efg’s R Notes: EBImage: Haralick Features
Basic | Haralick | Moment | Shape
Haralick Textural Features Details
The function computeFeatures.haralick computes features that quantify pixel texture. Features are named according to Haralick’s original paper. See Haralick Textural Features Details for details about the 26 features.
All Haralick features have a prefix “h.”.
library(EBImage)computeFeatures.haralick(x, ref , properties=FALSE, haralick.nbins=32, haralick.scales=c(1, 2), xs, ...)List properties of Haralick features
feature.properties <- computeFeatures.haralick(properties=TRUE)
feature.properties name translation.invariant rotation.invariant
1 h.asm.s1 TRUE TRUE
2 h.con.s1 TRUE TRUE
3 h.cor.s1 TRUE TRUE
4 h.var.s1 TRUE TRUE
5 h.idm.s1 TRUE TRUE
6 h.sav.s1 TRUE TRUE
7 h.sva.s1 TRUE TRUE
8 h.sen.s1 TRUE TRUE
9 h.ent.s1 TRUE TRUE
10 h.dva.s1 TRUE TRUE
11 h.den.s1 TRUE TRUE
12 h.f12.s1 TRUE TRUE
13 h.f13.s1 TRUE TRUE
14 h.asm.s2 TRUE TRUE
15 h.con.s2 TRUE TRUE
16 h.cor.s2 TRUE TRUE
17 h.var.s2 TRUE TRUE
18 h.idm.s2 TRUE TRUE
19 h.sav.s2 TRUE TRUE
20 h.sva.s2 TRUE TRUE
21 h.sen.s2 TRUE TRUE
22 h.ent.s2 TRUE TRUE
23 h.dva.s2 TRUE TRUE
24 h.den.s2 TRUE TRUE
25 h.f12.s2 TRUE TRUE
26 h.f13.s2 TRUE TRUELoad and segment nucleus
par(mfrow=c(1,2))
y <- readImage(system.file("images", "nuclei.tif", package="EBImage"))[,,1]
x <- thresh(y, 10, 10, 0.05)
x <- opening(x, makeBrush(5, shape='disc'))
x <- bwlabel(x)
display(y, title="Cell nuclei")
display(x, title="Segmented nuclei")
Compute Haralick features
haralickFeatures <- computeFeatures.haralick(x, y)
str(haralickFeatures) num [1:76, 1:26] 0.02222 0.01259 0.00712 0.02203 0.01764 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:26] "h.asm.s1" "h.con.s1" "h.cor.s1" "h.var.s1" ...options(digits=4, width=100)
haralickFeatures h.asm.s1 h.con.s1 h.cor.s1 h.var.s1 h.idm.s1 h.sav.s1 h.sva.s1 h.sen.s1 h.ent.s1 h.dva.s1
[1,] 0.022224 3.8455 0.7456 8.559 0.3909 16.21 250.38 1.2483 1.7418 3.8455
[2,] 0.012585 4.4215 0.8502 15.763 0.4295 29.07 818.19 1.4333 2.0212 4.4215
[3,] 0.007124 16.2582 0.7255 30.612 0.3025 45.20 2006.48 1.5651 2.3143 16.2582
[4,] 0.022026 1.8475 0.8924 9.582 0.5523 32.03 974.36 1.3421 1.7653 1.8475
[5,] 0.017644 2.0354 0.8970 10.879 0.5416 31.29 931.33 1.3878 1.8426 2.0354
[6,] 0.021749 1.7653 0.9078 10.573 0.5682 34.57 1139.58 1.3604 1.7779 1.7653
[7,] 0.013924 3.4527 0.8805 15.449 0.4718 39.01 1464.00 1.4603 1.9906 3.4527
[8,] 0.014018 2.8896 0.9029 15.887 0.4984 33.53 1085.51 1.4547 1.9549 2.8896
[9,] 0.118404 5.0848 0.8988 26.130 0.5633 55.21 3004.93 1.2674 1.7165 5.0848
[10,] 0.070508 0.7958 0.7841 2.843 0.6917 22.74 478.44 1.0142 1.2724 0.7958
[11,] 0.117755 0.7929 0.6469 2.123 0.7150 22.09 453.66 0.8806 1.0929 0.7929
[12,] 0.019052 2.1181 0.8822 9.988 0.5226 29.30 815.66 1.3435 1.7948 2.1181
[13,] 0.104005 0.8071 0.5875 1.978 0.7079 14.52 190.24 0.8417 1.0818 0.8071
[14,] 0.102355 6.7783 0.8584 24.933 0.5233 54.93 2968.50 1.2727 1.7536 6.7783
[15,] 0.494436 9.1845 0.5674 11.614 0.7602 61.20 3698.75 0.6524 0.8468 9.1845
[16,] 0.471465 6.8751 0.6229 10.115 0.7601 61.40 3716.50 0.6764 0.8991 6.8751
