ticket/nnnn/sync/stim/aligner

allensdk/brain_observatory/behavior/behavior_session.py

@@ -7,7 +7,7 @@
 
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import \
     JsonReadableInterface, NwbReadableInterface, \
     LimsReadableInterface
@@ -98,7 +98,7 @@ def from_json(cls,
 
         behavior_session_id = BehaviorSessionId.from_json(
             dict_repr=session_data)
-        stimulus_file = StimulusFile.from_json(dict_repr=session_data)
+        stimulus_file = BehaviorStimulusFile.from_json(dict_repr=session_data)
         stimulus_timestamps = StimulusTimestamps.from_json(
             dict_repr=session_data)
         running_acquisition = RunningAcquisition.from_json(
@@ -174,7 +174,7 @@ def from_lims(cls, behavior_session_id: int,
             monitor_delay = cls._get_monitor_delay()
 
         behavior_session_id = BehaviorSessionId(behavior_session_id)
-        stimulus_file = StimulusFile.from_lims(
+        stimulus_file = BehaviorStimulusFile.from_lims(
             db=lims_db, behavior_session_id=behavior_session_id.value)
         if stimulus_timestamps is None:
             stimulus_timestamps = StimulusTimestamps.from_stimulus_file(
@@ -878,7 +878,7 @@ def metadata(self) -> Dict[str, Any]:
 
     @classmethod
     def _read_data_from_stimulus_file(
-            cls, stimulus_file: StimulusFile,
+            cls, stimulus_file: BehaviorStimulusFile,
             stimulus_timestamps: StimulusTimestamps):
         """Helper method to read data from stimulus file"""
         licks = Licks.from_stimulus_file(

allensdk/brain_observatory/behavior/data_files/__init__.py

@@ -1,2 +1,6 @@
-from allensdk.brain_observatory.behavior.data_files.stimulus_file import StimulusFile  # noqa E501, F401
+from allensdk.brain_observatory.behavior.data_files.stimulus_file import (  # noqa F401
+    BehaviorStimulusFile,
+    ReplayStimulusFile,
+    MappingStimulusFile)
+
 from allensdk.brain_observatory.behavior.data_files.sync_file import SyncFile  # noqa E501, F401

allensdk/brain_observatory/behavior/data_files/stimulus_file.py

@@ -14,7 +14,7 @@
 from allensdk.core import DataObject
 
 # Query returns path to StimulusPickle file for given behavior session
-STIMULUS_FILE_QUERY_TEMPLATE = """
+BEHAVIOR_STIMULUS_FILE_QUERY_TEMPLATE = """
     SELECT
         wkf.storage_directory || wkf.filename AS stim_file
     FROM
@@ -37,7 +37,45 @@ def from_lims_cache_key(cls, db, behavior_session_id: int):
     return hashkey(behavior_session_id)
 
 
-class StimulusFile(DataFile):
+class _NumFramesMixin(object):
+    """
+    Mixin to implement num_frames for a generic (i.e. non-behavior)
+    StimulusFile
+    """
+
+    def _validate_frame_data(self) -> None:
+        """
+        Check that self.data['intervalsms'] is present and
+        that self.data['items']['behavior']['intervalsms'] is empty
+        """
+        msg = ""
+        if 'intervalsms' not in self.data:
+            msg += "self.data['intervalsms'] not present\n"
+        if "items" in self.data:
+            if "behavior" in self.data["items"]:
+                if "intervalsms" in self.data["items"]["behavior"]:
+                    val = self.data["items"]["behavior"]["intervalsms"]
+                    if len(val) > 0:
+                        msg += ("len(self.data['items']['behavior']"
+                                f"['intervalsms'] == {len(val)}; "
+                                "expected zero\n")
+        if len(msg) > 0:
+            full_msg = f"When getting num_frames from {type(self)}\n"
+            full_msg += msg
+            full_msg += f"\nfilepath: {self.filepath}"
+            raise RuntimeError(full_msg)
+
+        return None
+
+    def num_frames(self) -> int:
+        """
+        Return the number of frames associated with this StimulusFile
+        """
+        self._validate_frame_data()
+        return len(self.data['intervalsms']) + 1
+
+
+class _StimulusFile(DataFile):
     """A DataFile which contains methods for accessing and loading visual
     behavior stimulus *.pkl files.
 
