def clipping(self):
planeCollection = vtk.vtkPlaneCollection()
harden = slicer.vtkSlicerTransformLogic()
tempTransform = slicer.vtkMRMLLinearTransformNode()
tempTransform.HideFromEditorsOn()
slicer.mrmlScene.AddNode(tempTransform)
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
dictionnaryModel = dict()
hardenModelIDdict = dict()
landmarkDescriptionDict = dict()
modelIDdict = dict()
for i in range(3, numNodes):
planeCollection.RemoveAllItems()
mh = slicer.mrmlScene.GetNthNodeByClass(i, "vtkMRMLModelNode")
if mh.GetDisplayVisibility() == 0:
continue
model = slicer.util.getNode(mh.GetName())
transform = model.GetParentTransformNode()
if transform:
tempTransform.Copy(transform)
harden.hardenTransform(tempTransform)
m = vtk.vtkMatrix4x4()
tempTransform.GetMatrixTransformToParent(m)
m.Invert(m, m)
else:
m = vtk.vtkMatrix4x4()
for key, planeDef in self.planeDict.iteritems():
hardenP = m.MultiplyPoint(planeDef.P)
hardenN = m.MultiplyPoint(planeDef.n)
if planeDef.boxState:
planeDef.vtkPlane.SetOrigin(hardenP[0], hardenP[1], hardenP[2])
if planeDef.negState:
planeDef.vtkPlane.SetNormal(-hardenN[0], -hardenN[1], -hardenN[2])
if planeDef.posState:
planeDef.vtkPlane.SetNormal(hardenN[0], hardenN[1], hardenN[2])
planeCollection.AddItem(planeDef.vtkPlane)
dictionnaryModel[model.GetID()]= model.GetPolyData()
polyData = model.GetPolyData()
clipper = vtk.vtkClipClosedSurface()
clipper.SetClippingPlanes(planeCollection)
clipper.SetInputData(polyData)
clipper.SetGenerateFaces(1)
clipper.SetScalarModeToLabels()
clipper.Update()
polyDataNew = clipper.GetOutput()
model.SetAndObservePolyData(polyDataNew)
# Checking if one ore more fiducial list are connected to this model
list = slicer.mrmlScene.GetNodesByClass("vtkMRMLMarkupsFiducialNode")
end = list.GetNumberOfItems()
for i in range(0,end):
fidList = list.GetItemAsObject(i)
if fidList.GetAttribute("connectedModelID"):
if fidList.GetAttribute("connectedModelID") == model.GetID():
modelIDdict[fidList.GetID()], hardenModelIDdict[fidList.GetID()], landmarkDescriptionDict[fidList.GetID()] = \
self.unprojectLandmarks(fidList)
return dictionnaryModel, modelIDdict, hardenModelIDdict, landmarkDescriptionDict
def createIntermediateHardenModel(self, model):
hardenModel = slicer.mrmlScene.GetNodesByName("SurfaceRegistration_" + model.GetName() + "_hardenCopy_" + str(
slicer.app.applicationPid())).GetItemAsObject(0)
if hardenModel is None:
hardenModel = slicer.vtkMRMLModelNode()
hardenPolyData = vtk.vtkPolyData()
hardenPolyData.DeepCopy(model.GetPolyData())
hardenModel.SetAndObservePolyData(hardenPolyData)
hardenModel.SetName(
"SurfaceRegistration_" + model.GetName() + "_hardenCopy_" + str(slicer.app.applicationPid()))
if model.GetParentTransformNode():
hardenModel.SetAndObserveTransformNodeID(model.GetParentTransformNode().GetID())
hardenModel.HideFromEditorsOn()
slicer.mrmlScene.AddNode(hardenModel)
logic = slicer.vtkSlicerTransformLogic()
logic.hardenTransform(hardenModel)
return hardenModel
def createIntermediateHardenModel(self, model):
hardenModel = slicer.mrmlScene.GetNodesByName(
"SurfaceRegistration_" + model.GetName() + "_hardenCopy_" +
