From 239b0e24ba0d694f14cecaf261e0ef6ba1e01f67 Mon Sep 17 00:00:00 2001 From: "Kevin M. Rosenberg" Date: Sun, 11 Feb 2018 19:58:54 -0700 Subject: [PATCH] Added snark14m distribution examples --- examples/.more_run_scripts | 6 + examples/b1/b1.in | 48 ++ examples/b1/b1r.out | 342 ++++++++++++ examples/b1/run | 1 + examples/b1/snark.lock | 1 + examples/b10/b10.in | 51 ++ examples/b10/b10r.out | 305 +++++++++++ examples/b10/run | 1 + examples/b11/b11.in | 65 +++ examples/b11/b11r.out | 606 +++++++++++++++++++++ examples/b11/run | 1 + examples/b2/b2.in | 61 +++ examples/b2/b2r.out | 811 ++++++++++++++++++++++++++++ examples/b2/bin/README | 1 + examples/b2/build | 2 + examples/b2/run | 2 + examples/b2/src/Makefile | 60 ++ examples/b2/src/alp1.cpp | 154 ++++++ examples/b2/src/art_tset.cpp | 32 ++ examples/b3/b3.in | 52 ++ examples/b3/b3r.out | 148 +++++ examples/b3/run | 1 + examples/b4/b4.in | 46 ++ examples/b4/b4r.out | 243 +++++++++ examples/b4/run | 1 + examples/b5/b5.in | 75 +++ examples/b5/b5r.out | 503 +++++++++++++++++ examples/b5/run | 1 + examples/b6/b6.in | 60 ++ examples/b6/b6r.out | 379 +++++++++++++ examples/b6/run | 1 + examples/b7/b7.in | 64 +++ examples/b7/b7r.out | 534 ++++++++++++++++++ examples/b7/run | 1 + examples/b8/b8.in | 43 ++ examples/b8/b8r.out | 386 +++++++++++++ examples/b8/run | 1 + examples/b9/b.9.compare.ss | 9 + examples/b9/b.9.experimenter.in | 7 + examples/b9/b.9.projection.ss | 15 + examples/b9/b.9.recon.ss | 7 + examples/b9/b.9.virus.ens | 18 + examples/b9/b9r.out | 32 ++ examples/b9/bin/.donotdeletedir | 0 examples/b9/build | 4 + examples/b9/run | 2 + examples/b9/src/Makefile | 69 +++ examples/b9/src/user_fom1.c | 69 +++ examples/b9/virus_24_1_0.96_0.6.atl | 32 ++ examples/b9/virus_24_1_0.96_0.7.atl | 32 ++ examples/b9/virus_24_1_0.96_0.8.atl | 32 ++ examples/b9/virus_24_1_0.97_0.6.atl | 32 ++ examples/b9/virus_24_1_0.97_0.7.atl | 32 ++ examples/b9/virus_24_1_0.97_0.8.atl | 32 ++ examples/b9/virus_26_1_0.96_0.6.atl | 34 ++ examples/b9/virus_26_1_0.96_0.7.atl | 34 ++ examples/b9/virus_26_1_0.96_0.8.atl | 34 ++ examples/b9/virus_26_1_0.97_0.6.atl | 34 ++ examples/b9/virus_26_1_0.97_0.7.atl | 34 ++ examples/b9/virus_26_1_0.97_0.8.atl | 34 ++ examples/b9/virus_28_1_0.96_0.6.atl | 36 ++ examples/b9/virus_28_1_0.96_0.7.atl | 36 ++ examples/b9/virus_28_1_0.96_0.8.atl | 36 ++ examples/b9/virus_28_1_0.97_0.6.atl | 36 ++ examples/b9/virus_28_1_0.97_0.7.atl | 36 ++ examples/b9/virus_28_1_0.97_0.8.atl | 36 ++ examples/regression | 15 + examples/run_all | 19 + 68 files changed, 5967 insertions(+) create mode 100644 examples/.more_run_scripts create mode 100644 examples/b1/b1.in create mode 100644 examples/b1/b1r.out create mode 100755 examples/b1/run create mode 100644 examples/b1/snark.lock create mode 100644 examples/b10/b10.in create mode 100644 examples/b10/b10r.out create mode 100755 examples/b10/run create mode 100644 examples/b11/b11.in create mode 100644 examples/b11/b11r.out create mode 100755 examples/b11/run create mode 100644 examples/b2/b2.in create mode 100644 examples/b2/b2r.out create mode 100644 examples/b2/bin/README create mode 100755 examples/b2/build create mode 100755 examples/b2/run create mode 100644 examples/b2/src/Makefile create mode 100644 examples/b2/src/alp1.cpp create mode 100644 examples/b2/src/art_tset.cpp create mode 100644 examples/b3/b3.in create mode 100644 examples/b3/b3r.out create mode 100755 examples/b3/run create mode 100644 examples/b4/b4.in create mode 100644 examples/b4/b4r.out create mode 100755 examples/b4/run create mode 100644 examples/b5/b5.in create mode 100644 examples/b5/b5r.out create mode 100755 examples/b5/run create mode 100644 examples/b6/b6.in create mode 100644 examples/b6/b6r.out create mode 100755 examples/b6/run create mode 100644 examples/b7/b7.in create mode 100644 examples/b7/b7r.out create mode 100755 examples/b7/run create mode 100644 examples/b8/b8.in create mode 100644 examples/b8/b8r.out create mode 100755 examples/b8/run create mode 100644 examples/b9/b.9.compare.ss create mode 100644 examples/b9/b.9.experimenter.in create mode 100644 examples/b9/b.9.projection.ss create mode 100644 examples/b9/b.9.recon.ss create mode 100644 examples/b9/b.9.virus.ens create mode 100644 examples/b9/b9r.out create mode 100644 examples/b9/bin/.donotdeletedir create mode 100755 examples/b9/build create mode 100755 examples/b9/run create mode 100644 examples/b9/src/Makefile create mode 100644 examples/b9/src/user_fom1.c create mode 100644 examples/b9/virus_24_1_0.96_0.6.atl create mode 100644 examples/b9/virus_24_1_0.96_0.7.atl create mode 100644 examples/b9/virus_24_1_0.96_0.8.atl create mode 100644 examples/b9/virus_24_1_0.97_0.6.atl create mode 100644 examples/b9/virus_24_1_0.97_0.7.atl create mode 100644 examples/b9/virus_24_1_0.97_0.8.atl create mode 100644 examples/b9/virus_26_1_0.96_0.6.atl create mode 100644 examples/b9/virus_26_1_0.96_0.7.atl create mode 100644 examples/b9/virus_26_1_0.96_0.8.atl create mode 100644 examples/b9/virus_26_1_0.97_0.6.atl create mode 100644 examples/b9/virus_26_1_0.97_0.7.atl create mode 100644 examples/b9/virus_26_1_0.97_0.8.atl create mode 100644 examples/b9/virus_28_1_0.96_0.6.atl create mode 100644 examples/b9/virus_28_1_0.96_0.7.atl create mode 100644 examples/b9/virus_28_1_0.96_0.8.atl create mode 100644 examples/b9/virus_28_1_0.97_0.6.atl create mode 100644 examples/b9/virus_28_1_0.97_0.7.atl create mode 100644 examples/b9/virus_28_1_0.97_0.8.atl create mode 100755 examples/regression create mode 100755 examples/run_all diff --git a/examples/.more_run_scripts b/examples/.more_run_scripts new file mode 100644 index 0000000..261455e --- /dev/null +++ b/examples/.more_run_scripts @@ -0,0 +1,6 @@ +#!/bin/bash +#now need to modify run scripts in examples directory +for i in `seq 1 10`; + do + more b$i/run +done diff --git a/examples/b1/b1.in b/examples/b1/b1.in new file mode 100644 index 0000000..3763525 --- /dev/null +++ b/examples/b1/b1.in @@ -0,0 +1,48 @@ +* EXAMPLE 1 +* DAISY PATTERN +* CREATION OF PHANTOM AND DIVERGENT PROJECTION DATA +* RECONSTRUCTION WITH DCON +* ANALYSIS +CREATE +EXAMPLE 1 DAISY +SPECTRUM MONOCHROMATIC 75 +OBJECTS +TRIA 1.9 -3.7 0.5 4.1 20.0 2.5 +SEGM 4.0 0.1 2.9 4.3 47.0 2.2 +SEGM -2.1 -2.1 3.1 3.0 -15.0 2.2 +ELIP 0.0 2.5 1.0 1.0 0.0 1.5 +ELIP 0.1 4.3 1.3 1.2 0.0 1.0 +ELIP -2.0 3.5 1.3 1.3 0.0 1.0 +ELIP -1.0 1.5 1.3 1.1 0.0 1.0 +ELIP 1.5 1.6 1.5 1.3 0.0 1.0 +ELIP 1.8 3.3 1.2 1.2 0.0 1.0 +LAST 1.0 +PHANTOM AVERAGE 3 +31 0.4 +RAYSUM AVERAGE 1 +1 1 +GEOMETRY +DIVERGENT ARC 20.0 10000.0 +RAYS USER 65 150.0 +ANGLES 60 EQUALLY SPACED +0.0 352.5 +MEASUREMENT PERFECT +BACKGROUND 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +EXECUTE DCON +EXAMPLE 1 DIVERGENT CONVOLUTION FROM 60 VIEWS +-1 1 -1 0.5 0 +BANDLIMITING +* +LINES SCALE 100.0 COLUMN 16 +1 +* +PUNCH PHANTOM +1 +* +END diff --git a/examples/b1/b1r.out b/examples/b1/b1r.out new file mode 100644 index 0000000..f268c11 --- /dev/null +++ b/examples/b1/b1r.out @@ -0,0 +1,342 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> EXAMPLE 1 + + <*> DAISY PATTERN + + <*> CREATION OF PHANTOM AND DIVERGENT PROJECTION DATA + + <*> RECONSTRUCTION WITH DCON + + <*> ANALYSIS + + <#> CREATE + + EXAMPLE 1 DAISY + + + <#> SPECTRUM MONOCHROMATIC 75 + energy spectrum is monochromatic at energy level 75 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 tria 1.9000 -3.7000 0.5000 4.1000 20.0000 2.5000 2.5000 + + 2 segm 4.0000 0.1000 2.9000 4.3000 47.0000 2.2000 2.2000 + + 3 segm -2.1000 -2.1000 3.1000 3.0000 -15.0000 2.2000 2.2000 + + 4 elip 0.0000 2.5000 1.0000 1.0000 0.0000 1.5000 1.5000 + + 5 elip 0.1000 4.3000 1.3000 1.2000 0.0000 1.0000 1.0000 + + 6 elip -2.0000 3.5000 1.3000 1.3000 0.0000 1.0000 1.0000 + + 7 elip -1.0000 1.5000 1.3000 1.1000 0.0000 1.0000 1.0000 + + 8 elip 1.5000 1.6000 1.5000 1.3000 0.0000 1.0000 1.0000 + + 9 elip 1.8000 3.3000 1.2000 1.2000 0.