.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_gallery/mkh5/append_cals.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_examples_gallery_mkh5_append_cals.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_mkh5_append_cals.py:


append separate cals
====================

.. GENERATED FROM PYTHON SOURCE LINES 7-9

Set up
-------

.. GENERATED FROM PYTHON SOURCE LINES 9-18

.. code-block:: default


    from pathlib import Path
    from matplotlib import pyplot as plt  # for inspecting cal pulses
    from mkpy import mkh5

    MKDIG_PATH = Path("../mkdig_data")

    print("mkpy version", mkh5.__version__)





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

 Out:

 .. code-block:: none

    mkpy version 0.2.7




.. GENERATED FROM PYTHON SOURCE LINES 19-25

Create subject, append cals
---------------------------

Use :meth:`mkh5.append_mkdata()<mkpy.mkh5.mkh5.append_mkdata>` to
combine EEG recordings  and separately recorded calibration data in
a single .h5 file prior to converting A/D samples to :math:`\mu` V.

.. GENERATED FROM PYTHON SOURCE LINES 28-29

Set EEG and calibration data file names

.. GENERATED FROM PYTHON SOURCE LINES 29-37

.. code-block:: default

    crw = MKDIG_PATH / "sub000p3.crw"  # EEG recording
    log = MKDIG_PATH / "sub000p3.x.log"  # events
    yhdr = MKDIG_PATH / "sub000p3.yhdr"  # extra header info

    cals_crw = MKDIG_PATH / "sub000c.crw"
    cals_log = MKDIG_PATH / "sub000c.log"
    cals_yhdr = MKDIG_PATH / "sub000c.yhdr"








.. GENERATED FROM PYTHON SOURCE LINES 38-39

Convert .crw/.log to mkh5 format .h5.

.. GENERATED FROM PYTHON SOURCE LINES 39-44

.. code-block:: default

    p3_h5_f = "example_sub000p3.h5"
    p3_h5 = mkh5.mkh5(p3_h5_f)
    p3_h5.reset_all()
    p3_h5.create_mkdata("sub000", crw, log, yhdr)








.. GENERATED FROM PYTHON SOURCE LINES 45-46

Append calibration data to the existing ``sub000``.

.. GENERATED FROM PYTHON SOURCE LINES 46-48

.. code-block:: default

    p3_h5.append_mkdata("sub000", cals_crw, cals_log, cals_yhdr)








.. GENERATED FROM PYTHON SOURCE LINES 49-51

Convert EEG and calibration data A/D to microvolts.
set re-usable calibration parameters

.. GENERATED FROM PYTHON SOURCE LINES 51-59

.. code-block:: default

    cal_kws = dict(
        n_points=5,  # samples to average
        cal_size=10,  # uV
        lo_cursor=-36,  # lo_cursor ms
        hi_cursor=48,  # hi_cursor ms
        cal_ccode=0,  # condition code
    )








.. GENERATED FROM PYTHON SOURCE LINES 60-61

inspect the calibration pulses

.. GENERATED FROM PYTHON SOURCE LINES 61-64

.. code-block:: default

    f, ax = p3_h5.plotcals(p3_h5_f, "sub000", **cal_kws)
    plt.show()




.. image-sg:: /examples_gallery/mkh5/images/sphx_glr_append_cals_001.png
   :alt: calibration pulses (recorded N=209) from: example_sub000p3.h5 sub000 n_points=5 cal_size=10 lo_cursor=-36 hi_cursor=48 cal_ccode=0, scale=17.63, trimmed 4, scale=20.30, trimmed 6, scale=20.05, trimmed 2, scale=20.79, trimmed 5, scale=20.57, trimmed 2, scale=40.10, trimmed 5, scale=39.59, trimmed 9, scale=40.74, trimmed 25, scale=40.41, trimmed 12, scale=39.97, trimmed 5, scale=38.81, trimmed 16, scale=35.54, trimmed 12, scale=36.47, trimmed 6, scale=40.55, trimmed 10, scale=37.84, trimmed 13, scale=39.66, trimmed 9, scale=42.00, trimmed 11, scale=39.58, trimmed 7, scale=41.42, trimmed 5, scale=40.46, trimmed 18, scale=40.05, trimmed 22, scale=40.76, trimmed 12, scale=40.66, trimmed 3, scale=39.91, trimmed 13, scale=40.58, trimmed 12, scale=40.35, trimmed 14, scale=40.75, trimmed 21, scale=41.24, trimmed 12, scale=40.69, trimmed 8, scale=40.91, trimmed 8, scale=20.56, trimmed 23, scale=20.64, trimmed 10
   :srcset: /examples_gallery/mkh5/images/sphx_glr_append_cals_001.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    Plotting cals
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/mkh5.py:3666: UserWarning: negative event code(s) found for cal condition code 0 -16384
      warnings.warn(msg)
    Found cals in /sub000/dblock_4




.. GENERATED FROM PYTHON SOURCE LINES 65-66

Convert EEG and calibration data A/D to microvolts.

.. GENERATED FROM PYTHON SOURCE LINES 66-67

.. code-block:: default

    p3_h5.calibrate_mkdata("sub000", **cal_kws)




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

 Out:

 .. code-block:: none

    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/mkh5.py:3666: UserWarning: negative event code(s) found for cal condition code 0 -16384
      warnings.warn(msg)
    Found cals in /sub000/dblock_4
    Calibrating block /sub000/dblock_0 of 5: (31232,)  
    Calibrating block /sub000/dblock_1 of 5: (32768,)  
    Calibrating block /sub000/dblock_2 of 5: (31744,)  
    Calibrating block /sub000/dblock_3 of 5: (32512,)  
    Calibrating block /sub000/dblock_4 of 5: (28416,)  





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

   **Total running time of the script:** ( 0 minutes  6.914 seconds)


.. _sphx_glr_download_examples_gallery_mkh5_append_cals.py:


.. only :: html

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



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

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



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

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


.. only:: html

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

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