pymer

Collection of Python scripts for analyzing extracellular multielectrode array recordings from the retina in the Gollisch lab, Göttingen.

Installing

Install the latest version of Anaconda or Miniconda.

Creating conda environment

Open the terminal and navigate to the directory where you downloaded the repository.

conda env create --file environment.yml

This will create a new conda environment named pymer with the required packages.

Each time you want to use this environment, you need to activate it:

conda activate pymer

Adding path variables

A few folder paths need to be made available to python so that the scripts in those folders are reachable. This can be done by a single import when the directory is set to the pymer folder.

import pathadder

You should edit the pymer_path variable in this script to match the location of the folder where pymer is located.

The import needs to be done each time you launch the python interpreter or in the beginning of each script/notebook.

If you'd like to make this more permanent, the following lines can be added to your ~/.bashrc file, changing the PYMERPATH variable to tha appropriate path.

PYMERPATH='/home/user/repositories/pymer'
export PYTHONPATH="${PYTHONPATH}:$PYMERPATH"
export PYTHONPATH="${PYTHONPATH}:$PYMERPATH/modules"
export PYTHONPATH="${PYTHONPATH}:$PYMERPATH/external_libs"
export PYTHONPATH="${PYTHONPATH}:$PYMERPATH/classes"
export PYTHONPATH="${PYTHONPATH}:$PYMERPATH/generalizedmodels"

Random Number Generator

To set up the random number generator, run the following in the terminal with the pymer environment activated:

sudo apt install gcc g++

cd external_libs/randpy

python setup.py build_ext --inplace

User Configuration

A local setting root_experiment_dir is necessary for most functions.

This is a shortcut for all experiments, so that they are accessible from anywhere regardless of your current working directory. Once you set the root_experiment_directory, you can access experiments simply by their folder name instead of the full path.

To set your local configuration, create an empty file named ".pymer_config" at your home directory (/home/<username>/ for Linux and Mac and C:\Users\<username>\ for Windows) and add the desired options. See the default configuration file for all options.

A minimum working example to get you started would be:

{
        "root_experiment_dir" : "/home/<username>/mydata/"
}