def avgProjectionsVtk(self, filenames , extent):
'''Returns the average of the input images
Input is passed as filenames pointing to 2D TIFF
Output is a vtkImageData
gives the same result as avgProjections within machine precision.
'''
num = len(filenames)
readers = [vtk.vtkTIFFReader() for i in range(num)]
scalers = [vtk.vtkImageShiftScale() for i in range(num)]
vois = [vtk.vtkExtractVOI() for i in range(num)]
avger = vtk.vtkImageWeightedSum()
counter = 0
for reader, voi, scaler, filename in zip(readers, vois , scalers ,filenames):
reader.SetFileName(filename)
reader.Update()
print ("reading {0}".format(filename))
voi.SetInputData(reader.GetOutput())
voi.SetVOI(extent)
voi.Update()
print ("extracting VOI")
scaler.SetInputData(voi.GetOutput())
scaler.SetOutputScalarTypeToDouble()
scaler.SetScale(1)
scaler.SetShift(0)
scaler.Update()
avger.AddInputData(scaler.GetOutput())
avger.SetWeight(counter , 1/float(num))
counter = counter + 1
print ("adding input connection {0}".format(counter))
avger.Update()
return avger.GetOutput()
def onApply(self):
inputVolume = self.inputSelector.currentNode()
outputVolume = self.outputSelector.currentNode()
if not (inputVolume):
qt.QMessageBox.critical(slicer.util.mainWindow(), 'Averaging',
'Input volumes are required')
return
outVolumeNode = self.outputSelector.currentNode()
volumesLogic = slicer.modules.volumes.logic()
# newNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'average volume')
# create output volume by cloning the selected reference volume
# volumesLogic = slicer.modules.volumes.logic()
newNode = volumesLogic.CloneVolume(self.inputSelector.currentNode(),
"average volume")
# vtk function to average the images
imgsum = vtk.vtkImageWeightedSum()
imgsum.NormalizeByWeightOn()
# add all of the input image data
for (i, n) in enumerate(self.inputSelector.checkedNodes()):
print("adding input image: {0}".format(n.GetName()))
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToFloat()
cast.AddInputConnection(n.GetImageDataConnection())
imgsum.AddInputConnection(cast.GetOutputPort())
imgsum.SetWeight(i, 1.)
# run the filter and set the result to the output image
imgsum.Update()
newNode.SetAndObserveImageData(imgsum.GetOutput())
def onApply(self):
inputVolume = self.inputSelector.currentNode()
outputVolume = self.outputSelector.currentNode()
if not (inputVolume):
qt.QMessageBox.critical(
slicer.util.mainWindow(),
'Averaging', 'Input volumes are required')
return
outVolumeNode = self.outputSelector.currentNode()
volumesLogic = slicer.modules.volumes.logic()
# newNode = volumesLogic.CloneVolume(slicer.mrmlScene, sourceVolumeNode, 'average volume')
# create output volume by cloning the selected reference volume
# volumesLogic = slicer.modules.volumes.logic()
newNode = volumesLogic.CloneVolume(self.inputSelector.currentNode(), "average volume")
# vtk function to average the images
imgsum = vtk.vtkImageWeightedSum()
imgsum.NormalizeByWeightOn()
# add all of the input image data
for (i,n) in enumerate(self.inputSelector.checkedNodes()):
print("adding input image: {0}".format(n.GetName()))
cast = vtk.vtkImageCast()
cast.SetOutputScalarTypeToFloat()
cast.AddInputConnection(n.GetImageDataConnection())
imgsum.AddInputConnection(cast.GetOutputPort())
imgsum.SetWeight(i, 1.)
# run the filter and set the result to the output image
imgsum.Update()
newNode.SetAndObserveImageData(imgsum.GetOutput())
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImageWeightedSum(), 'Processing.',
('vtkImageData',), ('vtkImageData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def SumVTKImages(ImageSets, Weights):
NumOfImages = len(ImageSets)
SumFilter = vtk.vtkImageWeightedSum()
for x in range(0, NumOfImages, 1):
SumFilter.AddInputConnection(ImageSets[x])
SumFilter.SetWeight(x, Weights[x])
SumFilter.Update()
# Return summed Image as vtkImageData
return SumFilter.GetOutput()
def SumVTKImages(ImageSets, Weights):
NumOfImages = len(ImageSets)
SumFilter = vtk.vtkImageWeightedSum()
for x in range(0, NumOfImages, 1):
SumFilter.AddInputConnection(ImageSets[x])
SumFilter.SetWeight(x, Weights[x])
SumFilter.Update()
# Return summed Image as vtkImageData
return SumFilter.GetOutput()
def CombineGaussians(bounds, coords, weights, sizes):
"""Forms a linear combination of Gaussians"""
assert len(bounds) == 6, 'Invalid bounds'
assert len(coords) == len(weights) == len(sizes), 'Different numbers of coordinates and weights'
combo = vtk.vtkImageWeightedSum()
for i in range(len(coords)):
primitive = vtk.vtkImageGaussianSource()
primitive.SetWholeExtent(*bounds)
primitive.SetCenter(coords[i])
primitive.SetStandardDeviation(sizes[i])
primitive.SetMaximum(weights[i]) #WRONG normalization
combo.AddInputConnection(primitive.GetOutputPort())
combo.SetWeight(i, 1.0)
return combo
def average_all_images(image_datas, fname='average_image.raw'):
