Feature non behavior ophys nwb

allensdk/__init__.py

@@ -59,7 +59,7 @@ def one(x):
         return x
     if xlen != 1:
         raise OneResultExpectedError("Expected length one result, received: "
-                                     f"{x} results from queryr")
+                                     f"{x} results from query")
     if isinstance(x, set):
         return list(x)[0]
     else:

allensdk/brain_observatory/behavior/data_files/_data_file_abc.py

@@ -2,6 +2,8 @@
 from typing import Any, Union
 from pathlib import Path
 
+from allensdk.internal.core.lims_utilities import safe_system_path
+
 
 class DataFile(abc.ABC):
     """An abstract class that prototypes methods for accessing internal
@@ -15,7 +17,7 @@ class DataFile(abc.ABC):
     """
 
     def __init__(self, filepath: Union[str, Path]):  # pragma: no cover
-        self._filepath: str = str(filepath)
+        self._filepath: str = safe_system_path(str(filepath))
         self._data = self.load_data(filepath=self._filepath)
 
     @property

allensdk/brain_observatory/behavior/data_files/demix_file.py

@@ -61,6 +61,8 @@ def load_data(filepath: Union[str, Path]) -> pd.DataFrame:
         with h5py.File(filepath, 'r') as in_file:
             traces = in_file['data'][()]
             roi_id = in_file['roi_names'][()]
-            idx = pd.Index(roi_id, name='cell_roi_id', dtype=int)
+            roi_id = roi_id.astype(str)
+            roi_id = roi_id.astype(int)
+            idx = pd.Index(roi_id, name='cell_roi_id')
             return pd.DataFrame({'corrected_fluorescence': list(traces)},
                                 index=idx)

allensdk/brain_observatory/behavior/data_files/dff_file.py

@@ -54,12 +54,15 @@ def from_lims(
                 AND oe.id = {};
                 """.format(ophys_experiment_id)
         filepath = db.fetchone(query, strict=True)
+        print(filepath)
         return cls(filepath=filepath)
 
     @staticmethod
     def load_data(filepath: Union[str, Path]) -> pd.DataFrame:
         with h5py.File(filepath, 'r') as raw_file:
             traces = np.asarray(raw_file['data'], dtype=np.float64)
             roi_names = np.asarray(raw_file['roi_names'])
-            idx = pd.Index(roi_names, name='cell_roi_id', dtype=int)
+            roi_names = roi_names.astype(str)
+            roi_names = roi_names.astype(int)
+            idx = pd.Index(roi_names, name='cell_roi_id')
             return pd.DataFrame({'dff': [x for x in traces]}, index=idx)

allensdk/brain_observatory/behavior/data_files/eye_tracking_file.py

@@ -7,7 +7,7 @@
     load_eye_tracking_hdf
 from allensdk.internal.api import PostgresQueryMixin
 from allensdk.internal.core.lims_utilities import safe_system_path
-from allensdk.brain_observatory.behavior.data_files import DataFile
+from allensdk.internal.core import DataFile
 
 
 class EyeTrackingFile(DataFile):
@@ -29,16 +29,17 @@ def to_json(self) -> Dict[str, str]:
     @classmethod
     def from_lims(
         cls, db: PostgresQueryMixin,
-        ophys_experiment_id: Union[int, str]
+        behavior_session_id: Union[int, str]
     ) -> "EyeTrackingFile":
         query = f"""
                 SELECT wkf.storage_directory || wkf.filename AS eye_tracking_file
-                FROM ophys_experiments oe
-                LEFT JOIN well_known_files wkf ON wkf.attachable_id = oe.ophys_session_id
+                FROM behavior_sessions bs
+                JOIN ophys_sessions os ON os.id = bs.ophys_session_id
+                LEFT JOIN well_known_files wkf ON wkf.attachable_id = os.id
                 JOIN well_known_file_types wkft ON wkf.well_known_file_type_id = wkft.id
                 WHERE wkf.attachable_type = 'OphysSession'
                     AND wkft.name = 'EyeTracking Ellipses'
-                    AND oe.id = {ophys_experiment_id};
+                    AND bs.id = {behavior_session_id};
                 """  # noqa E501
         filepath = db.fetchone(query, strict=True)
         return cls(filepath=filepath)
@@ -47,4 +48,4 @@ def from_lims(
     def load_data(filepath: Union[str, Path]) -> pd.DataFrame:
         filepath = safe_system_path(file_name=filepath)
         # TODO move the contents of this function here
-        return load_eye_tracking_hdf(filepath)
+        return load_eye_tracking_hdf(filepath)

allensdk/brain_observatory/behavior/data_files/stimulus_file.py

@@ -12,7 +12,7 @@
 from allensdk.brain_observatory.behavior.data_files import DataFile
 
 # 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
@@ -27,13 +27,31 @@
 """
 
 
+NO_BEHAVIOR_STIMULUS_FILE_QUERY_TEMPLATE = """
+    SELECT
+        wkf.storage_directory || wkf.filename AS stim_file
+    FROM
+        well_known_files wkf
+    JOIN 
+        well_known_file_types wkft
+        ON wkf.well_known_file_type_id = wkft.id
+    WHERE
+        wkf.attachable_id = {behavior_session_id}
+        AND wkft.name = 'StimulusPickle'
+"""
+
+
+
 def from_json_cache_key(cls, dict_repr: dict):
     return hashkey(json.dumps(dict_repr))
 
 
 def from_lims_cache_key(cls, db, behavior_session_id: int):
     return hashkey(behavior_session_id)
 
