bluepyemodel.evaluation.protocol_configuration¶

ProtocolConfiguration

Classes

ProtocolConfiguration(name, stimuli[, ...])

Container for the definition of a protocol

class ProtocolConfiguration(name, stimuli, recordings_from_config=None, recordings=None, validation=False, ion_variables=None, protocol_type='ThresholdBasedProtocol', stochasticity=False)¶

Bases: object

Container for the definition of a protocol

Init.

The arguments efeatures and protocols are expected to be in the format used for the storage of the fitness calculator configuration. To store the results of an extraction, use the method init_from_bluepyefe.

Parameters:

name (str) – name of the protocol

stimuli (list of dict) –

contains the description of the stimuli. The exact format has to match what is expected by the related eCode class (see the classes defined in bluepyemodel.ecodes for more information). For example, for a Step protocol, the format will be:

[{
    'amp': float, 'thresh_perc': float, 'holding_current': float,
    'delay': float, 'duration': float, 'totduration': float, 'location': dict
}]
The location should have a format that can be read by
evaluation.evaluator.define_location()

recordings_from_config (list of dict) –
contains the description of the recordings. For a recording at a given compartment, the format is for example:
```
[{
    "type": "CompRecording",
    "name": f"{protocol_name}.soma.v",
    "location": "soma",
    "variable": "v",
}]
```
recordings (list of dict) – same as recordings_from_config. Is here for backward compatibility only.
ion_variables (list of str) – ion current names and ionic concentration names for all available mechanisms.
protocol_type (str) – type of the protocol. Can be “ThresholdBasedProtocol” or “Protocol”. When using “ThresholdBasedProtocol”, the current amplitude and step amplitude of the stimulus will be ignored and replaced by values obtained from the holding current and rheobase of the cell model respectively. When using “Protocol”, the current amplitude and step amplitude of the stimulus will be used directly, in this case, if a “thresh_perc” was informed, it will be ignored.
stochasticity (bool) – whether the mechanisms should be on stochastic mode when the protocol runs, or not.

as_dict()¶: Dictionary form