import os import sys import unittest import vtk, qt, ctk, slicer from slicer.ScriptedLoadableModule import * import logging import parseDicom import vtkInterface as vi import fileIO import slicer import numpy as np import slicerNetwork import resample import json import re # # cardiacSPECT # class cardiacSPECT(ScriptedLoadableModule): """Uses ScriptedLoadableModule base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self, parent): ScriptedLoadableModule.__init__(self, parent) parent.title = "Cardiac SPECT" parent.categories = ["Examples"] parent.dependencies = [] parent.contributors = ["Andrej Studen (FMF/JSI)"] # replace with "Firstname Lastname (Org)" parent.helpText = """ Load dynamic cardiac SPECT data to Slicer """ parent.acknowledgementText = """ This module was developed within the frame of the ARRS sponsored medical physics research programe to investigate quantitative measurements of cardiac function using sestamibi-like tracers """ # replace with organization, grant and thanks. self.parent.helpText += self.getDefaultModuleDocumentationLink() self.parent = parent # # cardiacSPECTWidget # class cardiacSPECTWidget(ScriptedLoadableModuleWidget): """Uses ScriptedLoadableModuleWidget base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def setup(self): ScriptedLoadableModuleWidget.setup(self) self.selectRemote=fileIO.remoteFileSelector() try: self.network=slicer.modules.labkeySlicerPythonExtensionWidget.network except: self.network=slicerNetwork.labkeyURIHandler() configFile=os.path.join(os.path.expanduser('~'),'.cardiacSPECT','cardiacSPECT.json') self.logic=cardiacSPECTLogic(configFile) self.logic.setURIHandler(self.network) self.selectRemote.setMaster(self) # Instantiate and connect widgets ... dataButton = ctk.ctkCollapsibleButton() dataButton.text = "Data" self.layout.addWidget(dataButton) # Layout within the sample collapsible button dataFormLayout = qt.QFormLayout(dataButton) self.patientId=qt.QLineEdit(); dataFormLayout.addRow('Patient ID', self.patientId) self.refPatientId=qt.QLineEdit(); dataFormLayout.addRow('Reference Patient ID', self.refPatientId) patientLoadButton = qt.QPushButton("Load") patientLoadButton.toolTip="Load data from DICOM" dataFormLayout.addRow("Patient",patientLoadButton) patientLoadButton.clicked.connect(self.onPatientLoadButtonClicked) patientLoadNRRDButton = qt.QPushButton("Load NRRD") patientLoadNRRDButton.toolTip="Load data from NRRD" dataFormLayout.addRow("Patient",patientLoadNRRDButton) patientLoadNRRDButton.clicked.connect(self.onPatientLoadNRRDButtonClicked) loadSegmentationButton = qt.QPushButton("Load") loadSegmentationButton.toolTip="Load segmentation from server" dataFormLayout.addRow("Segmentation",loadSegmentationButton) loadSegmentationButton.clicked.connect(self.onLoadSegmentationButtonClicked) saveVolumeButton = qt.QPushButton("Save") saveVolumeButton.toolTip="Save volume to NRRD" dataFormLayout.addRow("Volume",saveVolumeButton) saveVolumeButton.clicked.connect(self.onSaveVolumeButtonClicked) saveSegmentationButton = qt.QPushButton("Save") saveSegmentationButton.toolTip="Save segmentation to NRRD" dataFormLayout.addRow("Segmentation",saveSegmentationButton) saveSegmentationButton.clicked.connect(self.onSaveSegmentationButtonClicked) saveTransformationButton = qt.QPushButton("Save") saveTransformationButton.toolTip="Save transformation to