work in progress

Author: Justin Kiggins

tests/translator/test_translator_functional.py

@@ -1,5 +1,59 @@
-from visual_behavior.translator import schemas
+
+from visual_behavior.schemas.core import MetadataSchema, StimulusSchema, \
+    RunningSchema, LickSchema, RewardSchema, TrialSchema
+from visual_behavior.schemas.extended_trials import ExtendedTrialSchema
+from visual_behavior.translator import foraging2, foraging
+from visual_behavior.translator.core import create_extended_dataframe
 
 
 """test the schemas vs the outputs here
 """
+
+def _test_core_data_schemas(core_data):
+
+    # metadata
+
+    # core dataframes
+    dataframe_schemas = (
+        (StimulusSchema, core_data['visual_stimuli']),
+        (RunningSchema, core_data['running']),
+        (LickSchema, core_data['licks']),
+        (RewardSchema, core_data['rewards']),
+        (TrialSchema, core_data['trials']),
+    )
+
+    for Schema, data in dataframe_schemas:
+        errors = Schema(many=True).validate(data.to_dict(orient='records'))
+
+        for row, row_errors in errors.items():
+            assert len(row_errors)==0, (Schema, data, row_errors)
+
+    extended_trials = create_extended_dataframe(
+        trials=core_data['trials'],
+        metadata=core_data['metadata'],
+        licks=core_data['licks'],
+        time=core_data['time'],
+    )
+
+    errors = ExtendedTrialSchema(many=True).validate(
+        extended_trials.to_dict(orient='records')
+    )
+
+    for row, row_errors in errors.items():
+        assert len(row_errors)==0, row_errors
+
+    errors = MetadataSchema().validate(core_data['metadata'])
+    assert len(errors)==0, errors.keys()
+
+
+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
+    )
+    _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
+    )
+    _test_core_data_schemas(core_data)

visual_behavior/schemas/core.py

@@ -208,13 +208,13 @@ class StimulusSchema(TimeSeriesSchema):
         required=True,
         allow_none=True,
     )
-    contrast = fields.Float(
-        description='The contrast of a grating stimulus',
+    orientation = fields.Float(
+        description='The orientation of a grating stimulus',
         required=True,
         allow_none=True,
     )
-    orientation = fields.Float(
-        description='The orientation of a grating stimulus',
+    end_frame = fields.Int(
+        description='The last frame of this stimulus, non-inclusive',
         required=True,
     )
 
@@ -298,7 +298,7 @@ class MetadataSchema(Schema):
         description='total number of stimulus frames',
         required=True,
     )
-    auto_reward_volume = fields.Float(
+    auto_reward_vol = fields.Float(
         description='volume provided during autoreward trials',
         required=True,
     )
@@ -326,6 +326,26 @@ class MetadataSchema(Schema):
         description='maximum number of times to repeat parameters after a false alarm',
         required=True,
     )
+    initial_blank_duration = fields.Float(
+        description='duration of grey screen at start of each trial, in seconds',
+        required=True,
+    )
+    catch_frequency = fields.Float(
+        description='fraction of trials that should be catch trials',
+        required=True,
+    )
+    warm_up_trials = fields.Int(
+        description='number of warm up trials at start of session',
+        required=True,
+    )
+    stimulus_window = fields.Float(
+        description='start and stop times of stimulus window',
+        required=True,
+    )
+    volume_limit = fields.Float(
+        description='maximum volume of water to deliver in a session, in mL',
+        required=True,
+    )
 
 
 # class ChangeDetectionSessionCoreSchema(Schema):

visual_behavior/translator/foraging/__init__.py

@@ -282,6 +282,7 @@ def load_running_speed(data, smooth=False, time=None):
 
     running_speed = pd.DataFrame({
         'time': time,
+        'frame': range(len(time)),
         'speed': speed,
         # 'acceleration (cm/s^2)': accel,
         # 'jerk (cm/s^3)': jerk,
@@ -339,15 +340,15 @@ def load_visual_stimuli(data, time=None):
     stimdf = pd.DataFrame(data['stimuluslog'])
 
     stimdf = find_ends(stimdf)
-    stimdf['end'] = stimdf['frames_to_end'] + stimdf['frame']
+    stimdf['end_frame'] = stimdf['frames_to_end'] + stimdf['frame']
 
     def find_time(fr):
         try:
             return time[fr]
         except IndexError:
             return np.nan
 
-    stimdf['end_time'] = stimdf['end'].map(find_time)
+    stimdf['end_time'] = stimdf['end_frame'].map(find_time)
     stimdf['duration'] = stimdf['end_time'] - stimdf['time']
 
     onset_mask = (
@@ -358,13 +359,13 @@ def find_time(fr):
     ) > 0
 
     if pd.isnull(stimdf['image_name']).any() == False:  # 'image_category' in stimdf.columns:
-        cols = ['frame', 'time', 'duration', 'image_category', 'image_name']
+        cols = ['frame', 'end_frame', 'time', 'duration', 'image_category', 'image_name']
         stimuli = stimdf[onset_mask][cols]
         stimuli['orientation'] = None
         stimuli['contrast'] = None
 
     elif 'ori' in stimdf.columns:
-        cols = ['frame', 'time', 'duration', 'ori', 'contrast']
+        cols = ['frame', 'end_frame', 'time', 'duration', 'ori', 'contrast']
         stimuli = stimdf[onset_mask][cols]
         stimuli.rename(columns={'ori': 'orientation'}, inplace=True)
         stimuli['image_category'] = None

visual_behavior/translator/foraging2/extract.py

@@ -725,8 +725,8 @@ def get_running_speed(exp_data, smooth=False, time=None):
     running_speed = pd.DataFrame({
         'time': time,
         'speed (cm/s)': speed,
-        'acceleration (cm/s^2)': accel,
-        'jerk (cm/s^3)': jerk,
+        # 'acceleration (cm/s^2)': accel,
+        # 'jerk (cm/s^3)': jerk,
     })
     return running_speed