.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "auto_examples/plot_load_save_datasets.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
Click :ref:`here <sphx_glr_download_auto_examples_plot_load_save_datasets.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr_auto_examples_plot_load_save_datasets.py:
Load and save dataset example
=============================
In this example, we show how to load and save braindecode datasets.
.. GENERATED FROM PYTHON SOURCE LINES 7-20
.. code-block:: default
# Authors: Lukas Gemein <l.gemein@gmail.com>
#
# License: BSD (3-clause)
import tempfile
from braindecode.datasets import MOABBDataset
from braindecode.preprocessing import preprocess, Preprocessor
from braindecode.datautil import load_concat_dataset
from braindecode.preprocessing import create_windows_from_events
.. GENERATED FROM PYTHON SOURCE LINES 21-22
First, we load some dataset using MOABB.
.. GENERATED FROM PYTHON SOURCE LINES 22-27
.. code-block:: default
dataset = MOABBDataset(
dataset_name='BNCI2014001',
subject_ids=[1],
)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
.. GENERATED FROM PYTHON SOURCE LINES 28-30
We can apply preprocessing steps to the dataset. It is also possible to skip
this step and not apply any preprocessing.
.. GENERATED FROM PYTHON SOURCE LINES 30-35
.. code-block:: default
preprocess(
concat_ds=dataset,
preprocessors=[Preprocessor(fn='resample', sfreq=10)]
)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
48 events found
Event IDs: [1 2 3 4]
<braindecode.datasets.moabb.MOABBDataset object at 0x7f748ee50850>
.. GENERATED FROM PYTHON SOURCE LINES 36-42
We save the dataset to a an existing directory. It will create a '.fif' file
for every dataset in the concat dataset. Additionally it will create two
JSON files, the first holding the description of the dataset, the second
holding the name of the target. If you want to store to the same directory
several times, for example due to trying different preprocessing, you can
choose to overwrite the existing files.
.. GENERATED FROM PYTHON SOURCE LINES 42-49
.. code-block:: default
tmpdir = tempfile.mkdtemp() # write in a temporary directory
dataset.save(
path=tmpdir,
overwrite=False,
)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Writing /tmp/tmp4_0_urks/0/0-raw.fif
Closing /tmp/tmp4_0_urks/0/0-raw.fif
[done]
Writing /tmp/tmp4_0_urks/1/1-raw.fif
Closing /tmp/tmp4_0_urks/1/1-raw.fif
[done]
Writing /tmp/tmp4_0_urks/2/2-raw.fif
Closing /tmp/tmp4_0_urks/2/2-raw.fif
[done]
Writing /tmp/tmp4_0_urks/3/3-raw.fif
Closing /tmp/tmp4_0_urks/3/3-raw.fif
[done]
Writing /tmp/tmp4_0_urks/4/4-raw.fif
Closing /tmp/tmp4_0_urks/4/4-raw.fif
[done]
Writing /tmp/tmp4_0_urks/5/5-raw.fif
Closing /tmp/tmp4_0_urks/5/5-raw.fif
[done]
Writing /tmp/tmp4_0_urks/6/6-raw.fif
Closing /tmp/tmp4_0_urks/6/6-raw.fif
[done]
Writing /tmp/tmp4_0_urks/7/7-raw.fif
Closing /tmp/tmp4_0_urks/7/7-raw.fif
[done]
Writing /tmp/tmp4_0_urks/8/8-raw.fif
Closing /tmp/tmp4_0_urks/8/8-raw.fif
[done]
Writing /tmp/tmp4_0_urks/9/9-raw.fif
Closing /tmp/tmp4_0_urks/9/9-raw.fif
[done]
Writing /tmp/tmp4_0_urks/10/10-raw.fif
Closing /tmp/tmp4_0_urks/10/10-raw.fif
[done]
Writing /tmp/tmp4_0_urks/11/11-raw.fif
Closing /tmp/tmp4_0_urks/11/11-raw.fif
[done]
.. GENERATED FROM PYTHON SOURCE LINES 50-56
We load the saved dataset from a directory. Signals can be preloaded in
compliance with mne. Optionally, only specific '.fif' files can be loaded
by specifying their ids. The target name can be changed, if the dataset
supports it (TUHAbnormal for example supports 'pathological', 'age', and
'gender'. If you stored a preprocessed version with target 'pathological'
it is possible to change the target upon loading).
.. GENERATED FROM PYTHON SOURCE LINES 56-63
.. code-block:: default
dataset_loaded = load_concat_dataset(
path=tmpdir,
preload=True,
ids_to_load=[1, 3],
target_name=None,
)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Opening raw data file /tmp/tmp4_0_urks/1/1-raw.fif...
