Configuration files

A configuration file describes the components of a scaffold model. It contains the instructions to place and connect neurons, how to represent the cells and connections as models in simulators and what to stimulate and record in simulations.

The default configuration format is JSON and a standard configuration file is structured like this:

{
  "storage": {

  },
  "network": {

  },
  "regions": {

  },
  "partitions": {

  },
  "cell_types": {

  },
  "placement": {

  },
  "after_placement": {

  },
  "connectivity": {

  },
  "after_connectivity": {

  },
  "simulations": {

  }
}

The regions, partitions, cell_types, placement and connectivity spaceholders hold the configuration for Regions, Partitions, CellTypes, PlacementStrategies and ConnectionStrategies respectively.

When you’re configuring a model you’ll mostly be using configuration attributes, nodes, dictionaries, lists, and references. These configuration units can be declared through the config file, or programatically added.

Code

Most of the framework components pass the data on to Python classes, that determine the underlying code strategy of the component. In order to link your Python classes to the configuration file they should be an importable module. Here’s an example of how the MySpecialConnection class in the local Python file connectome.py would be available to the configuration:

{
  "connectivity": {
    "A_to_B": {
      "strategy": "connectome.MySpecialConnection",
      "value1": 15,
      "thingy2": [4, 13]
    }
  }
}

The framework will try to pass the additional keys value1 and thingy2 to the class. The class should be decorated as a configuration node for it to correctly receive and handle the values:

from bsb import config, ConnectionStrategy

@config.node
class MySpecialConnection(ConnectionStrategy):
  value1 = config.attr(type=int)
  thingy2 = config.list(type=int, size=2, required=True)

For more information on creating your own configuration nodes see Nodes.

JSON

The BSB uses a JSON parser with some extras. The parser has 2 special mechanisms, JSON references and JSON imports. This allows parts of the configuration file to be reusable across documents and to compose the document from prefab blocks.

See JSON parser to read more on the JSON parser.

Default configuration

You can create a default configuration by calling Configuration.default. It corresponds to the following JSON:

{
  "storage": {
    "engine": "hdf5"
  },
  "network": {
    "x": 200, "y": 200, "z": 200
  },
  "partitions": {

  },
  "cell_types": {

  },
  "placement": {

  },
  "connectivity": {

  }
}