.. note::
    :class: sphx-glr-download-link-note

    Click :ref:`here <sphx_glr_download_auto_examples_NeoAll_examples_plot_NeoAll_ex5.py>` to download the full example code
.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_NeoAll_examples_plot_NeoAll_ex5.py:


======================================================
    Neo All - example 5 - Channel Groups / Index
======================================================

This example show how to use the channel indexes in the NeoAll class. In NeoAll, channel indexes are defined for each
tetrode and each electrode **if the signal directory path is given at init**. Otherwise channel indexes are created
based on the probe file.




.. code-block:: python


    from neoStructures import *
    import pandas as pd
    import matplotlib.pyplot as plt
    from os.path import isdir, join







Import the data and create the NeoAll instance



.. code-block:: python

    data_dir = join('pySpikeAnalysis', 'sample_data') if isdir('pySpikeAnalysis') else join('..', '..', 'pySpikeAnalysis', 'sample_data')
    spykingcircus_dir = r'SpykingCircus_results'
    probe_filename = r'000_AA.prb'
    results_filename = r'spykingcircusres'
    artefact_csv_filepath = join(data_dir, r'artefact_free_periods.csv')

    neoAll = NeoAll(join(data_dir, spykingcircus_dir), results_filename, join(data_dir, probe_filename), save_fig=0)







See information about NeoAll



.. code-block:: python

    print(neoAll)





.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    NeoAll Instance with 54 units. 1 Neo segment per unit. Each segment contains 1 Neo spiketrain
    10 channel indexes


Let's look at the different channel indexes :



.. code-block:: python

    print(neoAll.channel_indexes)






.. rst-class:: sphx-glr-script-out

 Out:

 .. code-block:: none

    [<neo.core.channelindex.ChannelIndex object at 0x7f5595d02cc0>, <neo.core.channelindex.ChannelIndex object at 0x7f5595d02cf8>, <neo.core.channelindex.ChannelIndex object at 0x7f5595d020f0>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4550>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc47b8>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4a58>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4c18>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4cf8>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4d68>, <neo.core.channelindex.ChannelIndex object at 0x7f5595cc4f98>]


We can see that the first groups or ChannelIndex correpond to individual tetrodes and that the last groups
We can see that the first groups or ChannelIndex correpond to individual tetrodes and that the last groups
correpond to the entire electrode (i.e. group of 2 or 3 tetrodes)


We can use the channel indexes for plotting the firing rate evolution of multiple units in the same figure. Channel
indexes define groups of channel. By default, a channel index is defined for each tetrode.
Let's plot the firing rate evolution of all units of the tetrode 2 of electrode cp (ChannelIndex number 4,
thus index 3) :



.. code-block:: python

    neoAll.plot_spikerate_evolution_group(grp_index=3)



.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_NeoAll_ex5_001.png
    :class: sphx-glr-single-img




**Total running time of the script:** ( 0 minutes  3.032 seconds)


.. _sphx_glr_download_auto_examples_NeoAll_examples_plot_NeoAll_ex5.py:


.. only :: html

 .. container:: sphx-glr-footer
    :class: sphx-glr-footer-example



  .. container:: sphx-glr-download

     :download:`Download Python source code: plot_NeoAll_ex5.py <plot_NeoAll_ex5.py>`



  .. container:: sphx-glr-download

     :download:`Download Jupyter notebook: plot_NeoAll_ex5.ipynb <plot_NeoAll_ex5.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_