Recipes

The arb::recipe class documentation is below.

C++ best practices

Here, we collect rules of thumb to keep in mind when making recipes in C++.

Recipe

class recipe

A description of a model, describing the cells and network, without any information about how the model is to be represented or executed.

All recipes derive from this abstract base class, defined in src/recipe.hpp.

Recipes provide a cell-centric interface for describing a model. This means that model properties, such as connections, are queried using the global identifier (gid) of a cell. In the description below, the term gid is used as shorthand for “the cell with global identifier gid”.

Warning

All member functions must be thread safe, because the recipe is used by the multithreaded model-building stage. In practice, this means that multiple threads should be able to call member functions of a recipe simultaneously. Model building is multithreaded to reduce model building times, so recipe implementations should avoid using locks and mutexes to introduce thread safety. See recipe best practices for more information.

Required Member Functions

The following member functions must be implemented by every recipe:

virtual cell_size_type num_cells() const = 0

The number of cells in the model.

virtual cell_kind get_cell_kind(cell_gid_type gid) const = 0

The kind of gid (see arb::cell_kind).

virtual util::unique_any get_cell_description(cell_gid_type gid) const = 0

A description of the cell gid, for example the morphology, synapses and ion channels required to build a multi-compartment neuron.

The type used to describe a cell depends on the kind of the cell. The interface for querying the kind and description of a cell are separate to allow the cell type to be provided without building a full cell description, which can be very expensive.

Optional Member Functions

virtual std::vector<cell_connection> connections_on(cell_gid_type gid) const

Returns a list of all the incoming connections for gid . Each connection con should have a valid synapse label con.dest on the post-synaptic target gid, and a valid source label con.source.label on the pre-synaptic source con.source.gid. See cell_connection.

By default returns an empty list.

virtual std::vector<ext_cell_connection> external_connections_on(cell_gid_type gid) const

Returns a list of all the incoming connections for gid from a remote simulation. Each connection con should have a valid synapse label con.dest on the post-synaptic target gid, and a valid source label con.source.lid on the remote pre-synaptic source con.source.rid. See ext_cell_connection.

By default returns an empty list.

virtual std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const

Returns a list of all the gap junctions connected to gid. Each gap junction gj should have a valid gap junction site label gj.local on gid, and a valid gap junction site label gj.peer.label on gj.peer.gid. See gap_junction_connection.

By default returns an empty list.

virtual std::vector<event_generator> event_generators(cell_gid_type gid) const

Returns a list of all the event generators that are attached to gid.

By default returns an empty list.

virtual std::vector<probe_info> get_probes(cell_gid_type gid) const

Intended for use by cell group implementations to set up sampling data structures ahead of time and for putting in place any structures or information in the concrete cell implementations to allow monitoring.

Returns a vector containing (in order) all the probes on a given cell gid.

By default returns an empty vector.

virtual std::any get_global_properties(cell_kind) const

Global property type will be specific to a given cell kind.

By default returns an empty container.

Cells

See Cells.

Synapses

See Interconnectivity.

Probes

class probe_info

Probes are specified in the recipe objects that are used to initialize a model; the specification of the item or value that is subjected to a probe will be specific to a particular cell type.

cell_tag_type tag

User-defined tag; must be unique per cell or an exception of type dup_cell_probe will be thrown.

util::any address

Cell-type specific location info, specific to cell kind of id.gid.

Event generator and schedules

Example