# jupyterlab-h5web
[](https://badge.fury.io/py/jupyterlab-h5web)
[](https://mybinder.org/v2/gh/silx-kit/jupyterlab-h5web/HEAD?urlpath=lab/tree/example.ipynb)
**jupyterlab-h5web** is a JupyterLab extension to explore and visualize HDF5
file contents, using the web-based viewer
[h5web](https://github.com/silx-kit/h5web). h5web supports the
[NeXus](https://www.nexusformat.org/) format.
See [Usage](README.md#Usage) for more details.
## Requirements
- JupyterLab 4
See the table below for earlier JupyterLab versions
## Compatibility table
| | JupyterLab 2 | JupyterLab 3 | JupyterLab 4 |
| ----------------------- | ----------------- | ----------------- | -------------- |
| Extension version range | `0.0.1` - `0.3.0` | `1.0.0` - `8.0.0` | `10.0.0` - ... |
## Install
### With pip
```bash
pip install jupyterlab_h5web
```
To enable support for additional filters such as
[blosc](https://github.com/Blosc/hdf5-blosc) or
[bitshuffle](https://github.com/kiyo-masui/bitshuffle):
```bash
pip install jupyterlab_h5web[full]
```
This will install [hdf5plugin](https://pypi.org/project/hdf5plugin/) in addition
to the extension.
### With conda
```bash
conda install -c conda-forge jupyterlab-h5web
```
## 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`, `Heatmap` or `Matrix`
visualizations.
- _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:
```python
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](example.ipynb).
### Supported file formats
**jupyter-h5web** detects HDF5 files based on their file extensions. The viewer
works for the following extensions:
- "Classic" HDF5: `.h5`, `.hdf5`
- [NeXus](https://www.nexusformat.org/): `.nexus`, `.nx`, `.nxs`
- [CXI](https://cxidb.org/cxi.html): `.cxi`
- [NetCDF4](https://docs.unidata.ucar.edu/nug/current/): `.nc`, `.nc4`
- [Loom](http://linnarssonlab.org/loompy/format/index.html): `.loom`
For other types of files, you can change the extension to one of the supported
extensions or, if it is widespread,
[open an issue](https://github.com/silx-kit/jupyterlab-h5web/issues) to discuss
its support.
## Changelog
See https://github.com/silx-kit/jupyterlab-h5web/releases.
## Troubleshoot
If the following instructions do not solve your issue, you can open an
[issue on GitHub](https://github.com/silx-kit/jupyterlab-h5web/issues).
### 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:
```bash
jupyter server extension list
```
If `jupyterlab_h5web` does not appear or is disabled, try to enable it:
```
jupyter server extension 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:
```bash
jupyter labextension list
```
## Uninstall
```bash
pip uninstall jupyterlab_h5web
```
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"description": "# jupyterlab-h5web\n\n\n[](https://badge.fury.io/py/jupyterlab-h5web)\n[](https://mybinder.org/v2/gh/silx-kit/jupyterlab-h5web/HEAD?urlpath=lab/tree/example.ipynb)\n\n\n\n**jupyterlab-h5web** is a JupyterLab extension to explore and visualize HDF5\nfile contents, using the web-based viewer\n[h5web](https://github.com/silx-kit/h5web). h5web supports the\n[NeXus](https://www.nexusformat.org/) format.\n\nSee [Usage](README.md#Usage) for more details.\n\n## Requirements\n\n- JupyterLab 4\n\nSee the table below for earlier JupyterLab versions\n\n## Compatibility table\n\n| | JupyterLab 2 | JupyterLab 3 | JupyterLab 4 |\n| ----------------------- | ----------------- | ----------------- | -------------- |\n| Extension version range | `0.0.1` - `0.3.0` | `1.0.0` - `8.0.0` | `10.0.0` - ... |\n\n## Install\n\n### With pip\n\n```bash\npip install jupyterlab_h5web\n```\n\nTo enable support for additional filters such as\n[blosc](https://github.com/Blosc/hdf5-blosc) or\n[bitshuffle](https://github.com/kiyo-masui/bitshuffle):\n\n```bash\npip install jupyterlab_h5web[full]\n```\n\nThis will install [hdf5plugin](https://pypi.org/project/hdf5plugin/) in addition\nto the extension.\n\n### With conda\n\n```bash\nconda install -c conda-forge jupyterlab-h5web\n```\n\n## Usage\n\nThis extension enables opening HDF5 files in a JupyterLab tab and exploring HDF5\nfiles in Jupyter notebooks.\n\n### In JupyterLab\n\nYou can double-click on an HDF5 file or right-click _Open with_ -> _h5web_ to\nlaunch a tab.\n\nThis tab is composed of a sidebar, where you can explore the structure of the\nHDF5 file, and of a main area where the visualization of the selected entity\ntakes place. This visualization is controlled by the upper-right button that can\ntoggle between:\n\n- _Display_: visualize datasets using `Line`, `Heatmap` or `Matrix`\n visualizations.\n- _Inspect_: show the metadata and attributes of any entity\n\n### In Jupyter notebooks\n\nTo open a HDF5 file with H5Web, use the `H5Web` widget in a notebook cell:\n\n```python\nfrom jupyterlab_h5web import H5Web\n\nH5Web('<path to the HDF5 file>')\n```\n\nThe cell height can be resized with the handle at the bottom-right.\n\nAn example is provided in [example.ipynb](example.ipynb).\n\n### Supported file formats\n\n**jupyter-h5web** detects HDF5 files based on their file extensions. The viewer\nworks for the following extensions:\n\n- \"Classic\" HDF5: `.h5`, `.hdf5`\n- [NeXus](https://www.nexusformat.org/): `.nexus`, `.nx`, `.nxs`\n- [CXI](https://cxidb.org/cxi.html): `.cxi`\n- [NetCDF4](https://docs.unidata.ucar.edu/nug/current/): `.nc`, `.nc4`\n- [Loom](http://linnarssonlab.org/loompy/format/index.html): `.loom`\n\nFor other types of files, you can change the extension to one of the supported\nextensions or, if it is widespread,\n[open an issue](https://github.com/silx-kit/jupyterlab-h5web/issues) to discuss\nits support.\n\n## Changelog\n\nSee https://github.com/silx-kit/jupyterlab-h5web/releases.\n\n## Troubleshoot\n\nIf the following instructions do not solve your issue, you can open an\n[issue on GitHub](https://github.com/silx-kit/jupyterlab-h5web/issues).\n\n### Check the server extension\n\nIf you are seeing the frontend extension but it is not working, check that\n`jupyterlab_h5web` is installed and enabled.\n\nIt should be listed when running:\n\n```bash\njupyter server extension list\n```\n\nIf `jupyterlab_h5web` does not appear or is disabled, try to enable it:\n\n```\njupyter server extension enable jupyterlab_h5web\n```\n\n### Check the frontend extension\n\nIf `jupyterlab_h5web` is installed and enabled but you are not seeing the\nfrontend, check the frontend is installed:\n\n```bash\njupyter labextension list\n```\n\n## Uninstall\n\n```bash\npip uninstall jupyterlab_h5web\n```\n",
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