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

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

.. _sphx_glr_auto_examples_QESR.py:

Quantify the Double Integral of an ESR spectra (QESR)
========================================================
Calculate the concentration of spin label present in
a sample based on the double integral of an ESR spectra.

An ESR spectra should be collected for both the 
sample of interest as well as a "background" 
(typically water for aqueous samples). 
The spectra is rescaled according to it's acquisition parameters 
(e.g., Q value, diameter of capillaries, modulation amplitude,
gain, etc) and multiplied by a proportionality constant that 
is defined in your pyspecdata config file. 

In order to properly run this example, your config file
should have the following values under General:

::

    220720new propfactor = 1.715e-10
    220720new q = 4600
    qesr caps diameter = 0.704
    default calibration = 220720new
    default diameter = qesr caps

Note that the diameter is given in units of mm.

.. GENERATED FROM PYTHON SOURCE LINES 27-68



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


    *

      .. image-sg:: /auto_examples/images/sphx_glr_QESR_001.png
         :alt: zoomed-in baseline diagnostic showing only baseline (data and fit)
         :srcset: /auto_examples/images/sphx_glr_QESR_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_QESR_002.png
         :alt: abs mode: background subtracted, show baseline, $\left(\frac{dblint}{denom}\right)(calibration\ \rightarrow None)$
         :srcset: /auto_examples/images/sphx_glr_QESR_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_QESR_003.png
         :alt: zoomed-in baseline diagnostic showing only baseline (data and fit)
         :srcset: /auto_examples/images/sphx_glr_QESR_003.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_QESR_004.png
         :alt: abs mode: background subtracted, show baseline, $\left(\frac{dblint}{denom}\right)(calibration\ \rightarrow None)$
         :srcset: /auto_examples/images/sphx_glr_QESR_004.png
         :class: sphx-glr-multi-img


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

 .. code-block:: none

    the stored concentration is 69.93816677405941 millimolar
    the stored concentration is 521.3475578866337 micromolar
    1: ras baseline diagnostic
    {'print_string': '\\par'}
    {'width': 0.9}
    2: ras absorption, bg. no bl. |||G
    {'print_string': '\\textbf{\\texttt{220804_rasI36_MTSL.DSC}}\\par'}
    {'print_string': '\\par'}
    3: calibration experiment baseline diagnostic
    {'print_string': '\\par'}
    {'width': 0.9}
    4: calibration experiment absorption, bg. no bl. |||G
    {'print_string': '\\textbf{\\texttt{220720_stock_4.DSC}}\\par'}
    {'print_string': '\\par'}




    \par






    \textbf{\texttt{220804_rasI36_MTSL.DSC}}\par






    \par






    \par






    \textbf{\texttt{220720_stock_4.DSC}}\par






    \par









|

.. code-block:: Python


    from matplotlib.pyplot import rcParams
    from pyspecProcScripts import QESR
    from pyspecdata import figlist_var, find_file
    import pickle

    # sphinx_gallery_thumbnail_number = 2
    rcParams["image.aspect"] = "auto"  # needed for sphinx gallery

    pickle_file = "TEMPOL_rerun_conc.pickle"  # when complete, the
    #                                          concentration is stored here
    with figlist_var() as fl:
        fl.basename = "ras"  # I want different basenames so these show up on
        #                      different plots, because they have very
        #                      different concentrations
        c = QESR(
            "220804_rasI36_MTSL.DSC",  # filename
            label="kRas I36",  # label for legends
            exp_type="francklab_esr/Farhana",  # location of file
            diameter_name="QESR caps",
            background=find_file(
                "220804_water.DSC", exp_type="francklab_esr/Farhana"
            )[
                "harmonic", 0
            ],  # background used for background subtraction - loaded above
            pickle_file=pickle_file,
            fl=fl,
        )
        fl.basename = "calibration experiment"
        c = QESR(
            "220720_stock_4.DSC",  # filename
            label="70 mM ref",  # label for legends
            exp_type="francklab_esr/alex",  # location of file
            diameter_name="QESR caps",
            pickle_file=pickle_file,
            fl=fl,
        )
        with open(pickle_file, "rb") as fp:
            pickle_vars = pickle.load(fp)
        print("the stored concentration is", pickle_vars["70 mM ref"])
        print("the stored concentration is", pickle_vars["kRas I36"])


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

   **Total running time of the script:** (0 minutes 2.328 seconds)


.. _sphx_glr_download_auto_examples_QESR.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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