def removeIslands(self):
#
# change the label values based on the parameter node
#
if not self.sliceLogic:
self.sliceLogic = self.editUtil.getSliceLogic()
parameterNode = self.editUtil.getParameterNode()
minimumSize = int(parameterNode.GetParameter("IslandEffect,minimumSize"))
fullyConnected = bool(parameterNode.GetParameter("IslandEffect,fullyConnected"))
label = self.editUtil.getLabel()
# first, create an inverse binary version of the image
# so that islands inside segemented object will be detected, along
# with a big island of the background
preThresh = vtk.vtkImageThreshold()
preThresh.SetInValue( 0 )
preThresh.SetOutValue( 1 )
preThresh.ReplaceInOn()
preThresh.ReplaceOutOn()
preThresh.ThresholdBetween( label,label )
preThresh.SetInput( self.getScopedLabelInput() )
preThresh.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInput( preThresh.GetOutput() )
islandMath.SetFullyConnected( fullyConnected )
islandMath.SetMinimumSize( minimumSize )
# TODO: $this setProgressFilter $islandMath "Calculating Islands..."
islandMath.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# now rethreshold so that everything which is not background becomes the label
postThresh = vtk.vtkImageThreshold()
postThresh.SetInValue( label )
postThresh.SetOutValue( 0 )
postThresh.ReplaceInOn()
postThresh.ReplaceOutOn()
postThresh.ThresholdBetween( 0, 0 )
postThresh.SetOutputScalarTypeToShort()
postThresh.SetInput( islandMath.GetOutput() )
postThresh.SetOutput( self.getScopedLabelOutput() )
# TODO $this setProgressFilter $postThresh "Applying to Label Map..."
postThresh.Update()
self.applyScopedLabel()
def onApply(self):
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(
selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
segmentationNode.GetSegmentation().RemoveSegment(selectedSegmentID)
qt.QApplication.restoreOverrideCursor()
def onApply(self):
# TODO:
# self.logic.undoRedo = self.undoRedo
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" % (islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode(
multiLabelImage, segmentationNode, selectedSegmentName
)
# Set labelmap visibility to outline for the new segments
displayNode = segmentationNode.GetDisplayNode()
# for index in xrange(1,islandCount+1):
# segmentID = selectedSegmentName + "_" + str(index)
# displayNode.SetSegmentVisibility2DFill(segmentID, False)
# displayNode.SetSegmentVisibility2DOutline(segmentID, True)
displayNode.SetSegmentVisibility(selectedSegmentID, False)
def onApply(self):
#TODO:
#self.logic.undoRedo = self.undoRedo
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
# Set labelmap visibility to outline for the new segments
displayNode = segmentationNode.GetDisplayNode()
#for index in xrange(1,islandCount+1):
# segmentID = selectedSegmentName + "_" + str(index)
# displayNode.SetSegmentVisibility2DFill(segmentID, False)
# displayNode.SetSegmentVisibility2DOutline(segmentID, True)
displayNode.SetSegmentVisibility(selectedSegmentID, False)
def onApply(self):
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get parameters
fullyConnected = self.scriptedEffect.integerParameter("FullyConnected")
minimumSize = self.scriptedEffect.integerParameter("MinimumSize")
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedLong()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# Note that island operation happens in unsigned long space
# but the segment editor works in unsigned char
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToUnsignedChar()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(castOut.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName )
segmentationNode.GetSegmentation().RemoveSegment(selectedSegmentID)
qt.QApplication.restoreOverrideCursor()
def removeIslands(self):
#
# change the label values based on the parameter node
#
if not self.sliceLogic:
self.sliceLogic = self.editUtil.getSliceLogic()
parameterNode = self.editUtil.getParameterNode()
minimumSize = int(
parameterNode.GetParameter("IslandEffect,minimumSize"))
fullyConnected = bool(
parameterNode.GetParameter("IslandEffect,fullyConnected"))
label = self.editUtil.getLabel()
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castIn.SetInput(self.getScopedLabelInput())
else:
castIn.SetInputData(self.getScopedLabelInput())
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
if vtk.VTK_MAJOR_VERSION <= 5:
islandMath.SetInput(castIn.GetOutput())
else:
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# TODO: $this setProgressFilter $islandMath "Calculating Islands..."