str(slicer.app.applicationPid())).GetItemAsObject(0)
if hardenModel is None:
hardenModel = slicer.vtkMRMLModelNode()
hardenPolyData = vtk.vtkPolyData()
hardenPolyData.DeepCopy(model.GetPolyData())
hardenModel.SetAndObservePolyData(hardenPolyData)
hardenModel.SetName("SurfaceRegistration_" + model.GetName() +
"_hardenCopy_" + str(slicer.app.applicationPid()))
if model.GetParentTransformNode():
hardenModel.SetAndObserveTransformNodeID(
model.GetParentTransformNode().GetID())
hardenModel.HideFromEditorsOn()
slicer.mrmlScene.AddNode(hardenModel)
logic = slicer.vtkSlicerTransformLogic()
logic.hardenTransform(hardenModel)
return hardenModel
def clipping(self):
planeCollection = vtk.vtkPlaneCollection()
harden = slicer.vtkSlicerTransformLogic()
tempTransform = slicer.vtkMRMLLinearTransformNode()
tempTransform.HideFromEditorsOn()
slicer.mrmlScene.AddNode(tempTransform)
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
dictionnaryModel = dict()
hardenModelIDdict = dict()
landmarkDescriptionDict = dict()
modelIDdict = dict()
for i in range(3, numNodes):
planeCollection.RemoveAllItems()
mh = slicer.mrmlScene.GetNthNodeByClass(i, "vtkMRMLModelNode")
if mh.GetDisplayVisibility() == 0:
continue
model = slicer.util.getNode(mh.GetName())
transform = model.GetParentTransformNode()
if transform:
tempTransform.Copy(transform)
harden.hardenTransform(tempTransform)
m = vtk.vtkMatrix4x4()
tempTransform.GetMatrixTransformToParent(m)
m.Invert(m, m)
else:
m = vtk.vtkMatrix4x4()
for key, planeDef in self.planeDict.iteritems():
hardenP = m.MultiplyPoint(planeDef.P)
hardenN = m.MultiplyPoint(planeDef.n)
if planeDef.boxState:
planeDef.vtkPlane.SetOrigin(hardenP[0], hardenP[1],
hardenP[2])
if planeDef.negState:
planeDef.vtkPlane.SetNormal(-hardenN[0], -hardenN[1],
-hardenN[2])
if planeDef.posState:
planeDef.vtkPlane.SetNormal(hardenN[0], hardenN[1],
hardenN[2])
planeCollection.AddItem(planeDef.vtkPlane)
dictionnaryModel[model.GetID()] = model.GetPolyData()
polyData = model.GetPolyData()
clipper = vtk.vtkClipClosedSurface()
clipper.SetClippingPlanes(planeCollection)
clipper.SetInputData(polyData)
clipper.SetGenerateFaces(1)
clipper.SetScalarModeToLabels()
clipper.Update()
polyDataNew = clipper.GetOutput()
model.SetAndObservePolyData(polyDataNew)
# Checking if one ore more fiducial list are connected to this model
list = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLMarkupsFiducialNode")
end = list.GetNumberOfItems()
for i in range(0, end):
fidList = list.GetItemAsObject(i)
if fidList.GetAttribute("connectedModelID"):
if fidList.GetAttribute(
"connectedModelID") == model.GetID():
modelIDdict[fidList.GetID()], hardenModelIDdict[fidList.GetID()], landmarkDescriptionDict[fidList.GetID()] = \
self.unprojectLandmarks(fidList)
return dictionnaryModel, modelIDdict, hardenModelIDdict, landmarkDescriptionDict
def run(self, inputVolumeNode, inputFiducialNode, vtIDT, vtMethodID):
logging.info('Processing started')
self.vsc = VisSimCommon.VisSimCommonLogic()
self.vsc.setGlobalVariables(1)
print("setup local paths variables.........................")