NRRD" dataFormLayout.addRow("Transformation",saveTransformationButton) saveTransformationButton.clicked.connect(self.onSaveTransformationButtonClicked) saveInputFunctionButton = qt.QPushButton("Save") saveInputFunctionButton.toolTip="Save InputFunction to NRRD" dataFormLayout.addRow("InputFunction",saveInputFunctionButton) saveInputFunctionButton.clicked.connect(self.onSaveInputFunctionButtonClicked) transformNodeButton = qt.QPushButton("Transform Nodes") transformNodeButton.toolTip="Transform node with patient based transform" dataFormLayout.addRow("Transform Nodes",transformNodeButton) transformNodeButton.clicked.connect(self.onTransformNodeButtonClicked) # Add vertical spacer self.layout.addStretch(1) #addFrameButton=qt.QPushButton("Add Frame") #addFrameButton.toolTip="Add frame to VTK" #dataFormLayout.addWidget(addFrameButton) #addFrameButton.connect('clicked(bool)',self.onAddFrameButtonClicked) #addCTButton=qt.QPushButton("Add CT") #addCTButton.toolTip="Add CT to VTK" #dataFormLayout.addWidget(addCTButton) #addCTButton.connect('clicked(bool)',self.onAddCTButtonClicked) # # Parameters Area # parametersCollapsibleButton = ctk.ctkCollapsibleButton() parametersCollapsibleButton.text = "Parameters" self.layout.addWidget(parametersCollapsibleButton) # Layout within the dummy collapsible button parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton) # # check box to trigger taking screen shots for later use in tutorials # hbox1=qt.QHBoxLayout() frameLabel = qt.QLabel() frameLabel.setText("Select frame") hbox1.addWidget(frameLabel) self.time_frame_select=qt.QSlider(qt.Qt.Horizontal) self.time_frame_select.valueChanged.connect(self.onTimeFrameSelect) #self.time_frame_select.connect('valueChanged()', self.onTimeFrameSelect) self.time_frame_select.setMinimum(0) self.time_frame_select.setMaximum(0) self.time_frame_select.setValue(0) self.time_frame_select.setTickPosition(qt.QSlider.TicksBelow) self.time_frame_select.setTickInterval(5) self.time_frame_select.toolTip = "Select the time frame" hbox1.addWidget(self.time_frame_select) parametersFormLayout.addRow(hbox1) hbox2 = qt.QHBoxLayout() meanROILabel = qt.QLabel() meanROILabel.setText("MeanROI") hbox2.addWidget(meanROILabel) self.meanROIVolume = qt.QLineEdit() self.meanROIVolume.setText("testVolume15") hbox2.addWidget(self.meanROIVolume) self.meanROISegment = qt.QLineEdit() self.meanROISegment.setText("Segment_1") hbox2.addWidget(self.meanROISegment) computeMeanROI = qt.QPushButton("Compute mean ROI") computeMeanROI.connect('clicked(bool)',self.onComputeMeanROIClicked) hbox2.addWidget(computeMeanROI) self.meanROIResult = qt.QLineEdit() self.meanROIResult.setText("0") hbox2.addWidget(self.meanROIResult) parametersFormLayout.addRow(hbox2) #row 3 hbox3 = qt.QHBoxLayout() drawTimePlot=qt.QPushButton("Draw ROI time plot") drawTimePlot.connect('clicked(bool)',self.onDrawTimePlotClicked) hbox3.addWidget(drawTimePlot) parametersFormLayout.addRow(hbox3) #dataFormLayout.addWidget(hbox) #row 4 hbox4 = qt.QHBoxLayout() countSegments=qt.QPushButton("Count segmentation segments") countSegments.connect('clicked(bool)',self.onCountSegmentsClicked) hbox4.addWidget(countSegments) self.countSegmentsDisplay=qt.QLineEdit() self.countSegmentsDisplay.setText("0") hbox4.addWidget(self.countSegmentsDisplay) parametersFormLayout.addRow(hbox4) # # Apply Button # self.applyButton = qt.QPushButton("Apply") self.applyButton.toolTip = "Run the algorithm." self.applyButton.enabled = False parametersFormLayout.addRow(self.applyButton) # connections self.applyButton.connect('clicked(bool)', self.onApplyButton) #self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect) #self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect) # Add vertical spacer self.layout.addStretch(1) self.resetPosition=1 def cleanup(self): pass def onApplyButton(self): pass #logic = cardiacSPECTLogic() #imageThreshold = self.imageThresholdSliderWidget.value def onBrowseButtonClicked(self): startDir=self.dataPath.text inputDir=qt.QFileDialog.getExistingDirectory(None, 'Select DICOM directory',startDir) self.dataPath.setText("file://"+inputDir) def onRemoteBrowseButtonClicked(self): self.selectRemote.show() def onDataLoadButtonClicked(self): self.logic.loadData(self) def onRemotePathTextChanged(self,str): self.dataPath.setText('labkey://'+str) def onTimeFrameSelect(self): it=self.time_frame_select.value selectionNode = slicer.app.applicationLogic().GetSelectionNode() print("Propagating CT volume") nodeName=self.patientId.text+'CT' node=slicer.mrmlScene.GetFirstNodeByName(nodeName) selectionNode.SetReferenceActiveVolumeID(node.GetID()) if self.resetPosition==1: self.resetPosition=0 slicer.app.applicationLogic().PropagateVolumeSelection(1) else: slicer.app.applicationLogic().PropagateVolumeSelection(0) print("Propagating SPECT volume") nodeName=self.patientId.text+'Volume'+str(it) node=slicer.mrmlScene.GetFirstNodeByName(nodeName) selectionNode.SetSecondaryVolumeID(node.GetID()) slicer.app.applicationLogic().PropagateForegroundVolumeSelection(0) node.GetDisplayNode().SetAndObserveColorNodeID('vtkMRMLColorTableNodeRed') lm = slicer.app.layoutManager() sID=['Red','Yellow','Green'] for s in sID: sliceLogic = lm.sliceWidget(s).sliceLogic() compositeNode = sliceLogic.GetSliceCompositeNode() compositeNode.SetForegroundOpacity(0.5) #make sure the viewer is matched to the volume print("Done") #to access sliceLogic (slice control) use #lcol=slicer.app.layoutManager().mrmlSliceLogics() (vtkCollection) #vtkMRMLSliceLogic are named by colors (Red,Green,Blue) def onComputeMeanROIClicked(self): s=self.logic.meanROI(self.meanROIVolume.text,self.meanROISegment.text) self.meanROIResult.setText(str(s)) def onDrawTimePlotClicked(self): n=self.time_frame_select.maximum+1 ft=self.logic.frame_time #find number of segments ns = self.logic.countSegments() #add the chart node cn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode()) for j in range(0,ns): #add node for data dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode()) dn.SetSize(n) dn.SetName(self.patientId.text+'_'+self.logic.getSegmentName(j)) dt=0; t0=0; for i in range(0,n): vol=self.patientId.text+"Volume"+str(i) fx=ft[i] fy=self.logic.meanROI(vol,j) dt=2*ft[i]-t0 t0+=dt dn.SetValue(i, 0, fx) dn.SetValue(i, 1, fy/dt) dn.SetValue(i, 2, 0) print("[{0} at {1:.2f}:{2:.2f}]".format(vol,fx,fy)) #fish the number of the segment cn.AddArray(self.logic.getSegmentName(j), dn.GetID()) cn.SetProperty('default', 'title', 'ROI time plot') cn.SetProperty('default', 'xAxisLabel', 'time [ms]') cn.SetProperty('default', 'yAxisLabel', 'Activity (arb)') #update the chart node cvns = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode') if cvns.GetNumberOfItems() == 0: cvn = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartViewNode()) else: cvn = cvns.GetItemAsObject(0) cvn.SetChartNodeID(cn.GetID()) def onCountSegmentsClicked(self): self.countSegmentsDisplay.setText(self.logic.countSegments()) def onPatientLoadButtonClicked(self): self.logic.loadPatient(self.patientId.text) self.time_frame_select.setMaximum(self.logic.frame_data.shape[3]-1) def onPatientLoadNRRDButtonClicked(self): self.logic.loadPatientNRRD(self.patientId.text) self.time_frame_select.setMaximum(len(self.logic.frame_time)) def onLoadSegmentationButtonClicked(self): self.logic.loadSegmentation(self.patientId.text) def onSaveVolumeButtonClicked(self): self.logic.storeVolumeNodes(self.patientId.text, self.time_frame_select.minimum,self.time_frame_select.maximum) def onSaveSegmentationButtonClicked(self): self.logic.storeSegmentation(self.patientId.text) def onSaveTransformationButtonClicked(self): self.logic.storeTransformation(self.patientId.text) def onSaveInputFunctionButtonClicked(self): self.logic.storeInputFunction(self.patientId.text) def onTransformNodeButtonClicked(self): self.logic.applyTransform(self.patientId.text, self.refPatientId.text, self.time_frame_select.minimum,self.time_frame_select.maximum) #def onAddFrameButtonClicked(self): # it=int(self.time_frame_select.text) # self.logic.addFrame(it) # def onAddCTButtonClicked(self): # self.logic.addCT() # # # cardiacSPECTLogic # class cardiacSPECTLogic(ScriptedLoadableModuleLogic): """This class should implement all the actual computation done by your module. The interface should be such that other python code can import this class and make use of the functionality without requiring an instance of the Widget. Uses ScriptedLoadableModuleLogic base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def __init__(self,config): ScriptedLoadableModuleLogic.__init__(self) self.pd=parseDicom.parseDicomLogic(self) self.resampler=resample.resampleLogic(None) fname=config try: f=open(fname) except OSError as e: print "Confgiuration error: OS error({0}): {1}".format(e.errno, e.strerror) return self.cfg=json.load(f) self.coreRelativePath=self.cfg["project"]+'/'+self.cfg['atFiles'] def setURIHandler(self,net): self.net=net self.pd.setURIHandler(net) def loadData(self,widget): inputDir=str(widget.dataPath.text) self.pd.readMasterDirectory(inputDir) self.frame_data, self.frame_time, self.frame_origin, \ self.frame_pixel_size, self.frame_orientation=self.pd.readNMDirectory(inputDir) self.ct_data,self.ct_origin,self.ct_pixel_size, \ self.ct_orientation=self.pd.readCTDirectory(inputDir) self.ct_orientation=vi.completeOrientation(self.ct_orientation) self.frame_orientation=vi.completeOrientation(self.frame_orientation) self.addCT('test') self.addFrames('test') widget.time_frame_select.setMaximum(self.frame_data.shape[3]-1) #additional message via qt qt.QMessageBox.information( slicer.util.mainWindow(), 'Slicer Python','Data loaded') def getFilespecPath(self,r): if self.cfg["remote"]==True: path=r['_labkeyurl_Series'] path=path[:path.rfind('/')] return "labkey://"+path else: path=os.path.join(self.cfg["dicomPath"],r["Study"],r["Series"]) return "file://"+path def loadPatient(self,patientId): print("Loading {}").format(patientId) ds=self.net.loadDataset("dinamic_spect/Patients","Imaging") for r in ds['rows']: if r['aliasID']==patientId: visit=r print visit dicoms=self.net.loadDataset("Test/Transfer","Imaging") for r in dicoms['rows']: if not