[17,] 0.018188 3.1399 0.8390 10.752 0.4826 36.96 1302.91 1.3634 1.8676 3.1399
[18,] 0.398206 9.6490 0.6271 13.936 0.7046 60.46 3603.85 0.7798 1.0367 9.6490
[19,] 0.072663 6.5401 0.8631 24.880 0.4948 54.89 2958.74 1.3213 1.8221 6.5401
[20,] 0.021163 5.2949 0.6223 8.009 0.4286 23.09 500.35 1.2323 1.8300 5.2949
[21,] 0.011421 3.4193 0.8854 15.918 0.4416 36.37 1274.24 1.4718 2.0196 3.4193
[22,] 0.010491 4.8877 0.8690 19.648 0.4047 39.20 1491.54 1.4905 2.0666 4.8877
[23,] 0.031133 1.4491 0.8789 6.984 0.6097 27.50 710.41 1.2745 1.6548 1.4491
[24,] 0.040622 1.2458 0.8432 4.973 0.6328 26.62 662.07 1.1761 1.5235 1.2458
[25,] 0.025687 8.2625 0.8685 32.421 0.3862 50.09 2479.43 1.4932 2.1146 8.2625
[26,] 0.010082 5.0272 0.8692 20.218 0.4052 40.25 1572.32 1.5178 2.1160 5.0272
[27,] 0.014073 5.6684 0.8433 19.088 0.4313 46.30 2077.04 1.4605 2.0782 5.6684
[28,] 0.009097 4.8458 0.8840 21.881 0.3928 43.09 1806.17 1.5309 2.1400 4.8458
[29,] 0.025400 4.4500 0.5775 6.266 0.4156 33.37 1053.79 1.1648 1.6949 4.4500
[30,] 0.010761 5.4360 0.9030 29.018 0.4011 48.71 2330.38 1.5515 2.1595 5.4360
[31,] 0.011218 4.4797 0.8694 18.145 0.4337 43.00 1787.79 1.4807 2.0794 4.4797
[32,] 0.019212 4.3747 0.9194 28.133 0.4792 50.50 2503.18 1.5177 2.0593 4.3747
[33,] 0.009222 5.8258 0.8650 22.584 0.3973 42.12 1726.05 1.5506 2.1870 5.8258
[34,] 0.013840 6.4152 0.8893 29.986 0.4144 47.87 2255.38 1.5461 2.1593 6.4152
[35,] 0.329953 17.2167 0.5080 18.496 0.6483 59.76 3521.91 0.8610 1.1231 17.2167
[36,] 0.010473 4.6216 0.8466 16.061 0.3992 39.73 1519.99 1.4651 2.0598 4.6216
[37,] 0.083051 6.4902 0.8627 24.630 0.5080 54.66 2933.90 1.3114 1.8107 6.4902
[38,] 0.023596 2.5292 0.7938 7.133 0.4834 31.05 909.64 1.2526 1.7270 2.5292
[39,] 0.026801 1.6944 0.8657 7.310 0.5743 28.02 738.74 1.2772 1.6802 1.6944
[40,] 0.053604 9.2340 0.7684 20.938 0.4534 55.03 2953.18 1.3378 1.9122 9.2340
[41,] 0.017447 2.5536 0.8662 10.541 0.5106 31.94 969.96 1.3763 1.8740 2.5536
[42,] 0.010582 9.5952 0.7053 17.280 0.3182 36.23 1265.73 1.4422 2.0898 9.5952
[43,] 0.436319 10.2013 0.5770 13.059 0.7332 60.93 3662.32 0.7250 0.9569 10.2013
[44,] 0.258074 7.3100 0.7528 15.784 0.6363 59.30 3453.41 0.9733 1.3300 7.3100
[45,] 0.059910 1.4515 0.6942 3.374 0.5672 19.28 341.55 1.0221 1.3543 1.4515
[46,] 0.301235 7.6518 0.7383 15.618 0.6524 59.51 3484.18 0.9184 1.2562 7.6518
[47,] 0.016343 2.1269 0.9169 13.790 0.5362 35.06 1179.03 1.4469 1.9088 2.1269
[48,] 0.016675 6.1948 0.7189 12.021 0.4104 46.36 2063.93 1.3494 1.9703 6.1948
[49,] 0.013807 5.5517 0.8065 15.348 0.4164 47.74 2195.18 1.4403 2.0572 5.5517
[50,] 0.016387 2.7011 0.8530 10.185 0.4965 31.20 924.83 1.3580 1.8703 2.7011
[51,] 0.030667 1.4603 0.8664 6.463 0.5956 25.61 614.42 1.2324 1.6120 1.4603
[52,] 0.029860 1.7946 0.8140 5.823 0.5701 26.52 657.78 1.2137 1.6411 1.7946
[53,] 0.008802 5.1924 0.8643 20.130 0.3804 42.31 1735.24 1.5217 2.1479 5.1924
[54,] 0.014474 3.3030 0.8481 11.870 0.4527 35.34 1193.38 1.3793 1.9198 3.3030
[55,] 0.191807 5.9194 0.8573 21.734 0.6081 57.30 3235.12 1.1025 1.4992 5.9194
[56,] 0.028715 1.5953 0.9154 10.429 0.5989 25.87 638.17 1.3338 1.7186 1.5953
[57,] 0.010888 4.0323 0.9146 24.603 0.4467 47.90 2239.11 1.5478 2.1048 4.0323
