def startSegmentation(self):
if self.segmentationStarted:
# Already started
return
self.segmentationStarted = True
print("Start ." + str(self.detailedAirways) + ".")
import time
startTime = time.time()
# Clear previous segmentation
if self.outputSegmentation:
self.outputSegmentation.GetSegmentation().RemoveAllSegments()
if not self.rightLungFiducials:
self.rightLungFiducials = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", "R")
self.rightLungFiducials.CreateDefaultDisplayNodes()
self.rightLungFiducials.GetDisplayNode().SetSelectedColor(self.brighterColor(self.rightLungColor))
if not self.leftLungFiducials:
self.leftLungFiducials = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", "L")
self.leftLungFiducials.CreateDefaultDisplayNodes()
self.leftLungFiducials.GetDisplayNode().SetSelectedColor(self.brighterColor(self.leftLungColor))
if not self.tracheaFiducials:
self.tracheaFiducials = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode", "T")
self.tracheaFiducials.CreateDefaultDisplayNodes()
self.tracheaFiducials.GetDisplayNode().SetSelectedColor(self.brighterColor(self.tracheaColor))
if not self.resampledVolume:
self.resampledVolume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLScalarVolumeNode", "Resampled Volume")
# Create resampled volume with fixed 2.0mm spacing (for faster, standardized workflow)
self.showStatusMessage('Resampling volume, please wait...')
parameters = {"outputPixelSpacing": "2.0,2.0,2.0", "InputVolume": self.inputVolume, "interpolationType": "linear", "OutputVolume": self.resampledVolume}
cliParameterNode = slicer.cli.runSync(slicer.modules.resamplescalarvolume, None, parameters)
slicer.mrmlScene.RemoveNode(cliParameterNode)
if not self.outputSegmentation:
self.outputSegmentation = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode", "Lung segmentation")
self.outputSegmentation.CreateDefaultDisplayNodes()
# We show the current segmentation using markups, so let's hide the display node (seeds)
self.rightLungSegmentId = None
self.leftLungSegmentId = None
self.tracheaSegmentId = None
self.outputSegmentation.GetDisplayNode().SetVisibility(False)
self.outputSegmentation.SetReferenceImageGeometryParameterFromVolumeNode(self.resampledVolume)
# Create temporary segment editor to get access to effects
self.segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
self.segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
self.segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
self.segmentEditorWidget.setSegmentationNode(self.outputSegmentation)
if self.detailedAirways:
self.segmentEditorWidget.setMasterVolumeNode(self.inputVolume)
else:
self.segmentEditorWidget.setMasterVolumeNode(self.resampledVolume)
self.segmentEditorWidget.mrmlSegmentEditorNode().SetMasterVolumeIntensityMask(True)
self.segmentEditorWidget.mrmlSegmentEditorNode().SetMasterVolumeIntensityMaskRange(self.lungThresholdMin, self.lungThresholdMax)
stopTime = time.time()
logging.info('StartSegmentation completed in {0:.2f} seconds'.format(stopTime-startTime))
def __init__(self, parent=None):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.__init__(self, parent)
VTKObservationMixin.__init__(
self) # needed for parameter node observation
self.logic = None
self._parameterNode = None
# 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"):
if slicer.util.confirmOkCancelDisplay(
"SegmentEndocranium requires installation of the SurfaceWrapSolidify extension.\nClick OK to install and restart the application."
):
extensionName = 'SurfaceWrapSolidify'
em = slicer.app.extensionsManagerModel()
if not em.isExtensionInstalled(extensionName):
extensionMetaData = em.retrieveExtensionMetadataByName(
extensionName)
url = f"{em.serverUrl().toString()}/api/v1/item/{extensionMetaData['_id']}/download"
extensionPackageFilename = slicer.app.temporaryPath + '/' + extensionMetaData[
'_id']
slicer.util.downloadFile(url, extensionPackageFilename)
em.interactive = False # Disable popups (automatically install dependencies)
em.installExtension(extensionPackageFilename)
slicer.util.restart()
def seged(op, op_config, node, node_config, model, model_config):
"""Segment editor processing."""
sew = slicer.qMRMLSegmentEditorWidget()
sew.setMRMLScene(slicer.mrmlScene)
sen = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode")
sew.setMRMLSegmentEditorNode(sen)
segmentation = node.GetSegmentation()
sew.setSegmentationNode(node)
sew.setActiveEffectByName(op["action"])
if not op["targets"]:
op["targets"] = range(segmentation.GetNumberOfSegments())
if "master" in node_config:
mv = model_config["inputs"][node_config["master"]]["value"]
else:
mv = None
sew.setMasterVolumeNode(mv)
for n in op["targets"]:
logging.info("- Applying to segment %d" % n)
sew.setCurrentSegmentID(segmentation.GetNthSegmentID(n))
effect = sew.activeEffect()
if effect is None:
raise Exception("Unknown seged action: %s" % op["action"])
for p, v in op_config["params"].items():
effect.setParameter(p, str(v))
effect.self().onApply()
sew.setActiveEffectByName(None)
slicer.mrmlScene.RemoveNode(sen)
def buildSegment(self,
inputVolme,
masterSegment=None,
segmentationNode=None,
name='airway'):
if (segmentationNode == None):
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolme)
segmentID = segmentationNode.GetSegmentation().AddEmptySegment(name)
segmentationEditor = slicer.qMRMLSegmentEditorWidget()
segmentationEditor.setMRMLScene(slicer.mrmlScene)
segmentationEditor.setMRMLSegmentEditorNode(
slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentEditorNode'))
segmentationEditor.setSegmentationNode(segmentationNode)
#//segmentationEditor.ad & test &
# ? What was this line supposed to be? I can't remember but it doesn't seem to be causing problems for now
segmentationEditor.setMasterVolumeNode(inputVolme)
#import qSlicerSegmentationEditorEffectsPythonQt as effects
segmentationEditor.setActiveEffectByName('Threshold')
effect = segmentationEditor.activeEffect()
effect.setParameter('MinimumThreshold', '-1024')
effect.setParameter('MaximumThreshold', AIR_DENSITY_THRESHOLD)
effect.self().onApply()
# FIXME: part of the fix for handling out of bounds air - currently broken
#if masterSegment is not None:
#segmentationEditor.setActiveEffectByName('Logical operators')
#effect = segmentationEditor.activeEffect()
#effect.setParameter('ModifierSegmentID', masterSegment.GetName())
#effect.setParameter('Operation', 'INTERSECT')
#effect.self().onApply()
segmentationEditor.setActiveEffectByName('Islands')
effect = segmentationEditor.activeEffect()
effect.setParameter('KeepLargestIsland', True)
effect.self().onApply()
segmentationNode.CreateClosedSurfaceRepresentation()
surfaceMesh = segmentationNode.GetClosedSurfaceRepresentation(
segmentID)
normals = vtk.vtkPolyDataNormals()
normals.ConsistencyOn()
normals.SetInputData(surfaceMesh)
normals.Update()
surfaceMesh = normals.GetOutput()
return segmentationNode
def setup(self):
"""
Called when the user opens the module the first time and the widget is initialized.
"""
ScriptedLoadableModuleWidget.setup(self)
# Load widget from .ui file (created by Qt Designer)
uiWidget = slicer.util.loadUI(self.resourcePath('UI/BreastCalc.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Set scene in MRML widgets. Make sure that in Qt designer
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
uiWidget.setMRMLScene(slicer.mrmlScene)
# Example of adding widgets dynamically (without Qt designer).
# This approach is not recommended, but only shown as an illustrative example.
self.invertedOutputSelector = slicer.qMRMLNodeComboBox()
self.invertedOutputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.invertedOutputSelector.addEnabled = True
self.invertedOutputSelector.removeEnabled = True
self.invertedOutputSelector.noneEnabled = True
self.invertedOutputSelector.setMRMLScene(slicer.mrmlScene)
self.invertedOutputSelector.setToolTip(
"Result with inverted threshold will be written into this volume")
