From 762b7266f132e253ff79097a86ae95dbbdd8caa7 Mon Sep 17 00:00:00 2001
From: Circle Ci
Date: Mon, 25 Mar 2024 14:12:54 +0000
Subject: [PATCH] doc updates [skip ci]
---
dev/.buildinfo | 2 +-
.../auto_examples_python.zip | Bin 100936 -> 100936 bytes
.../auto_examples_jupyter.zip | Bin 155421 -> 155421 bytes
dev/_modules/index.html | 8 +--
dev/_modules/mne_bids/copyfiles.html | 8 +--
dev/_modules/mne_bids/dig.html | 8 +--
dev/_modules/mne_bids/inspect.html | 8 +--
dev/_modules/mne_bids/path.html | 8 +--
dev/_modules/mne_bids/read.html | 38 ++++++++---
dev/_modules/mne_bids/report/_report.html | 8 +--
dev/_modules/mne_bids/sidecar_updates.html | 8 +--
dev/_modules/mne_bids/stats.html | 8 +--
dev/_modules/mne_bids/utils.html | 8 +--
dev/_modules/mne_bids/write.html | 8 +--
dev/_static/documentation_options.js | 2 +-
dev/api.html | 8 +--
dev/authors.html | 8 +--
dev/auto_examples/anonymize_dataset.html | 62 +++++++++---------
dev/auto_examples/bidspath.html | 8 +--
dev/auto_examples/convert_eeg_to_bids.html | 14 ++--
dev/auto_examples/convert_empty_room.html | 10 +--
dev/auto_examples/convert_group_studies.html | 14 ++--
dev/auto_examples/convert_ieeg_to_bids.html | 10 +--
dev/auto_examples/convert_mne_sample.html | 14 ++--
dev/auto_examples/convert_mri_and_trans.html | 10 +--
dev/auto_examples/convert_nirs_to_bids.html | 14 ++--
dev/auto_examples/create_bids_folder.html | 8 +--
dev/auto_examples/mark_bad_channels.html | 10 +--
dev/auto_examples/read_bids_datasets.html | 55 ++++++++--------
.../rename_brainvision_files.html | 10 +--
dev/auto_examples/sg_execution_times.html | 32 ++++-----
dev/auto_examples/update_bids_datasets.html | 8 +--
dev/contribute.html | 8 +--
dev/generated/cli.html | 8 +--
dev/generated/mne_bids.BIDSPath.html | 8 +--
dev/generated/mne_bids.anonymize_dataset.html | 8 +--
.../mne_bids.convert_montage_to_mri.html | 8 +--
.../mne_bids.convert_montage_to_ras.html | 8 +--
...e_bids.copyfiles.copyfile_brainvision.html | 8 +--
.../mne_bids.copyfiles.copyfile_bti.html | 8 +--
.../mne_bids.copyfiles.copyfile_ctf.html | 8 +--
.../mne_bids.copyfiles.copyfile_edf.html | 8 +--
.../mne_bids.copyfiles.copyfile_eeglab.html | 8 +--
.../mne_bids.copyfiles.copyfile_kit.html | 8 +--
.../mne_bids.find_matching_paths.html | 8 +--
.../mne_bids.get_anat_landmarks.html | 8 +--
.../mne_bids.get_anonymization_daysback.html | 8 +--
.../mne_bids.get_bids_path_from_fname.html | 8 +--
dev/generated/mne_bids.get_datatypes.html | 8 +--
.../mne_bids.get_entities_from_fname.html | 8 +--
dev/generated/mne_bids.get_entity_vals.html | 8 +--
.../mne_bids.get_head_mri_trans.html | 8 +--
dev/generated/mne_bids.inspect_dataset.html | 8 +--
.../mne_bids.make_dataset_description.html | 8 +--
dev/generated/mne_bids.make_report.html | 8 +--
dev/generated/mne_bids.mark_channels.html | 8 +--
dev/generated/mne_bids.print_dir_tree.html | 8 +--
dev/generated/mne_bids.read_raw_bids.html | 8 +--
.../mne_bids.search_folder_for_text.html | 8 +--
.../mne_bids.stats.count_events.html | 10 +--
dev/generated/mne_bids.template_to_head.html | 8 +--
.../mne_bids.update_anat_landmarks.html | 8 +--
.../mne_bids.update_sidecar_json.html | 8 +--
dev/generated/mne_bids.write_anat.html | 8 +--
.../mne_bids.write_meg_calibration.html | 8 +--
.../mne_bids.write_meg_crosstalk.html | 8 +--
dev/generated/mne_bids.write_raw_bids.html | 8 +--
dev/genindex.html | 8 +--
dev/index.html | 8 +--
dev/install.html | 8 +--
dev/objects.inv | Bin 3746 -> 3746 bytes
dev/py-modindex.html | 8 +--
dev/search.html | 8 +--
dev/searchindex.js | 2 +-
