def createModel(self,labelVolume):
"""
Create the 3D model from the airway label
"""
modelHierarchyCollection = slicer.mrmlScene.GetNodesByName('AirwayModelHierarchy')
if( modelHierarchyCollection.GetNumberOfItems() >= 1 ):
modelHierarchy = modelHierarchyCollection.GetItemAsObject(0)
else:
nodeType = 'vtkMRMLModelHierarchyNode'
modelHierarchy = slicer.mrmlScene.CreateNodeByClass(nodeType)
modelHierarchy.SetScene(slicer.mrmlScene)
modelHierarchy.SetName(slicer.mrmlScene.GetUniqueNameByString('AirwayModelHierarchy'))
slicer.mrmlScene.AddNode(modelHierarchy)
parameters = {}
parameters["InputVolume"] = labelVolume.GetID()
parameters["ModelSceneFile"] = modelHierarchy.GetID()
parameters["Name"] = 'AirwayModel'
#parameters["FilterType"] = 'Laplacian'
parameters["Smooth"] = 20
parameters["Decimate"] = 0.10
modelMaker = slicer.modules.modelmaker
slicer.cli.run(modelMaker, None, parameters,True)
lm = slicer.app.layoutManager()
threeDView = lm.threeDWidget( 0 ).threeDView()
threeDView.resetFocalPoint()
threeDView.lookFromViewAxis(ctk.ctkAxesWidget().Anterior)
return True
def createModel(self,labelVolume):
"""
Create the 3D model from the airway label
"""
modelHierarchyCollection = slicer.mrmlScene.GetNodesByName('AirwayModelHierarchy')
if( modelHierarchyCollection.GetNumberOfItems() >= 1 ):
modelHierarchy = modelHierarchyCollection.GetItemAsObject(0)
else:
nodeType = 'vtkMRMLModelHierarchyNode'
modelHierarchy = slicer.mrmlScene.CreateNodeByClass(nodeType)
modelHierarchy.SetScene(slicer.mrmlScene)
modelHierarchy.SetName(slicer.mrmlScene.GetUniqueNameByString('AirwayModelHierarchy'))
slicer.mrmlScene.AddNode(modelHierarchy)
parameters = {}
parameters["InputVolume"] = labelVolume.GetID()
parameters["ModelSceneFile"] = modelHierarchy.GetID()
parameters["Name"] = 'AirwayModel'
#parameters["FilterType"] = 'Laplacian'
parameters["Smooth"] = 20
parameters["Decimate"] = 0.10
modelMaker = slicer.modules.modelmaker
slicer.cli.run(modelMaker, None, parameters,True)
lm = slicer.app.layoutManager()
threeDView = lm.threeDWidget( 0 ).threeDView()
threeDView.resetFocalPoint()
threeDView.lookFromViewAxis(ctk.ctkAxesWidget().Anterior)
return True
def onStartSegmentationButton(self):
inputVolume = self.inputSelector.currentNode()
inputName = inputVolume.GetName()
inputNode = slicer.util.getNode(inputName)
instUIDs = inputNode.GetAttribute('DICOM.instanceUIDs').split()
fileName = slicer.dicomDatabase.fileForInstance(instUIDs[0])
patientAge = slicer.dicomDatabase.fileValue(fileName,'0010,1010')
patientAge=patientAge[1:3]
age_str = str(patientAge)
self.age.setText(age_str)
# Analyze histogram of the image to work out the second peak intensity value
start = timeit.default_timer()
self.LungNoduleSegmentationButton.enabled = False
seedPoint = self.fiducialListSelector.currentNode()
inputNodeArray = slicer.util.array(inputVolume.GetID())
maskedImage = inputNodeArray[inputNodeArray >= -1024]
edges=[]
I_max = maskedImage.max()
I_min = maskedImage.min()
for val in range(I_min,I_max+2):
edges.append(val)
I_max =float(I_max)
I_min =float(I_min)
maskedImage = maskedImage.astype(float)
histogram,bins = numpy.histogram(maskedImage,bins=edges)
mx, mn = self.peakdetect(histogram)
threshold = (-1024+bins[mx[0][0]]) / 2
if threshold < -800:
maskedImage = inputNodeArray[inputNodeArray >= -1000]
edges=[]
I_max = maskedImage.max()
I_min = maskedImage.min()
for val in range(I_min,I_max+2):
edges.append(val)
I_max =float(I_max)
I_min =float(I_min)
maskedImage = maskedImage.astype(float)
histogram,bins = numpy.histogram(maskedImage,bins=edges)
mx, mn = self.peakdetect(histogram)
threshold = (-1024+bins[mx[0][0]]) / 2
print threshold
stop = timeit.default_timer()
print "Histogram anaylis: ", stop - start, "sec"
# Segment the lung surface
start = timeit.default_timer()
nodeType = 'vtkMRMLScalarVolumeNode'
self.lungLabelNode = slicer.mrmlScene.CreateNodeByClass(nodeType)
self.lungLabelNode.SetLabelMap(1)
self.lungLabelNode.SetScene(slicer.mrmlScene)
self.lungLabelNode.SetName(slicer.mrmlScene.GetUniqueNameByString('LungLabel'))
slicer.mrmlScene.AddNode(self.lungLabelNode)
LungSegmentationModule = slicer.modules.lungsegmentationcli
lungLabelColor = 1
parameters = {
"InputVolume": inputVolume,
"OutputVolume": self.lungLabelNode,
"Lower": -1024,
"Upper": threshold,
"lungColor": lungLabelColor,
}
slicer.cli.run( LungSegmentationModule, None, parameters, wait_for_completion = True )
stop = timeit.default_timer()
print "Lung segmentation: ", stop - start, "sec"
# Segment the selected nodule
start = timeit.default_timer()
