respdetect: A Matlab tool for detecting breath events from whale biologger data
respdetect: A Matlab tool for detecting breath events from whale biologger data - Published in JOSS (2025)
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Published in Journal of Open Source Software
Repository
A tool to detect respirations from kinematic data
Basic Info
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
respdetect
Summary
Respdetect is a MATLAB toolkit to detect respirations in whale DTAG or CATS tag records. The tools are especially useful for detecting respiration events using movement signatures in logging whales, in addition to single-breath surfacings. Respdetect exports the locations and type (single-breath surfacing or logging) of all detected breaths.
These files are intended to work alongside the DTAG Matlab Toolboxes by Mark Johnson which can be found here. The DTAG Matlab toolbox is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with D3. If not, see http://www.gnu.org/licenses/.
Installation
System Requirements
Respdetect was developed and tested on 64-bit Windows 10 and has not yet been tested on other platforms.
MATLAB
Respdetect was developed on MATLAB versions R2020a and has not yet been tested with other versions.
MATLAB toolbox dependencies:
- Audio Toolbox
- Signal Processing Toolbox
- Image Processing Toolbox
- Statistics and Machine Learning Toolbox
Installation Instructions
You may either 1) directly download this repository or 2) clone it using: git clone https://github.com/ashleyblawas/respdetect.git.
When you open the run_all.m file you will see that you have the option to specify the data path.. This setup is detailed in the repository Wiki here. You can alternatively leave the data_path variable empty which will force it to default to the tests folder in the GitHub repository. After running the first step of run_all.m, the respdetect tools will be on your path and no further installation is needed.
Usage
Check out the repository Wiki (linked above and to screenshot below) for detailed instructions on how to use these tools. The run_all.m script will guide you through the use of the tools.
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Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. More information on contributing can be found here.
License
Owner
- Name: Ashley Blawas
- Login: ashleyblawas
- Kind: user
- Company: Stanford University
- Website: ashleyblawas.me
- Twitter: a_blaw
- Repositories: 1
- Profile: https://github.com/ashleyblawas
Post-Doc at Hopkins Marine Station of Stanford University
JOSS Publication
respdetect: A Matlab tool for detecting breath events from whale biologger data
Authors
Nicholas School of the Environment, Duke University, Durham, NC, USA, Hopkins Marine Station, Stanford University, Pacific Grove, CA, USA
Editor
Kristen Thyng
Tags
Matlab DTAGs breaths whales physiologyGitHub Events
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