vtID =int(vtIDT)
# set the correct models paths:
modelPath = self.vsc.vtVars['modelPath']+ ',Default'+",Mdl" + self.vsc.vtVars['Styp']+ str(vtID) +self.vsc.vtVars['imgType']
modelPath = os.path.join(*modelPath.split(","))
modelSegPath = self.vsc.vtVars['modelPath'] + self.vsc.vtVars['segT']+",Mdl"+self.vsc.vtVars['Styp']+ str(vtID)+ self.vsc.vtVars['sgT'] +self.vsc.vtVars['imgType']
modelSegPath = os.path.join(*modelSegPath.split(","))
modelLigPtsPath = self.vsc.vtVars['modelLigPtsPath'] +str(vtID)+self.vsc.vtVars['vtPtsLigSuff']+".fcsv"
# set the results paths:
resTransPathOld = os.path.join(self.vsc.vtVars['outputPath'] ,"TransformParameters.0.txt")
resTransPath=resTransPathOld[0:-6]+'Pars.txt'
resOldDefPath = os.path.join(self.vsc.vtVars['outputPath'] , "deformationField"+self.vsc.vtVars['imgType'])
resDefPath = os.path.join(self.vsc.vtVars['outputPath'] , inputVolumeNode.GetName()+"_C"+str(vtID)+"_dFld"+self.vsc.vtVars['imgType'])
inputImgName = inputVolumeNode.GetStorageNode().GetFileName()
inputImgName = basename(os.path.splitext(inputImgName)[0])
segNodeName = inputVolumeNode.GetName() + "_C" +str(vtID)+".Seg"
ligPtsNodeName = inputVolumeNode.GetName() + "_C" +str(vtID)+"_LigPts"
transNodeName = inputVolumeNode.GetName() + "_C" +str(vtID)+ "_Transform"
print("removeOtputsFolderContents ........................ ")
#only for this vertebra
self.vsc.removeOtputsFolderContents()
# check if the model is found
if not isfile(modelPath):
print >> sys.stderr, "ERROR: model is not found"
print("modelPath: " + modelPath)
return -1
# endif
print("ptRAS2IJK ........................ ")
# for multiple vertebra, it is enough to have one markup node
# Get IJK point from the fiducial to use in cropping
newFid= True
for j in range (inputFiducialNode.GetNumberOfFiducials() ):
if inputFiducialNode.GetNthFiducialLabel(j)==("C"+str(vtID)) :
break
#endif
#endfor
# Get IJK point from the fiducial to use in cropping
inputPoint = self.vsc.ptRAS2IJK(inputFiducialNode,inputVolumeNode,j)
# TODO: add better condition
if np.sum(inputPoint)== 0 :
print("Error: select vertebra point")
return -1
#endif
fnm = os.path.join(self.vsc.vtVars['outputPath'] , inputVolumeNode.GetName()+"_C"+str(vtID)+"_vtLocations.fcsv")
sR = slicer.util.saveNode(inputFiducialNode, fnm )
#Remove old resulted nodes
for node in slicer.util.getNodes():
if ( ligPtsNodeName == node): slicer.mrmlScene.RemoveNode(node) #endif
if ( segNodeName == node): slicer.mrmlScene.RemoveNode(node) #endif
if ( transNodeName == node): slicer.mrmlScene.RemoveNode(node) #endif
#endfor
inputPointT = self.vsc.v2t(inputPoint)
print ("************ Cropping **********************")
self.vsc.vtVars['intputCropPath'] = self.vsc.runCropping(inputVolumeNode, inputPointT,self.vsc.vtVars['croppingLength'], self.vsc.vtVars['RSxyz'], self.vsc.vtVars['hrChk'], str(vtID) )
[success, croppedNode] = slicer.util.loadVolume(self.vsc.vtVars['intputCropPath'], returnNode=True)
croppedNode.SetName(inputVolumeNode.GetName()+"_C"+str(vtID)+"Crop")
print ("************ Register model to cropped input image **********************")
cTI = self.vsc.runElastix(self.vsc.vtVars['elastixBinPath'],self.vsc.vtVars['intputCropPath'], modelPath, self.vsc.vtVars['outputPath'], self.vsc.vtVars['parsPath'], self.vsc.vtVars['noOutput'], "554")
copyfile(resTransPathOld, resTransPath)
#genrates deformation field
cTR = self.vsc.runTransformix(self.vsc.vtVars['transformixBinPath'],modelPath, self.vsc.vtVars['outputPath'], resTransPath, self.vsc.vtVars['noOutput'], "556")
# rename fthe file:
os.rename(resOldDefPath,resDefPath)
print ("************ Load deformation field Transform **********************")
[success, vtTransformNode] = slicer.util.loadTransform(resDefPath, returnNode = True)
vtTransformNode.SetName(transNodeName)
print ("************ Transform segmentation **********************")
[success, vtSegNode] = slicer.util.loadSegmentation(modelSegPath, returnNode = True)
vtSegNode.SetName(segNodeName)
vtSegNode.SetAndObserveTransformNodeID(vtTransformNode.GetID()) # movingAllMarkupNode should be loaded, the file contains all points
slicer.vtkSlicerTransformLogic().hardenTransform(vtSegNode) # apply the transform
vtSegNode.CreateClosedSurfaceRepresentation()
fnm = os.path.join(self.vsc.vtVars['outputPath'] , vtSegNode.GetName()+".nrrd")
sR = slicer.util.saveNode(vtSegNode, fnm )
if self.vsc.s2b(self.vsc.vtVars['ligChk']):
print ("************ Transform Ligaments Points **********************")
[success, vtLigPtsNode] = slicer.util.loadMarkupsFiducialList (modelLigPtsPath, returnNode = True)
vtLigPtsNode.GetDisplayNode().SetSelectedColor(1,0,0)
vtLigPtsNode.GetDisplayNode().SetTextScale(0.5)
vtLigPtsNode.SetName(ligPtsNodeName)
vtLigPtsNode.SetAndObserveTransformNodeID(vtTransformNode.GetID())
slicer.vtkSlicerTransformLogic().hardenTransform(vtLigPtsNode) # apply the transform
# needed in extract scaled model
self.vtLigPtsNode = vtLigPtsNode
fnm = os.path.join(self.vsc.vtVars['outputPath'] , vtLigPtsNode.GetName()+".fcsv")
sR = slicer.util.saveNode(vtLigPtsNode, fnm )
#endif
# Display the result if no error
# Clear vertebra location labels
if (cTI==0) and (cTR==0):
# change the model type from vtk to stl
msn=slicer.vtkMRMLModelStorageNode()
msn.SetDefaultWriteFileExtension('stl')
slicer.mrmlScene.AddDefaultNode(msn)
print("get vertebra information")
tableName = inputVolumeNode.GetName()+"_tbl"
# create only if it does not exist
try:
