def erode(self,fill,neighborMode,iterations):
eroder = slicer.vtkImageErode()
eroder.SetInputData( self.getScopedLabelInput() )
eroder.SetOutput( self.getScopedLabelOutput() )
eroder.SetForeground( EditUtil.getLabel() )
eroder.SetBackground( fill )
if neighborMode == '8':
eroder.SetNeighborTo8()
elif neighborMode == '4':
eroder.SetNeighborTo4()
else:
# TODO: error feedback from effect logic?
# bad neighbor mode - silently use default
print('Bad neighborMode: %s' % neighborMode)
for i in range(iterations):
# TODO: $this setProgressFilter eroder "Erode ($i)"
print('updating')
eroder.Update()
self.applyScopedLabel()
eroder.SetOutput( None )
def erode(self,fill,neighborMode,iterations):
eroder = slicer.vtkImageErode()
eroder.SetInputData( self.getScopedLabelInput() )
eroder.SetOutput( self.getScopedLabelOutput() )
eroder.SetForeground( EditUtil.getLabel() )
eroder.SetBackground( fill )
if neighborMode == '8':
eroder.SetNeighborTo8()
elif neighborMode == '4':
eroder.SetNeighborTo4()
else:
# TODO: error feedback from effect logic?
# bad neighbor mode - silently use default
print('Bad neighborMode: %s' % neighborMode)
for i in range(iterations):
# TODO: $this setProgressFilter eroder "Erode ($i)"
print('updating')
eroder.Update()
self.applyScopedLabel()
eroder.SetOutput( None )
def onApply(self):
# Get parameters
neighborMode = self.scriptedEffect.integerParameter("NeighborMode")
iterations = self.scriptedEffect.integerParameter("Iterations")
# Get edited labelmap
editedLabelmap = self.scriptedEffect.parameterSetNode().GetEditedLabelmap()
# Perform erosion
eroder = slicer.vtkImageErode()
eroder.SetInputData(editedLabelmap)
eroder.SetForeground(1)
eroder.SetBackground(0)
if neighborMode == 8:
eroder.SetNeighborTo8()
elif neighborMode == 4:
eroder.SetNeighborTo4()
else:
logging.error("Invalid neighbor mode!")
for i in xrange(iterations):
eroder.Update()
editedLabelmap.DeepCopy(eroder.GetOutput())
# Notify editor about changes.
# This needs to be called so that the changes are written back to the edited segment
self.scriptedEffect.apply()
def close(self,fill,neighborMode,iterations):
dilater = slicer.vtkImageErode()
eroder = slicer.vtkImageErode()
if vtk.VTK_MAJOR_VERSION <= 5:
dilater.SetInput( self.getScopedLabelInput() )
else:
dilater.SetInputData( self.getScopedLabelInput() )
if vtk.VTK_MAJOR_VERSION <= 5:
eroder.SetInput( dilater.GetOutput() )
else:
eroder.SetInputData( dilater.GetOutput() )
eroder.SetOutput( self.getScopedLabelOutput() )
dilater.SetForeground( fill )
dilater.SetBackground( self.editUtil.getLabel() )
eroder.SetForeground( self.editUtil.getLabel() )
eroder.SetBackground( fill )
if neighborMode == '8':
dilater.SetNeighborTo8()
eroder.SetNeighborTo8()
elif neighborMode == '4':
dilater.SetNeighborTo4()
eroder.SetNeighborTo4()
else:
# TODO: error feedback from effect logic?
# bad neighbor mode - silently use default
print('Bad neighborMode: %s' % neighborMode)
for i in xrange(iterations):
# TODO: $this setProgressFilter dilater "Interpolate ($i)"
dilater.Update()
eroder.Update()
self.applyScopedLabel()
dilater.SetOutput( None )
eroder.SetOutput( None )
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 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())
for scan in range(numberOfScans):
# load CT file of sample CT-shest
slicer.util.loadVolume(dataPath + 'CT-chest.nrrd')
ctImage = slicer.util.getNode('CT-chest')
# use vtk to adjust the threshold value
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(ctImage.GetImageData())
# TODO: adjust a better threshold level
threshold.ThresholdBetween(300, 1000)
threshold.SetInValue(255)
threshold.SetOutValue(0)
# use a slicer serode
serode = slicer.vtkImageErode()
serode.SetInputConnection(threshold.GetOutputPort())
serode.SetNeighborTo4()
serode.Update()
ctImage.SetAndObserveImageData(serode.GetOutputDataObject(0))
# save label map
outFileName = 'CT_label_{}.nrrd'.format(scan)
outFilePath = os.path.join(dataPath, outFileName)
slicer.util.saveNode(ctImage, outFilePath)
# make model out of label
parameters = {}
parameters['InputVolume'] = ctImage.GetID()