A JupyterLab extension to explore and visualize HDF5 file contents.
Project description
jupyterlab-h5web
This extension is still in active development. Please report any encountered issue.
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.
Requirements
- JupyterLab 2 (JupyterLab 3 can be used up to 3.0.x but is not officially supported).
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.
Update
In the case you want to update jupyterlab_h5web after having already installed
it, do a clean reinstallation:
# Uninstall the old version
jupyter labextension uninstall jupyterlab-h5web
pip uninstall jupyterlab_h5web
# Install the new version
pip install jupyterlab_h5web
jupyter lab build
Otherwise, the labextension may not be updated correctly.
Usage
This extension enables opening HDF5 files in a JupyterLab tab and exploring HDF5 files in Jupyter notebooks.
In JupyterLab
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,HeatmaporMatrixvisualizations. - Inspect: show the metadata and attributes of any entity
In Jupyter notebooks
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>')
An example is provided in example.ipynb.
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
See https://github.com/silx-kit/jupyterlab-h5web/releases.
Troubleshoot
Check the server extension
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 serverextension list
If jupyterlab_h5web does not appear or is disabled, try to enable it:
jupyter serverextension enable jupyterlab_h5web
Check the frontend extension
If jupyterlab_h5web 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
Stale H5Web
In the case the displayed H5Web does not match the installed version, try to reinstall the package using the procedure described in Update.
Uninstall
jupyter labextension uninstall jupyterlab-h5web
pip uninstall jupyterlab_h5web
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