# if table exists, don't create a new one.
spTblNode = slicer.util.getNode(tableName)
print("table is found .........................................")
except:
#create a new table
spTblNode= None
#endtry
spTblNode = self.vsc.getItemInfo( vtSegNode, croppedNode, spTblNode, vtID)
else:
print("error happened during segmentation ")
#endif
#Remove temporary files and nodes:
self.vsc.removeTmpsFiles()
print("================= vertebra analysis is complete =====================")
logging.info('Processing completed')
return vtSegNode
def transformNodewithBspline(self, movingSimilarityLabel, BSPLINETransform): # tranform input node using bspline transform from registration movingSimilarityLabel.SetAndObserveTransformNodeID(BSPLINETransform.GetID()) slicer.vtkSlicerTransformLogic().hardenTransform(movingSimilarityLabel) # hardens transform
def run(self, fixedVolumeNode, fixedFiducialNode, movingVolumeNode,
movingFiducialNode):
logging.info('Processing started')
print(fixedVolumeNode.GetName())
print(movingVolumeNode.GetName())
self.vsc = VisSimCommon.VisSimCommonLogic()
self.vsc.setGlobalVariables(0)
self.vsc.removeOtputsFolderContents()
# results paths
resTransPath = os.path.join(self.vsc.vtVars['outputPath'],
"TransformParameters.0.txt")
resOldDefPath = os.path.join(
self.vsc.vtVars['outputPath'],
"deformationField" + self.vsc.vtVars['imgType'])
resDefPath = os.path.join(
self.vsc.vtVars['outputPath'],
movingVolumeNode.GetName() + "_dFld" + self.vsc.vtVars['imgType'])
transNodeName = movingVolumeNode.GetName() + "_Transform"
# Save original fixed and moving images
if fixedVolumeNode.GetStorageNode() is None:
fixedImgPath = os.path.join(self.vsc.vtVars['vissimPath'],
fixedVolumeNode.GetName() + ".nrrd")
slicer.util.saveNode(fixedVolumeNode, fixedImgPath)
fixedPath = fixedVolumeNode.GetStorageNode().GetFileName()
if movingVolumeNode.GetStorageNode() is None:
movingImgPath = os.path.join(self.vsc.vtVars['vissimPath'],
movingVolumeNode.GetName() + ".nrrd")
slicer.util.saveNode(movingVolumeNode, movingImgPath)
movingPath = movingVolumeNode.GetStorageNode().GetFileName()
# Get IJK point from the fiducial to use in cropping
fixedPoint = self.vsc.ptRAS2IJK(fixedFiducialNode, fixedVolumeNode, 0)
print("run fixed point: ============================")
print(fixedVolumeNode.GetName())
print(fixedPoint)
# TODO: add better condition
if np.sum(fixedPoint) == 0:
print("Error: select cochlea fixed point")
return -1
#endif
fnm = os.path.join(self.vsc.vtVars['outputPath'],
fixedVolumeNode.GetName() + "_F_Cochlea_Pos.fcsv")
sR = slicer.util.saveNode(fixedFiducialNode, fnm)
movingPoint = self.vsc.ptRAS2IJK(movingFiducialNode, movingVolumeNode,
0)
print("run moving point: ============================")
print(movingVolumeNode.GetName())
print(movingPoint)
# TODO: add better condition
if np.sum(fixedPoint) == 0:
print("Error: select cochlea moving point")
return -1
#endif
fnm = os.path.join(self.vsc.vtVars['outputPath'],
movingVolumeNode.GetName() + "_M_Cochlea_Pos.fcsv")
sR = slicer.util.saveNode(movingFiducialNode, fnm)
#Remove old resulted nodes
