fabiansinz / efish_locking

Analysis code for high frequency locking in weakly electric fish

Installation instructions

• install docker

• sudo pip install docker-compose

• Clone code: git clone https://github.com/fabiansinz/efish_locking.git

• Create a file .env with content

  DJ_HOST=<IP OF MYSQL-SERVER>
  DJ_USER=<USER FOR THIS DATABASE>
  DJ_PASS=<PASSWORD FOR THE USER>
  

  and replace the placeholders with the correct values. It has to be the IP, because the Docker container cannot look up servers. The mysql user (here it's efish) needs the rights GRANT ALL PRIVILEGES ON efish%.* TO 'efish'@'%';

• Build the docker container: sudo docker-compose build --pull --no-cache locking

• If you only want to use a populated database, read on. If you want to populate the tables, then you'll need a directory data/carolin in you home with the recordings. If the files are at a different location, change the location in docker-compose.yml.

• Start the docker container by sudo docker-compose run locking. That will start a shell in the docker container

• To import the data use: python3 scripts/populate_data.py

• To run analyses use: python3 scripts/populate_analyses.py

• To run modells use: python3 scripts/populate_modelling.py

• After that you can reproduce the figures with the respective figure scripts in the scripts directory. The current docker-compose.yml maps the local directory figures_docker to the directory where the figures are stored in the container. This means you either have to create that one locally or you need to change the docker-compose.yml to point to a different directory.