We will use distance between test segments computed in 140926-test-signal-jump to find sequence of segments that were likely together

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In [1]:

%matplotlib inline
from matplotlib import pylab as pl
import cPickle as pickle
import pandas as pd
import numpy as np
import os

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In [3]:

targets = ['Dog_1', 'Dog_2', 'Dog_3', 'Dog_4', 'Dog_5', 'Patient_1', 'Patient_2']

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In [5]:

for target in targets:
print
N = d.shape[0]
print target, N, N/6.
dord = np.unravel_index(d.ravel().argsort(),d.shape)
Nsequences = N/6

# find good pairs of segments that are likely to be paired in time
next_segment = [-1]*N
previous_segment = [-1]*N
for i,(s1,s2) in enumerate(np.array(dord).T):
dist = d[s1,s2]
if next_segment[s1] != -1:
print i,'right conflict',dist
break
if previous_segment[s2] != -1:
print i,'left conflict',dist
break
next_segment[s1] = s2
previous_segment[s2] = s1
if i < Nsequences:
print 'skip'
continue
# check code
for i in range(N):
if next_segment[i] != -1:
assert previous_segment[next_segment[i]] == i

# find good sequences
sequences = []
for i in range(N):
if previous_segment[i] == -1 and next_segment[i] != -1:
j = i
sequence = [j]
while next_segment[j] != -1:
j = next_segment[j]
sequence.append(j)
sequences.append(sequence)
len_sequences = [len(sequence) for sequence in sequences]
print '#sequences',len(sequences), '%segments that was sequenced',sum(len_sequences)/float(N), 'longest sequence', max(len_sequences)
print sequences

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Dog_1 502 83.6666666667
108 left conflict -0.9611050735
#sequences 74 %segments that was sequenced 0.362549800797 longest sequence 5
[[21, 32], [43, 20], [51, 497], [56, 24], [58, 371], [62, 42], [66, 134], [70, 495], [76, 127, 146, 106, 389], [77, 204], [79, 48], [93, 321], [95, 452], [97, 107, 219], [120, 141], [124, 88], [158, 140], [162, 287], [163, 131], [179, 194, 377, 99], [186, 473], [188, 259], [190, 463], [209, 263], [211, 117], [215, 197], [224, 31], [235, 37, 84], [236, 199], [239, 67], [240, 394], [247, 223, 249, 102], [248, 416, 132], [256, 262, 361], [260, 490], [291, 381, 92, 268], [301, 366, 342], [302, 343, 232], [303, 19], [304, 230], [307, 376], [310, 456], [320, 57, 413], [331, 424], [339, 153, 174], [340, 281, 229, 333], [341, 176, 245], [346, 26], [350, 319], [354, 181, 431, 338, 200], [360, 441, 4], [369, 439], [370, 316, 300], [375, 227, 109], [390, 383, 309], [392, 164], [393, 145], [406, 282, 161], [412, 154], [419, 195], [432, 332], [434, 267, 293, 442, 221], [445, 115], [450, 395], [453, 425], [455, 34], [459, 45], [461, 193], [476, 44], [479, 185], [481, 489, 430], [487, 206], [494, 63, 189], [499, 446, 182]]

