[BUG] Issues Rendering, Plotting and Saving Cubes

[abradley60]

Hi there,

I've tried in a few different environments and I can't seem to get a cube plotting or saving. I have tried in a vscode notebook, with a python file and in google collab.

os mac M1
python version = 3.10.18
pip install lexcube

>>> import lexcube
>>> lexcube.__version__
'1.0.3'

My python file based on the example notebook:

import lexcube
import numpy as np

data_source = np.sum(np.mgrid[0:256,0:256,0:256], axis=0)
w = lexcube.Cube3DWidget(data_source, cmap="prism", vmin=0, vmax=768)
w.savefig('tmp.png')

running this file prints out the following, but no file is saved to tmp.png:

When using Lexcube and generated images or videos, please acknowledge/cite: Söchting, M., Scheuermann, G., Montero, D., & Mahecha, M. D. (2025). Interactive Earth system data cube visualization in Jupyter notebooks. Big Earth Data, 1–15. https://doi.org/10.1080/20964471.2025.2471646

similarly, in a jupyter notebook I get the following. The plot is not showing, only the sliders. The file is also not saving:

Kind regards

[msoechting]

Hi Alex, sorry for the late response. You need to call .plot() and have the interactive widget open and visibly running in a Jupyter notebook before .savefig() has any effect.

• Pure python is not a Jupyter notebook and will therefore not work with Lexcube, since Lexcube depends on the Jupyter widget package.
• Google Colab and VSCode are not native Jupyter environments, but have their own implementation and quirks. In the Lexcube README, for each there is a description on how to get Lexcube running:
  Note on Google Collab
  Note on Jupyter for VSCode

If all fails, you can still use the regular Jupyter Lab interface in the web browser (opened from jupyter lab command) which will definitely work with Lexcube.

[abradley60]

Hi @msoechting thanks for your response and sorry for my delayed response. I'm still having some trouble. I have made another attempt at the numpy example in collab and am getting the same error. Apologies if there is something obvious I am missing, or should I opt for the Jupyter Lab interface in the web browser?

Thanks Again.

[msoechting]

Hi Alex, no worries! If you want to use Google Collab, you need to execute the code given in the README in the section "Notes on Google Collab" in a separate cell before you call or import Lexcube:

from google.colab import output
output.enable_custom_widget_manager()

Can you try that and let me know if that works for you? Otherwise, a simple jupyter lab should definitely work with the examples.