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castOut.SetInput(islandMath.GetOutput())
else:
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToShort()
castOut.SetOutput(self.getScopedLabelOutput())
# TODO $this setProgressFilter $postThresh "Applying to Label Map..."
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
self.applyScopedLabel()
castOut.SetOutput(None)
def removeIslands(self):
#
# change the label values based on the parameter node
#
if not self.sliceLogic:
self.sliceLogic = self.editUtil.getSliceLogic()
parameterNode = self.editUtil.getParameterNode()
minimumSize = int(parameterNode.GetParameter("IslandEffect,minimumSize"))
fullyConnected = bool(parameterNode.GetParameter("IslandEffect,fullyConnected"))
label = self.editUtil.getLabel()
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castIn.SetInput( self.getScopedLabelInput() )
else:
castIn.SetInputData( self.getScopedLabelInput() )
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
if vtk.VTK_MAJOR_VERSION <= 5:
islandMath.SetInput( castIn.GetOutput() )
else:
islandMath.SetInputConnection( castIn.GetOutputPort() )
islandMath.SetFullyConnected( fullyConnected )
islandMath.SetMinimumSize( minimumSize )
# TODO: $this setProgressFilter $islandMath "Calculating Islands..."
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castOut.SetInput( islandMath.GetOutput() )
else:
castOut.SetInputConnection( islandMath.GetOutputPort() )
castOut.SetOutputScalarTypeToShort()
castOut.SetOutput( self.getScopedLabelOutput() )
# TODO $this setProgressFilter $postThresh "Applying to Label Map..."
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
self.applyScopedLabel()
castOut.SetOutput( None )
def identIslands(self):
inputImage=self.volume.GetImageData()
labelImage=self.label.GetImageData()
#labelImage.SetSpacing(self.label.GetSpacing())
IJKToRAS = vtk.vtkMatrix4x4()
self.volume.GetIJKToRASMatrix(IJKToRAS)
self.label.SetIJKToRASMatrix(IJKToRAS)
eV=slicer.vtkFillVOIImageFilter()
eV.SetfillValue(0)
eV.SetInputData(inputImage)
if self.sliceidx>0:
VOIpre=[0,inputImage.GetDimensions()[0],0,inputImage.GetDimensions()[1],0,self.sliceidx-1]
eV.AddVOI(VOIpre)
if self.sliceidx<inputImage.GetDimensions()[2]:
VOIpost=[0,inputImage.GetDimensions()[0],0,inputImage.GetDimensions()[1],self.sliceidx+1,inputImage.GetDimensions()[2]]
eV.AddVOI(VOIpost)
eV.Update()
slice=eV.GetOutput()
thresh = vtk.vtkImageThreshold()
thresh.SetInputData(slice)
thresh.ThresholdBetween(self.thrRange[0],self.thrRange[1])
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.SetOutputScalarType(vtk.VTK_SHORT)
thresh.Modified()
thresh.Update()
islandM=vtkITK.vtkITKIslandMath()
islandM.SetInputData(thresh.GetOutput())
islandM.Update()
labelImage.DeepCopy(islandM.GetOutput())
def splitSegments(self, minimumSize=0, maxNumberOfSegments=0, split=True):
"""
minimumSize: if 0 then it means that all islands are kept, regardless of size
maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
"""
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedInt()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(False)
islandMath.SetMinimumSize(minimumSize)
islandMath.Update()
# Create a separate image for the first (largest) island
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
if split:
thresh.ThresholdBetween(1, 1)
else:
if maxNumberOfSegments != 0:
thresh.ThresholdBetween(1, maxNumberOfSegments)
else:
thresh.ThresholdByUpper(1)
thresh.SetInputData(islandMath.GetOutput())
thresh.SetOutValue(backgroundValue)
thresh.SetInValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
largestIslandImage = vtkSegmentationCore.vtkOrientedImageData()
largestIslandImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
largestIslandImage.SetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
if split and (maxNumberOfSegments != 1):
thresh2 = vtk.vtkImageThreshold()
# 0 is background, 1 is largest island; we need label 2 and higher
if maxNumberOfSegments != 0:
thresh2.ThresholdBetween(2, maxNumberOfSegments)
else:
thresh2.ThresholdByUpper(2)
thresh2.SetInputData(islandMath.GetOutput())
thresh2.SetOutValue(backgroundValue)
thresh2.ReplaceInOff()
thresh2.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(thresh2.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
selectedSegmentIndex = segmentationNode.GetSegmentation(
).GetSegmentIndex(selectedSegmentID)
insertBeforeSegmentID = segmentationNode.GetSegmentation(
).GetNthSegmentID(selectedSegmentIndex + 1)
selectedSegmentName = segmentationNode.GetSegmentation(
).GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName+" -", insertBeforeSegmentID )
self.scriptedEffect.modifySelectedSegmentByLabelmap(
largestIslandImage,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def removeIslands(self):
#
# change the label values based on the parameter node
#
if not self.sliceLogic:
self.sliceLogic = self.editUtil.getSliceLogic()
parameterNode = self.editUtil.getParameterNode()
minimumSize = int(parameterNode.GetParameter("IslandEffect,minimumSize"))
fullyConnected = bool(parameterNode.GetParameter("IslandEffect,fullyConnected"))
label = self.editUtil.getLabel()
# first, create an inverse binary version of the image
# so that islands inside segemented object will be detected, along
# with a big island of the background
preThresh = vtk.vtkImageThreshold()
preThresh.SetInValue( 0 )
preThresh.SetOutValue( 1 )
preThresh.ReplaceInOn()
preThresh.ReplaceOutOn()
preThresh.ThresholdBetween( label,label )
preThresh.SetInput( self.getScopedLabelInput() )
preThresh.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInput( preThresh.GetOutput() )
islandMath.SetFullyConnected( fullyConnected )
islandMath.SetMinimumSize( minimumSize )
