doc updates [skip ci]

mne-tools · Nov 20, 2023 · 2cce6a5 · 2cce6a5
1 parent 4d30494
commit 2cce6a5
Show file tree

Hide file tree

Showing 86 changed files with 173 additions and 1,753 deletions.
diff --git 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: 78dd81a548e2ebb3d89a89e7ec639028
+config: 570aec689683546ee3c7091db75f71da
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip
diff --git a/dev/_images/sphx_glr_convert_eeg_to_bids_001.png b/dev/_images/sphx_glr_convert_eeg_to_bids_001.png
diff --git a/dev/_images/sphx_glr_convert_ieeg_to_bids_001.png b/dev/_images/sphx_glr_convert_ieeg_to_bids_001.png
diff --git a/dev/_images/sphx_glr_convert_mne_sample_001.png b/dev/_images/sphx_glr_convert_mne_sample_001.png
diff --git a/dev/_images/sphx_glr_convert_mri_and_trans_001.png b/dev/_images/sphx_glr_convert_mri_and_trans_001.png
diff --git a/dev/_images/sphx_glr_convert_mri_and_trans_002.png b/dev/_images/sphx_glr_convert_mri_and_trans_002.png
diff --git a/dev/_images/sphx_glr_convert_mri_and_trans_003.png b/dev/_images/sphx_glr_convert_mri_and_trans_003.png
diff --git a/dev/_images/sphx_glr_convert_mri_and_trans_004.png b/dev/_images/sphx_glr_convert_mri_and_trans_004.png
diff --git a/dev/_images/sphx_glr_convert_nirs_to_bids_001.png b/dev/_images/sphx_glr_convert_nirs_to_bids_001.png
diff --git a/dev/_images/sphx_glr_mark_bad_channels_001.png b/dev/_images/sphx_glr_mark_bad_channels_001.png
diff --git a/dev/_images/sphx_glr_mark_bad_channels_002.png b/dev/_images/sphx_glr_mark_bad_channels_002.png
diff --git a/dev/_images/sphx_glr_read_bids_datasets_001.png b/dev/_images/sphx_glr_read_bids_datasets_001.png
diff --git a/dev/_modules/index.html b/dev/_modules/index.html
@@ -560,7 +560,7 @@ <h1>All modules for which code is available</h1>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html
@@ -1197,7 +1197,7 @@ <h1>Source code for mne_bids.copyfiles</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html
@@ -1345,7 +1345,7 @@ <h1>Source code for mne_bids.dig</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html
@@ -1008,7 +1008,7 @@ <h1>Source code for mne_bids.inspect</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html
@@ -3054,7 +3054,7 @@ <h1>Source code for mne_bids.path</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html
@@ -1707,7 +1707,7 @@ <h1>Source code for mne_bids.read</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/report/_report.html b/dev/_modules/mne_bids/report/_report.html
@@ -1091,7 +1091,7 @@ <h1>Source code for mne_bids.report._report</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/sidecar_updates.html b/dev/_modules/mne_bids/sidecar_updates.html
@@ -942,7 +942,7 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/stats.html b/dev/_modules/mne_bids/stats.html
@@ -677,7 +677,7 @@ <h1>Source code for mne_bids.stats</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html
@@ -1094,7 +1094,7 @@ <h1>Source code for mne_bids.utils</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
@@ -3702,7 +3702,7 @@ <h1>Source code for mne_bids.write</h1><div class="highlight"><pre>
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/api.html b/dev/api.html
@@ -770,7 +770,7 @@ <h2>mne_bids.copyfiles<a class="headerlink" href="#mne-bids-copyfiles" title="Pe
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/authors.html b/dev/authors.html
@@ -568,7 +568,7 @@
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html
@@ -672,18 +672,18 @@ <h2>Basic anonymization<a class="headerlink" href="#basic-anonymization" title="
     Input:  /home/circleci/mne_data/MNE-sample-data-bids
     Output: /home/circleci/mne_data/MNE-sample-data-bids-anon
 
