voxel_vote produces broken voted file for ultra-high res unsigned-int label files

[gdevenyi]

I'm putting in files that are properly aligned:

With the following properties:

$ mincinfo reg2_ABI_to_Dorr_2_10_1_NL.mnc
file: reg2_ABI_to_Dorr_2_10_1_NL.mnc
image: unsigned long 0 to 614454277
image dimensions: zspace yspace xspace
    dimension name         length         step        start
    --------------         ------         ----        -----
    zspace                    241         0.04         -4.2
    yspace                    478         0.04        -8.19
    xspace                    315         0.04        -6.27
$ $ print_all_labels reg2_ABI_to_Dorr_2_10_1_NL.mnc
Label: 1 1684
Label: 2 1459
Label: 6 19685
Label: 7 18351
Label: 9 3818
Label: 10 31582
Label: 12 1381
Label: 15 2152
Label: 17 14202
Label: 19 4331
Label: 20 30299
Label: 23 8509
Label: 26 5838
Label: 27 2115
Label: 28 15478
Label: 30 451
Label: 33 19907
Label: 35 573
Label: 36 2961
Label: 38 1671
Label: 41 4284
Label: 42 1945
Label: 50 1846
Label: 52 16301
Label: 54 597
Label: 56 57048
Label: 58 482
Label: 59 709
Label: 62 2631
Label: 63 997
Label: 64 2992
Label: 66 288
Label: 67 1302
Label: 68 3079
Label: 72 1561
Label: 74 2922
Label: 75 332
Label: 78 8460
Label: 81 38454
Label: 83 16515
Label: 84 7335
Label: 88 6782
Label: 91 13073
Label: 93 348
Label: 96 9634
Label: 97 9473
Label: 98 3974
Label: 100 172
Label: 101 17566
Label: 102 966
Label: 105 1962
Label: 106 165
Label: 108 18013
Label: 113 16956
Label: 114 4811
Label: 115 171
Label: 117 3189
Label: 118 2008
Label: 120 15531
Label: 121 619
Label: 122 4059
Label: 123 2940
Label: 125 8316
Label: 126 835
Label: 128 61826
Label: 129 12900
Label: 131 11482
Label: 132 415
Label: 133 1479
Label: 136 62363
Label: 139 15366
Label: 140 3367
Label: 143 505
Label: 145 6410
Label: 146 35897
Label: 147 102
Label: 148 2524
Label: 149 4285
Label: 153 6696
Label: 155 15994
Label: 156 2308
Label: 158 504
Label: 159 73170
Label: 162 2630
Label: 163 18467
Label: 164 1
Label: 169 3296
Label: 171 10506
Label: 173 2416
Label: 177 902
Label: 178 10047
Label: 180 6661
Label: 181 2919
Label: 186 2899
Label: 187 9711
Label: 188 1429
Label: 189 563
Label: 190 4749
Label: 194 28474
Label: 196 1184
Label: 197 810
Label: 198 1092
Label: 201 34751
Label: 202 38211
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Label: 204 3175
Label: 206 5309
Label: 207 407
Label: 209 4477
Label: 210 1624
Label: 211 15586
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Label: 215 10782
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Label: 222 1898
Label: 223 2014
Label: 225 12292
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Label: 312782590 1516
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Label: 312782640 578
Label: 312782644 4856
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Label: 312782652 558
Label: 484682470 22830
Label: 484682508 10003
Label: 484682512 12311
Label: 484682516 68028
Label: 484682520 22800
Label: 484682524 6131
Label: 484682528 460
Label: 496345664 4832
Label: 496345668 8903
Label: 496345672 1815
Label: 526157192 7436
Label: 526157196 2176
Label: 526322264 5
Label: 527696977 44
Label: 549009203 474
Label: 549009211 354
Label: 549009215 5314
Label: 549009219 277
Label: 549009223 1085
Label: 549009227 415
Label: 560581551 2847
Label: 560581559 453
Label: 560581563 1430
Label: 563807435 4014
Label: 563807439 484
Label: 576073699 315
Label: 576073704 3365
Label: 589508447 2922
Label: 589508451 1166
Label: 589508455 1117
Label: 599626923 207
Label: 599626927 306
Label: 606826647 3802
Label: 606826651 1483
Label: 606826655 738
Label: 606826659 686
Label: 606826663 182
Label: 607344830 449
Label: 607344834 3221
Label: 607344838 2454
Label: 607344842 513
Label: 607344846 1905
Label: 607344850 1238
Label: 607344854 261
Label: 607344858 1362
Label: 607344862 640
Label: 614454277 516

I've checked and the values are properly integers, with no slice/volume rescaling.

voxel_vote (after adjusting https://github.com/Mouse-Imaging-Centre/minc-stuffs/blob/master/python/voxel_vote#L32 to uint) produces:

 $ Display ../../Dorr-orig/DSURQE_40micron.mnc -label voxelvote.mnc 
Input ../../Dorr-orig/DSURQE_40micron.mnc
Objects input.
Input voxelvote.mnc
Error: tried to realloc invalid number of elements, 0.
Error: tried to realloc invalid number of elements, 0.
Segmentation fault

A crash on Display, and a broken (wrong location) and "grid-overlayed" output in register

[bcdarwin]

Hmm... a couple questions:

• Is ImageMath 3 <out.mnc> MajorityVoting <voting_files> similarly broken?
• Did you also alter line 34 in the code?
• Can you send me a subset of these files? (Does it happen with only two files with these label sets?)

[gdevenyi]

Is ImageMath 3 <out.mnc> MajorityVoting <voting_files> similarly broken?

No, it works with both ANTs, and SimpleITK (which is how I did it in the end, on a big high-mem machine)

Did you also alter line 34 in the code?

Yes. Good question.

Can you send me a subset of these files? (Does it happen with only two files with these label sets?)

I can send you everything, its not that many :) Of course I also want to contribute them back to you, since its my optimized Allen-on-Dorr labelset I made.

https://we.tl/t-NVgbDSakZX

[bcdarwin]

We have found another issue with voxel_vote producing broken labels. Strangely, it appears to have been introduced by pyminc changes between versions 0.52 and 0.54. I intend to investigate further shortly (more for the sake of pyminc than voxel_vote).

[bcdarwin]

According to git bisect the voxel_vote issue (unsure if related) on our data was introduced in Mouse-Imaging-Centre/pyminc@5487a47.

[bcdarwin]

If you are still interested in this issue and have a chance, could you check if this issue is still present with Pyminc 0.56?