| Name | simple-zarr-server JSON |
| Version |
0.2.0
JSON |
| download |
| home_page | |
| Summary | A simple server for sharing zarr over HTTP. |
| upload_time | 2023-06-12 15:51:10 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | BSD-3 |
| keywords |
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| VCS |
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| bugtrack_url |
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| requirements |
No requirements were recorded.
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# simple-zarr-server
[](https://github.com/manzt/simple-zarr-server/raw/main/LICENSE)
[](https://pypi.org/project/simple-zarr-server)
[](https://python.org)
[](https://github.com/manzt/simple-zarr-server/actions)
A minimal server for sharing zarr over HTTP.
----------------------------------
## Installation
You can install `simple-zarr-server` via [pip]:
pip install simple-zarr-server
## Usage
#### CLI:
```bash
$ simple-zarr-server --help
# Usage: simple-zarr-server [OPTIONS] PATH
#
# Options:
# --cors TEXT Origin to allow CORS. Use wildcard '*' to allow all.
# -w, --allow-write
# --host TEXT Bind socket to this host. [default: 127.0.0.1]
#
# --port INTEGER Bind socket to this port. [default: 8000]
# --reload Enable auto-reload.
# --loop [auto|asyncio|uvloop] Event loop implementation. [default: auto]
# --http [auto|h11|httptools] HTTP protocol implementation. [default: auto]
#
# --ws [auto|none|websockets|wsproto]
# WebSocket protocol implementation. [default: auto]
#
# --use-colors / --no-use-colors Enable/Disable colorized logging.
# --proxy-headers / --no-proxy-headers
# Enable/Disable X-Forwarded-Proto,
# X-Forwarded-For, X-Forwarded-Port to
# populate remote address info.
#
# --forwarded-allow-ips TEXT Comma seperated list of IPs to trust with
# proxy headers. Defaults to the
# $FORWARDED_ALLOW_IPS environment variable if
# available, or '127.0.0.1'.
$ simple-zarr-server /dataset.zarr # or /dataset.n5, or /dataset.zip
# INFO: Uvicorn running on http://127.0.0.1:8000 (Press CTRL+C to quit)
```
#### Python API:
The python API is more flexible than the CLI, and can serve any [`zarr.Array`](https://zarr.readthedocs.io/en/stable/api/core.html#zarr.core.Array),
[`zarr.Group`](https://zarr.readthedocs.io/en/stable/api/hierarchy.html#zarr.hierarchy.Group) or `np.ndarray`.
##### Server
```python
from simple_zarr_server import serve
import numpy as np
arr = np.random.rand(1024, 1024)
serve(arr) # creates an in-memory store if not zarr.Array or zarr.Group
```
##### Client
##### `zarr-python`
```python
import zarr
from fsspec import get_mapper
store = get_mapper("http://localhost:8000")
arr = zarr.open(store, mode='r')
# or
import dask.array as da
arr = da.from_zarr("http://localhost:8000")
```
##### `zarr.js`
```javascript
import { openArray } from 'zarr';
arr = await openArray({ store: 'http://localhost:8000' });
```
#### Advanced: Serving a remote pyramidal tiff as Zarr
##### Server
```python
from napari_lazy_openslide import OpenSlideStore
from simple_zarr_server import serve
import zarr
store = OpenSlideStore('tumor_004.tif') # custom zarr store
grp = zarr.open(store)
serve(grp)
```
##### Client
```python
import napari
import dask.array as da
import zarr
from fsspec import get_mapper
store = get_mapper("http://localhost:8000")
z_grp = zarr.open(store)
datasets = z_grp.attrs["multiscales"][0]["datasets"]
pyramid = [
da.from_zarr(store, component=d["path"]) for d in datasets
]
with napari.gui_qt():
napari.view_image(pyramid)
```
## Note
This package is experimental. It wraps *any* `zarr-python` store as a REST API, enabling remote access over HTTP.
It is similar to [`xpublish`](https://github.com/xarray-contrib/xpublish), but is more minimal and
does not provide special endpoints that are specific to Xarray datasets. If your data are Xarray dataset,
_please_ use `xpublish`! `simple-zarr-server` was designed with imaging data in mind, and when combined with a tool
like `ngrok` provides an interesting way to share local images with collaborators.
Some non-standard zarr stores that might be of interest include:
- [`napari_lazy_openslide.OpenSlideStore`](https://github.com/manzt/napari-lazy-openslide) - read multiscale RGB TIFFs as zarr
- [`HDF5Zarr`](https://github.com/catalystneuro/HDF5Zarr) - read HDF5 with zarr
## Contributing
Contributions are very welcome. Tests can be run with `hatch run cov`.
## License
Distributed under the terms of the [BSD-3] license,
"simple-zarr-server" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[file an issue]: https://github.com/manzt/simple-zarr-server/issues
[hatch]: https://hatch.pypa.io/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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