diff --git a/dev/.buildinfo b/dev/.buildinfo index 78c1afc..13e9d9c 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 4451fc236d997e67665e7d4e212ee7b1 +config: be500588654c21b1241230d680a456c6 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index b9c6cd7..bafcf6e 100644 Binary files a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip and b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip differ diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip index b4fbef9..a81506a 100644 Binary files a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip and b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip differ diff --git a/dev/_modules/autoreject/autoreject.html b/dev/_modules/autoreject/autoreject.html index 88b3a5a..6559b87 100644 --- a/dev/_modules/autoreject/autoreject.html +++ b/dev/_modules/autoreject/autoreject.html @@ -7,7 +7,7 @@
-autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/_modules/autoreject/ransac.html b/dev/_modules/autoreject/ransac.html index e5d629a..0491a4d 100644 --- a/dev/_modules/autoreject/ransac.html +++ b/dev/_modules/autoreject/ransac.html @@ -7,7 +7,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/_modules/autoreject/utils.html b/dev/_modules/autoreject/utils.html index 9635e52..03c81c2 100644 --- a/dev/_modules/autoreject/utils.html +++ b/dev/_modules/autoreject/utils.html @@ -7,7 +7,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/_modules/index.html b/dev/_modules/index.html index ae8664f..24db6ee 100644 --- a/dev/_modules/index.html +++ b/dev/_modules/index.html @@ -7,7 +7,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js index b31228f..5a49958 100644 --- a/dev/_static/documentation_options.js +++ b/dev/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.4.3', + VERSION: '0.5.0.dev3', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/dev/api.html b/dev/api.html index 1ebe661..277d0d3 100644 --- a/dev/api.html +++ b/dev/api.html @@ -8,7 +8,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/auto_examples/index.html b/dev/auto_examples/index.html index 1c40d1a..327c991 100644 --- a/dev/auto_examples/index.html +++ b/dev/auto_examples/index.html @@ -8,7 +8,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
diff --git a/dev/auto_examples/plot_auto_repair.html b/dev/auto_examples/plot_auto_repair.html index 87bbb9a..413548f 100644 --- a/dev/auto_examples/plot_auto_repair.html +++ b/dev/auto_examples/plot_auto_repair.html @@ -8,7 +8,7 @@ -autoreject 0.4.3 documentation
+autoreject 0.5.0.dev3 documentation
@@ -583,531 +583,531 @@Running autoreject on ch_type=grad
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+ 97%|█████████▋| Creating augmented epochs : 197/204 [00:34<00:01, 5.81it/s]
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0%| | Computing thresholds ... : 0/204 [00:00<?, ?it/s]
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0%| | n_interp : 0/3 [00:00<?, ?it/s]
@@ -1116,221 +1116,221 @@
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@@ -1930,221 +1930,221 @@
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No bad epochs were found for your data. Returning a copy of the data you wanted to clean. Interpolation may have been done.
NOTE: pick_channels() is a legacy function. New code should use inst.pick(...).
NOTE: pick_channels() is a legacy function. New code should use inst.pick(...).
@@ -2189,7 +2189,7 @@
<Figure size 1200x600 with 1 Axes>
-Total running time of the script: (1 minutes 32.265 seconds)
+Total running time of the script: (2 minutes 6.742 seconds)
Fitting ICA to data using 32 channels (please be patient, this may take a while)
Selecting by non-zero PCA components: 32 components
-Fitting ICA took 3.2s.
+Fitting ICA took 5.5s.
Total running time of the script: (0 minutes 2.824 seconds)
+Total running time of the script: (0 minutes 4.749 seconds)
-Total running time of the script: (0 minutes 1.868 seconds)
+Total running time of the script: (0 minutes 2.526 seconds)
-Total running time of the script: (1 minutes 4.505 seconds)
+Total running time of the script: (1 minutes 28.868 seconds)
- -We will create epochs with data starting 200 ms before trigger onset -and continuing up to 800 ms after that. The data contains visual stimuli for -famous faces, unfamiliar faces, as well as scrambled faces.
