def CreateNewNode(self, colorName, color, dim, origin):
# we add a pseudo-random number to the name of our empty volume to avoid the risk of having a volume called
# exactly the same by the user which could be confusing. We could also have used slicer.app.sessionId()
if colorName not in self.colorSliceVolumes.keys():
VolumeName = "EasyClip_EmptyVolume_" + str(slicer.app.applicationPid()) + "_" + colorName
# Do NOT set the spacing and the origin of imageData (vtkImageData)
# The spacing and the origin should only be set in the vtkMRMLScalarVolumeNode!!!!!!
# We only create an image of 1 voxel (as we only use it to color the planes
imageData = vtk.vtkImageData()
imageData.SetDimensions(1, 1, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
imageData.SetScalarComponentFromDouble(0, 0, 0, 0, color)
if hasattr(slicer, 'vtkMRMLLabelMapVolumeNode'):
sampleVolumeNode = slicer.vtkMRMLLabelMapVolumeNode()
else:
sampleVolumeNode = slicer.vtkMRMLScalarVolumeNode()
sampleVolumeNode = slicer.mrmlScene.AddNode(sampleVolumeNode)
sampleVolumeNode.SetName(VolumeName)
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
colorNode = slicer.util.getNode('GenericAnatomyColors')
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
sampleVolumeNode.SetAndObserveImageData(imageData)
sampleVolumeNode.SetAndObserveDisplayNodeID(labelmapVolumeDisplayNode.GetID())
labelmapVolumeDisplayNode.VisibilityOff()
self.colorSliceVolumes[colorName] = sampleVolumeNode.GetID()
sampleVolumeNode = slicer.mrmlScene.GetNodeByID(self.colorSliceVolumes[colorName])
sampleVolumeNode.HideFromEditorsOn()
sampleVolumeNode.SetOrigin(origin[0], origin[1], origin[2])
sampleVolumeNode.SetSpacing(dim[0], dim[1], dim[2])
if not hasattr(slicer, 'vtkMRMLLabelMapVolumeNode'):
sampleVolumeNode.SetLabelMap(1)
sampleVolumeNode.SetHideFromEditors(True)
sampleVolumeNode.SetSaveWithScene(False)
return sampleVolumeNode
def initializeNewLabel(newLabel, sourceVolume):
displayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLLabelMapVolumeDisplayNode())
threshold = vtk.vtkImageThreshold()
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetInValue(0)
threshold.SetOutValue(0)
threshold.SetOutputScalarTypeToUnsignedShort()
threshold.SetInput(sourceVolume.GetImageData())
threshold.Update()
labelImage = vtk.vtkImageData()
labelImage.DeepCopy(threshold.GetOutput())
newLabel.SetAndObserveStorageNodeID(None)
newLabel.SetLabelMap(1)
newLabel.CopyOrientation(sourceVolume)
ras2ijk = vtk.vtkMatrix4x4()
sourceVolume.GetRASToIJKMatrix(ras2ijk)
newLabel.SetRASToIJKMatrix(ras2ijk)
newLabel.SetAttribute('ReportingReportNodeID', sourceVolume.GetAttribute('ReportingReportNodeID'))
newLabel.SetAttribute('AssociatedNodeID', sourceVolume.GetID())
newLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
newLabel.SetAndObserveImageData(labelImage)
def createSampleLabelmapVolumeNode(self, volumeNode, name, label, colorNode=None):
self.assertTrue( volumeNode != None )
self.assertTrue( volumeNode.IsA('vtkMRMLScalarVolumeNode') )
self.assertTrue( label > 0 )
sampleLabelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
sampleLabelmapNode.SetName(name)
sampleLabelmapNode = slicer.mrmlScene.AddNode(sampleLabelmapNode)
sampleLabelmapNode.Copy(volumeNode)
imageData = vtk.vtkImageData()