Range : 0 ... 3868 = 0.000 ... 386.800 secs
Ready.
Reading 0 ... 3868 = 0.000 ... 386.800 secs...
Opening raw data file /tmp/tmp4_0_urks/3/3-raw.fif...
Range : 0 ... 3868 = 0.000 ... 386.800 secs
Ready.
Reading 0 ... 3868 = 0.000 ... 386.800 secs...
.. GENERATED FROM PYTHON SOURCE LINES 64-66
The serialization utility also supports WindowsDatasets, so we create
compute windows next.
.. GENERATED FROM PYTHON SOURCE LINES 66-74
.. code-block:: default
windows_dataset = create_windows_from_events(
concat_ds=dataset_loaded,
trial_start_offset_samples=0,
trial_stop_offset_samples=0,
)
windows_dataset.description
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Used Annotations descriptions: ['feet', 'left_hand', 'right_hand', 'tongue']
Adding metadata with 4 columns
Replacing existing metadata with 4 columns
48 matching events found
No baseline correction applied
0 projection items activated
Loading data for 48 events and 40 original time points ...
0 bad epochs dropped
Used Annotations descriptions: ['feet', 'left_hand', 'right_hand', 'tongue']
Adding metadata with 4 columns
Replacing existing metadata with 4 columns
48 matching events found
No baseline correction applied
0 projection items activated
Loading data for 48 events and 40 original time points ...
0 bad epochs dropped
.. 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>subject</th>
<th>session</th>
<th>run</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>1</td>
<td>session_T</td>
<td>run_1</td>
</tr>
<tr>
<th>1</th>
<td>1</td>
<td>session_T</td>
<td>run_3</td>
</tr>
</tbody>
</table>
</div>
</div>
<br />
<br />
.. GENERATED FROM PYTHON SOURCE LINES 75-81
Again, we save the dataset to an existing directory. It will create a
'-epo.fif' file for every dataset in the concat dataset. Additionally it
will create a JSON file holding the description of the dataset. If you
want to store to the same directory several times, for example due to
trying different windowing parameters, you can choose to overwrite the
existing files.
.. GENERATED FROM PYTHON SOURCE LINES 81-86
.. code-block:: default
windows_dataset.save(
path=tmpdir,
overwrite=True,
)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Loading data for 1 events and 40 original time points ...
Loading data for 48 events and 40 original time points ...
Loading data for 1 events and 40 original time points ...
Loading data for 48 events and 40 original time points ...
/home/runner/work/braindecode/braindecode/braindecode/datasets/base.py:569: UserWarning: The number of saved datasets (2) does not match the number of existing subdirectories (12). You may now encounter a mix of differently preprocessed datasets!
f"datasets!", UserWarning)
/home/runner/work/braindecode/braindecode/braindecode/datasets/base.py:573: UserWarning: Chosen directory /tmp/tmp4_0_urks contains other subdirectories or files ['10', '8', '5', '7', '3', '11', '6', '2', '4', '9'].
warnings.warn(f'Chosen directory {path} contains other '
.. GENERATED FROM PYTHON SOURCE LINES 87-90
Load the saved dataset from a directory. Signals can be preloaded in
compliance with mne. Optionally, only specific '-epo.fif' files can be
loaded by specifying their ids.
.. GENERATED FROM PYTHON SOURCE LINES 90-98
.. code-block:: default
windows_dataset_loaded = load_concat_dataset(
path=tmpdir,
preload=False,
ids_to_load=[0],
target_name=None,
)
windows_dataset_loaded.description
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Reading /tmp/tmp4_0_urks/0/0-epo.fif ...
Found the data of interest:
t = 0.00 ... 3900.00 ms
0 CTF compensation matrices available
Adding metadata with 4 columns
Replacing existing metadata with 4 columns
48 matching events found
No baseline correction applied
0 projection items activated
.. 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>subject</th>
<th>session</th>
<th>run</th>
</tr>
</thead>
<tbody>
<tr>
<th>0</th>
<td>1</td>
<td>session_T</td>
<td>run_1</td>
</tr>
</tbody>
</table>
</div>
</div>
<br />
<br />
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 4.979 seconds)
**Estimated memory usage:** 408 MB
.. _sphx_glr_download_auto_examples_plot_load_save_datasets.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: plot_load_save_datasets.py <plot_load_save_datasets.py>`
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: plot_load_save_datasets.ipynb <plot_load_save_datasets.ipynb>`
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_