#for node in slicer.util.getNodes():
# if ( "result" in [node].GetName() ): slicer.mrmlScene.RemoveNode(node) #endif
#endfor
# TODO: add better condition
if (np.sum(fixedPoint) == 0) and (np.sum(movingPoint) == 0):
#qt.QMessageBox.critical(slicer.util.mainWindow(),'SlicerCochleaRegistration', 'Cochlea locations are missing')
print("Error: select cochlea points in fixed and moving images")
return False
#endif
fixedPointT = self.vsc.v2t(fixedPoint)
movingPointT = self.vsc.v2t(movingPoint)
print("=================== Cropping =====================")
self.vsc.vtVars['fixedCropPath'] = self.vsc.runCropping(
fixedVolumeNode, fixedPointT, self.vsc.vtVars['croppingLength'],
self.vsc.vtVars['RSxyz'], self.vsc.vtVars['hrChk'], 0)
[success, croppedFixedNode
] = slicer.util.loadVolume(self.vsc.vtVars['fixedCropPath'],
returnNode=True)
croppedFixedNode.SetName(fixedVolumeNode.GetName() + "_F_Crop")
self.vsc.vtVars['movingCropPath'] = self.vsc.runCropping(
movingVolumeNode, movingPointT, self.vsc.vtVars['croppingLength'],
self.vsc.vtVars['RSxyz'], self.vsc.vtVars['hrChk'], 0)
[success, croppedMovingNode
] = slicer.util.loadVolume(self.vsc.vtVars['movingCropPath'],
returnNode=True)
croppedMovingNode.SetName(movingVolumeNode.GetName() + "_M_Crop")
print(
"************ Register cropped moving image to cropped fixed image **********************"
)
cTI = self.vsc.runElastix(self.vsc.vtVars['elastixBinPath'],
self.vsc.vtVars['fixedCropPath'],
self.vsc.vtVars['movingCropPath'],
self.vsc.vtVars['outputPath'],
self.vsc.vtVars['parsPath'],
self.vsc.vtVars['noOutput'], "336")
#copyfile(resTransPathOld, resTransPath)
#genrates deformation field
cTR = self.vsc.runTransformix(self.vsc.vtVars['transformixBinPath'],
self.vsc.vtVars['movingCropPath'],
self.vsc.vtVars['outputPath'],
resTransPath,
self.vsc.vtVars['noOutput'], "339")
# rename fthe file:
os.rename(resOldDefPath, resDefPath)
print(
"************ Load deformation field Transform **********************"
)
[success, vtTransformNode] = slicer.util.loadTransform(resDefPath,
returnNode=True)
vtTransformNode.SetName(transNodeName)
print(
"************ Transform The Original Moving image **********************"
)
movingVolumeNode.SetAndObserveTransformNodeID(vtTransformNode.GetID())
#export seg to lbl then export back with input image as reference
slicer.vtkSlicerTransformLogic().hardenTransform(
movingVolumeNode) # apply the transform
fnm = os.path.join(self.vsc.vtVars['outputPath'],
movingVolumeNode.GetName() + "_Registered.nrrd")
sR = slicer.util.saveNode(movingVolumeNode, fnm)
[success,
registeredMovingVolumeNode] = slicer.util.loadVolume(fnm,
returnNode=True)
registeredMovingVolumeNode.SetName(movingVolumeNode.GetName() +
"_Registered")
#remove the tempnode and load the original
slicer.mrmlScene.RemoveNode(movingVolumeNode)
[success, movingVolumeNode] = slicer.util.loadVolume(movingPath,
returnNode=True)
movingVolumeNode.SetName(
os.path.splitext(
os.path.basename(
movingVolumeNode.GetStorageNode().GetFileName()))[0])
if (cTI == 0) and (cTR == 0):
print("No error is reported during registeration ...")
