1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184
|
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
# Daniel McCloy <dan.mccloy@gmail.com>
#
# License: BSD-3-Clause
import os.path as op
from pathlib import Path
import sys
from collections import OrderedDict
from dataclasses import dataclass
from copy import deepcopy
from functools import partial
import string
from typing import Union
import numpy as np
from ..defaults import HEAD_SIZE_DEFAULT, _handle_default
from ..utils import (verbose, logger, warn,
_check_preload, _validate_type, fill_doc, _check_option,
_get_stim_channel, _check_fname, _check_dict_keys,
_on_missing)
from ..io.constants import FIFF
from ..io.meas_info import (anonymize_info, Info, MontageMixin, create_info,
_rename_comps)
from ..io.pick import (channel_type, pick_info, pick_types, _picks_by_type,
_check_excludes_includes, _contains_ch_type,
channel_indices_by_type, pick_channels, _picks_to_idx,
get_channel_type_constants,
_pick_data_channels)
from ..io.tag import _rename_list
from ..io.write import DATE_NONE
from ..io.proj import setup_proj
def _get_meg_system(info):
"""Educated guess for the helmet type based on channels."""
have_helmet = True
for ch in info['chs']:
if ch['kind'] == FIFF.FIFFV_MEG_CH:
# Only take first 16 bits, as higher bits store CTF grad comp order
coil_type = ch['coil_type'] & 0xFFFF
nmag = np.sum(
[c['kind'] == FIFF.FIFFV_MEG_CH for c in info['chs']])
if coil_type == FIFF.FIFFV_COIL_NM_122:
system = '122m'
break
elif coil_type // 1000 == 3: # All Vectorview coils are 30xx
system = '306m'
break
elif (coil_type == FIFF.FIFFV_COIL_MAGNES_MAG or
coil_type == FIFF.FIFFV_COIL_MAGNES_GRAD):
system = 'Magnes_3600wh' if nmag > 150 else 'Magnes_2500wh'
break
elif coil_type == FIFF.FIFFV_COIL_CTF_GRAD:
system = 'CTF_275'
break
elif coil_type == FIFF.FIFFV_COIL_KIT_GRAD:
system = 'KIT'
# Our helmet does not match very well, so let's just create it
have_helmet = False
break
elif coil_type == FIFF.FIFFV_COIL_BABY_GRAD:
system = 'BabySQUID'
break
elif coil_type == FIFF.FIFFV_COIL_ARTEMIS123_GRAD:
system = 'ARTEMIS123'
have_helmet = False
break
else:
system = 'unknown'
have_helmet = False
return system, have_helmet
def _get_ch_type(inst, ch_type, allow_ref_meg=False):
"""Choose a single channel type (usually for plotting).
Usually used in plotting to plot a single datatype, e.g. look for mags,
then grads, then ... to plot.
"""
if ch_type is None:
allowed_types = ['mag', 'grad', 'planar1', 'planar2', 'eeg', 'csd',
'fnirs_cw_amplitude', 'fnirs_fd_ac_amplitude',
'fnirs_fd_phase', 'fnirs_od', 'hbo', 'hbr',
'ecog', 'seeg', 'dbs']
allowed_types += ['ref_meg'] if allow_ref_meg else []
for type_ in allowed_types:
if isinstance(inst, Info):
if _contains_ch_type(inst, type_):
ch_type = type_
break
elif type_ in inst:
ch_type = type_
break
else:
raise RuntimeError('No plottable channel types found')
return ch_type
@verbose
def equalize_channels(instances, copy=True, verbose=None):
"""Equalize channel picks and ordering across multiple MNE-Python objects.
First, all channels that are not common to each object are dropped. Then,
using the first object in the list as a template, the channels of each
object are re-ordered to match the template. The end result is that all
given objects define the same channels, in the same order.
Parameters
----------
instances : list
A list of MNE-Python objects to equalize the channels for. Objects can
be of type Raw, Epochs, Evoked, AverageTFR, Forward, Covariance,
CrossSpectralDensity or Info.
copy : bool
When dropping and/or re-ordering channels, an object will be copied
when this parameter is set to ``True``. When set to ``False`` (the
default) the dropping and re-ordering of channels happens in-place.
.. versionadded:: 0.20.0
%(verbose)s
Returns
-------
equalized_instances : list
A list of MNE-Python objects that have the same channels defined in the
same order.
Notes
-----
This function operates inplace.
"""
from ..cov import Covariance
from ..io.base import BaseRaw
from ..io.meas_info import Info
from ..epochs import BaseEpochs
from ..evoked import Evoked
from ..forward import Forward
from ..time_frequency import _BaseTFR, CrossSpectralDensity
# Instances need to have a `ch_names` attribute and a `pick_channels`
# method that supports `ordered=True`.
allowed_types = (BaseRaw, BaseEpochs, Evoked, _BaseTFR, Forward,
Covariance, CrossSpectralDensity, Info)
allowed_types_str = ("Raw, Epochs, Evoked, TFR, Forward, Covariance, "
"CrossSpectralDensity or Info")
for inst in instances:
_validate_type(inst, allowed_types, "Instances to be modified",
allowed_types_str)
chan_template = instances[0].ch_names
logger.info('Identifying common channels ...')
channels = [set(inst.ch_names) for inst in instances]
common_channels = set(chan_template).intersection(*channels)
all_channels = set(chan_template).union(*channels)
dropped = list(set(all_channels - common_channels))
# Preserve the order of chan_template
order = np.argsort([chan_template.index(ch) for ch in common_channels])
common_channels = np.array(list(common_channels))[order].tolist()
# Update all instances to match the common_channels list
reordered = False
equalized_instances = []
for inst in instances:
# Only perform picking when needed
if inst.ch_names != common_channels:
if isinstance(inst, Info):
sel = pick_channels(inst.ch_names, common_channels, exclude=[],
ordered=True)
inst = pick_info(inst, sel, copy=copy, verbose=False)
else:
if copy:
inst = inst.copy()
inst.pick_channels(common_channels, ordered=True)
if len(inst.ch_names) == len(common_channels):
reordered = True
equalized_instances.append(inst)
if dropped:
logger.info('Dropped the following channels:\n%s' % dropped)
elif reordered:
logger.info('Channels have been re-ordered.')
return equalized_instances
channel_type_constants = get_channel_type_constants(include_defaults=True)
_human2fiff = {k: v.get('kind', FIFF.FIFFV_COIL_NONE) for k, v in
channel_type_constants.items()}
_human2unit = {k: v.get('unit', FIFF.FIFF_UNIT_NONE) for k, v in
channel_type_constants.items()}
_unit2human = {FIFF.FIFF_UNIT_V: 'V',
FIFF.FIFF_UNIT_T: 'T',
FIFF.FIFF_UNIT_T_M: 'T/m',
FIFF.FIFF_UNIT_MOL: 'M',
FIFF.FIFF_UNIT_NONE: 'NA',
FIFF.FIFF_UNIT_CEL: 'C',
FIFF.FIFF_UNIT_S: 'S'}
def _check_set(ch, projs, ch_type):
"""Ensure type change is compatible with projectors."""
new_kind = _human2fiff[ch_type]
if ch['kind'] != new_kind:
for proj in projs:
if ch['ch_name'] in proj['data']['col_names']:
raise RuntimeError('Cannot change channel type for channel %s '
'in projector "%s"'
% (ch['ch_name'], proj['desc']))
ch['kind'] = new_kind
class SetChannelsMixin(MontageMixin):
"""Mixin class for Raw, Evoked, Epochs."""
@verbose
def set_eeg_reference(self, ref_channels='average', projection=False,
ch_type='auto', forward=None, *, joint=False,
verbose=None):
"""Specify which reference to use for EEG data.
Use this function to explicitly specify the desired reference for EEG.
This can be either an existing electrode or a new virtual channel.
This function will re-reference the data according to the desired
reference.
Parameters
----------
%(ref_channels_set_eeg_reference)s
%(projection_set_eeg_reference)s
%(ch_type_set_eeg_reference)s
%(forward_set_eeg_reference)s
%(joint_set_eeg_reference)s
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
Data with EEG channels re-referenced. If ``ref_channels='average'``
and ``projection=True`` a projection will be added instead of
directly re-referencing the data.
%(set_eeg_reference_see_also_notes)s
"""
from ..io.reference import set_eeg_reference
return set_eeg_reference(self, ref_channels=ref_channels, copy=False,
projection=projection, ch_type=ch_type,
forward=forward, joint=joint)[0]
def _get_channel_positions(self, picks=None):
"""Get channel locations from info.
Parameters
----------
picks : str | list | slice | None
None gets good data indices.
Notes
-----
.. versionadded:: 0.9.0
"""
picks = _picks_to_idx(self.info, picks)
chs = self.info['chs']
pos = np.array([chs[k]['loc'][:3] for k in picks])
n_zero = np.sum(np.sum(np.abs(pos), axis=1) == 0)
if n_zero > 1: # XXX some systems have origin (0, 0, 0)
raise ValueError('Could not extract channel positions for '
'{} channels'.format(n_zero))
return pos
def _set_channel_positions(self, pos, names):
"""Update channel locations in info.
Parameters
----------
pos : array-like | np.ndarray, shape (n_points, 3)
The channel positions to be set.
names : list of str
The names of the channels to be set.
Notes
-----
.. versionadded:: 0.9.0
"""
if len(pos) != len(names):
raise ValueError('Number of channel positions not equal to '
'the number of names given.')
pos = np.asarray(pos, dtype=np.float64)
if pos.shape[-1] != 3 or pos.ndim != 2:
msg = ('Channel positions must have the shape (n_points, 3) '
'not %s.' % (pos.shape,))
raise ValueError(msg)
for name, p in zip(names, pos):
if name in self.ch_names:
idx = self.ch_names.index(name)
self.info['chs'][idx]['loc'][:3] = p
else:
msg = ('%s was not found in the info. Cannot be updated.'
% name)
raise ValueError(msg)
@verbose
def set_channel_types(self, mapping, verbose=None):
"""Define the sensor type of channels.
Parameters
----------
mapping : dict
A dictionary mapping a channel to a sensor type (str), e.g.,
``{'EEG061': 'eog'}``.
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The instance (modified in place).
.. versionchanged:: 0.20
Return the instance.
Notes
-----
The following sensor types are accepted:
ecg, eeg, emg, eog, exci, ias, misc, resp, seeg, dbs, stim, syst,
ecog, hbo, hbr, fnirs_cw_amplitude, fnirs_fd_ac_amplitude,
fnirs_fd_phase, fnirs_od, temperature, gsr
.. versionadded:: 0.9.0
"""
ch_names = self.info['ch_names']
# first check and assemble clean mappings of index and name
unit_changes = dict()
for ch_name, ch_type in mapping.items():
if ch_name not in ch_names:
raise ValueError("This channel name (%s) doesn't exist in "
"info." % ch_name)
c_ind = ch_names.index(ch_name)
if ch_type not in _human2fiff:
raise ValueError('This function cannot change to this '
'channel type: %s. Accepted channel types '
'are %s.'
% (ch_type,
", ".join(sorted(_human2unit.keys()))))
# Set sensor type
_check_set(self.info['chs'][c_ind], self.info['projs'], ch_type)
unit_old = self.info['chs'][c_ind]['unit']
unit_new = _human2unit[ch_type]
if unit_old not in _unit2human:
raise ValueError("Channel '%s' has unknown unit (%s). Please "
"fix the measurement info of your data."
% (ch_name, unit_old))
if unit_old != _human2unit[ch_type]:
this_change = (_unit2human[unit_old], _unit2human[unit_new])
if this_change not in unit_changes:
unit_changes[this_change] = list()
unit_changes[this_change].append(ch_name)
self.info['chs'][c_ind]['unit'] = _human2unit[ch_type]
if ch_type in ['eeg', 'seeg', 'ecog', 'dbs']:
coil_type = FIFF.FIFFV_COIL_EEG
elif ch_type == 'hbo':
coil_type = FIFF.FIFFV_COIL_FNIRS_HBO
elif ch_type == 'hbr':
coil_type = FIFF.FIFFV_COIL_FNIRS_HBR
elif ch_type == 'fnirs_cw_amplitude':
coil_type = FIFF.FIFFV_COIL_FNIRS_CW_AMPLITUDE
elif ch_type == 'fnirs_fd_ac_amplitude':
coil_type = FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE
elif ch_type == 'fnirs_fd_phase':
coil_type = FIFF.FIFFV_COIL_FNIRS_FD_PHASE
elif ch_type == 'fnirs_od':
coil_type = FIFF.FIFFV_COIL_FNIRS_OD
else:
coil_type = FIFF.FIFFV_COIL_NONE
self.info['chs'][c_ind]['coil_type'] = coil_type
msg = "The unit for channel(s) {0} has changed from {1} to {2}."
for this_change, names in unit_changes.items():
warn(msg.format(", ".join(sorted(names)), *this_change))
return self
@verbose
def rename_channels(self, mapping, allow_duplicates=False, verbose=None):
"""Rename channels.
Parameters
----------
%(mapping_rename_channels_duplicates)s
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The instance (modified in place).
.. versionchanged:: 0.20
Return the instance.
Notes
-----
.. versionadded:: 0.9.0
"""
from ..io import BaseRaw
ch_names_orig = list(self.info['ch_names'])
rename_channels(self.info, mapping, allow_duplicates)
# Update self._orig_units for Raw
if isinstance(self, BaseRaw):
# whatever mapping was provided, now we can just use a dict
mapping = dict(zip(ch_names_orig, self.info['ch_names']))
for old_name, new_name in mapping.items():
if old_name in self._orig_units:
self._orig_units[new_name] = self._orig_units.pop(old_name)
ch_names = self.annotations.ch_names
for ci, ch in enumerate(ch_names):
ch_names[ci] = tuple(mapping.get(name, name) for name in ch)
return self
@verbose
def plot_sensors(self, kind='topomap', ch_type=None, title=None,
show_names=False, ch_groups=None, to_sphere=True,
axes=None, block=False, show=True, sphere=None,
verbose=None):
"""Plot sensor positions.
Parameters
----------
kind : str
Whether to plot the sensors as 3d, topomap or as an interactive
sensor selection dialog. Available options 'topomap', '3d',
'select'. If 'select', a set of channels can be selected
interactively by using lasso selector or clicking while holding
control key. The selected channels are returned along with the
figure instance. Defaults to 'topomap'.
ch_type : None | str
The channel type to plot. Available options 'mag', 'grad', 'eeg',
'seeg', 'dbs', 'ecog', 'all'. If ``'all'``, all the available mag,
grad, eeg, seeg, dbs, and ecog channels are plotted. If
None (default), then channels are chosen in the order given above.
title : str | None
Title for the figure. If None (default), equals to ``'Sensor
positions (%%s)' %% ch_type``.
show_names : bool | array of str
Whether to display all channel names. If an array, only the channel
names in the array are shown. Defaults to False.
ch_groups : 'position' | array of shape (n_ch_groups, n_picks) | None
Channel groups for coloring the sensors. If None (default), default
coloring scheme is used. If 'position', the sensors are divided
into 8 regions. See ``order`` kwarg of :func:`mne.viz.plot_raw`. If
array, the channels are divided by picks given in the array.
.. versionadded:: 0.13.0
to_sphere : bool
Whether to project the 3d locations to a sphere. When False, the
sensor array appears similar as to looking downwards straight above
the subject's head. Has no effect when kind='3d'. Defaults to True.
.. versionadded:: 0.14.0
axes : instance of Axes | instance of Axes3D | None
Axes to draw the sensors to. If ``kind='3d'``, axes must be an
instance of Axes3D. If None (default), a new axes will be created.
.. versionadded:: 0.13.0
block : bool
Whether to halt program execution until the figure is closed.
Defaults to False.
.. versionadded:: 0.13.0
show : bool
Show figure if True. Defaults to True.
%(sphere_topomap_auto)s
%(verbose)s
Returns
-------
fig : instance of Figure
Figure containing the sensor topography.
selection : list
A list of selected channels. Only returned if ``kind=='select'``.
See Also
--------
mne.viz.plot_layout
Notes
-----
This function plots the sensor locations from the info structure using
matplotlib. For drawing the sensors using PyVista see
:func:`mne.viz.plot_alignment`.
.. versionadded:: 0.12.0
"""
from ..viz.utils import plot_sensors
return plot_sensors(self.info, kind=kind, ch_type=ch_type, title=title,
show_names=show_names, ch_groups=ch_groups,
to_sphere=to_sphere, axes=axes, block=block,
show=show, sphere=sphere, verbose=verbose)
@verbose
def anonymize(self, daysback=None, keep_his=False, verbose=None):
"""Anonymize measurement information in place.
Parameters
----------
%(daysback_anonymize_info)s
%(keep_his_anonymize_info)s
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The modified instance.
Notes
-----
%(anonymize_info_notes)s
.. versionadded:: 0.13.0
"""
anonymize_info(self.info, daysback=daysback, keep_his=keep_his,
verbose=verbose)
self.set_meas_date(self.info['meas_date']) # unify annot update
return self
def set_meas_date(self, meas_date):
"""Set the measurement start date.
Parameters
----------
meas_date : datetime | float | tuple | None
The new measurement date.
If datetime object, it must be timezone-aware and in UTC.
A tuple of (seconds, microseconds) or float (alias for
``(meas_date, 0)``) can also be passed and a datetime
object will be automatically created. If None, will remove
the time reference.
Returns
-------
inst : instance of Raw | Epochs | Evoked
The modified raw instance. Operates in place.
See Also
--------
mne.io.Raw.anonymize
Notes
-----
If you want to remove all time references in the file, call
:func:`mne.io.anonymize_info(inst.info) <mne.io.anonymize_info>`
after calling ``inst.set_meas_date(None)``.
.. versionadded:: 0.20
"""
from ..annotations import _handle_meas_date
meas_date = _handle_meas_date(meas_date)
with self.info._unlock():
self.info['meas_date'] = meas_date
# clear file_id and meas_id if needed
if meas_date is None:
for key in ('file_id', 'meas_id'):
value = self.info.get(key)
if value is not None:
assert 'msecs' not in value
value['secs'] = DATE_NONE[0]
value['usecs'] = DATE_NONE[1]
# The following copy is needed for a test CTF dataset
# otherwise value['machid'][:] = 0 would suffice
_tmp = value['machid'].copy()
_tmp[:] = 0
value['machid'] = _tmp
if hasattr(self, 'annotations'):
self.annotations._orig_time = meas_date
return self
class UpdateChannelsMixin(object):
"""Mixin class for Raw, Evoked, Epochs, Spectrum, AverageTFR."""
@verbose
def pick_types(self, meg=False, eeg=False, stim=False, eog=False,
ecg=False, emg=False, ref_meg='auto', *, misc=False,
resp=False, chpi=False, exci=False, ias=False, syst=False,
seeg=False, dipole=False, gof=False, bio=False,
ecog=False, fnirs=False, csd=False, dbs=False,
temperature=False, gsr=False,
include=(), exclude='bads', selection=None, verbose=None):
"""Pick some channels by type and names.
Parameters
----------
%(pick_types_params)s
%(verbose)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
pick_channels
Notes
-----
.. versionadded:: 0.9.0
"""
idx = pick_types(
self.info, meg=meg, eeg=eeg, stim=stim, eog=eog, ecg=ecg, emg=emg,
ref_meg=ref_meg, misc=misc, resp=resp, chpi=chpi, exci=exci,
ias=ias, syst=syst, seeg=seeg, dipole=dipole, gof=gof, bio=bio,
ecog=ecog, fnirs=fnirs, csd=csd, dbs=dbs, include=include,
exclude=exclude, selection=selection, temperature=temperature,
gsr=gsr)
self._pick_drop_channels(idx)
# remove dropped channel types from reject and flat
if getattr(self, 'reject', None) is not None:
# use list(self.reject) to avoid RuntimeError for changing
# dictionary size during iteration
for ch_type in list(self.reject):
if ch_type not in self:
del self.reject[ch_type]
if getattr(self, 'flat', None) is not None:
for ch_type in list(self.flat):
if ch_type not in self:
del self.flat[ch_type]
return self
@verbose
def pick_channels(self, ch_names, ordered=False, *, verbose=None):
"""Pick some channels.
Parameters
----------
ch_names : list
The list of channels to select.
ordered : bool
If True (default False), ensure that the order of the channels in
the modified instance matches the order of ``ch_names``.
.. versionadded:: 0.20.0
%(verbose)s
.. versionadded:: 1.1
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
pick_types
reorder_channels
Notes
-----
The channel names given are assumed to be a set, i.e. the order
does not matter. The original order of the channels is preserved.
You can use ``reorder_channels`` to set channel order if necessary.
.. versionadded:: 0.9.0
"""
picks = pick_channels(self.info['ch_names'], ch_names, ordered=ordered)
return self._pick_drop_channels(picks)
@verbose
def pick(self, picks, exclude=(), *, verbose=None):
"""Pick a subset of channels.
Parameters
----------
%(picks_all)s
exclude : list | str
Set of channels to exclude, only used when picking based on
types (e.g., exclude="bads" when picks="meg").
%(verbose)s
.. versionadded:: 0.24.0
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
"""
picks = _picks_to_idx(self.info, picks, 'all', exclude,
allow_empty=False)
return self._pick_drop_channels(picks)
def reorder_channels(self, ch_names):
"""Reorder channels.
Parameters
----------
ch_names : list
The desired channel order.
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
pick_types
pick_channels
Notes
-----
Channel names must be unique. Channels that are not in ``ch_names``
are dropped.
.. versionadded:: 0.16.0
"""
_check_excludes_includes(ch_names)
idx = list()
for ch_name in ch_names:
ii = self.ch_names.index(ch_name)
if ii in idx:
raise ValueError('Channel name repeated: %s' % (ch_name,))
idx.append(ii)
return self._pick_drop_channels(idx)
@fill_doc
def drop_channels(self, ch_names, on_missing='raise'):
"""Drop channel(s).
Parameters
----------
ch_names : iterable or str
Iterable (e.g. list) of channel name(s) or channel name to remove.
%(on_missing_ch_names)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
reorder_channels
pick_channels
pick_types
Notes
-----
.. versionadded:: 0.9.0
"""
if isinstance(ch_names, str):
ch_names = [ch_names]
try:
all_str = all([isinstance(ch, str) for ch in ch_names])
except TypeError:
raise ValueError("'ch_names' must be iterable, got "
"type {} ({}).".format(type(ch_names), ch_names))
if not all_str:
raise ValueError("Each element in 'ch_names' must be str, got "
"{}.".format([type(ch) for ch in ch_names]))
missing = [ch for ch in ch_names if ch not in self.ch_names]
if len(missing) > 0:
msg = "Channel(s) {0} not found, nothing dropped."
_on_missing(on_missing, msg.format(", ".join(missing)))
bad_idx = [self.ch_names.index(ch) for ch in ch_names
if ch in self.ch_names]
idx = np.setdiff1d(np.arange(len(self.ch_names)), bad_idx)
return self._pick_drop_channels(idx)
@verbose
def _pick_drop_channels(self, idx, *, verbose=None):
# avoid circular imports
from ..io import BaseRaw
from ..time_frequency import AverageTFR, EpochsTFR
from ..time_frequency.spectrum import BaseSpectrum
msg = 'adding, dropping, or reordering channels'
if isinstance(self, BaseRaw):
if self._projector is not None:
_check_preload(self, f'{msg} after calling .apply_proj()')
else:
_check_preload(self, msg)
if getattr(self, 'picks', None) is not None:
self.picks = self.picks[idx]
if getattr(self, '_read_picks', None) is not None:
self._read_picks = [r[idx] for r in self._read_picks]
if hasattr(self, '_cals'):
self._cals = self._cals[idx]
pick_info(self.info, idx, copy=False)
for key in ('_comp', '_projector'):
mat = getattr(self, key, None)
if mat is not None:
setattr(self, key, mat[idx][:, idx])
if isinstance(self, BaseSpectrum):
axis = self._dims.index('channel')
elif isinstance(self, (AverageTFR, EpochsTFR)):
axis = -3
else: # All others (Evoked, Epochs, Raw) have chs axis=-2
axis = -2
if hasattr(self, '_data'): # skip non-preloaded Raw
self._data = self._data.take(idx, axis=axis)
else:
assert isinstance(self, BaseRaw) and not self.preload
if isinstance(self, BaseRaw):
self.annotations._prune_ch_names(self.info, on_missing='ignore')
self._orig_units = {
k: v for k, v in self._orig_units.items()
if k in self.ch_names}
self._pick_projs()
return self
def _pick_projs(self):
"""Keep only projectors which apply to at least 1 data channel."""
drop_idx = []
for idx, proj in enumerate(self.info['projs']):
if not set(self.info['ch_names']) & set(proj['data']['col_names']):
drop_idx.append(idx)
for idx in drop_idx:
logger.info(f"Removing projector {self.info['projs'][idx]}")
if drop_idx and hasattr(self, 'del_proj'):
self.del_proj(drop_idx)
return self
def add_channels(self, add_list, force_update_info=False):
"""Append new channels to the instance.
