Note
Click here to download the full example code
Make an MNE-Report with a Slider¶
In this example, MEG evoked data are plotted in an HTML slider.
# Authors: Teon Brooks <teon.brooks@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
from mne.report import Report
from mne.datasets import sample
from mne import read_evokeds
from matplotlib import pyplot as plt
data_path = sample.data_path()
meg_path = data_path + '/MEG/sample'
subjects_dir = data_path + '/subjects'
evoked_fname = meg_path + '/sample_audvis-ave.fif'
Do standard folder parsing (this can take a couple of minutes):
report = Report(image_format='png', subjects_dir=subjects_dir,
info_fname=evoked_fname, subject='sample',
raw_psd=False) # use False for speed here
report.parse_folder(meg_path, on_error='ignore', mri_decim=10)
Out:
Embedding : jquery.js
Embedding : jquery-ui.min.js
Embedding : bootstrap.min.js
Embedding : jquery-ui.min.css
Embedding : bootstrap.min.css
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
Read a total of 4 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Average EEG reference (1 x 60) idle
Range : 6450 ... 48149 = 42.956 ... 320.665 secs
Ready.
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Iterating over 30 potential files (this may take some time)
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/all-trans.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise-cov.fif
306 x 306 full covariance (kind = 1) found.
Read a total of 3 projection items:
PCA-v1 (1 x 102) active
PCA-v2 (1 x 102) active
PCA-v3 (1 x 102) active
Computing rank from covariance with rank=None
Using tolerance 9.9e-16 (2.2e-16 eps * 102 dim * 0.044 max singular value)
Estimated rank (mag): 102
MAG: rank 102 computed from 102 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 8.8e-14 (2.2e-16 eps * 203 dim * 2 max singular value)
Estimated rank (grad): 203
GRAD: rank 203 computed from 203 data channels with 0 projectors
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise_raw-eve.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/ernoise_raw.fif...
Isotrak not found
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 19800 ... 85867 = 32.966 ... 142.965 secs
Ready.
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-ave.fif
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Multiple channel types selected, returning one figure per type.
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-cov.fif
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
Computing rank from covariance with rank=None
Using tolerance 2.5e-14 (2.2e-16 eps * 102 dim * 1.1 max singular value)
Estimated rank (mag): 102
MAG: rank 102 computed from 102 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 1.8e-13 (2.2e-16 eps * 203 dim * 3.9 max singular value)
Estimated rank (grad): 203
GRAD: rank 203 computed from 203 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 4.7e-14 (2.2e-16 eps * 59 dim * 3.6 max singular value)
Estimated rank (eeg): 59
EEG: rank 59 computed from 59 data channels with 0 projectors
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6-eeg-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6-eeg-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
59 x 59 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
Noise covariance matrix read.
22494 x 22494 diagonal covariance (kind = 2) found.
Source covariance matrix read.
22494 x 22494 diagonal covariance (kind = 6) found.
Orientation priors read.
22494 x 22494 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6-fwd.fif
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6-fwd.fif...
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
Desired named matrix (kind = 3523) not available
Read EEG forward solution (7498 sources, 60 channels, free orientations)
Source spaces transformed to the forward solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6p-fwd.fif
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-eeg-oct-6p-fwd.fif...
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-fwd.fif...
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
Desired named matrix (kind = 3523) not available
Read MEG forward solution (7498 sources, 306 channels, free orientations)
Desired named matrix (kind = 3523) not available
Read EEG forward solution (7498 sources, 60 channels, free orientations)
MEG and EEG forward solutions combined
Source spaces transformed to the forward solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-diagnoise-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-diagnoise-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
364 x 364 diagonal 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
Noise covariance matrix read.
22494 x 22494 diagonal covariance (kind = 2) found.
Source covariance matrix read.
22494 x 22494 diagonal covariance (kind = 6) found.
Orientation priors read.
22494 x 22494 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
364 x 364 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
Noise covariance matrix read.
22494 x 22494 diagonal covariance (kind = 2) found.
Source covariance matrix read.
22494 x 22494 diagonal covariance (kind = 6) found.
Orientation priors read.
22494 x 22494 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-fwd.fif
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-fwd.fif...
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
Desired named matrix (kind = 3523) not available
Read MEG forward solution (7498 sources, 306 channels, free orientations)
Source spaces transformed to the forward solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-diagnoise-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-diagnoise-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
305 x 305 diagonal 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
Noise covariance matrix read.
22494 x 22494 diagonal covariance (kind = 2) found.
Source covariance matrix read.
22494 x 22494 diagonal covariance (kind = 6) found.
Orientation priors read.
22494 x 22494 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-fixed-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-fixed-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
305 x 305 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
Noise covariance matrix read.
7498 x 7498 diagonal covariance (kind = 2) found.
Source covariance matrix read.
Did not find the desired covariance matrix (kind = 6)
7498 x 7498 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
305 x 305 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
Noise covariance matrix read.
22494 x 22494 diagonal covariance (kind = 2) found.
Source covariance matrix read.
22494 x 22494 diagonal covariance (kind = 6) found.
Orientation priors read.
22494 x 22494 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
305 x 305 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
Noise covariance matrix read.
7498 x 7498 diagonal covariance (kind = 2) found.
Source covariance matrix read.
Did not find the desired covariance matrix (kind = 6)
Did not find the desired covariance matrix (kind = 5)
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
Reading a source space...
Computing patch statistics...
Patch information added...
Distance information added...
[done]
2 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-fwd.fif
Reading forward solution from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-fwd.fif...
Reading a source space...
[done]
1 source spaces read
Desired named matrix (kind = 3523) not available
Read MEG forward solution (3757 sources, 306 channels, free orientations)
Source spaces transformed to the forward solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif
Reading inverse operator decomposition from /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-meg-vol-7-meg-inv.fif...
Reading inverse operator info...
[done]
Reading inverse operator decomposition...
[done]
305 x 305 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
Noise covariance matrix read.
11271 x 11271 diagonal covariance (kind = 2) found.
Source covariance matrix read.
Did not find the desired covariance matrix (kind = 6)
11271 x 11271 diagonal covariance (kind = 5) found.
Depth priors read.
Did not find the desired covariance matrix (kind = 3)
Reading a source space...
[done]
1 source spaces read
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
Source spaces transformed to the inverse solution coordinate frame
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-no-filter-ave.fif
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | PCA-v1, active : True, n_channels : 102>
Removing projector <Projection | PCA-v2, active : True, n_channels : 102>
Removing projector <Projection | PCA-v3, active : True, n_channels : 102>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Multiple channel types selected, returning one figure per type.
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
combining channels using "gfp"
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis-shrunk-cov.fif
365 x 365 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 59) active
Computing rank from covariance with rank=None
Using tolerance 2.8e-14 (2.2e-16 eps * 102 dim * 1.2 max singular value)
Estimated rank (mag): 102
MAG: rank 102 computed from 102 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 1.9e-13 (2.2e-16 eps * 203 dim * 4.2 max singular value)
Estimated rank (grad): 203
GRAD: rank 203 computed from 203 data channels with 0 projectors
Computing rank from covariance with rank=None
Using tolerance 1.1e-13 (2.2e-16 eps * 59 dim * 8.7 max singular value)
Estimated rank (eeg): 59
EEG: rank 59 computed from 59 data channels with 0 projectors
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_ecg-eve.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_ecg-proj.fif
Read a total of 6 projection items:
ECG-planar-999--0.200-0.400-PCA-01 (1 x 203) idle
ECG-planar-999--0.200-0.400-PCA-02 (1 x 203) idle
ECG-axial-999--0.200-0.400-PCA-01 (1 x 102) idle
ECG-axial-999--0.200-0.400-PCA-02 (1 x 102) idle
ECG-eeg-999--0.200-0.400-PCA-01 (1 x 59) idle
ECG-eeg-999--0.200-0.400-PCA-02 (1 x 59) idle
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_eog-eve.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_eog-proj.fif
Read a total of 6 projection items:
EOG-planar-998--0.200-0.200-PCA-01 (1 x 203) idle
EOG-planar-998--0.200-0.200-PCA-02 (1 x 203) idle
EOG-axial-998--0.200-0.200-PCA-01 (1 x 102) idle
EOG-axial-998--0.200-0.200-PCA-02 (1 x 102) idle
EOG-eeg-998--0.200-0.200-PCA-01 (1 x 59) idle
EOG-eeg-998--0.200-0.200-PCA-02 (1 x 59) idle
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw-eve.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_filt-0-40_raw.fif...
