def loadImageData(self, filePath, grayscale, volumeNode):
import vtkITK
if grayscale:
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
else:
reader = vtkITK.vtkITKArchetypeImageSeriesVectorReaderFile()
reader.SetArchetype(filePath)
reader.AddFileName(filePath)
reader.SetSingleFile(True)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
# GDCM is not particularly better in this than DCMTK, we just select one explicitly
# so that we know which one is used
reader.SetDICOMImageIOApproachToGDCM()
reader.Update()
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorString = vtk.vtkErrorCode.GetStringFromErrorCode(
reader.GetErrorCode())
raise ValueError(
f"Could not read image {loadable.name} from file {filePath}. Error is: {errorString}"
)
rasToIjk = reader.GetRasToIjkMatrix()
ijkToRas = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4.Invert(rasToIjk, ijkToRas)
return reader.GetOutput(), ijkToRas
def load(self, loadable):
"""Load the selection
"""
if loadable.grayscale:
volumeNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLScalarVolumeNode", loadable.name)
else:
volumeNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLVectorVolumeNode", loadable.name)
import vtkITK
if loadable.grayscale:
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
else:
reader = vtkITK.vtkITKArchetypeImageSeriesVectorReaderFile()
filePath = loadable.files[0]
reader.SetArchetype(filePath)
reader.AddFileName(filePath)
reader.SetSingleFile(True)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
# GDCM is not particularly better in this than DCMTK, we just select one explicitly
# so that we know which one is used
reader.SetDICOMImageIOApproachToGDCM()
reader.Update()
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorString = vtk.vtkErrorCode.GetStringFromErrorCode(
reader.GetErrorCode())
raise ValueError(
f"Could not read image {loadable.name} from file {filePath}. Error is: {errorString}"
)
rasToIjk = reader.GetRasToIjkMatrix()
ijkToRas = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4.Invert(rasToIjk, ijkToRas)
imageData = reader.GetOutput()
imageData.SetSpacing(1.0, 1.0, 1.0)
imageData.SetOrigin(0.0, 0.0, 0.0)
volumeNode.SetIJKToRASMatrix(ijkToRas)
volumeNode.SetAndObserveImageData(imageData)
# show volume
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetActiveVolumeID(volumeNode.GetID())
appLogic.PropagateVolumeSelection()
return volumeNode
def loadFilesWithSeriesReader(self,imageIOName,files,name,grayscale=True):
""" Explicitly use the named imageIO to perform the loading
"""
if grayscale:
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
else:
reader = vtkITK.vtkITKArchetypeImageSeriesVectorReaderFile()
reader.SetArchetype(files[0])
for f in files:
reader.AddFileName(f)
reader.SetSingleFile(0)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
if imageIOName == "GDCM":
reader.SetDICOMImageIOApproachToGDCM()
elif imageIOName == "DCMTK":
reader.SetDICOMImageIOApproachToDCMTK()
else:
raise Exception("Invalid imageIOName of %s" % imageIOName)
logging.info("Loading with imageIOName: %s" % imageIOName)
reader.Update()
slicer.modules.reader = reader
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorStrings = (imageIOName, vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode()))
logging.error("Could not read scalar volume using %s approach. Error is: %s" % errorStrings)
return
imageChangeInformation = vtk.vtkImageChangeInformation()
imageChangeInformation.SetInputConnection(reader.GetOutputPort())
imageChangeInformation.SetOutputSpacing( 1, 1, 1 )
imageChangeInformation.SetOutputOrigin( 0, 0, 0 )
imageChangeInformation.Update()
name = slicer.mrmlScene.GenerateUniqueName(name)
if grayscale:
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", name)
else:
volumeNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode", name)
volumeNode.SetAndObserveImageData(imageChangeInformation.GetOutputDataObject(0))
slicer.vtkMRMLVolumeArchetypeStorageNode.SetMetaDataDictionaryFromReader(volumeNode, reader)
volumeNode.SetRASToIJKMatrix(reader.GetRasToIjkMatrix())
volumeNode.CreateDefaultDisplayNodes()
slicer.modules.DICOMInstance.reader = reader
slicer.modules.DICOMInstance.imageChangeInformation = imageChangeInformation
return(volumeNode)
def load(self,loadable):
"""Load the selection
"""
outputSequenceNodes = []
for filePath in loadable.files:
import vtkITK
if loadable.grayscale:
reader = vtkITK.vtkITKArchetypeImageSeriesScalarReader()
else:
reader = vtkITK.vtkITKArchetypeImageSeriesVectorReaderFile()
reader.SetArchetype(filePath)
reader.AddFileName(filePath)
reader.SetSingleFile(True)
reader.SetOutputScalarTypeToNative()
reader.SetDesiredCoordinateOrientationToNative()
reader.SetUseNativeOriginOn()
# GDCM is not particularly better in this than DCMTK, we just select one explicitly
# so that we know which one is used
reader.SetDICOMImageIOApproachToGDCM()
reader.Update()
if reader.GetErrorCode() != vtk.vtkErrorCode.NoError:
errorString = vtk.vtkErrorCode.GetStringFromErrorCode(reader.GetErrorCode())
raise ValueError("Could not read image {0} from file {1}. Error is: {2}".format(loadable.name, filePath, errorString))
volume = reader.GetOutput()
[spacingX, spacingY, frameTimeMsec] = volume.GetSpacing()
volume.SetSpacing(1.0, 1.0, 1.0)
outputSequenceNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSequenceNode")
if frameTimeMsec == 1.0:
# frame time is not found, set it to 1.0fps
frameTime = 1
outputSequenceNode.SetIndexName("frame")
outputSequenceNode.SetIndexUnit("")
playbackRateFps = 10
else:
frameTime = frameTimeMsec * 0.001
outputSequenceNode.SetIndexName("time")
outputSequenceNode.SetIndexUnit("s")
playbackRateFps = 1.0/frameTime
if loadable.grayscale:
tempFrameVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode")
else:
tempFrameVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLVectorVolumeNode")
# Rotate 180deg, otherwise the image would appear upside down
ijkToRAS = vtk.vtkMatrix4x4()
ijkToRAS.SetElement(0,0,-1.0)
ijkToRAS.SetElement(1,1,-1.0)
tempFrameVolume.SetIJKToRASMatrix(ijkToRAS)
tempFrameVolume.SetSpacing(spacingX, spacingY, 1.0)
numberOfFrames = volume.GetDimensions()[2]
extent = volume.GetExtent()
numberOfFrames = extent[5]-extent[4]+1
for frame in range(numberOfFrames):
crop = vtk.vtkImageClip()
crop.SetInputData(volume)
crop.SetOutputWholeExtent(extent[0], extent[1], extent[2], extent[3], extent[4]+frame, extent[4]+frame)
crop.ClipDataOn()
crop.Update()
croppedOutput = crop.GetOutput()
croppedOutput.SetExtent(extent[0], extent[1], extent[2], extent[3], 0, 0)
tempFrameVolume.SetAndObserveImageData(croppedOutput)
if type(frameTime)==int:
timeStampSec = str(frame * frameTime)
else:
timeStampSec = "{:.3f}".format(frame * frameTime)
outputSequenceNode.SetDataNodeAtValue(tempFrameVolume, timeStampSec)
slicer.mrmlScene.RemoveNode(tempFrameVolume)
if len(loadable.files) == 1:
outputSequenceNode.SetName(loadable.name)
else:
ds = dicom.read_file(filePath, stop_before_pixels=True)
if hasattr(ds, 'PositionerPrimaryAngle') and hasattr(ds, 'PositionerSecondaryAngle'):
outputSequenceNode.SetName('{0} ({1}/{2})'.format(loadable.name, ds.PositionerPrimaryAngle,ds.PositionerSecondaryAngle))
else:
outputSequenceNode.SetName(loadable.name)
slicer.mrmlScene.AddNode(outputSequenceNode)
# Create storage node that allows saving node as nrrd
outputSequenceStorageNode = slicer.vtkMRMLVolumeSequenceStorageNode()
slicer.mrmlScene.AddNode(outputSequenceStorageNode)
outputSequenceNode.SetAndObserveStorageNodeID(outputSequenceStorageNode.GetID())
outputSequenceNodes.append(outputSequenceNode)
if not hasattr(loadable, 'createBrowserNode') or loadable.createBrowserNode:
# Add a browser node and show the volume in the slice viewer for user convenience
outputSequenceBrowserNode = slicer.vtkMRMLSequenceBrowserNode()
outputSequenceBrowserNode.SetName(slicer.mrmlScene.GenerateUniqueName(loadable.name+' browser'))
outputSequenceBrowserNode.SetPlaybackRateFps(playbackRateFps)
slicer.mrmlScene.AddNode(outputSequenceBrowserNode)
# Add all sequences to the sequence browser
first = True
for outputSequenceNode in outputSequenceNodes:
#outputSequenceBrowserNode.SetAndObserveMasterSequenceNodeID(outputSequenceNode.GetID())
outputSequenceBrowserNode.AddSynchronizedSequenceNode(outputSequenceNode)
proxyVolumeNode = outputSequenceBrowserNode.GetProxyNode(outputSequenceNode)
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, proxyVolumeNode)
if first:
first = False
# Automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(proxyVolumeNode.GetID())
appLogic.PropagateVolumeSelection()
appLogic.FitSliceToAll()
slicer.modules.sequences.setToolBarActiveBrowserNode(outputSequenceBrowserNode)
# Show sequence browser toolbar
slicer.modules.sequences.showSequenceBrowser(outputSequenceBrowserNode)
return outputSequenceNode