vtkImageReslice do not include the center point

Support
1

I am using vtkImageReslice to reslice a volume image. The vtkImageReslice need the direction and center point as the input. However, I find the center point do not located in the output of vtkImageReslice.

from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
import vtk
import numpy as np

def numpyToVTK(data):
    flat_data_array = data.transpose(2,1,0).flatten()
    vtk_data_array = numpy_to_vtk(flat_data_array)
    vtk_data = numpy_to_vtk(num_array=vtk_data_array, deep=True, array_type=vtk.VTK_FLOAT)
    img = vtk.vtkImageData()
    img.GetPointData().SetScalars(vtk_data)
    img.SetDimensions(data.shape)
    return img

img = np.zeros(shape=[512,512,120])
img[0:300,0:100,:] = 255

vtkImg = numpyToVTK(img)

reslice = vtk.vtkImageReslice()
reslice.SetInputData(vtkImg)
reslice.SetAutoCropOutput(True)
reslice.SetOutputDimensionality(2)
reslice.SetInterpolationModeToCubic()
reslice.SetSlabNumberOfSlices(1)
reslice.SetOutputSpacing(1.0,1.0,1.0)

center = [150, 50, 100]

axialElement = [
    1, 0, 0, center[0],
    0, 1, 0, center[1],
    0, 0, 1, center[2],
    0, 0, 0, 1
]

resliceAxes = vtk.vtkMatrix4x4()
resliceAxes.DeepCopy(axialElement)
reslice.SetResliceAxes(resliceAxes)
reslice.Update()

reslicedImg = reslice.GetOutput()

Then, I show the reslicedImg and the center as following:


imageActor = vtk.vtkImageActor()
windowLevel = vtk.vtkImageMapToWindowLevelColors()
imageActor.GetMapper().SetInputConnection(windowLevel.GetOutputPort())
windowLevel.SetInputData(reslicedImg)
windowLevel.Update()

sphere = vtk.vtkSphereSource()
sphere.SetCenter(center[0], center[1], center[2])
# sphere.SetCenter(center[0], center[1], -100)
sphere.SetRadius(50)
sphere.Update()
sphereMapper = vtk.vtkPolyDataMapper()
sphereMapper.SetInputData(sphere.GetOutput())
sphereActor = vtk.vtkActor()
sphereActor.SetMapper(sphereMapper)

ren = vtk.vtkRenderer()
ren.AddActor(imageActor)
ren.AddActor(sphereActor)
ren.SetBackground(0.1, 0.2, 0.4)

renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(400, 400)

iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
renWin.Render()
iren.Start()

and the result is:

image
image493×530 13.4 KB

The position of the showed sphere is the center point that is used by vtkImageReslice. We can see that the sphere and the image plane is seperated. However, in my understanding, the sphere should located at the output of vtkImageReslice.

Is there anything wrong with my code?

2

Finally, I know what’s the problem with my code.

Let’s say the original image is volumeImg, and the resliced image is reslicedImg. The coordinate system of volumeImg and reslicedImg is different.

The point of center is represented with the volumeImg coordinate system, while it has been shown in the reslicedImg coordinate system.

Thus, I need to covert the center from the volumeImg coordinate system to reslicedImg coordinate system and display it. The completed code should be:

from vtk.util.numpy_support import vtk_to_numpy, numpy_to_vtk
import vtk
import numpy as np

def numpyToVTK(data):
    flat_data_array = data.transpose(2,1,0).flatten()
    vtk_data_array = numpy_to_vtk(flat_data_array)
    vtk_data = numpy_to_vtk(num_array=vtk_data_array, deep=True, array_type=vtk.VTK_FLOAT)
    img = vtk.vtkImageData()
    img.GetPointData().SetScalars(vtk_data)
    img.SetDimensions(data.shape)
    return img

img = np.zeros(shape=[512,512,120])
img[0:300,0:100,:] = 255

vtkImg = numpyToVTK(img)

reslice = vtk.vtkImageReslice()
reslice.SetInputData(vtkImg)
reslice.SetAutoCropOutput(True)
reslice.SetOutputDimensionality(2)
reslice.SetInterpolationModeToCubic()
reslice.SetSlabNumberOfSlices(1)
reslice.SetOutputSpacing(1.0,1.0,1.0)

center = [256, 256, 60]

axialElement = [
    1, 0, 0, center[0],
    0, 1, 0, center[1],
    0, 0, 1, center[2],
    0, 0, 0, 1
]

resliceAxes = vtk.vtkMatrix4x4()
resliceAxes.DeepCopy(axialElement)
reslice.SetResliceAxes(resliceAxes)
reslice.Update()

reslicedImg = reslice.GetOutput()

imageActor = vtk.vtkImageActor()
windowLevel = vtk.vtkImageMapToWindowLevelColors()
imageActor.GetMapper().SetInputConnection(windowLevel.GetOutputPort())
windowLevel.SetInputData(reslicedImg)
windowLevel.Update()

invertAxes = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4.Invert(reslice.GetResliceAxes(), invertAxes)
coor = invertAxes.MultiplyPoint([center[0], center[1], center[2], 1])
# coor = reslice.GetResliceAxes().MultiplyPoint([center[0], center[1], center[2], 1])

sphere = vtk.vtkSphereSource()
sphere.SetCenter(coor[0], coor[1], coor[2])
# sphere.SetCenter(center[0], center[1], -100)
sphere.SetRadius(50)
sphere.Update()
sphereMapper = vtk.vtkPolyDataMapper()
sphereMapper.SetInputData(sphere.GetOutput())
sphereActor = vtk.vtkActor()
sphereActor.SetMapper(sphereMapper)

ren = vtk.vtkRenderer()
ren.AddActor(imageActor)
ren.AddActor(sphereActor)
ren.SetBackground(0.1, 0.2, 0.4)

renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(400, 400)

iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
renWin.Render()
iren.Start()

And the result is:

image
image502×534 11.8 KB

We can see that the converted center is located on the resliced image plane.

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