def ImageModelSnapshot(self,
dataNode,
labelNode,
outputDir,
IDcurrPatient,
ImageFilePath,
progress_filename,
selLabels=False,
levels=False):
cast1 = vtk.vtkImageCast()
cast1.SetOutputScalarTypeToInt()
cast1.SetInputConnection(labelNode.GetImageDataConnection())
cast1.Update()
labelNode.SetImageDataConnection(cast1.GetOutputPort())
cast2 = vtk.vtkImageCast()
cast2.SetOutputScalarTypeToInt()
cast2.SetInputConnection(dataNode.GetImageDataConnection())
cast2.Update()
dataNode.SetImageDataConnection(cast2.GetOutputPort())
labelNode.SetOrigin(dataNode.GetOrigin())
try:
imageNodeSITK = su.PullFromSlicer(dataNode.GetName())
labelNodeSITK = su.PullFromSlicer(labelNode.GetName())
labelArraySITK = sitk.GetArrayFromImage(labelNodeSITK)
lbound, hbound = squeeze(self, labelArraySITK, labelNode)
self.cmaj = sitk.CropImageFilter()
self.cmaj.SetLowerBoundaryCropSize(lbound)
self.cmaj.SetUpperBoundaryCropSize(hbound)
zoomLabelNodeSITK = self.cmaj.Execute(labelNodeSITK)
zoomImageNodeSITK = self.cmaj.Execute(imageNodeSITK)
zoomLabelNodeName = 'zoomLabelNode' + '_' + IDcurrPatient
zoomImageNodeName = 'zoomImageNode' + '_' + IDcurrPatient
su.PushToSlicer(zoomLabelNodeSITK, zoomLabelNodeName)
su.PushToSlicer(zoomImageNodeSITK, zoomImageNodeName)
zoomLabelNode = slicer.util.getNode(zoomLabelNodeName)
zoomImageNode = slicer.util.getNode(zoomImageNodeName)
zoomLabelNodeArraySITK = sitk.GetArrayFromImage(zoomLabelNodeSITK)
zoomLabelNodeArraySITK = numpy.where(zoomLabelNodeArraySITK == 0,
numpy.NAN, zoomLabelNodeArraySITK)
maxZind = find_LargestSlices(self, zoomLabelNodeArraySITK)
imgOutputDir = str(outputDir)
modelHandler(ImageFilePath, zoomImageNode, zoomLabelNode, imgOutputDir,
IDcurrPatient, maxZind)
return (maxZind)
except Exception, e:
with open(progress_filename, mode='a') as printfile:
printfile.write('ERROR: ' + str(e) + '\n')
os.makedirs(os.path.join(outputDir, IDcurrPatient + '_flagged'))
return (-1, -1, -1)
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 ImageModelSnapshot(self, dataNode, labelNode, outputDir, IDcurrPatient, ImageFilePath, progress_filename, selLabels=False, levels=False):
cast1 = vtk.vtkImageCast()
cast1.SetOutputScalarTypeToInt()
cast1.SetInputConnection(labelNode.GetImageDataConnection())
cast1.Update()
labelNode.SetImageDataConnection(cast1.GetOutputPort())
cast2 = vtk.vtkImageCast()
cast2.SetOutputScalarTypeToInt()
cast2.SetInputConnection(dataNode.GetImageDataConnection())
cast2.Update()
dataNode.SetImageDataConnection(cast2.GetOutputPort())
labelNode.SetOrigin(dataNode.GetOrigin())
try:
imageNodeSITK = su.PullFromSlicer(dataNode.GetName())
labelNodeSITK = su.PullFromSlicer(labelNode.GetName())
labelArraySITK = sitk.GetArrayFromImage(labelNodeSITK)
lbound, hbound = squeeze(self, labelArraySITK, labelNode)
self.cmaj = sitk.CropImageFilter()
self.cmaj.SetLowerBoundaryCropSize(lbound)
self.cmaj.SetUpperBoundaryCropSize(hbound)
zoomLabelNodeSITK = self.cmaj.Execute(labelNodeSITK)
zoomImageNodeSITK = self.cmaj.Execute(imageNodeSITK)
zoomLabelNodeName = 'zoomLabelNode'+'_'+IDcurrPatient
zoomImageNodeName = 'zoomImageNode'+'_'+IDcurrPatient
su.PushToSlicer(zoomLabelNodeSITK, zoomLabelNodeName)
su.PushToSlicer(zoomImageNodeSITK, zoomImageNodeName)
zoomLabelNode = slicer.util.getNode(zoomLabelNodeName)
zoomImageNode = slicer.util.getNode(zoomImageNodeName)
zoomLabelNodeArraySITK = sitk.GetArrayFromImage(zoomLabelNodeSITK)
zoomLabelNodeArraySITK = numpy.where(zoomLabelNodeArraySITK == 0, numpy.NAN, zoomLabelNodeArraySITK)
maxZind = find_LargestSlices(self, zoomLabelNodeArraySITK)
imgOutputDir = str(outputDir)
modelHandler(ImageFilePath, zoomImageNode, zoomLabelNode, imgOutputDir, IDcurrPatient, maxZind)
return(maxZind)
except Exception, e:
with open(progress_filename,mode='a') as printfile: printfile.write('ERROR: ' + str(e) + '\n')
os.makedirs(os.path.join(outputDir,IDcurrPatient+'_flagged'))
return(-1,-1,-1)
def castScalarToInt(volumeNode):
castScalarToInt = vtk.vtkImageCast()
castScalarToInt.SetOutputScalarTypeToInt()
castScalarToInt.SetInputConnection(volumeNode.GetImageDataConnection())
castScalarToInt.Update()
volumeNode.SetImageDataConnection(castScalarToInt.GetOutputPort())
def recolorLabelMap(self, modelNode, labelMap, initialValue, outputValue):
import vtkSlicerRtCommonPython
if (modelNode != None and labelMap != None):
self.labelMapImgData = labelMap.GetImageData()
self.resectionPolyData = modelNode.GetPolyData()
# IJK -> RAS
ijkToRasMatrix = vtk.vtkMatrix4x4()
labelMap.GetIJKToRASMatrix(ijkToRasMatrix)
# RAS -> IJK
rasToIjkMatrix = vtk.vtkMatrix4x4()
labelMap.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
rasToIjkTransform.Update()
# Transform Resection model from RAS -> IJK
polyDataTransformFilter = vtk.vtkTransformPolyDataFilter()
if (vtk.VTK_MAJOR_VERSION <= 5):
polyDataTransformFilter.SetInput(self.resectionPolyData)
else:
polyDataTransformFilter.SetInputData(self.resectionPolyData)
polyDataTransformFilter.SetTransform(rasToIjkTransform)
polyDataTransformFilter.Update()
# Convert Resection model to label map
polyDataToLabelmapFilter = vtkSlicerRtCommonPython.vtkPolyDataToLabelmapFilter()
polyDataToLabelmapFilter.SetInputPolyData(polyDataTransformFilter.GetOutput())
polyDataToLabelmapFilter.SetReferenceImage(self.labelMapImgData)
polyDataToLabelmapFilter.UseReferenceValuesOn()
polyDataToLabelmapFilter.SetBackgroundValue(0)
polyDataToLabelmapFilter.SetLabelValue(outputValue)
polyDataToLabelmapFilter.Update()
# Cast resection label map to unsigned char for use with mask filter
castFilter = vtk.vtkImageCast()
if (vtk.VTK_MAJOR_VERSION <= 5):
castFilter.SetInput(polyDataToLabelmapFilter.GetOutput())
else:
castFilter.SetInputData(polyDataToLabelmapFilter.GetOutput())
castFilter.SetOutputScalarTypeToUnsignedChar()
castFilter.Update()
