Weird behaviour of `Volume(img)`

Using Volume to render data from a numpy array seems to mess up the axes order (see screenshot below). At the same time building a vtkImageData manually works fine.

I’m getting this behaviour only after reinstalling my python environment and updating vtkplotter. Unfortunately I can’t find the configuration in which things would work as they did before, so here’s code illustrating the problem:

import vtk
import numpy as np
from vtkplotter import show, embedWindow, Volume

embedWindow('itkwidgets') # backends are: itkwidgets, k3d or False

import skimage.io as io
f = 'embryo.tif' # from the vtkplotter examples
raw = io.imread(f, plugin='simpleitk')

arr = vtk.util.numpy_support.numpy_to_vtk(raw.transpose(2,1,0).ravel(), array_type=vtk.VTK_FLOAT)
img = vtk.vtkImageData()
img.SetDimensions(raw.shape)
img.GetPointData().SetScalars(arr)

# doesn't work
# show(Volume(raw.transpose(2,1,0)))
show(Volume(raw))
# show(Volume(raw)._image)
# show(Volume(raw.transpose(2,1,0))._image)

# works
# show(img)

This is the output:

Thanks! Cheers, Marvin

[m-albert]

This works for me as well. Thanks so much for looking into this so quickly and fixing! Cheers, Marvin

[marcomusy]

Actually I said something completely wrong… the trasnpose thing doesn’t fix the spacing order… so in the end I believe the order=‘F’ would simplify the operation, so the above becomes:

from vtkplotter import *
from skimage.io import imread

f = datadir+'embryo.tif'

voriginal = load(f)
printc('voxel size is', voriginal.spacing(), c='cyan')

raw = imread(f)

vraw = Volume(raw, spacing=(104,104,104))
# Need to change axes and mirror
# NOTE: spacing specified above is now inverted: (z,y,x)
vraw.permuteAxes(2,1,0).mirror("y")

# Compare loading the volume directly with the numpy volume:
# they should be the same
show(voriginal, vraw, N=2, axes=1)

I committed the new version… sorry for the confusion and thanks a lot for the help! Let me know if this does the job… M.