r['PatientId']==visit['aliasID']: continue if abs(r['SequenceNum']-float(visit['nmMaster']))<0.1: masterPath=self.getFilespecPath(r) #masterPath="labkey://"+path if abs(r['SequenceNum']-float(visit['nmCorrData']))<0.1: nmPath=self.getFilespecPath(r) #nmPath="labkey://"+path if abs(r['SequenceNum']-float(visit['ctData']))<0.1: ctPath=self.getFilespecPath(r) #ctPath="labkey://"+path self.pd.readMasterDirectory(masterPath) self.frame_data, self.frame_time, self.frame_origin, \ self.frame_pixel_size, self.frame_orientation=self.pd.readNMDirectory(nmPath) self.ct_data,self.ct_origin,self.ct_pixel_size, \ self.ct_orientation=self.pd.readCTDirectory(ctPath) self.ct_orientation=vi.completeOrientation(self.ct_orientation) self.frame_orientation=vi.completeOrientation(self.frame_orientation) self.addCT(patientId) self.addFrames(patientId) def loadPatientNRRD(self,patientId): print("Loading NRRD {}").format(patientId) self.loadDummyInputFunction(patientId) dnsNode=slicer.util.getFirstNodeByName(patientId+'_Dummy') if dnsNode==None: print("Could not find dummy double array node") return n=dnsNode.GetSize(); self.frame_time=np.zeros(n); a=vtk.reference(1) for i in range(0,n): self.loadVolume(patientId,i) self.frame_time[i]=dnsNode.GetValue(i,0,a) self.loadCTVolume(patientId) self.loadSegmentation(patientId) def loadDummyInputFunction(self,patientId): self.loadNode(patientId,patientId+'_Dummy','DoubleArrayFile','.mcsv') def loadVolume(self,patientId,i): self.loadNode(patientId,patientId+'Volume'+str(i),'VolumeFile') def loadCTVolume(self,patientId): self.loadNode(patientId,patientId+'CT','VolumeFile') def loadSegmentation(self,patientId): self.loadNode(patientId,'Heart','SegmentationFile') def loadNode(self,patientId,fName,type,suffix='.nrrd'): relativePath=self.coreRelativePath+'/'+patientId labkeyFile=relativePath+'/'+fName+suffix print ("Remote: {}").format(labkeyFile) self.net.loadNode(labkeyFile,type,returnNode=True) def addNode(self,nodeName,v, lpsOrigin, pixel_size, lpsOrientation, dataType): # if dataType=0 it is CT data, which gets propagated to background an is #used to fit the view field dimensions # if dataType=1, it is SPECT data, which gets propagated to foreground #and is not fit; keeping window set from CT #nodeName='testVolume'+str(it) newNode=slicer.vtkMRMLScalarVolumeNode() newNode.SetName(nodeName) #pixel_size=[0,0,0] #pixel_size=v.GetSpacing() #print(pixel_size) #origin=[0,0,0] #origin=v.GetOrigin() v.SetOrigin([0,0,0]) v.SetSpacing([1,1,1]) ijkToRAS = vtk.vtkMatrix4x4() #think how to do this with image orientation rasOrientation=[-lpsOrientation[i] if (i%3 < 2) else lpsOrientation[i] for i in range(0,len(lpsOrientation))] rasOrigin=[-lpsOrigin[i] if (i%3<2) else lpsOrigin[i] for i in range(0,len(lpsOrigin))] for i in range(0,3): for j in range(0,3): ijkToRAS.SetElement(i,j,pixel_size[i]*rasOrientation[3*j+i]) ijkToRAS.SetElement(i,3,rasOrigin[i]) newNode.SetIJKToRASMatrix(ijkToRAS) newNode.SetAndObserveImageData(v) slicer.mrmlScene.AddNode(newNode) def addFrames(self,patientId): #convert data from numpy.array to vtkImageData #use time point it print "NFrames: {}".format(self.frame_data.shape[3]) for it in range(0,self.frame_data.shape[3]): frame_data=self.frame_data[:,:,:,it]; nodeName=patientId+'Volume'+str(it) self.addNode(nodeName, vi.numpyToVTK(frame_data,frame_data.shape), self.frame_origin, self.frame_pixel_size, self.frame_orientation,1) def