def addSequenceFromImageData(self, imageData, tempFrameVolume, filePath,
name, singleFileInLoadable):
# 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)
# z axis is time
[spacingX, spacingY, frameTimeMsec] = imageData.GetSpacing()
imageData.SetSpacing(1.0, 1.0, 1.0)
tempFrameVolume.SetSpacing(spacingX, spacingY, 1.0)
# Create new sequence
outputSequenceNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSequenceNode")
# Get sequence name
if singleFileInLoadable:
outputSequenceNode.SetName(name)
else:
ds = dicom.read_file(filePath, stop_before_pixels=True)
if hasattr(ds, 'PositionerPrimaryAngle') and hasattr(
ds, 'PositionerSecondaryAngle'):
outputSequenceNode.SetName(
f'{name} ({ds.PositionerPrimaryAngle}/{ds.PositionerSecondaryAngle})'
)
else:
outputSequenceNode.SetName(name)
if frameTimeMsec == 1.0:
# frame time is not found, set it to 1.0fps
frameTime = 1
outputSequenceNode.SetIndexName("frame")
outputSequenceNode.SetIndexUnit("")
playbackRateFps = 10
else:
# frame time is set, use it
frameTime = frameTimeMsec * 0.001
outputSequenceNode.SetIndexName("time")
outputSequenceNode.SetIndexUnit("s")
playbackRateFps = 1.0 / frameTime
# Add frames to the sequence
numberOfFrames = imageData.GetDimensions()[2]
extent = imageData.GetExtent()
numberOfFrames = extent[5] - extent[4] + 1
for frame in range(numberOfFrames):
# get current frame from multiframe
crop = vtk.vtkImageClip()
crop.SetInputData(imageData)
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)
croppedOutput.SetOrigin(0.0, 0.0, 0.0)
tempFrameVolume.SetAndObserveImageData(croppedOutput)
# get timestamp
if type(frameTime) == int:
timeStampSec = str(frame * frameTime)
else:
timeStampSec = f"{frame * frameTime:.3f}"
outputSequenceNode.SetDataNodeAtValue(tempFrameVolume,
timeStampSec)
# Create storage node that allows saving node as nrrd
outputSequenceStorageNode = slicer.vtkMRMLVolumeSequenceStorageNode()
slicer.mrmlScene.AddNode(outputSequenceStorageNode)
outputSequenceNode.SetAndObserveStorageNodeID(
outputSequenceStorageNode.GetID())
return outputSequenceNode, playbackRateFps
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
def loadPhilips4DUSAsSequence(self, loadable):
"""Load the selection as an Ultrasound, store in a Sequence node
"""
# get the key info from the "fake" dicom file
filePath = loadable.files[0]
ds = dicom.read_file(filePath, stop_before_pixels=True)
columns = ds.Columns
rows = ds.Rows
slices = ds[(0x3001, 0x1001)].value # private tag!
spacing = (
ds.PhysicalDeltaX * 10,
ds.PhysicalDeltaY * 10,
ds[(0x3001, 0x1003)].value * 10 # private tag!