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 3 + + this run will generate a phantom + density in each pixel is obtained as the average of 3 x 3 points + + + <#> 31 0.4 + picture size 31 x 31, 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 20.0 10000.0 + rays are divergent from point sources + source to origin distance 20.0000 + the detectors lie on an arc with source to detector distance = 10000.0000 + + + <#> RAYS USER 65 150.0 + number of rays per projection 65 + at detector spacing 150.0000 + + + <#> ANGLES 60 EQUALLY SPACED + total number of projections 60 + + projection angles 0.0000 5.9746 11.9492 17.9237 23.8983 29.8729 35.8475 41.8220 47.7966 53.7712 + 59.7458 65.7203 71.6949 77.6695 83.6441 89.6186 95.5932 101.5678 107.5424 113.5169 + 119.4915 125.4661 131.4407 137.4153 143.3898 149.3644 155.3390 161.3136 167.2881 173.2627 + 179.2373 185.2119 191.1864 197.1610 203.1356 209.1102 215.0847 221.0593 227.0339 233.0085 + 238.9831 244.9576 250.9322 256.9068 262.8814 268.8559 274.8305 280.8051 286.7797 292.7542 + 298.7288 304.7034 310.6780 316.6525 322.6271 328.6017 334.5763 340.5508 346.5254 352.5000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 0.0 + at levels + 75 + background absorption 0.0000 + + + <#> RUN + 0.001 seconds phantom creation + 0.004 seconds projection data creation + 0.005 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 1 DAISY + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 tria 1.9000 -3.7000 0.5000 4.1000 20.0000 2.5000 2.5000 + + 2 segm 4.0000 0.1000 2.9000 4.3000 47.0000 2.2000 2.2000 + + 3 segm -2.1000 -2.1000 3.1000 3.0000 -15.0000 2.2000 2.2000 + + 4 elip 0.0000 2.5000 1.0000 1.0000 0.0000 1.5000 1.5000 + + 5 elip 0.1000 4.3000 1.3000 1.2000 0.0000 1.0000 1.0000 + + 6 elip -2.0000 3.5000 1.3000 1.3000 0.0000 1.0000 1.0000 + + 7 elip -1.0000 1.5000 1.3000 1.1000 0.0000 1.0000 1.0000 + + 8 elip 1.5000 1.6000 1.5000 1.3000 0.0000 1.0000 1.0000 + + 9 elip 1.8000 3.3000 1.2000 1.2000 0.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 3 + + density in each pixel is obtained as the average of 3 x 3 points + + + <#> pixe 31 size 0.4000 + picture size 31 x 31, pixel size 0.4000 + + test picture read + EXAMPLE 1 DAISY + 0.000 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + EXAMPLE 1 DAISY + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 tria 1.9000 -3.7000 0.5000 4.1000 20.0000 2.5000 2.5000 + + 2 segm 4.0000 0.1000 2.9000 4.3000 47.0000 2.2000 2.2000 + + 3 segm -2.1000 -2.1000 3.1000 3.0000 -15.0000 2.2000 2.2000 + + 4 elip 0.0000 2.5000 1.0000 1.0000 0.0000 1.5000 1.5000 + + 5 elip 0.1000 4.3000 1.3000 1.2000 0.0000 1.0000 1.0000 + + 6 elip -2.0000 3.5000 1.3000 1.3000 0.0000 1.0000 1.0000 + + 7 elip -1.0000 1.5000 1.3000 1.1000 0.0000 1.0000 1.0000 + + 8 elip 1.5000 1.6000 1.5000 1.3000 0.0000 1.0000 1.0000 + + 9 elip 1.8000 3.3000 1.2000 1.2000 0.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> 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 20.0000 det dist10000.0000 + rays are divergent from point sources + source to origin distance 20.0000 + the detectors lie on an arc with source to detector distance = 10000.0000 + + + <#> rays user 65 spacing 150.0000 + number of rays per projection 65 + snark computed number of rays 63 + at detector spacing 150.0000 + + + <#> angl 60 + total number of projections 60 + + + projection angles 0.0000 5.9746 11.9492 17.9237 23.8983 29.8729 35.8475 41.8220 47.7966 53.7712 + 59.7458 65.7203 71.6949 77.6695 83.6441 89.6186 95.5932 101.5678 107.5424 113.5169 + 119.4915 125.4661 131.4407 137.4153 143.3898 149.3644 155.3390 161.3136 167.2881 173.2627 + 179.2373 185.2119 191.1864 197.1610 203.1356 209.1102 215.0847 221.0593 227.0339 233.0085 + 238.9831 244.9576 250.9322 256.9068 262.8814 268.8559 274.8305 280.8051 286.7797 292.7542 + 298.7288 304.7034 310.6780 316.6525 322.6271 328.6017 334.5763 340.5508 346.5254 352.5000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 75 + background absorption 0.0000 + + estimate of totlen = 31273.639204 + estimate of totden = 11129.885164 + estimate of average density = 0.3559 + projection data read + EXAMPLE 1 DAISY + 0.000 seconds used for processing command proj + + + <*> + + <#> EXECUTE DCON + + EXAMPLE 1 DIVERGENT CONVOLUTION FROM 60 VIEWS + + <#> -1 1 -1 0.5 0 + cubic spline interpolation + one out of every 1 projection(s) used for reconstruction + 64 points used on each side of convolution + pre-smoothing weight on center ray = 0.5000 + pre-smoothing weight on side rays = 0.2500 + accurate back-projection + + <#> BANDLIMITING + band-limiting filter + total time for obtaining smoothed projection data was 0.001 + total time for convoluting projection data was 0.000 + total time for back-projecting was 0.001 + algorithm executed in iteration 1 + 0.002 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.002 seconds for this iteration + 0.002 seconds used for processing command exec + + + <*> + + <#> LINES SCALE 100.0 COLUMN 16 + + last iteration + + lines display of reconstruction using DCON iter 1 + + phantom name: EXAMPLE 1 DAISY + projection data: EXAMPLE 1 DAISY + execution name: EXAMPLE 1 DIVERGENT CONVOLUTION FROM 60 VIEWS + scaling factor = 100.00000 + + column = 16 + row original estimate difference + 0 0.00000 -7.80005 -7.80005 + 1 22.22222 28.11589 5.89367 + 2 100.00000 88.37252 -11.62748 + 3 100.00000 104.43894 4.43894 + 4 100.00000 102.69494 2.69494 + 5 100.00000 107.73658 7.73658 + 6 100.00000 147.49863 47.49863 + 7 216.66667 188.04080 -28.62586 + 8 150.00000 180.51891 30.51891 + 9 216.66667 211.83020 -4.83647 + 10 250.00000 245.52265 -4.47735 + 11 216.66667 199.38366 -17.28301 + 12 111.11111 120.98082 9.86971 + 13 66.66667 68.05861 1.39194 + 14 0.00000 13.57312 13.57312 + 15 27.77778 12.48964 -15.28813 + 16 0.00000 27.99191 27.99191 + 17 0.00000 24.69207 24.69207 + 18 0.00000 10.47314 10.47314 + 19 0.00000 -0.41472 -0.41472 + 20 0.00000 0.60572 0.60572 + 21 0.00000 10.05671 10.05671 + 22 122.22222 102.66325 -19.55897 + 23 97.77778 87.82826 -9.94952 + 24 0.00000 5.13094 5.13094 + 25 0.00000 -2.85855 -2.85855 + 26 0.00000 -3.34366 -3.34366 + 27 0.00000 1.38876 1.38876 + 28 0.00000 3.44155 3.44155 + 29 0.00000 5.01602 5.01602 + 30 0.00000 -0.04334 -0.04334 + + + + 0.001 seconds used for processing command line + + + <*> + + <#> PUNCH PHANTOM + + last iteration + + reconstruction of EXAMPLE 1 DIVERGENT