.. _sphx_glr_auto_examples_plot_simulate_bo.py:


=============================
Simulating a brain object
=============================

In this example, we demonstrate the simulate_bo function.
First, we'll load in some example locations. Then we'll simulate 1
brain object specifying a noise parameter and the correlational structure
of the data (a toeplitz matrix). We'll then subsample 10 locations from the
original brain object.





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


    *

      .. image:: /auto_examples/images/sphx_glr_plot_simulate_bo_001.png
            :scale: 47

    *

      .. image:: /auto_examples/images/sphx_glr_plot_simulate_bo_002.png
            :scale: 47





.. code-block:: python


    # Code source: Lucy Owen & Andrew Heusser
    # License: MIT

    import supereeg as se
    from supereeg.helpers import _corr_column
    import numpy as np

    # simulate 100 locations
    locs = se.simulate_locations(n_elecs=100)

    # simulate brain object
    bo = se.simulate_bo(n_samples=1000, sample_rate=100, cov='random', locs=locs, noise =.1)

    # sample 10 locations, and get indices
    sub_locs = locs.sample(90, replace=False).sort_values(['x', 'y', 'z']).index.values.tolist()

    # index brain object to get sample patient
    bo_sample = bo[: ,sub_locs]

    # plot sample patient locations
    bo_sample.plot_locs()

    # plot sample patient data
    bo_sample.plot_data()

    # make model from brain object
    r_model = se.Model(data=bo, locs=locs)

    # predict
    bo_s = r_model.predict(bo_sample, nearest_neighbor=False)

    # find indices for reconstructed locations
    recon_labels = np.where(np.array(bo_s.label) != 'observed')

    # find correlations between predicted and actual data
    corrs = _corr_column(bo.get_data().as_matrix(), bo_s.get_data().as_matrix())

    # index reconstructed correlations
    corrs[recon_labels].mean()


**Total running time of the script:** ( 0 minutes  0.834 seconds)



.. only :: html

 .. container:: sphx-glr-footer


  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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