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

.. only:: html

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

        Click :ref:`here <sphx_glr_download_auto_examples_run_fieldtrip_IF.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_run_fieldtrip_IF.py:


.. _ft_seeg_example:

=========================================
Apply bipolar montage to depth electrodes
=========================================
This scripts shows a very simple example on how to create an Interface wrapping
a desired function of a Matlab toolbox (|FieldTrip|).

.. |FieldTrip| raw:: html

    <a href="http://www.fieldtriptoolbox.org/" target="_blank">FieldTrip</a>

The **input** data should be a **.mat** file containing a FieldTrip data struct

.. GENERATED FROM PYTHON SOURCE LINES 16-27

.. code-block:: default


    # Authors: Annalisa Pascarella <a.pascarella@iac.cnr.it>
    # License: BSD (3-clause)

    import os.path as op

    import ephypype
    from ephypype.nodes.FT_tools import Reference
    from ephypype.datasets import fetch_ieeg_dataset



.. GENERATED FROM PYTHON SOURCE LINES 28-29

Let us fetch the data first. It is around 675 MB download.

.. GENERATED FROM PYTHON SOURCE LINES 29-54

.. code-block:: default


    base_path = op.join(op.dirname(ephypype.__file__), '..', 'examples')
    data_path = fetch_ieeg_dataset(base_path)

    import json  # noqa
    import pprint  # noqa
    params = json.load(open("params.json"))
    pprint.pprint({'time frequency parameters': params["tfr"]})
    ft_path = params["tfr"]['fieldtrip_path']
    refmethod = params["tfr"]['refmethod']
    channels_name = params["tfr"]['channels_name']

    # channels_name = '{\'RAM*\', \'RHH*\', \'RTH*\', \'ROC*\', \'LAM*\',\'LHH*\', \'LTH*\'}'  # noqa

    # Now we call the interface Reference to apply a bipolar montage to sEEG data
    reference_if = Reference()
    reference_if.inputs.data_file = op.join(data_path, 'SubjectUCI29_data.mat')
    reference_if.inputs.channels = channels_name
    reference_if.inputs.ft_path = ft_path
    reference_if.inputs.refmethod = refmethod
    reference_if.inputs.script = ''

    out = reference_if.run()

    print('Rereferenced data saved at {}'.format(out.outputs.data_output))


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

   **Total running time of the script:** ( 0 minutes  0.000 seconds)


.. _sphx_glr_download_auto_examples_run_fieldtrip_IF.py:

.. only:: html

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


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

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

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

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


.. only:: html

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

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