# Create a new parameterNode
# This parameterNode stores all user choices in parameter values, node selections, etc.
# so that when the scene is saved and reloaded, these settings are restored.
self.logic = BreastCalcLogic()
# Connections
#self.ui.applyButton.connect('clicked(bool)', self.onApplyButton)
self.ui.confirmButton.connect('clicked(bool)', self.onConfirmButton)
self.ui.imageThresholdSliderWidget.connect('valueChanged(double)',
self.onThresholdSlider)
self.segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
self.segmentationNode.CreateDefaultDisplayNodes(
) # only needed for display
# Create temporary segment editor to get access to effects
self.segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
self.segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
self.segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
self.segmentEditorWidget.setMRMLSegmentEditorNode(
self.segmentEditorNode)
self.segmentEditorWidget.setSegmentationNode(self.segmentationNode)
self.mode = 0
def __init__(self):
StepBasedSession.__init__(self)
self.seriesTypeManager = SeriesTypeManager()
self.seriesTypeManager.addEventObserver(
self.seriesTypeManager.SeriesTypeManuallyAssignedEvent,
lambda caller, event: self.invokeEvent(
self.SeriesTypeManuallyAssignedEvent))
self.targetingPlugin = TargetsDefinitionPlugin(self)
self.needlePathCaculator = ZFrameGuidanceComputation(self)
self.segmentationEditor = slicer.qMRMLSegmentEditorWidget()
self.resetAndInitializeMembers()
self.resetAndInitializedTargetsAndSegments()
def test_Autoscroll(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: SegmentEditorAutoscroll)
"""
self.delayDisplay("Starting test_Autoscroll")
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 with an empty segment")
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)
segment = vtkSegmentationCore.vtkSegment()
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 autoscroll for 10 seconds")
segmentEditorWidget.setActiveEffectByName("Autoscroll")
effect = segmentEditorWidget.activeEffect()
qt.QTimer.singleShot(10000, effect.self().onApply)
effect.self().onApply()
self.delayDisplay('test_Autoscroll passed')
def TestSection_04_qMRMLSegmentatEditorWidget(self):
logging.info('Test section 4: qMRMLSegmentatEditorWidget')
self.segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentEditorNode')
self.assertIsNotNone(self.segmentEditorNode)
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLSegmentEditorNode(self.segmentEditorNode)
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorWidget.setSegmentationNode(self.inputSegmentationNode)
segmentEditorWidget.installKeyboardShortcuts(segmentEditorWidget)
segmentEditorWidget.setFocus(qt.Qt.OtherFocusReason)
segmentEditorWidget.show()
self.segmentEditorNode.SetSelectedSegmentID('first')
segmentEditorWidget.selectNextSegment()
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'second')
segmentEditorWidget.selectPreviousSegment()
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'first')
displayNode.SetSegmentVisibility('second', False)
segmentEditorWidget.selectNextSegment()
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'third')
# Trying to go out of bounds past first segment
segmentEditorWidget.selectPreviousSegment() #First
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'first')
segmentEditorWidget.selectPreviousSegment() #First
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'first')
segmentEditorWidget.selectPreviousSegment() #First
selectedSegmentID = self.segmentEditorNode.GetSelectedSegmentID()
self.assertEqual(selectedSegmentID, 'first')
# Wrap around
self.segmentEditorNode.SetSelectedSegmentID('third')
segmentEditorWidget.selectNextSegment()
self.assertEqual(selectedSegmentID, 'first')
def _setupSegmentEditorWidget(self):
self._segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
self._segmentEditorWidget.hide()
self._segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorSingletonTag = "SegmentEditor"
self.segmentEditorNode = slicer.mrmlScene.GetSingletonNode(segmentEditorSingletonTag, "vtkMRMLSegmentEditorNode")
if not self.segmentEditorNode:
self.segmentEditorNode = slicer.vtkMRMLSegmentEditorNode()
self.segmentEditorNode.SetSingletonTag(segmentEditorSingletonTag)
self.segmentEditorNode = slicer.mrmlScene.AddNode(self.segmentEditorNode)
self._segmentEditorWidget.setMRMLSegmentEditorNode(self.segmentEditorNode)
self.segmentEditorWidget.setSegmentationNode(self.segmentationNode)
self.logic.scriptedEffect = self._segmentEditorWidget.effectByName('Surface cut')
self.layout.addWidget(self._segmentEditorWidget, 1, 0)
def setupSegmentEditor(self):
self.segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
self.segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
self.segmentEditorWidget.visible = False
self.segmentEditorWidget.setSegmentationNodeSelectorVisible(False)
self.segmentEditorWidget.setMasterVolumeNodeSelectorVisible(False)
self.segmentEditorWidget.setSwitchToSegmentationsButtonVisible(False)
self.segmentEditorWidget.findChild(qt.QPushButton,
"AddSegmentButton").hide()
self.segmentEditorWidget.findChild(qt.QPushButton,
"RemoveSegmentButton").hide()
self.segmentEditorWidget.findChild(ctk.ctkMenuButton,
"Show3DButton").hide()
self.segmentEditorWidget.findChild(
ctk.ctkExpandableWidget, "SegmentsTableResizableFrame").hide()
self.segmentEditorWidget.setSizePolicy(qt.QSizePolicy.Maximum,
qt.QSizePolicy.Expanding)
def test_Engrave1(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: SegmentEditorEngrave)
"""
self.delayDisplay("Starting test_Engrave1")
##################################
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("ENgrave")
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.AddControlPoint(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_Engrave1 passed')
def run(self, inputVolume, Index):
logging.info('Processing started')
DosiFilmImage = inputVolume
logging.info(DosiFilmImage)
date = datetime.datetime.now()
savepath = u"//s-grp/grp/RADIOPHY/Personnel/Aurélien Corroyer-Dulmont/3dSlicer/Field_Center_vs_Jaw_setting_TOMOTHERAPY_QC_Results/Results_" + str(
date.day) + str(date.month) + str(date.year) + ".txt"
logging.info(savepath)
logging.info(Index)
#### To get background intensity for the thershold value of the bloc
# Create segmentation
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
DosiFilmImage)
# Create segment
backgroundSeed = vtk.vtkSphereSource()
backgroundSeed.SetCenter(-40, -30, 0)
backgroundSeed.SetRadius(5)
backgroundSeed.Update()
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
backgroundSeed.GetOutput(), "Segment A", [1.0, 0.0, 0.0])
mergedLabelmapNode = slicer.vtkMRMLLabelMapVolumeNode()
slicer.mrmlScene.AddNode(mergedLabelmapNode)
sa = vtk.vtkStringArray()
sa.InsertNextValue("Segment A")
slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(
segmentationNode, sa, mergedLabelmapNode, DosiFilmImage)
label = su.PullVolumeFromSlicer("LabelMapVolume")
image = su.PullVolumeFromSlicer(DosiFilmImage)
stat_filter_backgroundSeed = sitk.LabelIntensityStatisticsImageFilter()
stat_filter_backgroundSeed.Execute(label, image) #attention à l'ordre
meanBackground = stat_filter_backgroundSeed.GetMean(1)
print(meanBackground)
# Stockage du nom de la machine en utilisant le choix de l'utilisateur dans la class Widget
if Index == 0:
machineName = 'Tomotherapy 1'
else:
machineName = 'Tomotherapy 2'
# Création de la segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
DosiFilmImage)
logging.info(segmentationNode)
# Création des segments editors temporaires
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(DosiFilmImage)
# Création d'un segment après seuillage
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment(
"IrradiatedBlocks")
segmentEditorNode.SetSelectedSegmentID(addedSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
#effect.setParameter("MinimumThreshold",str(22000))
#effect.setParameter("MaximumThreshold",str(55000))
effect.setParameter("MinimumThreshold", str(meanBackground / 5))
effect.setParameter("MaximumThreshold", str(meanBackground / 1.2))
effect.self().onApply()
# Passage en mode closed surface pour calcul des centres
n = slicer.util.getNode('Segmentation_1')
s = n.GetSegmentation()
ss = s.GetSegment('IrradiatedBlocks')
ss.AddRepresentation('Closed surface', vtk.vtkPolyData())
# Division du segment en plusieurs segments (un par bloc d'irradiation)
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", str("SPLIT_ISLANDS_TO_SEGMENTS"))
effect.setParameter("MinimumSize", 1000)
effect.self().onApply()
######### Initialisation des variables fixes d'intérêt###########
Segmentation_Name = 'Segmentation_1'
Segment_Name = [
"IrradiatedBlocks", "IrradiatedBlocks -_1", "IrradiatedBlocks -_2",
"IrradiatedBlocks -_3", "IrradiatedBlocks -_4",
"IrradiatedBlocks -_5", "IrradiatedBlocks -_6"
]
ListYaxisCenterOfBlock = [
0, 0, 0, 0, 0, 0, 0
] # initialisation de la liste contenant les valeurs Y centrales des blocs
# Boucle de calcul des centres pour les 7 blocs (segment)
i = 0
while i < len(Segment_Name):
n = slicer.util.getNode(Segmentation_Name)
s = n.GetSegmentation()
ss = s.GetSegment(Segment_Name[i])
pd = ss.GetRepresentation('Closed surface')
com = vtk.vtkCenterOfMass()
com.SetInputData(pd)
com.Update()
com.GetCenter() # A voir mais je pense que cette ligne est inutile
CenterOfBlock = com.GetCenter(
) # CenterOfBlock est alors un tuple avec plusieurs variables (coordonées x,y,z)
YaxisCenterOfBlock = (
CenterOfBlock[1]
) # Sélection de la 2ème valeur du tuple (indice 1) qui est la valeur dans l'axe Y qui est l'unique valeure d'intérêt
YaxisCenterOfBlock = abs(
YaxisCenterOfBlock) # On passe en valeur absolue
ListYaxisCenterOfBlock[i] = YaxisCenterOfBlock
i += 1
logging.info(ListYaxisCenterOfBlock)
######### Calcul de la différence en Y entre les centres des différents blocs###########
MaxYaxisCenter = max(ListYaxisCenterOfBlock)
MinYaxisCenter = min(ListYaxisCenterOfBlock)
DifferenceMaxInPixelYCenters = MaxYaxisCenter - MinYaxisCenter
DifferenceMaxInMmYCenters = float(DifferenceMaxInPixelYCenters)
DifferenceMaxInMmYCenters = DifferenceMaxInMmYCenters * 0.3528 # Pas élégant mais si je ne fais pas ça, il initialise DifferenceMaxInMmYCenters en tuple et pas en variable...