Parameters
----------
add_list : list
A list of objects to append to self. Must contain all the same
type as the current object.
force_update_info : bool
If True, force the info for objects to be appended to match the
values in ``self``. This should generally only be used when adding
stim channels for which important metadata won't be overwritten.
.. versionadded:: 0.12
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
See Also
--------
drop_channels
Notes
-----
If ``self`` is a Raw instance that has been preloaded into a
:obj:`numpy.memmap` instance, the memmap will be resized.
"""
# avoid circular imports
from ..io import BaseRaw, _merge_info
from ..epochs import BaseEpochs
_validate_type(add_list, (list, tuple), 'Input')
# Object-specific checks
for inst in add_list + [self]:
_check_preload(inst, "adding channels")
if isinstance(self, BaseRaw):
con_axis = 0
comp_class = BaseRaw
elif isinstance(self, BaseEpochs):
con_axis = 1
comp_class = BaseEpochs
else:
con_axis = 0
comp_class = type(self)
for inst in add_list:
_validate_type(inst, comp_class, 'All input')
data = [inst._data for inst in [self] + add_list]
# Make sure that all dimensions other than channel axis are the same
compare_axes = [i for i in range(data[0].ndim) if i != con_axis]
shapes = np.array([dat.shape for dat in data])[:, compare_axes]
for shape in shapes:
if not ((shapes[0] - shape) == 0).all():
raise ValueError(
'All data dimensions except channels must match, got '
f'{shapes[0]} != {shape}')
del shapes
# Create final data / info objects
infos = [self.info] + [inst.info for inst in add_list]
new_info = _merge_info(infos, force_update_to_first=force_update_info)
# Now update the attributes
if isinstance(self._data, np.memmap) and con_axis == 0 and \
sys.platform != 'darwin': # resizing not available--no mremap
# Use a resize and fill in other ones
out_shape = (sum(d.shape[0] for d in data),) + data[0].shape[1:]
n_bytes = np.prod(out_shape) * self._data.dtype.itemsize
self._data.flush()
self._data.base.resize(n_bytes)
self._data = np.memmap(self._data.filename, mode='r+',
dtype=self._data.dtype, shape=out_shape)
assert self._data.shape == out_shape
assert self._data.nbytes == n_bytes
offset = len(data[0])
for d in data[1:]:
this_len = len(d)
self._data[offset:offset + this_len] = d
offset += this_len
else:
self._data = np.concatenate(data, axis=con_axis)
self.info = new_info
if isinstance(self, BaseRaw):
self._cals = np.concatenate([getattr(inst, '_cals')
for inst in [self] + add_list])
# We should never use these since data are preloaded, let's just
# set it to something large and likely to break (2 ** 31 - 1)
extra_idx = [2147483647] * sum(info['nchan'] for info in infos[1:])
assert all(len(r) == infos[0]['nchan'] for r in self._read_picks)
self._read_picks = [
np.concatenate([r, extra_idx]) for r in self._read_picks]
assert all(len(r) == self.info['nchan'] for r in self._read_picks)
for other in add_list:
self._orig_units.update(other._orig_units)
elif isinstance(self, BaseEpochs):
self.picks = np.arange(self._data.shape[1])
if hasattr(self, '_projector'):
activate = False if self._do_delayed_proj else self.proj
self._projector, self.info = setup_proj(self.info, False,
activate=activate)
return self
@fill_doc
def add_reference_channels(self, ref_channels):
"""Add reference channels to data that consists of all zeros.
Adds reference channels to data that were not included during
recording. This is useful when you need to re-reference your data
to different channels. These added channels will consist of all zeros.
Parameters
----------
%(ref_channels)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The modified instance.
"""
from ..io.reference import add_reference_channels
return add_reference_channels(self, ref_channels, copy=False)
class InterpolationMixin(object):
"""Mixin class for Raw, Evoked, Epochs."""
@verbose
def interpolate_bads(self, reset_bads=True, mode='accurate',
origin='auto', method=None, exclude=(),
verbose=None):
"""Interpolate bad MEG and EEG channels.
Operates in place.
Parameters
----------
reset_bads : bool
If True, remove the bads from info.
mode : str
Either ``'accurate'`` or ``'fast'``, determines the quality of the
Legendre polynomial expansion used for interpolation of channels
using the minimum-norm method.
origin : array-like, shape (3,) | str
Origin of the sphere in the head coordinate frame and in meters.
Can be ``'auto'`` (default), which means a head-digitization-based
origin fit.
.. versionadded:: 0.17
method : dict
Method to use for each channel type.
Currently only the key "eeg" has multiple options:
- ``"spline"`` (default)
Use spherical spline interpolation.
- ``"MNE"``
Use minimum-norm projection to a sphere and back.
This is the method used for MEG channels.
The value for "meg" is "MNE", and the value for
"fnirs" is "nearest". The default (None) is thus an alias for::
method=dict(meg="MNE", eeg="spline", fnirs="nearest")
.. versionadded:: 0.21
exclude : list | tuple
The channels to exclude from interpolation. If excluded a bad
channel will stay in bads.
%(verbose)s
Returns
-------
inst : instance of Raw, Epochs, or Evoked
The modified instance.
Notes
-----
.. versionadded:: 0.9.0
"""
from ..bem import _check_origin
from .interpolation import _interpolate_bads_eeg,\
_interpolate_bads_meeg, _interpolate_bads_nirs
_check_preload(self, "interpolation")
method = _handle_default('interpolation_method', method)
for key in method:
_check_option('method[key]', key, ('meg', 'eeg', 'fnirs'))
_check_option("method['eeg']", method['eeg'], ('spline', 'MNE'))
_check_option("method['meg']", method['meg'], ('MNE',))
_check_option("method['fnirs']", method['fnirs'], ('nearest',))
if len(self.info['bads']) == 0:
warn('No bad channels to interpolate. Doing nothing...')
return self
logger.info('Interpolating bad channels')
origin = _check_origin(origin, self.info)
if method['eeg'] == 'spline':
_interpolate_bads_eeg(self, origin=origin, exclude=exclude)
eeg_mne = False
else:
eeg_mne = True
_interpolate_bads_meeg(self, mode=mode, origin=origin, eeg=eeg_mne,
exclude=exclude)
_interpolate_bads_nirs(self, exclude=exclude)
if reset_bads is True:
self.info['bads'] = \
[ch for ch in self.info['bads'] if ch in exclude]
return self
@verbose
def rename_channels(info, mapping, allow_duplicates=False, verbose=None):
"""Rename channels.
Parameters
----------
%(info_not_none)s Note: modified in place.
%(mapping_rename_channels_duplicates)s
%(verbose)s
"""
_validate_type(info, Info, 'info')
info._check_consistency()
bads = list(info['bads']) # make our own local copies
ch_names = list(info['ch_names'])
# first check and assemble clean mappings of index and name
if isinstance(mapping, dict):
_check_dict_keys(mapping, ch_names, key_description="channel name(s)",
valid_key_source="info")
new_names = [(ch_names.index(ch_name), new_name)
for ch_name, new_name in mapping.items()]
elif callable(mapping):
new_names = [(ci, mapping(ch_name))
for ci, ch_name in enumerate(ch_names)]
else:
raise ValueError('mapping must be callable or dict, not %s'
% (type(mapping),))
# check we got all strings out of the mapping
for new_name in new_names:
_validate_type(new_name[1], 'str', 'New channel mappings')
# do the remapping locally
for c_ind, new_name in new_names:
for bi, bad in enumerate(bads):
if bad == ch_names[c_ind]:
bads[bi] = new_name
ch_names[c_ind] = new_name
# check that all the channel names are unique
if len(ch_names) != len(np.unique(ch_names)) and not allow_duplicates:
raise ValueError('New channel names are not unique, renaming failed')
# do the remapping in info
info['bads'] = bads
ch_names_mapping = dict()
for ch, ch_name in zip(info['chs'], ch_names):
ch_names_mapping[ch['ch_name']] = ch_name
ch['ch_name'] = ch_name
# .get b/c fwd info omits it
_rename_comps(info.get('comps', []), ch_names_mapping)
if 'projs' in info: # fwd might omit it
for proj in info['projs']:
proj['data']['col_names'][:] = \
_rename_list(proj['data']['col_names'], ch_names_mapping)
info._update_redundant()
info._check_consistency()
def _recursive_flatten(cell, dtype):
"""Unpack mat files in Python."""
if len(cell) > 0:
while not isinstance(cell[0], dtype):
cell = [c for d in cell for c in d]
return cell
@dataclass
class _BuiltinChannelAdjacency:
name: str
description: str
fname: str
source_url: Union[str, None]
_ft_neighbor_url_t = string.Template(
'https://github.com/fieldtrip/fieldtrip/raw/master/'
'template/neighbours/$fname'
)
_BUILTIN_CHANNEL_ADJACENCIES = [
_BuiltinChannelAdjacency(
name='biosemi16',
description='Biosemi 16-electrode cap',
fname='biosemi16_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='biosemi16_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='biosemi32',
description='Biosemi 32-electrode cap',
fname='biosemi32_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='biosemi32_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='biosemi64',
description='Biosemi 64-electrode cap',
fname='biosemi64_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='biosemi64_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='bti148',
description='BTI 148-channel system',
fname='bti148_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='bti148_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='bti248',
description='BTI 248-channel system',
fname='bti248_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='bti248_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='bti248grad',
description='BTI 248 gradiometer system',
fname='bti248grad_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='bti248grad_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='ctf64',
description='CTF 64 axial gradiometer',
fname='ctf64_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='ctf64_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='ctf151',
description='CTF 151 axial gradiometer',
fname='ctf151_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='ctf151_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='ctf275',
description='CTF 275 axial gradiometer',
fname='ctf275_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='ctf275_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='easycap32ch-avg',
description='',
fname='easycap32ch-avg_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycap32ch-avg_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='easycap64ch-avg',
description='',
fname='easycap64ch-avg_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycap64ch-avg_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='easycap128ch-avg',
description='',
fname='easycap128ch-avg_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycap128ch-avg_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='easycapM1',
description='Easycap M1',
fname='easycapM1_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycapM1_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='easycapM11',
description='Easycap M11',
fname='easycapM11_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycapM11_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='easycapM14',
description='Easycap M14',
fname='easycapM14_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycapM14_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='easycapM15',
description='Easycap M15',
fname='easycapM15_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='easycapM15_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='KIT-157',
description='',
fname='KIT-157_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-208',
description='',
fname='KIT-208_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-NYU-2019',
description='',
fname='KIT-NYU-2019_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-UMD-1',
description='',
fname='KIT-UMD-1_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-UMD-2',
description='',
fname='KIT-UMD-2_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-UMD-3',
description='',
fname='KIT-UMD-3_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='KIT-UMD-4',
description='',
fname='KIT-UMD-4_neighb.mat',
source_url=None,
),
_BuiltinChannelAdjacency(
name='neuromag306mag',
description='Neuromag306, only magnetometers',
fname='neuromag306mag_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='neuromag306mag_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='neuromag306planar',
description='Neuromag306, only planar gradiometers',
fname='neuromag306planar_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='neuromag306planar_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='neuromag122cmb',
description='Neuromag122, only combined planar gradiometers',
fname='neuromag122cmb_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='neuromag122cmb_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='neuromag306cmb',
description='Neuromag306, only combined planar gradiometers',
fname='neuromag306cmb_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='neuromag306cmb_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='ecog256',
description='ECOG 256channels, average referenced',
fname='ecog256_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='ecog256_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='ecog256bipolar',
description='ECOG 256channels, bipolar referenced',
fname='ecog256bipolar_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='ecog256bipolar_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='eeg1010_neighb',
description='',
fname='eeg1010_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='eeg1010_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='elec1005',
description='Standard 10-05 system',
fname='elec1005_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='elec1005_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='elec1010',
description='Standard 10-10 system',
fname='elec1010_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='elec1010_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='elec1020',
description='Standard 10-20 system',
fname='elec1020_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='elec1020_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='itab28',
description='ITAB 28-channel system',
fname='itab28_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='itab28_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='itab153',
description='ITAB 153-channel system',
fname='itab153_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='itab153_neighb.mat'),
),
_BuiltinChannelAdjacency(
name='language29ch-avg',
description='MPI for Psycholinguistic: Averaged 29-channel cap',
fname='language29ch-avg_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='language29ch-avg_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='mpi_59_channels',
description='MPI for Psycholinguistic: 59-channel cap',
fname='mpi_59_channels_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='mpi_59_channels_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='yokogawa160',
description='',
fname='yokogawa160_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='yokogawa160_neighb.mat'), # noqa: E501
),
_BuiltinChannelAdjacency(
name='yokogawa440',
description='',
fname='yokogawa440_neighb.mat',
source_url=_ft_neighbor_url_t.substitute(fname='yokogawa440_neighb.mat'), # noqa: E501
),
]
@fill_doc
def get_builtin_ch_adjacencies(*, descriptions=False):
"""Get a list of all FieldTrip neighbor definitions shipping with MNE.
The names of the these neighbor definitions can be passed to
:func:`read_ch_adjacency`.
Parameters
----------
descriptions : bool
Whether to return not only the neighbor definition names, but also
their corresponding descriptions. If ``True``, a list of tuples is
returned, where the first tuple element is the neighbor definition name
and the second is the description. If ``False`` (default), only the
names are returned.
Returns
-------
neighbor_name : list of str | list of tuple
If ``descriptions=False``, the names of all builtin FieldTrip neighbor
definitions that can be loaded directly via :func:`read_ch_adjacency`.
If ``descriptions=True``, a list of tuples ``(name, description)``.
Notes
-----
.. versionadded:: 1.1
"""
if descriptions:
return sorted(
[(m.name, m.description) for m in _BUILTIN_CHANNEL_ADJACENCIES],
key=lambda x: x[0].casefold() # only sort based on name
)
else:
return sorted(
[m.name for m in _BUILTIN_CHANNEL_ADJACENCIES],
key=str.casefold
)
@fill_doc
def read_ch_adjacency(fname, picks=None):
"""Read a channel adjacency ("neighbors") file that ships with MNE.
More information on these neighbor definitions can be found on the related
`FieldTrip documentation pages
<http://www.fieldtriptoolbox.org/template/neighbours/>`__.
Parameters
----------
fname : str
The path to the file to load, or the name of a channel adjacency
matrix that ships with MNE-Python.
.. note::
You can retrieve the names of all
built-in channel adjacencies via
:func:`mne.channels.get_builtin_ch_adjacencies`.
%(picks_all)s
Picks must match the template.
Returns
-------
ch_adjacency : scipy.sparse.csr_matrix, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
See Also
--------
get_builtin_ch_adjacencies
mne.viz.plot_ch_adjacency
find_ch_adjacency
mne.stats.combine_adjacency
Notes
-----
If the neighbor definition you need is not shipped by MNE-Python,
you may use :func:`find_ch_adjacency` to compute the
adjacency matrix based on your 2D sensor locations.
Note that depending on your use case, you may need to additionally use
:func:`mne.stats.combine_adjacency` to prepare a final "adjacency"
to pass to the eventual function.
"""
from scipy.io import loadmat
if op.isabs(fname):
fname = _check_fname(
fname=fname,
overwrite='read',
must_exist=True
)
else: # built-in FieldTrip neighbors
ch_adj_name = fname
del fname
if ch_adj_name.endswith('_neighb.mat'): # backward-compat
ch_adj_name = ch_adj_name.replace('_neighb.mat', '')
if ch_adj_name not in get_builtin_ch_adjacencies():
raise ValueError(
f'No built-in channel adjacency matrix found with name: '
f'{ch_adj_name}. Valid names are: '
f'{", ".join(get_builtin_ch_adjacencies())}'
)
ch_adj = [a for a in _BUILTIN_CHANNEL_ADJACENCIES
if a.name == ch_adj_name][0]
fname = ch_adj.fname
templates_dir = Path(__file__).resolve().parent / 'data' / 'neighbors'
fname = _check_fname( # only needed to convert to a string
fname=templates_dir / fname,
overwrite='read',
must_exist=True
)
nb = loadmat(fname)['neighbours']
ch_names = _recursive_flatten(nb['label'], str)
picks = _picks_to_idx(len(ch_names), picks)
neighbors = [_recursive_flatten(c, str) for c in
nb['neighblabel'].flatten()]
assert len(ch_names) == len(neighbors)
adjacency = _ch_neighbor_adjacency(ch_names, neighbors)
# picking before constructing matrix is buggy
adjacency = adjacency[picks][:, picks]
ch_names = [ch_names[p] for p in picks]
# make sure MEG channel names contain space after "MEG"
for idx, ch_name in enumerate(ch_names):
if ch_name.startswith('MEG') and not ch_name[3] == ' ':
ch_name = ch_name.replace('MEG', 'MEG ')
ch_names[idx] = ch_name
return adjacency, ch_names
def _ch_neighbor_adjacency(ch_names, neighbors):
"""Compute sensor adjacency matrix.
