.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_gallery/mkh5mne/from_mkh5.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

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

        Click :ref:`here <sphx_glr_download_examples_gallery_mkh5mne_from_mkh5.py>`
        to download the full example code

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

.. _sphx_glr_examples_gallery_mkh5mne_from_mkh5.py:


Options for converting to mne.Raw
#################################

.. GENERATED FROM PYTHON SOURCE LINES 7-9

Set up
-------

.. GENERATED FROM PYTHON SOURCE LINES 9-22

.. code-block:: default

    import os
    import mne
    from mkpy import mkh5
    from mkpy.io import mkh5mne

    mne.viz.set_browser_backend("matplotlib")  # for docs generation

    # FYI
    conda_env = os.environ["CONDA_DEFAULT_ENV"]
    print("conda env", conda_env)
    for pkg in [mkh5, mne]:
        print(pkg.__name__, pkg.__version__)





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

 Out:

 .. code-block:: none

    conda env env_3.8
    mkpy.mkh5 0.2.7
    mne 1.0.3




.. GENERATED FROM PYTHON SOURCE LINES 23-28

mkh5 data file format in a nutshell
===================================
This sample mkh5 data is for a single subject in an auditory oddball paradigm with
previously set epoch tables.


.. GENERATED FROM PYTHON SOURCE LINES 28-31

.. code-block:: default

    H5_F = "../mkh5_data/sub000p3.h5"
    h5_data = mkh5.mkh5(H5_F)








.. GENERATED FROM PYTHON SOURCE LINES 32-35

Stimulus and response events of interest have been tagged with an mkh5 codemap and stored
as named epochs tables ``mkh5.set_epochs(...)``. The epochs tables are whatever was deemed
useful.

.. GENERATED FROM PYTHON SOURCE LINES 35-60

.. code-block:: default

    h5_data.get_epochs_table_names()

    # The epochs tables have index information about where to find the
    # events in the mkh5 file, the experimental variables from
    # the codemap, and the epoch discrete time interval specs, relative
    # to the current mkh5 datablock.
    epochs_table = h5_data.get_epochs_table("ms1500")
    epochs_table[
        [
            "epoch_id",
            "data_group",
            "dblock_path",  # HDF5 data lookup info
            "log_evcodes",
            "log_ccodes",
            "log_flags",  # event code info
            "tone",
            "stim",
            "accuracy",
            "acc_type",  # codemap tags
            "diti_t_0",
            "diti_hop",
            "diti_len",  # epoch t_0, offset, duration
        ]
    ]






.. raw:: html

    <div class="output_subarea output_html rendered_html output_result">
    <div>
    <style scoped>
        .dataframe tbody tr th:only-of-type {
            vertical-align: middle;
        }

