def createVectorVolumeFromRoi(self,
exportRoi,
spacingMm,
numberOfComponents=3):
roiCenter = [0, 0, 0]
exportRoi.GetXYZ(roiCenter)
roiRadius = [0, 0, 0]
exportRoi.GetRadiusXYZ(roiRadius)
roiOrigin_Roi = [
roiCenter[0] - roiRadius[0], roiCenter[1] - roiRadius[1],
roiCenter[2] - roiRadius[2], 1
]
roiToRas = vtk.vtkMatrix4x4()
if exportRoi.GetTransformNodeID() != None:
roiBoxTransformNode = slicer.mrmlScene.GetNodeByID(
exportRoi.GetTransformNodeID())
roiBoxTransformNode.GetMatrixTransformToWorld(roiToRas)
exportVolumeSize = [
roiRadius[0] * 2 / spacingMm, roiRadius[1] * 2 / spacingMm,
roiRadius[2] * 2 / spacingMm
]
exportVolumeSize = [int(math.ceil(x)) for x in exportVolumeSize]
exportImageData = vtk.vtkImageData()
exportImageData.SetExtent(0, exportVolumeSize[0] - 1, 0,
exportVolumeSize[1] - 1, 0,
exportVolumeSize[2] - 1)
if vtk.VTK_MAJOR_VERSION <= 5:
exportImageData.SetScalarType(vtk.VTK_DOUBLE)
exportImageData.SetNumberOfScalarComponents(numberOfComponents)
exportImageData.AllocateScalars()
else:
exportImageData.AllocateScalars(vtk.VTK_DOUBLE, numberOfComponents)
exportVolume = None
if numberOfComponents == 1:
exportVolume = slicer.vtkMRMLScalarVolumeNode()
else:
exportVolume = slicer.vtkMRMLVectorVolumeNode()
exportVolume.SetAndObserveImageData(exportImageData)
exportVolume.SetIJKToRASDirections(roiToRas.GetElement(0, 0),
roiToRas.GetElement(0, 1),
roiToRas.GetElement(0, 2),
roiToRas.GetElement(1, 0),
roiToRas.GetElement(1, 1),
roiToRas.GetElement(1, 2),
roiToRas.GetElement(2, 0),
roiToRas.GetElement(2, 1),
roiToRas.GetElement(2, 2))
exportVolume.SetSpacing(spacingMm, spacingMm, spacingMm)
roiOrigin_Ras = roiToRas.MultiplyPoint(roiOrigin_Roi)
exportVolume.SetOrigin(roiOrigin_Ras[0:3])
return exportVolume
def resampleVectorVolume(self,vectorVolume,resample):
if not vectorVolume or not vectorVolume.IsA('vtkMRMLVectorVolumeNode'):
print "No vector volume for resampling."
return
if resample == []:
print "No resample values."
return
if not len(resample) == 3:
print "Too many values for resampling."
return
oldVectorVolume = vectorVolume
#Create new vector volume
newVectorVolume = slicer.vtkMRMLVectorVolumeNode()
newVectorVolume.SetName(oldVectorVolume.GetName())
slicer.mrmlScene.AddNode(newVectorVolume)
newStorageNode = newVectorVolume.CreateDefaultStorageNode()
newVectorVolume.SetAndObserveStorageNodeID(newStorageNode.GetID())
#Create strings for resampling
spacing = ''
size = ''
for i in range(0,len(resample)):
spacing += str(oldVectorVolume.GetSpacing()[i]*resample[i])
#extent = oldVectorVolume.GetImageData().GetExtent[2*i+1]
extent = oldVectorVolume.GetImageData().GetExtent()[2*i+1]+1
size += str(extent/resample[i])
if i < 2:
spacing += ','
size += ','
print "Resampling " + oldVectorVolume.GetName() + " to new pixel size " + size
#Set parameters
parameters = {}
parameters["inputVolume"] = oldVectorVolume.GetID()
parameters["outputVolume"] = newVectorVolume.GetID()
parameters["referenceVolume"] = ''
parameters["outputImageSpacing"] = spacing
parameters["outputImageSize"] = size
#Do resampling
resampleScalarVolume = slicer.modules.resamplescalarvectordwivolume
clNode = slicer.cli.run(resampleScalarVolume, None, parameters, wait_for_completion=True)
#Remove old vector node and set new:
return newVectorVolume
def resampleVectorVolume(self):
if not self.vectorVolume or not self.vectorVolume.IsA('vtkMRMLVectorVolumeNode'):
print "No vector volume for resampling."
