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