MRG, MAINT: Go back to OrderedDict

mne/annotations.py

@@ -2,6 +2,7 @@
 #
 # License: BSD (3-clause)
 
+from collections import OrderedDict
 from datetime import datetime, timedelta, timezone
 import os.path as op
 import re
@@ -249,7 +250,7 @@ def __getitem__(self, key):
             out_keys = ('onset', 'duration', 'description', 'orig_time')
             out_vals = (self.onset[key], self.duration[key],
                         self.description[key], self.orig_time)
-            return dict(zip(out_keys, out_vals))
+            return OrderedDict(zip(out_keys, out_vals))
         else:
             key = list(key) if isinstance(key, tuple) else key
             return Annotations(onset=self.onset[key],

mne/channels/_standard_montage_utils.py

@@ -2,6 +2,7 @@
 #          Alexandre Gramfort <alexandre.gramfort@inria.fr>
 #
 # License: BSD (3-clause)
+from collections import OrderedDict
 import os.path as op
 import numpy as np
 
@@ -90,7 +91,7 @@ def _mgh_or_standard(basename, head_size):
             ch_names_.append(line.strip(' ').strip('\n'))
 
     pos = np.array(pos)
-    ch_pos = dict(zip(ch_names_, pos))
+    ch_pos = OrderedDict(zip(ch_names_, pos))
     nasion, lpa, rpa = [ch_pos.pop(n) for n in fid_names]
     scale = head_size / np.median(np.linalg.norm(pos, axis=1))
     for value in ch_pos.values():
@@ -151,7 +152,7 @@ def _read_sfp(fname, head_size):
     ch_names, xs, ys, zs = _safe_np_loadtxt(fname, **options)
 
     pos = np.stack([xs, ys, zs], axis=-1)
-    ch_pos = dict(zip(ch_names, pos))
+    ch_pos = OrderedDict(zip(ch_names, pos))
     # no one grants that fid names are there.
     nasion, lpa, rpa = [ch_pos.pop(n, None) for n in fid_names]
 
@@ -177,7 +178,7 @@ def _read_csd(fname, head_size):
     if head_size is not None:
         pos *= head_size / np.median(np.linalg.norm(pos, axis=1))
 
-    return make_dig_montage(ch_pos=dict(zip(ch_names, pos)))
+    return make_dig_montage(ch_pos=OrderedDict(zip(ch_names, pos)))
 
 
 def _read_elc(fname, head_size):
@@ -225,7 +226,7 @@ def _read_elc(fname, head_size):
     if head_size is not None:
         pos *= head_size / np.median(np.linalg.norm(pos, axis=1))
 
-    ch_pos = dict(zip(ch_names_, pos))
+    ch_pos = OrderedDict(zip(ch_names_, pos))
     nasion, lpa, rpa = [ch_pos.pop(n, None) for n in fid_names]
 
     return make_dig_montage(ch_pos=ch_pos, coord_frame='unknown',
@@ -251,7 +252,7 @@ def _read_theta_phi_in_degrees(fname, head_size, fid_names=None,
 
     radii = np.full(len(phi), head_size)
     pos = _sph_to_cart(np.array([radii, np.deg2rad(phi), np.deg2rad(theta)]).T)
-    ch_pos = dict(zip(ch_names, pos))
+    ch_pos = OrderedDict(zip(ch_names, pos))
 
     nasion, lpa, rpa = None, None, None
     if fid_names is not None:
@@ -282,7 +283,7 @@ def _read_elp_besa(fname, head_size):
     if head_size is not None:
         pos *= head_size / np.median(np.linalg.norm(pos, axis=1))
 
-    ch_pos = dict(zip(ch_names, pos))
+    ch_pos = OrderedDict(zip(ch_names, pos))
 
     fid_names = ('Nz', 'LPA', 'RPA')
     # No one grants that the fid names actually exist.
@@ -310,4 +311,4 @@ def _read_brainvision(fname, head_size):
     if head_size is not None:
         pos *= head_size / np.median(np.linalg.norm(pos, axis=1))
 
