Does k3d-jupyter support to render a time series of 3D volume?

[tfunatomi]

• K3D version: 2.16.0
• Python version: 3.10.12
• Operating System: Ubuntu22.04

Description

I want to render a time series of a 3D volume.
It seems that the animation for the time series works, but the rendering result looks strange.

What I Did

When I try to render a time series of a 3D volume by passing a dictionary to k3d.mip or k3d.volume, there is no error but the rendering result becomes very different from the one when rendering a time step.

import k3d
import numpy as np
import SimpleITK as sitk

im_sitk = sitk.ReadImage('./heart.mhd')
img = sitk.GetArrayFromImage(im_sitk)

plot = k3d.plot()
plt_mip_o = k3d.mip(img.astype(np.float32), name='MIP of one timestep')
plt_mip_o.visible = False # Just for comparison
plot += plt_mip_o
plt_mip_t = k3d.mip({0:img.astype(np.float32)}, name='MIP of a time series')
plot += plt_mip_t
plot.display()

I would be grateful if you could help me.

[artur-trzesiok]

Hi @tfunatomi !

k3d.volume and k3d.mip have important parameter called "color_range". For static data it is calculated authomatically if user will not pass it. For time series data that automation is disabled. So if you will pass color_range like that:

plt_mip_t = k3d.mip({0:img.astype(np.float32)}, 
                    color_range = [0.0, 1000.0], 
                    name='MIP of a time series')

everything will be fine. Thanks for spoting that problem. I should either add infomation about that constraint to docs or implement feature to calculate color_range for timeseries data.

btw. Please remember that in animation parameters are interpolated using js. So in your case you will try to interpolate 317x 512 x 512 floats number in pure js. That will be slow. Animation in k3d have special rule that if time == exactly a keypoint interpolation will be avoided.

btw. I have in my mind idea to do interpolation for k3d.volume and k3d.mip on shader level.

[artur-trzesiok]

Thanks @tfunatomi . Fix is on devel

[artur-trzesiok]

Hi! Please check https://pypi.org/project/k3d/2.16.1/ :)

[tfunatomi]

I appreciate your quick response!
It's so helpful :)