Plane slicer at custom position

[IsabellaPa]

Hello,
I'm playing around with the slicer_plane function and I would like to define the output slice by handing 4 points that make a rectangle to the function. This way I would get a slice image of a specific region in the volume and with a certain orientation.
Unfortunately my rectangle-plane-output does not sick to the origin but slides around on the infinite plane. Any ideas what's going wrong?

I experienced the most problems if I define a tilted plane in middle part of the volume. For example this pointset does not work: [ 5. 40. 20.] [ 87.27681404 138.05368872 20. ] [-79.91698537 111.2538111 84. ] [ 2.35982867 209.30749982 84. ]

My code so far:

 def slice_plane_custom(volume, p0, p1, p2, p3):
        
        p0_vis = Sphere(pos=p0, r=3.0, res=24, quads=False, c='g5', alpha=1.0)
        p1_vis = Sphere(pos=p1, r=3.0, res=24, quads=False, c='g5', alpha=1.0)
        p2_vis = Sphere(pos=p2, r=3.0, res=24, quads=False, c='g5', alpha=1.0)
        p3_vis = Sphere(pos=p3, r=3.0, res=24, quads=False, c='g5', alpha=1.0)
        
        T = vtk.vtkTransform()

        Test_M= T.GetMatrix()
        Test_M.SetElement(0,0, cutting_plane_coordi[0, 0]) # cutting_plane_coordi[0,:] = e1 of the coordinate system between p0 and p1
        Test_M.SetElement(1,0, cutting_plane_coordi[0, 1])
        Test_M.SetElement(2,0, cutting_plane_coordi[0, 2])

        Test_M.SetElement(0,1, cutting_plane_coordi[1, 0])# cutting_plane_coordi[1,:] = e2 of the coordinate system between p0 and p2
        Test_M.SetElement(1,1, cutting_plane_coordi[1, 1])
        Test_M.SetElement(2,1, cutting_plane_coordi[1, 2])

        Test_M.SetElement(0,2, cutting_plane_coordi[2, 0])# cutting_plane_coordi[2,:] = e3 crossproduct of e1 and e2
        Test_M.SetElement(1,2, cutting_plane_coordi[2, 1])
        Test_M.SetElement(2,2, cutting_plane_coordi[2, 2])

        Test_M.SetElement(0,3, p0[0])
        Test_M.SetElement(1,3, p0[1])
        Test_M.SetElement(2,3, p0[2])



        reslice = vtk.new("ImageReslice")
        reslice.SetInputData(volume.dataset)
        reslice.SetOutputDimensionality(2)

        reslice.SetResliceAxes(Test_M)
        #reslice.SetResliceAxesOrigin(p0)
        reslice.SetOutputOrigin(p0) #both of the origin functions are not doing what I would expect them to do 
        reslice.SetInterpolationModeToLinear()
        reslice.SetAutoCropOutput(False)
        reslice.SetOutputExtent(0,128,0,128,0,0)
        reslice.SetOutputSpacing(1,1,1)
        reslice.Update()
        vslice = vtk.new("ImageDataGeometryFilter")
        vslice.SetInputData(reslice.GetOutput())
        vslice.Update()
        msh = Mesh(vslice.GetOutput())
        
        msh.apply_transform(Test_M)
        msh.pipeline = utils.OperationNode(
            "slice_plane", parents=[volume], c="#4cc9f0:#e9c46a")
        
        vslice = msh
        
        vslice.cmap('Purples_r').lighting('off').add_scalarbar('Slice', c='w')
        arr_shape = vslice.metadata["shape"]

        arr = np.reshape(np.array([vslice.pointdata[0]]), arr_shape)

        plot = Plotter(axes=9, bg='k', bg2='bb')
        plot.show(volume, vslice, p0_vis, p1_vis, p2_vis, p3_vis, __doc__)
        return arr

[marcomusy]

Hi I just created an example for you:

pip install -U git+https://github.com/marcomusy/vedo.git

https://github.com/marcomusy/vedo/blob/master/examples/volumetric/slice_plane3.py

Hope it helps!

[IsabellaPa]

That's great, thank you!