From: Kevin M. Rosenberg Date: Mon, 12 Feb 2018 22:05:42 +0000 (-0700) Subject: Exclude examples b7 and b11 from regression as use random number generator. Add PERFE... X-Git-Url: http://git.kpe.io/?p=snark14.git;a=commitdiff_plain;h=8fbca36cd1abc71c89e6d49611dbd58424881a96 Exclude examples b7 and b11 from regression as use random number generator. Add PERFECT measurement versions of examples as b12 and b13 --- diff --git a/examples/.gitignore b/examples/.gitignore index 58e9c64..98b08ac 100644 --- a/examples/.gitignore +++ b/examples/.gitignore @@ -12,6 +12,6 @@ b9/snark_e.in b9/snark_e.out b9/fomfil.1 b9/testem.1 -b11/RPRTsuperiorization -b11/RPRTklds +*/RPRTsuperiorization +*/RPRTklds .have_run diff --git a/examples/Makefile b/examples/Makefile index a1bfcde..5ed7d85 100644 --- a/examples/Makefile +++ b/examples/Makefile @@ -17,6 +17,6 @@ results: .have_run clean: @rm -f */b[0-9][0-9].out */b1[0-9].out */file11 */prjfil */recfil */eval */src/.o */punch b*/src/*.o */MAPUser1 */snark.lock b*/bin/* - @rm -f b11/RPRTsuperiorization b11/RPRTklds b9/snark_e.in b9/snark_e.out b9/testem.1 b9/fomfil.1 + @rm -f */RPRTsuperiorization */RPRTklds b9/snark_e.in b9/snark_e.out b9/testem.1 b9/fomfil.1 @rm -f .have_run diff --git a/examples/b11/README b/examples/b11/README new file mode 100644 index 0000000..a17892a --- /dev/null +++ b/examples/b11/README @@ -0,0 +1,7 @@ +SNARK14m's original b11 example uses 'MEASUREMENT NOISY' data which +causes inconsistencies in output across different random number +libraries. + +This version is excluded from regresstion testing, but b12 example +uses PERFECT data and is used for regression. + diff --git a/examples/b11/b11r.out b/examples/b11/b11r.out deleted file mode 100644 index 3458c1f..0000000 --- a/examples/b11/b11r.out +++ /dev/null @@ -1,606 +0,0 @@ - snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM - - - <*> *******EXAMPLE 11 - - <*> SUPERIORIZED MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION - - <*> OF BRAIN PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS - - <*> WITH EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. - - <*> COEFFICIENT OF PENALTLY TERM IS SET TO 0 - - <*> - - <#> CREATE - - EXAMPLE 11 Brain Phantom - - - <#> SPECTRUM MONOCHROMATIC 511 - energy spectrum is monochromatic at energy level 511 - - - <#> OBJECTS - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.9500 0.9500 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 1.0000 1.0000 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 1.0000 1.0000 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.9500 0.9500 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.9500 0.9500 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 1.0000 1.0000 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.9500 0.9500 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 1.0000 1.0000 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 1.0000 1.0000 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.9500 0.9500 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.9500 0.9500 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 1.0000 1.0000 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.9500 0.9500 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 1.0000 1.0000 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 1.0000 1.0000 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.9500 0.9500 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 1.0000 1.0000 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.9500 0.9500 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.9500 0.9500 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 1.0000 1.0000 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 1.0000 1.0000 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.9500 0.9500 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 1.0000 1.0000 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.9500 0.9500 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.9500 0.9500 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 1.0000 1.0000 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 1.0000 1.0000 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> PHANTOM AVERAGE 7 - - this run will generate a phantom - density in each pixel is obtained as the average of 7 x 7 points - - - <#> 381 PIXELS OF SIZE 0.4 - picture size 381 x 381, pixel size 0.4000 - - - <#> RAYSUM AVERAGE 1 - - this run will generate projection data - projection data are calculated by dividing each ray interval into 1 substrips - - with aperture (substrip) weights 1 - - - <#> GEOMETRY - - - <#> divergent arc 153 306 - rays are divergent from point sources - source to origin distance 153.0000 - the detectors lie on an arc with source to detector distance = 306.0000 - - - <#> RAYS USER 301 DETECTOR SPACING 1.1 - number of rays per projection 301 - at detector spacing 1.1000 - - - <#> ANGLES 500 EQUAL SPACING - total number of projections 500 - - projection angles 0.0000 0.7190 1.4381 2.1571 2.8762 3.5952 4.3142 5.0333 5.7523 6.4713 - 7.1904 7.9094 8.6285 9.3475 10.0665 10.7856 11.5046 12.2236 12.9427 13.6617 - 14.3808 15.0998 15.8188 16.5379 17.2569 17.9760 18.6950 19.4140 20.1331 20.8521 - 21.5711 22.2902 23.0092 23.7283 24.4473 25.1663 25.8854 26.6044 27.3234 28.0425 - 28.7615 29.4806 30.1996 30.9186 31.6377 32.3567 33.0758 33.7948 34.5138 35.2329 - 35.9519 36.6709 37.3900 38.1090 38.8281 39.5471 40.2661 40.9852 41.7042 42.4232 - 43.1423 43.8613 44.5804 45.2994 46.0184 46.7375 47.4565 48.1756 48.8946 49.6136 - 50.3327 51.0517 51.7707 52.4898 53.2088 53.9279 54.6469 55.3659 56.0850 56.8040 - 57.5230 58.2421 58.9611 59.6802 60.3992 61.1182 61.8373 62.5563 63.2754 63.9944 - 64.7134 65.4325 66.1515 66.8705 67.5896 68.3086 69.0277 69.7467 70.4657 71.1848 - 71.9038 72.6228 73.3419 74.0609 74.7800 75.4990 76.2180 76.9371 77.6561 78.3752 - 79.0942 79.8132 80.5323 81.2513 81.9703 82.6894 83.4084 84.1275 84.8465 85.5655 - 86.2846 87.0036 87.7226 88.4417 89.1607 89.8798 90.5988 91.3178 92.0369 92.7559 - 93.4749 94.1940 94.9130 95.6321 96.3511 97.0701 97.7892 98.5082 99.2273 99.9463 - 100.6653 101.3844 102.1034 102.8224 103.5415 104.2605 104.9796 105.6986 106.4176 107.1367 - 107.8557 108.5747 109.2938 110.0128 110.7319 111.4509 112.1699 112.8890 113.6080 114.3271 - 115.0461 115.7651 116.4842 117.2032 117.9222 118.6413 119.3603 120.0794 120.7984 121.5174 - 122.2365 122.9555 123.6745 124.3936 125.1126 125.8317 126.5507 127.2697 127.9888 128.7078 - 129.4269 130.1459 130.8649 131.5840 132.3030 133.0220 133.7411 134.4601 135.1792 135.8982 - 136.6172 137.3363 138.0553 138.7743 139.4934 140.2124 140.9315 141.6505 142.3695 143.0886 - 143.8076 144.5267 145.2457 145.9647 146.6838 147.4028 148.1218 148.8409 149.5599 150.2790 - 150.9980 151.7170 152.4361 153.1551 153.8741 154.5932 155.3122 156.0313 156.7503 157.4693 - 158.1884 158.9074 159.6265 160.3455 161.0645 161.7836 162.5026 163.2216 163.9407 164.6597 - 165.3788 166.0978 166.8168 167.5359 168.2549 168.9739 169.6930 170.4120 171.1311 171.8501 - 172.5691 173.2882 174.0072 174.7263 175.4453 176.1643 176.8834 177.6024 178.3214 179.0405 - 179.7595 180.4786 181.1976 181.9166 182.6357 183.3547 184.0737 184.7928 185.5118 186.2309 - 186.9499 187.6689 188.3880 189.1070 189.8261 190.5451 191.2641 191.9832 192.7022 193.4212 - 194.1403 194.8593 195.5784 196.2974 197.0164 197.7355 198.4545 199.1735 199.8926 200.6116 - 201.3307 202.0497 202.7687 203.4878 204.2068 204.9259 205.6449 206.3639 207.0830 207.8020 - 208.5210 209.2401 209.9591 210.6782 211.3972 212.1162 212.8353 213.5543 214.2733 214.9924 - 215.7114 216.4305 217.1495 217.8685 218.5876 219.3066 220.0257 220.7447 221.4637 222.1828 - 222.9018 223.6208 224.3399 225.0589 225.7780 226.4970 227.2160 227.9351 228.6541 229.3731 - 230.0922 230.8112 231.5303 232.2493 232.9683 233.6874 234.4064 235.1255 235.8445 236.5635 - 237.2826 238.0016 238.7206 239.4397 240.1587 240.8778 241.5968 242.3158 243.0349 243.7539 - 244.4729 245.1920 245.9110 246.6301 247.3491 248.0681 248.7872 249.5062 250.2253 250.9443 - 251.6633 252.3824 253.1014 253.8204 254.5395 255.2585 255.9776 256.6966 257.4156 258.1347 - 258.8537 259.5727 260.2918 261.0108 261.7299 262.4489 263.1679 263.8870 264.6060 265.3251 - 266.0441 266.7631 267.4822 268.2012 268.9202 269.6393 270.3583 271.0774 271.7964 272.5154 - 273.2345 273.9535 274.6725 275.3916 276.1106 276.8297 277.5487 278.2677 278.9868 279.7058 - 280.4248 281.1439 281.8629 282.5820 283.3010 284.0200 284.7391 285.4581 286.1772 286.8962 - 287.6152 288.3343 289.0533 289.7723 290.4914 291.2104 291.9295 292.6485 293.3675 294.0866 - 294.8056 295.5246 296.2437 296.9627 297.6818 298.4008 299.1198 299.8389 300.5579 301.2770 - 301.9960 302.7150 303.4341 304.1531 304.8721 305.5912 306.3102 307.0293 307.7483 308.4673 - 309.1864 309.9054 310.6244 311.3435 312.0625 312.7816 313.5006 314.2196 314.9387 315.6577 - 316.3768 317.0958 317.8148 318.5339 319.2529 319.9719 320.6910 321.4100 322.1291 322.8481 - 323.5671 324.2862 325.0052 325.7242 326.4433 327.1623 327.8814 328.6004 329.3194 330.0385 - 330.7575 331.4766 332.1956 332.9146 333.6337 