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

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

.. _sphx_glr_auto_examples_tutorial_fit_pfid.py:


Fitting the perturbed free induction decay
==========================================

Sometimes it is useful to fit the perturbed free induction (see explanation in
the PFID tutorial), maybe certain excited state features are not yet visible or
a more exact determination of the center frequency is required.


WORK IN PROGRESS

.. GENERATED FROM PYTHON SOURCE LINES 13-19

.. code-block:: Python

    import numpy as np
    import matplotlib.pyplot as plt
    import skultrafast.plot_helpers as ph
    import skultrafast.unit_conversions as uc
    from skultrafast.utils import pfid_r4, pfid_r6
    from skultrafast import messpy, data_io, dataset







.. GENERATED FROM PYTHON SOURCE LINES 20-34

.. code-block:: Python



    fname = data_io.get_example_path('messpy')
    print("Tutorial MessPy-file located at %s" % fname)
    mpf = messpy.MessPyFile(
        fname,
        invert_data=True,  # Changes the sign of the data
        is_pol_resolved=True,  # If the data was recored polarization resolved.
        pol_first_scan='perp',  # Polarisation of the first scan
        valid_channel=1,  # Which channel to use, recent IR data always uses 1
        # Recent visible data uses 0
    )

    mpf.recalculate_wavelengths(8.8)




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

 .. code-block:: none

    Tutorial MessPy-file located at /home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/skultrafast/examples/data/messpyv1_data.npz
    /home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/skultrafast/messpy.py:174: RuntimeWarning: overflow encountered in cast
      self.wavenumbers = 1e7 / self.wl




.. GENERATED FROM PYTHON SOURCE LINES 35-43

.. code-block:: Python


    para, perp, iso = mpf.avg_and_concat()

    pol_ds = dataset.PolTRSpec(para, perp)
    pol_ds.subtract_background()
    merged_ds = pol_ds.merge_nearby_channels(8)
    merged_ds.plot.spec(-.5, n_average=3);



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

.. code-block:: pytb

    Traceback (most recent call last):
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/checkouts/latest/skultrafast/examples/tutorial_fit_pfid.py", line 41, in <module>
        merged_ds.plot.spec(-.5, n_average=3);
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/skultrafast/dataset.py", line 1887, in spec
        l1 = pa.plot.spec(*times,
             ^^^^^^^^^^^^^^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/skultrafast/dataset.py", line 1415, in spec
        dat = filter.uniform_filter(ds, (2*n_average + 1, 1)).data[idx, :]
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/skultrafast/filter.py", line 39, in uniform_filter
        f = nd.uniform_filter(d, size=sigma, mode="nearest")
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/scipy/ndimage/_filters.py", line 1613, in uniform_filter
        uniform_filter1d(input, int(size), axis, output, mode,
      File "/home/docs/checkouts/readthedocs.org/user_builds/skultrafast/envs/latest/lib/python3.11/site-packages/scipy/ndimage/_filters.py", line 1539, in uniform_filter1d
        _nd_image.uniform_filter1d(input, size, axis, output, mode, cval,
    RuntimeError: array type dtype('float16') not supported




.. GENERATED FROM PYTHON SOURCE LINES 44-48

.. code-block:: Python

    merged_ds.plot.spec(-1.5, n_average=1);




.. GENERATED FROM PYTHON SOURCE LINES 49-51

.. code-block:: Python

    merged_ds.t



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

   **Total running time of the script:** (0 minutes 0.150 seconds)


.. _sphx_glr_download_auto_examples_tutorial_fit_pfid.py:

.. only:: html

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

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

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

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

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

    .. container:: sphx-glr-download sphx-glr-download-zip

      :download:`Download zipped: tutorial_fit_pfid.zip <tutorial_fit_pfid.zip>`


.. only:: html

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

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