CONVOLUTIO using DCON iter 1, EXAMPLE 1 DAISY + 0.000 seconds used for processing command punc + + + <*> + + <#> END diff --git a/examples/b1/run b/examples/b1/run new file mode 100755 index 0000000..54b080b --- /dev/null +++ b/examples/b1/run @@ -0,0 +1 @@ +snark14 b1.in diff --git a/examples/b1/snark.lock b/examples/b1/snark.lock new file mode 100644 index 0000000..84e0d24 --- /dev/null +++ b/examples/b1/snark.lock @@ -0,0 +1 @@ +2660 diff --git a/examples/b10/b10.in b/examples/b10/b10.in new file mode 100644 index 0000000..ab58b8a --- /dev/null +++ b/examples/b10/b10.in @@ -0,0 +1,51 @@ +********EXAMPLE 10 +* ROTATED RECTANGLE WITH PSEUDO PROJECTION DATA +* RECONSTRUCTION BY ART WITH BLOB BASIS +* +*TRACE 1 +CREATE +EXAMPLE 10 ROTATED RECTANGLE +SPECTRUM MONOCHROMATIC 10 +OBJECTS +RECT 0.0 0.0 2.0 10.0 -30.0 1.0 +LAST 1.0 +PHANTOM AVERAGE 1 +25 PIXELS OF SIZE 1.0 +RAYSUM +RUN +* +PICTURE TEST +* +PROJECTION PSEUDO +EXAMPLE 10 PSEUDO PROJECTION DATA FOR TWELVE VIEWS +GEOMETRY +PARALLEL UNIFORM LINE +RAYS PROGRAM 25 2.0 DETECTOR SPACING AT 2.0 +ANGLES 12 EQUALLY SPACED +0.0 165.0 +MEASUREMENT PERFECT +BACKGROUND 50.0 +* +BASIS BLOB +* +SELECT SNARK RAYSEQ +STEP 3 1 +* +STOP ITERATION 10 +* +EXECUTE AVERAGE ART +ART WITH BLOB BASIS +ART3 +CONSTRAINT ART2 +* +BASIS PIXEL +EXECUTE AVERAGE ART +ART WITH PIXEL BASIS +ART3 +CONSTRAINT ART2 +* +EVALUATE BOTH +COMPARING BLOB AND PIXEL BASIS +WHOLEPIC +2222222222 +END diff --git a/examples/b10/b10r.out b/examples/b10/b10r.out new file mode 100644 index 0000000..1953ccc --- /dev/null +++ b/examples/b10/b10r.out @@ -0,0 +1,305 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> *******EXAMPLE 10 + + <*> ROTATED RECTANGLE WITH PSEUDO PROJECTION DATA + + <*> RECONSTRUCTION BY ART WITH BLOB BASIS + + <*> + + <*> TRACE 1 + + <#> CREATE + + EXAMPLE 10 ROTATED RECTANGLE + + + <#> SPECTRUM MONOCHROMATIC 10 + energy spectrum is monochromatic at energy level 10 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 rect 0.0000 0.0000 2.0000 10.0000 -30.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 1 + + this run will generate a phantom + density in each pixel is obtained as the average of 1 x 1 points + + + <#> 25 PIXELS OF SIZE 1.0 + picture size 25 x 25, pixel size 1.0000 + + + <#> RAYSUM + + 0.000 seconds phantom creation + 0.000 seconds used for processing command crea + + + <*> RUN + + <*> + + <#> PICTURE TEST + + EXAMPLE 10 ROTATED RECTANGLE + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 rect 0.0000 0.0000 2.0000 10.0000 -30.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 1 + + density in each pixel is obtained as the average of 1 x 1 points + + + <#> pixe 25 size 1.0000 + picture size 25 x 25, pixel size 1.0000 + + test picture read + EXAMPLE 10 ROTATED RECTANGLE + 0.000 seconds used for processing command pict + + + <*> + + <#> PROJECTION PSEUDO + + EXAMPLE 10 PSEUDO PROJECTION DATA FOR TWELVE VIEWS + + + + <#> GEOMETRY + + + <#> PARALLEL UNIFORM LINE + rays are parallel with uniform spacing between rays + data collected along lines + + + + <#> RAYS PROGRAM 25 2.0 DETECTOR SPACING AT 2.0 + number of rays per projection 37 + snark computed number of rays 19 + at detector spacing 2.0000 + + + <#> ANGLES 12 EQUALLY SPACED + total number of projections 12 + + projection angles 0.0000 15.0000 30.0000 45.0000 60.0000 75.0000 90.0000 105.0000 120.0000 135.0000 + 150.0000 165.0000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 50.0 + at levels + 10 + background absorption 50.0000 + + estimate of totlen = 3776.330760 + estimate of totden = 498.725717 + estimate of average density = 0.1321 + projection data read + EXAMPLE 10 PSEUDO PROJECTION DATA FOR TWELVE VIEWS + 0.000 seconds used for processing command proj + + + <*> + + <#> BASIS BLOB + hexagonal grid: there are 25 rows, the middle row has 21 grid points and the row next to the middle one has 22 grid points + blob basis with parameters: support = 2.0629 shape = 11.2829 delta = 1.1547 + 0.083 seconds used for processing command basi + + + <*> + + <#> SELECT SNARK RAYSEQ + + <#> STEP 3 1 + sequential ray selection with ray-step 1 and projection-step 3 + 0.000 seconds used for processing command sele + + + <*> + + <#> STOP ITERATION 10 + 10 iterations + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE AVERAGE ART + + ART WITH BLOB BASIS + + <#> ART3 + art3 method + relaxation parameter is 1.0 + norm is 2 + tolerance is 0.0 + + <#> CONSTRAINT ART2 + constraint art2 way + relaxation constraints with cr = 1.0 + picture is not normalized + 228 rays are used for each iteration + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iteration 2 completed + 0.001 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iteration 3 completed + 0.001 seconds for this iteration + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.001 seconds for this iteration + algorithm executed in iteration 5 + 0.000 seconds for the execution of the algorithm + iteration 5 completed + 0.001 seconds for this iteration + algorithm executed in iteration 6 + 0.000 seconds for the execution of the algorithm + iteration 6 completed + 0.001 seconds for this iteration + algorithm executed in iteration 7 + 0.000 seconds for the execution of the algorithm + iteration 7 completed + 0.001 seconds for this iteration + algorithm executed in iteration 8 + 0.000 seconds for the execution of the algorithm + iteration 8 completed + 0.001 seconds for this iteration + algorithm executed in iteration 9 + 0.000 seconds for the execution of the algorithm + iteration 9 completed + 0.001 seconds for this iteration + algorithm executed in iteration 10 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 10 + 0.001 seconds for this iteration + 0.007 seconds for all iterations + 0.008 seconds used for processing command exec + + + <*> + + <#> BASIS PIXEL + pixel basis + 0.000 seconds used for processing command basi + + + <#> EXECUTE AVERAGE ART + + ART WITH PIXEL BASIS + + <#> ART3 + art3 method + relaxation parameter is 1.0 + norm is 2 + tolerance is 0.0 + + <#> CONSTRAINT ART2 + constraint art2 way + relaxation constraints with cr = 1.0 + picture is not normalized + 228 rays are used for each iteration + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + iteration 1 completed + 0.000 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iteration 2 completed + 0.000 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iteration 3 completed + 0.000 seconds for this iteration + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.000 seconds for this iteration + algorithm executed in iteration 5 + 0.000 seconds for the execution of the algorithm + iteration 5 completed + 0.000 seconds for this iteration + algorithm executed in iteration 6 + 0.000 seconds for the execution of the algorithm + iteration 6 completed + 0.000 seconds for this iteration + algorithm executed in iteration 7 + 0.000 seconds for the execution of the algorithm + iteration 7 completed + 0.000 seconds for this iteration + algorithm executed in iteration 8 + 0.000 seconds for the execution of the algorithm + iteration 8 completed + 0.000 seconds for this iteration + algorithm executed in iteration 9 + 0.000 seconds for the execution of the algorithm + iteration 9 completed + 0.000 seconds for this iteration + algorithm executed in iteration 10 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 10 + 0.000 seconds for this iteration + 0.001 seconds for all iterations + 0.002 seconds used for processing command exec + + + <*> + + <#> EVALUATE BOTH + + COMPARING BLOB AND PIXEL BASIS + + <#> WHOLEPIC + Region cx cy u v ang t1 t2 + + wholepic -1e+20 1e+20 + + iterations 1 2 3 4 5 6 7 8 9 + last iteration + + residual calculation using line integration + 0.004 seconds used for processing command eval + + + <#> END diff --git a/examples/b10/run b/examples/b10/run new file mode 100755 index 0000000..f16b9ac --- /dev/null +++ b/examples/b10/run @@ -0,0 +1 @@ +snark14 b10.in diff --git a/examples/b11/b11.in b/examples/b11/b11.in new file mode 100644 index 0000000..81b8b95 --- /dev/null +++ b/examples/b11/b11.in @@ -0,0 +1,65 @@ +********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 NOISY +QUANTUM 1.0 1.0 CALIBRATION 4 +SEED 0 +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/b11/b11r.out b/examples/b11/b11r.out new file mode 100644 index 0000000..3458c1f --- /dev/null +++ b/examples/b11/b11r.out @@ -0,0 +1,606 @@ + 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 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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 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 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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 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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 new file mode 100755 index 0000000..4e5107b --- /dev/null +++ b/examples/b11/run @@ -0,0 +1 @@ +snark14 b11.in diff --git a/examples/b2/b2.in b/examples/b2/b2.in new file mode 100644 index 0000000..7b8a21c --- /dev/null +++ b/examples/b2/b2.in @@ -0,0 +1,61 @@ +**** EXAMPLE 2 +* Creation of a small test pattern and projection data with execution of +* a user-defined reconstruction algorithm and analysis. +* +CREATE +Example 2, A simple test pattern and projection data +SPECTRUM MONOCHROMATIC with energy at 75 KeV +OBJECTS cx cy u v ang den +ELIP 0.00 0.00 0.90 0.90 0.00 2.50 +ELIP 0.00 0.00 0.80 0.60 0.00 -1.25 +ELIP 0.00 0.00 0.21 0.25 0.00 0.10 +LAST 1.00 +PHANTOM AVERAGE 1 point for estimating pixel density +number of elements is 31 Size of a pixel is 0.07 +RAYSUM AVERAGE 1 line for estimation of ray sum with weight + 1 +GEOMETRY +PARALLEL UNIFORM LINE +RAYS USER-defined 63 rays per projection at spacing 0.05 +ANGLES 30 EQUAL SPACING between the first and last angles which are + 0.0 174.0 +MEASUREMENT PERFECT +BACKGROUND absorption is 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +MODE LOWER constraint set at 0.0 UPPER constraint set at 2.5 +* +SELECT USER RAYSEQ +STEP projections by 10 and rays by 1 +* +STOP TERMINATION VARIANCE at 0.01 +* +EXECUTE AVERAGE ART SMOOTH +Example 2a underrelaxed art4 with variable tolerance +smoothing threshold is 0.2 Weights are 2.25 1.5 1.0 +111111111111111111111111111111111111111111111111111 +ART4 RELAXATION CONSTANT = 0.025 TOLERANCE VARIABLE decreasing +CONSTRAINT BOUND CONRELAX CONSTANT = 0.5 NOMLIZE at each iteration +* +STOP ITERATIONS = 30 +* +EXECUTE ALP1 +Example 2b underrelaxed art with extrapolation +* +* Reset mode to unconstrained +MODE +* +EVALUATE RESOLUTION +Example 2a underrelaxed art4 +WHOLEPIC +2222222222222222222222222222222222222222 +* +LINES COLUMNS 15 and 18 are to be printed +1 1 1 1 +* +END + diff --git a/examples/b2/b2r.out b/examples/b2/b2r.out new file mode 100644 index 0000000..009ba70 --- /dev/null +++ b/examples/b2/b2r.out @@ -0,0 +1,811 @@ + snark14UserDefined.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> *** EXAMPLE 2 + + <*> Creation of a small test pattern and projection data with execution of + + <*> a user-defined reconstruction algorithm and analysis. + + <*> + + <#> CREATE + + Example 2, A simple test pattern and projection data + + + <#> SPECTRUM MONOCHROMATIC with energy at 75 KeV + energy spectrum is monochromatic at energy level 75 + + + <#> OBJECTS cx cy u v ang den + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 0.9000 0.9000 0.0000 2.5000 2.5000 + + 2 elip 0.0000 0.0000 0.8000 0.6000 0.0000 -1.2500 -1.2500 + + 3 elip 0.0000 0.0000 0.2100 0.2500 0.0000 0.1000 0.1000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 1 point for estimating pixel density + + this run will generate a phantom + density in each pixel is obtained as the average of 1 x 1 points + + + <#> number of elements is 31 Size of a pixel is 0.07 + picture size 31 x 31, pixel size 0.0700 + + + <#> RAYSUM AVERAGE 1 line for estimation of ray sum with weight + + this run will generate projection data + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> GEOMETRY + + + <#> PARALLEL UNIFORM LINE + rays are parallel with uniform spacing between rays + data collected along lines + + + + <#> RAYS USER-defined 63 rays per projection at spacing 0.05 + number of rays per projection 63 + at detector spacing 0.0500 + + + <#> ANGLES 30 EQUAL SPACING between the first and last angles which are + total number of projections 30 + + projection angles 0.0000 6.0000 12.0000 18.0000 24.0000 30.0000 36.0000 42.0000 48.0000 54.0000 + 60.0000 66.0000 72.0000 78.0000 84.0000 90.0000 96.0000 102.0000 108.0000 114.0000 + 120.0000 126.0000 132.0000 138.0000 144.0000 150.0000 156.0000 162.0000 168.0000 174.0000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND absorption is 0.0 + at levels + 75 + background absorption 0.0000 + + + <#> RUN + 0.004 seconds phantom creation + 0.000 seconds projection data creation + 0.004 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + Example 2, A simple test pattern and projection data + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 0.9000 0.9000 0.0000 2.5000 2.5000 + + 2 elip 0.0000 0.0000 0.8000 0.6000 0.0000 -1.2500 -1.2500 + + 3 elip 0.0000 0.0000 0.2100 0.2500 0.0000 0.1000 0.1000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 1 + + density in each pixel is obtained as the average of 1 x 1 points + + + <#> pixe 31 size 0.0700 + picture size 31 x 31, pixel size 0.0700 + + test picture read + Example 2, A simple test pattern and projection data + 0.000 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + Example 2, A simple test pattern and projection data + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 0.9000 0.9000 0.0000 2.5000 2.5000 + + 2 elip 0.0000 0.0000 0.8000 0.6000 0.0000 -1.2500 -1.2500 + + 3 elip 0.0000 0.0000 0.2100 0.2500 0.0000 0.1000 0.1000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> rays aver 1 + + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> geom + + + <#> para unif line + rays are parallel with uniform spacing between rays + data collected along lines + + + + <#> rays user 63 spacing 0.0500 + number of rays per projection 63 + snark computed number of rays 63 + at detector spacing 0.0500 + + + <#> angl 30 + total number of projections 30 + + + projection angles 0.0000 6.0000 