foraging translator conforms to schema

Author: neuromusic

tests/translator/test_translator_functional.py

@@ -4,6 +4,7 @@
 from visual_behavior.schemas.extended_trials import ExtendedTrialSchema
 from visual_behavior.translator import foraging2, foraging
 from visual_behavior.translator.core import create_extended_dataframe
+from visual_behavior.uuid_utils import create_session_uuid
 
 
 """test the schemas vs the outputs here
@@ -50,10 +51,20 @@ def test_foraging2_translator_schema(foraging2_data_stage4_2018_05_10):
     core_data = foraging2.data_to_change_detection_core(
         foraging2_data_stage4_2018_05_10
     )
+    core_data['metadata']['behavior_session_uuid'] = create_session_uuid(
+        core_data['metadata']['mouseid'],
+        core_data['metadata']['startdatetime'],
+    )
     _test_core_data_schemas(core_data)
 
 def test_foraging_translator_schema(behavioral_session_output_fixture):
     core_data = foraging.data_to_change_detection_core(
         behavioral_session_output_fixture
     )
+
+    core_data['metadata']['behavior_session_uuid'] = create_session_uuid(
+        str(core_data['metadata']['mouseid']),
+        core_data['metadata']['startdatetime'],
+    )
+
     _test_core_data_schemas(core_data)

visual_behavior/schemas/core.py

@@ -20,10 +20,10 @@ class RewardSchema(TimeSeriesSchema):
     """ schema for water reward presentations
 
     """
-    volume = fields.Float(
-        description='Volume of water dispensed on this reward presentation in mL',
-        required=True,
-    )
+    # volume = fields.Float(
+    #     description='Volume of water dispensed on this reward presentation in mL',
+    #     required=True,
+    # )
     # lickspout = fields.Int(
     #     description='The water line on which this reward was dispensed',
     #     required=True,

visual_behavior/translator/foraging/__init__.py

@@ -2,6 +2,7 @@
 import pandas as pd
 import numpy as np
 from scipy.signal import medfilt
+from .extract import get_end_time
 from ...utilities import calc_deriv, rad_to_dist, local_time
 
 warnings.warn(
@@ -83,13 +84,23 @@ def load_metadata(data):
 
 
     metadata['auto_reward_vol'] = 0.05 # hard coded
-    metadata['max_session_duration'] = None
-    metadata['min_no_lick_time'] = data.get('minimum_no_lick_time', None)
-    metadata['free_reward_trials'] = data.get('warm_up_trials', None)
-    metadata['abort_on_early_response'] = data.get('ignore_false_alarms', False) == False
-    metadata['even_sampling_enabled'] = data.get('image_category_sampling_mode','') == 'even_sampling'
-    metadata['failure_repeats'] = data.get('max_number_trial_repeats', None)
+    metadata['max_session_duration'] = 60.0 # hard coded
+    metadata['min_no_lick_time'] = data['minimum_no_lick_time']
+    metadata['abort_on_early_response'] = data['ignore_false_alarms'] == False
+    metadata['even_sampling_enabled'] = data['image_category_sampling_mode'] == 'even_sampling'
+    metadata['failure_repeats'] = data['max_number_trial_repeats']
+    metadata['catch_frequency'] = data['catch_frequency']
+    metadata['volume_limit'] = data['volumelimit']
+    metadata['initial_blank_duration'] = data['initial_blank']
+    metadata['warm_up_trials'] = data['warmup_trials']
+    metadata['stimulus_window'] = data['trial_duration'] - data['delta_minimum']
+
+    block_length = data['lick_detect_training_block_length']
 
+    try:
+        metadata['free_reward_trials'] = block_length[0]
+    except TypeError:
+        metadata['free_reward_trials'] = block_length
 
     return metadata
 
@@ -107,6 +118,9 @@ def load_trials(data, time=None):
 
     """
 
+    if time is None:
+        time = load_time(data)
+
     columns = (
         'auto_rewarded',
         'change_contrast',
@@ -185,7 +199,10 @@ def stringify(x):
 
     # add endframe column as startframe of last frame. Last endframe is last frame of session
     trials['endframe'] = trials['startframe'].shift(periods=-1)
-    trials.at[trials.index[-1], 'endframe'] = len(load_time(data)) - 1
+    trials.at[trials.index[-1], 'endframe'] = len(time) - 1
+
+    trials['endtime'] = get_end_time(trials, time)
+    trials['trial_length'] = trials['endtime'] - trials['starttime']
 
     return trials