else:
print("error happened during registration ")
#endif
#Remove temporary files and nodes:
self.vsc.removeTmpsFiles()
print(
"================= Cochlea registration is complete ====================="
)
logging.info('Processing completed')
return registeredMovingVolumeNode
def run(self, inputVolumeNode, inputFiducialNode, cochleaSide):
logging.info('Processing started')
self.vsc = VisSimCommon.VisSimCommonLogic()
self.vsc.setGlobalVariables(0)
self.inputVolumeNode = inputVolumeNode
self.inputFiducialNode = inputFiducialNode
# modality type CBCT, CT or MRI
# it seems using CBCT atlas is enough
Styp = "Dv"
# segmentation atlas model paths
modelPath = os.path.join(
self.vsc.vtVars['modelPath'],
"Mdl" + Styp + cochleaSide + "c" + self.vsc.vtVars['imgType'])
modelSegPath = os.path.join(
self.vsc.vtVars['modelPath'],
"Mdl" + Styp + cochleaSide + "cS.seg" + self.vsc.vtVars['imgType'])
modelImgStPath = os.path.join(self.vsc.vtVars['modelPath'],
"Mdl" + Styp + cochleaSide + "cSt.fcsv")
# set the results paths:
resTransPathOld = os.path.join(self.vsc.vtVars['outputPath'],
"TransformParameters.0.txt")
resTransPath = resTransPathOld[0:-6] + 'Pars.txt'
resOldDefPath = os.path.join(
self.vsc.vtVars['outputPath'],
"deformationField" + self.vsc.vtVars['imgType'])
resDefPath = os.path.join(
self.vsc.vtVars['outputPath'],
inputVolumeNode.GetName() + "_dFld" + self.vsc.vtVars['imgType'])
inputImgName = os.path.basename(
os.path.splitext(
inputVolumeNode.GetStorageNode().GetFileName())[0])
segNodeName = inputVolumeNode.GetName() + "_S.Seg"
stpNodeName = inputVolumeNode.GetName() + "_StPts"
transNodeName = inputVolumeNode.GetName() + "_Transform"
self.vsc.removeOtputsFolderContents()
# check if the model is found
if not os.path.isfile(modelPath):
print("ERROR: model is not found", file=sys.stderr)
print("modelPath: " + modelPath)
return -1
# endif
# Get IJK point from the fiducial to use in cropping
inputPoint = self.vsc.ptRAS2IJK(inputFiducialNode, inputVolumeNode, 0)
# TODO: add better condition
if np.sum(inputPoint) == 0:
print("Error: select cochlea point")
return -1
#endif
fnm = os.path.join(self.vsc.vtVars['outputPath'],
inputVolumeNode.GetName() + "_Cochlea_Pos.fcsv")
sR = slicer.util.saveNode(inputFiducialNode, fnm)
#Remove old resulted nodes
for node in slicer.util.getNodes():
if (segNodeName == node): slicer.mrmlScene.RemoveNode(node) #endif
if (transNodeName == node):
slicer.mrmlScene.RemoveNode(node) #endif
#endfor
inputPointT = self.vsc.v2t(inputPoint)
print("=================== Cropping =====================")
self.vsc.vtVars['intputCropPath'] = self.vsc.runCropping(
inputVolumeNode, inputPointT, self.vsc.vtVars['croppingLength'],
self.vsc.vtVars['RSxyz'], self.vsc.vtVars['hrChk'], 0)
[success, croppedNode
] = slicer.util.loadVolume(self.vsc.vtVars['intputCropPath'],
returnNode=True)
croppedNode.SetName(inputVolumeNode.GetName() + "_Crop")
print(
"************ Register model to cropped input image **********************"
)
cTI = self.vsc.runElastix(self.vsc.vtVars['elastixBinPath'],
self.vsc.vtVars['intputCropPath'], modelPath,
self.vsc.vtVars['outputPath'],
self.vsc.vtVars['parsPath'],
self.vsc.vtVars['noOutput'], "292")
copyfile(resTransPathOld, resTransPath)
#genrates deformation field
cTR = self.vsc.runTransformix(self.vsc.vtVars['transformixBinPath'],
modelPath, self.vsc.vtVars['outputPath'],
resTransPath,
self.vsc.vtVars['noOutput'], "295")
# rename fthe file:
os.rename(resOldDefPath, resDefPath)
print(
"************ Load deformation field Transform **********************"
)
[success, vtTransformNode] = slicer.util.loadTransform(resDefPath,
returnNode=True)
vtTransformNode.SetName(transNodeName)
print(
"************ Transform The Segmentation **********************")
[success, vtSegNode] = slicer.util.loadSegmentation(modelSegPath,
returnNode=True)