### Enonciation des résultats ###
logging.info("Coordonnee Max en Y : " + str(MaxYaxisCenter))
logging.info("Coordonnee Min en Y : " + str(MinYaxisCenter))
logging.info("Difference maximale entre les blocs (en pixel) : " +
str(DifferenceMaxInPixelYCenters))
logging.info("Difference maximale entre les blocs (en mm) : " +
str(DifferenceMaxInMmYCenters))
######### Création et remplissage fichier text pour stocker les résultats###########
file = open(savepath, 'w')
### encodage du fichier pour écriture incluant les "é" ###
file = codecs.open(savepath, encoding='utf-8')
txt = file.read()
file = codecs.open(savepath, "w", encoding='mbcs')
date = datetime.datetime.now()
file.write(u"Résultats test -Field Center vs Jaw setting-")
file.write("\n\n")
file.write("Machine : " + str(machineName))
file.write("\n\n")
file.write("Date : " + str(date.day) + "/" + str(date.month) + "/" +
str(date.year))
file.write("\n\n")
file.write("\n\n")
i = 0
for i in range(
len(ListYaxisCenterOfBlock)
): # Boucle pour obtenir les coordonées Y des centres des 7 blocs
file.write(u"Coordonnée Y du centre du bloc n°" + str(i + 1) +
": ")
file.write(str(ListYaxisCenterOfBlock[i]))
file.write("\n\n")
file.write("\n\n")
file.write(u"Coordonnée Max en Y : " + str(MaxYaxisCenter))
file.write("\n\n")
file.write(u"Coordonnée Min en Y : " + str(MinYaxisCenter))
file.write("\n\n")
file.write(u"Différence maximale entre les blocs (en pixel) : " +
str(DifferenceMaxInPixelYCenters))
file.write("\n\n")
file.write(u"Différence maximale entre les blocs (en mm) : " +
str(DifferenceMaxInMmYCenters))
######### Calcul de la conformité et mention dans le fichier résultats###########
if 0 <= DifferenceMaxInMmYCenters < 0.5:
Result = "Conforme"
elif DifferenceMaxInMmYCenters > 0.5:
Result = "Hors tolerance"
else:
Result = "Limite" #car si pas < ou > à 0.5 alors = à 0.5
if DifferenceMaxInMmYCenters < 0:
logging.info(
u"Valeur de la différence négative, problème dans l'image ou dans le programme, contactez Aurélien Corroyer-Dulmont tel : 5768"
)
logging.info(Result)
file.write("\n\n")
file.write("\n\n")
file.write(u"Résultat : " + str(Result))
file.close()
logging.info('Processing completed')
logging.info('\n\nResults are in the following file : ' + savepath)
return True
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 setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Add margin to the sides
self.layout.setContentsMargins(8, 0, 8, 0)
#
# Pre-Setup
#
self.previewImageNodesCollapsibleButton = ctk.ctkCollapsibleButton()
self.previewImageNodesCollapsibleButton.text = "Image Nodes"
self.layout.addWidget(self.previewImageNodesCollapsibleButton)
self.previewImageNodesCollapsibleButton.collapsed = False #True
presetPS = qt.QFormLayout(self.previewImageNodesCollapsibleButton)
self.grayscaleSelectorFrame = qt.QFrame(self.parent)
self.grayscaleSelectorFrame.setLayout(
qt.QHBoxLayout()) #qt.QHBoxLayout()
self.parent.layout().addWidget(self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel = qt.QLabel("Gray Image: ",
self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel.setToolTip(
"Select the grayscale volume (background grayscale scalar volume node) for statistics calculations"
)
self.grayscaleSelectorFrame.layout().addWidget(
self.grayscaleSelectorLabel)
self.grayscaleSelector = slicer.qMRMLNodeComboBox(
) # self.grayscaleSelectorFrame)
self.grayscaleSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.grayscaleSelector.selectNodeUponCreation = False
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = True
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene(slicer.mrmlScene)
self.grayscaleSelector.setToolTip(
'Setting to pick up as slicer.mrmlScene')
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.grayscaleSelectorFrame.layout().addWidget(self.grayscaleSelector)
presetPS.addRow(self.grayscaleSelectorFrame)
# hide this part, no use . .... aiden 2019.08.13
#...........................................................................................................................
self.labelSelectorFrame = qt.QFrame(
self.parent
) # original code: no-definition of parent self.labelSelectorFrame = qt.QFrame()
self.labelSelectorFrame.setLayout(qt.QHBoxLayout())
#self.labelSelectorFrame.setToolTip('Where am I? self.labelSelectorFrame')
self.parent.layout().addWidget(self.labelSelectorFrame)
self.labelSelectorLabel = qt.QLabel()
self.labelSelectorLabel.setText("Label Map: ")
self.labelSelectorFrame.layout().addWidget(self.labelSelectorLabel)
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.removeEnabled = False
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = True
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to edit")
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
self.labelSelectorFrame.layout().addWidget(self.labelSelector)
# Load label into segmentation
self.applyLabelMapToSegmentationButton = qt.QPushButton(
'Labels to Segments')
self.applyLabelMapToSegmentationButton.setToolTip(
'Pick up a label-map and convert to segments')
self.applyLabelMapToSegmentationButton.connect(
'clicked(bool)', self.onApplyLabels2Segments)
self.labelSelectorFrame.layout().addWidget(
self.applyLabelMapToSegmentationButton)
#...........................................................................................................................
presetPS.addRow(self.labelSelectorFrame)
#
#BeFixed CheckBox
# under development.............The goal is try to get customized settings to fix some segments during segment-editing
#
self.setBeFixedCheckBox = ctk.ctkCollapsibleButton()
self.setBeFixedCheckBox.text = 'Set up Fixed Segments'
self.setBeFixedCheckBox.collapsed = False
self.layout.addWidget(self.setBeFixedCheckBox)
beFixedFormLayout = qt.QFormLayout(self.setBeFixedCheckBox)
self.setBeFixedCheckBox = []
qt_form1 = qt.QFrame(self.parent)
qt_form1_layout = qt.QHBoxLayout()
qt_form1.setLayout(qt_form1_layout)
for i_chbx in range(10):
tmp_s = str(i_chbx)
#print(tmp_s)
CheckBox = qt.QCheckBox(tmp_s)
CheckBox.checked = False
CheckBox.setToolTip('Segment # ' + str(i_chbx))
#CheckBox.setFixedWidth(25)
CheckBox.connect('clicked(bool)', self.onCheckBoxBeFixedUpdated)
self.setBeFixedCheckBox.append(CheckBox)
qt_form1.layout().addWidget(CheckBox)
beFixedFormLayout.addRow(qt_form1)
qt_form2 = qt.QFrame()
qt_form2_layout = qt.QHBoxLayout()
qt_form2.setLayout(qt_form2_layout)
for i_chbx in range(10, 20, 1):
tmp_s = str(i_chbx)
#print(tmp_s)
CheckBox = qt.QCheckBox(tmp_s)
CheckBox.checked = False
CheckBox.setToolTip('Segment # ' + str(i_chbx))
#CheckBox.setFixedWidth(25)
CheckBox.connect('clicked(bool)', self.onCheckBoxBeFixedUpdated)
self.setBeFixedCheckBox.append(CheckBox)
qt_form2.layout().addWidget(CheckBox)
beFixedFormLayout.addRow(qt_form2)
# set them up to be disabled and hiden
for i in range(20):
self.setBeFixedCheckBox[i].enabled = False
self.setBeFixedCheckBox[i].hide()
#
# Above still under development
#print('&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&')
#
#
# Segment editor widget
#
#
#import qSlicerSegmentationsModuleWidgetsPythonQt
#self.editor = qSlicerSegmentationsModuleWidgetsPythonQt.qMRMLSegmentEditorWidget()
self.editor = slicer.qMRMLSegmentEditorWidget()
#slicer.util.delayDisplay('edited: self.editor = qSlicerSegmentationsModuleWidgetsPythonQt.qMRMLSegmentEditorWidget() ')
#self.editor.switchToSegmentationsButtonVisible =True
#print(get_class_members(self.editor))
#print(get_object_attrs(self.editor))
self.editor.setMaximumNumberOfUndoStates(15)
# Set parameter node first so that the automatic selections made when the scene is set are saved
self.selectParameterNode()
self.editor.setMRMLScene(slicer.mrmlScene)
self.layout.addWidget(
self.editor) # adding the Widgets here to the layout
# Observe editor effect registrations to make sure that any effects that are registered
# later will show up in the segment editor widget. For example, if Segment Editor is set
# as startup module, additional effects are registered after the segment editor widget is created.
#Events of onSegmentAddedRemoved???