[58,] 0.017029 3.2836 0.8518 12.081 0.4722 33.06 1045.14 1.3737 1.8770 3.2836
[59,] 0.022553 2.1714 0.8476 8.125 0.5126 26.74 672.82 1.3102 1.7707 2.1714
[60,] 0.036504 7.5008 0.8765 31.370 0.4186 51.55 2622.73 1.4646 2.0486 7.5008
[61,] 0.015874 3.1103 0.8586 12.002 0.4805 38.67 1429.44 1.4022 1.9256 3.1103
[62,] 0.023382 2.3135 0.8250 7.611 0.5282 31.23 920.36 1.2943 1.7558 2.3135
[63,] 0.015938 2.7924 0.8810 12.731 0.4989 36.09 1246.74 1.4158 1.9202 2.7924
[64,] 0.027671 1.6003 0.8596 6.698 0.5716 24.39 557.02 1.2406 1.6263 1.6003
[65,] 0.071228 0.7895 0.7929 2.906 0.6986 17.48 277.82 1.0184 1.2734 0.7895
[66,] 0.014803 2.2884 0.9253 16.313 0.5228 38.69 1443.71 1.4769 1.9496 2.2884
[67,] 0.019140 3.2590 0.8372 11.010 0.4753 36.05 1239.76 1.3680 1.8759 3.2590
[68,] 0.051484 1.0102 0.8203 3.812 0.6596 22.23 456.15 1.1116 1.4238 1.0102
[69,] 0.015627 3.8377 0.8479 13.615 0.4516 37.29 1334.65 1.3975 1.9362 3.8377
[70,] 0.032586 1.6664 0.8289 5.869 0.5924 26.72 667.98 1.2228 1.6255 1.6664
[71,] 0.048703 1.0672 0.8295 4.130 0.6579 20.75 396.15 1.1358 1.4567 1.0672
[72,] 0.154361 6.4140 0.8551 23.138 0.5641 56.69 3164.78 1.1730 1.6006 6.4140
[73,] 0.016355 3.9383 0.8524 14.340 0.4415 37.59 1359.13 1.3969 1.9385 3.9383
[74,] 0.025208 1.9476 0.8507 7.523 0.5493 28.18 747.37 1.2852 1.7277 1.9476
[75,] 0.076100 0.7171 0.8216 3.009 0.7208 20.66 393.17 1.0139 1.2382 0.7171
[76,] 0.097994 1.6667 0.0625 1.889 0.5000 9.00 70.86 0.6951 1.0343 1.6667
h.den.s1 h.f12.s1 h.f13.s1 h.asm.s2 h.con.s2 h.cor.s2 h.var.s2 h.idm.s2 h.sav.s2 h.sva.s2
[1,] 0.6232 0.2212 0.5929 0.025992 13.609 0.2132 9.648 0.2278 18.13 307.5
[2,] 0.6944 0.2508 0.6632 0.012431 14.217 0.5565 17.027 0.2982 29.27 827.0
[3,] 0.9491 0.1821 0.6091 0.007236 44.679 0.3663 36.252 0.1919 45.43 2022.7
[4,] 0.5288 0.3290 0.7078 0.019348 5.011 0.6825 8.890 0.4067 32.51 1001.4
[5,] 0.5503 0.3246 0.7143 0.013385 5.340 0.7327 10.991 0.4020 31.72 956.3
[6,] 0.5266 0.3407 0.7198 0.016636 4.178 0.7566 9.583 0.4325 35.28 1184.3
[7,] 0.6541 0.2975 0.7080 0.010355 8.755 0.6597 13.864 0.3313 39.95 1528.1
[8,] 0.6178 0.3199 0.7246 0.010343 8.369 0.7037 15.122 0.3203 33.91 1104.2
[9,] 0.7124 0.3223 0.6949 0.108581 11.313 0.7616 24.731 0.4872 56.04 3086.0
[10,] 0.3927 0.2828 0.5851 0.066460 1.467 0.5896 2.787 0.5901 22.70 478.0
[11,] 0.4063 0.2484 0.5163 0.151627 1.000 0.2194 1.641 0.6385 21.77 446.8
[12,] 0.5476 0.3103 0.6948 0.014531 6.074 0.6471 9.607 0.3587 29.97 850.1
[13,] 0.4073 0.1793 0.4381 0.070749 1.931 0.3148 2.409 0.5310 14.14 179.5
[14,] 0.7669 0.2876 0.6672 0.106626 18.774 0.5907 23.934 0.4380 55.73 3043.0
[15,] 0.5480 0.1835 0.3966 0.473235 12.362 0.2224 8.949 0.7462 61.90 3774.7
[16,] 0.5455 0.1982 0.4237 0.417110 9.374 0.2986 7.682 0.7168 61.89 3764.0
[17,] 0.6339 0.2590 0.6529 0.016725 7.675 0.5390 9.324 0.3715 37.57 1341.8
[18,] 0.6294 0.2090 0.4636 0.446429 16.085 0.2688 11.999 0.7061 61.22 3691.0
[19,] 0.7737 0.2828 0.6717 0.069931 16.516 0.6044 21.874 0.4024 56.03 3063.6
[20,] 0.7273 0.1318 0.4770 0.026783 14.040 0.1085 8.875 0.3096 22.71 482.3
[21,] 0.6356 0.3003 0.7143 0.010048 9.325 0.6894 16.014 0.2815 36.76 1298.4