# how cool is this, this class was from my masters' thesis.
# though the new vtk coding is not recognizable anymore...
sum = vtk.vtkImageWeightedSum()
weights = vtk.vtkDoubleArray()
for image in image_datas:
weights.InsertNextTuple1(1.0)
sum.AddInput(image)
sum.SetWeights(weights)
sum.NormalizeByWeightOn()
sum.Update()
writer = vtk.vtkImageWriter()
writer.SetInput(sum.GetOutput())
writer.SetFileName(fname)
writer.SetFileDimensionality(3)
writer.Write()
return(sum.GetOutput())
def CombineGaussians(bounds, coords, weights, sizes):
"""Forms a linear combination of Gaussians"""
assert len(bounds) == 6, 'Invalid bounds'
assert len(coords) == len(weights) == len(
sizes), 'Different numbers of coordinates and weights'
combo = vtk.vtkImageWeightedSum()
for i in range(len(coords)):
primitive = vtk.vtkImageGaussianSource()
primitive.SetWholeExtent(*bounds)
primitive.SetCenter(coords[i])
primitive.SetStandardDeviation(sizes[i])
primitive.SetMaximum(weights[i]) #WRONG normalization
combo.AddInputConnection(primitive.GetOutputPort())
combo.SetWeight(i, 1.0)
return combo
def runConversionMethodAverage(self, inputVolumeNode, outputVolumeNode):
ijkToRAS = vtk.vtkMatrix4x4()
inputVolumeNode.GetIJKToRASMatrix(ijkToRAS)
outputVolumeNode.SetIJKToRASMatrix(ijkToRAS)
numberOfComponents = inputVolumeNode.GetImageData(
).GetNumberOfScalarComponents()
weightedSum = vtk.vtkImageWeightedSum()
weights = vtk.vtkDoubleArray()
weights.SetNumberOfValues(numberOfComponents)
# TODO: Average could be extended to let the user choose the weights of the components.
evenWeight = 1.0 / numberOfComponents
logging.debug("ImageWeightedSum: weight value for all components: %s" %
evenWeight)
for comp in range(numberOfComponents):
weights.SetValue(comp, evenWeight)
weightedSum.SetWeights(weights)
for comp in range(numberOfComponents):
extract = vtk.vtkImageExtractComponents()
extract.SetInputConnection(
inputVolumeNode.GetImageDataConnection())
extract.SetComponents(comp)
extract.Update()
# Cast component to Double
compToDouble = vtk.vtkImageCast()
compToDouble.SetInputConnection(0, extract.GetOutputPort())
compToDouble.SetOutputScalarTypeToDouble()
# Add to the weighted sum
weightedSum.AddInputConnection(compToDouble.GetOutputPort())
logging.debug("TotalInputConnections in weightedSum: %s" %
weightedSum.GetTotalNumberOfInputConnections())
weightedSum.SetNormalizeByWeight(
False) # It is already normalized in the evenWeight case.
weightedSum.Update()
# Cast back to the type of the InputVolume, for consistency with other ConversionMethods
castBack = vtk.vtkImageCast()
castBack.SetInputConnection(0, weightedSum.GetOutputPort())
castBack.SetOutputScalarType(
inputVolumeNode.GetImageData().GetScalarType())
outputVolumeNode.SetImageDataConnection(castBack.GetOutputPort())
def runConversionMethodAverage(self, inputVolumeNode, outputVolumeNode):
ijkToRAS = vtk.vtkMatrix4x4()
inputVolumeNode.GetIJKToRASMatrix(ijkToRAS)
outputVolumeNode.SetIJKToRASMatrix(ijkToRAS)
numberOfComponents = inputVolumeNode.GetImageData().GetNumberOfScalarComponents()
weightedSum = vtk.vtkImageWeightedSum()
weights = vtk.vtkDoubleArray()
weights.SetNumberOfValues(numberOfComponents)
