def setup(self):
print(" ")
print("=======================================================")
print(" Remeshing Tools 2019 ")
print("=======================================================")
ScriptedLoadableModuleWidget.setup(self)
# Declare global labels
self.imtimeLbl = qt.QLabel(" Time: 00:00")
self.imtimeLbl.setFixedWidth(300)
self.qhtimeLbl = qt.QLabel(" Time: 00:00")
self.qhtimeLbl.setFixedWidth(300)
# Initialize GUI
self.initMainPanel()
self.logic = SlicerRemeshingLogic()
self.logic.setGlobalVariables()
self.logic.checkBinaries()
# change the model type from vtk to stl
msn = slicer.vtkMRMLModelStorageNode()
msn.SetDefaultWriteFileExtension('stl')
slicer.mrmlScene.AddDefaultNode(msn)
def initializeModelNode(node): displayNode = slicer.vtkMRMLModelDisplayNode() storageNode = slicer.vtkMRMLModelStorageNode() displayNode.SetScene(slicer.mrmlScene) storageNode.SetScene(slicer.mrmlScene) slicer.mrmlScene.AddNode(displayNode) slicer.mrmlScene.AddNode(storageNode) node.SetAndObserveDisplayNodeID(displayNode.GetID()) node.SetAndObserveStorageNodeID(storageNode.GetID())
def initializeModelNode(node):
displayNode = slicer.vtkMRMLModelDisplayNode()
storageNode = slicer.vtkMRMLModelStorageNode()
displayNode.SetScene(slicer.mrmlScene)
storageNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(displayNode)
slicer.mrmlScene.AddNode(storageNode)
node.SetAndObserveDisplayNodeID(displayNode.GetID())
node.SetAndObserveStorageNodeID(storageNode.GetID())
def runBtnClick(self):
self.runBtn.setText("...please wait")
self.runBtn.setStyleSheet("QPushButton{ background-color: red }")
slicer.app.processEvents()
# Get the cochlea location point
sr = self.inputPointEdt.text.strip()
sr = sr[1:-1]
self.inputPoint = map(int, sr.split(','))
#remove old files
shutil.rmtree(self.outputPath)
os.mkdir(self.outputPath)
Styp = "Dv"
side = "L"
if self.sideActivated: # right side
side = "R"
self.modelCropPath = self.modelPath + "/Mdl" + Styp + side + "c.nrrd"
self.modelCropSegPath = self.modelPath + "/Mdl" + Styp + side + "cS.nrrd"
self.modelCropImgStPath = self.modelPath + "/Mdl" + Styp + side + "cSt.nrrd"
resTransPath = self.outputPath + "/TransformParameters.0.txt"
res0ImgPath = self.outputPath + "/result.0.nrrd"
resImgPath = self.outputPath + "/result.nrrd"
# check if the model is found
if not isfile(self.modelCropPath):
print >> sys.stderr, "ERROR: model is not found"
return False
# endif
try: # is there a node loaded
self.inputNode = self.inputSelectorCoBx.currentNode()
except AttributeError:
print >> sys.stderr, "ERROR: No input volume, Bad Path or DICOM."
self.suppDICOM()
#end try
self.inputPath = self.inputNode.GetStorageNode().GetFileName()
self.inputFnm = basename(os.path.splitext(self.inputPath)[0])
# Remove old result
rNodes = slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode")
for f in rNodes:
if f.GetName()[0:3] == 'res':
slicer.mrmlScene.RemoveNode(f)
self.stm = time.time()
print("time:" + str(self.stm))
self.timeLbl.setText(" Time: 00:00")
if self.inputPointEdt.text == "[0, 0, 0]":
print("Error: select cochlea point")
return False
#endif
self.intputCropPath = self.doCropping(self.inputNode, self.inputPoint)
print("=================== Segmentation =====================")
print
print("************ Compute the Transform **********************")
# register the cropped image of the model
cmd = self.elastixBinPath + " -f " + self.intputCropPath + " -m " + self.modelCropPath + " -out " + self.outputPath + " -p " + self.parsPath + self.noOutput
print("Executing: " + cmd)
cTI = os.system(cmd)
errStr = "elastix error at line 601, check the log files"
self.chkElxER(
cTI, errStr) # Check if errors happen during elastix execution
print(
"************ Transform The Segmentation **********************")
# Apply the transformation to the segmentation image:
Cmd = self.transformixBinPath + " -in " + self.modelCropSegPath + " -out " + self.outputPath + " -tp " + resTransPath + self.noOutput
print("Executing... " + str(Cmd))
cTS = os.system(Cmd)
errStr = "Transformix error at line 611, check the log file"
self.chkElxER(
cTS, errStr) # Check if errors happen during elastix execution
#rename the result file
self.resImgLabelPath = self.outputPath + "/" + self.inputNode.GetName(
) + "-label.nrrd"
self.resultFnm = basename(os.path.splitext(self.resImgLabelPath)[0])
os.rename(resImgPath, self.resImgLabelPath)
print("************ Transform The Points **********************")
# transform the Scala Tympani Points for length Computation
Cmd = self.transformixBinPath + " -in " + self.modelCropImgStPath + " -out " + self.outputPath + " -tp " + resTransPath + self.noOutput
print("Executing... " + str(Cmd))
cTP = os.system(Cmd)
errStr = "Transformix error, transform points at line 623, check the log file"
self.chkElxER(
cTP, errStr) # Check if errors happen during elastix execution
#rename the result image file
self.resImgPtsPath = self.outputPath + "/" + self.inputNode.GetName(
) + "-IPtsSt.nrrd"
os.rename(resImgPath, self.resImgPtsPath)
# Load the image poins, calculat the length and crete the points
[success,
self.resImgPtsNode] = slicer.util.loadVolume(self.resImgPtsPath,
returnNode=True)
# Convert to points
self.image2points(self.resImgPtsNode)
# Display the result if no error
# Clear cochlea location labels
if (cTS == 0) and (cTP == 0):
#remove the temprary cropped file and node
os.remove(self.inputCropPath)
slicer.mrmlScene.RemoveNode(self.croppedNode)
# Remove old Fiducial nodes
nodes = slicer.util.getNodesByClass('vtkMRMLMarkupsFiducialNode')
for f in nodes:
if ((f.GetName() == "CochleaLocation")):
slicer.mrmlScene.RemoveNode(f)
# The result image file is loaded into the slicer scene.
[success, self.resultNode
] = slicer.util.loadLabelVolume(self.resImgLabelPath,
returnNode=True)
nodes = slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode")
for f in nodes:
match = re.search(r"result_[0-9]*", f.GetName())
if match:
self.resultFnm = f.GetName()
self.resultNode = slicer.util.getNode(self.resultFnm)
self.resultNode.SetName('result')
# Generate a .seg node
self.segNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLSegmentationNode')
self.segNode.SetName(self.inputFnm + "S")
slicer.modules.segmentations.logic(
).ImportLabelmapToSegmentationNode(self.resultNode, self.segNode)
#self.segNode.SetName(self.inputFnm+"S") #TODO check if this shoud be removed
sg = self.segNode.GetSegmentation()
st = sg.GetSegment("7")
st.SetName(self.inputFnm + "_St")
sv = sg.GetSegment("300")
sv.SetName(self.inputFnm + "_Sv")
#remove the temprary labelmap
slicer.mrmlScene.RemoveNode(self.resultNode)
# change the model type from vtk to stl
msn = slicer.vtkMRMLModelStorageNode()
msn.SetDefaultWriteFileExtension('stl')
slicer.mrmlScene.AddDefaultNode(msn)
# get Cochlea measuerments
self.getCochleaSize()
else:
print("error happened during segmentation ")
# TODO: find a reduced code to replace this block
lm = slicer.app.layoutManager()
r_logic = lm.sliceWidget("Red").sliceLogic()
r_cn = r_logic.GetSliceCompositeNode()
r_cn.SetBackgroundVolumeID(self.inputNode.GetID())
y_logic = lm.sliceWidget("Yellow").sliceLogic()
y_cn = y_logic.GetSliceCompositeNode()
y_cn.SetBackgroundVolumeID(self.inputNode.GetID())
g_logic = lm.sliceWidget("Green").sliceLogic()
g_cn = g_logic.GetSliceCompositeNode()
g_cn.SetBackgroundVolumeID(self.inputNode.GetID())
print(
"================= Cochlea analysis is complete ====================="
)
# Update time label
self.etm = time.time()
tm = self.etm - self.stm
self.timeLbl.setText("Time: " + str(tm) + " seconds")
self.runBtn.setText("Run")
self.runBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
slicer.app.processEvents()
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 run(self, inputVolumeNode, inputFiducialNode, side):
#to be used fromoutside we need to do:
# import CochleaSeg
# logic= CochleaSeg.CochleaSegLogic()
# logic.run(with the parameters above)
"""
Run the actual algorithm
"""
# we need to run this again in case of external call
self.setGlobalVariables()
self.hasImageData(inputVolumeNode)
self.inputVolumeNode = inputVolumeNode
self.inputFiducialNode = inputFiducialNode
# Create a temporary node as workaround for bad path or filename
#TODO: create a temp folder and remove temp node before display
tmpName= self.vissimPath+"/inputImage.nrrd"
slicer.util.saveNode( inputVolumeNode, tmpName)
[success, self.inputVolumeNode] = slicer.util.loadVolume(tmpName, returnNode=True)
self.inputVolumeNode.SetName("inputImage")
logging.info('Processing started')
# Get IJK point from the fiducial to use in cropping
self.inputPoint = self.ptRAS2IJK(self.inputFiducialNode,inputVolumeNode)
#remove old files if exist
if os.path.isdir(self.outputPath.strip()):
print("removing old output folder!")