12.0000 18.0000 24.0000 30.0000 36.0000 42.0000 48.0000 54.0000 + 60.0000 66.0000 72.0000 78.0000 84.0000 90.0000 96.0000 102.0000 108.0000 114.0000 + 120.0000 126.0000 132.0000 138.0000 144.0000 150.0000 156.0000 162.0000 168.0000 174.0000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 75 + background absorption 0.0000 + + estimate of totlen = 2823.757863 + estimate of totden = 2677.896607 + estimate of average density = 0.9483 + projection data read + Example 2, A simple test pattern and projection data + 0.001 seconds used for processing command proj + + + <*> + + <#> MODE LOWER constraint set at 0.0 UPPER constraint set at 2.5 + lower constraint set to 0.0000 + upper constraint set to 2.5000 + 0.000 seconds used for processing command mode + + + <*> + + <#> SELECT USER RAYSEQ + + <#> STEP projections by 10 and rays by 1 + sequential ray selection with ray-step 1 and projection-step 10 + 0.000 seconds used for processing command sele + + + <*> + + <#> STOP TERMINATION VARIANCE at 0.01 + termination test vari + epsilon = 0.010000 + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE AVERAGE ART SMOOTH + + Example 2a underrelaxed art4 with variable tolerance + + <#> smoothing threshold is 0.2 Weights are 2.25 1.5 1.0 + reconstruction is smoothed after + + iterations 1 2 3 4 5 6 7 8 9 10 + 11 12 13 14 15 16 17 18 19 20 + 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 40 + 41 42 43 44 45 46 47 48 49 50 + last iteration + + threshold = 0.20000 w1 = 2.25000 w2 = 1.50000 w3 = 1.00000 + + <#> ART4 RELAXATION CONSTANT = 0.025 TOLERANCE VARIABLE decreasing + art4 method + relaxation parameter is 0.0250 + tolerance is variable + + <#> CONSTRAINT BOUND CONRELAX CONSTANT = 0.5 NOMLIZE at each iteration + constraint set to boundaries + relax constraints with cr= 0.5000 + picture is normalized to 0.9483 after each iteration + 1890 rays are used for each iteration + lower constraint = 0.0000 + upper constraint = 2.5000 + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.001 seconds for the execution of the algorithm + iteration 2 completed + 0.001 seconds for this iteration + algorithm executed in iteration 3 + 0.002 seconds for the execution of the algorithm + iteration 3 completed + 0.002 seconds for this iteration + algorithm executed in iteration 4 + 0.001 seconds for the execution of the algorithm + iteration 4 completed + 0.001 seconds for this iteration + algorithm executed in iteration 5 + 0.003 seconds for the execution of the algorithm + iteration 5 completed + 0.003 seconds for this iteration + algorithm executed in iteration 6 + 0.002 seconds for the execution of the algorithm + iteration 6 completed + 0.002 seconds for this iteration + algorithm executed in iteration 7 + 0.001 seconds for the execution of the algorithm + iteration 7 completed + 0.001 seconds for this iteration + algorithm executed in iteration 8 + 0.001 seconds for the execution of the algorithm + iteration 8 completed + 0.001 seconds for this iteration + algorithm executed in iteration 9 + 0.001 seconds for the execution of the algorithm + iteration 9 completed + 0.001 seconds for this iteration + algorithm executed in iteration 10 + 0.002 seconds for the execution of the algorithm + iteration 10 completed + 0.002 seconds for this iteration + algorithm executed in iteration 11 + 0.001 seconds for the execution of the algorithm + iteration 11 completed + 0.001 seconds for this iteration + algorithm executed in iteration 12 + 0.002 seconds for the execution of the algorithm + iteration 12 completed + 0.002 seconds for this iteration + algorithm executed in iteration 13 + 0.001 seconds for the execution of the algorithm + iteration 13 completed + 0.001 seconds for this iteration + algorithm executed in iteration 14 + 0.001 seconds for the execution of the algorithm + iteration 14 completed + 0.001 seconds for this iteration + algorithm executed in iteration 15 + 0.001 seconds for the execution of the algorithm + iteration 15 completed + 0.001 seconds for this iteration + algorithm executed in iteration 16 + 0.000 seconds for the execution of the algorithm + iteration 16 completed + 0.000 seconds for this iteration + algorithm executed in iteration 17 + 0.002 seconds for the execution of the algorithm + iteration 17 completed + 0.002 seconds for this iteration + algorithm executed in iteration 18 + 0.001 seconds for the execution of the algorithm + iteration 18 completed + 0.001 seconds for this iteration + algorithm executed in iteration 19 + 0.001 seconds for the execution of the algorithm + iteration 19 completed + 0.001 seconds for this iteration + algorithm executed in iteration 20 + 0.001 seconds for the execution of the algorithm + iteration 20 completed + 0.001 seconds for this iteration + algorithm executed in iteration 21 + 0.002 seconds for the execution of the algorithm + iterative process stops at iteration 21 + the change in variance is less than 0.009852 of the variance + reconstruction completed after iteration 21 + 0.002 seconds for this iteration + 0.031 seconds for all iterations + 0.031 seconds used for processing command exec + + + <*> + + <#> STOP ITERATIONS = 30 + 30 iterations + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE ALP1 + + Example 2b underrelaxed art with extrapolation + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.001 seconds for the execution of the algorithm + iteration 2 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 5.062718796778e-01 + algorithm executed in iteration 3 + 0.001 seconds for the execution of the algorithm + iteration 3 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 5.062718796778e-01 + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 6.560964044719e-01 + algorithm executed in iteration 5 + 0.001 seconds for the execution of the algorithm + iteration 5 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 6.560964044719e-01 + algorithm executed in iteration 6 + 0.000 seconds for the execution of the algorithm + iteration 6 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 7.480594958675e-01 + algorithm executed in iteration 7 + 0.001 seconds for the execution of the algorithm + iteration 7 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 7.480594958675e-01 + algorithm executed in iteration 8 + 0.000 seconds for the execution of the algorithm + iteration 8 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 7.951514183812e-01 + algorithm executed in iteration 9 + 0.001 seconds for the execution of the algorithm + iteration 9 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 7.951514183812e-01 + algorithm executed in iteration 10 + 0.000 seconds for the execution of the algorithm + iteration 10 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.250655739411e-01 + algorithm executed in iteration 11 + 0.002 seconds for the execution of the algorithm + iteration 11 completed + 0.002 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.250655739411e-01 + algorithm executed in iteration 12 + 0.000 seconds for the execution of the algorithm + iteration 12 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.467169748437e-01 + algorithm executed in iteration 13 + 0.001 seconds for the execution of the algorithm + iteration 13 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.467169748437e-01 + algorithm executed in iteration 14 + 0.000 seconds for the execution of the algorithm + iteration 14 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.628058734349e-01 + algorithm executed in iteration 15 + 0.002 seconds for the execution of the algorithm + iteration 15 completed + 0.002 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.628058734349e-01 + algorithm executed in iteration 16 + 0.000 seconds for the execution of the algorithm + iteration 16 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.749346145383e-01 + algorithm executed in iteration 17 + 0.001 seconds for the execution of the algorithm + iteration 17 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.749346145383e-01 + algorithm executed in iteration 18 + 0.000 seconds for the execution of the algorithm + iteration 18 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.843623393369e-01 + algorithm executed in iteration 19 + 0.001 seconds for the execution of the algorithm + iteration 19 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.843623393369e-01 + algorithm executed in iteration 20 + 0.000 seconds for the execution of the algorithm + iteration 20 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.920147280181e-01 + algorithm executed in iteration 21 + 0.001 seconds for the execution of the algorithm + iteration 21 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.920147280181e-01 + algorithm executed in iteration 22 + 0.000 seconds for the execution of the algorithm + iteration 22 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.985122210336e-01 + algorithm executed in iteration 23 + 0.001 seconds for the execution of the algorithm + iteration 23 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 8.985122210336e-01 + algorithm executed in iteration 24 + 0.000 seconds for the execution of the algorithm + iteration 24 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.042443038619e-01 + algorithm executed in iteration 25 + 0.001 seconds for the execution of the algorithm + iteration 25 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.042443038619e-01 + algorithm executed in iteration 26 + 0.000 seconds for the execution of the algorithm + iteration 26 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.094448804097e-01 + algorithm executed in iteration 27 + 0.001 seconds for the execution of the algorithm + iteration 27 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.094448804097e-01 + algorithm executed in iteration 28 + 0.000 seconds for the execution of the algorithm + iteration 28 completed + 0.000 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.142500229503e-01 + algorithm executed in iteration 29 + 0.001 seconds for the execution of the algorithm + iteration 29 completed + 0.001 seconds for this iteration + EXTRAPOLATION PARAMETER IN EXTRAP IS 9.142500229503e-01 + algorithm executed in iteration 30 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 30 + 0.000 seconds for this iteration + 0.017 seconds for all iterations + 0.018 seconds used for processing command exec + + + <*> + + <*> Reset mode to unconstrained + + <#> MODE + 0.000 seconds used for processing command mode + + + <*> + + <#> EVALUATE RESOLUTION + + Example 2a underrelaxed art4 + + <#> WHOLEPIC + Region cx cy u v ang t1 t2 + + wholepic -1e+20 1e+20 + + iterations 1 2 3 4 5 6 7 8 9 10 + 11 12 13 14 15 16 17 18 19 20 + 21 22 23 24 25 26 27 28 29 30 + 31 32 33 34 35 36 37 38 39 + last iteration + + residual calculation using line integration + 0.047 seconds used for processing command eval + + + <*> + + <#> LINES COLUMNS 15 and 18 are to be printed + + iterations 10 20 30 + last iteration + + lines display of reconstruction using ART iter 10 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2a underrelaxed art4 with variable tolerance + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 0.18210 0.18210 0.00000 0.00909 0.00909 + 1 0.00000 0.20450 0.20450 0.00000 0.24753 0.24753 + 2 0.00000 1.10539 1.10539 0.00000 0.52569 0.52569 + 3 2.50000 2.13754 -0.36246 2.50000 1.94767 -0.55233 + 4 2.50000 2.16437 -0.33563 2.50000 2.18812 -0.31188 + 5 2.50000 2.16394 -0.33606 2.50000 2.20758 -0.29242 + 6 2.50000 2.13317 -0.36683 2.50000 2.17610 -0.32390 + 7 1.25000 1.49667 0.24667 1.25000 1.68287 0.43287 + 8 1.25000 1.44121 0.19121 1.25000 1.41529 0.16529 + 9 1.25000 1.37200 0.12200 1.25000 1.38374 0.13374 + 10 1.25000 1.34328 0.09328 1.25000 1.34276 0.09276 + 11 1.25000 1.33396 0.08396 1.25000 1.32222 0.07222 + 12 1.35000 1.34036 -0.00964 1.25000 1.31411 0.06411 + 13 1.35000 1.34676 -0.00324 1.25000 1.31521 0.06521 + 14 1.35000 1.35058 0.00058 1.25000 1.31568 0.06568 + 15 1.35000 1.35053 0.00053 1.35000 1.31710 -0.03290 + 16 1.35000 1.35058 0.00058 1.25000 1.31607 0.06607 + 17 1.35000 1.34676 -0.00324 1.25000 1.31587 0.06587 + 18 1.35000 1.34035 -0.00965 1.25000 1.31417 0.06417 + 19 1.25000 1.33395 0.08395 1.25000 1.32131 0.07131 + 20 1.25000 1.34326 0.09326 1.25000 1.34021 0.09021 + 21 1.25000 1.37196 0.12196 1.25000 1.38008 0.13008 + 22 1.25000 1.44114 0.19114 1.25000 1.41090 0.16090 + 23 1.25000 1.49658 0.24658 1.25000 1.68040 0.43040 + 24 2.50000 2.13333 -0.36667 2.50000 2.17405 -0.32595 + 25 2.50000 2.16414 -0.33586 2.50000 2.20535 -0.29465 + 26 2.50000 2.16455 -0.33545 2.50000 2.18655 -0.31345 + 27 2.50000 2.13774 -0.36226 2.50000 1.94456 -0.55544 + 28 0.00000 1.10534 1.10534 0.00000 0.44393 0.44393 + 29 0.00000 0.20439 0.20439 0.00000 0.29112 0.29112 + 30 0.00000 0.18198 0.18198 0.00000 0.01326 0.01326 + + + lines display of reconstruction using ART iter 20 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2a underrelaxed art4 with variable tolerance + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 0.00164 0.00164 0.00000 0.02169 0.02169 + 1 0.00000 0.00132 0.00132 0.00000 0.04480 0.04480 + 2 0.00000 0.94940 0.94940 0.00000 0.13226 0.13226 + 3 2.50000 2.43151 -0.06849 2.50000 2.25420 -0.24580 + 4 2.50000 2.43097 -0.06903 2.50000 2.44794 -0.05206 + 5 2.50000 2.37936 -0.12064 2.50000 2.44383 -0.05617 + 6 2.50000 2.31917 -0.18083 2.50000 2.39051 -0.10949 + 7 1.25000 1.46751 0.21751 1.25000 1.65881 0.40881 + 8 1.25000 1.31935 0.06935 1.25000 1.33707 0.08707 + 9 1.25000 1.29770 0.04770 1.25000 1.31051 0.06051 + 10 1.25000 1.27744 0.02744 1.25000 1.27762 0.02762 + 11 1.25000 1.28043 0.03043 1.25000 1.26720 0.01720 + 12 1.35000 1.30399 -0.04601 1.25000 1.26843 0.01843 + 13 1.35000 1.32095 -0.02905 1.25000 1.27985 0.02985 + 14 1.35000 1.32945 -0.02055 1.25000 1.28645 0.03645 + 15 1.35000 1.32847 -0.02153 1.35000 1.29098 -0.05902 + 16 1.35000 1.32944 -0.02056 1.25000 1.28714 0.03714 + 17 1.35000 1.32093 -0.02907 1.25000 1.28136 0.03136 + 18 1.35000 1.30399 -0.04601 1.25000 1.27000 0.02000 + 19 1.25000 1.28044 0.03044 1.25000 1.26871 0.01871 + 20 1.25000 1.27744 0.02744 1.25000 1.27815 0.02815 + 21 1.25000 1.29767 0.04767 1.25000 1.30973 0.05973 + 22 1.25000 1.31930 0.06930 1.25000 1.33504 0.08504 + 23 1.25000 1.46737 0.21737 1.25000 1.71927 0.46927 + 24 2.50000 2.31941 -0.18059 2.50000 2.39181 -0.10819 + 25 2.50000 2.37969 -0.12031 2.50000 2.44490 -0.05510 + 26 2.50000 2.43125 -0.06875 2.50000 2.44917 -0.05083 + 27 2.50000 2.43179 -0.06821 2.50000 2.25444 -0.24556 + 28 0.00000 0.94928 0.94928 0.00000 0.12809 0.12809 + 29 0.00000 0.00158 0.00158 0.00000 0.04576 0.04576 + 30 0.00000 0.00199 0.00199 0.00000 0.02628 0.02628 + + + lines display of reconstruction using ART iter 21 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2a underrelaxed art4 with variable tolerance + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 0.00100 0.00100 0.00000 0.01742 0.01742 + 1 0.00000 0.00070 0.00070 0.00000 0.03672 0.03672 + 2 0.00000 0.93506 0.93506 0.00000 0.11759 0.11759 + 3 2.50000 2.44949 -0.05051 2.50000 2.27648 -0.22352 + 4 2.50000 2.44615 -0.05385 2.50000 2.45838 -0.04162 + 5 2.50000 2.39029 -0.10971 2.50000 2.45205 -0.04795 + 6 2.50000 2.32845 -0.17155 2.50000 2.39929 -0.10071 + 7 1.25000 1.46233 0.21233 1.25000 1.65516 0.40516 + 8 1.25000 1.31367 0.06367 1.25000 1.33085 0.08085 + 9 1.25000 1.29279 0.04279 1.25000 1.30546 0.05546 + 10 1.25000 1.27400 0.02400 1.25000 1.27412 0.02412 + 11 1.25000 1.27844 0.02844 1.25000 1.26496 0.01496 + 12 1.35000 1.30374 -0.04626 1.25000 1.26714 0.01714 + 13 1.35000 1.32159 -0.02841 1.25000 1.27948 0.02948 + 14 1.35000 1.33036 -0.01964 1.25000 1.28660 0.03660 + 15 1.35000 1.32919 -0.02081 1.35000 1.29140 -0.05860 + 16 1.35000 1.33034 -0.01966 1.25000 1.28726 0.03726 + 17 1.35000 1.32157 -0.02843 1.25000 1.28096 0.03096 + 18 1.35000 1.30372 -0.04628 1.25000 1.26874 0.01874 + 19 1.25000 1.27844 0.02844 1.25000 1.26657 0.01657 + 20 1.25000 1.27400 0.02400 1.25000 1.27479 0.02479 + 21 1.25000 1.29277 0.04277 1.25000 1.30483 0.05483 + 22 1.25000 1.31362 0.06362 1.25000 1.32898 0.07898 + 23 1.25000 1.46218 0.21218 1.25000 1.65781 0.40781 + 24 2.50000 2.32869 -0.17131 2.50000 2.40065 -0.09935 + 25 2.50000 2.39063 -0.10937 2.50000 2.45318 -0.04682 + 26 2.50000 2.44644 -0.05356 2.50000 2.45967 -0.04033 + 27 2.50000 2.44977 -0.05023 2.50000 2.27692 -0.22308 + 28 0.00000 0.93489 0.93489 0.00000 0.11431 0.11431 + 29 0.00000 0.00120 0.00120 0.00000 0.03840 0.03840 + 30 0.00000 0.00161 0.00161 0.00000 0.02249 0.02249 + + + lines display of reconstruction using ALP1 iter 10 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2b underrelaxed art with extrapolation + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 0.12670 0.12670 0.00000 -0.02567 -0.02567 + 1 0.00000 0.17187 0.17187 0.00000 0.16958 0.16958 + 2 0.00000 1.20151 1.20151 0.00000 0.48350 0.48350 + 3 2.50000 2.23551 -0.26449 2.50000 2.01480 -0.48520 + 4 2.50000 2.39456 -0.10544 2.50000 2.31508 -0.18492 + 5 2.50000 2.34966 -0.15034 2.50000 2.46624 -0.03376 + 6 2.50000 2.31124 -0.18876 2.50000 2.29509 -0.20491 + 7 1.25000 1.63106 0.38106 1.25000 1.81482 0.56482 + 8 1.25000 1.35183 0.10183 1.25000 1.44203 0.19203 + 9 1.25000 1.42885 0.17885 1.25000 1.45015 0.20015 + 10 1.25000 1.31859 0.06859 1.25000 1.36973 0.11973 + 11 1.25000 1.42731 0.17731 1.25000 1.34954 0.09954 + 12 1.35000 1.31939 -0.03061 1.25000 1.31390 0.06390 + 13 1.35000 1.37323 0.02323 1.25000 1.32415 0.07415 + 14 1.35000 1.46590 0.11590 1.25000 1.37584 0.12584 + 15 1.35000 1.13749 -0.21251 1.35000 1.25214 -0.09786 + 16 1.35000 1.46594 0.11594 1.25000 1.36902 0.11902 + 17 1.35000 1.37317 0.02317 1.25000 1.30699 0.05699 + 18 1.35000 1.31944 -0.03056 1.25000 1.34043 0.09043 + 19 1.25000 1.42727 0.17727 1.25000 1.33982 0.08982 + 20 1.25000 1.31861 0.06861 1.25000 1.35654 0.10654 + 21 1.25000 1.42880 0.17880 1.25000 1.44218 0.19218 + 22 1.25000 1.35172 0.10172 1.25000 1.45375 0.20375 + 23 1.25000 1.63100 0.38100 1.25000 1.80751 0.55751 + 24 2.50000 2.31161 -0.18839 2.50000 2.27967 -0.22033 + 25 2.50000 2.34937 -0.15063 2.50000 2.50118 0.00118 + 26 2.50000 2.39545 -0.10455 2.50000 2.30942 -0.19058 + 27 2.50000 2.23526 -0.26474 2.50000 1.99542 -0.50458 + 28 0.00000 1.20133 1.20133 0.00000 0.49478 0.49478 + 29 0.00000 0.17173 0.17173 0.00000 0.15734 0.15734 + 30 0.00000 0.12647 0.12647 0.00000 -0.02832 -0.02832 + + + lines display of reconstruction using ALP1 iter 20 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2b underrelaxed art with extrapolation + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 -0.09663 -0.09663 0.00000 -0.18986 -0.18986 + 1 0.00000 -0.12331 -0.12331 0.00000 -0.05402 -0.05402 + 2 0.00000 1.04579 1.04579 0.00000 0.12373 0.12373 + 3 2.50000 2.51540 0.01540 2.50000 2.25540 -0.24460 + 4 2.50000 2.59753 0.09753 2.50000 2.56869 0.06869 + 5 2.50000 2.55529 0.05529 2.50000 2.67846 0.17846 + 6 2.50000 2.40841 -0.09159 2.50000 2.45046 -0.04954 + 7 1.25000 1.52857 0.27857 1.25000 1.73851 0.48851 + 8 1.25000 1.19882 -0.05118 1.25000 1.29003 0.04003 + 9 1.25000 1.28220 0.03220 1.25000 1.30029 0.05029 + 10 1.25000 1.18525 -0.06475 1.25000 1.24281 -0.00719 + 11 1.25000 1.27819 0.02819 1.25000 1.24380 -0.00620 + 12 1.35000 1.25011 -0.09989 1.25000 1.22237 -0.02763 + 13 1.35000 1.30966 -0.04034 1.25000 1.24476 -0.00524 + 14 1.35000 1.38630 0.03630 1.25000 1.28583 0.03583 + 15 1.35000 1.11801 -0.23199 1.35000 1.20027 -0.14973 + 16 1.35000 1.38636 0.03636 1.25000 1.28050 0.03050 + 17 1.35000 1.30959 -0.04041 1.25000 1.23298 -0.01702 + 18 1.35000 1.25014 -0.09986 1.25000 1.24848 -0.00152 + 19 1.25000 1.27817 0.02817 1.25000 1.23597 -0.01403 + 20 1.25000 1.18526 -0.06474 1.25000 1.23189 -0.01811 + 21 1.25000 1.28211 0.03211 1.25000 1.29998 0.04998 + 22 1.25000 1.19865 -0.05135 1.25000 1.30195 0.05195 + 23 1.25000 1.52839 0.27839 1.25000 1.73195 0.48195 + 24 2.50000 2.40899 -0.09101 2.50000 2.44156 -0.05844 + 25 2.50000 2.55477 0.05477 2.50000 2.70939 0.20939 + 26 2.50000 2.59890 0.09890 2.50000 2.56774 0.06774 + 27 2.50000 2.51498 0.01498 2.50000 2.24565 -0.25435 + 28 0.00000 1.04557 1.04557 0.00000 0.14374 0.14374 + 29 0.00000 -0.12338 -0.12338 0.00000 -0.05331 -0.05331 + 30 0.00000 -0.09670 -0.09670 0.00000 -0.17428 -0.17428 + + + lines display of reconstruction using ALP1 iter 30 + + phantom name: Example 2, A simple test pattern and projection data + projection data: Example 2, A simple test pattern and projection data + execution name: Example 2b underrelaxed art with extrapolation + scaling factor = 1.00000 + + column = 15 18 + row original estimate difference original estimate difference + 0 0.00000 -0.10295 -0.10295 0.00000 -0.15511 -0.15511 + 1 0.00000 -0.21068 -0.21068 0.00000 -0.09236 -0.09236 + 2 0.00000 0.92855 0.92855 0.00000 -0.06300 -0.06300 + 3 2.50000 2.64511 0.14511 2.50000 2.37419 -0.12581 + 4 2.50000 2.61843 0.11843 2.50000 2.63291 0.13291 + 5 2.50000 2.61277 0.11277 2.50000 2.68002 0.18002 + 6 2.50000 2.39593 -0.10407 2.50000 2.48350 -0.01650 + 7 1.25000 1.47574 0.22574 1.25000 1.66721 0.41721 + 8 1.25000 1.11475 -0.13525 1.25000 1.19787 -0.05213 + 9 1.25000 1.24880 -0.00120 1.25000 1.25371 0.00371 + 10 1.25000 1.15550 -0.09450 1.25000 1.22544 -0.02456 + 11 1.25000 1.25545 0.00545 1.25000 1.24429 -0.00571 + 12 1.35000 1.26430 -0.08570 1.25000 1.22826 -0.02174 + 13 1.35000 1.32865 -0.02135 1.25000 1.25347 0.00347 + 14 1.35000 1.40845 0.05845 1.25000 1.28571 