def getNIFTIHeader(self, volumeNode):
reader = vtk.vtkNIFTIImageReader()
filepath = self.getNodeFilepath(volumeNode)
reader.SetFileName(filepath)
reader.Update()
header = reader.GetNIFTIHeader()
return header
def load_image(self, ImgFileName):
# Load an image using the vtk image reader
imgReader = vtk.vtkNIFTIImageReader()
imgReader.SetFileName(ImgFileName)
imgReader.Update()
# This is needed for working on the Mac
# Perhaps the imgReader don't finish running in time?
# VTK uses 'lazy functions'
from vtk.util.numpy_support import vtk_to_numpy
array = vtk_to_numpy(imgReader.GetOutput().GetPointData().GetScalars())
return imgReader
def loadDevelopmentalAtlas(self):
# get the header - this reader doesn't support 4D
# but can query the header.
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(self.developmentalPath)
reader.Update()
niftiHeader = reader.GetNIFTIHeader()
print(self.developmentalPath)
if niftiHeader.GetDataType() != 16:
print(niftiHeader.GetDataType())
raise Exception('Can only load float data')
# create the correct size and shape vtkImageData
columns = niftiHeader.GetDim(1)
rows = niftiHeader.GetDim(2)
slices = niftiHeader.GetDim(3)
frames = niftiHeader.GetDim(4)
fp = open(self.developmentalPath, 'rb')
headerThrowaway = fp.read(niftiHeader.GetVoxOffset())
niiArray = numpy.fromfile(fp, numpy.dtype('float32'))
niiShape = (frames, slices, rows, columns)
niiArray = niiArray.reshape(niiShape)
image = vtk.vtkImageData()
image.SetDimensions(columns, rows, slices)
image.AllocateScalars(vtk.VTK_FLOAT, frames)
from vtk.util.numpy_support import vtk_to_numpy
imageShape = (slices, rows, columns, frames)
imageArray = vtk_to_numpy(
image.GetPointData().GetScalars()).reshape(imageShape)
# copy the data from numpy to vtk (need to shuffle frames to components)
for frame in range(frames):
imageArray[:, :, :, frame] = niiArray[frame]
# create the multivolume node and display it
multiVolumeNode = slicer.vtkMRMLMultiVolumeNode()
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(frames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(frames)
for frame in xrange(frames):
volumeLabels.SetComponent(frame, 0, self.agesInYears[frame])
multiVolumeNode.SetScene(slicer.mrmlScene)
multiVolumeDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
multiVolumeDisplayNode.SetReferenceCount(
multiVolumeDisplayNode.GetReferenceCount() - 1)
multiVolumeDisplayNode.SetScene(slicer.mrmlScene)
multiVolumeDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(multiVolumeDisplayNode)
multiVolumeNode.SetAndObserveDisplayNodeID(
multiVolumeDisplayNode.GetID())
multiVolumeNode.SetAndObserveImageData(image)
multiVolumeNode.SetNumberOfFrames(frames)
multiVolumeNode.SetName("DevelopmentalAtlas")
multiVolumeNode.SetLabelArray(volumeLabels)
multiVolumeNode.SetLabelName("Years")
multiVolumeNode.SetAttribute("MultiVolume.FrameLabels",
str(self.agesInYears)[1:-1])
multiVolumeNode.SetAttribute("MultiVolume.NumberOfFrames", str(frames))
multiVolumeNode.SetAttribute(
"MultiVolume.FrameIdentifyingDICOMTagName", "Age")
multiVolumeNode.SetAttribute(
"MultiVolume.FrameIdentifyingDICOMTagUnits", "(Years)")
slicer.mrmlScene.AddNode(multiVolumeNode)
return multiVolumeNode
def read4DNIfTI(self, mvNode, fileName):
"""Try to read a 4D nifti file as a multivolume"""
print('trying to read %s' % fileName)
# use the vtk reader which seems to handle most nifti variants well
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(fileName)
reader.SetTimeAsVector(True)
reader.Update()
header = reader.GetNIFTIHeader()
qFormMatrix = reader.GetQFormMatrix()
if not qFormMatrix:
print('Warning: %s does not have a QFormMatrix - using Identity')
qFormMatrix = vtk.vtkMatrix4x4()
spacing = reader.GetOutputDataObject(0).GetSpacing()
timeSpacing = reader.GetTimeSpacing()
nFrames = reader.GetTimeDimension()
if header.GetIntentCode() != header.IntentTimeSeries:
intentName = header.GetIntentName()
if not intentName:
intentName = 'Nothing'
print(
f'Warning: {fileName} does not have TimeSeries intent, instead it has \"{intentName}\"'
)
print('Trying to read as TimeSeries anyway')
units = header.GetXYZTUnits()
# try to account for some of the unit options
# (Note: no test data available but we hope these are right)
if units & header.UnitsMSec == header.UnitsMSec:
timeSpacing /= 1000.