[22,] 0.7076 0.2811 0.7009 0.018870 14.477 0.5907 18.685 0.2722 39.41 1503.9
[23,] 0.5004 0.3300 0.6929 0.023655 3.555 0.7043 7.011 0.4642 27.88 729.8
[24,] 0.4718 0.3013 0.6461 0.030493 2.752 0.6028 4.465 0.4828 27.25 694.0
[25,] 0.8256 0.2625 0.6871 0.029419 24.114 0.5924 30.584 0.2865 51.69 2619.4
[26,] 0.7189 0.2750 0.7005 0.009247 14.284 0.6488 21.334 0.2523 40.91 1622.4
[27,] 0.7496 0.2484 0.6673 0.013193 14.969 0.5635 18.146 0.3176 47.25 2156.4
[28,] 0.7047 0.2836 0.7120 0.008587 14.797 0.6470 21.960 0.2341 43.78 1856.8
[29,] 0.6919 0.1446 0.4819 0.070312 11.750 -0.3875 5.234 0.2181 33.25 1061.3
[30,] 0.7367 0.2931 0.7236 0.008997 15.886 0.6949 27.030 0.2692 49.56 2396.7
[31,] 0.7013 0.2617 0.6822 0.010505 11.390 0.6369 16.685 0.2873 43.88 1854.2
[32,] 0.7047 0.3322 0.7481 0.016839 13.410 0.7574 28.642 0.3444 50.81 2528.8
[33,] 0.7480 0.2609 0.6937 0.010777 15.306 0.6646 23.815 0.2885 42.27 1737.9
[34,] 0.7750 0.2822 0.7128 0.014349 15.726 0.7329 30.436 0.3078 48.52 2310.3
[35,] 0.7370 0.1660 0.4289 0.312643 21.179 0.2088 14.385 0.6343 60.52 3600.0
[36,] 0.6946 0.2634 0.6817 0.012893 10.528 0.5878 13.770 0.2674 40.76 1591.7
[37,] 0.7683 0.2878 0.6752 0.094428 14.932 0.6701 23.628 0.4530 55.53 3021.1
[38,] 0.5694 0.2505 0.6246 0.021910 5.515 0.4617 6.123 0.3521 32.07 970.6
[39,] 0.5211 0.3033 0.6720 0.022210 4.474 0.6376 7.172 0.4297 28.49 763.2
[40,] 0.8349 0.2038 0.5933 0.029757 22.777 0.4294 20.958 0.3274 55.49 2989.9
[41,] 0.5920 0.2883 0.6842 0.013745 5.744 0.6807 9.995 0.3701 32.52 1002.8
[42,] 0.8353 0.1958 0.6038 0.015163 21.962 0.3538 17.994 0.1802 36.85 1306.0
[43,] 0.6010 0.1792 0.4144 0.428952 13.080 0.2918 10.236 0.7093 61.52 3724.9
[44,] 0.6974 0.2369 0.5482 0.268438 14.853 0.3982 13.342 0.5959 60.05 3531.3
[45,] 0.4657 0.2393 0.5549 0.103448 4.103 -0.2081 2.698 0.4282 19.00 335.2
[46,] 0.6820 0.2349 0.5331 0.253679 14.493 0.4967 15.399 0.5862 59.76 3502.4
[47,] 0.5587 0.3514 0.7462 0.011913 5.355 0.7780 13.061 0.3745 35.69 1218.2
[48,] 0.7609 0.1720 0.5567 0.016197 13.776 0.3289 11.264 0.2826 47.14 2132.9
[49,] 0.7388 0.2283 0.6415 0.012400 14.015 0.4779 14.422 0.2888 48.54 2264.1
[50,] 0.6005 0.2639 0.6585 0.012180 8.167 0.5929 11.032 0.3172 31.35 932.7
[51,] 0.4929 0.3112 0.6693 0.020517 3.831 0.6558 6.565 0.4274 25.87 626.5
[52,] 0.5335 0.2543 0.6165 0.025794 3.923 0.5741 5.605 0.4314 26.85 674.2
[53,] 0.7167 0.2604 0.6887 0.007411 14.708 0.5993 19.352 0.2311 42.97 1781.3
[54,] 0.6309 0.2569 0.6574 0.012706 9.527 0.5873 12.541 0.3559 35.36 1193.0
[55,] 0.7032 0.2888 0.6302 0.205532 13.208 0.6358 19.133 0.5567 58.14 3318.4
[56,] 0.5134 0.3617 0.7293 0.020497 4.014 0.7790 10.083 0.4377 26.10 646.3
[57,] 0.6821 0.3262 0.7481 0.007444 11.473 0.7403 23.091 0.2926 48.69 2303.2
[58,] 0.6418 0.2810 0.6772 0.016475 8.455 0.5982 11.521 0.3496 33.84 1092.9
[59,] 0.5493 0.2786 0.6605 0.014844 5.627 0.6335 8.677 0.3487 27.31 701.8
[60,] 0.8079 0.2755 0.6930 0.033490 22.957 0.6245 31.570 0.3188 52.22 2678.7
[61,] 0.6293 0.2787 0.6811 0.013102 8.797 0.6183 12.525 0.3143 38.85 1442.0
[62,] 0.5756 0.2702 0.6497 0.019669 5.350 0.5683 7.196 0.3892 32.06 969.5