-Let us now load all the epochs into memory and concatenate them
-import mne # noqa
-epochs = list()
-for run in range(3, 7):
- run_fname = os.path.join(target_dir, f'sub-{subject_id}', 'ses-meg', 'meg',
- f'sub-{subject_id}_ses-meg_task-facerecognition'
- '_run-{:02d}_meg.fif'.format(run))
- raw = mne.io.read_raw_fif(run_fname, preload=True)
- raw.pick_types(eeg=True, meg=False, stim=True) # less memory + computation
- raw.filter(1., 40., l_trans_bandwidth=0.5, n_jobs=1, verbose='INFO')
+sub-16_ses-meg_task-facerecognition_run-03_meg.fif: 64%|██████▎ | 530M/832M [01:16<00:34, 9.19MB/s]
- raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
- 'EEG063': 'ecg', 'EEG064': 'misc'})
- raw.rename_channels({'EEG061': 'EOG061', 'EEG062': 'EOG062',
- 'EEG063': 'ECG063', 'EEG064': 'MISC'})
- events = mne.find_events(raw, stim_channel='STI101',
- consecutive='increasing',
- min_duration=0.003, verbose=True)
- # Read epochs
- mne.io.set_eeg_reference(raw)
- epoch = mne.Epochs(raw, events, events_id, tmin, tmax, proj=True,
- baseline=None,
- preload=False, reject=None, decim=4)
- epochs.append(epoch)
- # Same `dev_head_t` for all runs so that we can concatenate them.
- epoch.info['dev_head_t'] = epochs[0].info['dev_head_t']
+sub-16_ses-meg_task-facerecognition_run-04_meg.fif: 80%|███████▉ | 664M/830M [01:16<00:19, 9.14MB/s]
+sub-16_ses-meg_task-facerecognition_run-01_meg.fif: 82%|████████▏ | 674M/824M [01:17<00:17, 9.23MB/s]
+sub-16_ses-meg_task-facerecognition_run-02_meg.fif: 46%|████▌ | 384M/835M [01:16<01:29, 5.30MB/s]
-epochs = mne.epochs.concatenate_epochs(epochs)
-
Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-03_meg.fif...
- Read a total of 8 projection items:
- mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
- Range : 40700 ... 588499 = 37.000 ... 534.999 secs
-Ready.
-Reading 0 ... 547799 = 0.000 ... 497.999 secs...
-NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
-Filtering raw data in 1 contiguous segment
-Setting up band-pass filter from 1 - 40 Hz
-FIR filter parameters
----------------------
-Designing a one-pass, zero-phase, non-causal bandpass filter:
-- Windowed time-domain design (firwin) method
-- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
-- Lower passband edge: 1.00
-- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
-- Upper passband edge: 40.00 Hz
-- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
-- Filter length: 7261 samples (6.601 s)
+sub-16_ses-meg_task-facerecognition_run-06_meg.fif: 66%|██████▌ | 539M/822M [01:16<00:32, 9.23MB/s]
-/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
- raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
-296 events found
-Event IDs: [ 5 6 7 13 14 15 17 18 19 261 262 263 269 271
- 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
-EEG channel type selected for re-referencing
-Applying average reference.
-Applying a custom ('EEG',) reference.
-Not setting metadata
-49 matching events found
-No baseline correction applied
-0 projection items activated
-Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-04_meg.fif...
- Read a total of 8 projection items:
- mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
- Range : 36300 ... 582999 = 33.000 ... 529.999 secs
-Ready.
-Reading 0 ... 546699 = 0.000 ... 496.999 secs...
-NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
-Filtering raw data in 1 contiguous segment
-Setting up band-pass filter from 1 - 40 Hz
-FIR filter parameters
----------------------
-Designing a one-pass, zero-phase, non-causal bandpass filter:
-- Windowed time-domain design (firwin) method
-- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
-- Lower passband edge: 1.00
-- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
-- Upper passband edge: 40.00 Hz
-- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
-- Filter length: 7261 samples (6.601 s)
-/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
- raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
-296 events found
-Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
- 271 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
-EEG channel type selected for re-referencing
-Applying average reference.