-    return make_dig_montage(ch_pos=dict(zip(ch_names, pos)))
+    return make_dig_montage(ch_pos=OrderedDict(zip(ch_names, pos)))

mne/channels/montage.py

@@ -11,10 +11,11 @@
 #
 # License: Simplified BSD
 
-import os.path as op
-import re
+from collections import OrderedDict
 from copy import deepcopy
 from functools import partial
+import os.path as op
+import re
 
 import numpy as np
 
@@ -289,7 +290,7 @@ def __add__(self, other):
     def _get_ch_pos(self):
         pos = [d['r'] for d in _get_dig_eeg(self.dig)]
         assert len(self.ch_names) == len(pos)
-        return dict(zip(self.ch_names, pos))
+        return OrderedDict(zip(self.ch_names, pos))
 
     def _get_dig_names(self):
         NAMED_KIND = (FIFF.FIFFV_POINT_EEG,)
@@ -302,9 +303,12 @@ def _get_dig_names(self):
         return dig_names
 
 
-def _check_unit_and_get_scaling(unit, valid_scales):
-    _check_option('unit', unit, list(valid_scales.keys()))
-    return valid_scales[unit]
+VALID_SCALES = dict(mm=1e-3, cm=1e-2, m=1)
+
+
+def _check_unit_and_get_scaling(unit):
+    _check_option('unit', unit, sorted(VALID_SCALES.keys()))
+    return VALID_SCALES[unit]
 
 
 def transform_to_head(montage):
@@ -514,8 +518,7 @@ def read_dig_hpts(fname, unit='mm'):
 
     """
     from ._standard_montage_utils import _str_names, _str
-    VALID_SCALES = dict(mm=1e-3, cm=1e-2, m=1)
-    _scale = _check_unit_and_get_scaling(unit, VALID_SCALES)
+    _scale = _check_unit_and_get_scaling(unit)
 
     out = np.genfromtxt(fname, comments='#',
                         dtype=(_str, _str, 'f8', 'f8', 'f8'))
@@ -705,7 +708,8 @@ def _backcompat_value(pos, ref_pos):
             info_names_use = info_names
             dig_names_use = dig_names
         else:
-            ch_pos_use = {name.lower(): pos for name, pos in ch_pos.items()}
+            ch_pos_use = OrderedDict(
+                (name.lower(), pos) for name, pos in ch_pos.items())
             info_names_use = [name.lower() for name in info_names]
             dig_names_use = [name.lower() if name is not None else name
                              for name in dig_names]
@@ -738,15 +742,14 @@ def _backcompat_value(pos, ref_pos):
                 logger.info(missing_coord_msg)
 
             # set ch coordinates and names from digmontage or nan coords
-            _ch_pos_use = dict(ch_pos_use)  # make a copy
-            for name in info_names:
-                if name not in ch_pos_use:
-                    _ch_pos_use[name] = [np.nan, np.nan, np.nan]
-            ch_pos_use = _ch_pos_use
+            ch_pos_use = dict(
+                (name, ch_pos_use.get(name, [np.nan] * 3))
+                for name in info_names)  # order does not matter here
 
         for name, use in zip(info_names, info_names_use):
             _loc_view = info['chs'][info['ch_names'].index(name)]['loc']
             _loc_view[:6] = _backcompat_value(ch_pos_use[use], eeg_ref_pos)
+        del ch_pos_use
 
         # XXX this is probably wrong as it uses the order from the montage
         # rather than the order of our info['ch_names'] ...
@@ -868,8 +871,7 @@ def read_dig_polhemus_isotrak(fname, ch_names=None, unit='m'):
     read_dig_fif
     """
     VALID_FILE_EXT = ('.hsp', '.elp', '.eeg')
-    VALID_SCALES = dict(mm=1e-3, cm=1e-2, m=1)
-    _scale = _check_unit_and_get_scaling(unit, VALID_SCALES)
+    _scale = _check_unit_and_get_scaling(unit)
 
