vtkResliceCursorWidget: output images are cropped

pasquamatt · September 18, 2020, 8:37am

Hi to all,

I am trying to set up a four pane medical image viewer in Python, but I notice that the displayed images seem to be cropped, especially when more than one cursor has been rotated. Here you can see a GIF showing my problem in the green pane when the cursors on the other two planes have been rotated:
FourPaneViewer
At first I thought the problem was somehow correlated with this option of vtkImageReslice:

SetAutoCropOutput(): Turn this on if you want to guarantee that the extent of the output will be large enough to ensure that none of the data will be cropped (default: Off).

So I set it on, but it didn’t work.

Here you can find my code:

from vtk import *

# Reslice cursor callback
def ResliceCursorCallback(obj,event):
    for i in range(0,3):
        ps = planeWidgetArray[i].GetPolyDataAlgorithm();
        origin = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetOrigin();
        ps.SetOrigin(origin);
        point1 = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetPoint1();
        ps.SetPoint1(point1);
        point2 = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetPoint2();
        ps.SetPoint2(point2);
        planeWidgetArray[i].UpdatePlacement();

# DICOM reader
reader = vtkDICOMImageReader();
reader.SetDirectoryName("CT");
reader.Update();
imageDims = reader.GetOutput().GetDimensions();

# // Bounding box
outline = vtkOutlineFilter();
outline.SetInputConnection(reader.GetOutputPort());

outlineMapper = vtkPolyDataMapper();
outlineMapper.SetInputConnection(outline.GetOutputPort());

outlineActor = vtkActor();
outlineActor.SetMapper(outlineMapper);
outlineActor.GetProperty().SetColor(1,1,0);

# // Mapper and actors for volume
volumeMapper = vtkPolyDataMapper();
volumeMapper.SetInputConnection(reader.GetOutputPort());

volumeActor = vtkActor();
volumeActor.SetMapper(volumeMapper);

# // Renderers
renWin = vtkRenderWindow();
RendererArray = [None]*4;
for i in range(0,4):
    RendererArray[i] = vtkRenderer();
    renWin.AddRenderer(RendererArray[i]);
renWin.SetMultiSamples(0);

# // Render window interactor
iren = vtkRenderWindowInteractor();
renWin.SetInteractor(iren);

# // Picker
picker = vtkCellPicker();
picker.SetTolerance(0.005);

# // Properties
ipwProp = vtkProperty();

# // 3D plane widgets
planeWidgetArray = [None]*3;
for i in range(0,3):
    planeWidgetArray[i] = vtkImagePlaneWidget();
    planeWidgetArray[i].SetInteractor(iren);
    planeWidgetArray[i].SetPicker(picker);
    planeWidgetArray[i].RestrictPlaneToVolumeOn();
    color = [0, 0, 0 ];
    color[i] = 1;
    planeWidgetArray[i].GetPlaneProperty().SetColor(color);
    planeWidgetArray[i].SetTexturePlaneProperty(ipwProp);
    planeWidgetArray[i].TextureInterpolateOff();
    planeWidgetArray[i].SetResliceInterpolateToLinear();
    planeWidgetArray[i].SetInputConnection(reader.GetOutputPort());
    planeWidgetArray[i].SetPlaneOrientation(i);
    planeWidgetArray[i].SetSliceIndex(int(imageDims[i] / 2));
    planeWidgetArray[i].DisplayTextOn();
    planeWidgetArray[i].SetDefaultRenderer(RendererArray[3]);
    planeWidgetArray[i].SetWindowLevel(1358, -27, 0);
    planeWidgetArray[i].On();
    planeWidgetArray[i].InteractionOff();

planeWidgetArray[1].SetLookupTable(planeWidgetArray[0].GetLookupTable()); 
planeWidgetArray[2].SetLookupTable(planeWidgetArray[0].GetLookupTable());

# // ResliceCursor
resliceCursor = vtkResliceCursor();
center = reader.GetOutput().GetCenter();
resliceCursor.SetCenter(center[0], center[1], center[2]);
resliceCursor.SetThickMode(0);
resliceCursor.SetThickness(10, 10, 10);
resliceCursor.SetHole(0);
resliceCursor.SetImage(reader.GetOutput());

