[![Issues][issues-shield]][issues-url]
[![Issues][closed-issues-shield]][closed-issues-url]
[![GNU General Public License v3.0][license-shield]][license-url]
<!-- PROJECT LOGO -->
<br/>
<div align="center">
<img
src="https://raw.githubusercontent.com/mrdrzit/Behavython/main/logo/logo.png"
style="max-width: 100%; height: 100%;"
alt="Behavython software"
<p align="center">
<span style="font-size:14px">To be used in conjunction with <a href=https://bonsai-rx.org>Bonsai-RX</a> to extract behavior from video </span>
<br />
·
<a href="https://github.com/mrdrzit/Behavython/issues">Report Bug</a>
·
<a href="https://github.com/mrdrzit/Behavython/issues">Request Feature</a>
</p>
</div>
<!-- TABLE OF CONTENTS -->
<summary>Table of Contents</summary>
<ol>
<li>
<a href="#about">About the project</a>
<ul>
<li><a href="#built-with">Built With</a></li>
</ul>
</li>
<li>
<a href="#getting-started">Getting Started</a>
<ul>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#installation">Installation</a></li>
</ul>
</li>
<li><a href="#usage">Usage</a></li>
<li><a href="#contributing">Contributing</a></li>
<li><a href="#license">License</a></li>
<li><a href="#contact">Contact</a></li>
<li><a href="#acknowledgments">Acknowledgments</a></li>
</ol>
<!-- ABOUT THE PROJECT -->
<br/>
### About
- <span style="font-size:14px">This software was developed to be used in conjunction with <a href=https://bonsai-rx.org>Bonsai-RX</a> to extract behavior from video. It is a simple interface that allows the user to select the data and image files that were generated by Bonsai and then run the analysis. The results are saved in a csv file that can be used for further analysis. </span>
- <span style="font-size:14px">The software also implements bindings to the <a href=https://github.com/DeepLabCut/DeepLabCut>DeepLabCut</a> package, allowwing users to run the analysis using pretrained models on their data. </span>
### Built With
* [Python](https://www.python.org/)
* [Qt Designer](https://doc.qt.io/qt-5/qtdesigner-manual.html)
<!-- GETTING STARTED -->
## Getting Started
### Prerequisites
- deeplabcut
- seaborn
- pyside6
- openpyxl
- scikit-image
- pandas
- numpy
- matplotlib
- tk
- scipy
***For a simple way to keep up to date with requirements, reference the requirements.txt file***
### Installation as a pip package
For the installation you need a simple command that you can get by one of two ways:
1. Copying and pasting from here:
- "pip install behavython" (without quotation[""] marks)
2. Going to the Pypi site and copying from there:
- [PyPi frontpage](https://pypi.org/project/behavython/)
_At the moment, Behavython was mainly tested on Windows_
<br/>
<!-- USAGE EXAMPLES -->
## Usage
- Windows
1. Open the interface typing "behavython" on the command line
- If you installed it as a pip package you can just type "behavython" on the command line
- If you downloaded the source code you need to go to the folder where you downloaded it and type "python Bbehavython_front.py" on the command line
<p align="center">
<img src="https://user-images.githubusercontent.com/83073576/184265356-f986cfba-65bf-4e18-a297-75e0f956e2dc.png" width="600" heigth="600" title="With this you'll be almost set">
</p>
2. Select all the photo-data pairs that you want to analyze
- In this step is important that you don't forget to verify that you got all the bonsai files, including the data and a image of the arena that you are analyzing
<p align="center">
<img src="https://user-images.githubusercontent.com/83073576/184265915-4ed017de-3b79-4bbe-9d36-5b2c449317ad.png" width="600" heigth="600" title="Don't forget tha data files in the csv format">
</p>
3. Wait for the program to finish the analysis
- Currently the program looks like it freezed when running. It is expected behavior but we are looking into it. Right now you only need to wait a little bit.
<p align="center">
<img src="https://user-images.githubusercontent.com/83073576/184266129-8221c85a-a2cc-4024-9301-49e721d4477f.png" width="600" heigth="600" title="Don't forget tha data files in the csv format">
</p>
4. When finished the progress bar will show 100% and a preview of the results will be available on the right
<p align="center">
<img src="https://user-images.githubusercontent.com/83073576/184266218-3f14f4d6-f979-478e-9b36-1fe4f0631635.png" width="600" heigth="600" title="You just need to wait now:)">
</p>
See the [open issues](https://github.com/mrdrzit/Behavython/issues) for a full list of proposed features (and known issues).
<br/>
<!-- CONTRIBUTING -->
## Contributing
Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are **greatly appreciated.** If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue explaining what is the problem. Also, you can reach us by mail - listed at the end :)
<br/>
<!-- LICENSE -->
## License
Distributed under the GNU General Public License v3.0. See `LICENSE.txt` for more information.
<br/>
<!-- CONTACT -->
## Contact
João Pedro Carvalho Moreira - mcjpedro@gmail.com<br />
Matheus Costa - matheuscosta3004@gmail.com
<br/>
<!-- ACKNOWLEDGMENTS -->
## Acknowledgments
* Flávio Mourão:<br/>
Github: [Flávio Mourão](https://github.com/fgmourao) Twitter: [@F_Mourao_](https://twitter.com/F_Mourao_)
* Lab:<br/>
[Núcleo de Neurociências](http://www.nnc.ufmg.br)
### Developed at
Nucleo de Neurociencias - NNC<br/>
Universidade Federal de Minas Gerais - UFMG<br/>
Brazil<br/>
<!-- MARKDOWN LINKS & IMAGES -->
[issues-shield]: https://img.shields.io/github/issues/mrdrzit/Behavython
[issues-url]: https://github.com/mrdrzit/Behavython/issues
[closed-issues-shield]: https://img.shields.io/github/issues-closed/mrdrzit/Behavython?color=%2321e00b
[closed-issues-url]: https://github.com/mrdrzit/Behavython/issues?q=is%3Aissue+is%3Aclosed
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[license-url]: https://github.com/mrdrzit/Behavython/blob/main/LICENSE
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