bids_fname -> bids_basename

examples/convert_eeg_to_bids.py

@@ -109,7 +109,7 @@
 # however optional. The required inputs are:
 #
 # * raw
-# * bids_fname
+# * bids_basename
 # * output_path
 #
 # ... as you can see in the docstring:
@@ -132,8 +132,8 @@
 trial_type = {'rest': 0, 'imagine left fist': 1, 'imagine right fist': 2}
 
 # Now convert our data to be in a new BIDS dataset.
-bids_fname = make_bids_basename(subject=subject_id, task=task)
-write_raw_bids(raw_file, bids_fname, output_path, event_id=trial_type,
+bids_basename = make_bids_basename(subject=subject_id, task=task)
+write_raw_bids(raw_file, bids_basename, output_path, event_id=trial_type,
                events_data=events, overwrite=True)
 ###############################################################################
 # What does our fresh BIDS directory look like?
@@ -170,7 +170,7 @@
         make_bids_basename(
             subject='{:03}'.format(subj_idx), task=task_names[task_idx],
             run=run_mapping[task_idx])
-        write_raw_bids(raw, bids_fname, output_path, event_id=trial_type,
+        write_raw_bids(raw, bids_basename, output_path, event_id=trial_type,
                        events_data=events, overwrite=True)
 
 ###############################################################################

examples/convert_group_studies.py

@@ -69,9 +69,9 @@
                             'run_%02d_raw.fif' % run)
 
         raw = mne.io.read_raw_fif(raw_fname)
-        bids_fname = ('sub-%02d_ses-01_task-VisualFaces_run-%d'
-                      % (subject_id, run))
-        write_raw_bids(raw, bids_fname, output_path, event_id=event_id,
+        bids_basename = ('sub-%02d_ses-01_task-VisualFaces_run-%d'
+                         % (subject_id, run))
+        write_raw_bids(raw, bids_basename, output_path, event_id=event_id,
                        overwrite=True)
 
 ###############################################################################

examples/convert_mne_sample.py

@@ -39,8 +39,8 @@
 # Finally, we specify the raw_file and events_data
 
 raw = mne.io.read_raw_fif(raw_fname)
-bids_fname = 'sub-01_ses-01_task-audiovisual_run-01'
-write_raw_bids(raw, bids_fname, output_path, events_data=events_data,
+bids_basename = 'sub-01_ses-01_task-audiovisual_run-01'
+write_raw_bids(raw, bids_basename, output_path, events_data=events_data,
                event_id=event_id, overwrite=True)
 
 ###############################################################################

examples/create_bids_folder.py

@@ -9,8 +9,8 @@
 
 .. note::
 
-   You may automatically convert Raw files to a BIDS-compatible folder with
-   `raw_to_bids`. This example is for manually creating files/folders.
+   You may automatically convert Raw objects to BIDS-compatible files with
+   `write_raw_bids`. This example is for manually creating files/folders.
 """
 
 # Authors: Chris Holdgraf <choldgraf@berkeley.edu>
@@ -30,16 +30,16 @@
 # pieces of metadata, ensuring that they are in the correct order in the
 # final file path. Omitted keys will not be included in the file path.
 
-my_name = make_bids_basename(subject='test', session='two', task='mytask',
-                             suffix='data.csv')
-print(my_name)
+bids_basename = make_bids_basename(subject='test', session='two',
+                                   task='mytask', suffix='data.csv')
+print(bids_basename)
 
 ###############################################################################
 # You may also omit the suffix, which will result in *only* a prefix for a
 # file name. This could then prepended to many more files.
 
-my_name = make_bids_basename(subject='test', task='mytask')
-print(my_name)
+bids_basename = make_bids_basename(subject='test', task='mytask')
+print(bids_basename)
 
 ###############################################################################
 # Creating folders

mne_bids/commands/mne_bids_raw_to_bids.py

@@ -57,12 +57,12 @@ def run():
 
     opt, args = parser.parse_args()
 
-    bids_fname = make_bids_basename(
+    bids_basename = make_bids_basename(
         subject=opt.subject_id, session=opt.session_id, run=opt.run,
         acquisition=opt.acq, task=opt.task)
     raw = _read_raw(opt.raw_fname, hpi=opt.hpi, electrode=opt.electrode,
                     hsp=opt.hsp, config=opt.config)
-    write_raw_bids(raw, bids_fname, opt.output_path, event_id=opt.event_id,
+    write_raw_bids(raw, bids_basename, opt.output_path, event_id=opt.event_id,
                    events_data=opt.events_data, overwrite=opt.overwrite,
                    verbose=True)
 

mne_bids/mne_bids.py

@@ -517,7 +517,7 @@ def _sidecar_json(raw, task, manufacturer, fname, kind, overwrite=False,
     return fname
 
 
-def write_raw_bids(raw, bids_fname, output_path, events_data=None,
+def write_raw_bids(raw, bids_basename, output_path, events_data=None,
                    event_id=None, overwrite=False, verbose=True):
     """Walk over a folder of files and create BIDS compatible folder.
 
@@ -529,7 +529,7 @@ def write_raw_bids(raw, bids_fname, output_path, events_data=None,
     raw : instance of mne.Raw
         The raw data. It must be an instance of mne.Raw. The data should not be
         loaded on disk, i.e., raw.preload must be False.
-    bids_fname : str
+    bids_basename : str
         The base filename of the BIDS compatible files. Typically, this can be
         generated using make_bids_basename.
         Example: sub-01_ses-01_task-testing_acq-01_run-01
@@ -549,7 +549,7 @@ def write_raw_bids(raw, bids_fname, output_path, events_data=None,
     output_path : str
         The path of the root of the BIDS compatible folder. The session and
         subject specific folders will be populated automatically by parsing
-        bids_fname.
+        bids_basename.
     events_data : str | array | None
         The events file. If a string, a path to the events file. If an array,
         the MNE events array (shape n_events, 3). If None, events will be
@@ -602,12 +602,12 @@ def write_raw_bids(raw, bids_fname, output_path, events_data=None,
                        "raw.times should not have changed since reading"
                        " in from the file. It may have been cropped.")
 
-    params = _parse_bids_filename(bids_fname, verbose)
+    params = _parse_bids_filename(bids_basename, verbose)
     subject_id, session_id = params['sub'], params['ses']
     acquisition, task, run = params['acq'], params['task'], params['run']
     kind = _handle_kind(raw)
 
-    bids_fname = bids_fname + '_%s%s' % (kind, ext)
+    bids_fname = bids_basename + '_%s%s' % (kind, ext)
     data_path = make_bids_folders(subject=subject_id, session=session_id,
                                   kind=kind, root=output_path,
                                   overwrite=False, verbose=verbose)
@@ -677,7 +677,7 @@ def write_raw_bids(raw, bids_fname, output_path, events_data=None,
     _mkdir_p(os.path.dirname(bids_fname))
 
     if verbose:
-        print('Writing data files to %s' % bids_fname)
+        print('Copying data files to %s' % bids_fname)
 
     if ext not in ALLOWED_EXTENSIONS:
         raise ValueError('ext must be in %s, got %s'

mne_bids/tests/test_mne_bids.py

@@ -72,36 +72,36 @@ def test_fif():
     raw_fname2 = op.join(data_path2, 'sample_audvis_raw.fif')
     raw.save(raw_fname2)
 
-    bids_fname = bids_basename.replace(subject_id, subject_id2)
-    write_raw_bids(raw, bids_fname, output_path, events_data=events_fname,
+    bids_basename2 = bids_basename.replace(subject_id, subject_id2)
+    write_raw_bids(raw, bids_basename2, output_path, events_data=events_fname,
                    event_id=event_id, overwrite=False)
     # check that the overwrite parameters work correctly for the participant
     # data
     # change the gender but don't force overwrite.
     raw.info['subject_info'] = {'his_id': subject_id2,
                                 'birthday': (1994, 1, 26), 'sex': 2}
     with pytest.raises(OSError, match="already exists"):
-        write_raw_bids(raw, bids_fname, output_path,
+        write_raw_bids(raw, bids_basename2, output_path,
                        events_data=events_fname, event_id=event_id,
                        overwrite=False)
     # now force the overwrite
-    write_raw_bids(raw, bids_fname, output_path, events_data=events_fname,
+    write_raw_bids(raw, bids_basename2, output_path, events_data=events_fname,
                    event_id=event_id, overwrite=True)
 
     with pytest.raises(ValueError, match='raw_file must be'):
         write_raw_bids('blah', bids_basename, output_path)
 
-    bids_fname = 'sub-01_ses-01_xyz-01_run-01'
+    bids_basename2 = 'sub-01_ses-01_xyz-01_run-01'
     with pytest.raises(KeyError, match='Unexpected entity'):
-        write_raw_bids(raw, bids_fname, output_path)
+        write_raw_bids(raw, bids_basename2, output_path)
 
-    bids_fname = 'sub-01_run-01_task-auditory'
+    bids_basename2 = 'sub-01_run-01_task-auditory'
     with pytest.raises(ValueError, match='ordered correctly'):
-        write_raw_bids(raw, bids_fname, output_path, overwrite=True)
+        write_raw_bids(raw, bids_basename2, output_path, overwrite=True)
 
     del raw._filenames
     with pytest.raises(ValueError, match='raw.filenames is missing'):
-        write_raw_bids(raw, bids_fname, output_path)
+        write_raw_bids(raw, bids_basename2, output_path)
 
     cmd = ['bids-validator', output_path]
     run_subprocess(cmd, shell=shell)