+def from_lims_nb_cache_key(cls, db, ophys_experiment_id: int):
+    return hashkey(ophys_experiment_id)
+
 
 class StimulusFile(DataFile):
     """A DataFile which contains methods for accessing and loading visual
@@ -62,11 +80,23 @@ def from_lims(
         cls, db: PostgresQueryMixin,
         behavior_session_id: Union[int, str]
     ) -> "StimulusFile":
-        query = STIMULUS_FILE_QUERY_TEMPLATE.format(
+        query = NO_BEHAVIOR_STIMULUS_FILE_QUERY_TEMPLATE.format(
             behavior_session_id=behavior_session_id
         )
         filepath = db.fetchone(query, strict=True)
         return cls(filepath=filepath)
+
+    @classmethod
+    @cached(cache=LRUCache(maxsize=10), key=from_lims_nb_cache_key)
+    def no_behavior_from_lims(
+        cls, db: PostgresQueryMixin,
+        ophys_experiment_id: Union[int, str]
+    ) -> "StimulusFile":
+        query = NO_BEHAVIOR_STIMULUS_FILE_QUERY_TEMPLATE.format(
+            experiment_id = ophys_experiment_id
+        )
+        filepath = db.fetchone(query, strict=True)
+        return cls(filepath=filepath)
 
     @staticmethod
     def load_data(filepath: Union[str, Path]) -> dict:

allensdk/brain_observatory/behavior/data_objects/__init__.py

@@ -1,6 +1,8 @@
 from allensdk.brain_observatory.behavior.data_objects.base._data_object_abc import DataObject  # noqa: E501, F401
 from allensdk.brain_observatory.behavior.data_objects.metadata\
     .behavior_metadata.behavior_session_id import BehaviorSessionId  # noqa: E501, F401
+from allensdk.brain_observatory.behavior.data_objects.metadata\
+    .ophys_experiment_metadata.ophys_session_id import OphysSessionId
 from allensdk.brain_observatory.behavior.data_objects.timestamps\
     .stimulus_timestamps.stimulus_timestamps import StimulusTimestamps  # noqa: E501, F401
 from allensdk.brain_observatory.behavior.data_objects.running_speed.running_speed import RunningSpeed  # noqa: E501, F401

allensdk/brain_observatory/behavior/data_objects/cell_specimens/cell_specimens.py

@@ -185,6 +185,7 @@ def __init__(self,
             roi_ids=cell_specimen_table['cell_roi_id'].values,
             raise_if_rois_missing=False)
 
+
         self._meta = meta
         self._cell_specimen_table = cell_specimen_table
         self._dff_traces = dff_traces
@@ -299,6 +300,7 @@ def _get_events():
         corrected_fluorescence_traces = _get_corrected_fluorescence_traces()
         events = _get_events()
 
+
         return CellSpecimens(
             cell_specimen_table=cell_specimen_table, meta=meta,
             dff_traces=dff_traces,
@@ -525,7 +527,6 @@ def _get_segmentation_mask_image(self, spacing: tuple) -> Image:
             metadata
         """
         mask_data = np.sum(self.roi_masks['roi_mask']).astype(int)
-
         mask_image = Image(
             data=mask_data,
             spacing=spacing,
@@ -578,6 +579,9 @@ def _validate_traces(
         for traces in (dff_traces, corrected_fluorescence_traces):
             # validate traces contain expected roi ids
             if not np.in1d(traces.value.index, cell_roi_ids).all():
+#                print(traces.value.index)
+#                print("roi table")
+#                print(cell_roi_ids)
                 raise RuntimeError(f"{traces.name} contains ROI IDs that "
                                    f"are not in "
                                    f"cell_specimen_table.cell_roi_id")

allensdk/brain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/multi_plane_metadata/multi_plane_metadata.py

@@ -29,15 +29,15 @@ class MultiplaneMetadata(OphysExperimentMetadata):
     def __init__(self,
                  ophys_experiment_id: int,
                  ophys_session_id: OphysSessionId,
-                 experiment_container_id: ExperimentContainerId,
+                 #experiment_container_id: ExperimentContainerId,
                  field_of_view_shape: FieldOfViewShape,
                  imaging_depth: ImagingDepth,
                  imaging_plane_group: ImagingPlaneGroup,
                  project_code: ProjectCode):
         super().__init__(
             ophys_experiment_id=ophys_experiment_id,
             ophys_session_id=ophys_session_id,
-            experiment_container_id=experiment_container_id,
+            #experiment_container_id=experiment_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
             project_code=project_code
@@ -55,7 +55,7 @@ def from_lims(
         return cls(
             ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
             ophys_session_id=ophys_experiment_metadata._ophys_session_id,
-            experiment_container_id=ophys_experiment_metadata._experiment_container_id,     # noqa E501
+            #experiment_container_id=ophys_experiment_metadata._experiment_container_id,     # noqa E501
             field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
             imaging_depth=ophys_experiment_metadata._imaging_depth,
             project_code=ophys_experiment_metadata._project_code,