def testStorageValue(self, logic):
print " Test storage of Values: "
bool = True
arrayValue = vtk.vtkDoubleArray()
arrayMask = vtk.vtkDoubleArray()
for i in range(0, 1000, 2):
arrayValue.InsertNextValue(i)
arrayValue.InsertNextValue(i)
arrayMask.InsertNextValue(0.0)
arrayMask.InsertNextValue(0.0)
listOfRandomNumber = list()
del listOfRandomNumber[:]
for i in range(0, 250):
listOfRandomNumber.append(randint(0, 998))
listOfRandomNumber = set(listOfRandomNumber)
listOfRandomNumber = sorted(listOfRandomNumber)
for index in listOfRandomNumber:
arrayMask.SetValue(index, 1.0)
array = logic.defineArray(arrayValue, arrayMask)
array = sorted(array)
a = 0
for i in listOfRandomNumber:
if arrayValue.GetValue(i) != array[a]:
bool = False
print " Failed", a, array[a], i, arrayValue.GetValue(i)
break
a += 1
if bool:
print " Passed"
def testStorageValue(self):
logic = MeshStatisticsLogic()
print " Test storage of Values: "
arrayValue = vtk.vtkDoubleArray()
arrayMask = vtk.vtkDoubleArray()
for i in range(0, 1000, 2):
arrayValue.InsertNextValue(i)
arrayValue.InsertNextValue(i)
arrayMask.InsertNextValue(0.0)
arrayMask.InsertNextValue(0.0)
listOfRandomNumber = list()
del listOfRandomNumber[:]
for i in range(0, 250):
listOfRandomNumber.append(randint(0, 998))
listOfRandomNumber = list(set(listOfRandomNumber))
listOfRandomNumber = sorted(listOfRandomNumber)
for index in listOfRandomNumber:
arrayMask.SetValue(index, 1.0)
bool, array = logic.defineArray(arrayValue, arrayMask)
array = sorted(array)
a = 0
for i in listOfRandomNumber:
if arrayValue.GetValue(i) != array[a]:
print " Failed", a, array[a], i, arrayValue.GetValue(i)
return False
a += 1
print " Passed"
return True
def testStorageValue(self):
logic = MeshStatisticsLogic()
print ' Test storage of Values: '
arrayValue = vtk.vtkDoubleArray()
arrayMask = vtk.vtkDoubleArray()
for i in range(0, 1000, 2):
arrayValue.InsertNextValue(i)
arrayValue.InsertNextValue(i)
arrayMask.InsertNextValue(0.0)
arrayMask.InsertNextValue(0.0)
listOfRandomNumber = list()
del listOfRandomNumber[:]
for i in range(0, 250):
listOfRandomNumber.append(randint(0, 998))
listOfRandomNumber = list(set(listOfRandomNumber))
listOfRandomNumber = sorted(listOfRandomNumber)
for index in listOfRandomNumber:
arrayMask.SetValue(index, 1.0)
bool, array = logic.defineArray(arrayValue, arrayMask)
array = sorted(array)
a = 0
for i in listOfRandomNumber:
if arrayValue.GetValue(i) != array[a]:
print ' Failed', a, array[a], i, arrayValue.GetValue(i)
return False
a += 1
print ' Passed'
return True
def defineArrays(self, logic, firstValue, lastValue):
arrayValue = vtk.vtkDoubleArray()
ROIArray = vtk.vtkDoubleArray()
for i in range(firstValue, lastValue):
arrayValue.InsertNextValue(i)
ROIArray.InsertNextValue(1.0)
array = logic.defineArray(arrayValue, ROIArray)
return array
def defineArrays(self, logic, firstValue, lastValue):
arrayValue = vtk.vtkDoubleArray()
ROIArray = vtk.vtkDoubleArray()
for i in range(firstValue, lastValue):
arrayValue.InsertNextValue(i)
ROIArray.InsertNextValue(1.0)
bool, array = logic.defineArray(arrayValue, ROIArray)
if bool:
return array
return False
def populateChart(self):
# strip elements from 2nd 3d view
# and add our own chart renderer to it
self.aModeImageNode = slicer.util.getNode('Image_NeedleTip')
if self.aModeImageNode is None:
logging.debug(
"Cannot locate Image_NeedleTip, can't visualize chart")
return
self.imageData = self.aModeImageNode.GetImageData()
if not self.table is None:
# We already have created all of the things, don't recreate
self.view.GetInteractor().Initialize()
self.chart.RecalculateBounds()
return
self.table = vtk.vtkTable()
self.chart = vtk.vtkChartXY()
self.line = self.chart.AddPlot(0)
self.view = vtk.vtkContextView()
self.signalArray = vtk.vtkDoubleArray()
self.signalArray.SetName("RF Signal")
self.distanceArray = vtk.vtkDoubleArray()
self.distanceArray.SetName("Distance (mm)")
self.imageDimensions = self.imageData.GetDimensions()
self.signalArray.SetNumberOfTuples(self.imageDimensions[0])
self.distanceArray.SetNumberOfTuples(self.imageDimensions[0])
self.table.AddColumn(self.distanceArray)
self.table.AddColumn(self.signalArray)
self.line = self.chart.AddPlot(0)
self.line.SetInputData(self.table, 0, 1)
self.line.SetColor(0, 255, 0, 255)
self.line.SetWidth(1.0)
inc = 1000 * 1480 / (
2 * 420e6
) # distance in mm. The delay distance is added to the increments. (2e-6*1480/2) +
distanceDelay = 1000 * 2e-6 * 1480 / 2
for i in range(self.imageDimensions[0]):
self.distanceArray.SetComponent(i, 0, distanceDelay + inc * i)
self.view.GetRenderer().SetBackground(1.0, 1.0, 1.0)
self.view.GetRenderWindow().SetSize(400, 300)
# self.contextScene = vtk.vtkContextScene()
# self.contextScene.AddItem(self.chart)
# self.contextActor = vtk.vtkContextActor()
self.view.GetScene().AddItem(self.chart)
self.view.GetRenderWindow().SetMultiSamples(0)
# self.layoutManager.threeDWidget(1).threeDView.renderWindow().GetRenderer().GetFirstRenderer().AddActor(self.contextActor)
self.view.GetInteractor().Initialize()
def ConvertTextureToPointAttribute(modelNode, textureImageNode):
polyData=modelNode.GetPolyData()
textureImageFlipVert=vtk.vtkImageFlip()
textureImageFlipVert.SetFilteredAxis(1)
textureImageFlipVert.SetInputConnection(textureImageNode.GetImageDataConnection())
textureImageFlipVert.Update()
textureImageData=textureImageFlipVert.GetOutput()
pointData=polyData.GetPointData()
tcoords=pointData.GetTCoords()
numOfPoints=pointData.GetNumberOfTuples()
assert numOfPoints==tcoords.GetNumberOfTuples(), "Number of texture coordinates does not equal number of points"
textureSamplingPointsUv=vtk.vtkPoints()
textureSamplingPointsUv.SetNumberOfPoints(numOfPoints)
for pointIndex in xrange(numOfPoints):
uv=tcoords.GetTuple2(pointIndex)
textureSamplingPointsUv.SetPoint(pointIndex, uv[0], uv[1], 0)
textureSamplingPointDataUv=vtk.vtkPolyData()
uvToXyz=vtk.vtkTransform()
textureImageDataSpacingSpacing=textureImageData.GetSpacing()
textureImageDataSpacingOrigin=textureImageData.GetOrigin()
textureImageDataSpacingDimensions=textureImageData.GetDimensions()
uvToXyz.Scale(textureImageDataSpacingDimensions[0]/textureImageDataSpacingSpacing[0], textureImageDataSpacingDimensions[1]/textureImageDataSpacingSpacing[1], 1)
uvToXyz.Translate(textureImageDataSpacingOrigin)
textureSamplingPointDataUv.SetPoints(textureSamplingPointsUv)
transformPolyDataToXyz=vtk.vtkTransformPolyDataFilter()
transformPolyDataToXyz.SetInputData(textureSamplingPointDataUv)
transformPolyDataToXyz.SetTransform(uvToXyz)
probeFilter=vtk.vtkProbeFilter()
probeFilter.SetInputConnection(transformPolyDataToXyz.GetOutputPort())
probeFilter.SetSourceData(textureImageData)
probeFilter.Update()
rgbPoints=probeFilter.GetOutput().GetPointData().GetArray('ImageScalars')
colorArrayRed=vtk.vtkDoubleArray()
colorArrayRed.SetName('ColorRed')
colorArrayRed.SetNumberOfTuples(numOfPoints)
colorArrayGreen=vtk.vtkDoubleArray()
colorArrayGreen.SetName('ColorGreen')
colorArrayGreen.SetNumberOfTuples(numOfPoints)
colorArrayBlue=vtk.vtkDoubleArray()
colorArrayBlue.SetName('ColorBlue')
colorArrayBlue.SetNumberOfTuples(numOfPoints)
for pointIndex in xrange(numOfPoints):
rgb=rgbPoints.GetTuple3(pointIndex)
colorArrayRed.SetValue(pointIndex,rgb[0])
colorArrayGreen.SetValue(pointIndex,rgb[1])
colorArrayBlue.SetValue(pointIndex,rgb[2])
colorArrayRed.Modified()
colorArrayGreen.Modified()
colorArrayBlue.Modified()
pointData.AddArray(colorArrayRed)
pointData.AddArray(colorArrayGreen)
pointData.AddArray(colorArrayBlue)
pointData.Modified()
polyData.Modified()
def CalculatePlane( self, inPoints, base, dir1, dir2, normal ):
# Create arrays for the dataset
points2D = vtk.vtkPoints()
arrayX = vtk.vtkDoubleArray()
arrayX.SetNumberOfComponents( 1 )
arrayX.SetName ( 'X' )
arrayY = vtk.vtkDoubleArray()
arrayY.SetNumberOfComponents( 1 )
arrayY.SetName ( 'Y' )
arrayZ = vtk.vtkDoubleArray()
arrayZ.SetNumberOfComponents( 1 )
arrayZ.SetName ( 'Z' )
# Add the points to the table
for i in range( 0, inPoints.GetNumberOfPoints() ):
currPoint = [ 0, 0, 0 ]
inPoints.GetPoint( i, currPoint )
arrayX.InsertNextValue( currPoint[ 0 ] )
arrayY.InsertNextValue( currPoint[ 1 ] )
arrayZ.InsertNextValue( currPoint[ 2 ] )
# Create a table for the dataset
table = vtk.vtkTable()
table.AddColumn( arrayX )
table.AddColumn( arrayY )
table.AddColumn( arrayZ )
# Setting up the PCA
pca = vtk.vtkPCAStatistics()
pca.SetInputData( vtk.vtkStatisticsAlgorithm.INPUT_DATA, table )
pca.SetColumnStatus( 'X', 1 )
pca.SetColumnStatus( 'Y', 1 )
pca.SetColumnStatus( 'Z', 1 )
pca.RequestSelectedColumns()
pca.SetDeriveOption( True )
pca.Update()
eigvec = vtk.vtkDoubleArray()
pca.GetEigenvectors( eigvec )
eigvec.GetTuple( 0, dir1 )
eigvec.GetTuple( 1, dir2 )
eigvec.GetTuple( 2, normal )
mean = self.CalculateMean( inPoints )
base[0] = mean[0]
base[1] = mean[1]
base[2] = mean[2]
def importFunction(self):
# check if the output container exists
mvNode = self.outputSelector.currentNode()
#print(mvNode)
if mvNode == None:
self.__status.text = 'Status: Select output node!'