# Create mask for recoloring the original label map
maskFilter = vtk.vtkImageMask()
if (vtk.VTK_MAJOR_VERSION <= 5):
maskFilter.SetImageInput(self.labelMapImgData)
maskFilter.SetMaskInput(castFilter.GetOutput())
else:
maskFilter.SetImageInputData(self.labelMapImgData)
maskFilter.SetMaskInputData(castFilter.GetOutput())
maskFilter.SetMaskedOutputValue(outputValue)
maskFilter.NotMaskOn()
maskFilter.Update()
self.labelMapImgData = maskFilter.GetOutput()
self.labelMapImgData.Modified()
labelMap.SetAndObserveImageData(self.labelMapImgData)
def run(self,inputVolume,outputVolume,algorithm=0,variance=2,thresholdmin=0,thresholdmax=0):
"""
Run the edge detection algorithm
"""
self.input=inputVolume
self.output=outputVolume
self.algorithm=algorithm
self.variance=variance
self.threshold=[thresholdmin,thresholdmax]
slicer.util.delayDisplay('Running the edge detection aglorithm')
im=self.input.GetImageData()
cast=vtk.vtkImageCast()
cast.SetOutputScalarTypeToDouble()
cast.SetInputData(im)
cast.Update()
em=slicer.vtkITKEdgeDetection()
em.SetInputData(cast.GetOutput())
em.SetAlgorithmInt(self.algorithm)
em.Setvariance(self.variance)
em.Setthreshold(self.threshold)
em.Update()
self.output.GetImageData().DeepCopy(em.GetOutput())
return True
def performFrangiVesselness( self, image, minimumDiameter, maximumDiameter, discretizationSteps, alpha, beta, gamma ):
'''
'''
# import the vmtk libraries
try:
#from libvtkvmtkSegmentationPython import *
import libvtkvmtkSegmentationPython as s
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk libraries!"
cast = vtk.vtkImageCast()
cast.SetInput( image )
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = s.vtkvmtkVesselnessMeasureImageFilter()
v.SetInput( image )
v.SetSigmaMin( minimumDiameter )
v.SetSigmaMax( maximumDiameter )
v.SetNumberOfSigmaSteps( discretizationSteps )
v.SetAlpha( alpha )
v.SetBeta( beta )
v.SetGamma( gamma )
v.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy( v.GetOutput() )
outImageData.Update()
outImageData.GetPointData().GetScalars().Modified()
return outImageData
def castVolumeNodeToShort(self, volumeNode): imageData = volumeNode.GetImageData() cast = vtk.vtkImageCast() cast.SetInputData(imageData) cast.SetOutputScalarTypeToShort() cast.SetOutput(imageData) cast.Update()
def castVolumeNodeToDouble(self, volumeNode): castFilter = vtk.vtkImageCast() castFilter.SetInputData(volumeNode.GetImageData()) castFilter.SetOutputScalarTypeToDouble() castFilter.Update() volumeNode.SetAndObserveImageData(castFilter.GetOutput()) logging.info(volumeNode.GetName() + ' was casted to double.')
def castScalarToInt(volumeNode):
castScalarToInt = vtk.vtkImageCast()
castScalarToInt.SetOutputScalarTypeToInt()
castScalarToInt.SetInputConnection(volumeNode.GetImageDataConnection())
castScalarToInt.Update()
volumeNode.SetImageDataConnection(castScalarToInt.GetOutputPort())
def performFrangiVesselness(self, image, minimumDiameter, maximumDiameter,
discretizationSteps, alpha, beta, gamma):
'''
'''
# import the vmtk libraries
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cast = vtk.vtkImageCast()
cast.SetInputData(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
v = vtkvmtkSegmentation.vtkvmtkVesselnessMeasureImageFilter()
v.SetInputData(image)
v.SetSigmaMin(minimumDiameter)
v.SetSigmaMax(maximumDiameter)
v.SetNumberOfSigmaSteps(discretizationSteps)
v.SetAlpha(alpha)
v.SetBeta(beta)
v.SetGamma(gamma)
v.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(v.GetOutput())
outImageData.GetPointData().GetScalars().Modified()
return outImageData
def buildGradientBasedFeatureImage(self, imageData):
'''
'''
# import the vmtk libraries
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
derivativeSigma = 0.0
sigmoidRemapping = 1
cast = vtk.vtkImageCast()
cast.SetInputData(imageData)
cast.SetOutputScalarTypeToFloat()
cast.Update()
if (derivativeSigma > 0.0):
gradientMagnitude = vtkvmtkSegmentation.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter(
)
gradientMagnitude.SetInputData(cast.GetOutput())
gradientMagnitude.SetSigma(derivativeSigma)
gradientMagnitude.SetNormalizeAcrossScale(0)
gradientMagnitude.Update()
else:
gradientMagnitude = vtkvmtkSegmentation.vtkvmtkGradientMagnitudeImageFilter(
)
gradientMagnitude.SetInputData(cast.GetOutput())
gradientMagnitude.Update()
featureImage = None
if sigmoidRemapping == 1:
scalarRange = gradientMagnitude.GetOutput().GetPointData(
).GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = -(inputMaximum - inputMinimum) / 6.0
beta = (inputMaximum + inputMinimum) / 2.0
sigmoid = vtkvmtkSegmentation.vtkvmtkSigmoidImageFilter()
sigmoid.SetInputData(gradientMagnitude.GetOutput())
sigmoid.SetAlpha(alpha)
sigmoid.SetBeta(beta)
sigmoid.SetOutputMinimum(0.0)
sigmoid.SetOutputMaximum(1.0)
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = vtkvmtkSegmentation.vtkvmtkBoundedReciprocalImageFilter(
)
boundedReciprocal.SetInputData(gradientMagnitude.GetOutput())
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(featureImage)
return outImageData
def castVolumeNodeToDouble(self, volumeNode):
castFilter = vtk.vtkImageCast()
castFilter.SetInputData(volumeNode.GetImageData())
castFilter.SetOutputScalarTypeToDouble()
castFilter.Update()
volumeNode.SetAndObserveImageData(castFilter.GetOutput())
return True
def castVolumeNodeToDouble(self, volumeNode):
castFilter = vtk.vtkImageCast()
castFilter.SetInputData(volumeNode.GetImageData())
castFilter.SetOutputScalarTypeToDouble()
castFilter.Update()
volumeNode.SetAndObserveImageData(castFilter.GetOutput())
return True
def buildGradientBasedFeatureImage( self, imageData ):
'''
'''
# import the vmtk libraries
try:
#from libvtkvmtkSegmentationPython import *
import libvtkvmtkSegmentationPython as s
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk libraries!"
derivativeSigma = 0.0
sigmoidRemapping = 1
cast = vtk.vtkImageCast()
cast.SetInput( imageData )
cast.SetOutputScalarTypeToFloat()
cast.Update()
if ( derivativeSigma > 0.0 ):
gradientMagnitude = s.vtkvmtkGradientMagnitudeRecursiveGaussianImageFilter()
gradientMagnitude.SetInput( cast.GetOutput() )
gradientMagnitude.SetSigma( derivativeSigma )
gradientMagnitude.SetNormalizeAcrossScale( 0 )
gradientMagnitude.Update()
else:
gradientMagnitude = s.vtkvmtkGradientMagnitudeImageFilter()
gradientMagnitude.SetInput( cast.GetOutput() )
gradientMagnitude.Update()
featureImage = None
if sigmoidRemapping == 1:
scalarRange = gradientMagnitude.GetOutput().GetPointData().GetScalars().GetRange()
inputMinimum = scalarRange[0]
inputMaximum = scalarRange[1]
alpha = -( inputMaximum - inputMinimum ) / 6.0
beta = ( inputMaximum + inputMinimum ) / 2.0
sigmoid = s.vtkvmtkSigmoidImageFilter()
sigmoid.SetInput( gradientMagnitude.GetOutput() )
sigmoid.SetAlpha( alpha )
sigmoid.SetBeta( beta )
sigmoid.SetOutputMinimum( 0.0 )
sigmoid.SetOutputMaximum( 1.0 )
sigmoid.Update()
featureImage = sigmoid.GetOutput()
else:
boundedReciprocal = s.vtkvmtkBoundedReciprocalImageFilter()
boundedReciprocal.SetInput( gradientMagnitude.GetOutput() )
boundedReciprocal.Update()
featureImage = boundedReciprocal.GetOutput()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy( featureImage )
outImageData.Update()
return outImageData
def onSliderChanged(self, newValue):
value = self.__mdSlider.value
if self.__mvNode != None:
mvDisplayNode = self.__mvNode.GetDisplayNode()
mvDisplayNode.SetFrameComponent(newValue)
if self.extractFrame == True:
frameVolume = self.__vfSelector.currentNode()
if frameVolume == None or self.__mvNode == None:
return
mvImage = self.__mvNode.GetImageData()
frameId = newValue
extract = vtk.vtkImageExtractComponents()
cast = vtk.vtkImageCast()
extract.SetInput(mvImage)
extract.SetComponents(frameId)
cast.SetInput(extract.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.Update()
frame = cast.GetOutput()
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
self.__mvNode.GetRASToIJKMatrix(ras2ijk)
self.__mvNode.GetIJKToRASMatrix(ijk2ras)
frameImage = frameVolume.GetImageData()
if frameImage == None:
frameVolume.SetAndObserveImageData(frame)
frameVolume.SetRASToIJKMatrix(ras2ijk)
frameVolume.SetIJKToRASMatrix(ijk2ras)
frameImage = frame
frameImage.DeepCopy(frame)
displayNode = frameVolume.GetDisplayNode()
if displayNode == None:
displayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLScalarVolumeDisplayNode')
displayNode.SetReferenceCount(1)
displayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(displayNode)
displayNode.SetDefaultColorMap()
frameVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
frameName = '%s frame %d' % (self.__mvNode.GetName(), frameId)
frameVolume.SetName(frameName)
def detectEdgeInROI(self,edge,alternateEdge=None):
qu=QCLib.QCUtil()
VOIROI=qu.getVOIfromRectROI(self.ROI)
eV=vtk.vtkExtractVOI()
eV.SetInputData(self.input.GetImageData())
eV.SetVOI(VOIROI)
eV.Update()
imROI=eV.GetOutput()
thr=[0,0]
if self.algorithm==0:
#find threshold for edge detection
mL=makeROIGhostLogic()
ghost=vtk.vtkImageData()
ghnode=slicer.vtkMRMLScalarVolumeNode()
ghnode.SetAndObserveImageData(ghost)
mL.run(self.input,ghnode)
rL=ROIStatisticsLogic()
rL.run(self.input,ghnode)
zROI=VOIROI[4]
ghVals=[]
stats=rL.stats.values()
for n in range(rL.stats.__len__()):
ghVals.append(stats[n][zROI]['mean']+stats[n][zROI]['sd'])
thr=[max(ghVals),2*max(ghVals)]
else:
alternateEdge=None
cast=vtk.vtkImageCast()
cast.SetOutputScalarTypeToDouble()
cast.SetInputData(imROI)
cast.Update()
em=slicer.vtkITKEdgeDetection()
em.SetInputData(cast.GetOutput())
em.SetAlgorithmInt(self.algorithm)
em.Setthreshold(thr)
em.Setvariance(5)
em.Update()
edge.DeepCopy(em.GetOutput())
if alternateEdge:
self.signedDistance(edge,alternateEdge)
def savePNGs(self, node, pattern):
wlc = vtk.vtkImageMapToWindowLevelColors()
wlc.SetInputData(node.GetImageData())
if not node.GetLabelMap():
displayNode = node.GetDisplayNode()
wlc.SetWindow(displayNode.GetWindow())
wlc.SetLevel(displayNode.GetLevel())
wlc.Update()
print(wlc.GetOutput().GetScalarRange())
cast = vtk.vtkImageCast()
cast.SetInputConnection(wlc.GetOutputPort())
cast.SetOutputScalarTypeToUnsignedChar()
pngWriter = vtk.vtkPNGWriter()
pngWriter.SetFilePattern(pattern)
pngWriter.SetInputConnection(cast.GetOutputPort())
pngWriter.Write()
slicer.modules.BitmapGeneratorWidget.pngWriter = pngWriter
def DoIt(inputDir, labelFile, outputDir, forceLabel, forceResample):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
if not hasattr(slicer.modules, 'reporting'):
print 'The Reporting module has not been loaded into Slicer, script cannot run!\n\tTry setting the --additional-module-path parameter.'
