Пример #1
0
  def vtkImageDataToPNG(self,imageData,method='VTK'):
    """Return a buffer of png data using the data
    from the vtkImageData.
    """
    if method == 'PIL':
      if imageData:
        imageData.Update()
        imageScalars = imageData.GetPointData().GetScalars()
        imageArray = vtk.util.numpy_support.vtk_to_numpy(imageScalars)
        d = imageData.GetDimensions()
        im = Image.fromarray( numpy.flipud( imageArray.reshape([d[1],d[0],4]) ) )
      else:
        # no data available, make a small black opaque image
        a = numpy.zeros(100*100*4, dtype='uint8').reshape([100,100,4])
        a[:,:,3] = 255
        im = Image.fromarray( a )
      if size:
        im.thumbnail((size,size), Image.ANTIALIAS)
      pngStringIO = StringIO.StringIO()
      im.save(pngStringIO, format="PNG")
      pngData = pngStringIO.getvalue()
    elif method == 'VTK':
      writer = vtk.vtkPNGWriter()
      writer.SetWriteToMemory(True)
      writer.SetInput(imageData)
      writer.Write()
      result = writer.GetResult()
      pngArray = vtk.util.numpy_support.vtk_to_numpy(result)
      pngStringIO = StringIO.StringIO()
      pngStringIO.write(pngArray)
      pngData = pngStringIO.getvalue()

    return pngData
def ImageModelSnapshot(imageNode, labelNode, outputImagePath, progress_filename):   
    castScalarToInt(imageNode)
    castScalarToInt(labelNode)
     
    # center label to origin of image, if needed 
    #labelNode.SetOrigin(imageNode.GetOrigin()) 
    
    try:
        minBounds, maxBounds = getCropBoundaries(labelNode)
        
        zoomImageNode = cropToZoom(imageNode, minBounds, maxBounds, label=False)
        zoomLabelNode = cropToZoom(labelNode, minBounds, maxBounds, label=True)
        
        sitkZoomLabelNode = su.PullFromSlicer(zoomLabelNode.GetName())
        zoomLabelNodeArray = sitk.GetArrayFromImage(sitkZoomLabelNode)
        zoomLabelNodeArray = np.where(zoomLabelNodeArray == 0, np.NAN, zoomLabelNodeArray)
        
        # Find index of Z axis slice with largest surface area in the label node
        maxZind = findLargestSurfaceAreaSlice(zoomLabelNodeArray)
        
        outputImage = modelHandler(zoomImageNode, zoomLabelNode, maxZind)
        
        writer=vtk.vtkPNGWriter()
        writer.SetFileName(outputImagePath)
        writer.SetInputData(outputImage)
        writer.Write()
        
        return(maxZind)
      
    except Exception, e:
        with open(progress_filename,mode='a') as printfile: printfile.write('ERROR: ' + str(e) + '\n\n')
        print "ERROR: Error Creating", outputImagePath, str(e) 
        return(-1,-1,-1)
Пример #3
0
    def picasaUploadPicture(self, snapshotNodeId, snapshotName, snapshotDescription, albumId, tags=[]):
        """Upload a snapshot node to the specified album, with a list of tags."""
        self.checkLogin()

        if SlicerUtil.IsDevelopment:
            print ("Uploading image to Picasa")
            print ("Id: %s" % snapshotNodeId)
            print ("Name: %s" % snapshotName)
            print ("Description: %s" % snapshotDescription)
            print ("Album: %s" % albumId)
            print ("Tags:")
            print (tags)

        #     time.sleep(3)
        #     return

        snapshotNode = slicer.mrmlScene.GetNodeByID(snapshotNodeId)

        # Save the image to a temp file
        pngWriter = vtk.vtkPNGWriter()
        snapShotImage = snapshotNode.GetScreenShot()
        pngWriter.SetInputData(snapShotImage)
        filePath = "{0}/{1}.png".format(self.localStoragePath, snapshotName)
        pngWriter.SetFileName(filePath)
        pngWriter.Write()

        albumUrl = "/data/feed/api/user/default/albumid/" + albumId

        # Upload to Picasa
        self.gd_client.InsertPhotoSimple(
            albumUrl, snapshotName, snapshotDescription, filePath, content_type="image/png", keywords=tags
        )
Пример #4
0
  def picasaUploadPicture(self, snapshotNodeId, snapshotName, snapshotDescription, albumId, tags=[]):
    """Upload a snapshot node to the specified album, with a list of tags."""
    self.checkLogin()
   
    if (SlicerUtil.IsDevelopment):
      print ("Uploading image to Picasa")
      print(("Id: %s" % snapshotNodeId))
      print(("Name: %s" % snapshotName))
      print(("Description: %s" % snapshotDescription))
      print(("Album: %s" % albumId))
      print ("Tags:")
      print (tags)    
       
