add example convert_session script

src/constantinople_lab_to_nwb/optogenetics/__init__.py

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+from .optogenetics_nwbconverter import OptogeneticsNWBConverter

src/constantinople_lab_to_nwb/optogenetics/optogenetics_convert_session.py

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+from pathlib import Path
+from typing import Union
+
+from dateutil import tz
+from neuroconv.utils import load_dict_from_file, dict_deep_update
+
+from constantinople_lab_to_nwb.optogenetics import OptogeneticsNWBConverter
+
+
+def session_to_nwb(
+    raw_behavior_file_path: Union[str, Path],
+    nwbfile_path: Union[str, Path],
+    overwrite: bool = False,
+    verbose: bool = False,
+):
+    """
+    Convert a session of data to NWB format.
+
+    Parameters
+    ----------
+    raw_behavior_file_path : str or Path
+        The path to the raw behavior file.
+    nwbfile_path : str or Path
+        The path to the NWB file to write.
+    overwrite : bool, default: False
+        Whether to overwrite an existing NWB file.
+    verbose : bool, default: False
+        Whether to display verbose output.
+    """
+    source_data = dict()
+    conversion_options = dict()
+
+    # Add Behavior
+    source_data.update(dict(Behavior=dict(file_path=raw_behavior_file_path)))
+    # Exclude some task arguments from the trials table that are the same for all trials
+    task_arguments_to_exclude = [
+        "BlockLengthTest",
+        "BlockLengthAd",
+        "TrialsStage2",
+        "TrialsStage3",
+        "TrialsStage4",
+        "TrialsStage5",
+        "TrialsStage6",
+        "TrialsStage8",
+        "CTrial",
+    ]
+    conversion_options.update(dict(Behavior=dict(task_arguments_to_exclude=task_arguments_to_exclude)))
+
+    converter = OptogeneticsNWBConverter(source_data=source_data, verbose=verbose)
+
+    subject_id, session_id = Path(raw_behavior_file_path).stem.split("_", maxsplit=1)
+    protocol = session_id.split("_")[0]
+    session_id = session_id.replace("_", "-")
+
+    # Add datetime to conversion
+    metadata = converter.get_metadata()
+    session_start_time = metadata["NWBFile"]["session_start_time"]
+    tzinfo = tz.gettz("America/New_York")
+    metadata["NWBFile"].update(
+        session_start_time=session_start_time.replace(tzinfo=tzinfo),
+        session_id=session_id,
+        protocol=protocol,
+    )
+
+    # Update default metadata with the editable in the corresponding yaml file
+    editable_metadata_path = Path(__file__).parent / "metadata" / "optogenetics_general_metadata.yaml"
+    editable_metadata = load_dict_from_file(editable_metadata_path)
+    metadata = dict_deep_update(metadata, editable_metadata)
+
+    # Update behavior metadata
+    behavior_metadata_path = Path(__file__).parent / "metadata" / "optogenetics_behavior_metadata.yaml"
+    behavior_metadata = load_dict_from_file(behavior_metadata_path)
+    metadata = dict_deep_update(metadata, behavior_metadata)
+
+    # Update ogen metadata
+    ogen_metadata_path = Path(__file__).parent / "metadata" / "optogenetics_stimulation_metadata.yaml"
+    ogen_metadata = load_dict_from_file(ogen_metadata_path)
+    metadata = dict_deep_update(metadata, ogen_metadata)
+
+    metadata["Subject"].update(subject_id=subject_id, sex="U", age="P7D")
+    # if subject_metadata is not None:
+    #     metadata["Subject"].update(subject_metadata)
+
+    # Run conversion
+    converter.run_conversion(
+        nwbfile_path=nwbfile_path,
+        metadata=metadata,
+        conversion_options=conversion_options,
+        overwrite=overwrite,
+    )
+
+
+if __name__ == "__main__":
+    # Parameters for conversion
+    # The raw behavior data is stored in a .mat file (contains data for a single session)
+    bpod_file_path = Path(
+        "/Volumes/T9/Constantinople/raw_Bpod/L047/DataFiles/L047_RWTautowait2OptoTest_20240816_085658.mat"
+    )
+    nwbfile_path = "/Volumes/T9/Constantinople/nwbfiles/L047_RWTautowait2OptoTest_20240816_085658k.nwb"
+    overwrite = True
+    verbose = False
+
+    # Run conversion
+    session_to_nwb(
+        raw_behavior_file_path=bpod_file_path,
+        nwbfile_path=nwbfile_path,
+        overwrite=overwrite,
+        verbose=verbose,
+    )