Merge branch 'main' into electrodes_dev

Author: hoechenberger

examples/convert_mne_sample.py

@@ -10,7 +10,10 @@
 In this example we will use MNE-BIDS to organize the MNE sample data according
 to the BIDS standard.
 In a second step we will read the organized dataset using MNE-BIDS.
-"""  # noqa: D400 D205
+
+.. _BIDS dataset_description.json definition: https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset-description
+.. _ds000248 dataset_description.json: https://github.com/sappelhoff/bids-examples/blob/master/ds000248/dataset_description.json
+"""  # noqa: D400 D205 E501
 
 # Authors: Mainak Jas <[email protected]>
 #          Alexandre Gramfort <[email protected]>
@@ -24,14 +27,17 @@
 # First we import some basic Python libraries, followed by MNE-Python and its
 # sample data, and then finally the MNE-BIDS functions we need for this example
 
+import json
 import os.path as op
+from pprint import pprint
 import shutil
 
 import mne
 from mne.datasets import sample
 
 from mne_bids import (write_raw_bids, read_raw_bids, write_meg_calibration,
-                      write_meg_crosstalk, BIDSPath, print_dir_tree)
+                      write_meg_crosstalk, BIDSPath, print_dir_tree,
+                      make_dataset_description)
 from mne_bids.stats import count_events
 
 # %%
@@ -82,10 +88,11 @@
 raw.info['line_freq'] = 60
 raw_er.info['line_freq'] = 60
 
+task = 'audiovisual'
 bids_path = BIDSPath(
     subject='01',
     session='01',
-    task='audiovisual',
+    task=task,
     run='1',
     root=output_path
 )
@@ -170,3 +177,57 @@
 with open(readme, 'r', encoding='utf-8-sig') as fid:
     text = fid.read()
 print(text)
+
+# %%
+# It is also generally a good idea to add a description of your dataset,
+# see the `BIDS dataset_description.json definition`_ for more information.
+
+how_to_acknowledge = """\
+If you reference this dataset in a publication, please acknowledge its \
+authors and cite MNE papers: A. Gramfort, M. Luessi, E. Larson, D. Engemann, \
+D. Strohmeier, C. Brodbeck, L. Parkkonen, M. Hämäläinen, \
+MNE software for processing MEG and EEG data, NeuroImage, Volume 86, \
+1 February 2014, Pages 446-460, ISSN 1053-8119 \
+and \
+A. Gramfort, M. Luessi, E. Larson, D. Engemann, D. Strohmeier, C. Brodbeck, \
+R. Goj, M. Jas, T. Brooks, L. Parkkonen, M. Hämäläinen, MEG and EEG data \
+analysis with MNE-Python, Frontiers in Neuroscience, Volume 7, 2013, \
+ISSN 1662-453X"""
+
+make_dataset_description(
+    path=bids_path.root,
+    name=task,
+    authors=["Alexandre Gramfort", "Matti Hämäläinen"],
+    how_to_acknowledge=how_to_acknowledge,
+    acknowledgements="""\
+Alexandre Gramfort, Mainak Jas, and Stefan Appelhoff prepared and updated the \
+data in BIDS format.""",
+    data_license='CC0',
+    ethics_approvals=['Human Subjects Division at the University of Washington'],  # noqa: E501
+    funding=[
+        "NIH 5R01EB009048",
+        "NIH 1R01EB009048",
+        "NIH R01EB006385",
+        "NIH 1R01HD40712",
+        "NIH 1R01NS44319",
+        "NIH 2R01NS37462",
+        "NIH P41EB015896",
+        "ANR-11-IDEX-0003-02",
+        "ERC-StG-263584",
+        "ERC-StG-676943",
+        "ANR-14-NEUC-0002-01"
+    ],
+    references_and_links=[
+        "https://doi.org/10.1016/j.neuroimage.2014.02.017",
+        "https://doi.org/10.3389/fnins.2013.00267",
+        "https://mne.tools/stable/overview/datasets_index.html#sample"
+    ],
+    doi="doi:10.18112/openneuro.ds000248.v1.2.4",
+    overwrite=True
+)
+desc_json_path = bids_path.root / 'dataset_description.json'
+with open(desc_json_path, 'r', encoding='utf-8-sig') as fid:
+    pprint(json.loads(fid.read()))
+
+# %%
+# This should be very similar to the `ds000248 dataset_description.json`_!

mne_bids/path.py

@@ -1622,7 +1622,7 @@ def get_entity_vals(root, entity_key, *, ignore_subjects='emptyroom',
 
     References
     ----------
-    .. [1] https://bids-specification.rtfd.io/en/latest/02-common-principles.html#file-name-structure  # noqa: E501
+    .. [1] https://bids-specification.rtfd.io/en/latest/02-common-principles.html#entities  # noqa: E501
 
     """
     root = _check_fname(