def onInputChanged(self):
self.__chartTable.SetNumberOfRows(self.numFrames)
self.plotFrame.enabled = True
# self.plotFrame.collapsed = 0
self.__xArray.SetNumberOfTuples(self.numFrames)
self.__xArray.SetNumberOfComponents(1)
self.__xArray.Allocate(self.numFrames)
self.__xArray.SetName('frame')
self.__yArray.SetNumberOfTuples(self.numFrames)
self.__yArray.SetNumberOfComponents(1)
self.__yArray.Allocate(self.numFrames)
self.__yArray.SetName('signal intensity')
self.__chartTable = vtk.vtkTable()
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.__chartTable.SetNumberOfRows(self.numFrames)
# get the range of intensities for the
self.__mvRange = [0, 0]
for v in self.nodeImgList[0][0]:
frame = v
frameRange = frame.GetScalarRange()
self.__mvRange[0] = min(self.__mvRange[0], frameRange[0])
self.__mvRange[1] = max(self.__mvRange[1], frameRange[1])
# self.__mvLabels = string.split(self.__mvNode.GetAttribute('MultiVolume.FrameLabels'),',')
#if len(self.__mvLabels) != nFrames:
# return
self.__mvLabels = []
for l in range(self.numFrames):
self.__mvLabels.append(float(l))
def updateChart(self):
outputTransformSequenceNode = self.outputTransformSequenceSelector.currentNode()
self.__chart.RemovePlot(0)
if outputTransformSequenceNode == None:
return
if outputTransformSequenceNode.GetDataNodeClassName() != "vtkMRMLLinearTransformNode":
return
numOfDataNodes = outputTransformSequenceNode.GetNumberOfDataNodes()
indexName = outputTransformSequenceNode.GetIndexName()
self.__xArray.SetNumberOfTuples(numOfDataNodes)
self.__xArray.SetNumberOfComponents(1)
self.__xArray.Allocate(numOfDataNodes)
self.__xArray.SetName(indexName)
self.__yArray.SetNumberOfTuples(numOfDataNodes)
self.__yArray.SetNumberOfComponents(1)
self.__yArray.Allocate(numOfDataNodes)
self.__yArray.SetName('DisplacementX')
self.__zArray.SetNumberOfTuples(numOfDataNodes)
self.__zArray.SetNumberOfComponents(1)
self.__zArray.Allocate(numOfDataNodes)
self.__zArray.SetName('DisplacementY')
self.__mArray.SetNumberOfTuples(numOfDataNodes)
self.__mArray.SetNumberOfComponents(1)
self.__mArray.Allocate(numOfDataNodes)
self.__mArray.SetName('DisplacementZ')
self.__chartTable = vtk.vtkTable()
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.__chartTable.AddColumn(self.__zArray)
self.__chartTable.AddColumn(self.__mArray)
self.__chartTable.SetNumberOfRows(numOfDataNodes)
for i in range(numOfDataNodes):
self.__chartTable.SetValue(i, 0, float(outputTransformSequenceNode.GetNthIndexValue(i)))
linearTransformNode = outputTransformSequenceNode.GetNthDataNode(i)
vtkMatrix = linearTransformNode.GetTransformToParent().GetMatrix()
self.__chartTable.SetValue(i, 1, vtkMatrix.GetElement(0,3))
self.__chartTable.SetValue(i, 2, vtkMatrix.GetElement(1,3))
self.__chartTable.SetValue(i, 3, vtkMatrix.GetElement(2,3))
self.__chart.GetAxis(0).SetTitle('displacement(mm)')
self.__chart.GetAxis(1).SetTitle('time(s)')
plot = self.__chart.AddPlot(0)
if self.chartingDisplayOption == 'LR':
plot.SetInput(self.__chartTable, 0, 1)
if self.chartingDisplayOption == 'AP':
plot.SetInput(self.__chartTable, 0, 2)
if self.chartingDisplayOption == 'SI':
plot.SetInput(self.__chartTable, 0, 3)
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 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 onInputChanged(self):
self.__mvNode = self.__mvSelector.currentNode()
if self.__mvNode != None:
Helper.SetBgFgVolumes(self.__mvNode.GetID(), None)
nFrames = self.__mvNode.GetNumberOfFrames()
self.__mdSlider.minimum = 0
self.__mdSlider.maximum = nFrames - 1
self.__chartTable.SetNumberOfRows(nFrames)
# if self.__cvn != None:
# self.__cvn.SetChartNodeID(self.__cn.GetID())
self.ctrlFrame.enabled = True
self.plotFrame.enabled = True
self.ctrlFrame.collapsed = 0
self.plotFrame.collapsed = 0
self.__vfSelector.setCurrentNode(None)
self.__xArray.SetNumberOfTuples(nFrames)
self.__xArray.SetNumberOfComponents(1)
self.__xArray.Allocate(nFrames)
self.__xArray.SetName('frame')
self.__yArray.SetNumberOfTuples(nFrames)
self.__yArray.SetNumberOfComponents(1)
self.__yArray.Allocate(nFrames)
self.__yArray.SetName('signal intensity')
self.__chartTable = vtk.vtkTable()
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.__chartTable.SetNumberOfRows(nFrames)
# get the range of intensities for the
mvi = self.__mvNode.GetImageData()
self.__mvRange = [0, 0]
for f in range(nFrames):
extract = vtk.vtkImageExtractComponents()
extract.SetInput(mvi)
extract.SetComponents(f)
extract.Update()
frame = extract.GetOutput()
frameRange = frame.GetScalarRange()
self.__mvRange[0] = min(self.__mvRange[0], frameRange[0])
self.__mvRange[1] = max(self.__mvRange[1], frameRange[1])
self.__mvLabels = string.split(
self.__mvNode.GetAttribute('MultiVolume.FrameLabels'), ',')
if len(self.__mvLabels) != nFrames:
return
for l in range(nFrames):
self.__mvLabels[l] = float(self.__mvLabels[l])
self.baselineFrames.maximum = nFrames
else:
self.ctrlFrame.enabled = False
self.plotFrame.enabled = False
self.ctrlFrame.collapsed = 1
self.plotFrame.collapsed = 1
self.__mvLabels = []
def setup(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
plotFrameLayout.addWidget(self.plotSettingsFrame, 0, 1)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
label = qt.QLabel('Input secondary multivolume')
self.fgSelector = slicer.qMRMLNodeComboBox()
self.fgSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.fgSelector.setMRMLScene(slicer.mrmlScene)
self.fgSelector.addEnabled = 0
self.fgSelector.noneEnabled = 1
self.fgSelector.toolTip = "Secondary multivolume will be used for the secondary \
plot in interactive charting. As an example, this can be used to overlay the \
curve obtained by fitting a model to the data"
inputFrameLayout.addRow(label, self.fgSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
label = qt.QLabel('Current frame number')
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector, 1, 1, 1, 2)
ctrlFrameLayout.addWidget(self.extractButton, 2, 0, 1, 3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode', 'LabelMap',
'1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.chartButton = qt.QPushButton('Chart')
self.chartButton.checkable = False
self.chartButton.connect('clicked()', self.onChartRequested)
plotSettingsFrameLayout.addWidget(label, 0, 0)
plotSettingsFrameLayout.addWidget(self.__fSelector, 0, 1)
plotSettingsFrameLayout.addWidget(self.chartButton, 0, 2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotSettingsFrameLayout.addWidget(self.iCharting, 1, 0, 1, 3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
groupLabel = qt.QLabel('Interactive plotting mode:')
self.iChartingMode = qt.QButtonGroup()
self.iChartingIntensity = qt.QRadioButton('Signal intensity')
#self.iChartingIntensity.tooltip = 'Plot range adjusted dynamically to the range over the time course for the selected pixel'
self.iChartingIntensityFixedAxes = qt.QRadioButton(
'Fixed range intensity')
#self.iChartingIntensityFixedAxes.tooltip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.iChartingPercent = qt.QRadioButton('Percent change')
#self.iChartingPercent.tooltip = 'Percent change relative to the average of the first N frames (parameter set below)'
self.iChartingIntensity.setChecked(1)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(groupLabel)
self.groupLayout.addRow(self.iChartingIntensity)
self.groupLayout.addRow(self.iChartingIntensityFixedAxes)
self.groupLayout.addRow(self.iChartingPercent)
self.baselineFrames = qt.QSpinBox()
self.baselineFrames.minimum = 1
label = qt.QLabel('Number of frames for baseline calculation')
self.groupLayout.addRow(label, self.baselineFrames)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for X axis')
self.groupLayout.addRow(self.xLogScaleCheckBox, label)
self.xLogScaleCheckBox.connect('stateChanged(int)',
self.onXLogScaleRequested)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for Y axis')
self.groupLayout.addRow(self.yLogScaleCheckBox, label)
self.yLogScaleCheckBox.connect('stateChanged(int)',
self.onYLogScaleRequested)
plotSettingsFrameLayout.addWidget(self.groupWidget, 2, 0)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView, 3, 0, 1, 3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def createChart(self, sliceWidget, xy, ignoreCurrentBackground=False):
if not sliceWidget and not xy:
return
sliceLogic = sliceWidget.sliceLogic()
bgLayer = sliceLogic.GetBackgroundLayer()
doIJKToRASTransformation = False
bgVolumeNode = bgLayer.GetVolumeNode()
if not bgVolumeNode or bgVolumeNode.GetID() != self.__bgMultiVolumeNode.GetID() or \
bgVolumeNode != self.__bgMultiVolumeNode:
if not ignoreCurrentBackground:
return
else:
doIJKToRASTransformation = True
xyz = sliceWidget.sliceView().convertDeviceToXYZ(xy)
xyToIJK = bgLayer.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
if doIJKToRASTransformation:
RAStoIJK = vtk.vtkMatrix4x4()
self.__bgMultiVolumeNode.GetRASToIJKMatrix(RAStoIJK)
ras = self.xyToRAS(sliceLogic, xy)
ijkFloat = RAStoIJK.MultiplyPoint([ras[0], ras[1], ras[2], 1])[:3]
bgijk = self.getIJKIntFromIJKFloat(ijkFloat)
bgImage = self.__bgMultiVolumeNode.GetImageData()
if not self.arePixelsWithinImageExtent(bgImage, bgijk):
self.clearPlots()
return
nComponents = self.__bgMultiVolumeNode.GetNumberOfFrames()
useFg = False
fgImage = None
fgijk = None
if self.__fgMultiVolumeNode:
fgijkFloat = xyToIJK.TransformDoublePoint(xyz)
fgijk = self.getIJKIntFromIJKFloat(fgijkFloat)
fgImage = self.__fgMultiVolumeNode.GetImageData()
fgChartTable = vtk.vtkTable()
if fgijk[0] == bgijk[0] and fgijk[1] == bgijk[1] and fgijk[2] == bgijk[2] and \
fgImage.GetNumberOfScalarComponents() == bgImage.GetNumberOfScalarComponents():
useFg = True
fgxArray = vtk.vtkFloatArray()
self.refreshArray(fgxArray, nComponents, '')
fgyArray = vtk.vtkFloatArray()
self.refreshArray(fgyArray, nComponents, '2nd multivolume')
# will crash if there is no name
fgChartTable.AddColumn(fgxArray)
fgChartTable.AddColumn(fgyArray)
fgChartTable.SetNumberOfRows(nComponents)
# get the vector of values at IJK
for c in range(nComponents):
val = bgImage.GetScalarComponentAsDouble(bgijk[0],bgijk[1],bgijk[2],c)
if math.isnan(val):
val = 0
self.__chartTable.SetValue(c, 0, self.__mvLabels[c])
self.__chartTable.SetValue(c, 1, val)
if useFg:
fgValue = fgImage.GetScalarComponentAsDouble(bgijk[0],bgijk[1],bgijk[2],c)
if math.isnan(fgValue):
fgValue = 0
fgChartTable.SetValue(c,0,self.__mvLabels[c])
fgChartTable.SetValue(c,1,fgValue)
self.baselineAverageSignal = 0
if self.__chartMode == self.PERCENTAGE_CHANGE_MODE:
self.computePercentageChangeWithRespectToBaseline(self.__bgMultiVolumeNode, self.__chartTable, bgijk)
if useFg:
self.computePercentageChangeWithRespectToBaseline(self.__fgMultiVolumeNode, fgChartTable, fgijk)
self.clearPlots()
self.setAxesTitle()
bgPlot = self.chart.AddPlot(vtk.vtkChart.POINTS if useFg else vtk.vtkChart.LINE)
# bgPlot.SetLabel("Primary multivolume ")
self.setPlotInputTable(bgPlot, self.__chartTable)
if useFg:
fgPlot = self.chart.AddPlot(vtk.vtkChart.LINE)
# bgPlot.SetLabel("Primary multivolume ")
self.setPlotInputTable(fgPlot, fgChartTable)
def createNewVTKTable(self, xArray, yArray): chartTable = vtk.vtkTable() chartTable.AddColumn(xArray) chartTable.AddColumn(yArray) return chartTable
def onInputChanged(self):
self.__mvNode = self.__mvSelector.currentNode()
if self.__mvNode != None:
Helper.SetBgFgVolumes(self.__mvNode.GetID(), None)
nFrames = self.__mvNode.GetNumberOfFrames()
self.__mdSlider.minimum = 0
self.__mdSlider.maximum = nFrames-1
self.__chartTable.SetNumberOfRows(nFrames)
# if self.__cvn != None:
# self.__cvn.SetChartNodeID(self.__cn.GetID())
self.ctrlFrame.enabled = True
self.plotFrame.enabled = True
self.ctrlFrame.collapsed = 0
self.plotFrame.collapsed = 0
self.__vfSelector.setCurrentNode(None)
self.__xArray.SetNumberOfTuples(nFrames)
self.__xArray.SetNumberOfComponents(1)
self.__xArray.Allocate(nFrames)
self.__xArray.SetName('frame')
self.__yArray.SetNumberOfTuples(nFrames)
self.__yArray.SetNumberOfComponents(1)
self.__yArray.Allocate(nFrames)
self.__yArray.SetName('signal intensity')
self.__chartTable = vtk.vtkTable()
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.__chartTable.SetNumberOfRows(nFrames)
# get the range of intensities for the
mvi = self.__mvNode.GetImageData()
self.__mvRange = [0,0]
for f in range(nFrames):
extract = vtk.vtkImageExtractComponents()
extract.SetInput(mvi)
extract.SetComponents(f)
extract.Update()
frame = extract.GetOutput()
frameRange = frame.GetScalarRange()
self.__mvRange[0] = min(self.__mvRange[0], frameRange[0])
self.__mvRange[1] = max(self.__mvRange[1], frameRange[1])
self.__mvLabels = string.split(self.__mvNode.GetAttribute('MultiVolume.FrameLabels'),',')
if len(self.__mvLabels) != nFrames:
return
for l in range(nFrames):
self.__mvLabels[l] = float(self.__mvLabels[l])
self.baselineFrames.maximum = nFrames
else:
self.ctrlFrame.enabled = False
self.plotFrame.enabled = False
self.ctrlFrame.collapsed = 1
self.plotFrame.collapsed = 1
self.__mvLabels = []
def setup(self, wName, parent):
if self.ctrlWidget:
return
self.LinkViewers()
self.numFrames = len(self.nodeImgList[0][0])
if parent:
self.ctrlWidget = parent
else:
# Create seperate window
self.ctrlWidget = slicer.qMRMLWidget()
self.ctrlWidget.setMRMLScene(slicer.mrmlScene)
self.ctrlWidget.setLayout(qt.QFormLayout())
self.ctrlWidget.setWindowTitle(wName)
ctrlLayout = self.ctrlWidget.layout()
# Create Slider Panel
self.sliderPanel = qt.QWidget()
self.sliderPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.sliderPanel)
sliderLayout = self.sliderPanel.layout()
if self.numFrames > 1:
self.ctrlFrameLabel = qt.QLabel('Frame')
self.ctrlFrameSlider = ctk.ctkSliderWidget()
self.ctrlFrameSlider.connect('valueChanged(double)',
self.onSliderFrameChanged)
sliderLayout.addWidget(self.ctrlFrameLabel, 0, 0)
sliderLayout.addWidget(self.ctrlFrameSlider, 0, 1)
self.ctrlLevelLabel = qt.QLabel('Level')
self.ctrlLevelSlider = ctk.ctkSliderWidget()
self.ctrlLevelSlider.connect('valueChanged(double)',
self.onSliderLevelChanged)
sliderLayout.addWidget(self.ctrlLevelLabel, 1, 0)
sliderLayout.addWidget(self.ctrlLevelSlider, 1, 1)
self.ctrlWindowLabel = qt.QLabel('Window')
self.ctrlWindowSlider = ctk.ctkSliderWidget()
self.ctrlWindowSlider.connect('valueChanged(double)',
self.onSliderWindowChanged)
sliderLayout.addWidget(self.ctrlWindowLabel, 2, 0)
sliderLayout.addWidget(self.ctrlWindowSlider, 2, 1)
self.setSliderRangesAndValues()
if self.sliceNodeList:
self.orientPanel = qt.QWidget()
self.orientPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.orientPanel)
self.orientationButtons = {}
index = 0
for orientation in self.orientations:
self.orientationButtons[orientation] = qt.QRadioButton()
self.orientationButtons[orientation].text = orientation
# self.orientationBox.layout().addWidget(self.orientationButtons[orientation])
self.orientPanel.layout().addWidget(
self.orientationButtons[orientation], 0, index)
self.orientationButtons[orientation].connect(
"clicked()", lambda o=orientation: self.setOrientation(o))
index += 1
self.setOrientation(self.selectedOrientation)
if False:
#self.plotFrame = ctk.ctkCollapsibleButton()
#self.plotFrame.text = "Plotting"
#self.plotFrame.collapsed = 0
self.plotFrame = qt.QWidget()
plotFrameLayout = qt.QGridLayout(self.plotFrame)
ctrlLayout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
#plotFrameLayout.addWidget(self.plotSettingsFrame,0,1)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
# taken from https://github.com/fedorov/MultiVolumeExplorer
self.__chartView = ctk.ctkVTKChartView(self.ctrlWidget)
# self.plotFrame)
# self.ctrlWidget
plotFrameLayout.addWidget(self.__chartView, 0, 0)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.onInputChanged()
self.refreshObservers()
self.buttonPanel = qt.QWidget()
self.buttonPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.buttonPanel)
self.exitButton = qt.QPushButton("Exit")
self.exitButton.toolTip = "Close down slicer."
self.exitButton.name = "sviewer exit"
self.buttonPanel.layout().addWidget(self.exitButton, 0, 0)
self.exitButton.connect('clicked()', exit)
# do not do ctrlWin.show() here - for some reason window does not pop up then
return self.ctrlWidget
def createChart(self, sliceWidget, xy, ignoreCurrentBackground=False):
if not sliceWidget and not xy:
return
sliceLogic = sliceWidget.sliceLogic()
bgLayer = sliceLogic.GetBackgroundLayer()
doIJKToRASTransformation = False
bgVolumeNode = bgLayer.GetVolumeNode()
if not bgVolumeNode or bgVolumeNode.GetID() != self.__bgMultiVolumeNode.GetID() or \
bgVolumeNode != self.__bgMultiVolumeNode:
if not ignoreCurrentBackground:
return
else:
doIJKToRASTransformation = True
xyz = sliceWidget.sliceView().convertDeviceToXYZ(xy)
xyToIJK = bgLayer.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
if doIJKToRASTransformation:
RAStoIJK = vtk.vtkMatrix4x4()
self.__bgMultiVolumeNode.GetRASToIJKMatrix(RAStoIJK)
ras = self.xyToRAS(sliceLogic, xy)
ijkFloat = RAStoIJK.MultiplyPoint([ras[0], ras[1], ras[2], 1])[:3]
bgijk = self.getIJKIntFromIJKFloat(ijkFloat)
bgImage = self.__bgMultiVolumeNode.GetImageData()
if not self.arePixelsWithinImageExtent(bgImage, bgijk):
self.clearPlots()
return
nComponents = self.__bgMultiVolumeNode.GetNumberOfFrames()
useFg = False
fgImage = None
fgijk = None
if self.__fgMultiVolumeNode:
fgijkFloat = xyToIJK.TransformDoublePoint(xyz)
fgijk = self.getIJKIntFromIJKFloat(fgijkFloat)
fgImage = self.__fgMultiVolumeNode.GetImageData()
fgChartTable = vtk.vtkTable()
if fgijk[0] == bgijk[0] and fgijk[1] == bgijk[1] and fgijk[2] == bgijk[2] and \
fgImage.GetNumberOfScalarComponents() == bgImage.GetNumberOfScalarComponents():
useFg = True
fgxArray = vtk.vtkFloatArray()
self.refreshArray(fgxArray, nComponents, '')
fgyArray = vtk.vtkFloatArray()
self.refreshArray(fgyArray, nComponents, '2nd multivolume')
# will crash if there is no name
fgChartTable.AddColumn(fgxArray)
fgChartTable.AddColumn(fgyArray)
fgChartTable.SetNumberOfRows(nComponents)
# get the vector of values at IJK
for c in range(nComponents):
val = bgImage.GetScalarComponentAsDouble(bgijk[0], bgijk[1],
bgijk[2], c)
if math.isnan(val):
val = 0
self.__chartTable.SetValue(c, 0, self.__mvLabels[c])
self.__chartTable.SetValue(c, 1, val)
if useFg:
fgValue = fgImage.GetScalarComponentAsDouble(
bgijk[0], bgijk[1], bgijk[2], c)
if math.isnan(fgValue):
fgValue = 0
fgChartTable.SetValue(c, 0, self.__mvLabels[c])
fgChartTable.SetValue(c, 1, fgValue)
self.baselineAverageSignal = 0
if self.__chartMode == self.PERCENTAGE_CHANGE_MODE:
self.computePercentageChangeWithRespectToBaseline(
self.__bgMultiVolumeNode, self.__chartTable, bgijk)
if useFg:
self.computePercentageChangeWithRespectToBaseline(
self.__fgMultiVolumeNode, fgChartTable, fgijk)
self.clearPlots()
self.setAxesTitle()
bgPlot = self.chart.AddPlot(
vtk.vtkChart.POINTS if useFg else vtk.vtkChart.LINE)
# bgPlot.SetLabel("Primary multivolume ")
self.setPlotInputTable(bgPlot, self.__chartTable)
if useFg:
fgPlot = self.chart.AddPlot(vtk.vtkChart.LINE)
# bgPlot.SetLabel("Primary multivolume ")
self.setPlotInputTable(fgPlot, fgChartTable)
def createNewVTKTable(self, xArray, yArray):
chartTable = vtk.vtkTable()
chartTable.AddColumn(xArray)
chartTable.AddColumn(yArray)
return chartTable
def setup(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
##self.layout.addWidget(label)
##self.layout.addWidget(self.__mvSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
#self.__mdSlider.setRange(0,10)
#self.__mdSlider.setValue(5)
label = qt.QLabel('Current frame number')
##self.layout.addWidget(label)
##self.layout.addWidget(self.__mdSlider)
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector, 1, 1, 1, 2)
ctrlFrameLayout.addWidget(self.extractButton, 2, 0, 1, 3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode', 'LabelMap',
'1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.__fSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelVolumeChanged)
self.__fSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onLVMRMLSceneChanged)
plotFrameLayout.addWidget(label, 0, 0, 1, 1)
plotFrameLayout.addWidget(self.__fSelector, 0, 1, 1, 2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotFrameLayout.addWidget(self.iCharting, 1, 0, 1, 3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
label = qt.QLabel("Use intensity range to fix axis extent")
label.toolTip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.__fixedAxesCheckbox = qt.QCheckBox()
self.__fixedAxesCheckbox.toolTip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.__fixedAxesCheckbox.checked = False
plotFrameLayout.addWidget(label, 2, 0)
plotFrameLayout.addWidget(self.__fixedAxesCheckbox, 2, 1, 1, 2)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView, 3, 0, 1, 3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def processEvent(self, observee, event):
if not self.iCharting.checked:
return
if self.__mvNode == None:
return
