FIX: More

Author: larsoner

doc/whats_new.rst

@@ -36,7 +36,7 @@ Detailed list of changes
 - :func:`mne_bids.write_raw_bids()` can now handle mne `Raw` objects with `eyegaze` and `pupil` channels, by `Christian O'Reilly`_ (:gh:`1344`)
 - :func:`mne_bids.get_entity_vals()` has a new parameter ``ignore_suffixes`` to easily ignore sidecar files, by `Daniel McCloy`_ (:gh:`1362`)
 - Empty-room matching now preferentially finds recordings in the subject directory tagged as `task-noise` before looking in the `sub-emptyroom` directories. This adds support for a part of the BIDS specification for ER recordings, by `Berk Gerçek`_ (:gh:`1364`)
-- Path matching is now implemenented in a more efficient manner within `_return_root_paths`, by `Arne Gottwald` (:gh:`1355`)
+- Path matching is now implemenented in a more efficient manner within :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
 - :func:`mne_bids.get_entity_vals()` has a new parameter ``include_match`` to prefilter item matching and ignore non-matched items from begin of directory scan, by `Arne Gottwald` (:gh:`1355`)
 
 
@@ -56,7 +56,7 @@ Detailed list of changes
 - :func:`mne_bids.read_raw_bids` can optionally return an ``event_id`` dictionary suitable for use with :func:`mne.events_from_annotations`, and if a ``values`` column is present in ``events.tsv`` it will be used as the source of the integer event ID codes, by `Daniel McCloy`_ (:gh:`1349`)
 - BIDS dictates that the recording entity should be displayed as "_recording-" in the filename. This PR makes :class:`mne_bids.BIDSPath`  correctly display "_recording-" (instead of "_rec-") in BIDSPath.fpath. By `Scott Huberty`_ (:gh:`1348`)
 - :func:`mne_bids.make_dataset_description` now correctly encodes the dataset description as UTF-8 on disk, by `Scott Huberty`_ (:gh:`1357`)
-- Corrects extension match within `_filter_fnames` at end of filename, by `Arne Gottwald` (:gh:`1355`)
+- Corrects extension when filtering filenames in :meth:`mne_bids.BIDSPath.match()` and :func:`mne_bids.find_matching_paths()`, by `Arne Gottwald` (:gh:`1355`)
 
 ⚕️ Code health
 ^^^^^^^^^^^^^^

mne_bids/path.py

@@ -12,7 +12,6 @@
 from copy import deepcopy
 from datetime import datetime
 from io import StringIO
-from itertools import chain as iter_chain
 from os import path as op
 from pathlib import Path
 from textwrap import indent
@@ -2017,8 +2016,9 @@ def get_entity_vals(
 
         .. versionadded:: 0.17
     include_match : str | array-like of str | None
-        Apply a starting match pragma following Unix style pattern syntax from
-        package glob to prefilter search criterion.
+        Glob-style match string(s) of directories to include in the search (i.e., each
+        must end with ``"/"``). ``None`` (the default) is equivalent to ``"**/"``
+        (within any subdirectory of the BIDS root).
 
         .. versionadded:: 0.17
     with_key : bool
@@ -2119,8 +2119,7 @@ def get_entity_vals(
     search_str = f"**/*{entity_long_abbr_map[entity_key]}-*_*"
     if include_match is not None:
         include_match = _ensure_tuple(include_match)
-        filenames = [root.glob(im + search_str) for im in include_match]
-        filenames = iter_chain(*filenames)
+        filenames = [f for im in include_match for f in root.glob(im + search_str)]
     else:
         filenames = root.glob(search_str)
 
@@ -2543,8 +2542,7 @@ def _return_root_paths(root, datatype=None, ignore_json=True, ignore_nosub=False
     root = Path(root)  # if root is str
 
     if datatype is None and not ignore_nosub:
-        search_str = "*.*"
-        paths = root.rglob(search_str)
+        paths = root.rglob("*.*")
     else:
         if datatype is not None:
             datatype = _ensure_tuple(datatype)
@@ -2557,6 +2555,7 @@ def _return_root_paths(root, datatype=None, ignore_json=True, ignore_nosub=False
         if ignore_nosub:
             search_str = f"sub-*/{search_str}"
         # TODO: Why is this not equivalent to list(root.rglob(search_str)) ?
+        # Most of the speedup is from using glob.iglob here.
         paths = [
             Path(root, fn)
             for fn in glob.iglob(search_str, root_dir=root, recursive=True)

mne_bids/tests/test_path.py

@@ -171,8 +171,8 @@ def test_path_benchmark(tmp_path_factory):
     """Benchmark exploring bids tree."""
     # This benchmark is to verify the speed-up in function call get_entity_vals with
     # `include_match=sub-*/` in face of a bids tree hosting derivatives and sourcedata.
-    n_subjects = 20
-    n_sessions = 10
+    n_subjects = 10
+    n_sessions = 5
     n_derivatives = 17
     tmp_bids_root = tmp_path_factory.mktemp("mnebids_utils_test_bids_ds")
 
@@ -251,6 +251,15 @@ def test_path_benchmark(tmp_path_factory):
     target = 2 * timed_entity / len(bids_subdirectories)
     assert timed_entity_match < target
 
+    # and these should be equivalent
+    out_1 = get_entity_vals(tmp_bids_root, "session")
+    out_2 = get_entity_vals(tmp_bids_root, "session", include_match="**/")
+    assert out_1 == out_2
+    out_3 = get_entity_vals(tmp_bids_root, "session", include_match="sub-*/")
+    assert out_2 == out_3  # all are sub-* vals
+    out_4 = get_entity_vals(tmp_bids_root, "session", include_match="none/")
+    assert out_4 == []
+
 
 def test_search_folder_for_text(capsys):
     """Test finding entries."""