NWBConverter#

Contains core class definitions for the NWBConverter and ConverterPipe.

class NWBConverter(source_data: dict[str, dict], verbose: bool = False)[source]#

Bases: object

Primary class for all NWB conversion classes.

Validate source_data against source_schema and initialize all data interfaces.

display_name: Optional[str] = None#
keywords: tuple[str] = ()#
associated_suffixes: tuple[str] = ()#
info: Optional[str] = None#
data_interface_classes = None#
classmethod get_source_schema() → dict[source]#

Compile input schemas from each of the data interface classes.

Returns

The compiled source schema from all data interface classes.

Return type

dict

classmethod validate_source(source_data: dict[str, dict], verbose: bool = False)[source]#

Validate source_data against Converter source_schema.

get_metadata_schema() → dict[source]#

Compile metadata schemas from each of the data interface objects.

Returns

The compiled metadata schema from all data interface objects.

Return type

dict

get_metadata() → DeepDict[source]#

Auto-fill as much of the metadata as possible. Must comply with metadata schema.

Returns

The metadata dictionary containing auto-filled metadata from all interfaces.

Return type

DeepDict

validate_metadata(metadata: dict[str, dict], append_mode: bool = False)[source]#

Validate metadata against Converter metadata_schema.

get_conversion_options_schema() → dict[source]#

Compile conversion option schemas from each of the data interface classes.

Returns

The compiled conversion options schema from all data interface classes.

Return type

dict

validate_conversion_options(conversion_options: dict[str, dict])[source]#

Validate conversion_options against Converter conversion_options_schema.

create_nwbfile(metadata: Optional[dict] = None, conversion_options: Optional[dict] = None) → NWBFile[source]#

Create and return an in-memory pynwb.NWBFile object with the conversion data added to it.

Parameters

  • metadata (dict, optional) – Metadata dictionary with information used to create the NWBFile.

  • conversion_options (dict, optional) – Similar to source_data, a dictionary containing keywords for each interface for which non-default conversion specification is requested.

Returns

nwbfile – The in-memory object with this interface’s data added to it.

Return type

pynwb.NWBFile

add_to_nwbfile(nwbfile: NWBFile, metadata, conversion_options: Optional[dict] = None)[source]#

Add data from the instantiated data interfaces to the given NWBFile.

Parameters

  • nwbfile (NWBFile) – The NWB file object to which the data from the data interfaces will be added.

  • metadata (dict) – The metadata dictionary that contains information used to describe the data.

  • conversion_options (dict, optional) – A dictionary containing conversion options for each interface, where non-default behavior is requested. Each key corresponds to a data interface name, and the values are dictionaries with options for that interface. By default, None.

run_conversion(nwbfile_path: Path, nwbfile: Optional[NWBFile] = None, metadata: Optional[dict] = None, overwrite: bool = False, backend: Optional[Literal['hdf5', 'zarr']] = None, backend_configuration: Optional[Union[HDF5BackendConfiguration, ZarrBackendConfiguration]] = None, conversion_options: Optional[dict] = None) → None[source]#

Run the NWB conversion over all the instantiated data interfaces.

Parameters

  • nwbfile_path (FilePath) – Path for where to write or load (if overwrite=False) the NWBFile. If specified, the context will always write to this location.

  • nwbfile (NWBFile, optional) – An in-memory NWBFile object to write to the location.

  • metadata (dict, optional) – Metadata dictionary with information used to create the NWBFile when one does not exist or overwrite=True.

  • overwrite (bool, default: False) – Whether to overwrite the NWBFile if one exists at the nwbfile_path. The default is False (append mode).

  • backend ({“hdf5”, “zarr”}, optional) – The type of backend to use when writing the file. If a backend_configuration is not specified, the default type will be “hdf5”. If a backend_configuration is specified, then the type will be auto-detected.

  • backend_configuration (HDF5BackendConfiguration or ZarrBackendConfiguration, optional) – The configuration model to use when configuring the datasets for this backend. To customize, call the .get_default_backend_configuration(…) method, modify the returned BackendConfiguration object, and pass that instead. Otherwise, all datasets will use default configuration settings.

  • conversion_options (dict, optional) – Similar to source_data, a dictionary containing keywords for each interface for which non-default conversion specification is requested.

temporally_align_data_interfaces(metadata: Optional[dict] = None, conversion_options: Optional[dict] = None)[source]#

Override this method to implement custom alignment.

static get_default_backend_configuration(nwbfile: NWBFile, backend: Literal['hdf5', 'zarr'] = 'hdf5') → Union[HDF5BackendConfiguration, ZarrBackendConfiguration][source]#

Fill and return a default backend configuration to serve as a starting point for further customization.

Parameters

  • nwbfile (pynwb.NWBFile) – The in-memory object with this interface’s data already added to it.

  • backend (“hdf5” or “zarr”, default: “hdf5”) – The type of backend to use when creating the file.

Returns

The default configuration for the specified backend type.

Return type

Union[HDF5BackendConfiguration, ZarrBackendConfiguration]

class ConverterPipe(data_interfaces: Union[list[neuroconv.basedatainterface.BaseDataInterface], dict[str, neuroconv.basedatainterface.BaseDataInterface]], verbose=False)[source]#

Bases: NWBConverter

Takes a list or dict of pre-initialized interfaces as arguments to build an NWBConverter class.

Validate source_data against source_schema and initialize all data interfaces.

classmethod get_source_schema() → dict[source]#

Compile input schemas from each of the data interface classes.

Returns

The compiled source schema from all data interface classes.

Return type

dict

classmethod validate_source()[source]#

Validate source_data against Converter source_schema.

get_conversion_options_schema() → dict[source]#

Compile conversion option schemas from each of the data interface classes.

Returns

The compiled conversion options schema containing: - root: True - id: “conversion_options.schema.json” - title: “Conversion options schema” - description: “Schema for the conversion options” - version: “0.1.0” - properties: Dictionary mapping interface names to their unrooted schemas

Return type

dict