dev/sg_execution_times.html | 32 ++++-----
dev/use.html | 8 +--
dev/whats_new.html | 10 +--
dev/whats_new_previous_releases.html | 8 +--
78 files changed, 411 insertions(+), 388 deletions(-)
diff --git a/dev/.buildinfo b/dev/.buildinfo
index d3fb79525..c9265b1a3 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: d2c8736a61e27479173708aea8053788
+config: 80b0d55387f22bebbe14ace688568fdd
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip
index e40e990b01c775c3edb5d1e6736042054f9a7507..a44b3c33ba0dad1b7ad464814b5a91579b2ddfe2 100644
GIT binary patch
delta 273
zcmX>xh3&)?Hr@blW)=|!5J)Pl+{l|I&zxOYxw%Z9Plve{$Y}R2m0->SGX5u@Q~*nz
zZV}~YZUu@wp6n*hTm@w4to{+m+yG>#|NSA$oKjf1T}hhJS&}$jUHb%#>lS0kWqOCrqEv#^?aDX!_+gMrV*4rc1Unnt_y0
z4{B$01WQe8XLJL(Vfy`cMkkOPrmJ)S89>9QXLc~!gWNEEHHZOp!t}QtKm&m;m~PMs
YWPsEZcLEiI4BXKPv;rjZuanUW0H?2Gxh3&)?Hr@blW)=|!5K!Atw2?PWp4nhS(dIIFJ{@KkAfw&8RDxL_$oQXpQUNS=
zxw!P1g>9aIgti_jU3okR!5!0=snVdncnBEx8j{_
- Overview: module code — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ Overview: module code — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -568,7 +568,7 @@ All modules for which code is available
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html
index af0207daa..1b0267b21 100644
--- a/dev/_modules/mne_bids/copyfiles.html
+++ b/dev/_modules/mne_bids/copyfiles.html
@@ -7,7 +7,7 @@
- mne_bids.copyfiles — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.copyfiles — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -1221,7 +1221,7 @@ Source code for mne_bids.copyfiles
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html
index f9115602d..57ffd2a18 100644
--- a/dev/_modules/mne_bids/dig.html
+++ b/dev/_modules/mne_bids/dig.html
@@ -7,7 +7,7 @@
- mne_bids.dig — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.dig — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -1363,7 +1363,7 @@ Source code for mne_bids.dig
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html
index c9680ba6d..2ea05bb0f 100644
--- a/dev/_modules/mne_bids/inspect.html
+++ b/dev/_modules/mne_bids/inspect.html
@@ -7,7 +7,7 @@
- mne_bids.inspect — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.inspect — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -1017,7 +1017,7 @@ Source code for mne_bids.inspect
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html
index 277ff7ffb..9c4ff14ff 100644
--- a/dev/_modules/mne_bids/path.html
+++ b/dev/_modules/mne_bids/path.html
@@ -7,7 +7,7 @@
- mne_bids.path — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.path — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -3099,7 +3099,7 @@ Source code for mne_bids.path
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html
index 7012cdd52..1a509e0da 100644
--- a/dev/_modules/mne_bids/read.html
+++ b/dev/_modules/mne_bids/read.html
@@ -7,7 +7,7 @@
- mne_bids.read — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.read — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -847,12 +847,32 @@ Source code for mne_bids.read
# extract the acquisition time from scans file
acq_time = acq_times [ row_ind ]
if acq_time != "n/a" :
- # microseconds in the acquisition time is optional
+ # BIDS allows the time to be stored in UTC with a zero time-zone offset, as
+ # indicated by a trailing "Z" in the datetime string. If the "Z" is missing, the
+ # time is represented as "local" time. We have no way to know what the local
+ # time zone is at the *acquisition* site; so we simply assume the same time zone
+ # as the user's current system (this is what the spec demands anyway).