shutil.rmtree(self.outputPath)
#endif
os.mkdir(self.outputPath)
# modality type CBCT, CT or MRI
# it seems using CBCT atlas is enough
Styp="Dv"
# segmentation atlas model paths
self.modelCropPath = self.modelPath + "/Mdl"+Styp+side+"c.nrrd"
self.modelCropSegPath = self.modelPath + "/Mdl"+Styp+side+"cS.nrrd"
self.modelCropImgStPath = self.modelPath + "/Mdl"+Styp+side+"cSt.nrrd"
# results paths
resTransPath = self.outputPath + "/TransformParameters.0.txt"
res0ImgPath = self.outputPath + "/result.0.nrrd"
resImgPath = self.outputPath + "/result.nrrd"
# check if the model is found
if not isfile(self.modelCropPath):
print >> sys.stderr, "ERROR: model is not found"
return False
# endif
self.inputPath = self.inputVolumeNode.GetStorageNode().GetFileName()
self.inputFnm = basename(os.path.splitext(self.inputPath)[0])
# Remove old nodes
rNodes = slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode")
for f in rNodes:
if f.GetName()[0:3]=='res':
slicer.mrmlScene.RemoveNode(f)
#endif
#endfor
# TODO: add better condition
if np.sum(self.inputPoint)== 0 :
print("Error: select cochlea point")
return False
#endif
print("=================== Cropping =====================")
self.intputCropPath = self.doCropping(self.inputVolumeNode, self.inputPoint, self.croppingLength)
print ("************ Register model to cropped input image **********************")
cTI = self.runElastix(self.intputCropPath, self.modelCropPath, self.outputPath, self.parsPath, self.noOutput, "554")
print ("************ Transform The Segmentation **********************")
cTS = self.runTransformix(self.modelCropSegPath, self.outputPath, resTransPath , self.noOutput, "556")
#rename the result file
self.resImgLabelPath = self.outputPath +"/"+ self.inputVolumeNode.GetName() +"-label.nrrd"
self.resultFnm = basename(os.path.splitext(self.resImgLabelPath)[0])
os.rename(resImgPath, self.resImgLabelPath)
print ("************ Transform The Points **********************")
# transform the Scala Tympani Points for length Computation
cTP = self.runTransformix(self.modelCropImgStPath, self.outputPath, resTransPath , self.noOutput, "556")
#rename the result image file
self.resImgPtsPath = self.outputPath +"/"+ self.inputVolumeNode.GetName() + "-IPtsSt.nrrd"
os.rename(resImgPath, self.resImgPtsPath )
# Load the image poins, calculat the length and crete the points
[success, self.resImgPtsNode] = slicer.util.loadVolume(self.resImgPtsPath, returnNode=True)
# Convert the image points to fiducials
print ("************ create fiducial from the scala transformed image **********************")
self.image2points(self.resImgPtsNode)
# Display the result if no error
# Clear cochlea location labels
if (cTS==0) and (cTP==0):
#remove the temprary cropped file and node
os.remove(self.inputCropPath)
slicer.mrmlScene.RemoveNode(self.croppedNode )
# Remove old Fiducial nodes
nodes = slicer.util.getNodesByClass('vtkMRMLMarkupsFiducialNode')
for f in nodes:
if ((f.GetName() == "CochleaLocation") ):
slicer.mrmlScene.RemoveNode(f)
# The result image file is loaded into the slicer scene.
[success , self.resultNode]=slicer.util.loadLabelVolume(self.resImgLabelPath,returnNode=True)
nodes = slicer.util.getNodesByClass("vtkMRMLScalarVolumeNode")
for f in nodes:
match = re.search(r"result_[0-9]*", f.GetName())
if match:
self.resultFnm = f.GetName()
self.resultNode = f
self.resultNode.SetName('result')
#endif
#endfor
# Generate a .seg node
self.segNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSegmentationNode')
self.segNode.SetName(self.inputFnm+"S")
slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(self.resultNode, self.segNode)
sg=self.segNode.GetSegmentation()
st=sg.GetSegment("7")
st.SetName(self.inputFnm+"_St")
sv=sg.GetSegment("300")
sv.SetName(self.inputFnm+"_Sv")
#remove the temprary loaded labelmap
slicer.mrmlScene.RemoveNode(self.resultNode )
# change the model type from vtk to stl
msn=slicer.vtkMRMLModelStorageNode()
msn.SetDefaultWriteFileExtension('stl')
slicer.mrmlScene.AddDefaultNode(msn)
# get Cochlea measuerments
self.getCochleaSize()
else:
print("error happened during segmentation ")
#endif
# TODO: find a reduced code to replace this block
lm = slicer.app.layoutManager()
r_logic = lm.sliceWidget("Red").sliceLogic()
r_cn = r_logic.GetSliceCompositeNode()
r_cn.SetBackgroundVolumeID(self.inputVolumeNode.GetID())
y_logic = lm.sliceWidget("Yellow").sliceLogic()
y_cn = y_logic.GetSliceCompositeNode()
y_cn.SetBackgroundVolumeID(self.inputVolumeNode.GetID())
g_logic = lm.sliceWidget("Green").sliceLogic()
g_cn = g_logic.GetSliceCompositeNode()
g_cn.SetBackgroundVolumeID(self.inputVolumeNode.GetID())
print("================= Cochlea analysis is complete =====================")
logging.info('Processing completed')
return True
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