Update examples/convert_empty_room.py

Co-authored-by: Richard Höchenberger <[email protected]>

Author: sappelhoff

doc/sphinxext/gen_cli.py

@@ -8,10 +8,9 @@
 # SPDX-License-Identifier: BSD-3-Clause
 
 import glob
-import os
 import shutil
 import sys
-from os import path as op
+from pathlib import Path
 
 import sphinx.util
 from mne.utils import hashfunc, run_subprocess
@@ -57,16 +56,12 @@ def setup(app):
 
 def generate_cli_rst(app=None):
     """Generate the command line interface docs."""
-    out_dir = op.abspath(op.join(op.dirname(__file__), "..", "generated"))
-    if not op.isdir(out_dir):
-        os.mkdir(out_dir)
-    out_fname = op.join(out_dir, "cli.rst.new")
-
-    cli_path = op.abspath(
-        op.join(os.path.dirname(__file__), "..", "..", "mne_bids", "commands")
-    )
+    out_dir = Path(__file__).resolve().parent.parent / "generated"
+    out_dir.mkdir(exist_ok=True)
+    out_fname = out_dir / "cli.rst.new"
+    cli_path = Path(__file__).resolve().parent.parent / "mne_bids" / "commands"
     fnames = sorted(
-        [op.basename(fname) for fname in glob.glob(op.join(cli_path, "mne_bids*.py"))]
+        [Path(fname).name for fname in glob.glob(str(cli_path / "mne_bids*.py"))]
     )
     iterator = sphinx.util.display.status_iterator(
         fnames, "generating MNE-BIDS cli help ... ", length=len(fnames)
@@ -75,7 +70,7 @@ def generate_cli_rst(app=None):
         f.write(header)
         for fname in iterator:
             cmd_name = fname[:-3]
-            run_name = op.join(cli_path, fname)
+            run_name = cli_path / fname
             output, _ = run_subprocess(
                 [sys.executable, run_name, "--help"], verbose=False
             )
@@ -118,10 +113,10 @@ def generate_cli_rst(app=None):
 def _replace_md5(fname):
     """Replace a file based on MD5sum."""
     # adapted from sphinx-gallery
-    assert fname.endswith(".new")
-    fname_old = fname[:-4]
-    if os.path.isfile(fname_old) and hashfunc(fname) == hashfunc(fname_old):
-        os.remove(fname)
+    assert fname.suffix == ".new"
+    fname_old = fname.with_suffix("")
+    if fname_old.is_file() and hashfunc(fname) == hashfunc(fname_old):
+        fname.unlink()
     else:
         shutil.move(fname, fname_old)
 

examples/convert_eeg_to_bids.py

@@ -26,8 +26,8 @@
 
 # %%
 # We are importing everything we need for this example:
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 from mne.datasets import eegbci
@@ -66,8 +66,8 @@
 # of the directory tree.
 
 # get MNE directory with example data
-mne_data_dir = mne.get_config("MNE_DATASETS_EEGBCI_PATH")
-data_dir = op.join(mne_data_dir, "MNE-eegbci-data")
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_EEGBCI_PATH"))
+data_dir = mne_data_dir / "MNE-eegbci-data"
 
 print_dir_tree(data_dir)
 
@@ -156,7 +156,7 @@
 
 # define a task name and a directory where to save the data to
 task = "RestEyesClosed"
-bids_root = op.join(mne_data_dir, "eegmmidb_bids_eeg_example")
+bids_root = mne_data_dir / "eegmmidb_bids_eeg_example"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -218,7 +218,7 @@
 #
 # If you are preparing a manuscript, please make sure to also cite MNE-BIDS
 # there.
-readme = op.join(bids_root, "README")
+readme = bids_root / "README"
 with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)

examples/convert_empty_room.py

@@ -42,7 +42,7 @@
 data_path = sample.data_path()
 raw_fname = data_path / "MEG" / "sample" / "sample_audvis_raw.fif"
 
-bids_root = data_path / ".." / "MNE-sample-data-bids"
+bids_root = data_path.parent / "MNE-sample-data-bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous

examples/convert_group_studies.py

@@ -17,8 +17,8 @@
 # %%
 # Let us import ``mne_bids``
 
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 from mne.datasets import eegbci
@@ -53,14 +53,14 @@
     eegbci.load_data(subject=subject_id, runs=runs, update_path=True)
 
 # get path to MNE directory with the downloaded example data
-mne_data_dir = mne.get_config("MNE_DATASETS_EEGBCI_PATH")
-data_dir = op.join(mne_data_dir, "MNE-eegbci-data")
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_EEGBCI_PATH"))
+data_dir = mne_data_dir / "MNE-eegbci-data"
 
