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 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 convertToLabelMap(self, volumeNode, name):
volumesLogic = slicer.modules.volumes.logic()
newLabelNode = slicer.vtkMRMLLabelMapVolumeNode()
newLabelNode.SetName(volumeNode.GetName())
newLabelNode.SetHideFromEditors(volumeNode.GetHideFromEditors())
newLabelNode.SetSaveWithScene(volumeNode.GetSaveWithScene())
newLabelNode.SetSelectable(volumeNode.GetSelectable())
newLabelNode.SetSingletonTag(volumeNode.GetSingletonTag())
newLabelNode.SetDescription(volumeNode.GetDescription())
#TODO: Attributes
slicer.mrmlScene.AddNode(newLabelNode)
volumesLogic.CreateLabelVolumeFromVolume(slicer.mrmlScene,
newLabelNode, volumeNode)
slicer.mrmlScene.RemoveNode(volumeNode)
def ConvertStructureSetToLabelmap(self):
import vtkSlicerDicomRtImportExportModuleLogic
import vtkSegmentationCore
import vtkSlicerSegmentationsModuleMRML
import vtkSlicerSegmentationsModuleLogic
labelmapsToSave = []
# Get all segmentation nodes from the scene
segmentationNodes = slicer.util.getNodes('vtkMRMLSegmentationNode*')
for segmentationNode in segmentationNodes.values():
logging.info(' Converting structure set ' + segmentationNode.GetName())
# Set referenced volume as rasterization reference
referenceVolume = vtkSlicerDicomRtImportExportModuleLogic.vtkSlicerDicomRtImportExportModuleLogic.GetReferencedVolumeByDicomForSegmentation(segmentationNode)
if referenceVolume == None:
logging.error('No reference volume found for segmentation ' + segmentationNode.GetName())
continue
# Perform conversion
binaryLabelmapRepresentationName = vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName()
segmentation = segmentationNode.GetSegmentation()
segmentation.CreateRepresentation(binaryLabelmapRepresentationName)
# Create labelmap volume nodes from binary labelmaps
segmentIDs = vtk.vtkStringArray()
segmentation.GetSegmentIDs(segmentIDs)
for segmentIndex in xrange(0,segmentIDs.GetNumberOfValues()):
segmentID = segmentIDs.GetValue(segmentIndex)
segment = segmentation.GetSegment(segmentID)
binaryLabelmap = segment.GetRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationBinaryLabelmapRepresentationName())
if not binaryLabelmap:
logging.error('Failed to retrieve binary labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
continue
labelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(labelmapNode)
labelmapName = segmentationNode.GetName() + "_" + segmentID
labelmapNode.SetName(labelmapName)
if not vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic.CreateLabelmapVolumeFromOrientedImageData(binaryLabelmap,labelmapNode):
logging.error('Failed to create labelmap from segment ' + segmentID + ' in segmentation ' + segmentationNode.GetName())
continue
# Append volume to list
labelmapsToSave.append(labelmapNode)
return labelmapsToSave
def CreateNewLabelVolume(self,name):
""" Creates a new labelmap volume with the inputted name
"""
# Create labelmap node
labelNode=slicer.vtkMRMLLabelMapVolumeNode()
labelNode.SetName(name)
# Add volume to scene
slicer.mrmlScene.AddNode(labelNode)
displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.util.getNode('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
labelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
labelNode.CreateDefaultStorageNode()
return labelNode
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 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)