[63,] 0.6096 0.2979 0.6995 0.014074 7.330 0.7032 13.347 0.3764 36.45 1271.9
[64,] 0.5023 0.3189 0.6786 0.025222 3.807 0.6696 6.761 0.4113 24.19 548.2
[65,] 0.3931 0.2940 0.5961 0.056230 1.452 0.6207 2.913 0.5793 17.62 282.6
[66,] 0.5724 0.3601 0.7584 0.010258 6.300 0.7948 16.355 0.3572 39.32 1488.2
[67,] 0.6385 0.2690 0.6647 0.014965 8.870 0.5630 11.149 0.3378 36.89 1296.8
[68,] 0.4353 0.2932 0.6220 0.040242 1.829 0.6780 3.840 0.5545 22.33 461.0
[69,] 0.6690 0.2712 0.6748 0.014542 11.234 0.5655 13.926 0.3194 37.55 1351.3
[70,] 0.5244 0.2807 0.6417 0.025063 4.172 0.5720 5.874 0.4539 27.19 691.4
[71,] 0.4483 0.3035 0.6374 0.032932 2.470 0.6348 4.382 0.5135 20.80 398.8
[72,] 0.7389 0.2798 0.6371 0.171786 16.396 0.6086 21.946 0.5096 57.48 3245.0
[73,] 0.6732 0.2638 0.6672 0.020161 11.496 0.5679 14.301 0.3368 37.78 1370.6
[74,] 0.5447 0.2837 0.6597 0.019987 4.475 0.6256 6.975 0.4007 28.64 771.1
[75,] 0.3830 0.3312 0.6231 0.058423 1.351 0.6959 3.221 0.6306 20.74 396.3
[76,] 0.4260 0.1387 0.3780 0.000000 0.000 0.0000 0.000 0.0000 0.00 0.0
h.sen.s2 h.ent.s2 h.dva.s2 h.den.s2 h.f12.s2 h.f13.s2
[1,] 1.2031 1.6636 13.609 0.8430 0.16833 0.5133
[2,] 1.3979 2.0907 14.217 0.9226 0.17791 0.5790
[3,] 1.5400 2.2309 44.679 1.1333 0.21550 0.6454
[4,] 1.2907 1.8594 5.011 0.7142 0.18325 0.5593
[5,] 1.3616 1.9794 5.340 0.7311 0.18096 0.5705
[6,] 1.3104 1.8777 4.178 0.6815 0.20337 0.5885
[7,] 1.4114 2.0854 8.755 0.8189 0.16992 0.5666
[8,] 1.4176 2.0677 8.369 0.8077 0.18022 0.5797
[9,] 1.2468 1.7031 11.313 0.8479 0.23748 0.6067
[10,] 0.9708 1.3235 1.467 0.4909 0.15028 0.4399
[11,] 0.6696 0.9144 1.000 0.4125 0.07828 0.2679
[12,] 1.3008 1.9191 6.074 0.7445 0.15260 0.5212
[13,] 0.8809 1.2328 1.931 0.5221 0.08477 0.3215
[14,] 1.2351 1.6631 18.774 0.9239 0.20476 0.5619
[15,] 0.6215 0.7609 12.362 0.5800 0.13762 0.3261
[16,] 0.6797 0.8643 9.374 0.6122 0.10784 0.3063
[17,] 1.2855 1.9052 7.675 0.8056 0.12811 0.4791
[18,] 0.6946 0.8409 16.085 0.6244 0.15695 0.3653
[19,] 1.2881 1.8154 16.516 0.9411 0.18475 0.5558
[20,] 1.1472 1.7517 14.040 0.9178 0.14428 0.4883
[21,] 1.4326 2.0913 9.325 0.8137 0.19497 0.6029
[22,] 1.3665 1.8243 14.477 0.9086 0.22084 0.6035
[23,] 1.2497 1.7629 3.555 0.6548 0.18747 0.5528
[24,] 1.1216 1.6111 2.752 0.5935 0.14288 0.4686
[25,] 1.4400 2.0156 24.114 1.0236 0.20522 0.6077
[26,] 1.4713 2.1546 14.284 0.9126 0.20692 0.6259
[27,] 1.3905 2.0718 14.969 0.9304 0.16400 0.5562
[28,] 1.4955 2.1494 14.797 0.9139 0.17173 0.5764
[29,] 0.7526 1.1665 11.750 0.6773 0.42019 0.6799
[30,] 1.5106 2.1981 15.886 0.9419 0.19914 0.6205
[31,] 1.4158 2.1209 11.390 0.8746 0.16071 0.5565
[32,] 1.4998 2.1558 13.410 0.9132 0.21728 0.6393
[33,] 1.5066 2.1798 15.306 0.9340 0.20851 0.6308
[34,] 1.5256 2.1418 15.726 0.9471 0.23375 0.6578
[35,] 0.7948 0.9775 21.179 0.7217 0.13295 0.3605
[36,] 1.3794 1.9636 10.528 0.8353 0.14995 0.5221
[37,] 1.2604 1.7077 14.932 0.8770 0.25045 0.6219
[38,] 1.1568 1.7269 5.515 0.7025 0.14575 0.4876
[39,] 1.2371 1.8123 4.474 0.6968 0.16237 0.5235
[40,] 1.3332 1.9154 22.777 0.9835 0.15756 0.5285
[41,] 1.3294 1.9557 5.744 0.7369 0.16646 0.5467
[42,] 1.3496 1.8578 21.962 0.9672 0.24512 0.6363
[43,] 0.6819 0.8319 13.080 0.6239 0.11202 0.3066
