Metadata-Version: 2.1
Name: snouty_viewer
Version: 0.0.3
Summary: A plugin to visualize and convert Snouty data.
Home-page: https://github.com/aelefebv/snouty-viewer
Author: Austin E. Y. T. Lefebvre
Author-email: austin.e.lefebvre@gmail.com
License: MIT
Project-URL: Bug Tracker, https://github.com/aelefebv/snouty-viewer/issues
Project-URL: Documentation, https://github.com/aelefebv/snouty-viewer#README.md
Project-URL: Source Code, https://github.com/aelefebv/snouty-viewer
Project-URL: User Support, https://github.com/aelefebv/snouty-viewer/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: testing
License-File: LICENSE

# snouty-viewer

[![License MIT](https://img.shields.io/pypi/l/snouty-viewer.svg?color=green)](https://github.com/aelefebv/snouty-viewer/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/snouty-viewer.svg?color=green)](https://pypi.org/project/snouty-viewer)
[![Python Version](https://img.shields.io/pypi/pyversions/snouty-viewer.svg?color=green)](https://python.org)
[![tests](https://github.com/aelefebv/snouty-viewer/workflows/tests/badge.svg)](https://github.com/aelefebv/snouty-viewer/actions/workflows/test_and_deploy.yml)
[![codecov](https://codecov.io/gh/aelefebv/snouty-viewer/branch/main/graph/badge.svg)](https://codecov.io/gh/aelefebv/snouty-viewer)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/snouty-viewer)](https://napari-hub.org/plugins/snouty-viewer)

## Description
Easy to use plugin for opening raw Snouty files and converting them to native view.

![Example](https://i.imgur.com/VirE5DM.gif)

## Intended Audience & Supported Data
This plugin is intended for those using a SOLS (Snouty) microscope collected via
[Alfred Millett-Sikking's code](https://github.com/amsikking/SOLS_microscope).

This plugin accepts a folder with at least subdirectories of data and metadata as an input.
The metadata must have a 000000.txt file for the metadata to be properly parsed.

## Quickstart

### A. Getting the plugin working (choose either a or b, you don't have to do both)
#### a. Through pip-install:
1. pip install snouty-viewer (within a virtual environment of Python 3.8, 3.9, or 3.10 recommended)
2. Open up napari
#### b. Through Napari:
1. Open up napari
2. Plugins > Install/Uninstall plugins
3. Search for "snouty-viewer"
4. Install
5. (Maybe need to) reopen napari

### B. Viewing raw Snouty data
- Drag and drop a root folder of your Snouty data. This is the folder that includes the data and metadata subfolders.
- Select "Snouty Viewer" for opening.

### C. Converting raw Snouty data to its native view
1. Click plugins, snouty-viewer: Native View
2. Select the file you want to convert
3. Press Run

### D. Saving your native view file
1. Select the file you want to save
2. File > Save Selected Layer(s)...
3. Select where you want to save your file
4. Write your file name (recommended to end in .tif)
5. Save
6. Wait (this could take a few minutes depending on your file's size)

## Getting Help
- Open up an issue on [GitHub](https://github.com/aelefebv/snouty-viewer/issues).
- Start a thread on [image.sc](https://forum.image.sc/)

----------------------------------

This [napari] plugin was generated with [Cookiecutter] using [@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:
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-->

## Installation

You can install `snouty-viewer` via [pip]:

    pip install snouty-viewer



To install latest development version :

    pip install git+https://github.com/aelefebv/snouty-viewer.git


## 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,
"snouty-viewer" 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/aelefebv/snouty-viewer/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