# // 2D Reslice cursor widgets
resliceCursorRepArray = [None]*3;
resliceCursorWidgetArray = [None]*3;
viewUp = [[0, 0, -1],[0, 0, -1],[0, 1, 0]];
for i in range(0,3):
    resliceCursorWidgetArray[i] = vtkResliceCursorWidget();
    resliceCursorRepArray[i] = vtkResliceCursorLineRepresentation();
    resliceCursorWidgetArray[i].SetInteractor(iren);
    resliceCursorWidgetArray[i].SetRepresentation(resliceCursorRepArray[i]);
    resliceCursorRepArray[i].GetResliceCursorActor().GetCursorAlgorithm().SetResliceCursor(resliceCursor);
    resliceCursorRepArray[i].GetResliceCursorActor().GetCursorAlgorithm().SetReslicePlaneNormal(i);
    minVal = reader.GetOutput().GetScalarRange()[0];
    reslice = resliceCursorRepArray[i].GetReslice();
    reslice.SetInputConnection(reader.GetOutputPort());
    reslice.SetBackgroundColor(minVal, minVal, minVal, minVal);
    reslice.AutoCropOutputOn();
    reslice.Update();
    resliceCursorWidgetArray[i].SetDefaultRenderer(RendererArray[i]);
    resliceCursorWidgetArray[i].SetEnabled(1);
    RendererArray[i].GetActiveCamera().SetFocalPoint(0, 0, 0);
    camPos = [0, 0, 0];
    camPos[i] = 1;
    RendererArray[i].GetActiveCamera().SetPosition(camPos[0], camPos[1], camPos[2]);
    RendererArray[i].GetActiveCamera().ParallelProjectionOn();
    RendererArray[i].GetActiveCamera().SetViewUp(viewUp[i][0], viewUp[i][1], viewUp[i][2]);
    RendererArray[i].ResetCamera();
    resliceCursorWidgetArray[i].AddObserver('InteractionEvent',ResliceCursorCallback)
    range_color = reader.GetOutput().GetScalarRange();
    resliceCursorRepArray[i].SetWindowLevel(range_color[1] - range_color[0], (range_color[0] + range_color[1]) / 2.0, 0);
    planeWidgetArray[i].SetWindowLevel(range_color[1] - range_color[0], (range_color[0] + range_color[1]) / 2.0, 0);
    resliceCursorRepArray[i].SetLookupTable(resliceCursorRepArray[0].GetLookupTable());
    planeWidgetArray[i].GetColorMap().SetLookupTable(resliceCursorRepArray[0].GetLookupTable());
    
# // Background
RendererArray[0].SetBackground(0.3, 0.1, 0.1);
RendererArray[1].SetBackground(0.1, 0.3, 0.1);
RendererArray[2].SetBackground(0.1, 0.1, 0.3);
RendererArray[3].AddActor(volumeActor);
RendererArray[3].AddActor(outlineActor);
RendererArray[3].SetBackground(0.1, 0.1, 0.1);
renWin.SetSize(600, 600);

# // Render
RendererArray[0].SetViewport(0, 0, 0.5, 0.5);
RendererArray[1].SetViewport(0.5, 0, 1, 0.5);
RendererArray[2].SetViewport(0, 0.5, 0.5, 1);
RendererArray[3].SetViewport(0.5, 0.5, 1, 1);
renWin.Render();

# // Camera in 3D view
RendererArray[3].GetActiveCamera().Elevation(110);
RendererArray[3].GetActiveCamera().SetViewUp(0, 0, -1);
RendererArray[3].GetActiveCamera().Azimuth(45);
RendererArray[3].GetActiveCamera().Dolly(1.15);
RendererArray[3].ResetCameraClippingRange();

iren.Initialize()
iren.Start()

Has someone any idea about which can be the cause of this weird behaviour?

Thanks in advance for any help or hints.

zist8888 · November 22, 2024, 8:53am

can you resoved it?

lgivord · November 22, 2024, 10:15am

maybe @lassoan or @LucasGandel can have already encounter this issue and have some insight ?

LucasGandel · November 22, 2024, 11:46am

This was the behavior 4 years ago, but it should have been fixed in https://gitlab.kitware.com/vtk/vtk/-/commit/0e0af1b9a9a96efafcf8ce863ff87a3e67b665e3 which is available in vtk 9.1.
@zist8888 do you reproduce with recent versions of VTK?

zist8888 · November 25, 2024, 2:59am

yes,output images show correct.but I have an other question,when move navigator lines in near other view,the line also can operate at same direction.I think the line is not show this view,so cant operate.can you give some suggestion,thanks!

