Pecking Analysis

pecking test preprocessing

Setup

pip install -r requirements.txt

Setup file save paths:

• copy the file configs/plump_config.py and name it configs/XXX_config.py.

• edit the new file and fill in behavior_data_dir to be the location of the trialdata csvs, metadata_dir to be a place where metadata will live about lesions (you need to set up that file).

• edit configs/project_lesions_2021.py to import your new config

If you need to download data, see the Downloading Data section at the bottom.

Steps

1. Download data OR point behavior_data_dir to where your data is

2. Run python cli.py package-data OUTPUT_PATH. a single csv with all trials will be saved at OUTPUT_PATH.

Lesion metadata file

Should look something like this

Subject,Lesion Date,Treatment,Drug
BluYel2571F,5/2/2019,CTRL,
GreBlu5039F,5/2/2019,NCM,NMA
...

Downloading Data

To download data, install gdrive_access, easiest way will be to do pip install git+https://github.com/theunissenlab/gdrive_python.git@main.

Follow the setup instructions in that project's readme to get google drive API credentials. In the config file, set up gdrive_credentials_dir to be the folder containing your settings.yaml file.

Make sure to share the folder pecking_test_data (from fetlab) with yourself. You should see it at the top level of your "sharedWithMe" folder on Google Drive.

Note: it is important to specify main branch of gdrive_access which has a fix that lets you see shared folders.

Run python cli.py locate-data to see if the subject folders are being found on google drive properly.