vtSegNode.SetName(segNodeName)
vtSegNode.SetAndObserveTransformNodeID(vtTransformNode.GetID())
#export seg to lbl then export back with input image as reference
slicer.vtkSlicerTransformLogic().hardenTransform(
vtSegNode) # apply the transform
vtSegNode.CreateClosedSurfaceRepresentation()
fnm = os.path.join(self.vsc.vtVars['outputPath'],
vtSegNode.GetName() + ".nrrd")
sR = slicer.util.saveNode(vtSegNode, fnm)
print(
"************ Transform The Scala Points **********************")
#TODO:check the right side model
#TODO:add scala vestibuli model
# transform the Scala Tympani Points for length Computation
[success,
vtImgStNode] = slicer.util.loadMarkupsFiducialList(modelImgStPath,
returnNode=True)
vtImgStNode.GetDisplayNode().SetSelectedColor(1, 0, 0)
vtImgStNode.GetDisplayNode().SetTextScale(0.5)
vtImgStNode.SetName(stpNodeName)
vtImgStNode.SetAndObserveTransformNodeID(vtTransformNode.GetID())
slicer.vtkSlicerTransformLogic().hardenTransform(
vtImgStNode) # apply the transform
fnm = os.path.join(self.vsc.vtVars['outputPath'],
vtImgStNode.GetName() + ".fcsv")
sR = slicer.util.saveNode(vtImgStNode, fnm)
# Display the result if no error
# Clear cochlea location labels
if (cTI == 0) and (cTR == 0):
# change the model type from vtk to stl
msn = slicer.vtkMRMLModelStorageNode()
msn.SetDefaultWriteFileExtension('stl')
slicer.mrmlScene.AddDefaultNode(msn)
print("get Cochlea information")
tableName = inputVolumeNode.GetName() + "_tbl"
# create only if it does not exist
try:
spTblNode = slicer.util.getNode(tableName)
except Exception as e:
print(e)
spTblNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLTableNode")
spTblNode.SetName(tableName)
#endtry
spTblNode = self.vsc.getItemInfo(vtSegNode, croppedNode, spTblNode,
0)
for i in range(0, 8):
spTblNode.RemoveColumn(3)
#endfor
spTblNode.GetTable().GetColumn(1).SetName("Size (mm^3)")
spTblNode.GetTable().GetColumn(2).SetName("Length (mm)")
spTblNode.SetCellText(0, 0, "Scala Tympani")
spTblNode.SetCellText(1, 0, "Scala Vestibuli")
#spTblNode.resultsTableNode.SetCellText(0,2,"ST value")
#spTblNode.resultsTableNode.SetCellText(1,2,"0")
self.vsc.getFiducilsDistance(vtImgStNode, spTblNode)
spTblNode.RemoveRow(spTblNode.GetNumberOfRows())
self.spTblNode = spTblNode
else:
print("error happened during segmentation ")
#endif
#Remove temporary files and nodes:
self.vsc.removeTmpsFiles()
print(
"================= Cochlea analysis is complete ====================="
)
logging.info('Processing completed')
return vtSegNode
def run(self, inputVolumeNode, inputFiducialNode, methodID):
self.vsc = VisSimCommon.VisSimCommonLogic()
self.vsc.setGlobalVariables(1)
self.inputVolumeNode = inputVolumeNode
self.inputFiducialNode = inputFiducialNode
self.outputPaths = []
self.intputCropPaths = []
self.inputPoints = []
self.modelPaths = []
vtIDsLst = []
missingVt = list(range(1, 8))
rng = 7 # number of vertebra
for j in range(7):
vtIDsLst.append([0, 0, 0])
self.intputCropPaths.append("")
self.inputPoints.append([0, 0, 0])
#endfor
for j in range(inputFiducialNode.GetNumberOfFiducials()):
l = inputFiducialNode.GetNthFiducialLabel(j)
k = int(l[1])
missingVt[k - 1] = 0
inputFiducialNode.GetNthFiducialPosition(j, vtIDsLst[k - 1])
#endfor
if sum(missingVt) > 0:
vtIDsLst = self.getAllVertebraePoints(vtIDsLst, inputFiducialNode)
#endif
#create a table for vertebra information
tableName = inputVolumeNode.GetName() + "_tbl"
spTblNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLTableNode")
spTblNode.SetName(tableName)
spTblNode.AddEmptyRow()
spTblNode.GetTable().GetColumn(0).SetName("Vertebra")
spTblNode.AddColumn()
spTblNode.GetTable().GetColumn(1).SetName("Volume mm3")
spTblNode.AddColumn()
spTblNode.GetTable().GetColumn(2).SetName("CoM X")
spTblNode.AddColumn()
spTblNode.GetTable().GetColumn(3).SetName("CoM Y")
spTblNode.AddColumn()