return
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ''
frameFileListAttr = ''
dicomTagNameAttr = self.__dicomTag.text
dicomTagUnitsAttr = self.__veLabel.text
teAttr = self.__te.text
trAttr = self.__tr.text
faAttr = self.__fa.text
# each frame is saved as a separate volume
# first filter valid file names and sort alphabetically
frames = []
frame0 = None
inputDir = self.__fDialog.directory
print(inputDir)
def performPostProcessing(self, snrThreshold, distanceMinimumValue, distanceMaximumValue):
# Create new vtkPolyData
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
# Filter accordingly to the input parameters
recordedDataBufferFiltered = []
for idx in range(len(self.recordedDataBuffer)):
d = self.recordedDataBuffer[idx][3]
snr = self.recordedDataBuffer[idx][4]
if (snr > snrThreshold and
d < distanceMaximumValue and
d > distanceMinimumValue):
recordedDataBufferFiltered.append(self.recordedDataBuffer[idx])
self.addPointToPolyData(newPolyData, self.recordedDataBuffer[idx][0:3])
# Update recorded model and buffer
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
self.recordedDataBuffer = recordedDataBufferFiltered
def getArrayFromTable(self, outputTable, arrayName):
distanceArray = outputTable.GetTable().GetColumnByName(arrayName)
if distanceArray:
return distanceArray
newArray = vtk.vtkDoubleArray()
newArray.SetName(arrayName)
outputTable.GetTable().AddColumn(newArray)
return newArray
def clearPointsInRecordedModel(self):
self.recordedDataBuffer = []
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
def undoPostProcessing(self):
# Create new vtkPolyData
newPoints = vtk.vtkPoints()
newVertices = vtk.vtkCellArray()
newPolyData = vtk.vtkPolyData()
newPolyData.SetPoints(newPoints)
newPolyData.SetVerts(newVertices)
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
newPolyData.GetPointData().SetScalars(colorArray)
# Filter accordingly to the input parameters
recordedDataBufferFiltered = []
for idx in range(len(self.recordedDataBufferDefault)):
self.addPointToPolyData(newPolyData, self.recordedDataBufferDefault[idx][0:3])
# Update recorded model and buffer
self.recordedModelNode.GetPolyData().DeepCopy(newPolyData)
self.recordedModelNode.GetPolyData().Modified()
self.recordedDataBuffer = self.recordedDataBufferDefault
def onImportButtonClicked(self):
# check if the output container exists
mvNode = self.__mvSelector.currentNode()
if mvNode == None:
self.__status.text = 'Status: Select output node!'
return
modeIdx = self.__modeSelector.currentIndex
processingMode = self.__processingModes[modeIdx]
# There are two options:
# 1. DICOM series in a directory, with either predefined or custom parse tag
# 2. Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
if modeIdx < len(self.__processingModes)-1:
# DICOM series
# get logic
logic = slicer.modules.multivolumeexplorer.logic()
# create a clean temporary directory
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
tmpDir = tmpDir+'/MultiVolumeImporter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
else:
# clean it up
print("tmpDir: %s" % tmpDir)
oldFileNames = os.listdir(tmpDir)
for f in oldFileNames:
print("%s will be unlinked" % f)
os.unlink(tmpDir+'/'+f)
nFrames = logic.ProcessDICOMSeries(self.__fDialog.directory, tmpDir, self.__dicomTag.text, volumeLabels)
self.__status.text = 'Series processed OK, '+str(nFrames)+' volumes identified'
print("Location of files: %s" % tmpDir)
for f in os.listdir(tmpDir):
if not f.startswith('.'):
fileNames.append(f)
fileNames.sort()
frameFolder = tmpDir
else:
# each frame is saved as a separate volume
for f in os.listdir(self.__fDialog.directory):
if not f.startswith('.'):
fileNames.append(f)
fileNames.sort()
frameFolder = self.__fDialog.directory
nFrames = len(fileNames)
volumeLabels.SetNumberOfTuples(nFrames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(nFrames)
for i in range(len(fileNames)):
frameId = self.__veInitial.value+self.__veStep.value*i
volumeLabels.SetComponent(i, 0, frameId)
# read the first frame to get the extent for DWI node
fullName = frameFolder+'/'+fileNames[0]
volumesLogic = slicer.modules.volumes.logic()
frame = volumesLogic.AddArchetypeVolume(fullName, processingMode[3]+' Frame 0', 0)
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
nFrames = len(fileNames)
mvImage = vtk.vtkImageData()
mvImage.SetExtent(frameExtent)
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.AllocateScalars()
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
self.annihilateScalarNode(frame)
for frameId in range(0,nFrames):
fullName = frameFolder+'/'+fileNames[frameId]
print("Processing frame %d: %s" % (frameId, fullName))
frame = volumesLogic.AddArchetypeVolume(fullName, 'Frame'+str(frameId), 0)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
self.annihilateScalarNode(frame)
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
slicer.mrmlScene.AddNode(mvNode)
mvNode.SetReferenceCount(mvNode.GetReferenceCount()-1)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
print("MultiVolume node setup complete !")
Helper.SetBgFgVolumes(mvNode.GetID(),None)
def onImportButtonClicked(self):
# check if the output container exists
mvNode = self.__mvSelector.currentNode()
if mvNode == None:
self.__status.text = 'Status: Select output node!'