Dog_2 1000 166.666666667
324 right conflict -0.932151727252
#sequences 193 %segments that was sequenced 0.517 longest sequence 6
[[3, 226, 140], [6, 386], [16, 862], [23, 956, 935], [26, 37, 276], [28, 489], [31, 614], [34, 143], [35, 175], [44, 346], [48, 552, 542], [52, 737, 268], [58, 315, 772, 124], [64, 435], [66, 938, 17], [67, 254], [74, 302, 775, 588, 673, 184], [80, 776], [86, 387, 641], [90, 265], [92, 306], [93, 598, 695, 699, 638], [95, 131, 941], [97, 907], [100, 507], [102, 865, 604], [104, 889, 798, 733, 50, 72], [109, 63], [114, 79, 87, 216], [127, 998, 170, 32], [130, 10], [133, 30], [146, 634, 281, 498], [152, 340, 606], [157, 731], [162, 213], [169, 257], [173, 954], [180, 20], [185, 341], [194, 877], [202, 600, 277, 196, 296], [206, 71], [209, 509], [214, 419], [222, 990, 203, 275], [225, 384, 582, 251], [232, 792], [233, 292], [234, 352, 820, 14], [235, 118], [236, 783, 291], [238, 578], [239, 122], [245, 546, 514, 657, 323], [250, 892, 702, 555], [253, 405], [264, 317, 939, 645], [267, 347, 46], [274, 248, 227], [284, 663], [289, 616], [293, 9], [295, 332, 466, 24, 558, 853], [297, 45], [305, 283, 917, 136, 510], [325, 545], [327, 438], [334, 298, 452], [336, 161], [339, 846], [342, 730], [348, 240], [357, 221, 764], [360, 413], [370, 608], [393, 2], [400, 139], [402, 121], [404, 447, 365, 763], [408, 707], [409, 218, 622], [411, 750, 511], [415, 841, 832, 255, 612, 581], [424, 312, 160], [430, 910], [431, 824], [440, 839], [448, 619, 810], [454, 412], [455, 101], [456, 874], [461, 423], [463, 960, 613], [467, 911], [469, 977], [474, 471], [480, 880, 304, 421, 569], [484, 392], [494, 147], [501, 278], [504, 760, 630], [506, 199, 426], [512, 401], [537, 995, 77, 442], [551, 629], [567, 75, 53], [568, 468], [570, 924], [571, 599], [572, 60], [575, 682], [580, 927], [583, 107, 905], [584, 549, 916, 285], [585, 261, 43, 754], [586, 991], [587, 154], [601, 262], [631, 125], [633, 273, 807, 150], [642, 126], [648, 453], [653, 688], [654, 186, 487], [658, 652, 566], [665, 538], [666, 177], [672, 476], [678, 635, 208], [686, 718, 649], [689, 492], [691, 908, 741], [703, 19], [705, 590, 15], [719, 345], [725, 369], [732, 906], [734, 970, 866], [740, 519], [742, 428], [748, 318], [753, 379], [755, 465, 459, 550], [758, 462, 174], [766, 714, 418, 815, 316, 851], [771, 932, 972, 191, 138, 524], [774, 816, 868], [789, 948], [794, 751], [795, 690], [803, 362, 562, 767, 508], [804, 576, 182], [812, 382], [835, 385], [838, 301], [842, 921, 770, 377], [844, 738], [845, 505, 746, 172, 724, 320], [848, 372, 592, 872], [849, 88], [850, 560], [854, 934, 231, 704], [855, 836], [857, 515], [859, 858, 785], [879, 813, 333], [884, 898, 137], [891, 171], [894, 12], [897, 117], [899, 368, 110, 779], [902, 944, 490, 488, 337], [903, 187], [904, 609], [912, 151], [915, 134], [925, 636, 444], [940, 244], [952, 540, 679, 119], [953, 356], [964, 78], [966, 39], [968, 324], [969, 266, 532], [975, 364], [976, 314], [979, 594], [981, 155], [985, 29, 801], [988, 864, 527, 800], [994, 331], [997, 811]]

