modify conversions to use subject extension

src/pinto_lab_to_nwb/general/subject.py

@@ -24,16 +24,19 @@ def make_subject_metadata(subject_id: str, subject_metadata_file_path: str) -> d
     date_of_birth = date_of_birth.replace(tzinfo=tzinfo)
 
     sex_mapping = dict(Male="M", Female="F")
-    # TODO: ear_tag_id, and zygosity are in the metadata file, but would require an extension of Subject to add, should it be added?
     subject_kwargs = dict(
         date_of_birth=date_of_birth,
         subject_id=subject_id,
         sex=sex_mapping[subject_metadata["sex"][subject_ind]],
         genotype=subject_metadata["line"][subject_ind],
+        zygosity=subject_metadata["zygosity"][subject_ind],
     )
     subject_description = subject_metadata["subject_description"][subject_ind]
     if subject_description:
         subject_kwargs["description"] = subject_description
+    ear_tag = subject_metadata["ear_tag_id"][subject_ind]
+    if ear_tag:
+        subject_kwargs["ear_tag_id"] = ear_tag
 
     metadata = dict(Subject=subject_kwargs, NWBFile=dict(protocol=subject_metadata["protocol"][subject_ind]))
     return metadata

src/pinto_lab_to_nwb/into_the_void/into_the_void_convert_session.py

@@ -1,6 +1,8 @@
 """Primary script to run to convert an entire session for of data using the NWBConverter."""
 import re
 from pathlib import Path
+from typing import Optional
+
 from dateutil import tz
 from neuroconv.utils import (
     load_dict_from_file,
@@ -9,6 +11,7 @@
     FilePathType,
 )
 
+from pinto_lab_to_nwb.general import make_subject_metadata
 from pinto_lab_to_nwb.into_the_void import IntoTheVoidNWBConverter
 from pinto_lab_to_nwb.into_the_void.into_the_voidnwbconverter import get_default_segmentation_to_imaging_name_mapping
 
@@ -17,6 +20,7 @@ def session_to_nwb(
     nwbfile_path: FilePathType,
     two_photon_imaging_folder_path: FolderPathType,
     segmentation_folder_path: FolderPathType,
+    subject_metadata_file_path: Optional[FilePathType] = None,
     segmentation_to_imaging_plane_map: dict = None,
     stub_test: bool = False,
 ):
@@ -31,6 +35,8 @@ def session_to_nwb(
         The folder path that contains the Bruker TIF imaging output (.ome.tif files).
     segmentation_folder_path: FolderPathType
         The folder that contains the Suite2P segmentation output.
+    subject_metadata_file_path: FilePathType, optional
+        The file path to the subject metadata file ('subject_metadata.mat').
     segmentation_to_imaging_plane_map: dict, optional
         The optional mapping between the imaging and segmentation planes.
     stub_test: bool, optional
@@ -42,7 +48,7 @@ def session_to_nwb(
         imaging_folder_path=imaging_folder_path,
         segmentation_folder_path=segmentation_folder_path,
         segmentation_to_imaging_map=segmentation_to_imaging_plane_map,
-        verbose=False,
+        verbose=True,
     )
 
     conversion_options = {
@@ -70,6 +76,15 @@ def session_to_nwb(
         metadata["NWBFile"].update(session_id=groups_dict["session_id"].replace("_", "-"))
         metadata["Subject"].update(subject_id=groups_dict["subject_id"])
 
