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

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

.. _sphx_glr_auto_examples_phaseCycNoise_example.py:


Phase Cycling Noise
===================

A demo of the correlation alignment on a dataset
with a lot of phase cycling noise

.. GENERATED FROM PYTHON SOURCE LINES 7-47



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


    *

      .. image-sg:: /auto_examples/images/sphx_glr_phaseCycNoise_example_001.png
         :alt: raw data FIR_27dBm
         :srcset: /auto_examples/images/sphx_glr_phaseCycNoise_example_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_phaseCycNoise_example_002.png
         :alt: Correlation Diagnostic, before correlation sig. energy=1.54363e+09, correlation function (t),  after apod, correlation function (v),  after apod, after correlation before ph0 restore, after correlation ph0 restored  sig. energy=1.54363e+09
         :srcset: /auto_examples/images/sphx_glr_phaseCycNoise_example_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_phaseCycNoise_example_003.png
         :alt: correlation convergence
         :srcset: /auto_examples/images/sphx_glr_phaseCycNoise_example_003.png
         :class: sphx-glr-multi-img


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

 .. code-block:: none

    You didn't set units for t2 before saving the data!!!
    [(12, 'vd'), (2, 'ph2'), (2, 'ph1'), (2048, 't2')]
    1: raw data FIR_27dBm |||(None, None)
    2: Correlation Diagnostics |||(None, None)
    3: correlation convergence |||(None, None)







|

.. code-block:: Python

    from pyspecdata import figlist_var, find_file
    from pyspecProcScripts import correl_align
    from numpy import exp, pi

    save_fig = False
    this_figsize = (9, 5.56)
    with figlist_var() as fl:
        for date, id_string, node_name in [
            ("210607", "TEMPOL_100mM_cap_probe_DNP", "FIR_27dBm"),
        ]:
            filename = date + "_" + id_string + ".h5"
            nodename = "signal"
            nodename = node_name
            s = find_file(filename, expno=nodename, exp_type="ODNP_NMR_comp/ODNP")
            s = s["nScans", 0]
            print(s.shape)
            s.reorder(["ph2", "ph1", "vd", "t2"])
            s.setaxis("vd", "#")
            s.ft(["ph1", "ph2"])
            fl.next("raw data %s" % node_name)
            s["vd", 0] *= -1
            s.setaxis("t2", lambda x: x - 1.06e-3)
            s.ft("t2", shift=True)
            s.ift(["ph1", "ph2"])
            s *= exp(s.fromaxis("ph2") * 2 * pi * 1j)
            fl.image(s)
            s.ift("t2")
            s /= exp(s.fromaxis("ph2") * 2 * pi * 1j)
            s.ft(["ph1", "ph2"])
            s.ift(["ph1", "ph2"])
            signal_pathway = {"ph1": 0, "ph2": 1}
            s.ft("t2")
            opt_shift, sigma, mask_func = correl_align(
                s,
                indirect_dim="vd",
                signal_pathway=signal_pathway,
                sigma=3000 / 2.355,
                max_shift=300,
                fl=fl,
            )


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

   **Total running time of the script:** (0 minutes 10.721 seconds)


.. _sphx_glr_download_auto_examples_phaseCycNoise_example.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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