return
# Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ''
frameFileListAttr = ''
dicomTagNameAttr = self.__dicomTag.text
dicomTagUnitsAttr = self.__veLabel.text
teAttr = self.__te.text
trAttr = self.__tr.text
faAttr = self.__fa.text
# each frame is saved as a separate volume
for f in os.listdir(self.__fDialog.directory):
if not f.startswith('.'):
fileNames.append(f)
frameFileListAttr += f + ','
fileNames.sort()
frameFileListAttr = frameFileListAttr[:-1]
frameFolder = self.__fDialog.directory
nFrames = len(fileNames)
volumeLabels.SetNumberOfTuples(nFrames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(nFrames)
for i in range(len(fileNames)):
frameId = self.__veInitial.value + self.__veStep.value * i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ','
frameLabelsAttr = frameLabelsAttr[:-1]
# read the first frame to get the extent
fullName = frameFolder + '/' + fileNames[0]
volumesLogic = slicer.modules.volumes.logic()
frame = self.readFrame(fullName)
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1] * frameExtent[3] * frameExtent[5]
nFrames = len(fileNames)
mvImage = vtk.vtkImageData()
mvImage.SetExtent(frameExtent)
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.AllocateScalars()
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars())
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
for frameId in range(0, nFrames):
fullName = frameFolder + '/' + fileNames[frameId]
print("Processing frame %d: %s" % (frameId, fullName))
frame = self.readFrame(fullName)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName',
dicomTagNameAttr)
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits',
dicomTagUnitsAttr)
if dicomTagNameAttr == 'TriggerTime' or dicomTagNameAttr == 'AcquisitionTime':
if teTag != '':
mvNode.SetAttribute('MultiVolume.DICOM.EchoTime', teTag)
if trTag != '':
mvNode.SetAttribute('MultiVolume.DICOM.RepetitionTime', trTag)
if faTag != '':
mvNode.SetAttribute('MultiVolume.DICOM.FlipAngle', faTag)
mvNode.SetName(str(nFrames) + ' frames 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(
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 __init__(self):
# Member variables
self.outputLabels = None
self.recordedDataBuffer = []
self.record = False
self.reset = False
self.outputObserverTag = -1
self.rigidBodyToTrackerTransformNode = None
self.measurementToMeasurerTransformNode = None
self.parametersToMeasurerTransformNode = None
self.plus = None
self.m = vtk.vtkMatrix4x4()
self.direction = -1
self.ras = [0, 0, 0, 1]
self.d = 0.0
self.snr = 0
self.total = 0
self.LABEL_UPDATE_RATE = 10
self.labelUpdateCount = 0
self.snrThreshold = 40
self.distanceMaximumValue = 1000.0
self.distanceMinimumValue = 0.0
self.lensMaxDistance = 0.0
self.lensMinDistance = 0.0
self.normalizingConstant = 0.0
self.min = -1000.0
self.addColours = True
import Viewpoint # Viewpoint
self.viewpointLogic = Viewpoint.ViewpointLogic()
self.stopWatch = None # StopWatch
# Create style sheets
self.errorStyleSheet = "QLabel { color : #FF0000; \
font: bold 14px}"
self.defaultStyleSheet = "QLabel { color : #000000; \
font: bold 14px}"
# Create rainbow colour table
self.colorTable=slicer.vtkMRMLColorTableNode()
self.colorTable.SetTypeToRainbow ()
# Add MeasurementPoint
self.measurementPointMarkupsFiducialNode = slicer.util.getNode('MeasurementPoint')
if not self.measurementPointMarkupsFiducialNode:
self.measurementPointMarkupsFiducialNode = slicer.vtkMRMLMarkupsFiducialNode()
self.measurementPointMarkupsFiducialNode.SetName('MeasurementPoint')
self.measurementPointMarkupsFiducialNode.AddFiducial(0, 0, 0)
self.measurementPointMarkupsFiducialNode.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.measurementPointMarkupsFiducialNode)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphScale(2.0)
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetGlyphType(13) # Sphere3D
self.measurementPointMarkupsFiducialNode.GetDisplayNode().SetSelectedColor(1, 0, 0)
# Add RecordedModel
self.recordedModelNode = slicer.util.getNode('RecordedModel')
if not self.recordedModelNode:
recordedPoints = vtk.vtkPoints()
recordedVertices = vtk.vtkCellArray()
recordedPolyData = vtk.vtkPolyData()
recordedPolyData.SetPoints(recordedPoints)
recordedPolyData.SetVerts(recordedVertices)
self.recordedModelNode = self.addModelToScene(recordedPolyData, "RecordedModel")
self.recordedModelNode.GetModelDisplayNode().SetPointSize(3)
# Set up coloured scalars
colorArray = vtk.vtkDoubleArray()
colorArray.SetNumberOfComponents(4)
colorArray.SetName('Colors')
self.recordedModelNode.GetPolyData().GetPointData().SetScalars(colorArray)
# Create share directory
self.pathToCreatedSaveDir = self.createShareDirectory()
# Post-Processing default (for undo)
self.recordedDataBufferDefault = []
def onImportButtonClicked(self):
# check if the output container exists
mvNode = self.__mvSelector.currentNode()
if mvNode == None:
self.__status.text = "Status: Select output node!"
return
print("Before processing: " + mvNode.GetID())
# Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ""
frameFileListAttr = ""
dicomTagNameAttr = self.__dicomTag.text
dicomTagUnitsAttr = self.__veLabel.text
teAttr = self.__te.text
trAttr = self.__tr.text
faAttr = self.__fa.text
# each frame is saved as a separate volume
for f in os.listdir(self.__fDialog.directory):
if not f.startswith("."):
fileNames.append(f)
frameFileListAttr += f + ","
fileNames.sort()
frameFileListAttr = frameFileListAttr[:-1]
frameFolder = self.__fDialog.directory
nFrames = len(fileNames)
volumeLabels.SetNumberOfTuples(nFrames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(nFrames)
for i in range(len(fileNames)):
frameId = self.__veInitial.value + self.__veStep.value * i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ","
frameLabelsAttr = frameLabelsAttr[:-1]
# read the first frame to get the extent
fullName = frameFolder + "/" + fileNames[0]
volumesLogic = slicer.modules.volumes.logic()
frame = self.readFrame(fullName)
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1] * frameExtent[3] * frameExtent[5]
nFrames = len(fileNames)
mvImage = vtk.vtkImageData()
mvImage.SetExtent(frameExtent)
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.AllocateScalars()
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
for frameId in range(0, nFrames):
fullName = frameFolder + "/" + fileNames[frameId]
print("Processing frame %d: %s" % (frameId, fullName))
frame = self.readFrame(fullName)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLMultiVolumeDisplayNode")
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute("MultiVolume.FrameFileList", frameFileListAttr)
mvNode.SetAttribute("MultiVolume.FrameLabels", frameLabelsAttr)
mvNode.SetAttribute("MultiVolume.NumberOfFrames", str(nFrames))
mvNode.SetAttribute("MultiVolume.FrameIdentifyingDICOMTagName", dicomTagNameAttr)
mvNode.SetAttribute("MultiVolume.FrameIdentifyingDICOMTagUnits", dicomTagUnitsAttr)
if dicomTagNameAttr == "TriggerTime" or dicomTagNameAttr == "AcquisitionTime":
if teTag != "":
mvNode.SetAttribute("MultiVolume.DICOM.EchoTime", teTag)
if trTag != "":
mvNode.SetAttribute("MultiVolume.DICOM.RepetitionTime", trTag)
if faTag != "":
mvNode.SetAttribute("MultiVolume.DICOM.FlipAngle", faTag)
print("MultiVolume node setup complete !")
Helper.SetBgFgVolumes(mvNode.GetID(), None)
print("After processing: " + mvNode.GetID())
def onImportButtonClicked(self):
# check if the output container exists
mvNode = self.__mvSelector.currentNode()
if mvNode == None:
self.__status.text = 'Status: Select output node!'
return
# Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ''
frameFileListAttr = ''
dicomTagNameAttr = self.__dicomTag.text
dicomTagUnitsAttr = self.__veLabel.text
teAttr = self.__te.text
trAttr = self.__tr.text
faAttr = self.__fa.text
# each frame is saved as a separate volume
# first filter valid file names and sort alphabetically
frames = []
frame0 = None
inputDir = self.__fDialog.directory
for f in os.listdir(inputDir):
if not f.startswith('.'):
fileName = inputDir + '/' + f
fileNames.append(fileName)
self.humanSort(fileNames)
# check for nifti file that may be 4D as special case
niftiFiles = []
for fileName in fileNames:
if fileName.lower().endswith(
'.nii.gz') or fileName.lower().endswith('.nii'):
niftiFiles.append(fileName)
if len(niftiFiles) == 1:
self.read4DNIfTI(mvNode, niftiFiles[0])
return
# not 4D nifti, so keep trying
for fileName in fileNames:
(s, f) = self.readFrame(fileName)
if s:
if not frame0:
frame0 = f
frame0Image = frame0.GetImageData()
frame0Extent = frame0Image.GetExtent()
else:
frameImage = f.GetImageData()
frameExtent = frameImage.GetExtent()
if frameExtent[1] != frame0Extent[1] or frameExtent[
3] != frame0Extent[3] or frameExtent[
5] != frame0Extent[5]:
continue
frames.append(f)
nFrames = len(frames)
print('Successfully read ' + str(nFrames) + ' frames')
if nFrames == 1:
print('Single frame dataset - not reading as multivolume!')
return
# convert seconds data to milliseconds, which is expected by pkModeling.cxx line 81
if dicomTagUnitsAttr == 's':
frameIdMultiplier = 1000.0
dicomTagUnitsAttr = 'ms'
else:
frameIdMultiplier = 1.0
volumeLabels.SetNumberOfComponents(1)
volumeLabels.SetNumberOfTuples(nFrames)
for i in range(nFrames):
frameId = frameIdMultiplier * (self.__veInitial.value +
self.__veStep.value * i)
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ','
frameLabelsAttr = frameLabelsAttr[:-1]
# allocate multivolume
mvImage = vtk.vtkImageData()
mvImage.SetExtent(frame0Extent)
mvImage.AllocateScalars(frame0.GetImageData().GetScalarType(), nFrames)
extent = frame0.GetImageData().GetExtent()
numPixels = float(extent[1] + 1) * (extent[3] + 1) * (extent[5] +
1) * nFrames
scalarType = frame0.GetImageData().GetScalarType()
print('Will now try to allocate memory for ' + str(numPixels) +
' pixels of VTK scalar type ' + str(scalarType))
print('Memory allocated successfully')
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars())
mat = vtk.vtkMatrix4x4()
frame0.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame0.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
for frameId in range(nFrames):
# TODO: check consistent size and orientation!
frame = frames[frameId]
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName',
dicomTagNameAttr)
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits',
dicomTagUnitsAttr)
if dicomTagNameAttr == 'TriggerTime' or dicomTagNameAttr == 'AcquisitionTime':
if teAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.EchoTime', teAttr)
if trAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.RepetitionTime', trAttr)
if faAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.FlipAngle', faAttr)
mvNode.SetName(str(nFrames) + ' frames MultiVolume')
Helper.SetBgFgVolumes(mvNode.GetID(), None)
def onImportButtonClicked(self):
# check if the output container exists
vcNode = self.__vcSelector.currentNode()
if vcNode == None:
self.__status.text = 'Status: Select output node!'
return
modeIdx = self.__modeSelector.currentIndex
processingMode = self.__processingModes[modeIdx]
# There are two options:
# 1. DICOM series in a directory, with either predefined or custom parse tag
# 2. Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
if modeIdx < len(self.__processingModes)-1:
# DICOM series
# get logic
logic = slicer.modules.multivolumeexplorer.logic()
# create a clean temporary directory
tmpDir = slicer.app.settings().value('Modules/TemporaryDirectory')
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
tmpDir = tmpDir+'/MultiVolumeImporter'
if not os.path.exists(tmpDir):
os.mkdir(tmpDir)
else:
# clean it up
print 'tmpDir = '+tmpDir
fileNames = os.listdir(tmpDir)
for f in fileNames:
print f,' will be unlinked'
os.unlink(tmpDir+'/'+f)
nFrames = logic.ProcessDICOMSeries(self.__fDialog.directory, tmpDir, self.__dicomTag.text, volumeLabels)
self.__status.text = 'Series processed OK, '+str(nFrames)+' volumes identified'
Helper.Info('Location of files:'+tmpDir)
fileNames = os.listdir(tmpDir)
fileNames.sort()
frameFolder = tmpDir
else:
# each frame is saved as a separate volume
fileNames = os.listdir(self.__fDialog.directory)
fileNames.sort()
frameFolder = self.__fDialog.directory
nFrames = len(fileNames)
volumeLabels.SetNumberOfTuples(nFrames)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(nFrames)
for i in range(len(fileNames)):
frameId = self.__veInitial.value+self.__veStep.value*i
volumeLabels.SetComponent(i, 0, frameId)
# read the first frame to get the extent for DWI node
fullName = frameFolder+'/'+fileNames[0]
volumesLogic = slicer.modules.volumes.logic()
frame = volumesLogic.AddArchetypeVolume(fullName, processingMode[3]+' Frame 0', 0)
frameImage = frame.GetImageData()
frameExtent = frameImage.GetExtent()
frameSize = frameExtent[1]*frameExtent[3]*frameExtent[5]
nFrames = len(fileNames)
dwiImage = vtk.vtkImageData()
dwiImage.SetExtent(frameExtent)
dwiImage.SetNumberOfScalarComponents(nFrames)
dwiImage.AllocateScalars()
dwiImageArray = vtk.util.numpy_support.vtk_to_numpy(dwiImage.GetPointData().GetScalars())
# create and initialize a blank DWI node
bValues = vtk.vtkDoubleArray()
bValues.Allocate(nFrames)
bValues.SetNumberOfComponents(1)
bValues.SetNumberOfTuples(nFrames)
gradients = vtk.vtkDoubleArray()
gradients.Allocate(nFrames*3)
gradients.SetNumberOfComponents(3)
gradients.SetNumberOfTuples(nFrames)
bValuesArray = vtk.util.numpy_support.vtk_to_numpy(bValues)
gradientsArray = vtk.util.numpy_support.vtk_to_numpy(gradients)
bValuesArray[:] = 0
gradientsArray[:] = 1
dwiNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLDiffusionWeightedVolumeNode')
dwiNode.SetName(processingMode[3]+'DisplayVolume')
dwiNode.SetScene(slicer.mrmlScene)
dwiNode.SetBValues(bValues)
dwiNode.SetDiffusionGradients(gradients)
mat = vtk.vtkMatrix4x4()
frame.GetRASToIJKMatrix(mat)
dwiNode.SetRASToIJKMatrix(mat)
frame.GetIJKToRASMatrix(mat)
dwiNode.SetIJKToRASMatrix(mat)
self.annihilateScalarNode(frame)
for frameId in range(0,nFrames):
fullName = frameFolder+'/'+fileNames[frameId]
Helper.Info('Processing frame '+str(frameId)+': '+fullName)
frame = volumesLogic.AddArchetypeVolume(fullName, 'Frame'+str(frameId), 0)
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
dwiImageArray.T[frameId] = frameImageArray
self.annihilateScalarNode(frame)
dwiDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLDiffusionWeightedVolumeDisplayNode')
dwiDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(dwiDisplayNode)
dwiDisplayNode.SetDefaultColorMap()
dwiNode.SetAndObserveDisplayNodeID(dwiDisplayNode.GetID())
dwiNode.SetAndObserveImageData(dwiImage)
slicer.mrmlScene.AddNode(dwiNode)
Helper.Info('DWI node added to the scene')
vcNode.SetDWVNodeID(dwiNode.GetID())
vcNode.SetLabelArray(volumeLabels)
vcNode.SetLabelName(self.__veLabel.text)
Helper.Info('VC node setup complete!')
Helper.SetBgFgVolumes(dwiNode.GetID(),None)
def setup(self):
# Instantiate and connect widgets ...
if self.developerMode:
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "VolumeProbe Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test All")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# reload and run specific tests
scenarios = ("Three Volume", "View Watcher", "ROIManager",)
for scenario in scenarios:
button = qt.QPushButton("Reload and Test %s" % scenario)
self.reloadAndTestButton.toolTip = "Reload this module and then run the %s self test." % scenario
reloadFormLayout.addWidget(button)
button.connect('clicked()', lambda s=scenario: self.onReloadAndTest(scenario=s))
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
"""
#
# target volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ( ("vtkMRMLVolumeNode"), "" )
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = True
self.inputSelector.setMRMLScene( slicer.mrmlScene )
self.inputSelector.setToolTip( "Pick the input to the algorithm." )
parametersFormLayout.addRow("Target Volume: ", self.inputSelector)
"""
#
# Add ROI
#
self.drawROICheck = qt.QCheckBox()
parametersFormLayout.addRow("Draw ROI", self.drawROICheck)
self.drawROICheck.connect("toggled(bool)", self.onDrawROIToggled)
self.ROIRadiusSlider = ctk.ctkSliderWidget()
#self.ROIRadiusSlider.setMinimum(1)
#self.ROIRadiusSlider.setMaximum(100)
self.ROIRadiusSlider.setValue(self.ROIRadius)
parametersFormLayout.addRow("ROI Radius", self.ROIRadiusSlider)
self.ROIRadiusSlider.connect("valueChanged(double)", self.onROIRadiusChanged)
#
# Add Histogram
self.numBins = qt.QSpinBox()
self.numBins.setRange(0, 200)
self.numBins.setEnabled(1)
self.numBins.setValue(20)
parametersFormLayout.addRow("Number of Bins", self.numBins)
self.histogramArray = vtk.vtkDoubleArray()
self.histogramArray.SetNumberOfComponents(1)
self.histogramArray.SetNumberOfTuples(0)
self.histogram = ctk.ctkVTKHistogram()
self.histogram.setDataArray(self.histogramArray)
self.histogram.numberOfBins = self.numBins.value
self.histogramView = ctk.ctkTransferFunctionView()
self.histogramItem = ctk.ctkTransferFunctionBarsItem(self.histogram)
self.histogramItem.barWidth = 0.7
self.histogramView.scene().addItem(self.histogramItem)
parametersFormLayout.addRow("Histogram", self.histogramView)
self.histogramView.show()
self.minField = qt.QSpinBox()
self.minField.setRange(-100000, 100000)
self.minField.setEnabled(0)
parametersFormLayout.addRow("Min Value", self.minField)
self.maxField = qt.QSpinBox()
self.maxField.setRange(-100000, 100000)
self.maxField.setEnabled(0)
parametersFormLayout.addRow("Max Value", self.maxField)
self.meanField = qt.QSpinBox()
self.meanField.setRange(-100000, 100000)
self.meanField.setEnabled(0)
parametersFormLayout.addRow("Mean Value", self.meanField)
self.medianField = qt.QSpinBox()
self.medianField.setRange(-100000, 100000)
self.medianField.setEnabled(0)
parametersFormLayout.addRow("Median Value", self.medianField)
self.stdField = qt.QSpinBox()
self.stdField.setRange(-100000, 100000)
self.stdField.setEnabled(0)
parametersFormLayout.addRow("STD Value", self.stdField)
# Add vertical spacer
self.layout.addStretch(1)
def convertTextureToPointAttribute(self, modelNode, textureImageNode,
colorAsVector):
polyData = modelNode.GetPolyData()
textureImageFlipVert = vtk.vtkImageFlip()
textureImageFlipVert.SetFilteredAxis(1)
textureImageFlipVert.SetInputConnection(
textureImageNode.GetImageDataConnection())
textureImageFlipVert.Update()
textureImageData = textureImageFlipVert.GetOutput()
pointData = polyData.GetPointData()
tcoords = pointData.GetTCoords()
numOfPoints = pointData.GetNumberOfTuples()
assert numOfPoints == tcoords.GetNumberOfTuples(
), "Number of texture coordinates does not equal number of points"
textureSamplingPointsUv = vtk.vtkPoints()
textureSamplingPointsUv.SetNumberOfPoints(numOfPoints)
for pointIndex in range(numOfPoints):
uv = tcoords.GetTuple2(pointIndex)
textureSamplingPointsUv.SetPoint(pointIndex, uv[0], uv[1], 0)
textureSamplingPointDataUv = vtk.vtkPolyData()
uvToXyz = vtk.vtkTransform()
textureImageDataSpacingSpacing = textureImageData.GetSpacing()
textureImageDataSpacingOrigin = textureImageData.GetOrigin()
textureImageDataSpacingDimensions = textureImageData.GetDimensions()
uvToXyz.Scale(
textureImageDataSpacingDimensions[0] /
textureImageDataSpacingSpacing[0],
textureImageDataSpacingDimensions[1] /
textureImageDataSpacingSpacing[1], 1)
uvToXyz.Translate(textureImageDataSpacingOrigin)
textureSamplingPointDataUv.SetPoints(textureSamplingPointsUv)
transformPolyDataToXyz = vtk.vtkTransformPolyDataFilter()
transformPolyDataToXyz.SetInputData(textureSamplingPointDataUv)
transformPolyDataToXyz.SetTransform(uvToXyz)
probeFilter = vtk.vtkProbeFilter()
probeFilter.SetInputConnection(transformPolyDataToXyz.GetOutputPort())
probeFilter.SetSourceData(textureImageData)
probeFilter.Update()
rgbPoints = probeFilter.GetOutput().GetPointData().GetArray(
'ImageScalars')
if colorAsVector:
colorArray = vtk.vtkDoubleArray()
colorArray.SetName('Color')
colorArray.SetNumberOfComponents(3)
colorArray.SetNumberOfTuples(numOfPoints)
for pointIndex in range(numOfPoints):
rgb = rgbPoints.GetTuple3(pointIndex)
colorArray.SetTuple3(pointIndex, rgb[0] / 255., rgb[1] / 255.,
rgb[2] / 255.)
