.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/fluorescence_decay/plot_decay_fit_irf_bg.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_decay_fit_irf_bg.py>`
        to download the full example code

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

.. _sphx_glr_auto_examples_fluorescence_decay_plot_decay_fit_irf_bg.py:


===============================
Fluorescence decay analysis - 3
===============================

.. GENERATED FROM PYTHON SOURCE LINES 7-71



.. image-sg:: /auto_examples/fluorescence_decay/images/sphx_glr_plot_decay_fit_irf_bg_001.png
   :alt: plot decay fit irf bg
   :srcset: /auto_examples/fluorescence_decay/images/sphx_glr_plot_decay_fit_irf_bg_001.png
   :class: sphx-glr-single-img





.. code-block:: Python

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


    def objective_function(
            x: np.ndarray,
            x_min: int,
            x_max: int,
            irf: np.array,
            max_irf_fraction: float = 0.05
    ):
        max_irf = np.max(irf) * max_irf_fraction
        w = np.copy(irf[x_min:x_max])
        w[w < 1] = 1
        w[np.where(irf > max_irf)[0]] = 1
        chi2 = (((irf[x_min:x_max] - x[0])/w)**2).sum(axis=0)
        return chi2

    # Read TTTR
    spc132_filename = '../../tttr-data/bh/bh_spc132_sm_dna/m000.spc'
    data = tttrlib.TTTR(spc132_filename, 'SPC-130')
    data_green = data[data.get_selection_by_channel([0, 8])]
    # the macro time clock in ms
    macro_time_resolution = data.header.macro_time_resolution

    # Make histograms
    n_bins = 512  # number of bins in histogram
    x_min, x_max = 1, 512  # fit range
    dt = data.header.micro_time_resolution * 4096 / n_bins  # time resolution
    time_axis = np.arange(0, n_bins) * dt

    # IRF
    # select background / scatter, maximum 7 photons in 6 ms
    time_window_irf = 6.e-3
    n_ph_max_irf = 7
    irf, _ = np.histogram(
        data_green[
            data_green.get_selection_by_count_rate(
                time_window=time_window_irf,
                n_ph_max=n_ph_max_irf
            )
        ].micro_times, bins=n_bins
    )

    x0 = np.array([4])
    fit = scipy.optimize.minimize(
        objective_function, x0,
        args=(x_min, x_max, irf),
        method='BFGS'
    )
    irf_bg = fit.x


    fig, ax = p.subplots(nrows=2, ncols=1, sharex=True, sharey=False)
    ax[1].semilogy(time_axis, irf, label="IRF")
    ax[1].semilogy(
        time_axis[x_min:x_max],
        np.ones_like(time_axis)[x_min:x_max] * irf_bg, label="IRF Bg"
    )
    ax[1].legend()
    p.show()


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

   **Total running time of the script:** (0 minutes 0.917 seconds)


.. _sphx_glr_download_auto_examples_fluorescence_decay_plot_decay_fit_irf_bg.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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