imageData.DeepCopy(volumeNode.GetImageData())
sampleLabelmapNode.SetAndObserveImageData(imageData)
extent = imageData.GetExtent()
for x in xrange(extent[0], extent[1]+1):
for y in xrange(extent[2], extent[3]+1):
for z in xrange(extent[4], extent[5]+1):
if (x >= (extent[1]/4) and x <= (extent[1]/4) * 3) and (y >= (extent[3]/4) and y <= (extent[3]/4) * 3) and (z >= (extent[5]/4) and z <= (extent[5]/4) * 3):
imageData.SetScalarComponentFromDouble(x,y,z,0,label)
else:
imageData.SetScalarComponentFromDouble(x,y,z,0,0)
# Display labelmap
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
if colorNode == None:
colorNode = slicer.util.getNode('GenericAnatomyColors')
self.assertTrue( colorNode != None )
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelmapVolumeDisplayNode.VisibilityOn()
sampleLabelmapNodeName = slicer.mrmlScene.GenerateUniqueName(name)
sampleLabelmapNode.SetName(sampleLabelmapNodeName)
sampleLabelmapNode.SetAndObserveDisplayNodeID(labelmapVolumeDisplayNode.GetID())
return sampleLabelmapNode
def initializeNewLabel(newLabel, sourceVolume):
displayNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLLabelMapVolumeDisplayNode())
threshold = vtk.vtkImageThreshold()
threshold.ReplaceInOn()
threshold.ReplaceOutOn()
threshold.SetInValue(0)
threshold.SetOutValue(0)
threshold.SetOutputScalarTypeToUnsignedShort()
threshold.SetInput(sourceVolume.GetImageData())
threshold.Update()
labelImage = vtk.vtkImageData()
labelImage.DeepCopy(threshold.GetOutput())
newLabel.SetAndObserveStorageNodeID(None)
newLabel.SetLabelMap(1)
newLabel.CopyOrientation(sourceVolume)
ras2ijk = vtk.vtkMatrix4x4()
sourceVolume.GetRASToIJKMatrix(ras2ijk)
newLabel.SetRASToIJKMatrix(ras2ijk)
newLabel.SetAttribute('AssociatedNodeID', sourceVolume.GetID())
newLabel.SetAndObserveDisplayNodeID(displayNode.GetID())
newLabel.SetAndObserveImageData(labelImage)
def renderLabelMap(self):
# Initializes a vtkMRMLScalarVolumeNode for the SegmentCAD Output and copies ijkToRAS matrix and Image data from nodeLabel
ijkToRASMatrix = vtk.vtkMatrix4x4()
self.volumePre.GetIJKToRASMatrix(ijkToRASMatrix)
self.SegmentCADLabelMap.SetIJKToRASMatrix(ijkToRASMatrix)
SegmentCADLabelMapImageData = vtk.vtkImageData()
SegmentCADLabelMapImageData.DeepCopy(self.volumePre.GetImageData())
SegmentCADLabelMapPointData = SegmentCADLabelMapImageData.GetPointData()
# Numpy array is converted from signed int16 to signed vtkShortArray
scalarArray = vtk.vtkShortArray()
dims1D = SegmentCADLabelMapPointData.GetScalars().GetSize()
self.nodeArraySegmentCADLabel = self.nodeArraySegmentCADLabel.reshape(dims1D, order='C')
scalarArray = vtk.util.numpy_support.numpy_to_vtk(self.nodeArraySegmentCADLabel)
# PointData() of SegmentCAD label output pointed to new vtkShortArray for scalar values
SegmentCADLabelMapImageData.SetScalarTypeToShort()
SegmentCADLabelMapPointData.SetScalars(scalarArray)
SegmentCADLabelMapPointData.Update()
SegmentCADLabelMapImageData.Update()
self.SegmentCADLabelMap.SetAndObserveImageData(SegmentCADLabelMapImageData)
# Corresponding display node and color table nodes created for SegmentCAD label Output
self.SegmentCADLabelMapDisplay = slicer.vtkMRMLLabelMapVolumeDisplayNode()
self.SegmentCADLabelMapDisplay.SetScene(slicer.mrmlScene)
self.SegmentCADLabelMapDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
