Source code for neuroconv.datainterfaces.ophys.miniscope.miniscopeconverter

from typing import Optional

from pynwb import NWBFile

from ... import MiniscopeBehaviorInterface, MiniscopeImagingInterface
from ....nwbconverter import NWBConverter
from ....tools.nwb_helpers import make_or_load_nwbfile
from ....utils import FolderPathType, get_schema_from_method_signature


class MiniscopeConverter(NWBConverter):
    """Primary conversion class for handling Miniscope data streams."""

    @classmethod
    def get_source_schema(cls):
        return get_schema_from_method_signature(cls)

    def __init__(self, folder_path: FolderPathType, verbose: bool = True):
        """
        Initializes the data interfaces for the Miniscope recording and behavioral data stream.

        The main Miniscope folder is expected to contain both data streams organized as follows:

        C6-J588_Disc5/ (main folder)
        ├── 15_03_28/ (subfolder corresponding to the recording time)
        │   ├── Miniscope/ (subfolder containing the microscope video stream)
        │   │   ├── 0.avi (microscope video)
        │   │   ├── metaData.json (metadata for the microscope device)
        │   │   └── timeStamps.csv (timing of this video stream)
        │   ├── BehavCam_2/ (subfolder containing the behavioral video stream)
        │   │   ├── 0.avi (bevavioral video)
        │   │   ├── metaData.json (metadata for the behavioral camera)
        │   │   └── timeStamps.csv (timing of this video stream)
        │   └── metaData.json (metadata for the recording, such as the start time)
        ├── 15_06_28/
        │   ├── Miniscope/
        │   ├── BehavCam_2/
        │   └── metaData.json
        └── 15_12_28/

        Parameters
        ----------
        folder_path : FolderPathType
            The path to the main Miniscope folder.
        verbose : bool, default: True
            Controls verbosity.
        """
        self.verbose = verbose
        self.data_interface_objects = dict(
            MiniscopeImaging=MiniscopeImagingInterface(folder_path=folder_path),
            MiniscopeBehavCam=MiniscopeBehaviorInterface(folder_path=folder_path),
        )

    def get_conversion_options_schema(self) -> dict:
        return self.data_interface_objects["MiniscopeImaging"].get_conversion_options_schema()

    def add_to_nwbfile(
        self,
        nwbfile: NWBFile,
        metadata,
        stub_test: bool = False,
        stub_frames: int = 100,
    ):
        self.data_interface_objects["MiniscopeImaging"].add_to_nwbfile(
            nwbfile=nwbfile,
            metadata=metadata,
            stub_test=stub_test,
            stub_frames=stub_frames,
        )
        self.data_interface_objects["MiniscopeBehavCam"].add_to_nwbfile(
            nwbfile=nwbfile,
            metadata=metadata,
        )

    def run_conversion(
        self,
        nwbfile_path: Optional[str] = None,
        nwbfile: Optional[NWBFile] = None,
        metadata: Optional[dict] = None,
        overwrite: bool = False,
        stub_test: bool = False,
        stub_frames: int = 100,
    ) -> None:
        if metadata is None:
            metadata = self.get_metadata()

        self.validate_metadata(metadata=metadata)

        self.temporally_align_data_interfaces()

        with make_or_load_nwbfile(
            nwbfile_path=nwbfile_path,
            nwbfile=nwbfile,
            metadata=metadata,
            overwrite=overwrite,
            verbose=self.verbose,
        ) as nwbfile_out:
            self.add_to_nwbfile(nwbfile=nwbfile_out, metadata=metadata, stub_test=stub_test, stub_frames=stub_frames)