334.3527 335.0717 335.7908 336.5098 337.2289 - 337.9479 338.6669 339.3860 340.1050 340.8240 341.5431 342.2621 342.9812 343.7002 344.4192 - 345.1383 345.8573 346.5764 347.2954 348.0144 348.7335 349.4525 350.1715 350.8906 351.6096 - 352.3287 353.0477 353.7667 354.4858 355.2048 355.9238 356.6429 357.3619 358.0810 358.8000 - - - <#> MEASUREMENT NOISY - noise characteristics of projection data follow - nature characteristics - - <#> QUANTUM 1.0 1.0 CALIBRATION 4 - Emission tomography - - <#> SEED 0 - seed for random number generator is 0 - - - <#> BACKGROUND 0.0 - at levels - 511 - background absorption 0.0000 - - - <#> RUN - 0.358 seconds phantom creation - 1.289 seconds projection data creation - 1.647 seconds used for processing command crea - - - <*> - - <#> PICTURE TEST - - EXAMPLE 11 Brain Phantom - - - <#> spec mono 511 - energy spectrum is monochromatic at energy level 511 - - - <#> obje - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> phan aver 7 - - density in each pixel is obtained as the average of 7 x 7 points - - - <#> pixe 381 size 0.4000 - picture size 381 x 381, pixel size 0.4000 - - test picture read - EXAMPLE 11 Brain Phantom - 0.042 seconds used for processing command pict - - - <*> - - <#> PROJECTION REAL - - EXAMPLE 11 Brain Phantom - - - <#> spec mono 511 - energy spectrum is monochromatic at energy level 511 - - - <#> obje - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> rays aver 1 - - projection data are calculated by dividing each ray interval into 1 substrips - - with aperture (substrip) weights 1 - - - <#> geom - - - <#> dive arc source at 153.0000 det dist 306.0000 - rays are divergent from point sources - source to origin distance 153.0000 - the detectors lie on an arc with source to detector distance = 306.0000 - - - <#> rays user 301 spacing 1.1000 - number of rays per projection 301 - snark computed number of rays 437 - at detector spacing 1.1000 - - - <#> angl 500 - total number of projections 500 - - - projection angles 0.0000 0.7190 1.4381 2.1571 2.8762 3.5952 4.3142 5.0333 5.7523 6.4713 - 7.1904 7.9094 8.6285 9.3475 10.0665 10.7856 11.5046 12.2236 12.9427 13.6617 - 14.3808 15.0998 15.8188 16.5379 17.2569 17.9760 18.6950 19.4140 20.1331 20.8521 - 21.5711 22.2902 23.0092 23.7283 24.4473 25.1663 25.8854 26.6044 27.3234 28.0425 - 28.7615 29.4806 30.1996 30.9186 31.6377 32.3567 33.0758 33.7948 34.5138 35.2329 - 35.9519 36.6709 37.3900 38.1090 38.8281 39.5471 40.2661 40.9852 41.7042 42.4232 - 43.1423 43.8613 44.5804 45.2994 46.0184 46.7375 47.4565 48.1756 48.8946 49.6136 - 50.3327 51.0517 51.7707 52.4898 53.2088 53.9279 54.6469 55.3659 56.0850 56.8040 - 57.5230 58.2421 58.9611 59.6802 60.3992 61.1182 61.8373 62.5563 63.2754 63.9944 - 64.7134 65.4325 66.1515 66.8705 67.5896 68.3086 69.0277 69.7467 70.4657 71.1848 - 71.9038 72.6228 73.3419 74.0609 74.7800 75.4990 76.2180 76.9371 77.6561 78.3752 - 79.0942 79.8132 80.5323 81.2513 81.9703 82.6894 83.4084 84.1275 84.8465 85.5655 - 86.2846 87.0036 87.7226 88.4417 89.1607 89.8798 90.5988 91.3178 92.0369 92.7559 - 93.4749 94.1940 94.9130 95.6321 96.3511 97.0701 97.7892 98.5082 99.2273 99.9463 - 100.6653 101.3844 102.1034 102.8224 103.5415 104.2605 104.9796 105.6986 106.4176 107.1367 - 107.8557 108.5747 109.2938 110.0128 110.7319 111.4509 112.1699 112.8890 113.6080 114.3271 - 115.0461 115.7651 116.4842 117.2032 117.9222 118.6413 119.3603 120.0794 120.7984 121.5174 - 122.2365 122.9555 123.6745 124.3936 125.1126 125.8317 126.5507 127.2697 127.9888 128.7078 - 129.4269 130.1459 130.8649 131.5840 132.3030 133.0220 133.7411 134.4601 135.1792 135.8982 - 136.6172 137.3363 138.0553 138.7743 139.4934 140.2124 140.9315 141.6505 142.3695 143.0886 - 143.8076 144.5267 145.2457 145.9647 146.6838 147.4028 148.1218 148.8409 149.5599 150.2790 - 150.9980 151.7170 152.4361 153.1551 153.8741 154.5932 155.3122 156.0313 156.7503 157.4693 - 158.1884 158.9074 159.6265 160.3455 161.0645 161.7836 162.5026 163.2216 163.9407 164.6597 - 165.3788 166.0978 166.8168 167.5359 168.2549 168.9739 169.6930 170.4120 171.1311 171.8501 - 172.5691 173.2882 174.0072 174.7263 175.4453 176.1643 176.8834 177.6024 178.3214 179.0405 - 179.7595 180.4786 181.1976 181.9166 182.6357 183.3547 184.0737 184.7928 185.5118 186.2309 - 186.9499 187.6689 188.3880 189.1070 189.8261 190.5451 191.2641 191.9832 192.7022 193.4212 - 194.1403 194.8593 195.5784 196.2974 197.0164 197.7355 198.4545 199.1735 199.8926 200.6116 - 201.3307 202.0497 202.7687 203.4878 204.2068 204.9259 205.6449 206.3639 207.0830 207.8020 - 208.5210 209.2401 209.9591 210.6782 211.3972 212.1162 212.8353 213.5543 214.2733 214.9924 - 215.7114 216.4305 217.1495 217.8685 218.5876 219.3066 220.0257 220.7447 221.4637 222.1828 - 222.9018 223.6208 224.3399 225.0589 225.7780 226.4970 227.2160 227.9351 228.6541 229.3731 - 230.0922 230.8112 231.5303 232.2493 232.9683 233.6874 234.4064 235.1255 235.8445 236.5635 - 237.2826 238.0016 238.7206 239.4397 240.1587 240.8778 241.5968 242.3158 243.0349 243.7539 - 244.4729 245.1920 245.9110 246.6301 247.3491 248.0681 248.7872 249.5062 250.2253 250.9443 - 251.6633 252.3824 253.1014 253.8204 254.5395 255.2585 255.9776 256.6966 257.4156 258.1347 - 258.8537 259.5727 260.2918 261.0108 261.7299 262.4489 263.1679 263.8870 264.6060 265.3251 - 266.0441 266.7631 267.4822 268.2012 268.9202 269.6393 270.3583 271.0774 271.7964 272.5154 - 273.2345 273.9535 274.6725 275.3916 276.1106 276.8297 277.5487 278.2677 278.9868 279.7058 - 280.4248 281.1439 281.8629 282.5820 283.3010 284.0200 284.7391 285.4581 286.1772 286.8962 - 287.6152 288.3343 289.0533 289.7723 290.4914 291.2104 291.9295 292.6485 293.3675 294.0866 - 294.8056 295.5246 296.2437 296.9627 297.6818 298.4008 299.1198 299.8389 300.5579 301.2770 - 301.9960 302.7150 303.4341 304.1531 304.8721 305.5912 306.3102 307.0293 307.7483 308.4673 - 309.1864 309.9054 310.6244 311.3435 312.0625 312.7816 313.5006 314.2196 314.9387 315.6577 - 316.3768 317.0958 317.8148 318.5339 319.2529 319.9719 320.6910 321.4100 322.1291 322.8481 - 323.5671 324.2862 325.0052 325.7242 326.4433 327.1623 327.8814 328.6004 329.3194 330.0385 - 330.7575 331.4766 332.1956 332.9146 333.6337 334.3527 335.0717 335.7908 336.5098 337.2289 - 337.9479 338.6669 339.3860 340.1050 340.8240 341.5431 342.2621 342.9812 343.7002 344.4192 - 345.1383 345.8573 346.5764 347.2954 348.0144 348.7335 349.4525 350.1715 350.8906 351.6096 - 352.3287 353.0477 353.7667 354.4858 355.2048 355.9238 356.6429 357.3619 358.0810 358.8000 - - - <#> meas nois - noise characteristics of projection data follow - nature characteristics - - <#> quan 1.0000 1.0000 cali 4 - Emission tomography - - <#> seed 0 - seed for random number generator is 0 - - - <#> back 0.0000 - at levels - 511 - background absorption 0.0000 - - estimate of totlen = 20962469.574466 - estimate of totden = 9802000.000000 - estimate of average density = 0.4676 - projection data read - EXAMPLE 11 Brain Phantom - 0.054 seconds used for processing command proj - - - <*> - - <#> STOP TERMINATION KLDS 100000 RPRT - termination test klds - reporting is enabled - reporting file: RPRTklds - reporting on every iteration - epsilon = 100000 - 0.000 seconds used for processing command stop - - - <*> - - <#> SUPERIORIZE 16 0.999 1 SMOO RPRT - Superiorization is enabled - N = 16 - a = 0.999 - b = 1 - secondary criterion: smoo - reporting is enabled - reporting file: RPRTsuperiorization - reporting on every iteration - 0.000 seconds used for processing command supe - - - <#> EXECUTE AVERAGE EMAP - - Example 11 Illustrating the Superiorized MAP EM algorithm for PET - - <#> gamma is 0 EVAL - - ----------------------------------------------------------- - - maximum a-posteriori probability expectation maximization - - gamma: 0.000 - evaluation flag is set - - ----------------------------------------------------------- - - value of l: 15 - value of phi before algorithm operator: 4.42622e-28 - value of phi after algorithm operator: 3.14467 - algorithm executed in iteration 1 - 3.847 seconds for the execution of the algorithm - current epsilon (KL distance) = 638282 - iteration 1 completed - 4.805 seconds for this iteration - value of l: 31 - value of phi before algorithm operator: 0.429607 - value of phi after algorithm operator: 1.65065 - algorithm executed in iteration 2 - 2.144 seconds for the execution of the algorithm - current epsilon (KL distance) = 446785 - iteration 2 completed - 3.149 seconds for this iteration - value of l: 47 - value of phi before algorithm operator: 0.706119 - value of phi after algorithm operator: 2.49879 - algorithm executed in iteration 3 - 2.148 seconds for the execution of the algorithm - current epsilon (KL distance) = 331430 - iteration 3 completed - 3.106 seconds for this iteration - value of l: 63 - value of phi before algorithm operator: 0.564997 - value of phi after algorithm operator: 2.14542 - algorithm executed in iteration 4 - 2.143 seconds for the execution of the algorithm - current epsilon (KL distance) = 257464 - iteration 4 completed - 3.090 seconds for this iteration - value of l: 79 - value of phi before algorithm operator: 0.577605 - value of phi after algorithm