return
if self.resample == []:
print "No resample values."
return
if not len(self.resample) == 3:
print "Too many values for resampling."
return
oldVectorVolume = self.vectorVolume
#Create new vector volume
newVectorVolume = slicer.vtkMRMLVectorVolumeNode()
newVectorVolume.SetName(oldVectorVolume.GetName())
slicer.mrmlScene.AddNode(newVectorVolume)
#Create strings for resampling
spacing = ''
size = ''
for i in range(0, len(self.resample)):
spacing += str(oldVectorVolume.GetSpacing()[i] * self.resample[i])
#extent = oldVectorVolume.GetImageData().GetExtent[2*i+1]
extent = oldVectorVolume.GetImageData().GetExtent()[2 * i + 1] + 1
size += str(extent / self.resample[i])
if i < 2:
spacing += ','
size += ','
print "Resampling " + oldVectorVolume.GetName() + " to new pixel size " + size
#Set parameters
parameters = {}
parameters["inputVolume"] = oldVectorVolume.GetID()
parameters["outputVolume"] = newVectorVolume.GetID()
parameters["referenceVolume"] = ''
parameters["outputImageSpacing"] = spacing
parameters["outputImageSize"] = size
#Do resampling
resampleScalarVolume = slicer.modules.resamplescalarvectordwivolume
clNode = slicer.cli.run(resampleScalarVolume, None, parameters, wait_for_completion=True)
#Remove old vector node and set new:
self.vectorVolume = newVectorVolume
slicer.mrmlScene.RemoveNode(oldVectorVolume)
def resampleVolume(self, inputVolume, referenceVolume):
parameters = {}
parameters["inputVolume"] = inputVolume.GetID()
parameters["referenceVolume"] = referenceVolume.GetID()
outputVolume = slicer.vtkMRMLVectorVolumeNode()
outputVolume.SetName('ResampledVolume')
slicer.mrmlScene.AddNode( outputVolume )
parameters["outputVolume"] = outputVolume.GetID()
# Instead of
# slicer.cli.run(slicer.modules.resamplescalarvectordwivolume, None, parameters, wait_for_completion=True)
# apply using custom code to allow disabling DisplayData in ApplyAndWait
module = slicer.modules.resamplescalarvectordwivolume
node = slicer.cli.createNode(module, parameters)
logic = module.logic()
logic.ApplyAndWait(node, False)
return outputVolume
def resampleVolume(self, inputVolume, referenceVolume):
parameters = {}
parameters["inputVolume"] = inputVolume.GetID()
parameters["referenceVolume"] = referenceVolume.GetID()
outputVolume = slicer.vtkMRMLVectorVolumeNode()
outputVolume.SetName('ResampledVolume')
slicer.mrmlScene.AddNode(outputVolume)
parameters["outputVolume"] = outputVolume.GetID()
# Instead of
# slicer.cli.run(slicer.modules.resamplescalarvectordwivolume, None, parameters, wait_for_completion=True)
# apply using custom code to allow disabling DisplayData in ApplyAndWait
module = slicer.modules.resamplescalarvectordwivolume
node = slicer.cli.createNode(module, parameters)
logic = module.logic()
logic.ApplyAndWait(node, False)
return outputVolume
def createVectorVolumeFromRoi(self, exportRoi, spacingMm, numberOfComponents=3):
roiCenter = [0, 0, 0]
exportRoi.GetXYZ( roiCenter )
roiRadius = [0, 0, 0]
exportRoi.GetRadiusXYZ( roiRadius )
roiOrigin_Roi = [roiCenter[0] - roiRadius[0], roiCenter[1] - roiRadius[1], roiCenter[2] - roiRadius[2], 1 ]
roiToRas = vtk.vtkMatrix4x4()
if exportRoi.GetTransformNodeID() != None:
roiBoxTransformNode = slicer.mrmlScene.GetNodeByID(exportRoi.GetTransformNodeID())
roiBoxTransformNode.GetMatrixTransformToWorld(roiToRas)
exportVolumeSize = [roiRadius[0]*2/spacingMm, roiRadius[1]*2/spacingMm, roiRadius[2]*2/spacingMm]
exportVolumeSize = [int(math.ceil(x)) for x in exportVolumeSize]
exportImageData = vtk.vtkImageData()
exportImageData.SetExtent(0, exportVolumeSize[0]-1, 0, exportVolumeSize[1]-1, 0, exportVolumeSize[2]-1)
if vtk.VTK_MAJOR_VERSION <= 5:
exportImageData.SetScalarType(vtk.VTK_DOUBLE)
exportImageData.SetNumberOfScalarComponents(numberOfComponents)
exportImageData.AllocateScalars()
else:
exportImageData.AllocateScalars(vtk.VTK_DOUBLE, numberOfComponents)
exportVolume = None
if numberOfComponents==1:
exportVolume = slicer.vtkMRMLScalarVolumeNode()
else:
exportVolume = slicer.vtkMRMLVectorVolumeNode()
exportVolume.SetAndObserveImageData(exportImageData)
exportVolume.SetIJKToRASDirections( roiToRas.GetElement(0,0), roiToRas.GetElement(0,1), roiToRas.GetElement(0,2), roiToRas.GetElement(1,0), roiToRas.GetElement(1,1), roiToRas.GetElement(1,2), roiToRas.GetElement(2,0), roiToRas.GetElement(2,1), roiToRas.GetElement(2,2))
exportVolume.SetSpacing(spacingMm, spacingMm, spacingMm)
roiOrigin_Ras = roiToRas.MultiplyPoint(roiOrigin_Roi)
exportVolume.SetOrigin(roiOrigin_Ras[0:3])
return exportVolume
def exportTransformToVectorVolume(self, positionErrorVectorTransform, exportRoi, magnitudeOnly):
if not positionErrorVectorTransform:
return
roiBounds_Ras = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
exportRoi.GetRASBounds(roiBounds_Ras)
exportVolumeSize = [(roiBounds_Ras[1]-roiBounds_Ras[0]+1)/self.exportVolumeSpacingMm, (roiBounds_Ras[3]-roiBounds_Ras[2]+1)/self.exportVolumeSpacingMm, (roiBounds_Ras[5]-roiBounds_Ras[4]+1)/self.exportVolumeSpacingMm]
exportVolumeSize = [int(math.ceil(x)) for x in exportVolumeSize]
exportImageData = vtk.vtkImageData()
exportImageData.SetExtent(0, exportVolumeSize[0]-1, 0, exportVolumeSize[1]-1, 0, exportVolumeSize[2]-1)
if vtk.VTK_MAJOR_VERSION <= 5:
exportImageData.SetScalarType(vtk.VTK_DOUBLE)
exportImageData.SetNumberOfScalarComponents(1)
exportImageData.AllocateScalars()
else:
exportImageData.AllocateScalars(vtk.VTK_DOUBLE, 1)
exportVolume = slicer.vtkMRMLVectorVolumeNode()
exportVolume.SetAndObserveImageData(exportImageData)
exportVolume.SetSpacing(self.exportVolumeSpacingMm, self.exportVolumeSpacingMm, self.exportVolumeSpacingMm)
exportVolume.SetOrigin(roiBounds_Ras[0], roiBounds_Ras[2], roiBounds_Ras[4])
slicer.modules.transforms.logic().CreateDisplacementVolumeFromTransform(positionErrorVectorTransform, exportVolume, magnitudeOnly)
def exportTransformToVectorVolume(self, positionErrorVectorTransform, exportRoi, magnitudeOnly):
if not positionErrorVectorTransform:
return
roiBounds_Ras = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
exportRoi.GetRASBounds(roiBounds_Ras)
exportVolumeSize = [(roiBounds_Ras[1]-roiBounds_Ras[0]+1)/self.exportVolumeSpacingMm, (roiBounds_Ras[3]-roiBounds_Ras[2]+1)/self.exportVolumeSpacingMm, (roiBounds_Ras[5]-roiBounds_Ras[4]+1)/self.exportVolumeSpacingMm]
exportVolumeSize = [int(math.ceil(x)) for x in exportVolumeSize]
exportImageData = vtk.vtkImageData()
exportImageData.SetExtent(0, exportVolumeSize[0]-1, 0, exportVolumeSize[1]-1, 0, exportVolumeSize[2]-1)
if vtk.VTK_MAJOR_VERSION <= 5:
exportImageData.SetScalarType(vtk.VTK_DOUBLE)
exportImageData.SetNumberOfScalarComponents(1)
exportImageData.AllocateScalars()
else:
exportImageData.AllocateScalars(vtk.VTK_DOUBLE, 1)
exportVolume = slicer.vtkMRMLVectorVolumeNode()
exportVolume.SetAndObserveImageData(exportImageData)
exportVolume.SetSpacing(self.exportVolumeSpacingMm, self.exportVolumeSpacingMm, self.exportVolumeSpacingMm)
exportVolume.SetOrigin(roiBounds_Ras[0], roiBounds_Ras[2], roiBounds_Ras[4])
slicer.modules.transforms.logic().CreateDisplacementVolumeFromTransform(positionErrorVectorTransform, exportVolume, magnitudeOnly)
