def hausdorffDistance(self,fiber1,fiber2):
"""
calculate the distance between two fiber bundles
Based on code from Laurent Chauvin
"""
polyA = fiber1.GetPolyData()
polyB = fiber2.GetPolyData()
locA = vtk.vtkMergePoints()
locB = vtk.vtkMergePoints()
locA.SetDataSet(polyA)
locB.SetDataSet(polyB)
locs = (locA,locB)
for loc in locs:
loc.AutomaticOn()
loc.BuildLocator()
ptsA = polyA.GetPoints()
ptsB = polyB.GetPoints()
rangeA = ptsA.GetNumberOfPoints()
rangeB = ptsB.GetNumberOfPoints()
maxd = 0.0
maxd1 = 0.0
avgd = 0.0
avgd1 = 0.0
distanceA = vtk.vtkFloatArray()
distanceA.SetName("Distance")
for i in range(rangeA):
pt = ptsA.GetPoint(i)
bid = locB.FindClosestPoint(pt)
ptb = ptsB.GetPoint(bid)
d = self.pointDistance(pt,ptb)
distanceA.InsertNextValue(d)
avgd += d
if d > maxd:
maxd = d
avgd = avgd / rangeA
distanceB = vtk.vtkFloatArray()
distanceB.SetName("Distance")
for i in range(rangeB):
pt = ptsB.GetPoint(i)
bid = locA.FindClosestPoint(pt)
ptb = ptsA.GetPoint(bid)
d = self.pointDistance(pt,ptb)
distanceB.InsertNextValue(d)
avgd1 += d
if d > maxd1:
maxd1 = d
avgd1 = avgd1 / rangeB
polyA.GetPointData().SetScalars(distanceA)
polyB.GetPointData().SetScalars(distanceB)
return max(maxd,maxd1)
def __init__(self):
self.__chartView = ctk.ctkVTKChartView()
self.__bgxArray = vtk.vtkFloatArray()
self.__bgyArray = vtk.vtkFloatArray()
self.__bgxArray.SetName('')
self.__bgyArray.SetName('1st multivolume')
self.__chartTable = self.createNewVTKTable(self.__bgxArray, self.__bgyArray)
self.__bgMultiVolumeNode = None
self.__fgMultiVolumeNode = None
self.__mvLabels = []
self.__xLogScaleEnabled = False
self.__yLogScaleEnabled = False
self.__mvRange = [0,0]
self.__nFramesForBaselineCalculation = 1
self.__chartMode = None
self.activateSignalIntensityMode()
self.baselineAverageSignal = 0
self.__showLegend = False
def __init__(self):
self.__chartView = ctk.ctkVTKChartView()
self.__bgxArray = vtk.vtkFloatArray()
self.__bgyArray = vtk.vtkFloatArray()
self.__bgxArray.SetName('')
self.__bgyArray.SetName('1st multivolume')
self.__chartTable = self.createNewVTKTable(self.__bgxArray,
self.__bgyArray)
self.__bgMultiVolumeNode = None
self.__fgMultiVolumeNode = None
self.__mvLabels = []
self.__xLogScaleEnabled = False
self.__yLogScaleEnabled = False
self.__mvRange = [0, 0]
self.__nFramesForBaselineCalculation = 1
self.__chartMode = None
self.activateSignalIntensityMode()
self.baselineAverageSignal = 0
self.__showLegend = False
def onThresholdValuesChanged(self,lower,upper):
# Check if this is the first update of the threshold range
if self.thresholdFlag == 1:
newScalars = vtk.vtkFloatArray()
newScalars.SetNumberOfComponents( self.scalars.GetNumberOfComponents() )
newScalars.SetNumberOfValues ( self.numberOfPoints )
newScalars.SetName( "NewScalars" )
# Set values of new scalars according to threshold
for i in xrange( self.numberOfPoints ):
value = self.scalars.GetValue( i )
if value < lower:
newScalars.SetValue( i, 0 )
elif value > upper:
newScalars.SetValue( i, self.range[1] )
else:
newScalars.SetValue( i, value )
# Update the polydata with the new scalars
self.polyData.GetPointData().AddArray( newScalars )
self.polyData.GetPointData().RemoveArray( "NRRDImage" )
self.polyData.Modified()
self.outputModel.SetAndObservePolyData( self.polyData )
self.outputModel.GetDisplayNode().SetScalarVisibility( 1 )
self.outputModel.GetDisplayNode().SetActiveScalarName( "NewScalars" )
def onThresholdValuesChanged(self, lower, upper):
# Check if this is the first update of the threshold range
if self.thresholdFlag == 1:
newScalars = vtk.vtkFloatArray()
newScalars.SetNumberOfComponents(
self.scalars.GetNumberOfComponents())
newScalars.SetNumberOfValues(self.numberOfPoints)
newScalars.SetName("NewScalars")
# Set values of new scalars according to threshold
for i in xrange(self.numberOfPoints):
value = self.scalars.GetValue(i)
if value < lower:
newScalars.SetValue(i, 0)
elif value > upper:
newScalars.SetValue(i, self.range[1])
else:
newScalars.SetValue(i, value)
# Update the polydata with the new scalars
self.polyData.GetPointData().AddArray(newScalars)
self.polyData.GetPointData().RemoveArray("NRRDImage")
self.polyData.Modified()
self.outputModel.SetAndObservePolyData(self.polyData)
self.outputModel.GetDisplayNode().SetScalarVisibility(1)
self.outputModel.GetDisplayNode().SetActiveScalarName("NewScalars")
def generateVTKFloatArrayFromNumpy(self, np_array):
size = np_array.size
vtk_float = vtk.vtkFloatArray()
vtk_float.SetNumberOfComponents(1)
for i in range(size):
vtk_float.InsertNextTuple([np_array[i]])
return vtk_float
def __init__(self):
self.__chartView = slicer.qMRMLPlotView()
self.__chartView.setMRMLScene(slicer.mrmlScene)
self.__chartViewNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotViewNode")
self.__chartView.setMRMLPlotViewNode(self.__chartViewNode)
self.__chart = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotChartNode")
self.__chart.LegendVisibilityOff()
self.__chart.SetAxisTitleFontSize(15)
self.__chartViewNode.SetPlotChartNodeID(self.__chart.GetID())
self.__chartView.show()
self.__bgxArray = vtk.vtkFloatArray()
self.__bgyArray = vtk.vtkFloatArray()
self.__bgxArray.SetName('x')
self.__bgyArray.SetName('1st multivolume')
self.__chartTableNode = self.createNewVTKTableNode(
self.__bgxArray, self.__bgyArray)
self.__chartTable = self.__chartTableNode.GetTable()
self.__fgChartTableNode = None
self.__bgPlot = None
self.__fgPlot = None
self.__bgMultiVolumeNode = None
self.__fgMultiVolumeNode = None
self.__mvLabels = []
self.__xLogScaleEnabled = False
self.__yLogScaleEnabled = False
self.__mvRange = [0, 0]
self.__nFramesForBaselineCalculation = 1
self.__chartMode = None
self.activateSignalIntensityMode()
self.baselineAverageSignal = 0
self.__showLegend = False
def onProbeVolumeButtonClicked(self):
# Set flag to prevent model from being thresholded without user input
self.thresholdFlag = 0
wallModel = self.inputModelSelector.currentNode()
inputVol = self.inputVolumeSelector.currentNode()
self.polyData = vtk.vtkPolyData()
if not (wallModel):
qt.QMessageBox.critical(slicer.util.mainWindow(),
'Scar Visualization',
'Wall model is required to proceed.')
elif not (inputVol):
qt.QMessageBox.critical(slicer.util.mainWindow(),
'Scar Visualization',
'Input volume is required to proceed.')
else:
self.outputModel = slicer.vtkMRMLModelNode()
self.outputModel.SetName("Output Model")
slicer.mrmlScene.AddNode(self.outputModel)
paramProbe = {}
paramProbe['InputVolume'] = inputVol
paramProbe['InputModel'] = wallModel
paramProbe['OutputModel'] = self.outputModel
# Pass parameters to Probe Volume Model
slicer.cli.run(slicer.modules.probevolumewithmodel,
None,
paramProbe,
wait_for_completion=True)
# Set color of output model
labelsColorNode = slicer.modules.colors.logic(
).GetColorTableNodeID(35) # Color Warm Tint 3
self.outputModel.GetDisplayNode().SetAndObserveColorNodeID(
labelsColorNode)
# Delete input model which is not required anymore
slicer.mrmlScene.RemoveNode(wallModel)
# Update threshold widget with scalar values from model
self.polyData = self.outputModel.GetPolyData()
self.numberOfPoints = self.polyData.GetNumberOfPoints()
self.scalars = vtk.vtkFloatArray()
self.scalars = self.polyData.GetPointData().GetScalars("NRRDImage")
self.range = [0] * 2
numberOfComponents = self.scalars.GetNumberOfComponents()
for i in xrange(numberOfComponents):
self.scalars.GetRange(self.range, i)
lowerThreshold = self.range[0]
upperThreshold = self.range[1]
# Set threshold range according to current model
self.threshold.minimum = lowerThreshold
self.threshold.maximum = upperThreshold
self.thresholdFlag = 1
def onProbeVolumeButtonClicked(self):
# Set flag to prevent model from being thresholded without user input
self.thresholdFlag = 0
wallModel = self.inputModelSelector.currentNode()
inputVol = self.inputVolumeSelector.currentNode()
self.polyData = vtk.vtkPolyData()
if not (wallModel):
qt.QMessageBox.critical(slicer.util.mainWindow(),
'Scar Visualization', 'Wall model is required to proceed.')