addCT(self,patientId): nodeName=patientId+'CT' self.addNode(nodeName, #vi.numpyToVTK3D(self.ct_data, # self.ct_origin,self.ct_pixel_size), vi.numpyToVTK(self.ct_data,self.ct_data.shape), self.ct_origin,self.ct_pixel_size, self.ct_orientation,0) def rFromI(i,volumeNode): ijkToRas = vtk.vtkMatrix4x4() volumeNode.GetIJKToRASMatrix(ijkToRas) vImage=volumeNode.GetImageData() i1=list(vImage.GetPoint(i)) i1=i1.append(1) #ras are global coordinates (in mm) position_ras=ijkToRas.MultiplyPoint(i1) return position_ras[0:3] def IfromR(pos,volumeNode): fM=vtk.vtkMatrix4x4() volumeNode.GetRASToIJKMatrix(fM) fM.MultiplyPoint(pos) vImage=volumeNode.GetImageData() #nearest neighbor return vImage.FindPoint(pos[0:3]) def getMaskPos(self,mask,i): maskIJK=mask.GetPoint(i) maskIJK=[r-c for r,c in zip(maskIJK,mask.GetOrigin())] maskIJK=[r/s for r,s in zip(maskIJK,mask.GetSpacing())] #this is now in extent spacing, whitch ImageToWorldMatrix understands #to 4D vector for vtkMatrix4x4 handling maskIJK.append(1) #go to ras, global coordinates (in mm) maskImageToWorldMatrix=vtk.vtkMatrix4x4() mask.GetImageToWorldMatrix(maskImageToWorldMatrix) maskPos=maskImageToWorldMatrix.MultiplyPoint(maskIJK) return maskPos[0:3] def meanROI(self, volName1, i): s=0 #get the segmentation mask fNode=slicer.mrmlScene.GetNodesByClass("vtkMRMLSegmentationNode").GetItemAsObject(0) print "Found segmentation node: {}".format(fNode.GetName()) segNode=slicer.vtkMRMLSegmentationNode.SafeDownCast(fNode) #no python bindings for vtkSegmentation #if segNode.GetSegmentation().GetNumberOfSegments()==0 : # print("No segments available") # return 0 #edit here to change for more segments segment=segNode.GetSegmentation().GetNthSegmentID(int(i)) mask = segNode.GetBinaryLabelmapRepresentation(segment) if mask==None: print("Segment {} not found".format(segment)) return s print "Got mask for segment {}, npts {}".format(segment,mask.GetNumberOfPoints()) #get mask at (x,y,z) #mask.GetPointData().GetScalars().GetTuple1(mask.FindPoint([x,y,z])) #get the image data dataNode=slicer.mrmlScene.GetFirstNodeByName(volName1) dataImage=dataNode.GetImageData() # use IJK2RAS to get global coordinates dataRAStoIJK = vtk.vtkMatrix4x4() dataNode.GetRASToIJKMatrix(dataRAStoIJK) #allow for interpolation in segmentation pixels coeff=vtk.vtkImageBSplineCoefficients() coeff.SetInputData(dataImage) coeff.SetBorderMode(vtk.VTK_IMAGE_BORDER_CLAMP) #between 3 and 5 coeff.SetSplineDegree(5) coeff.Update() maskImageToWorldMatrix=vtk.vtkMatrix4x4() mask.GetImageToWorldMatrix(maskImageToWorldMatrix) ns=0 maskN=mask.GetNumberOfPoints() maskScalars=mask.GetPointData().GetScalars() maskOrigin=[0,0,0] maskOrigin=mask.GetOrigin() for i in range(0,maskN): #skip all points that are 0 if maskScalars.GetTuple1(i)==0: continue #get global coordinates of point i maskPos=self.getMaskPos(mask,i) #print("Evaluating at {}").format(maskPos) #convert from global to local dataPos=[0,0,0] #account for potentially applied transform on dataNode dataNode.TransformPointFromWorld(maskPos,dataPos) dataPos.append(1) dataIJK=dataRAStoIJK.MultiplyPoint(dataPos) #drop the 4th index dataIJK=dataIJK[0:3] #interpolate s+=coeff.Evaluate(dataIJK) ns+=1 return s/ns def countSegments(self): segNodeList=slicer.mrmlScene.GetNodesByClass("vtkMRMLSegmentationNode") if segNodeList.GetNumberOfItems()==0: return 0 