Backport #9972 (#9977)

* Backport #9972

* Fix defaults

* MRG: Add argument overwrite to export for raws and epochs to match save. (#9975)

* Add argument overwrite to export for Raws.

* Add argument overwrite to export for epochs.

* Add tests.

* Add entry to changelog.

* Move entry to changelog to Bugs and fix spelling typo.

* fix indentation for ..versionadded

* typo fix.

* fix tests.

* Change versionadded from 1.0 to 0.24.1 [skip azp] [skip actions]

* Add overwrite for evoked instances (mffpy related).

* FIX: replace else statement with finally.

* Use shutil.rmtree instead of os.remove since mffpy creates a directory.

* Remove finally.

* Update changelog.

* improve comment preceding folder deletion.

* Update mne/epochs.py [skip ci]

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Update mne/export/_egimff.py [skip ci]

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Update mne/export/_export.py [skip ci]

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Update mne/export/_export.py [skip ci]

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Update mne/export/_export.py [skip ci]

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Update mne/export/_egimff.py

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* Fix behavior when pathlib.Path are passed instead of strings.

* Fix import and style.

* add test for epochs as well.

* Remove str(fname) as it's not needed.

* fix positional/keyword arguments.

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

* remove dead link (no suitable alternative) [skip actions][skip azp] (#9979)

* FIX: Backport fix

* import fix for scipy 1.8 pre (#9973)

* import fix for scipy 1.8 pre

* fix arg oversight

* FIX: A couple more

* FIX: Found another

* FIX: More [skip azp] [skip circle]

* FIX: Correct [skip circle] [skip azp]

* FIX: One more

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

Co-authored-by: Mathieu Scheltienne <73893616+mscheltienne@users.noreply.github.com>
Co-authored-by: Eric Larson <larson.eric.d@gmail.com>
Co-authored-by: Daniel McCloy <dan@mccloy.info>

Author: 4 people

doc/changes/0.18.inc

@@ -145,7 +145,7 @@ Bug
 
 - Fix :func:`mne.gui.coregistration` and :ref:`mne coreg` crashing with segmentation fault when switching subjects by `Eric Larson`_
 
-- Fix :func:`mne.io.read_raw_brainvision` to accommodate vmrk files which do not have any annotations by `Alexander Kovrig`_
+- Fix :func:`mne.io.read_raw_brainvision` to accommodate vmrk files which do not have any annotations by Alexander Kovrig
 
 - Fix :meth:`mne.io.Raw.plot` and :meth:`mne.Epochs.plot` to auto-scale ``misc`` channel types by default by `Eric Larson`_
 

doc/changes/0.24.inc

@@ -21,6 +21,10 @@ Version 0.24.1 (Unreleased)
 
 - Fix bug with :class:`mne.Report` where figures were saved with ``bbox_inches='tight'``, which led to inconsistent sizes in sliders (:gh:`9966` by `Eric Larson`_)
 
+- :func:`mne.gui.coregistration` and the ``mne coreg`` command didn't respect the ``inspect`` parameter (:gh:`9972` by `Richard Höchenberger`_)
+
+- Add missing argument ``overwrite`` to :func:`mne.export.export_raw`, :func:`mne.export.export_epochs`, :func:`mne.export.export_evokeds` and :func:`mne.export.export_evokeds_mff` (:gh:`9975` by `Mathieu Scheltienne`_)
+
 .. _changes_0_24_0:
 
 Version 0.24.0 (2021-11-03)

doc/changes/names.inc

@@ -244,8 +244,6 @@
 
 .. _Quentin Bertrand: https://github.com/QB3
 
-.. _Alexander Kovrig: https://github.com/OpenSatori
-
 .. _Kostiantyn Maksymenko: https://github.com/makkostya
 
 .. _Thomas Radman: https://github.com/tradman

doc/conf.py

@@ -855,6 +855,7 @@ def reset_warnings(gallery_conf, fname):
                 "default value of type 'dict' in an Any trait will",  # traits
                 'rcParams is deprecated',  # PyVista rcParams -> global_theme
                 'to mean no clipping',
+                'Call to deprecated method ThresholdBetween',
                 ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             'ignore', message=".*%s.*" % key, category=DeprecationWarning)

mne/epochs.py

@@ -1914,7 +1914,7 @@ def save(self, fname, split_size='2GB', fmt='single', overwrite=False,
                         split_naming, overwrite)
 
     @verbose
-    def export(self, fname, fmt='auto', verbose=None):
+    def export(self, fname, fmt='auto', *, overwrite=False, verbose=None):
         """Export Epochs to external formats.
 
         Supported formats: EEGLAB (set, uses :mod:`eeglabio`)
@@ -1924,14 +1924,17 @@ def export(self, fname, fmt='auto', verbose=None):
         ----------
         %(export_params_fname)s
         %(export_params_fmt)s
+        %(overwrite)s
+
+            .. versionadded:: 0.24.1
         %(verbose)s
 
         Notes
         -----
         %(export_eeglab_note)s
         """
         from .export import export_epochs
-        export_epochs(fname, self, fmt, verbose)
+        export_epochs(fname, self, fmt, overwrite=overwrite, verbose=verbose)
 
     def equalize_event_counts(self, event_ids=None, method='mintime'):
         """Equalize the number of trials in each condition.

mne/export/_egimff.py

@@ -3,17 +3,21 @@
 #
 # License: BSD-3-Clause
 
+import os
+import shutil
 import datetime
+import os.path as op
 
 import numpy as np
 
 from ..io.egi.egimff import _import_mffpy
 from ..io.pick import pick_types, pick_channels
-from ..utils import verbose
+from ..utils import verbose, _check_fname
 
 
 @verbose
-def export_evokeds_mff(fname, evoked, history=None, *, verbose=None):
+def export_evokeds_mff(fname, evoked, history=None, *, overwrite=False,
+                       verbose=None):
     """Export evoked dataset to MFF.
 
     Parameters
@@ -28,6 +32,9 @@ def export_evokeds_mff(fname, evoked, history=None, *, verbose=None):
         history.xml. This must adhere to the format described in
         mffpy.xml_files.History.content. If None, no history.xml will be
         written.
+    %(overwrite)s
+
+        .. versionadded:: 0.24.1
     %(verbose)s
 
     Notes
@@ -48,6 +55,11 @@ def export_evokeds_mff(fname, evoked, history=None, *, verbose=None):
     sampling_rate = int(info['sfreq'])
 
     # Initialize writer
+    # Future changes: conditions based on version or mffpy requirement if
+    # https://github.com/BEL-Public/mffpy/pull/92 is merged and released.
+    fname = _check_fname(fname, overwrite=overwrite)
+    if op.exists(fname):
+        os.remove(fname) if op.isfile(fname) else shutil.rmtree(fname)
     writer = mffpy.Writer(fname)
     current_time = pytz.utc.localize(datetime.datetime.utcnow())
     writer.addxml('fileInfo', recordTime=current_time)

mne/export/_export.py

@@ -6,12 +6,12 @@
 import os.path as op
 
 from ._egimff import export_evokeds_mff
-from ..utils import verbose, logger, _validate_type
+from ..utils import verbose, logger, _validate_type, _check_fname
 
 
 @verbose
 def export_raw(fname, raw, fmt='auto', physical_range='auto',
-               add_ch_type=False, verbose=None):
+               add_ch_type=False, *, overwrite=False, verbose=None):
     """Export Raw to external formats.
 
     Supported formats:
@@ -27,13 +27,17 @@ def export_raw(fname, raw, fmt='auto', physical_range='auto',
     %(export_params_fmt)s
     %(export_params_physical_range)s
     %(export_params_add_ch_type)s
+    %(overwrite)s
+
+        .. versionadded:: 0.24.1
     %(verbose)s
 
     Notes
     -----
     %(export_eeglab_note)s
     %(export_edf_note)s
     """
+    fname = _check_fname(fname, overwrite=overwrite)
     supported_export_formats = {  # format : extensions
         'eeglab': ('set',),
         'edf': ('edf',),
@@ -52,7 +56,7 @@ def export_raw(fname, raw, fmt='auto', physical_range='auto',
 
 
 @verbose
-def export_epochs(fname, epochs, fmt='auto', verbose=None):
+def export_epochs(fname, epochs, fmt='auto', *, overwrite=False, verbose=None):
     """Export Epochs to external formats.
 
     Supported formats: EEGLAB (set, uses :mod:`eeglabio`)
@@ -64,12 +68,16 @@ def export_epochs(fname, epochs, fmt='auto', verbose=None):
     epochs : instance of Epochs
         The epochs to export.
     %(export_params_fmt)s
+    %(overwrite)s
+
+        .. versionadded:: 0.24.1
     %(verbose)s
 
     Notes
     -----
     %(export_eeglab_note)s
     """
+    fname = _check_fname(fname, overwrite=overwrite)
     supported_export_formats = {
         'eeglab': ('set',),
         'edf': ('edf',),
@@ -87,7 +95,8 @@ def export_epochs(fname, epochs, fmt='auto', verbose=None):
 
 
 @verbose
-def export_evokeds(fname, evoked, fmt='auto', verbose=None):
+def export_evokeds(fname, evoked, fmt='auto', *, overwrite=False,
+                   verbose=None):
     """Export evoked dataset to external formats.
 
     This function is a wrapper for format-specific export functions. The export
@@ -109,6 +118,9 @@ def export_evokeds(fname, evoked, fmt='auto', verbose=None):
         Format of the export. Defaults to ``'auto'``, which will infer the
         format from the filename extension. See supported formats above for
         more information.
+    %(overwrite)s
+
+        .. versionadded:: 0.24.1
     %(verbose)s
 
     See Also
@@ -120,6 +132,7 @@ def export_evokeds(fname, evoked, fmt='auto', verbose=None):
     -----
     .. versionadded:: 0.24
     """
+    fname = _check_fname(fname, overwrite=overwrite)
     supported_export_formats = {
         'mff': ('mff',),
         'eeglab': ('set',),
@@ -134,7 +147,7 @@ def export_evokeds(fname, evoked, fmt='auto', verbose=None):
     logger.info(f'Exporting evoked dataset to {fname}...')
 
     if fmt == 'mff':
-        export_evokeds_mff(fname, evoked)
+        export_evokeds_mff(fname, evoked, overwrite=overwrite)
     elif fmt == 'eeglab':
         raise NotImplementedError('Export to EEGLAB not implemented.')
     elif fmt == 'edf':

mne/export/tests/test_export.py

@@ -51,6 +51,14 @@ def test_export_raw_eeglab(tmp_path):
     assert_allclose(raw.times, raw_read.times)
     assert_allclose(raw.get_data(), raw_read.get_data())
 
+    # test overwrite
+    with pytest.raises(FileExistsError, match='Destination file exists'):
+        raw.export(temp_fname, overwrite=False)
+    raw.export(temp_fname, overwrite=True)
+
+    # test pathlib.Path files
+    raw.export(Path(temp_fname), overwrite=True)
+
 
 @pytest.mark.skipif(not _check_edflib_installed(strict=False),
                     reason='edflib-python not installed')
@@ -78,7 +86,7 @@ def test_double_export_edf(tmp_path):
 
     # export again
     raw_read.load_data()
-    raw_read.export(temp_fname, add_ch_type=True)
+    raw_read.export(temp_fname, add_ch_type=True, overwrite=True)
     raw_read = read_raw_edf(temp_fname, preload=True)
 
     # stim channel should be dropped
@@ -180,28 +188,28 @@ def test_rawarray_edf(tmp_path):
     raw_bad.rename_channels({'1': 'abcdefghijklmnopqrstuvwxyz'})
     with pytest.raises(RuntimeError, match='Signal label'), \
             pytest.warns(RuntimeWarning, match='Data has a non-integer'):
-        raw_bad.export(temp_fname)
+        raw_bad.export(temp_fname, overwrite=True)
 
     # include bad birthday that is non-EDF compliant
     bad_info = info.copy()
     bad_info['subject_info']['birthday'] = (1700, 1, 20)
     raw = RawArray(data, bad_info)
     with pytest.raises(RuntimeError, match='Setting patient birth date'):
-        raw.export(temp_fname)
+        raw.export(temp_fname, overwrite=True)
 
     # include bad measurement date that is non-EDF compliant
     raw = RawArray(data, info)
     meas_date = datetime(year=1984, month=1, day=1, tzinfo=timezone.utc)
     raw.set_meas_date(meas_date)
     with pytest.raises(RuntimeError, match='Setting start date time'):
-        raw.export(temp_fname)
+        raw.export(temp_fname, overwrite=True)
 
     # test that warning is raised if there are non-voltage based channels
     raw = RawArray(data, info)
     with pytest.warns(RuntimeWarning, match='The unit'):
         raw.set_channel_types({'9': 'hbr'})
     with pytest.warns(RuntimeWarning, match='Non-voltage channels'):
-        raw.export(temp_fname)
+        raw.export(temp_fname, overwrite=True)
 
     # data should match up to the non-accepted channel
     raw_read = read_raw_edf(temp_fname, preload=True)
@@ -313,6 +321,14 @@ def test_export_epochs_eeglab(tmp_path, preload):
     assert_allclose(epochs.times, epochs_read.times)
     assert_allclose(epochs.get_data(), epochs_read.get_data())
 
+    # test overwrite
+    with pytest.raises(FileExistsError, match='Destination file exists'):
+        epochs.export(temp_fname, overwrite=False)
+    epochs.export(temp_fname, overwrite=True)
+
+    # test pathlib.Path files
+    epochs.export(Path(temp_fname), overwrite=True)
+
 
 @requires_version('mffpy', '0.5.7')
 @testing.requires_testing_data
@@ -355,6 +371,20 @@ def test_export_evokeds_to_mff(tmp_path, fmt, do_history):
         assert ave_exported.comment == ave.comment
         assert_allclose(ave_exported.times, ave.times)
 
+    # test overwrite
+    with pytest.raises(FileExistsError, match='Destination file exists'):
+        if do_history:
+            export_evokeds_mff(export_fname, evoked, history=history,
+                               overwrite=False)
+        else:
+            export_evokeds(export_fname, evoked, overwrite=False)
+
+    if do_history:
+        export_evokeds_mff(export_fname, evoked, history=history,
+                           overwrite=True)
+    else:
+        export_evokeds(export_fname, evoked, overwrite=True)
+
 
 @requires_version('mffpy', '0.5.7')
 @testing.requires_testing_data

mne/externals/pymatreader/pymatreader.py

@@ -31,9 +31,8 @@
 import scipy.io
 import os
 
-from scipy.io.matlab.miobase import get_matfile_version
-
-from .utils import _import_h5py, _hdf5todict, _check_for_scipy_mat_struct
+from .utils import (_import_h5py, _hdf5todict, _check_for_scipy_mat_struct,
+                    get_matfile_version)
 
 __all__ = 'read_mat'
 

mne/externals/pymatreader/utils.py

@@ -33,6 +33,15 @@
 import numpy
 import scipy.io
 
+try:
+    from scipy.io.matlab.miobase import get_matfile_version
+    from scipy.io.matlab.mio5_params import MatlabOpaque
+    from scipy.io.matlab.mio5 import MatlabFunction
+except ModuleNotFoundError:  # scipy 1.8
+    from scipy.io._matlab.miobase import get_matfile_version
+    from scipy.io._matlab.mio5_params import MatlabOpaque
+    from scipy.io._matlab.mio5 import MatlabFunction
+
 if sys.version_info <= (2, 7):
     chr = unichr  # noqa This is needed for python 2 and 3 compatibility
 
@@ -209,7 +218,7 @@ def _check_for_scipy_mat_struct(data):
         for key in data:
             data[key] = _check_for_scipy_mat_struct(data[key])
 
-    if isinstance(data, scipy.io.matlab.mio5_params.MatlabOpaque):
+    if isinstance(data, MatlabOpaque):
         warn('Complex objects (like classes) are not supported. '
              'They are imported on a best effort base '
              'but your mileage will vary.')
@@ -222,7 +231,7 @@ def _check_for_scipy_mat_struct(data):
 
 def _handle_scipy_ndarray(data):
     if data.dtype == numpy.dtype('object') and not \
-            isinstance(data, scipy.io.matlab.mio5.MatlabFunction):
+            isinstance(data, MatlabFunction):
         as_list = []
         for element in data:
             as_list.append(_check_for_scipy_mat_struct(element))