jupyterlab-h5web is a JupyterLab extension to explore and visualize HDF5 file contents, using the web-based viewer h5web. h5web supports the NeXus format.
See Usage for more details.
See the table below for earlier JupyterLab versions
| JupyterLab 2 | JupyterLab 3 | JupyterLab 4 | |
|---|---|---|---|
| Extension version range | 0.0.1 - 0.3.0 | 1.0.0 - 8.0.0 | 10.0.0 - ... |
pip install jupyterlab_h5web
To enable support for additional filters such as blosc or bitshuffle:
pip install jupyterlab_h5web[full]
This will install hdf5plugin in addition to the extension.
conda install -c conda-forge jupyterlab-h5web
This extension enables opening HDF5 files in a JupyterLab tab and exploring HDF5 files in Jupyter notebooks.
You can double-click on an HDF5 file or right-click Open with -> h5web to launch a tab.
This tab is composed of a sidebar, where you can explore the structure of the HDF5 file, and of a main area where the visualization of the selected entity takes place. This visualization is controlled by the upper-right button that can toggle between:
Line, Heatmap or Matrix
visualizations.To open a HDF5 file with H5Web, use the H5Web widget in a notebook cell:
from jupyterlab_h5web import H5Web
H5Web('<path to the HDF5 file>')
The cell height can be resized with the handle at the bottom-right.
An example is provided in example.ipynb.
jupyter-h5web detects HDF5 files based on their file extensions. The viewer works for the following extensions:
For other types of files, you can change the extension to one of the supported extensions or, if it is widespread, open an issue to discuss its support.
See https://github.com/silx-kit/jupyterlab-h5web/releases.
If the following instructions do not solve your issue, you can open an issue on GitHub.
If you are seeing the frontend extension but it is not working, check that
jupyterlab_h5web is installed and enabled.
It should be listed when running:
jupyter server extension list
If jupyterlab_h5web does not appear or is disabled, try to enable it:
jupyter server extension enable jupyterlab_h5web
If jupyterlab_h5web is installed and enabled but you are not seeing the
frontend, check the frontend is installed:
jupyter labextension list
pip uninstall jupyterlab_h5web
FAQs
A JupyterLab extension to explore and visualize HDF5 file contents.
We found that jupyterlab-h5web demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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