#self.addObserver(self.editor, self.editor.InvokeCustomModifiedEvent, self.editorAddOrRemoveSegments)
#Modified by Aiden
#import qSlicerSegmentationsEditorEffectsPythonQt
#TODO: For some reason the instance() function cannot be called as a class function although it's static
#factory = qSlicerSegmentationsEditorEffectsPythonQt.qSlicerSegmentEditorEffectFactory()
#qSlicerSegmentEditorEffectFactory--> Singleton class managing segment editor effect plugins.
factory = slicer.qSlicerSegmentEditorEffectFactory()
#slicer.util.delayDisplay('factory = qSlicerSegmentationsEditorEffectsPythonQt.qSlicerSegmentEditorEffectFactory()')
self.effectFactorySingleton = factory.instance()
self.effectFactorySingleton.connect('effectRegistered(QString)',
self.editorEffectRegistered)
# Connect observers to scene events
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent,
self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent,
self.onSceneEndClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndImportEvent,
self.onSceneEndImport)
# It seems it will work until a 3D-view exists
layoutManager = slicer.app.layoutManager()
if layoutManager:
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
def run(self,
inputVolume,
imageThreshold_min,
imageThreshold_max,
minimumVoxelsize,
tls_per_min,
enableScreenshots=0):
"""
Run the actual algorithm
"""
if not self.isValidInputData(inputVolume):
slicer.util.errorDisplay('Input volume error.')
return False
logging.info('Processing started')
masterVolumeNode = inputVolume
# Create segmentation
SegmentationNodeCol = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLSegmentationNode")
SegmentationNodeCol.UnRegister(slicer.mrmlScene)
b = True
for SegmentationNode in SegmentationNodeCol:
if SegmentationNode.GetName() == "rc_seg":
SegmentationNode.GetSegmentation().RemoveAllSegments()
SegmentationNode.GetDisplayNode(
).ClearSegmentDisplayProperties()
print("segmantation rc_seg cleared ")
b = False
break
if b:
SegmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
SegmentationNode.UnRegister(slicer.mrmlScene)
SegmentationNode.SetName("rc_seg")
print("segmantation created : ", SegmentationNode.GetName())
SegmentationNode.CreateDefaultDisplayNodes(
) # only needed for display
SegmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
addedSegmentID = SegmentationNode.GetSegmentation().AddEmptySegment(
SegmentationNode.GetName() + "_")
# Create temporary segment editor to get access to effects
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorNode.SetSelectedSegmentID(addedSegmentID)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(SegmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
# Fill by thresholding
effect.setParameter("MinimumThreshold", str(imageThreshold_min))
effect.setParameter("MaximumThreshold", str(imageThreshold_max))
effect.self().onApply()
# Fill by thresholding
if minimumVoxelsize is not None:
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", "SPLIT_ISLANDS_TO_SEGMENTS")
effect.setParameter("MinimumSize", minimumVoxelsize)
effect.self().onApply()
# Compute segment volumes
resultsTableNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLTableNode')
resultsTableNode.UnRegister(slicer.mrmlScene)
import SegmentStatistics
segStatLogic = SegmentStatistics.SegmentStatisticsLogic()
segStatLogic.getParameterNode().SetParameter("Segmentation",
SegmentationNode.GetID())
segStatLogic.getParameterNode().SetParameter("ScalarVolume",
masterVolumeNode.GetID())
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.surface_mm2.enabled",
"False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.volume_cm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ClosedSurfaceSegmentStatisticsPlugin.volume_mm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.volume_cm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.volume_mm3.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"LabelmapSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.max.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.mean.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.median.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.min.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.stdev.enabled", "False")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.volume_mm3.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.volume_cm3.enabled", "True")
segStatLogic.getParameterNode().SetParameter(
"ScalarVolumeSegmentStatisticsPlugin.voxel_count.enabled", "False")
segStatLogic.computeStatistics()
segStatLogic.exportToTable(resultsTableNode)
col = resultsTableNode.AddColumn()
col.SetName("Time of lithotripsy [min:sec:1/100s]")
id_colone_vmm3 = resultsTableNode.GetColumnIndex("Volume [mm3]")
id_colone_Tl = resultsTableNode.GetColumnIndex(
"Time of lithotripsy [min:sec:1/100s]")
import math
for i in range(resultsTableNode.GetNumberOfRows()):
vol_i = float(resultsTableNode.GetCellText(i, id_colone_vmm3))
tl_i = math.modf(vol_i / tls_per_min)
tl_i_min = int(tl_i[1])
tli_1 = math.modf(60. * tl_i[0])
tli_sec = int(tli_1[1])
tli_cent = 100 * tli_1[0]
resultsTableNode.SetCellText(
i, id_colone_Tl,
"{:d}:{:d}:{:.0f}".format(tl_i_min, tli_sec, tli_cent))
segStatLogic.showTable(resultsTableNode)
logging.info('Processing completed !')
return True
def test_SegmentEditorHollow1(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: SegmentEditorHollow)
"""
self.delayDisplay("Starting test_SegmentEditorHollow1")
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("Hollow")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("ShellThicknessMm", 3.0)
effect.setParameter("ShellMode", "MEDIAL_SURFACE")
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('test_SegmentEditorHollow1 passed')
def process_segmentation(threshold_range, image, update_status):
print(threshold_range)
# Fix Volume Orientation
update_status(text="Rotating views to volume plane...", progress=2)
manager = slicer.app.layoutManager()
for name in manager.sliceViewNames():
widget = manager.sliceWidget(name)
node = widget.mrmlSliceNode()
node.RotateToVolumePlane(image)
# Create segmentation
update_status(text="Creating segmentation...", progress=5)
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
image)
segmentId = segmentationNode.GetSegmentation().AddEmptySegment("Bone")
segmentationNode.GetSegmentation().GetSegment(segmentId).SetColor(
[0.9, 0.8, 0.7])
# Create segment editor to get access to effects
update_status(text="Starting segmentation editor...", progress=6)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(image)
# Threshold
update_status(text="Processing threshold segmentation...", progress=8)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold",
str(threshold_range[0])) # 1460 #1160 # 223
effect.setParameter("MaximumThreshold", str(threshold_range[1]))
effect.self().onApply()
# Smoothing
update_status(text="Processing smoothing segmentation...", progress=10)
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_OPENING")
effect.setParameter("KernelSizeMm", 0.5)
effect.self().onApply()
# Islands
update_status(text="Processing island segmentation...", progress=11)
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", "KEEP_LARGEST_ISLAND")
effect.setParameter("MinimumSize", 1000)
effect.self().onApply()
# Crop
# update_status("Cropping segmentation...")
# segmentEditorWidget.setActiveEffectByName("Scissors")
# effect = segmentEditorWidget.activeEffect()
# effect.setParameter("MinimumThreshold", "223")
# effect.setParameter("MaximumThreshold", "3071")
# effect.self().onApply()
# Clean up
update_status(text="Cleaning up...", progress=13)
segmentEditorWidget.setActiveEffectByName(None)
slicer.mrmlScene.RemoveNode(segmentEditorNode)
# Make segmentation results visible in 3D and set focal
update_status(text="Rendering...", progress=15)
segmentationNode.CreateClosedSurfaceRepresentation()
# Make sure surface mesh cells are consistently oriented
update_status(text="Retrieving surface mesh...", progress=18)
polyData = segmentationNode.GetClosedSurfaceRepresentation(segmentId)
return polyData
def ProceduralSegmentation(self, inputDir, outputDir):
# Importing Dicom into temporary database
dicomDataDir = inputDir
from DICOMLib import DICOMUtils
loadedNodeIDs = []
with DICOMUtils.TemporaryDICOMDatabase() as db:
DICOMUtils.importDicom(dicomDataDir, db)
