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 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779
|
"""Utility functions for plotting M/EEG data."""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
# Clemens Brunner <clemens.brunner@gmail.com>
#
# License: Simplified BSD
import math
from functools import partial
import difflib
import webbrowser
import tempfile
import numpy as np
from copy import deepcopy
from distutils.version import LooseVersion
from itertools import cycle
import warnings
from ..channels.layout import _auto_topomap_coords
from ..channels.channels import _contains_ch_type
from ..defaults import _handle_default
from ..io import show_fiff, Info
from ..io.pick import (channel_type, channel_indices_by_type, pick_channels,
_pick_data_channels, _DATA_CH_TYPES_SPLIT,
pick_info, _picks_by_type)
from ..io.proc_history import _get_rank_sss
from ..io.proj import setup_proj
from ..utils import logger, verbose, set_config, warn, _check_ch_locs
from ..externals.six import string_types
from ..selection import (read_selection, _SELECTIONS, _EEG_SELECTIONS,
_divide_to_regions)
from ..annotations import _sync_onset
_channel_type_prettyprint = {'eeg': "EEG channel", 'grad': "Gradiometer",
'mag': "Magnetometer", 'seeg': "sEEG channel",
'eog': "EOG channel", 'ecg': "ECG sensor",
'emg': "EMG sensor", 'ecog': "ECoG channel",
'misc': "miscellaneous sensor"}
def _setup_vmin_vmax(data, vmin, vmax, norm=False):
"""Handle vmin and vmax parameters for visualizing topomaps.
For the normal use-case (when `vmin` and `vmax` are None), the parameter
`norm` drives the computation. When norm=False, data is supposed to come
from a mag and the output tuple (vmin, vmax) is symmetric range
(-x, x) where x is the max(abs(data)). When norm=False (aka data is the L2
norm of a gradiometer pair) the output tuple corresponds to (0, x).
Otherwise, vmin and vmax are callables that drive the operation.
"""
should_warn = False
if vmax is None and vmin is None:
vmax = np.abs(data).max()
vmin = 0. if norm else -vmax
if vmin == 0 and np.min(data) < 0:
should_warn = True
else:
if callable(vmin):
vmin = vmin(data)
elif vmin is None:
vmin = 0. if norm else np.min(data)
if vmin == 0 and np.min(data) < 0:
should_warn = True
if callable(vmax):
vmax = vmax(data)
elif vmax is None:
vmax = np.max(data)
if should_warn:
warn_msg = ("_setup_vmin_vmax output a (min={vmin}, max={vmax})"
" range whereas the minimum of data is {data_min}")
warn_val = {'vmin': vmin, 'vmax': vmax, 'data_min': np.min(data)}
warn(warn_msg.format(**warn_val), UserWarning)
return vmin, vmax
def plt_show(show=True, fig=None, **kwargs):
"""Show a figure while suppressing warnings.
Parameters
----------
show : bool
Show the figure.
fig : instance of Figure | None
If non-None, use fig.show().
**kwargs : dict
Extra arguments for :func:`matplotlib.pyplot.show`.
"""
import matplotlib
import matplotlib.pyplot as plt
if show and matplotlib.get_backend() != 'agg':
(fig or plt).show(**kwargs)
def tight_layout(pad=1.2, h_pad=None, w_pad=None, fig=None):
"""Adjust subplot parameters to give specified padding.
.. note:: For plotting please use this function instead of
``plt.tight_layout``.
Parameters
----------
pad : float
padding between the figure edge and the edges of subplots, as a
fraction of the font-size.
h_pad : float
Padding height between edges of adjacent subplots.
Defaults to `pad_inches`.
w_pad : float
Padding width between edges of adjacent subplots.
Defaults to `pad_inches`.
fig : instance of Figure
Figure to apply changes to.
"""
import matplotlib.pyplot as plt
fig = plt.gcf() if fig is None else fig
fig.canvas.draw()
try: # see https://github.com/matplotlib/matplotlib/issues/2654
with warnings.catch_warnings(record=True) as ws:
fig.tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad)
except Exception:
try:
with warnings.catch_warnings(record=True) as ws:
fig.set_tight_layout(dict(pad=pad, h_pad=h_pad, w_pad=w_pad))
except Exception:
warn('Matplotlib function "tight_layout" is not supported.'
' Skipping subplot adjustment.')
return
for w in ws:
w_msg = str(w.message) if hasattr(w, 'message') else w.get_message()
if not w_msg.startswith('This figure includes Axes'):
warn(w_msg, w.category, 'matplotlib')
def _check_delayed_ssp(container):
"""Handle interactive SSP selection."""
if container.proj is True or\
all(p['active'] for p in container.info['projs']):
raise RuntimeError('Projs are already applied. Please initialize'
' the data with proj set to False.')
elif len(container.info['projs']) < 1:
raise RuntimeError('No projs found in evoked.')
def _validate_if_list_of_axes(axes, obligatory_len=None):
"""Validate whether input is a list/array of axes."""
import matplotlib as mpl
if obligatory_len is not None and not isinstance(obligatory_len, int):
raise ValueError('obligatory_len must be None or int, got %d',
'instead' % type(obligatory_len))
if not isinstance(axes, (list, np.ndarray)):
raise ValueError('axes must be a list or numpy array of matplotlib '
'axes objects, got %s instead.' % type(axes))
if isinstance(axes, np.ndarray) and axes.ndim > 1:
raise ValueError('if input is a numpy array, it must be '
'one-dimensional. The received numpy array has %d '
'dimensions however. Try using ravel or flatten '
'method of the array.' % axes.ndim)
is_correct_type = np.array([isinstance(x, mpl.axes.Axes)
for x in axes])
if not np.all(is_correct_type):
first_bad = np.where(np.logical_not(is_correct_type))[0][0]
raise ValueError('axes must be a list or numpy array of matplotlib '
'axes objects while one of the list elements is '
'%s.' % type(axes[first_bad]))
if obligatory_len is not None and not len(axes) == obligatory_len:
raise ValueError('axes must be a list/array of length %d, while the'
' length is %d' % (obligatory_len, len(axes)))
def mne_analyze_colormap(limits=[5, 10, 15], format='mayavi'):
"""Return a colormap similar to that used by mne_analyze.
Parameters
----------
limits : list (or array) of length 3 or 6
Bounds for the colormap, which will be mirrored across zero if length
3, or completely specified (and potentially asymmetric) if length 6.
format : str
Type of colormap to return. If 'matplotlib', will return a
matplotlib.colors.LinearSegmentedColormap. If 'mayavi', will
return an RGBA array of shape (256, 4).
Returns
-------
cmap : instance of matplotlib.pyplot.colormap | array
A teal->blue->gray->red->yellow colormap.
Notes
-----
For this will return a colormap that will display correctly for data
that are scaled by the plotting function to span [-fmax, fmax].
Examples
--------
The following code will plot a STC using standard MNE limits:
colormap = mne.viz.mne_analyze_colormap(limits=[5, 10, 15])
brain = stc.plot('fsaverage', 'inflated', 'rh', colormap)
brain.scale_data_colormap(fmin=-15, fmid=0, fmax=15, transparent=False)
"""
# Ensure limits is an array
limits = np.asarray(limits, dtype='float')
if len(limits) != 3 and len(limits) != 6:
raise ValueError('limits must have 3 or 6 elements')
if len(limits) == 3 and any(limits < 0.):
raise ValueError('if 3 elements, limits must all be non-negative')
if any(np.diff(limits) <= 0):
raise ValueError('limits must be monotonically increasing')
if format == 'matplotlib':
from matplotlib import colors
if len(limits) == 3:
limits = (np.concatenate((-np.flipud(limits), limits)) +
limits[-1]) / (2 * limits[-1])
else:
limits = (limits - np.min(limits)) / np.max(limits -
np.min(limits))
cdict = {'red': ((limits[0], 0.0, 0.0),
(limits[1], 0.0, 0.0),
(limits[2], 0.5, 0.5),
(limits[3], 0.5, 0.5),
(limits[4], 1.0, 1.0),
(limits[5], 1.0, 1.0)),
'green': ((limits[0], 1.0, 1.0),
(limits[1], 0.0, 0.0),
(limits[2], 0.5, 0.5),
(limits[3], 0.5, 0.5),
(limits[4], 0.0, 0.0),
(limits[5], 1.0, 1.0)),
'blue': ((limits[0], 1.0, 1.0),
(limits[1], 1.0, 1.0),
(limits[2], 0.5, 0.5),
(limits[3], 0.5, 0.5),
(limits[4], 0.0, 0.0),
(limits[5], 0.0, 0.0)),
'alpha': ((limits[0], 1.0, 1.0),
(limits[1], 1.0, 1.0),
(limits[2], 0.0, 0.0),
(limits[3], 0.0, 0.0),
(limits[4], 1.0, 1.0),
(limits[5], 1.0, 1.0)),
}
return colors.LinearSegmentedColormap('mne_analyze', cdict)
elif format == 'mayavi':
if len(limits) == 3:
limits = np.concatenate((-np.flipud(limits), [0], limits)) /\
limits[-1]
else:
limits = np.concatenate((limits[:3], [0], limits[3:]))
limits /= np.max(np.abs(limits))
r = np.array([0, 0, 0, 0, 1, 1, 1])
g = np.array([1, 0, 0, 0, 0, 0, 1])
b = np.array([1, 1, 1, 0, 0, 0, 0])
a = np.array([1, 1, 0, 0, 0, 1, 1])
xp = (np.arange(256) - 128) / 128.0
colormap = np.r_[[np.interp(xp, limits, 255 * c)
for c in [r, g, b, a]]].T
return colormap
else:
raise ValueError('format must be either matplotlib or mayavi')
def _toggle_options(event, params):
"""Toggle options (projectors) dialog."""
import matplotlib.pyplot as plt
if len(params['projs']) > 0:
if params['fig_proj'] is None:
_draw_proj_checkbox(event, params, draw_current_state=False)
else:
# turn off options dialog
plt.close(params['fig_proj'])
del params['proj_checks']
params['fig_proj'] = None
def _toggle_proj(event, params):
"""Perform operations when proj boxes clicked."""