spTblNode.GetTable().GetColumn(4).SetName("CoM Z")
self.spTblNode = spTblNode
# create output paths
for i in range(rng):
#get other points
#create a list from the points
vtID = i + 1
outputPath = self.vsc.vtVars[
'outputPath'] + "," + inputVolumeNode.GetName() + "_C" + str(
vtID)
outputPath = os.path.join(*outputPath.split(","))
self.outputPaths.append(outputPath)
modelCropPath = self.vsc.vtVars[
'modelPath'] + ',Default' + ",Mdl" + self.vsc.vtVars[
'Styp'] + str(vtID) + self.vsc.vtVars['imgType']
modelCropPath = os.path.join(*modelCropPath.split(","))
self.modelPaths.append(modelCropPath)
if not os.path.exists(self.outputPaths[i]):
os.makedirs(self.outputPaths[i])
#endif
#endfor
# try parallel but slicer crash
# try if we collect information then run popen
"""
i=range(rng)
pool = ThreadPool(9)
b=pool.map(self.runCroppingAll,i)
pool.close()
pool.join()
"""
#--------------------- process ------------------------------------
for i in range(rng):
vtID = i + 1
segNodeName = self.inputVolumeNode.GetName() + "_C" + str(
vtID) + ".Seg"
ligPtsNodeName = self.inputVolumeNode.GetName() + "_C" + str(
vtID) + "_LigPts"
transNodeName = self.inputVolumeNode.GetName() + "_C" + str(
vtID) + "_Transform"
self.runCroppingAll(i)
self.runElastixAll(i)
self.resTransPath = os.path.join(self.outputPaths[i],
"TransformParameters.0.txt")
resOldDefPath = os.path.join(
self.outputPaths[i],
"deformationField" + self.vsc.vtVars['imgType'])
resDefPath = os.path.join(
self.outputPaths[i],
self.inputVolumeNode.GetName() + "_C" + str(vtID) + "_dFld" +
self.vsc.vtVars['imgType'])
#remove old result files:
if os.path.isfile(resOldDefPath):
os.remove(resOldDefPath)
if os.path.isfile(resDefPath):
os.remove(resDefPath)
self.runTransformixAll(i)
os.rename(resOldDefPath, resDefPath)
[success,
vtTransformNode] = slicer.util.loadTransform(resDefPath,
returnNode=True)
vtTransformNode.SetName(transNodeName)
modelSegPath = self.vsc.vtVars['modelPath'] + self.vsc.vtVars[
'segT'] + ",Mdl" + self.vsc.vtVars['Styp'] + str(
vtID) + self.vsc.vtVars['sgT'] + self.vsc.vtVars['imgType']
modelSegPath = os.path.join(*modelSegPath.split(","))
[success,
vtResultSegNode] = slicer.util.loadSegmentation(modelSegPath,
returnNode=True)
vtResultSegNode.SetName(segNodeName)
vtResultSegNode.SetAndObserveTransformNodeID(
vtTransformNode.GetID()
) # movingAllMarkupNode should be loaded, the file contains all points
slicer.vtkSlicerTransformLogic().hardenTransform(vtResultSegNode)
vtResultSegNode.CreateClosedSurfaceRepresentation()
fnm = os.path.join(self.outputPaths[i],
vtResultSegNode.GetName() + ".nrrd")
sR = slicer.util.saveNode(vtResultSegNode, fnm)
if self.vsc.s2b(self.vsc.vtVars['ligChk']):
modelCropImgLigPtsPath = self.vsc.vtVars[
'modelPath'] + self.vsc.vtVars[
'vtPtsLigDir'] + "," + self.vsc.vtVars['Styp'] + str(
vtID) + self.vsc.vtVars['vtPtsLigSuff'] + ".fcsv"
modelCropImgLigPtsPath = os.path.join(
*modelCropImgLigPtsPath.split(","))
[success, vtLigPtsNode] = slicer.util.loadMarkupsFiducialList(
modelCropImgLigPtsPath, returnNode=True)
vtLigPtsNode.GetDisplayNode().SetSelectedColor(1, 0, 0)
vtLigPtsNode.GetDisplayNode().SetTextScale(0.5)
vtLigPtsNode.SetName(ligPtsNodeName)
vtLigPtsNode.SetAndObserveTransformNodeID(
vtTransformNode.GetID()
) # movingAllMarkupNode should be loaded, the file contains all points
slicer.vtkSlicerTransformLogic().hardenTransform(
vtLigPtsNode) # apply the transform
# needed in extract scaled model
self.vtLigPtsNode = vtLigPtsNode
fnm = os.path.join(self.outputPaths[i],
vtLigPtsNode.GetName() + ".fcsv")
sR = slicer.util.saveNode(vtLigPtsNode, fnm)
#endif
self.getVertebraInfoAll(i)
#endfor
self.spTblNode.RemoveRow(0)
self.vsc.vtVars['segNodeCoM'] = self.vsc.vtVars['segNodeCoM']
self.vtResultSegNode = vtResultSegNode
#Remove temporary files and nodes:
self.vsc.removeTmpsFiles()
return vtResultSegNode