-Applying a custom ('EEG',) reference.
-Not setting metadata
-49 matching events found
-No baseline correction applied
-0 projection items activated
-Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-05_meg.fif...
- Read a total of 8 projection items:
- mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
- Range : 60500 ... 602799 = 55.000 ... 547.999 secs
-Ready.
-Reading 0 ... 542299 = 0.000 ... 492.999 secs...
-NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
-Filtering raw data in 1 contiguous segment
-Setting up band-pass filter from 1 - 40 Hz
+sub-16_ses-meg_task-facerecognition_run-03_meg.fif: 64%|██████▍ | 531M/832M [01:16<00:34, 9.17MB/s]
-FIR filter parameters
----------------------
-Designing a one-pass, zero-phase, non-causal bandpass filter:
-- Windowed time-domain design (firwin) method
-- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
-- Lower passband edge: 1.00
-- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
-- Upper passband edge: 40.00 Hz
-- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
-- Filter length: 7261 samples (6.601 s)
-/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
- raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
-292 events found
-Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 269 271 273
- 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
-EEG channel type selected for re-referencing
-Applying average reference.
-Applying a custom ('EEG',) reference.
-Not setting metadata
-49 matching events found
-No baseline correction applied
-0 projection items activated
-Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-06_meg.fif...
- Read a total of 8 projection items:
- mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
- mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
- grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
- Range : 27500 ... 568699 = 25.000 ... 516.999 secs
-Ready.
-Reading 0 ... 541199 = 0.000 ... 491.999 secs...
-NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
-Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
-Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
-Filtering raw data in 1 contiguous segment
-Setting up band-pass filter from 1 - 40 Hz
-FIR filter parameters
----------------------
-Designing a one-pass, zero-phase, non-causal bandpass filter:
-- Windowed time-domain design (firwin) method
-- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
-- Lower passband edge: 1.00
-- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
-- Upper passband edge: 40.00 Hz
-- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
-- Filter length: 7261 samples (6.601 s)
-/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
- raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
-295 events found
-Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
- 270 271 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114
- 4115]
-EEG channel type selected for re-referencing
-Applying average reference.
-Applying a custom ('EEG',) reference.
+sub-16_ses-meg_task-facerecognition_run-04_meg.fif: 80%|████████ | 665M/830M [01:16<00:18, 9.24MB/s]
+sub-16_ses-meg_task-facerecognition_run-01_meg.fif: 82%|████████▏ | 675M/824M [01:17<00:16, 9.35MB/s]
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+sub-16_ses-meg_task-facerecognition_run-03_meg.fif: 64%|██████▍ | 531M/832M [01:16<00:34, 9.11MB/s]
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+sub-16_ses-meg_task-facerecognition_run-04_meg.fif: 80%|████████ | 666M/830M [01:16<00:18, 9.10MB/s]
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+
+✅ Finished downloading ds000117.
+
+🧠 Please enjoy your brains.
+
We will create epochs with data starting 200 ms before trigger onset +and continuing up to 800 ms after that. The data contains visual stimuli for +famous faces, unfamiliar faces, as well as scrambled faces.
+Let us now load all the epochs into memory and concatenate them
+import mne # noqa
+
+epochs = list()
+for run in range(3, 7):
+ run_fname = os.path.join(target_dir, f'sub-{subject_id}', 'ses-meg', 'meg',
+ f'sub-{subject_id}_ses-meg_task-facerecognition'
+ '_run-{:02d}_meg.fif'.format(run))
+ raw = mne.io.read_raw_fif(run_fname, preload=True)
+ raw.pick_types(eeg=True, meg=False, stim=True) # less memory + computation
+ raw.filter(1., 40., l_trans_bandwidth=0.5, n_jobs=1, verbose='INFO')
+
+ raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
+ 'EEG063': 'ecg', 'EEG064': 'misc'})
+ raw.rename_channels({'EEG061': 'EOG061', 'EEG062': 'EOG062',
+ 'EEG063': 'ECG063', 'EEG064': 'MISC'})
+
+ events = mne.find_events(raw, stim_channel='STI101',
+ consecutive='increasing',
+ min_duration=0.003, verbose=True)
+ # Read epochs
+ mne.io.set_eeg_reference(raw)
+
+ epoch = mne.Epochs(raw, events, events_id, tmin, tmax, proj=True,
+ baseline=None,
+ preload=False, reject=None, decim=4)
+ epochs.append(epoch)
+
+ # Same `dev_head_t` for all runs so that we can concatenate them.
