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

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

.. _sphx_glr_auto_examples_single_molecule_plot_single_molecule_mcs.py:


================
Intensity traces
================
The function ``tttrlib.intensity_trace`` can be applied to a sequences of event
times traces to calculate the time-dependent counts for a given time window size.
In single-molecule FRET experiments such traces are particularly useful to illustrate
single-molecule bursts. The function takes an array of macro times as an input
the macro times are binned and the counts per bin are returned.

#.. plot:: ../examples/single_molecule/single_molecule_mcs.py

Above, for a donor and acceptor detection channel a histogram trace for is shown
in green and red.

There are two options to compute intensity traces. Intensity traces can either be
computed using the function ``tttrlib.compute_intensity_trace`` or using the method
``intensity_trace`` of a ``TTTR`` object.

.. code-block:: python

    tttr_object = tttrlib.TTTR('../../tttr-data/bh/bh_spc132.spc', 'SPC-130')
    # option 1
    tttr_object = tttrlib.compute_intensity_trace(
        data.macro_times,
        time_window_length=1.0, # this is one millisecond
        macro_time_resolution=data.get_header().macro_time_resolution / 1e6
    )
    # option 2
    tttr_object = data.intensity_trace(
        time_window_length=1.0, # this is one millisecond
    )

When the first option is used, a calibration for the macro time array needs to be
provided. If the second option is used, the macro time calibration of the header
information that was processes from the tttr file when the ``TTTR`` object was
created is already considered. The time window length are in units of milli seconds.

.. GENERATED FROM PYTHON SOURCE LINES 41-83



.. image-sg:: /auto_examples/single_molecule/images/sphx_glr_plot_single_molecule_mcs_001.png
   :alt: plot single molecule mcs
   :srcset: /auto_examples/single_molecule/images/sphx_glr_plot_single_molecule_mcs_001.png
   :class: sphx-glr-single-img


.. rst-class:: sphx-glr-script-out

 .. code-block:: none

    /builds/skf/tttrlib/examples/single_molecule/plot_single_molecule_mcs.py:64: RuntimeWarning: divide by zero encountered in divide
      SgSr_ratio = (green_trace[:m] / red_trace[:m])
    /builds/skf/tttrlib/examples/single_molecule/plot_single_molecule_mcs.py:64: RuntimeWarning: invalid value encountered in divide
      SgSr_ratio = (green_trace[:m] / red_trace[:m])
    /builds/skf/tttrlib/examples/single_molecule/plot_single_molecule_mcs.py:65: RuntimeWarning: invalid value encountered in multiply
      SgSr_ratio[np.where((green_trace[:m] + red_trace[:m]) < 2)] *= 0






|

.. code-block:: Python

    import matplotlib.pylab as p
    import numpy as np

    import tttrlib

    data = tttrlib.TTTR('../../tttr-data/bh/bh_spc132.spc', 'SPC-130')
    mt = data.get_macro_times()

    green_indeces = data.get_selection_by_channel([0, 8])
    red_indeces = data.get_selection_by_channel([1, 9])

    fig, ax = p.subplots(3, 1, sharex=True, sharey=False)

    p.setp(ax[0].get_xticklabels(), visible=False)
    green_trace = tttrlib.compute_intensity_trace(
        mt[green_indeces],
        time_window_length=1.0e-3, # this is one millisecond
        macro_time_resolution=data.get_header().macro_time_resolution
    )
    red_trace = data[red_indeces].get_intensity_trace(
        time_window_length=1.0e-3
    )
    m = min(len(green_trace), len(red_trace))
    SgSr_ratio = (green_trace[:m] / red_trace[:m])
    SgSr_ratio[np.where((green_trace[:m] + red_trace[:m]) < 2)] *= 0

    ax[0].plot(green_trace, 'g', label='Green signal, Sg')
    ax[1].plot(red_trace, 'r', label='Red signal, Sr')
    ax[1].invert_yaxis()
    ax[0].legend()
    ax[1].legend()
    ax[2].plot(SgSr_ratio, 'b', label='Sg/Sr')
    ax[2].legend()
    p.subplots_adjust(
        left=None,
        bottom=None,
        right=None,
        top=None,
        wspace=None, hspace=0
    )
    p.show()
    #


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

   **Total running time of the script:** (0 minutes 0.374 seconds)


.. _sphx_glr_download_auto_examples_single_molecule_plot_single_molecule_mcs.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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