Merge pull request #1924 from AllenInstitute/rc/2.8.0

rc/2.8.0

.circleci/config.yml

@@ -105,9 +105,7 @@ version: 2.1
 workflows:
   main:
     jobs:
-      # disable lint build, for merge to default branch
-      # turn back on when rc/2.8.0 is started
-      # - lint
+      - lint
       - linux-py36
       - linux-py37
       # disabled osx build. covered by github-actions

CHANGELOG.md

@@ -1,7 +1,12 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
-## [2.7.0] = TBD
+## [2.8.0] = TBD
+- Created lookup table to get monitor_delay for cases where calculation from data fails
+- If sync timestamp file has more timestamps than eye tracking moving has frame, trim excess timestamps (up to 15)
+- Session API returns both warped and unwarped stimulus images, and both are written to NWB
+
+## [2.7.0] = 2021-02-19
 - Refactored behavior and ophys session and data APIs to remove a circular inheritance issue
 - Fixed segmentation mask and roi_mask misregistration in 'BehaviorOphysSession'
 - Replaces BehaviorOphysSession.get_roi_masks() method with roi_masks property

allensdk/__init__.py

@@ -35,10 +35,7 @@
 #
 import logging
 
-
-
-
-__version__ = '2.7.0'
+__version__ = '2.8.0'
 
 
 try:
@@ -61,7 +58,8 @@ def one(x):
     except TypeError:
         return x
     if xlen != 1:
-        raise OneResultExpectedError('Expected length one result, received: {} results from query'.format(x))
+        raise OneResultExpectedError("Expected length one result, received: "
+                                     f"{x} results from queryr")
     if isinstance(x, set):
         return list(x)[0]
     else:
@@ -75,6 +73,7 @@ def one(x):
         'allensdk.api.api.retrieve_file_over_http')
     file_download_log.setLevel(logging.INFO)
     console = logging.StreamHandler()
-    formatter = logging.Formatter('%(asctime)s %(name)-12s %(levelname)-8s %(message)s')
+    formatter = logging.Formatter("%(asctime)s %(name)-12s "
+                                  "%(levelname)-8s %(message)s")
     console.setFormatter(formatter)
     file_download_log.addHandler(console)

allensdk/brain_observatory/behavior/behavior_ophys_session.py

@@ -234,7 +234,7 @@ def events(self) -> pd.DataFrame:
 
     @events.setter
     def events(self, value):
-        self_events = value
+        self._events = value
 
     @property
     def cell_specimen_table(self) -> pd.DataFrame:

allensdk/brain_observatory/behavior/behavior_session.py

@@ -174,7 +174,7 @@ def get_performance_metrics(self, engaged_trial_reward_rate_threshold=2):
         performance_metrics['total_reward_count'] = len(self.rewards)
         performance_metrics['total_reward_volume'] = self.rewards.volume.sum()
 
-        rpdf = self.get_rpdf()
+        rpdf = self.get_rolling_performance_df()
         engaged_trial_mask = (
                 rpdf['reward_rate'] >
                 engaged_trial_reward_rate_threshold)
@@ -313,24 +313,17 @@ def stimulus_presentations(self, value):
         self._stimulus_presentations = value
 
     @property
-    def stimulus_templates(self) -> StimulusTemplate:
+    def stimulus_templates(self) -> pd.DataFrame:
         """Get stimulus templates (movies, scenes) for behavior session.
 
         Returns
         -------
-        StimulusTemplate
-            A StimulusTemplate object containing the stimulus images for the
-            experiment. Relevant properties include:
-                image_set_name: The name of the image set that the
-                    StimulusTemplate encapsulates
-                image_names: A list of individual image names in the image set
-                images: A list of StimulusImage (inherits from np.ndarray)
-                    objects.
-            Also has a to_dataframe() method to convert to a dataframe
-            where indices are image names, an 'image' column contains image
-            arrays, and the df.name is the image set.
+        pd.DataFrame
+            A pandas DataFrame object containing the stimulus images for the
+            experiment. Indices are image names, 'warped' and 'unwarped'
+            columns contains image arrays, and the df.name is the image set.
         """
-        return self._stimulus_templates
+        return self._stimulus_templates.to_dataframe()
 
     @stimulus_templates.setter
     def stimulus_templates(self, value):

allensdk/brain_observatory/behavior/eye_tracking_processing.py

@@ -44,7 +44,7 @@ def load_eye_tracking_hdf(eye_tracking_file: Path) -> pd.DataFrame:
 
