bluepyefe.auto_targets

class AutoTarget

Functions

default_auto_targets()

Define a set of 3 generic AutoTarget for firing pattern properties, AP waveform properties and hyperpolarizing step properties.

Classes

AutoTarget(protocols, amplitudes, efeatures)

Fuzzy targets defined by lists of ecodes, amplitudes and efeatures.
class AutoTarget(protocols, amplitudes, efeatures, min_recordings_per_amplitude=10, preferred_number_protocols=1, tolerance=10)[source]

Bases: object

Fuzzy targets defined by lists of ecodes, amplitudes and efeatures. The AutoTarget will try to find the best combination of ecodes, amplitudes and efeatures that match the data available in the recordings.

Extract efeatures.

Parameters:

  • protocols (list of str) – list of eCodes, by order of priority.

  • amplitudes (list of int) – list of amplitudes, expressed as percentages of the rheobase, by order of priority

  • efeatures (list str) – list of efeatures.

  • min_recordings_per_amplitude (int) – minimum number of recordings a amplitude should have to be considered as a target.

  • preferred_number_protocols (int) – out of all the available amplitudes, how many should be used.

  • tolerance (float) – tolerance used to bin the efeatures around the target amplitudes.

generate_targets()[source]

Build a list of targets in the format expected by the main extraction function of BluePyEfe using the targets presently active.

is_valid()[source]

Check if the present AutoTarget has active targets (if matching ephys data were found)

select_ecode_and_amplitude(recordings)[source]

Based on what ephys data is available, builds an effective (active) set of targets.

default_auto_targets()[source]

Define a set of 3 generic AutoTarget for firing pattern properties, AP waveform properties and hyperpolarizing step properties.