Merge pull request #293 from AllenNeuralDynamics/more_fib_plus_pav_updates

More fib plus pav updates

Author: dougollerenshaw

scripts/example_create_fiber_and_pav_sessions.py

@@ -31,7 +31,6 @@
     # Optional parameters with defaults:
     experimenter_full_name=["test_experimenter_1", "test_experimenter_2"],
     rig_id="428_9_B_20240617",
-    task_version="1.0.0",
     iacuc_protocol="2115",
     mouse_platform_name="mouse_tube_foraging",
     active_mouse_platform=False,
@@ -62,13 +61,14 @@ def create_metadata(
         "test_experimenter_2",
     ],
     rig_id: str = "428_9_0_20240617",
-    task_version: str = "1.0.0",
     iacuc_protocol: str = "2115",
     mouse_platform_name: str = "mouse_tube_foraging",
     active_mouse_platform: bool = False,
-    session_type: str = "Foraging_Photometry",
-    task_name: str = "Fiber Photometry",
-    notes: str = "Example configuration for fiber photometry rig",
+    session_type: str = "FIB",
+    notes: str = "",
+    anaesthesia: Optional[str] = None,
+    animal_weight_post: Optional[float] = None,
+    animal_weight_prior: Optional[float] = None,
 ) -> bool:
     """Create fiber photometry metadata with default settings.
 
@@ -79,13 +79,14 @@ def create_metadata(
         output_filename: Name of the output JSON file
         experimenter_full_name: List of experimenter names
         rig_id: Identifier for the experimental rig
-        task_version: Version of the experimental task
         iacuc_protocol: Protocol identifier
         mouse_platform_name: Name of the mouse platform
         active_mouse_platform: Whether platform is active
         session_type: Type of experimental session
-        task_name: Name of the experimental task
         notes: Additional notes about the session
+        anaesthesia: Anaesthesia used
+        animal_weight_post: Animal weight after session
+        animal_weight_prior: Animal weight before session
 
     Returns:
         bool: True if metadata was successfully
@@ -99,13 +100,14 @@ def create_metadata(
         "output_directory": str(output_directory),
         "output_filename": output_filename,
         "rig_id": rig_id,
-        "task_version": task_version,
         "iacuc_protocol": iacuc_protocol,
         "mouse_platform_name": mouse_platform_name,
         "active_mouse_platform": active_mouse_platform,
         "session_type": session_type,
-        "task_name": task_name,
         "notes": notes,
+        "anaesthesia": anaesthesia,
+        "animal_weight_post": animal_weight_post,
+        "animal_weight_prior": animal_weight_prior,
         "data_streams": [
             {
                 "stream_start_time": None,
@@ -184,7 +186,7 @@ def create_metadata(
                     {
                         "name": "Bonsai",
                         "parameters": {},
-                        "url": "",
+                        "url": "https://github.com/AllenNeuralDynamics/PavlovianCond_Bonsai/tree/dafd7dfe0f347f781e91466b3d16b83cf32f8b6d",  # noqa E501
                         "version": "",
                     }
                 ],
@@ -232,6 +234,32 @@ def create_metadata(
         default="session_fip.json",
         help="Name of the output JSON file (default: session_fip.json)",
     )
+    parser.add_argument(
+        "--active-mouse-platform",
+        action="store_true",
+        help="Whether the mouse platform was active",
+    )
+    parser.add_argument(
+        "--anaesthesia", type=str, default=None, help="Anaesthesia used"
+    )
+    parser.add_argument(
+        "--animal-weight-post",
+        type=float,
+        default=None,
+        help="Animal weight after session",
+    )
+    parser.add_argument(
+        "--animal-weight-prior",
+        type=float,
+        default=None,
+        help="Animal weight before session",
+    )
+    parser.add_argument(
+        "--mouse-platform-name",
+        type=str,
+        default="mouse_tube_foraging",
+        help="Name of the mouse platform",
+    )
 
     args = parser.parse_args()
 
@@ -240,6 +268,11 @@ def create_metadata(
         data_directory=args.data_directory,
         output_directory=args.output_directory,
         output_filename=args.output_filename,
+        active_mouse_platform=args.active_mouse_platform,
+        anaesthesia=args.anaesthesia,
+        animal_weight_post=args.animal_weight_post,
+        animal_weight_prior=args.animal_weight_prior,
+        mouse_platform_name=args.mouse_platform_name,
     )
 
     output_path = args.output_directory / args.output_filename

src/aind_metadata_mapper/fip/example_create_session.py

@@ -36,6 +36,12 @@ class JobSettings(BaseJobSettings):
         IACUC protocol identifier
     notes : str
         Session notes
+    anaesthesia : Optional[str]
+        Anaesthesia used
+    animal_weight_post : Optional[float]
+        Animal weight after session
+    animal_weight_prior : Optional[float]
+        Animal weight before session
     protocol_id : List[str], optional
         List of protocol identifiers, defaults to empty list
     data_directory : Optional[Union[str, Path]], optional
@@ -60,6 +66,9 @@ class JobSettings(BaseJobSettings):
     session_type: str = "FIB"
     iacuc_protocol: str
     notes: str
+    anaesthesia: Optional[str] = None
+    animal_weight_post: Optional[float] = None
+    animal_weight_prior: Optional[float] = None
 
     # Optional Session fields with defaults
     protocol_id: List[str] = []

src/aind_metadata_mapper/fip/models.py

@@ -40,7 +40,51 @@
 
 @dataclass
 class FiberData:
-    """Intermediate data model for fiber photometry data."""
+    """Intermediate data model for fiber photometry data.
+
+    This model holds the extracted and processed data before final
+    transformation into a Session object. It serves as a structured
+    intermediate representation of the fiber photometry session data.
+
+    Parameters
+    ----------
+    start_time : datetime
+        Session start time from fiber photometry files
+    end_time : Optional[datetime]
+        Session end time from fiber photometry files
+    data_files : List[Path]
+        List of paths to fiber photometry data files
+    timestamps : List[float]
+        List of timestamps from fiber photometry recordings
+    light_source_configs : List[dict]
+        List of light source configuration dictionaries
+    detector_configs : List[dict]
+        List of detector configuration dictionaries
+    fiber_configs : List[dict]
+        List of fiber configuration dictionaries
+    subject_id : str
+        Subject identifier
+    experimenter_full_name : List[str]
+        List of experimenter names
+    rig_id : str
+        Identifier for the experimental rig
+    iacuc_protocol : str
+        IACUC protocol number
+    notes : str
+        Additional notes about the session
+    mouse_platform_name : str
+        Name of the mouse platform used
+    active_mouse_platform : bool
+        Whether the mouse platform was active
+    session_type : str
+        Type of session (e.g. "FIB")
+    anaesthesia : Optional[str]
+        Anaesthesia used, if any
+    animal_weight_post : Optional[float]
+        Animal weight after session
+    animal_weight_prior : Optional[float]
+        Animal weight before session
+    """
 
     start_time: datetime
     end_time: Optional[datetime]
@@ -56,6 +100,10 @@ class FiberData:
     notes: str
     mouse_platform_name: str
     active_mouse_platform: bool
+    session_type: str
+    anaesthesia: Optional[str]
+    animal_weight_post: Optional[float]
+    animal_weight_prior: Optional[float]
 
 
 class FIBEtl(GenericEtl[JobSettings]):
@@ -141,6 +189,10 @@ def _extract(self) -> FiberData:
             notes=settings.notes,
             mouse_platform_name=settings.mouse_platform_name,
             active_mouse_platform=settings.active_mouse_platform,
+            session_type=settings.session_type,
+            anaesthesia=settings.anaesthesia,
+            animal_weight_post=settings.animal_weight_post,
+            animal_weight_prior=settings.animal_weight_prior,
         )
 
     def _transform(self, fiber_data: FiberData) -> Session:
@@ -177,14 +229,17 @@ def _transform(self, fiber_data: FiberData) -> Session:
             experimenter_full_name=fiber_data.experimenter_full_name,
             session_start_time=fiber_data.start_time,
             session_end_time=fiber_data.end_time,
-            session_type="FIB",
+            session_type=fiber_data.session_type,
             rig_id=fiber_data.rig_id,
             subject_id=fiber_data.subject_id,
             iacuc_protocol=fiber_data.iacuc_protocol,
             notes=fiber_data.notes,
             data_streams=[stream],
             mouse_platform_name=fiber_data.mouse_platform_name,
             active_mouse_platform=fiber_data.active_mouse_platform,
+            anaesthesia=fiber_data.anaesthesia,
+            animal_weight_post=fiber_data.animal_weight_post,
+            animal_weight_prior=fiber_data.animal_weight_prior,
         )
 
         return session