+ epoch.info['dev_head_t'] = epochs[0].info['dev_head_t']
+
+
+epochs = mne.epochs.concatenate_epochs(epochs)
+
Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-03_meg.fif...
+ Read a total of 8 projection items:
+ mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
+ Range : 40700 ... 588499 = 37.000 ... 534.999 secs
+Ready.
+Reading 0 ... 547799 = 0.000 ... 497.999 secs...
+NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
+Filtering raw data in 1 contiguous segment
+Setting up band-pass filter from 1 - 40 Hz
+
+FIR filter parameters
+---------------------
+Designing a one-pass, zero-phase, non-causal bandpass filter:
+- Windowed time-domain design (firwin) method
+- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
+- Lower passband edge: 1.00
+- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
+- Upper passband edge: 40.00 Hz
+- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
+- Filter length: 7261 samples (6.601 s)
+
+/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
+ raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
+296 events found
+Event IDs: [ 5 6 7 13 14 15 17 18 19 261 262 263 269 271
+ 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
+EEG channel type selected for re-referencing
+Applying average reference.
+Applying a custom ('EEG',) reference.
+Not setting metadata
+49 matching events found
+No baseline correction applied
+0 projection items activated
+Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-04_meg.fif...
+ Read a total of 8 projection items:
+ mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
+ Range : 36300 ... 582999 = 33.000 ... 529.999 secs
+Ready.
+Reading 0 ... 546699 = 0.000 ... 496.999 secs...
+NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
+Filtering raw data in 1 contiguous segment
+Setting up band-pass filter from 1 - 40 Hz
+
+FIR filter parameters
+---------------------
+Designing a one-pass, zero-phase, non-causal bandpass filter:
+- Windowed time-domain design (firwin) method
+- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
+- Lower passband edge: 1.00
+- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
+- Upper passband edge: 40.00 Hz
+- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
+- Filter length: 7261 samples (6.601 s)
+
+/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
+ raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
+296 events found
+Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
+ 271 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
+EEG channel type selected for re-referencing
+Applying average reference.
+Applying a custom ('EEG',) reference.
+Not setting metadata
+49 matching events found
+No baseline correction applied
+0 projection items activated
+Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-05_meg.fif...
+ Read a total of 8 projection items:
+ mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
+ Range : 60500 ... 602799 = 55.000 ... 547.999 secs
+Ready.
+Reading 0 ... 542299 = 0.000 ... 492.999 secs...
+NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
+Filtering raw data in 1 contiguous segment
+Setting up band-pass filter from 1 - 40 Hz
+
+FIR filter parameters
+---------------------
+Designing a one-pass, zero-phase, non-causal bandpass filter:
+- Windowed time-domain design (firwin) method
+- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
+- Lower passband edge: 1.00
+- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
+- Upper passband edge: 40.00 Hz
+- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
+- Filter length: 7261 samples (6.601 s)
+
+/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
+ raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
+292 events found
+Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 269 271 273
+ 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114 4115]
+EEG channel type selected for re-referencing
+Applying average reference.
+Applying a custom ('EEG',) reference.
+Not setting metadata
+49 matching events found
+No baseline correction applied
+0 projection items activated
+Opening raw data file /home/circleci/project/autoreject/../examples/ds000117/sub-16/ses-meg/meg/sub-16_ses-meg_task-facerecognition_run-06_meg.fif...
