Merge branch 'int-brain-lab:main' into main

Author: mdmelin

iblrig_custom_tasks/nate_adaptiveTimeoutChoiceWorld/__init__.py

@@ -0,0 +1,99 @@
+"""
+This task inherits TrainingChoiceWorldSession with the addition of configurable, adaptive timeouts for incorrect
+choices depending on the stimulus contrast.
+"""
+
+import logging
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+import yaml
+from pydantic import NonNegativeFloat
+
+from iblrig.misc import get_task_arguments
+from iblrig_tasks._iblrig_tasks_trainingChoiceWorld.task import Session as TrainingCWSession
+
+log = logging.getLogger('iblrig.task')
+
+
+# read defaults from task_parameters.yaml
+with open(Path(__file__).parent.joinpath('task_parameters.yaml')) as f:
+    DEFAULTS = yaml.safe_load(f)
+
+
+class AdaptiveTimeoutChoiceWorldTrialData(TrainingCWSession.TrialDataModel):
+    adaptive_delay_nogo: NonNegativeFloat
+    adaptive_delay_error: NonNegativeFloat
+
+
+class Session(TrainingCWSession):
+    protocol_name = 'nate_adaptiveTimeoutChoiceWorld'
+    TrialDataModel = AdaptiveTimeoutChoiceWorldTrialData
+
+    def __init__(
+        self,
+        *args,
+        adaptive_delay_nogo=DEFAULTS['ADAPTIVE_FEEDBACK_NOGO_DELAY_SECS'],
+        adaptive_delay_error=DEFAULTS['ADAPTIVE_FEEDBACK_ERROR_DELAY_SECS'],
+        **kwargs,
+    ):
+        self._adaptive_delay_nogo = adaptive_delay_nogo
+        self._adaptive_delay_error = adaptive_delay_error
+        super().__init__(*args, **kwargs)
+        assert len(self._adaptive_delay_nogo) == len(self.task_params.CONTRAST_SET)
+        assert len(self._adaptive_delay_error) == len(self.task_params.CONTRAST_SET)
+
+    def draw_next_trial_info(self, **kwargs):
+        super().draw_next_trial_info(**kwargs)
+        contrast = self.trials_table.at[self.trial_num, 'contrast']
+        index = np.flatnonzero(np.array(self.task_params['CONTRAST_SET']) == contrast)[0]
+        self.trials_table.at[self.trial_num, 'adaptive_delay_nogo'] = self._adaptive_delay_nogo[index]
+        self.trials_table.at[self.trial_num, 'adaptive_delay_error'] = self._adaptive_delay_error[index]
+
+    @property
+    def feedback_nogo_delay(self):
+        return self.trials_table.at[self.trial_num, 'adaptive_delay_nogo']
+
+    @property
+    def feedback_error_delay(self):
+        return self.trials_table.at[self.trial_num, 'adaptive_delay_error']
+
+    def show_trial_log(self, extra_info: dict[str, Any] | None = None, log_level: int = logging.INFO):
+        trial_info = self.trials_table.iloc[self.trial_num]
+        info_dict = {
+            'Adaptive no-go delay': f'{trial_info.adaptive_delay_nogo:.2f} s',
+            'Adaptive error delay': f'{trial_info.adaptive_delay_error:.2f} s',
+        }
+        if isinstance(extra_info, dict):
+            info_dict.update(extra_info)
+        super().show_trial_log(extra_info=info_dict, log_level=log_level)
+
+    @staticmethod
+    def extra_parser():
+        parser = super(Session, Session).extra_parser()
+        parser.add_argument(
+            '--adaptive_delay_nogo',
+            option_strings=['--adaptive_delay_nogo'],
+            dest='adaptive_delay_nogo',
+            default=DEFAULTS['ADAPTIVE_FEEDBACK_NOGO_DELAY_SECS'],
+            nargs='+',
+            type=float,
+            help='list of delays for no-go condition (contrasts: 1.0, 0.5, 0.25, 0.125, 0.0625, 0.0)',
+        )
+        parser.add_argument(
+            '--adaptive_delay_error',
+            option_strings=['--adaptive_delay_error'],
+            dest='adaptive_delay_error',
+            default=DEFAULTS['ADAPTIVE_FEEDBACK_ERROR_DELAY_SECS'],
+            nargs='+',
+            type=float,
+            help='list of delays for error condition (contrasts: 1.0, 0.5, 0.25, 0.125, 0.0625, 0.0)',
+        )
+        return parser
+
+
+if __name__ == '__main__':  # pragma: no cover
+    kwargs = get_task_arguments(parents=[Session.extra_parser()])
+    sess = Session(**kwargs)
+    sess.run()

iblrig_custom_tasks/nate_adaptiveTimeoutChoiceWorld/task.py

@@ -0,0 +1,10 @@
+'ADAPTIVE_GAIN': True
+'ADAPTIVE_REWARD': True
+'AG_INIT_VALUE': 8.0  # Adaptive Gain init value. Once the mouse completes 200 response trials whithin a session, this reverts to STIM_GAIN
+'CONTRAST_SET_PROBABILITY_TYPE': skew_zero  # uniform, skew_zero
+'DEBIAS': True  # Whether to use debiasing rule or not by repeating error trials
+'REWARD_AMOUNT_UL': 3.0  # Reward amount (uL), will oscillate between 1.5 and 3 uL depending on previous sessions if adaptive_reward is True
+
+'CONTRAST_SET': [1.0, 0.5, 0.25, 0.125, 0.0625, 0.0]
+'ADAPTIVE_FEEDBACK_NOGO_DELAY_SECS': [2.0, 2.0, 2.0, 2.0, 2.0, 2.0]
+'ADAPTIVE_FEEDBACK_ERROR_DELAY_SECS': [2.0, 2.0, 2.0, 2.0, 2.0, 2.0]

iblrig_custom_tasks/nate_adaptiveTimeoutChoiceWorld/task_parameters.yaml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name            = "project_extraction"
-version         = "0.3.0"
+version         = "0.4.0"
 description     = "Custom extractors for satellite tasks"
 dynamic         = [ "readme" ]
 keywords        = [ "IBL", "neuro-science" ]