patientUIDs = db.patients()
for patientUID in patientUIDs:
loadedNodeIDs.extend(DICOMUtils.loadPatientByUID(patientUID))
# Loading Dicom into scene
seriesVolumeNode = slicer.util.getNode(loadedNodeIDs[0])
storageVolumeNode = seriesVolumeNode.CreateDefaultStorageNode()
slicer.mrmlScene.AddNode(storageVolumeNode)
storageVolumeNode.UnRegister(slicer.mrmlScene)
seriesVolumeNode.SetAndObserveStorageNodeID(storageVolumeNode.GetID())
# Access segmentation module
slicer.util.selectModule('Segment Editor')
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
seriesVolumeNode)
# TODO Automate creation of different segments in the future (using some form of -type argument)
# Create spine segment
segmentTypeID = "Spine"
newSegment = slicer.vtkSegment()
newSegment.SetName(segmentTypeID)
newSegment.SetColor([0.89, 0.85, 0.78])
segmentationNode.GetSegmentation().AddSegment(newSegment,
segmentTypeID)
# Create segment editor widget to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
# Access segment editor node
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
slicer.mrmlScene.AddNode(segmentEditorNode)
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(seriesVolumeNode)
# Segment Editor Effect: Thresholding
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", "90")
effect.setParameter("MaximumThreshold", "1600")
effect.self().onApply()
# Setting Closed Surface Representation Values
segmentationNode.GetSegmentation().SetConversionParameter(
"Oversampling factor", "1.0")
segmentationNode.GetSegmentation().SetConversionParameter(
"Joint smoothing", "0.50")
segmentationNode.GetSegmentation().SetConversionParameter(
"Smoothing factor", "0.50")
# Segment Editor Effect: Smoothing
segmentEditorWidget.setActiveEffectByName("Smoothing")
effect = segmentEditorWidget.activeEffect()
# 2mm MEDIAN Smoothing
effect.setParameter("SmoothingMethod", "MEDIAN")
effect.setParameter("KernelSizeMm", 2.5)
effect.self().onApply()
# 2mm OPEN Smoothing
#effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_OPENING")
#effect.setParameter("KernelSizeMm", 2)
#effect.self().onApply
# 1.5mm CLOSED Smoothing
#effect.setParameter("SmoothingMethod", "MORPHOLOGICAL_CLOSING")
#effect.setParameter("KernelSizeMm", 1.5)
#effect.self().onApply
# Create Closed Surface Representation
segmentationNode.CreateClosedSurfaceRepresentation()
# Export Segmentation to Model Node
shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
exportFolderItemId = shNode.CreateFolderItem(shNode.GetSceneItemID(),
"Segments")
slicer.modules.segmentations.logic().ExportAllSegmentsToModels(
segmentationNode, exportFolderItemId)
segmentID = segmentationNode.GetSegmentation().GetNthSegmentID(0)
surfaceMesh = segmentationNode.GetClosedSurfaceInternalRepresentation(
segmentID)
# Decimate Model
decimator = vtk.vtkDecimatePro()
decimator.SplittingOff()
decimator.PreserveTopologyOn()
decimator.SetTargetReduction(0.95)
decimator.SetInputData(surfaceMesh)
decimator.Update()
surfaceMesh = decimator.GetOutput()
# Smooth the Model
smoothingFactor = 0.5
smoother = vtk.vtkWindowedSincPolyDataFilter()
smoother.SetInputData(surfaceMesh)
smoother.SetNumberOfIterations(50)
smoother.SetPassBand(pow(10.0, -4.0 * smoothingFactor))
smoother.BoundarySmoothingOff()
smoother.FeatureEdgeSmoothingOff()
smoother.NonManifoldSmoothingOn()
smoother.NormalizeCoordinatesOn()
smoother.Update()
surfaceMesh = smoother.GetOutput()
# Clean up Model
cleaner = vtk.vtkCleanPolyData()
#cleaner.PointMergingOff()
#cleaner.ConvertLinesToPointsOn()
#cleaner.ConvertPolysToLinesOn()
#cleaner.ConvertStripsToPolysOn()
cleaner.SetInputData(surfaceMesh)
cleaner.Update()
surfaceMesh = cleaner.GetOutput()
# Write to OBJ File
outputFileName = outputDir + "segmentation.obj"
writer = vtk.vtkOBJWriter()
writer.SetFileName(outputFileName)
writer.SetInputData(surfaceMesh)
writer.Update()
# Clean up
segmentEditorWidget = None
slicer.mrmlScene.RemoveNode(segmentEditorNode)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
parametersCollapsibleButton.setFont(qt.QFont("Times", 12))
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# ROI selector
#
self.ROISelector = slicer.qMRMLNodeComboBox()
self.ROISelector.nodeTypes = ["vtkMRMLAnnotationROINode"]
self.ROISelector.selectNodeUponCreation = True
self.ROISelector.addEnabled = False
self.ROISelector.removeEnabled = True
self.ROISelector.noneEnabled = True
self.ROISelector.showHidden = False
self.ROISelector.showChildNodeTypes = False
self.ROISelector.setMRMLScene(slicer.mrmlScene)
self.ROISelector.setToolTip("Pick the ROI to the algorithm.")
parametersFormLayout.addRow("Select ROI: ", self.ROISelector)
#
# Pectoral Smoothing Iterations Spin Box
#
self.pectoralSmoothingIterationSpinBox = qt.QSpinBox()
self.pectoralSmoothingIterationSpinBox.setRange(0, 20000)
self.pectoralSmoothingIterationSpinBox.setSingleStep(500)
self.pectoralSmoothingIterationSpinBox.setValue(4000)
parametersFormLayout.addRow("Pectoral Smoothing Iterations: ",
self.pectoralSmoothingIterationSpinBox)
#
# Breast Implants Collapsible Button
#
breastImplantsCollapsibleButton = ctk.ctkCollapsibleButton()
breastImplantsCollapsibleButton.text = "Breast Implants"
breastImplantsCollapsibleButton.setFont(qt.QFont("Times", 12))
breastImplantsCollapsibleButton.collapsed = True
self.layout.addWidget(breastImplantsCollapsibleButton)
# Layout within the dummy collapsible button
breastImplantsFormLayout = qt.QFormLayout(
breastImplantsCollapsibleButton)
#
# Breast implants algorithm hint label
#
self.breastImplantsHintLabel = qt.QLabel()
self.breastImplantsHintLabel.setText(
"Please pick one point for one side or two points for both sides.")
# Align Center
self.breastImplantsHintLabel.setAlignment(4)
self.breastImplantsHintLabel.setFrameStyle(qt.QFrame.WinPanel)
self.breastImplantsHintLabel.setFrameShadow(qt.QFrame.Sunken)
self.breastImplantsHintLabel.setMargin(2)
self.breastImplantsHintLabel.setFont(
qt.QFont("Times", 14, qt.QFont.Black))
breastImplantsFormLayout.addRow(self.breastImplantsHintLabel)
#
# GACM initial point selector
#
self.pointSelector = slicer.qMRMLNodeComboBox()
self.pointSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.pointSelector.selectNodeUponCreation = True
self.pointSelector.addEnabled = True
self.pointSelector.removeEnabled = True
self.pointSelector.noneEnabled = True
self.pointSelector.showHidden = False
self.pointSelector.showChildNodeTypes = False
self.pointSelector.baseName = "P"
self.pointSelector.setMRMLScene(slicer.mrmlScene)
self.pointSelector.setToolTip("Pick the initial points for GACM.")
breastImplantsFormLayout.addRow("Initial Points: ", self.pointSelector)
#
# Place the fiducial point(s) on screen
#
self.markupPointWidget = slicer.qSlicerMarkupsPlaceWidget()
self.markupPointWidget.setMRMLScene(slicer.mrmlScene)
self.markupPointWidget.setPlaceModePersistency(False)
breastImplantsFormLayout.addRow(self.markupPointWidget)
#
# Estimate Volume Button
#
self.estimateButton = qt.QPushButton("Estimate Volume")
self.estimateButton.toolTip = "Run the algorithm."
self.estimateButton.enabled = False
self.estimateButton.setFont(qt.QFont("Times", 24, qt.QFont.Black))
self.layout.addWidget(self.estimateButton)
#
# Spacer
#
self.spacer = qt.QLabel()
self.layout.addWidget(self.spacer)
#
# Editting Segmentation
#
segmentationEditorCollapsibleButton = ctk.ctkCollapsibleButton()
segmentationEditorCollapsibleButton.text = "Editting Segmentation"
segmentationEditorCollapsibleButton.setFont(qt.QFont("Times", 12))
segmentationEditorCollapsibleButton.collapsed = True
self.layout.addWidget(segmentationEditorCollapsibleButton)
# Layout within the dummy collapsible button
segmentationEditorFormLayout = qt.QFormLayout(
segmentationEditorCollapsibleButton)
self.segmentationEditorWidget = slicer.qMRMLSegmentEditorWidget()
self.segmentationEditorWidget.setMaximumNumberOfUndoStates(10)
self.parameterSetNode = None
self.selectParameterNode()
self.segmentationEditorWidget.setSwitchToSegmentationsButtonVisible(
False)
self.segmentationEditorWidget.setUndoEnabled(True)
self.segmentationEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentationEditorFormLayout.addWidget(self.segmentationEditorWidget)
#
# Calculate Statistics Button
#
self.statButton = qt.QPushButton("Calculate Statistics")
self.statButton.toolTip = "Calculate statistics."
