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

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

.. _sphx_glr_auto_examples_pac_plot_compare_surrogates.py:


====================================================
Compare methods to correct PAC for spurious coupling
====================================================

This example illustrates the different implemented methods in order to generate
the distribution of surrogates and then to correct the PAC for spurious
couplings. This includes :

    * Swapping phase / amplitude trials (Tort et al. 2010,
      :cite:`tort2010measuring`)
    * Swapping amplitudes time blocks [RECOMMENDED] (Bahramisharif et al. 2013,
      :cite:`bahramisharif2013propagating`, Aru et al. 2015,
      :cite:`aru2015untangling`)
    * Introducing a time lag on phase series (Canolty et al. 2006,
      :cite:`canolty2006high`)



.. code-block:: default

    import matplotlib.pyplot as plt

    from tensorpac import Pac
    from tensorpac.signals import pac_signals_wavelet







Simulate artificial coupling
##############################################################################
 first, we generate several trials that contains a coupling between a 6z phase
 and a 90hz amplitude. By default, the returned dataset is organized as
 (n_epochs, n_times) where n_times is the number of time points and n_epochs
 is the number of trials


.. code-block:: default


    f_pha = 6       # frequency phase for the coupling
    f_amp = 70      # frequency amplitude for the coupling
    n_epochs = 20   # number of trials
    n_times = 4000  # number of time points
    sf = 512.       # sampling frequency
    data, time = pac_signals_wavelet(sf=sf, f_pha=f_pha, f_amp=f_amp, noise=3.,
                                     n_epochs=n_epochs, n_times=n_times)







Extract phases and amplitudes
##############################################################################
 now, we are going to extract all the phases and amplitudes. This is going to
 be useful then because it avoid to do it each time we're going to compute the
 PAC.


.. code-block:: default


    # define a :class:`tensorpac.Pac` object and use the MVL as the main method
    # for measuring PAC
    p = Pac(idpac=(1, 0, 0), f_pha=(3, 10, 1, .2), f_amp=(50, 90, 5, 1),
            dcomplex='wavelet', width=12)

    # Now, extract all of the phases and amplitudes
    phases = p.filter(sf, data, ftype='phase')
    amplitudes = p.filter(sf, data, ftype='amplitude')








Compute PAC and surrogates
##############################################################################
 now the phases and amplitudes are extracted, we can compute the true PAC such
 as the surrogates. Then the true value of PAC is going to be normalized using
 a z-score normalization and using the distribution of surrogates


.. code-block:: default


    plt.figure(figsize=(16, 12))
    for i, k in enumerate(range(4)):
        # change the pac method
        p.idpac = (5, k, 1)
        # compute only the pac without filtering
        xpac = p.fit(phases, amplitudes, n_perm=20)
        # plot
        title = p.str_surro.replace(' (', '\n(')
        plt.subplot(2, 2, k + 1)
        p.comodulogram(xpac.mean(-1), title=title, cmap='Reds', vmin=0,
                       fz_labels=18, fz_title=20, fz_cblabel=18)

    plt.tight_layout()

    plt.show()



.. image:: /auto_examples/pac/images/sphx_glr_plot_compare_surrogates_001.png
    :class: sphx-glr-single-img





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

   **Total running time of the script:** ( 0 minutes  10.278 seconds)


.. _sphx_glr_download_auto_examples_pac_plot_compare_surrogates.py:


.. only :: html

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



  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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