-Shifting recording dates by 31035 days (85.0 years).
+Shifting recording dates by 29415 days (80.6 years).
 Using the following subject ID anonymization mapping:
 
     sub-ABC123 → sub-1
     sub-emptyroom → sub-emptyroom
 
 
   0%|          | Anonymizing : 0/5 [00:00&lt;?,       ?it/s]
- 20%|██        | Anonymizing : 1/5 [00:00&lt;00:01,    2.64it/s]
- 40%|████      | Anonymizing : 2/5 [00:02&lt;00:04,    1.44s/it]
- 60%|██████    | Anonymizing : 3/5 [00:03&lt;00:02,    1.23s/it]
-100%|██████████| Anonymizing : 5/5 [00:03&lt;00:00,    1.36it/s]
+ 20%|██        | Anonymizing : 1/5 [00:00&lt;00:01,    3.50it/s]
+ 40%|████      | Anonymizing : 2/5 [00:02&lt;00:03,    1.24s/it]
+ 60%|██████    | Anonymizing : 3/5 [00:03&lt;00:02,    1.06s/it]
+100%|██████████| Anonymizing : 5/5 [00:03&lt;00:00,    1.58it/s]
 </pre></div>
 </div>
 <p>That’s it! Let’s have a look at directory structure of the anonymized
@@ -711,12 +711,12 @@ <h2>Basic anonymization<a class="headerlink" href="#basic-anonymization" title="
 |--------- sub-1_task-audiovisual_meg.fif
 |--------- sub-1_task-audiovisual_meg.json
 |--- sub-emptyroom/
-|------ ses-19171217/
-|--------- sub-emptyroom_ses-19171217_scans.tsv
+|------ ses-19220525/
+|--------- sub-emptyroom_ses-19220525_scans.tsv
 |--------- meg/
-|------------ sub-emptyroom_ses-19171217_task-noise_channels.tsv
-|------------ sub-emptyroom_ses-19171217_task-noise_meg.fif
-|------------ sub-emptyroom_ses-19171217_task-noise_meg.json
+|------------ sub-emptyroom_ses-19220525_task-noise_channels.tsv
+|------------ sub-emptyroom_ses-19220525_task-noise_meg.fif
+|------------ sub-emptyroom_ses-19220525_task-noise_meg.json
 </pre></div>
 </div>
 <p>You can see that the subject ID was changed to a number (in this case, the
@@ -754,8 +754,8 @@ <h2>Limiting to specific data types<a class="headerlink" href="#limiting-to-spec
 
 
   0%|          | Anonymizing : 0/1 [00:00&lt;?,       ?it/s]
-100%|██████████| Anonymizing : 1/1 [00:02&lt;00:00,    2.31s/it]
-100%|██████████| Anonymizing : 1/1 [00:02&lt;00:00,    2.31s/it]
+100%|██████████| Anonymizing : 1/1 [00:02&lt;00:00,    2.14s/it]
+100%|██████████| Anonymizing : 1/1 [00:02&lt;00:00,    2.14s/it]
 |MNE-sample-data-bids-anon/
 |--- README
 |--- dataset_description.json
@@ -797,9 +797,9 @@ <h2>Specifying time shift<a class="headerlink" href="#specifying-time-shift" tit
 
 
   0%|          | Anonymizing : 0/4 [00:00&lt;?,       ?it/s]
- 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:01,    2.61it/s]
- 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.69it/s]
-100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.38it/s]
+ 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:00,    3.38it/s]
+ 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.95it/s]
+100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.91it/s]
 |sub-emptyroom/
 |--- ses-20021126/
 |------ sub-emptyroom_ses-20021126_scans.tsv
@@ -837,17 +837,17 @@ <h2>Specifying subject IDs<a class="headerlink" href="#specifying-subject-ids" t
     Input:  /home/circleci/mne_data/MNE-sample-data-bids
     Output: /home/circleci/mne_data/MNE-sample-data-bids-anon
 