# TODO: $this setProgressFilter $islandMath "Calculating Islands..."
islandMath.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
if islandCount == 0:
return
bgPixel = self.findNonZeroBorderPixel(islandMath.GetOutput())
# now rethreshold so that everything which is not background becomes the label
postThresh = vtk.vtkImageThreshold()
postThresh.SetInValue( 0 )
postThresh.SetOutValue( label )
postThresh.ReplaceInOn()
postThresh.ReplaceOutOn()
postThresh.ThresholdBetween( bgPixel, bgPixel )
postThresh.SetOutputScalarTypeToShort()
postThresh.SetInput( islandMath.GetOutput() )
postThresh.SetOutput( self.getScopedLabelOutput() )
# TODO $this setProgressFilter $postThresh "Applying to Label Map..."
postThresh.Update()
self.applyScopedLabel()
if False:
# some code for debugging - leave it in
layerLogic = self.sliceLogic.GetLabelLayer()
labelNode = layerLogic.GetVolumeNode()
volumesLogic = slicer.modules.volumes.logic()
thresh1 = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode, 'thres1')
islands = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode, 'islands')
thresh2 = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode, 'thres2')
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToShort()
cast.SetInput(preThresh.GetOutput())
cast.Update()
thresh1.SetAndObserveImageData(cast.GetOutput())
cast2 = vtk.vtkImageCast()
cast2.SetOutputScalarTypeToShort()
cast2.SetInput(islandMath.GetOutput())
cast2.Update()
islands.SetAndObserveImageData(cast2.GetOutput())
thresh2.SetAndObserveImageData(postThresh.GetOutput())
def splitSegments(self, minimumSize=0, maxNumberOfSegments=0, split=True):
"""
minimumSize: if 0 then it means that all islands are kept, regardless of size
maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
"""
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedInt()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(False)
islandMath.SetMinimumSize(minimumSize)
islandMath.Update()
islandImage = slicer.vtkOrientedImageData()
islandImage.ShallowCopy(islandMath.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
islandImage.SetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
baseSegmentName = "Label"
selectedSegmentID = self.scriptedEffect.parameterSetNode(
).GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode(
).GetSegmentationNode()
with slicer.util.NodeModify(segmentationNode):
segmentation = segmentationNode.GetSegmentation()
selectedSegment = segmentation.GetSegment(selectedSegmentID)
selectedSegmentName = selectedSegment.GetName()
if selectedSegmentName is not None and selectedSegmentName != "":
baseSegmentName = selectedSegmentName
labelValues = vtk.vtkIntArray()
slicer.vtkSlicerSegmentationsModuleLogic.GetAllLabelValues(
labelValues, islandImage)
# Erase segment from in original labelmap.
# Individuall islands will be added back later.
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(selectedSegmentLabelmap)
threshold.ThresholdBetween(0, 0)
threshold.SetInValue(0)
threshold.SetOutValue(0)
threshold.Update()
emptyLabelmap = slicer.vtkOrientedImageData()
emptyLabelmap.ShallowCopy(threshold.GetOutput())
emptyLabelmap.CopyDirections(selectedSegmentLabelmap)
self.scriptedEffect.modifySegmentByLabelmap(
segmentationNode, selectedSegmentID, emptyLabelmap,
slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
for i in range(labelValues.GetNumberOfTuples()):
if (maxNumberOfSegments > 0 and i >= maxNumberOfSegments):
# We only care about the segments up to maxNumberOfSegments.
# If we do not want to split segments, we only care about the first.
break
labelValue = int(labelValues.GetTuple1(i))
segment = selectedSegment
segmentID = selectedSegmentID
if i != 0 and split:
segment = slicer.vtkSegment()
name = baseSegmentName + "_" + str(i + 1)
segment.SetName(name)
segment.AddRepresentation(
slicer.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName(),
selectedSegment.GetRepresentation(
slicer.vtkSegmentationConverter.
GetSegmentationBinaryLabelmapRepresentationName()))
segmentation.AddSegment(segment)
segmentID = segmentation.GetSegmentIdBySegment(segment)
segment.SetLabelValue(
segmentation.GetUniqueLabelValueForSharedLabelmap(
selectedSegmentID))
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(islandMath.GetOutput())
threshold.ThresholdBetween(labelValue, labelValue)
threshold.SetInValue(1)
threshold.SetOutValue(0)
threshold.Update()
modificationMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd
if i == 0:
modificationMode = slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet
# Create oriented image data from output
modifierImage = slicer.vtkOrientedImageData()
modifierImage.DeepCopy(threshold.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
modifierImage.SetGeometryFromImageToWorldMatrix(
selectedSegmentLabelmapImageToWorldMatrix)
# We could use a single slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode
# method call to import all the resulting segments at once but that would put all the imported segments
# in a new layer. By using modifySegmentByLabelmap, the number of layers will not increase.
self.scriptedEffect.modifySegmentByLabelmap(
segmentationNode, segmentID, modifierImage,
modificationMode)
qt.QApplication.restoreOverrideCursor()
def splitSegments(self, minimumSize = 0, maxNumberOfSegments = 0, split = True):
"""
minimumSize: if 0 then it means that all islands are kept, regardless of size
maxNumberOfSegments: if 0 then it means that all islands are kept, regardless of how many
"""
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.scriptedEffect.saveStateForUndo()
# Get modifier labelmap
selectedSegmentLabelmap = self.scriptedEffect.selectedSegmentLabelmap()
castIn = vtk.vtkImageCast()
castIn.SetInputData(selectedSegmentLabelmap)
castIn.SetOutputScalarTypeToUnsignedInt()
# Identify the islands in the inverted volume and
# find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(False)
islandMath.SetMinimumSize(minimumSize)
islandMath.Update()
# Create a separate image for the first (largest) island
labelValue = 1
backgroundValue = 0
thresh = vtk.vtkImageThreshold()
if split:
thresh.ThresholdBetween(1, 1)
else:
if maxNumberOfSegments != 0:
thresh.ThresholdBetween(1, maxNumberOfSegments)
else:
thresh.ThresholdByUpper(1)
thresh.SetInputData(islandMath.GetOutput())
thresh.SetOutValue(backgroundValue)
thresh.SetInValue(labelValue)
thresh.SetOutputScalarType(selectedSegmentLabelmap.GetScalarType())
thresh.Update()
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
largestIslandImage = vtkSegmentationCore.vtkOrientedImageData()
largestIslandImage.ShallowCopy(thresh.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
largestIslandImage.SetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
if split and (maxNumberOfSegments != 1):
thresh2 = vtk.vtkImageThreshold()
# 0 is background, 1 is largest island; we need label 2 and higher
if maxNumberOfSegments != 0:
thresh2.ThresholdBetween(2, maxNumberOfSegments)
else:
thresh2.ThresholdByUpper(2)
thresh2.SetInputData(islandMath.GetOutput())
thresh2.SetOutValue(backgroundValue)
thresh2.ReplaceInOff()
thresh2.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
logging.info( "%d islands created (%d ignored)" % (islandCount, ignoredIslands) )
# Create oriented image data from output
import vtkSegmentationCorePython as vtkSegmentationCore
multiLabelImage = vtkSegmentationCore.vtkOrientedImageData()
multiLabelImage.DeepCopy(thresh2.GetOutput())
selectedSegmentLabelmapImageToWorldMatrix = vtk.vtkMatrix4x4()
selectedSegmentLabelmap.GetImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
multiLabelImage.SetGeometryFromImageToWorldMatrix(selectedSegmentLabelmapImageToWorldMatrix)
# Import multi-label labelmap to segmentation
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
selectedSegmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
selectedSegmentIndex = segmentationNode.GetSegmentation().GetSegmentIndex(selectedSegmentID)
insertBeforeSegmentID = segmentationNode.GetSegmentation().GetNthSegmentID(selectedSegmentIndex + 1)
selectedSegmentName = segmentationNode.GetSegmentation().GetSegment(selectedSegmentID).GetName()
slicer.vtkSlicerSegmentationsModuleLogic.ImportLabelmapToSegmentationNode( \
multiLabelImage, segmentationNode, selectedSegmentName+" -", insertBeforeSegmentID )