self.statButton.enabled = True
self.statButton.setFont(qt.QFont("Times", 24, qt.QFont.Black))
segmentationEditorFormLayout.addWidget(self.statButton)
# connections
self.estimateButton.connect('clicked(bool)', self.onEstimateButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.pointSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.setPoint)
self.segmentationEditorWidget.connect(
"masterVolumeNodeChanged(vtkMRMLVolumeNode*)", self.saveState)
self.statButton.connect('clicked(bool)', self.calculateStatistics)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
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 run(self, inputVolume, Index):
logging.info('Processing started')
DosiFilmImage = inputVolume
date = datetime.datetime.now()
# Stockage du nom de la machine en utilisant le choix de l'utilisateur dans la class Widget
if Index == 0:
machineName = 'Tomotherapy 1'
else:
machineName = 'Tomotherapy 2'
# To obtain fiducial position from user
markups = slicer.util.getNode('F')
FiducialCoordinatesF1 = [0, 0, 0, 0]
FiducialCoordinatesF2 = [0, 0, 0, 0]
FiducialCoordinatesF3 = [0, 0, 0, 0]
markups.GetNthFiducialWorldCoordinates(0, FiducialCoordinatesF1)
markups.GetNthFiducialWorldCoordinates(1, FiducialCoordinatesF2)
markups.GetNthFiducialWorldCoordinates(2, FiducialCoordinatesF3)
# Création de la segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
DosiFilmImage)
# Création des segments editors temporaires
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(DosiFilmImage)
# Création d'un segment après seuillage
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment(
"IrradiatedBlocks")
segmentEditorNode.SetSelectedSegmentID(addedSegmentID)
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", str(10000))
effect.setParameter("MaximumThreshold", str(30000))
effect.self().onApply()
# Passage en mode closed surface pour calcul des centres
n = slicer.util.getNode('Segmentation')
s = n.GetSegmentation()
ss = s.GetSegment('IrradiatedBlocks')
ss.AddRepresentation('Closed surface', vtk.vtkPolyData())
# Division du segment en plusieurs segments (un par bloc d'irradiation)
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", str("SPLIT_ISLANDS_TO_SEGMENTS"))
effect.setParameter("MinimumSize", 1000)
effect.self().onApply()
# Boucle de calcul des centres pour les 7 blocs (segment)
n = slicer.util.getNode('Segmentation')
s = n.GetSegmentation()
ss = s.GetSegment("IrradiatedBlocks")
pd = ss.GetRepresentation('Closed surface')
com = vtk.vtkCenterOfMass()
com.SetInputData(pd)
com.Update()
CenterOfBlock = com.GetCenter(
) # CenterOfBlock est alors un tuple avec plusieurs variables (coordonées x,y,z)
XaxisCenterOfBlock = (
CenterOfBlock[0]
) # Sélection de la 2ème valeur du tuple (indice 1) qui est la valeur dans l'axe Y qui est l'unique valeure d'intérêt
YaxisCenterOfBlock = (CenterOfBlock[1])
YaxisCenterOfBlock = abs(
YaxisCenterOfBlock) # On passe en valeur absolue
XaxisCenterOfBlock = abs(
XaxisCenterOfBlock) # On passe en valeur absolue
######### Calcul des éléments d'intérêt ###########
VerticalOffsetInMm = (abs((
(abs(FiducialCoordinatesF1[1]) + abs(FiducialCoordinatesF2[1])) /
2) - YaxisCenterOfBlock)) * 0.3528
VerticalDistanceInMm = (
abs(abs(FiducialCoordinatesF1[1]) -
abs(FiducialCoordinatesF2[1]))) * 0.3528
LateralOffsetInMm = (abs(FiducialCoordinatesF3[0]) -
XaxisCenterOfBlock) * 0.3528
######### Enonciation des résultats ###########
print(u"\n\nRésultats du test -Real and Virtual Isocentre-\n")
print("Machine : " + str(machineName) + "\n")
print(u"Coordonnée X du centre du bloc d'irradiation: " +
str(XaxisCenterOfBlock) + "\n")
print(u"Coordonnée Y du centre du bloc d'irradiation: " +
str(YaxisCenterOfBlock) + "\n")
print(u"Coordonnée du fiducial F1: " + str(FiducialCoordinatesF1) +
"\n")
print(u"Coordonnée du fiducial F1: " + str(FiducialCoordinatesF2) +
"\n")
print(u"Coordonnée du fiducial F1: " + str(FiducialCoordinatesF3) +
"\n\n")
print(u"Vertical Offset (mm): " + str(VerticalOffsetInMm) + "\n")
print(u"Vertical Distance (mm): " + str(VerticalDistanceInMm) + "\n")
print(u"Lateral Offset (mm): " + str(LateralOffsetInMm) + "\n")
######### Calcul de la conformité et mention des résultats ###########
if 0 <= VerticalOffsetInMm < 1:
ResultVerticalOffset = "Conforme"
elif VerticalOffsetInMm > 1:
ResultVerticalOffset = "Hors tolerance"
else:
ResultVerticalOffset = "Limite" #car si pas < ou > à 1 alors = à 1
print(u"Résultat pour Vertical Offset: " + str(ResultVerticalOffset))
if 0 <= VerticalDistanceInMm < 1:
ResultVerticalDistance = "Conforme"
elif VerticalDistanceInMm > 1:
ResultVerticalDistance = "Hors tolerance"
else:
ResultVerticalDistance = "Limite" #car si pas < ou > à 1 alors = à 1
print(u"Résultat pour Vertical Distance: " +
str(ResultVerticalDistance))
if 0 <= LateralOffsetInMm < 1:
ResultLateralOffset = "Conforme"
elif LateralOffsetInMm > 1:
ResultLateralOffset = "Hors tolerance"
else:
ResultLateralOffset = "Limite" #car si pas < ou > à 1 alors = à 1
print(u"Résultat pour Lateral Offset: " + str(ResultLateralOffset) +
"\n")
"""### Au cas ou problème dans l'image ##
if VerticalOffsetInMm or VerticalDistanceInMm or LateralOffsetInMm < 0:
logging.info(u"Valeur de la différence négative, problème dans l'image ou dans le programme, contactez Aurélien Corroyer-Dulmont tel : 5768")"""
logging.info('Processing completed')
return True
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')
def run(self,
inputVolume,
directory,
exportlabelmaps=True,
exportOBJ=True,
medianFilter=True,
exportDICOM=True,
showResult=True):
"""
Run the processing algorithm.
Can be used without GUI widget.
:param inputVolume: volume to be segmented
:param exportOBJ: export to OBJ files
:param exportlabelmaps: export to labelmaps
:param medianFilter: Whether the medial filter is used for improving the segmentation
:param exportDICOM: Whether the isotropic volume is exported as a DICOM series
:param showResult: show output volume in slice viewers
"""
if not inputVolume:
raise ValueError("Input volume is invalid")
logging.info('Processing started')
# Perform the temporal bone autosegmentation
InputVolume: inputVolume.GetID()
spacing = inputVolume.GetSpacing()[2]
# resample
if spacing <= 0.25:
parameters = {
"outputPixelSpacing": "0.25,0.25,0.25",
"InputVolume": inputVolume,
"interpolationType": 'linear',
"OutputVolume": inputVolume
}
slicer.cli.runSync(slicer.modules.resamplescalarvolume, None,
parameters)
else:
parameters = {
"outputPixelSpacing": "0.25,0.25,0.25",
"InputVolume": inputVolume,
"interpolationType": 'bspline',
"OutputVolume": inputVolume
}
slicer.cli.runSync(slicer.modules.resamplescalarvolume, None,
parameters)
print('\nResampling...\n')
spacing = inputVolume.GetSpacing()[2]
volumeName = inputVolume.GetName()
# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
otic_capsule_segment = segmentationNode.GetSegmentation(
).AddEmptySegment("otic_capsule")
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(inputVolume)
segmentationNode1 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode1.CreateDefaultDisplayNodes(
) # only needed for display
segmentationNode1.SetReferenceImageGeometryParameterFromVolumeNode(
inputVolume)
# Create segment editor to get access to effects
segmentEditorWidget1 = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget1.setMRMLScene(slicer.mrmlScene)
segmentEditorNode1 = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget1.setMRMLSegmentEditorNode(segmentEditorNode1)
segmentEditorWidget1.setSegmentationNode(segmentationNode1)
segmentEditorWidget1.setMasterVolumeNode(inputVolume)
## Autosegmentation of the otic capsule
# NVIDIA auto segmentation
segmentEditorWidget.setActiveEffectByName("Nvidia AIAA")
effect = segmentEditorWidget.activeEffect()
serverUrl = "http://tbone.onthewifi.com:956/v1/models"
effect.self().ui.serverComboBox.currentText = serverUrl
effect.self().onClickFetchModels()
effect.self().ui.segmentationModelSelector.currentText = "inner_ear"
effect.self().onClickSegmentation()
inner_ear = segmentationNode.GetSegmentation(
).GetSegmentIdBySegmentName("inner_ear")
segmentEditorWidget.setCurrentSegmentID(inner_ear)
segmentationNode.GetSegmentation().GetSegment(inner_ear).SetColor(
1, 0, 0)
segmentationNode.GetSegmentation().GetSegment(
otic_capsule_segment).SetColor(0.89, 0.92, 0.65)
segmentEditorNode.SetMasterVolumeIntensityMaskRange(-300, 550)
#Turn mask range on
segmentEditorNode.MasterVolumeIntensityMaskOn()
#growing the membranous labyrinth
# Margin effect
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", 0.3)
effect.self().onApply()
segmentEditorWidget.setCurrentSegmentID('otic_capsule')
#Copying the inner ear segment to otic capsule
# Logical effect
segmentEditorWidget.setActiveEffectByName("Logical operators")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", 'COPY')
effect.setParameter("ModifierSegmentID", inner_ear)
effect.setParameter("BypassMasking", 1)
effect.self().onApply()
# Define the Mask range for bony labyrinth
segmentEditorNode.SetMasterVolumeIntensityMaskRange(650, 2500)
#Turn mask range on
segmentEditorNode.MasterVolumeIntensityMaskOn()
#segmenting the otic capsule from the inner ear
# Margin effect
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", spacing * 5)
effect.self().onApply()
segmentEditorNode.MasterVolumeIntensityMaskOff()
# Islands effect
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", 'KEEP_LARGEST_ISLAND')
effect.self().onApply()
#Make the inner ear not visible to export only the otic capsule