# TODO: Average could be extended to let the user choose the weights of the components.
evenWeight = 1.0/numberOfComponents
logging.debug("ImageWeightedSum: weight value for all components: %s" % evenWeight)
for comp in range(numberOfComponents):
weights.SetValue(comp, evenWeight)
weightedSum.SetWeights(weights)
for comp in range(numberOfComponents):
extract = vtk.vtkImageExtractComponents()
extract.SetInputConnection(inputVolumeNode.GetImageDataConnection())
extract.SetComponents(comp)
extract.Update()
# Cast component to Double
compToDouble = vtk.vtkImageCast()
compToDouble.SetInputConnection(0, extract.GetOutputPort())
compToDouble.SetOutputScalarTypeToDouble()
# Add to the weighted sum
weightedSum.AddInputConnection(compToDouble.GetOutputPort())
logging.debug("TotalInputConnections in weightedSum: %s" % weightedSum.GetTotalNumberOfInputConnections())
weightedSum.SetNormalizeByWeight(False) # It is already normalized in the evenWeight case.
weightedSum.Update()
# Cast back to the type of the InputVolume, for consistency with other ConversionMethods
castBack = vtk.vtkImageCast()
castBack.SetInputConnection(0, weightedSum.GetOutputPort())
castBack.SetOutputScalarType(inputVolumeNode.GetImageData().GetScalarType())
outputVolumeNode.SetImageDataConnection(castBack.GetOutputPort())
def main():
colors = vtk.vtkNamedColors()
colors.SetColor('leftBkg', [0.6, 0.5, 0.4, 1.0])
colors.SetColor('centreBkg', [0.1, 0.5, 0.4, 1.0])
colors.SetColor('rightBkg', [0.4, 0.5, 0.6, 1.0])
# Create image 1
source1 = vtk.vtkImageMandelbrotSource()
source1.SetWholeExtent(0, 255, 0, 255, 0, 0)
source1.Update()
source1Double = vtk.vtkImageCast()
source1Double.SetInputConnection(0, source1.GetOutputPort())
source1Double.SetOutputScalarTypeToDouble()
# Create image 2
source2 = vtk.vtkImageSinusoidSource()
source2.SetWholeExtent(0, 255, 0, 255, 0, 0)
source2.Update()
# Do the sum
sumFilter = vtk.vtkImageWeightedSum()
sumFilter.SetWeight(0, 0.8)
sumFilter.SetWeight(1, 0.2)
sumFilter.AddInputConnection(source1Double.GetOutputPort())
sumFilter.AddInputConnection(source2.GetOutputPort())
sumFilter.Update()
# Display the images
source1CastFilter = vtk.vtkImageCast()
source1CastFilter.SetInputConnection(source1.GetOutputPort())
source1CastFilter.SetOutputScalarTypeToUnsignedChar()
source1CastFilter.Update()
source2CastFilter = vtk.vtkImageCast()
source2CastFilter.SetInputConnection(source2.GetOutputPort())
source2CastFilter.SetOutputScalarTypeToUnsignedChar()
source2CastFilter.Update()
summedCastFilter = vtk.vtkImageCast()
summedCastFilter.SetInputConnection(sumFilter.GetOutputPort())
summedCastFilter.SetOutputScalarTypeToUnsignedChar()
summedCastFilter.Update()
# Create actors
source1Actor = vtk.vtkImageActor()
source1Actor.GetMapper().SetInputConnection(
source1CastFilter.GetOutputPort())
source2Actor = vtk.vtkImageActor()
source2Actor.GetMapper().SetInputConnection(
source2CastFilter.GetOutputPort())
summedActor = vtk.vtkImageActor()
summedActor.GetMapper().SetInputConnection(
summedCastFilter.GetOutputPort())
# There will be one render window
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(600, 300)
# And one interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
leftViewport = [0.0, 0.0, 0.33, 1.0]
centerViewport = [0.33, 0.0, .66, 1.0]
rightViewport = [0.66, 0.0, 1.0, 1.0]
# Setup renderers
leftRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(leftRenderer)
leftRenderer.SetViewport(leftViewport)
leftRenderer.SetBackground(colors.GetColor3d('leftBkg'))
centerRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(centerRenderer)
centerRenderer.SetViewport(centerViewport)
centerRenderer.SetBackground(colors.GetColor3d('centreBkg'))
rightRenderer = vtk.vtkRenderer()
renderWindow.AddRenderer(rightRenderer)
rightRenderer.SetViewport(rightViewport)
