added arguments to temporally_align_data_interfaces

pyproject.toml

@@ -17,7 +17,7 @@ classifiers = [
 dependencies = [
   "neuroconv==0.6.6",
   "ndx-events==0.2.0",
-  "pymatreader==1.0.0"
+  "pymatreader==1.0.0",
   "spikeinterface==0.101.2"
 ]
 

src/schneider_lab_to_nwb/zempolich_2024/zempolich_2024_nwbconverter.py

@@ -1,6 +1,7 @@
 """Primary NWBConverter class for this dataset."""
 from pathlib import Path
 from pymatreader import read_mat
+from typing import Optional
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import (
     PhySortingInterface,
@@ -14,6 +15,19 @@
     Zempolich2024IntrinsicSignalOpticalImagingInterface,
 )
 
+# neuroconv.NWBConverter.run_conversion imports
+import warnings
+from pathlib import Path
+from typing import Literal, Optional
+from pydantic import FilePath
+from pynwb import NWBFile
+from neuroconv.tools.nwb_helpers._metadata_and_file_helpers import _resolve_backend
+from neuroconv.tools.nwb_helpers import (
+    HDF5BackendConfiguration,
+    configure_backend,
+    make_or_load_nwbfile,
+)
+
 
 class Zempolich2024NWBConverter(NWBConverter):
     """Primary conversion class."""
@@ -28,7 +42,9 @@ class Zempolich2024NWBConverter(NWBConverter):
         ISOI=Zempolich2024IntrinsicSignalOpticalImagingInterface,
     )
 
-    def temporally_align_data_interfaces(self):
+    def temporally_align_data_interfaces(
+        self, metadata: Optional[dict] = None, conversion_options: Optional[dict] = None
+    ) -> None:
         """Align timestamps between data interfaces.
 
         It is called by run_conversion() after the data interfaces have been initialized but before the data is added
@@ -39,5 +55,61 @@ def temporally_align_data_interfaces(self):
         behavior_file_path = Path(behavior_interface.source_data["file_path"])
         file = read_mat(behavior_file_path)
         cam1_timestamps, cam2_timestamps = file["continuous"]["cam"]["time"]
+        if conversion_options["Behavior"].get("normalize_timestamps", False):
+            starting_timestamp = file["continuous"][metadata["Behavior"]["TimeSeries"][0]["name"]]["time"][0]
+            cam1_timestamps -= starting_timestamp
+            cam2_timestamps -= starting_timestamp
         self.data_interface_objects["VideoCamera1"].set_aligned_timestamps([cam1_timestamps])
         self.data_interface_objects["VideoCamera2"].set_aligned_timestamps([cam2_timestamps])
+
+    # NOTE: run_conversion is copy-pasted from neuroconv.NWBConverter and only modified to call
+    # temporally_align_data_interfaces with the correct arguments. This is a temporary solution until the neuroconv
+    # library is updated to allow for easier customization of the conversion process
+    # (see https://github.com/catalystneuro/neuroconv/pull/1162).
+    def run_conversion(
+        self,
+        nwbfile_path: Optional[FilePath] = None,
+        nwbfile: Optional[NWBFile] = None,
+        metadata: Optional[dict] = None,
+        overwrite: bool = False,
+        backend: Optional[Literal["hdf5"]] = None,
+        backend_configuration: Optional[HDF5BackendConfiguration] = None,
+        conversion_options: Optional[dict] = None,
+    ) -> None:
+
+        if nwbfile_path is None:
+            warnings.warn(  # TODO: remove on or after 2024/12/26
+                "Using Converter.run_conversion without specifying nwbfile_path is deprecated. To create an "
+                "NWBFile object in memory, use Converter.create_nwbfile. To append to an existing NWBFile object,"
+                " use Converter.add_to_nwbfile."
+            )
+
+        backend = _resolve_backend(backend, backend_configuration)
+        no_nwbfile_provided = nwbfile is None  # Otherwise, variable reference may mutate later on inside the context
+
+        file_initially_exists = Path(nwbfile_path).exists() if nwbfile_path is not None else False
+        append_mode = file_initially_exists and not overwrite
+
+        if metadata is None:
+            metadata = self.get_metadata()
+
+        self.validate_metadata(metadata=metadata, append_mode=append_mode)
+        self.validate_conversion_options(conversion_options=conversion_options)
+
+        self.temporally_align_data_interfaces(metadata=metadata, conversion_options=conversion_options)
+
+        with make_or_load_nwbfile(
+            nwbfile_path=nwbfile_path,
+            nwbfile=nwbfile,
+            metadata=metadata,
+            overwrite=overwrite,
+            backend=backend,
+            verbose=getattr(self, "verbose", False),
+        ) as nwbfile_out:
+            if no_nwbfile_provided:
+                self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, conversion_options=conversion_options)
+
+            if backend_configuration is None:
+                backend_configuration = self.get_default_backend_configuration(nwbfile=nwbfile_out, backend=backend)
+
+            configure_backend(nwbfile=nwbfile_out, backend_configuration=backend_configuration)