brainbox.behavior.training

Functions

compute_bias_info	Compute all relevant performance metrics for when subject is on biasedChoiceWorld
compute_median_reaction_time	Compute median reaction time on zero contrast trials from trials object
compute_n_trials	Compute number of trials in trials object
compute_performance	Compute performance on all trials at each contrast level from trials object
compute_performance_easy	Compute performance on easy trials (stimulus >= 50 %) from trials object
compute_psychometric	Compute psychometric fit parameters for trials object
compute_reaction_time	Compute median reaction time for all contrasts
compute_training_info	Compute all relevant performance metrics for when subject is on trainingChoiceWorld
concatenate_trials	Concatenate trials from different training sessions
criterion_1a	Returns bool indicating whether criterion for trained_1a is met.
criterion_1b	Returns bool indicating whether criterion for trained_1b is met.
criterion_delay	Returns bool indicating whether criterion for ready4delay is met.
criterion_ephys	Returns bool indicating whether criterion for ready4ephysrig or ready4recording is met.
display_status	Display training status of subject to terminal
get_lab_training_status	Computes the training status of all alive and water restricted subjects in a specified lab
get_sessions	Download and load in training data for a specfied subject.
get_signed_contrast	Compute signed contrast from trials object
get_subject_training_status	Computes the training status of specified subject
get_training_status	Compute training status of a subject from three consecutive training datasets
plot_psychometric	Function to plot pyschometric curve plots a la datajoint webpage
plot_reaction_time	Function to plot reaction time against contrast a la datajoint webpage (inversed for some reason??)
plot_reaction_time_over_trials	Function to plot reaction time with trial number a la datajoint webpage

get_lab_training_status(lab, date=None, details=True, one=None)

Computes the training status of all alive and water restricted subjects in a specified lab

Parameters

• lab (string) – lab name (must match the name registered on Alyx)

• date – the date from which to compute training status from. If not specified will compute

from the latest date with available data :type date: string of format ‘YYYY-MM-DD’ :param details: whether to display all information about training status computation e.g performance, number of trials, psychometric fit parameters :type details: bool :param one: instantiation of ONE class

get_subject_training_status(subj, date=None, details=True, one=None)

Computes the training status of specified subject

Parameters

• subj (string) – subject nickname (must match the name registered on Alyx)

• date – the date from which to compute training status from. If not specified will compute

from the latest date with available data :type date: string of format ‘YYYY-MM-DD’ :param details: whether to display all information about training status computation e.g performance, number of trials, psychometric fit parameters :type details: bool :param one: instantiation of ONE class

get_sessions(subj, date=None, one=None)

Download and load in training data for a specfied subject. If a date is given it will load data from the three (or as many are available) previous sessions up to the specified date, if not it will load data from the last three training sessions that have data available

Parameters

• subj (string) – subject nickname (must match the name registered on Alyx)

• date – the date from which to compute training status from. If not specified will compute

from the latest date with available data :type date: string of format ‘YYYY-MM-DD’ :param one: instantiation of ONE class :returns:

• trials - dict of trials objects where each key is the session date

• task_protocol - list of the task protocol used for each of the sessions

• ephys_sess_data - list of dates where training was conducted on ephys rig. Empty list if

  all sessions on training rig

• n_delay - number of sessions on ephys rig that had delay prior to starting session

  > 15min. Returns 0 is no sessions detected

get_training_status(trials, task_protocol, ephys_sess_dates, n_delay)

Compute training status of a subject from three consecutive training datasets

Parameters

• trials (Bunch) – dict containing trials objects from three consective training sessions

• task_protocol – task protocol used for the three training session, can be ‘training’,

‘biased’ or ‘ephys’ :type task_protocol: list of strings :param ephys_sess_dates: dates of sessions conducted on ephys rig :type ephys_sess_dates: list of strings :param n_delay: number of sessions on ephys rig with delay before start > 15 min :type n_delay: int :returns:

• status - training status of subject

• info - Bunch containing performance metrics that decide training status e.g performance

  on easy trials, number of trials, psychometric fit parameters, reaction time

display_status(subj, sess_dates, status, perf_easy=None, n_trials=None, psych=None, psych_20=None, psych_80=None, rt=None)

Display training status of subject to terminal

Parameters

• subj (string) – subject nickname

• sess_dates (list of strings) – training session dates used to determine training status

• status (string) – training status of subject

• perf_easy (np.array) – performance on easy trials for each training sessions

• n_trials (np.array) – number of trials for each training sessions

• psych (np.array - bias, threshold, lapse high, lapse low) – parameters of psychometric curve fit to data from all training sessions

• psych_20 – parameters of psychometric curve fit to data in 20 (probability left) block

from all training sessions :type psych_20: np.array - bias, threshold, lapse high, lapse low :param psych_80: parameters of psychometric curve fit to data in 80 (probability left) block from all training sessions :type psych_80: np.array - bias, threshold, lapse high, lapse low :param rt: median reaction time on zero contrast trials across all training sessions (if nan indicates no zero contrast stimuli in training sessions)

concatenate_trials(trials)