self.scriptedEffect.modifySelectedSegmentByLabelmap(largestIslandImage, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet)
qt.QApplication.restoreOverrideCursor()
def removeIslandsMorphologyDecruft(self,
image,
foregroundLabel,
backgroundLabel,
iterations=1):
#
# make binary mask foregroundLabel->1, backgroundLabel->0
#
binThresh = vtk.vtkImageThreshold()
binThresh.SetInputData(image)
binThresh.ThresholdBetween(foregroundLabel, foregroundLabel)
binThresh.SetInValue(1)
binThresh.SetOutValue(0)
binThresh.Update()
#
# first, erode iterations number of times
#
eroder = slicer.vtkImageErode()
eroderImage = vtk.vtkImageData()
eroderImage.DeepCopy(binThresh.GetOutput())
eroder.SetInputData(eroderImage)
for iteration in range(iterations):
eroder.SetForeground(1)
eroder.SetBackground(0)
eroder.SetNeighborTo8()
eroder.Update()
eroderImage.DeepCopy(eroder.GetOutput())
#
# now save only islands bigger than a specified size
#
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
castIn.SetInputConnection(eroder.GetInputConnection(0, 0))
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(self.fullyConnected)
islandMath.SetMinimumSize(self.minimumSize)
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToShort()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
#
# now map everything back to 0 and 1
#
thresh = vtk.vtkImageThreshold()
thresh.SetInputConnection(castOut.GetOutputPort())
thresh.ThresholdByUpper(1)
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.Update()
#
# now, dilate back (erode background) iterations_plus_one number of times
#
dilater = slicer.vtkImageErode()
dilaterImage = vtk.vtkImageData()
dilaterImage.DeepCopy(thresh.GetOutput())
dilater.SetInputData(dilaterImage)
for iteration in range(1 + iterations):
dilater.SetForeground(0)
dilater.SetBackground(1)
dilater.SetNeighborTo8()
dilater.Update()
dilaterImage.DeepCopy(dilater.GetOutput())
#
# only keep pixels in both original and dilated result
#
logic = vtk.vtkImageLogic()
logic.SetInputConnection(0, dilater.GetInputConnection(0, 0))
logic.SetInputConnection(1, binThresh.GetOutputPort())
#if foregroundLabel == 0:
# logic.SetOperationToNand()
#else:
logic.SetOperationToAnd()
logic.SetOutputTrueValue(1)
logic.Update()
#
# convert from binary mask to 1->foregroundLabel, 0->backgroundLabel
#
unbinThresh = vtk.vtkImageThreshold()
unbinThresh.SetInputConnection(logic.GetOutputPort())
unbinThresh.ThresholdBetween(1, 1)
unbinThresh.SetInValue(foregroundLabel)
unbinThresh.SetOutValue(backgroundLabel)
unbinThresh.Update()
image.DeepCopy(unbinThresh.GetOutput())
def removeIslandsConnectivity(self):
#
# change the label values based on the parameter node
#
if not self.sliceLogic:
self.sliceLogic = self.editUtil.getSliceLogic()
parameterNode = self.editUtil.getParameterNode()
minimumSize = int(
parameterNode.GetParameter("IslandEffect,minimumSize"))
fullyConnected = bool(
parameterNode.GetParameter("IslandEffect,fullyConnected"))
label = self.editUtil.getLabel()
# first, create an inverse binary version of the image
# so that islands inside segemented object will be detected, along
# with a big island of the background
preThresh = vtk.vtkImageThreshold()
preThresh.SetInValue(0)
preThresh.SetOutValue(1)
preThresh.ReplaceInOn()
preThresh.ReplaceOutOn()
preThresh.ThresholdBetween(label, label)
preThresh.SetInputData(self.getScopedLabelInput())
preThresh.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
islandMath.SetInputConnection(preThresh.GetOutputPort())
islandMath.SetFullyConnected(fullyConnected)
islandMath.SetMinimumSize(minimumSize)
# TODO: $this setProgressFilter $islandMath "Calculating Islands..."
islandMath.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print("%d islands created (%d ignored)" %
(islandCount, ignoredIslands))
if islandCount == 0:
return
bgPixel = self.findNonZeroBorderPixel(islandMath.GetOutput())
# now rethreshold so that everything which is not background becomes the label
postThresh = vtk.vtkImageThreshold()
postThresh.SetInValue(0)
postThresh.SetOutValue(label)
postThresh.ReplaceInOn()
postThresh.ReplaceOutOn()
postThresh.ThresholdBetween(bgPixel, bgPixel)
postThresh.SetOutputScalarTypeToShort()
postThresh.SetInputConnection(islandMath.GetOutputPort())
postThresh.SetOutput(self.getScopedLabelOutput())