[44,] 0.9209 1.2305 14.853 0.7805 0.17361 0.4567
[45,] 0.7642 1.0807 4.103 0.6600 0.17684 0.4349
[46,] 0.9457 1.2551 14.493 0.7899 0.18020 0.4691
[47,] 1.4077 2.0132 5.355 0.7182 0.21488 0.6198
[48,] 1.2554 1.9517 13.776 0.9048 0.10130 0.4336
[49,] 1.3752 2.0820 14.015 0.9111 0.12542 0.4931
[50,] 1.3419 2.0189 8.167 0.8018 0.13535 0.5040
[51,] 1.2084 1.7689 3.831 0.6565 0.15230 0.5029
[52,] 1.1625 1.7101 3.923 0.6643 0.12201 0.4464
[53,] 1.4688 2.2105 14.708 0.9090 0.16790 0.5772
[54,] 1.3551 2.0023 9.527 0.8425 0.17273 0.5614
[55,] 1.0549 1.4180 13.208 0.8010 0.21490 0.5378
[56,] 1.3215 1.8294 4.014 0.6598 0.24728 0.6350
[57,] 1.5102 2.2275 11.473 0.8771 0.20095 0.6261
[58,] 1.2990 1.9210 8.455 0.8162 0.18263 0.5659
[59,] 1.2979 1.9320 5.627 0.7185 0.14407 0.5091
[60,] 1.4335 2.0291 22.957 1.0073 0.21006 0.6155
[61,] 1.3683 2.0252 8.797 0.8222 0.15747 0.5409
[62,] 1.2409 1.8537 5.350 0.7182 0.14423 0.5003
[63,] 1.3844 1.9997 7.330 0.7932 0.20579 0.6065
[64,] 1.1938 1.6611 3.807 0.6439 0.19474 0.5488
[65,] 0.9947 1.3560 1.452 0.4786 0.16146 0.4604
[66,] 1.4597 2.0875 6.300 0.7553 0.22474 0.6407
[67,] 1.3262 1.9658 8.870 0.8251 0.15125 0.5245
[68,] 1.0839 1.5054 1.829 0.5243 0.17910 0.5063
[69,] 1.3483 1.9751 11.234 0.8667 0.18169 0.5711
[70,] 1.1854 1.7241 4.172 0.6897 0.15411 0.5001
[71,] 1.1119 1.5940 2.470 0.5784 0.16389 0.4976
[72,] 1.1107 1.5097 16.396 0.8601 0.22324 0.5619
[73,] 1.3292 1.9241 11.496 0.8803 0.17627 0.5573
[74,] 1.2242 1.7943 4.475 0.6818 0.16536 0.5257
[75,] 1.0277 1.3571 1.351 0.4846 0.21405 0.5270
[76,] 0.0000 0.0000 0.000 0.0000 0.00000 0.0000Correlations of Haralick features
correlationMatrix <- cor(haralickFeatures)
correlationMatrix## h.asm.s1 h.con.s1 h.cor.s1 h.var.s1 h.idm.s1 h.sav.s1 h.sva.s1 h.sen.s1 h.ent.s1 h.dva.s1
## h.asm.s1 1.00000 0.47368 -0.51077 -0.031988 0.66446 0.52951 0.64284 -0.80003 -0.76562 0.47368
## h.con.s1 0.47368 1.00000 -0.27150 0.634937 -0.20300 0.75491 0.76844 -0.06138 0.04364 1.00000
## h.cor.s1 -0.51077 -0.27150 1.00000 0.330692 -0.26615 0.07788 -0.05427 0.72823 0.62964 -0.27150
## h.var.s1 -0.03199 0.63494 0.33069 1.000000 -0.53337 0.73935 0.68147 0.51746 0.56754 0.63494
## h.idm.s1 0.66446 -0.20300 -0.26615 -0.533369 1.00000 -0.05902 0.05482 -0.82354 -0.89955 -0.20300
## h.sav.s1 0.52951 0.75491 0.07788 0.739352 -0.05902 1.00000 0.98299 0.01296 0.07189 0.75491
## h.sva.s1 0.64284 0.76844 -0.05427 0.681472 0.05482 0.98299 1.00000 -0.14337 -0.07953 0.76844
## h.sen.s1 -0.80003 -0.06138 0.72823 0.517460 -0.82354 0.01296 -0.14337 1.00000 0.98501 -0.06138
## h.ent.s1 -0.76562 0.04364 0.62964 0.567538 -0.89955 0.07189 -0.07953 0.98501 1.00000 0.04364
## h.dva.s1 0.47368 1.00000 -0.27150 0.634937 -0.20300 0.75491 0.76844 -0.06138 0.04364 1.00000
## h.den.s1 -0.07778 0.74726 0.16229 0.859731 -0.70482 0.68825 0.61617 0.51238 0.61817 0.74726
## h.f12.s1 -0.40751 -0.52940 0.80732 0.080132 0.06648 -0.14641 -0.22123 0.45178 0.30345 -0.52940
## h.f13.s1 -0.71545 -0.33387 0.90495 0.370768 -0.47526 -0.05803 -0.19477 0.86404 0.77495 -0.33387
## h.asm.s2 0.98538 0.49199 -0.45537 -0.004335 0.63909 0.55795 0.65999 -0.76453 -0.73129 0.49199