# read options if possible
if 'proj_checks' in params:
bools = [x[0].get_visible() for x in params['proj_checks'].lines]
for bi, (b, p) in enumerate(zip(bools, params['projs'])):
# see if they tried to deactivate an active one
if not b and p['active']:
bools[bi] = True
else:
proj = params.get('apply_proj', True)
bools = [proj] * len(params['projs'])
compute_proj = False
if 'proj_bools' not in params:
compute_proj = True
elif not np.array_equal(bools, params['proj_bools']):
compute_proj = True
# if projectors changed, update plots
if compute_proj is True:
params['plot_update_proj_callback'](params, bools)
def _get_help_text(params):
"""Customize help dialogs text."""
text, text2 = list(), list()
text.append(u'\u2190 : \n') # left arrow
text.append(u'\u2192 : \n') # right arrow
text.append(u'\u2193 : \n') # down arrow
text.append(u'\u2191 : \n') # up arrow
text.append(u'- : \n')
text.append(u'+ or = : \n')
text.append(u'Home : \n')
text.append(u'End : \n')
if 'fig_selection' not in params:
text.append(u'Page down : \n')
text.append(u'Page up : \n')
text.append(u'F11 : \n')
text.append(u'? : \n')
text.append(u'Esc : \n\n')
text.append(u'Mouse controls\n')
text.append(u'click on data :\n')
text2.append('Navigate left\n')
text2.append('Navigate right\n')
text2.append('Scale down\n')
text2.append('Scale up\n')
text2.append('Toggle full screen mode\n')
text2.append('Open help box\n')
text2.append('Quit\n\n\n')
if 'raw' in params:
text2.insert(4, 'Reduce the time shown per view\n')
text2.insert(5, 'Increase the time shown per view\n')
text.append(u'click elsewhere in the plot :\n')
if 'ica' in params:
text.append(u'click component name :\n')
text2.insert(2, 'Navigate components down\n')
text2.insert(3, 'Navigate components up\n')
text2.insert(8, 'Reduce the number of components per view\n')
text2.insert(9, 'Increase the number of components per view\n')
text2.append('Mark bad channel\n')
text2.append('Vertical line at a time instant\n')
text2.append('Show topography for the component\n')
else:
text.append(u'click channel name :\n')
text2.insert(2, 'Navigate channels down\n')
text2.insert(3, 'Navigate channels up\n')
text.insert(6, u'a : \n')
text2.insert(6, 'Toggle annotation mode\n')
text.insert(7, u'b : \n')
text2.insert(7, 'Toggle butterfly plot on/off\n')
if 'fig_selection' not in params:
text2.insert(10, 'Reduce the number of channels per view\n')
text2.insert(11, 'Increase the number of channels per view\n')
text2.append('Mark bad channel\n')
text2.append('Vertical line at a time instant\n')
text2.append('Mark bad channel\n')
elif 'epochs' in params:
text.append(u'right click :\n')
text2.insert(4, 'Reduce the number of epochs per view\n')
text2.insert(5, 'Increase the number of epochs per view\n')
if 'ica' in params:
text.append(u'click component name :\n')
text2.insert(2, 'Navigate components down\n')
text2.insert(3, 'Navigate components up\n')
text2.insert(8, 'Reduce the number of components per view\n')
text2.insert(9, 'Increase the number of components per view\n')
text2.append('Mark component for exclusion\n')
text2.append('Vertical line at a time instant\n')
text2.append('Show topography for the component\n')
else:
text.append(u'click channel name :\n')
text.append(u'right click channel name :\n')
text2.insert(2, 'Navigate channels down\n')
text2.insert(3, 'Navigate channels up\n')
text2.insert(8, 'Reduce the number of channels per view\n')
text2.insert(9, 'Increase the number of channels per view\n')
text.insert(10, u'b : \n')
text2.insert(10, 'Toggle butterfly plot on/off\n')
text.insert(11, u'h : \n')
text2.insert(11, 'Show histogram of peak-to-peak values\n')
text2.append('Mark bad epoch\n')
text2.append('Vertical line at a time instant\n')
text2.append('Mark bad channel\n')
text2.append('Plot ERP/ERF image\n')
text.append(u'middle click :\n')
text2.append('Show channel name (butterfly plot)\n')
text.insert(11, u'o : \n')
text2.insert(11, 'View settings (orig. view only)\n')
return ''.join(text), ''.join(text2)
def _prepare_trellis(n_cells, max_col):
import matplotlib.pyplot as plt
if n_cells == 1:
nrow = ncol = 1
elif n_cells <= max_col:
nrow, ncol = 1, n_cells
else:
nrow, ncol = int(math.ceil(n_cells / float(max_col))), max_col
fig, axes = plt.subplots(nrow, ncol, figsize=(1.3 * ncol + 1,
1.5 * nrow + 1))
axes = [axes] if ncol == nrow == 1 else axes.flatten()
for ax in axes[n_cells:]: # hide unused axes
# XXX: Previously done by ax.set_visible(False), but because of mpl
# bug, we just hide the frame.
from .topomap import _hide_frame
_hide_frame(ax)
return fig, axes
def _draw_proj_checkbox(event, params, draw_current_state=True):
"""Toggle options (projectors) dialog."""
from matplotlib import widgets
projs = params['projs']
# turn on options dialog
labels = [p['desc'] for p in projs]
actives = ([p['active'] for p in projs] if draw_current_state else
params.get('proj_bools', [params['apply_proj']] * len(projs)))
width = max([4., max([len(p['desc']) for p in projs]) / 6.0 + 0.5])
height = len(projs) / 6.0 + 1.5
fig_proj = figure_nobar(figsize=(width, height))
fig_proj.canvas.set_window_title('SSP projection vectors')
params['fig_proj'] = fig_proj # necessary for proper toggling
ax_temp = fig_proj.add_axes((0, 0, 1, 0.8), frameon=False)
ax_temp.set_title('Projectors marked with "X" are active')
proj_checks = widgets.CheckButtons(ax_temp, labels=labels, actives=actives)
# make edges around checkbox areas
[rect.set_edgecolor('0.5') for rect in proj_checks.rectangles]
[rect.set_linewidth(1.) for rect in proj_checks.rectangles]
# change already-applied projectors to red
for ii, p in enumerate(projs):
if p['active']:
for x in proj_checks.lines[ii]:
x.set_color('#ff0000')
# make minimal size
# pass key presses from option dialog over
proj_checks.on_clicked(partial(_toggle_proj, params=params))
params['proj_checks'] = proj_checks
fig_proj.canvas.mpl_connect('key_press_event', _key_press)
# this should work for non-test cases
try:
fig_proj.canvas.draw()
plt_show(fig=fig_proj, warn=False)
except Exception:
pass
def _layout_figure(params):
"""Set figure layout. Shared with raw and epoch plots."""
size = params['fig'].get_size_inches() * params['fig'].dpi
scroll_width = 25
hscroll_dist = 25
vscroll_dist = 10
l_border = 100
r_border = 10
t_border = 35
b_border = 45
# only bother trying to reset layout if it's reasonable to do so
if size[0] < 2 * scroll_width or size[1] < 2 * scroll_width + hscroll_dist:
return
# convert to relative units
scroll_width_x = scroll_width / size[0]
scroll_width_y = scroll_width / size[1]
vscroll_dist /= size[0]
hscroll_dist /= size[1]
l_border /= size[0]
r_border /= size[0]
t_border /= size[1]
b_border /= size[1]
# main axis (traces)
ax_width = 1.0 - scroll_width_x - l_border - r_border - vscroll_dist
ax_y = hscroll_dist + scroll_width_y + b_border
ax_height = 1.0 - ax_y - t_border
pos = [l_border, ax_y, ax_width, ax_height]
params['ax'].set_position(pos)
if 'ax2' in params:
params['ax2'].set_position(pos)
params['ax'].set_position(pos)
# vscroll (channels)
pos = [ax_width + l_border + vscroll_dist, ax_y,
scroll_width_x, ax_height]
params['ax_vscroll'].set_position(pos)
# hscroll (time)
pos = [l_border, b_border, ax_width, scroll_width_y]
params['ax_hscroll'].set_position(pos)
if 'ax_button' in params:
# options button
pos = [l_border + ax_width + vscroll_dist, b_border,
scroll_width_x, scroll_width_y]
params['ax_button'].set_position(pos)
if 'ax_help_button' in params:
pos = [l_border - vscroll_dist - scroll_width_x * 2, b_border,
scroll_width_x * 2, scroll_width_y]
params['ax_help_button'].set_position(pos)
params['fig'].canvas.draw()
@verbose
def compare_fiff(fname_1, fname_2, fname_out=None, show=True, indent=' ',
read_limit=np.inf, max_str=30, verbose=None):
"""Compare the contents of two fiff files using diff and show_fiff.
Parameters
----------
fname_1 : str
First file to compare.
fname_2 : str
Second file to compare.
fname_out : str | None
Filename to store the resulting diff. If None, a temporary
file will be created.
show : bool
If True, show the resulting diff in a new tab in a web browser.
indent : str
How to indent the lines.
read_limit : int
Max number of bytes of data to read from a tag. Can be np.inf
to always read all data (helps test read completion).
max_str : int
Max number of characters of string representation to print for
each tag's data.
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).
Returns
-------
fname_out : str
The filename used for storing the diff. Could be useful for
when a temporary file is used.
"""
file_1 = show_fiff(fname_1, output=list, indent=indent,
read_limit=read_limit, max_str=max_str)
file_2 = show_fiff(fname_2, output=list, indent=indent,
read_limit=read_limit, max_str=max_str)
diff = difflib.HtmlDiff().make_file(file_1, file_2, fname_1, fname_2)
if fname_out is not None:
f = open(fname_out, 'wb')
else:
f = tempfile.NamedTemporaryFile('wb', delete=False, suffix='.html')
fname_out = f.name
with f as fid:
fid.write(diff.encode('utf-8'))
if show is True:
webbrowser.open_new_tab(fname_out)
return fname_out
def figure_nobar(*args, **kwargs):
"""Make matplotlib figure with no toolbar."""
from matplotlib import rcParams, pyplot as plt
old_val = rcParams['toolbar']
try:
rcParams['toolbar'] = 'none'
fig = plt.figure(*args, **kwargs)
# remove button press catchers (for toolbar)
cbs = list(fig.canvas.callbacks.callbacks['key_press_event'].keys())
for key in cbs:
fig.canvas.callbacks.disconnect(key)
finally:
rcParams['toolbar'] = old_val
return fig
def _helper_raw_resize(event, params):
"""Resize."""
size = ','.join([str(s) for s in params['fig'].get_size_inches()])
set_config('MNE_BROWSE_RAW_SIZE', size, set_env=False)
_layout_figure(params)
def _plot_raw_onscroll(event, params, len_channels=None):
"""Interpret scroll events."""
if 'fig_selection' in params:
if params['butterfly']:
return
_change_channel_group(event.step, params)
return
if len_channels is None:
len_channels = len(params['inds'])
orig_start = params['ch_start']
if event.step < 0:
params['ch_start'] = min(params['ch_start'] + params['n_channels'],
len_channels - params['n_channels'])
else: # event.key == 'up':
params['ch_start'] = max(params['ch_start'] - params['n_channels'], 0)
if orig_start != params['ch_start']:
_channels_changed(params, len_channels)
def _channels_changed(params, len_channels):
"""Deal with the vertical shift of the viewport."""
if params['ch_start'] + params['n_channels'] > len_channels:
params['ch_start'] = len_channels - params['n_channels']
if params['ch_start'] < 0:
params['ch_start'] = 0
params['plot_fun']()
def _plot_raw_time(value, params):
"""Deal with changed time value."""
info = params['info']
max_times = params['n_times'] / float(info['sfreq']) + \
params['first_time'] - params['duration']
if value > max_times:
value = params['n_times'] / float(info['sfreq']) + \
params['first_time'] - params['duration']
if value < params['first_time']:
value = params['first_time']
if params['t_start'] != value:
params['t_start'] = value
params['hsel_patch'].set_x(value)
def _radio_clicked(label, params):
"""Handle radio buttons in selection dialog."""
from .evoked import _rgb
# First the selection dialog.
labels = [l._text for l in params['fig_selection'].radio.labels]
idx = labels.index(label)
params['fig_selection'].radio._active_idx = idx
channels = params['selections'][label]
ax_topo = params['fig_selection'].get_axes()[1]
types = np.array([], dtype=int)
for this_type in _DATA_CH_TYPES_SPLIT:
if this_type in params['types']:
types = np.concatenate(
[types, np.where(np.array(params['types']) == this_type)[0]])
colors = np.zeros((len(types), 4)) # alpha = 0 by default
locs3d = np.array([ch['loc'][:3] for ch in params['info']['chs']])
x, y, z = locs3d.T
color_vals = _rgb(x, y, z)
for color_idx, pick in enumerate(types):
if pick in channels: # set color and alpha = 1
colors[color_idx] = np.append(color_vals[pick], 1.)
ax_topo.collections[0]._facecolors = colors
params['fig_selection'].canvas.draw()
if params['butterfly']:
return
# Then the plotting window.
params['ax_vscroll'].set_visible(True)
nchan = sum([len(params['selections'][l]) for l in labels[:idx]])
params['vsel_patch'].set_y(nchan)
n_channels = len(channels)
params['n_channels'] = n_channels
params['inds'] = channels
for line in params['lines'][n_channels:]: # To remove lines from view.
line.set_xdata([])
line.set_ydata([])
if n_channels > 0: # Can be 0 with lasso selector.