if units & header.UnitsUSec == header.UnitsUSec:
timeSpacing /= 1000. / 1000.
spaceScaling = 1.
if units & header.UnitsMeter == header.UnitsMeter:
spaceScaling *= 1000.
if units & header.UnitsMicron == header.UnitsMicron:
spaceScaling /= 1000.
spacing = [e * spaceScaling for e in spacing]
# create frame labels using the timing info from the file
# but use the advanced info so user can specify offset and scale
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(nFrames)
frameLabelsAttr = ''
for i in range(nFrames):
frameId = self.__veInitial.value + timeSpacing * self.__veStep.value * i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ','
frameLabelsAttr = frameLabelsAttr[:-1]
# create the display node
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
# spacing and origin are in the ijkToRAS, so clear them from image data
imageChangeInformation = vtk.vtkImageChangeInformation()
imageChangeInformation.SetInputConnection(reader.GetOutputPort())
imageChangeInformation.SetOutputSpacing(1, 1, 1)
imageChangeInformation.SetOutputOrigin(0, 0, 0)
imageChangeInformation.Update()
# QForm includes directions and origin, but not spacing so add that
# here by multiplying by a diagonal matrix with the spacing
scaleMatrix = vtk.vtkMatrix4x4()
for diag in range(3):
scaleMatrix.SetElement(diag, diag, spacing[diag])
ijkToRAS = vtk.vtkMatrix4x4()
ijkToRAS.DeepCopy(qFormMatrix)
vtk.vtkMatrix4x4.Multiply4x4(ijkToRAS, scaleMatrix, ijkToRAS)
mvNode.SetIJKToRASMatrix(ijkToRAS)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(
imageChangeInformation.GetOutputDataObject(0))
mvNode.SetNumberOfFrames(nFrames)
# set the labels and other attributes, then display the volume
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName', '')
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits', '')
mvNode.SetName(str(nFrames) + ' frames NIfTI MultiVolume')
Helper.SetBgFgVolumes(mvNode.GetID(), None)
def read4DNIfTI(self, mvNode, fileName):
"""Try to read a 4D nifti file as a multivolume"""
print('trying to read %s' % fileName)
# use the vtk reader which seems to handle most nifti variants well
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(fileName)
reader.SetTimeAsVector(True)
reader.Update()
header = reader.GetNIFTIHeader()
qFormMatrix = reader.GetQFormMatrix()
if not qFormMatrix:
print('Warning: %s does not have a QFormMatrix - using Identity')
qFormMatrix = vtk.vtkMatrix4x4()
spacing = reader.GetOutputDataObject(0).GetSpacing()
timeSpacing = reader.GetTimeSpacing()
nFrames = reader.GetTimeDimension()
if header.GetIntentCode() != header.IntentTimeSeries:
intentName = header.GetIntentName()
if not intentName:
intentName = 'Nothing'
print('Warning: %s does not have TimeSeries intent, instead it has \"%s\"' % (fileName,intentName))
print('Trying to read as TimeSeries anyway')
units = header.GetXYZTUnits()
# try to account for some of the unit options
# (Note: no test data available but we hope these are right)
if units & header.UnitsMSec:
timeSpacing /= 1000.
if units & header.UnitsUSec:
timeSpacing /= 1000. / 1000.
spaceScaling = 1.
if units & header.UnitsMeter:
spaceScaling *= 1000.
if units & header.UnitsMicron:
spaceScaling /= 1000.