## h.con.s2 0.11126 0.88462 -0.01167 0.796214 -0.52568 0.65910 0.62901 0.29491 0.40239 0.88462
## h.cor.s2 -0.36699 -0.28246 0.80558 0.292590 -0.07508 0.05687 -0.03050 0.55226 0.44286 -0.28246
## h.var.s2 -0.11763 0.60768 0.36636 0.986518 -0.58778 0.66518 0.59946 0.58057 0.63002 0.60768
## h.idm.s2 0.74432 0.05073 -0.10203 -0.284392 0.91269 0.22607 0.31156 -0.71574 -0.77833 0.05073
## h.sav.s2 0.50918 0.74434 0.13332 0.740204 -0.06375 0.99689 0.97284 0.04255 0.09564 0.74434
## h.sva.s2 0.63628 0.76705 -0.04399 0.685802 0.04908 0.98424 0.99974 -0.13465 -0.07154 0.76705
## h.sen.s2 -0.67092 -0.02304 0.85486 0.525040 -0.65815 0.10492 -0.04762 0.94298 0.90534 -0.02304
## h.ent.s2 -0.72583 -0.07937 0.82090 0.460260 -0.69448 0.03900 -0.11829 0.95599 0.92510 -0.07937
## h.dva.s2 0.11126 0.88462 -0.01167 0.796214 -0.52568 0.65910 0.62901 0.29491 0.40239 0.88462
## h.den.s2 -0.30263 0.49041 0.54702 0.782777 -0.71850 0.52556 0.40945 0.73274 0.78407 0.49041
## h.f12.s2 -0.23789 0.11785 0.44471 0.404242 -0.30697 0.20950 0.13411 0.42094 0.40285 0.11785
## h.f13.s2 -0.56680 0.02066 0.81045 0.530306 -0.56863 0.15805 0.01967 0.82777 0.78886 0.02066
## h.den.s1 h.f12.s1 h.f13.s1 h.asm.s2 h.con.s2 h.cor.s2 h.var.s2 h.idm.s2 h.sav.s2
## h.asm.s1 -0.0777753 -0.40751 -0.71545 0.985377 0.11126 -0.3669857 -0.1176 0.74432 0.50918
## h.con.s1 0.7472575 -0.52940 -0.33387 0.491994 0.88462 -0.2824569 0.6077 0.05073 0.74434
## h.cor.s1 0.1622943 0.80732 0.90495 -0.455366 -0.01167 0.8055827 0.3664 -0.10203 0.13332
## h.var.s1 0.8597313 0.08013 0.37077 -0.004335 0.79621 0.2925897 0.9865 -0.28439 0.74020
## h.idm.s1 -0.7048215 0.06648 -0.47526 0.639095 -0.52568 -0.0750848 -0.5878 0.91269 -0.06375
## h.sav.s1 0.6882488 -0.14641 -0.05803 0.557952 0.65910 0.0568716 0.6652 0.22607 0.99689
## h.sva.s1 0.6161698 -0.22123 -0.19477 0.659991 0.62901 -0.0305023 0.5995 0.31156 0.97284
## h.sen.s1 0.5123797 0.45178 0.86404 -0.764532 0.29491 0.5522633 0.5806 -0.71574 0.04255
## h.ent.s1 0.6181704 0.30345 0.77495 -0.731293 0.40239 0.4428624 0.6300 -0.77833 0.09564
## h.dva.s1 0.7472575 -0.52940 -0.33387 0.491994 0.88462 -0.2824569 0.6077 0.05073 0.74434
## h.den.s1 1.0000000 -0.26105 0.18333 -0.036403 0.90495 0.0002202 0.8615 -0.42969 0.69092
## h.f12.s1 -0.2610455 1.00000 0.83367 -0.396447 -0.38053 0.8437773 0.0936 0.04258 -0.11589
## h.f13.s1 0.1833271 0.83367 1.00000 -0.686852 -0.02759 0.8129299 0.4144 -0.41805 -0.02310
## h.asm.s2 -0.0364032 -0.39645 -0.68685 1.000000 0.14633 -0.3913314 -0.0901 0.75994 0.54466
## h.con.s2 0.9049452 -0.38053 -0.02759 0.146329 1.00000 -0.1366918 0.8158 -0.25596 0.65833
## h.cor.s2 0.0002202 0.84378 0.81293 -0.391331 -0.13669 1.0000000 0.3143 -0.02785 0.08360
## h.var.s2 0.8614716 0.09360 0.41441 -0.090100 0.81579 0.3142634 1.0000 -0.34368 0.66829
## h.idm.s2 -0.4296859 0.04258 -0.41805 0.759940 -0.25596 -0.0278492 -0.3437 1.00000 0.23883
## h.sav.s2 0.6909192 -0.11589 -0.02310 0.544662 0.65833 0.0836040 0.6683 0.23883 1.00000
## h.sva.s2 0.6200413 -0.21461 -0.18540 0.654751 0.62992 -0.0239530 0.6029 0.30867 0.97518
## h.sen.s2 0.4781344 0.53303 0.87337 -0.635392 0.29878 0.6879302 0.5894 -0.48626 0.14942
## h.ent.s2 0.4514830 0.49026 0.85757 -0.693474 0.25287 0.6415864 0.5288 -0.55074 0.08136
## h.dva.s2 0.9049452 -0.38053 -0.02759 0.146329 1.00000 -0.1366918 0.8158 -0.25596 0.65833
## h.den.s2 0.8760303 0.04816 0.48780 -0.240788 0.74927 0.2599108 0.8158 -0.40946 0.55871
## h.f12.s2 0.3685400 0.30712 0.42017 -0.155883 0.29319 0.1387164 0.4277 -0.15529 0.23450
## h.f13.s2 0.4809108 0.53445 0.80056 -0.497678 0.32453 0.5271276 0.5861 -0.37637 0.20186
## h.sva.s2 h.sen.s2 h.ent.s2 h.dva.s2 h.den.s2 h.f12.s2 h.f13.s2
## h.asm.s1 0.63628 -0.67092 -0.72583 0.11126 -0.30263 -0.2379 -0.56680
## h.con.s1 0.76705 -0.02304 -0.07937 0.88462 0.49041 0.1178 0.02066
## h.cor.s1 -0.04399 0.85486 0.82090 -0.01167 0.54702 0.4447 0.81045
## h.var.s1 0.68580 0.52504 0.46026 0.79621 0.78278 0.4042 0.53031
## h.idm.s1 0.04908 -0.65815 -0.69448 -0.52568 -0.71850 -0.3070 -0.56863
## h.sav.s1 0.98424 0.10492 0.03900 0.65910 0.52556 0.2095 0.15805
## h.sva.s1 0.99974 -0.04762 -0.11829 0.62901 0.40945 0.1341 0.01967
## h.sen.s1 -0.13465 0.94298 0.95599 0.29491 0.73274 0.4209 0.82777
## h.ent.s1 -0.07154 0.90534 0.92510 0.40239 0.78407 0.4029 0.78886
## h.dva.s1 0.76705 -0.02304 -0.07937 0.88462 0.49041 0.1178 0.02066
## h.den.s1 0.62004 0.47813 0.45148 0.90495 0.87603 0.3685 0.48091
## h.f12.s1 -0.21461 0.53303 0.49026 -0.38053 0.04816 0.3071 0.53445
## h.f13.s1 -0.18540 0.87337 0.85757 -0.02759 0.48780 0.4202 0.80056
## h.asm.s2 0.65475 -0.63539 -0.69347 0.14633 -0.24079 -0.1559 -0.49768
## h.con.s2 0.62992 0.29878 0.25287 1.00000 0.74927 0.2932 0.32453
## h.cor.s2 -0.02395 0.68793 0.64159 -0.13669 0.25991 0.1387 0.52713
## h.var.s2 0.60295 0.58939 0.52878 0.81579 0.81585 0.4277 0.58611
## h.idm.s2 0.30867 -0.48626 -0.55074 -0.25596 -0.40946 -0.1553 -0.37637
## h.sav.s2 0.97518 0.14942 0.08136 0.65833 0.55871 0.2345 0.20186
## h.sva.s2 1.00000 -0.03817 -0.10903 0.62992 0.41666 0.1372 0.02746
## h.sen.s2 -0.03817 1.00000 0.98851 0.29878 0.77925 0.3986 0.85776
## h.ent.s2 -0.10903 0.98851 1.00000 0.25287 0.75239 0.3475 0.82312
## h.dva.s2 0.62992 0.29878 0.25287 1.00000 0.74927 0.2932 0.32453
## h.den.s2 0.41666 0.77925 0.75239 0.74927 1.00000 0.4349 0.72616
## h.f12.s2 0.13719 0.39862 0.34749 0.29319 0.43488 1.0000 0.80844
## h.f13.s2 0.02746 0.85776 0.82312 0.32453 0.72616 0.8084 1.00000Heatmaps of correlation matrix
Color-coded display of correlation matrix
library(gplots) # heatmap.2
library(RColorBrewer) # brewer.palheatmap.2(correlationMatrix, dendrogram="none", Rowv=FALSE, symm=TRUE,
main="Texture Features",
scale="none", col=brewer.pal(11,"RdBu"), margins=c(7,7), trace="none")
Dendrograms show relationships in correlation matrix
heatmap.2(correlationMatrix, key=FALSE,
main="Haralick Texture Features",
scale="none", col=brewer.pal(11,"RdBu"), margins=c(7,7), trace="none")
A diverging palette from RColorBrewer is used for the heatmaps since correlations can range from -1 to +1. In the RdBu pallete, red is low and blue is high.
packageVersion("EBImage")## [1] '4.8.2'packageVersion("gplots")## [1] '2.16.0'packageVersion("RColorBrewer")## [1] '1.1.2'efg
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