Histogram plot of volume masked by segments

MaskVolumeHistogramPlot.py

# Generate input data
################################################

import SampleData
import numpy as np

# Load master volume
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()

# Create segmentation
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

# Create seed segment inside tumor
tumorSeed = vtk.vtkSphereSource()
tumorSeed.SetCenter(-6, 30, 28)
tumorSeed.SetRadius(10)
tumorSeed.Update()
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(tumorSeed.GetOutput(), "Tumor", [1.0,0.0,0.0])

# Create seed segment inside tumor 2
referenceSeed = vtk.vtkSphereSource()
referenceSeed.SetCenter(-6, -50, -10)
referenceSeed.SetRadius(20)
referenceSeed.Update()
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(referenceSeed.GetOutput(), "Reference", [0.0,0.0,1.0])

# Create seed segment outside tumor
backgroundSeedPositions = [[0,65,32], [1, -14, 30], [0, 28, -7], [0,30,64], [31, 33, 27], [-42, 30, 27]]
append = vtk.vtkAppendPolyData()
for backgroundSeedPosition in backgroundSeedPositions:
  backgroundSeed = vtk.vtkSphereSource()
  backgroundSeed.SetCenter(backgroundSeedPosition)
  backgroundSeed.SetRadius(10)
  backgroundSeed.Update()
  append.AddInputData(backgroundSeed.GetOutput())

append.Update()
backgroundSegmentId = segmentationNode.AddSegmentFromClosedSurfaceRepresentation(append.GetOutput(), "Background", [0.0,1.0,0.0])

# Perform analysis
################################################

# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
# To show segment editor widget (useful for debugging): segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)

# Set up masking parameters
segmentEditorWidget.setActiveEffectByName("Mask volume")
effect = segmentEditorWidget.activeEffect()
# set fill value to be outside the valid intensity range
intensityRange = masterVolumeNode.GetImageData().GetScalarRange()
effect.setParameter("FillValue", str(intensityRange[0]-1))
# Blank out voxels that are outside the segment
effect.setParameter("Operation", "FILL_OUTSIDE")
# Create a volume that will store temporary masked volumes
maskedVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Temporary masked volume")
effect.self().outputVolumeSelector.setCurrentNode(maskedVolume)

# Create chart
plotChartNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotChartNode", "Histogram")

# Create histogram plot data series for each masked volume
for segmentIndex in range(segmentationNode.GetSegmentation().GetNumberOfSegments()):
  # Set active segment
  segmentID = segmentationNode.GetSegmentation().GetNthSegmentID(segmentIndex)
  segmentEditorWidget.setCurrentSegmentID(segmentID)
  # Apply mask
  effect.self().onApply()
  # Compute histogram values
  histogram = np.histogram(arrayFromVolume(maskedVolume), bins=100, range=intensityRange)
  # Save results to a new table node
  segment = segmentationNode.GetSegmentation().GetNthSegment(segmentIndex)
  tableNode=slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode", segment.GetName() + " histogram table")
  updateTableFromArray(tableNode, histogram)
  tableNode.GetTable().GetColumn(0).SetName("Count")
  tableNode.GetTable().GetColumn(1).SetName("Intensity")
  # Create new plot data series node
  plotSeriesNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLPlotSeriesNode", segment.GetName() + " histogram")
  plotSeriesNode.SetAndObserveTableNodeID(tableNode.GetID())
  plotSeriesNode.SetXColumnName("Intensity")
  plotSeriesNode.SetYColumnName("Count")
  plotSeriesNode.SetPlotType(slicer.vtkMRMLPlotSeriesNode.PlotTypeScatter)
  plotSeriesNode.SetMarkerStyle(slicer.vtkMRMLPlotSeriesNode.MarkerStyleNone)
  plotSeriesNode.SetUniqueColor()
  # Add plot to chart
  plotChartNode.AddAndObservePlotSeriesNodeID(plotSeriesNode.GetID())

# Show chart in layout
slicer.modules.plots.logic().ShowChartInLayout(plotChartNode)

# Delete temporary node
slicer.mrmlScene.RemoveNode(maskedVolume)
slicer.mrmlScene.RemoveNode(segmentEditorNode)

Line-71: plotSeriesNode is not defined yet.
Need be deleted.

Line-71: plotSeriesNode is not defined yet.
Need be deleted.

Good catch, thank you, fixed in rev3.