        .dataframe tbody tr th {
            vertical-align: top;
        }

        .dataframe thead th {
            text-align: right;
        }
    </style>
    <table border="1" class="dataframe">
      <thead>
        <tr style="text-align: right;">
          <th></th>
          <th>epoch_id</th>
          <th>data_group</th>
          <th>dblock_path</th>
          <th>log_evcodes</th>
          <th>log_ccodes</th>
          <th>log_flags</th>
          <th>tone</th>
          <th>stim</th>
          <th>accuracy</th>
          <th>acc_type</th>
          <th>diti_t_0</th>
          <th>diti_hop</th>
          <th>diti_len</th>
        </tr>
      </thead>
      <tbody>
        <tr>
          <th>0</th>
          <td>0</td>
          <td>sub000</td>
          <td>sub000/dblock_0</td>
          <td>11</td>
          <td>1</td>
          <td>0</td>
          <td>hi</td>
          <td>target</td>
          <td>correct</td>
          <td>hit</td>
          <td>1468</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>1</th>
          <td>1</td>
          <td>sub000</td>
          <td>sub000/dblock_0</td>
          <td>11</td>
          <td>1</td>
          <td>0</td>
          <td>hi</td>
          <td>target</td>
          <td>correct</td>
          <td>hit</td>
          <td>2396</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>2</th>
          <td>2</td>
          <td>sub000</td>
          <td>sub000/dblock_0</td>
          <td>11</td>
          <td>1</td>
          <td>0</td>
          <td>hi</td>
          <td>target</td>
          <td>correct</td>
          <td>hit</td>
          <td>2943</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>3</th>
          <td>3</td>
          <td>sub000</td>
          <td>sub000/dblock_0</td>
          <td>11</td>
          <td>1</td>
          <td>0</td>
          <td>hi</td>
          <td>target</td>
          <td>correct</td>
          <td>hit</td>
          <td>3308</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>4</th>
          <td>4</td>
          <td>sub000</td>
          <td>sub000/dblock_0</td>
          <td>11</td>
          <td>1</td>
          <td>0</td>
          <td>hi</td>
          <td>target</td>
          <td>correct</td>
          <td>hit</td>
          <td>4574</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>...</th>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
          <td>...</td>
        </tr>
        <tr>
          <th>595</th>
          <td>596</td>
          <td>sub000</td>
          <td>sub000/dblock_4</td>
          <td>4</td>
          <td>0</td>
          <td>0</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>27315</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>596</th>
          <td>597</td>
          <td>sub000</td>
          <td>sub000/dblock_4</td>
          <td>2</td>
          <td>0</td>
          <td>0</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>27444</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>597</th>
          <td>598</td>
          <td>sub000</td>
          <td>sub000/dblock_4</td>
          <td>3</td>
          <td>0</td>
          <td>0</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>27573</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>598</th>
          <td>599</td>
          <td>sub000</td>
          <td>sub000/dblock_4</td>
          <td>4</td>
          <td>0</td>
          <td>0</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>27703</td>
          <td>-187</td>
          <td>375</td>
        </tr>
        <tr>
          <th>599</th>
          <td>600</td>
          <td>sub000</td>
          <td>sub000/dblock_4</td>
          <td>2</td>
          <td>0</td>
          <td>0</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>cal</td>
          <td>27832</td>
          <td>-187</td>
          <td>375</td>
        </tr>
      </tbody>
    </table>
    <p>600 rows × 13 columns</p>
    </div>
    </div>
    <br />
    <br />

.. GENERATED FROM PYTHON SOURCE LINES 61-63

The mkh5 EEG and event channel data are stored in datablocks (HDF5
Dataset) at the end of an HDF5 "slash" path:

.. GENERATED FROM PYTHON SOURCE LINES 64-67

.. code-block:: default

    h5_data.dblock_paths






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

 Out:

 .. code-block:: none


    ['sub000/dblock_0', 'sub000/dblock_1', 'sub000/dblock_2', 'sub000/dblock_3', 'sub000/dblock_4']



.. GENERATED FROM PYTHON SOURCE LINES 68-75

Electrode locations
===================

Converting mkh5 to mne.Raw **requires** an mkh5 format apparatus map
with the coordinate space, fiducal landmarks and electrode
locations. If the appartus map was included with the YAML .yhdr when
the mkh5 file was created it will be used automatically.

.. GENERATED FROM PYTHON SOURCE LINES 75-78

.. code-block:: default


    mne_raw = mkh5mne.from_mkh5(H5_F)





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

 Out:

 .. code-block:: none

    ../mkh5_data/sub000p3.h5
    looking up data block paths, larger files take longer ...
    ok
    checking info, montage sub000/dblock_1
    checking info, montage sub000/dblock_2
    checking info, montage sub000/dblock_3
    checking info, montage sub000/dblock_4
    Creating RawArray with float64 data, n_channels=39, n_times=31232
        Range : 0 ... 31231 =      0.000 ...   124.924 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
    Creating RawArray with float64 data, n_channels=39, n_times=32768
        Range : 0 ... 32767 =      0.000 ...   131.068 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
    Creating RawArray with float64 data, n_channels=39, n_times=31744
        Range : 0 ... 31743 =      0.000 ...   126.972 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
    Creating RawArray with float64 data, n_channels=39, n_times=32512
        Range : 0 ... 32511 =      0.000 ...   130.044 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
    Creating RawArray with float64 data, n_channels=39, n_times=28416
        Range : 0 ... 28415 =      0.000 ...   113.660 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
    EEG data marked as already having the desired reference.




.. GENERATED FROM PYTHON SOURCE LINES 79-84

This sample mkh5 data file was created with coordinates for an
idealized "average" head, based on 3D digitized
locations. Head-shaped locations are called for when working with
realistic head geometry in MNE but they don't line up exactly with
circular topographic maps.

.. GENERATED FROM PYTHON SOURCE LINES 85-87

.. code-block:: default

    _ = mne.viz.plot_sensors(mne_raw.info, sphere="auto")




.. image-sg:: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_001.png
   :alt: from mkh5
   :srcset: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_001.png
   :class: sphx-glr-single-img





.. GENERATED FROM PYTHON SOURCE LINES 88-96

If original .yhdr did not include an apparatus map or a different
set of locations is preferred, they can be specified when converting
to MNE and used instead.