-Shifting recording dates by 36058 days (98.8 years).
+Shifting recording dates by 32725 days (89.7 years).
 Using the following subject ID anonymization mapping:
 
     sub-ABC123 → sub-anonymous
     sub-emptyroom → sub-emptyroom
 
 
   0%|          | Anonymizing : 0/4 [00:00&lt;?,       ?it/s]
- 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:01,    2.70it/s]
- 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.70it/s]
-100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.42it/s]
+ 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:00,    3.34it/s]
+ 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.93it/s]
+100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.88it/s]
 |MNE-sample-data-bids-anon/
 |--- README
 |--- dataset_description.json
@@ -865,12 +865,12 @@ <h2>Specifying subject IDs<a class="headerlink" href="#specifying-subject-ids" t
 |--------- sub-anonymous_task-audiovisual_meg.fif
 |--------- sub-anonymous_task-audiovisual_meg.json
 |--- sub-emptyroom/
-|------ ses-19040317/
-|--------- sub-emptyroom_ses-19040317_scans.tsv
+|------ ses-19130502/
+|--------- sub-emptyroom_ses-19130502_scans.tsv
 |--------- meg/
-|------------ sub-emptyroom_ses-19040317_task-noise_channels.tsv
-|------------ sub-emptyroom_ses-19040317_task-noise_meg.fif
-|------------ sub-emptyroom_ses-19040317_task-noise_meg.json
+|------------ sub-emptyroom_ses-19130502_task-noise_channels.tsv
+|------------ sub-emptyroom_ses-19130502_task-noise_meg.fif
+|------------ sub-emptyroom_ses-19130502_task-noise_meg.json
 </pre></div>
 </div>
 </section>
@@ -927,9 +927,9 @@ <h2>Reproducibility<a class="headerlink" href="#reproducibility" title="Permalin
 
 
   0%|          | Anonymizing : 0/4 [00:00&lt;?,       ?it/s]
- 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:01,    2.72it/s]
- 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.70it/s]
-100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.41it/s]
+ 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:00,    3.43it/s]
+ 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.96it/s]
+100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.94it/s]
 |MNE-sample-data-bids-anon/
 |--- README
 |--- dataset_description.json
@@ -972,9 +972,9 @@ <h2>Reproducibility<a class="headerlink" href="#reproducibility" title="Permalin
 
 
   0%|          | Anonymizing : 0/4 [00:00&lt;?,       ?it/s]
- 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:01,    2.65it/s]
- 50%|█████     | Anonymizing : 2/4 [00:01&lt;00:01,    1.62it/s]
-100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.25it/s]
+ 25%|██▌       | Anonymizing : 1/4 [00:00&lt;00:00,    3.53it/s]
+ 50%|█████     | Anonymizing : 2/4 [00:00&lt;00:01,    1.98it/s]
+100%|██████████| Anonymizing : 4/4 [00:01&lt;00:00,    3.98it/s]
 |MNE-sample-data-bids-anon/
 |--- README
 |--- dataset_description.json
@@ -1000,7 +1000,7 @@ <h2>Reproducibility<a class="headerlink" href="#reproducibility" title="Permalin
 |------------ sub-emptyroom_ses-19221211_task-noise_meg.json
 </pre></div>
 </div>
-<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 12.727 seconds)</p>
+<p class="sphx-glr-timing"><strong>Total running time of the script:</strong> (0 minutes 11.064 seconds)</p>
 <div class="sphx-glr-footer sphx-glr-footer-example docutils container" id="sphx-glr-download-auto-examples-anonymize-dataset-py">
 <div class="binder-badge docutils container">
 <a class="reference external image-reference" href="https://mybinder.org/v2/gh/mne-tools/mne-bids/gh-pages?filepath=dev/notebooks/auto_examples/anonymize_dataset.ipynb"><img alt="Launch binder" src="../_images/binder_badge_logo.svg" width="150px" /></a>
@@ -1091,7 +1091,7 @@ <h2>Reproducibility<a class="headerlink" href="#reproducibility" title="Permalin
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>

diff --git a/dev/auto_examples/bidspath.html b/dev/auto_examples/bidspath.html
@@ -818,7 +818,7 @@
         <div class="footer-item">
   <p class="copyright">
 
-      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-16.
+      © Copyright 2017-2023, MNE Developers. Last updated on 2023-11-20.
       <br/>
 
   </p>