From f8c1ef790ecbbad71d49a5f316f815569ac2a83f Mon Sep 17 00:00:00 2001 From: weiglszonja Date: Tue, 26 Nov 2024 15:17:59 +0100 Subject: [PATCH] update session_to_nwb --- .../schierek_embargo_2024_convert_session.py | 95 ++++++++++++++++++- 1 file changed, 92 insertions(+), 3 deletions(-) diff --git a/src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_convert_session.py b/src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_convert_session.py index ca140ec..7868149 100644 --- a/src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_convert_session.py +++ b/src/constantinople_lab_to_nwb/schierek_embargo_2024/schierek_embargo_2024_convert_session.py @@ -4,14 +4,65 @@ from pathlib import Path from typing import Union, Optional +import numpy as np +import pandas as pd from dateutil import tz from neuroconv.datainterfaces import OpenEphysRecordingInterface from neuroconv.utils import load_dict_from_file, dict_deep_update +from nwbinspector import inspect_nwbfile, save_report, format_messages +from pymatreader import read_mat from spikeinterface.extractors import OpenEphysBinaryRecordingExtractor +from constantinople_lab_to_nwb.utils import get_subject_metadata_from_rat_info_folder from constantinople_lab_to_nwb.schierek_embargo_2024 import SchierekEmbargo2024NWBConverter +def update_ephys_device_metadata_for_subject( + epys_registry_file_path: Union[str, Path], + subject_id: str, + metadata: dict, +): + if not os.path.exists(epys_registry_file_path): + raise FileNotFoundError(f"File not found: {epys_registry_file_path}") + + ephys_registry = read_mat(epys_registry_file_path) + if "Registry" not in ephys_registry: + raise ValueError(f"'Registry' key not found in {epys_registry_file_path}.") + ephys_registry = pd.DataFrame(ephys_registry["Registry"]) + if "ratname" not in ephys_registry.columns: + raise ValueError(f"'ratname' column not found in {epys_registry_file_path}.") + filtered_ephys_registry = ephys_registry[ephys_registry["ratname"] == subject_id] + + metadata["Ecephys"]["ElectrodeGroup"][0].update( + description="The electrode group on the Neuropixels probe.", + ) + if not filtered_ephys_registry.empty: + ap_value = filtered_ephys_registry["AP"].values[0] + ml_value = filtered_ephys_registry["ML"].values[0] + dv_value = filtered_ephys_registry["DV"].values[0] + + coordinates_in_mm = f"AP: {ap_value} mm, ML: {ml_value} mm" + if not np.isnan(dv_value): + coordinates_in_mm += f", DV: {dv_value}." + + recording_hemisphere = filtered_ephys_registry["recordinghemisphere"].values[0] + recording_hemisphere = dict(L="left", R="right").get(recording_hemisphere, recording_hemisphere) + probe_type = filtered_ephys_registry["probetype"].values[0] + + brain_region = filtered_ephys_registry["recordingsite"].values[0] + description = f"The {probe_type} probe implanted in {brain_region} brain region, at {coordinates_in_mm}, {recording_hemisphere} hemisphere." + if "distance2LO" in filtered_ephys_registry.columns: + distance_to_LO_um = filtered_ephys_registry["distance2LO"].values[0] + # TODO: confirm unit + description += f" Distance to LO: {distance_to_LO_um} μm." + + metadata["Ecephys"]["Device"][0].update( + description=description, + ) + + return metadata + + def session_to_nwb( openephys_recording_folder_path: Union[str, Path], spike_sorting_folder_path: Union[str, Path], @@ -20,6 +71,8 @@ def session_to_nwb( nwbfile_path: Union[str, Path], column_name_mapping: Optional[dict] = None, column_descriptions: Optional[dict] = None, + ephys_registry_file_path: Optional[Union[str, Path]] = None, + subject_metadata: Optional[dict] = None, stub_test: bool = False, overwrite: bool = False, ): @@ -36,6 +89,10 @@ def session_to_nwb( The path to the processed spike sorting file (.mat). nwbfile_path : str or Path The path to the NWB file to write. + ephys_registry_file_path: str or Path + The path to the ephys registry (.mat) file. + subject_metadata: dict, optional + Additional subject metadata. e.g. dict( stub_test : bool, default: False Whether to run a stub test conversion. overwrite : bool, default: False @@ -145,7 +202,15 @@ def session_to_nwb( behavior_metadata = load_dict_from_file(behavior_metadata_path) metadata = dict_deep_update(metadata, behavior_metadata) - metadata["Subject"].update(subject_id=subject_id) + if ephys_registry_file_path is not None: + metadata = update_ephys_device_metadata_for_subject( + epys_registry_file_path=ephys_registry_file_path, + subject_id=subject_id, + metadata=metadata, + ) + + if subject_metadata is not None: + metadata["Subject"].update(subject_id=subject_id, **subject_metadata) # Run conversion converter.run_conversion( @@ -155,6 +220,17 @@ def session_to_nwb( overwrite=overwrite, ) + results = list(inspect_nwbfile(nwbfile_path=nwbfile_path)) + report_path = Path(nwbfile_path).parent / f"{subject_id}-{session_id}_nwbinspector_result.txt" + if not report_path.exists(): + save_report( + report_file_path=report_path, + formatted_messages=format_messages( + results, + levels=["importance", "file_path"], + ), + ) + if __name__ == "__main__": @@ -225,13 +301,24 @@ def session_to_nwb( wait_thresh="The threshold in seconds to remove wait-times (mean + 1*std of all cumulative wait-times).", ) - nwbfile_path = Path("/Volumes/T9/Constantinople/nwbfiles/J076_2023-12-12_14-52-04.nwb") + nwbfile_path = Path("/Users/weian/data/demo/J076_2023-12-12_14-52-04.nwb") if not nwbfile_path.parent.exists(): os.makedirs(nwbfile_path.parent, exist_ok=True) - stub_test = True + # Ephys registry file path (constains metadata for the neuropixels probe) + ephys_registry_file_path = "/Volumes/T9/Constantinople/Ephys Data/Ephys_registry.mat" + + stub_test = False overwrite = True + # Get subject metadata from rat registry + rat_registry_folder_path = "/Volumes/T9/Constantinople/Rat_info" + subject_metadata = get_subject_metadata_from_rat_info_folder( + folder_path=rat_registry_folder_path, + subject_id="J076", + date="2023-12-12", + ) + session_to_nwb( openephys_recording_folder_path=openephys_recording_folder_path, spike_sorting_folder_path=phy_sorting_folder_path, @@ -239,6 +326,8 @@ def session_to_nwb( raw_behavior_file_path=bpod_file_path, column_name_mapping=column_name_mapping, column_descriptions=column_descriptions, + ephys_registry_file_path=ephys_registry_file_path, + subject_metadata=subject_metadata, nwbfile_path=nwbfile_path, stub_test=stub_test, overwrite=overwrite,