mvImage = self.__mvNode.GetImageData()
nComponents = self.__mvNode.GetNumberOfFrames()
# TODO: use a timer to delay calculation and compress events
if event == 'LeaveEvent':
# reset all the readouts
# TODO: reset the label text
return
if not self.sliceWidgetsPerStyle.has_key(observee):
return
sliceWidget = self.sliceWidgetsPerStyle[observee]
sliceLogic = sliceWidget.sliceLogic()
interactor = observee.GetInteractor()
xy = interactor.GetEventPosition()
xyz = sliceWidget.sliceView().convertDeviceToXYZ(xy)
ras = sliceWidget.sliceView().convertXYZToRAS(xyz)
bgLayer = sliceLogic.GetBackgroundLayer()
fgLayer = sliceLogic.GetForegroundLayer()
volumeNode = bgLayer.GetVolumeNode()
fgVolumeNode = self.fgSelector.currentNode()
if not volumeNode or volumeNode.GetID() != self.__mvNode.GetID():
return
if volumeNode != self.__mvNode:
return
nameLabel = volumeNode.GetName()
xyToIJK = bgLayer.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
ijk = []
for element in ijkFloat:
try:
index = int(round(element))
except ValueError:
index = 0
ijk.append(index)
extent = mvImage.GetExtent()
if not (ijk[0]>=extent[0] and ijk[0]<=extent[1] and \
ijk[1]>=extent[2] and ijk[1]<=extent[3] and \
ijk[2]>=extent[4] and ijk[2]<=extent[5]):
# pixel outside the valid extent
return
useFg = False
if fgVolumeNode:
fgxyToIJK = fgLayer.GetXYToIJKTransform()
fgijkFloat = xyToIJK.TransformDoublePoint(xyz)
fgijk = []
for element in fgijkFloat:
try:
index = int(round(element))
except ValueError:
index = 0
fgijk.append(index)
fgImage = fgVolumeNode.GetImageData()
fgChartTable = vtk.vtkTable()
if fgijk[0] == ijk[0] and fgijk[1] == ijk[1] and fgijk[2] == ijk[2] and \
fgImage.GetNumberOfScalarComponents() == mvImage.GetNumberOfScalarComponents():
useFg = True
fgxArray = vtk.vtkFloatArray()
fgxArray.SetNumberOfTuples(nComponents)
fgxArray.SetNumberOfComponents(1)
fgxArray.Allocate(nComponents)
fgxArray.SetName('frame')
fgyArray = vtk.vtkFloatArray()
fgyArray.SetNumberOfTuples(nComponents)
fgyArray.SetNumberOfComponents(1)
fgyArray.Allocate(nComponents)
fgyArray.SetName('signal intensity')
# will crash if there is no name
fgChartTable.AddColumn(fgxArray)
fgChartTable.AddColumn(fgyArray)
fgChartTable.SetNumberOfRows(nComponents)
# get the vector of values at IJK
for c in range(nComponents):
val = mvImage.GetScalarComponentAsDouble(ijk[0], ijk[1], ijk[2], c)
self.__chartTable.SetValue(c, 0, self.__mvLabels[c])
self.__chartTable.SetValue(c, 1, val)
if useFg:
fgValue = fgImage.GetScalarComponentAsDouble(
ijk[0], ijk[1], ijk[2], c)
fgChartTable.SetValue(c, 0, self.__mvLabels[c])
fgChartTable.SetValue(c, 1, fgValue)
baselineAverageSignal = 0
if self.iChartingPercent.checked:
# check if percent plotting was requested and recalculate
nBaselines = min(self.baselineFrames.value, nComponents)
for c in range(nBaselines):
baselineAverageSignal += mvImage.GetScalarComponentAsDouble(
ijk[0], ijk[1], ijk[2], c)
baselineAverageSignal /= nBaselines
if baselineAverageSignal != 0:
for c in range(nComponents):
intensity = mvImage.GetScalarComponentAsDouble(
ijk[0], ijk[1], ijk[2], c)
self.__chartTable.SetValue(
c, 1, (intensity / baselineAverageSignal - 1) * 100.)
self.__chart.RemovePlot(0)
self.__chart.RemovePlot(0)
if self.iChartingPercent.checked and baselineAverageSignal != 0:
self.__chart.GetAxis(0).SetTitle('change relative to baseline, %')
else:
self.__chart.GetAxis(0).SetTitle('signal intensity')
tag = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(
self.__mvNode.GetAttribute(
'MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag + ', ' + units
self.__chart.GetAxis(1).SetTitle(xTitle)
if self.iChartingIntensityFixedAxes.checked == True:
self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.FIXED)
self.__chart.GetAxis(0).SetRange(self.__mvRange[0],
self.__mvRange[1])
else:
self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.AUTO)
if useFg:
plot = self.__chart.AddPlot(vtk.vtkChart.POINTS)
plot.SetInput(self.__chartTable, 0, 1)
fgplot = self.__chart.AddPlot(vtk.vtkChart.LINE)
fgplot.SetInput(fgChartTable, 0, 1)
else:
plot = self.__chart.AddPlot(vtk.vtkChart.LINE)
plot.SetInput(self.__chartTable, 0, 1)
if self.xLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(1).GetTitle()
self.__chart.GetAxis(1).SetTitle('log of ' + title)
if self.yLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(0).GetTitle()
self.__chart.GetAxis(0).SetTitle('log of ' + title)
def __init__(self,param):
super(LesionFormWidget,self).__init__()
# parameters node keeps all that is needed to render
# the form and to store the scores
self.param = param
self.widget = qt.QWidget()
self.layout = qt.QHBoxLayout(self.widget)
lesionNameWidget = qt.QWidget()
scoreSheetWidget = qt.QWidget()
plotWidget = qt.QWidget()
lnLayout = qt.QVBoxLayout(lesionNameWidget)
ssLayout = qt.QVBoxLayout(scoreSheetWidget)
pLayout = qt.QVBoxLayout(plotWidget)
lesionName = qt.QLabel(self.param.lesionName)
lnLayout.addWidget(lesionName)
w = qt.QWidget()
wl = qt.QHBoxLayout(w)
for i in range(0,6):
if i:
label = qt.QLabel(str(i))
else:
label = qt.QLabel('')
wl.addWidget(label)
ssLayout.addWidget(w)
w = qt.QWidget()
wl = qt.QHBoxLayout(w)
t2label = qt.QLabel('T2W')
wl.addWidget(t2label)
t2radios = []
self.t2group = qt.QButtonGroup()
for i in range(1,6):
t2radios.append(qt.QRadioButton())
self.t2group.addButton(t2radios[-1],i)
wl.addWidget(t2radios[-1])
self.t2group.connect('buttonClicked(int)', self.onT2scoreUpdated)
ssLayout.addWidget(w)
w = qt.QWidget()
wl = qt.QHBoxLayout(w)
dwilabel = qt.QLabel('DWI')
wl.addWidget(dwilabel)
dwiradios = []
self.dwigroup = qt.QButtonGroup()
for i in range(1,6):
dwiradios.append(qt.QRadioButton())
self.dwigroup.addButton(dwiradios[-1],i)
wl.addWidget(dwiradios[-1])
self.dwigroup.connect('buttonClicked(int)', self.onDWIscoreUpdated)
ssLayout.addWidget(w)
w = qt.QWidget()
wl = qt.QHBoxLayout(w)
dcelabel = qt.QLabel('DCE')
wl.addWidget(dcelabel)
dceradios = []
self.dcegroup = qt.QButtonGroup()
for i in range(1,6):
dceradios.append(qt.QRadioButton())
self.dcegroup.addButton(dceradios[-1],i)
wl.addWidget(dceradios[-1])
self.dcegroup.connect('buttonClicked(int)', self.onDCEscoreUpdated)
ssLayout.addWidget(w)
chartView = ctk.ctkVTKChartView(plotWidget)
chart = chartView.chart()
table = vtk.vtkTable()
x = vtk.vtkFloatArray()
y = vtk.vtkFloatArray()
x.SetName('time point')
y.SetName('signal intensity')
table.AddColumn(x)
table.AddColumn(y)
table.SetNumberOfRows(100)
for c in range(len(self.param.x)):
table.SetValue(c,0,self.param.x[c])
table.SetValue(c,1,self.param.y[c])
plot = chart.AddPlot(0)
plot.SetInput(table,0,1)
chart.AddPlot(0)
cw = qt.QWidget()
cwl = qt.QVBoxLayout(cw)
cwl.addWidget(chartView)
pLayout.addWidget(cw)
self.layout.addWidget(lesionNameWidget)
self.layout.addWidget(scoreSheetWidget)
self.layout.addWidget(plotWidget)
def setup( self ):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
plotFrameLayout.addWidget(self.plotSettingsFrame,0,1)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
label = qt.QLabel('Input secondary multivolume')
self.fgSelector = slicer.qMRMLNodeComboBox()
self.fgSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.fgSelector.setMRMLScene(slicer.mrmlScene)
self.fgSelector.addEnabled = 0
self.fgSelector.noneEnabled = 1
self.fgSelector.toolTip = "Secondary multivolume will be used for the secondary \
plot in interactive charting. As an example, this can be used to overlay the \
curve obtained by fitting a model to the data"
inputFrameLayout.addRow(label, self.fgSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
label = qt.QLabel('Current frame number')
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector,1,1,1,2)
ctrlFrameLayout.addWidget(self.extractButton,2,0,1,3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode','LabelMap','1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.chartButton = qt.QPushButton('Chart')
self.chartButton.checkable = False
self.chartButton.connect('clicked()', self.onChartRequested)
plotSettingsFrameLayout.addWidget(label,0,0)
plotSettingsFrameLayout.addWidget(self.__fSelector,0,1)
plotSettingsFrameLayout.addWidget(self.chartButton,0,2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotSettingsFrameLayout.addWidget(self.iCharting,1,0,1,3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)', self.onInteractiveChartingChanged)
groupLabel = qt.QLabel('Interactive plotting mode:')
self.iChartingMode = qt.QButtonGroup()
self.iChartingIntensity = qt.QRadioButton('Signal intensity')
#self.iChartingIntensity.tooltip = 'Plot range adjusted dynamically to the range over the time course for the selected pixel'
self.iChartingIntensityFixedAxes = qt.QRadioButton('Fixed range intensity')
#self.iChartingIntensityFixedAxes.tooltip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.iChartingPercent = qt.QRadioButton('Percent change')
#self.iChartingPercent.tooltip = 'Percent change relative to the average of the first N frames (parameter set below)'
self.iChartingIntensity.setChecked(1)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(groupLabel)
self.groupLayout.addRow(self.iChartingIntensity)
self.groupLayout.addRow(self.iChartingIntensityFixedAxes)
self.groupLayout.addRow(self.iChartingPercent)
self.baselineFrames = qt.QSpinBox()
self.baselineFrames.minimum = 1
label = qt.QLabel('Number of frames for baseline calculation')
self.groupLayout.addRow(label,self.baselineFrames)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for X axis')
self.groupLayout.addRow(self.xLogScaleCheckBox,label)
self.xLogScaleCheckBox.connect('stateChanged(int)', self.onXLogScaleRequested)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for Y axis')
self.groupLayout.addRow(self.yLogScaleCheckBox,label)
self.yLogScaleCheckBox.connect('stateChanged(int)', self.onYLogScaleRequested)
plotSettingsFrameLayout.addWidget(self.groupWidget,2,0)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView,3,0,1,3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def setup( self ):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
##self.layout.addWidget(label)
##self.layout.addWidget(self.__mvSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
#self.__mdSlider.setRange(0,10)
#self.__mdSlider.setValue(5)
label = qt.QLabel('Current frame number')
##self.layout.addWidget(label)
##self.layout.addWidget(self.__mdSlider)
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector,1,1,1,2)
ctrlFrameLayout.addWidget(self.extractButton,2,0,1,3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode','LabelMap','1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.__fSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onLabelVolumeChanged)
self.__fSelector.connect('mrmlSceneChanged(vtkMRMLScene*)', self.onLVMRMLSceneChanged)
plotFrameLayout.addWidget(label,0,0,1,1)
plotFrameLayout.addWidget(self.__fSelector,0,1,1,2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotFrameLayout.addWidget(self.iCharting,1,0,1,3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)', self.onInteractiveChartingChanged)
label = qt.QLabel("Use intensity range to fix axis extent")
label.toolTip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.__fixedAxesCheckbox = qt.QCheckBox()
self.__fixedAxesCheckbox.toolTip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.__fixedAxesCheckbox.checked = False
plotFrameLayout.addWidget(label, 2, 0)
plotFrameLayout.addWidget(self.__fixedAxesCheckbox, 2,1,1,2)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView,3,0,1,3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def processEvent(self,observee,event):
if not self.iCharting.checked:
return
if self.__mvNode == None:
return
mvImage = self.__mvNode.GetImageData()
nComponents = self.__mvNode.GetNumberOfFrames()
# TODO: use a timer to delay calculation and compress events
if event == 'LeaveEvent':
# reset all the readouts
# TODO: reset the label text
return
if not self.sliceWidgetsPerStyle.has_key(observee):
return
sliceWidget = self.sliceWidgetsPerStyle[observee]
sliceLogic = sliceWidget.sliceLogic()
interactor = observee.GetInteractor()
xy = interactor.GetEventPosition()
xyz = sliceWidget.sliceView().convertDeviceToXYZ(xy);
ras = sliceWidget.sliceView().convertXYZToRAS(xyz)
bgLayer = sliceLogic.GetBackgroundLayer()
fgLayer = sliceLogic.GetForegroundLayer()
volumeNode = bgLayer.GetVolumeNode()
fgVolumeNode = self.fgSelector.currentNode()
if not volumeNode or volumeNode.GetID() != self.__mvNode.GetID():
return
if volumeNode != self.__mvNode:
return
nameLabel = volumeNode.GetName()
xyToIJK = bgLayer.GetXYToIJKTransform()
ijkFloat = xyToIJK.TransformDoublePoint(xyz)
ijk = []
for element in ijkFloat:
try:
index = int(round(element))
except ValueError:
index = 0
ijk.append(index)
extent = mvImage.GetExtent()
if not (ijk[0]>=extent[0] and ijk[0]<=extent[1] and \
ijk[1]>=extent[2] and ijk[1]<=extent[3] and \
ijk[2]>=extent[4] and ijk[2]<=extent[5]):
# pixel outside the valid extent
return
useFg = False
if fgVolumeNode:
fgxyToIJK = fgLayer.GetXYToIJKTransform()
fgijkFloat = xyToIJK.TransformDoublePoint(xyz)
fgijk = []
for element in fgijkFloat:
try:
index = int(round(element))
except ValueError:
index = 0
fgijk.append(index)
fgImage = fgVolumeNode.GetImageData()
fgChartTable = vtk.vtkTable()
if fgijk[0] == ijk[0] and fgijk[1] == ijk[1] and fgijk[2] == ijk[2] and \
fgImage.GetNumberOfScalarComponents() == mvImage.GetNumberOfScalarComponents():
useFg = True
fgxArray = vtk.vtkFloatArray()
fgxArray.SetNumberOfTuples(nComponents)
fgxArray.SetNumberOfComponents(1)
fgxArray.Allocate(nComponents)
fgxArray.SetName('frame')
fgyArray = vtk.vtkFloatArray()
fgyArray.SetNumberOfTuples(nComponents)
fgyArray.SetNumberOfComponents(1)
fgyArray.Allocate(nComponents)
fgyArray.SetName('signal intensity')
# will crash if there is no name
fgChartTable.AddColumn(fgxArray)
fgChartTable.AddColumn(fgyArray)
fgChartTable.SetNumberOfRows(nComponents)
# get the vector of values at IJK
for c in range(nComponents):
val = mvImage.GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
self.__chartTable.SetValue(c, 0, self.__mvLabels[c])
self.__chartTable.SetValue(c, 1, val)
if useFg:
fgValue = fgImage.GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
fgChartTable.SetValue(c,0,self.__mvLabels[c])
fgChartTable.SetValue(c,1,fgValue)
baselineAverageSignal = 0
if self.iChartingPercent.checked:
# check if percent plotting was requested and recalculate
nBaselines = min(self.baselineFrames.value,nComponents)
for c in range(nBaselines):
baselineAverageSignal += mvImage.GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
baselineAverageSignal /= nBaselines
if baselineAverageSignal != 0:
for c in range(nComponents):
intensity = mvImage.GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
self.__chartTable.SetValue(c,1,(intensity/baselineAverageSignal-1)*100.)
self.__chart.RemovePlot(0)
self.__chart.RemovePlot(0)
if self.iChartingPercent.checked and baselineAverageSignal != 0:
self.__chart.GetAxis(0).SetTitle('change relative to baseline, %')
else:
self.__chart.GetAxis(0).SetTitle('signal intensity')
tag = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagName'))
units = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits'))
xTitle = tag+', '+units
self.__chart.GetAxis(1).SetTitle(xTitle)
if self.iChartingIntensityFixedAxes.checked == True:
self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.FIXED)
self.__chart.GetAxis(0).SetRange(self.__mvRange[0],self.__mvRange[1])
else:
self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.AUTO)
if useFg:
plot = self.__chart.AddPlot(vtk.vtkChart.POINTS)
plot.SetInput(self.__chartTable, 0, 1)
fgplot = self.__chart.AddPlot(vtk.vtkChart.LINE)
fgplot.SetInput(fgChartTable, 0, 1)
else:
plot = self.__chart.AddPlot(vtk.vtkChart.LINE)
plot.SetInput(self.__chartTable, 0, 1)
if self.xLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(1).GetTitle()
self.__chart.GetAxis(1).SetTitle('log of '+title)
if self.yLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(0).GetTitle()
self.__chart.GetAxis(0).SetTitle('log of '+title)
def processEvent(self, observee, event):
#if not self.iCharting.checked:
# return
fgImages = self.nodeImgList[0]
mvImage = fgImages[0]
fgNodes = self.nodeList[0]
nComponents = self.numFrames
# TODO: use a timer to delay calculation and compress events
if event == 'LeaveEvent':
# reset all the readouts
# TODO: reset the label text
return
if not self.sliceWidgetsPerStyle.has_key(observee):
return
sliceWidget = self.sliceWidgetsPerStyle[observee]
sliceLogic = sliceWidget.sliceLogic()
interactor = observee.GetInteractor()
xy = interactor.GetEventPosition()
coordinates = []
# we need a 4 element point to be able to multiply further down
coordinates.append(xy[0])
coordinates.append(xy[1])
coordinates.append(0)
coordinates.append(1)
xyToRas = sliceLogic.GetSliceNode().GetXYToRAS()
rasPos = xyToRas.MultiplyPoint(coordinates)
# VTK_CREATE(vtkMatrix4x4, rasToijk);
rasToijk = vtk.vtkMatrix4x4()
fgNodes[0].GetRASToIJKMatrix(rasToijk)
ijkFloat = rasToijk.MultiplyPoint(rasPos)
ijk = []
for element in ijkFloat:
try:
index = int(round(element))
except ValueError:
index = 0
ijk.append(index)
extent = mvImage[0].GetExtent()
if not (ijk[0]>=extent[0] and ijk[0]<=extent[1] and \
ijk[1]>=extent[2] and ijk[1]<=extent[3] and \
ijk[2]>=extent[4] and ijk[2]<=extent[5]):
return
nComponents = self.numFrames
# for testing
# nComponents=1
if True:
fgxArray = vtk.vtkFloatArray()
fgxArray.SetNumberOfTuples(nComponents)
fgxArray.SetNumberOfComponents(1)
fgxArray.Allocate(nComponents)
fgxArray.SetName('frame')
fgyArray = vtk.vtkFloatArray()
fgyArray.SetNumberOfTuples(nComponents)
fgyArray.SetNumberOfComponents(1)
fgyArray.Allocate(nComponents)
fgyArray.SetName('signal intensity')
# will crash if there is no name
fgChartTable = vtk.vtkTable()
fgChartTable.AddColumn(fgxArray)
fgChartTable.AddColumn(fgyArray)
fgChartTable.SetNumberOfRows(nComponents)
# get the vector of values at IJK
if (self.ctrlLevelSlider.maximum - self.ctrlLevelSlider.minimum) > 20:
intFlag = True
else:
intFlag = False
disVal = []
if self.ctrlFrameSlider:
cInd = int(self.ctrlFrameSlider.value)
else:
cInd = 0
for c in range(nComponents):
for img in fgImages:
# for c in range(1):
iLen = len(img)
if c < iLen:
val = img[c].GetScalarComponentAsDouble(
ijk[0], ijk[1], ijk[2], 0)
else:
val = img[iLen - 1].GetScalarComponentAsDouble(
ijk[0], ijk[1], ijk[2], 0)
if intFlag:
val = int(val)
else:
val = round(val * 100) / 100.0
# Kilian: will only show last image - change later
self.__chartTable.SetValue(c, 0, self.__mvLabels[c])
self.__chartTable.SetValue(c, 1, val)
if cInd == c:
disVal.append(val)
#if useFg:
# fgValue = fgImage.GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],0)
# fgChartTable.SetValue(c,0,self.__mvLabels[c])
# fgChartTable.SetValue(c,1,fgValue)
self.valueFrameValues.setText(disVal)
# To disable plot uncomment
# return
baselineAverageSignal = 0
# if self.iChartingPercent.checked:
# # check if percent plotting was requested and recalculate
# nBaselines = min(self.baselineFrames.value,nComponents)
# for c in range(nBaselines):
# baselineAverageSignal += mvImage[0].GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
# baselineAverageSignal /= nBaselines
# if baselineAverageSignal != 0:
# for c in range(nComponents):
# intensity = mvImage[0].GetScalarComponentAsDouble(ijk[0],ijk[1],ijk[2],c)
# self.__chartTable.SetValue(c,1,(intensity/baselineAverageSignal-1)*100.)
self.__chart.RemovePlot(0)
self.__chart.RemovePlot(0)
#if self.iChartingPercent.checked and baselineAverageSignal != 0:
# self.__chart.GetAxis(0).SetTitle('change relative to baseline, %')
#else:
self.__chart.GetAxis(0).SetTitle('signal intensity')
#tag = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagName'))
#units = str(self.__mvNode.GetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits'))
#xTitle = tag+', '+units
self.__chart.GetAxis(1).SetTitle("Time")
#if self.iChartingIntensityFixedAxes.checked == True:
# self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.FIXED)
# self.__chart.GetAxis(0).SetRange(self.__mvRange[0],self.__mvRange[1])
# self.__chart.GetAxis(0).SetRange(2000,6000)
# self.__chart.GetAxis(1).SetBehavior(vtk.vtkAxis.FIXED)
# self.__chart.GetAxis(1).SetRange(2000,6000)
#else:
# self.__chart.GetAxis(0).SetBehavior(vtk.vtkAxis.AUTO)
# if useFg:
useFg = False
if useFg:
plot = self.__chart.AddPlot(vtk.vtkChart.POINTS)
if vtk.VTK_MAJOR_VERSION <= 5:
plot.SetInput(self.__chartTable, 0, 1)
else:
plot.SetInputData(self.__chartTable, 0, 1)
fgplot = self.__chart.AddPlot(vtk.vtkChart.LINE)
if vtk.VTK_MAJOR_VERSION <= 5:
fgplot.SetInput(fgChartTable, 0, 1)
else:
fgplot.SetInputData(fgChartTable, 0, 1)
else:
plot = self.__chart.AddPlot(vtk.vtkChart.LINE)
if vtk.VTK_MAJOR_VERSION <= 5:
plot.SetInput(self.__chartTable, 0, 1)
else:
plot.SetInputData(self.__chartTable, 0, 1)
if self.xLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(1).GetTitle()
self.__chart.GetAxis(1).SetTitle('log of ' + title)
if self.yLogScaleCheckBox.checkState() == 2:
title = self.__chart.GetAxis(0).GetTitle()
self.__chart.GetAxis(0).SetTitle('log of ' + title)