LucasGandel · November 25, 2024, 8:35am

Do you mean that the line is not always visible? It’s probably related to this issue: https://gitlab.kitware.com/vtk/vtk/-/issues/18441

Using the following properties for the lines should fix it:

    resliceCursorRep[i]->GetResliceCursorActor()->GetCenterlineProperty(0)->SetRepresentationToWireframe();
    resliceCursorRep[i]->GetResliceCursorActor()->GetCenterlineProperty(1)->SetRepresentationToWireframe();
    resliceCursorRep[i]->GetResliceCursorActor()->GetCenterlineProperty(2)->SetRepresentationToWireframe();

zist8888 · November 25, 2024, 10:33am

no,It meas that navigator lines show correct,but the line was operated part is incorrect.because in other view also can operate, it should be operated by own view.

LucasGandel · November 25, 2024, 3:39pm

OK thanks for the additional information. This probably happens because you have multiple renderers but only one render window and one interactor. In this case can you try to set the DefaultRenderer for every widgets to see if it helps? If you could share your code that would help a lot.

zist8888 · November 26, 2024, 12:56am

(post deleted by author)

zist8888 · November 26, 2024, 1:03am

from vtk import *

# Reslice cursor callback
def ResliceCursorCallback(obj,event):
    for i in range(0,3):
        ps = planeWidgetArray[i].GetPolyDataAlgorithm();
        origin = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetOrigin();
        ps.SetOrigin(origin);
        point1 = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetPoint1();
        ps.SetPoint1(point1);
        point2 = resliceCursorWidgetArray[i].GetResliceCursorRepresentation().GetPlaneSource().GetPoint2();
        ps.SetPoint2(point2);
        planeWidgetArray[i].UpdatePlacement();

# DICOM reader
reader = vtkDICOMImageReader();
reader.SetDirectoryName('/data/VTK/TestVTK/bin/dcmdata/');
reader.Update();
imageDims = reader.GetOutput().GetDimensions();

# // Bounding box
outline = vtkOutlineFilter();
outline.SetInputConnection(reader.GetOutputPort());

outlineMapper = vtkPolyDataMapper();
outlineMapper.SetInputConnection(outline.GetOutputPort());

outlineActor = vtkActor();
outlineActor.SetMapper(outlineMapper);
outlineActor.GetProperty().SetColor(1,1,0);

# // Mapper and actors for volume
volumeMapper = vtkPolyDataMapper();
volumeMapper.SetInputConnection(reader.GetOutputPort());

volumeActor = vtkActor();
volumeActor.SetMapper(volumeMapper);

# // Renderers
renWin = vtkRenderWindow();
RendererArray = [None]*4;
for i in range(0,4):
    RendererArray[i] = vtkRenderer();
    renWin.AddRenderer(RendererArray[i]);
renWin.SetMultiSamples(0);

# // Render window interactor
iren = vtkRenderWindowInteractor();
renWin.SetInteractor(iren);

# // Picker
picker = vtkCellPicker();
picker.SetTolerance(0.005);

# // Properties
ipwProp = vtkProperty();

# // 3D plane widgets
planeWidgetArray = [None]*3;
for i in range(0,3):
    planeWidgetArray[i] = vtkImagePlaneWidget();
    planeWidgetArray[i].SetInteractor(iren);
    planeWidgetArray[i].SetPicker(picker);
    planeWidgetArray[i].RestrictPlaneToVolumeOn();
    color = [0, 0, 0 ];
    color[i] = 1;
    planeWidgetArray[i].GetPlaneProperty().SetColor(color);
    planeWidgetArray[i].SetTexturePlaneProperty(ipwProp);
    planeWidgetArray[i].TextureInterpolateOff();
    planeWidgetArray[i].SetResliceInterpolateToLinear();
    planeWidgetArray[i].SetInputConnection(reader.GetOutputPort());
    planeWidgetArray[i].SetPlaneOrientation(i);
    planeWidgetArray[i].SetSliceIndex(int(imageDims[i] / 2));
    planeWidgetArray[i].DisplayTextOn();
    planeWidgetArray[i].SetDefaultRenderer(RendererArray[3]);
    planeWidgetArray[i].SetWindowLevel(1358, -27, 0);
    planeWidgetArray[i].On();
    planeWidgetArray[i].InteractionOff();

planeWidgetArray[1].SetLookupTable(planeWidgetArray[0].GetLookupTable()); 
planeWidgetArray[2].SetLookupTable(planeWidgetArray[0].GetLookupTable());

