A JupyterLab extension to explore and visualize HDF5 file contents.
Project description
jupyterlab-h5web
A JupyterLab extension to explore and visualize HDF5 file contents. Based on h5web.
WARNING: This extension is still in active development. Please report any encountered issue.
Requirements
- JupyterLab ~= 2.0 (not JupyterLab 3)
Install
Note: You will need NodeJS to install the extension.
pip install jupyterlab_h5web
jupyter lab build
To enable support for additional filters such as blosc or bitshuffle:
pip install jupyterlab_h5web[full]
jupyter lab build
This will install hdf5plugin in addition to the extension.
Usage
Once the extension is installed, 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:
- Display: visualize datasets using
Line
,Heatmap
orMatrix
visualizations. - Inspect: show the metadata and attributes of any entity
Supported file formats
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.
Changelog
0.0.4
- Added optional support of filters through
hdf5plugin
- Added
.nexus
,.nx
,.nxs
and.cxi
to the supported extensions - Fixed unwanted background changes when switching themes in JupyterLab
0.0.3
- Added wheels
0.0.2
- Removed
npm
from the build process
0.0.1
- First release :tada:
Troubleshoot
If you are seeing the frontend extension but it is not working, check
that the jupyterlab_hdf
extension is enabled:
jupyter serverextension list
If the jupyterlab_hdf
is installed and enabled but you are not seeing
the frontend, check the frontend is installed:
jupyter labextension list
If it is installed, try:
jupyter lab clean
jupyter lab build
Uninstall
pip uninstall jupyterlab_h5web
jupyter labextension uninstall jupyterlab-h5web
Project details
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