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

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

.. _sphx_glr_gallery_calcium_deconvolve.py:


Deconvolve synthetic calcium traces
==============================

This is an example of how to infer spike events



First, we'll generate some fake data



.. code-block:: python


    import numpy as np
    import pandas as pd
    from neuroglia.datasets import make_calcium_traces

    data = make_calcium_traces(duration=10.0,oscillation=False)

    traces = data['traces']
    spikes = data['spikes']


let's plot the data



.. code-block:: python


    import matplotlib.pyplot as plt
    traces.plot()
    plt.show()


Now, we'll deconvolve the data



.. code-block:: python


    from neuroglia.calcium import CalciumDeconvolver

    deconvolver = CalciumDeconvolver()
    detected_events = deconvolver.transform(traces)

    neuron_ids = traces.columns

    for neuron in neuron_ids:
        y_true = spikes[neuron]
        y_pred = detected_events[neuron]
        corr = np.corrcoef(y_pred,y_true)[0,1]
        print("{}: {:0.2f}".format(neuron,corr))

    detected_events.plot()
    plt.show()


Now, we'll predict spikes



.. code-block:: python


    spikes_pred = deconvolver.predict(traces)
    spikes_true = (spikes>0).astype(int)

    for neuron in neuron_ids:
        y_true = spikes_true[neuron]
        y_pred = spikes_pred[neuron]
        corr = np.corrcoef(y_pred,y_true)[0,1]
        print("{}: {:0.2f}".format(neuron,corr))


.. _sphx_glr_download_gallery_calcium_deconvolve.py:


.. only :: html

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



  .. container:: sphx-glr-download

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



  .. container:: sphx-glr-download

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


.. only:: html

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

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