The Animal Data Organization (AnDO) is a set of specifications for the organization of a directory containing experimental data recorded in animals. It is very inspired by the BIDS specifications ( https://bids-specification.readthedocs.io ). The main difference lies in the fact that in experiments conducted with animals, it is very common to have different settings for different sessions, and more importantly for different animals (whereas research on human subjects tends to have exactly the same protocol used for all subjects, as looked after by the BIDS specifications).
This project is composed of three main scrip :
-AnDOChecker script that check if your dataset follows AnDO rules -AnDOGenerator script that create a dataset based on a CSV files -AnDOViewer script that display your dataset directory in a convenient way.
Futher information on Specs : https://bids.neuroimaging.io/bep032
AnDOChecker requires:
- Python (>= 3.6)
- Pip3
> pip install AnDOCheckerBy installing AnDOChecker all three of the scripts will be installed
usage: AnDOChecker.py [-h] [-v] path
positional arguments:
path Path to your folder
optional arguments: -h, --help show this help message and exit
-v, --verbose increase output verbosity
> python checker/AnDOChecker.py tests/dataset001/LandingOR verbose usage
> python checker/AnDOChecker.py -v tests/dataset001/Landing
OR, in an equivalent manner, you can use the command line interface (CLI) provided with the package:
> AnDOChecker -v tests/dataset001/Landing
usage: AnDOGenerator.py [-h] pathToCsv pathToDir
positional arguments:
pathToCsv Path to your folder
pathToDir Path to your csv file
optional arguments:
-h, --help show this help message and exit
OR, in an equivalent manner, you can use the command line interface (CLI) provided with the package:
> AnDOGenerator data.csv data/
usage: AnDOViewer.py [-h] [-S] [-Se] [-Su] [-Ss] pathToDir
positional arguments:
pathToDir Path to the folder to show
optional arguments:
-h, --help show this help message and exit
-S, --show show dir structure
-Se, --show_experiments show experiments folder only
-Su, --show_subjects show subjects folder only
-Ss, --show_sessions show sessions folder only
OR, in an equivalent manner, you can use the command line interface (CLI) provided with the package:
> AnDOViewer data/
We welcome new contributors of all experience levels. The [Development Guide][] has detailed information about contributing code, documentation, tests, and more. We've included some basic information in this README.
- Official source code repo: https://github.com/INT-NIT/AnDOChecker
- Download releases: https://pypi.org/project/AnDOChecker/
- Issue tracker:https://github.com/INT-NIT/AnDOChecker/issues
You can check the latest sources with the command:
git clone https://github.com/INT-NIT/AnDOChecker.git
To learn more about making a contribution to AnDoChecker, please see our [Contributing guide][].