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

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

.. _sphx_glr_auto_examples_proc_CPMG.py:


CPMG-specific processing
========================
`py proc_CPMG.py NODENAME FILENAME EXP_TYPE`

Based on `proc_raw.py`:
Here we apply the postprocessing, and then do some stuff specific to a CPMG.

Tested with:

``py proc_CPMG.py CPMG_9 240620_200uM_TEMPOL_pm_generic_CPMG.h5 ODNP_NMR_comp/Echoes``

.. GENERATED FROM PYTHON SOURCE LINES 14-80



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


    *

      .. image-sg:: /auto_examples/images/sphx_glr_proc_CPMG_001.png
         :alt: raw data
         :srcset: /auto_examples/images/sphx_glr_proc_CPMG_001.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_proc_CPMG_002.png
         :alt: time domain
         :srcset: /auto_examples/images/sphx_glr_proc_CPMG_002.png
         :class: sphx-glr-multi-img

    *

      .. image-sg:: /auto_examples/images/sphx_glr_proc_CPMG_003.png
         :alt: plot as time trace
         :srcset: /auto_examples/images/sphx_glr_proc_CPMG_003.png
         :class: sphx-glr-multi-img


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

 .. code-block:: none

    You didn't set units for indirect before saving the data!!!
    You didn't set units for nEcho before saving the data!!!
    You didn't set units for t2 before saving the data!!!
    WARNING! the file doesn't have coherence_pathway set, so I'm assuming {'ph1': 1, 'ph_overall': -1}
    1: raw data |||(None, None)
    2: time domain |||(None, None)
    3: plot as time trace |||None







|

.. code-block:: Python


    from pyspecProcScripts.load_data import lookup_table
    from pyspecProcScripts import select_pathway
    import pyspecdata as psd
    import sys, os
    import numpy as np
    from itertools import cycle
    import matplotlib.pylab as plt

    # sphinx_gallery_thumbnail_number = 3

    if (
        "SPHINX_GALLERY_RUNNING" in os.environ
        and os.environ["SPHINX_GALLERY_RUNNING"] == "True"
    ):
        sys.argv = [
            sys.argv[0],
            "CPMG_9",
            "240620_200uM_TEMPOL_pm_generic_CPMG.h5",
            "ODNP_NMR_comp/Echoes",
        ]

    filter_data = False
    colorcyc_list = plt.rcParams["axes.prop_cycle"].by_key()["color"]
    colorcyc = cycle(colorcyc_list)

    assert len(sys.argv) == 4
    d = psd.find_file(
        sys.argv[2], exp_type=sys.argv[3], expno=sys.argv[1], lookup=lookup_table
    )
    with psd.figlist_var() as fl:
        d.squeeze()
        fl.next("raw data")
        rows = np.prod([d.shape[j] for j in d.dimlabels[:-1]])
        fl.image(d, interpolation="auto")
        # {{{ allows us to see how filtering affects things
        #     -- relevant to considerations about
        #     integration, etc
        if filter_data:
            d["t2":(None, -750)] = 0
            d["t2":(750, None)] = 0
            fl.next("filtered data")
            fl.image(d)
        # }}}
        d.ift("t2")
        fl.next("time domain")
        cohpth = d.get_prop("coherence_pathway")
        if cohpth is None:
            cohpth = {
                "ph1": +1,
                "ph_overall": -1,
            }  # this should be stored as the coherence_pathway property of the
            #    data, but for CPMG_9, it appears that it is not
            print(
                "WARNING! the file doesn't have coherence_pathway set, so I'm"
                " assuming",
                cohpth,
            )
        d = select_pathway(d, cohpth)
        fl.image(d)
        fl.next("plot as time trace")
        d.smoosh(["nEcho", "t2"], "t2")
        acq = d.get_prop("acq_params")
        echo_time = 1e-6 * 2 * (acq["tau_us"] + acq["p90_us"])
        d["t2"] = (1 + d["t2"]["nEcho"]) * echo_time + d["t2"]["t2"]
        fl.plot(abs(d), "o-", markersize=2)


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

   **Total running time of the script:** (0 minutes 1.053 seconds)


.. _sphx_glr_download_auto_examples_proc_CPMG.py:

.. only:: html

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

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

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

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

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


.. only:: html

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

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