+ Read a total of 8 projection items:
+ mag_ssp_upright.fif : PCA-mags-v1 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v2 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v3 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v4 (1 x 306) idle
+ mag_ssp_upright.fif : PCA-mags-v5 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v1 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v2 (1 x 306) idle
+ grad_ssp_upright.fif : PCA-grad-v3 (1 x 306) idle
+ Range : 27500 ... 568699 = 25.000 ... 516.999 secs
+Ready.
+Reading 0 ... 541199 = 0.000 ... 491.999 secs...
+NOTE: pick_types() is a legacy function. New code should use inst.pick(...).
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v1, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v2, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v3, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v4, active : False, n_channels : 306>
+Removing projector <Projection | mag_ssp_upright.fif : PCA-mags-v5, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v1, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v2, active : False, n_channels : 306>
+Removing projector <Projection | grad_ssp_upright.fif : PCA-grad-v3, active : False, n_channels : 306>
+Filtering raw data in 1 contiguous segment
+Setting up band-pass filter from 1 - 40 Hz
+
+FIR filter parameters
+---------------------
+Designing a one-pass, zero-phase, non-causal bandpass filter:
+- Windowed time-domain design (firwin) method
+- Hamming window with 0.0194 passband ripple and 53 dB stopband attenuation
+- Lower passband edge: 1.00
+- Lower transition bandwidth: 0.50 Hz (-6 dB cutoff frequency: 0.75 Hz)
+- Upper passband edge: 40.00 Hz
+- Upper transition bandwidth: 10.00 Hz (-6 dB cutoff frequency: 45.00 Hz)
+- Filter length: 7261 samples (6.601 s)
+
+/home/circleci/project/examples/plot_visualize_bad_epochs.py:57: RuntimeWarning: The unit for channel(s) EEG064 has changed from V to NA.
+ raw.set_channel_types({'EEG061': 'eog', 'EEG062': 'eog',
+295 events found
+Event IDs: [ 5 6 7 13 14 15 17 18 19 256 261 262 263 269
+ 270 271 273 274 275 4096 4101 4102 4103 4109 4110 4111 4113 4114
+ 4115]
+EEG channel type selected for re-referencing
+Applying average reference.
+Applying a custom ('EEG',) reference.
Not setting metadata
50 matching events found
No baseline correction applied
@@ -12186,1533 +16706,2028 @@
No baseline correction applied
Now, we apply autoreject
-from autoreject import AutoReject, compute_thresholds # noqa
+Now, we apply autoreject
+from autoreject import AutoReject, compute_thresholds # noqa
+
+this_epoch = epochs['famous']
+exclude = [] # XXX
+picks = mne.pick_types(epochs.info, meg=False, eeg=True, stim=False,
+ eog=False, exclude=exclude)
+
+
+Note that autoreject.AutoReject
by design supports multiple
+channels. If no picks are passed separate solutions will be computed for each
+channel type and internally combines. This then readily supports cleaning
+unseen epochs from the different channel types used during fit.
+Here we only use a subset of channels to save time.
+Also note that once the parameters are learned, any data can be repaired
+that contains channels that were used during fit. This also means that time
+may be saved by fitting autoreject.AutoReject
on a
+representative subsample of the data.
+ar = AutoReject(picks=picks, random_state=42, n_jobs=1, verbose=True)
+
+epochs_ar, reject_log = ar.fit_transform(this_epoch, return_log=True)
+
+
+Running autoreject on ch_type=eeg
+
+ 0%| | Creating augmented epochs : 0/70 [00:00<?, ?it/s]
+ 1%|▏ | Creating augmented epochs : 1/70 [00:00<00:01, 44.57it/s]
+ 3%|▎ | Creating augmented epochs : 2/70 [00:00<00:01, 38.94it/s]
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+100%|██████████| Creating augmented epochs : 70/70 [00:03<00:00, 22.39it/s]
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+ 0%| | Computing thresholds ... : 0/70 [00:00<?, ?it/s]
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-this_epoch = epochs['famous']
-exclude = [] # XXX
-picks = mne.pick_types(epochs.info, meg=False, eeg=True, stim=False,
- eog=False, exclude=exclude)
-
-
-Note that autoreject.AutoReject
by design supports multiple
-channels. If no picks are passed separate solutions will be computed for each
-channel type and internally combines. This then readily supports cleaning
-unseen epochs from the different channel types used during fit.
