Translate the volume to origin

[gungui98]

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Sample Code What is the problem, question, or error?

Write a short description telling me what you are doing, what you expect to happen, and what is currently happening.

import numpy as np
import pyvista as pv
from pyvista import examples


# Download a volumetric dataset
vol = examples.download_knee_full()
print(vol.center)
print(vol.origin)
vol = vol.translate(-np.array(vol.center).astype(np.float64))

cpos = [(-381.74, -46.02, 216.54), (74.8305, 89.2905, 100.0), (0.23, 0.072, 0.97)]
pl = pv.Plotter()
pl.add_volume(vol, cmap="bone", opacity="sigmoid")
pl.add_point_labels(vol.center, ['Center'], point_color='blue', point_size=20, text_color='black', font_size=20,)
pl.add_point_labels(vol.origin, ['Origin'], point_color='red', point_size=20, text_color='black', font_size=20,)
pl.camera_position = cpos
pl.show()

Description

I want to translate the volume that moves the center to the origin using the code, but when I visualize the volume, it is still in the same position. I also tried to assign the return value of vol.translate to the vol but the code seemed to freeze when rendering.

System Information

--------------------------------------------------------------------------------
  Date: Thu May 02 12:04:26 2024 SE Asia Standard Time
                OS : Windows
            CPU(s) : 12
           Machine : AMD64
      Architecture : 64bit
       Environment : IPython
        GPU Vendor : ATI Technologies Inc.
      GPU Renderer : AMD Radeon(TM) Graphics
       GPU Version : 4.5.14802 Core Profile Context 21.40.52 30.0.14052.5
  MathText Support : False
  Python 3.9.18 (main, Sep 11 2023, 14:09:26) [MSC v.1916 64 bit (AMD64)]
           pyvista : 0.43.6
               vtk : 9.3.0
             numpy : 1.26.4
        matplotlib : 3.8.2
            scooby : 0.9.2
             pooch : 1.8.1
            pillow : 9.4.0
           imageio : 2.34.1
           IPython : 8.18.1
             scipy : 1.11.4
      nest_asyncio : 1.5.8
--------------------------------------------------------------------------------

Screenshots

No response

[tkoyama010]

Sorry for the inconvenience, the translate method does not seem to work well with the ImageData class. We recommend updating the origin property as follows instead.

vol.origin = vol.origin - np.array(vol.center)

You can expect to get the results you request by executing the following code.

import numpy as np
import pyvista as pv
from pyvista import examples


# Download a volumetric dataset
vol = examples.download_knee_full()
center = vol.center
origin = vol.origin
print(center)
print(origin)

# vol = vol.translate(-np.array(vol.center).astype(np.float64))
vol.origin = vol.origin - np.array(vol.center)

cpos = [(-381.74, -46.02, 216.54), (74.8305, 89.2905, 100.0), (0.23, 0.072, 0.97)]
pl = pv.Plotter()
pl.add_volume(vol, cmap="bone", opacity="sigmoid")
pl.add_point_labels(center, ['Center'], point_color='blue', point_size=20, text_color='black', font_size=20,)
pl.add_point_labels(origin, ['Origin'], point_color='red', point_size=20, text_color='black', font_size=20,)
pl.camera_position = cpos
pl.show()

[gungui98]

@tkoyama010 Thanks for your quick response, it seems to solve my problem. Another question, which may be unrelated to the post, but I am trying to visualize some markup points exported from the 3D slicer application to the pyvista, but the coordinate from keypoint doesn't seem to match with the coordinate of pyvista, I am using pv.wrap(numpy_volume) to load the volume data from dicom files, and the coordinate from 3D slicer is a tuple of R,A,S coordinates. Do you have any idea how to sync between the two applications?

[tkoyama010]

I'm sorry. I can't advise you on the 3D slicer; if you share the file you are trying to visualize in PyVista, I can advise you. A new thread would be better for getting advice from other community members.