_setup_browser_offsets(params, n_channels)
params['plot_fun']()
def _get_active_radiobutton(radio):
"""Find out active radio button."""
# XXX: In mpl 1.5 you can do: fig.radio.value_selected
colors = np.array([np.sum(circle.get_facecolor()) for circle
in radio.circles])
return np.where(colors < 4.0)[0][0] # return idx where color != white
def _set_annotation_radio_button(idx, params):
"""Set active button."""
radio = params['fig_annotation'].radio
for circle in radio.circles:
circle.set_facecolor('white')
radio.circles[idx].set_facecolor('#cccccc')
_annotation_radio_clicked('', radio, params['ax'].selector)
def _set_radio_button(idx, params):
"""Set radio button."""
# XXX: New version of matplotlib has this implemented for radio buttons,
# This function is for compatibility with old versions of mpl.
radio = params['fig_selection'].radio
radio.circles[radio._active_idx].set_facecolor((1., 1., 1., 1.))
radio.circles[idx].set_facecolor((0., 0., 1., 1.))
_radio_clicked(radio.labels[idx]._text, params)
def _change_channel_group(step, params):
"""Deal with change of channel group."""
radio = params['fig_selection'].radio
idx = radio._active_idx
if step < 0:
if idx < len(radio.labels) - 1:
_set_radio_button(idx + 1, params)
elif idx > 0:
_set_radio_button(idx - 1, params)
def _handle_change_selection(event, params):
"""Handle clicks on vertical scrollbar using selections."""
radio = params['fig_selection'].radio
ydata = event.ydata
labels = [label._text for label in radio.labels]
offset = 0
for idx, label in enumerate(labels):
nchans = len(params['selections'][label])
offset += nchans
if ydata < offset:
_set_radio_button(idx, params)
return
def _plot_raw_onkey(event, params):
"""Interpret key presses."""
import matplotlib.pyplot as plt
if event.key == params['close_key']:
plt.close(params['fig'])
if params['fig_annotation'] is not None:
plt.close(params['fig_annotation'])
elif event.key == 'down':
if 'fig_selection' in params.keys():
_change_channel_group(-1, params)
return
elif params['butterfly']:
return
params['ch_start'] += params['n_channels']
_channels_changed(params, len(params['inds']))
elif event.key == 'up':
if 'fig_selection' in params.keys():
_change_channel_group(1, params)
return
elif params['butterfly']:
return
params['ch_start'] -= params['n_channels']
_channels_changed(params, len(params['inds']))
elif event.key == 'right':
value = params['t_start'] + params['duration'] / 4
_plot_raw_time(value, params)
params['update_fun']()
params['plot_fun']()
elif event.key == 'shift+right':
value = params['t_start'] + params['duration']
_plot_raw_time(value, params)
params['update_fun']()
params['plot_fun']()
elif event.key == 'left':
value = params['t_start'] - params['duration'] / 4
_plot_raw_time(value, params)
params['update_fun']()
params['plot_fun']()
elif event.key == 'shift+left':
value = params['t_start'] - params['duration']
_plot_raw_time(value, params)
params['update_fun']()
params['plot_fun']()
elif event.key in ['+', '=']:
params['scale_factor'] *= 1.1
params['plot_fun']()
elif event.key == '-':
params['scale_factor'] /= 1.1
params['plot_fun']()
elif event.key == 'pageup' and 'fig_selection' not in params:
n_channels = params['n_channels'] + 1
_setup_browser_offsets(params, n_channels)
_channels_changed(params, len(params['inds']))
elif event.key == 'pagedown' and 'fig_selection' not in params:
n_channels = params['n_channels'] - 1
if n_channels == 0:
return
_setup_browser_offsets(params, n_channels)
if len(params['lines']) > n_channels: # remove line from view
params['lines'][n_channels].set_xdata([])
params['lines'][n_channels].set_ydata([])
_channels_changed(params, len(params['inds']))
elif event.key == 'home':
duration = params['duration'] - 1.0
if duration <= 0:
return
params['duration'] = duration
params['hsel_patch'].set_width(params['duration'])
params['update_fun']()
params['plot_fun']()
elif event.key == 'end':
duration = params['duration'] + 1.0
if duration > params['raw'].times[-1]:
duration = params['raw'].times[-1]
params['duration'] = duration
params['hsel_patch'].set_width(params['duration'])
params['update_fun']()
params['plot_fun']()
elif event.key == '?':
_onclick_help(event, params)
elif event.key == 'f11':
mng = plt.get_current_fig_manager()
mng.full_screen_toggle()
elif event.key == 'a':
if 'ica' in params.keys():
return
if params['fig_annotation'] is None:
_setup_annotation_fig(params)
else:
params['fig_annotation'].canvas.close_event()
elif event.key == 'b':
_setup_butterfly(params)
elif event.key == 'w':
params['use_noise_cov'] = not params['use_noise_cov']
params['plot_update_proj_callback'](params, None)
def _setup_annotation_fig(params):
"""Initialize the annotation figure."""
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.widgets import RadioButtons, SpanSelector, Button
if params['fig_annotation'] is not None:
params['fig_annotation'].canvas.close_event()
annotations = params['raw'].annotations
labels = list(set(annotations.description))
labels = np.union1d(labels, params['added_label'])
fig = figure_nobar(figsize=(4.5, 2.75 + len(labels) * 0.75))
fig.patch.set_facecolor('white')
ax = plt.subplot2grid((len(labels) + 2, 2), (0, 0),
rowspan=max(len(labels), 1),
colspan=2, frameon=False)
ax.set_title('Labels')
ax.set_aspect('equal')
button_ax = plt.subplot2grid((len(labels) + 2, 2), (len(labels), 1),
rowspan=1, colspan=1)
label_ax = plt.subplot2grid((len(labels) + 2, 2), (len(labels), 0),
rowspan=1, colspan=1)
plt.axis('off')
text_ax = plt.subplot2grid((len(labels) + 2, 2), (len(labels) + 1, 0),
rowspan=1, colspan=2)
text_ax.text(0.5, 0.9, 'Left click & drag - Create/modify annotation\n'
'Right click - Delete annotation\n'
'Letter/number keys - Add character\n'
'Backspace - Delete character\n'
'Esc - Close window/exit annotation mode', va='top',
ha='center')
plt.axis('off')
annotations_closed = partial(_annotations_closed, params=params)
fig.canvas.mpl_connect('close_event', annotations_closed)
fig.canvas.set_window_title('Annotations')
fig.radio = RadioButtons(ax, labels, activecolor='#cccccc')
radius = 0.15
circles = fig.radio.circles
for circle, label in zip(circles, fig.radio.labels):
circle.set_edgecolor(params['segment_colors'][label.get_text()])
circle.set_linewidth(4)
circle.set_radius(radius / (len(labels)))
label.set_x(circle.center[0] + (radius + 0.1) / len(labels))
if len(fig.radio.circles) < 1:
col = '#ff0000'
else:
col = circles[0].get_edgecolor()
fig.canvas.mpl_connect('key_press_event', partial(
_change_annotation_description, params=params))
fig.button = Button(button_ax, 'Add label')
fig.label = label_ax.text(0.5, 0.5, '"BAD_"', va='center', ha='center')
fig.button.on_clicked(partial(_onclick_new_label, params=params))
plt_show(fig=fig)
params['fig_annotation'] = fig
ax = params['ax']
cb_onselect = partial(_annotate_select, params=params)
selector = SpanSelector(ax, cb_onselect, 'horizontal', minspan=.1,
rectprops=dict(alpha=0.5, facecolor=col))
if len(labels) == 0:
selector.active = False
params['ax'].selector = selector
if LooseVersion(mpl.__version__) < LooseVersion('1.5'):
# XXX: Hover event messes up callback ids in old mpl.
warn('Modifying existing annotations is not possible for '
'matplotlib versions < 1.4. Upgrade matplotlib.')
return
hover_callback = partial(_on_hover, params=params)
params['hover_callback'] = params['fig'].canvas.mpl_connect(
'motion_notify_event', hover_callback)
radio_clicked = partial(_annotation_radio_clicked, radio=fig.radio,
selector=selector)
fig.radio.on_clicked(radio_clicked)
def _onclick_new_label(event, params):
"""Add new description on button press."""
text = params['fig_annotation'].label.get_text()[1:-1]
params['added_label'].append(text)
_setup_annotation_colors(params)
_setup_annotation_fig(params)
idx = [label.get_text() for label in
params['fig_annotation'].radio.labels].index(text)
_set_annotation_radio_button(idx, params)
def _mouse_click(event, params):
"""Handle mouse clicks."""
if event.button not in (1, 3):
return
if event.button == 3: # right click
if params['fig_annotation'] is not None: # annotation mode
raw = params['raw']
if any(c.contains(event)[0] for c in params['ax'].collections):
xdata = event.xdata - params['first_time']
onset = _sync_onset(raw, raw.annotations.onset)
ends = onset + raw.annotations.duration
ann_idx = np.where((xdata > onset) & (xdata < ends))[0]
raw.annotations.delete(ann_idx) # only first one deleted
_remove_segment_line(params)
_plot_annotations(raw, params)
params['plot_fun']()
else: # right click in browse mode does nothing
return
if event.inaxes is None: # check if channel label is clicked
if params['n_channels'] > 100:
return
ax = params['ax']
ylim = ax.get_ylim()
pos = ax.transData.inverted().transform((event.x, event.y))
if pos[0] > params['t_start'] or pos[1] < 0 or pos[1] > ylim[0]:
return
params['label_click_fun'](pos)
# vertical scrollbar changed
elif event.inaxes == params['ax_vscroll']:
if 'fig_selection' in params.keys():
_handle_change_selection(event, params)
else:
ch_start = max(int(event.ydata) - params['n_channels'] // 2, 0)
if params['ch_start'] != ch_start:
params['ch_start'] = ch_start
params['plot_fun']()
# horizontal scrollbar changed
elif event.inaxes == params['ax_hscroll']:
_plot_raw_time(event.xdata - params['duration'] / 2, params)
params['update_fun']()
params['plot_fun']()
elif event.inaxes == params['ax']:
params['pick_bads_fun'](event)
def _handle_topomap_bads(ch_name, params):
"""Color channels in selection topomap when selecting bads."""
for t in _DATA_CH_TYPES_SPLIT:
if t in params['types']:
types = np.where(np.array(params['types']) == t)[0]
break
color_ind = np.where(np.array(
params['info']['ch_names'])[types] == ch_name)[0]
if len(color_ind) > 0:
sensors = params['fig_selection'].axes[1].collections[0]
this_color = sensors._edgecolors[color_ind][0]
if all(this_color == [1., 0., 0., 1.]): # is red
sensors._edgecolors[color_ind] = [0., 0., 0., 1.]
else: # is black
sensors._edgecolors[color_ind] = [1., 0., 0., 1.]
params['fig_selection'].canvas.draw()
def _find_channel_idx(ch_name, params):
"""Find all indices when using selections."""
indices = list()
offset = 0
labels = [l._text for l in params['fig_selection'].radio.labels]
for label in labels:
if label == 'Custom':
continue # Custom selection not included as it shifts the indices.
selection = params['selections'][label]
hits = np.where(np.array(params['raw'].ch_names)[selection] == ch_name)
for idx in hits[0]:
indices.append(offset + idx)
offset += len(selection)
return indices
def _draw_vert_line(xdata, params):
"""Draw vertical line."""
params['ax_vertline'].set_xdata(xdata)
params['ax_hscroll_vertline'].set_xdata(xdata)
params['vertline_t'].set_text('%0.2f ' % xdata)
def _select_bads(event, params, bads):
"""Select bad channels onpick. Returns updated bads list."""
# trade-off, avoid selecting more than one channel when drifts are present
# however for clean data don't click on peaks but on flat segments
if params['butterfly']:
_draw_vert_line(event.xdata, params)
return bads
def f(x, y):
return y(np.mean(x), x.std() * 2)
lines = event.inaxes.lines
for line in lines:
ydata = line.get_ydata()
if not isinstance(ydata, list) and not np.isnan(ydata).any():
ymin, ymax = f(ydata, np.subtract), f(ydata, np.add)
if ymin <= event.ydata <= ymax:
this_chan = vars(line)['ch_name']
if this_chan in params['info']['ch_names']:
if 'fig_selection' in params:
ch_idx = _find_channel_idx(this_chan, params)
_handle_topomap_bads(this_chan, params)
else:
ch_idx = [params['ch_start'] + lines.index(line)]
if this_chan not in bads:
bads.append(this_chan)
color = params['bad_color']
line.set_zorder(-1)
else:
while this_chan in bads:
bads.remove(this_chan)
color = vars(line)['def_color']
line.set_zorder(0)
line.set_color(color)
for idx in ch_idx:
params['ax_vscroll'].patches[idx].set_color(color)
break
else:
_draw_vert_line(event.xdata, params)
return bads
def _onclick_help(event, params):
"""Draw help window."""
import matplotlib.pyplot as plt
text, text2 = _get_help_text(params)
width = 6
height = 5
fig_help = figure_nobar(figsize=(width, height), dpi=80)
fig_help.canvas.set_window_title('Help')
params['fig_help'] = fig_help
ax = plt.subplot2grid((8, 5), (0, 0), colspan=5)
ax.set_title('Keyboard shortcuts')
plt.axis('off')
ax1 = plt.subplot2grid((8, 5), (1, 0), rowspan=7, colspan=2)
ax1.set_yticklabels(list())
plt.text(0.99, 1, text, fontname='STIXGeneral', va='top', ha='right')
plt.axis('off')
ax2 = plt.subplot2grid((8, 5), (1, 2), rowspan=7, colspan=3)
ax2.set_yticklabels(list())
plt.text(0, 1, text2, fontname='STIXGeneral', va='top')
plt.axis('off')
fig_help.canvas.mpl_connect('key_press_event', _key_press)
tight_layout(fig=fig_help)
# this should work for non-test cases
try:
fig_help.canvas.draw()
plt_show(fig=fig_help, warn=False)
except Exception:
pass
def _key_press(event):
"""Handle key press in dialog."""
import matplotlib.pyplot as plt
if event.key == 'escape':
plt.close(event.canvas.figure)
def _setup_browser_offsets(params, n_channels):
"""Compute viewport height and adjust offsets."""
ylim = [n_channels * 2 + 1, 0]
offset = ylim[0] / n_channels
params['offsets'] = np.arange(n_channels) * offset + (offset / 2.)
params['n_channels'] = n_channels
params['ax'].set_yticks(params['offsets'])
params['ax'].set_ylim(ylim)
params['vsel_patch'].set_height(n_channels)
line = params['ax_vertline']
line.set_data(line._x, np.array(params['ax'].get_ylim()))
class ClickableImage(object):
"""Display an image so you can click on it and store x/y positions.
Takes as input an image array (can be any array that works with imshow,
but will work best with images. Displays the image and lets you
click on it. Stores the xy coordinates of each click, so now you can
superimpose something on top of it.
Upon clicking, the x/y coordinate of the cursor will be stored in
self.coords, which is a list of (x, y) tuples.
Parameters
----------
imdata : ndarray
The image that you wish to click on for 2-d points.
**kwargs : dict
Keyword arguments. Passed to ax.imshow.
Notes
-----
.. versionadded:: 0.9.0
"""
def __init__(self, imdata, **kwargs):
"""Display the image for clicking."""
from matplotlib.pyplot import figure
self.coords = []
self.imdata = imdata
self.fig = figure()
self.ax = self.fig.add_subplot(111)
self.ymax = self.imdata.shape[0]
self.xmax = self.imdata.shape[1]
self.im = self.ax.imshow(imdata,
extent=(0, self.xmax, 0, self.ymax),
picker=True, **kwargs)
self.ax.axis('off')
self.fig.canvas.mpl_connect('pick_event', self.onclick)
plt_show(block=True)
def onclick(self, event):
"""Handle Mouse clicks.
Parameters
----------
event : matplotlib event object
The matplotlib object that we use to get x/y position.
"""
mouseevent = event.mouseevent
self.coords.append((mouseevent.xdata, mouseevent.ydata))
def plot_clicks(self, **kwargs):
"""Plot the x/y positions stored in self.coords.
Parameters
----------
**kwargs : dict
Arguments are passed to imshow in displaying the bg image.
"""
from matplotlib.pyplot import subplots
if len(self.coords) == 0:
raise ValueError('No coordinates found, make sure you click '
'on the image that is first shown.')
f, ax = subplots()
ax.imshow(self.imdata, extent=(0, self.xmax, 0, self.ymax), **kwargs)
xlim, ylim = [ax.get_xlim(), ax.get_ylim()]
xcoords, ycoords = zip(*self.coords)
ax.scatter(xcoords, ycoords, c='#ff0000')
ann_text = np.arange(len(self.coords)).astype(str)
for txt, coord in zip(ann_text, self.coords):
ax.annotate(txt, coord, fontsize=20, color='#ff0000')
ax.set_xlim(xlim)
ax.set_ylim(ylim)
plt_show()
def to_layout(self, **kwargs):
"""Turn coordinates into an MNE Layout object.
Normalizes by the image you used to generate clicks
Parameters
----------
**kwargs : dict
Arguments are passed to generate_2d_layout
"""
from ..channels.layout import generate_2d_layout
coords = np.array(self.coords)
lt = generate_2d_layout(coords, bg_image=self.imdata, **kwargs)
return lt
def _fake_click(fig, ax, point, xform='ax', button=1, kind='press'):
"""Fake a click at a relative point within axes."""
if xform == 'ax':
x, y = ax.transAxes.transform_point(point)
elif xform == 'data':
x, y = ax.transData.transform_point(point)
elif xform == 'pix':
x, y = point
else:
raise ValueError('unknown transform')
if kind == 'press':
func = partial(fig.canvas.button_press_event, x=x, y=y, button=button)
elif kind == 'release':
func = partial(fig.canvas.button_release_event, x=x, y=y,
button=button)
elif kind == 'motion':
func = partial(fig.canvas.motion_notify_event, x=x, y=y)
try:
func(guiEvent=None)
except Exception: # for old MPL
func()
def add_background_image(fig, im, set_ratios=None):
"""Add a background image to a plot.
Adds the image specified in `im` to the
figure `fig`. This is generally meant to
be done with topo plots, though it could work
for any plot.
Note: This modifies the figure and/or axes
in place.
Parameters
----------
fig : plt.figure
The figure you wish to add a bg image to.
im : array, shape (M, N, {3, 4})
A background image for the figure. This must be a valid input to
`matplotlib.pyplot.imshow`. Defaults to None.
set_ratios : None | str
Set the aspect ratio of any axes in fig
to the value in set_ratios. Defaults to None,
which does nothing to axes.
Returns
-------
ax_im : instance of the created matplotlib axis object
corresponding to the image you added.
Notes
-----
.. versionadded:: 0.9.0
"""
if im is None:
# Don't do anything and return nothing
return None
if set_ratios is not None:
for ax in fig.axes:
ax.set_aspect(set_ratios)
ax_im = fig.add_axes([0, 0, 1, 1], label='background')
ax_im.imshow(im, aspect='auto')
ax_im.set_zorder(-1)
return ax_im
def _find_peaks(evoked, npeaks):
"""Find peaks from evoked data.
Returns ``npeaks`` biggest peaks as a list of time points.
"""
from scipy.signal import argrelmax
gfp = evoked.data.std(axis=0)
order = len(evoked.times) // 30
if order < 1:
order = 1
peaks = argrelmax(gfp, order=order, axis=0)[0]
if len(peaks) > npeaks:
max_indices = np.argsort(gfp[peaks])[-npeaks:]
peaks = np.sort(peaks[max_indices])
times = evoked.times[peaks]
if len(times) == 0:
times = [evoked.times[gfp.argmax()]]
return times
def _process_times(inst, use_times, n_peaks=None, few=False):
"""Return a list of times for topomaps."""
if isinstance(use_times, string_types):
if use_times == 'interactive':
use_times, n_peaks = 'peaks', 1
if use_times == 'peaks':
if n_peaks is None:
n_peaks = min(3 if few else 7, len(inst.times))
use_times = _find_peaks(inst, n_peaks)
elif use_times == 'auto':
if n_peaks is None:
n_peaks = min(5 if few else 10, len(use_times))
use_times = np.linspace(inst.times[0], inst.times[-1], n_peaks)
else:
raise ValueError("Got an unrecognized method for `times`. Only "
"'peaks', 'auto' and 'interactive' are supported "
"(or directly passing numbers).")
elif np.isscalar(use_times):
use_times = [use_times]
use_times = np.array(use_times, float)
if use_times.ndim != 1:
raise ValueError('times must be 1D, got %d dimensions'
% use_times.ndim)
if len(use_times) > 20:
raise RuntimeError('Too many plots requested. Please pass fewer '
'than 20 time instants.')
return use_times
def plot_sensors(info, kind='topomap', ch_type=None, title=None,
show_names=False, ch_groups=None, to_sphere=True, axes=None,
block=False, show=True):
"""Plot sensors positions.
Parameters
----------
info : Instance of Info
Info structure containing the channel locations.
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', 'ecog', 'all'. If ``'all'``, all the available mag, grad, eeg,
seeg 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 (ch_groups, 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.
Returns
-------
fig : instance of matplotlib 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 mayavi see
:func:`mne.viz.plot_alignment`.
.. versionadded:: 0.12.0
"""
from .evoked import _rgb
if kind not in ['topomap', '3d', 'select']:
raise ValueError("Kind must be 'topomap', '3d' or 'select'. Got %s." %
kind)
if not isinstance(info, Info):
raise TypeError('info must be an instance of Info not %s' % type(info))
ch_indices = channel_indices_by_type(info)
allowed_types = _DATA_CH_TYPES_SPLIT
if ch_type is None:
for this_type in allowed_types:
if _contains_ch_type(info, this_type):
ch_type = this_type
break
picks = ch_indices[ch_type]
elif ch_type == 'all':
picks = list()
for this_type in allowed_types:
picks += ch_indices[this_type]
elif ch_type in allowed_types:
picks = ch_indices[ch_type]
else:
raise ValueError("ch_type must be one of %s not %s!" % (allowed_types,
ch_type))
if len(picks) == 0:
raise ValueError('Could not find any channels of type %s.' % ch_type)
chs = [info['chs'][pick] for pick in picks]
if not _check_ch_locs(chs):
raise RuntimeError('No valid channel positions found')
pos = np.array([ch['loc'][:3] for ch in chs])
ch_names = np.array([ch['ch_name'] for ch in chs])
bads = [idx for idx, name in enumerate(ch_names) if name in info['bads']]
if ch_groups is None:
def_colors = _handle_default('color')
colors = ['red' if i in bads else def_colors[channel_type(info, pick)]
for i, pick in enumerate(picks)]
else:
if ch_groups in ['position', 'selection']:
if ch_groups == 'position':
ch_groups = _divide_to_regions(info, add_stim=False)
ch_groups = list(ch_groups.values())
else:
ch_groups, color_vals = list(), list()
for selection in _SELECTIONS + _EEG_SELECTIONS:
channels = pick_channels(
info['ch_names'], read_selection(selection, info=info))
ch_groups.append(channels)
color_vals = np.ones((len(ch_groups), 4))
for idx, ch_group in enumerate(ch_groups):
color_picks = [np.where(picks == ch)[0][0] for ch in ch_group
if ch in picks]
if len(color_picks) == 0:
continue
x, y, z = pos[color_picks].T
color = np.mean(_rgb(x, y, z), axis=0)
color_vals[idx, :3] = color # mean of spatial color
else:
import matplotlib.pyplot as plt
colors = np.linspace(0, 1, len(ch_groups))
color_vals = [plt.cm.jet(colors[i]) for i in range(len(ch_groups))]
if not isinstance(ch_groups, (np.ndarray, list)):
raise ValueError("ch_groups must be None, 'position', "
"'selection', or an array. Got %s." % ch_groups)
colors = np.zeros((len(picks), 4))
for pick_idx, pick in enumerate(picks):
for ind, value in enumerate(ch_groups):
if pick in value:
colors[pick_idx] = color_vals[ind]
break
if kind in ('topomap', 'select'):
pos = _auto_topomap_coords(info, picks, True, to_sphere=to_sphere)
title = 'Sensor positions (%s)' % ch_type if title is None else title
fig = _plot_sensors(pos, colors, bads, ch_names, title, show_names, axes,
show, kind == 'select', block=block,
to_sphere=to_sphere)
if kind == 'select':
return fig, fig.lasso.selection
return fig
def _onpick_sensor(event, fig, ax, pos, ch_names, show_names):
"""Pick a channel in plot_sensors."""
if event.mouseevent.key == 'control' and fig.lasso is not None:
for ind in event.ind:
fig.lasso.select_one(ind)
return
if show_names:
return # channel names already visible
ind = event.ind[0] # Just take the first sensor.
ch_name = ch_names[ind]
this_pos = pos[ind]
# XXX: Bug in matplotlib won't allow setting the position of existing
# text item, so we create a new one.
ax.texts.pop(0)
if len(this_pos) == 3:
ax.text(this_pos[0], this_pos[1], this_pos[2], ch_name)
else:
ax.text(this_pos[0], this_pos[1], ch_name)
fig.canvas.draw()
def _close_event(event, fig):
"""Listen for sensor plotter close event."""
if getattr(fig, 'lasso') is not None:
fig.lasso.disconnect()
def _plot_sensors(pos, colors, bads, ch_names, title, show_names, ax, show,
select, block, to_sphere):
"""Plot sensors."""
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from .topomap import _check_outlines, _draw_outlines
edgecolors = np.repeat('black', len(colors))
edgecolors[bads] = 'red'
if ax is None:
fig = plt.figure(figsize=(max(plt.rcParams['figure.figsize']),) * 2)
if pos.shape[1] == 3:
Axes3D(fig)
ax = fig.gca(projection='3d')
else:
ax = fig.add_subplot(111)
else:
fig = ax.get_figure()
if pos.shape[1] == 3:
ax.text(0, 0, 0, '', zorder=1)
ax.scatter(pos[:, 0], pos[:, 1], pos[:, 2], picker=True, c=colors,
s=75, edgecolor=edgecolors, linewidth=2)
ax.azim = 90
ax.elev = 0
ax.xaxis.set_label_text('x')
ax.yaxis.set_label_text('y')
ax.zaxis.set_label_text('z')
else:
ax.text(0, 0, '', zorder=1)
# Equal aspect for 3D looks bad, so only use for 2D
ax.set(xticks=[], yticks=[], aspect='equal')
fig.subplots_adjust(left=0, bottom=0, right=1, top=1, wspace=None,
hspace=None)
if to_sphere:
pos, outlines = _check_outlines(pos, 'head')
else:
pos, outlines = _check_outlines(pos, np.array([0.5, 0.5]),
{'center': (0, 0),
'scale': (4.5, 4.5)})
_draw_outlines(ax, outlines)
pts = ax.scatter(pos[:, 0], pos[:, 1], picker=True, c=colors, s=25,
edgecolor=edgecolors, linewidth=2, clip_on=False)
if select:
fig.lasso = SelectFromCollection(ax, pts, ch_names)
else:
fig.lasso = None
ax.axis("off") # remove border around figure
connect_picker = True
if show_names:
if isinstance(show_names, (list, np.ndarray)): # only given channels
indices = [list(ch_names).index(name) for name in show_names]
else: # all channels
indices = range(len(pos))
for idx in indices:
this_pos = pos[idx]
if pos.shape[1] == 3:
ax.text(this_pos[0], this_pos[1], this_pos[2], ch_names[idx])
else:
ax.text(this_pos[0] + 0.015, this_pos[1], ch_names[idx])
connect_picker = select
if connect_picker:
picker = partial(_onpick_sensor, fig=fig, ax=ax, pos=pos,
ch_names=ch_names, show_names=show_names)
fig.canvas.mpl_connect('pick_event', picker)
fig.suptitle(title)
closed = partial(_close_event, fig=fig)
fig.canvas.mpl_connect('close_event', closed)
plt_show(show, block=block)
return fig
def _compute_scalings(scalings, inst):
"""Compute scalings for each channel type automatically.
Parameters
----------
scalings : dict
The scalings for each channel type. If any values are
'auto', this will automatically compute a reasonable
scaling for that channel type. Any values that aren't
'auto' will not be changed.
inst : instance of Raw or Epochs
The data for which you want to compute scalings. If data
is not preloaded, this will read a subset of times / epochs
up to 100mb in size in order to compute scalings.
Returns
-------
scalings : dict
A scalings dictionary with updated values
"""
from ..io.base import BaseRaw
from ..epochs import BaseEpochs
if not isinstance(inst, (BaseRaw, BaseEpochs)):
raise ValueError('Must supply either Raw or Epochs')
if scalings is None:
# If scalings is None just return it and do nothing
return scalings
ch_types = channel_indices_by_type(inst.info)
ch_types = dict([(i_type, i_ixs)
for i_type, i_ixs in ch_types.items() if len(i_ixs) != 0])
if scalings == 'auto':
# If we want to auto-compute everything
scalings = dict((i_type, 'auto') for i_type in ch_types.keys())
if not isinstance(scalings, dict):
raise ValueError('scalings must be a dictionary of ch_type: val pairs,'
' not type %s ' % type(scalings))
scalings = deepcopy(scalings)
if inst.preload is False:
if isinstance(inst, BaseRaw):
# Load a window of data from the center up to 100mb in size
n_times = 1e8 // (len(inst.ch_names) * 8)
n_times = np.clip(n_times, 1, inst.n_times)
n_secs = n_times / float(inst.info['sfreq'])
time_middle = np.mean(inst.times)
tmin = np.clip(time_middle - n_secs / 2., inst.times.min(), None)
tmax = np.clip(time_middle + n_secs / 2., None, inst.times.max())
data = inst._read_segment(tmin, tmax)
elif isinstance(inst, BaseEpochs):
# Load a random subset of epochs up to 100mb in size
n_epochs = 1e8 // (len(inst.ch_names) * len(inst.times) * 8)
n_epochs = int(np.clip(n_epochs, 1, len(inst)))
ixs_epochs = np.random.choice(range(len(inst)), n_epochs, False)
inst = inst.copy()[ixs_epochs].load_data()
else:
data = inst._data
if isinstance(inst, BaseEpochs):
data = inst._data.reshape([len(inst.ch_names), -1])
# Iterate through ch types and update scaling if ' auto'
for key, value in scalings.items():
if value != 'auto':
continue
if key not in ch_types.keys():
raise ValueError("Sensor {0} doesn't exist in data".format(key))
this_data = data[ch_types[key]]
scale_factor = np.percentile(this_data.ravel(), [0.5, 99.5])
scale_factor = np.max(np.abs(scale_factor))
scalings[key] = scale_factor
return scalings
def _setup_cmap(cmap, n_axes=1, norm=False):
"""Set color map interactivity."""
if cmap == 'interactive':
cmap = ('Reds' if norm else 'RdBu_r', True)
elif not isinstance(cmap, tuple):
if cmap is None:
cmap = 'Reds' if norm else 'RdBu_r'
cmap = (cmap, False if n_axes > 2 else True)
return cmap
def _prepare_joint_axes(n_maps, figsize=None):
"""Prepare axes for topomaps and colorbar in joint plot figure.
Parameters
----------
n_maps: int
Number of topomaps to include in the figure
figsize: tuple
Figure size, see plt.figsize
Returns
-------
fig : matplotlib.figure.Figure
Figure with initialized axes
main_ax: matplotlib.axes._subplots.AxesSubplot
Axes in which to put the main plot
map_ax: list
List of axes for each topomap
cbar_ax: matplotlib.axes._subplots.AxesSubplot
Axes for colorbar next to topomaps
"""
import matplotlib.pyplot as plt
fig = plt.figure(figsize=figsize)
main_ax = fig.add_subplot(212)
ts = n_maps + 2
map_ax = [plt.subplot(4, ts, x + 2 + ts) for x in range(n_maps)]
# Position topomap subplots on the second row, starting on the
# second column
cbar_ax = plt.subplot(4, 5 * (ts + 1), 10 * (ts + 1))
# Position colorbar at the very end of a more finely divided
# second row of subplots
return fig, main_ax, map_ax, cbar_ax
class DraggableColorbar(object):
"""Enable interactive colorbar.
See http://www.ster.kuleuven.be/~pieterd/python/html/plotting/interactive_colorbar.html
""" # noqa: E501
def __init__(self, cbar, mappable):
import matplotlib.pyplot as plt
self.cbar = cbar
self.mappable = mappable
self.press = None
self.cycle = sorted([i for i in dir(plt.cm) if
hasattr(getattr(plt.cm, i), 'N')])
self.index = self.cycle.index(cbar.get_cmap().name)
self.lims = (self.cbar.norm.vmin, self.cbar.norm.vmax)
self.connect()
def connect(self):
"""Connect to all the events we need."""
self.cidpress = self.cbar.patch.figure.canvas.mpl_connect(
'button_press_event', self.on_press)
self.cidrelease = self.cbar.patch.figure.canvas.mpl_connect(
'button_release_event', self.on_release)
self.cidmotion = self.cbar.patch.figure.canvas.mpl_connect(
'motion_notify_event', self.on_motion)
self.keypress = self.cbar.patch.figure.canvas.mpl_connect(
'key_press_event', self.key_press)
self.scroll = self.cbar.patch.figure.canvas.mpl_connect(
'scroll_event', self.on_scroll)
def on_press(self, event):
"""Handle button press."""
if event.inaxes != self.cbar.ax:
return
self.press = event.y
def key_press(self, event):
"""Handle key press."""
if event.key == 'down':
self.index += 1
elif event.key == 'up':
self.index -= 1
elif event.key == ' ': # space key resets scale
self.cbar.norm.vmin = self.lims[0]
self.cbar.norm.vmax = self.lims[1]
else:
return
if self.index < 0:
self.index = len(self.cycle) - 1
elif self.index >= len(self.cycle):
self.index = 0
cmap = self.cycle[self.index]
self.cbar.set_cmap(cmap)
self.cbar.draw_all()
self.mappable.set_cmap(cmap)
self.cbar.patch.figure.canvas.draw()
def on_motion(self, event):
"""Handle mouse movements."""
if self.press is None:
return
if event.inaxes != self.cbar.ax:
return
yprev = self.press
dy = event.y - yprev
self.press = event.y
scale = self.cbar.norm.vmax - self.cbar.norm.vmin
perc = 0.03
if event.button == 1:
self.cbar.norm.vmin -= (perc * scale) * np.sign(dy)
self.cbar.norm.vmax -= (perc * scale) * np.sign(dy)
elif event.button == 3:
self.cbar.norm.vmin -= (perc * scale) * np.sign(dy)
self.cbar.norm.vmax += (perc * scale) * np.sign(dy)
self.cbar.draw_all()
self.mappable.set_norm(self.cbar.norm)
self.cbar.patch.figure.canvas.draw()
def on_release(self, event):
"""Handle release."""
self.press = None
self.mappable.set_norm(self.cbar.norm)
self.cbar.patch.figure.canvas.draw()
def on_scroll(self, event):
"""Handle scroll."""
scale = 1.1 if event.step < 0 else 1. / 1.1
self.cbar.norm.vmin *= scale
self.cbar.norm.vmax *= scale
self.cbar.draw_all()
self.mappable.set_norm(self.cbar.norm)
self.cbar.patch.figure.canvas.draw()
class SelectFromCollection(object):
"""Select channels from a matplotlib collection using ``LassoSelector``.
Selected channels are saved in the ``selection`` attribute. This tool
highlights selected points by fading other points out (i.e., reducing their
alpha values).
Parameters
----------
ax : Instance of Axes
Axes to interact with.
collection : Instance of matplotlib collection
Collection you want to select from.
alpha_other : 0 <= float <= 1
To highlight a selection, this tool sets all selected points to an
alpha value of 1 and non-selected points to `alpha_other`.
Defaults to 0.3.
Notes
-----
This tool selects collection objects based on their *origins*
(i.e., `offsets`). Emits mpl event 'lasso_event' when selection is ready.
"""
def __init__(self, ax, collection, ch_names,
alpha_other=0.3):
import matplotlib as mpl
if LooseVersion(mpl.__version__) < LooseVersion('1.2.1'):
raise ImportError('Interactive selection not possible for '
'matplotlib versions < 1.2.1. Upgrade '
'matplotlib.')
from matplotlib.widgets import LassoSelector
self.canvas = ax.figure.canvas
self.collection = collection
self.ch_names = ch_names
self.alpha_other = alpha_other
self.xys = collection.get_offsets()
self.Npts = len(self.xys)
# Ensure that we have separate colors for each object
self.fc = collection.get_facecolors()
if len(self.fc) == 0:
raise ValueError('Collection must have a facecolor')
elif len(self.fc) == 1:
self.fc = np.tile(self.fc, self.Npts).reshape(self.Npts, -1)
self.fc[:, -1] = self.alpha_other # deselect in the beginning
self.lasso = LassoSelector(ax, onselect=self.on_select,
lineprops={'color': 'red', 'linewidth': .5})
self.selection = list()
def on_select(self, verts):
"""Select a subset from the collection."""
from matplotlib.path import Path
if len(verts) <= 3: # Seems to be a good way to exclude single clicks.
return
path = Path(verts)
inds = np.nonzero([path.contains_point(xy) for xy in self.xys])[0]
if self.canvas._key == 'control': # Appending selection.
sels = [np.where(self.ch_names == c)[0][0] for c in self.selection]
inters = set(inds) - set(sels)
inds = list(inters.union(set(sels) - set(inds)))
while len(self.selection) > 0:
self.selection.pop(0)
self.selection.extend(self.ch_names[inds])
self.fc[:, -1] = self.alpha_other
self.fc[inds, -1] = 1
self.collection.set_facecolors(self.fc)
self.canvas.draw_idle()
self.canvas.callbacks.process('lasso_event')
def select_one(self, ind):
"""Select or deselect one sensor."""
ch_name = self.ch_names[ind]
if ch_name in self.selection:
sel_ind = self.selection.index(ch_name)
self.selection.pop(sel_ind)
this_alpha = self.alpha_other
else:
self.selection.append(ch_name)
this_alpha = 1
self.fc[ind, -1] = this_alpha
self.collection.set_facecolors(self.fc)
self.canvas.draw_idle()
self.canvas.callbacks.process('lasso_event')
def disconnect(self):
"""Disconnect the lasso selector."""
self.lasso.disconnect_events()
self.fc[:, -1] = 1
self.collection.set_facecolors(self.fc)
self.canvas.draw_idle()
def _annotate_select(vmin, vmax, params):
"""Handle annotation span selector."""
raw = params['raw']
onset = _sync_onset(raw, vmin, True) - params['first_time']
duration = vmax - vmin
active_idx = _get_active_radiobutton(params['fig_annotation'].radio)
description = params['fig_annotation'].radio.labels[active_idx].get_text()
_merge_annotations(onset, onset + duration, description,
raw.annotations)
_plot_annotations(params['raw'], params)
params['plot_fun']()
def _plot_annotations(raw, params):
"""Set up annotations for plotting in raw browser."""
while len(params['ax_hscroll'].collections) > 0:
params['ax_hscroll'].collections.pop()
segments = list()
# sort the segments by start time
ann_order = raw.annotations.onset.argsort(axis=0)
descriptions = raw.annotations.description[ann_order]
_setup_annotation_colors(params)
for idx, onset in enumerate(raw.annotations.onset[ann_order]):
annot_start = _sync_onset(raw, onset) + params['first_time']
annot_end = annot_start + raw.annotations.duration[ann_order][idx]
segments.append([annot_start, annot_end])
dscr = descriptions[idx]
params['ax_hscroll'].fill_betweenx(
(0., 1.), annot_start, annot_end, alpha=0.3,
color=params['segment_colors'][dscr])
# Do not adjust half a sample backward (even though this would make it
# clearer what is included) because this breaks click-drag functionality
params['segments'] = np.array(segments)
params['annot_description'] = descriptions
def _get_color_list(annotations=False):
"""Get the current color list from matplotlib rcParams.
Parameters
----------
annotations : boolean
Has no influence on the function if false. If true, check if color
"red" (#ff0000) is in the cycle and remove it.
Returns
-------
colors : list
"""
import matplotlib.pyplot as plt
color_cycle = plt.rcParams.get('axes.prop_cycle')
if not color_cycle:
# Use deprecated color_cycle to avoid KeyErrors in environments
# with Python 2.7 and Matplotlib < 1.5
# this will already be a list
colors = plt.rcParams.get('axes.color_cycle')
else:
# we were able to use the prop_cycle. Now just convert to list
colors = color_cycle.by_key()['color']
# If we want annotations, red is reserved ... remove if present
if annotations and '#ff0000' in colors:
colors.remove('#ff0000')
return colors
def _setup_annotation_colors(params):
"""Set up colors for annotations."""
raw = params['raw']
segment_colors = params.get('segment_colors', dict())
# sort the segments by start time
ann_order = raw.annotations.onset.argsort(axis=0)
descriptions = raw.annotations.description[ann_order]
color_keys = np.union1d(descriptions, params['added_label'])
color_cycle = cycle(_get_color_list(annotations=True)) # no red
for key, color in segment_colors.items():
if color != '#ff0000' and key in color_keys:
next(color_cycle)
for idx, key in enumerate(color_keys):
if key in segment_colors:
continue
elif key.lower().startswith('bad') or key.lower().startswith('edge'):
segment_colors[key] = '#ff0000'
else:
segment_colors[key] = next(color_cycle)
params['segment_colors'] = segment_colors
def _annotations_closed(event, params):
"""Clean up on annotation dialog close."""
import matplotlib as mpl
import matplotlib.pyplot as plt
plt.close(params['fig_annotation'])
if params['ax'].selector is not None:
params['ax'].selector.disconnect_events()
params['ax'].selector = None
params['fig_annotation'] = None
if params['segment_line'] is not None:
params['segment_line'].remove()
params['segment_line'] = None
if LooseVersion(mpl.__version__) >= LooseVersion('1.5'):
params['fig'].canvas.mpl_disconnect(params['hover_callback'])
params['fig_annotation'] = None
params['fig'].canvas.draw()
def _on_hover(event, params):
"""Handle hover event."""
from matplotlib.patheffects import Stroke, Normal
if (event.button is not None or
event.inaxes != params['ax'] or event.xdata is None):
return
for coll in params['ax'].collections:
if coll.contains(event)[0]:
path = coll.get_paths()
assert len(path) == 1
path = path[0]
color = coll.get_edgecolors()[0]
mn = path.vertices[:, 0].min()
mx = path.vertices[:, 0].max()
# left/right line
x = mn if abs(event.xdata - mn) < abs(event.xdata - mx) else mx
mask = path.vertices[:, 0] == x
ylim = params['ax'].get_ylim()
def drag_callback(x0):
path.vertices[mask, 0] = x0
if params['segment_line'] is None:
modify_callback = partial(_annotation_modify, params=params)
line = params['ax'].plot([x, x], ylim, color=color,
linewidth=2., picker=5.)[0]
dl = DraggableLine(line, modify_callback, drag_callback)
params['segment_line'] = dl
else:
params['segment_line'].set_x(x)
params['segment_line'].drag_callback = drag_callback
line = params['segment_line'].line
pe = [Stroke(linewidth=4, foreground=color, alpha=0.5), Normal()]
line.set_path_effects(pe if line.contains(event)[0] else pe[1:])
params['ax'].selector.active = False
params['fig'].canvas.draw()
return
_remove_segment_line(params)
def _remove_segment_line(params):
"""Remove annotation line from the view."""
if params['segment_line'] is not None:
params['segment_line'].remove()
params['segment_line'] = None
params['ax'].selector.active = True
def _annotation_modify(old_x, new_x, params):
"""Modify annotation."""
raw = params['raw']
segment = np.array(np.where(params['segments'] == old_x))
if segment.shape[1] == 0:
return
annotations = params['raw'].annotations
idx = [segment[0][0], segment[1][0]]
onset = _sync_onset(raw, params['segments'][idx[0]][0], True)
ann_idx = np.where(annotations.onset == onset - params['first_time'])[0]
if idx[1] == 0: # start of annotation
onset = _sync_onset(raw, new_x, True) - params['first_time']
duration = annotations.duration[ann_idx] + old_x - new_x
else: # end of annotation
onset = annotations.onset[ann_idx]
duration = _sync_onset(raw, new_x, True) - onset - params['first_time']
if duration < 0:
onset += duration
duration *= -1.
_merge_annotations(onset, onset + duration,
annotations.description[ann_idx], annotations, ann_idx)
_plot_annotations(params['raw'], params)
_remove_segment_line(params)
params['plot_fun']()
def _merge_annotations(start, stop, description, annotations, current=()):
"""Handle drawn annotations."""
ends = annotations.onset + annotations.duration
idx = np.intersect1d(np.where(ends >= start)[0],
np.where(annotations.onset <= stop)[0])
idx = np.intersect1d(idx,
np.where(annotations.description == description)[0])
new_idx = np.setdiff1d(idx, current) # don't include modified annotation
end = max(np.append((annotations.onset[new_idx] +
annotations.duration[new_idx]), stop))
onset = min(np.append(annotations.onset[new_idx], start))
duration = end - onset
annotations.delete(idx)
annotations.append(onset, duration, description)
def _change_annotation_description(event, params):
"""Handle keys in annotation dialog."""
import matplotlib.pyplot as plt
fig = event.canvas.figure
text = fig.label.get_text()[1:-1]
if event.key == 'backspace':
text = text[:-1]
elif event.key == 'escape':
plt.close(fig)
return
elif event.key == 'enter':
_onclick_new_label(event, params)
elif len(event.key) > 1 or event.key == ';': # ignore modifier keys
return
else:
text = text + event.key
fig.label.set_text('"' + text + '"')
fig.canvas.draw()
def _annotation_radio_clicked(label, radio, selector):
"""Handle annotation radio buttons."""
idx = _get_active_radiobutton(radio)
color = radio.circles[idx].get_edgecolor()
selector.rect.set_color(color)
selector.rectprops.update(dict(facecolor=color))
def _setup_butterfly(params):
"""Set butterfly view of raw plotter."""
from .raw import _setup_browser_selection
if 'ica' in params:
return
butterfly = not params['butterfly']
ax = params['ax']
params['butterfly'] = butterfly
if butterfly:
types = np.array(params['types'])[params['orig_inds']]
if params['group_by'] in ['type', 'original']:
inds = params['inds']
labels = [t for t in _DATA_CH_TYPES_SPLIT + ['eog', 'ecg']
if t in types] + ['misc']
ticks = np.arange(5, 5 * (len(labels) + 1), 5)
offs = {l: t for (l, t) in zip(labels, ticks)}
params['offsets'] = np.zeros(len(params['types']))
for ind in inds:
params['offsets'][ind] = offs.get(params['types'][ind],
5 * (len(labels)))
ax.set_yticks(ticks)
params['ax'].set_ylim(5 * (len(labels) + 1), 0)
ax.set_yticklabels(labels)
else:
if 'selections' not in params:
params['selections'] = _setup_browser_selection(
params['raw'], 'position', selector=False)
sels = params['selections']
selections = _SELECTIONS[1:] # Vertex not used
if ('Misc' in sels and len(sels['Misc']) > 0):
selections += ['Misc']
if params['group_by'] == 'selection' and 'eeg' in types:
for sel in _EEG_SELECTIONS:
if sel in sels:
selections += [sel]
picks = list()
for selection in selections:
picks.append(sels.get(selection, list()))
labels = ax.yaxis.get_ticklabels()
for label in labels:
label.set_visible(True)
ylim = (5. * len(picks), 0.)
ax.set_ylim(ylim)
offset = ylim[0] / (len(picks) + 1)
ticks = np.arange(0, ylim[0], offset)
ticks = [ticks[x] if x < len(ticks) else 0 for x in range(20)]
ax.set_yticks(ticks)
offsets = np.zeros(len(params['types']))
for group_idx, group in enumerate(picks):
for idx, pick in enumerate(group):
offsets[pick] = offset * (group_idx + 1)
params['inds'] = params['orig_inds'].copy()
params['offsets'] = offsets
ax.set_yticklabels([''] + selections, color='black', rotation=45,
va='top')
else:
params['inds'] = params['orig_inds'].copy()
if 'fig_selection' not in params:
for idx in np.arange(params['n_channels'], len(params['lines'])):
params['lines'][idx].set_xdata([])
params['lines'][idx].set_ydata([])
_setup_browser_offsets(params, max([params['n_channels'], 1]))
if 'fig_selection' in params:
radio = params['fig_selection'].radio
active_idx = _get_active_radiobutton(radio)
_radio_clicked(radio.labels[active_idx]._text, params)
# For now, italics only work in non-grouped mode
_set_ax_label_style(ax, params, italicize=not butterfly)
params['ax_vscroll'].set_visible(not butterfly)
params['plot_fun']()
def _connection_line(x, fig, sourceax, targetax, y=1.,
y_source_transform="transAxes"):
"""Connect source and target plots with a line.
Connect source and target plots with a line, such as time series
(source) and topolots (target). Primarily used for plot_joint
functions.
"""
from matplotlib.lines import Line2D
trans_fig = fig.transFigure
trans_fig_inv = fig.transFigure.inverted()
xt, yt = trans_fig_inv.transform(targetax.transAxes.transform([.5, 0.]))
xs, _ = trans_fig_inv.transform(sourceax.transData.transform([x, 0.]))
_, ys = trans_fig_inv.transform(getattr(sourceax, y_source_transform
).transform([0., y]))
return Line2D((xt, xs), (yt, ys), transform=trans_fig, color='grey',
linestyle='-', linewidth=1.5, alpha=.66, zorder=1,
clip_on=False)
class DraggableLine(object):
"""Custom matplotlib line for moving around by drag and drop.
Parameters
----------
line : instance of matplotlib Line2D
Line to add interactivity to.
callback : function
Callback to call when line is released.
"""
def __init__(self, line, modify_callback, drag_callback):
self.line = line
self.press = None
self.x0 = line.get_xdata()[0]
self.modify_callback = modify_callback
self.drag_callback = drag_callback
self.cidpress = self.line.figure.canvas.mpl_connect(
'button_press_event', self.on_press)
self.cidrelease = self.line.figure.canvas.mpl_connect(
'button_release_event', self.on_release)
self.cidmotion = self.line.figure.canvas.mpl_connect(
'motion_notify_event', self.on_motion)
def set_x(self, x):
"""Repoisition the line."""
self.line.set_xdata([x, x])
self.x0 = x
def on_press(self, event):
"""Store button press if on top of the line."""
if event.inaxes != self.line.axes or not self.line.contains(event)[0]:
return
x0 = self.line.get_xdata()
y0 = self.line.get_ydata()
self.press = x0, y0, event.xdata, event.ydata
def on_motion(self, event):
"""Move the line on drag."""
if self.press is None:
return
if event.inaxes != self.line.axes:
return
x0, y0, xpress, ypress = self.press
dx = event.xdata - xpress
self.line.set_xdata(x0 + dx)
self.drag_callback((x0 + dx)[0])
self.line.figure.canvas.draw()
def on_release(self, event):
"""Handle release."""
if event.inaxes != self.line.axes or self.press is None:
return
self.press = None
self.line.figure.canvas.draw()
self.modify_callback(self.x0, event.xdata)
self.x0 = event.xdata
def remove(self):
"""Remove the line."""
self.line.figure.canvas.mpl_disconnect(self.cidpress)
self.line.figure.canvas.mpl_disconnect(self.cidrelease)
self.line.figure.canvas.mpl_disconnect(self.cidmotion)
self.line.figure.axes[0].lines.remove(self.line)
def _set_ax_facecolor(ax, face_color):
"""Fix call for old MPL."""
try:
ax.set_facecolor(face_color)
except AttributeError:
ax.set_axis_bgcolor(face_color)
def _setup_ax_spines(axes, vlines, tmin, tmax, invert_y=False,
ymax_bound=None, unit=None, truncate_xaxis=True):
ymin, ymax = axes.get_ylim()
y_range = -np.subtract(ymin, ymax)
# style the spines/axes
axes.spines["top"].set_position('zero')
if truncate_xaxis is True:
axes.spines["top"].set_smart_bounds(True)
else:
axes.spines['top'].set_bounds(tmin, tmax)
axes.tick_params(direction='out')
axes.tick_params(right=False)
current_ymin = axes.get_ylim()[0]
# set x label
axes.set_xlabel('Time (s)')
axes.xaxis.get_label().set_verticalalignment('center')
# set y label and ylabel position
if unit is not None:
axes.set_ylabel(unit + "\n", rotation=90)
ylabel_height = (-(current_ymin / y_range)
if 0 > current_ymin # ... if we have negative values
else (axes.get_yticks()[-1] / 2 / y_range))
axes.yaxis.set_label_coords(-0.05, 1 - ylabel_height
if invert_y else ylabel_height)
xticks = sorted(list(set([x for x in axes.get_xticks()] + vlines)))
axes.set_xticks(xticks)
x_extrema = [t for t in xticks if tmax >= t >= tmin]
if truncate_xaxis is True:
axes.spines['bottom'].set_bounds(x_extrema[0], x_extrema[-1])
else:
axes.spines['bottom'].set_bounds(tmin, tmax)
if ymin >= 0:
axes.spines["top"].set_color('none')
axes.spines["left"].set_zorder(0)
# finishing touches
if invert_y:
axes.invert_yaxis()
axes.spines['right'].set_color('none')
axes.set_xlim(tmin, tmax)
if truncate_xaxis is False:
axes.axis("tight")
axes.set_autoscale_on(False)
def _handle_decim(info, decim, lowpass):
"""Handle decim parameter for plotters."""
from ..evoked import _check_decim
from ..utils import _ensure_int
if isinstance(decim, string_types) and decim == 'auto':
lp = info['sfreq'] if info['lowpass'] is None else info['lowpass']
lp = min(lp, info['sfreq'] if lowpass is None else lowpass)
info['lowpass'] = lp
decim = max(int(info['sfreq'] / (lp * 3) + 1e-6), 1)
decim = _ensure_int(decim, 'decim', must_be='an int or "auto"')
if decim <= 0:
raise ValueError('decim must be "auto" or a positive integer, got %s'
% (decim,))
decim = _check_decim(info, decim, 0)[0]
data_picks = _pick_data_channels(info, exclude=())
return decim, data_picks
def _grad_pair_pick_and_name(info, picks):
"""Deal with grads. (Helper for a few viz functions)."""
from ..channels.layout import _pair_grad_sensors
picked_chans = list()
pairpicks = _pair_grad_sensors(info, topomap_coords=False)
for ii in np.arange(0, len(pairpicks), 2):
first, second = pairpicks[ii], pairpicks[ii + 1]
if first in picks or second in picks:
picked_chans.append(first)
picked_chans.append(second)
picks = list(sorted(set(picked_chans)))
ch_names = [info["ch_names"][pick] for pick in picks]
return picks, ch_names
def _setup_plot_projector(info, noise_cov, proj=True, use_noise_cov=True,
nave=1):
from ..cov import compute_whitener
projector = np.eye(len(info['ch_names']))
whitened_ch_names = []
if noise_cov is not None and use_noise_cov:
# any channels in noise_cov['bads'] but not in info['bads'] get
# set to nan, which means that they are not plotted.
data_picks = _pick_data_channels(info, with_ref_meg=False, exclude=())
data_names = set(info['ch_names'][pick] for pick in data_picks)
# these can be toggled by the user
bad_names = set(info['bads'])
# these can't in standard pipelines be enabled (we always take the
# union), so pretend they're not in cov at all
cov_names = ((set(noise_cov['names']) & set(info['ch_names'])) -
set(noise_cov['bads']))
# Actually compute the whitener only using the difference
whiten_names = cov_names - bad_names
whiten_picks = pick_channels(info['ch_names'], whiten_names)
whiten_info = pick_info(info, whiten_picks)
rank = _triage_rank_sss(whiten_info, [noise_cov])[1][0]
whitener, whitened_ch_names = compute_whitener(
noise_cov, whiten_info, rank=rank, verbose=False)
whitener *= np.sqrt(nave) # proper scaling for Evoked data
assert set(whitened_ch_names) == whiten_names
projector[whiten_picks, whiten_picks[:, np.newaxis]] = whitener
# Now we need to change the set of "whitened" channels to include
# all data channel names so that they are properly italicized.
whitened_ch_names = data_names
# We would need to set "bad_picks" to identity to show the traces
# (but in gray), but here we don't need to because "projector"
# starts out as identity. So all that is left to do is take any
# *good* data channels that are not in the noise cov to be NaN
nan_names = data_names - (bad_names | cov_names)
# XXX conditional necessary because of annoying behavior of
# pick_channels where an empty list means "all"!
if len(nan_names) > 0:
nan_picks = pick_channels(info['ch_names'], nan_names)
projector[nan_picks] = np.nan
elif proj:
projector, _ = setup_proj(info, add_eeg_ref=False, verbose=False)
return projector, whitened_ch_names
def _set_ax_label_style(ax, params, italicize=True):
import matplotlib.text
for tick in params['ax'].get_yaxis().get_major_ticks():
for text in tick.get_children():
if isinstance(text, matplotlib.text.Text):
whitened = text.get_text() in params['whitened_ch_names']
whitened = whitened and italicize
text.set_style('italic' if whitened else 'normal')
def _check_sss(info):
"""Check SSS history in info."""
ch_used = [ch for ch in _DATA_CH_TYPES_SPLIT
if _contains_ch_type(info, ch)]
has_meg = 'mag' in ch_used and 'grad' in ch_used
has_sss = (has_meg and len(info['proc_history']) > 0 and
info['proc_history'][0].get('max_info') is not None)
return ch_used, has_meg, has_sss
def _triage_rank_sss(info, covs, rank=None, scalings=None):
from ..cov import _estimate_rank_meeg_cov
rank = dict() if rank is None else rank
scalings = _handle_default('scalings_cov_rank', scalings)
# Only look at good channels
picks = _pick_data_channels(info, with_ref_meg=False, exclude='bads')
info = pick_info(info, picks)
ch_used, has_meg, has_sss = _check_sss(info)
if has_sss:
if 'mag' in rank or 'grad' in rank:
raise ValueError('When using SSS, pass "meg" to set the rank '
'(separate rank values for "mag" or "grad" are '
'meaningless).')
elif 'meg' in rank:
raise ValueError('When not using SSS, pass separate rank values '
'for "mag" and "grad" (do not use "meg").')
picks_list = _picks_by_type(info, meg_combined=has_sss)
if has_sss:
# reduce ch_used to combined mag grad
ch_used = list(zip(*picks_list))[0]
# order pick list by ch_used (required for compat with plot_evoked)
picks_list = [x for x, y in sorted(zip(picks_list, ch_used))]
n_ch_used = len(ch_used)
# make sure we use the same rank estimates for GFP and whitening
picks_list2 = [k for k in picks_list]
# add meg picks if needed.
if has_meg:
# append ("meg", picks_meg)
picks_list2 += _picks_by_type(info, meg_combined=True)
rank_list = [] # rank dict for each cov
for cov in covs:
# We need to add the covariance projectors, compute the projector,
# and apply it, just like we will do in prepare_noise_cov, otherwise
# we risk the rank estimates being incorrect (i.e., if the projectors
# do not match).
info_proj = info.copy()
info_proj['projs'] += cov['projs']
this_rank = {}
C = cov['data'].copy()
# assemble rank dict for this cov, such that we have meg
for ch_type, this_picks in picks_list2:
# if we have already estimates / values for mag/grad but not
# a value for meg, combine grad and mag.
if ('mag' in this_rank and 'grad' in this_rank and
'meg' not in rank):
this_rank['meg'] = this_rank['mag'] + this_rank['grad']
# and we're done here
break
if rank.get(ch_type) is None:
this_info = pick_info(info_proj, this_picks)
idx = np.ix_(this_picks, this_picks)
projector = setup_proj(this_info, add_eeg_ref=False)[0]
this_C = C[idx]
if projector is not None:
this_C = np.dot(np.dot(projector, this_C), projector.T)
this_estimated_rank = _estimate_rank_meeg_cov(
this_C, this_info, scalings)
_check_estimated_rank(
this_estimated_rank, this_picks, this_info, info,
cov, ch_type, has_meg, has_sss)
this_rank[ch_type] = this_estimated_rank
elif rank.get(ch_type) is not None:
this_rank[ch_type] = rank[ch_type]
rank_list.append(this_rank)
return n_ch_used, rank_list, picks_list, has_sss
def _check_estimated_rank(this_estimated_rank, this_picks, this_info, info,
cov, ch_type, has_meg, has_sss):
"""Compare estimated against expected rank."""
expected_rank = len(this_picks)
expected_rank_reduction = 0
if has_meg and has_sss and ch_type == 'meg':
sss_rank = _get_rank_sss(info)
expected_rank_reduction += (expected_rank - sss_rank)
n_ssp = sum(_match_proj_type(pp, this_info['ch_names'])
for pp in cov['projs'])
expected_rank_reduction += n_ssp
expected_rank -= expected_rank_reduction
if this_estimated_rank != expected_rank:
logger.debug(
'For (%s) the expected and estimated rank diverge '
'(%i VS %i). \nThis may lead to surprising reults. '
'\nPlease consider using the `rank` parameter to '
'manually specify the spatial degrees of freedom.' % (
ch_type, expected_rank, this_estimated_rank
))
def _match_proj_type(proj, ch_names):
"""See if proj should be counted."""
proj_ch_names = proj['data']['col_names']
select = any(kk in ch_names for kk in proj_ch_names)
return select
def _check_cov(noise_cov, info):
"""Check the noise_cov for whitening and issue an SSS warning."""
from ..cov import read_cov, Covariance
if noise_cov is None:
return None
if isinstance(noise_cov, string_types):
noise_cov = read_cov(noise_cov)
if not isinstance(noise_cov, Covariance):
raise TypeError('noise_cov must be a str or Covariance, got %s'
% (type(noise_cov),))
if _check_sss(info)[2]: # has_sss
warn('Data have been processed with SSS, which changes the relative '
'scaling of magnetometers and gradiometers when viewing data '
'whitened by a noise covariance')
return noise_cov
def _set_title_multiple_electrodes(title, combine, ch_names, max_chans=6,
all=False, ch_type=None):
"""Prepare a title string for multiple electrodes."""
if title is None:
title = ", ".join(ch_names[:max_chans])
ch_type = _channel_type_prettyprint.get(ch_type, ch_type)
if ch_type is None:
ch_type = "sensor"
if len(ch_names) > 1:
ch_type += "s"
if all is True and isinstance(combine, string_types):
combine = combine[0].upper() + combine[1:]
title = "{} of {} {}".format(
combine, len(ch_names), ch_type)
elif len(ch_names) > max_chans and combine is not "gfp":
warn("More than {} channels, truncating title ...".format(
max_chans))
title += ", ...\n({} of {} {})".format(
combine, len(ch_names), ch_type,)
return title
def _check_time_unit(time_unit, times):
if not isinstance(time_unit, string_types):
raise TypeError('time_unit must be str, got %s' % (type(time_unit),))
if time_unit == 's':
times = times
elif time_unit == 'ms':
times = 1e3 * times
else:
raise ValueError("time_unit must be 's' or 'ms', got %r" % time_unit)
return time_unit, times
def _plot_masked_image(ax, data, times, mask=None, picks=None, yvals=None,
cmap="RdBu_r", vmin=None, vmax=None, ylim=None,
mask_style="both", mask_alpha=.25, mask_cmap="Greys",
yscale="linear"):
"""Plot a potentially masked (evoked, TFR, ...) 2D image."""
from matplotlib import ticker, __version__ as v
if mask_style is None and mask is not None:
mask_style = "both" # default
draw_mask = mask_style in {"both", "mask"}
draw_contour = mask_style in {"both", "contour"}
if cmap is None:
mask_cmap = cmap
# mask param check and preparation
if draw_mask is None:
if mask is not None:
draw_mask = True
else:
draw_mask = False
if draw_contour is None:
if mask is not None:
draw_contour = True
else:
draw_contour = False
if mask is None:
if draw_mask:
warn("`mask` is None, not masking the plot ...")
draw_mask = False
if draw_contour:
warn("`mask` is None, not adding contour to the plot ...")
draw_contour = False
if draw_mask:
if mask.shape != data.shape:
raise ValueError(
"The mask must have the same shape as the data, "
"i.e., %s, not %s" % (data.shape, mask.shape))
if draw_contour and yscale == "log":
warn("Cannot draw contours with linear yscale yet ...")
if yvals is None: # for e.g. Evoked images
yvals = np.arange(data.shape[0])
# else, if TFR plot, yvals will be freqs
# test yscale
if yscale == 'log' and not yvals[0] > 0:
raise ValueError('Using log scale for frequency axis requires all your'
' frequencies to be positive (you cannot include'
' the DC component (0 Hz) in the TFR).')
if len(yvals) < 2 or yvals[0] == 0:
yscale = 'linear'
elif yscale != 'linear':
ratio = yvals[1:] / yvals[:-1]
if yscale == 'auto':
if yvals[0] > 0 and np.allclose(ratio, ratio[0]):
yscale = 'log'
else:
yscale = 'linear'
# https://github.com/matplotlib/matplotlib/pull/9477
if yscale == "log" and v == "2.1.0":
warn("With matplotlib version 2.1.0, lines may not show up in "
"`AverageTFR.plot_joint`. Upgrade to a more recent version.")
if yscale is "log": # pcolormesh for log scale
# compute bounds between time samples
time_diff = np.diff(times) / 2. if len(times) > 1 else [0.0005]
time_lims = np.concatenate([[times[0] - time_diff[0]], times[:-1] +
time_diff, [times[-1] + time_diff[-1]]])
log_yvals = np.concatenate([[yvals[0] / ratio[0]], yvals,
[yvals[-1] * ratio[0]]])
yval_lims = np.sqrt(log_yvals[:-1] * log_yvals[1:])
# construct a time-yvaluency bounds grid
time_mesh, yval_mesh = np.meshgrid(time_lims, yval_lims)
if mask is not None:
ax.pcolormesh(time_mesh, yval_mesh, data, cmap=mask_cmap,
vmin=vmin, vmax=vmax, alpha=mask_alpha)
im = ax.pcolormesh(time_mesh, yval_mesh,
np.ma.masked_where(~mask, data), cmap=cmap,
vmin=vmin, vmax=vmax, alpha=1)
else:
im = ax.pcolormesh(time_mesh, yval_mesh, data, cmap=cmap,
vmin=vmin, vmax=vmax)
if ylim is None:
ylim = yval_lims[[0, -1]]
if yscale == 'log':
ax.set_yscale('log')
ax.get_yaxis().set_major_formatter(ticker.ScalarFormatter())
ax.yaxis.set_minor_formatter(ticker.NullFormatter())
# get rid of minor ticks
ax.yaxis.set_minor_locator(ticker.NullLocator())
tick_vals = yvals[np.unique(np.linspace(
0, len(yvals) - 1, 12).round().astype('int'))]
ax.set_yticks(tick_vals)
else:
# imshow for linear because the y ticks are nicer
# and the masked areas look better
extent = [times[0], times[-1], yvals[0], yvals[-1] + 1]
im_args = dict(interpolation='nearest', origin='lower',
extent=extent, aspect='auto', vmin=vmin, vmax=vmax)
if draw_mask:
ax.imshow(data, alpha=mask_alpha, cmap=mask_cmap, **im_args)
im = ax.imshow(
np.ma.masked_where(~mask, data), cmap=cmap, **im_args)
else:
im = ax.imshow(data, cmap=cmap, **im_args)
if draw_contour and np.unique(mask).size == 2:
big_mask = np.kron(mask, np.ones((10, 10)))
ax.contour(big_mask, colors=["k"], extent=extent,
linewidths=[.75], corner_mask=False,
antialiased=False, levels=[.5])
time_lims = times[[0, -1]]
ylim = yvals[0], yvals[-1] + 1
ax.set_xlim(time_lims[0], time_lims[-1])
ax.set_ylim(ylim)
if (draw_mask or draw_contour) and mask is not None:
if mask.all():
t_end = ", all points masked)"
else:
fraction = 1 - (np.float(mask.sum()) / np.float(mask.size))
t_end = ", %0.3g%% of points masked)" % (fraction * 100,)
else:
t_end = ")"
return im, t_end
def center_cmap(cmap, vmin, vmax, name="cmap_centered"):
"""Center given colormap (ranging from vmin to vmax) at value 0.
Parameters
----------
cmap : matplotlib.colors.Colormap
The colormap to center around 0.
vmin : float
Minimum value in the data to map to the lower end of the colormap.
vmax : float
Maximum value in the data to map to the upper end of the colormap.
name : str
Name of the new colormap. Defaults to 'cmap_centered'.
Returns
-------
cmap_centered : matplotlib.colors.Colormap
The new colormap centered around 0.
Notes
-----
This function can be used in situations where vmin and vmax are not
symmetric around zero. Normally, this results in the value zero not being
mapped to white anymore in many colormaps. Using this function, the value
zero will be mapped to white even for asymmetric positive and negative
value ranges. Note that this could also be achieved by re-normalizing a
given colormap by subclassing matplotlib.colors.Normalize as described
here:
https://matplotlib.org/users/colormapnorms.html#custom-normalization-two-linear-ranges
""" # noqa: E501
from matplotlib.colors import LinearSegmentedColormap
vzero = abs(vmin) / float(vmax - vmin)
index_old = np.linspace(0, 1, cmap.N)
index_new = np.hstack([np.linspace(0, vzero, cmap.N // 2, endpoint=False),
np.linspace(vzero, 1, cmap.N // 2)])
colors = "red", "green", "blue", "alpha"
cdict = {name: [] for name in colors}
for old, new in zip(index_old, index_new):
for color, name in zip(cmap(old), colors):
cdict[name].append((new, color, color))
return LinearSegmentedColormap(name, cdict)
|