# TODO $this setProgressFilter $postThresh "Applying to Label Map..."
postThresh.Update()
self.applyScopedLabel()
postThresh.SetOutput(None)
if False:
# some code for debugging - leave it in
layerLogic = self.sliceLogic.GetLabelLayer()
labelNode = layerLogic.GetVolumeNode()
volumesLogic = slicer.modules.volumes.logic()
thresh1 = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode,
'thres1')
islands = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode,
'islands')
thresh2 = volumesLogic.CloneVolume(slicer.mrmlScene, labelNode,
'thres2')
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToShort()
cast.SetInputConnection(preThresh.GetOutputPort())
thresh1.SetImageDataConnection(cast.GetOutputPort())
cast2 = vtk.vtkImageCast()
cast2.SetOutputScalarTypeToShort()
cast2.SetInputConnection(islandMath.GetOutputPort())
islands.SetImageDataConnection(cast2.GetOutputPort())
thresh2.SetImageDataConnection(postThresh.GetOutputPort())
def removeIslandsMorphologyDecruft(self, image, foregroundLabel, backgroundLabel, iterations=1):
#
# make binary mask foregroundLabel->1, backgroundLabel->0
#
binThresh = vtk.vtkImageThreshold()
if vtk.VTK_MAJOR_VERSION <= 5:
binThresh.SetInput(image)
else:
binThresh.SetInputData(image)
binThresh.ThresholdBetween(foregroundLabel, foregroundLabel)
binThresh.SetInValue(1)
binThresh.SetOutValue(0)
binThresh.Update()
#
# first, erode iterations number of times
#
eroder = slicer.vtkImageErode()
eroderImage = vtk.vtkImageData()
eroderImage.DeepCopy(binThresh.GetOutput())
if vtk.VTK_MAJOR_VERSION <= 5:
eroder.SetInput(eroderImage)
else:
eroder.SetInputData(eroderImage)
for iteration in range(iterations):
eroder.SetForeground(1)
eroder.SetBackground(0)
eroder.SetNeighborTo8()
eroder.Update()
eroderImage.DeepCopy(eroder.GetOutput())
#
# now save only islands bigger than a specified size
#
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castIn = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castIn.SetInput(eroderImage)
else:
castIn.SetInputConnection(eroder.GetInputConnection(0, 0))
castIn.SetOutputScalarTypeToUnsignedLong()
# now identify the islands in the inverted volume
# and find the pixel that corresponds to the background
islandMath = vtkITK.vtkITKIslandMath()
if vtk.VTK_MAJOR_VERSION <= 5:
islandMath.SetInput(castIn.GetOutput())
else:
islandMath.SetInputConnection(castIn.GetOutputPort())
islandMath.SetFullyConnected(self.fullyConnected)
islandMath.SetMinimumSize(self.minimumSize)
# note that island operation happens in unsigned long space
# but the slicer editor works in Short
castOut = vtk.vtkImageCast()
if vtk.VTK_MAJOR_VERSION <= 5:
castOut.SetInput(islandMath.GetOutput())
else:
castOut.SetInputConnection(islandMath.GetOutputPort())
castOut.SetOutputScalarTypeToShort()
castOut.Update()
islandCount = islandMath.GetNumberOfIslands()
islandOrigCount = islandMath.GetOriginalNumberOfIslands()
ignoredIslands = islandOrigCount - islandCount
print("%d islands created (%d ignored)" % (islandCount, ignoredIslands))
#
# now map everything back to 0 and 1
#
thresh = vtk.vtkImageThreshold()
if vtk.VTK_MAJOR_VERSION <= 5:
thresh.SetInput(castOut.GetOutput())
else:
thresh.SetInputConnection(castOut.GetOutputPort())
thresh.ThresholdByUpper(1)
thresh.SetInValue(1)
thresh.SetOutValue(0)
thresh.Update()
#
# now, dilate back (erode background) iterations_plus_one number of times
#
dilater = slicer.vtkImageErode()
dilaterImage = vtk.vtkImageData()
dilaterImage.DeepCopy(thresh.GetOutput())
if vtk.VTK_MAJOR_VERSION <= 5:
dilater.SetInput(dilaterImage)
else:
dilater.SetInputData(dilaterImage)
for iteration in range(1 + iterations):
dilater.SetForeground(0)
dilater.SetBackground(1)
dilater.SetNeighborTo8()
dilater.Update()
dilaterImage.DeepCopy(dilater.GetOutput())
#
# only keep pixels in both original and dilated result
#
logic = vtk.vtkImageLogic()
if vtk.VTK_MAJOR_VERSION <= 5:
logic.SetInput1(dilaterImage)
logic.SetInput2(binThresh.GetOutput())
else:
logic.SetInputConnection(0, dilater.GetInputConnection(0, 0))
logic.SetInputConnection(1, binThresh.GetOutputPort())
# if foregroundLabel == 0:
# logic.SetOperationToNand()
# else:
logic.SetOperationToAnd()
logic.SetOutputTrueValue(1)
logic.Update()
#
# convert from binary mask to 1->foregroundLabel, 0->backgroundLabel
#
unbinThresh = vtk.vtkImageThreshold()
if vtk.VTK_MAJOR_VERSION <= 5:
unbinThresh.SetInput(logic.GetOutput())
else:
unbinThresh.SetInputConnection(logic.GetOutputPort())
unbinThresh.ThresholdBetween(1, 1)
unbinThresh.SetInValue(foregroundLabel)
unbinThresh.SetOutValue(backgroundLabel)
unbinThresh.Update()
image.DeepCopy(unbinThresh.GetOutput())
def apply(self, ijkPoints):
kernelSizePixel = self.getKernelSizePixel()
if kernelSizePixel[0]<=0 and kernelSizePixel[1]<=0 and kernelSizePixel[2]<=0:
return
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
# Get parameter set node
parameterSetNode = self.scriptedEffect.parameterSetNode()
# Get parameters
minimumThreshold = self.scriptedEffect.doubleParameter("MinimumThreshold")
maximumThreshold = self.scriptedEffect.doubleParameter("MaximumThreshold")
# Get modifier labelmap
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
# Get master volume image data
masterImageData = self.scriptedEffect.masterVolumeImageData()
# Set intensity range
oldMasterVolumeIntensityMask = parameterSetNode.GetMasterVolumeIntensityMask()
parameterSetNode.MasterVolumeIntensityMaskOn()
oldIntensityMaskRange = parameterSetNode.GetMasterVolumeIntensityMaskRange()
intensityRange = [265.00, 1009.00]
if oldMasterVolumeIntensityMask:
intensityRange = [max(oldIntensityMaskRange[0], minimumThreshold), min(oldIntensityMaskRange[1], maximumThreshold)]
parameterSetNode.SetMasterVolumeIntensityMaskRange(intensityRange)
roiNode = lumbarSeed ##self.roiSelector.currentNode()
clippedMasterImageData = masterImageData
if roiNode is not None:
worldToImageMatrix = vtk.vtkMatrix4x4()
masterImageData.GetWorldToImageMatrix(worldToImageMatrix)
bounds = [0,0,0,0,0,0]
roiNode.GetRASBounds(bounds)
corner1RAS = [bounds[0], bounds[2], bounds[4], 1]
corner1IJK = [0, 0, 0, 0]
worldToImageMatrix.MultiplyPoint(corner1RAS, corner1IJK)
corner2RAS = [bounds[1], bounds[3], bounds[5], 1]
corner2IJK = [0, 0, 0, 0]
worldToImageMatrix.MultiplyPoint(corner2RAS, corner2IJK)
extent = [0, -1, 0, -1, 0, -1]
for i in range(3):
lowerPoint = min(corner1IJK[i], corner2IJK[i])
upperPoint = max(corner1IJK[i], corner2IJK[i])
extent[2*i] = int(math.floor(lowerPoint))
extent[2*i+1] = int(math.ceil(upperPoint))
imageToWorldMatrix = vtk.vtkMatrix4x4()
masterImageData.GetImageToWorldMatrix(imageToWorldMatrix)
clippedMasterImageData = slicer.vtkOrientedImageData()
self.padder = vtk.vtkImageConstantPad()
self.padder.SetInputData(masterImageData)
self.padder.SetOutputWholeExtent(extent)
self.padder.Update()
clippedMasterImageData.ShallowCopy(self.padder.GetOutput())
clippedMasterImageData.SetImageToWorldMatrix(imageToWorldMatrix)
# Pipeline
self.thresh = vtk.vtkImageThreshold()
self.thresh.SetInValue(LABEL_VALUE)
self.thresh.SetOutValue(BACKGROUND_VALUE)
self.thresh.SetInputData(clippedMasterImageData)
self.thresh.ThresholdBetween(minimumThreshold, maximumThreshold)
self.thresh.SetOutputScalarTypeToUnsignedChar()
self.thresh.Update()
self.erode = vtk.vtkImageDilateErode3D()
self.erode.SetInputConnection(self.thresh.GetOutputPort())
self.erode.SetDilateValue(BACKGROUND_VALUE)
self.erode.SetErodeValue(LABEL_VALUE)
self.erode.SetKernelSize(
kernelSizePixel[0],
kernelSizePixel[1],
kernelSizePixel[2])
self.erodeCast = vtk.vtkImageCast()
self.erodeCast.SetInputConnection(self.erode.GetOutputPort())
self.erodeCast.SetOutputScalarTypeToUnsignedInt()
self.erodeCast.Update()
# Remove small islands
self.islandMath = vtkITK.vtkITKIslandMath()
self.islandMath.SetInputConnection(self.erodeCast.GetOutputPort())
self.islandMath.SetFullyConnected(False)
self.islandMath.SetMinimumSize(125) # remove regions smaller than 5x5x5 voxels
self.islandThreshold = vtk.vtkImageThreshold()
self.islandThreshold.SetInputConnection(self.islandMath.GetOutputPort())
self.islandThreshold.ThresholdByLower(BACKGROUND_VALUE)
self.islandThreshold.SetInValue(BACKGROUND_VALUE)
self.islandThreshold.SetOutValue(LABEL_VALUE)
self.islandThreshold.SetOutputScalarTypeToUnsignedChar()
self.islandThreshold.Update()