+ acq_time_is_utc = acq_time . endswith ( "Z" )
+
+ # microseconds part in the acquisition time is optional; add it if missing
if "." not in acq_time :
- # acquisition time ends with '.%fZ' microseconds string
- acq_time += ".0Z"
- acq_time = datetime . strptime ( acq_time , "%Y-%m- %d T%H:%M:%S. %f Z" )
- acq_time = acq_time . replace ( tzinfo = timezone . utc )
+ if acq_time_is_utc :
+ acq_time = acq_time . replace ( "Z" , ".0Z" )
+ else :
+ acq_time += ".0"
+
+ date_format = "%Y-%m- %d T%H:%M:%S. %f "
+ if acq_time_is_utc :
+ date_format += "Z"
+
+ acq_time = datetime . strptime ( acq_time , date_format )
+
+ if acq_time_is_utc :
+ # Enforce setting timezone to UTC without additonal conversion
+ acq_time = acq_time . replace ( tzinfo = timezone . utc )
+ else :
+ # Convert time offset to UTC
+ acq_time = acq_time . astimezone ( timezone . utc )
logger . debug (
f "Loaded { scans_fname } scans file to set " f "acq_time as { acq_time } ."
@@ -1721,7 +1741,7 @@ Source code for mne_bids.read
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/report/_report.html b/dev/_modules/mne_bids/report/_report.html
index 4c6245a99..92b4fde30 100644
--- a/dev/_modules/mne_bids/report/_report.html
+++ b/dev/_modules/mne_bids/report/_report.html
@@ -7,7 +7,7 @@
- mne_bids.report._report — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.report._report — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -1102,7 +1102,7 @@ Source code for mne_bids.report._report
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/sidecar_updates.html b/dev/_modules/mne_bids/sidecar_updates.html
index 72da2b72f..8f841dafd 100644
--- a/dev/_modules/mne_bids/sidecar_updates.html
+++ b/dev/_modules/mne_bids/sidecar_updates.html
@@ -7,7 +7,7 @@
- mne_bids.sidecar_updates — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.sidecar_updates — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -956,7 +956,7 @@ Source code for mne_bids.sidecar_updates
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/stats.html b/dev/_modules/mne_bids/stats.html
index e160d2c8d..f1fa35db9 100644
--- a/dev/_modules/mne_bids/stats.html
+++ b/dev/_modules/mne_bids/stats.html
@@ -7,7 +7,7 @@
- mne_bids.stats — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.stats — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -694,7 +694,7 @@ Source code for mne_bids.stats
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html
index 19a905ab5..306577ce8 100644
--- a/dev/_modules/mne_bids/utils.html
+++ b/dev/_modules/mne_bids/utils.html
@@ -7,7 +7,7 @@
- mne_bids.utils — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.utils — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -1106,7 +1106,7 @@ Source code for mne_bids.utils
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
index 68db44781..544466d07 100644
--- a/dev/_modules/mne_bids/write.html
+++ b/dev/_modules/mne_bids/write.html
@@ -7,7 +7,7 @@
- mne_bids.write — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ mne_bids.write — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -40,7 +40,7 @@
-
+
@@ -144,7 +144,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -3713,7 +3713,7 @@ Source code for mne_bids.write
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index c402432d6..a3ec2e35a 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '0.15.0.dev43+g17d20c13',
+ VERSION: '0.15.0.dev44+gc75ac58d',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/dev/api.html b/dev/api.html
index b53287553..77e29d6c1 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -8,7 +8,7 @@
- API Documentation — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ API Documentation — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -41,7 +41,7 @@
-
+
@@ -147,7 +147,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -778,7 +778,7 @@ mne_bids.copyfiles
@@ -577,7 +577,7 @@
- © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-18.
+ © Copyright 2017-2024, MNE Developers. Last updated on 2024-03-25.
diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html
index dc928975b..cb635ae78 100644
--- a/dev/auto_examples/anonymize_dataset.html
+++ b/dev/auto_examples/anonymize_dataset.html
@@ -8,7 +8,7 @@
- 13. Anonymizing a BIDS dataset — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ 13. Anonymizing a BIDS dataset — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -41,7 +41,7 @@
-
+
@@ -148,7 +148,7 @@
- MNE-BIDS 0.15.0.dev43+g17d20c13 documentation
+ MNE-BIDS 0.15.0.dev44+gc75ac58d documentation
@@ -678,7 +678,7 @@ Basic anonymization
+Total running time of the script: (0 minutes 11.046 seconds)
@@ -1035,8 +1035,8 @@ Convert to BIDS