sys.exit(1)
reportingLogic = slicer.modules.reporting.logic()
print('Temporary directory location: '+dbDir1)
qt.QDir().mkpath(dbDir1)
dbDir0 = None
if slicer.dicomDatabase:
dbDir0 = os.path.split(slicer.dicomDatabase.databaseFilename)[0]
dicomWidget = slicer.modules.dicom.widgetRepresentation().self()
dicomWidget.onDatabaseDirectoryChanged(dbDir1)
# import DICOM study
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir, None)
indexer.waitForImportFinished()
print('DICOM import finished!')
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
sys.exit(1)
inputVolume = scalarVolumePlugin.load(loadables[0])
print 'Input volume loaded! ID = ', inputVolume.GetID()
# read the label volume
labelVolume = slicer.vtkMRMLLabelMapVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
if forceLabel>0:
# print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
thresh.SetInput(labelImage)
else:
thresh.SetInputData(labelImage)
thresh.ThresholdBetween(1, labelImage.GetScalarRange()[1])
thresh.SetInValue(int(forceLabel))
thresh.SetOutValue(0)
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.Update()
labelImage = thresh.GetOutput()
labelVolume.SetAndObserveImageData(labelImage)
slicer.mrmlScene.AddNode(labelVolume)
print 'Label volume added, id = ', labelVolume.GetID()
# ensure that the label volume scalar type is unsigned short
if labelVolume.GetImageData() != None:
scalarType = labelVolume.GetImageData().GetScalarType()
if scalarType != vtk.VTK_UNSIGNED_SHORT:
print 'Label volume has pixel type of ',vtk.vtkImageScalarTypeNameMacro(scalarType),', casting to unsigned short'
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToUnsignedShort()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(labelVolume.GetImageData())
cast.Update()
labelVolume.SetAndObserveImageData(cast.GetOutput())
else:
cast.SetInputConnection(labelVolume.GetImageDataConnection())
cast.Update()
labelVolume.SetImageDataConnection(cast.GetOutputPort())
if labelVolume.GetImageData().GetScalarType() != vtk.VTK_UNSIGNED_SHORT:
print 'Failed to cast label volume to unsigned short, type is ', vtk.vtkImageScalarTypeNameMacro(labelVolume.GetImageData().GetScalarType())
sys.exit(1)
volumesLogic = slicer.modules.volumes.logic()
geometryCheckString = volumesLogic.CheckForLabelVolumeValidity(inputVolume, labelVolume)
if geometryCheckString != "":
# has the user specified that forced resampling is okay?
if forceResample == False:
print 'Label volume mismatch with input volume:\n',geometryCheckString,'\nForced resample not specified, aborting. Re-run with --force option to ignore geometric inconsistencies'
sys.exit(1)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
print 'Resampled label added, id = ', resampledLabel.GetID()
resampledLabel = volumesLogic.ResampleVolumeToReferenceVolume(labelVolume, inputVolume)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.SetAndObserveDisplayNodeID(displayNode.GetID())
# initialize the DICOM DB for Reporting logic, save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(labelVolume)
print('About to write DICOM SEG!')
dbFileName = slicer.dicomDatabase.databaseFilename
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
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 createSyntheticMask(self, maskVolumeNode, radius):
"""
Run the actual algorithm
"""
roiSphere = vtk.vtkSphere()
roiCenter = [0, 0, 0]
roiOrigin = [0, 0, 0]
roiSpacing = [1, 1, 1]
roiDimension = [100, 100, 100]
# roiDimension = refVolumeNode.GetImageData().GetDimensions()
roiCenter[0] = roiOrigin[0] + roiDimension[0] * roiSpacing[0] / 2
roiCenter[1] = roiOrigin[1] + roiDimension[1] * roiSpacing[1] / 2
roiCenter[2] = roiOrigin[2] + roiDimension[2] * roiSpacing[2] / 2
print "roiCenter", roiCenter
"""
ijkToRas = vtk.vtkMatrix4x4()
refVolumeNode.GetIJKToRASMatrix( ijkToRas )
roiPoint = [0,0,0,1];
roiPoint[0] = roiCenter[0]
roiPoint[1] = roiCenter[1]
roiPoint[2] = roiCenter[2]
roiPoint = ijkToRas.MultiplyPoint(roiPoint)
roiCenter[0] = roiPoint[0]
roiCenter[1] = roiPoint[1]
roiCenter[2] = roiPoint[2]
print "roiCenter", roiCenter
"""
roiSphere.SetCenter(roiCenter)
roiSphere.SetRadius(radius)
# Determine the transform between the box and the image IJK coordinate systems
rasToSphere = vtk.vtkMatrix4x4()
