How can I use the module of "Markups to Model" in command line?

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1

Hi
Dear developers and users

How can I use the module of “Markups to Model” in command line?
I noticed that I can create a tube model around of centerline using the module of “Markups to Model” . At now, I want create this tube using this module in the command line. How can I do it?
Is it another module to create the tube around centerline?

Please guide me.
Shahrokh

2

Hi shahrokh,

You mean through python interactor?

There is no public function in the module yet to do this, but I can add one. In the meantime you can use vtk.vtkTubeFilter (https://www.vtk.org/doc/nightly/html/classvtkTubeFilter.html) to create tube poly data around the points. Something like this (note I haven’t personally tried running this so you may need to tweak it):

  numPoints = pointsToConnect.GetNumberOfPoints()
  lineCellArray = vtk.vtkCellArray()
  lineCellArray.InsertNextCell( numPoints )

  for i in xrange(0,numPoints)
  {
    lineCellArray.InsertCellPoint( i )
  }

  linePolyData = vtk.vtkPolyData()
  linePolyData.SetPoints( pointsToConnect )
  linePolyData.SetLines( lineCellArray )

  tubeSegmentFilter = vtk.vtkTubeFilter()
  tubeSegmentFilter.SetInputData( linePolyData )
  tubeSegmentFilter.SetRadius( tubeRadius ) #INSERT VALUE
  tubeSegmentFilter.SetNumberOfSides( tubeNumberOfSides ) #INSERT VALUE
  tubeSegmentFilter.CappingOn()
  tubeSegmentFilter.Update()

  # Access poly data by calling tubeSegmentFilter.GetOutput()

If you want to assign it to a vtkMRMLModelNode you’ll need to do:

  modelNode.SetAndObservePolyData( tubeSegmentFilter.GetOutput() )
  modelNode.CreateDefaultDisplayNodes()

I hope that helps. If it doesn’t answer your question please let me know.

Thomas

3

Hello
Dear Thomas,

Thanks a lot for your guidance. At now, I want to create tube poly data around the points in my vtp centerline file according with your commands.
I have some problems to do it.
I enter the following commands in python interactor of Slicer.

import vtk
filename = “~/centerlineRodCT001.vtp”
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
numPoints = reader.GetNumberOfPoints()
lineCellArray = vtk.vtkCellArray()
lineCellArray.InsertNextCell(numPoints)
for i in range(0,numPoints):
lineCellArray.InsertCellPoint( i )
linePolyData = vtk.vtkPolyData()
linePolyData.SetPoints(reader)

At this moment, I get the following error.
Traceback (most recent call last):
File “”, line 1, in
TypeError: SetPoints argument 1: method requires a vtkPoints, a vtkXMLPolyDataReader was provided.

Please guide me. How can I get vtkPoints argument?
Best regards,
Shahrokh

4

Excuse me. Unfortunately I can not find any python code example about reading centelines vtp file and applying vtktubefilter to it. Please let me know where I wrong it.
Thanks a lot.
Shahrokh

5

Assuming that the points saved in the file are already in the correct order…

This should get you a vtkPolyData object:
polydata = reader.GetOutput()

This should get you a vtkPoints object from the vtkPolyData object:
points = polydata.GetPoints()

6

Dear Thomas
Thanks a lot for your guidance. I’m sure this solves my problem.
Best regards.

7

Dear Thomas

Thanks a lot for your guidance. Finally, I can create a tube around the centerline vtp file with the following lines:

import vtk

filename = “/home/sn/centerlineRodCT001.vtp”
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
polydata = reader.GetOutput()
points = polydata.GetPoints()
numPoints = reader.GetNumberOfPoints()
lineCellArray = vtk.vtkCellArray()
lineCellArray.InsertNextCell(numPoints)
for i in range(0,numPoints):
lineCellArray.InsertCellPoint( i )
linePolyData = vtk.vtkPolyData()
linePolyData.SetPoints(points)
linePolyData.SetLines( lineCellArray )
tubeSegmentFilter = vtk.vtkTubeFilter()
tubeSegmentFilter.SetInputData( linePolyData )
tubeSegmentFilter.SetRadius(2)
tubeSegmentFilter.SetNumberOfSides(10)
tubeSegmentFilter.SetOutputPointsPrecision(1)
tubeSegmentFilter.CappingOn()
tubeSegmentFilter.Update()
tubeSegmentFilter.GetOutput()
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName(“tube.vtp”)
writer.SetInputDataObject(tubeSegmentFilter.GetOutput())
writer.Write()

Best regards,
Shahrokh