colorArray.Modified()
pointData.AddArray(colorArray)
else:
colorArrayRed = vtk.vtkDoubleArray()
colorArrayRed.SetName('ColorRed')
colorArrayRed.SetNumberOfTuples(numOfPoints)
colorArrayGreen = vtk.vtkDoubleArray()
colorArrayGreen.SetName('ColorGreen')
colorArrayGreen.SetNumberOfTuples(numOfPoints)
colorArrayBlue = vtk.vtkDoubleArray()
colorArrayBlue.SetName('ColorBlue')
colorArrayBlue.SetNumberOfTuples(numOfPoints)
for pointIndex in range(numOfPoints):
rgb = rgbPoints.GetTuple3(pointIndex)
colorArrayRed.SetValue(pointIndex, rgb[0])
colorArrayGreen.SetValue(pointIndex, rgb[1])
colorArrayBlue.SetValue(pointIndex, rgb[2])
colorArrayRed.Modified()
colorArrayGreen.Modified()
colorArrayBlue.Modified()
pointData.AddArray(colorArrayRed)
pointData.AddArray(colorArrayGreen)
pointData.AddArray(colorArrayBlue)
pointData.Modified()
polyData.Modified()
def calcApproachScore(self,
point,
skinPolyData,
obstacleBspTree,
skinModelNode=None):
pTarget = point
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface = [0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0, 0.0)
bspTree = obstacleBspTree
cp0 = [0.0, 0.0, 0.0]
cp1 = [0.0, 0.0, 0.0]
cp2 = [0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids = vtk.vtkIdList()
minDistance = -1
for index in range(nCells):
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
iD = bspTree.IntersectWithLine(pSurface, pTarget, tolerance, t,
x, pcoords, subId)
if iD < 1:
if skinModelNode != None:
d = vtk.vtkMath.Distance2BetweenPoints(
pSurface, pTarget)
d = math.sqrt(d)
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [
pSurface[0], pSurface[1], pSurface[2]
]
v = d + 101
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print("ERROR: Non-triangular cell.")
score = accessibleArea / (accessibleArea + inaccessibleArea)
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars(
"Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0, 200.0)
return (score, minDistance, minDistancePoint)
def calcApproachScore(self, point, skinPolyData, obstacleBspTree, skinModelNode=None):
pTarget = point
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface=[0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0,0.0);
bspTree = obstacleBspTree
cp0=[0.0, 0.0, 0.0]
cp1=[0.0, 0.0, 0.0]
cp2=[0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids=vtk.vtkIdList()
minDistance = -1;
for index in range(nCells):
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
iD = bspTree.IntersectWithLine(pSurface, pTarget, tolerance, t, x, pcoords, subId)
if iD < 1:
if skinModelNode != None:
d = vtk.vtkMath.Distance2BetweenPoints(pSurface, pTarget)
d = math.sqrt(d)
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [pSurface[0],pSurface[1],pSurface[2]]
v = d+101
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print ("ERROR: Non-triangular cell.")
score = accessibleArea / (accessibleArea + inaccessibleArea)
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars("Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0,200.0)
return (score, minDistance, minDistancePoint)
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 registrarButton(self):
mvNode = self.outputRegSelector.currentNode()
inputVolume = self.inputRegSelector.currentNode()
"""
Run the actual algorithm
"""
#se obtiene la escena y se obtiene el volumen 4D a partir del Volumen 4D de
#entrada de la ventana desplegable
escena = slicer.mrmlScene
imagenvtk4D = inputVolume.GetImageData()
#Se obtiene el número de volúmenes que tiene el volumen 4D
numero_imagenes = inputVolume.GetNumberOfFrames()
print('imagenes: ' + str(numero_imagenes))
#filtro vtk para descomponer un volumen 4D
extract1 = vtk.vtkImageExtractComponents()
extract1.SetInputData(imagenvtk4D)
#matriz de transformación
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
#le solicitamos al volumen original que nos devuelva sus matrices
inputVolume.GetRASToIJKMatrix(ras2ijk)
inputVolume.GetIJKToRASMatrix(ijk2ras)
#creo un volumen nuevo
volumenFijo = slicer.vtkMRMLScalarVolumeNode()
volumenSalida = slicer.vtkMRMLMultiVolumeNode()
#le asigno las transformaciones
volumenFijo.SetRASToIJKMatrix(ras2ijk)
volumenFijo.SetIJKToRASMatrix(ijk2ras)
#le asigno el volumen 3D fijo
imagen_fija = extract1.SetComponents(0)
extract1.Update()
volumenFijo.SetName('fijo')
volumenFijo.SetAndObserveImageData(extract1.GetOutput())
#anado el nuevo volumen a la escena
escena.AddNode(volumenFijo)
#se crea un vector para guardar el número del volumen que tenga un
#desplazamiento de mas de 4mm en cualquier dirección
v = []
#se hace un ciclo for para registrar todos los demás volúmenes del volumen 4D
#con el primer volumen que se definió como fijo
frameLabelsAttr = ''
frames = []
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(numero_imagenes)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(numero_imagenes)
for i in range(numero_imagenes):
# extraigo la imagen móvil en la posición i+1 ya que el primero es el fijo
imagen_movil = extract1.SetComponents(
i + 1) #Seleccionar un volumen i+1
extract1.Update()
#Creo el volumen móvil, y realizo el mismo procedimiento que con el fijo
volumenMovil = slicer.vtkMRMLScalarVolumeNode()
volumenMovil.SetRASToIJKMatrix(ras2ijk)
volumenMovil.SetIJKToRASMatrix(ijk2ras)
volumenMovil.SetAndObserveImageData(extract1.GetOutput())
volumenMovil.SetName('movil ' + str(i + 1))
escena.AddNode(volumenMovil)
#creamos la transformada para alinear los volúmenes
transformadaSalida = slicer.vtkMRMLLinearTransformNode()
transformadaSalida.SetName('Transformadaderegistro' + str(i + 1))
slicer.mrmlScene.AddNode(transformadaSalida)
#parámetros para la operación de registro
parameters = {}
#parameters['InitialTransform'] = transI.GetID()
parameters['fixedVolume'] = volumenFijo.GetID()
parameters['movingVolume'] = volumenMovil.GetID()
parameters['transformType'] = 'Rigid'
parameters['outputTransform'] = transformadaSalida.GetID()
frames.append(volumenMovil)
## parameters['outputVolume']=volumenSalida.GetID()
#Realizo el registro
cliNode = slicer.cli.run(slicer.modules.brainsfit,
None,
parameters,
wait_for_completion=True)
#obtengo la transformada lineal que se usó en el registro
transformada = escena.GetFirstNodeByName('Transformadaderegistro' +
str(i + 1))
#Obtengo la matriz de la transformada, esta matriz es de dimensiones 4x4
#en la cual estan todos los desplazamientos y rotaciones que se hicieron
#en la transformada, a partir de ella se obtienen los volumenes que se
#desplazaron mas de 4mm en cualquier direccion
hm = vtk.vtkMatrix4x4()
transformadaSalida.GetMatrixTransformToWorld(hm)
volumenMovil.ApplyTransformMatrix(hm)
volumenMovil.SetAndObserveTransformNodeID(None)
frameId = i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ','
## Matriz=transformada.GetMatrixTransformToParent()
## LR=Matriz.GetElement(0,3)#dirección izquierda o derecha en la fila 1, columna 4
## PA=Matriz.GetElement(1,3)#dirección anterior o posterior en la fila 2, columna 4
## IS=Matriz.GetElement(2,3)#dirección inferior o superior en la fila 3, columna 4
## #Se mira si el volumen "i" en alguna dirección tuvo un desplazamiento
## #mayor a 4mm, en caso de ser cierto se guarda en el vector "v"
## if abs(LR)>4:
## v.append(i+2)
## elif abs(PA)>4:
## v.append(i+2)
## elif abs(IS)>4:
## v.append(i+2)
## print("MovilExtent: "+str(volumenMovil.GetImageData().GetExtent()))
#### print("valor de f: "+ str(volumenMovil))
## frameLabelsAttr = frameLabelsAttr[:-1]
mvImage = vtk.vtkImageData()
mvImage.SetExtent(volumenMovil.GetImageData().GetExtent()
) ##Se le asigna la dimensión del miltuvolumen
mvImage.AllocateScalars(
volumenMovil.GetImageData().GetScalarType(), numero_imagenes
) ##Se le asigna el tipo y número de cortes al multivolumen
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars()
) ## Se crea la matriz de datos donde va a ir la imagen
mat = vtk.vtkMatrix4x4()
##Se hace la conversión y se obtiene la matriz de transformación del nodo
volumenMovil.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
volumenMovil.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
print("frameId: " + str(frameId))
print("# imag: " + str(numero_imagenes))
## print("Long frame1: "+str(len(frame)))
print("Long frames: " + str(len(frames)))
##
for frameId in range(numero_imagenes):