# if roiNode.GetTransformNodeID() != None:
# roiSphereTransformNode = slicer.mrmlScene.GetNodeByID(roiNode.GetTransformNodeID())
# sphereToRas = vtk.vtkMatrix4x4()
# roiSphereTransformNode.GetMatrixTransformToWorld(sphereToRas)
# rasToSphere.DeepCopy(sphereToRas)
# rasToSphere.Invert()
"""
ijkToSphere = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4.Multiply4x4(rasToSphere,ijkToRas,ijkToSphere)
ijkToSphereTransform = vtk.vtkTransform()
ijkToSphereTransform.SetMatrix(ijkToSphere)
roiSphere.SetTransform(ijkToSphereTransform)
# Use the stencil to fill the volume
refImageData = refVolumeNode.GetImageData()
"""
imageSource = vtk.vtkImageNoiseSource()
imageSource.SetMinimum(0)
imageSource.SetMaximum(0)
imageSource.SetWholeExtent(0, roiDimension[0] - 1, 0,
roiDimension[1] - 1, 0, roiDimension[2] - 1)
imageSource.Update()
imageCast = vtk.vtkImageCast()
imageCast.SetInputData(imageSource.GetOutput())
imageCast.SetOutputScalarTypeToUnsignedChar()
imageCast.Update()
"""
changeInfo = vtk.vtkImageChangeInformation()
changeInfo.SetInputData(imageCast.GetOutput())
changeInfo.SetOutputOrigin(refImageData.GetOrigin())
changeInfo.SetOutputSpacing(refImageData.GetSpacing())
changeInfo.Update()
"""
# Convert the implicit function to a stencil
functionToStencil = vtk.vtkImplicitFunctionToImageStencil()
functionToStencil.SetInput(roiSphere)
functionToStencil.SetOutputOrigin(0, 0, 0)
functionToStencil.SetOutputSpacing(1, 1, 1)
functionToStencil.SetOutputWholeExtent(0, roiDimension[0] - 1, 0,
roiDimension[1] - 1, 0,
roiDimension[2] - 1)
functionToStencil.Update()
# Apply the stencil to the volume
stencilToImage = vtk.vtkImageStencil()
stencilToImage.SetInputData(imageCast.GetOutput())
stencilToImage.SetStencilData(functionToStencil.GetOutput())
stencilToImage.ReverseStencilOn()
stencilToImage.SetBackgroundValue(1)
stencilToImage.Update()
"""
extent = refImageData.GetWholeExtent()
resample = vtk.vtkImageReslice()
resample.SetInputData(stencilToImage.GetOutput())
resample.SetOutputOrigin(refImageData.GetOrigin())
resample.SetOutputSpacing(refImageData.GetSpacing()[0]/2, refImageData.GetSpacing()[1]/2, refImageData.GetSpacing()[2]/2 )
resample.SetOutputExtent(extent[0], (extent[1]-extent[0])*2-1,
extent[2], (extent[3]-extent[2])*2-1,
extent[4], (extent[5]-extent[4])*2-1)
resample.Update()
changeInfo2 = vtk.vtkImageChangeInformation()
changeInfo2.SetInputData(resample.GetOutput())
changeInfo2.SetOutputOrigin(refImageData.GetOrigin())
changeInfo2.SetOutputSpacing(refImageData.GetSpacing())
changeInfo2.Update()
"""
# Update the volume with the stencil operation result
maskVolumeNode.SetAndObserveImageData(stencilToImage.GetOutput())
maskVolumeNode.SetOrigin(0, 0, 0)
maskVolumeNode.SetSpacing(1, 1, 1)
# maskVolumeNode.CopyOrientation(refVolumeNode)
mgr = slicer.app.layoutManager()
mgr.sliceWidget(
'Red').sliceLogic().GetSliceCompositeNode().SetLabelVolumeID(
maskVolumeNode.GetID())
mgr.sliceWidget(
'Yellow').sliceLogic().GetSliceCompositeNode().SetLabelVolumeID(
maskVolumeNode.GetID())
mgr.sliceWidget(
'Green').sliceLogic().GetSliceCompositeNode().SetLabelVolumeID(
maskVolumeNode.GetID())
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 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 fastMarching(self, percentMax):
self.fm = None
# allocate a new filter each time March is hit
bgImage = self.editUtil.getBackgroundImage()
labelImage = self.editUtil.getLabelImage()
# collect seeds
dim = bgImage.GetWholeExtent()
# initialize the filter
self.fm = slicer.vtkPichonFastMarching()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1] - scalarRange[0]
# this is more or less arbitrary; large depth values will bring the
# algorithm to the knees
scaleValue = 0
shiftValue = 0
if depth > 300:
scaleValue = 300. / depth
if scalarRange[0] < 0:
shiftValue = scalarRange[0] * -1
if scaleValue or shiftValue:
rescale = vtk.vtkImageShiftScale()
rescale.SetInput(bgImage)
rescale.SetScale(scaleValue)
rescale.SetShift(shiftValue)
rescale.Update()
bgImage = rescale.GetOutput()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1] - scalarRange[0]
print('Input scalar range: ' + str(depth))
self.fm.init(dim[1] + 1, dim[3] + 1, dim[5] + 1, depth, 1, 1, 1)
caster = vtk.vtkImageCast()
caster.SetOutputScalarTypeToShort()
caster.SetInput(bgImage)
caster.Update()
self.fm.SetInput(caster.GetOutput())
# self.fm.SetOutput(labelImage)
npoints = int(
(dim[1] + 1) * (dim[3] + 1) * (dim[5] + 1) * percentMax / 100.)
