.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "tutorials/extractors/plot_1_read_various_formats.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        :ref:`Go to the end <sphx_glr_download_tutorials_extractors_plot_1_read_various_formats.py>`
        to download the full example code.

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_tutorials_extractors_plot_1_read_various_formats.py:


Read various format into SpikeInterface
=======================================

SpikeInterface can read various formats of "recording" (traces) and "sorting" (spike train) data.

Internally, to read different formats, SpikeInterface either uses:
  * a wrapper to `neo <https://github.com/NeuralEnsemble/python-neo>`_ rawio classes
  * or a direct implementation

Note that:

  * file formats contain a "recording", a "sorting",  or "both"
  * file formats can be file-based (NWB, ...)  or folder based (SpikeGLX, OpenEphys, ...)

In this example we demonstrate how to read different file formats into SI

.. GENERATED FROM PYTHON SOURCE LINES 18-24

.. code-block:: Python


    import matplotlib.pyplot as plt

    import spikeinterface.core as si
    import spikeinterface.extractors as se








.. GENERATED FROM PYTHON SOURCE LINES 25-30

Let's download some datasets in different formats from the
`ephy_testing_data <https://gin.g-node.org/NeuralEnsemble/ephy_testing_data>`_ repo:

  * MEArec: a simulator format which is hdf5-based. It contains both a "recording" and a "sorting" in the same file.
  * Spike2: file from spike2 devices. It contains "recording" information only.

.. GENERATED FROM PYTHON SOURCE LINES 30-38

.. code-block:: Python



    spike2_file_path = si.download_dataset(remote_path="spike2/130322-1LY.smr")
    print(spike2_file_path)

    mearec_folder_path = si.download_dataset(remote_path="mearec/mearec_test_10s.h5")
    print(mearec_folder_path)





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

 .. code-block:: none


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    /home/docs/spikeinterface_datasets/ephy_testing_data/spike2/130322-1LY.smr
    /home/docs/spikeinterface_datasets/ephy_testing_data/mearec/mearec_test_10s.h5




.. GENERATED FROM PYTHON SOURCE LINES 39-47

Now that we have downloaded the files, let's load them into SI.

The :py:func:`~spikeinterface.extractors.read_spike2` function returns one object,
a :py:class:`~spikeinterface.core.BaseRecording`.

Note that internally this file contains 2 data streams ('0' and '1'), so we need to specify which one we
want to retrieve ('0' in our case).
the stream information can be retrieved by using the :py:func:`~spikeinterface.extractors.get_neo_streams` function.

.. GENERATED FROM PYTHON SOURCE LINES 47-59

.. code-block:: Python


    stream_names, stream_ids = se.get_neo_streams("spike2", spike2_file_path)
    print(stream_names)
    print(stream_ids)
    stream_id = stream_ids[0]
    print("stream_id", stream_id)

    recording = se.read_spike2(spike2_file_path, stream_id="0")
    print(recording)
    print(type(recording))
    print(isinstance(recording, si.BaseRecording))





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

 .. code-block:: none

    ['Signal stream 0', 'Signal stream 1']
    ['0', '1']
    stream_id 0
    Spike2RecordingExtractor: 1 channels - 20833.333333 Hz - 1 segments - 4,126,365 samples 
                              198.07s (3.30 minutes) - int16 dtype - 7.87 MiB
      file_path: /home/docs/spikeinterface_datasets/ephy_testing_data/spike2/130322-1LY.smr
    <class 'spikeinterface.extractors.neoextractors.spike2.Spike2RecordingExtractor'>
    True




.. GENERATED FROM PYTHON SOURCE LINES 60-63

The :py:func:`~spikeinterface.extractors.read_spike2`` function is equivalent to instantiating a
:py:class:`~spikeinterface.extractors.Spike2RecordingExtractor` object:


.. GENERATED FROM PYTHON SOURCE LINES 63-67

.. code-block:: Python


    recording = se.Spike2RecordingExtractor(spike2_file_path, stream_id="0")
    print(recording)





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

 .. code-block:: none

    Spike2RecordingExtractor: 1 channels - 20833.333333 Hz - 1 segments - 4,126,365 samples 
                              198.07s (3.30 minutes) - int16 dtype - 7.87 MiB
      file_path: /home/docs/spikeinterface_datasets/ephy_testing_data/spike2/130322-1LY.smr




.. GENERATED FROM PYTHON SOURCE LINES 68-70

The :py:func:`~spikeinterface.extractors.read_mearec` function returns two objects,
a :py:class:`~spikeinterface.core.BaseRecording` and a :py:class:`~spikeinterface.core.BaseSorting`:

.. GENERATED FROM PYTHON SOURCE LINES 70-78

.. code-block:: Python


    recording, sorting = se.read_mearec(mearec_folder_path)
    print(recording)
    print(type(recording))
    print()
    print(sorting)
    print(type(sorting))





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

 .. code-block:: none

    MEArecRecordingExtractor: 32 channels - 32.0kHz - 1 segments - 320,000 samples - 10.00s 
                              float32 dtype - 39.06 MiB
      file_path: /home/docs/spikeinterface_datasets/ephy_testing_data/mearec/mearec_test_10s.h5
    <class 'spikeinterface.extractors.neoextractors.mearec.MEArecRecordingExtractor'>

    MEArecSortingExtractor: 10 units - 1 segments - 32.0kHz
      file_path: /home/docs/spikeinterface_datasets/ephy_testing_data/mearec/mearec_test_10s.h5
    <class 'spikeinterface.extractors.neoextractors.mearec.MEArecSortingExtractor'>




.. GENERATED FROM PYTHON SOURCE LINES 79-80

The :py:func:`~spikeinterface.extractors.read_mearec` function is equivalent to:

.. GENERATED FROM PYTHON SOURCE LINES 80-84

.. code-block:: Python


    recording = se.MEArecRecordingExtractor(mearec_folder_path)
    sorting = se.MEArecSortingExtractor(mearec_folder_path)








.. GENERATED FROM PYTHON SOURCE LINES 85-87

SI objects (:py:class:`~spikeinterface.core.BaseRecording` and :py:class:`~spikeinterface.core.BaseSorting`)
can be plotted quickly with the :py:mod:`spikeinterface.widgets` submodule:

.. GENERATED FROM PYTHON SOURCE LINES 87-94

.. code-block:: Python


    import spikeinterface.widgets as sw

    w_ts = sw.plot_traces(recording, time_range=(0, 5))
    w_rs = sw.plot_rasters(sorting, time_range=(0, 5))

    plt.show()



.. rst-class:: sphx-glr-horizontal


    *

      .. image-sg:: /tutorials/extractors/images/sphx_glr_plot_1_read_various_formats_001.png
         :alt: plot 1 read various formats
         :srcset: /tutorials/extractors/images/sphx_glr_plot_1_read_various_formats_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /tutorials/extractors/images/sphx_glr_plot_1_read_various_formats_002.png
         :alt: plot 1 read various formats
         :srcset: /tutorials/extractors/images/sphx_glr_plot_1_read_various_formats_002.png
         :class: sphx-glr-multi-img






.. rst-class:: sphx-glr-timing

   **Total running time of the script:** (0 minutes 42.646 seconds)


.. _sphx_glr_download_tutorials_extractors_plot_1_read_various_formats.py:

.. only:: html

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

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download Jupyter notebook: plot_1_read_various_formats.ipynb <plot_1_read_various_formats.ipynb>`

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: plot_1_read_various_formats.py <plot_1_read_various_formats.py>`

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: plot_1_read_various_formats.zip <plot_1_read_various_formats.zip>`


.. only:: html

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

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