fNode=segNodeList.GetItemAsObject(0) segNode=slicer.vtkMRMLSegmentationNode.SafeDownCast(fNode) if fNode==None: return 0 return segNode.GetSegmentation().GetNumberOfSegments() def getSegmentName(self,i): segNodeList=slicer.mrmlScene.GetNodesByClass("vtkMRMLSegmentationNode") if segNodeList.GetNumberOfItems()==0: return "NONE" fNode=segNodeList.GetItemAsObject(0) segNode=slicer.vtkMRMLSegmentationNode.SafeDownCast(fNode) if fNode==None: return "NONE" return segNode.GetSegmentation().GetSegment(segNode.GetSegmentation().GetNthSegmentID(i)).GetName() def storeNodeRemote(self,relativePath,nodeName): labkeyPath=self.pd.net.GetLabkeyPathFromRelativePath(relativePath) print ("Remote: {}").format(labkeyPath) #checks if exists self.pd.net.mkdir(labkeyPath) localPath=self.pd.net.GetLocalPathFromRelativePath(relativePath) localPath.replace('/',os.path.sep) node=slicer.mrmlScene.GetFirstNodeByName(nodeName) if node==None: print("Node {} not found").format(nodeName) return suffix=".nrrd" if node.__class__.__name__=="vtkMRMLDoubleArrayNode": suffix=".mcsv" if (node.__class__.__name__=="vtkMRMLTransformNode" or node.__class__.__name__=="vtkMRMLGridTransformNode"): suffix=".h5" fileName=re.sub(r'_RS$',r'',nodeName)+suffix if not os.path.isdir(localPath): os.mkdir(localPath) file=os.path.join(localPath,fileName) slicer.util.saveNode(node,file) print("Stored to: {}").format(file) f=open(file,"rb") remoteFile=labkeyPath+'/'+fileName self.pd.net.put(remoteFile,f.read()) def storeVolumeNodes(self,patientId,n1,n2): #n1=self.time_frame.minimum; #n2=self.time_frame.maximum relativePath=self.coreRelativePath+'/'+patientId print("Store CT") nodeName=patientId+'CT' #prefer resampled testNode=slicer.util.getFirstNodeByName(nodeName+"_RS") if testNode: nodeName=nodeName+"_RS" self.storeNodeRemote(relativePath,nodeName) print("Storing NM from {} to {}").format(n1,n2) n=n2-n1+1 for i in range(n): it=i+n1 nodeName=patientId+'Volume'+str(it) #prefer resampled testNode=slicer.util.getFirstNodeByName(nodeName+"_RS") if testNode: nodeName=nodeName+"_RS" self.storeNodeRemote(relativePath,nodeName) self.storeDummyInputFunction(patientId) def storeSegmentation(self,patientId): relativePath=self.coreRelativePath+'/'+patientId segNodeName="Heart" self.storeNodeRemote(relativePath,segNodeName) def storeInputFunction(self,patientId): self.calculateInputFunction(patientId) relativePath=self.coreRelativePath+'/'+patientId doubleArrayNodeName=patientId+'_Ventricle' self.storeNodeRemote(relativePath,doubleArrayNodeName) def storeDummyInputFunction(self,patientId): self.calculateDummyInputFunction(patientId) relativePath=self.coreRelativePath+'/'+patientId doubleArrayNodeName=patientId+'_Dummy' self.storeNodeRemote(relativePath,doubleArrayNodeName) def storeTransformation(self,patientId): relativePath=self.coreRelativePath+'/'+patientId transformNodeName=patientId+"_DF" self.storeNodeRemote(relativePath,transformNodeName) def applyTransform(self, patientId,refPatientId,n1,n2): if patientId == refPatientId: print("Transform [{}] and reference [{}] are the same".format(patientId, refPatientId)) return transformNodeName=patientId+"_DF" transformNode=slicer.util.getFirstNodeByName(transformNodeName) if transformNode==None: print("Transform node [{}] not found").format(transformNodeName) return n=n2-n1+1 for i in range(n): it=i+n1 nodeName=patientId+'Volume'+str(it) node=slicer.util.getFirstNodeByName(nodeName) if node==None: continue node.SetAndObserveTransformNodeID(transformNode.GetID()) refNodeName=refPatientId+'Volume'+str(it) refNode=slicer.util.getFirstNodeByName(refNodeName) if refNode!