Is there any code to control 'specify geometry in Segment editor?

telomere · August 7, 2023, 8:35am

I made a shortcut to go Segment Editor module and automatically load source volume and add segmentation and segment.
In this situation, I also want to control “specify geometry” button which is next to source volume.
I want to choose ROI that I made previously and set spacing as 0.15mm.
But I never could find the function codes for controlling ‘specify geometry’

I also saw the script of Segment Editor module but I can’t find the ‘specify geometry’ part…

simonoxen · August 7, 2023, 9:07am

hi, not an expert here, but this test seems to have examples that could help:

github.com

Slicer/Slicer/blob/7ef59614c2458e4f693ab77834e6726cf6ae0540/Modules/Loadable/Segmentations/Testing/Python/SegmentationWidgetsTest1.py#L171


      
              if imageData is None:
                  logging.error('Invalid input image data')
                  return False
              imageAccumulate = vtk.vtkImageAccumulate()
              imageAccumulate.SetInputData(imageData)
              imageAccumulate.SetIgnoreZero(1)
              imageAccumulate.Update()
              return imageAccumulate.GetVoxelCount()
          
          # ------------------------------------------------------------------------------
          def TestSection_03_qMRMLSegmentationGeometryWidget(self):
              logging.info('Test section 2: qMRMLSegmentationGeometryWidget')
          
              binaryLabelmapReprName = slicer.vtkSegmentationConverter.GetBinaryLabelmapRepresentationName()
              closedSurfaceReprName = slicer.vtkSegmentationConverter.GetClosedSurfaceRepresentationName()
          
              # Use MRHead and Tinypatient for testing
              import SampleData
              mrVolumeNode = SampleData.downloadSample("MRHead")
              [tinyVolumeNode, tinySegmentationNode] = SampleData.downloadSamples('TinyPatient')

Also using ROIs as inputs

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Is there any code to control 'specify geometry in Segment editor?

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