self.fm.setNPointsEvolution(npoints)
print('Setting active label to ' + str(self.editUtil.getLabel()))
self.fm.setActiveLabel(self.editUtil.getLabel())
nSeeds = self.fm.addSeedsFromImage(labelImage)
if nSeeds == 0:
return 0
self.fm.Modified()
self.fm.Update()
# TODO: need to call show() twice for data to be updated
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.undoRedo.saveState()
self.editUtil.getLabelImage().DeepCopy(self.fm.GetOutput())
self.editUtil.markVolumeNodeAsModified(
self.sliceLogic.GetLabelLayer().GetVolumeNode())
# print('FastMarching output image: '+str(output))
print('FastMarching march update completed')
return npoints
def DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm)-dcm.rfind('.dcm') == 4:
dcmList.append(inputDir+'/'+dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
print 'Will examine: ',dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb)-rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir+'/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir+'/'+f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.')+1:len(rgbList[0])]
print 'Extension for RGBs: ',rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ',len(dcmFileList), ' and rgb files: ',len(rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/')+1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx),5)
rgbCnt = rgbCnt+1
src = rgbDir+'/'+rgb
dest = tmpDir+'/'+name+'.'+rgbExt
rgbRenamedList.append(dest)
shutil.copy(src,dest)
break
rgbIdx = rgbIdx+1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file '+dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx+1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0,1,2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir,'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID',inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory','')
if dbFileName =='':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName +'/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def performInitialization(self,
image,
lowerThreshold,
upperThreshold,
sourceSeedIds,
targetSeedIds,
ignoreSideBranches=0):
'''
'''
# import the vmtk libraries
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cast = vtk.vtkImageCast()
cast.SetInputData(image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max(imageDimensions)
threshold = vtk.vtkImageThreshold()
threshold.SetInputData(image)
threshold.ThresholdBetween(lowerThreshold, upperThreshold)
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue(scalarRange[0] - scalarRange[1])
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInputData(thresholdedImage)
shiftScale.SetShift(-scalarRange[0])
shiftScale.SetScale(1.0 / (scalarRange[1] - scalarRange[0]))
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if ignoreSideBranches:
# ignore sidebranches, use colliding fronts
fastMarching = vtkvmtkSegmentation.vtkvmtkCollidingFrontsImageFilter(
)
fastMarching.SetInputData(speedImage)
fastMarching.SetSeeds1(sourceSeedIds)
fastMarching.SetSeeds2(targetSeedIds)
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = vtk.vtkImageMathematics()
subtract.SetInputData(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-10 * fastMarching.GetNegativeEpsilon())
subtract.Update()
else:
fastMarching = vtkvmtkSegmentation.vtkvmtkFastMarchingUpwindGradientImageFilter(
)
fastMarching.SetInputData(speedImage)
fastMarching.SetSeeds(sourceSeedIds)
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset(0.0)
fastMarching.SetTargets(targetSeedIds)
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = vtk.vtkImageMathematics()
subtract.SetInputData(fastMarching.GetOutput())
subtract.SetOperationToAddConstant()
subtract.SetConstantC(-fastMarching.GetTargetValue())
subtract.Update()
else:
subtract = vtk.vtkImageThreshold()
subtract.SetInputData(fastMarching.GetOutput())
subtract.ThresholdByLower(2000) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue(-1)
subtract.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(subtract.GetOutput())
return outImageData
def performInitialization( self, image, lowerThreshold, upperThreshold, sourceSeedIds, targetSeedIds, ignoreSideBranches=0 ):
'''
'''
# import the vmtk libraries
try:
#from libvtkvmtkSegmentationPython import *
import libvtkvmtkSegmentationPython as s
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk libraries!"
cast = vtk.vtkImageCast()
cast.SetInput( image )
cast.SetOutputScalarTypeToFloat()
cast.Update()
image = cast.GetOutput()
scalarRange = image.GetScalarRange()
imageDimensions = image.GetDimensions()
maxImageDimensions = max( imageDimensions )
threshold = vtk.vtkImageThreshold()
threshold.SetInput( image )
threshold.ThresholdBetween( lowerThreshold, upperThreshold )
threshold.ReplaceInOff()
threshold.ReplaceOutOn()
threshold.SetOutValue( scalarRange[0] - scalarRange[1] )
threshold.Update()
thresholdedImage = threshold.GetOutput()
scalarRange = thresholdedImage.GetScalarRange()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInput( thresholdedImage )
shiftScale.SetShift( -scalarRange[0] )
shiftScale.SetScale( 1.0 / ( scalarRange[1] - scalarRange[0] ) )
shiftScale.Update()
speedImage = shiftScale.GetOutput()
if ignoreSideBranches:
# ignore sidebranches, use colliding fronts
fastMarching = s.vtkvmtkCollidingFrontsImageFilter()
fastMarching.SetInput( speedImage )
fastMarching.SetSeeds1( sourceSeedIds )
fastMarching.SetSeeds2( targetSeedIds )
fastMarching.ApplyConnectivityOn()
fastMarching.StopOnTargetsOn()
fastMarching.Update()
subtract = vtk.vtkImageMathematics()
subtract.SetInput( fastMarching.GetOutput() )
subtract.SetOperationToAddConstant()
subtract.SetConstantC( -10 * fastMarching.GetNegativeEpsilon() )
subtract.Update()
else:
fastMarching = s.vtkvmtkFastMarchingUpwindGradientImageFilter()
fastMarching.SetInput( speedImage )
fastMarching.SetSeeds( sourceSeedIds )
fastMarching.GenerateGradientImageOn()
fastMarching.SetTargetOffset( 0.0 )
fastMarching.SetTargets( targetSeedIds )
if targetSeedIds.GetNumberOfIds() > 0:
fastMarching.SetTargetReachedModeToOneTarget()
else:
fastMarching.SetTargetReachedModeToNoTargets()
fastMarching.Update()
if targetSeedIds.GetNumberOfIds() > 0:
subtract = vtk.vtkImageMathematics()
subtract.SetInput( fastMarching.GetOutput() )
subtract.SetOperationToAddConstant()
subtract.SetConstantC( -fastMarching.GetTargetValue() )
subtract.Update()
else:
subtract = vtk.vtkImageThreshold()
subtract.SetInput( fastMarching.GetOutput() )
subtract.ThresholdByLower( 2000 ) # TODO find robuste value
subtract.ReplaceInOff()
subtract.ReplaceOutOn()
subtract.SetOutValue( -1 )
subtract.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy( subtract.GetOutput() )
outImageData.Update()
return outImageData
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 DoIt(inputDir, rgbDir, outputDir):
#
# Read the input DICOM series as a volume
#
dcmList = []
for dcm in os.listdir(inputDir):
if len(dcm) - dcm.rfind('.dcm') == 4:
dcmList.append(inputDir + '/' + dcm)
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
print 'Will examine: ', dcmList
indexer = ctk.ctkDICOMIndexer()
indexer.addDirectory(slicer.dicomDatabase, inputDir)
indexer.waitForImportFinished()
loadables = scalarVolumePlugin.examine([dcmList])
if len(loadables) == 0:
print 'Could not parse the DICOM Study!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
'''
sNode.ResetFileNameList()
for f in loadables[0].files:
sNode.AddFileName(f)
sNode.SetFileName(loadables[0].files[0])
sNode.SetSingleFile(0)
inputVolume = slicer.vtkMRMLScalarVolumeNode()
sNode.ReadData(inputVolume)
'''
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'input_volume.nrrd'))
sNode.WriteData(inputVolume)
#
# Order the input RGBs and rename in a temp directory
#
rgbList = []
for rgb in os.listdir(rgbDir):
if len(rgb) - rgb.rfind('.bmp') == 4:
rgbList.append(rgb)
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
tmpDir = tmpDir + '/PNGStackLabelConverter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
oldFiles = os.listdir(tmpDir)
# just in case there is anything in that directory
for f in oldFiles:
os.unlink(tmpDir + '/' + f)
rgbOrdered = [None] * len(loadables[0].files)
rgbCnt = 0
rgbExt = rgbList[0][rgbList[0].rfind('.') + 1:len(rgbList[0])]
print 'Extension for RGBs: ', rgbExt
dcmFileList = loadables[0].files
rgbRenamedList = []
print 'Number of dcm files: ', len(dcmFileList), ' and rgb files: ', len(
rgbOrdered)
dcmIdx = 0
for dcm in dcmFileList:
rgbIdx = 0
for rgb in rgbList:
dcmPrefix = dcm[dcm.rfind('/') + 1:dcm.rfind('.')]