self.SegmentCADLabelMapDisplay.SetInputImageData(SegmentCADLabelMapImageData)
self.SegmentCADLabelMapDisplay.UpdateImageDataPipeline()
slicer.mrmlScene.AddNode(self.SegmentCADLabelMapDisplay)
self.SegmentCADLabelMap.SetAndObserveDisplayNodeID(self.SegmentCADLabelMapDisplay.GetID())
self.SegmentCADLabelMapDisplay.UpdateScene(slicer.mrmlScene)
def renderLabelMap(self):
# Initializes a vtkMRMLScalarVolumeNode for the SegmentCAD Output and copies ijkToRAS matrix and Image data from nodeLabel
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
self.nodePre.GetRASToIJKMatrix(ras2ijk)
self.nodePre.GetIJKToRASMatrix(ijk2ras)
self.SegmentCADLabelMap.SetRASToIJKMatrix(ras2ijk)
self.SegmentCADLabelMap.SetIJKToRASMatrix(ijk2ras)
SegmentCADLabelMapImageData = vtk.vtkImageData()
SegmentCADLabelMapImageData.DeepCopy(self.nodePre.GetImageData())
SegmentCADLabelMapPointData = SegmentCADLabelMapImageData.GetPointData()
# Numpy array is converted from signed int16 to signed vtkShortArray
scalarArray = vtk.vtkShortArray()
dims1D = SegmentCADLabelMapPointData.GetScalars().GetSize()
self.nodeArraySegmentCADLabel = self.nodeArraySegmentCADLabel.reshape(dims1D, order='C') #use a flattening function
scalarArray = vtk.util.numpy_support.numpy_to_vtk(self.nodeArraySegmentCADLabel)
# PointData() of SegmentCAD label output pointed to new vtkShortArray for scalar values
if vtk.VTK_MAJOR_VERSION <= 5:
#SegmentCADLabelMapImageData.SetScalarTypeToShort()
SegmentCADLabelMapPointData.SetScalars(scalarArray)
SegmentCADLabelMapPointData.Update()
else:
#SegmentCADLabelMapImageData.SetScalarType(4)
SegmentCADLabelMapPointData.SetScalars(scalarArray)
SegmentCADLabelMapImageData.Modified()
self.SegmentCADLabelMap.SetAndObserveImageData(SegmentCADLabelMapImageData)
# Corresponding display node and color table nodes created for SegmentCAD label Output
self.SegmentCADLabelMapDisplay = slicer.vtkMRMLLabelMapVolumeDisplayNode()
self.SegmentCADLabelMapDisplay.SetScene(slicer.mrmlScene)
self.SegmentCADLabelMapDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
if vtk.VTK_MAJOR_VERSION <= 5:
self.SegmentCADLabelMapDisplay.SetInputImageData(self.SegmentCADLabelMap.GetImageData())
else:
self.SegmentCADLabelMapDisplay.SetInputImageDataConnection(self.SegmentCADLabelMap.GetImageDataConnection())
self.SegmentCADLabelMapDisplay.UpdateImageDataPipeline()
slicer.mrmlScene.AddNode(self.SegmentCADLabelMapDisplay)
self.SegmentCADLabelMap.SetAndObserveDisplayNodeID(self.SegmentCADLabelMapDisplay.GetID())
self.SegmentCADLabelMapDisplay.UpdateScene(slicer.mrmlScene)
#red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
#red_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
#yellow_logic = slicer.app.layoutManager().sliceWidget("Yellow").sliceLogic()
#yellow_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
#green_logic = slicer.app.layoutManager().sliceWidget("Green").sliceLogic()
#green_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID(self.nodePre.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(self.SegmentCADLabelMap.GetID())
#selectionNode.SetReferenceSecondaryVolumeID(self.node1.GetID())
appLogic.PropagateVolumeSelection()
def loadData(self):
""" Load some default data for development and set up a viewing scenario for it.
