Metadata-Version: 2.1
Name: napari-sentinel-to-zarr
Version: 0.0.2
Summary: Writer plugin for napari to save Sentinel tiffs into ome-zarr format
Home-page: https://github.com/DragaDoncila/napari-sentinel-to-zarr
Author: Draga Doncila Pop
Author-email: ddon0001@student.monash.edu
License: MIT
Description: # napari-sentinel-to-zarr
        
        [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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        [![tests](https://github.com/DragaDoncila/napari-sentinel-to-zarr/workflows/tests/badge.svg)](https://github.com/DragaDoncila/napari-sentinel-to-zarr/actions)
        <!-- [![codecov](https://codecov.io/gh/DragaDoncila/napari-sentinel-to-zarr/branch/master/graph/badge.svg)](https://codecov.io/gh/DragaDoncila/napari-sentinel-to-zarr) -->
        
        Writer plugin for napari to save Sentinel tiffs into ome-zarr format
        
        ----------------------------------
        
        This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
        
        <!--
        Don't miss the full getting started guide to set up your new package:
        https://github.com/napari/cookiecutter-napari-plugin#getting-started
        
        and review the napari docs for plugin developers:
        https://napari.org/docs/plugins/index.html
        -->
        
        ## Installation
        
        You can install `napari-sentinel-to-zarr` via [pip]:
        
            `pip install napari-sentinel-to-zarr`
        
        
        ## Usage
        This package provides command-line utilities for:
        - Processing raw Sentinel zips of a tile into multiscale zarr
        - Processing interpolated “GapFilled” tif for that tile into zarr, rechunking along time axis
        - Processing the zarr from step 2 into multiscale OME-zarr
        
        
        ### Raw Zipped Images to Zarr
        Install the latest version of napari using
        
        `pip install -U napari`
        
        Install napari-sentinel-to-zarr using 
        
        `pip install napari-sentinel-to-zarr`
        
        Run `sentinel-to-zarr zip-to-zarr path/to/tile/55HBU out/path/dir/55HBU.zarr`
        
        where `path/to/tile/55HBU` is a directory full of Sentinel zips
        
        ### Interpolated Images to Zarr
        Run `sentinel-to-zarr interpolated-to-zarr path/to/interpolated/55HBU_GapFilled_Image.tif out/dir/Image.zarr`
        
        You can pass in optional arguments:
        - `--step-size` - how many slices to convert at once. The default is 20 which will require ~5GB RAM. A larger step size means more slices can be loaded at once, and will speed up performance. A full image is typically ~175GB.
        - `--chunk-size` - the chunk size of the resulting zarr. Default is 1024 which is typically considered a good option and provides good performance
        
        
        ### Interpolated Zarr to Multiscale Zarr
        Run `sentinel-to-zarr zarr-to-multiscale-zarr path/to/interpolated/zarr out/path/interpolated_multiscale.zarr tilename`
        
        Where `path/to/interpolated/zarr` is the output file from step 2
        
        You can pass in optional arguments
        - `--min-shape-` the smallest pyramid level you wish to generate. Default is 1024px
        
        ## Napari Plugin
        This package also comes with a napari writer plugin which allows you to open the raw tiles directly by dragging one into a napari viewer, and saving out while you browse using `File>Save Layers`
        <<<<<<< HEAD
        >>>>>>> Stashed changes
        =======
        >>>>>>> fb66ae98f8a36fe3d90cd02f1892b326fc180b52
        
        ## Contributing
        
        Contributions are very welcome. Tests can be run with [tox], please ensure
        the coverage at least stays the same before you submit a pull request.
        
        ## License
        
        Distributed under the terms of the [MIT] license,
        "napari-sentinel-to-zarr" is free and open source software
        
        ## Issues
        
        If you encounter any problems, please [file an issue] along with a detailed description.
        
        [napari]: https://github.com/napari/napari
        [Cookiecutter]: https://github.com/audreyr/cookiecutter
        [@napari]: https://github.com/napari
        [MIT]: http://opensource.org/licenses/MIT
        [BSD-3]: http://opensource.org/licenses/BSD-3-Clause
        [GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
        [GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
        [Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
        [Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
        [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
        [file an issue]: https://github.com/DragaDoncila/napari-sentinel-to-zarr/issues
        [napari]: https://github.com/napari/napari
        [tox]: https://tox.readthedocs.io/en/latest/
        [pip]: https://pypi.org/project/pip/
        [PyPI]: https://pypi.org/
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
