Software Architecture

The main goal of PyNWB is to enable users and developers to efficiently interact with the NWB data format, format files, and specifications. The following figures provide an overview of the high-level architecture of PyNWB and functionality of the various components.

PyNWB Software Architecture

Overview of the high-level software architecture of PyNWB.

PyNWB Software Architecture Functions

We choose a modular design for PyNWB to enable flexibility and separate the various aspects of the NWB:N ecosystem.

Main Concepts

PyNWB Software Architecture Concepts

Overview of the main concepts/classes in PyNWB and their location in the overall software architecture.

Container

Builder

Spec

  • Interact with format specifications

  • Data structures to specify data types and what said types consist of

  • Python representation for YAML specifications

  • Interface for writing extensions or custom specification

  • There are several main specification classes:

  • Main Modules:

Note

A data_type (or more specifically a neurodata_type in the context of NWB) defines a reusable type in a format specification that can be referenced and used elsewhere in other specifications. The specification of the NWB format is basically a collection of neurodata_types, e.g.: NWBFile defines a GroupSpec for the top-level group of an NWB format file which includes TimeSeries, ElectrodeGroup, ImagingPlane and many other neurodata_types . When creating a specification, two main keys are used to include and define new neurodata_types : i) neurodata_type_inc is used to include an existing type and ii) neurodata_type_def is used to defines a new type I.e, if both keys are defined then we create a new type that uses/inherits an existing type as a base.

ObjectMapper

  • Maintains the mapping between Container attributes and Spec components

  • Provides a way of converting between Container and Builders

  • ObjectMappers are constructed using a Spec

  • Ideally, one ObjectMapper for each data type

  • Things an ObjectMapper should do:

    • Given a Builder, return a Container representation
    • Given a Container, return a Builder representation
  • PyNWB has many of these – one for each type in NWB schema

  • Main Module: pynwb.form.build.map

    • NWB-specific ObjectMappers are locate in submodules of pynwb.io
PyNWB Software Architecture Main Concepts

Relationship between Containers, Builders, ObjectMappers, and Specs

Additional Concepts

Namespace, NamespaceCatalog, NamespaceBuilder

  • Namespace

    • A namespace for specifications

    • Necessary for making extensions

    • Contains basic info about who created extensions

    • Core NWB:N schema has namespace “core”

    • Get from pynwb.spec.NWBNamespace

      • extension of generic Namespace class that will include core
  • NamespaceCatalog – A class for managing namespaces

  • NamespaceBuilder – A utility for building extensions

TypeMap

  • Map between data types, Container classes (i.e. a Python class object) and corresponding ObjectMapper classes

  • Constructed from a NamespaceCatalog

  • Things a TypeMap does:

    • Given an NWB data type, return the associated Container class
    • Given a Container class, return the associated ObjectMapper
  • PyNWB has two of these classes:

    • the base class (i.e. TypeMap) - handles NWB 2.x
    • pynwb.legacy.TypeMapLegacy - handles NWB 1.x
  • PyNWB provides a “global” instance of TypeMap created at runtime

  • TypeMaps can be merged, which is useful when combining extensions

BuildManager

PyNWB Software Architecture BuildManager and TypeMap

Overview of BuildManager (and TypeMap).

FORMIO

  • Abstract base class for I/O

  • FORMIO has two key abstract methods:

    • write_builder – given a builder, write data to storage format
    • read_builder – given a handle to storage format, return builder representation
    • Others: open and close
  • Constructed with a BuildManager

  • Extend this for creating a new I/O backend

  • PyNWB has one extension of this:

    • pynwb.form.backends.hdf5.HDF5IO - reading and writing HDF5
    • pynwb.NWBHDF5IO - wrapper that pulls in core NWB specification
PyNWB Software Architecture FormIO

Overview of FORMIO.