ENH: Expose origin parameter (mne-tools#5588)

doc/whats_new.rst

@@ -57,6 +57,8 @@ Changelog
 
 - Add `split_naming` parameter to the `Raw.save` method to allow for BIDS-compatible raw file name construction by `Teon Brooks`_
 
+- Add ``origin`` parameter to :meth:`mne.Evoked.interpolate_bads` and related methods by `Eric Larson`_
+
 - Add capability to save a :class:`mne.Report` to an HDF5 file to :meth:`mne.Report.save` by `Marijn van Vliet`_
 
 - Add :func:`mne.open_report` to read back a :class:`mne.Report` object that was saved to an HDF5 file by `Marijn van Vliet`_

mne/channels/channels.py

@@ -888,7 +888,7 @@ class InterpolationMixin(object):
 
     @verbose
     def interpolate_bads(self, reset_bads=True, mode='accurate',
-                         verbose=None):
+                         origin=(0., 0., 0.04), verbose=None):
         """Interpolate bad MEG and EEG channels.
 
         Operates in place.
@@ -901,6 +901,12 @@ def interpolate_bads(self, reset_bads=True, mode='accurate',
             Either ``'accurate'`` or ``'fast'``, determines the quality of the
             Legendre polynomial expansion used for interpolation of MEG
             channels.
+        origin : array-like, shape (3,) | str
+            Origin of the sphere in the head coordinate frame and in meters.
+            Can be ``'auto'``, which means a head-digitization-based origin
+            fit. Default is ``(0., 0., 0.04)``.
+
+            .. versionadded:: 0.17
         verbose : bool, str, int, or None
             If not None, override default verbose level (see
             :func:`mne.verbose` and :ref:`Logging documentation <tut_logging>`
@@ -924,7 +930,7 @@ def interpolate_bads(self, reset_bads=True, mode='accurate',
             return self
 
         _interpolate_bads_eeg(self)
-        _interpolate_bads_meg(self, mode=mode)
+        _interpolate_bads_meg(self, mode=mode, origin=origin)
 
         if reset_bads is True:
             self.info['bads'] = []

mne/channels/interpolation.py

@@ -156,7 +156,8 @@ def _interpolate_bads_eeg(inst, verbose=None):
 
 
 @verbose
-def _interpolate_bads_meg(inst, mode='accurate', verbose=None):
+def _interpolate_bads_meg(inst, mode='accurate', origin=(0., 0., 0.04),
+                          verbose=None):
     """Interpolate bad channels from data in good channels.
 
     Parameters
@@ -167,6 +168,10 @@ def _interpolate_bads_meg(inst, mode='accurate', verbose=None):
         Either `'accurate'` or `'fast'`, determines the quality of the
         Legendre polynomial expansion used for interpolation. `'fast'` should
         be sufficient for most applications.
+    origin : array-like, shape (3,) | str
+        Origin of the sphere in the head coordinate frame and in meters.
+        Can be ``'auto'``, which means a head-digitization-based origin
+        fit. Default is ``(0., 0., 0.04)``.
     verbose : bool, str, int, or None
         If not None, override default verbose level (see :func:`mne.verbose`
         and :ref:`Logging documentation <tut_logging>` for more).
@@ -192,5 +197,5 @@ def _interpolate_bads_meg(inst, mode='accurate', verbose=None):
     inst_info['comps'] = []
     info_from = pick_info(inst_info, picks_good)
     info_to = pick_info(inst_info, picks_bad)
-    mapping = _map_meg_channels(info_from, info_to, mode=mode)
+    mapping = _map_meg_channels(info_from, info_to, mode=mode, origin=origin)
     _do_interp_dots(inst, mapping, picks_good, picks_bad)

mne/channels/tests/test_interpolation.py

@@ -145,10 +145,10 @@ def test_interpolation():
     assert np.corrcoef(data1, data2)[0, 1] > thresh
     assert len(epochs_meg.info['bads']) == 0
 
-    # MEG -- evoked
+    # MEG -- evoked (plus auto origin)
     data1 = evoked.data[pick]
     evoked.info.normalize_proj()
-    data2 = evoked.interpolate_bads().data[pick]
+    data2 = evoked.interpolate_bads(origin='auto').data[pick]
     assert np.corrcoef(data1, data2)[0, 1] > thresh
 
 

mne/forward/_field_interpolation.py

@@ -118,6 +118,10 @@ def _map_meg_channels(info_from, info_to, mode='fast', origin=(0., 0., 0.04)):
         Either `'accurate'` or `'fast'`, determines the quality of the
         Legendre polynomial expansion used. `'fast'` should be sufficient
         for most applications.
+    origin : array-like, shape (3,) | str
+        Origin of the sphere in the head coordinate frame and in meters.
+        Can be ``'auto'``, which means a head-digitization-based origin
+        fit. Default is ``(0., 0., 0.04)``.
 
     Returns
     -------
@@ -239,9 +243,9 @@ def _make_surface_mapping(info, surf, ch_type='meg', trans=None, mode='fast',
     n_jobs : int
         Number of permutations to run in parallel (requires joblib package).
     origin : array-like, shape (3,) | str
-        Origin of internal and external multipolar moment space in head
-        coords and in meters. The default is ``'auto'``, which means
-        a head-digitization-based origin fit.
+        Origin of the sphere in the head coordinate frame and in meters.
+        The default is ``'auto'``, which means a head-digitization-based
+        origin fit.
     verbose : bool, str, int, or None
         If not None, override default verbose level (see :func:`mne.verbose`
         and :ref:`Logging documentation <tut_logging>` for more).
@@ -363,20 +367,17 @@ def make_field_map(evoked, trans='auto', subject=None, subjects_dir=None,
         Should be ``'helmet'`` or ``'head'`` to specify in which surface
         to compute the MEG field map. The default value is ``'helmet'``
     origin : array-like, shape (3,) | str
-        Origin of internal and external multipolar moment space in head
-        coords and in meters. Can be ``'auto'``, which means
-        a head-digitization-based origin fit. Default is ``(0., 0., 0.04)``.
+        Origin of the sphere in the head coordinate frame and in meters.
+        Can be ``'auto'``, which means a head-digitization-based origin
+        fit. Default is ``(0., 0., 0.04)``.
 
         .. versionadded:: 0.11
-
     n_jobs : int
         The number of jobs to run in parallel.
     verbose : bool, str, int, or None
         If not None, override default verbose level (see :func:`mne.verbose`
         and :ref:`Logging documentation <tut_logging>` for more).
 
-        .. versionadded:: 0.11
-
     Returns
     -------
     surf_maps : list