Concatenate trials from different training sessions

Parameters

trials – dict containing trials objects from three consecutive training sessions,

keys are session dates :type trials: Bunch :return: trials object with data concatenated over three training sessions :rtype: dict

compute_training_info(trials, trials_all)

Compute all relevant performance metrics for when subject is on trainingChoiceWorld

Parameters

trials – dict containing trials objects from three consective training sessions,

keys are session dates :type trials: Bunch :param trials_all: trials object with data concatenated over three training sessions :type trials_all: Bunch :returns:

• perf_easy - performance of easy trials for each session

• n_trials - number of trials in each session

• psych - parameters for psychometric curve fit to all sessions

• rt - median reaction time for zero contrast stimuli over all sessions

compute_bias_info(trials, trials_all)

Compute all relevant performance metrics for when subject is on biasedChoiceWorld

Parameters

trials – dict containing trials objects from three consective training sessions,

keys are session dates :type trials: Bunch :param trials_all: trials object with data concatenated over three training sessions :type trials_all: Bunch :returns:

• perf_easy - performance of easy trials for each session

• n_trials - number of trials in each session

• psych_20 - parameters for psychometric curve fit to trials in 20 block over all sessions

• psych_80 - parameters for psychometric curve fit to trials in 80 block over all sessions

• rt - median reaction time for zero contrast stimuli over all sessions

get_signed_contrast(trials)

Compute signed contrast from trials object

Parameters

trials (dict) – trials object that must contain contrastLeft and contrastRight keys

returns: array of signed contrasts in percent, where -ve values are on the left

compute_performance_easy(trials)

Compute performance on easy trials (stimulus >= 50 %) from trials object

Parameters

trials – trials object that must contain contrastLeft, contrastRight and feedbackType

keys :type trials: dict returns: float containing performance on easy contrast trials

compute_performance(trials, signed_contrast=None, block=None, prob_right=False)

Compute performance on all trials at each contrast level from trials object

Parameters

trials – trials object that must contain contrastLeft, contrastRight and feedbackType

keys :type trials: dict returns: float containing performance on easy contrast trials

compute_n_trials(trials)

Compute number of trials in trials object

Parameters

trials (dict) – trials object

returns: int containing number of trials in session

compute_psychometric(trials, signed_contrast=None, block=None, plotting=False, compute_ci=False, alpha=0.32)

Compute psychometric fit parameters for trials object

Parameters

• trials (dict) – trials object that must contain contrastLeft, contrastRight and probabilityLeft

• signed_contrast (np.array) – array of signed contrasts in percent, where -ve values are on the left

• block (float) – biased block can be either 0.2 or 0.8

Returns

array of psychometric fit parameters - bias, threshold, lapse high, lapse low

compute_median_reaction_time(trials, stim_on_type='stimOn_times', contrast=None, signed_contrast=None)

Compute median reaction time on zero contrast trials from trials object

Parameters

• trials (dict) – trials object that must contain response_times and stimOn_times

• stim_on_type – feedback from which to compute the reaction time. Default is stimOn_times

i.e when stimulus is presented :type stim_on_type: string (must be a valid key in trials object) :param signed_contrast: array of signed contrasts in percent, where -ve values are on the left :type signed_contrast: np.array :return: float of median reaction time at zero contrast (returns nan if no zero contrast trials in trials object)

compute_reaction_time(trials, stim_on_type='stimOn_times', stim_off_type='response_times', signed_contrast=None, block=None, compute_ci=False, alpha=0.32)

Compute median reaction time for all contrasts

Parameters

• trials – trials object that must contain response_times and stimOn_times

• stim_on_type –

• stim_off_type –

• signed_contrast –

• block –

Returns

criterion_1a(psych, n_trials, perf_easy)

Returns bool indicating whether criterion for trained_1a is met. All criteria documented here (https://figshare.com/articles/preprint/A_standardized_and_reproducible_method_to_measure_ decision-making_in_mice_Appendix_2_IBL_protocol_for_mice_training/11634729)

criterion_1b(psych, n_trials, perf_easy, rt)

Returns bool indicating whether criterion for trained_1b is met.

criterion_ephys(psych_20, psych_80, n_trials, perf_easy, rt)

Returns bool indicating whether criterion for ready4ephysrig or ready4recording is met.

criterion_delay(n_trials, perf_easy)

Returns bool indicating whether criterion for ready4delay is met.

plot_psychometric(trials, ax=None, title=None, plot_ci=False, ci_aplha=0.32, **kwargs)

Function to plot pyschometric curve plots a la datajoint webpage

Parameters

trials –

Returns

plot_reaction_time(trials, ax=None, title=None, plot_ci=False, ci_alpha=0.32, **kwargs)

Function to plot reaction time against contrast a la datajoint webpage (inversed for some reason??)

Parameters

trials –

Returns

plot_reaction_time_over_trials(trials, stim_on_type='stimOn_times', ax=None, title=None, **kwargs)

Function to plot reaction time with trial number a la datajoint webpage

Parameters

• trials –

• stim_on_type –

• ax –

• title –

• kwargs –

Returns