operator: 2.1505 - algorithm executed in iteration 5 - 2.241 seconds for the execution of the algorithm - current epsilon (KL distance) = 207738 - iteration 5 completed - 3.451 seconds for this iteration - value of l: 95 - value of phi before algorithm operator: 0.579469 - value of phi after algorithm operator: 2.11049 - algorithm executed in iteration 6 - 2.264 seconds for the execution of the algorithm - current epsilon (KL distance) = 173224 - iteration 6 completed - 3.188 seconds for this iteration - value of l: 111 - value of phi before algorithm operator: 0.581496 - value of phi after algorithm operator: 2.08666 - algorithm executed in iteration 7 - 2.374 seconds for the execution of the algorithm - current epsilon (KL distance) = 148708 - iteration 7 completed - 3.408 seconds for this iteration - value of l: 127 - value of phi before algorithm operator: 0.587932 - value of phi after algorithm operator: 2.07545 - algorithm executed in iteration 8 - 2.618 seconds for the execution of the algorithm - current epsilon (KL distance) = 130971 - iteration 8 completed - 3.687 seconds for this iteration - value of l: 143 - value of phi before algorithm operator: 0.598034 - value of phi after algorithm operator: 2.07283 - algorithm executed in iteration 9 - 2.448 seconds for the execution of the algorithm - current epsilon (KL distance) = 117930 - iteration 9 completed - 3.523 seconds for this iteration - value of l: 159 - value of phi before algorithm operator: 0.610951 - value of phi after algorithm operator: 2.07635 - algorithm executed in iteration 10 - 2.199 seconds for the execution of the algorithm - current epsilon (KL distance) = 108196 - iteration 10 completed - 3.139 seconds for this iteration - value of l: 175 - value of phi before algorithm operator: 0.625866 - value of phi after algorithm operator: 2.08405 - algorithm executed in iteration 11 - 2.215 seconds for the execution of the algorithm - current epsilon (KL distance) = 100827 - iteration 11 completed - 3.599 seconds for this iteration - value of l: 191 - value of phi before algorithm operator: 0.64192 - value of phi after algorithm operator: 2.09414 - algorithm executed in iteration 12 - 2.428 seconds for the execution of the algorithm - current epsilon (KL distance) = 95173.6 - reconstruction completed after iteration 12 - 3.422 seconds for this iteration - 41.565 seconds for all iterations - 41.706 seconds used for processing command exec - - - <*> - - <#> END diff --git a/examples/b11/run b/examples/b11/run index 4e5107b..cc6392d 100755 --- a/examples/b11/run +++ b/examples/b11/run @@ -1 +1 @@ -snark14 b11.in +snark14 b11.in diff --git a/examples/b12/README b/examples/b12/README new file mode 100644 index 0000000..9127728 --- /dev/null +++ b/examples/b12/README @@ -0,0 +1,7 @@ +SNARK14m's original b11 example uses 'MEASUREMENT NOISY' data which +causes inconsistencies in output across different random number +libraries. + +This version uses PERFECT data so it can be used to test regression +across different platforms. + diff --git a/examples/b12/b12.in b/examples/b12/b12.in new file mode 100644 index 0000000..ee3d74d --- /dev/null +++ b/examples/b12/b12.in @@ -0,0 +1,63 @@ +********EXAMPLE 11 +* SUPERIORIZED MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION +* OF BRAIN PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS +* WITH EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. +* COEFFICIENT OF PENALTLY TERM IS SET TO 0 +* +CREATE +EXAMPLE 11 Brain Phantom +SPECTRUM MONOCHROMATIC 511 +OBJECTS + 1 elip -7.0 46.0 3.0 6.0 17.0 0.95 1.0 + 2 elip 7.0 46.0 3.0 6.0 -17.0 1.0 0.95 + 3 rect -12.0 64.0 7.5 4.5 5.0 1.0 1.0 + 4 rect 12.0 64.0 7.5 4.5 -5.0 0.95 0.95 + 5 rect -38.0 51.0 3.5 13.0 -39.0 0.95 1.0 + 6 rect 38.0 51.0 3.5 13.0 39.0 1.0 0.95 + 7 rect -46.0 24.0 6.5 6.0 -18.0 0.95 1.0 + 8 rect 46.0 24.0 6.5 6.0 18.0 1.0 0.95 + 9 rect -49.0 6.0 2.5 10.0 63.0 1.0 1.0 + 10 rect 49.0 6.0 2.5 10.0 -63.0 0.95 0.95 + 11 rect -52.0 -14.0 9.0 7.0 -14.0 0.95 1.0 + 12 rect 52.0 -14.0 9.0 7.0 14.0 1.0 0.95 + 13 rect -10.0 -56.0 5.5 10.0 -1.0 0.95 1.0 + 14 rect 10.0 -56.0 5.5 10.0 1.0 1.0 0.95 + 15 elip -40.0 -47.0 9.0 22.5 48.0 1.0 1.0 + 16 elip 40.0 -47.0 9.0 22.5 -48.0 0.95 0.95 + 17 elip -8.0 -22.0 3.5 15.5 -9.0 1.0 1.0 + 18 elip 8.0 -22.0 3.5 15.5 9.0 0.95 0.95 + 19 elip -27.0 -6.0 5.5 23.5 -5.0 0.95 1.0 + 20 elip 27.0 -6.0 5.5 23.5 5.0 1.0 0.95 + 21 elip -25.0 38.0 6.5 10.5 -14.0 1.0 1.0 + 22 elip 25.0 38.0 6.5 10.5 14.0 0.95 0.95 + 23 rect -8.0 32.0 1.5 6.5 38.0 1.0 1.0 + 24 rect 8.0 32.0 1.5 6.5 -38.0 0.95 0.95 + 25 rect -8.0 3.0 1.0 9.0 -33.0 0.95 1.0 + 26 rect 8.0 3.0 1.0 9.0 33.0 1.0 0.95 + 27 elip 0.0 0.0 66.5 74.0 0.0 1.0 1.0 +LAST .51 1 0.05 +PHANTOM AVERAGE 7 +381 PIXELS OF SIZE 0.4 +RAYSUM AVERAGE 1 +1 +GEOMETRY +divergent arc 153 306 +RAYS USER 301 DETECTOR SPACING 1.1 +ANGLES 500 EQUAL SPACING +0.0 358.8 +MEASUREMENT PERFECT +BACKGROUND 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +STOP TERMINATION KLDS 100000 RPRT +* +SUPERIORIZE 16 0.999 1 SMOO RPRT +EXECUTE AVERAGE EMAP +Example 11 Illustrating the Superiorized MAP EM algorithm for PET +gamma is 0 EVAL +* +END diff --git a/examples/b12/b12r.out b/examples/b12/b12r.out new file mode 100644 index 0000000..e8f9220 --- /dev/null +++ b/examples/b12/b12r.out @@ -0,0 +1,505 @@ + snark14.s170710 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> *******EXAMPLE 11 + + <*> SUPERIORIZED MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION + + <*> OF BRAIN PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS + + <*> WITH EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. + + <*> COEFFICIENT OF PENALTLY TERM IS SET TO 0 + + <*> + + <#> CREATE + + EXAMPLE 11 Brain Phantom + + + <#> SPECTRUM MONOCHROMATIC 511 + energy spectrum is monochromatic at energy level 511 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 511 + + 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.9500 0.9500 + + 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 1.0000 1.0000 + + 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 1.0000 1.0000 + + 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.9500 0.9500 + + 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.9500 0.9500 + + 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 1.0000 1.0000 + + 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.9500 0.9500 + + 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 1.0000 1.0000 + + 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 1.0000 1.0000 + + 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.9500 0.9500 + + 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.9500 0.9500 + + 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 1.0000 1.0000 + + 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.9500 0.9500 + + 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 1.0000 1.0000 + + 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 1.0000 1.0000 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.9500 0.9500 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 1.0000 1.0000 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.9500 0.9500 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.9500 0.9500 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 1.0000 1.0000 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 1.0000 1.0000 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.9500 0.9500 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 1.0000 1.0000 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.9500 0.9500 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.9500 0.9500 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 1.0000 1.0000 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 1.0000 1.0000 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> PHANTOM AVERAGE 7 + + this run will generate a phantom + density in each pixel is obtained as the average of 7 x 7 points + + + <#> 381 PIXELS OF SIZE 0.4 + picture size 381 x 381, pixel size 0.4000 + + + <#> RAYSUM AVERAGE 1 + + this run will generate projection data + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> GEOMETRY + + + <#> divergent arc 153 306 + rays are divergent from point sources + source to origin distance 153.0000 + the detectors lie on an arc with source to detector distance = 306.0000 + + + <#> RAYS USER 301 DETECTOR SPACING 1.1 + number of rays per projection 301 + at detector spacing 1.1000 + + + <#> ANGLES 500 EQUAL SPACING + total number of projections 500 + + projection angles 0.0000 0.7190 1.4381 2.1571 2.8762 3.5952 4.3142 5.0333 5.7523 6.4713 + 7.1904 7.9094 8.6285 9.3475 10.0665 10.7856 11.5046 12.2236 12.9427 13.6617 + 14.3808 15.0998 15.8188 16.5379 17.2569 17.9760 18.6950 19.4140 20.1331 20.8521 + 21.5711 22.2902 23.0092 23.7283 24.4473 25.1663 25.8854 26.6044 27.3234 28.0425 + 28.7615 29.4806 30.1996 30.9186 31.6377 32.3567 33.0758 33.7948 34.5138 35.2329 + 35.9519 36.6709 37.3900 38.1090 38.8281 39.5471 40.2661 40.9852 41.7042 42.4232 + 43.1423 43.8613 44.5804 45.2994 46.0184 46.7375 47.4565 48.1756 48.8946 49.6136 + 50.3327 51.0517 51.7707 52.4898 