pysonata

pySONATA

A python library for the SONATA data format

Installation

Using pip:

$ pip install sonata

Install from source:

$ python setup.py install

Usage

Reading Configuration files

You can parse and validate a config json file using the from_json function in config.py. It will take care of manifest variables, combine links to other parts of the config (simulation.json, circuit.json) and return a completed json in python dictionary.

from config import from_json
cfg = from_json('path/to/config.json')
print(cfg['run']['tstart'])

Note:

• You can also pass in a jsonschema IValidator object which will check if the json file follows the schema. The AIBS BMTK uses our own custom validators, and if desired I can add the code to this repo.

Reading in circuit (nodes and edges) files

See tutorial

Reading and writing compartment reports

See tutorial

Reading and writing spike train reports

See tutorial