=None: self.resampler.rebinNode(node,refNode) print("Completed transformation {}").format(it) nodeName=patientId+'CT' node=slicer.util.getFirstNodeByName(nodeName) if not node==None: node.SetAndObserveTransformNodeID(transformNode.GetID()) refNodeName=refPatientId+'CT' refNode=slicer.util.getFirstNodeByName(refNodeName) if refNode!=None: self.resampler.rebinNode(node,refNode) def calculateInputFunction(self,patientId): n=len(self.frame_time) dnsNodeName=patientId+'_Ventricle' dns = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLDoubleArrayNode',dnsNodeName) if dns.GetNumberOfItems() == 0: dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode()) dn.SetName(dnsNodeName) else: dn = dns.GetItemAsObject(0) dn.SetSize(n) fNodes=slicer.mrmlScene.GetNodesByClass("vtkMRMLSegmentationNode") if fNodes.GetNumberOfItems() == 0: return fNode=fNodes.GetItemAsObject(0) segNode=slicer.vtkMRMLSegmentationNode.SafeDownCast(fNode) segmentation=segNode.GetSegmentation() juse=-1 for j in range(0,segmentation.GetNumberOfSegments()): segmentID=segNode.GetSegmentation().GetNthSegmentID(j) segment=segNode.GetSegmentation().GetSegment(segmentID) if segment.GetName()=='Ventricle': juse=j break if juse<0: print 'Failed to find Ventricle segment' return dt=0; t0=0; ft=self.frame_time for i in range(0,n): vol=patientId+"Volume"+str(i) fx=ft[i] fy=self.meanROI(vol,juse) dt=2*ft[i]-t0 t0+=dt dn.SetValue(i, 0, fx) dn.SetValue(i, 1, fy/dt) dn.SetValue(i, 2, 0) print("[{0} at {1:.2f}:{2:.2f}]".format(vol,fx,fy)) def calculateDummyInputFunction(self,patientId): n=self.frame_data.shape[3] dnsNodeName=patientId+'_Dummy' dns = slicer.mrmlScene.GetNodesByClassByName('vtkMRMLDoubleArrayNode',dnsNodeName) if dns.GetNumberOfItems() == 0: dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode()) dn.SetName(dnsNodeName) else: dn = dns.GetItemAsObject(0) dn.SetSize(n) ft=self.frame_time for i in range(0,n): fx=ft[i] dn.SetValue(i, 0, fx) dn.SetValue(i, 1, 0) dn.SetValue(i, 2, 0) class cardiacSPECTTest(ScriptedLoadableModuleTest): """ This is the test case for your scripted module. Uses ScriptedLoadableModuleTest base class, available at: https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py """ def setUp(self): """ Do whatever is needed to reset the state - typically a scene clear will be enough. """ slicer.mrmlScene.Clear(0) def runTest(self): """Run as few or as many tests as needed here. """ self.setUp() self.test_cardiacSPECT1() def test_cardiacSPECT1(self): """ Ideally you should have several levels of tests. At the lowest level tests should exercise the functionality of the logic with different inputs (both valid and invalid). At higher levels your tests should emulate the way the user would interact with your code and confirm that it still works the way you intended. One of the most important features of the tests is that it should alert other developers when their changes will have an impact on the behavior of your module. For example, if a developer removes a feature that you depend on, your test should break so they know that the feature is needed. """ self.delayDisplay("Starting the test") # # first, get some data # self.delayDisplay('Test passed!')