#     time.sleep(3)
#     return
   
    snapshotNode = slicer.mrmlScene.GetNodeByID(snapshotNodeId)
    
    # Save the image to a temp file
    pngWriter = vtk.vtkPNGWriter()  
    snapShotImage = snapshotNode.GetScreenShot()
    pngWriter.SetInputData(snapShotImage)
    filePath = "{0}/{1}.png".format(self.localStoragePath, snapshotName)
    pngWriter.SetFileName(filePath)
    pngWriter.Write()
    
    albumUrl = '/data/feed/api/user/default/albumid/' + albumId
    
    # Upload to Picasa
    self.gd_client.InsertPhotoSimple(albumUrl,
      snapshotName,
      snapshotDescription,
      filePath,
      content_type='image/png',
      keywords=tags)  
Пример #5
0
 def savePNGs(self, node, pattern):
     wlc = vtk.vtkImageMapToWindowLevelColors()
     wlc.SetInputData(node.GetImageData())
     if not node.GetLabelMap():
         displayNode = node.GetDisplayNode()
         wlc.SetWindow(displayNode.GetWindow())
         wlc.SetLevel(displayNode.GetLevel())
     wlc.Update()
     print(wlc.GetOutput().GetScalarRange())
     cast = vtk.vtkImageCast()
     cast.SetInputConnection(wlc.GetOutputPort())
     cast.SetOutputScalarTypeToUnsignedChar()
     pngWriter = vtk.vtkPNGWriter()
     pngWriter.SetFilePattern(pattern)
     pngWriter.SetInputConnection(cast.GetOutputPort())
     pngWriter.Write()
     slicer.modules.BitmapGeneratorWidget.pngWriter = pngWriter
def ImageModelSnapshot(imageNode, labelNode, outputImagePath,
                       progress_filename):
    castScalarToInt(imageNode)
    castScalarToInt(labelNode)

    # center label to origin of image, if needed
    #labelNode.SetOrigin(imageNode.GetOrigin())

    try:
        minBounds, maxBounds = getCropBoundaries(labelNode)

        zoomImageNode = cropToZoom(imageNode,
                                   minBounds,
                                   maxBounds,
                                   label=False)
        zoomLabelNode = cropToZoom(labelNode, minBounds, maxBounds, label=True)

        sitkZoomLabelNode = su.PullFromSlicer(zoomLabelNode.GetName())
        zoomLabelNodeArray = sitk.GetArrayFromImage(sitkZoomLabelNode)
        zoomLabelNodeArray = np.where(zoomLabelNodeArray == 0, np.NAN,
                                      zoomLabelNodeArray)

        # Find index of Z axis slice with largest surface area in the label node
        maxZind = findLargestSurfaceAreaSlice(zoomLabelNodeArray)

        outputImage = modelHandler(zoomImageNode, zoomLabelNode, maxZind)

        writer = vtk.vtkPNGWriter()
        writer.SetFileName(outputImagePath)
        writer.SetInputData(outputImage)
        writer.Write()

        return (maxZind)