@@ -46,41 +84,119 @@ class StimulusFile(DataFile):
     trials, and timing for all of the above.
     """
 
+    @classmethod
+    def file_path_key(cls) -> str:
+        """
+        The key in the dict_repr that maps to the path
+        to this StimulusFile's pickle file on disk.
+        """
+        raise NotImplementedError()
+
     def __init__(self, filepath: Union[str, Path]):
         super().__init__(filepath=filepath)
 
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_json_cache_key)
-    def from_json(cls, dict_repr: dict) -> "StimulusFile":
-        filepath = dict_repr["behavior_stimulus_file"]
+    def from_json(cls, dict_repr: dict) -> "_StimulusFile":
+        filepath = dict_repr[cls.file_path_key()]
         return cls(filepath=filepath)
 
     def to_json(self) -> Dict[str, str]:
-        return {"behavior_stimulus_file": str(self.filepath)}
+        return {self.file_path_key(): str(self.filepath)}
 
     @classmethod
     @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
     def from_lims(
         cls, db: PostgresQueryMixin,
         behavior_session_id: Union[int, str]
-    ) -> "StimulusFile":
-        query = STIMULUS_FILE_QUERY_TEMPLATE.format(
-            behavior_session_id=behavior_session_id
-        )
-        filepath = db.fetchone(query, strict=True)
-        return cls(filepath=filepath)
+    ) -> "_StimulusFile":
+        raise NotImplementedError()
 
     @staticmethod
     def load_data(filepath: Union[str, Path]) -> dict:
         filepath = safe_system_path(file_name=filepath)
         return pd.read_pickle(filepath)
 
+    def num_frames(self) -> int:
+        """
+        Return the number of frames associated with this StimulusFile
+        """
+        raise NotImplementedError()
+
+
+class BehaviorStimulusFile(_StimulusFile):
+
+    @classmethod
+    def file_path_key(cls) -> str:
+        return "behavior_stimulus_file"
+
+    @classmethod
+    @cached(cache=LRUCache(maxsize=10), key=from_lims_cache_key)
+    def from_lims(
+        cls, db: PostgresQueryMixin,
+        behavior_session_id: Union[int, str]
+    ) -> "BehaviorStimulusFile":
+        query = BEHAVIOR_STIMULUS_FILE_QUERY_TEMPLATE.format(
+            behavior_session_id=behavior_session_id
+        )
+        filepath = db.fetchone(query, strict=True)
+        return cls(filepath=filepath)
+
+    def _validate_frame_data(self):
+        """
+        Make sure that self.data['intervalsms'] does not exist and that
+        self.data['items']['behavior']['intervalsms'] does exist.
+        """
+        msg = ""
+        if "intervalsms" in self.data:
+            msg += "self.data['intervalsms'] present; did not expect that\n"
+        if "items" not in self.data:
+            msg += "self.data['items'] not present\n"
+        else:
+            if "behavior" not in self.data["items"]:
+                msg += "self.data['items']['behavior'] not present\n"
+            else:
+                if "intervalsms" not in self.data["items"]["behavior"]:
+                    msg += ("self.data['items']['behavior']['intervalsms'] "
+                            "not present\n")
+
+        if len(msg) > 0:
+            full_msg = f"When getting num_frames from {type(self)}\n"
+            full_msg += msg
+            full_msg += f"\nfilepath: {self.filepath}"
+            raise RuntimeError(full_msg)
+
+        return None
+
+    def num_frames(self) -> int:
+        """
+        Return the number of frames associated with this StimulusFile
+        """
+        self._validate_frame_data()
+        return len(self.data['items']['behavior']['intervalsms']) + 1
+
+
+class ReplayStimulusFile(_NumFramesMixin, _StimulusFile):
+
+    @classmethod
+    def file_path_key(cls) -> str:
+        return "replay_stimulus_file"
+
+
+class MappingStimulusFile(_NumFramesMixin, _StimulusFile):
+
+    @classmethod
+    def file_path_key(cls) -> str:
+        return "mapping_stimulus_file"
+
 
 class StimulusFileReadableInterface(abc.ABC):
     """Marks a data object as readable from stimulus file"""
     @classmethod
     @abc.abstractmethod
-    def from_stimulus_file(cls, stimulus_file: StimulusFile) -> "DataObject":
+    def from_stimulus_file(
+            cls,
+            stimulus_file: BehaviorStimulusFile) -> "DataObject":
         """Populate a DataObject from the stimulus file
 
         Returns

allensdk/brain_observatory/behavior/data_objects/licks.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from pynwb import NWBFile, TimeSeries, ProcessingModule
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.brain_observatory.behavior.data_objects import StimulusTimestamps
 from allensdk.core import \
@@ -31,7 +31,7 @@ def __init__(self, licks: pd.DataFrame):
         super().__init__(name='licks', value=licks)
 
     @classmethod
-    def from_stimulus_file(cls, stimulus_file: StimulusFile,
+    def from_stimulus_file(cls, stimulus_file: BehaviorStimulusFile,
                            stimulus_timestamps: StimulusTimestamps) -> "Licks":
         """Get lick data from pkl file.
         This function assumes that the first sensor in the list of

