713b631155 · vmtk/SlicerExtension-VMTK · GitHub). I have not tried running the auto-detect endpoints this way, but I have done the centerline extraction with supplied endpoints using VMTK using the above methods in one of my own python modules.