1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
|
.. _software-architecture:
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.
.. _fig-software-architecture:
.. figure:: figures/software_architecture.*
:width: 100%
:alt: PyNWB Software Architecture
Overview of the high-level software architecture of PyNWB (click to enlarge).
.. _fig-software-architecture-purpose:
.. figure:: figures/software_architecture_design_choices.*
:width: 100%
:alt: PyNWB Software Architecture Functions
We choose a modular design for PyNWB to enable flexibility and separate the
various aspects of the NWB:N ecosystem (click to enlarge).
.. raw:: latex
\clearpage \newpage
Main Concepts
-------------
.. _fig-software-architecture-concepts:
.. figure:: figures/software_architecture_concepts.*
:width: 100%
:alt: PyNWB Software Architecture Concepts
Overview of the main concepts/classes in PyNWB and their location in the overall software architecture (click to enlarge).
Container
^^^^^^^^^
* In memory objects
* Interface for (most) applications
* Like a table row
* PyNWB has many of these -- one for each neurodata_type in the NWB schema. PyNWB organizes the containers
into a set of modules based on their primary application (e.g., ophys for optophysiology):
* :py:class:`pynwb.base`, :py:class:`pynwb.file`
* :py:class:`pynwb.ecephys`
* :py:class:`pynwb.ophys`
* :py:class:`pynwb.icephys`
* :py:class:`pynwb.ogen`
* :py:class:`pynwb.behavior`
Builder
^^^^^^^
* Intermediary objects for I/O
* Interface for I/O
* Backend readers and writers must return and accept these
* There are different kinds of builders for different base types:
* :py:class:`~hdmf.build.builders.GroupBuilder` - represents a collection of objects
* :py:class:`~hdmf.build.builders.DatasetBuilder` - represents data
* :py:class:`~hdmf.build.builders.LinkBuilder` - represents soft-links
* :py:class:`~hdmf.build.builders.RegionBuilder` - represents a slice into data (Subclass of :py:class:`~hdmf.build.builders.DatasetBuilder`)
* **Main Module:** :py:mod:`hdmf.build.builders`
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:
* :py:class:`~pynwb.spec.NWBAttributeSpec` - specification for metadata
* :py:class:`~pynwb.spec.NWBGroupSpec` - specification for a collection of
objects (i.e. subgroups, datasets, link)
* :py:class:`~pynwb.spec.NWBDatasetSpec` - specification for dataset (like
and n-dimensional array). Specifies data type, dimensions, etc.
* :py:class:`~pynwb.spec.NWBLinkSpec` - specification for link (like a POSIX
soft link)
* :py:class:`~hdmf.spec.spec.RefSpec` - specification for references
(References are like links, but stored as data)
* :py:class:`~pynwb.spec.NWBDtypeSpec` - specification for compound data
types. Used to build complex data type specification, e.g., to define
tables (used only in :py:class:`~hdmf.spec.spec.DatasetSpec` and
correspondingly :py:class:`~pynwb.spec.NWBDatasetSpec`)
* **Main Modules:**
* :py:mod:`hdmf.spec` -- General specification classes.
* :py:mod:`pynwb.spec` -- NWB specification classes. (Most of these are
specializations of the classes from :py:mod:`hdmf.spec`)
.. 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``
* ``neurodata_type_inc`` is used to include an existing type and
* ``neurodata_type_def`` is used to define 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 `Builder`_
* 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:** :py:mod:`hdmf.build.objectmapper`
* NWB-specific ObjectMappers are locate in submodules of :py:class:`pynwb.io`
.. _fig-software-architecture-mainconcepts:
.. figure:: figures/software_architecture_mainconcepts.*
:width: 100%
:alt: PyNWB Software Architecture Main Concepts
Relationship between `Container`_, `Builder`_, `ObjectMapper`_, and `Spec`_
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 :py:class:`pynwb.spec.NWBNamespace`
* extension of generic Namespace class that will include core
* :py:class:`~hdmf.spec.namespace.NamespaceCatalog` -- A class for managing namespaces
* :py:class:`~hdmf.spec.write.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. :py:class:`~hdmf.build.manager.TypeMap`) - handles NWB 2.x
* :py:class:`pynwb.legacy.map.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
^^^^^^^^^^^^
* Responsible for `memoizing <https://en.wikipedia.org/wiki/Memoization>`_ `Builder`_ and `Container`_
* Constructed from a `TypeMap`_
* PyNWB only has one of these: :py:class:`hdmf.build.manager.BuildManager`
.. _fig-software-architecture-buildmanager:
.. figure:: figures/software_architecture_buildmanager.*
:width: 100%
:alt: PyNWB Software Architecture BuildManager and TypeMap
Overview of `BuildManager`_ (and `TypeMap`_) (click to enlarge).
HDMFIO
^^^^^^
* Abstract base class for I/O
* :py:class:`HDMFIO <hdmf.backends.io.HDMFIO>` has two key abstract methods:
* :py:meth:`~hdmf.backends.io.HDMFIO.write_builder` – given a builder, write data to storage format
* :py:meth:`~hdmf.backends.io.HDMFIO.read_builder` – given a handle to storage format, return builder representation
* Others: :py:meth:`~hdmf.backends.io.HDMFIO.open` and :py:meth:`~hdmf.backends.io.HDMFIO.close`
* Constructed with a `BuildManager`_
* Extend this for creating a new I/O backend
* PyNWB has one extension of this:
* :py:class:`~hdmf.backends.hdf5.h5tools.HDF5IO` - reading and writing HDF5
* :py:class:`~pynwb.NWBHDF5IO` - wrapper that pulls in core NWB specification
.. _fig-software-architecture-formio:
.. figure:: figures/software_architecture_formio.*
:width: 100%
:alt: PyNWB Software Architecture FormIO
Overview of `HDMFIO`_ (click to enlarge).
|