    except Exception, e:
        with open(progress_filename, mode='a') as printfile:
            printfile.write('ERROR: ' + str(e) + '\n\n')
        print "ERROR: Error Creating", outputImagePath, str(e)
        return (-1, -1, -1)
Пример #7
0
    def vtkImageDataToPNG(self, imageData, method='VTK'):
        """Return a buffer of png data using the data
    from the vtkImageData.
    """
        if method == 'PIL':
            if imageData:
                imageData.Update()
                imageScalars = imageData.GetPointData().GetScalars()
                imageArray = vtk.util.numpy_support.vtk_to_numpy(imageScalars)
                d = imageData.GetDimensions()
                im = Image.fromarray(
                    numpy.flipud(imageArray.reshape([d[1], d[0], 4])))
            else:
                # no data available, make a small black opaque image
                a = numpy.zeros(100 * 100 * 4,
                                dtype='uint8').reshape([100, 100, 4])
                a[:, :, 3] = 255
                im = Image.fromarray(a)
            #if size:
            #im.thumbnail((size,size), Image.ANTIALIAS)
            pngStringIO = StringIO.StringIO()
            im.save(pngStringIO, format="PNG")
            pngData = pngStringIO.getvalue()
        elif method == 'VTK':
            writer = vtk.vtkPNGWriter()
            writer.SetWriteToMemory(True)
            writer.SetInputDataObject(imageData)
            writer.SetCompressionLevel(0)
            writer.Write()
            result = writer.GetResult()
            pngArray = vtk.util.numpy_support.vtk_to_numpy(result)
            pngStringIO = StringIO.StringIO()
            pngStringIO.write(pngArray)
            pngData = pngStringIO.getvalue()

        return pngData
Пример #8
0
    def generate(self,
                 volumeRenderingNode,
                 filePattern="/tmp/slice_%04d.png"):  # underscore not dash
        """

    """
        lm = slicer.app.layoutManager()
        # switch on the type to get the requested window
        # just the 3D window
        mainThreeDWidget = lm.threeDWidget(0).threeDView()
        viewNode = mainThreeDWidget.mrmlViewNode()

        # create the dummy threeD widget
        threeDWidget = slicer.qMRMLThreeDWidget()
        threeDWidget.resize(self.width, self.height)
        threeDWidget.setObjectName("ThreeDWidget%s" %
                                   viewNode.GetLayoutLabel())
        threeDWidget.setMRMLScene(slicer.mrmlScene)
        threeDWidget.setMRMLViewNode(viewNode)
        self.threeDWidget = threeDWidget
        threeDWidget.show()

        # configure the view
        cacheViewNode = slicer.vtkMRMLViewNode()
        cacheViewNode.Copy(viewNode)
        viewNode.SetBoxVisible(0)
        viewNode.SetAxisLabelsVisible(0)
        viewNode.SetBackgroundColor((1, 1, 1))
        viewNode.SetBackgroundColor2((1, 1, 1))

        roi = volumeRenderingNode.GetROINode()
        roiCenter = [
            0,
        ] * 3
        roiRadius = [
            0,
        ] * 3
        roi.GetXYZ(roiCenter)
        roi.GetRadiusXYZ(roiRadius)
        roi.SetDisplayVisibility(0)
        camera = vtk.vtkCamera()
        camera.SetFocalPoint(roiCenter)
        camera.SetPosition(roiCenter[0], roiCenter[1],
                           roiCenter[2] + roiRadius[2])
        camera.SetViewUp((0, 1, 0))

        mrmlCamera = slicer.util.getNode('Default Scene Camera')
        cacheCamera = vtk.vtkCamera()
        cacheCamera.DeepCopy(mrmlCamera.GetCamera())

        mrmlCamera.GetCamera().DeepCopy(camera)
        viewNode.SetRenderMode(slicer.vtkMRMLViewNode.Orthographic)

        # cycle through the slabs
        slabRadius = list(roiRadius)
        slabRadius[2] = self.slabThickness
        roi.SetRadiusXYZ(slabRadius)
        slabCounter = 0
        slabCenter = [roiCenter[0], roiCenter[1], roiCenter[2] - roiRadius[2]]
        slabTop = roiCenter[2] + roiRadius[2]

        threeDView = threeDWidget.threeDView()
        renderWindow = threeDView.renderWindow()
        self.delayDisplay("Starting render...", 300)

        while slabCenter[2] <= slabTop:
            roi.SetXYZ(slabCenter)
            threeDView.forceRender()
            windowToImage = vtk.vtkWindowToImageFilter()
            windowToImage.SetInput(renderWindow)
            writer = vtk.vtkPNGWriter()
            writer.SetInputConnection(windowToImage.GetOutputPort())
            filePath = filePattern % slabCounter
            windowToImage.Update()
            writer.SetFileName(filePath)
            writer.Write()
            slabCounter += 1
            slabCenter[2] = slabCenter[2] + self.slabSpacing