Read a total of 4 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Average EEG reference (1 x 60) idle
Range : 6450 ... 48149 = 42.956 ... 320.665 secs
Ready.
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw-eve.fif
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw-trans.fif
Using outer_skin.surf for head surface.
Getting helmet for system 306m
Rendering : /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif
Opening raw data file /home/circleci/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif...
Read a total of 3 projection items:
PCA-v1 (1 x 102) idle
PCA-v2 (1 x 102) idle
PCA-v3 (1 x 102) idle
Range : 25800 ... 192599 = 42.956 ... 320.670 secs
Ready.
Rendering BEM
Using surface: /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/inner_skull.surf
Using surface: /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/outer_skull.surf
Using surface: /home/circleci/mne_data/MNE-sample-data/subjects/sample/bem/outer_skin.surf
Add a custom section with an evoked slider:
# Load the evoked data
evoked = read_evokeds(evoked_fname, condition='Left Auditory',
baseline=(None, 0), verbose=False)
evoked.crop(0, .2)
times = evoked.times[::4]
# Create a list of figs for the slider
figs = list()
for t in times:
figs.append(evoked.plot_topomap(t, vmin=-300, vmax=300, res=100,
show=False))
plt.close(figs[-1])
report.add_slider_to_section(figs, times, 'Evoked Response',
image_format='png') # can also use 'svg'
# Save the report
report.save('my_report.html', overwrite=True)
The HTML document written by mne.Report.save():
Out:
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Removing projector <Projection | Average EEG reference, active : True, n_channels : 60>
Saving report to location /home/circleci/project/examples/visualization/my_report.html
Rendering : Table of Contents
covariance
... ernoise-cov.fif
... sample_audvis-cov.fif
... sample_audvis-shrunk-cov.fif
events
... ernoise_raw-eve.fif
... sample_audvis_ecg-eve.fif
... sample_audvis_eog-eve.fif
... sample_audvis_filt-0-40_raw-eve.fif
... sample_audvis_raw-eve.fif
evoked
... sample_audvis-ave.fif
... sample_audvis-no-filter-ave.fif
forward
... sample_audvis-eeg-oct-6-fwd.fif
... sample_audvis-meg-eeg-oct-6-fwd.fif
... sample_audvis-meg-oct-6-fwd.fif
... sample_audvis-meg-vol-7-fwd.fif
inverse
... sample_audvis-eeg-oct-6-eeg-inv.fif
... sample_audvis-meg-eeg-oct-6-meg-eeg-diagnoise-inv.fif
... sample_audvis-meg-eeg-oct-6-meg-eeg-inv.fif
... sample_audvis-meg-oct-6-meg-diagnoise-inv.fif
... sample_audvis-meg-oct-6-meg-fixed-inv.fif
... sample_audvis-meg-oct-6-meg-inv.fif
... sample_audvis-meg-oct-6-meg-nodepth-fixed-inv.fif
... sample_audvis-meg-vol-7-meg-inv.fif
raw
... ernoise_raw.fif
... sample_audvis_filt-0-40_raw.fif
... sample_audvis_raw.fif
ssp
... sample_audvis_ecg-proj.fif
... sample_audvis_eog-proj.fif
trans
... sample_audvis_raw-trans.fif
bem
... bem
Evoked Response
... BEM
Total running time of the script: ( 0 minutes 46.523 seconds)
Estimated memory usage: 254 MB