Parameters
----------
ch_names : list of str
The channel names.
neighbors : list of list
A list of list of channel names. The neighbors to
which the channels in ch_names are connected with.
Must be of the same length as ch_names.
Returns
-------
ch_adjacency : scipy.sparse.spmatrix
The adjacency matrix.
"""
from scipy import sparse
if len(ch_names) != len(neighbors):
raise ValueError('`ch_names` and `neighbors` must '
'have the same length')
set_neighbors = {c for d in neighbors for c in d}
rest = set_neighbors - set(ch_names)
if len(rest) > 0:
raise ValueError('Some of your neighbors are not present in the '
'list of channel names')
for neigh in neighbors:
if (not isinstance(neigh, list) and
not all(isinstance(c, str) for c in neigh)):
raise ValueError('`neighbors` must be a list of lists of str')
ch_adjacency = np.eye(len(ch_names), dtype=bool)
for ii, neigbs in enumerate(neighbors):
ch_adjacency[ii, [ch_names.index(i) for i in neigbs]] = True
ch_adjacency = sparse.csr_matrix(ch_adjacency)
return ch_adjacency
@fill_doc
def find_ch_adjacency(info, ch_type):
"""Find the adjacency matrix for the given channels.
This function tries to infer the appropriate adjacency matrix template
for the given channels. If a template is not found, the adjacency matrix
is computed using Delaunay triangulation based on 2D sensor locations.
Parameters
----------
%(info_not_none)s
ch_type : str | None
The channel type for computing the adjacency matrix. Currently
supports ``'mag'``, ``'grad'``, ``'eeg'`` and ``None``.
If ``None``, the info must contain only one channel type.
Returns
-------
ch_adjacency : scipy.sparse.csr_matrix, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
See Also
--------
mne.viz.plot_ch_adjacency
mne.stats.combine_adjacency
get_builtin_ch_adjacencies
read_ch_adjacency
Notes
-----
.. versionadded:: 0.15
Automatic detection of an appropriate adjacency matrix template only
works for MEG data at the moment. This means that the adjacency matrix
is always computed for EEG data and never loaded from a template file. If
you want to load a template for a given montage use
:func:`read_ch_adjacency` directly.
.. warning::
If Delaunay triangulation is used to calculate the adjacency matrix it
may yield partially unexpected results (e.g., include unwanted edges
between non-adjacent sensors). Therefore, it is recommended to check
(and, if necessary, manually modify) the result by inspecting it
via :func:`mne.viz.plot_ch_adjacency`.
Note that depending on your use case, you may need to additionally use
:func:`mne.stats.combine_adjacency` to prepare a final "adjacency"
to pass to the eventual function.
"""
if ch_type is None:
picks = channel_indices_by_type(info)
if sum([len(p) != 0 for p in picks.values()]) != 1:
raise ValueError('info must contain only one channel type if '
'ch_type is None.')
ch_type = channel_type(info, 0)
else:
_check_option('ch_type', ch_type, ['mag', 'grad', 'eeg'])
(has_vv_mag, has_vv_grad, is_old_vv, has_4D_mag, ctf_other_types,
has_CTF_grad, n_kit_grads, has_any_meg, has_eeg_coils,
has_eeg_coils_and_meg, has_eeg_coils_only,
has_neuromag_122_grad, has_csd_coils) = _get_ch_info(info)
conn_name = None
if has_vv_mag and ch_type == 'mag':
conn_name = 'neuromag306mag'
elif has_vv_grad and ch_type == 'grad':
conn_name = 'neuromag306planar'
elif has_4D_mag:
if 'MEG 248' in info['ch_names']:
idx = info['ch_names'].index('MEG 248')
grad = info['chs'][idx]['coil_type'] == FIFF.FIFFV_COIL_MAGNES_GRAD
mag = info['chs'][idx]['coil_type'] == FIFF.FIFFV_COIL_MAGNES_MAG
if ch_type == 'grad' and grad:
conn_name = 'bti248grad'
elif ch_type == 'mag' and mag:
conn_name = 'bti248'
elif 'MEG 148' in info['ch_names'] and ch_type == 'mag':
idx = info['ch_names'].index('MEG 148')
if info['chs'][idx]['coil_type'] == FIFF.FIFFV_COIL_MAGNES_MAG:
conn_name = 'bti148'
elif has_CTF_grad and ch_type == 'mag':
if info['nchan'] < 100:
conn_name = 'ctf64'
elif info['nchan'] > 200:
conn_name = 'ctf275'
else:
conn_name = 'ctf151'
elif n_kit_grads > 0:
from ..io.kit.constants import KIT_NEIGHBORS
conn_name = KIT_NEIGHBORS.get(info['kit_system_id'])
if conn_name is not None:
logger.info(f'Reading adjacency matrix for {conn_name}.')
return read_ch_adjacency(conn_name)
logger.info('Could not find a adjacency matrix for the data. '
'Computing adjacency based on Delaunay triangulations.')
return _compute_ch_adjacency(info, ch_type)
@fill_doc
def _compute_ch_adjacency(info, ch_type):
"""Compute channel adjacency matrix using Delaunay triangulations.
Parameters
----------
%(info_not_none)s
ch_type : str
The channel type for computing the adjacency matrix. Currently
supports 'mag', 'grad' and 'eeg'.
Returns
-------
ch_adjacency : scipy.sparse.csr_matrix, shape (n_channels, n_channels)
The adjacency matrix.
ch_names : list
The list of channel names present in adjacency matrix.
"""
from scipy import sparse
from scipy.spatial import Delaunay
from .. import spatial_tris_adjacency
from ..channels.layout import _find_topomap_coords, _pair_grad_sensors
combine_grads = (ch_type == 'grad'
and any([coil_type in [ch['coil_type']
for ch in info['chs']]
for coil_type in
[FIFF.FIFFV_COIL_VV_PLANAR_T1,
FIFF.FIFFV_COIL_NM_122]]))
picks = dict(_picks_by_type(info, exclude=[]))[ch_type]
ch_names = [info['ch_names'][pick] for pick in picks]
if combine_grads:
pairs = _pair_grad_sensors(info, topomap_coords=False, exclude=[])
if len(pairs) != len(picks):
raise RuntimeError('Cannot find a pair for some of the '
'gradiometers. Cannot compute adjacency '
'matrix.')
# only for one of the pair
xy = _find_topomap_coords(info, picks[::2], sphere=HEAD_SIZE_DEFAULT)
else:
xy = _find_topomap_coords(info, picks, sphere=HEAD_SIZE_DEFAULT)
tri = Delaunay(xy)
neighbors = spatial_tris_adjacency(tri.simplices)
if combine_grads:
ch_adjacency = np.eye(len(picks), dtype=bool)
for idx, neigbs in zip(neighbors.row, neighbors.col):
for ii in range(2): # make sure each pair is included
for jj in range(2):
ch_adjacency[idx * 2 + ii, neigbs * 2 + jj] = True
ch_adjacency[idx * 2 + ii, idx * 2 + jj] = True # pair
ch_adjacency = sparse.csr_matrix(ch_adjacency)
else:
ch_adjacency = sparse.lil_matrix(neighbors)
ch_adjacency.setdiag(np.repeat(1, ch_adjacency.shape[0]))
ch_adjacency = ch_adjacency.tocsr()
return ch_adjacency, ch_names
@fill_doc
def fix_mag_coil_types(info, use_cal=False):
"""Fix magnetometer coil types.
Parameters
----------
%(info_not_none)s Corrections are done in-place.
use_cal : bool
If True, further refine the check for old coil types by checking
``info['chs'][ii]['cal']``.
Notes
-----
This function changes magnetometer coil types 3022 (T1: SQ20483N) and
3023 (T2: SQ20483-A) to 3024 (T3: SQ20950N) in the channel definition
records in the info structure.
Neuromag Vectorview systems can contain magnetometers with two
different coil sizes (3022 and 3023 vs. 3024). The systems
incorporating coils of type 3024 were introduced last and are used at
the majority of MEG sites. At some sites with 3024 magnetometers,
the data files have still defined the magnetometers to be of type
3022 to ensure compatibility with older versions of Neuromag software.
In the MNE software as well as in the present version of Neuromag
software coil type 3024 is fully supported. Therefore, it is now safe
to upgrade the data files to use the true coil type.
.. note:: The effect of the difference between the coil sizes on the
current estimates computed by the MNE software is very small.
Therefore the use of ``fix_mag_coil_types`` is not mandatory.
"""
old_mag_inds = _get_T1T2_mag_inds(info, use_cal)
for ii in old_mag_inds:
info['chs'][ii]['coil_type'] = FIFF.FIFFV_COIL_VV_MAG_T3
logger.info('%d of %d magnetometer types replaced with T3.' %
(len(old_mag_inds),
len(pick_types(info, meg='mag', exclude=[]))))
info._check_consistency()
def _get_T1T2_mag_inds(info, use_cal=False):
"""Find T1/T2 magnetometer coil types."""
picks = pick_types(info, meg='mag', exclude=[])
old_mag_inds = []
# From email exchanges, systems with the larger T2 coil only use the cal
# value of 2.09e-11. Newer T3 magnetometers use 4.13e-11 or 1.33e-10
# (Triux). So we can use a simple check for > 3e-11.
for ii in picks:
ch = info['chs'][ii]
if ch['coil_type'] in (FIFF.FIFFV_COIL_VV_MAG_T1,
FIFF.FIFFV_COIL_VV_MAG_T2):
if use_cal:
if ch['cal'] > 3e-11:
old_mag_inds.append(ii)
else:
old_mag_inds.append(ii)
return old_mag_inds
def _get_ch_info(info):
"""Get channel info for inferring acquisition device."""
chs = info['chs']
# Only take first 16 bits, as higher bits store CTF comp order
coil_types = {ch['coil_type'] & 0xFFFF for ch in chs}
channel_types = {ch['kind'] for ch in chs}
has_vv_mag = any(k in coil_types for k in
[FIFF.FIFFV_COIL_VV_MAG_T1, FIFF.FIFFV_COIL_VV_MAG_T2,
FIFF.FIFFV_COIL_VV_MAG_T3])
has_vv_grad = any(k in coil_types for k in [FIFF.FIFFV_COIL_VV_PLANAR_T1,
FIFF.FIFFV_COIL_VV_PLANAR_T2,
FIFF.FIFFV_COIL_VV_PLANAR_T3])
has_neuromag_122_grad = any(k in coil_types
for k in [FIFF.FIFFV_COIL_NM_122])
is_old_vv = ' ' in chs[0]['ch_name']
has_4D_mag = FIFF.FIFFV_COIL_MAGNES_MAG in coil_types
ctf_other_types = (FIFF.FIFFV_COIL_CTF_REF_MAG,
FIFF.FIFFV_COIL_CTF_REF_GRAD,
FIFF.FIFFV_COIL_CTF_OFFDIAG_REF_GRAD)
has_CTF_grad = (FIFF.FIFFV_COIL_CTF_GRAD in coil_types or
(FIFF.FIFFV_MEG_CH in channel_types and
any(k in ctf_other_types for k in coil_types)))
# hack due to MNE-C bug in IO of CTF
# only take first 16 bits, as higher bits store CTF comp order
n_kit_grads = sum(ch['coil_type'] & 0xFFFF == FIFF.FIFFV_COIL_KIT_GRAD
for ch in chs)
has_any_meg = any([has_vv_mag, has_vv_grad, has_4D_mag, has_CTF_grad,
n_kit_grads])
has_eeg_coils = (FIFF.FIFFV_COIL_EEG in coil_types and
FIFF.FIFFV_EEG_CH in channel_types)
has_eeg_coils_and_meg = has_eeg_coils and has_any_meg
has_eeg_coils_only = has_eeg_coils and not has_any_meg
has_csd_coils = (FIFF.FIFFV_COIL_EEG_CSD in coil_types and
FIFF.FIFFV_EEG_CH in channel_types)
return (has_vv_mag, has_vv_grad, is_old_vv, has_4D_mag, ctf_other_types,
has_CTF_grad, n_kit_grads, has_any_meg, has_eeg_coils,
has_eeg_coils_and_meg, has_eeg_coils_only, has_neuromag_122_grad,
has_csd_coils)
@fill_doc
def make_1020_channel_selections(info, midline="z"):
"""Return dict mapping from ROI names to lists of picks for 10/20 setups.
This passes through all channel names, and uses a simple heuristic to
separate channel names into three Region of Interest-based selections:
Left, Midline and Right. The heuristic is that channels ending on any of
the characters in ``midline`` are filed under that heading, otherwise those
ending in odd numbers under "Left", those in even numbers under "Right".
Other channels are ignored. This is appropriate for 10/20 files, but not
for other channel naming conventions.
If an info object is provided, lists are sorted from posterior to anterior.
Parameters
----------
%(info_not_none)s If possible, the channel lists will be sorted
posterior-to-anterior; otherwise they default to the order specified in
``info["ch_names"]``.
midline : str
Names ending in any of these characters are stored under the
``Midline`` key. Defaults to 'z'. Note that capitalization is ignored.
Returns
-------
selections : dict
A dictionary mapping from ROI names to lists of picks (integers).
"""
_validate_type(info, "info")
try:
from .layout import find_layout
layout = find_layout(info)
pos = layout.pos
ch_names = layout.names
except RuntimeError: # no channel positions found
ch_names = info["ch_names"]
pos = None
selections = dict(Left=[], Midline=[], Right=[])
for pick, channel in enumerate(ch_names):
last_char = channel[-1].lower() # in 10/20, last char codes hemisphere
if last_char in midline:
selection = "Midline"
elif last_char.isdigit():
selection = "Left" if int(last_char) % 2 else "Right"
else: # ignore the channel
continue
selections[selection].append(pick)
if pos is not None:
# sort channels from front to center
# (y-coordinate of the position info in the layout)
selections = {selection: np.array(picks)[pos[picks, 1].argsort()]
for selection, picks in selections.items()}
return selections
@verbose
def combine_channels(inst, groups, method='mean', keep_stim=False,
drop_bad=False, verbose=None):
"""Combine channels based on specified channel grouping.
Parameters
----------
inst : instance of Raw, Epochs, or Evoked
An MNE-Python object to combine the channels for. The object can be of
type Raw, Epochs, or Evoked.
groups : dict
Specifies which channels are aggregated into a single channel, with
aggregation method determined by the ``method`` parameter. One new
pseudo-channel is made per dict entry; the dict values must be lists of
picks (integer indices of ``ch_names``). For example::
groups=dict(Left=[1, 2, 3, 4], Right=[5, 6, 7, 8])
Note that within a dict entry all channels must have the same type.
method : str | callable
Which method to use to combine channels. If a :class:`str`, must be one
of 'mean', 'median', or 'std' (standard deviation). If callable, the
callable must accept one positional input (data of shape ``(n_channels,
n_times)``, or ``(n_epochs, n_channels, n_times)``) and return an
:class:`array <numpy.ndarray>` of shape ``(n_times,)``, or ``(n_epochs,
n_times)``. For example with an instance of Raw or Evoked::
method = lambda data: np.mean(data, axis=0)
Another example with an instance of Epochs::
method = lambda data: np.median(data, axis=1)
Defaults to ``'mean'``.
keep_stim : bool
If ``True``, include stimulus channels in the resulting object.
Defaults to ``False``.
drop_bad : bool
If ``True``, drop channels marked as bad before combining. Defaults to
``False``.
%(verbose)s
Returns
-------
combined_inst : instance of Raw, Epochs, or Evoked
An MNE-Python object of the same type as the input ``inst``, containing
one virtual channel for each group in ``groups`` (and, if ``keep_stim``
is ``True``, also containing stimulus channels).
"""
from ..io import BaseRaw, RawArray
from .. import BaseEpochs, EpochsArray, Evoked, EvokedArray
ch_axis = 1 if isinstance(inst, BaseEpochs) else 0
ch_idx = list(range(inst.info['nchan']))
ch_names = inst.info['ch_names']
ch_types = inst.get_channel_types()
inst_data = inst.data if isinstance(inst, Evoked) else inst.get_data()
groups = OrderedDict(deepcopy(groups))
# Convert string values of ``method`` into callables
# XXX Possibly de-duplicate with _make_combine_callable of mne/viz/utils.py
if isinstance(method, str):
method_dict = {key: partial(getattr(np, key), axis=ch_axis)
for key in ('mean', 'median', 'std')}
try:
method = method_dict[method]
except KeyError:
raise ValueError('"method" must be a callable, or one of "mean", '
f'"median", or "std"; got "{method}".')
# Instantiate channel info and data
new_ch_names, new_ch_types, new_data = [], [], []
if not isinstance(keep_stim, bool):
raise TypeError('"keep_stim" must be of type bool, not '
f'{type(keep_stim)}.')
if keep_stim:
stim_ch_idx = list(pick_types(inst.info, meg=False, stim=True))
if stim_ch_idx:
new_ch_names = [ch_names[idx] for idx in stim_ch_idx]
new_ch_types = [ch_types[idx] for idx in stim_ch_idx]
new_data = [np.take(inst_data, idx, axis=ch_axis)
for idx in stim_ch_idx]
else:
warn('Could not find stimulus channels.')
# Get indices of bad channels
ch_idx_bad = []
if not isinstance(drop_bad, bool):
raise TypeError('"drop_bad" must be of type bool, not '
f'{type(drop_bad)}.')
if drop_bad and inst.info['bads']:
ch_idx_bad = pick_channels(ch_names, inst.info['bads'])
# Check correctness of combinations
for this_group, this_picks in groups.items():
# Check if channel indices are out of bounds
if not all(idx in ch_idx for idx in this_picks):
raise ValueError('Some channel indices are out of bounds.')
# Check if heterogeneous sensor type combinations
this_ch_type = np.array(ch_types)[this_picks]
if len(set(this_ch_type)) > 1:
types = ', '.join(set(this_ch_type))
raise ValueError('Cannot combine sensors of different types; '
f'"{this_group}" contains types {types}.')
# Remove bad channels
these_bads = [idx for idx in this_picks if idx in ch_idx_bad]
this_picks = [idx for idx in this_picks if idx not in ch_idx_bad]
if these_bads:
logger.info('Dropped the following channels in group '
f'{this_group}: {these_bads}')
# Check if combining less than 2 channel
if len(set(this_picks)) < 2:
warn(f'Less than 2 channels in group "{this_group}" when '
f'combining by method "{method}".')
# If all good create more detailed dict without bad channels
groups[this_group] = dict(picks=this_picks, ch_type=this_ch_type[0])
# Combine channels and add them to the new instance
for this_group, this_group_dict in groups.items():
new_ch_names.append(this_group)
new_ch_types.append(this_group_dict['ch_type'])
this_picks = this_group_dict['picks']
this_data = np.take(inst_data, this_picks, axis=ch_axis)
new_data.append(method(this_data))
new_data = np.swapaxes(new_data, 0, ch_axis)
info = create_info(sfreq=inst.info['sfreq'], ch_names=new_ch_names,
ch_types=new_ch_types)
# create new instances and make sure to copy important attributes
if isinstance(inst, BaseRaw):
combined_inst = RawArray(new_data, info, first_samp=inst.first_samp)
elif isinstance(inst, BaseEpochs):
combined_inst = EpochsArray(new_data, info, events=inst.events,
tmin=inst.times[0], baseline=inst.baseline)
if inst.metadata is not None:
combined_inst.metadata = inst.metadata.copy()
elif isinstance(inst, Evoked):
combined_inst = EvokedArray(new_data, info, tmin=inst.times[0],
baseline=inst.baseline)
return combined_inst
# NeuroMag channel groupings
_SELECTIONS = ['Vertex', 'Left-temporal', 'Right-temporal', 'Left-parietal',
'Right-parietal', 'Left-occipital', 'Right-occipital',
'Left-frontal', 'Right-frontal']
_EEG_SELECTIONS = ['EEG 1-32', 'EEG 33-64', 'EEG 65-96', 'EEG 97-128']
def _divide_to_regions(info, add_stim=True):
"""Divide channels to regions by positions."""
from scipy.stats import zscore
picks = _pick_data_channels(info, exclude=[])
chs_in_lobe = len(picks) // 4
pos = np.array([ch['loc'][:3] for ch in info['chs']])
x, y, z = pos.T
frontal = picks[np.argsort(y[picks])[-chs_in_lobe:]]
picks = np.setdiff1d(picks, frontal)
occipital = picks[np.argsort(y[picks])[:chs_in_lobe]]
picks = np.setdiff1d(picks, occipital)
temporal = picks[np.argsort(z[picks])[:chs_in_lobe]]
picks = np.setdiff1d(picks, temporal)
lt, rt = _divide_side(temporal, x)
lf, rf = _divide_side(frontal, x)
lo, ro = _divide_side(occipital, x)
lp, rp = _divide_side(picks, x) # Parietal lobe from the remaining picks.
# Because of the way the sides are divided, there may be outliers in the
# temporal lobes. Here we switch the sides for these outliers. For other
# lobes it is not a big problem because of the vicinity of the lobes.
with np.errstate(invalid='ignore'): # invalid division, greater compare
zs = np.abs(zscore(x[rt]))
outliers = np.array(rt)[np.where(zs > 2.)[0]]
rt = list(np.setdiff1d(rt, outliers))
with np.errstate(invalid='ignore'): # invalid division, greater compare
zs = np.abs(zscore(x[lt]))
outliers = np.append(outliers, (np.array(lt)[np.where(zs > 2.)[0]]))
lt = list(np.setdiff1d(lt, outliers))
l_mean = np.mean(x[lt])
r_mean = np.mean(x[rt])
for outlier in outliers:
if abs(l_mean - x[outlier]) < abs(r_mean - x[outlier]):
lt.append(outlier)
else:
rt.append(outlier)
if add_stim:
stim_ch = _get_stim_channel(None, info, raise_error=False)
if len(stim_ch) > 0:
for region in [lf, rf, lo, ro, lp, rp, lt, rt]:
region.append(info['ch_names'].index(stim_ch[0]))
return OrderedDict([('Left-frontal', lf), ('Right-frontal', rf),
('Left-parietal', lp), ('Right-parietal', rp),
('Left-occipital', lo), ('Right-occipital', ro),
('Left-temporal', lt), ('Right-temporal', rt)])
def _divide_side(lobe, x):
"""Make a separation between left and right lobe evenly."""
lobe = np.asarray(lobe)
median = np.median(x[lobe])
left = lobe[np.where(x[lobe] < median)[0]]
right = lobe[np.where(x[lobe] > median)[0]]
medians = np.where(x[lobe] == median)[0]
left = np.sort(np.concatenate([left, lobe[medians[1::2]]]))
right = np.sort(np.concatenate([right, lobe[medians[::2]]]))
return list(left), list(right)
@verbose
def read_vectorview_selection(name, fname=None, info=None, verbose=None):
"""Read Neuromag Vector View channel selection from a file.
Parameters
----------
name : str | list of str
Name of the selection. If a list, the selections are combined.
Supported selections are: ``'Vertex'``, ``'Left-temporal'``,
``'Right-temporal'``, ``'Left-parietal'``, ``'Right-parietal'``,
``'Left-occipital'``, ``'Right-occipital'``, ``'Left-frontal'`` and
``'Right-frontal'``. Selections can also be matched and combined by
spcecifying common substrings. For example, ``name='temporal`` will
produce a combination of ``'Left-temporal'`` and ``'Right-temporal'``.
fname : str
Filename of the selection file (if ``None``, built-in selections are
used).
%(info)s Used to determine which channel naming convention to use, e.g.
``'MEG 0111'`` (with space) for old Neuromag systems and ``'MEG0111'``
(without space) for new ones.
%(verbose)s
Returns
-------
sel : list of str
List with channel names in the selection.
"""
# convert name to list of string
if not isinstance(name, (list, tuple)):
name = [name]
if isinstance(info, Info):
picks = pick_types(info, meg=True, exclude=())
if len(picks) > 0 and ' ' not in info['ch_names'][picks[0]]:
spacing = 'new'
else:
spacing = 'old'
elif info is not None:
raise TypeError('info must be an instance of Info or None, not %s'
% (type(info),))
else: # info is None
spacing = 'old'
# use built-in selections by default
if fname is None:
fname = op.join(op.dirname(__file__), '..', 'data', 'mne_analyze.sel')
fname = _check_fname(fname, must_exist=True, overwrite='read')
# use this to make sure we find at least one match for each name
name_found = {n: False for n in name}
with open(fname, 'r') as fid:
sel = []
for line in fid:
line = line.strip()
# skip blank lines and comments
if len(line) == 0 or line[0] == '#':
continue
# get the name of the selection in the file
pos = line.find(':')
if pos < 0:
logger.info('":" delimiter not found in selections file, '
'skipping line')
continue
sel_name_file = line[:pos]
# search for substring match with name provided
for n in name:
if sel_name_file.find(n) >= 0:
sel.extend(line[pos + 1:].split('|'))
name_found[n] = True
break
# make sure we found at least one match for each name
for n, found in name_found.items():
if not found:
raise ValueError('No match for selection name "%s" found' % n)
# make the selection a sorted list with unique elements
sel = list(set(sel))
sel.sort()
if spacing == 'new': # "new" or "old" by now, "old" is default
sel = [s.replace('MEG ', 'MEG') for s in sel]
return sel
|