elif not (inputVol):
qt.QMessageBox.critical(slicer.util.mainWindow(),
'Scar Visualization', 'Input volume is required to proceed.')
else:
self.outputModel = slicer.vtkMRMLModelNode()
self.outputModel.SetName( "Output Model" )
slicer.mrmlScene.AddNode(self.outputModel)
paramProbe = {}
paramProbe['InputVolume'] = inputVol
paramProbe['InputModel'] = wallModel
paramProbe['OutputModel'] = self.outputModel
# Pass parameters to Probe Volume Model
slicer.cli.run( slicer.modules.probevolumewithmodel, None, paramProbe, wait_for_completion=True )
# Set color of output model
labelsColorNode = slicer.modules.colors.logic().GetColorTableNodeID(35) # Color Warm Tint 3
self.outputModel.GetDisplayNode().SetAndObserveColorNodeID(labelsColorNode)
# Delete input model which is not required anymore
slicer.mrmlScene.RemoveNode( wallModel )
# Update threshold widget with scalar values from model
self.polyData = self.outputModel.GetPolyData()
self.numberOfPoints = self.polyData.GetNumberOfPoints()
self.scalars = vtk.vtkFloatArray()
self.scalars = self.polyData.GetPointData().GetScalars( "NRRDImage" )
self.range = [0] * 2
numberOfComponents = self.scalars.GetNumberOfComponents()
for i in xrange ( numberOfComponents ):
self.scalars.GetRange(self.range, i)
lowerThreshold = self.range[0]
upperThreshold = self.range[1]
# Set threshold range according to current model
self.threshold.minimum = lowerThreshold
self.threshold.maximum = upperThreshold
self.thresholdFlag = 1
def onApplyThreshold(self):
min, max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length <= self.thresholdMax.value and length >= self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i, newId)
newScalars.InsertNextValue(((length - min) / (max - min)))
newId += 1
tensorValue = [0] * 9
if (tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(
ids.GetId(i), j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max - min) / 10
interMin = min
interMax = min + step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length <= interMax and length >= interMin and length <= self.thresholdMax.value and length >= self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i, 0, (interMin + interMax) / 2)
array.SetComponent(i, 1, numberOfFibers)
array.SetComponent(i, 2, 0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
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 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 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 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()
if self.__fgChartTableNode:
slicer.mrmlScene.RemoveNode(self.__fgChartTableNode)
self.__fgChartTableNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLTableNode", "fgChartTable")
fgChartTable = self.__fgChartTableNode.GetTable()
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, 'fg')
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()
self.__bgPlot = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotSeriesNode", "1st multivolume")
self.__bgPlot.SetAndObserveTableNodeID(self.__chartTableNode.GetID())
self.__bgPlot.SetXColumnName('x')
self.__bgPlot.SetYColumnName('1st multivolume')
self.__bgPlot.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
if useFg:
self.__bgPlot.SetLineStyle(
slicer.vtkMRMLPlotSeriesNode.LineStyleNone)
else:
self.__bgPlot.SetMarkerStyle(
slicer.vtkMRMLPlotSeriesNode.MarkerStyleNone)
self.__chart.AddAndObservePlotSeriesNodeID(self.__bgPlot.GetID())
# bgPlot.SetLabel("Primary multivolume ")
if useFg:
self.__fgPlot = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotSeriesNode", "2nd multivolume")
self.__fgPlot.SetAndObserveTableNodeID(
self.__fgChartTableNode.GetID())
self.__fgPlot.SetXColumnName('fg')
self.__fgPlot.SetYColumnName('2nd multivolume')
self.__fgPlot.SetPlotType(
slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
self.__fgPlot.SetColor(1, 0, 0)
self.__fgPlot.SetMarkerStyle(
slicer.vtkMRMLPlotSeriesNode.MarkerStyleNone)
self.__chart.AddAndObservePlotSeriesNodeID(self.__fgPlot.GetID())
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 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 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 __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 chartContact(self, screwCount):
# Show this chart in the plot view
plotWidget = slicer.app.layoutManager().plotWidget(0)
plotViewNode = plotWidget.mrmlPlotViewNode()
# Retrieve/Create plot chart
plotChartNode = plotViewNode.GetPlotChartNode()
if not plotChartNode:
plotChartNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotChartNode", "Screw - Bone Contact chart")
plotViewNode.SetPlotChartNodeID(plotChartNode.GetID())
plotChartNode.SetTitle("Screw - Bone Contact")
plotChartNode.SetXAxisTitle('Screw Percentile (Head - Tip)')
plotChartNode.SetYAxisTitle('Average HU Contact')
# Retrieve/Create plot table
firstPlotSeries = plotChartNode.GetNthPlotSeriesNode(0)
plotTableNode = firstPlotSeries.GetTableNode(
) if firstPlotSeries else None
if not plotTableNode:
plotTableNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLTableNode", "Screw - Bone Contact table")
# Set x, cortical bone, and cancellous bone columns
plotTableNode.RemoveAllColumns()
arrX = vtk.vtkFloatArray()
arrX.SetName("Screw Percentile")
plotTableNode.AddColumn(arrX)
arrCortical = vtk.vtkFloatArray()
arrCortical.SetName("Cortical Bone")
plotTableNode.AddColumn(arrCortical)
arrCancellous = vtk.vtkFloatArray()
arrCancellous.SetName("Cancellous Bone")
plotTableNode.AddColumn(arrCancellous)
numPoints = 10
plotTable = plotTableNode.GetTable()
plotTable.SetNumberOfRows(numPoints)
for i in range(numPoints):
plotTable.SetValue(i, 0, i * 10)
plotTable.SetValue(i, 1, 250)
plotTable.SetValue(i, 2, 130)
arrays = [arrCortical, arrCancellous]
for i in range(screwCount):
# Create an Array Node and add some data
arrScrew = vtk.vtkFloatArray()
arrScrew.SetName('Screw %s' % i)
arrScrew.SetNumberOfValues(numPoints)
screwValues = self.screwContact[i]
for j in range(numPoints):
arrScrew.SetValue(j, screwValues[j])
plotTableNode.AddColumn(arrScrew)
arrays.append(arrScrew)
# Update/Create plot series
for arrIndex, arr in enumerate(arrays):
plotSeriesNode = plotChartNode.GetNthPlotSeriesNode(arrIndex)
if not plotSeriesNode:
plotSeriesNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLPlotSeriesNode")
plotChartNode.AddAndObservePlotSeriesNodeID(
plotSeriesNode.GetID())
plotSeriesNode.SetName("{0}".format(arr.GetName()))
plotSeriesNode.SetAndObserveTableNodeID(plotTableNode.GetID())
plotSeriesNode.SetXColumnName(arrX.GetName())
plotSeriesNode.SetYColumnName(arr.GetName())
plotSeriesNode.SetPlotType(
slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
if arrIndex < 2:
# two constant lines
plotSeriesNode.SetLineStyle(
slicer.vtkMRMLPlotSeriesNode.LineStyleDash)
else:
plotSeriesNode.SetLineStyle(
slicer.vtkMRMLPlotSeriesNode.LineStyleSolid)
plotSeriesNode.SetMarkerStyle(
slicer.vtkMRMLPlotSeriesNode.MarkerStyleNone)
plotSeriesNode.SetUniqueColor()
# Remove extra series nodes
for i in range(plotChartNode.GetNumberOfPlotSeriesNodes() -
len(arrays)):
plotChartNode.RemoveNthPlotSeriesNodeID(
plotChartNode.GetNumberOfPlotSeriesNodes() - 1)
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)
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 onApplyThreshold(self):
min,max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length<=self.thresholdMax.value and length>=self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i,newId)
newScalars.InsertNextValue(((length-min)/(max-min)))
newId += 1
tensorValue = [0]*9
if(tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(ids.GetId(i),j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max-min)/10
interMin = min
interMax = min+step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length<=interMax and length>=interMin and length<=self.thresholdMax.value and length>=self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i,0,(interMin+interMax)/2)
array.SetComponent(i,1,numberOfFibers)
array.SetComponent(i,2,0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length",arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
