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

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

 
   
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

 
   
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

 
   
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

 
   
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-%dT%H:%M:%S.%fZ")
-        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-%dT%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

 
   
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

 
   
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

 
   
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

 
   
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

 
   
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

 
   
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 - © 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/authors.html b/dev/authors.html index c500de492..eef0714d9 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -8,7 +8,7 @@ - <no title> — MNE-BIDS 0.15.0.dev43+g17d20c13 documentation + <no title> — MNE-BIDS 0.15.0.dev44+gc75ac58d documentation @@ -41,7 +41,7 @@ - + @@ -145,7 +145,7 @@ -

MNE-BIDS 0.15.0.dev43+g17d20c13 documentation

+

MNE-BIDS 0.15.0.dev44+gc75ac58d documentation

@@ -577,7 +577,7 @@ 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 anonymizationSpecifying subject IDsSpecifying subject IDsSpecifying subject IDs @@ -933,9 +933,9 @@

ReproducibilityTotal running time of the script: (0 minutes 11.101 seconds)

+

Total running time of the script: (0 minutes 11.046 seconds)

@@ -1035,8 +1035,8 @@

Convert to BIDS -

Total running time of the script: (0 minutes 1.895 seconds)

+

Total running time of the script: (0 minutes 1.899 seconds)

Now let’s get an overview of the events on the whole dataset

-
counts = count_events(bids_root)
-counts
+
 
@@ -957,7 +957,7 @@ 0.0 were removed from analysis).
-

Total running time of the script: (0 minutes 1.340 seconds)

+

Total running time of the script: (0 minutes 1.215 seconds)

Now let’s get an overview of the events on the whole dataset

-

This should be very similar to the ds000248 dataset_description.json!

-

Total running time of the script: (0 minutes 3.875 seconds)

+

Total running time of the script: (0 minutes 3.768 seconds)