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silx-kit / jupyterlab-h5web

A JupyterLab extension to explore and visualize HDF5 file contents. Based on https://github.com/silx-kit/h5web.
MIT License
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Custom selection of dimensions to be plotted #107

Closed freiburgermsu closed 7 months ago

freiburgermsu commented 1 year ago

Hello!

My group is interested to explore an H5 dataset through plotting various dimensions across each other. Your JupyterLab plugin interface is awesome, but we cannot seem select our own dimensions to plot. Can your plugin accommodate selecting data dimensions for plotting, or can the code be expanded to add this functionality?

Andrew

loichuder commented 1 year ago

Getting back to this after a long time, sorry.

Can your plugin accommodate selecting data dimensions for plotting, or can the code be expanded to add this functionality?

We support the NeXus standard where metadata can be added to the file to define plottable data: https://manual.nexusformat.org/datarules.html#find-plottable-data. In essence, this means adding structure and attributes to the HDF5 groups/datasets that is then interpreted by H5Web to generate the plot.

The example notebook shows an example of NeXus data generation.

We don't really plan to go beyond that since there are already many amazing tools to do customizable plots in Jupyter (matplotlib, bokeh, plotly to name a few). The advantage of the integration in Jupyter ecosystem is that you can use those directly by using h5py to get the data from the HDF5 file.

loichuder commented 7 months ago

Closing this. Can be reopened if needed.