From 24bbdac54a9b2392e5f71652fe4cb7697f184976 Mon Sep 17 00:00:00 2001 From: Circle Ci Date: Mon, 5 Aug 2024 07:43:25 +0000 Subject: [PATCH] doc updates [skip ci] --- dev/.buildinfo | 2 +- .../auto_examples_python.zip | Bin 100203 -> 100203 bytes .../read_bids_datasets.zip | Bin 19850 -> 19850 bytes .../mark_bad_channels.zip | Bin 16499 -> 16499 bytes .../convert_mne_sample.zip | Bin 20493 -> 20493 bytes .../convert_nirs_to_bids.zip | Bin 16296 -> 16296 bytes .../convert_group_studies.zip | Bin 11192 -> 11192 bytes .../rename_brainvision_files.zip | Bin 8931 -> 8931 bytes .../auto_examples_jupyter.zip | Bin 154556 -> 154556 bytes .../bidspath.zip | Bin 17550 -> 17550 bytes .../convert_ieeg_to_bids.zip | Bin 47945 -> 47945 bytes .../update_bids_datasets.zip | Bin 11262 -> 11262 bytes .../create_bids_folder.zip | Bin 5694 -> 5694 bytes .../anonymize_dataset.zip | Bin 18580 -> 18580 bytes .../convert_eeg_to_bids.zip | Bin 21351 -> 21351 bytes .../convert_mri_and_trans.zip | Bin 27386 -> 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dev/_modules/mne_bids/path.html | 61 +++++++++++++---- dev/_modules/mne_bids/read.html | 8 +-- 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 | 64 +++++++++--------- dev/auto_examples/bidspath.html | 8 +-- dev/auto_examples/convert_eeg_to_bids.html | 10 +-- dev/auto_examples/convert_empty_room.html | 10 +-- dev/auto_examples/convert_group_studies.html | 10 +-- dev/auto_examples/convert_ieeg_to_bids.html | 10 +-- dev/auto_examples/convert_mne_sample.html | 56 +++++++-------- dev/auto_examples/convert_mri_and_trans.html | 10 +-- dev/auto_examples/convert_nirs_to_bids.html | 10 +-- dev/auto_examples/create_bids_folder.html | 8 +-- dev/auto_examples/mark_bad_channels.html | 10 +-- dev/auto_examples/read_bids_datasets.html | 47 ++++++------- .../rename_brainvision_files.html | 8 +-- dev/auto_examples/sg_execution_times.html | 32 ++++----- dev/auto_examples/update_bids_datasets.html | 10 +-- dev/contribute.html | 8 +-- dev/generated/cli.html | 8 +-- dev/generated/mne_bids.BIDSPath.html | 15 ++-- 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 | 15 ++-- .../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 | 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MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -564,7 +564,7 @@

All modules for which code is available

diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html index 01e9b7cc1..22965d55b 100644 --- a/dev/_modules/mne_bids/copyfiles.html +++ b/dev/_modules/mne_bids/copyfiles.html @@ -7,7 +7,7 @@ - mne_bids.copyfiles — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation + mne_bids.copyfiles — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1211,7 +1211,7 @@

Source code for mne_bids.copyfiles

 
   
diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html
index a11e225dd..8c3e83191 100644
--- a/dev/_modules/mne_bids/dig.html
+++ b/dev/_modules/mne_bids/dig.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.dig — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.dig — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1357,7 +1357,7 @@

Source code for mne_bids.dig

 
   
diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html
index f5052237c..e866051f0 100644
--- a/dev/_modules/mne_bids/inspect.html
+++ b/dev/_modules/mne_bids/inspect.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.inspect — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.inspect — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1012,7 +1012,7 @@

Source code for mne_bids.inspect

 
   
diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html
index 7646dd344..f78df8c5c 100644
--- a/dev/_modules/mne_bids/path.html
+++ b/dev/_modules/mne_bids/path.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.path — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.path — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1223,7 +1223,9 @@

Source code for mne_bids.path

             raise RuntimeError("The root must not be None to remove files.")
 
