def __init__(self, scriptedEffect):
AbstractScriptedSegmentEditorEffect.__init__(self, scriptedEffect)
scriptedEffect.name = 'Threshold'
# Effect-specific members
import vtkITK
self.autoThresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
self.timer = qt.QTimer()
self.previewState = 0
self.previewStep = 1
self.previewSteps = 5
self.timer.connect('timeout()', self.preview)
self.previewPipelines = {}
self.setupPreviewDisplay()
def __init__(self, scriptedEffect):
AbstractScriptedSegmentEditorEffect.__init__(self, scriptedEffect)
scriptedEffect.name = 'Threshold'
# Effect-specific members
import vtkITK
self.autoThresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
self.timer = qt.QTimer()
self.previewState = 0
self.previewStep = 1
self.previewSteps = 5
self.timer.connect('timeout()', self.preview)
self.previewPipelines = {}
self.setupPreviewDisplay()
def run(self, inputVolume, outputSegmentation, smoothingKernelSize=3.0):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be segmented
:param outputSegmentation: segmentation to sore the result in
:param smoothingKernelSize: this is used for closing small holes in the segmentation
"""
if not inputVolume or not outputSegmentation:
raise ValueError("Input volume or output segmentation is invalid")
logging.info('Processing started')
# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(inputVolume.GetImageData())
thresholdCalculator.SetMethodToOtsu()
thresholdCalculator.Update()
boneThresholdValue = thresholdCalculator.GetThreshold()
volumeScalarRange = inputVolume.GetImageData().GetScalarRange()
logging.debug(
"Volume minimum = {0}, maximum = {1}, bone threshold = {2}".format(
volumeScalarRange[0], volumeScalarRange[1],
boneThresholdValue))
# Set up segmentation
outputSegmentation.CreateDefaultDisplayNodes()
outputSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
# To show segment editor widget (useful for debugging): segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
if not segmentEditorWidget.effectByName("Wrap Solidify"):
raise NotImplementedError(
"SurfaceWrapSolidify extension is required")
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(outputSegmentation)
segmentEditorWidget.setMasterVolumeNode(inputVolume)
# Create bone segment by thresholding
boneSegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"bone")
segmentEditorNode.SetSelectedSegmentID(boneSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(boneThresholdValue))
effect.setParameter("MaximumThreshold", str(volumeScalarRange[1]))
effect.self().onApply()
# Smooth bone segment (just to reduce solidification computation time)
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING")
effect.setParameter("KernelSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Solidify bone
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
effect.self().onApply()
# Create segment for cavity within bone region using thresholding
segmentEditorNode.SetOverwriteMode(
slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
segmentEditorNode.SetMaskMode(
slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideAllSegments)
cavitySegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"cavity")
segmentEditorNode.SetSelectedSegmentID(cavitySegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(volumeScalarRange[0]))
effect.setParameter("MaximumThreshold", str(boneThresholdValue))
effect.self().onApply()
# Cavity shrink
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", str(-smoothingKernelSize))
effect.self().onApply()
# Find largest cavity
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameterDefault("Operation", "KEEP_LARGEST_ISLAND")
effect.self().onApply()
# Cavity restore
segmentEditorNode.SetMaskMode(
slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideAllSegments
) # ensure we don't leak into bone
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Clean up
slicer.mrmlScene.RemoveNode(segmentEditorNode)
outputSegmentation.RemoveSegment(boneSegmentID)
segmentEditorWidget = None
logging.info('Processing completed')
def run(self,
inputVolume,
outputSegmentation,
smoothingKernelSize=3.0,
splitCavitiesDiameter=15.0):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be segmented
:param outputSegmentation: segmentation to sore the result in
:param smoothingKernelSize: this is used for closing small holes in the segmentation
:param splitCavitiesDiameter: plugs in holes smaller than splitCavitiesDiamater.
"""
if not inputVolume or not outputSegmentation:
raise ValueError("Input volume or output segmentation is invalid")
logging.info('Processing started')
# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(inputVolume.GetImageData())
# thresholdCalculator.SetMethodToOtsu() - this does not always work (see for example CTHead example data set)
thresholdCalculator.SetMethodToMaximumEntropy()
thresholdCalculator.Update()
boneThresholdValue = thresholdCalculator.GetThreshold()
volumeScalarRange = inputVolume.GetImageData().GetScalarRange()
logging.debug(
f"Volume minimum = {volumeScalarRange[0]}, maximum = {volumeScalarRange[1]}, bone threshold = {boneThresholdValue}"
)
# Set up segmentation
outputSegmentation.CreateDefaultDisplayNodes()
outputSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
# To show segment editor widget (useful for debugging): segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
if not segmentEditorWidget.effectByName("Wrap Solidify"):
raise NotImplementedError(
"SurfaceWrapSolidify extension is required")
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(outputSegmentation)
segmentEditorWidget.setMasterVolumeNode(inputVolume)
# Create bone segment by thresholding
boneSegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"bone")
segmentEditorNode.SetSelectedSegmentID(boneSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(boneThresholdValue))
effect.setParameter("MaximumThreshold", str(volumeScalarRange[1]))
effect.self().onApply()
# Smooth bone segment (just to reduce solidification computation time)
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING")
effect.setParameter("KernelSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Solidify bone
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("region", "largestCavity")
effect.setParameter("splitCavities",
"True" if splitCavitiesDiameter > 0 else "False")
effect.setParameter("splitCavitiesDiameter",
str(splitCavitiesDiameter)) # in mm
effect.setParameter("outputType", "newSegment") # in mm
effect.self().onApply()
# Clean up
#slicer.mrmlScene.RemoveNode(segmentEditorNode)
#outputSegmentation.RemoveSegment(boneSegmentID)
#segmentEditorWidget = None
logging.info('Processing completed')