绘制由3d numpy数组表示的3d体积数据

Question

I've seen that vtkplotter supports a wide range of volumetric image formats, but does it support plotting numpy arrays? I have an image in a .mhd format that I converted to .npz file and would like to plot it using the mentioned library. Is there a way to do so?

import numpy as np
data = np.zeros((3,3,3))
# how to plot this?

If you know any other tools for visualizing volumetric data, suited for medical analysis, please tell so. I've tried mayavi but it consumes so much memory that it crashes my computer.

Answer 1

You can use numpy_support to convert numpy arrays to vtkImageData (ie a VTK 3D image).

An example follows, there's a numpy warning about type conversion: I don't think it's relevant but I'm not a python guru...

from vtk.util import numpy_support
import vtk
import numpy as np

data = np.zeros((3,3,3))

# vtkImageData is the vtk image volume type
imdata = vtk.vtkImageData()
# this is where the conversion happens
depthArray = numpy_support.numpy_to_vtk(data.ravel(), deep=True, array_type=vtk.VTK_DOUBLE)

# fill the vtk image data object
imdata.SetDimensions(data.shape)
imdata.SetSpacing([1,1,1])
imdata.SetOrigin([0,0,0])
imdata.GetPointData().SetScalars(depthArray)

# f.ex. save it as mhd file
writer = vtk.vtkMetaImageWriter()
writer.SetFileName("test.mhd")
writer.SetInputData(imdata)
writer.Write()

... and to visualize vtk volume data you can use Paraview.