This map overrides the original head-shaped electrode locations with
spherical 3D coordinates which are unrealistic as human head
geometry but line up neatly with circles for painting pretty 2D
pictures.

.. GENERATED FROM PYTHON SOURCE LINES 97-102

.. code-block:: default


    mne_raw_a = mkh5mne.from_mkh5(H5_F, apparatus_yaml="mne_32chan_xyz_spherical.yml")
    _ = mne.viz.plot_sensors(mne_raw_a.info)





.. image-sg:: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_002.png
   :alt: from mkh5
   :srcset: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_002.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    ../mkh5_data/sub000p3.h5
    looking up data block paths, larger files take longer ...
    ok
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    checking info, montage sub000/dblock_1
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    checking info, montage sub000/dblock_2
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    checking info, montage sub000/dblock_3
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    checking info, montage sub000/dblock_4
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_0 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    Creating RawArray with float64 data, n_channels=39, n_times=31232
        Range : 0 ... 31231 =      0.000 ...   124.924 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
    ['HEOG']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_1 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    Creating RawArray with float64 data, n_channels=39, n_times=32768
        Range : 0 ... 32767 =      0.000 ...   131.068 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
    ['HEOG']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_2 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    Creating RawArray with float64 data, n_channels=39, n_times=31744
        Range : 0 ... 31743 =      0.000 ...   126.972 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
    ['HEOG']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_3 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    Creating RawArray with float64 data, n_channels=39, n_times=32512
        Range : 0 ... 32511 =      0.000 ...   130.044 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
    ['HEOG']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1190: UserWarning: Overriding /sub000/dblock_4 with sensor locations from mne_32chan_xyz_spherical.yml
      warnings.warn(msg)
    Creating RawArray with float64 data, n_channels=39, n_times=28416
        Range : 0 ... 28415 =      0.000 ...   113.660 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting position of 1 eog channel found in montage:
    ['HEOG']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
    EEG data marked as already having the desired reference.




.. GENERATED FROM PYTHON SOURCE LINES 103-115

Selecting which datablocks to convert to mne.Raw
================================================

By default :py:meth:`.read_raw_mkh5` converts the entire mkh5 file.
The mkh5 data groups and EEG datablocks are appended in the order
order returned by :py:meth:`.dblock_paths` which sorts HDF5 the HDF5
paths to data group alphabetically and preserves data block order
within each group.

An mkh5 file might have multiple subjects or experiments, if
you don't want to make it all one mne.Raw object, you can
 select which data blocks to convert with ``datablock_paths=``.

.. GENERATED FROM PYTHON SOURCE LINES 115-123

.. code-block:: default

    mne_raw_b = mkh5mne.read_raw_mkh5(
        H5_F, dblock_paths=["sub000/dblock_0", "sub000/dblock_1"]
    )

    # only dblock_0 and dblock_1 appear in the Raw data
    mne_raw_b.annotations.description






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

 Out:

 .. code-block:: none

    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1688: UserWarning: mkh5mne.read_raw_mkh5() is deprecated and will be removed in a future release, use mkh5mn3.from_mkh5() instead
      warnings.warn(
    ok
    checking info, montage sub000/dblock_1
    Creating RawArray with float64 data, n_channels=39, n_times=31232
        Range : 0 ... 31231 =      0.000 ...   124.924 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
    Creating RawArray with float64 data, n_channels=39, n_times=32768
        Range : 0 ... 32767 =      0.000 ...   131.068 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
    EEG data marked as already having the desired reference.

    array(['sub000/dblock_0', 'sub000/dblock_1', 'BAD boundary',
           'EDGE boundary'], dtype='<U15')



.. GENERATED FROM PYTHON SOURCE LINES 124-131

Marking garv artifacts in mne.Raw
----------------------------------

If you prepared the mkh5 file with the .log file log_flags set to
track garv artifacts (``avg -x``) you can automatically mark the
garv artifacts in the mne.Raw with BAD_garv mne.Annotations by
passing in the ``garv_annotations`` options.

