def runGrowCut(self, masterImageData, seedLabelmap, outputLabelmap):
self.clippedMaskImageData = slicer.vtkOrientedImageData()
intensityBasedMasking = self.scriptedEffect.parameterSetNode(
).GetMasterVolumeIntensityMask()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
success = segmentationNode.GenerateEditMask(
self.clippedMaskImageData,
self.scriptedEffect.parameterSetNode().GetMaskMode(),
masterImageData, # reference geometry
"", # edited segment ID
self.scriptedEffect.parameterSetNode().GetMaskSegmentID() if
self.scriptedEffect.parameterSetNode().GetMaskSegmentID() else "",
masterImageData if intensityBasedMasking else None,
self.scriptedEffect.parameterSetNode(
).GetMasterVolumeIntensityMaskRange()
if intensityBasedMasking else None)
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment(
)
self.growCutFilter.SetIntensityVolume(masterImageData)
self.growCutFilter.SetSeedLabelVolume(seedLabelmap)
self.growCutFilter.SetMaskVolume(self.clippedMaskImageData)
self.growCutFilter.Update()
outputLabelmap.ShallowCopy(self.growCutFilter.GetOutput())
def computePreviewLabelmap(self, mergedImage, outputLabelmap):
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
if not self.growCutFilter:
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment(
)
self.growCutFilter.SetIntensityVolume(self.clippedMasterImageData)
self.growCutFilter.SetMaskVolume(self.clippedMaskImageData)
maskExtent = self.clippedMaskImageData.GetExtent(
) if self.clippedMaskImageData else None
if maskExtent is not None and maskExtent[0] <= maskExtent[
1] and maskExtent[2] <= maskExtent[3] and maskExtent[
4] <= maskExtent[5]:
# Mask is used.
# Grow the extent more, as background segment does not surround region of interest.
self.extentGrowthRatio = 0.50
else:
# No masking is used.
# Background segment is expected to surround region of interest, so narrower margin is enough.
self.extentGrowthRatio = 0.20
self.extentGrowthRatio
if self.scriptedEffect.parameterDefined("SeedLocalityFactor"):
seedLocalityFactor = self.scriptedEffect.doubleParameter(
"SeedLocalityFactor")
else:
seedLocalityFactor = 0.0
self.growCutFilter.SetDistancePenalty(seedLocalityFactor)
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
outputLabelmap.DeepCopy(self.growCutFilter.GetOutput())
def computePreviewLabelmap(self, mergedImage, outputLabelmap):
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
if not self.growCutFilter:
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment()
self.growCutFilter.SetIntensityVolume(self.clippedMasterImageData)
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
outputLabelmap.DeepCopy( self.growCutFilter.GetOutput() )
def computePreviewLabelmap(self, mergedImage, outputLabelmap):
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
if not self.growCutFilter:
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment(
)
self.growCutFilter.SetIntensityVolume(self.clippedMasterImageData)
self.growCutFilter.SetMaskVolume(self.clippedMaskImageData)
maskExtent = self.clippedMaskImageData.GetExtent(
) if self.clippedMaskImageData else None
if maskExtent is not None and maskExtent[0] <= maskExtent[
1] and maskExtent[2] <= maskExtent[3] and maskExtent[
4] <= maskExtent[5]:
# Mask is used.
# Grow the extent more, as background segment does not surround region of interest.
self.extentGrowthRatio = 0.50
else:
# No masking is used.
# Background segment is expected to surround region of interest, so narrower margin is enough.
self.extentGrowthRatio = 0.20
if self.scriptedEffect.parameterDefined("SeedLocalityFactor"):
seedLocalityFactor = self.scriptedEffect.doubleParameter(
"SeedLocalityFactor")
else:
seedLocalityFactor = 0.0
self.growCutFilter.SetDistancePenalty(seedLocalityFactor)
self.growCutFilter.SetSeedLabelVolume(mergedImage)
startTime = time.time()
self.growCutFilter.Update()
logging.info(
'Grow-cut operation on volume of {}x{}x{} voxels was completed in {:3.1f} seconds.'
