allensdk.brain_observatory.behavior.trials_processing module¶
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allensdk.brain_observatory.behavior.trials_processing.calculate_reward_rate(response_latency=None, starttime=None, window=0.75, trial_window=25, initial_trials=10)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.create_extended_trials(trials=None, metadata=None, time=None, licks=None)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.find_licks(reward_times, licks, window=3.5)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.get_change_time_frame_response_latency(trial)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.get_even_sampling(data)[source]¶ Get status of even_sampling
Parameters: - data: Mapping
foraging2 experiment output data
Returns: - bool:
True if even_sampling is enabled
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allensdk.brain_observatory.behavior.trials_processing.get_image_info_from_trial(trial_log, ti)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.get_ori_info_from_trial(trial_log, ti)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.get_response_latency(change_event, trial)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.get_stimulus_attr_changes(stim_dict, change_frame, first_frame, last_frame)[source]¶ Notes
- assumes only two stimuli are ever shown
- converts attr_names to lowercase
- gets the net attr changes from the start of a trial to the end of a trial
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allensdk.brain_observatory.behavior.trials_processing.get_trial_image_names(trial, stimuli) → Dict[str, str][source]¶ Gets the name of the stimulus presented at the beginning of the trial and what is it changed to at the end of the trial. Parameters ———- trial: A trial in a behavior ophys session stimuli: The stimuli presentation log for the behavior session
Returns: - A dictionary indicating the starting_stimulus and what the stimulus is
changed to.
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allensdk.brain_observatory.behavior.trials_processing.get_trial_lick_times(lick_times, start_time, stop_time)[source]¶ extract lick times in time range
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allensdk.brain_observatory.behavior.trials_processing.get_trial_reward_time(rebased_reward_times, start_time, stop_time)[source]¶ extract reward times in time range
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allensdk.brain_observatory.behavior.trials_processing.get_trial_timing(event_dict: dict, stimulus_presentations_df: pandas.core.frame.DataFrame, licks: List[float], go: bool, catch: bool, auto_rewarded: bool, hit: bool, false_alarm: bool, aborted: bool)[source]¶ Extract a dictionary of trial timing data. See trial_data_from_log for a description of the trial types.
Parameters: - event_dict: dict
Dictionary of trial events in the well-known pkl file
- stimulus_presentations_df: pd.DataFrame
pandas dataframe of stimulus presentations, from the get_stimulus_presentations response for the BehaviorOphysSession.api.
- licks: List[float]
list of lick timestamps, from the get_licks response for the BehaviorOphysSession.api.
- go: bool
True if “go” trial, False otherwise. Mutually exclusive with catch.
- catch: bool
True if “catch” trial, False otherwise. Mutually exclusive with go.
- auto_rewarded: bool
True if “auto_rewarded” trial, False otherwise.
- hit: bool
True if “hit” trial, False otherwise
- false_alarm: bool
True if “false_alarm” trial, False otherwise
- aborted: bool
True if “aborted” trial, False otherwise
Returns: - dict
- start_time: float
The time the trial started (in seconds elapsed from recording start)
- stop_time: float
The time the trial ended (in seconds elapsed from recording start)
- trial_length: float
Duration of the trial in seconds
- response_time: float
The response time, for non-aborted trials. This is equal to the first lick in the trial. For aborted trials or trials without licks, response_time is NaN.
- change_frame: int
The frame number that the stimulus changed
- change_time: float
The time in seconds that the stimulus changed
- response_latency: float or None
The time in seconds between the stimulus change and the animal’s lick response, if the trial is a “go”, “catch”, or “auto_rewarded” type. If the animal did not respond, return float(“inf”). In all other cases, return None.
Notes
The following parameters are mutually exclusive (exactly one can be true):
hit, miss, false_alarm, aborted, auto_rewarded
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allensdk.brain_observatory.behavior.trials_processing.get_trials(data, licks_df, rewards_df, stimulus_presentations_df, rebase)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.local_time(iso_timestamp, timezone=None)[source]¶
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allensdk.brain_observatory.behavior.trials_processing.resolve_initial_image(stimuli, start_frame)[source]¶ Attempts to resolve the initial image for a given start_frame for a trial
Parameters: - stimuli: Mapping
foraging2 shape stimuli mapping
- start_frame: int
start frame of the trial
Returns: - initial_image_category_name: str
stimulus category of initial image
- initial_image_group: str
group name of the initial image
- initial_image_name: str
name of the initial image
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allensdk.brain_observatory.behavior.trials_processing.trial_data_from_log(trial)[source]¶ Infer trial logic from trial log. Returns a dictionary.
- reward volume: volume of water delivered on the trial, in mL
Each of the following values is boolean:
Trial category values are mutually exclusive * go: trial was a go trial (trial with a stimulus change) * catch: trial was a catch trial (trial with a sham stimulus change)
stimulus_change/sham_change are mutually exclusive * stimulus_change: did the stimulus change (True on ‘go’ trials) * sham_change: stimulus did not change, but response was evaluated (True on ‘catch’ trials)
Each trial can be one (and only one) of the following: * hit (stimulus changed, animal responded in response window) * miss (stimulus changed, animal did not respond in response window) * false_alarm (stimulus did not change, animal responded in response window) * correct_reject (stimulus did not change, animal did not respond in response window) * aborted (animal responded before change time) * auto_rewarded (reward was automatically delivered following the change. This will bias the animals choice and should not be categorized as hit/miss)