Metadata-Version: 2.4
Name: frontveg
Version: 0.2.0
Summary: Segmentation of vegetation located to close to camera
Author: Herearii Metuarea
Author-email: herearii.metuarea@univ-angers.fr
License: 
        Copyright (c) 2025, Herearii Metuarea
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of copyright holder nor the names of its
          contributors may be used to endorse or promote products derived from
          this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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Project-URL: Bug Tracker, https://github.com/hereariim/frontveg/issues
Project-URL: Documentation, https://github.com/hereariim/frontveg#README.md
Project-URL: Source Code, https://github.com/hereariim/frontveg
Project-URL: User Support, https://github.com/hereariim/frontveg/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD 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 :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: magicgui
Requires-Dist: qtpy
Requires-Dist: scikit-image
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: pytest; extra == "testing"
Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari; extra == "testing"
Requires-Dist: pyqt5; extra == "testing"
Dynamic: license-file

# frontveg

[![License BSD-3](https://img.shields.io/pypi/l/frontveg.svg?color=green)](https://github.com/hereariim/frontveg/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/frontveg.svg?color=green)](https://pypi.org/project/frontveg)
[![Python Version](https://img.shields.io/pypi/pyversions/frontveg.svg?color=green)](https://python.org)
[![tests](https://github.com/hereariim/frontveg/workflows/tests/badge.svg)](https://github.com/hereariim/frontveg/actions)
[![codecov](https://codecov.io/gh/hereariim/frontveg/branch/main/graph/badge.svg)](https://codecov.io/gh/hereariim/frontveg)
[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/frontveg)](https://napari-hub.org/plugins/frontveg)
[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)

A plugin for foreground vegetation segmentation, tailored for trellised vegetation row images. It uses RGB images to perform inference and allows users to manually refine the generated mask.

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

The method was developped by Herearii Metuarea, PHENET PhD at LARIS (French laboratory located in Angers, France) and Abdoul-Djalil Hamza Ousseini, AgroEcoPhen Engineer at IRHS (French Institute located in INRAe Angers, France) in Imhorphen team (bioimaging research group lead) under the supervision of Eric Duchêne (Research Engineer), Morgane Roth (Research Engineer) and David Rousseau (Full professor). This plugin was written by Herearii Metuarea and was designed in the context of the european project PHENET.


![Data Warehouse](https://github.com/user-attachments/assets/781dc1ef-3ae0-47ff-9771-6de2879ed602)

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

This [napari] plugin was generated with [copier] using the [napari-plugin-template].

<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/napari-plugin-template#getting-started

and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->

## Installation

You can install `frontveg` via [pip]:

    pip install frontveg



To install latest development version :

    pip install git+https://github.com/hereariim/frontveg.git

## Description

This plugin is a tool to perform image inference. This plugin contained two steps of image processing. First, from RGB image, an depth map is estimated and then thresholded to detect foreground and background in image. Second, grounding dino model detect foliage in foreground. The output is a binary mask where white colour are associated to foliage in foreground.

## Contact

Imhorphen team, bioimaging research group

42 rue George Morel, Angers, France

- Pr David Rousseau, david.rousseau@univ-angers.fr
- Abdoul-djalil ousseini-hamza, abdoul-djalil.ousseini-hamza@inrae.fr
- Herearii Metuarea, herearii.metuarea@univ-angers.fr

## 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 [BSD-3] license,
"frontveg" 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
[copier]: https://copier.readthedocs.io/en/stable/
[@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
[napari-plugin-template]: https://github.com/napari/napari-plugin-template

[file an issue]: https://github.com/hereariim/frontveg/issues

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