        # reset things
        viewNode.Copy(cacheViewNode)
        mrmlCamera.GetCamera().DeepCopy(cacheCamera)
        roi.SetXYZ(roiCenter)
        roi.SetRadiusXYZ(roiRadius)
        roi.SetDisplayVisibility(1)
Пример #9
0
  def takeScreenshot(self,name,type=-1):
    # show the message even if not taking a screen shot
    
    filePath = '/u/kanderle/Transfer/Movie/'+name+'.png'

    if self.enableScreenshots == 0:
      return

    lm = slicer.app.layoutManager()
    description = '4D'
    # switch on the type to get the requested window
    widget = 0
    if type == -1:
      # full window
      widget = slicer.util.mainWindow()
    elif type == slicer.qMRMLScreenShotDialog().FullLayout:
      # full layout
      widget = lm.viewport()
    elif type == slicer.qMRMLScreenShotDialog().ThreeD:
      # just the 3D window
      widget = lm.threeDWidget(0).threeDView()
    elif type == slicer.qMRMLScreenShotDialog().Red:
      # red slice window
      widget = lm.sliceWidget("Red")
    elif type == slicer.qMRMLScreenShotDialog().Yellow:
      # yellow slice window
      widget = lm.sliceWidget("Yellow")
    elif type == slicer.qMRMLScreenShotDialog().Green:
      # green slice window
      widget = lm.sliceWidget("Green")

    # grab and convert to vtk image data
    
    
    
    if type == slicer.qMRMLScreenShotDialog().ThreeD:
      degrees = 71
      n = 0 #
      heartBeat = 0
      heartDisplayNode = None
      color = [0.56,0,0]
      widget = lm.threeDWidget(0).threeDView()
      for i in range(0,degrees):
	if i < 10:
	  number = '0' + str(i)
	else:
	  number = str(i)
	filePath = '/u/kanderle/Transfer/Movie/'+name+'_'+number+'.png'
	#if i%heartBeat == 0:
	  #if heartDisplayNode:
	    #heartDisplayNode.SetVisibility(0)
	  #n += 1
	  #if n>10:
	    #n = 1
          #print "Changing state to: " + str(n)
	#heartNode = slicer.util.getNode('Heart_' + str(n))
	#if not heartNode:
	  #print "No Heart Node"
	  #n = n+1
	  #continue
	#heartDisplayNode = heartNode.GetDisplayNode()
	#heartDisplayNode.SetColor(color)
	#heartDisplayNode.SetVisibility(1)
	#heartDisplayNode.SetOpacity(0.8)
	  
	rw = widget.renderWindow()
	wti = vtk.vtkWindowToImageFilter()
	wti.SetInput(rw)
	wti.Update()
	writer = vtk.vtkPNGWriter()
	writer.SetFileName(filePath)
	writer.SetInputConnection(wti.GetOutputPort())
	writer.Write()
	widget.yaw()
	widget.forceRender()
	
    else:
      qpixMap = qt.QPixmap().grabWidget(widget)
      qimage = qpixMap.toImage()
      imageData = vtk.vtkImageData()
      slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)

      annotationLogic = slicer.modules.annotations.logic()
      annotationLogic.CreateSnapShot(name, description, type, self.screenshotScaleFactor, imageData)
def modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir,
                 IDcurrPatient, Zind):
    """
  imageBuffer = vtk.vtkImageData()
  label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
  q = labelNode.GetImageData()
  q.DeepCopy(label)
  if labelNode.GetImageDataConnection():
    labelNode.GetImageDataConnection().GetProducer().Update()
  if labelNode.GetImageData().GetPointData().GetScalars() != None:
    labelNode.GetImageData().GetPointData().GetScalars().Modified()
  labelNode.GetImageData().Modified()
  labelNode.Modified()
  pdb.set_trace()
  """
    imageSeriesDescription = os.path.basename(ImageFilePath).replace(
        '.nrrd', '')
    imagePatientID = os.path.basename(
        os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
    imageStudyDate = os.path.basename(
        os.path.dirname(os.path.dirname((ImageFilePath))))
    imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate

    inputImage = su.PullFromSlicer(imageNode.GetName())
    inputLabel = su.PullFromSlicer(labelNode.GetName())
    pixelID = inputImage.GetPixelIDValue()
    FlipYAxis = sitk.FlipImageFilter()
    FlipYAxis.SetFlipAxes([False, True, False])
    sizeZ = list(inputImage.GetSize())
    sizeZ[2] = 0
    indexZ = [0, 0, Zind]
    ExtractorZ = sitk.ExtractImageFilter()
    ExtractorZ.SetSize(sizeZ)
    ExtractorZ.SetIndex(indexZ)
    sliceZImage = ExtractorZ.Execute(inputImage)
    sliceZLabel = ExtractorZ.Execute(inputLabel)
    imageName = 'Axial_Slice_Image' + IDcurrPatient
    labelName = 'Axial_Slice_Label' + IDcurrPatient
    su.PushToSlicer(sliceZImage, imageName)
    su.PushToSlicer(sliceZLabel, labelName)

    sliceZImageNode = slicer.util.getNode(imageName)
    sliceZLabelNode = slicer.util.getNode(labelName)
    volumesLogic = slicer.vtkSlicerVolumesLogic()
    volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
    volumesLogic.SetVolumeAsLabelMap(labelNode, True)

    #sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
    #labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)

    sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
    sliceZLabelNodeDisplay.SetAndObserveColorNodeID(
        'vtkMRMLColorTableNodeFileGenericColors.txt')
    sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
    labelNodeDisplay = labelNode.GetDisplayNode()
    labelNodeDisplay.SetAndObserveColorNodeID(
        'vtkMRMLColorTableNodeFileGenericColors.txt')
    labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())

    ##
    appLogic = slicer.app.applicationLogic()
    selectionNode = appLogic.GetSelectionNode()
    selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
    selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())
    appLogic.PropagateVolumeSelection()

    ##
    lm = slicer.app.layoutManager()
    lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
    redWidget = lm.sliceWidget('Red')
    redLogic = redWidget.sliceLogic()
    redView = redWidget.sliceView()
    #redLogic.SetBackgroundWindowLevel(*windowLevel)

    sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
    dims = list(sliceZImageNode.GetImageData().GetDimensions())
    # dims[0] is x, dims[1] is y, dims [2] is Z
    redWidget.setFixedSize(720, 660)
    slncw = redWidget.sliceController()
    slncw.showLabelOutline(1)
    slncw.fitSliceToBackground()
    #sln.SetFieldOfView(dims[0],dims[1],1)
    #sln.SetDimensions(dims[0],dims[1],1)

    sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
    if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
        sliceannotations.sliceViewAnnotationsCheckBox.click()

    slicer.app.processEvents()
    wti = vtk.vtkWindowToImageFilter()
    wti.SetInput(redView.renderWindow())
    wti.Update()
    imgDataRedSlice = wti.GetOutput()

    modelMakerCLI(labelNode)
    imgData3D = GetModelSnapshot()

    append = vtk.vtkImageAppend()
    append.SetAppendAxis(0)
    append.AddInputData(imgDataRedSlice)
    append.AddInputData(imgData3D)
    append.Update()
    finalImage = append.GetOutput()

    #finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
    finalImagePath = str(
        os.path.join(
            imgOutputDir,
            imagePatientID_StudyDate + '_' + imageSeriesDescription + '.png'))
    writer = vtk.vtkPNGWriter()
    writer.SetFileName(finalImagePath)
    writer.SetInputData(finalImage)
    writer.Write()
Пример #11
0
def modelHandler(ImageFilePath, imageNode, labelNode, imgOutputDir, IDcurrPatient, Zind):
  """
  imageBuffer = vtk.vtkImageData()
  label = growCut(imageNode.GetImageData(),labelNode.GetImageData(),imageBuffer)
  q = labelNode.GetImageData()
  q.DeepCopy(label)
  if labelNode.GetImageDataConnection():
    labelNode.GetImageDataConnection().GetProducer().Update()
  if labelNode.GetImageData().GetPointData().GetScalars() != None:
    labelNode.GetImageData().GetPointData().GetScalars().Modified()
  labelNode.GetImageData().Modified()
  labelNode.Modified()
  pdb.set_trace()
  """
  imageSeriesDescription = os.path.basename(ImageFilePath).replace('.nrrd','')
  imagePatientID = os.path.basename(os.path.dirname(os.path.dirname(os.path.dirname((ImageFilePath)))))
  imageStudyDate = os.path.basename(os.path.dirname(os.path.dirname((ImageFilePath))))
  imagePatientID_StudyDate = imagePatientID + '_' + imageStudyDate
  