-Here we only use a subset of channels to save time.
-Also note that once the parameters are learned, any data can be repaired
-that contains channels that were used during fit. This also means that time
-may be saved by fitting autoreject.AutoReject
on a
-representative subsample of the data.
-ar = AutoReject(picks=picks, random_state=42, n_jobs=1, verbose=True)
-epochs_ar, reject_log = ar.fit_transform(this_epoch, return_log=True)
-
-
-Running autoreject on ch_type=eeg
+ 43%|████▎ | Repairing epochs : 85/197 [00:02<00:03, 34.25it/s]
- 0%| | Creating augmented epochs : 0/70 [00:00<?, ?it/s]
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-100%|██████████| Creating augmented epochs : 70/70 [00:02<00:00, 31.50it/s]
- 0%| | Computing thresholds ... : 0/70 [00:00<?, ?it/s]
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-100%|██████████| Computing thresholds ... : 70/70 [00:39<00:00, 1.76it/s]
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+ 51%|█████ | Repairing epochs : 100/197 [00:02<00:03, 31.17it/s]
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+ 51%|█████▏ | Repairing epochs : 101/197 [00:03<00:03, 31.01it/s]
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+ 53%|█████▎ | Repairing epochs : 105/197 [00:03<00:02, 33.65it/s]
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+ 54%|█████▍ | Repairing epochs : 106/197 [00:03<00:02, 33.43it/s]
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+ 80%|███████▉ | Repairing epochs : 157/197 [00:03<00:00, 46.18it/s]
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+ 80%|████████ | Repairing epochs : 158/197 [00:03<00:00, 45.98it/s]
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+ 81%|████████ | Repairing epochs : 159/197 [00:03<00:00, 45.86it/s]
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+ 81%|████████ | Repairing epochs : 160/197 [00:03<00:00, 45.48it/s]
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+ 82%|████████▏ | Repairing epochs : 161/197 [00:03<00:00, 44.74it/s]
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+ 83%|████████▎ | Repairing epochs : 163/197 [00:03<00:00, 47.10it/s]
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+ 85%|████████▌ | Repairing epochs : 168/197 [00:03<00:00, 47.44it/s]
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+ 94%|█████████▍| Repairing epochs : 185/197 [00:04<00:00, 40.39it/s]
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+ 94%|█████████▍| Repairing epochs : 186/197 [00:04<00:00, 39.15it/s]
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+ 95%|█████████▍| Repairing epochs : 187/197 [00:04<00:00, 39.30it/s]
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+ 95%|█████████▌| Repairing epochs : 188/197 [00:04<00:00, 39.11it/s]
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+ 96%|█████████▋| Repairing epochs : 190/197 [00:04<00:00, 40.18it/s]
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+ 97%|█████████▋| Repairing epochs : 191/197 [00:04<00:00, 39.10it/s]
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+ 97%|█████████▋| Repairing epochs : 192/197 [00:04<00:00, 39.05it/s]
- 97%|█████████▋| Repairing epochs : 191/197 [00:02<00:00, 64.12it/s]
+ 98%|█████████▊| Repairing epochs : 193/197 [00:04<00:00, 39.37it/s]
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+ 98%|█████████▊| Repairing epochs : 194/197 [00:04<00:00, 39.59it/s]
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+100%|██████████| Repairing epochs : 197/197 [00:04<00:00, 42.29it/s]
No bad epochs were found for your data. Returning a copy of the data you wanted to clean. Interpolation may have been done.
@@ -14179,7 +19401,7 @@
<Figure size 640x300 with 2 Axes>
Total running time of the script: (3 minutes 6.021 seconds)
+Total running time of the script: (4 minutes 21.923 seconds)