.format(self.clippedMasterImageData.GetDimensions()[0],
self.clippedMasterImageData.GetDimensions()[1],
self.clippedMasterImageData.GetDimensions()[2],
time.time() - startTime))
outputLabelmap.DeepCopy(self.growCutFilter.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
mergedImage.GetImageToWorldMatrix(imageToWorld)
outputLabelmap.SetImageToWorldMatrix(imageToWorld)
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
method = self.scriptedEffect.parameter("AutoCompleteMethod")
previewNode = self.scriptedEffect.parameterSetNode().GetNodeReference(ResultPreviewNodeReferenceRole)
if not previewNode or not self.mergedLabelmapGeometryImage \
or (method == GROWCUT and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
minimumNumberOfSegments = 2 if method == GROWCUT else 1
if self.selectedSegmentIds.GetNumberOfValues() < minimumNumberOfSegments:
logging.info("Auto-complete operation skipped: at least {0} visible segments are required".format(minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.setPreviewOpacity(0.6)
if method == GROWCUT:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
if method == MORPHOLOGICAL_SLICE_INTERPOLATION:
import vtkITK
interpolator = vtkITK.vtkITKMorphologicalContourInterpolator()
interpolator.SetInputData(mergedImage)
interpolator.Update()
outputLabelmap.DeepCopy(interpolator.GetOutput())
elif method == GROWCUT:
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
# if self.growCutFilter exists but previewNode is empty then probably the scene was closed
# while in preview mode
if self.growCutFilter:
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
else:
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment()
self.growCutFilter.SetIntensityVolume(self.clippedMasterImageData)
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
outputLabelmap.DeepCopy( self.growCutFilter.GetOutput() )
else:
logging.error("Invalid auto-complete method {0}".format(smoothingMethod))
return
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
previewNode.GetDisplayNode().SetSegmentColor(segmentID, segmentationNode.GetDisplayNode().GetSegmentColor(segmentID))
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
def preview(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
method = self.scriptedEffect.parameter("AutoCompleteMethod")
previewNode = self.scriptedEffect.parameterSetNode().GetNodeReference(ResultPreviewNodeReferenceRole)
if not previewNode or not self.mergedLabelmapGeometryImage \
or (method == GROWCUT and not self.clippedMasterImageData):
self.reset()
# Compute merged labelmap extent (effective extent slightly expanded)
self.selectedSegmentIds = vtk.vtkStringArray()
segmentationNode.GetDisplayNode().GetVisibleSegmentIDs(self.selectedSegmentIds)
minimumNumberOfSegments = 2 if method == GROWCUT else 1
if self.selectedSegmentIds.GetNumberOfValues() < minimumNumberOfSegments:
logging.info("Auto-complete operation skipped: at least {0} visible segments are required".format(minimumNumberOfSegments))
return
if not self.mergedLabelmapGeometryImage:
self.mergedLabelmapGeometryImage = vtkSegmentationCore.vtkOrientedImageData()
commonGeometryString = segmentationNode.GetSegmentation().DetermineCommonLabelmapGeometry(
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.selectedSegmentIds)
if not commonGeometryString:
logging.info("Auto-complete operation skipped: all visible segments are empty")
return
vtkSegmentationCore.vtkSegmentationConverter.DeserializeImageGeometry(commonGeometryString, self.mergedLabelmapGeometryImage)
masterImageExtent = masterImageData.GetExtent()
labelsEffectiveExtent = self.mergedLabelmapGeometryImage.GetExtent()
margin = [17, 17, 17]
labelsExpandedExtent = [
max(masterImageExtent[0], labelsEffectiveExtent[0]-margin[0]),