+        if subject_metadata_file_path:
+            subject_metadata = make_subject_metadata(
+                subject_id=groups_dict["subject_id"], subject_metadata_file_path=subject_metadata_file_path
+            )
+            metadata = dict_deep_update(metadata, subject_metadata)
+
+    # Separate subject metadata from NWBFile metadata to add SubjectExtension
+    metadata["SubjectExtension"] = metadata.pop("Subject", None)
+
     # Run conversion
     converter.run_conversion(
         nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True, conversion_options=conversion_options
@@ -83,6 +98,8 @@ def session_to_nwb(
     imaging_folder_path = Path("/Volumes/t7-ssd/Pinto/NCCR32_2022_11_03_IntoTheVoid_t_series-005")
     # The folder that contains the Suite2P segmentation output.
     segmentation_folder_path = imaging_folder_path / "suite2p"
+    # The file path to the subject metadata file.
+    subject_metadata_file_path = "/Volumes/t7-ssd/Pinto/Behavior/subject_metadata.mat"
     # The folder path that will contain the NWB files.
     nwbfile_folder_path = Path("/Volumes/t7-ssd/Pinto/nwbfiles")
     # For testing purposes, when stub_test=True only writes a subset of imaging and segmentation data.
@@ -99,6 +116,7 @@ def session_to_nwb(
     session_to_nwb(
         nwbfile_path=nwbfile_path,
         two_photon_imaging_folder_path=imaging_folder_path,
+        subject_metadata_file_path=subject_metadata_file_path,
         segmentation_folder_path=segmentation_folder_path,
         segmentation_to_imaging_plane_map=plane_map,
         stub_test=stub_test,

src/pinto_lab_to_nwb/into_the_void/into_the_voidnwbconverter.py

@@ -1,10 +1,12 @@
 """Primary NWBConverter class for this dataset."""
 from typing import Optional
 
+from ndx_pinto_metadata import SubjectExtension
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import Suite2pSegmentationInterface, BrukerTiffMultiPlaneImagingInterface
 from neuroconv.converters import BrukerTiffSinglePlaneConverter, BrukerTiffMultiPlaneConverter
-from neuroconv.utils import FolderPathType, DeepDict, dict_deep_update
+from neuroconv.utils import FolderPathType, DeepDict
+from pynwb import NWBFile
 
 
 def get_default_segmentation_to_imaging_name_mapping(
@@ -150,3 +152,10 @@ def get_metadata(self) -> DeepDict:
             metadata["Ophys"]["ImagingPlane"][metadata_ind]["device"] = device_name
 
         return metadata
+
+    def add_to_nwbfile(self, nwbfile: NWBFile, metadata, conversion_options: Optional[dict] = None) -> None:
+        super().add_to_nwbfile(nwbfile=nwbfile, metadata=metadata, conversion_options=conversion_options)
+
+        # Add subject (from extension)
+        if metadata["SubjectExtension"] is not None:
+            nwbfile.subject = SubjectExtension(**metadata["SubjectExtension"])

src/pinto_lab_to_nwb/widefield/widefield_convert_session.py

@@ -146,6 +146,8 @@ def session_to_nwb(
             )
             metadata = dict_deep_update(metadata, subject_metadata)
 
+    # Separate subject metadata from NWBFile metadata to add SubjectExtension
+    metadata["SubjectExtension"] = metadata.pop("Subject", None)
     # Run conversion
     converter.run_conversion(
         nwbfile_path=nwbfile_path, metadata=metadata, overwrite=True, conversion_options=conversion_options

src/pinto_lab_to_nwb/widefield/widefieldnwbconverter.py

@@ -4,10 +4,10 @@
 
 import numpy as np
 from natsort import natsorted
+from ndx_pinto_metadata import SubjectExtension
 from neuroconv import NWBConverter
 from pynwb import NWBFile
 
-from pinto_lab_to_nwb.widefield.interfaces import WidefieldImagingInterface, WidefieldProcessedImagingInterface
 from pinto_lab_to_nwb.widefield.utils import load_motion_correction_data
 from pinto_lab_to_nwb.widefield.utils.motion_correction import add_motion_correction
 from pinto_lab_to_nwb.widefield.interfaces import (
@@ -46,6 +46,10 @@ def __init__(self, source_data: Dict[str, dict], verbose: bool = True):
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata, conversion_options: Optional[dict] = None) -> None:
         super().add_to_nwbfile(nwbfile=nwbfile, metadata=metadata, conversion_options=conversion_options)
 
+        # Add subject (from extension)
+        if metadata["SubjectExtension"] is not None:
+            nwbfile.subject = SubjectExtension(**metadata["SubjectExtension"])
+
         # Add motion correction for blue and violet frames
         imaging_interface_names = ["ImagingBlue", "ImagingViolet"]
         for interface_name in imaging_interface_names: