def growCut(self):
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
background = self.getScopedBackground()
gestureInput = self.getScopedLabelInput()
growCutOutput = self.getScopedLabelOutput()
if not self.areInputsValid():
logging.warning(self.getInvalidInputsMessage())
# set the make a zero-valued volume for the output
# TODO: maybe this should be done in numpy as a one-liner
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType( vtk.VTK_SHORT )
if vtk.VTK_MAJOR_VERSION <= 5:
thresh.SetInput( gestureInput )
else:
thresh.SetInputData( gestureInput )
thresh.SetOutput( growCutOutput )
thresh.Update()
growCutOutput.DeepCopy( gestureInput )
if vtk.VTK_MAJOR_VERSION <= 5:
growCutFilter.SetInput( 0, background )
growCutFilter.SetInput( 1, gestureInput )
growCutFilter.SetInput( 2, growCutOutput )
else:
growCutFilter.SetInputData( 0, background )
growCutFilter.SetInputData( 1, gestureInput )
growCutFilter.SetInputConnection( 2, thresh.GetOutputPort() )
objectSize = 5. # TODO: this is a magic number
contrastNoiseRatio = 0.8 # TODO: this is a magic number
priorStrength = 0.003 # TODO: this is a magic number
segmented = 2 # TODO: this is a magic number
conversion = 1000 # TODO: this is a magic number
spacing = gestureInput.GetSpacing()
voxelVolume = reduce(lambda x,y: x*y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1./3.
oSize = int(round(pow(voxelNumber,cubeRoot)))
growCutFilter.SetObjectSize( oSize )
growCutFilter.SetContrastNoiseRatio( contrastNoiseRatio )
growCutFilter.SetPriorSegmentConfidence( priorStrength )
growCutFilter.Update()
growCutOutput.DeepCopy( growCutFilter.GetOutput() )
self.applyScopedLabel()
def growCut(background, gestureInput, growCutOutput):
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
# set the make a zero-valued volume for the output
# TODO: maybe this should be done in numpy as a one-liner
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType(vtk.VTK_SHORT)
thresh.SetInputData(gestureInput)
thresh.SetOutput(growCutOutput)
thresh.Update()
growCutOutput.DeepCopy(gestureInput)
growCutFilter.SetInputData(0, background)
growCutFilter.SetInputData(1, gestureInput)
growCutFilter.SetInputConnection(2, thresh.GetOutputPort())
objectSize = 10. # TODO: this is a magic number
contrastNoiseRatio = 0.8 # TODO: this is a magic number
priorStrength = 0.003 # TODO: this is a magic number
segmented = 2 # TODO: this is a magic number
conversion = 1000 # TODO: this is a magic number
spacing = gestureInput.GetSpacing()
voxelVolume = reduce(lambda x, y: x * y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1. / 3.
oSize = int(round(pow(voxelNumber, cubeRoot)))
growCutFilter.SetObjectSize(oSize)
growCutFilter.SetContrastNoiseRatio(contrastNoiseRatio)
growCutFilter.SetPriorSegmentConfidence(priorStrength)
growCutFilter.Update()
growCutOutput.DeepCopy(growCutFilter.GetOutput())
return growCutOutput
def growCut(background,gestureInput,growCutOutput): growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter() # set the make a zero-valued volume for the output # TODO: maybe this should be done in numpy as a one-liner thresh = vtk.vtkImageThreshold() thresh.ReplaceInOn() thresh.ReplaceOutOn() thresh.SetInValue(0) thresh.SetOutValue(0) thresh.SetOutputScalarType( vtk.VTK_SHORT ) thresh.SetInputData( gestureInput ) thresh.SetOutput( growCutOutput ) thresh.Update() growCutOutput.DeepCopy( gestureInput ) growCutFilter.SetInputData( 0, background ) growCutFilter.SetInputData( 1, gestureInput ) growCutFilter.SetInputConnection( 2, thresh.GetOutputPort() ) objectSize = 10. # TODO: this is a magic number contrastNoiseRatio = 0.8 # TODO: this is a magic number priorStrength = 0.003 # TODO: this is a magic number segmented = 2 # TODO: this is a magic number conversion = 1000 # TODO: this is a magic number spacing = gestureInput.GetSpacing() voxelVolume = reduce(lambda x,y: x*y, spacing) voxelAmount = objectSize / voxelVolume voxelNumber = round(voxelAmount) * conversion cubeRoot = 1./3. oSize = int(round(pow(voxelNumber,cubeRoot))) growCutFilter.SetObjectSize( oSize ) growCutFilter.SetContrastNoiseRatio( contrastNoiseRatio ) growCutFilter.SetPriorSegmentConfidence( priorStrength ) growCutFilter.Update() growCutOutput.DeepCopy( growCutFilter.GetOutput() ) return growCutOutput
def growCut(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.DeepCopy(imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(masterImageData) # Copy geometry
masterImageData = masterImageDataShort
# Generate merged labelmap as input to GrowCut
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(mergedImage, vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS, masterImageData)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType( vtk.VTK_SHORT )
thresh.SetInputData( mergedImage )
thresh.SetOutput( outputLabelmap )
thresh.Update()
outputLabelmap.DeepCopy( mergedImage ) #TODO: It was thresholded just above, why deep copy now?
