merszym / caro

A project to get a GPIO module to run over Raspian

Caro

A Program to run 'THE CAROUSSEL' - A Raspberry/GPIO-based machine built by Dr. Wolf Hütteroth and Dr. Tilman Triphan from the University of Leipzig/Konstanz to test the behavior of Drosophila in the presence of a turning disc. This Script regulates the light, the turning of the discs and the camera. Input = Experiment-File (s. 3.), Output = Video-files for downstream analysis of Drosophila movement-patterns

Dependencies:

• see Point 1.3 and use the caro.yml-file to create a fitting environment!

1. Getting started:

(I assume, that you have a Raspberry prepared)

1. Clone this repository onto your Raspberry by typing:

git clone https://github.com/MerlinSzymanski/Carousel

2. Change your working-directory:

cd path/to/Carousel/

3. Create and activate the Environment

conda env create -f caro.yml
conda activate caro 

4. Set up a Shortcut in the Terminal by running

python3 main.py -s

5. Run a functionality-Test

python3 main.py -t

If something is not working, check the pin-numbering in the Caroussel.py-module

2. Running the experiment:

You can now access the program by opening the terminal and typing

caro

which start the Userunterface.

If you want to go directly over the python-file, change to the Carousel/ directory and type:

python3 main.py

Available flags are:

• i: The program starts without a GUI and reads the data from a file. Default file = files/template.json to use the same data as in the previous experiment, you can use -i save_files/temp/exp_settings.json
• g: The program starts with a GUI
• t: The Functionality test
• c: A cleanup-programm, if the Caroussel runs after the programm crashed

3. Data to provide:

You can see in the GUI what should be provided...

Necessary for the Script:

• circRythm: e.g. "6:22LD" = from 06:00 - 22:00 white light, from 22:00 - 06:00 Red Light. Please specify your regimes in files/circrythm.json
• motor_switchtime: e.g. "5" = After 5 minutes one disc stops turning and the other one starts
• motor1_direction: "cw" or "ccw" = clockwise or counterclockwise
• motor2_direction: "same" or "different" = relative to motor 1
• video_length: e.g. "9000" = Lenght in frames. Should be switched back to seconds to avoid confusion!
• FPS: e.g. "5" = Frames per second

Everything else is just piped into the archive, but can be specified using the files/*.json files

4. Additional functions

If some of the functions dont work - check the pin-numbers in the "caroussel.py" module. To shutdown a running caroussel after a crash,use

python3 main.py -c