use converter.create_nwbfile

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_week_session.py

@@ -1,17 +1,15 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
 
 import time
-import uuid
-from copy import deepcopy
 from natsort import natsorted
 from pathlib import Path
 from typing import Union
 import re
 import pandas as pd
 from datetime import datetime
+from mne.io import read_raw_edf
 
-from pynwb import NWBFile
-from neuroconv.utils import load_dict_from_file
+from neuroconv.utils import load_dict_from_file, dict_deep_update
 from neuroconv.tools.nwb_helpers import configure_and_write_nwbfile
 
 from utils import get_session_slicing_time_range, get_session_run_time
@@ -72,24 +70,22 @@ def session_to_nwb(
     source_data.update(dict(CellRegistration=dict(file_paths=file_paths)))
     conversion_options.update(dict(CellRegistration=dict(stub_test=stub_test, subject_id=subject_id)))
 
-    from mne.io import read_raw_edf
+    converter = Zaki2024NWBConverter(source_data=source_data)
+    # Add datetime to conversion
+    metadata = converter.get_metadata()
+    # Update default metadata with the editable in the corresponding yaml file
+    editable_metadata_path = Path(__file__).parent / "zaki_2024_metadata.yaml"
+    editable_metadata = load_dict_from_file(editable_metadata_path)
+    metadata = dict_deep_update(metadata, editable_metadata)
+
+    metadata["Subject"]["subject_id"] = subject_id
 
     edf_reader = read_raw_edf(input_fname=edf_file_paths[0], verbose=verbose)
     session_start_time = edf_reader.info["meas_date"]
 
-    editable_metadata_path = Path(__file__).parent / "zaki_2024_metadata.yaml"
-    editable_metadata = load_dict_from_file(editable_metadata_path)
-    nwbfile_kwargs = deepcopy(editable_metadata["NWBFile"])
+    metadata["NWBFile"]["session_start_time"] = session_start_time
 
-    nwbfile_kwargs.update(
-        dict(
-            session_id=f"{subject_id}_week_session",
-            identifier=str(uuid.uuid4()),
-            session_start_time=session_start_time,
-        )
-    )
-
-    nwbfile = NWBFile(**nwbfile_kwargs)
+    nwbfile = converter.create_nwbfile(metadata=metadata, conversion_options=conversion_options)
 
     # Add epochs table to store time range of conditioning and offline sessions
     sessions_summary_file = data_dir_path / f"Ca_EEG_Experiment/{subject_id}/{subject_id}_SessionTimes.csv"
@@ -140,14 +136,7 @@ def session_to_nwb(
 
         nwbfile.add_epoch(start_time=start_time, stop_time=stop_time, session_ids=session_id)
 
-    converter = Zaki2024NWBConverter(source_data=source_data)
-
-    # Add datetime to conversion
-    metadata = converter.get_metadata()
-    metadata["Subject"]["subject_id"] = subject_id
-
     # Run conversion
-    converter.add_to_nwbfile(metadata=metadata, nwbfile=nwbfile, conversion_options=conversion_options)
     configure_and_write_nwbfile(nwbfile=nwbfile, backend="hdf5", output_filepath=nwbfile_path)
 
     if verbose: