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functions_baffle planner.py
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functions_baffle planner.py
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def subtract():
"""
Subtracts the skull (first segment) from the baffle (second segment)
"""
masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')
segmentationNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLSegmentationNode')
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
#getnames
bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
skullname = segmentationNode.GetSegmentation().GetNthSegment(0).GetName()#get name of skull
##run subtaction
segmentEditorWidget.setActiveEffectByName('Logical operators')
effect = segmentEditorWidget.activeEffect()
segmentEditorNode.SetSelectedSegmentID(bafflename)######perform operations
effect.setParameter("Operation", "SUBTRACT")
effect.setParameter("ModifierSegmentID", skullname)#subtract this selection
effect.self().onApply()
#remove segment editor connection
segmentEditorWidget = None
slicer.mrmlScene.RemoveNode(segmentEditorNode)
def smooth(mm):
"""
Smooth the baffle (the second segment) using median smoothing. Takes an argument in mm.
"""
masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')
segmentationNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLSegmentationNode')
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
#getnames of segments in segmentation
bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
skullname = segmentationNode.GetSegmentation().GetNthSegment(0).GetName()#get name of skull
##run Smoothing
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
segmentEditorNode.SetSelectedSegmentID(bafflename)
effect.setParameter("SmoothingMethod", "MEDIAN")
effect.setParameter("KernelSizeMm", mm)
effect.self().onApply()
#remove segment editor connection
segmentEditorWidget = None
slicer.mrmlScene.RemoveNode(segmentEditorNode)
def connect():
"""
Connects the segmentation and volume nodes together in preparation for subsequent functions. Adds a segmentation node to the scene
"""
global masterVolumeNode
#Connect the volumes and segmentation to allow programatic access to model-segmentation conversion and segmentation effects
masterVolumeNode = slicer.mrmlScene.GetNthNodeByClass(0, 'vtkMRMLScalarVolumeNode')#detects the first scalar volume
global segmentationNode
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
def modelToSeg():
"""
Converts model and baffle to segmentations. Takes the first and second models in the scene (besides from the 3 slice models already present in the
scene by default). Skull should be the first model, baffle the second.
"""
modelskull = slicer.mrmlScene.GetNthNodeByClass(3, 'vtkMRMLModelNode')
modelbaffle = slicer.mrmlScene.GetNthNodeByClass(4, 'vtkMRMLModelNode')
# Import the model into the segmentation node
slicer.modules.segmentations.logic().ImportModelToSegmentationNode(modelskull, segmentationNode)
slicer.modules.segmentations.logic().ImportModelToSegmentationNode(modelbaffle, segmentationNode)
def seg_to_obj(path, segmentationNode):
"""
Convert baffle to obj. Converts the second segmentation. Takes as arguments the name of the segmentation("Segmentation" by default), and saves an obj file as the name of the segmentation .
Example usage: seg_to_obj("c:/tmp", "Segmentation")
"""
segmentationNode = getNode(segmentationNode)
bafflename = segmentationNode.GetSegmentation().GetNthSegment(1).GetName()#get name of baffle
segmentIds = vtk.vtkStringArray()
segmentIds.InsertNextValue(bafflename)
# Write to STL file
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsClosedSurfaceRepresentationToFiles(path, segmentationNode, segmentIds, "OBJ")