def updateWindowLevelRectangle(self, sliceLayer, xyBounds):
# conversion as done in LabelEffect.py:applyImageMask
xlo, xhi, ylo, yhi, zlo, zhi = xyBounds
if xlo == xhi or ylo == yhi: return
sliceNode = sliceLayer.GetVolumeNode()
sliceImage = sliceNode.GetImageData()
if not sliceImage:
return [0,0,0,0]
xyToIJK = sliceLayer.GetXYToIJKTransform()
tlIJK = xyToIJK.TransformPoint( (xlo, yhi, 0) )
trIJK = xyToIJK.TransformPoint( (xhi, yhi, 0) )
blIJK = xyToIJK.TransformPoint( (xlo, ylo, 0) )
brIJK = xyToIJK.TransformPoint( (xhi, ylo, 0) )
#
# get the mask bounding box in ijk coordinates
# - get the xy bounds
# - transform to ijk
# - clamp the bounds to the dimensions of the label image
#
# do the clamping of the four corners
dims = sliceImage.GetDimensions()
tl = [0,] * 3
tr = [0,] * 3
bl = [0,] * 3
br = [0,] * 3
corners = ((tlIJK, tl),(trIJK, tr),(blIJK, bl),(brIJK, br))
for corner,clampedCorner in corners:
for d in xrange(3):
clamped = int(round(corner[d]))
if clamped < 0: clamped = 0
if clamped >= dims[d]: clamped = dims[d]-1
clampedCorner[d] = clamped
# calculate the statistics for the selected region
clip = vtk.vtkImageClip()
extentMin = [min(tl[0],min(tr[0],min(bl[0],br[0]))),min(tl[1],min(tr[1],min(bl[1],br[1]))),min(tl[2],min(tr[2],min(bl[2],br[2])))]
extentMax = [max(tl[0],max(tr[0],max(bl[0],br[0]))),max(tl[1],max(tr[1],max(bl[1],br[1]))),max(tl[2],max(tr[2],max(bl[2],br[2])))]
clip.SetOutputWholeExtent(extentMin[0],extentMax[0],extentMin[1],extentMax[1],extentMin[2],extentMax[2])
if vtk.VTK_MAJOR_VERSION <= 5:
clip.SetInput(sliceNode.GetImageData())
else:
clip.SetInputData(sliceNode.GetImageData())
clip.ClipDataOn()
clip.Update()
stats = vtk.vtkImageHistogramStatistics()
if vtk.VTK_MAJOR_VERSION <= 5:
stats.SetInput(clip.GetOutput())
else:
stats.SetInputData(clip.GetOutput())
stats.Update()
minIntensity = stats.GetMinimum()
maxIntensity = stats.GetMaximum()
sliceNode.GetDisplayNode().SetAutoWindowLevel(False)
sliceNode.GetDisplayNode().SetAutoWindowLevel(0)
sliceNode.GetDisplayNode().SetWindowLevel(maxIntensity-minIntensity, (maxIntensity-minIntensity)/2.+minIntensity)
sliceNode.GetDisplayNode().Modified()
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 updateWindowLevelRectangle(self, sliceLayer, xyBounds):
# conversion as done in LabelEffect.py:applyImageMask
xlo, xhi, ylo, yhi, zlo, zhi = xyBounds
if xlo == xhi or ylo == yhi:
return
sliceNode = sliceLayer.GetVolumeNode()
sliceImage = sliceNode.GetImageData()
if not sliceImage:
return [0, 0, 0, 0]
xyToIJK = sliceLayer.GetXYToIJKTransform()
tlIJK = xyToIJK.TransformPoint((xlo, yhi, 0))
trIJK = xyToIJK.TransformPoint((xhi, yhi, 0))
blIJK = xyToIJK.TransformPoint((xlo, ylo, 0))
brIJK = xyToIJK.TransformPoint((xhi, ylo, 0))
#
# get the mask bounding box in ijk coordinates
# - get the xy bounds
# - transform to ijk
# - clamp the bounds to the dimensions of the label image
#
# do the clamping of the four corners
dims = sliceImage.GetDimensions()
tl = [0] * 3
tr = [0] * 3
bl = [0] * 3
br = [0] * 3
corners = ((tlIJK, tl), (trIJK, tr), (blIJK, bl), (brIJK, br))
for corner, clampedCorner in corners:
for d in xrange(3):
clamped = int(round(corner[d]))
if clamped < 0:
clamped = 0
if clamped >= dims[d]:
clamped = dims[d] - 1
clampedCorner[d] = clamped
# calculate the statistics for the selected region
clip = vtk.vtkImageClip()
extentMin = [
min(tl[0], min(tr[0], min(bl[0], br[0]))),
min(tl[1], min(tr[1], min(bl[1], br[1]))),
min(tl[2], min(tr[2], min(bl[2], br[2]))),
]
extentMax = [
max(tl[0], max(tr[0], max(bl[0], br[0]))),
max(tl[1], max(tr[1], max(bl[1], br[1]))),
max(tl[2], max(tr[2], max(bl[2], br[2]))),
]
clip.SetOutputWholeExtent(extentMin[0], extentMax[0], extentMin[1], extentMax[1], extentMin[2], extentMax[2])
if vtk.VTK_MAJOR_VERSION <= 5:
clip.SetInput(sliceNode.GetImageData())
else:
clip.SetInputData(sliceNode.GetImageData())
clip.ClipDataOn()
clip.Update()
stats = vtk.vtkImageHistogramStatistics()
if vtk.VTK_MAJOR_VERSION <= 5:
stats.SetInput(clip.GetOutput())
else:
stats.SetInputData(clip.GetOutput())
stats.Update()
minIntensity = stats.GetMinimum()
maxIntensity = stats.GetMaximum()
sliceNode.GetDisplayNode().SetAutoWindowLevel(False)
sliceNode.GetDisplayNode().SetAutoWindowLevel(0)
sliceNode.GetDisplayNode().SetWindowLevel(
maxIntensity - minIntensity, (maxIntensity - minIntensity) / 2.0 + minIntensity
)
sliceNode.GetDisplayNode().Modified()
def clipImageWithPolyData(self,
inputImageData,
outputImageData,
clippingPolyData,
rasToModel,
inputIjkToRas,
outputIjkToRas,
clipOutsideSurface=True,
fillValue=0,
reduceExtent=False):
"""
Fill voxels of the input volume inside/outside the clipping model with the provided fill value
If reduceExtent is True then the extent of the volume will be reduced to the smallest possible box that still contains all the non-zero voxels.
