Slicer - Convert centerlines to a graph {V,E}

som1197 · July 16, 2021, 4:42am

Thank you @lassoan for the piece of code. Yes I will send out a pull request with the proposed changes soon.

Moreover, I also wanted to know if scalar values of ‘GroupIDsarray’, ‘TortuosityArray’ , ‘BlankingArray’ etc. can be incorporated in the centerline model. I generated the following plots by using the conventional vmtkscripts, but it does not always work correctly.

Currently there are only 3 ways to postprocess the centerline data as shown here.

However, can we make any changes here in the base code to store values of other arrays as well?
Also would it be possible to run this function independently in a separate python code given the vtkpolymesh surface data and the endpoint co ordinates?

github.com

vmtk/SlicerExtension-VMTK/blob/995027f17f195d802134f799aab095ea31f3e6c5/ExtractCenterline/ExtractCenterline.py#L635-L723


      
          def extractCenterline(self, surfacePolyData, endPointsMarkupsNode, curveSamplingDistance=1.0):

              """Compute centerline.

              This is more robust and accurate but takes longer than the network extraction.

              :param surfacePolyData:

              :param endPointsMarkupsNode:

              :return:

              """

          

              import vtkvmtkComputationalGeometryPython as vtkvmtkComputationalGeometry

              import vtkvmtkMiscPython as vtkvmtkMisc

          

              # Cap all the holes that are in the mesh that are not marked as endpoints

              # Maybe this is not needed.

              capDisplacement = 0.0

              surfaceCapper = vtkvmtkComputationalGeometry.vtkvmtkCapPolyData()

              surfaceCapper.SetInputData(surfacePolyData)

              surfaceCapper.SetDisplacement(capDisplacement)

              surfaceCapper.SetInPlaneDisplacement(capDisplacement)

              surfaceCapper.Update()

This file has been truncated. show original

This has been done for the network curves but the centerline curves hold the real information.

github.com

vmtk/SlicerExtension-VMTK/blob/995027f17f195d802134f799aab095ea31f3e6c5/ExtractCenterline/ExtractCenterline.py#L616-L633


      
          if computeGeometry:

              centerlineGeometry = vtkvmtkComputationalGeometry.vtkvmtkCenterlineGeometry()

              centerlineGeometry.SetInputData(networkExtraction.GetOutput())

              centerlineGeometry.SetLengthArrayName(self.lengthArrayName)

              centerlineGeometry.SetCurvatureArrayName(self.curvatureArrayName)

              centerlineGeometry.SetTorsionArrayName(self.torsionArrayName)

              centerlineGeometry.SetTortuosityArrayName(self.tortuosityArrayName)

              centerlineGeometry.SetFrenetTangentArrayName(self.frenetTangentArrayName)

              centerlineGeometry.SetFrenetNormalArrayName(self.frenetNormalArrayName)

              centerlineGeometry.SetFrenetBinormalArrayName(self.frenetBinormalArrayName)

              # centerlineGeometry.SetLineSmoothing(0)

              # centerlineGeometry.SetOutputSmoothedLines(0)

              # centerlineGeometry.SetNumberOfSmoothingIterations(100)

              # centerlineGeometry.SetSmoothingFactor(0.1)

              centerlineGeometry.Update()

              return centerlineGeometry.GetOutput()

          else:

              return networkExtraction.GetOutput()

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Slicer - Convert centerlines to a graph {V,E}

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