shalevy1 / ipyvolume

3d plotting for Python in the Jupyter notebook based on IPython widgets using WebGL

ipyvolume

Try out in mybinder:

3d plotting for Python in the Jupyter notebook based on IPython widgets using WebGL.

Ipyvolume currenty can

• Do (multi) volume rendering.
• Create scatter plots (up to ~1 million glyphs).
• Create quiver plots (like scatter, but with an arrow pointing in a particular direction).
• Render isosurfaces.
• Do lasso mouse selections.
• Render in the Jupyter notebook, or create a standalone html page (or snippet to embed in your page).
• Render in stereo, for virtual reality with Google Cardboard.
• Animate in d3 style, for instance if the x coordinates or color of a scatter plots changes.
• Animations / sequences, all scatter/quiver plot properties can be a list of arrays, which can represent time snapshots.
• Stylable (although still basic)
• Integrates with
• ipywidgets for adding gui controls (sliders, button etc), see an example at the documentation homepage
• bokeh by linking the selection
• bqplot by linking the selection

Ipyvolume will probably, but not yet:

• Render labels in latex.
• Show a custom popup on hovering over a glyph.

Documentation

Documentation is generated at readthedocs:

Screencast demos

Animation

(see more at the documentation)

Volume rendering

Glyphs (quiver plots)

Installation

Using pip

Advice: Make sure you use conda or virtualenv. If you are not a root user and want to use the --user argument for pip, you expose the installation to all python environments, which is a bad practice, make sure you know what you are doing.

$ pip install ipyvolume

Conda/Anaconda

$ conda install -c conda-forge ipyvolume

For Jupyter lab users

The Jupyter lab extension is not enabled by default (yet).

$ conda install -c conda-forge nodejs  # or some other way to have a recent node
$ jupyter labextension install @jupyter-widgets/jupyterlab-manager
$ jupyter labextension install ipyvolume
$ jupyter labextension install jupyter-threejs

Pre-notebook 5.3

If you are still using an old notebook version, ipyvolume and its dependend extension (widgetsnbextension) need to be enabled manually. If unsure, check which extensions are enabled:

$ jupyter nbextention list

If not enabled, enable them:

$ jupyter nbextension enable --py --sys-prefix ipyvolume
$ jupyter nbextension enable --py --sys-prefix widgetsnbextension

Pip as user: (but really, do not do this)

You have been warned, do this only if you know what you are doing, this might hunt you in the future, and now is a good time to consider learning virtualenv or conda.

$ pip install ipyvolume --user
$ jupyter nbextension enable --py --user ipyvolume
$ jupyter nbextension enable --py --user widgetsnbextension

Developer installation

$ git clone https://github.com/maartenbreddels/ipyvolume.git
$ cd ipyvolume
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix ipyvolume
$ jupyter nbextension enable --py --sys-prefix ipyvolume

For all cases make sure ipywidgets is enabled if you use Jupyter notebook version < 5.3 (using --user instead of --sys-prefix if doing a local install):

$ jupyter nbextension enable --py --sys-prefix widgetsnbextension
$ jupyter nbextension enable --py --sys-prefix pythreejs
$ jupyter nbextension enable --py --sys-prefix ipywebrtc
$ jupyter nbextension enable --py --sys-prefix ipyvolume

Developer workflow

Jupyter notebook (classical)

Note: There is never a need to restart the notebook server, nbextensions are picked up after a page reload.

Start this command:

$ (cd js; npm run watch)

It will

• Watch for changes in the sourcecode and run the typescript compiler for transpilation of the src dir to the lib dir.
• Watch the lib dir, and webpack will build (among other things), ROOT/ipyvolume/static/index.js.

Refresh the page.