multielectrode_grasp/code/python-neo/doc/source/releases/0.5.0.rst

=======================
Neo 0.5.0 release notes
=======================

22nd March 2017


For Neo 0.5, we have taken the opportunity to simplify the Neo object model.

Although this will require an initial time investment for anyone who has written code with
an earlier version of Neo, the benefits will be greater simplicity, both in your own code and
within the Neo code base, which should allow us to move more quickly in fixing bugs, improving
performance and adding new features.

More detail on these changes follows:


Merging of "single-value" and "array" versions of data classes
==============================================================

In previous versions of Neo, we had :class:`AnalogSignal` for one-dimensional (single channel)
signals, and :class:`AnalogSignalArray` for two-dimensional (multi-channel) signals.
In Neo 0.5.0, these have been merged under the name :class:`AnalogSignal`.
:class:`AnalogSignal` has the same behaviour as the old :class:`AnalogSignalArray`.

It is still possible to create an :class:`AnalogSignal` from a one-dimensional array, but
this will be converted to an array with shape `(n, 1)`, e.g.:

.. code-block:: python

    >>> signal = neo.AnalogSignal([0.0, 0.1, 0.2, 0.5, 0.6, 0.5, 0.4, 0.3, 0.0],
    ...                           sampling_rate=10*kHz,
    ...                           units=nA)
    >>> signal.shape
    (9, 1)

Multi-channel arrays are created as before, but using :class:`AnalogSignal` instead of
:class:`AnalogSignalArray`:

.. code-block:: python

    >>> signal = neo.AnalogSignal([[0.0, 0.1, 0.2, 0.5, 0.6, 0.5, 0.4, 0.3, 0.0],
    ...                            [0.0, 0.2, 0.4, 0.7, 0.9, 0.8, 0.7, 0.6, 0.3]],
    ...                           sampling_rate=10*kHz,
    ...                           units=nA)
    >>> signal.shape
    (9, 2)


Similarly, the :class:`Epoch` and :class:`EpochArray` classes have been merged into an
array-valued class :class:`Epoch`, ditto for :class:`Event` and :class:`EventArray`, and the
:class:`Spike` class, whose main function was to contain the waveform data for an individual spike,
has been suppressed; waveform data are now available as the :attr:`waveforms` attribute
of the :class:`SpikeTrain` class.


Recording channels
==================

As a consequence of the removal of "single-value" data classes, information on recording channels
and the relationship between analog signals and spike trains is also stored differently.

In Neo 0.5, we have introduced a new class, :class:`ChannelIndex`, which replaces both
:class:`RecordingChannel` and :class:`RecordingChannelGroup`.

In older versions of Neo, a :class:`RecordingChannel` object held metadata about a logical
recording channel (a name and/or integer index) together with references to one or more
:class:`AnalogSignal`\s recorded on that channel at different points in time
(different :class:`Segment`\s); redundantly, the :class:`AnalogSignal` also had a
:attr:`channel_index` attribute, which could be used in addition to or instead of creating a
:class:`RecordingChannel`.

Metadata about :class:`AnalogSignalArray`\s could be contained in a :class:`RecordingChannelGroup`
in a similar way, i.e. :class:`RecordingChannelGroup` functioned as an array-valued version of
:class:`RecordingChannel`, but :class:`RecordingChannelGroup` could also be used to group together
individual :class:`RecordingChannel` objects.

With Neo 0.5, information about the channel names and ids of an :class:`AnalogSignal` is contained
in a :class:`ChannelIndex`, e.g.:

.. code-block:: python

    >>> signal = neo.AnalogSignal([[0.0, 0.1, 0.2, 0.5, 0.6, 0.5, 0.4, 0.3, 0.0],
    ...                            [0.0, 0.2, 0.4, 0.7, 0.9, 0.8, 0.7, 0.6, 0.3]],
    ...                            [0.0, 0.1, 0.3, 0.6, 0.8, 0.7, 0.6, 0.5, 0.3]],
    ...                           sampling_rate=10*kHz,
    ...                           units=nA)
    >>> channels = neo.ChannelIndex(index=[0, 1, 2],
    ...                             channel_names=["chan1", "chan2", "chan3"])
    >>> signal.channel_index = channels

In this use, it replaces :class:`RecordingChannel`.

:class:`ChannelIndex` may also be used to group together a subset of the channels of a
multi-channel signal, for example:

.. code-block:: python

    >>> channel_group = neo.ChannelIndex(index=[0, 2])
    >>> channel_group.analogsignals.append(signal)
    >>> unit = neo.Unit()  # will contain the spike train recorded from channels 0 and 2.
    >>> unit.channel_index = channel_group


Checklist for updating code from 0.3/0.4 to 0.5
===============================================

To update your code from Neo 0.3/0.4 to 0.5, run through the following checklist:

    1. Change all usages of :class:`AnalogSignalArray` to :class:`AnalogSignal`.
    2. Change all usages of :class:`EpochArray` to :class:`Epoch`.
    3. Change all usages of :class:`EventArray` to :class:`Event`.
    4. Where you have a list of (single channel) :class:`AnalogSignal`\s all of the same length,
       consider converting them to a single, multi-channel :class:`AnalogSignal`.
    5. Replace :class:`RecordingChannel` and :class:`RecordingChannelGroup` with
       :class:`ChannelIndex`.


.. note:: in points 1-3, the data structure is still an array, it just has a shorter name.


Other changes
=============

    * added :class:`NixIO` (`about the NIX format`_)
    * added :class:`IgorIO`
    * added :class:`NestIO` (for data files produced by the `NEST simulator`_)
    * :class:`NeoHdf5IO` is now read-only. It will read data files produced by earlier versions
      of Neo, but another HDF5-based IO, e.g. :class:`NixIO`, should be used for writing data.
    * many fixes/improvements to existing IO modules. All IO modules should now work with Python 3.

.. https://github.com/NeuralEnsemble/python-neo/issues?utf8=✓&q=is%3Aissue%20is%3Aclosed%20created%3A%3E2014-02-01%20

.. _`about the NIX format`: https://github.com/G-Node/nix/wiki
.. _`NEST simulator`: https://www.nest-simulator.org/