53.2088 53.9279 54.6469 55.3659 56.0850 56.8040 + 57.5230 58.2421 58.9611 59.6802 60.3992 61.1182 61.8373 62.5563 63.2754 63.9944 + 64.7134 65.4325 66.1515 66.8705 67.5896 68.3086 69.0277 69.7467 70.4657 71.1848 + 71.9038 72.6228 73.3419 74.0609 74.7800 75.4990 76.2180 76.9371 77.6561 78.3752 + 79.0942 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+ 316.3768 317.0958 317.8148 318.5339 319.2529 319.9719 320.6910 321.4100 322.1291 322.8481 + 323.5671 324.2862 325.0052 325.7242 326.4433 327.1623 327.8814 328.6004 329.3194 330.0385 + 330.7575 331.4766 332.1956 332.9146 333.6337 334.3527 335.0717 335.7908 336.5098 337.2289 + 337.9479 338.6669 339.3860 340.1050 340.8240 341.5431 342.2621 342.9812 343.7002 344.4192 + 345.1383 345.8573 346.5764 347.2954 348.0144 348.7335 349.4525 350.1715 350.8906 351.6096 + 352.3287 353.0477 353.7667 354.4858 355.2048 355.9238 356.6429 357.3619 358.0810 358.8000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 0.0 + at levels + 511 + background absorption 0.0000 + + + <#> RUN + 0.214 seconds phantom creation + 0.604 seconds projection data creation + 0.820 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 11 Brain Phantom + + + <#> spec mono 511 + energy spectrum is monochromatic at energy level 511 + + + <#> obje + description of 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15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> phan aver 7 + + density in each pixel is obtained as the average of 7 x 7 points + + + <#> pixe 381 size 0.4000 + picture size 381 x 381, pixel size 0.4000 + + test picture read + EXAMPLE 11 Brain Phantom + 0.043 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + EXAMPLE 11 Brain Phantom + + + <#> spec mono 511 + energy spectrum is monochromatic at energy level 511 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 511 + + 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 + + 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 + + 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 + + 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 + + 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 + + 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 + + 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 + + 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 + + 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 + + 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 + + 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 + + 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 + + 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 + + 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 + + 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> rays aver 1 + + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> geom + + + <#> dive arc source at 153.0000 det dist 306.0000 + rays are divergent from point sources + source to origin distance 153.0000 + the detectors lie on an arc with source to detector distance = 306.0000 + + + <#> rays user 301 spacing 1.1000 + number of rays per projection 301 + snark computed number of rays 437 + at detector spacing 1.1000 + + + <#> angl 500 + total number of projections 500 + + + projection angles 0.0000 0.7190 1.4381 2.1571 2.8762 3.5952 4.3142 5.0333 5.7523 6.4713 + 7.1904 7.9094 8.6285 9.3475 10.0665 10.7856 11.5046 12.2236 12.9427 13.6617 + 14.3808 15.0998 15.8188 16.5379 17.2569 17.9760 18.6950 19.4140 20.1331 20.8521 + 21.5711 22.2902 23.0092 23.7283 24.4473 25.1663 25.8854 26.6044 27.3234 28.0425 + 28.7615 29.4806 30.1996 30.9186 31.6377 32.3567 33.0758 33.7948 34.5138 35.2329 + 35.9519 36.6709 37.3900 38.1090 38.8281 39.5471 40.2661 40.9852 41.7042 42.4232 + 43.1423 43.8613 44.5804 45.2994 46.0184 46.7375 47.4565 48.1756 48.8946 49.6136 + 50.3327 51.0517 51.7707 52.4898 53.2088 53.9279 54.6469 55.3659 56.0850 56.8040 + 57.5230 58.2421 58.9611 59.6802 60.3992 61.1182 61.8373 62.5563 63.2754 63.9944 + 64.7134 65.4325 66.1515 66.8705 67.5896 68.3086 69.0277 69.7467 70.4657 71.1848 + 71.9038 72.6228 73.3419 74.0609 74.7800 75.4990 76.2180 76.9371 77.6561 78.3752 + 79.0942 79.8132 80.5323 81.2513 81.9703 82.6894 83.4084 84.1275 84.8465 85.5655 + 86.2846 87.0036 87.7226 88.4417 89.1607 89.8798 90.5988 91.3178 92.0369 92.7559 + 93.4749 94.1940 94.9130 95.6321 96.3511 97.0701 97.7892 98.5082 99.2273 99.9463 + 100.6653 101.3844 102.1034 102.8224 103.5415 104.2605 104.9796 105.6986 106.4176 107.1367 + 107.8557 108.5747 109.2938 110.0128 110.7319 111.4509 112.1699 112.8890 113.6080 114.3271 + 115.0461 115.7651 116.4842 117.2032 117.9222 118.6413 119.3603 120.0794 120.7984 121.5174 + 122.2365 122.9555 123.6745 124.3936 125.1126 125.8317 126.5507 127.2697 127.9888 128.7078 + 129.4269 130.1459 130.8649 131.5840 132.3030 133.0220 133.7411 134.4601 135.1792 135.8982 + 136.6172 137.3363 138.0553 138.7743 139.4934 140.2124 140.9315 141.6505 142.3695 143.0886 + 143.8076 144.5267 145.2457 145.9647 146.6838 147.4028 148.1218 148.8409 149.5599 150.2790 + 150.9980 151.7170 152.4361 153.1551 153.8741 154.5932 155.3122 156.0313 156.7503 157.4693 + 158.1884 158.9074 159.6265 160.3455 161.0645 161.7836 162.5026 163.2216 163.9407 164.6597 + 165.3788 166.0978 166.8168 167.5359 168.2549 168.9739 169.6930 170.4120 171.1311 171.8501 + 172.5691 173.2882 174.0072 174.7263 175.4453 176.1643 176.8834 177.6024 178.3214 179.0405 + 179.7595 180.4786 181.1976 181.9166 182.6357 183.3547 184.0737 184.7928 185.5118 186.2309 + 186.9499 187.6689 188.3880 189.1070 189.8261 190.5451 191.2641 191.9832 192.7022 193.4212 + 194.1403 194.8593 195.5784 196.2974 197.0164 197.7355 198.4545 199.1735 199.8926 200.6116 + 201.3307 202.0497 202.7687 203.4878 204.2068 204.9259 205.6449 206.3639 207.0830 207.8020 + 208.5210 209.2401 209.9591 210.6782 211.3972 212.1162 212.8353 213.5543 214.2733 214.9924 + 215.7114 216.4305 217.1495 217.8685 218.5876 219.3066 220.0257 220.7447 221.4637 222.1828 + 222.9018 223.6208 224.3399 225.0589 225.7780 226.4970 227.2160 227.9351 228.6541 229.3731 + 230.0922 230.8112 231.5303 232.2493 232.9683 233.6874 234.4064 235.1255 235.8445 236.5635 + 237.2826 238.0016 238.7206 239.4397 240.1587 240.8778 241.5968 242.3158 243.0349 243.7539 + 244.4729 245.1920 245.9110 246.6301 247.3491 248.0681 248.7872 249.5062 250.2253 250.9443 + 251.6633 252.3824 253.1014 253.8204 254.5395 255.2585 255.9776 256.6966 257.4156 258.1347 + 258.8537 259.5727 260.2918 261.0108 261.7299 262.4489 263.1679 263.8870 264.6060 265.3251 + 266.0441 266.7631 267.4822 268.2012 268.9202 269.6393 270.3583 271.0774 271.7964 272.5154 + 273.2345 273.9535 274.6725 275.3916 276.1106 276.8297 277.5487 278.2677 278.9868 279.7058 + 280.4248 281.1439 281.8629 282.5820 283.3010 284.0200 284.7391 285.4581 286.1772 286.8962 + 287.6152 288.3343 289.0533 289.7723 290.4914 291.2104 291.9295 292.6485 293.3675 294.0866 + 294.8056 295.5246 296.2437 296.9627 297.6818 298.4008 299.1198 299.8389 300.5579 301.2770 + 301.9960 302.7150 303.4341 304.1531 304.8721 305.5912 306.3102 307.0293 307.7483 308.4673 + 309.1864 309.9054 310.6244 311.3435 312.0625 312.7816 313.5006 314.2196 314.9387 315.6577 + 316.3768 317.0958 317.8148 318.5339 319.2529 319.9719 320.6910 321.4100 322.1291 322.8481 + 323.5671 324.2862 325.0052 325.7242 326.4433 327.1623 327.8814 328.6004 329.3194 330.0385 + 330.7575 331.4766 332.1956 332.9146 333.6337 334.3527 335.0717 335.7908 336.5098 337.2289 + 337.9479 338.6669 339.3860 340.1050 340.8240 341.5431 342.2621 342.9812 343.7002 344.4192 + 345.1383 345.8573 346.5764 347.2954 348.0144 348.7335 349.4525 350.1715 350.8906 351.6096 + 352.3287 353.0477 353.7667 354.4858 355.2048 355.9238 356.6429 357.3619 358.0810 358.8000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 511 + background absorption 0.0000 + + estimate of totlen = 20962469.574466 + estimate of totden = 9804758.593222 + estimate of average density = 0.4677 + projection data read + EXAMPLE 11 Brain Phantom + 0.070 seconds used for processing command proj + + + <*> + + <#> STOP TERMINATION KLDS 100000 RPRT + termination test klds + reporting is enabled + reporting file: RPRTklds + reporting on every iteration + epsilon = 100000 + 0.000 seconds used for processing command stop + + + <*> + + <#> SUPERIORIZE 16 0.999 1 SMOO RPRT + Superiorization is enabled + N = 16 + a = 0.999 + b = 1 + secondary criterion: smoo + reporting is enabled + reporting file: RPRTsuperiorization + reporting on every iteration + 0.000 seconds used for processing command supe + + + <#> EXECUTE AVERAGE EMAP + + Example 11 Illustrating the Superiorized MAP EM algorithm for PET + + <#> gamma is 0 EVAL + + ----------------------------------------------------------- + + maximum a-posteriori probability expectation maximization + + gamma: 0.000 + evaluation flag is set + + ----------------------------------------------------------- + + *** WARNING - There exist negative values in the projection data *** + *** Negative values set to 0.0 *** + value of l: 15 + value of phi before algorithm operator: 0 + value of phi after algorithm operator: 2.39758 + algorithm executed in iteration 1 + 1.266 seconds for the execution of the algorithm +****Error: Negative raysum in prjfil detected, KLDS is not applicable! Terminating algorithm execution. + reconstruction completed after iteration 1 + 1.268 seconds for this iteration + 1.392 seconds used for processing command exec + + + <*> + + <#> END diff --git a/examples/b12/run b/examples/b12/run new file mode 100755 index 0000000..b981a8a --- /dev/null +++ b/examples/b12/run @@ -0,0 +1 @@ +snark14 b12.in diff --git a/examples/b13/README b/examples/b13/README new file mode 100644 index 0000000..d6aab0e --- /dev/null +++ b/examples/b13/README @@ -0,0 +1,7 @@ +SNARK14m's original b7 example uses 'MEASUREMENT NOISY' data which +causes inconsistencies in output across different random number +libraries. + +This version uses PERFECT data so it can be used to test regression +across different platforms. + diff --git a/examples/b13/b13.in b/examples/b13/b13.in new file mode 100644 index 0000000..835896e --- /dev/null +++ b/examples/b13/b13.in @@ -0,0 +1,62 @@ +********EXAMPLE 7 +* MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION OF BRAIN +* PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS WITH +* EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. +* COEFFICIENT OF PENALTLY TERM IS SET TO 10.0 +* +CREATE +EXAMPLE 7 Brain Phantom +SPECTRUM MONOCHROMATIC 511 +OBJECTS + 1 elip -7.0 46.0 3.0 6.0 17.0 0.95 1.0 + 2 elip 7.0 46.0 3.0 6.0 -17.0 1.0 0.95 + 3 rect -12.0 64.0 7.5 4.5 5.0 1.0 1.0 + 4 rect 12.0 64.0 7.5 4.5 -5.0 0.95 0.95 + 5 rect -38.0 51.0 3.5 13.0 -39.0 0.95 1.0 + 6 rect 38.0 51.0 3.5 13.0 39.0 1.0 0.95 + 7 rect -46.0 24.0 6.5 6.0 -18.0 0.95 1.0 + 8 rect 46.0 24.0 6.5 6.0 18.0 1.0 0.95 + 9 rect -49.0 6.0 2.5 10.0 63.0 1.0 1.0 + 10 rect 49.0 6.0 2.5 10.0 -63.0 0.95 0.95 + 11 rect -52.0 -14.0 9.0 7.0 -14.0 0.95 1.0 + 12 rect 52.0 -14.0 9.0 7.0 14.0 1.0 0.95 + 13 rect -10.0 -56.0 5.5 10.0 -1.0 0.95 1.0 + 14 rect 10.0 -56.0 5.5 10.0 1.0 1.0 0.95 + 15 elip -40.0 -47.0 9.0 22.5 48.0 1.0 1.0 + 16 elip 40.0 -47.0 9.0 22.5 -48.0 0.95 0.95 + 17 elip -8.0 -22.0 3.5 15.5 -9.0 1.0 1.0 + 18 elip 8.0 -22.0 3.5 15.5 9.0 0.95 0.95 + 19 elip -27.0 -6.0 5.5 23.5 -5.0 0.95 1.0 + 20 elip 27.0 -6.0 5.5 23.5 5.0 1.0 0.95 + 21 elip -25.0 38.0 6.5 10.5 -14.0 1.0 1.0 + 22 elip 25.0 38.0 6.5 10.5 14.0 0.95 0.95 + 23 rect -8.0 32.0 1.5 6.5 38.0 1.0 1.0 + 24 rect 8.0 32.0 1.5 6.5 -38.0 0.95 0.95 + 25 rect -8.0 3.0 1.0 9.0 -33.0 0.95 1.0 + 26 rect 8.0 3.0 1.0 9.0 33.0 1.0 0.95 + 27 elip 0.0 0.0 66.5 74.0 0.0 1.0 1.0 +LAST .51 1 0.05 +PHANTOM AVERAGE 7 +95 PIXELS OF SIZE 1.6 +RAYSUM AVERAGE 1 +1 +GEOMETRY +divergent arc 153 306 +RAYS USER 101 DETECTOR SPACING 3.2 +ANGLES 300 EQUAL SPACING +0.0 358.8 +MEASUREMENT PERFECT +BACKGROUND 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +STOP ITERATION 20 +* +EXECUTE AVERAGE EMAP +Example 7 Illustrating the MAP EM algorithm for PET +gamma is 10.0 EVAL +* +END diff --git a/examples/b13/b13r.out b/examples/b13/b13r.out new file mode 100644 index 0000000..e419bf7 --- /dev/null +++ b/examples/b13/b13r.out @@ -0,0 +1,522 @@ + snark14.s170710 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> *******EXAMPLE 7 + + <*> MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION OF BRAIN + + <*> PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS WITH + + <*> EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. + + <*> COEFFICIENT OF PENALTLY TERM IS SET TO 10.0 + + <*> + + <#> CREATE + + EXAMPLE 7 Brain Phantom + + + <#> SPECTRUM MONOCHROMATIC 511 + energy spectrum is monochromatic at energy level 511 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 511 + + 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.9500 0.9500 + + 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 1.0000 1.0000 + + 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 1.0000 1.0000 + + 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.9500 0.9500 + + 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.9500 0.9500 + + 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 1.0000 1.0000 + + 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.9500 0.9500 + + 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 1.0000 1.0000 + + 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 1.0000 1.0000 + + 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.9500 0.9500 + + 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.9500 0.9500 + + 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 1.0000 1.0000 + + 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.9500 0.9500 + + 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 1.0000 1.0000 + + 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 1.0000 1.0000 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.9500 0.9500 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 1.0000 1.0000 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.9500 0.9500 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.9500 0.9500 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 1.0000 1.0000 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 1.0000 1.0000 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.9500 0.9500 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 1.0000 1.0000 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.9500 0.9500 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.9500 0.9500 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 1.0000 1.0000 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 1.0000 1.0000 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> PHANTOM AVERAGE 7 + + this run will generate a phantom + density in each pixel is obtained as the average of 7 x 7 points + + + <#> 95 PIXELS OF SIZE 1.6 + picture size 95 x 95, pixel size 1.6000 + + + <#> RAYSUM AVERAGE 1 + + this run will generate projection data + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> GEOMETRY + + + <#> divergent arc 153 306 + rays are divergent from point sources + source to origin distance 153.0000 + the detectors lie on an arc with source to detector distance = 306.0000 + + + <#> RAYS USER 101 DETECTOR SPACING 3.2 + number of rays per projection 101 + at detector spacing 3.2000 + + + <#> ANGLES 300 EQUAL SPACING + total number of projections 300 + + projection angles 0.0000 1.2000 2.4000 3.6000 4.8000 6.0000 7.2000 8.4000 9.6000 10.8000 + 12.0000 13.2000 14.4000 15.6000 16.8000 18.0000 19.2000 20.4000 21.6000 22.8000 + 24.0000 25.2000 26.4000 27.6000 28.8000 30.0000 31.2000 32.4000 33.6000 34.8000 + 36.0000 37.2000 38.4000 39.6000 40.8000 42.0000 43.2000 44.4000 45.6000 46.8000 + 48.0000 49.2000 50.4000 51.6000 52.8000 54.0000 55.2000 56.4000 57.6000 58.8000 + 60.0000 61.2000 62.4000 63.6000 64.8000 66.0000 67.2000 68.4000 69.6000 70.8000 + 72.0000 73.2000 74.4000 75.6000 76.8000 78.0000 79.2000 80.4000 81.6000 82.8000 + 84.0000 85.2000 86.4000 87.6000 88.8000 90.0000 91.2000 92.4000 93.6000 94.8000 + 96.0000 97.2000 98.4000 99.6000 100.8000 102.0000 103.2000 104.4000 105.6000 106.8000 + 108.0000 109.2000 110.4000 111.6000 112.8000 114.0000 115.2000 116.4000 117.6000 118.8000 + 120.0000 121.2000 122.4000 123.6000 124.8000 126.0000 127.2000 128.4000 129.6000 130.8000 + 132.0000 133.2000 134.4000 135.6000 136.8000 138.0000 139.2000 140.4000 141.6000 142.8000 + 144.0000 145.2000 146.4000 147.6000 148.8000 150.0000 151.2000 152.4000 153.6000 154.8000 + 156.0000 157.2000 158.4000 159.6000 160.8000 162.0000 163.2000 164.4000 165.6000 166.8000 + 168.0000 169.2000 170.4000 171.6000 172.8000 174.0000 175.2000 176.4000 177.6000 178.8000 + 180.0000 181.2000 182.4000 183.6000 184.8000 186.0000 187.2000 188.4000 189.6000 190.8000 + 192.0000 193.2000 194.4000 195.6000 196.8000 198.0000 199.2000 200.4000 201.6000 202.8000 + 204.0000 205.2000 206.4000 207.6000 208.8000 210.0000 211.2000 212.4000 213.6000 214.8000 + 216.0000 217.2000 218.4000 219.6000 220.8000 222.0000 223.2000 224.4000 225.6000 226.8000 + 228.0000 229.2000 230.4000 231.6000 232.8000 234.0000 235.2000 236.4000 237.6000 238.8000 + 240.0000 241.2000 242.4000 243.6000 244.8000 246.0000 247.2000 248.4000 249.6000 250.8000 + 252.0000 253.2000 254.4000 255.6000 256.8000 258.0000 259.2000 260.4000 261.6000 262.8000 + 264.0000 265.2000 266.4000 267.6000 268.8000 270.0000 271.2000 272.4000 273.6000 274.8000 + 276.0000 277.2000 278.4000 279.6000 280.8000 282.0000 283.2000 284.4000 285.6000 286.8000 + 288.0000 289.2000 290.4000 291.6000 292.8000 294.0000 295.2000 296.4000 297.6000 298.8000 + 300.0000 301.2000 302.4000 303.6000 304.8000 306.0000 307.2000 308.4000 309.6000 310.8000 + 312.0000 313.2000 314.4000 315.6000 316.8000 318.0000 319.2000 320.4000 321.6000 322.8000 + 324.0000 325.2000 326.4000 327.6000 328.8000 330.0000 331.2000 332.4000 333.6000 334.8000 + 336.0000 337.2000 338.4000 339.6000 340.8000 342.0000 343.2000 344.4000 345.6000 346.8000 + 348.0000 349.2000 350.4000 351.6000 352.8000 354.0000 355.2000 356.4000 357.6000 358.8000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 0.0 + at levels + 511 + background absorption 0.0000 + + + <#> RUN + 0.014 seconds phantom creation + 0.078 seconds projection data creation + 0.093 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 