  inputImage = su.PullFromSlicer(imageNode.GetName())
  inputLabel = su.PullFromSlicer(labelNode.GetName())
  pixelID = inputImage.GetPixelIDValue()
  FlipYAxis = sitk.FlipImageFilter()
  FlipYAxis.SetFlipAxes([False, True, False])  
  sizeZ = list(inputImage.GetSize())
  sizeZ[2] = 0
  indexZ = [0, 0, Zind]
  ExtractorZ = sitk.ExtractImageFilter()
  ExtractorZ.SetSize(sizeZ)
  ExtractorZ.SetIndex(indexZ)
  sliceZImage = ExtractorZ.Execute(inputImage)
  sliceZLabel = ExtractorZ.Execute(inputLabel)
  imageName = 'Axial_Slice_Image' + IDcurrPatient
  labelName = 'Axial_Slice_Label' + IDcurrPatient
  su.PushToSlicer(sliceZImage, imageName)
  su.PushToSlicer(sliceZLabel, labelName)
  
  sliceZImageNode = slicer.util.getNode(imageName)
  sliceZLabelNode = slicer.util.getNode(labelName)
  volumesLogic = slicer.vtkSlicerVolumesLogic()
  volumesLogic.SetVolumeAsLabelMap(sliceZLabelNode, True)
  volumesLogic.SetVolumeAsLabelMap(labelNode, True)
   
  #sliceZLabelNode = binarizeLabelMapToValue(sliceZLabelNode, labelValue=296)
  #labelNode = binarizeLabelMapToValue(labelNode, labelValue=296)
  
  sliceZLabelNodeDisplay = sliceZLabelNode.GetDisplayNode()
  sliceZLabelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
  sliceZLabelNode.SetAndObserveDisplayNodeID(sliceZLabelNodeDisplay.GetID())
  labelNodeDisplay = labelNode.GetDisplayNode()
  labelNodeDisplay.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericColors.txt')
  labelNode.SetAndObserveDisplayNodeID(labelNodeDisplay.GetID())
  
  ##
  appLogic = slicer.app.applicationLogic()
  selectionNode = appLogic.GetSelectionNode()
  selectionNode.SetReferenceActiveVolumeID(sliceZImageNode.GetID())
  selectionNode.SetReferenceActiveLabelVolumeID(sliceZLabelNode.GetID())  
  appLogic.PropagateVolumeSelection()
  
  ##
  lm = slicer.app.layoutManager()
  lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutFourUpView)
  redWidget = lm.sliceWidget('Red')
  redLogic = redWidget.sliceLogic()
  redView = redWidget.sliceView()
  #redLogic.SetBackgroundWindowLevel(*windowLevel)
   
  sln = slicer.util.getNode('vtkMRMLSliceNodeRed')
  dims = list(sliceZImageNode.GetImageData().GetDimensions())
  # dims[0] is x, dims[1] is y, dims [2] is Z 
  redWidget.setFixedSize(720,660)
  slncw = redWidget.sliceController()
  slncw.showLabelOutline(1)
  slncw.fitSliceToBackground()
  #sln.SetFieldOfView(dims[0],dims[1],1)
  #sln.SetDimensions(dims[0],dims[1],1)
  
  sliceannotations = slicer.modules.DataProbeInstance.infoWidget.sliceAnnoations
  if sliceannotations.sliceViewAnnotationsCheckBox.checkState() == 2:
    sliceannotations.sliceViewAnnotationsCheckBox.click()
  
  slicer.app.processEvents()
  wti=vtk.vtkWindowToImageFilter()  
  wti.SetInput(redView.renderWindow())
  wti.Update()
  imgDataRedSlice = wti.GetOutput()
 
  modelMakerCLI(labelNode) 
  imgData3D = GetModelSnapshot()
  
  append = vtk.vtkImageAppend() 
  append.SetAppendAxis(0)
  append.AddInputData(imgDataRedSlice)
  append.AddInputData(imgData3D)
  append.Update()
  finalImage = append.GetOutput()
  
  #finalImagePath = str(os.path.join(imgOutputDir, IDcurrPatient + '_axial_sliceZ.png'))
  finalImagePath = str(os.path.join(imgOutputDir, imagePatientID_StudyDate + '_' + imageSeriesDescription +'.png'))
  writer=vtk.vtkPNGWriter()
  writer.SetFileName(finalImagePath)
  writer.SetInputData(finalImage)
  writer.Write()