if rgb.find(dcmPrefix) != -1:
name = string.zfill(str(dcmIdx), 5)
rgbCnt = rgbCnt + 1
src = rgbDir + '/' + rgb
dest = tmpDir + '/' + name + '.' + rgbExt
rgbRenamedList.append(dest)
shutil.copy(src, dest)
break
rgbIdx = rgbIdx + 1
# remove the matched DICOM file from the list
if rgbIdx == len(rgbList):
print('ERROR: failed to find matching label file for DICOM file ' +
dcm)
return
del rgbList[rgbIdx]
dcmIdx = dcmIdx + 1
if len(rgbRenamedList) == 0:
print 'Could not parse the DICOM Study!'
return
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.ResetFileNameList()
for f in rgbRenamedList:
sNode.AddFileName(f)
sNode.SetFileName(rgbRenamedList[0])
sNode.SetSingleFile(0)
inputRGBVolume = slicer.vtkMRMLVectorVolumeNode()
sNode.ReadData(inputRGBVolume)
# run the filter
# - extract the RGB portions
extract = vtk.vtkImageExtractComponents()
extract.SetComponents(0, 1, 2)
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
extract.SetInput(inputRGBVolume.GetImageData())
else:
extract.SetInputData(inputRGBVolume.GetImageData())
luminance = vtk.vtkImageLuminance()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
luminance.SetInput(extract.GetOutput())
else:
luminance.SetInputData(extract.GetOutput())
cast = vtk.vtkImageCast()
if vtk.vtkVersion().GetVTKMajorVersion() < 6:
cast.SetInput(luminance.GetOutput())
else:
cast.SetInputData(luminance.GetOutput())
cast.SetOutputScalarTypeToShort()
cast.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputLabel = slicer.vtkMRMLLabelMapVolumeNode()
outputLabel.SetIJKToRASMatrix(ijkToRAS)
outputLabel.SetAndObserveImageData(cast.GetOutput())
reportingLogic = slicer.modules.reporting.logic()
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(
reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
outputLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
sNode.SetWriteFileFormat('nrrd')
sNode.SetFileName(os.path.join(outputDir, 'label_output.nrrd'))
sNode.WriteData(outputLabel)
# save as DICOM SEG
labelCollection = vtk.vtkCollection()
labelCollection.AddItem(outputLabel)
slicer.mrmlScene.AddNode(inputVolume)
outputLabel.SetAttribute('AssociatedNodeID', inputVolume.GetID())
slicer.mrmlScene.AddNode(outputLabel)
# initialize the DICOM DB for Reporting logic
settings = qt.QSettings()
dbFileName = settings.value('DatabaseDirectory', '')
if dbFileName == '':
print('ERROR: database must be initialized')
else:
dbFileName = dbFileName + '/ctkDICOM.sql'
reportingLogic.InitializeDICOMDatabase(dbFileName)
reportingLogic.DicomSegWrite(labelCollection, outputDir)
def fastMarching(self,percentMax):
self.fm = None
# allocate a new filter each time March is hit
bgImage = EditUtil.getBackgroundImage()
labelImage = EditUtil.getLabelImage()
# collect seeds
if vtk.VTK_MAJOR_VERSION <= 5:
dim = bgImage.GetWholeExtent()
else:
dim = bgImage.GetDimensions()
print dim
# initialize the filter
self.fm = slicer.vtkPichonFastMarching()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1]-scalarRange[0]
# this is more or less arbitrary; large depth values will bring the
# algorithm to the knees
scaleValue = 0
shiftValue = 0
if depth>300:
scaleValue = 300./depth
if scalarRange[0] < 0:
shiftValue = scalarRange[0]*-1
if scaleValue or shiftValue:
rescale = vtk.vtkImageShiftScale()
if vtk.VTK_MAJOR_VERSION <= 5:
rescale.SetInput(bgImage)
else:
rescale.SetInputData(bgImage)
rescale.SetScale(scaleValue)
rescale.SetShift(shiftValue)
rescale.Update()
bgImage = rescale.GetOutput()
scalarRange = bgImage.GetScalarRange()
depth = scalarRange[1]-scalarRange[0]
print('Input scalar range: '+str(depth))
if vtk.VTK_MAJOR_VERSION <= 5:
self.fm.init(dim[1]+1, dim[3]+1, dim[5]+1, depth, 1, 1, 1)
else:
self.fm.init(dim[0], dim[1], dim[2], depth, 1, 1, 1)
caster = vtk.vtkImageCast()
caster.SetOutputScalarTypeToShort()
if vtk.VTK_MAJOR_VERSION <= 5:
caster.SetInput(bgImage)
caster.Update()
self.fm.SetInput(caster.GetOutput())
else:
caster.SetInputData(bgImage)
self.fm.SetInputConnection(caster.GetOutputPort())
# self.fm.SetOutput(labelImage)
if vtk.VTK_MAJOR_VERSION <= 5:
npoints = int((dim[1]+1)*(dim[3]+1)*(dim[5]+1)*percentMax/100.)
else:
npoints = int(dim[0]*dim[1]*dim[2]*percentMax/100.)