# TODO: check consistent size and orientation!
frame = frames[frameId]
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
##Se crea el nodo del multivolumen
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(numero_imagenes)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName('na')
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(numero_imagenes))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName', 'NA')
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits', 'na')
mvNode.SetName('MultiVolume Registrado')
Helper.SetBgFgVolumes(mvNode.GetID(), None)
print('Registro completo')
#al terminar el ciclo for con todos los volúmenes registrados se genera una
#ventana emergente con un mensaje("Registro completo!") y mostrando los
#volúmenes que se desplazaron mas de 4mm
qt.QMessageBox.information(slicer.util.mainWindow(), 'Slicer Python',
'Registro completo')
return True
def clipSurfaceAtEndPoints( self, networkPolyData, surfacePolyData ):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
import vtkvmtkComputationalGeometryPython as vtkvmtkComputationalGeometry
import vtkvmtkMiscPython as vtkvmtkMisc
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData( networkPolyData )
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks( 0 )
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray( 'Radius' )
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName( 'Radius' )
endpoints.SetPoints( endpointsPoints )
endpoints.GetPointData().AddArray( endpointsRadius )
radiusFactor = 1.2
minRadius = 0.01
for i in range( network.GetNumberOfCells() ):
numberOfCellPoints = network.GetCell( i ).GetNumberOfPoints()
pointId0 = network.GetCell( i ).GetPointId( 0 )
pointId1 = network.GetCell( i ).GetPointId( numberOfCellPoints - 1 )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId0, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId0 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId0 )
radius = radiusArray.GetValue( pointId0 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId1, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId1 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId1 )
radius = radiusArray.GetValue( pointId1 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
polyBall = vtkvmtkComputationalGeometry.vtkvmtkPolyBall()
#polyBall.SetInputData( endpoints )
polyBall.SetInput( endpoints )
polyBall.SetPolyBallRadiusArrayName( 'Radius' )
clipper = vtk.vtkClipPolyData()
clipper.SetInputData( surfacePolyData )
clipper.SetClipFunction( polyBall )
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputData( clipper.GetOutput() )
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy( clippedSurface )
return [outPolyData, endpointsPoints]
def initMultiVolumes(self, files, prescribedTags=None):
tag2ValueFileList = {}
multivolumes = []
if prescribedTags == None:
consideredTags = self.multiVolumeTags.keys()
else:
consideredTags = prescribedTags
# iterate over all files
for file in files:
# iterate over the tags that can be used to separate individual frames
for frameTag in consideredTags:
try:
tagValue2FileList = tag2ValueFileList[frameTag]
except:
tagValue2FileList = {}
tag2ValueFileList[frameTag] = tagValue2FileList
tagValueStr = slicer.dicomDatabase.fileValue(file,self.tags[frameTag])
if tagValueStr == '':
# not found?
continue
if frameTag == 'AcquisitionTime' or frameTag == 'SeriesTime':
# extra parsing is needed to convert from DICOM TM VR into ms
tagValue = self.tm2ms(tagValueStr) # convert to ms
else:
tagValue = float(tagValueStr)
try:
tagValue2FileList[tagValue].append(file)
except:
tagValue2FileList[tagValue] = [file]
# iterate over the parsed items and decide which ones can qualify as mv
for frameTag in self.multiVolumeTags.keys():
try:
tagValue2FileList = tag2ValueFileList[frameTag]
except:
# didn't find the tag
continue
if len(tagValue2FileList)<2:
# not enough frames for this tag to be a multivolume
continue
tagValues = tagValue2FileList.keys()
# sort the frames
tagValues.sort()
firstFrameSize = len(tagValue2FileList[tagValues[0]])
frameInvalid = False
for tagValue in tagValues:
if len(tagValue2FileList[tagValue]) != firstFrameSize:
# number of frames does not match
frameInvalid = True
if frameInvalid == True:
continue
# TODO: add a check to confirm individual frames have the same geometry
# (check pixel dimensions, orientation, position)
# now this looks like a serious mv!
# initialize the needed attributes for a new mvNode
frameFileListStr = ""
frameLabelsStr = ""
frameLabelsArray = vtk.vtkDoubleArray()
tagValue0 = tagValues[0]
for tagValue in tagValues:
frameFileList = tagValue2FileList[tagValue]
for file in frameFileList:
frameFileListStr = frameFileListStr+file+','
frameLabelsStr = frameLabelsStr+str(tagValue)+','
# if mv was parsed by series time, probably makes sense to start from
# 0
if frameTag == 'SeriesTime':
frameLabelsArray.InsertNextValue(tagValue-tagValue0)
else:
frameLabelsArray.InsertNextValue(tagValue)
#print 'File list: ',frameFileList
#print 'Labels: ',frameLabelsStr
frameFileListStr = frameFileListStr[:-1]
frameLabelsStr = frameLabelsStr[:-1]
mvNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeNode')
mvNode.SetReferenceCount(mvNode.GetReferenceCount()-1)
mvNode.SetScene(slicer.mrmlScene)
mvNode.SetAttribute("MultiVolume.FrameFileList",frameFileListStr)
mvNode.SetAttribute("MultiVolume.FrameLabels",frameLabelsStr)
mvNode.SetAttribute("MultiVolume.FrameIdentifyingDICOMTagName",frameTag)
mvNode.SetAttribute('MultiVolume.NumberOfFrames',str(len(tagValue2FileList)))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits',self.multiVolumeTagsUnits[frameTag])
mvNode.SetNumberOfFrames(len(tagValue2FileList))
mvNode.SetLabelName(self.multiVolumeTagsUnits[frameTag])
mvNode.SetLabelArray(frameLabelsArray)
if frameTag == 'TriggerTime' or frameTag == 'AcquisitionTime':
# this is DCE, so let's keep the tag values that will be needed for
# the analysis
firstFile = frameFileList[0]
echoTime = slicer.dicomDatabase.fileValue(firstFile, self.tags['EchoTime'])
repetitionTime = slicer.dicomDatabase.fileValue(firstFile, self.tags['RepetitionTime'])
flipAngle = slicer.dicomDatabase.fileValue(firstFile, self.tags['FlipAngle'])
mvNode.SetAttribute('MultiVolume.DICOM.EchoTime',echoTime)
mvNode.SetAttribute('MultiVolume.DICOM.RepetitionTime',repetitionTime)
mvNode.SetAttribute('MultiVolume.DICOM.FlipAngle',flipAngle)
# add the node
multivolumes.append(mvNode)
return multivolumes
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 updateCurve(self):
if self.AutomaticUpdate == False:
return
if self.SourceNode and self.DestinationNode:
if self.SourceNode.GetNumberOfFiducials() < 2:
if self.CurvePoly != None:
self.CurvePoly.Initialize()
self.CurveLength = 0.0
else:
if self.CurvePoly == None:
self.CurvePoly = vtk.vtkPolyData()
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
if self.InterpolationMethod == 0:
if self.RingMode > 0:
self.nodeToPoly(self.SourceNode, self.CurvePoly, True)
else:
self.nodeToPoly(self.SourceNode, self.CurvePoly, False)
elif self.InterpolationMethod == 1: # Cardinal Spline
if self.RingMode > 0:
self.nodeToPolyCardinalSpline(self.SourceNode,
self.CurvePoly, True)
else:
self.nodeToPolyCardinalSpline(self.SourceNode,
self.CurvePoly, False)
elif self.InterpolationMethod == 2: # Hermite Spline
if self.RingMode > 0:
self.nodeToPolyHermiteSpline(self.SourceNode,
self.CurvePoly, True)
else:
self.nodeToPolyHermiteSpline(self.SourceNode,
self.CurvePoly, False)
self.CurveLength = self.calculateLineLength(self.CurvePoly)
tubeFilter = vtk.vtkTubeFilter()
curvatureValues = vtk.vtkDoubleArray()
if self.Curvature:
## If the curvature option is ON, calculate the curvature along the curve.
(meanKappa, minKappa,
maxKappa) = self.computeCurvatures(self.CurvePoly,
curvatureValues)
self.CurvePoly.GetPointData().AddArray(curvatureValues)
self.curvatureMeanKappa = meanKappa
self.curvatureMinKappa = minKappa
self.curvatureMaxKappa = maxKappa
else:
self.curvatureMeanKappa = None
self.curvatureMinKappa = None
self.curvatureMaxKappa = None
tubeFilter.SetInputData(self.CurvePoly)
tubeFilter.SetRadius(self.TubeRadius)
tubeFilter.SetNumberOfSides(20)
tubeFilter.CappingOn()
tubeFilter.Update()
# self.DestinationNode.SetAndObservePolyData(tubeFilter.GetOutput())
self.DestinationNode.SetAndObservePolyData(self.CurvePoly)
self.DestinationNode.Modified()
if self.DestinationNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.DestinationNode)
displayNode = self.DestinationNode.GetDisplayNode()
if displayNode:
if self.Curvature:
displayNode.SetActiveScalarName('Curvature')
else:
displayNode.SetActiveScalarName('')
def updateCurve(self):
if self.AutomaticUpdate == False:
return
if self.SourceNode and self.DestinationNode:
if self.SourceNode.GetNumberOfFiducials() < 2:
if self.CurvePoly != None:
self.CurvePoly.Initialize()
self.CurveLength = 0.0
else:
if self.CurvePoly == None:
self.CurvePoly = vtk.vtkPolyData()
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
if self.InterpolationMethod == 0:
if self.RingMode > 0:
self.nodeToPoly(self.SourceNode, self.CurvePoly, True)
else:
self.nodeToPoly(self.SourceNode, self.CurvePoly, False)
elif self.InterpolationMethod == 1: # Cardinal Spline
if self.RingMode > 0:
self.nodeToPolyCardinalSpline(self.SourceNode, self.CurvePoly, True)
else:
self.nodeToPolyCardinalSpline(self.SourceNode, self.CurvePoly, False)
elif self.InterpolationMethod == 2: # Hermite Spline
if self.RingMode > 0:
self.nodeToPolyHermiteSpline(self.SourceNode, self.CurvePoly, True)
else:
self.nodeToPolyHermiteSpline(self.SourceNode, self.CurvePoly, False)
self.CurveLength = self.calculateLineLength(self.CurvePoly)
tubeFilter = vtk.vtkTubeFilter()
curvatureValues = vtk.vtkDoubleArray()
if self.Curvature:
## If the curvature option is ON, calculate the curvature along the curve.
(meanKappa, minKappa, maxKappa) = self.computeCurvatures(self.CurvePoly, curvatureValues)
self.CurvePoly.GetPointData().AddArray(curvatureValues)
self.curvatureMeanKappa = meanKappa
self.curvatureMinKappa = minKappa
self.curvatureMaxKappa = maxKappa
else:
self.curvatureMeanKappa = None
self.curvatureMinKappa = None
self.curvatureMaxKappa = None
tubeFilter.SetInputData(self.CurvePoly)
tubeFilter.SetRadius(self.TubeRadius)
tubeFilter.SetNumberOfSides(20)
tubeFilter.CappingOn()
tubeFilter.Update()
self.DestinationNode.SetAndObservePolyData(tubeFilter.GetOutput())
self.DestinationNode.Modified()
if self.DestinationNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.DestinationNode)
displayNode = self.DestinationNode.GetDisplayNode()
if displayNode:
if self.Curvature:
displayNode.SetActiveScalarName('Curvature')
else:
displayNode.SetActiveScalarName('')
def onImportButtonClicked(self):
# check if the output container exists
mvNode = self.__mvSelector.currentNode()
if mvNode == None:
self.__status.text = 'Status: Select output node!'
return
# Series of frames alpha-ordered, all in the input directory
# Assume here that the last mode in the list is for parsing a list of
# non-DICOM frames
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ''
frameFileListAttr = ''
dicomTagNameAttr = self.__dicomTag.text
dicomTagUnitsAttr = self.__veLabel.text
teAttr = self.__te.text
trAttr = self.__tr.text
faAttr = self.__fa.text
# each frame is saved as a separate volume
# first filter valid file names and sort alphabetically
frames = []
frame0 = None
inputDir = self.__fDialog.directory
for f in os.listdir(inputDir):
if not f.startswith('.'):
fileName = inputDir+'/'+f
fileNames.append(fileName)
self.humanSort(fileNames)
# check for nifti file that may be 4D as special case
niftiFiles = []
for fileName in fileNames:
if fileName.lower().endswith('.nii.gz') or fileName.lower().endswith('.nii'):
niftiFiles.append(fileName)
if len(niftiFiles) == 1:
self.read4DNIfTI(mvNode, niftiFiles[0])
return
# not 4D nifti, so keep trying
for fileName in fileNames:
(s,f) = self.readFrame(fileName)
if s:
if not frame0:
frame0 = f
frame0Image = frame0.GetImageData()
frame0Extent = frame0Image.GetExtent()
else:
frameImage = f.GetImageData()
frameExtent = frameImage.GetExtent()
if frameExtent[1]!=frame0Extent[1] or frameExtent[3]!=frame0Extent[3] or frameExtent[5]!=frame0Extent[5]:
continue
frames.append(f)
nFrames = len(frames)
print('Successfully read '+str(nFrames)+' frames')
if nFrames == 1:
print('Single frame dataset - not reading as multivolume!')
return
# convert seconds data to milliseconds, which is expected by pkModeling.cxx line 81
if dicomTagUnitsAttr == 's':
frameIdMultiplier = 1000.0
dicomTagUnitsAttr = 'ms'
else:
frameIdMultiplier = 1.0
volumeLabels.SetNumberOfComponents(1)
volumeLabels.SetNumberOfTuples(nFrames)
for i in range(nFrames):
frameId = frameIdMultiplier*(self.__veInitial.value+self.__veStep.value*i)
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId)+','
frameLabelsAttr = frameLabelsAttr[:-1]
# allocate multivolume
mvImage = vtk.vtkImageData()
mvImage.SetExtent(frame0Extent)
if vtk.VTK_MAJOR_VERSION <= 5:
mvImage.SetNumberOfScalarComponents(nFrames)
mvImage.SetScalarType(frame0.GetImageData().GetScalarType())
mvImage.AllocateScalars()
else:
mvImage.AllocateScalars(frame0.GetImageData().GetScalarType(), nFrames)
extent = frame0.GetImageData().GetExtent()
numPixels = float(extent[1]+1)*(extent[3]+1)*(extent[5]+1)*nFrames
scalarType = frame0.GetImageData().GetScalarType()
print('Will now try to allocate memory for '+str(numPixels)+' pixels of VTK scalar type '+str(scalarType))
print('Memory allocated successfully')
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(mvImage.GetPointData().GetScalars())
mat = vtk.vtkMatrix4x4()
frame0.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame0.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
for frameId in range(nFrames):
# TODO: check consistent size and orientation!
frame = frames[frameId]
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass('vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount()-1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel.text)
mvNode.SetAttribute('MultiVolume.FrameLabels',frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames',str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName',dicomTagNameAttr)
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits',dicomTagUnitsAttr)
if dicomTagNameAttr == 'TriggerTime' or dicomTagNameAttr == 'AcquisitionTime':
if teAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.EchoTime',teAttr)
if trAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.RepetitionTime',trAttr)
if faAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.FlipAngle',faAttr)
mvNode.SetName(str(nFrames)+' frames MultiVolume')
Helper.SetBgFgVolumes(mvNode.GetID(),None)
def clipSurfaceAtEndPoints(self, networkPolyData, surfacePolyData):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
from libvtkvmtkComputationalGeometryPython import *
from libvtkvmtkMiscPython import *
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk4 libraries!"
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(networkPolyData)
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks(0)
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray('Radius')
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName('Radius')
endpoints.SetPoints(endpointsPoints)
endpoints.GetPointData().AddArray(endpointsRadius)
radiusFactor = 1.2
minRadius = 0.01
for i in range(network.GetNumberOfCells()):
numberOfCellPoints = network.GetCell(i).GetNumberOfPoints()
pointId0 = network.GetCell(i).GetPointId(0)
pointId1 = network.GetCell(i).GetPointId(numberOfCellPoints - 1)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId0, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId0)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId0)
radius = radiusArray.GetValue(pointId0)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId1, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId1)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId1)
radius = radiusArray.GetValue(pointId1)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
polyBall = vtkvmtkPolyBall()
polyBall.SetInput(endpoints)
polyBall.SetPolyBallRadiusArrayName('Radius')
clipper = vtk.vtkClipPolyData()
clipper.SetInput(surfacePolyData)
clipper.SetClipFunction(polyBall)
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInput(clipper.GetOutput())
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy(clippedSurface)
outPolyData.Update()
return [outPolyData, endpointsPoints]
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 importFunction(self):
self.__dicomTag = 'NA'
self.__veLabel = 'na'
self.__veInitial = 0
self.__veStep = 1
self.__te = 1
self.__tr = 1
self.__fa = 1
nameFrame = self.__nameFrame.text
inputVolume = self.inputSelector.currentNode()
# check if the output container exists
mvNode = self.outputSelector.currentNode()
## if mvNode == None:
## self.__status.text = 'Status: Select output node!'
## return
fileNames = [] # file names on disk
frameList = [] # frames as MRMLScalarVolumeNode's
frameFolder = ""
volumeLabels = vtk.vtkDoubleArray()
frameLabelsAttr = ''
frameFileListAttr = ''
dicomTagNameAttr = self.__dicomTag
dicomTagUnitsAttr = self.__veLabel
teAttr = self.__te
trAttr = self.__tr
faAttr = self.__fa
# each frame is saved as a separate volume
# first filter valid file names and sort alphabetically
frames = []
frame0 = None
inputDir = self.__fDialog.directory
metadatos = []
print('hola' + str(len(os.listdir(inputDir))))
for f in os.listdir(inputDir):
if not f.startswith('.'):
fileName = inputDir + '/' + f
fileName1 = str(inputDir + '/' + f)
metadato = dicom.read_file(fileName1)
metadatos.append(metadato)
fileNames.append(fileName)
self.humanSort(fileNames)
n = 0
for fileName in fileNames:
#f: información de cada scalar volume de cada corte
(s, f) = self.readFrame(fileName)
if s:
if not frame0:
## print("valor de f: "+ str(f));
frame0 = f
## print("frame0: "+str(frame0));
frame0Image = frame0.GetImageData()
frame0Extent = frame0Image.GetExtent()
## print("frame0Extent: " + str(frame0Extent));
else:
## print("valor de f1: "+ str(f))
frameImage = f.GetImageData()
## print("frameImage: "+str(frameImage))
frameExtent = frameImage.GetExtent()
## print("frameExtent: " + str(frameExtent));
if frameExtent[1] != frame0Extent[1] or frameExtent[
3] != frame0Extent[3] or frameExtent[
5] != frame0Extent[5]:
continue
## n=n+1
## print("for: "+str(n))
frames.append(f)
nFrames = len(frames)
## print("nFrames: "+str(nFrames))
print('Successfully read ' + str(nFrames) + ' frames')
if nFrames == 1:
print('Single frame dataset - not reading as multivolume!')
return
# convert seconds data to milliseconds, which is expected by pkModeling.cxx line 81
if dicomTagUnitsAttr == 's':
frameIdMultiplier = 1000.0
dicomTagUnitsAttr = 'ms'
else:
frameIdMultiplier = 1.0
## print("volumeLabelsAntes: "+ str(volumeLabels))
volumeLabels.SetNumberOfTuples(nFrames)
## print("volumeLabelsIntermedio: "+ str(volumeLabels))
volumeLabels.SetNumberOfComponents(1)
## print("volumeLabelsDespues: "+ str(volumeLabels))
volumeLabels.Allocate(nFrames)
## print("volumeLabelsTotal: "+ str(volumeLabels))
### Después de los 3 pasos el único cambio es size, en vez de 0 pasa a ser nFrames
for i in range(nFrames):
frameId = frameIdMultiplier * (self.__veInitial +
self.__veStep * i)
## print("frameId: "+str(frameId))
volumeLabels.SetComponent(i, 0, frameId) ##no hay necesidad
#### print("volumeLabelsTotal: "+ str(volumeLabels))##Aparentemente no hay cambio en volumeLabels
frameLabelsAttr += str(frameId) + ','
## print("frameLabelsAttr: "+str(frameLabelsAttr))
frameLabelsAttr = frameLabelsAttr[:-1] ##No hay cambio
## print("frameLabelsAttrTOTAL: "+str(frameLabelsAttr))
# allocate multivolume
mvImage = vtk.vtkImageData()
## print("mvImage: "+str(mvImage))
mvImage.SetExtent(frame0Extent)
## print("mvImageExtent: "+str(mvImage))
## print("vtk.VTK_MAJOR_VERSION: "+str(vtk.VTK_MAJOR_VERSION))
if vtk.VTK_MAJOR_VERSION <= 5: ##Versión 7
mvImage.SetNumberOfScalarComponents(nFrames)
print("mvImageSC: " + str(mvImage))
mvImage.SetScalarType(frame0.GetImageData().GetScalarType())
print("mvImageST: " + str(mvImage))
mvImage.AllocateScalars()
print("mvImageAllocate: " + str(mvImage))
else:
mvImage.AllocateScalars(frame0.GetImageData().GetScalarType(),
nFrames)
## print("mvImageElse: "+str(mvImage))
extent = frame0.GetImageData().GetExtent()
numPixels = float(extent[1] + 1) * (extent[3] + 1) * (extent[5] +
1) * nFrames
scalarType = frame0.GetImageData().GetScalarType()
print('Will now try to allocate memory for ' + str(numPixels) +
' pixels of VTK scalar type' + str(scalarType))
print('Memory allocated successfully')
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars())
## print("mvImageEArray: "+str(mvImageArray))
## print("mvImage.GetPointData().GetScalars(): " + str(mvImage.GetPointData().GetScalars()));
## print("ID mvImagearray " + str(id(mvImageArray)));
## print("ID 2: " + str(mvImage.GetPointData().GetScalars()));
## print("Que es frame0: " + str(frame0));
##EMPIEZA A FORMARCE EL VOLUMEN###############
mat = vtk.vtkMatrix4x4()
frame0.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
frame0.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
print("frameId: " + str(frameId))
print("# imag: " + str(nFrames))
## print("Long frame: "+str(len(frame)))
for frameId in range(nFrames):
# TODO: check consistent size and orientation!
frame = frames[frameId]
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(nFrames)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName(self.__veLabel)
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(nFrames))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName',
dicomTagNameAttr)
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits',
dicomTagUnitsAttr)
if dicomTagNameAttr == 'TriggerTime' or dicomTagNameAttr == 'AcquisitionTime':
if teAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.EchoTime', teAttr)
if trAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.RepetitionTime', trAttr)
if faAttr != '':
mvNode.SetAttribute('MultiVolume.DICOM.FlipAngle', faAttr)
mvNode.SetName(nameFrame)
NameFrame = nameFrame
self.Diccionario = {
NameFrame: metadato
}
print(self.Diccionario.get(NameFrame))
Helper.SetBgFgVolumes(mvNode.GetID(), None)
def calcApproachScore(self,
targetPointNode,
skinPolyData,
obstacleBspTree,
skinModelNode=None):
#pTargetA = targetPointNode.GetMarkupPointVector(0, 0)
tListNumber = targetPointNode.GetNumberOfFiducials()
#pTargetA = pointA
#pTargetB = pointB
#pTargetC = pointC
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface = [0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0, 0.0)
bspTree = obstacleBspTree
cp0 = [0.0, 0.0, 0.0]
cp1 = [0.0, 0.0, 0.0]
cp2 = [0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids = vtk.vtkIdList()
minDistance = -1
#iDA = 0
#iDAFlag = 0
#d = 0
for index in range(nCells):
iDA = 0
iDAFlag = 0
d = 0
i = 0
j = 0
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
#####
for i in range(0, tListNumber, 1):
pTargetA = targetPointNode.GetMarkupPointVector(i, 0)
iDA = bspTree.IntersectWithLine(pSurface, pTargetA,
tolerance, t, x, pcoords,
subId)
if iDA >= 1:
iDAFlag = 10
#####
if iDAFlag < 1:
if skinModelNode != None:
for j in range(0, tListNumber, 1):
pTargetA = targetPointNode.GetMarkupPointVector(
j, 0)
d += (vtk.vtkMath.Distance2BetweenPoints(
pSurface, pTargetA))
d = d / tListNumber
d = math.sqrt(d)
if 100 < d < 240:
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [
pSurface[0], pSurface[1], pSurface[2]
]
v = d + 51
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print("ERROR: Non-triangular cell.")
score = accessibleArea
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars(
"Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0, 200.0)
return (score, minDistance, minDistancePoint)