min(masterImageExtent[1], labelsEffectiveExtent[1]+margin[0]),
max(masterImageExtent[2], labelsEffectiveExtent[2]-margin[1]),
min(masterImageExtent[3], labelsEffectiveExtent[3]+margin[1]),
max(masterImageExtent[4], labelsEffectiveExtent[4]-margin[2]),
min(masterImageExtent[5], labelsEffectiveExtent[5]+margin[2]) ]
self.mergedLabelmapGeometryImage.SetExtent(labelsExpandedExtent)
previewNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLSegmentationNode')
previewNode.UnRegister(None)
previewNode = slicer.mrmlScene.AddNode(previewNode)
previewNode.CreateDefaultDisplayNodes()
previewNode.GetDisplayNode().SetVisibility2DOutline(False)
if segmentationNode.GetParentTransformNode():
previewNode.SetAndObserveTransformNodeID(segmentationNode.GetParentTransformNode().GetID())
self.scriptedEffect.parameterSetNode().SetNodeReferenceID(ResultPreviewNodeReferenceRole, previewNode.GetID())
self.setPreviewOpacity(0.6)
if method == GROWCUT:
self.clippedMasterImageData = vtkSegmentationCore.vtkOrientedImageData()
masterImageClipper = vtk.vtkImageConstantPad()
masterImageClipper.SetInputData(masterImageData)
masterImageClipper.SetOutputWholeExtent(self.mergedLabelmapGeometryImage.GetExtent())
masterImageClipper.Update()
self.clippedMasterImageData.ShallowCopy(masterImageClipper.GetOutput())
self.clippedMasterImageData.CopyDirections(self.mergedLabelmapGeometryImage)
previewNode.SetName(segmentationNode.GetName()+" preview")
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_EFFECTIVE_SEGMENTS, self.mergedLabelmapGeometryImage, self.selectedSegmentIds)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
if method == MORPHOLOGICAL_SLICE_INTERPOLATION:
import vtkITK
interpolator = vtkITK.vtkITKMorphologicalContourInterpolator()
interpolator.SetInputData(mergedImage)
interpolator.Update()
outputLabelmap.DeepCopy(interpolator.GetOutput())
elif method == GROWCUT:
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
# if self.growCutFilter exists but previewNode is empty then probably the scene was closed
# while in preview mode
if self.growCutFilter:
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
else:
self.growCutFilter = vtkSlicerSegmentationsModuleLogic.vtkImageGrowCutSegment()
self.growCutFilter.SetIntensityVolume(self.clippedMasterImageData)
self.growCutFilter.SetSeedLabelVolume(mergedImage)
self.growCutFilter.Update()
outputLabelmap.DeepCopy( self.growCutFilter.GetOutput() )
else:
logging.error("Invalid auto-complete method {0}".format(smoothingMethod))
return
# Write output segmentation results in segments
for index in xrange(self.selectedSegmentIds.GetNumberOfValues()):
segmentID = self.selectedSegmentIds.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Disable save with scene?
# Get only the label of the current segment from the output image
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(1)
thresh.SetOutValue(0)
labelValue = index + 1 # n-th segment label value = n + 1 (background label value is 0)
thresh.ThresholdBetween(labelValue, labelValue);
thresh.SetOutputScalarType(vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(outputLabelmap)
thresh.Update()
# Write label to segment
newSegmentLabelmap = vtkSegmentationCore.vtkOrientedImageData()
newSegmentLabelmap.ShallowCopy(thresh.GetOutput())
newSegmentLabelmap.CopyDirections(mergedImage)
newSegment = previewNode.GetSegmentation().GetSegment(segmentID)
if not newSegment:
newSegment = vtkSegmentationCore.vtkSegment()
newSegment.SetName(segment.GetName())
color = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
newSegment.SetColor(color)
previewNode.GetSegmentation().AddSegment(newSegment, segmentID)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, previewNode, segmentID)
self.updateGUIFromMRML()
