This extension is still in active development. Please report any encountered issue.
See Usage for more details.
- JupyterLab 2 (JupyterLab 3 can be used but is not officially supported).
Note: You will need NodeJS to install the extension.
pip install jupyterlab_h5web jupyter lab build
pip install jupyterlab_h5web[full] jupyter lab build
This will install hdf5plugin in addition to the extension.
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:
- Display: visualize datasets using
- Inspect: show the metadata and attributes of any entity
Note: Opening a file this way will fetch the whole file. This is a limitation for heavy files and should be fixed soon.
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.
Note: The limitation of the JupyterLab tab does not apply here: the widget will only fetch HDF5 contents on-demand.
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.
Check the server extension
If you are seeing the frontend extension but it is not working, check that
jupyterlab_hdf is installed and enabled.
It should be listed when running:
jupyter serverextension list
jupyterlab_hdf does not appear, try to install it manually:
pip install jupyterlab_hdf
and to enable it:
jupyter serverextension enable jupyterlab_hdf
Check the frontend extension
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
pip uninstall jupyterlab_h5web jupyter labextension uninstall jupyterlab-h5web