)
frames = int(ds.NumberOfFrames)
imageComponents = frames
frameTimeMsec = ds.FrameTime
pixelShape = (frames, slices, rows, columns)
pixelSize = pixelShape[0] * pixelShape[1] * pixelShape[2] * pixelShape[
3]
totalFileSize = os.path.getsize(filePath)
headerSize = totalFileSize - pixelSize
outputSequenceNode = slicer.vtkMRMLSequenceNode()
for frame in range(frames):
imgReader = vtk.vtkImageReader()
imgReader.SetFileDimensionality(3)
imgReader.SetFileName(filePath)
imgReader.SetNumberOfScalarComponents(1)
imgReader.SetDataScalarTypeToUnsignedChar()
imgReader.SetDataExtent(0, columns - 1, 0, rows - 1, 0, slices - 1)
imgReader.SetHeaderSize(headerSize +
frame * slices * rows * columns)
imgReader.FileLowerLeftOn()
imgReader.Update()
outputNode = slicer.vtkMRMLScalarVolumeNode()
outputNode.SetAndObserveImageData(imgReader.GetOutput())
outputNode.SetSpacing(spacing)
timeStampSec = "{:.3f}".format(frame * frameTimeMsec * 0.001)
outputSequenceNode.SetDataNodeAtValue(outputNode, timeStampSec)
outputSequenceNode.SetName(
slicer.mrmlScene.GenerateUniqueName(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())
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(
outputSequenceNode.GetName() + ' browser'))
slicer.mrmlScene.AddNode(outputSequenceBrowserNode)
outputSequenceBrowserNode.SetAndObserveMasterSequenceNodeID(
outputSequenceNode.GetID())
masterOutputNode = outputSequenceBrowserNode.GetProxyNode(
outputSequenceNode)
# Automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(masterOutputNode.GetID())
appLogic.PropagateVolumeSelection()
appLogic.FitSliceToAll()
slicer.modules.sequencebrowser.setToolBarActiveBrowserNode(
outputSequenceBrowserNode)
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, masterOutputNode)
return outputSequenceNode
def loadAsSequence(self,loadable):
"""Load the selection as an Ultrasound, store in a Sequence node
"""
# get the key info from the "fake" dicom file
filePath = loadable.files[0]
ds = dicom.read_file(filePath, stop_before_pixels=True)
columns = ds.Columns
rows = ds.Rows
slices = ds[(0x3001,0x1001)].value # private tag!
spacing = (
ds.PhysicalDeltaX * 10,
ds.PhysicalDeltaY * 10,
ds[(0x3001,0x1003)].value * 10 # private tag!
)
frames = int(ds.NumberOfFrames)
imageComponents = frames
frameTimeMsec = ds.FrameTime
pixelShape = (frames, slices, rows, columns)
pixelSize = reduce(lambda x,y : x*y, pixelShape)
totalFileSize = os.path.getsize(filePath)
headerSize = totalFileSize-pixelSize
outputSequenceNode = slicer.vtkMRMLSequenceNode()
for frame in range(frames):
imgReader = vtk.vtkImageReader()
imgReader.SetFileDimensionality(3)
imgReader.SetFileName(filePath);
imgReader.SetNumberOfScalarComponents(1)
imgReader.SetDataScalarTypeToUnsignedChar()
imgReader.SetDataExtent(0,columns-1, 0,rows-1, 0,slices-1)
imgReader.SetHeaderSize(headerSize+frame*slices*rows*columns)
imgReader.FileLowerLeftOn();
imgReader.Update()
outputNode = slicer.vtkMRMLScalarVolumeNode()
outputNode.SetAndObserveImageData(imgReader.GetOutput())
outputNode.SetSpacing(spacing)
timeStampSec = "{:.3f}".format(frame * frameTimeMsec * 0.001)
outputSequenceNode.SetDataNodeAtValue(outputNode, timeStampSec)
outputSequenceNode.SetName(slicer.mrmlScene.GenerateUniqueName(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())
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(outputSequenceNode.GetName()+' browser'))
slicer.mrmlScene.AddNode(outputSequenceBrowserNode)
outputSequenceBrowserNode.SetAndObserveMasterSequenceNodeID(outputSequenceNode.GetID())
masterOutputNode = outputSequenceBrowserNode.GetVirtualOutputDataNode(outputSequenceNode)
# Automatically select the volume to display
appLogic = slicer.app.applicationLogic()
selNode = appLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(masterOutputNode.GetID())
appLogic.PropagateVolumeSelection()
appLogic.FitSliceToAll()
outputSequenceBrowserNode.ScalarVolumeAutoWindowLevelOff() # for performance optimization
# create Subject hierarchy nodes for the loaded series
self.addSeriesInSubjectHierarchy(loadable, masterOutputNode)
return outputSequenceNode