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 writeTRiPdata(self, filePath, pytripCube=None, extension='.ctx', nodeID = None, binfoName='',aix = False, resample = []):
if nodeID is not None:
node = slicer.util.getNode( nodeID )
print "Node to write:" + node.GetID()
else:
node = None
if pytripCube is None and node is not None:
print "Converting slicer node into pytrip cube " + str(node.GetID())
#Getting vector field from transform node
if node.IsA('vtkMRMLGridTransformNode') or node.IsA('vtkMRMLBSplineTransformNode'):
print "Converting Transform Node to Vector Field"
trans = node.GetTransformFromParent()#.GetConcatenatedTransform(0)
#trans.Inverse()
#trans.Update()
im = trans.GetDisplacementGrid()
if im is None:
print "Can't get image data. " + str(im)
return
vectorVolume = slicer.vtkMRMLVectorVolumeNode()
slicer.mrmlScene.AddNode( vectorVolume )
vectorVolume.SetAndObserveImageData( im )
vectorVolume.SetName( node.GetName() )
vectorVolume.SetSpacing( im.GetSpacing() )
#vectorVolume.SetOrigin( im.GetOrigin() )
#Get Right Direction For Vector Volume
#matrix = vtk.vtkMatrix4x4()
matrix = trans.GetGridDirectionMatrix()
#matrix.DeepCopy((-1,0,0,0,0,-1,0,0,0,0,1,0,0,0,0,1))
vectorVolume.SetIJKToRASDirectionMatrix(matrix)
if not resample == []:
newVectorVolume = self.resampleVectorVolume(vectorVolume,resample)
slicer.mrmlScene.RemoveNode(vectorVolume)
vectorVolume = newVectorVolume
node = vectorVolume
pytripCube = self.getPyTRiPCubeFromNode(node)
if aix:
pytripCube.byte_order = 'aix'
pytripCube.cube.byteswap()
else:
pytripCube.byte_order = 'vms'
if pytripCube is None:
if node is None:
print "Input slicer node or pytrip Cube!"
return
else:
print "Cannot create/find pytripCube"
return
if not filePath[-1] == '/':
filePath += '/'
fName = str(filePath)+binfoName+ pytripCube.patient_name
if node is not None:
if node.IsA('vtkMRMLVectorVolumeNode'):
if not extension == '.cbt':
print "Error, vector volume can be exported only as .cbt (no: "+extension+" )"
return
array = slicer.util.array(node.GetID())
#Change precision from double to float
if array.dtype == np.float64:
array = array.astype(np.float32)
if pytripCube.byte_order == 'aix':
print "Changing array to aix byte order."
array.byteswap()
pName = pytripCube.patient_name
for i in range(0,3):
# Vector field components in cbt are divided with voxel spacing due to historical reasons.
if i == 2:
pytripCube.cube = np.array(array[:,:,:,i])/pytripCube.slice_distance
else:
if nodeID.find('GridTransform') > -1:
print "Changing sign"
pytripCube.cube = -np.array(array[:,:,:,i])/pytripCube.pixel_size
else:
pytripCube.cube = np.array(array[:,:,:,i])/pytripCube.pixel_size
#if i == 2:
#print "Converting vector components."
#pytripCube.cube = np.array(array[:,:,:,i]/pytripCube.slice_distance
#elif i < 2:
#pytripCube.cube = np.array(array[:,:,:,i]/pytripCube.pixel_size
#pytripCube.cube = array
if i==0:
fNameNew = fName + "_x"
pytripCube.patient_name = pName + "_x"
elif i==1:
fNameNew = fName + "_y"
pytripCube.patient_name = pName + "_y"
elif i==2:
fNameNew = fName + "_z"
pytripCube.patient_name = pName + "_z"
print("Saving: "+fNameNew)
pytripCube.write_trip_data(fNameNew+extension)
pytripCube.write_trip_header(fNameNew+".hed")
if nodeID.find('GridTransform') > -1:
slicer.mrmlScene.RemoveNode(vectorVolume)
elif node.IsA('vtkMRMLScalarVolumeNode'):
pytripCube.write_trip_data(fName+extension)
pytripCube.write_trip_header(fName+".hed")
else:
if extension == '.cbt':
print "Error, input is not vector volume for exporting cbt."
return
pytripCube.write_trip_data(fName+extension)
pytripCube.write_trip_header(fName+".hed")
print("Saved: "+fName+extension)