np-nwb 0.1.1

Tools for quickly generating `.nwb` files from non-standard Mindscope Neuropixels experiments.

np_nwb

Tools for quickly generating .nwb files from non-standard Mindscope Neuropixels experiments.

np_nwb

Tools for quickly generating .nwb files from non-standard Mindscope Neuropixels experiments.

Generating an .nwb file will entail:

• inputting a path to a folder of raw data from a single experiment (session_folder)
• creating an instance of pynwb.NWBFile and writing to disk (nwb_file)
• passing nwb_file + session_folder, to various modules that add nwb components
• each module should:
  • accept or load an instance of pynwb.NWBFile from nwb_file
  • recognize the type of experiment contained in session_folder
  • process raw data in session_folder accordingly
  • append tables to the pynwb.NWBFile instance
  • optionally write to disk
  • return the pynwb.NWBFile instance

Each module should therefore provide a single function or method which implements the following append() interface:

import logging
import pathlib
import tempfile
from typing import Optional

import pynwb

logger = logging.getLogger(__name__)


def append(
    session_folder: str | pathlib.Path,
    nwb_file: str | pathlib.Path | pynwb.NWBFile,
    output_file: Optional[str | pathlib.Path] = None,
    ) -> pynwb.NWBFile:
    """Append one or more new components to an `.nwb` file.

    - callable from within a Python process, by accepting & returning instances of `pynwb.  NWBFile` 
    - callable from the command line, in which case all three input arguments are required, with `nwb_file` specified as a path
    """
    session_folder = pathlib.Path(session_folder)

    # ... process session_folder

    if not isinstance(nwb_file, pynwb.NWBFile):
        nwb_file = load_nwb_from_disk(nwb_file) 
    
    # ... append new components to nwb_file

    if output_file is not None:
        write_nwb_to_disk(nwb_file, output_file)
    
    return nwb_file


def load_nwb_from_disk(
    nwb_path: str | pathlib.Path,
    ) -> pynwb.NWBFile:
    logger.info(f'Loading nwb file at {nwb_path}')
    with pynwb.NWBHDF5IO(nwb_path, mode='r') as f:
        return f.read()


def write_nwb_to_disk(
    nwb_file: pynwb.NWBFile, output_path: Optional[str | pathlib.Path] = None
    ) -> None:
    if output_path is None:
        output_path = pathlib.Path(tempfile.mkdtemp()) / f'{nwb_file.session_id}.nwb'
    
    nwb_file.set_modified()

    logger.info(f'Writing nwb file `{nwb_file.session_id!r}` to {output_path}')
    with pynwb.NWBHDF5IO(output_path, mode='w') as f:
        f.write(nwb_file, cache_spec=True)
    logger.debug(f'Writing complete for nwb file `{nwb_file.session_id!r}`')