     # Values in the hdf5 may be complex (likely an artifact of the ellipse
     # fitting process). Take only the real component.
-    eye_tracking_data = eye_tracking_data.apply(lambda x: np.real(x.to_numpy()))
+    eye_tracking_data = eye_tracking_data.apply(lambda x: np.real(x.to_numpy()))  # noqa: E501
 
     return eye_tracking_data.astype(float)
 
@@ -186,9 +186,23 @@ def process_eye_tracking_data(eye_data: pd.DataFrame,
         eye tracking frames.
     """
 
-    if len(frame_times) != len(eye_data.index):
+    n_sync = len(frame_times)
+    n_eye_frames = len(eye_data.index)
+
+    # If n_sync exceeds n_eye_frames by <= 15,
+    # just trim the excess sync pulses from the end
+    # of the timestamps array.
+    #
+    # This solution was discussed in
+    # https://github.com/AllenInstitute/AllenSDK/issues/1545
+
+    if n_sync > n_eye_frames and n_sync <= n_eye_frames+15:
+        frame_times = frame_times[:n_eye_frames]
+        n_sync = len(frame_times)
+
+    if n_sync != n_eye_frames:
         raise RuntimeError(f"Error! The number of sync file frame times "
-                           f"({len(frame_times)} does not match the "
+                           f"({len(frame_times)}) does not match the "
                            f"number of eye tracking frames "
                            f"({len(eye_data.index)})!")
 
@@ -217,7 +231,7 @@ def process_eye_tracking_data(eye_data: pd.DataFrame,
     cr_areas[likely_blinks] = np.nan
     eye_areas[likely_blinks] = np.nan
 
-    eye_data.insert(0, "time", frame_times)
+    eye_data.insert(0, "timestamps", frame_times)
     eye_data.insert(1, "cr_area", cr_areas)
     eye_data.insert(2, "eye_area", eye_areas)
     eye_data.insert(3, "pupil_area", pupil_areas)

allensdk/brain_observatory/behavior/metadata_processing.py

@@ -1,4 +1,6 @@
+from typing import Dict
 import re
+import numpy as np
 
 description_dict = {
     # key is a regex and value is returned on match
@@ -55,25 +57,82 @@ def get_expt_description(session_type: str) -> str:
     return match.popitem()[1]
 
 
-def get_task_parameters(data):
+def get_task_parameters(data: Dict) -> Dict:
+    """
+    Read task_parameters metadata from the behavior stimulus pickle file.
+
+    Parameters
+    ----------
+    data: dict
+        The nested dict read in from the behavior stimulus pickle file.
+        All of the data expected by this method lives under
+        data['items']['behavior']
+
+    Returns
+    -------
+    dict
+        A dict containing the task_parameters associated with this session.
+    """
     behavior = data["items"]["behavior"]
+    stimuli = behavior['stimuli']
+    config = behavior["config"]
+    doc = config["DoC"]
 
     task_parameters = {}
+
     task_parameters['blank_duration_sec'] = \
-        [float(x) for x in behavior['config']['DoC']['blank_duration_range']]
-    task_parameters['stimulus_duration_sec'] = \
-        behavior['config']['DoC']['stimulus_window']
+        [float(x) for x in doc['blank_duration_range']]
+
+    if 'images' in stimuli:
+        stim_key = 'images'
+    elif 'grating' in stimuli:
+        stim_key = 'grating'
+    else:
+        msg = "Cannot get stimulus_duration_sec\n"
+        msg += "'images' and/or 'grating' not a valid "
+        msg += "key in pickle file under "
+        msg += "['items']['behavior']['stimuli']\n"
+        msg += f"keys: {list(stimuli.keys())}"
+        raise RuntimeError(msg)
+
+    stim_duration = stimuli[stim_key]['flash_interval_sec']
+
+    # from discussion in
+    # https://github.com/AllenInstitute/AllenSDK/issues/1572
+    #
+    # 'flash_interval' contains (stimulus_duration, gray_screen_duration)
+    # (as @matchings said above). That second value is redundant with
+    # 'blank_duration_range'. I'm not sure what would happen if they were
+    # set to be conflicting values in the params. But it looks like
+    # they're always consistent. It should always be (0.25, 0.5),
+    # except for TRAINING_0 and TRAINING_1, which have statically
+    # displayed stimuli (no flashes).
+
+    if stim_duration is None:
+        stim_duration = np.NaN
+    else:
+        stim_duration = stim_duration[0]
+
+    task_parameters['stimulus_duration_sec'] = stim_duration
+
     task_parameters['omitted_flash_fraction'] = \
         behavior['params'].get('flash_omit_probability', float('nan'))
     task_parameters['response_window_sec'] = \
-        [float(x) for x in behavior["config"]["DoC"]["response_window"]]
-    task_parameters['reward_volume'] = \
-        behavior["config"]["reward"]["reward_volume"]
-    task_parameters['stage'] = behavior["params"]["stage"]
+        [float(x) for x in doc["response_window"]]
+    task_parameters['reward_volume'] = config["reward"]["reward_volume"]
+    task_parameters['auto_reward_volume'] = doc['auto_reward_volume']
+    task_parameters['session_type'] = behavior["params"]["stage"]
     task_parameters['stimulus'] = next(iter(behavior["stimuli"]))
-    task_parameters['stimulus_distribution'] = \
-        behavior["config"]["DoC"]["change_time_dist"]
-    task_parameters['task'] = behavior["config"]["behavior"]["task_id"]
+    task_parameters['stimulus_distribution'] = doc["change_time_dist"]
+
+    task_id = config['behavior']['task_id']
+    if 'DoC' in task_id:
+        task_parameters['task'] = 'change detection'
+    else:
+        msg = "metadata_processing.get_task_parameters does not "
+        msg += f"know how to parse 'task_id' = {task_id}"
+        raise RuntimeError(msg)
+
     n_stimulus_frames = 0
     for stim_type, stim_table in behavior["stimuli"].items():
         n_stimulus_frames += sum(stim_table.get("draw_log", []))

allensdk/brain_observatory/behavior/rewards_processing.py

@@ -1,7 +1,6 @@
 from typing import Dict
 import numpy as np
 import pandas as pd
-from collections import defaultdict
 
 
 def get_rewards(data: Dict,
@@ -31,13 +30,14 @@ def get_rewards(data: Dict,
     trial_df = pd.DataFrame(data["items"]["behavior"]["trial_log"])
     rewards_dict = {"volume": [], "timestamps": [], "autorewarded": []}
     for idx, trial in trial_df.iterrows():
-        rewards = trial["rewards"]  # as i write this there can only ever be one reward per trial
+        rewards = trial["rewards"]
+        # as i write this there can only ever be one reward per trial
         if rewards:
             rewards_dict["volume"].append(rewards[0][0])
             rewards_dict["timestamps"].append(timestamps[rewards[0][2]])
             auto_rwrd = trial["trial_params"]["auto_reward"]
             rewards_dict["autorewarded"].append(auto_rwrd)
 
-    df = pd.DataFrame(rewards_dict).set_index("timestamps", drop=True)
+    df = pd.DataFrame(rewards_dict)
 
     return df

allensdk/brain_observatory/behavior/schemas.py

@@ -215,6 +215,7 @@ class BehaviorTaskParametersSchema(RaisingSchema):
     stimulus_duration_sec = fields.Float(
         doc='Duration of each stimulus presentation in seconds',
         required=True,
+        allow_nan=True
     )
     omitted_flash_fraction = fields.Float(
         doc='Fraction of flashes/image presentations that were omitted',
@@ -232,7 +233,11 @@ class BehaviorTaskParametersSchema(RaisingSchema):
         doc='Volume of water (in mL) delivered as reward',
         required=True,
     )
-    stage = fields.String(
+    auto_reward_volume = fields.Float(
+        doc='Volume of water (in mL) delivered as an automatic reward',
+        required=True,
+    )
+    session_type = fields.String(
         doc='Stage of behavioral task',
         required=True,
     )

allensdk/brain_observatory/behavior/session_apis/data_io/behavior_nwb_api.py

@@ -18,7 +18,7 @@
 from allensdk.brain_observatory.behavior.schemas import (
     BehaviorTaskParametersSchema, OphysBehaviorMetadataSchema)
 from allensdk.brain_observatory.behavior.stimulus_processing import \
-    StimulusTemplate
+    StimulusTemplate, StimulusTemplateFactory
 from allensdk.brain_observatory.behavior.trials_processing import (
     TRIAL_COLUMN_DESCRIPTION_DICT
 )
@@ -75,12 +75,14 @@ def save(self, session_object):
                                          from_dataframe=True)
 
         # Add stimulus template data to NWB in-memory object:
-        # Not all sessions will have stimulus_templates (e.g. gratings)
-        if session_object.stimulus_templates:
-            self._add_stimulus_templates(
-                nwbfile=nwbfile,
-                stimulus_templates=session_object.stimulus_templates,
-                stimulus_presentations=session_object.stimulus_presentations)
+        # Use the semi-private _stimulus_templates attribute because it is
+        # a StimulusTemplate object. The public stimulus_templates property
+        # of the session_object returns a DataFrame.
+        session_stimulus_templates = session_object._stimulus_templates
+        self._add_stimulus_templates(
+            nwbfile=nwbfile,
+            stimulus_templates=session_stimulus_templates,
+            stimulus_presentations=session_object.stimulus_presentations)
 
         # search for omitted rows and add stop_time before writing to NWB file
         set_omitted_stop_time(
@@ -200,12 +202,10 @@ def get_stimulus_templates(self, **kwargs) -> Optional[StimulusTemplate]:
 
         image_attributes = [{'image_name': image_name}
                             for image_name in image_data.control_description]
-        stimulus_templates = StimulusTemplate(
-            image_set_name=image_set_name,
-            image_attributes=image_attributes,
-            images=image_data.data[:]
+        return StimulusTemplateFactory.from_processed(
+            image_set_name=image_set_name, image_attributes=image_attributes,
+            warped=image_data.data[:], unwarped=image_data.unwarped[:]
         )
-        return stimulus_templates
 
     def get_stimulus_timestamps(self) -> np.ndarray:
         stim_module = self.nwbfile.processing['stimulus']
@@ -224,7 +224,7 @@ def get_licks(self) -> np.ndarray:
             licks = lick_module.get_data_interface('licks')
 
             return pd.DataFrame({
-                'time': licks.timestamps[:],
+                'timestamps': licks.timestamps[:],
                 'frame': licks.data[:]
             })
         else:
@@ -238,11 +238,11 @@ def get_rewards(self) -> np.ndarray:
             volume = rewards.get_data_interface('volume').data[:]
             return pd.DataFrame({
                 'volume': volume, 'timestamps': time,
-                'autorewarded': autorewarded}).set_index('timestamps')
+                'autorewarded': autorewarded})
         else:
             return pd.DataFrame({
                 'volume': [], 'timestamps': [],
-                'autorewarded': []}).set_index('timestamps')
+                'autorewarded': []})
 
     def get_metadata(self) -> dict:
 

allensdk/brain_observatory/behavior/session_apis/data_io/behavior_ophys_json_api.py

@@ -14,9 +14,10 @@ class BehaviorOphysJsonApi(BehaviorOphysDataTransforms):
     a specified raw data source (extractor). Contains all methods
     needed to fill a BehaviorOphysSession."""
 
-    def __init__(self, data):
+    def __init__(self, data: dict, skip_eye_tracking: bool = False):
         extractor = BehaviorOphysJsonExtractor(data=data)
-        super().__init__(extractor=extractor)
+        super().__init__(extractor=extractor,
+                         skip_eye_tracking=skip_eye_tracking)
 
 
 class BehaviorOphysJsonExtractor(BehaviorJsonExtractor,

allensdk/brain_observatory/behavior/session_apis/data_io/behavior_ophys_lims_api.py

@@ -27,7 +27,8 @@ def __init__(self,
                  ophys_experiment_id: Optional[int] = None,
                  lims_credentials: Optional[DbCredentials] = None,
                  mtrain_credentials: Optional[DbCredentials] = None,
-                 extractor: Optional[BehaviorOphysDataExtractorBase] = None):
+                 extractor: Optional[BehaviorOphysDataExtractorBase] = None,
+                 skip_eye_tracking: bool = False):
 
         if extractor is None:
             if ophys_experiment_id is not None:
@@ -40,7 +41,8 @@ def __init__(self,
                     "BehaviorOphysLimsApi must be provided either an "
                     "instantiated 'extractor' or an 'ophys_experiment_id'!")
 
-        super().__init__(extractor=extractor)
+        super().__init__(extractor=extractor,
+                         skip_eye_tracking=skip_eye_tracking)
 
 
 class BehaviorOphysLimsExtractor(OphysLimsExtractor, BehaviorLimsExtractor,