def selectParameterNode(self):
# Select parameter set node if one is found in the scene, and create one otherwise
segmentEditorSingletonTag = "SegmentEditor"
segmentEditorNode = slicer.mrmlScene.GetSingletonNode(segmentEditorSingletonTag, "vtkMRMLSegmentEditorNode")
if segmentEditorNode is None:
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
segmentEditorNode.SetSingletonTag(segmentEditorSingletonTag)
segmentEditorNode = slicer.mrmlScene.AddNode(segmentEditorNode)
if self.parameterSetNode == segmentEditorNode:
# nothing changed
return
self.parameterSetNode = segmentEditorNode
self.editor.setMRMLSegmentEditorNode(self.parameterSetNode)
def test_ScriptedSegmentEditorEffectModuleTemplate1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing sphere-shaped seeds
- Run segmentation
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorScriptedSegmentEditorEffectModuleTemplate)
"""
self.delayDisplay("Starting test_ScriptedSegmentEditorEffectModuleTemplate1")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
import SampleData
from SegmentStatistics import SegmentStatisticsLogic
##################################
self.delayDisplay("Load master volume")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
##################################
self.delayDisplay("Create segmentation containing a few spheres")
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
# Segments are defined by a list of: name and a list of sphere [radius, posX, posY, posZ]
segmentGeometries = [
['Tumor', [[10, -6,30,28]]],
['Background', [[10, 0,65,22], [15, 1, -14, 30], [12, 0, 28, -7], [5, 0,30,54], [12, 31, 33, 27], [17, -42, 30, 27], [6, -2,-17,71]]],
['Air', [[10, 76,73,0], [15, -70,74,0]]] ]
for segmentGeometry in segmentGeometries:
segmentName = segmentGeometry[0]
appender = vtk.vtkAppendPolyData()
for sphere in segmentGeometry[1]:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentationNode.GetSegmentation().GenerateUniqueSegmentID(segmentName))
appender.Update()
segment.AddRepresentation(vtkSegmentationCore.vtkSegmentationConverter.GetSegmentationClosedSurfaceRepresentationName(), appender.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Create segment editor")
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
##################################
self.delayDisplay("Run segmentation")
segmentEditorWidget.setActiveEffectByName("ScriptedSegmentEditorEffectModuleTemplate")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("ObjectScaleMm", 3.0)
effect.self().onApply()
##################################
self.delayDisplay("Make segmentation results nicely visible in 3D")
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility("Air", False)
segmentationDisplayNode.SetSegmentOpacity3D("Background",0.5)
##################################
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)
# Export results to table (just to see all results)
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
self.delayDisplay("Check a few numerical results")
self.assertEqual( round(segStatLogic.statistics["Tumor","LM volume cc"]), 16)
self.assertEqual( round(segStatLogic.statistics["Background","LM volume cc"]), 3010)
self.delayDisplay('test_ScriptedSegmentEditorEffectModuleTemplate1 passed')
def test_SurfaceCut1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing sphere-shaped seeds
- Run segmentation
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorSurfaceCut)
"""
self.delayDisplay("Starting test_SurfaceCut1")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
import SampleData
from SegmentStatistics import SegmentStatisticsLogic
##################################
self.delayDisplay("Load master volume")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
##################################
self.delayDisplay("Create segmentation containing a few spheres")
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
# Segments are defined by a list of: name and a list of sphere [radius, posX, posY, posZ]
segmentGeometries = [['Tumor', [[10, -6, 30, 28]]],
[
'Background',
[[10, 0, 65, 22], [15, 1, -14, 30],
[12, 0, 28, -7], [5, 0, 30, 54],
[12, 31, 33, 27], [17, -42, 30, 27],
[6, -2, -17, 71]]
], ['Air', [[10, 76, 73, 0], [15, -70, 74, 0]]]]
for segmentGeometry in segmentGeometries:
segmentName = segmentGeometry[0]
appender = vtk.vtkAppendPolyData()
for sphere in segmentGeometry[1]:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
segmentName))
appender.Update()
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
appender.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Create segment editor")
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
##################################
self.delayDisplay("Run segmentation")
segmentEditorWidget.setActiveEffectByName("SurfaceCut")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("ObjectScaleMm", 3.0)