# // ResliceCursor
resliceCursor = vtkResliceCursor();
center = reader.GetOutput().GetCenter();
resliceCursor.SetCenter(center[0], center[1], center[2]);
resliceCursor.SetThickMode(0);
resliceCursor.SetThickness(10, 10, 10);
resliceCursor.SetHole(0);
resliceCursor.SetImage(reader.GetOutput());

# // 2D Reslice cursor widgets
resliceCursorRepArray = [None]*3;
resliceCursorWidgetArray = [None]*3;
viewUp = [[0, 0, -1],[0, 0, -1],[0, 1, 0]];
for i in range(0,3):
    resliceCursorWidgetArray[i] = vtkResliceCursorWidget();
    resliceCursorRepArray[i] = vtkResliceCursorLineRepresentation();
    resliceCursorWidgetArray[i].SetInteractor(iren);
    resliceCursorWidgetArray[i].SetRepresentation(resliceCursorRepArray[i]);
    resliceCursorRepArray[i].GetResliceCursorActor().GetCursorAlgorithm().SetResliceCursor(resliceCursor);
    resliceCursorRepArray[i].GetResliceCursorActor().GetCursorAlgorithm().SetReslicePlaneNormal(i);
    
    for j in range(3):
        resliceCursorRepArray[i].GetResliceCursorActor().GetCenterlineProperty(j).SetRepresentationToWireframe()
        resliceCursorRepArray[i].GetResliceCursorActor().GetCenterlineProperty(j).RenderLinesAsTubesOn()
        resliceCursorRepArray[i].GetResliceCursorActor().GetCenterlineProperty(j).SetLineWidth(1)
                
    minVal = reader.GetOutput().GetScalarRange()[0];
    reslice = resliceCursorRepArray[i].GetReslice();
    reslice.SetInputConnection(reader.GetOutputPort());
    reslice.SetBackgroundColor(minVal, minVal, minVal, minVal);
    reslice.AutoCropOutputOn();
    reslice.Update();
    resliceCursorWidgetArray[i].SetDefaultRenderer(RendererArray[i]);
    resliceCursorWidgetArray[i].SetEnabled(1);
    RendererArray[i].GetActiveCamera().SetFocalPoint(0, 0, 0);
    camPos = [0, 0, 0];
    camPos[i] = 1;
    RendererArray[i].GetActiveCamera().SetPosition(camPos[0], camPos[1], camPos[2]);
    RendererArray[i].GetActiveCamera().ParallelProjectionOn();
    RendererArray[i].GetActiveCamera().SetViewUp(viewUp[i][0], viewUp[i][1], viewUp[i][2]);
    RendererArray[i].ResetCamera();
    resliceCursorWidgetArray[i].AddObserver('InteractionEvent',ResliceCursorCallback)
    range_color = reader.GetOutput().GetScalarRange();
    resliceCursorRepArray[i].SetWindowLevel(range_color[1] - range_color[0], (range_color[0] + range_color[1]) / 2.0, 0);
    planeWidgetArray[i].SetWindowLevel(range_color[1] - range_color[0], (range_color[0] + range_color[1]) / 2.0, 0);
    resliceCursorRepArray[i].SetLookupTable(resliceCursorRepArray[0].GetLookupTable());
    planeWidgetArray[i].GetColorMap().SetLookupTable(resliceCursorRepArray[0].GetLookupTable());
    
# // Background
RendererArray[0].SetBackground(0.3, 0.1, 0.1);
RendererArray[1].SetBackground(0.1, 0.3, 0.1);
RendererArray[2].SetBackground(0.1, 0.1, 0.3);
RendererArray[3].AddActor(volumeActor);
RendererArray[3].AddActor(outlineActor);
RendererArray[3].SetBackground(0.1, 0.1, 0.1);
renWin.SetSize(600, 600);

# // Render
RendererArray[0].SetViewport(0, 0, 0.5, 0.5);
RendererArray[1].SetViewport(0.5, 0, 1, 0.5);
RendererArray[2].SetViewport(0, 0.5, 0.5, 1);
RendererArray[3].SetViewport(0.5, 0.5, 1, 1);
renWin.Render();

# // Camera in 3D view
RendererArray[3].GetActiveCamera().Elevation(110);
RendererArray[3].GetActiveCamera().SetViewUp(0, 0, -1);
RendererArray[3].GetActiveCamera().Azimuth(45);
RendererArray[3].GetActiveCamera().Dolly(1.15);
RendererArray[3].ResetCameraClippingRange();

iren.Initialize()
iren.Start()

thank for you response,this is my test code,i have add defaultrenderer,but the promble is not resolved.