rightRenderer.SetBackground(colors.GetColor3d('rightBkg'))
leftRenderer.AddActor(source1Actor)
centerRenderer.AddActor(source2Actor)
rightRenderer.AddActor(summedActor)
leftRenderer.ResetCamera()
centerRenderer.ResetCamera()
rightRenderer.ResetCamera()
renderWindow.Render()
interactor.Start()
th.SetInputConnection(mag.GetOutputPort()) th.SetReplaceIn(1) th.SetReplaceOut(1) th.ThresholdBetween(-1000, 1000) th.SetOutValue(0) th.SetInValue(2000) cast = vtk.vtkImageCast() cast.SetInputConnection(mag.GetOutputPort()) cast.SetOutputScalarTypeToFloat() cast2 = vtk.vtkImageCast() cast2.SetInputConnection(th.GetOutputPort()) cast2.SetOutputScalarTypeToFloat() sum = vtk.vtkImageWeightedSum() sum.AddInputConnection(cast.GetOutputPort()) sum.AddInputConnection(cast2.GetOutputPort()) sum.SetWeight(0, 10) sum.SetWeight(1, 4) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(sum.GetOutputPort()) viewer.SetZSlice(22) viewer.SetColorWindow(1819) viewer.SetColorLevel(939) sum.SetWeight(0, 1) # make interface viewer.SetSize(256, 256) viewer.Render()
th.SetInputConnection(mag.GetOutputPort()) th.SetReplaceIn(1) th.SetReplaceOut(1) th.ThresholdBetween(-1000, 1000) th.SetOutValue(0) th.SetInValue(2000) cast = vtk.vtkImageCast() cast.SetInputConnection(mag.GetOutputPort()) cast.SetOutputScalarTypeToFloat() cast2 = vtk.vtkImageCast() cast2.SetInputConnection(th.GetOutputPort()) cast2.SetOutputScalarTypeToFloat() sum = vtk.vtkImageWeightedSum() sum.AddInputConnection(cast.GetOutputPort()) sum.AddInputConnection(cast2.GetOutputPort()) sum.SetWeight(0, 10) sum.SetWeight(1, 4) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(sum.GetOutputPort()) viewer.SetZSlice(22) viewer.SetColorWindow(1819) viewer.SetColorLevel(939) sum.SetWeight(0, 1) # make interface viewer.SetSize(256, 256) viewer.Render()
# Create image 1 source1 = vtk.vtkImageMandelbrotSource() source1.SetWholeExtent(0, 255, 0, 255, 0, 0) source1.Update() source1Double = vtk.vtkImageCast() source1Double.SetInputConnection(0, source1.GetOutputPort()) source1Double.SetOutputScalarTypeToDouble() # Create image 2 source2 = vtk.vtkImageSinusoidSource() source2.SetWholeExtent(0, 255, 0, 255, 0, 0) source2.Update() # Do the sum sumFilter = vtk.vtkImageWeightedSum() sumFilter.SetWeight(0, 0.8) sumFilter.SetWeight(1, 0.2) sumFilter.AddInputConnection(source1Double.GetOutputPort()) sumFilter.AddInputConnection(source2.GetOutputPort()) sumFilter.Update() # Display the images source1CastFilter = vtk.vtkImageCast() source1CastFilter.SetInputConnection(source1.GetOutputPort()) source1CastFilter.SetOutputScalarTypeToUnsignedChar() source1CastFilter.Update() source2CastFilter = vtk.vtkImageCast() source2CastFilter.SetInputConnection(source2.GetOutputPort()) source2CastFilter.SetOutputScalarTypeToUnsignedChar()
# Create image 1 source1 = vtk.vtkImageMandelbrotSource() source1.SetWholeExtent(0, 255, 0, 255, 0, 0) source1.Update() source1Double = vtk.vtkImageCast() source1Double.SetInputConnection(0, source1.GetOutputPort()) source1Double.SetOutputScalarTypeToDouble() # Create image 2 source2 = vtk.vtkImageSinusoidSource() source2.SetWholeExtent(0, 255, 0, 255, 0, 0) source2.Update() # Do the sum sumFilter = vtk.vtkImageWeightedSum() sumFilter.SetWeight(0, 0.8) sumFilter.SetWeight(1, 0.2) sumFilter.AddInputConnection(source1Double.GetOutputPort()) sumFilter.AddInputConnection(source2.GetOutputPort()) sumFilter.Update() # Display the images source1CastFilter = vtk.vtkImageCast() source1CastFilter.SetInputConnection(source1.GetOutputPort()) source1CastFilter.SetOutputScalarTypeToUnsignedChar() source1CastFilter.Update() source2CastFilter = vtk.vtkImageCast() source2CastFilter.SetInputConnection(source2.GetOutputPort()) source2CastFilter.SetOutputScalarTypeToUnsignedChar()