     _, ext = op.splitext(fname)
     _check_option('fname', ext, VALID_FILE_EXT)
@@ -892,7 +894,7 @@ def read_dig_polhemus_isotrak(fname, ch_names=None, unit='m'):
     else:
         points = data.pop('points')
         if points.shape[0] == len(ch_names):
-            data['ch_pos'] = dict(zip(ch_names, points))
+            data['ch_pos'] = OrderedDict(zip(ch_names, points))
         else:
             raise ValueError((
                 "Length of ``ch_names`` does not match the number of points"
@@ -938,8 +940,7 @@ def read_polhemus_fastscan(fname, unit='mm'):
     make_dig_montage
     """
     VALID_FILE_EXT = ['.txt']
-    VALID_SCALES = dict(mm=1e-3, cm=1e-2, m=1)
-    _scale = _check_unit_and_get_scaling(unit, VALID_SCALES)
+    _scale = _check_unit_and_get_scaling(unit)
 
     _, ext = op.splitext(fname)
     _check_option('fname', ext, VALID_FILE_EXT)
@@ -1031,7 +1032,7 @@ def read_custom_montage(fname, head_size=HEAD_SIZE_DEFAULT, coord_frame=None):
         pos *= scale
 
         montage = make_dig_montage(
-            ch_pos=dict(zip(ch_names, pos)),
+            ch_pos=OrderedDict(zip(ch_names, pos)),
             coord_frame='head',
         )
 

mne/datasets/utils.py

@@ -5,6 +5,7 @@
 #          Stefan Appelhoff <stefan.appelhoff@mailbox.org>
 # License: BSD Style.
 
+from collections import OrderedDict
 import os
 import os.path as op
 import shutil
@@ -701,7 +702,7 @@ def fetch_hcp_mmp_parcellation(subjects_dir=None, combine=True, verbose=None):
             return
         # otherwise, let's make them
         logger.info('Creating combined labels')
-        groups = dict([
+        groups = OrderedDict([
             ('Primary Visual Cortex (V1)',
              ('V1',)),
             ('Early Visual Cortex',

mne/io/what.py

@@ -3,6 +3,8 @@
 #
 # License: BSD (3-clause)
 
+from collections import OrderedDict
+
 from ..fixes import _get_args
 from ..utils import _check_fname, logger
 
@@ -38,7 +40,7 @@ def what(fname):
     from ..proj import read_proj
     from .meas_info import read_fiducials
     _check_fname(fname, overwrite='read', must_exist=True)
-    checks = dict()
+    checks = OrderedDict()
     checks['raw'] = read_raw_fif
     checks['ica'] = read_ica
     checks['epochs'] = read_epochs

mne/tests/test_annotations.py

@@ -2,6 +2,7 @@
 #
 # License: BSD 3 clause
 
+from collections import OrderedDict
 from datetime import datetime, timezone
 from itertools import repeat
 import sys
@@ -967,7 +968,7 @@ def test_annotations_simple_iteration():
                         orig_time=None)
 
     for ii, elements in enumerate(annot[:2]):
-        assert isinstance(elements, dict)
+        assert isinstance(elements, OrderedDict)
         expected_values = (ii, ii, str(ii))
         for elem, expected_type, expected_value in zip(elements.values(),
                                                        EXPECTED_ELEMENTS_TYPE,

mne/utils/mixin.py

@@ -4,7 +4,7 @@
 #
 # License: BSD (3-clause)
 
-
+from collections import OrderedDict
 from copy import deepcopy
 import logging
 import json
@@ -413,7 +413,7 @@ def _prepare_read_metadata(metadata):
         pd = _check_pandas_installed(strict=False)
         # use json.loads because this preserves ordering
         # (which is necessary for round-trip equivalence)
-        metadata = json.loads(metadata, object_pairs_hook=dict)
+        metadata = json.loads(metadata, object_pairs_hook=OrderedDict)
         assert isinstance(metadata, list)
         if pd:
             metadata = pd.DataFrame.from_records(metadata)