brainbox.task.trials

Functions

filter_by_trial

Select trials of interest for raster

filter_correct_incorrect

Return psth for correct and incorrect trials and raster sorted by correct incorrect

filter_correct_incorrect_left_right

Return psth for left correct, left incorrect, right correct, right incorrect and raster sorted by these trials

filter_left_right

Return psth for left and right trials and raster sorted by left right

filter_trials

Wrapper to get out psth and raster for trial choice

find_trial_ids

Finds trials that match criterion

get_event_aligned_raster

Get event aligned raster

get_psth

Compute psth averaged over chosen trials

find_trial_ids(trials, side='all', choice='all', order='trial num', sort='idx', contrast=(1, 0.5, 0.25, 0.125, 0.0625, 0), event=None)[source]

Finds trials that match criterion

Parameters

trials – trials object. Must contain attributes contrastLeft, contrastRight and

feedbackType :param side: stimulus side, options are ‘all’, ‘left’ or ‘right’ :param choice: trial choice, options are ‘all’, ‘correct’ or ‘incorrect’ :param contrast: contrast of stimulus, pass in list/tuple of all contrasts that want to be considered e.g [1, 0.5] would only look for trials with 100 % and 50 % contrast :param order: how to order the trials, options are ‘trial num’ or ‘reaction time’ :param sort: how to sort the trials, options are ‘side’ (split left right trials), ‘choice’ (split correct incorrect trials), ‘choice and side’ (split left right and correct incorrect) :param event: trial event to align to (in order to remove nan trials for this event) :return: np.array of trial ids, list of dividers to indicate how trials are sorted

get_event_aligned_raster(times, events, tbin=0.02, values=None, epoch=[- 0.4, 1], bin=True)[source]

Get event aligned raster

Parameters
  • times – array of times e.g spike times or dlc points

  • events – array of events to epoch around

  • tbin – bin size to over which to count events

  • values – values to scale counts by

  • epoch – window around each event

  • bin – whether to bin times in tbin windows or not

Returns

get_psth(raster, trial_ids=None)[source]

Compute psth averaged over chosen trials

Parameters
  • raster – output from event aligned raster, window of activity around event

  • trial_ids – the trials from the raster to average over

Returns

filter_by_trial(raster, trial_id)[source]

Select trials of interest for raster

Parameters
  • raster

  • trial_id

Returns

filter_correct_incorrect_left_right(trials, event_raster, event, contrast, order='trial num')[source]

Return psth for left correct, left incorrect, right correct, right incorrect and raster sorted by these trials

Parameters
  • trials – trials object

  • event_raster – output from get_event_aligned_activity

  • event – event to align to e.g ‘goCue_times’, ‘stimOn_times’

  • contrast – contrast of stimulus, pass in list/tuple of all contrasts that want to be

considered e.g [1, 0.5] would only look for trials with 100 % and 50 % contrast :param order: order to sort trials by either ‘trial num’ or ‘reaction time’ :return:

filter_correct_incorrect(trials, event_raster, event, contrast, order='trial num')[source]

Return psth for correct and incorrect trials and raster sorted by correct incorrect

Parameters
  • trials – trials object

  • event_raster – output from get_event_aligned_activity

  • event – event to align to e.g ‘goCue_times’, ‘stimOn_times’

  • contrast – contrast of stimulus, pass in list/tuple of all contrasts that want to be

considered e.g [1, 0.5] would only look for trials with 100 % and 50 % contrast :param order: order to sort trials by either ‘trial num’ or ‘reaction time’ :return:

filter_left_right(trials, event_raster, event, contrast, order='trial num')[source]

Return psth for left and right trials and raster sorted by left right

Parameters
  • trials – trials object

  • event_raster – output from get_event_aligned_activity

  • event – event to align to e.g ‘goCue_times’, ‘stimOn_times’

  • contrast – contrast of stimulus, pass in list/tuple of all contrasts that want to be

considered e.g [1, 0.5] would only look for trials with 100 % and 50 % contrast :param order: order to sort trials by either ‘trial num’ or ‘reaction time’ :return:

filter_trials(trials, event_raster, event, contrast=(1, 0.5, 0.25, 0.125, 0.0625, 0), order='trial num', sort='choice')[source]

Wrapper to get out psth and raster for trial choice

Parameters
  • trials – trials object

  • event_raster – output from get_event_aligned_activity

  • event – event to align to e.g ‘goCue_times’, ‘stimOn_times’

  • contrast – contrast of stimulus, pass in list/tuple of all contrasts that want to be

considered e.g [1, 0.5] would only look for trials with 100 % and 50 % contrast :param order: order to sort trials by either ‘trial num’ or ‘reaction time’ :param sort: how to divide trials options are ‘choice’ (e.g correct vs incorrect), ‘side’ (e.g left vs right’) and ‘choice and side’ (e.g correct vs incorrect and left vs right) :return: