Update metadata yaml

src/jdb_to_nwb/convert.py

@@ -3,9 +3,11 @@
 import yaml
 
 from pynwb import NWBFile, NWBHDF5IO
+from pynwb.file import Subject
 from datetime import datetime
 from dateutil import tz
 
+from . import __version__
 from .convert_raw_ephys import add_raw_ephys
 from .convert_spikes import add_spikes
 from .convert_behavior import add_behavior
@@ -19,17 +21,42 @@ def create_nwbs(
     with open(metadata_file_path, "r") as f:
         metadata = yaml.safe_load(f)
 
+    # parse subject metadata
+    subject = Subject(**metadata["subject"])
+
+    # parse surgery metadata
+    surgery = "..."  # TODO parse from structured metadata
+
     # TODO: read these from metadata
     nwbfile = NWBFile(
-        session_description="Mock session",
-        session_start_time=datetime.now(tz.tzlocal()),
-        identifier="mock_session",
+        session_description="Mock session",  # TODO: generate this from metadata
+        session_start_time=datetime.now(tz.tzlocal()),  # TODO: update this 
+        identifier="mock_session",  # TODO: update this
+        session_id=metadata.get("session_id"),
+        surgery=surgery,
+        notes=metadata.get("notes"),
+        experimenter=metadata.get("experimenter"),
+        institution=metadata.get("institution"),
+        lab=metadata.get("lab"),
+        keywords=metadata.get("keywords"),
+        experiment_description=metadata.get("experiment_description"),
+        related_publications=metadata.get("related_publications"),
+        subject=subject,
+        source_script="jdb_to_nwb " + __version__,
+        source_script_file_name="convert.py",
     )
 
+    # if photometry is present, timestamps should be aligned to the photometry
+    add_photometry(nwbfile=nwbfile, metadata=metadata)
+    photometry_start_in_arduino_time = add_behavior(nwbfile=nwbfile, metadata=metadata)
+
     add_raw_ephys(nwbfile=nwbfile, metadata=metadata)
     add_spikes(nwbfile=nwbfile, metadata=metadata)
-    photometry_start_in_arduino_time = add_behavior(nwbfile=nwbfile, metadata=metadata)
-    add_photometry(nwbfile=nwbfile, metadata=metadata)
+
+    # TODO: time alignment
+
+    # reset the session start time to the earliest of the data streams
+    nwbfile.fields["session_start_time"] = datetime.now(tz.tzlocal())
 
     print(f"Writing file, including iterative read from raw ephys data...")
 
@@ -45,4 +72,4 @@ def cli():
     parser.add_argument("output_nwb_file_path", type=Path, help="Path to the output NWB file.")
     args = parser.parse_args()
 
-    create_nwbs(args.metadata_file_path, args.output_nwb_file_path)
+    create_nwbs(args.metadata_file_path, args.output_nwb_file_path)

src/plotting/plot_ephys.py

@@ -0,0 +1,2 @@
+def plot_channel_map():
+    pass

tests/metadata_full.yaml

@@ -10,9 +10,10 @@ ephys:
   plug_order: "chip_first" # must be either "chip_first" or "cable_first", "chip_first" is the default if none specified
   # For now, there is just one device, which is the probe
   device:
-    name: "Probe"
-    description: "Berke Lab Probe"
-    manufacturer: "My Manufacturer"
+    name: "256-ch Silicon Probe, 3mm length, 66um pitch"
+    # 3mm will be always 66, and 6mm will be always 80
+    description: "32 shanks, 8 electrodes per shank. Each shank is 66um apart. The length of each shank is 3mm."
+    manufacturer: "Daniel Egert, Berke Lab"
 
 # Specify both "phot_file_path" and "box_file_path" for raw LabVIEW data,
 # OR "signals_mat_file_path" for preprocessed LabVIEW data,
@@ -23,11 +24,71 @@ photometry:
   box_file_path: "tests/test_data/downloaded/IM-1478/07252022/IM-1478_2022-07-25_15-24-22____Tim_Conditioning.box"
   # ppd_file_path: ""
 
+  # TODO
+  # virus_injection_metadata:
+  #   - 
+  # fiber_metadata:
+  #   - 
+
+
 behavior:
   arduino_text_file_path: "tests/test_data/behavior/arduinoraw0.txt"
   arduino_timestamps_file_path: "tests/test_data/behavior/ArduinoStamps0.csv"
   maze_configuration_file_path: "tests/test_data/behavior/barriers.txt"
+  behavioral_info:
+    reward_type: sucrose solution (10% sucrose, 0.1% NaCl) 
+    reward_amount_in_uL: 15
+    deprivation_type: water  # water (default) or food
 
 video:
   file_path: "../data/video/video.mp4"
-  timestamps_file_path: "../data/photometry/07252022/timestamps.csv"
+  timestamps_file_path: "../data/photometry/07252022/timestamps.csv"
+
+animal_name: "IM-1478"
+date: "07252022"  # MMDDYYYY or YYYYMMDD
+
+subject:
+  subject_id: "IM-1478"
+  species: Rattus norvegicus
+  strain: Long Evans
+  sex: M
+  date_of_birth: "2022-07-25"
+  description: A male, Long Evans, wild-type rat.
+
+session_id: "IM-1478_07252022"
+
+# surgical notes, one dictionary per surgery
+surgeries:
+  - description: The virus was injected in the left nucleus accumbens core on 2022-01-01.
+    date: 2022-01-01
+    type: virus_injection  # virus_injection OR probe_implantation
+  - description: The probe was implanted in the left nucleus accumbens core on 2022-02-01.
+    date: 2022-02-01
+    type: probe_implantation  # virus_injection OR probe_implantation
+
+notes:
+  This was a barrier shift task.
+
+experimenter:
+  - Crater, Stephanie
+  - Figueroa, Jose
+  - Hwang, Yang-Sun
+  - Krausz, Tim
+
+institution: University of California, San Francisco
+
+lab: Berke Lab
+
+keywords:
+  - photometry
+  - ephys
+  - behavior
+  - video
+  - hex maze
+  - dopamine
+  - reward
+
+experiment_description: |
+  This experiment was performed to test the effects of dopamine on behavior.
+
+# related_publications: "doi: 10.1016/j.neuron.2023.07.017"