write_synapse_activation_file¶

single_cell_parser.writer.write_synapse_activation_file(fname=None, cell=None, synTypes=None, synDistances=None, synTimes=None, activeSyns=None)¶

Write out a Synapse activation file.

Used in compute_synapse_distances_times() to write out a synapse activation file.

The following information is saved:

• synapse type: to which presynaptic cell type this synapse belongs to.

• synapse ID: unique identifier for the synapse.

• soma distance: distance from the synapse to the soma.

• section ID: ID of the section of the postsynaptic cell that contains this synapse.

• section pt ID: ID of the point in the section that contains this synapse.

• dendrite label: label of the dendrite that contains this synapse.

• activation times: times at which the synapse was active (ms).

Parameters:¶

fname : str¶

The output file name as a ful path, including the file extension. Preferably unique (see e.g. _evoked_activity() for the generation of unique syapse activation filenames)

cell : single_cell_parser.cell.Cell¶

Cell object.

synTypes : list¶

list of synapse types.

synDistances : dict¶

dictionary of synapse distances per synapse type.

synTimes : dict¶

dictionary of synapse activation times per synapse type. Values are a list of the activation times for each synapse within that type.

activeSyns : dict¶

dictionary of active synapses per synapse type. Values are a list of booleans indicating whether each synapse of that type is active.

Returns:¶

None. Writes out the synapse activation file to fname.

Example

>>> synTypes = ['cell_type_1']  # 1 synapse type
>>> synTimes = {'cell_type_1': [[0.1, 0.2, 0.3], [0.15, 0.25, 0.35], [0.2, 0.3, 0.4]]}  # 3 synapses of that type
>>> synDistances = {'cell_type_1': [150.0, 200.0, 250.0]}
>>> activeSyns = {'cell_type_1': [True, True, True]}  # all 3 synapses are active
>>> write_synapse_activation_file(
...     'synapse_activation.csv',
...     cell,
...     synTypes,
...     synDistances,
...     synTimes,
...     activeSyns
... )