 # %%
 # Let us loop over the subjects and create BIDS-compatible folder
 
 # Make a path where we can save the data to
-bids_root = op.join(mne_data_dir, "eegmmidb_bids_group_conversion")
+bids_root = mne_data_dir / "eegmmidb_bids_group_conversion"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous

examples/convert_ieeg_to_bids.py

@@ -45,8 +45,8 @@
 
 # %%
 
-import os.path as op
 import shutil
+from pathlib import Path
 
 import mne
 import nibabel as nib
@@ -77,9 +77,9 @@
 
 # The electrode coords data are in the tsv file format
 # which is easily read in using numpy
-raw = mne.io.read_raw_fif(op.join(misc_path, "seeg", "sample_seeg_ieeg.fif"))
+raw = mne.io.read_raw_fif(misc_path / "seeg" / "sample_seeg_ieeg.fif")
 raw.info["line_freq"] = 60  # specify power line frequency as required by BIDS
-subjects_dir = op.join(misc_path, "seeg")  # Freesurfer recon-all directory
+subjects_dir = misc_path / "seeg"  # Freesurfer recon-all directory
 
 # %%
 # When the locations of the channels in this dataset were found in
@@ -153,10 +153,10 @@
 task = "motor"
 
 # get MNE-Python directory w/ example data
-mne_data_dir = mne.get_config("MNE_DATASETS_MISC_PATH")
+mne_data_dir = Path(mne.get_config("MNE_DATASETS_MISC_PATH"))
 
 # There is the root directory for where we will write our data.
-bids_root = op.join(mne_data_dir, "ieeg_bids")
+bids_root = mne_data_dir / "ieeg_bids"
 
 # %%
 # To ensure the output path doesn't contain any leftover files from previous
@@ -182,7 +182,7 @@
 # plot T1 to show that it is ACPC-aligned
 # note that the origin is centered on the anterior commissure (AC)
 # with the y-axis passing through the posterior commissure (PC)
-T1_fname = op.join(subjects_dir, "sample_seeg", "mri", "T1.mgz")
+T1_fname = subjects_dir / "sample_seeg" / "mri" / "T1.mgz"
 fig = plot_anat(T1_fname, cut_coords=(0, 0, 0))
 fig.axes["x"].ax.annotate(
     "AC",
@@ -295,7 +295,7 @@
 # We can see that the appropriate citations are already written in the README.
 # If you are preparing a manuscript, please make sure to also cite MNE-BIDS
 # there.
-readme = op.join(bids_root, "README")
+readme = bids_root / "README"
 with open(readme, encoding="utf-8-sig") as fid:
     text = fid.read()
 print(text)
@@ -334,7 +334,7 @@
     shutil.rmtree(bids_root)
 
 # load our raw data again
-raw = mne.io.read_raw_fif(op.join(misc_path, "seeg", "sample_seeg_ieeg.fif"))
+raw = mne.io.read_raw_fif(misc_path / "seeg" / "sample_seeg_ieeg.fif")
 raw.info["line_freq"] = 60  # specify power line frequency as required by BIDS
 
 # get Talairach transform
@@ -463,15 +463,15 @@
     shutil.rmtree(bids_root)
 
 # get a template mgz image to transform the montage to voxel coordinates
-subjects_dir = op.join(mne.datasets.sample.data_path(), "subjects")
-template_T1 = nib.load(op.join(subjects_dir, "fsaverage", "mri", "T1.mgz"))
+subjects_dir = mne.datasets.sample.data_path() / "subjects"
+template_T1 = nib.load(subjects_dir / "fsaverage" / "mri" / "T1.mgz")
 
 # get voxels to surface RAS and scanner RAS transforms
 vox_mri_t = template_T1.header.get_vox2ras_tkr()  # surface RAS
 vox_ras_t = template_T1.header.get_vox2ras()  # scanner RAS
 
 raw = mne.io.read_raw_fif(
-    op.join(misc_path, "seeg", "sample_seeg_ieeg.fif")  # load our raw data again
+    misc_path / "seeg" / "sample_seeg_ieeg.fif"  # load our raw data again
 )
 montage = raw.get_montage()  # get the original montage
 montage.apply_trans(trans)  # head->mri

examples/mark_bad_channels.py

@@ -25,7 +25,6 @@
 # Let's start by importing the required modules and functions, reading the
 # "sample" data, and writing it in the BIDS format.
 
-import os.path as op
 import shutil
 
 import mne
@@ -39,8 +38,8 @@
 )
 
 data_path = mne.datasets.sample.data_path()
-raw_fname = op.join(data_path, "MEG", "sample", "sample_audvis_raw.fif")
-events_fname = op.join(data_path, "MEG", "sample", "sample_audvis_raw-eve.fif")
+raw_fname = data_path / "MEG" / "sample" / "sample_audvis_raw.fif"
+events_fname = data_path / "MEG" / "sample" / "sample_audvis_raw-eve.fif"
 event_id = {
     "Auditory/Left": 1,
     "Auditory/Right": 2,
@@ -49,7 +48,7 @@
     "Smiley": 5,
     "Button": 32,
 }
-bids_root = op.join(data_path, "..", "MNE-sample-data-bids")
+bids_root = data_path.parent / "MNE-sample-data-bids"
 bids_path = BIDSPath(
     subject="01", session="01", task="audiovisual", run="01", root=bids_root
 )