allensdk.brain_observatory.nwb.nwb_utils module

class allensdk.brain_observatory.nwb.nwb_utils.NWBWriter(nwb_filepath: str, session_data: dict, serializer: JsonReadableInterface | NwbReadableInterface | NwbWritableInterface)

Bases: object

Base class for writing NWB files

property nwb_filepath: str

Path to write nwb file

write_nwb(id_column_name: str = 'behavior_session_id', skip_metadata: List[str] | None = None, skip_stim: List[str] | None = None, **kwargs)

Tries to write nwb to disk. If it fails, the filepath has “.error” appended

Parameters:

id_column_namestr

Name of the id column to pull from metadata.

skip_metadatalist of str

Name of key in session_data to skip when comparing to session.

skip_stimlist of str

Name of key in stimulus file to skip when comparing to session.

kwargs: kwargs sent to `from_nwb`, `to_nwb`

allensdk.brain_observatory.nwb.nwb_utils.add_image_to_nwb(nwbfile: NWBFile, image_data: Image, image_name: str)

Adds image given by image_data with name image_name to nwbfile

Parameters:

nwbfile

nwbfile to add image to

image_data

The image data

image_name

Image name

Returns:

None

allensdk.brain_observatory.nwb.nwb_utils.get_column_name(table_cols: list, possible_names: set) → str

This function returns a column name, given a table with unknown column names and a set of possible column names which are expected. The table column name returned should be the only name contained in the “expected” possible names. :param table_cols: the table columns to search for the possible name within :param possible_names: the names that could exist within the data columns :return: the first entry of the intersection between the possible names

and the names of the columns of the stimulus table

allensdk.brain_observatory.nwb.nwb_utils.get_image(nwbfile: NWBFile, name: str, module: str) → Image