effect.self().onApply()
##################################
self.delayDisplay("Make segmentation results nicely visible in 3D")
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility("Air", False)
segmentationDisplayNode.SetSegmentOpacity3D("Background", 0.5)
##################################
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)
# Export results to table (just to see all results)
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
self.delayDisplay("Check a few numerical results")
self.assertEqual(
round(segStatLogic.statistics["Tumor", "LM volume cc"]), 16)
self.assertEqual(
round(segStatLogic.statistics["Background", "LM volume cc"]), 3010)
self.delayDisplay('test_SurfaceCut1 passed')
def run(self, inputVolume, outputSegmentation, smoothingKernelSize=3.0):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be segmented
:param outputSegmentation: segmentation to sore the result in
:param smoothingKernelSize: this is used for closing small holes in the segmentation
"""
if not inputVolume or not outputSegmentation:
raise ValueError("Input volume or output segmentation is invalid")
logging.info('Processing started')
# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(inputVolume.GetImageData())
thresholdCalculator.SetMethodToOtsu()
thresholdCalculator.Update()
boneThresholdValue = thresholdCalculator.GetThreshold()
volumeScalarRange = inputVolume.GetImageData().GetScalarRange()
logging.debug(
"Volume minimum = {0}, maximum = {1}, bone threshold = {2}".format(
volumeScalarRange[0], volumeScalarRange[1],
boneThresholdValue))
# Set up segmentation
outputSegmentation.CreateDefaultDisplayNodes()
outputSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
# 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)
if not segmentEditorWidget.effectByName("Wrap Solidify"):
raise NotImplementedError(
"SurfaceWrapSolidify extension is required")
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(outputSegmentation)
segmentEditorWidget.setMasterVolumeNode(inputVolume)
# Create bone segment by thresholding
boneSegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"bone")
segmentEditorNode.SetSelectedSegmentID(boneSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(boneThresholdValue))
effect.setParameter("MaximumThreshold", str(volumeScalarRange[1]))
effect.self().onApply()
# Smooth bone segment (just to reduce solidification computation time)
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING")
effect.setParameter("KernelSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Solidify bone
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
effect.self().onApply()
# Create segment for cavity within bone region using thresholding
segmentEditorNode.SetOverwriteMode(
slicer.vtkMRMLSegmentEditorNode.OverwriteNone)
segmentEditorNode.SetMaskMode(
slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideAllSegments)
cavitySegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"cavity")
segmentEditorNode.SetSelectedSegmentID(cavitySegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(volumeScalarRange[0]))
effect.setParameter("MaximumThreshold", str(boneThresholdValue))
effect.self().onApply()
# Cavity shrink
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", str(-smoothingKernelSize))
effect.self().onApply()
# Find largest cavity
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameterDefault("Operation", "KEEP_LARGEST_ISLAND")
effect.self().onApply()
# Cavity restore
segmentEditorNode.SetMaskMode(
slicer.vtkMRMLSegmentEditorNode.PaintAllowedInsideAllSegments
) # ensure we don't leak into bone
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Clean up
slicer.mrmlScene.RemoveNode(segmentEditorNode)
outputSegmentation.RemoveSegment(boneSegmentID)
segmentEditorWidget = None
logging.info('Processing completed')
def test_WrapSolidify1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing sphere-shaped seeds
- Run segmentation
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorWrapSolidify)
"""
self.delayDisplay("Starting test_WrapSolidify1")
import vtkSegmentationCorePython as vtkSegmentationCore
import vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic
import SampleData
from SegmentStatistics import SegmentStatisticsLogic
##################################
self.delayDisplay("Load master volume")
masterVolumeNode = SampleData.downloadSample('MRBrainTumor1')
##################################
self.delayDisplay("Create segmentation containing a two spheres")
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
features = ["none", "carveCavities", "createShell", "both"]
spheres = [[20, 5, 5, 5], [20, -5, -5, -5]]
appender = vtk.vtkAppendPolyData()
for sphere in spheres:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