spacing = map(lambda e: e * spaceScaling, spacing)
# create frame labels using the timing info from the file
# but use the advanced info so user can specify offset and scale
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(nFrames)
frameLabelsAttr = ''
for i in range(nFrames):
frameId = self.__veInitial.value + timeSpacing * self.__veStep.value * i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId)+','
frameLabelsAttr = frameLabelsAttr[:-1]
# create the display node
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetDefaultColorMap()
# spacing and origin are in the ijkToRAS, so clear them from image data
imageChangeInformation = vtk.vtkImageChangeInformation()
imageChangeInformation.SetInputConnection(reader.GetOutputPort())
imageChangeInformation.SetOutputSpacing( 1, 1, 1 )
imageChangeInformation.SetOutputOrigin( 0, 0, 0 )
imageChangeInformation.Update()
# QForm includes directions and origin, but not spacing so add that
# here by multiplying by a diagonal matrix with the spacing
scaleMatrix = vtk.vtkMatrix4x4()
for diag in range(3):
scaleMatrix.SetElement(diag, diag, spacing[diag])
ijkToRAS = vtk.vtkMatrix4x4()
ijkToRAS.DeepCopy(qFormMatrix)
vtk.vtkMatrix4x4.Multiply4x4(ijkToRAS, scaleMatrix, ijkToRAS)
mvNode.SetIJKToRASMatrix(ijkToRAS)
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(imageChangeInformation.GetOutputDataObject(0))
mvNode.SetNumberOfFrames(nFrames)
# set the labels and other attributes, then display the volume
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute('MultiVolume.FrameLabels',frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames',str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName','')
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits','')
mvNode.SetName(str(nFrames)+' frames NIfTI MultiVolume')
Helper.SetBgFgVolumes(mvNode.GetID(),None)
def loadDevelopmentalAtlas(self):
# get the header - this reader doesn't support 4D
# but can query the header.
reader = vtk.vtkNIFTIImageReader()
reader.SetFileName(self.developmentalPath)
reader.Update()
niftiHeader = reader.GetNIFTIHeader()
print(self.developmentalPath)
if niftiHeader.GetDataType() != 16:
print (niftiHeader.GetDataType())
raise Exception('Can only load float data')
# create the correct size and shape vtkImageData
columns = niftiHeader.GetDim(1)
rows = niftiHeader.GetDim(2)
slices = niftiHeader.GetDim(3)
frames = niftiHeader.GetDim(4)
fp = open(self.developmentalPath, 'rb')
headerThrowaway = fp.read(niftiHeader.GetVoxOffset())
niiArray = numpy.fromfile(fp, numpy.dtype('float32'))
niiShape = (frames, slices, rows, columns)
niiArray = niiArray.reshape(niiShape)
image = vtk.vtkImageData()
image.SetDimensions(columns, rows, slices)
image.AllocateScalars(vtk.VTK_FLOAT, frames)
from vtk.util.numpy_support import vtk_to_numpy
imageShape = (slices, rows, columns, frames)
imageArray = vtk_to_numpy(image.GetPointData().GetScalars()).reshape(imageShape)
# copy the data from numpy to vtk (need to shuffle frames to components)
for frame in range(frames):
imageArray[:,:,:,frame] = niiArray[frame]
# create the multivolume node and display it
multiVolumeNode = slicer.vtkMRMLMultiVolumeNode()
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(frames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(frames)
for frame in xrange(frames):
volumeLabels.SetComponent(frame,0,self.agesInYears[frame])
multiVolumeNode.SetScene(slicer.mrmlScene)
multiVolumeDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
multiVolumeDisplayNode.SetReferenceCount(multiVolumeDisplayNode.GetReferenceCount()-1)
multiVolumeDisplayNode.SetScene(slicer.mrmlScene)
multiVolumeDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(multiVolumeDisplayNode)
multiVolumeNode.SetAndObserveDisplayNodeID(multiVolumeDisplayNode.GetID())
multiVolumeNode.SetAndObserveImageData(image)
multiVolumeNode.SetNumberOfFrames(frames)
multiVolumeNode.SetName("DevelopmentalAtlas")
multiVolumeNode.SetLabelArray(volumeLabels)
multiVolumeNode.SetLabelName("Years")
multiVolumeNode.SetAttribute("MultiVolume.FrameLabels", str(self.agesInYears)[1:-1])
multiVolumeNode.SetAttribute("MultiVolume.NumberOfFrames", str(frames))
multiVolumeNode.SetAttribute("MultiVolume.FrameIdentifyingDICOMTagName", "Age")
multiVolumeNode.SetAttribute("MultiVolume.FrameIdentifyingDICOMTagUnits", "(Years)")
slicer.mrmlScene.AddNode(multiVolumeNode)
return multiVolumeNode