#segmentationNode.GetDisplayNode().SetSegmentVisibility(inner_ear, False)
#copy the inner ear segment to another segmentation Node
#segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(segmentationNode.GetSegmentation(),inner_ear)
# Remove the inner ear to export only the otic capsule
segmentationNode.GetSegmentation().RemoveSegment(inner_ear)
if exportlabelmaps == True:
#Create labelmap for otic capsule and export the segment
oticcapsule_labelmap = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
oticcapsule_labelmap.SetName('oticcapsule_labelmap')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode,
oticcapsule_labelmap,
inputVolume)
slicer.util.saveNode(oticcapsule_labelmap,
directory + '/oticcapsule_labelmap.nrrd')
if exportOBJ == True:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
segnumber = shNode.GetItemByDataNode(segmentationNode)
shNode.SetItemName(segnumber, volumeName + '_otic capsule')
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic(
).ExportSegmentsClosedSurfaceRepresentationToFiles(
directory, segmentationNode, segmentIDs, "OBJ", True, 1.0,
False)
#copy the otic capsule segment to another segmentation Node
segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(
segmentationNode.GetSegmentation(), otic_capsule_segment)
# Remove the otic capsule after exporting
segmentationNode.GetSegmentation().RemoveSegment('otic_capsule')
# Autosegmentation of the ossicles
segmentEditorWidget.setActiveEffectByName("Nvidia AIAA")
effect = segmentEditorWidget.activeEffect()
effect.self().ui.segmentationModelSelector.currentText = 'ossicles'
effect.self().onClickSegmentation()
ossicles = segmentationNode.GetSegmentation(
).GetSegmentIdBySegmentName("ossicles")
segmentationNode.GetSegmentation().GetSegment(ossicles).SetColor(
1, 1, 0.88)
segmentEditorWidget.setCurrentSegmentID(ossicles)
# Islands effect
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", 'REMOVE_SMALL_ISLANDS')
effect.setParameter("MinimumSize", 50)
effect.self().onApply()
if exportlabelmaps == True:
#Create labelmap for ossicles and export the segment
ossicles_labelmap = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
ossicles_labelmap.SetName('ossicles_labelmap')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode,
ossicles_labelmap,
inputVolume)
slicer.util.saveNode(ossicles_labelmap,
directory + '/ossicles_labelmap.nrrd')
if exportOBJ == True:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
segnumber = shNode.GetItemByDataNode(segmentationNode)
shNode.SetItemName(segnumber, volumeName + '_ossicles')
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic(
).ExportSegmentsClosedSurfaceRepresentationToFiles(
directory, segmentationNode, segmentIDs, "OBJ", True, 1.0,
False)
#copy the ossicles segment to another segmentation Node
segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(
segmentationNode.GetSegmentation(), ossicles)
# Remove the ossicles after exporting
segmentationNode.GetSegmentation().RemoveSegment(ossicles)
# Autosegmentation of Cochlear duct
segmentEditorWidget.setActiveEffectByName("Nvidia AIAA")
effect = segmentEditorWidget.activeEffect()
effect.self(
).ui.segmentationModelSelector.currentText = "cochlear_duct"
effect.self().onClickSegmentation()
cochlear_duct = segmentationNode.GetSegmentation(
).GetSegmentIdBySegmentName("cochlear_duct")
segmentEditorWidget.setCurrentSegmentID(cochlear_duct)
segmentationNode.GetSegmentation().GetSegment(cochlear_duct).SetColor(
1, 0, 0)
segmentEditorNode.SetMasterVolumeIntensityMaskRange(-410, 750)
#Turn mask range on
segmentEditorNode.MasterVolumeIntensityMaskOn()
#growing the membranous labyrinth
# Margin effect
segmentEditorWidget.setActiveEffectByName("Margin")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MarginSizeMm", 0.3)
effect.self().onApply()
if exportlabelmaps == True:
#Create labelmap for cochlear duct and export the segment
cochlear_duct_labelmap = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
cochlear_duct_labelmap.SetName('cochlear_duct_labelmap')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode,
cochlear_duct_labelmap,
inputVolume)
slicer.util.saveNode(cochlear_duct_labelmap,
directory + '/cochlear_duct_labelmap.nrrd')
if exportOBJ == True:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
segnumber = shNode.GetItemByDataNode(segmentationNode)
shNode.SetItemName(segnumber, volumeName + '_cochlear_duct')
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic(
).ExportSegmentsClosedSurfaceRepresentationToFiles(
directory, segmentationNode, segmentIDs, "OBJ", True, 1.0,
False)
#copy the cochlear_duct segment to another segmentation Node
segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(
segmentationNode.GetSegmentation(), cochlear_duct)
# Remove the cochlear_duct after exporting
segmentationNode.GetSegmentation().RemoveSegment(cochlear_duct)
if medianFilter == True:
volumesLogic = slicer.modules.volumes.logic()
median = volumesLogic.CloneVolume(slicer.mrmlScene, inputVolume,
'Volume_median_filter')
parameters = {
"neighborhood": "1,1,1",
"inputVolume": inputVolume,
"outputVolume": median
}
slicer.cli.runSync(slicer.modules.medianimagefilter, None,
parameters)
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
median)
segmentEditorWidget.setMasterVolumeNode(median)
# Autosegmentation of Facial Nerve
segmentEditorWidget.setActiveEffectByName("Nvidia AIAA")
effect = segmentEditorWidget.activeEffect()
effect.self().ui.segmentationModelSelector.currentText = 'facial_nerve'
effect.self().onClickSegmentation()
facial_nerve = segmentationNode.GetSegmentation(
).GetSegmentIdBySegmentName("facial_nerve")
segmentationNode.GetSegmentation().GetSegment(facial_nerve).SetColor(
0.9, 1, 0)
if exportlabelmaps == True:
#Create labelmap for facial nerve and export the segment
facial_labelmap = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode,
facial_labelmap, inputVolume)
facial_labelmap.SetName('facial_labelmap')
slicer.util.saveNode(facial_labelmap,
directory + '/facial_labelmap.nrrd')
if exportOBJ == True:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
segnumber = shNode.GetItemByDataNode(segmentationNode)
shNode.SetItemName(segnumber, volumeName + '_facial_nerve')
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic(
).ExportSegmentsClosedSurfaceRepresentationToFiles(
directory, segmentationNode, segmentIDs, "OBJ", True, 1.0,
False)
#copy the facial nerve segment to another segmentation Node
segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(
segmentationNode.GetSegmentation(), facial_nerve)
# Remove the facial_nerve after exporting
segmentationNode.GetSegmentation().RemoveSegment(facial_nerve)
# Autosegmentation of Sigmoid sinus
segmentEditorWidget.setActiveEffectByName("Nvidia AIAA")
effect = segmentEditorWidget.activeEffect()
effect.self(
).ui.segmentationModelSelector.currentText = 'sigmoid_sinus'
effect.self().onClickSegmentation()
sigmoid = segmentationNode.GetSegmentation().GetSegmentIdBySegmentName(
"sigmoid_sinus")
segmentEditorWidget.setCurrentSegmentID(sigmoid)
# Islands effect
segmentEditorWidget.setActiveEffectByName("Islands")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("Operation", 'REMOVE_SMALL_ISLANDS')
effect.setParameter("MinimumSize", 500)
effect.self().onApply()
if exportlabelmaps == True:
# Create labelmap for sigmoid sinus and export the segment
sigmoid_labelmap = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
sigmoid_labelmap.SetName('sigmoid_labelmap')
slicer.modules.segmentations.logic(
).ExportVisibleSegmentsToLabelmapNode(segmentationNode,
sigmoid_labelmap,
inputVolume)
slicer.util.saveNode(sigmoid_labelmap,
directory + '/sigmoid_labelmap.nrrd')
if exportOBJ == True:
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
segnumber = shNode.GetItemByDataNode(segmentationNode)
shNode.SetItemName(segnumber, volumeName + '_sigmoid')
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic(
).ExportSegmentsClosedSurfaceRepresentationToFiles(
directory, segmentationNode, segmentIDs, "OBJ", True, 1.0,
False)
#copy the sigmoid segment to another segmentation Node
segmentationNode1.GetSegmentation().CopySegmentFromSegmentation(
segmentationNode.GetSegmentation(), sigmoid)
# Remove the sigmoid after exporting
segmentationNode.GetSegmentation().RemoveSegment(sigmoid)
# Remove the empty segmentation node
slicer.mrmlScene.RemoveNode(segmentationNode)
# Export the isotropic volume as nrrd file
slicer.util.saveNode(inputVolume, directory + '/Volume.nrrd')
# Export the isotropic volume as a DICOM series
if exportDICOM == True:
from datetime import datetime
now = datetime.now()
patient = now.strftime("%b-%d-%Y_%H-%M-%S")
# Create patient and study and put the volume under the study
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
patientItemID = shNode.CreateSubjectItem(shNode.GetSceneItemID(),
patient)
studyItemID = shNode.CreateStudyItem(patientItemID,
"Auto-segmentation Study")
volumeShItemID = shNode.GetItemByDataNode(inputVolume)
shNode.SetItemParent(volumeShItemID, studyItemID)
import DICOMScalarVolumePlugin
exporter = DICOMScalarVolumePlugin.DICOMScalarVolumePluginClass()
exportables = exporter.examineForExport(volumeShItemID)
for exp in exportables:
exp.directory = directory
exporter.export(exportables)
# Make segmentation results visible in 3D
segmentationNode1.CreateClosedSurfaceRepresentation()
layoutManager = slicer.app.layoutManager()
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
# Remove volume
#slicer.mrmlScene.RemoveNode(median)