"""
self.logging.debug("call")
dataDialog = qt.QPushButton();
dataDialog.setText('Loading files for session %s...' % self.currentSession);
dataDialog.show()
volumeLogic = slicer.modules.volumes.logic()
t1NodeName = '%s_t1_average' % self.currentSession
t1VolumeNode = slicer.util.getNode(t1NodeName)
if t1VolumeNode is None:
self.logging.debug("%s = %s", 't1_average', self.sessionFiles['t1_average'])
try:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles['t1_average'], t1NodeName, 0, None)
except TypeError:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles['t1_average'], t1NodeName, 0)
if slicer.util.getNode(t1NodeName) is None:
self.logging.error("Could not load session file for T1: %s", self.sessionFiles['t1_average'])
t1VolumeNode = slicer.util.getNode(t1NodeName)
t1VolumeNode.CreateDefaultDisplayNodes()
t1VolumeNode.GetDisplayNode().AutoWindowLevelOn()
t2NodeName = '%s_t2_average' % self.currentSession
t2VolumeNode = slicer.util.getNode(t2NodeName)
if t2VolumeNode is None:
self.logging.debug("%s = %s", 't2_average', self.sessionFiles['t2_average'])
try:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles['t2_average'], t2NodeName, 0, None)
except TypeError:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles['t2_average'], t2NodeName, 0)
if slicer.util.getNode(t2NodeName) is None:
self.logging.error("Could not load session file for T2: %s", self.sessionFiles['t2_average'])
t2VolumeNode = slicer.util.getNode(t2NodeName)
t2VolumeNode.CreateDefaultDisplayNodes()
t2VolumeNode.GetDisplayNode().AutoWindowLevelOn()
for region in self.regions:
regionNodeName = '%s_%s' % (self.currentSession, region)
regionNode = slicer.util.getNode(regionNodeName)
if regionNode is None:
self.logging.debug("%s = %s", region, self.sessionFiles[region])
try:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles[region], regionNodeName, 1, None)
except TypeError:
volumeLogic.AddArchetypeScalarVolume(self.sessionFiles[region], regionNodeName, 1)
if slicer.util.getNode(regionNodeName) is None:
self.logging.error("Could not load session file for region %s! File: %s", region, self.sessionFiles[region])
regionNode = slicer.util.getNode(regionNodeName)
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
regionNode.SetAndObserveNthDisplayNodeID(0, displayNode.GetID())
dataDialog.close()
def CreateNewNode(self, colorName, color, dim, origin):
# we add a pseudo-random number to the name of our empty volume to avoid the risk of having a volume called
# exactly the same by the user which could be confusing. We could also have used slicer.app.sessionId()
if colorName not in self.colorSliceVolumes.keys():
