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

.. only:: html

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

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

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

.. _sphx_glr_auto_examples_fluorescence_decay_plot_pile_up.py:


===============================
Pile-up
===============================
This example illustrates the effect of pile up on the shape of fluorescence decay
curves and demonstrates how the shape of a model function can be modified to
account for pile up.

.. GENERATED FROM PYTHON SOURCE LINES 9-99



.. image-sg:: /auto_examples/fluorescence_decay/images/sphx_glr_plot_pile_up_001.png
   :alt: plot pile up
   :srcset: /auto_examples/fluorescence_decay/images/sphx_glr_plot_pile_up_001.png
   :class: sphx-glr-single-img





.. code-block:: Python

    import pylab as p
    import numpy as np
    import scipy.stats
    import tttrlib

    # Set seed to make results reproducible
    np.random.seed(42)

    # Define number of channels and excitation period
    n_channels = 512
    period = 32
    time_axis = np.linspace(0, period, n_channels)
    conv_stop = n_channels // 2

    # compute a irf
    irf_width = 0.25
    irf_position = 2.0
    dt = time_axis[1] - time_axis[0]
    irf_p = scipy.stats.norm.pdf(time_axis, loc=irf_position, scale=irf_width)
    irf_s = irf_p

    """
    In this example first an ideal fluorescence decay is computed for the parallel (p)
    and perpendicular (s) channel using fit23.
    """

    # Compute model fo a single photon
    n_photons = 1
    period, g, l1, l2 = 32, 1.0, 0.1, 0.1
    tau, gamma, r0, rho = 2.0, 0.01, 0.38, 1.2

    model = np.zeros(n_channels * 2)  # For parallel and perpendicualr
    bg = np.zeros_like(model)
    tttrlib.DecayFit23.modelf(
        np.array([tau, gamma, r0, rho]),
        np.hstack([irf_p, irf_s]),
        bg, dt,
        np.array([period, g, l1, l2, conv_stop]),
        model
    )

    """
    The number the model is scaled to a number of photons typically recorded in a eTCSPC 
    experiment. In an eTCSPC experiment usually 1e6 - 20e6 photons are recorded. 
    """

    n_photons = 5.5e5
    model *= n_photons

    # Add pileup to parallel (p) and perpendicular (s)
    model_p = model[:len(model) // 2]
    model_p_with_pileup = np.copy(model_p)
    model_s = model[len(model) // 2:]
    model_s_with_pileup = np.copy(model_s)

    """
    The pile up depends on the instrument dead time, the repetition rate used to excite
    the sample and the total number of registered photons. Here, to highlight the effect
    of pile up an unrealistic combination of the measurement time and the number of photons 
    is used. In modern counting electronics the dead time is often around 100 nano
    seconds.

    In this example there is no data. Thus, the model without pile up is used as
    "data". In a real experiment use the experimental histogram in the data argument.
    """

    pile_up_parameter = {
        'repetition_rate': 1./period * 1000,  # Repetition rate is in MHz
        'instrument_dead_time': 120.,  # Instrument dead time nano seconds
        'measurement_time': 0.05,  # Measurement time in seconds
        'pile_up_model': "coates"
    }

    tttrlib.add_pile_up_to_model(
        model=model_p_with_pileup,
        decay=model_p,
        **pile_up_parameter
    )
    tttrlib.add_pile_up_to_model(
        model=model_s_with_pileup,
        decay=model_s,
        **pile_up_parameter
    )

    model_ps_pile_up = np.hstack([model_p_with_pileup, model_s_with_pileup])
    p.semilogy(model_ps_pile_up, label='with pileup')
    p.semilogy(model, label='no pileup')
    p.legend()
    p.show()



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

   **Total running time of the script:** (0 minutes 0.348 seconds)


.. _sphx_glr_download_auto_examples_fluorescence_decay_plot_pile_up.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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