#saveNode(inputVolume, directory+'/inputVolume.nrrd')
#slicer.mrmlScene.RemoveNode(segmentationNode)
#print(path)
logging.info('Processing completed')
def test_SplitVolume1(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: SegmentEditorSplitVolume)
"""
self.delayDisplay("Starting test_SplitVolume1")
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("SplitVolume")
effect = segmentEditorWidget.activeEffect()
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("Check extent of cropped volumes")
expectedBounds = [[
100.31225000000003, 119.99975000000003, 101.24974999999999,
119.99974999999999, -78.4, -58.8
],
[
19.68725000000002, 119.99975000000003,
16.874749999999977, 119.99974999999999, -78.4,
16.80000000000001
],
[
-49.687749999999994, 119.99975000000003,
90.93724999999999, 119.99974999999999, -78.4,
-47.6
]]
for segmentIndex in range(
segmentationNode.GetSegmentation().GetNumberOfSegments()):
segmentID = segmentationNode.GetSegmentation().GetNthSegmentID(
segmentIndex)
outputVolumeName = masterVolumeNode.GetName() + '_' + segmentID
outputVolume = slicer.util.getNode(outputVolumeName)
bounds = [0, 0, 0, 0, 0, 0]
outputVolume.GetBounds(bounds)
self.assertEqual(bounds, expectedBounds)
##################################
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_SplitVolume1 passed')
def generateMask(self):
#masterVolumeNode = slicer.util.getNode('1*')
try:
slicer.mrmlScene.RemoveNode(slicer.util.getNode("*masked"))
except slicer.util.MRMLNodeNotFoundException:
pass
try:
slicer.mrmlScene.RemoveNode(slicer.util.getNode("*masked*"))
except slicer.util.MRMLNodeNotFoundException:
pass
# Create segmentation if mesh objects are present/selected
if not self.selectedModelsList == []:
for model in self.selectedModelsList:
if model.currentNode() is not None:
try:
masterVolumeNode = slicer.util.getNode("*masked")
except slicer.util.MRMLNodeNotFoundException:
masterVolumeNode = slicer.util.getNode('1*')
try:
masterVolumeNode = slicer.util.getNode("*masked*")
except slicer.util.MRMLNodeNotFoundException:
masterVolumeNode = slicer.util.getNode('1*')
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
#segmentationNode.CreateDefaultDisplayNodes() # only needed for display
slicer.vtkSlicerSegmentationsModuleLogic.ImportModelToSegmentationNode(
model.currentNode(), segmentationNode)
segmentationNode.CreateBinaryLabelmapRepresentation()
# 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
effect.setParameter("FillValue", str(20000))
# Blank out voxels that are outside the segment
effect.setParameter("Operation", "FILL_INSIDE")
for segmentIndex in range(segmentationNode.GetSegmentation(
).GetNumberOfSegments()):
# Set active segment
segmentID = segmentationNode.GetSegmentation(
).GetNthSegmentID(segmentIndex)
segmentEditorWidget.setCurrentSegmentID(segmentID)
# Apply mask
effect.self().onApply()
if "masked" in masterVolumeNode.GetName():
slicer.mrmlScene.RemoveNode(masterVolumeNode)
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 TestSection_04_qMRMLSegmentEditorWidget(self):
logging.info('Test section 4: qMRMLSegmentEditorWidget')
self.segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentEditorNode')
self.assertIsNotNone(self.segmentEditorNode)
self.inputSegmentationNode.SetSegmentListFilterEnabled(False)
self.inputSegmentationNode.SetSegmentListFilterOptions("")
displayNode = self.inputSegmentationNode.GetDisplayNode()
self.assertIsNotNone(displayNode)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLSegmentEditorNode(self.segmentEditorNode)
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorWidget.setSegmentationNode(self.inputSegmentationNode)
segmentEditorWidget.installKeyboardShortcuts(segmentEditorWidget)
segmentEditorWidget.setFocus(qt.Qt.OtherFocusReason)
segmentEditorWidget.show()
self.segmentEditorNode.SetSelectedSegmentID('first')
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
slicer.app.processEvents()
slicer.util.delayDisplay("First selected")
segmentEditorWidget.selectNextSegment()
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'second')
slicer.app.processEvents()
slicer.util.delayDisplay("Next segment")
segmentEditorWidget.selectPreviousSegment()
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
slicer.app.processEvents()
slicer.util.delayDisplay("Previous segment")
displayNode.SetSegmentVisibility('second', False)
segmentEditorWidget.selectNextSegment()
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'third')
slicer.app.processEvents()
slicer.util.delayDisplay("Next segment (with second segment hidden)")
# Trying to go out of bounds past first segment
segmentEditorWidget.selectPreviousSegment() #First
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
segmentEditorWidget.selectPreviousSegment() #First
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
segmentEditorWidget.selectPreviousSegment() #First
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
slicer.app.processEvents()
slicer.util.delayDisplay("Multiple previous segment")
# Wrap around
self.segmentEditorNode.SetSelectedSegmentID('third')
segmentEditorWidget.selectNextSegment()
self.assertEqual(self.segmentEditorNode.GetSelectedSegmentID(),
'first')
slicer.util.delayDisplay("Wrap around segments")
def convertSegmentsToSegment(self, probeNode, nodeIds):
thisScene = probeNode.GetScene()
#probeNode.GetSegmentation().CreateRepresentation("Binary labelmap") #added 2/22
#probeNode.GetSegmentation().SetMasterRepresentationName("Binary labelmap") #added 2/22
probeName = "ablation zone"
if len(nodeIds) > 1:
print(
"Found multiple probe nodes, combining them into a single segment!: ",
nodeIds)
probeName = "combined ablation zone"
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
slicer.app.processEvents()
for probeNodeID in nodeIds:
duplicateProbeNode = thisScene.GetNodeByID(probeNodeID)
#duplicateProbeNode.GetSegmentation().SetMasterRepresentationName("Binary labelmap") #ADDED 2/22
segmentType = duplicateProbeNode.GetSegmentation(
).GetMasterRepresentationName()
slicer.app.processEvents()
if (segmentType == "Closed surface"):
mergedImage = vtk.vtkPolyData()
duplicateProbeNode.GetClosedSurfaceRepresentation(
duplicateProbeNode.GetSegmentation().GetNthSegmentID(0),
mergedImage)
newSegmentID = segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
mergedImage, probeNodeID, [0, 1, 0])
newSegment = segmentationNode.GetSegmentation().GetSegment(
newSegmentID)
newSegment.SetName(probeName)
else:
labelmapImage = vtkSegmentationCore.vtkOrientedImageData()
duplicateProbeNode.GetBinaryLabelmapRepresentation(
duplicateProbeNode.GetSegmentation().GetNthSegmentID(0),
labelmapImage)
newSegmentID = segmentationNode.AddSegmentFromBinaryLabelmapRepresentation(
labelmapImage, probeNodeID, [1, 0, 0])
newSegment = segmentationNode.GetSegmentation().GetSegment(
newSegmentID)
newSegment.SetName(probeName)
duplicateProbeNode.GetSegmentation().CreateRepresentation(
"Closed Surface")
#segmentationNode.GetSegmentation().CreateRepresentation("Closed surface")
#segmentationNode.GetSegmentation().SetMasterRepresentationName("Closed surface")
#slicer.mrmlScene.RemoveNode(duplicateProbeNode)
duplicateProbeNode.SetDisplayVisibility(0)
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
for i in range(
1,
segmentationNode.GetSegmentation().GetNumberOfSegments() +
1): #TWO ADDITIONAL PROBES
segmentEditorWidget.setActiveEffectByName("Logical operators")
effect = segmentEditorWidget.activeEffect()
effect.self().scriptedEffect.setParameter("Operation", "UNION")
effect.self().scriptedEffect.setParameter(
"ModifierSegmentID",
segmentationNode.GetSegmentation().GetNthSegmentID(i))
effect.self().onApply()
#segmentationNode.GetSegmentation().RemoveSegment(segmentationNode.GetSegmentation().GetNthSegmentID(i))
#for i in range(1, segmentationNode.GetSegmentation().GetNumberOfSegments()): #TWO ADDITIONAL PROBES
# segmentationNode.GetSegmentation().RemoveSegment(segmentationNode.GetSegmentation().GetNthSegmentID(i))
segDisplayNode = segmentationNode.GetDisplayNode()
segDisplayNode.SetOpacity(0.3)
segmentationNode.GetSegmentation().CreateRepresentation(
"Closed surface")
segmentationNode.GetSegmentation().SetMasterRepresentationName(
"Closed surface")
segNum = segmentationNode.GetSegmentation().GetNumberOfSegments()
for i in range(0, segNum):
segmentationNode.GetSegmentation().RemoveSegment(
segmentationNode.GetSegmentation().GetNthSegmentID(1))
segmentationNode.SetName("translated probe")
#segmentationNode.GetSegmentation().GetNthSegment(0).SetName(probeName)
return segmentationNode
def test_NvidiaAIAA1(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: SegmentEditorNvidiaAIAA)
"""
self.delayDisplay("Starting test_NvidiaAIAA1")
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 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("NvidiaAIAA")
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_NvidiaAIAA1 passed')
loadedVolumeNode = slicer.util.loadVolume(TestFile, returnNode=True)
vol = slicer.util.getNode('*ORIG')
VoxelSize = vol.GetSpacing()
Origin = vol.GetOrigin()
VolDims = vol.GetImageData().GetDimensions()
# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
loadedVolumeNode)
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment("skin")
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(loadedVolumeNode)
# Thresholding
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", "35")
effect.setParameter("MaximumThreshold", "695")
effect.self().onApply()
# Smoothing