# Perform grow cut
import vtkITK
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
growCutFilter.SetInputData( 0, masterImageData )
growCutFilter.SetInputData( 1, mergedImage )
#TODO: This call sets an empty image for the optional "previous segmentation", and
# is apparently needed for the first segmentation too. Why?
growCutFilter.SetInputConnection( 2, thresh.GetOutputPort() )
#TODO: These are magic numbers inherited from EditorLib/GrowCut.py
objectSize = 5.
contrastNoiseRatio = 0.8
priorStrength = 0.003
segmented = 2
conversion = 1000
spacing = mergedImage.GetSpacing()
voxelVolume = reduce(lambda x,y: x*y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1./3.
oSize = int(round(pow(voxelNumber,cubeRoot)))
growCutFilter.SetObjectSize( oSize )
growCutFilter.SetContrastNoiseRatio( contrastNoiseRatio )
growCutFilter.SetPriorSegmentConfidence( priorStrength )
growCutFilter.Update()
outputLabelmap.DeepCopy( growCutFilter.GetOutput() )
# Write output segmentation results in segments
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
for index in xrange(segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Get label corresponding to segment in merged labelmap (and so GrowCut output)
colorIndexStr = vtk.mutable("")
tagFound = segment.GetTag(slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(), colorIndexStr);
if not tagFound:
logging.error('Failed to apply GrowCut result on segment ' + segmentID)
continue
colorIndex = int(colorIndexStr.get())
# 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)
thresh.ThresholdBetween(colorIndex, colorIndex);
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)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(newSegmentLabelmap, segmentationNode, segmentID, slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE, newSegmentLabelmap.GetExtent())
def growCut(self):
# Get master volume image data
import vtkSegmentationCorePython as vtkSegmentationCore
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Get segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
# Cast master image if not short
if masterImageData.GetScalarType() != vtk.VTK_SHORT:
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(masterImageData)
imageCast.SetOutputScalarTypeToShort()
imageCast.ClampOverflowOn()
imageCast.Update()
masterImageDataShort = vtkSegmentationCore.vtkOrientedImageData()
masterImageDataShort.DeepCopy(
imageCast.GetOutput()) # Copy image data
masterImageDataShort.CopyDirections(
masterImageData) # Copy geometry
masterImageData = masterImageDataShort
# Generate merged labelmap as input to GrowCut
mergedImage = vtkSegmentationCore.vtkOrientedImageData()
segmentationNode.GenerateMergedLabelmapForAllSegments(
mergedImage,
vtkSegmentationCore.vtkSegmentation.EXTENT_UNION_OF_SEGMENTS,
masterImageData)
# Make a zero-valued volume for the output
outputLabelmap = vtkSegmentationCore.vtkOrientedImageData()
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(0)
thresh.SetOutValue(0)
thresh.SetOutputScalarType(vtk.VTK_SHORT)
thresh.SetInputData(mergedImage)
thresh.SetOutput(outputLabelmap)
thresh.Update()
outputLabelmap.DeepCopy(
mergedImage
) #TODO: It was thresholded just above, why deep copy now?
# Perform grow cut
import vtkITK
growCutFilter = vtkITK.vtkITKGrowCutSegmentationImageFilter()
growCutFilter.SetInputData(0, masterImageData)
growCutFilter.SetInputData(1, mergedImage)
#TODO: This call sets an empty image for the optional "previous segmentation", and
# is apparently needed for the first segmentation too. Why?
growCutFilter.SetInputConnection(2, thresh.GetOutputPort())
#TODO: These are magic numbers inherited from EditorLib/GrowCut.py
objectSize = 5.
contrastNoiseRatio = 0.8
priorStrength = 0.003
segmented = 2
conversion = 1000
spacing = mergedImage.GetSpacing()
voxelVolume = reduce(lambda x, y: x * y, spacing)
voxelAmount = objectSize / voxelVolume
voxelNumber = round(voxelAmount) * conversion
cubeRoot = 1. / 3.
oSize = int(round(pow(voxelNumber, cubeRoot)))
growCutFilter.SetObjectSize(oSize)
growCutFilter.SetContrastNoiseRatio(contrastNoiseRatio)
growCutFilter.SetPriorSegmentConfidence(priorStrength)
growCutFilter.Update()
outputLabelmap.DeepCopy(growCutFilter.GetOutput())
# Write output segmentation results in segments
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
for index in xrange(segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(index)
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
# Get label corresponding to segment in merged labelmap (and so GrowCut output)
colorIndexStr = vtk.mutable("")
tagFound = segment.GetTag(
slicer.vtkMRMLSegmentationDisplayNode.GetColorIndexTag(),
colorIndexStr)
if not tagFound:
logging.error('Failed to apply GrowCut result on segment ' +
segmentID)
continue
colorIndex = int(colorIndexStr.get())
# 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)
thresh.ThresholdBetween(colorIndex, colorIndex)
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)
slicer.vtkSlicerSegmentationsModuleLogic.SetBinaryLabelmapToSegment(
newSegmentLabelmap, segmentationNode, segmentID,
slicer.vtkSlicerSegmentationsModuleLogic.MODE_REPLACE,
newSegmentLabelmap.GetExtent())