self.fm.setNPointsEvolution(npoints)
print('Setting active label to '+str(EditUtil.getLabel()))
self.fm.setActiveLabel(EditUtil.getLabel())
nSeeds = self.fm.addSeedsFromImage(labelImage)
if nSeeds == 0:
return 0
self.fm.Modified()
self.fm.Update()
# TODO: need to call show() twice for data to be updated
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.fm.show(1)
self.fm.Modified()
self.fm.Update()
self.undoRedo.saveState()
EditUtil.getLabelImage().DeepCopy(self.fm.GetOutput())
EditUtil.markVolumeNodeAsModified(self.sliceLogic.GetLabelLayer().GetVolumeNode())
# print('FastMarching output image: '+str(output))
print('FastMarching march update completed')
return npoints
def GetDistanceMap(self,edgeImg,altedgeImg):
tmpimage=vtk.vtkImageData()
cast=vtk.vtkImageCast()
cast.SetOutputScalarTypeToDouble()
cast.SetInputData(edgeImg)
cast.Update()
#invert edge image edge=0 and background=2x
Math=vtk.vtkImageMathematics()
Math.SetInput1Data(cast.GetOutput())
Math.SetConstantC(0)
Math.SetConstantK(2)
Math.SetOperationToReplaceCByK()
Math.Update()
tmpimage.DeepCopy(Math.GetOutput())
Math.SetInput1Data(tmpimage)
Math.SetConstantC(1)
Math.SetConstantK(0)
Math.Update()
cast.SetInputData(Math.GetOutput())
cast.Update()
tmpimage.DeepCopy(cast.GetOutput())
tmpimage2=vtk.vtkImageData()
#calculate distance map
if self.distalg==0:
dm=slicer.vtkITKSignedDistanceTransform()
# tmpimage.SetSpacing(self.input.GetSpacing())
# dm.SetUseImageSpacing(True)
dm.SetAlgorithmToSignedMaurer()
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==1:
dm=slicer.vtkITKSignedDistanceTransform()
dm.SetAlgorithmToApproximateSigned()
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==2:
dm=slicer.vtkITKSignedDistanceTransform()
# tmpimage.SetSpacing(self.input.GetSpacing())
# dm.SetUseImageSpacing(True)
dm.SetAlgorithmToSignedDanielsson()
dm.SetObjectValue(2)
dm.SetInputData(tmpimage)
dm.Update()
tmpimage2.DeepCopy(dm.GetOutput())
elif self.distalg==3:
dm=vtk.vtkImageEuclideanDistance()
#tmpimage.SetSpacing(self.input.GetSpacing())
dm.InitializeOn()
#dm.ConsiderAnisotropyOn()
dm.SetInputData(tmpimage)
dm.Update()
Math.SetInputData(dm.GetOutput())
Math.SetOperationToSquareRoot()
Math.Update()
tmpimage2.DeepCopy(Math.GetOutput())
if not altedgeImg:
altedgeImg=tmpimage2
qu=QCLib.QCUtil()
rect=qu.minRectangle(self.ROI)
for i in range(rect['xmin'].__len__()):
if rect['xmin'][i]>=0:
index=i
break
xmin=rect['xmin'][index]
xmax=rect['xmax'][index]
ymin=rect['ymin'][index]
ymax=rect['ymax'][index]
distMap=vtk.vtkImageData()
distMap.DeepCopy(edgeImg)
for x in range(xmin,xmax+1):
for y in range(ymin,ymax+1):
isedge=math.copysign(edgeImg.GetScalarComponentAsDouble(x,y,index,0)-1,1)
if self.distalg!=3:
val=math.copysign((math.fabs(tmpimage2.GetScalarComponentAsDouble(x,y,index,0))+1)*isedge,altedgeImg.GetScalarComponentAsDouble(x,y,index,0))
else:
val=math.copysign((math.fabs(tmpimage2.GetScalarComponentAsDouble(x,y,index,0)))*isedge,altedgeImg.GetScalarComponentAsDouble(x,y,index,0))
distMap.SetScalarComponentFromDouble(x,y,index,0,val)
return distMap
def recolorLabelMap(self, modelNode, labelMap, initialValue, outputValue):
import vtkSlicerRtCommonPython
if (modelNode != None and labelMap != None):
self.labelMapImgData = labelMap.GetImageData()
self.resectionPolyData = modelNode.GetPolyData()
# IJK -> RAS
ijkToRasMatrix = vtk.vtkMatrix4x4()
labelMap.GetIJKToRASMatrix(ijkToRasMatrix)
# RAS -> IJK
rasToIjkMatrix = vtk.vtkMatrix4x4()
labelMap.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
rasToIjkTransform.Update()
# Transform Resection model from RAS -> IJK
polyDataTransformFilter = vtk.vtkTransformPolyDataFilter()
if (vtk.VTK_MAJOR_VERSION <= 5):
polyDataTransformFilter.SetInput(self.resectionPolyData)
else:
polyDataTransformFilter.SetInputData(self.resectionPolyData)
polyDataTransformFilter.SetTransform(rasToIjkTransform)
polyDataTransformFilter.Update()
# Convert Resection model to label map
polyDataToLabelmapFilter = vtkSlicerRtCommonPython.vtkPolyDataToLabelmapFilter(
)
polyDataToLabelmapFilter.SetInputPolyData(
polyDataTransformFilter.GetOutput())
polyDataToLabelmapFilter.SetReferenceImage(self.labelMapImgData)
polyDataToLabelmapFilter.UseReferenceValuesOn()
polyDataToLabelmapFilter.SetBackgroundValue(0)
polyDataToLabelmapFilter.SetLabelValue(outputValue)
polyDataToLabelmapFilter.Update()
# Cast resection label map to unsigned char for use with mask filter
castFilter = vtk.vtkImageCast()
if (vtk.VTK_MAJOR_VERSION <= 5):
castFilter.SetInput(polyDataToLabelmapFilter.GetOutput())
else:
castFilter.SetInputData(polyDataToLabelmapFilter.GetOutput())
castFilter.SetOutputScalarTypeToUnsignedChar()
castFilter.Update()
# Create mask for recoloring the original label map
maskFilter = vtk.vtkImageMask()
if (vtk.VTK_MAJOR_VERSION <= 5):
maskFilter.SetImageInput(self.labelMapImgData)
maskFilter.SetMaskInput(castFilter.GetOutput())
else:
maskFilter.SetImageInputData(self.labelMapImgData)
maskFilter.SetMaskInputData(castFilter.GetOutput())
maskFilter.SetMaskedOutputValue(outputValue)
maskFilter.NotMaskOn()
maskFilter.Update()
self.labelMapImgData = maskFilter.GetOutput()
self.labelMapImgData.Modified()
labelMap.SetAndObserveImageData(self.labelMapImgData)