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

    Click :ref:`here <sphx_glr_download_auto_examples_NeoAll_examples_plot_NeoAll_ex1.py>` to download the full example code
.. rst-class:: sphx-glr-example-title

.. _sphx_glr_auto_examples_NeoAll_examples_plot_NeoAll_ex1.py:


=====================
Neo All - example 1
=====================

This example shows how to use create a NeoAll instance.

.. note::

    NeoAll instances are created from the SpykingCircus files. See `here <https://spyking-circus.readthedocs.io/en/latest/advanced/files.html>`_
    for details about these results files. NeoAll needs at least three arguments to be initiated :

    * spikesorting_dirpath : the path of the directory containng the spyking circus result file
    * spikesorting_filename : the name of the Spiking Circus result file
    * probe_filepath : the path to the Spiking Circus probe file


For instance, the Spyking Cirucs files may look like these :

.. image:: ./../../_static/images/spykingcircus_files.png

Details of the files :
 * The *000_AA.prb* file is the probe file, it contains information about how contacts are organized on the electrodes, see `here <https://spyking-circus.readthedocs.io/en/latest/code/probe.html>`_ for more info. This file is needed for launching the spike-sorting. It is used in NeoAll for creating channel indexes and knowing the number of tetrodes.
 * The *.result.hdf5* file is used to store the spike times for each unit, at the end of the spike sorting procedure.
 * The *.template.hdf5* file contains the preffered contact of each unit.
 * In order to generate the units template, three files are used : *.basis.hdf5*, *.templates.hdf5* and *.clusters.hdf5* files. Unit template is computed using the :func:`~spykingcircus_utils.get_templates_from_spykingcircus_file` function.



First import the neoStructures :



.. code-block:: python

    from neoStructures import *
    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'

    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


neoAll contains a list of Neo Segments (1 segment per unit)



.. code-block:: python

    print(type(neoAll.segments[0]))





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

 Out:

 .. code-block:: none

    <class 'neo.core.segment.Segment'>


Computing the mean firing rate is easy, e.g. for unit 3:



.. code-block:: python

    mean_spkrate_3 = len(neoAll.segments[3].spiketrains[0]) / (neoAll.segments[3].t_stop - neoAll.segments[3].t_start)
    print(mean_spkrate_3)





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

 Out:

 .. code-block:: none

    2.410294521750985 1/s


The method :func:`neoStructures.NeoAll.plot_spikerate_evolution` can be used to visualize the firing-rate over time
The firing rate is computed by kernel convolution. The kernel is gaussian and the standard deviation can be set using
the sigma_gauss_kernel parameter.
The package `Elephant <http://elephant.readthedocs.io/en/latest/index.html>`_ is used for the estimation.



.. code-block:: python

    neoAll.plot_spikerate_evolution(unit_pos=3, sigma_gauss_kernel=30*s)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_NeoAll_ex1_001.png
    :class: sphx-glr-single-img




The shape of each unit can be plotted using the plot_unit_shape method :



.. code-block:: python

    neoAll.plot_unit_shape(2)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_NeoAll_ex1_002.png
    :class: sphx-glr-single-img




As well as the ISI (Inter-Spike Interval), e.g. for unit 22 :



.. code-block:: python

    neoAll.plot_isi(unit_pos=22)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_NeoAll_ex1_003.png
    :class: sphx-glr-single-img




Zoom on the x-origin and increase the number of bins for the histogram



.. code-block:: python

    neoAll.plot_isi(22, bin_duration_ms=0.1, tmax_ms=15)




.. image:: /auto_examples/NeoAll_examples/images/sphx_glr_plot_NeoAll_ex1_004.png
    :class: sphx-glr-single-img




**Total running time of the script:** ( 0 minutes  0.740 seconds)


.. _sphx_glr_download_auto_examples_NeoAll_examples_plot_NeoAll_ex1.py:


.. only :: html

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



  .. container:: sphx-glr-download

     :download:`Download Python source code: plot_NeoAll_ex1.py <plot_NeoAll_ex1.py>`



  .. container:: sphx-glr-download

     :download:`Download Jupyter notebook: plot_NeoAll_ex1.ipynb <plot_NeoAll_ex1.ipynb>`


.. only:: html

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

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