Dog_3 907 151.166666667
33 left conflict -0.989490150071
skip

Dog_4 990 165.0
556 right conflict -0.960661574506
#sequences 241 %segments that was sequenced 0.805050505051 longest sequence 6
[[0, 399], [1, 260, 101, 478, 415, 236], [7, 759, 635, 264], [11, 10], [13, 321, 132, 889], [14, 581, 429], [15, 24], [25, 315], [28, 8], [33, 631], [36, 964, 75, 141, 790], [38, 978, 678], [44, 875, 116], [45, 462], [46, 402, 971, 446], [48, 70, 483, 840, 986], [55, 170, 319, 767], [60, 127, 847], [63, 528], [67, 937, 987, 148, 948], [79, 126, 249], [86, 789], [87, 584], [98, 144], [103, 737, 721], [107, 664, 546, 18], [112, 827, 155, 106, 890, 244], [120, 122], [121, 573, 324, 544], [123, 383, 809, 970, 82, 333], [125, 647, 374], [128, 134], [129, 915], [135, 311], [136, 853, 417, 230], [138, 235, 613], [140, 499, 604], [142, 341, 860, 409, 655], [147, 200], [161, 896, 76], [163, 817, 648], [172, 680, 295, 68, 214], [174, 508, 488], [175, 976, 16], [177, 795, 520, 713], [179, 495], [184, 479, 829, 139, 724], [186, 22, 444, 859], [187, 585, 728, 154], [189, 855], [190, 682], [191, 89, 364], [193, 885], [197, 545, 531, 17], [203, 760], [207, 878], [208, 349, 413], [209, 143], [211, 638, 376, 102, 373], [216, 848], [220, 502, 770, 908, 985, 828], [225, 813], [233, 231, 459, 612], [251, 618], [253, 956], [255, 224, 47, 195], [256, 516, 473], [257, 658, 954], [263, 288], [268, 442, 934, 171, 241], [273, 932, 73], [279, 222, 327, 448, 729, 504], [281, 727, 406, 820], [282, 957, 497, 269, 656, 426], [283, 717], [289, 50], [294, 156], [297, 940, 455, 284], [299, 152, 183, 456], [300, 239, 926, 851], [307, 753, 862], [309, 361], [310, 377], [312, 730], [313, 662, 272], [316, 487], [318, 229, 731], [328, 740, 637, 167, 942], [329, 685, 523, 673], [335, 501], [338, 768, 703, 927, 511, 893], [340, 532], [343, 951, 943], [344, 907, 465, 652], [348, 562, 416], [350, 766, 835, 807, 837, 365], [356, 782], [357, 733, 698, 891], [362, 359], [366, 454, 428, 438], [372, 165, 923], [379, 720], [384, 640, 557], [385, 726, 526, 250], [386, 708, 911, 856, 792], [389, 355], [390, 578, 599, 706], [394, 51], [395, 110, 419, 606, 977, 217], [396, 984], [401, 286, 514, 398], [403, 162, 659, 754], [404, 846], [405, 118, 565], [407, 339, 457, 363], [422, 716], [430, 894, 711], [434, 27, 748], [441, 619], [443, 794, 843, 77, 234, 808], [450, 221, 521], [451, 449, 935, 873, 19, 592], [461, 906], [468, 470], [469, 796, 146, 226], [472, 958, 834, 761], [475, 677, 205, 601], [481, 877, 826, 973, 969, 247], [486, 825], [489, 322, 292, 552], [492, 188, 2, 505, 306, 3], [493, 561, 421, 74], [494, 966], [500, 301], [506, 901], [507, 824, 895], [509, 423], [513, 630], [515, 547, 605, 553, 52, 683], [522, 182], [524, 850, 670, 797], [527, 323], [535, 278], [536, 836, 869, 115, 503], [537, 248, 572, 905, 886, 477], [555, 920], [558, 484, 266, 979, 181], [559, 903], [564, 739], [566, 815, 124, 296], [575, 151, 71, 574], [577, 81, 653, 550], [583, 569], [589, 725, 801], [591, 803], [593, 331], [596, 694], [597, 485], [602, 265], [615, 369, 228, 892, 784, 368], [616, 517, 408], [620, 178, 567], [628, 261], [632, 883, 518], [642, 96, 665, 414, 270, 317], [643, 212], [649, 32], [650, 158, 427], [651, 668, 736, 833, 510, 149], [667, 594, 342, 360], [675, 936, 97], [684, 914], [686, 543], [688, 924, 262], [692, 83, 245, 695, 746, 541], [699, 622, 666], [700, 772, 201], [704, 482], [714, 660, 582], [715, 378], [719, 928, 435, 922, 237, 804], [723, 206], [735, 35, 466], [743, 196, 972, 702, 173], [745, 351, 391], [747, 988, 554], [749, 876, 471, 114, 866], [750, 982, 352, 744], [751, 287, 274, 5], [755, 718, 453, 168, 223], [756, 674], [757, 336], [758, 345, 491], [762, 865], [773, 669], [777, 912], [778, 285], [779, 732, 64], [780, 549, 609, 293], [781, 705, 467], [783, 830, 672, 412], [786, 533, 410, 939], [787, 290], [798, 53], [810, 690, 930, 679], [811, 938, 347], [812, 326, 219, 989, 62, 420], [814, 802], [816, 400, 246, 277, 192, 334], [818, 304, 397, 874], [819, 563, 26, 243, 325], [821, 6, 104, 105], [823, 480, 180, 199, 57, 841], [831, 463, 539], [838, 576, 579], [844, 393, 113], [845, 981, 254, 884, 381, 198], [861, 880], [863, 460, 21, 799], [864, 512, 43, 882, 267, 769], [867, 946, 707, 84], [871, 100], [879, 227, 358], [888, 644], [904, 963, 117, 587, 600, 69], [910, 742], [919, 354, 90, 625, 548], [921, 375, 586], [929, 476, 534, 218, 94, 59], [944, 909, 380, 160, 788], [949, 150, 153], [950, 629, 917, 854], [952, 785, 91], [953, 42, 298], [955, 621, 611], [959, 897, 388], [960, 519, 931], [961, 66, 464], [962, 580], [967, 654], [974, 542]]

Dog_5 191 31.8333333333
42 left conflict -0.959496774214
#sequences 33 %segments that was sequenced 0.392670157068 longest sequence 4
[[1, 131, 105, 139], [6, 36, 140], [10, 7], [22, 112], [32, 74], [33, 23, 190], [34, 49], [38, 84, 107], [41, 21], [42, 160], [57, 133], [62, 51], [69, 188], [77, 113], [78, 158], [79, 119, 55, 2], [90, 159], [91, 115], [93, 148], [99, 43], [116, 16], [120, 180], [128, 48], [129, 75], [138, 92, 109], [144, 14], [145, 130], [147, 154], [152, 5], [161, 171], [166, 182], [177, 26, 143], [179, 187]]

Patient_1 195 32.5
10 left conflict -0.909383819823
skip

Patient_2 150 25.0
1 right conflict -0.999516626264
skip

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In [ ]:

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