nodeType = 'vtkMRMLScalarVolumeNode'
self.noduleLabelNode = slicer.mrmlScene.CreateNodeByClass(nodeType)
self.noduleLabelNode.SetLabelMap(1)
self.noduleLabelNode.SetScene(slicer.mrmlScene)
self.noduleLabelNode.SetName(slicer.mrmlScene.GetUniqueNameByString('NoduleLabel'))
slicer.mrmlScene.AddNode(self.noduleLabelNode)
LungNoduleSegmentationModule = slicer.modules.lungnodulesegmentationcli
labelColor = 6
parameters = {
"InputVolume": inputVolume,
"InputLungLabel": self.lungLabelNode,
"OutputVolume": self.noduleLabelNode,
"seed": seedPoint,
"noduleColor": labelColor,
}
NoduleSegmentationNode = slicer.cli.run( LungNoduleSegmentationModule, None, parameters, wait_for_completion = True )
stop = timeit.default_timer()
print "Nodule segmentation: ", stop - start, "sec"
self.FissuresNode = slicer.mrmlScene.CreateNodeByClass(nodeType)
self.FissuresNode.SetLabelMap(1)
self.FissuresNode.SetScene(slicer.mrmlScene)
self.FissuresNode.SetName(slicer.mrmlScene.GetUniqueNameByString('FissuresVolume'))
slicer.mrmlScene.AddNode(self.FissuresNode)
FissuresSegmentationModule = slicer.modules.lungfissuresegmentationcli
params = {
"InputVolume": inputVolume,
"InputLungLabel": self.lungLabelNode,
"OutputVolume": self.FissuresNode,
}
slicer.cli.run( FissuresSegmentationModule, None, params, wait_for_completion = True )
self.LobesNode = slicer.mrmlScene.CreateNodeByClass(nodeType)
self.LobesNode.SetLabelMap(1)
self.LobesNode.SetScene(slicer.mrmlScene)
self.LobesNode.SetName(slicer.mrmlScene.GetUniqueNameByString('LobesVolume'))
slicer.mrmlScene.AddNode(self.LobesNode)
LobesSegmentationModule = slicer.modules.lunglobesegmentationcli
params = {
"InputVolume": inputVolume,
"LabelMapVolume": self.lungLabelNode,
"FissuresVolume": self.FissuresNode,
"OutputVolume": self.LobesNode
}
slicer.cli.run( LobesSegmentationModule, None, params, wait_for_completion = True )
# Create 3D model of the segment nodule
start = timeit.default_timer()
modelHierarchyCollection = slicer.mrmlScene.GetNodesByName('NoduleModelHierarchy')
if( modelHierarchyCollection.GetNumberOfItems() >= 1 ):
modelHierarchy = modelHierarchyCollection.GetItemAsObject(0)
else:
modelHierarchy = slicer.vtkMRMLModelHierarchyNode()
modelHierarchy.SetName(slicer.mrmlScene.GetUniqueNameByString('NoduleModelHierarchy'))
slicer.mrmlScene.AddNode(modelHierarchy)
parameters = {}
parameters["InputVolume"] = self.noduleLabelNode.GetID()
parameters["ModelSceneFile"] = modelHierarchy.GetID()
parameters["Name"] = 'NoduleModel'
parameters["Smooth"] = 20
parameters["Decimate"] = 0.10
modelMaker = slicer.modules.modelmaker
slicer.cli.run( modelMaker, None, parameters, wait_for_completion = True )
lm = slicer.app.layoutManager()
threeDView = lm.threeDWidget( 0 ).threeDView()
threeDView.resetFocalPoint()
threeDView.lookFromViewAxis(ctk.ctkAxesWidget().Anterior)
stop = timeit.default_timer()
print "Model maker: ", stop - start, "sec"
# Evaluate malignancy of the nodule
nodulePosition = NoduleSegmentationNode.GetParameterDefault(2,0)
noduleSize = NoduleSegmentationNode.GetParameterDefault(2,1)
noduleRoundness = NoduleSegmentationNode.GetParameterDefault(2,2)
noduleCavityWallThickness = NoduleSegmentationNode.GetParameterDefault(2,3)
noduleCalcificationPattern = NoduleSegmentationNode.GetParameterDefault(2,4)
size_str = str(noduleSize) + ' mm'
self.size.setText(size_str)
smoothness_str = 'Smooth'
noduleRoundness = float(noduleRoundness)
if noduleRoundness < 0.7:
smoothness_str = 'Spiculated'
self.spiculation.setText(smoothness_str)
thickness_str = 'Not Cavitated'
noduleCavityWallThickness = float(noduleCavityWallThickness)
if (noduleCavityWallThickness >= 0.1 and noduleCavityWallThickness < 100.0):
print noduleCavityWallThickness
thickness_str = str(noduleCavityWallThickness) + ' mm'
self.thickness.setText(thickness_str)
lobesImageData = self.LobesNode.GetImageData()
nodulePosition = eval(nodulePosition)
lobeValue = lobesImageData.GetScalarComponentAsDouble(int(nodulePosition[0]),int(nodulePosition[1]),int(nodulePosition[2]), 0)
position_str = 'Right Upper Lobe'
if lobeValue == 5:
position_str = 'Right Middle Lobe'
elif lobeValue == 6:
position_str = 'Right Lower Lobe'
elif lobeValue == 7:
position_str = 'Left Upper Lobe'
elif lobeValue == 8:
position_str = 'Left Lower Lobe'
self.location.setText(position_str)
calc_str = 'Benign Pattern'
if noduleCalcificationPattern == 'false':
calc_str = 'No Calcification'
self.calcification.setText(calc_str)
self.LungNoduleSegmentationButton.enabled = True
self.calculateProbability()
self.RecomputeButton.enabled = True