# Points may be outside the region after it is eroded.
# Snap the points to LABEL_VALUE voxels,
snappedIJKPoints = self.snapIJKPointsToLabel(ijkPoints, self.islandThreshold.GetOutput())
if snappedIJKPoints.GetNumberOfPoints() == 0:
qt.QApplication.restoreOverrideCursor()
return
# Convert points to real data coordinates. Required for vtkImageThresholdConnectivity.
seedPoints = vtk.vtkPoints()
origin = masterImageData.GetOrigin()
spacing = masterImageData.GetSpacing()
for i in range(snappedIJKPoints.GetNumberOfPoints()):
ijkPoint = snappedIJKPoints.GetPoint(i)
seedPoints.InsertNextPoint(
origin[0]+ijkPoint[0]*spacing[0],
origin[1]+ijkPoint[1]*spacing[1],
origin[2]+ijkPoint[2]*spacing[2])
segmentationAlgorithm = self.scriptedEffect.parameter(SEGMENTATION_ALGORITHM_PARAMETER_NAME)
if segmentationAlgorithm == SEGMENTATION_ALGORITHM_MASKING:
self.runMasking(seedPoints, self.islandThreshold.GetOutput(), modifierLabelmap)
else:
self.floodFillingFilterIsland = vtk.vtkImageThresholdConnectivity()
self.floodFillingFilterIsland.SetInputConnection(self.islandThreshold.GetOutputPort())
self.floodFillingFilterIsland.SetInValue(SELECTED_ISLAND_VALUE)
self.floodFillingFilterIsland.ReplaceInOn()
self.floodFillingFilterIsland.ReplaceOutOff()
self.floodFillingFilterIsland.ThresholdBetween(265.00, 1009.00)
self.floodFillingFilterIsland.SetSeedPoints(seedPoints)
self.floodFillingFilterIsland.Update()
self.maskCast = vtk.vtkImageCast()
self.maskCast.SetInputData(self.thresh.GetOutput())
self.maskCast.SetOutputScalarTypeToUnsignedChar()
self.maskCast.Update()
self.imageMask = vtk.vtkImageMask()
self.imageMask.SetInputConnection(self.floodFillingFilterIsland.GetOutputPort())
self.imageMask.SetMaskedOutputValue(OUTSIDE_THRESHOLD_VALUE)
self.imageMask.SetMaskInputData(self.maskCast.GetOutput())
self.imageMask.Update()
imageMaskOutput = slicer.vtkOrientedImageData()
imageMaskOutput.ShallowCopy(self.imageMask.GetOutput())
imageMaskOutput.CopyDirections(clippedMasterImageData)
imageToWorldMatrix = vtk.vtkMatrix4x4()
imageMaskOutput.GetImageToWorldMatrix(imageToWorldMatrix)
segmentOutputLabelmap = slicer.vtkOrientedImageData()
if segmentationAlgorithm == SEGMENTATION_ALGORITHM_GROWCUT:
self.runGrowCut(clippedMasterImageData, imageMaskOutput, segmentOutputLabelmap)
elif segmentationAlgorithm == SEGMENTATION_ALGORITHM_WATERSHED:
self.runWatershed(clippedMasterImageData, imageMaskOutput, segmentOutputLabelmap)
else:
logging.error("Unknown segmentation algorithm: \"" + segmentationAlgorithm + "\"")
segmentOutputLabelmap.SetImageToWorldMatrix(imageToWorldMatrix)
self.selectedSegmentThreshold = vtk.vtkImageThreshold()
self.selectedSegmentThreshold.SetInputData(segmentOutputLabelmap)
self.selectedSegmentThreshold.ThresholdBetween(SELECTED_ISLAND_VALUE, SELECTED_ISLAND_VALUE)
self.selectedSegmentThreshold.SetInValue(LABEL_VALUE)
self.selectedSegmentThreshold.SetOutValue(BACKGROUND_VALUE)
self.selectedSegmentThreshold.SetOutputScalarType(modifierLabelmap.GetScalarType())
self.selectedSegmentThreshold.Update()
modifierLabelmap.ShallowCopy(self.selectedSegmentThreshold.GetOutput())
self.scriptedEffect.saveStateForUndo()
self.scriptedEffect.modifySelectedSegmentByLabelmap(modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeAdd)
parameterSetNode.SetMasterVolumeIntensityMask(oldMasterVolumeIntensityMask)
parameterSetNode.SetMasterVolumeIntensityMaskRange(oldIntensityMaskRange)
qt.QApplication.restoreOverrideCursor()
