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