VolumeName = "EasyClip_EmptyVolume_" + str(
slicer.app.applicationPid()) + "_" + colorName
# Do NOT set the spacing and the origin of imageData (vtkImageData)
# The spacing and the origin should only be set in the vtkMRMLScalarVolumeNode!!!!!!
# We only create an image of 1 voxel (as we only use it to color the planes
imageData = vtk.vtkImageData()
imageData.SetDimensions(1, 1, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
imageData.SetScalarComponentFromDouble(0, 0, 0, 0, color)
if hasattr(slicer, 'vtkMRMLLabelMapVolumeNode'):
sampleVolumeNode = slicer.vtkMRMLLabelMapVolumeNode()
else:
sampleVolumeNode = slicer.vtkMRMLScalarVolumeNode()
sampleVolumeNode = slicer.mrmlScene.AddNode(sampleVolumeNode)
sampleVolumeNode.SetName(VolumeName)
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode(
)
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
colorNode = slicer.util.getNode('GenericAnatomyColors')
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(
colorNode.GetID())
sampleVolumeNode.SetAndObserveImageData(imageData)
sampleVolumeNode.SetAndObserveDisplayNodeID(
labelmapVolumeDisplayNode.GetID())
labelmapVolumeDisplayNode.VisibilityOff()
self.colorSliceVolumes[colorName] = sampleVolumeNode.GetID()
sampleVolumeNode = slicer.mrmlScene.GetNodeByID(
self.colorSliceVolumes[colorName])
sampleVolumeNode.HideFromEditorsOn()
sampleVolumeNode.SetOrigin(origin[0], origin[1], origin[2])
sampleVolumeNode.SetSpacing(dim[0], dim[1], dim[2])
if not hasattr(slicer, 'vtkMRMLLabelMapVolumeNode'):
sampleVolumeNode.SetLabelMap(1)
sampleVolumeNode.SetHideFromEditors(True)
sampleVolumeNode.SetSaveWithScene(False)
return sampleVolumeNode
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 renderLabelMap(self):
# Initializes a vtkMRMLScalarVolumeNode for the SegmentCAD Output and copies ijkToRAS matrix and Image data from nodeLabel
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
self.nodePre.GetRASToIJKMatrix(ras2ijk)
self.nodePre.GetIJKToRASMatrix(ijk2ras)
self.SegmentCADLabelMap.SetRASToIJKMatrix(ras2ijk)
self.SegmentCADLabelMap.SetIJKToRASMatrix(ijk2ras)
SegmentCADLabelMapImageData = vtk.vtkImageData()
SegmentCADLabelMapImageData.DeepCopy(self.nodePre.GetImageData())
SegmentCADLabelMapPointData = SegmentCADLabelMapImageData.GetPointData(
)
# Numpy array is converted from signed int16 to signed vtkShortArray
scalarArray = vtk.vtkShortArray()
dims1D = SegmentCADLabelMapPointData.GetScalars().GetSize()
self.nodeArraySegmentCADLabel = self.nodeArraySegmentCADLabel.reshape(
dims1D, order='C') #use a flattening function
scalarArray = vtk.util.numpy_support.numpy_to_vtk(
self.nodeArraySegmentCADLabel)
# PointData() of SegmentCAD label output pointed to new vtkShortArray for scalar values
if vtk.VTK_MAJOR_VERSION <= 5:
#SegmentCADLabelMapImageData.SetScalarTypeToShort()
SegmentCADLabelMapPointData.SetScalars(scalarArray)
SegmentCADLabelMapPointData.Update()
else:
#SegmentCADLabelMapImageData.SetScalarType(4)
SegmentCADLabelMapPointData.SetScalars(scalarArray)
SegmentCADLabelMapImageData.Modified()
self.SegmentCADLabelMap.SetAndObserveImageData(
SegmentCADLabelMapImageData)
# Corresponding display node and color table nodes created for SegmentCAD label Output
self.SegmentCADLabelMapDisplay = slicer.vtkMRMLLabelMapVolumeDisplayNode(
)
self.SegmentCADLabelMapDisplay.SetScene(slicer.mrmlScene)
self.SegmentCADLabelMapDisplay.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericColors.txt')
if vtk.VTK_MAJOR_VERSION <= 5:
self.SegmentCADLabelMapDisplay.SetInputImageData(
self.SegmentCADLabelMap.GetImageData())
else:
self.SegmentCADLabelMapDisplay.SetInputImageDataConnection(
self.SegmentCADLabelMap.GetImageDataConnection())
