Reading/Writing a noise covariance matrix¶

Plot a noise covariance matrix.

# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)

from os import path as op
import mne
from mne.datasets import sample

print(__doc__)

data_path = sample.data_path()
fname_cov = op.join(data_path, 'MEG', 'sample', 'sample_audvis-cov.fif')
fname_evo = op.join(data_path, 'MEG', 'sample', 'sample_audvis-ave.fif')

cov = mne.read_cov(fname_cov)
print(cov)
evoked = mne.read_evokeds(fname_evo)[0]

Out:

366 x 366 full covariance (kind = 1) found.
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
<Covariance  |  size : 366 x 366, n_samples : 15972, data : [[  2.27235589e-23   4.79818505e-24   7.12852747e-25 ...,   4.85348042e-18
    2.02846360e-18   8.26727393e-18]
 [  4.79818505e-24   5.33468523e-24   1.80261790e-25 ...,   2.33583009e-19
   -6.93161055e-19   2.35199238e-18]
 [  7.12852747e-25   1.80261790e-25   5.79073915e-26 ...,   1.09498615e-19
    6.16924072e-21   2.93873875e-19]
 ...,
 [  4.85348042e-18   2.33583009e-19   1.09498615e-19 ...,   1.40677185e-11
    1.27444183e-11   1.08634620e-11]
 [  2.02846360e-18  -6.93161055e-19   6.16924072e-21 ...,   1.27444183e-11
    1.59818134e-11   8.51070563e-12]
 [  8.26727393e-18   2.35199238e-18   2.93873875e-19 ...,   1.08634620e-11
    8.51070563e-12   1.53708918e-11]]>
Reading /home/ubuntu/mne_data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif ...
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Found the data of interest:
        t =    -199.80 ...     499.49 ms (Left Auditory)
        0 CTF compensation matrices available
        nave = 55 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
No baseline correction applied
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Found the data of interest:
        t =    -199.80 ...     499.49 ms (Right Auditory)
        0 CTF compensation matrices available
        nave = 61 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
No baseline correction applied
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Found the data of interest:
        t =    -199.80 ...     499.49 ms (Left visual)
        0 CTF compensation matrices available
        nave = 67 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
No baseline correction applied
    Read a total of 4 projection items:
        PCA-v1 (1 x 102) active
        PCA-v2 (1 x 102) active
        PCA-v3 (1 x 102) active
        Average EEG reference (1 x 60) active
    Found the data of interest:
        t =    -199.80 ...     499.49 ms (Right visual)
        0 CTF compensation matrices available
        nave = 58 - aspect type = 100
Projections have already been applied. Setting proj attribute to True.
No baseline correction applied

Show covariance

cov.plot(evoked.info, exclude='bads', show_svd=False)

../../_images/sphx_glr_plot_read_noise_covariance_matrix_001.png

Total running time of the script: ( 0 minutes 0.676 seconds)

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