.. GENERATED FROM PYTHON SOURCE LINES 131-143

.. code-block:: default


    # Mark *all* the log stim and response events events with lots of overlap
    mne_raw_c = mkh5mne.from_mkh5(
        H5_F,
        garv_annotations={
            "event_channel": "log_flags",
            "tmin": -500,
            "tmax": 1000,
            "units": "ms",
        },
    )





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

 Out:

 .. code-block:: none

    ../mkh5_data/sub000p3.h5
    looking up data block paths, larger files take longer ...
    ok
    checking info, montage sub000/dblock_1
    checking info, montage sub000/dblock_2
    checking info, montage sub000/dblock_3
    checking info, montage sub000/dblock_4
    Creating RawArray with float64 data, n_channels=39, n_times=31232
        Range : 0 ... 31231 =      0.000 ...   124.924 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'log_flags', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=32768
        Range : 0 ... 32767 =      0.000 ...   131.068 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'log_flags', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=31744
        Range : 0 ... 31743 =      0.000 ...   126.972 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'log_flags', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=32512
        Range : 0 ... 32511 =      0.000 ...   130.044 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'log_flags', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=28416
        Range : 0 ... 28415 =      0.000 ...   113.660 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'log_flags', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    EEG data marked as already having the desired reference.




.. GENERATED FROM PYTHON SOURCE LINES 144-148

.. note::

   ``avg -x`` flags **all** event codes in the log that fail a test whether or
   not these are the timelocking events of interest.

.. GENERATED FROM PYTHON SOURCE LINES 150-157

annotation intervals for log events upstream or downstream of the
timelock of interest may overlap the epoch interval and
``mne.Epochs(..., reject_by_annotation=True)`` will exclude them for
being (partially) polluted. To avoid this, define your mkh5 codemap
and named epochs table so that epochs of interest do not overlap and
use that same-named MNE event channel to set the garv annoations
like so:

.. GENERATED FROM PYTHON SOURCE LINES 157-170

.. code-block:: default


    mne_raw_c = mkh5mne.from_mkh5(
        H5_F,
        garv_annotations={
            "event_channel": "ms1500",
            "tmin": -500,
            "tmax": 1000,
            "units": "ms",
        },
    )


    mne_raw_c.plot(scalings={"eeg": 5e-5, "eog": 1e-4}, start=10.0, n_channels=39)



.. image-sg:: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_003.png
   :alt: from mkh5
   :srcset: /examples_gallery/mkh5mne/images/sphx_glr_from_mkh5_003.png
   :class: sphx-glr-single-img


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

 Out:

 .. code-block:: none

    ../mkh5_data/sub000p3.h5
    looking up data block paths, larger files take longer ...
    ok
    checking info, montage sub000/dblock_1
    checking info, montage sub000/dblock_2
    checking info, montage sub000/dblock_3
    checking info, montage sub000/dblock_4
    Creating RawArray with float64 data, n_channels=39, n_times=31232
        Range : 0 ... 31231 =      0.000 ...   124.924 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_0 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_0 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=32768
        Range : 0 ... 32767 =      0.000 ...   131.068 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_1 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_1 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=31744
        Range : 0 ... 31743 =      0.000 ...   126.972 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_2 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_2 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=32512
        Range : 0 ... 32511 =      0.000 ...   130.044 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_3 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_3 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    Creating RawArray with float64 data, n_channels=39, n_times=28416
        Range : 0 ... 28415 =      0.000 ...   113.660 secs
    Ready.
    /usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/io/mkh5mne.py:1478: RuntimeWarning: Not setting positions of 5 eog channels found in montage:
    ['lle', 'lhz', 'HEOG', 'rle', 'rhz']
    Consider setting the channel types to be of EEG/sEEG/ECoG/DBS/fNIRS using inst.set_channel_types before calling inst.set_montage, or omit these channels when creating your montage.
      raw_dblock.set_montage(montage)
    sub000/dblock_4 setting mkh5 epochs table ms100 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms10000 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms1500 events and metadata
    sub000/dblock_4 setting mkh5 epochs table ms3000 events and metadata
    annotating garv artifacts {'event_channel': 'ms1500', 'tmin': -500, 'tmax': 1000, 'units': 'ms'}
    EEG data marked as already having the desired reference.
    Opening raw-browser...

    <MNEBrowseFigure size 800x800 with 4 Axes>




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

   **Total running time of the script:** ( 1 minutes  28.220 seconds)


.. _sphx_glr_download_examples_gallery_mkh5mne_from_mkh5.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: from_mkh5.py <from_mkh5.py>`



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

     :download:`Download Jupyter notebook: from_mkh5.ipynb <from_mkh5.ipynb>`


.. only:: html

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

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