         # Planning:
-        paths_matched = self.match(ignore_json=False, check=self.check)
+        paths_matched = self.match(
+            ignore_json=False, ignore_nosub=False, check=self.check
+        )
         subjects = set()
         paths_to_delete = list()
         paths_to_update = {}
@@ -1539,7 +1541,7 @@ 

Source code for mne_bids.path

 
 
[docs] - def match(self, ignore_json=True, check=False): + def match(self, *, ignore_json=True, ignore_nosub=False, check=False): """Get a list of all matching paths in the root directory. Performs a recursive search, starting in ``.root`` (if set), based on @@ -1549,6 +1551,9 @@

Source code for mne_bids.path

         ----------
         ignore_json : bool
             If ``True``, ignores json files. Defaults to ``True``.
+        ignore_nosub : bool
+            If ``True``, ignores all files that are not of the form ``root/sub-*``.
+            Defaults to ``False``.
         check : bool
             If ``True``, only returns paths that conform to BIDS. If ``False``
             (default), the ``.check`` attribute of the returned
@@ -1569,7 +1574,10 @@ 

Source code for mne_bids.path

             )
 
         paths = _return_root_paths(
-            self.root, datatype=self.datatype, ignore_json=ignore_json
+            self.root,
+            datatype=self.datatype,
+            ignore_json=ignore_json,
+            ignore_nosub=ignore_nosub,
         )
 
         fnames = _filter_fnames(
@@ -2890,6 +2898,9 @@ 

Source code for mne_bids.path

     extensions=None,
     datatypes=None,
     check=False,
+    *,
+    ignore_json=False,
+    ignore_nosub=False,
 ):
     """Get list of all matching paths for all matching entity values.
 
@@ -2949,6 +2960,11 @@ 

Source code for mne_bids.path

         (default), the ``.check`` attribute of the returned
         :class:`mne_bids.BIDSPath` object will be set to ``True`` for paths that
         do conform to BIDS, and to ``False`` for those that don't.
+    ignore_json : bool
+        If ``True``, ignores json files. Defaults to ``False``.
+    ignore_nosub : bool
+        If ``True``, ignores all files that are not of the form ``root/sub-*``.
+        Defaults to ``False``.
 
     Returns
     -------
@@ -2956,7 +2972,9 @@ 

Source code for mne_bids.path

         The matching paths.
 
     """
-    fpaths = _return_root_paths(root, datatype=datatypes, ignore_json=False)
+    fpaths = _return_root_paths(
+        root, datatype=datatypes, ignore_json=ignore_json, ignore_nosub=ignore_nosub
+    )
 
     fpaths_filtered = _filter_fnames(
         fpaths,
@@ -2979,16 +2997,29 @@ 

Source code for mne_bids.path

 
 
 
-def _return_root_paths(root, datatype=None, ignore_json=True):
-    """Return all paths in root.
+def _return_root_paths(root, datatype=None, ignore_json=True, ignore_nosub=False):
+    """Return all file paths in root.
 
     Can be filtered by datatype (which is present in the path but not in
     the BIDSPath basename). Can also be list of datatypes.
+
+    Parameters
+    ----------
     root : pathlib.Path | str
         The root of the BIDS path.
     datatype : str | array-like of str | None
         The BIDS data type, e.g., ``'anat'``, ``'func'``, ``'eeg'``, ``'meg'``,
         ``'ieeg'``.
+    ignore_json : bool
+        If ``True`` (default), do not return files ending with ``.json``.
+    ignore_nosub : bool
+        If ``True``, return only files of the form ``root/sub-*``. Defaults to
+        ``False``.
+
+    Returns
+    -------
+    paths : list of pathlib.Path
+        All paths in `root`, filtered according to the function parameters.
     """
     root = Path(root)  # if root is str
 
@@ -2999,13 +3030,19 @@ 

Source code for mne_bids.path

         search_str = "*.*"
 
     paths = root.rglob(search_str)
-    # Only keep files (not directories), and omit the JSON sidecars
-    # if ignore_json is True.
+    # Only keep files (not directories), ...
+    # and omit the JSON sidecars if `ignore_json` is True.
     if ignore_json:
         paths = [p for p in paths if p.is_file() and p.suffix != ".json"]
     else:
         paths = [p for p in paths if p.is_file()]
 