for m in features:
segmentName = str(m)
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
segmentName))
appender.Update()
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
appender.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Create segment editor")
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
##################################
self.delayDisplay("Run WrapSolidify Effect")
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
for t in ["SEGMENTATION", "MODEL"]:
effect.setParameter("outputType", t)
self.delayDisplay(
"Creating Output Type %s, activated feature none" % (t))
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'none'))
effect.setParameter("carveCavities", False)
effect.setParameter("createShell", False)
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature carveCavities" %
(t))
effect.setParameter("carveCavities", True)
effect.setParameter("createShell", False)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'carveCavities'))
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature createShell" % (t))
effect.setParameter("carveCavities", False)
effect.setParameter("createShell", True)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'createShell'))
effect.self().onApply()
self.delayDisplay(
"Creating Output Type %s, activated feature both" % (t))
effect.setParameter("carveCavities", True)
effect.setParameter("createShell", True)
segmentEditorWidget.setCurrentSegmentID(
segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
'both'))
effect.self().onApply()
##################################
self.delayDisplay("Creating Segments from Models")
for m in features:
model = slicer.util.getNode(m)
segmentName = "MODEL_%s" % m
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
segmentName))
segment.SetColor(model.GetDisplayNode().GetColor())
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
model.GetPolyData())
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Compute statistics")
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.computeStatistics()
statistics = segStatLogic.getStatistics()
##################################
self.delayDisplay("Check a few numerical results")
# logging.info(round(statistics["none",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_none",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["carveCavities",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_carveCavities",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["createShell",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_createShell",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["both",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
# logging.info(round(statistics["MODEL_both",'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']))
self.assertEqual(
round(
statistics["none",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46605)
self.assertEqual(
round(
statistics["MODEL_none",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46320)
self.assertEqual(
round(
statistics["carveCavities",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46605)
self.assertEqual(
round(
statistics["MODEL_carveCavities",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
46321)
self.assertEqual(
round(
statistics["createShell",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9257)
self.assertEqual(
round(
statistics["MODEL_createShell",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9230)
self.assertEqual(
round(
statistics["both",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9254)
self.assertEqual(
round(
statistics["MODEL_both",
'ScalarVolumeSegmentStatisticsPlugin.volume_mm3']),
9245)
self.delayDisplay('test_WrapSolidify1 passed')
def test_SurfaceCut1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing fiducials around tumor
- Apply
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorSurfaceCut)
"""
self.delayDisplay("Starting test_SurfaceCut1")
##################################
self.delayDisplay("Load master volume")
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()
##################################
self.delayDisplay("Create tumor segmentation")
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
segmentName = "Tumor"
import vtkSegmentationCorePython as vtkSegmentationCore
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(segmentationNode.GetSegmentation().GenerateUniqueSegmentID(segmentName))
segmentationNode.GetSegmentation().AddSegment(segment)
##################################
self.delayDisplay("Create segment editor")
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
##################################
self.delayDisplay("Run segmentation")
segmentEditorWidget.setActiveEffectByName("Surface cut")
effect = segmentEditorWidget.activeEffect()
effect.self().fiducialPlacementToggle.placeButton().click()
points =[[2.589283578714074, 44.60536690073953, 27.299999999999997], [8.515228351086698, 35.22262101114956, 27.299999999999997],
[13.700430026912741, 25.099132025013006, 27.299999999999997], [5.799170330415919, 19.17318725264039, 27.299999999999997],
[2.589283578714074, 9.296612632019361, 27.299999999999997], [-10.250263428093263, 12.25958501820567, 27.299999999999997],
[-16.17620820046588, 18.185529790578286, 27.299999999999997], [-20.373752414229813, 27.568275680168263, 27.299999999999997],
[-15.929293834950343, 38.679422128366916, 27.299999999999997], [-11.484835255670887, 44.11153816970849, 27.299999999999997],
[6.539913426962492, 33.49422045254088, 31.499999999999993], [1.354711751136449, 42.383137611099805, 31.499999999999993],
[-8.768777235000101, 44.35845253522401, 31.499999999999993], [-14.200893276341674, 36.70410720424271, 31.499999999999993],
[-18.398437490105607, 27.07444694913721, 31.499999999999993], [-12.719407083248512, 16.704043597485132, 31.499999999999993],
[-7.534205407422476, 11.765756287174618, 31.499999999999993], [0.12013992355882408, 12.25958501820567, 31.499999999999993],
[5.799170330415919, 16.21021486645408, 31.499999999999993], [8.268313985571176, 21.642330907795646, 31.499999999999993],
[13.947344392428263, 26.827532583621682, 31.499999999999993], [-3.0897468281430065, 32.50656299047878, 45.49999999999998],
[2.589283578714074, 27.32136131465274, 45.49999999999998], [-5.3119761177827485, 21.642330907795646, 45.49999999999998],
[-8.02803413845352, 27.32136131465274, 45.49999999999998], [-14.694722007372718, 30.778162431870093, 38.499999999999986],
[-8.02803413845352, 12.01267065269014, 38.499999999999986], [-3.583575559174065, 39.66707959042902, 11.900000000000007],
[3.576941040776184, 31.765819893932196, 11.900000000000007], [0.12013992355882408, 20.901587811249065, 11.900000000000007],
[-9.26260596603116, 28.555933142230366, 11.900000000000007], [6.046084695931441, 38.432507762851394, 17.500000000000007],
[-17.163865662527982, 33.7411348180564, 17.500000000000007], [-14.200893276341674, 21.889245273311168, 17.500000000000007]]
for p in points:
effect.self().segmentMarkupNode.AddFiducialFromArray(p)
effect.self().onApply()
##################################
self.delayDisplay("Make segmentation results nicely visible in 3D")
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility(segmentName, True)
slicer.util.findChild(segmentEditorWidget, "Show3DButton").checked = True
segmentationDisplayNode.SetSegmentOpacity3D("Background",0.5)
##################################
self.delayDisplay("Compute statistics")
from SegmentStatistics import SegmentStatisticsLogic
segStatLogic = SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation", segmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume", masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter("visibleSegmentsOnly", "False")
segStatLogic.computeStatistics()
# Export results to table (just to see all results)
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
self.delayDisplay("Check a few numerical results")
stats = segStatLogic.getStatistics()
self.assertEqual( round(stats['Tumor', 'LabelmapSegmentStatisticsPlugin.volume_mm3']), 19498.0)
self.delayDisplay('test_SurfaceCut1 passed')
def test_TDIO1(self):
"""
Basic automated test of the segmentation method:
- Create segmentation by placing sphere-shaped seeds
- Run segmentation
- Verify results using segment statistics
The test can be executed from SelfTests module (test name: SegmentEditorTDIO)
"""
self.delayDisplay('Starting test_TDIO1')
import vtkSegmentationCorePython as vtkSegmentationCore, vtkSlicerSegmentationsModuleLogicPython as vtkSlicerSegmentationsModuleLogic, SampleData
from SegmentStatistics import SegmentStatisticsLogic
self.delayDisplay('Load master volume')
masterVolumeNode = SampleData.downloadSample('MRBrainTumor1')
self.delayDisplay('Create segmentation containing a few spheres')
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
segmentGeometries = [['Tumor', [[10, -6, 30, 28]]],
[
'Background',
[[10, 0, 65, 22], [15, 1, -14, 30],
[12, 0, 28, -7], [5, 0, 30, 54],
[12, 31, 33, 27], [17, -42, 30, 27],
[6, -2, -17, 71]]
], ['Air', [[10, 76, 73, 0], [15, -70, 74, 0]]]]
for segmentGeometry in segmentGeometries:
segmentName = segmentGeometry[0]
appender = vtk.vtkAppendPolyData()
for sphere in segmentGeometry[1]:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(sphere[0])
sphereSource.SetCenter(sphere[1], sphere[2], sphere[3])
appender.AddInputConnection(sphereSource.GetOutputPort())
segment = vtkSegmentationCore.vtkSegment()
segment.SetName(
segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
segmentName))
appender.Update()
segment.AddRepresentation(
vtkSegmentationCore.vtkSegmentationConverter.
