snudda.neurons.neuron_prototype

class snudda.neurons.neuron_prototype.NeuronPrototype(neuron_path, neuron_name, morphology_path=None, parameter_path=None, mechanism_path=None, modulation_path=None, snudda_data=None, meta_path=None, virtual_neuron=False, load_morphology=True, axon_stump_id_flag=False, verbose=False)[source]

Helper class, returns a neuron prototype based on parameter_id, morph_id and modulation_id

apply(function_name, arguments)[source]

Applies function to all morphology prototypes

clone(parameter_id=None, morphology_id=None, modulation_id=None, parameter_key=None, morphology_key=None, modulation_key=None, position=None, rotation=None, get_cache_original=False)[source]

Creates a clone of the neuron prototype, with given position and rotation.

Use either keys or id (keys have precedence if both given)

Parameters

  • parameter_id (int) – parameter set to use

  • morphology_id (int) – morphology set to use, a parameter set can have multiple morphology variations

  • modulation_id (int) – neuro-modulation parameter set to use

  • parameter_key (str) – parameter key for parameter set in parameters.json

  • morphology_key (str) – morphology key for morphology in meta.json

  • modulation_key (str) – modulation key for neuromodulation in modulation.json

  • position (float,float,float) – position of neuron clone

  • rotation – rotation (3x3 numpy matrix)

  • get_cache_original (bool) – return the original rather than a clone

get_modulation_parameters(modulation_key=None, modulation_id=None)[source]

Returns modulation parameter set, give either ID or key

Parameters

  • modulation_key (str) – modulation key

  • modulation_id (int) – modulation ID, which of the modulation parameter sets to use

Returns

One parameter set as a list of dictionaries

get_morphology(parameter_key=None, morphology_key=None, parameter_id=None, morphology_id=None)[source]

Returns morphology for a given parameter_id, morphology_id combination. (Each parameter set has a set of morphologies that it is valid for)

get_parameters(parameter_key=None, parameter_id=None)[source]

Returns neuron parameter set

Parameters

  • parameter_key (str) – parameter key for the parameter set

  • parameter_id (int) – parameter ID, which of the parameter sets to use

Returns

One parameter set as a list of dictionaries

instantiate()[source]

Instantiates all morphologies at once, instead of on demand.

load_info()[source]

Reads information about the neuron prototype.