self.SegmentCADLabelMapDisplay.UpdateImageDataPipeline()
slicer.mrmlScene.AddNode(self.SegmentCADLabelMapDisplay)
self.SegmentCADLabelMap.SetAndObserveDisplayNodeID(
self.SegmentCADLabelMapDisplay.GetID())
self.SegmentCADLabelMapDisplay.UpdateScene(slicer.mrmlScene)
#red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
#red_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
#yellow_logic = slicer.app.layoutManager().sliceWidget("Yellow").sliceLogic()
#yellow_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
#green_logic = slicer.app.layoutManager().sliceWidget("Green").sliceLogic()
#green_logic.GetSliceCompositeNode().SetLabelVolumeID(self.SegmentCADLabelMap.GetID())
appLogic = slicer.app.applicationLogic()
selectionNode = appLogic.GetSelectionNode()
#selectionNode.SetReferenceActiveVolumeID(self.nodePre.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
self.SegmentCADLabelMap.GetID())
#selectionNode.SetReferenceSecondaryVolumeID(self.node1.GetID())
appLogic.PropagateVolumeSelection()
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 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 onComputeBox(self):
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
bound = [MAXINT, -MAXINT, MAXINT, -MAXINT, MAXINT, -MAXINT]
for i in range (3,numNodes):
self.elements = slicer.mrmlScene.GetNthNodeByClass(i,"vtkMRMLModelNode" )
node = slicer.util.getNode(self.elements.GetName())
polydata = node.GetPolyData()
tempbound = polydata.GetBounds()
bound[0] = min(bound[0], tempbound[0])
bound[2] = min(bound[2], tempbound[2])
bound[4] = min(bound[4], tempbound[4])
bound[1] = max(bound[1], tempbound[1])
bound[3] = max(bound[3], tempbound[3])
bound[5] = max(bound[5], tempbound[5])
#--------------------------- Box around the model --------------------------#
# print "bound", bound
dimX = bound[1]-bound[0]
dimY = bound[3]-bound[2]
dimZ = bound[5]-bound[4]
# print "dimension X :", dimX
# print "dimension Y :", dimY
# print "dimension Z :", dimZ
dimX = dimX + 10
dimY = dimY + 10
dimZ = dimZ + 10
sampleVolumeNode = slicer.vtkMRMLScalarVolumeNode()
sampleVolumeNode = slicer.mrmlScene.AddNode(sampleVolumeNode)
imageData = vtk.vtkImageData()
# Do NOT set the spacing and the origin of imageData (vtkImageData)
# The spacing and the origin should only be set in the vtkMRMLScalarVolumeNode!!!!!!
imageData.SetDimensions(int(dimX), int(dimY), int(dimZ))
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
extent = imageData.GetExtent()
for x in xrange(extent[0], extent[1]+1):
for y in xrange(extent[2], extent[3]+1):
for z in xrange(extent[4], extent[5]+1):
imageData.SetScalarComponentFromDouble(x,y,z,0,0)
sampleVolumeNode.SetSpacing(1, 1, 1)
sampleVolumeNode.SetOrigin(bound[0], bound[2], bound[4])
sampleVolumeNode.SetName("Empty_volume")
sampleVolumeNode.SetAndObserveImageData(imageData)
sampleVolumeNode.SetLabelMap(1)
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
colorNode = slicer.util.getNode('GenericAnatomyColors')
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelmapVolumeDisplayNode.VisibilityOn()
sampleVolumeNode.SetAndObserveDisplayNodeID(labelmapVolumeDisplayNode.GetID())
count = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLSliceCompositeNode')
for n in xrange(count):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLSliceCompositeNode')
compNode.SetBackgroundVolumeID(sampleVolumeNode.GetID())
def DoIt(inputDir, labelFile, outputDir, forceLabel):
dbDir1 = slicer.app.temporaryPath+'/LabelConverter'
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]
try:
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!'
exit()
inputVolume = scalarVolumePlugin.load(loadables[0])
slicer.mrmlScene.AddNode(inputVolume)
print('Input volume loaded!')
# read the label volume
labelVolume = slicer.vtkMRMLScalarVolumeNode()
sNode = slicer.vtkMRMLVolumeArchetypeStorageNode()
sNode.SetFileName(labelFile)
sNode.ReadData(labelVolume)
labelVolume.LabelMapOn()
if forceLabel>0:
print('Forcing label to '+str(forceLabel))
labelImage = labelVolume.GetImageData()
thresh = vtk.vtkImageThreshold()
thresh.SetInput(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)
# resample label to the input volume raster
resampledLabel = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(resampledLabel)
eye = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(eye)
parameters = {}
parameters['inputVolume'] = labelVolume.GetID()
parameters['referenceVolume'] = inputVolume.GetID()
parameters['outputVolume'] = resampledLabel.GetID()
parameters['warpTransform'] = eye.GetID()
parameters['interpolationMode'] = 'NearestNeighbor'
parameters['pixelType'] = 'ushort'
cliNode = None
cliNode = slicer.cli.run(slicer.modules.brainsresample, None, parameters, 1)
labelVolume = resampledLabel
displayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
displayNode.SetAndObserveColorNodeID(reportingLogic.GetDefaultColorNode().GetID())
slicer.mrmlScene.AddNode(displayNode)
labelVolume.SetAttribute('AssociatedNodeID',inputVolume.GetID())
labelVolume.LabelMapOn()
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)
except:
print('Error occurred!')
dicomWidget.onDatabaseDirectoryChanged(dbDir0)
exit()
def onComputeBox(self):
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
bound = [MAXINT, -MAXINT, MAXINT, -MAXINT, MAXINT, -MAXINT]
for i in range(3, numNodes):
self.elements = slicer.mrmlScene.GetNthNodeByClass(
i, "vtkMRMLModelNode")
node = slicer.util.getNode(self.elements.GetName())
polydata = node.GetPolyData()
tempbound = polydata.GetBounds()
bound[0] = min(bound[0], tempbound[0])
bound[2] = min(bound[2], tempbound[2])
bound[4] = min(bound[4], tempbound[4])
bound[1] = max(bound[1], tempbound[1])
bound[3] = max(bound[3], tempbound[3])
bound[5] = max(bound[5], tempbound[5])
#--------------------------- Box around the model --------------------------#
# print "bound", bound
dimX = bound[1] - bound[0]
dimY = bound[3] - bound[2]
dimZ = bound[5] - bound[4]
# print "dimension X :", dimX
# print "dimension Y :", dimY
# print "dimension Z :", dimZ
dimX = dimX + 10
dimY = dimY + 10
dimZ = dimZ + 10
sampleVolumeNode = slicer.vtkMRMLScalarVolumeNode()
sampleVolumeNode = slicer.mrmlScene.AddNode(sampleVolumeNode)
imageData = vtk.vtkImageData()
# Do NOT set the spacing and the origin of imageData (vtkImageData)
# The spacing and the origin should only be set in the vtkMRMLScalarVolumeNode!!!!!!
imageData.SetDimensions(int(dimX), int(dimY), int(dimZ))
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
extent = imageData.GetExtent()
for x in xrange(extent[0], extent[1] + 1):
for y in xrange(extent[2], extent[3] + 1):
for z in xrange(extent[4], extent[5] + 1):
imageData.SetScalarComponentFromDouble(x, y, z, 0, 0)
sampleVolumeNode.SetSpacing(1, 1, 1)
sampleVolumeNode.SetOrigin(bound[0], bound[2], bound[4])
sampleVolumeNode.SetName("Empty_volume")
sampleVolumeNode.SetAndObserveImageData(imageData)
sampleVolumeNode.SetLabelMap(1)
labelmapVolumeDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
slicer.mrmlScene.AddNode(labelmapVolumeDisplayNode)
colorNode = slicer.util.getNode('GenericAnatomyColors')
labelmapVolumeDisplayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelmapVolumeDisplayNode.VisibilityOn()
sampleVolumeNode.SetAndObserveDisplayNodeID(
labelmapVolumeDisplayNode.GetID())
count = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceCompositeNode')
for n in xrange(count):
compNode = slicer.mrmlScene.GetNthNodeByClass(
n, 'vtkMRMLSliceCompositeNode')
compNode.SetBackgroundVolumeID(sampleVolumeNode.GetID())