+    # only keep files which are of the form root/sub-*,
+    # such that we only look in 'sub'-folders:
+    if ignore_nosub:
+        root_sub = str(root / "sub-")
+        paths = [p for p in paths if str(p).startswith(root_sub)]
+
     return paths
 
 
@@ -3094,7 +3131,7 @@ 

Source code for mne_bids.path

 
   
diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html
index a6369d394..e3c483fe4 100644
--- a/dev/_modules/mne_bids/read.html
+++ b/dev/_modules/mne_bids/read.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.read — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.read — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1744,7 +1744,7 @@

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 bd4a64d58..2a1e8c3c4 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 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.report._report — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1098,7 +1098,7 @@

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 55b25da94..0b9feb27c 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 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.sidecar_updates — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -949,7 +949,7 @@

Source code for mne_bids.sidecar_updates

 
   
diff --git a/dev/_modules/mne_bids/stats.html b/dev/_modules/mne_bids/stats.html
index e66e77a0d..3d4265cb7 100644
--- a/dev/_modules/mne_bids/stats.html
+++ b/dev/_modules/mne_bids/stats.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.stats — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.stats — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -689,7 +689,7 @@

Source code for mne_bids.stats

 
   
diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html
index 2dd0417ce..02f22bd47 100644
--- a/dev/_modules/mne_bids/utils.html
+++ b/dev/_modules/mne_bids/utils.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.utils — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.utils — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -1097,7 +1097,7 @@

Source code for mne_bids.utils

 
   
diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
index 17ab3d0a3..17818575a 100644
--- a/dev/_modules/mne_bids/write.html
+++ b/dev/_modules/mne_bids/write.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.write — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    mne_bids.write — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -3725,7 +3725,7 @@

Source code for mne_bids.write

 
   
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index 73bf67477..f4bdaf439 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.16.0.dev20+g3cbdbab8',
+    VERSION: '0.16.0.dev21+ge37d3b51',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/dev/api.html b/dev/api.html
index 1d486cb1c..44ccdd1c6 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -8,7 +8,7 @@
     
     
 
-    API Documentation — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation
+    API Documentation — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -150,7 +150,7 @@
   
   
   
-    

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -779,7 +779,7 @@

mne_bids.copyfiles - © Copyright 2017, The MNE-BIDS developers. Last updated on 2024-07-30. + © Copyright 2017, The MNE-BIDS developers. Last updated on 2024-08-05.

diff --git a/dev/authors.html b/dev/authors.html index 3af5c66ff..f62c4e27d 100644 --- a/dev/authors.html +++ b/dev/authors.html @@ -8,7 +8,7 @@ - <no title> — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation + <no title> — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation @@ -41,7 +41,7 @@ - + @@ -148,7 +148,7 @@ -

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -575,7 +575,7 @@ diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html index 12c39adab..5a425f3b7 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 0.16.0.dev20+g3cbdbab8 documentation + 13. Anonymizing a BIDS dataset — MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation @@ -41,7 +41,7 @@ - + @@ -151,7 +151,7 @@ -

MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation

+

MNE-BIDS 0.16.0.dev21+ge37d3b51 documentation

@@ -675,7 +675,7 @@

Basic anonymizationSpecifying subject IDsSpecifying subject IDsSpecifying subject IDs

@@ -930,9 +930,9 @@

ReproducibilityTotal running time of the script: (0 minutes 11.307 seconds)

+

Total running time of the script: (0 minutes 11.182 seconds)

@@ -1127,7 +1127,7 @@

Cite mne-bidshttps://bids-standard.github.io/bids-validator/

Command line tool: https://www.npmjs.com/package/bids-validator

-

Total running time of the script: (0 minutes 0.354 seconds)

+

Total running time of the script: (0 minutes 0.352 seconds)

-

Total running time of the script: (0 minutes 2.069 seconds)

+

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

-

Total running time of the script: (0 minutes 1.302 seconds)

+

Total running time of the script: (0 minutes 1.266 seconds)

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

-

Total running time of the script: (0 minutes 3.800 seconds)

+

Total running time of the script: (0 minutes 3.653 seconds)

-

Total running time of the script: (0 minutes 13.008 seconds)

+

Total running time of the script: (0 minutes 12.878 seconds)