"""
# Determine the transform between the box and the image IJK coordinate systems
ijkToModel = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4.Multiply4x4(rasToModel, inputIjkToRas, ijkToModel)
modelToIjkTransform = vtk.vtkTransform()
modelToIjkTransform.SetMatrix(ijkToModel)
modelToIjkTransform.Inverse()
transformModelToIjk = vtk.vtkTransformPolyDataFilter()
transformModelToIjk.SetTransform(modelToIjkTransform)
transformModelToIjk.SetInputData(clippingPolyData)
# Use the stencil to fill the volume
# Convert model to stencil
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetInputConnection(transformModelToIjk.GetOutputPort())
polyToStencil.SetOutputSpacing(inputImageData.GetSpacing())
polyToStencil.SetOutputOrigin(inputImageData.GetOrigin())
polyToStencil.SetOutputWholeExtent(inputImageData.GetExtent())
# Apply the stencil to the volume
stencilToImage = vtk.vtkImageStencil()
stencilToImage.SetInputData(inputImageData)
stencilToImage.SetStencilConnection(polyToStencil.GetOutputPort())
if clipOutsideSurface:
stencilToImage.ReverseStencilOff()
else:
stencilToImage.ReverseStencilOn()
stencilToImage.SetBackgroundValue(fillValue)
stencilToImage.Update()
# Update the volume with the stencil operation result
if reduceExtent:
clippingPolyDataBounds_Ijk = [0, 0, 0, 0, 0, 0]
transformModelToIjk.GetOutput().GetBounds(
clippingPolyDataBounds_Ijk)
inputVolumeExtent_Ijk = inputImageData.GetExtent()
outputVolumeExtent_Ijk = list(inputVolumeExtent_Ijk) # make a copy
for i in range(3):
a = int(math.floor(clippingPolyDataBounds_Ijk[i * 2]))
if a > outputVolumeExtent_Ijk[i * 2]:
outputVolumeExtent_Ijk[i * 2] = a
b = int(math.ceil(clippingPolyDataBounds_Ijk[i * 2 + 1]))
if b < outputVolumeExtent_Ijk[i * 2 + 1]:
outputVolumeExtent_Ijk[i * 2 + 1] = b
clipper = vtk.vtkImageClip()
clipper.SetOutputWholeExtent(outputVolumeExtent_Ijk)
clipper.ClipDataOn()
clipper.SetInputConnection(stencilToImage.GetOutputPort())
clipper.Update()
outputImageData.DeepCopy(clipper.GetOutput())
# Offset the extent to start at [0,0,0]
# (maybe this is not needed, but we do it because some code may assume the image extent starts from zero)
outputVolumeExtent_Ijk = list(outputImageData.GetExtent())
outputIjkToInputIjk = vtk.vtkMatrix4x4()
for i in range(3):
outputVolumeExtentOffset = outputVolumeExtent_Ijk[i * 2]
outputVolumeExtent_Ijk[i * 2] = outputVolumeExtent_Ijk[
i * 2] - outputVolumeExtentOffset
outputVolumeExtent_Ijk[i * 2 + 1] = outputVolumeExtent_Ijk[
i * 2 + 1] - outputVolumeExtentOffset
outputIjkToInputIjk.SetElement(i, 3, outputVolumeExtentOffset)
outputImageData.SetExtent(outputVolumeExtent_Ijk)
vtk.vtkMatrix4x4.Multiply4x4(inputIjkToRas, outputIjkToInputIjk,
outputIjkToRas)
else:
outputImageData.DeepCopy(stencilToImage.GetOutput())
outputIjkToRas.DeepCopy(inputIjkToRas)