diff --git a/dev/.buildinfo b/dev/.buildinfo index eb09dea40..86dd9f920 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: afb9502624699115ff79eeba506855de +config: 4683779c88973204f281741250e6435d tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index afb2e9016..af8a763d0 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/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip b/dev/_downloads/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip index 9ad5edcdd..77c45c2c4 100644 Binary files a/dev/_downloads/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip and b/dev/_downloads/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip differ diff --git a/dev/_downloads/2d16cae3d55264a4b7d58ed70766e580/mark_bad_channels.zip 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b/dev/_images/sphx_glr_read_bids_datasets_001.png index eee0de2fe..59f3b4f3d 100644 Binary files a/dev/_images/sphx_glr_read_bids_datasets_001.png and b/dev/_images/sphx_glr_read_bids_datasets_001.png differ diff --git a/dev/_modules/index.html b/dev/_modules/index.html index ace62cdaa..a2237267f 100644 --- a/dev/_modules/index.html +++ b/dev/_modules/index.html @@ -7,7 +7,7 @@ - Overview: module code — MNE-BIDS 0.16.0.dev20+g3cbdbab8 documentation + Overview: module code — 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

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

All modules for which code is available

- © 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/_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

 
   

     
-      © 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/_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

 
   

     
-      © 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/_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

 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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
 
   

     
-      © 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/_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 @@
 
   

     
-      © 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/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)