GetSegmentationClosedSurfaceRepresentationName(),
appender.GetOutput())
segmentationNode.GetSegmentation().AddSegment(segment)
self.delayDisplay('Create segment editor')
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.show()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
self.delayDisplay('Run segmentation')
segmentEditorWidget.setActiveEffectByName('TDIO')
effect = segmentEditorWidget.activeEffect()
effect.setParameter('ObjectScaleMm', 3.0)
effect.self().onApply()
self.delayDisplay('Make segmentation results nicely visible in 3D')
segmentationDisplayNode = segmentationNode.GetDisplayNode()
segmentationDisplayNode.SetSegmentVisibility('Air', False)
segmentationDisplayNode.SetSegmentOpacity3D('Background', 0.5)
self.delayDisplay('Compute statistics')
segStatLogic = SegmentStatisticsLogic()
segStatLogic.computeStatistics(segmentationNode, masterVolumeNode)
resultsTableNode = slicer.vtkMRMLTableNode()
slicer.mrmlScene.AddNode(resultsTableNode)
segStatLogic.exportToTable(resultsTableNode)
segStatLogic.showTable(resultsTableNode)
self.delayDisplay('Check a few numerical results')
self.assertEqual(
round(segStatLogic.statistics[('Tumor', 'LM volume cc')]), 16)
self.assertEqual(
round(segStatLogic.statistics[('Background', 'LM volume cc')]),
3010)
self.delayDisplay('test_TDIO1 passed')
def run(self,
inputVolume,
outputSegmentation,
smoothingKernelSize=3.0,
splitCavitiesDiameter=15.0):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be segmented
:param outputSegmentation: segmentation to sore the result in
:param smoothingKernelSize: this is used for closing small holes in the segmentation
:param splitCavitiesDiameter: plugs in holes smaller than splitCavitiesDiamater.
"""
if not inputVolume or not outputSegmentation:
raise ValueError("Input volume or output segmentation is invalid")
logging.info('Processing started')
# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(inputVolume.GetImageData())
# thresholdCalculator.SetMethodToOtsu() - this does not always work (see for example CTHead example data set)
thresholdCalculator.SetMethodToMaximumEntropy()
thresholdCalculator.Update()
boneThresholdValue = thresholdCalculator.GetThreshold()
volumeScalarRange = inputVolume.GetImageData().GetScalarRange()
logging.debug(
f"Volume minimum = {volumeScalarRange[0]}, maximum = {volumeScalarRange[1]}, bone threshold = {boneThresholdValue}"
)
# Set up segmentation
outputSegmentation.CreateDefaultDisplayNodes()
outputSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
# 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)
if not segmentEditorWidget.effectByName("Wrap Solidify"):
raise NotImplementedError(
"SurfaceWrapSolidify extension is required")
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(outputSegmentation)
segmentEditorWidget.setMasterVolumeNode(inputVolume)
# Create bone segment by thresholding
boneSegmentID = outputSegmentation.GetSegmentation().AddEmptySegment(
"bone")
segmentEditorNode.SetSelectedSegmentID(boneSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(boneThresholdValue))
effect.setParameter("MaximumThreshold", str(volumeScalarRange[1]))
effect.self().onApply()
# Smooth bone segment (just to reduce solidification computation time)
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING")
effect.setParameter("KernelSizeMm", str(smoothingKernelSize))
effect.self().onApply()
# Solidify bone
segmentEditorWidget.setActiveEffectByName("Wrap Solidify")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("region", "largestCavity")
effect.setParameter("splitCavities",
"True" if splitCavitiesDiameter > 0 else "False")
effect.setParameter("splitCavitiesDiameter",
str(splitCavitiesDiameter)) # in mm
effect.setParameter("outputType", "newSegment") # in mm
effect.self().onApply()
# Clean up
#slicer.mrmlScene.RemoveNode(segmentEditorNode)
#outputSegmentation.RemoveSegment(boneSegmentID)
#segmentEditorWidget = None
logging.info('Processing completed')
2
) # small sphere for small features. Change depending on size of objects in your phantom
featSeed.Update()
appendFeat.AddInputData(featSeed.GetOutput())
appendFeat.Update()
# add feature segmentation seeds to the segmentationNode. Change the name or colour based on preference.
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
appendFeat.GetOutput(), "Feature", [0.0, 0.0, 1.0])
# segmentEditorWidget.show() # this is for debugging if you need to!
slicer.app.processEvents()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
# grow from seeds
segmentEditorWidget.setActiveEffectByName("Grow from seeds")
effect = segmentEditorWidget.activeEffect()
effect.self().onPreview()
# for troubleshooting / editing the seed growth, stop before the onApply() function
effect.self().onApply()
# grow the background further into the phantom volume segmentation
# i needed this as my images had a noisy edge to the phantom volume, so it picked up to much noise as phantom volume