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/behavior_metadata.py

@@ -4,7 +4,7 @@
 import numpy as np
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 
 from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
@@ -208,7 +208,7 @@ def from_lims(
         equipment = Equipment.from_lims(
             behavior_session_id=behavior_session_id.value, lims_db=lims_db)
 
-        stimulus_file = StimulusFile.from_lims(
+        stimulus_file = BehaviorStimulusFile.from_lims(
             db=lims_db, behavior_session_id=behavior_session_id.value)
         stimulus_frame_rate = StimulusFrameRate.from_stimulus_file(
             stimulus_file=stimulus_file)
@@ -238,7 +238,7 @@ def from_json(cls, dict_repr: dict) -> "BehaviorMetadata":
         behavior_session_id = BehaviorSessionId.from_json(dict_repr=dict_repr)
         equipment = Equipment.from_json(dict_repr=dict_repr)
 
-        stimulus_file = StimulusFile.from_json(dict_repr=dict_repr)
+        stimulus_file = BehaviorStimulusFile.from_json(dict_repr=dict_repr)
         stimulus_frame_rate = StimulusFrameRate.from_stimulus_file(
             stimulus_file=stimulus_file)
         session_type = SessionType.from_stimulus_file(

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/behavior_session_uuid.py

@@ -3,7 +3,7 @@
 
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.core import \
     NwbReadableInterface
@@ -20,7 +20,8 @@ def __init__(self, behavior_session_uuid: Optional[uuid.UUID]):
 
     @classmethod
     def from_stimulus_file(
-            cls, stimulus_file: StimulusFile) -> "BehaviorSessionUUID":
+            cls,
+            stimulus_file: BehaviorStimulusFile) -> "BehaviorSessionUUID":
         id = stimulus_file.data.get('session_uuid')
         if id:
             id = uuid.UUID(id)
@@ -34,7 +35,7 @@ def from_nwb(cls, nwbfile: NWBFile) -> "BehaviorSessionUUID":
 
     def validate(self, behavior_session_id: int,
                  foraging_id: int,
-                 stimulus_file: StimulusFile) -> "BehaviorSessionUUID":
+                 stimulus_file: BehaviorStimulusFile) -> "BehaviorSessionUUID":
         """
         Sanity check to ensure that pkl file data matches up with
         the behavior session that the pkl file has been associated with.

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/date_of_acquisition.py

@@ -4,7 +4,7 @@
 import pytz
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.core import \
     JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
@@ -48,7 +48,7 @@ def from_lims(
     def from_nwb(cls, nwbfile: NWBFile) -> "DateOfAcquisition":
         return cls(date_of_acquisition=nwbfile.session_start_time)
 
-    def validate(self, stimulus_file: StimulusFile,
+    def validate(self, stimulus_file: BehaviorStimulusFile,
                  behavior_session_id: int) -> "DateOfAcquisition":
         """raise a warning if the date differs too much from the
         datetime obtained from the behavior stimulus (*.pkl) file."""

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/session_type.py

@@ -1,6 +1,6 @@
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.core import \
     NwbReadableInterface
@@ -17,7 +17,7 @@ def __init__(self, session_type: str):
     @classmethod
     def from_stimulus_file(
             cls,
-            stimulus_file: StimulusFile) -> "SessionType":
+            stimulus_file: BehaviorStimulusFile) -> "SessionType":
         try:
             stimulus_name = \
                 stimulus_file.data["items"]["behavior"]["cl_params"]["stage"]

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_metadata/stimulus_frame_rate.py

@@ -1,6 +1,6 @@
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.core import \
     NwbReadableInterface
@@ -22,7 +22,7 @@ def __init__(self, stimulus_frame_rate: float):
     @classmethod
     def from_stimulus_file(
             cls,
-            stimulus_file: StimulusFile) -> "StimulusFrameRate":
+            stimulus_file: BehaviorStimulusFile) -> "StimulusFrameRate":
 
         # in this data object, we only care about the difference between
         # timestamps, so we can set the monitor_delay to any

allensdk/brain_observatory/behavior/data_objects/rewards.py

@@ -3,7 +3,7 @@
 import pandas as pd
 from pynwb import NWBFile, TimeSeries, ProcessingModule
 
-from allensdk.brain_observatory.behavior.data_files import StimulusFile
+from allensdk.brain_observatory.behavior.data_files import BehaviorStimulusFile
 from allensdk.core import DataObject
 from allensdk.brain_observatory.behavior.data_objects import StimulusTimestamps
 from allensdk.core import \
@@ -21,7 +21,7 @@ def __init__(self, rewards: pd.DataFrame):
 
     @classmethod
     def from_stimulus_file(
-            cls, stimulus_file: StimulusFile,
+            cls, stimulus_file: BehaviorStimulusFile,
             stimulus_timestamps: StimulusTimestamps) -> "Rewards":
         """Get reward data from pkl file, based on timestamps
         (not sync file).