7 Brain Phantom + + + <#> spec mono 511 + energy spectrum is monochromatic at energy level 511 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 511 + + 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 + + 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 + + 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 + + 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 + + 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 + + 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 + + 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 + + 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 + + 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 + + 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 + + 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 + + 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 + + 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 + + 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 + + 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> phan aver 7 + + density in each pixel is obtained as the average of 7 x 7 points + + + <#> pixe 95 size 1.6000 + picture size 95 x 95, pixel size 1.6000 + + test picture read + EXAMPLE 7 Brain Phantom + 0.003 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + EXAMPLE 7 Brain Phantom + + + <#> spec mono 511 + energy spectrum is monochromatic at energy level 511 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 511 + + 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 + + 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 + + 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 + + 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 + + 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 + + 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 + + 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 + + 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 + + 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 + + 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 + + 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 + + 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 + + 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 + + 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 + + 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 + + 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 + + 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 + + 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 + + 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 + + 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 + + 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 + + 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 + + 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 + + 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 + + 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 + + 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 + + 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 + + scale factor multiplying object densities 0.5100 + + seed set to 1 + inhomogeneity set to 0.0500 + + <#> rays aver 1 + + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> geom + + + <#> dive arc source at 153.0000 det dist 306.0000 + rays are divergent from point sources + source to origin distance 153.0000 + the detectors lie on an arc with source to detector distance = 306.0000 + + + <#> rays user 101 spacing 3.2000 + number of rays per projection 101 + snark computed number of rays 151 + at detector spacing 3.2000 + + + <#> angl 300 + total number of projections 300 + + + projection angles 0.0000 1.2000 2.4000 3.6000 4.8000 6.0000 7.2000 8.4000 9.6000 10.8000 + 12.0000 13.2000 14.4000 15.6000 16.8000 18.0000 19.2000 20.4000 21.6000 22.8000 + 24.0000 25.2000 26.4000 27.6000 28.8000 30.0000 31.2000 32.4000 33.6000 34.8000 + 36.0000 37.2000 38.4000 39.6000 40.8000 42.0000 43.2000 44.4000 45.6000 46.8000 + 48.0000 49.2000 50.4000 51.6000 52.8000 54.0000 55.2000 56.4000 57.6000 58.8000 + 60.0000 61.2000 62.4000 63.6000 64.8000 66.0000 67.2000 68.4000 69.6000 70.8000 + 72.0000 73.2000 74.4000 75.6000 76.8000 78.0000 79.2000 80.4000 81.6000 82.8000 + 84.0000 85.2000 86.4000 87.6000 88.8000 90.0000 91.2000 92.4000 93.6000 94.8000 + 96.0000 97.2000 98.4000 99.6000 100.8000 102.0000 103.2000 104.4000 105.6000 106.8000 + 108.0000 109.2000 110.4000 111.6000 112.8000 114.0000 115.2000 116.4000 117.6000 118.8000 + 120.0000 121.2000 122.4000 123.6000 124.8000 126.0000 127.2000 128.4000 129.6000 130.8000 + 132.0000 133.2000 134.4000 135.6000 136.8000 138.0000 139.2000 140.4000 141.6000 142.8000 + 144.0000 145.2000 146.4000 147.6000 148.8000 150.0000 151.2000 152.4000 153.6000 154.8000 + 156.0000 157.2000 158.4000 159.6000 160.8000 162.0000 163.2000 164.4000 165.6000 166.8000 + 168.0000 169.2000 170.4000 171.6000 172.8000 174.0000 175.2000 176.4000 177.6000 178.8000 + 180.0000 181.2000 182.4000 183.6000 184.8000 186.0000 187.2000 188.4000 189.6000 190.8000 + 192.0000 193.2000 194.4000 195.6000 196.8000 198.0000 199.2000 200.4000 201.6000 202.8000 + 204.0000 205.2000 206.4000 207.6000 208.8000 210.0000 211.2000 212.4000 213.6000 214.8000 + 216.0000 217.2000 218.4000 219.6000 220.8000 222.0000 223.2000 224.4000 225.6000 226.8000 + 228.0000 229.2000 230.4000 231.6000 232.8000 234.0000 235.2000 236.4000 237.6000 238.8000 + 240.0000 241.2000 242.4000 243.6000 244.8000 246.0000 247.2000 248.4000 249.6000 250.8000 + 252.0000 253.2000 254.4000 255.6000 256.8000 258.0000 259.2000 260.4000 261.6000 262.8000 + 264.0000 265.2000 266.4000 267.6000 268.8000 270.0000 271.2000 272.4000 273.6000 274.8000 + 276.0000 277.2000 278.4000 279.6000 280.8000 282.0000 283.2000 284.4000 285.6000 286.8000 + 288.0000 289.2000 290.4000 291.6000 292.8000 294.0000 295.2000 296.4000 297.6000 298.8000 + 300.0000 301.2000 302.4000 303.6000 304.8000 306.0000 307.2000 308.4000 309.6000 310.8000 + 312.0000 313.2000 314.4000 315.6000 316.8000 318.0000 319.2000 320.4000 321.6000 322.8000 + 324.0000 325.2000 326.4000 327.6000 328.8000 330.0000 331.2000 332.4000 333.6000 334.8000 + 336.0000 337.2000 338.4000 339.6000 340.8000 342.0000 343.2000 344.4000 345.6000 346.8000 + 348.0000 349.2000 350.4000 351.6000 352.8000 354.0000 355.2000 356.4000 357.6000 358.8000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 511 + background absorption 0.0000 + + estimate of totlen = 4263169.769963 + estimate of totden = 2023083.983824 + estimate of average density = 0.4745 + projection data read + EXAMPLE 7 Brain Phantom + 0.017 seconds used for processing command proj + + + <*> + + <#> STOP ITERATION 20 + 20 iterations + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE AVERAGE EMAP + + Example 7 Illustrating the MAP EM algorithm for PET + + <#> gamma is 10.0 EVAL + + ----------------------------------------------------------- + + maximum a-posteriori probability expectation maximization + + gamma: 10.000 + evaluation flag is set + + ----------------------------------------------------------- + + *** WARNING - There exist negative values in the projection data *** + *** Negative values set to 0.0 *** + algorithm executed in iteration 1 + 0.063 seconds for the execution of the algorithm + iteration 1 completed + 0.064 seconds for this iteration + algorithm executed in iteration 2 + 0.040 seconds for the execution of the algorithm + iteration 2 completed + 0.040 seconds for this iteration + algorithm executed in iteration 3 + 0.040 seconds for the execution of the algorithm + iteration 3 completed + 0.040 seconds for this iteration + algorithm executed in iteration 4 + 0.040 seconds for the execution of the algorithm + iteration 4 completed + 0.040 seconds for this iteration + algorithm executed in iteration 5 + 0.041 seconds for the execution of the algorithm + iteration 5 completed + 0.041 seconds for this iteration + algorithm executed in iteration 6 + 0.042 seconds for the execution of the algorithm + iteration 6 completed + 0.042 seconds for this iteration + algorithm executed in iteration 7 + 0.044 seconds for the execution of the algorithm + iteration 7 completed + 0.044 seconds for this iteration + algorithm executed in iteration 8 + 0.041 seconds for the execution of the algorithm + iteration 8 completed + 0.041 seconds for this iteration + algorithm executed in iteration 9 + 0.040 seconds for the execution of the algorithm + iteration 9 completed + 0.040 seconds for this iteration + algorithm executed in iteration 10 + 0.041 seconds for the execution of the algorithm + iteration 10 completed + 0.041 seconds for this iteration + algorithm executed in iteration 11 + 0.040 seconds for the execution of the algorithm + iteration 11 completed + 0.040 seconds for this iteration + algorithm executed in iteration 12 + 0.040 seconds for the execution of the algorithm + iteration 12 completed + 0.040 seconds for this iteration + algorithm executed in iteration 13 + 0.040 seconds for the execution of the algorithm + iteration 13 completed + 0.040 seconds for this iteration + algorithm executed in iteration 14 + 0.040 seconds for the execution of the algorithm + iteration 14 completed + 0.040 seconds for this iteration + algorithm executed in iteration 15 + 0.040 seconds for the execution of the algorithm + iteration 15 completed + 0.040 seconds for this iteration + algorithm executed in iteration 16 + 0.040 seconds for the execution of the algorithm + iteration 16 completed + 0.041 seconds for this iteration + algorithm executed in iteration 17 + 0.040 seconds for the execution of the algorithm + iteration 17 completed + 0.040 seconds for this iteration + algorithm executed in iteration 18 + 0.040 seconds for the execution of the algorithm + iteration 18 completed + 0.040 seconds for this iteration + algorithm executed in iteration 19 + 0.041 seconds for the execution of the algorithm + iteration 19 completed + 0.041 seconds for this iteration + algorithm executed in iteration 20 + 0.041 seconds for the execution of the algorithm + reconstruction completed after iteration 20 + 0.041 seconds for this iteration + 0.836 seconds for all iterations + 0.883 seconds used for processing command exec + + + <*> + + <#> END diff --git a/examples/b13/run b/examples/b13/run new file mode 100755 index 0000000..9634ec9 --- /dev/null +++ b/examples/b13/run @@ -0,0 +1 @@ +snark14 b13.in diff --git a/examples/b7/b7r.out b/examples/b7/b7r.out deleted file mode 100644 index fec9182..0000000 --- a/examples/b7/b7r.out +++ /dev/null @@ -1,534 +0,0 @@ - snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM - - - <*> *******EXAMPLE 7 - - <*> MAP EM ALGORITHM FOR EMISSION TOMOGRAPHY. RECONSTRUCTION OF BRAIN - - <*> PHANTOM. SIMULATING PET GEOMETRY WITH A RING OF 300 DETECTORS WITH - - <*> EACH DETECTOR IN COINCIDENCE WITH 101 DETECTORS OPPOSITE IT. - - <*> COEFFICIENT OF PENALTLY TERM IS SET TO 10.0 - - <*> - - <#> CREATE - - EXAMPLE 7 Brain Phantom - - - <#> SPECTRUM MONOCHROMATIC 511 - energy spectrum is monochromatic at energy level 511 - - - <#> OBJECTS - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.9500 0.9500 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 1.0000 1.0000 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 1.0000 1.0000 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.9500 0.9500 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.9500 0.9500 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 1.0000 1.0000 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.9500 0.9500 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 1.0000 1.0000 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 1.0000 1.0000 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.9500 0.9500 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.9500 0.9500 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 1.0000 1.0000 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.9500 0.9500 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 1.0000 1.0000 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 1.0000 1.0000 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.9500 0.9500 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 1.0000 1.0000 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.9500 0.9500 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.9500 0.9500 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 1.0000 1.0000 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 1.0000 1.0000 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.9500 0.9500 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 1.0000 1.0000 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.9500 0.9500 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.9500 0.9500 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 1.0000 1.0000 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 1.0000 1.0000 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> PHANTOM AVERAGE 7 - - this run will generate a phantom - density in each pixel is obtained as the average of 7 x 7 points - - - <#> 95 PIXELS OF SIZE 1.6 - picture size 95 x 95, pixel size 1.6000 - - - <#> RAYSUM AVERAGE 1 - - this run will generate projection data - projection data are calculated by dividing each ray interval into 1 substrips - - with aperture (substrip) weights 1 - - - <#> GEOMETRY - - - <#> divergent arc 153 306 - rays are divergent from point sources - source to origin distance 153.0000 - the detectors lie on an arc with source to detector distance = 306.0000 - - - <#> RAYS USER 101 DETECTOR SPACING 3.2 - number of rays per projection 101 - at detector spacing 3.2000 - - - <#> ANGLES 300 EQUAL SPACING - total number of projections 300 - - projection angles 0.0000 1.2000 2.4000 3.6000 4.8000 6.0000 7.2000 8.4000 9.6000 10.8000 - 12.0000 13.2000 14.4000 15.6000 16.8000 18.0000 19.2000 20.4000 21.6000 22.8000 - 24.0000 25.2000 26.4000 27.6000 28.8000 30.0000 31.2000 32.4000 33.6000 34.8000 - 36.0000 37.2000 38.4000 39.6000 40.8000 42.0000 43.2000 44.4000 45.6000 46.8000 - 48.0000 49.2000 50.4000 51.6000 52.8000 54.0000 55.2000 56.4000 57.6000 58.8000 - 60.0000 61.2000 62.4000 63.6000 64.8000 66.0000 67.2000 68.4000 69.6000 70.8000 - 72.0000 73.2000 74.4000 75.6000 76.8000 78.0000 79.2000 80.4000 81.6000 82.8000 - 84.0000 85.2000 86.4000 87.6000 88.8000 90.0000 91.2000 92.4000 93.6000 94.8000 - 96.0000 97.2000 98.4000 99.6000 100.8000 102.0000 103.2000 104.4000 105.6000 106.8000 - 108.0000 109.2000 110.4000 111.6000 112.8000 114.0000 115.2000 116.4000 117.6000 118.8000 - 120.0000 121.2000 122.4000 123.6000 124.8000 126.0000 127.2000 128.4000 129.6000 130.8000 - 132.0000 133.2000 134.4000 135.6000 136.8000 138.0000 139.2000 140.4000 141.6000 142.8000 - 144.0000 145.2000 146.4000 147.6000 148.8000 150.0000 151.2000 152.4000 153.6000 154.8000 - 156.0000 157.2000 158.4000 159.6000 160.8000 162.0000 163.2000 164.4000 165.6000 166.8000 - 168.0000 169.2000 170.4000 171.6000 172.8000 174.0000 175.2000 176.4000 177.6000 178.8000 - 180.0000 181.2000 182.4000 183.6000 184.8000 186.0000 187.2000 188.4000 189.6000 190.8000 - 192.0000 193.2000 194.4000 195.6000 196.8000 198.0000 199.2000 200.4000 201.6000 202.8000 - 204.0000 205.2000 206.4000 207.6000 208.8000 210.0000 211.2000 212.4000 213.6000 214.8000 - 216.0000 217.2000 218.4000 219.6000 220.8000 222.0000 223.2000 224.4000 225.6000 226.8000 - 228.0000 229.2000 230.4000 231.6000 232.8000 234.0000 235.2000 236.4000 237.6000 238.8000 - 240.0000 241.2000 242.4000 243.6000 244.8000 246.0000 247.2000 248.4000 249.6000 250.8000 - 252.0000 253.2000 254.4000 255.6000 256.8000 258.0000 259.2000 260.4000 261.6000 262.8000 - 264.0000 265.2000 266.4000 267.6000 268.8000 270.0000 271.2000 272.4000 273.6000 274.8000 - 276.0000 277.2000 278.4000 279.6000 280.8000 282.0000 283.2000 284.4000 285.6000 286.8000 - 288.0000 289.2000 290.4000 291.6000 292.8000 294.0000 295.2000 296.4000 297.6000 298.8000 - 300.0000 301.2000 302.4000 303.6000 304.8000 306.0000 307.2000 308.4000 309.6000 310.8000 - 312.0000 313.2000 314.4000 315.6000 316.8000 318.0000 319.2000 320.4000 321.6000 322.8000 - 324.0000 325.2000 326.4000 327.6000 328.8000 330.0000 331.2000 332.4000 333.6000 334.8000 - 336.0000 337.2000 338.4000 339.6000 340.8000 342.0000 343.2000 344.4000 345.6000 346.8000 - 348.0000 349.2000 350.4000 351.6000 352.8000 354.0000 355.2000 356.4000 357.6000 358.8000 - - - <#> MEASUREMENT NOISY - noise characteristics of projection data follow - nature characteristics - - <#> QUANTUM 1.0 1.0 CALIBRATION 4 - Emission tomography - - <#> SEED 0 - seed for random number generator is 0 - - - <#> BACKGROUND 0.0 - at levels - 511 - background absorption 0.0000 - - - <#> RUN - 0.025 seconds phantom creation - 0.100 seconds projection data creation - 0.125 seconds used for processing command crea - - - <*> - - <#> PICTURE TEST - - EXAMPLE 7 Brain Phantom - - - <#> spec mono 511 - energy spectrum is monochromatic at energy level 511 - - - <#> obje - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> phan aver 7 - - density in each pixel is obtained as the average of 7 x 7 points - - - <#> pixe 95 size 1.6000 - picture size 95 x 95, pixel size 1.6000 - - test picture read - EXAMPLE 7 Brain Phantom - 0.000 seconds used for processing command pict - - - <*> - - <#> PROJECTION REAL - - EXAMPLE 7 Brain Phantom - - - <#> spec mono 511 - energy spectrum is monochromatic at energy level 511 - - - <#> obje - description of objects - density at levels - numb type x-coord y-coord x-length y-length angle av dens 511 - - 1 elip -7.0000 46.0000 3.0000 6.0000 17.0000 0.4845 0.4845 - - 2 elip 7.0000 46.0000 3.0000 6.0000 -17.0000 0.5100 0.5100 - - 3 rect -12.0000 64.0000 7.5000 4.5000 5.0000 0.5100 0.5100 - - 4 rect 12.0000 64.0000 7.5000 4.5000 -5.0000 0.4845 0.4845 - - 5 rect -38.0000 51.0000 3.5000 13.0000 -39.0000 0.4845 0.4845 - - 6 rect 38.0000 51.0000 3.5000 13.0000 39.0000 0.5100 0.5100 - - 7 rect -46.0000 24.0000 6.5000 6.0000 -18.0000 0.4845 0.4845 - - 8 rect 46.0000 24.0000 6.5000 6.0000 18.0000 0.5100 0.5100 - - 9 rect -49.0000 6.0000 2.5000 10.0000 63.0000 0.5100 0.5100 - - 10 rect 49.0000 6.0000 2.5000 10.0000 -63.0000 0.4845 0.4845 - - 11 rect -52.0000 -14.0000 9.0000 7.0000 -14.0000 0.4845 0.4845 - - 12 rect 52.0000 -14.0000 9.0000 7.0000 14.0000 0.5100 0.5100 - - 13 rect -10.0000 -56.0000 5.5000 10.0000 -1.0000 0.4845 0.4845 - - 14 rect 10.0000 -56.0000 5.5000 10.0000 1.0000 0.5100 0.5100 - - 15 elip -40.0000 -47.0000 9.0000 22.5000 48.0000 0.5100 0.5100 - - 16 elip 40.0000 -47.0000 9.0000 22.5000 -48.0000 0.4845 0.4845 - - 17 elip -8.0000 -22.0000 3.5000 15.5000 -9.0000 0.5100 0.5100 - - 18 elip 8.0000 -22.0000 3.5000 15.5000 9.0000 0.4845 0.4845 - - 19 elip -27.0000 -6.0000 5.5000 23.5000 -5.0000 0.4845 0.4845 - - 20 elip 27.0000 -6.0000 5.5000 23.5000 5.0000 0.5100 0.5100 - - 21 elip -25.0000 38.0000 6.5000 10.5000 -14.0000 0.5100 0.5100 - - 22 elip 25.0000 38.0000 6.5000 10.5000 14.0000 0.4845 0.4845 - - 23 rect -8.0000 32.0000 1.5000 6.5000 38.0000 0.5100 0.5100 - - 24 rect 8.0000 32.0000 1.5000 6.5000 -38.0000 0.4845 0.4845 - - 25 rect -8.0000 3.0000 1.0000 9.0000 -33.0000 0.4845 0.4845 - - 26 rect 8.0000 3.0000 1.0000 9.0000 33.0000 0.5100 0.5100 - - 27 elip 0.0000 0.0000 66.5000 74.0000 0.0000 0.5100 0.5100 - - scale factor multiplying object densities 0.5100 - - seed set to 1 - inhomogeneity set to 0.0500 - - <#> rays aver 1 - - projection data are calculated by dividing each ray interval into 1 substrips - - with aperture (substrip) weights 1 - - - <#> geom - - - <#> dive arc source at 153.0000 det dist 306.0000 - rays are divergent from point sources - source to origin distance 153.0000 - the detectors lie on an arc with source to detector distance = 306.0000 - - - <#> rays user 101 spacing 3.2000 - number of rays per projection 101 - snark computed number of rays 151 - at detector spacing 3.2000 - - - <#> angl 300 - total number of projections 300 - - - projection angles 0.0000 1.2000 2.4000 3.6000 4.8000 6.0000 7.2000 8.4000 9.6000 10.8000 - 12.0000 13.2000 14.4000 15.6000 16.8000 18.0000 19.2000 20.4000 21.6000 22.8000 - 24.0000 25.2000 26.4000 27.6000 28.8000 30.0000 31.2000 32.4000 33.6000 34.8000 - 36.0000 37.2000 38.4000 39.6000 40.8000 42.0000 43.2000 44.4000 45.6000 46.8000 - 48.0000 49.2000 50.4000 51.6000 52.8000 54.0000 55.2000 56.4000 57.6000 58.8000 - 60.0000 61.2000 62.4000 63.6000 64.8000 66.0000 67.2000 68.4000 69.6000 70.8000 - 72.0000 73.2000 74.4000 75.6000 76.8000 78.0000 79.2000 80.4000 81.6000 82.8000 - 84.0000 85.2000 86.4000 87.6000 88.8000 90.0000 91.2000 92.4000 93.6000 94.8000 - 96.0000 97.2000 98.4000 99.6000 100.8000 102.0000 103.2000 104.4000 105.6000 106.8000 - 108.0000 109.2000 110.4000 111.6000 112.8000 114.0000 115.2000 116.4000 117.6000 118.8000 - 120.0000 121.2000 122.4000 123.6000 124.8000 126.0000 127.2000 128.4000 129.6000 130.8000 - 132.0000 133.2000 134.4000 135.6000 136.8000 138.0000 139.2000 140.4000 141.6000 142.8000 - 144.0000 145.2000 146.4000 147.6000 148.8000 150.0000 151.2000 152.4000 153.6000 154.8000 - 156.0000 157.2000 158.4000 159.6000 160.8000 162.0000 163.2000 164.4000 165.6000 166.8000 - 168.0000 169.2000 170.4000 171.6000 172.8000 174.0000 175.2000 176.4000 177.6000 178.8000 - 180.0000 181.2000 182.4000 183.6000 184.8000 186.0000 187.2000 188.4000 189.6000 190.8000 - 192.0000 193.2000 194.4000 195.6000 196.8000 198.0000 199.2000 200.4000 201.6000 202.8000 - 204.0000 205.2000 206.4000 207.6000 208.8000 210.0000 211.2000 212.4000 213.6000 214.8000 - 216.0000 217.2000 218.4000 219.6000 220.8000 222.0000 223.2000 224.4000 225.6000 226.8000 - 228.0000 229.2000 230.4000 231.6000 232.8000 234.0000 235.2000 236.4000 237.6000 238.8000 - 240.0000 241.2000 242.4000 243.6000 244.8000 246.0000 247.2000 248.4000 249.6000 250.8000 - 252.0000 253.2000 254.4000 255.6000 256.8000 258.0000 259.2000 260.4000 261.6000 262.8000 - 264.0000 265.2000 266.4000 267.6000 268.8000 270.0000 271.2000 272.4000 273.6000 274.8000 - 276.0000 277.2000 278.4000 279.6000 280.8000 282.0000 283.2000 284.4000 285.6000 286.8000 - 288.0000 289.2000 290.4000 291.6000 292.8000 294.0000 295.2000 296.4000 297.6000 298.8000 - 300.0000 301.2000 302.4000 303.6000 304.8000 306.0000 307.2000 308.4000 309.6000 310.8000 - 312.0000 313.2000 314.4000 315.6000 316.8000 318.0000 319.2000 320.4000 321.6000 322.8000 - 324.0000 325.2000 326.4000 327.6000 328.8000 330.0000 331.2000 332.4000 333.6000 334.8000 - 336.0000 337.2000 338.4000 339.6000 340.8000 342.0000 343.2000 344.4000 345.6000 346.8000 - 348.0000 349.2000 350.4000 351.6000 352.8000 354.0000 355.2000 356.4000 357.6000 358.8000 - - - <#> meas nois - noise characteristics of projection data follow - nature characteristics - - <#> quan 1.0000 1.0000 cali 4 - Emission tomography - - <#> seed 0 - seed for random number generator is 0 - - - <#> back 0.0000 - at levels - 511 - background absorption 0.0000 - - estimate of totlen = 4263169.769963 - estimate of totden = 2020362.000000 - estimate of average density = 0.4739 - projection data read - EXAMPLE 7 Brain Phantom - 0.012 seconds used for processing command proj - - - <*> - - <#> STOP ITERATION 20 - 20 iterations - 0.000 seconds used for processing command stop - - - <*> - - <#> EXECUTE AVERAGE EMAP - - Example 7 Illustrating the MAP EM algorithm for PET - - <#> gamma is 10.0 EVAL - - ----------------------------------------------------------- - - maximum a-posteriori probability expectation maximization - - gamma: 10.000 - evaluation flag is set - - ----------------------------------------------------------- - - algorithm executed in iteration 1 - 0.167 seconds for the execution of the algorithm - iteration 1 completed - 0.167 seconds for this iteration - algorithm executed in iteration 2 - 0.096 seconds for the execution of the algorithm - iteration 2 completed - 0.096 seconds for this iteration - algorithm executed in iteration 3 - 0.106 seconds for the execution of the algorithm - iteration 3 completed - 0.106 seconds for this iteration - algorithm executed in iteration 4 - 0.097 seconds for the execution of the algorithm - iteration 4 completed - 0.097 seconds for this iteration - algorithm executed in iteration 5 - 0.096 seconds for the execution of the algorithm - iteration 5 completed - 0.096 seconds for this iteration - algorithm executed in iteration 6 - 0.097 seconds for the execution of the algorithm - iteration 6 completed - 0.097 seconds for this iteration - algorithm executed in iteration 7 - 0.096 seconds for the execution of the algorithm - iteration 7 completed - 0.097 seconds for this iteration - algorithm executed in iteration 8 - 0.097 seconds for the execution of the algorithm - iteration 8 completed - 0.097 seconds for this iteration - algorithm executed in iteration 9 - 0.112 seconds for the execution of the algorithm - iteration 9 completed - 0.112 seconds for this iteration - algorithm executed in iteration 10 - 0.116 seconds for the execution of the algorithm - iteration 10 completed - 0.116 seconds for this iteration - algorithm executed in iteration 11 - 0.100 seconds for the execution of the algorithm - iteration 11 completed - 0.100 seconds for this iteration - algorithm executed in iteration 12 - 0.106 seconds for the execution of the algorithm - iteration 12 completed - 0.106 seconds for this iteration - algorithm executed in iteration 13 - 0.117 seconds for the execution of the algorithm - iteration 13 completed - 0.117 seconds for this iteration - algorithm executed in iteration 14 - 0.115 seconds for the execution of the algorithm - iteration 14 completed - 0.115 seconds for this iteration - algorithm executed in iteration 15 - 0.115 seconds for the execution of the algorithm - iteration 15 completed - 0.115 seconds for this iteration - algorithm executed in iteration 16 - 0.109 seconds for the execution of the algorithm - iteration 16 completed - 0.109 seconds for this iteration - algorithm executed in iteration 17 - 0.102 seconds for the execution of the algorithm - iteration 17 completed - 0.102 seconds for this iteration - algorithm executed in iteration 18 - 0.089 seconds for the execution of the algorithm - iteration 18 completed - 0.089 seconds for this iteration - algorithm executed in iteration 19 - 0.101 seconds for the execution of the algorithm - iteration 19 completed - 0.101 seconds for this iteration - algorithm executed in iteration 20 - 0.099 seconds for the execution of the algorithm - reconstruction completed after iteration 20 - 0.099 seconds for this iteration - 2.135 seconds for all iterations - 2.183 seconds used for processing command exec - - - <*> - - <#> END diff --git a/examples/regression b/examples/regression index 281ebe7..fb4c2f1 100755 --- a/examples/regression +++ b/examples/regression @@ -1,5 +1,8 @@ #!/bin/bash -for i in `seq 1 11`; + +# Exclude examples 7 and 11 as they use random number generator not compatible across platforms + +for i in 1 2 3 4 5 6 8 9 10 12 13; do echo Computing the diff for example b"$i". cd b"$i" diff --git a/examples/run_all b/examples/run_all index e4ed0e4..82da88f 100755 --- a/examples/run_all +++ b/examples/run_all @@ -1,7 +1,7 @@ #!/bin/bash echo "Running all examples. This may take a few minutes." -for i in 1 3 4 5 6 7 8 10 11 20; +for i in 1 3 4 5 6 7 8 10 11 12 13 20; do cd b$i snark14 b${i}.in > b${i}.out