single_cell_parser ❭ writer ❭ write_synapse_activation_file

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
... )