0.03571 + 15 1.35000 1.14519 -0.20481 1.35000 1.22750 -0.12250 + 16 1.35000 1.40851 0.05851 1.25000 1.28178 0.03178 + 17 1.35000 1.32857 -0.02143 1.25000 1.24374 -0.00626 + 18 1.35000 1.26433 -0.08567 1.25000 1.25314 0.00314 + 19 1.25000 1.25545 0.00545 1.25000 1.23609 -0.01391 + 20 1.25000 1.15550 -0.09450 1.25000 1.21469 -0.03531 + 21 1.25000 1.24869 -0.00131 1.25000 1.25626 0.00626 + 22 1.25000 1.11456 -0.13544 1.25000 1.20898 -0.04102 + 23 1.25000 1.47547 0.22547 1.25000 1.65907 0.40907 + 24 2.50000 2.39664 -0.10336 2.50000 2.47619 -0.02381 + 25 2.50000 2.61204 0.11204 2.50000 2.70609 0.20609 + 26 2.50000 2.62009 0.12009 2.50000 2.63048 0.13048 + 27 2.50000 2.64455 0.14455 2.50000 2.36445 -0.13555 + 28 0.00000 0.92830 0.92830 0.00000 -0.04433 -0.04433 + 29 0.00000 -0.21071 -0.21071 0.00000 -0.09436 -0.09436 + 30 0.00000 -0.10286 -0.10286 0.00000 -0.14676 -0.14676 + + + + 0.002 seconds used for processing command line + + + <*> + + <#> END diff --git a/examples/b2/bin/README b/examples/b2/bin/README new file mode 100644 index 0000000..fb05f91 --- /dev/null +++ b/examples/b2/bin/README @@ -0,0 +1 @@ +Ececutable for example b.2 diff --git a/examples/b2/build b/examples/b2/build new file mode 100755 index 0000000..d1fe295 --- /dev/null +++ b/examples/b2/build @@ -0,0 +1,2 @@ +cd src +make install diff --git a/examples/b2/run b/examples/b2/run new file mode 100755 index 0000000..f710f63 --- /dev/null +++ b/examples/b2/run @@ -0,0 +1,2 @@ +./build >&2 +bin/snark14UserDefined b2.in diff --git a/examples/b2/src/Makefile b/examples/b2/src/Makefile new file mode 100644 index 0000000..bf3ba58 --- /dev/null +++ b/examples/b2/src/Makefile @@ -0,0 +1,60 @@ +# + +ifndef SNARKINCLUDE +SNARKINCLUDE=/usr/local/snark14/src/snark14/snark +endif + +ifndef SNARKLIBDIR +SNARKLIBDIR=/usr/local/snark14/lib +endif + +ifndef SNARKLIBINCLUDEDIR +SNARKLIBINCLUDEDIR=/usr/local/snark14/include +endif + +ifndef DIGFILEINCLUDE +DIGFILEINCLUDE=/usr/local/snark14/include/DIGFile +endif + +ifndef DIGFILESNARKINCLUDE +DIGFILESNARKINCLUDE=/usr/local/snark14/include/DIGFileSnark +endif + +ifndef DIGRANDINCLUDE +DIGRANDINCLUDE=/usr/local/snark14/include/DIGRand +endif + +OUTDIR=../bin +INCLUDEDIR = -I/usr/include -I$(XERCESINCLUDE)/.. \ +-I$(DIGFILEINCLUDE) -I$(DIGFILESNARKINCLUDE) -I$(DIGRANDINCLUDE) -I$(SNARKINCLUDE) \ +-I$(SNARKLIBINCLUDEDIR) + +OBJ = \ + alp1.o \ + art_tset.o + +LIBS= -L$(SNARKLIBDIR) -lsnark14 -lDIGFile -lDIGFileSnark -lDIGRand -lxerces-c -lm + +###################################### +# setings for testing +#LIBS=/usr/lib/libm.a +#FLAGS= -ffloat-store -O0 -DFFCOMPARE +###################################### + +all: snark14UserDefined + mv snark14UserDefined $(OUTDIR) + +snark14UserDefined: $(OBJ) + $(CXX) $(OBJ) $(CXXFLAGS) -o snark14UserDefined $(LIBS) + +clean: + rm -f $(OBJ) + rm -f snark14UserDefined + +install: all + +uninstall: + rm -f $(OUTDIR)/snark14UserDefined + +%.o: %.cpp + $(CXX) -c -I $(SRCDIR) $(CXXFLAGS) $(INCLUDEDIR) $< -o $@ diff --git a/examples/b2/src/alp1.cpp b/examples/b2/src/alp1.cpp new file mode 100644 index 0000000..c4835a3 --- /dev/null +++ b/examples/b2/src/alp1.cpp @@ -0,0 +1,154 @@ +/* + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * * + * S N A R K 1 4 * + * * + * A PICTURE RECONSTRUCTION PROGRAM * + * * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + + alp1.cpp,v 1.1 2009/06/01 23:26:59 jklukowska Exp + +*/ +// Example 2 user-written reconstruction function + + +#include +#include + +#include "blkdta.h" +#include "pseudo.h" +#include "projfile.h" +#include "uiod.h" +#include "consts.h" + +#include "alp1.h" + +void extrap(REAL* newrec, REAL* oldrec, REAL c, INTEGER area); +void itrun(REAL* recon, REAL* oldrec, REAL* proj, INTEGER* list, REAL* weight); + +BOOLEAN alp1_class::Run(REAL* recon, INTEGER* list, REAL* weight, INTEGER iter) +{ + + static REAL* oldrec; + static INTEGER curprj; + static REAL* proj; + INTEGER i; + static REAL newdif; + static REAL olddif; + static REAL c; + + if(iter == 1) { + + oldrec = new REAL[GeoPar.area]; + + proj = new REAL[GeoPar.nrays]; + + for(i = 0; i < GeoPar.area; i++) { + oldrec[i] = 0; + } + + // The previous art iteration is in OLDREC + itrun(recon, oldrec, proj, list, weight); + + for(i = 0; i < GeoPar.area; i++) { + oldrec[i] = recon[i]; + } + + curprj = 1; + return FALSE; + } + else if(iter == 2) { + itrun(recon, oldrec, proj, list, weight); + newdif = 0.0; + curprj = 2; + + for(i = 0; i < GeoPar.area; i++) { + newdif += SQR(recon[i] - oldrec[i]); + oldrec[i] = recon[i]; + } + + newdif = (REAL) sqrt(newdif); + return FALSE; + } + else if((iter/2)*2 != iter) { + curprj += 1; + itrun(recon, oldrec, proj, list, weight); + olddif = newdif; + newdif = 0.0; + + for(i = 0; i < GeoPar.area; i++) { + newdif += SQR(recon[i] - oldrec[i]); + } + + newdif = (REAL) sqrt(newdif); + if(olddif <= Consts.zero * newdif) { + fprintf(output, "\nCONVERGENCE DIFFERENCES %20.12e, %20.12e", olddif, newdif); + return FALSE; + } + c = newdif/olddif; + fprintf(output, "\n EXTRAPOLATION PARAMETER IN EXTRAP IS %20.12e", c); + + return FALSE; + } + + extrap(recon, oldrec, c, GeoPar.area); + + return FALSE; +} + +// NEWREC will contain extrapolated values +// OLDREC will contain the old values of NEWREC + +void extrap(REAL* newrec, REAL* oldrec, REAL c, INTEGER area) +{ + REAL d, save; + INTEGER i; + + if(fabs(1.0 - c) > Consts.zero) { + fprintf(output, "\n EXTRAPOLATION PARAMETER IN EXTRAP IS %20.12e", c); + d = c / ((REAL) 1.0 - c); + + for(i = 0; i < area; i++) { + save = newrec[i]; + newrec[i] += d * (newrec[i] - oldrec[i]); + oldrec[i] = save; + } + return; + } + fprintf(output, "\n EXTRAPOLATION PARAMETER IN EXTRAP IS %20.12e", c); + + fprintf(output, "\n EXTRAPOLATION PARAMETER TOO CLOSE TO 1 "); + + + for(i = 0; i < area; i++) { + oldrec[i] = newrec[i]; + } + return; +} + +void itrun(REAL* recon, REAL* oldrec, REAL* proj, INTEGER* list, REAL* weight) +{ + INTEGER i, nr, np, numb, j; + REAL snorm, raysum; + + for(i = 0; i < GeoPar.area; i++) { + recon[i] = oldrec[i]; + } + + for(np = 0; np < GeoPar.prjnum; np++) { + + ProjFile.ReadProj(np, proj, GeoPar.nrays); + + for(nr = 0; nr < GeoPar.nrays; nr++) { + raysum = pseudo(recon, np, nr, list, weight, &numb, &snorm, TRUE, FALSE); + + for(i = 0; i < numb; i++) { + j = list[i]; + recon[j] += (proj[nr]-raysum)* weight[i] * (REAL) 0.025 / snorm; + } + } + } + + return; +} diff --git a/examples/b2/src/art_tset.cpp b/examples/b2/src/art_tset.cpp new file mode 100644 index 0000000..4f85e9e --- /dev/null +++ b/examples/b2/src/art_tset.cpp @@ -0,0 +1,32 @@ +/* + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + * * + * S N A R K 1 4 * + * * + * A PICTURE RECONSTRUCTION PROGRAM * + * * + * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * + + art_tset.cpp,v 1.2 2008/09/06 15:18:05 rdavidi Exp + +*/ + +// Example 2 user-written tolerance function +// This function returns RAYSUM/(10*ITER) as tolerance. + +#include + +#include "blkdta.h" +#include "uiod.h" + +#include "art.h" + +REAL art_class::tset(REAL* recon, INTEGER iter, INTEGER np, INTEGER nr,INTEGER i, REAL raysum, INTEGER* list, REAL* weight, BOOLEAN* flag) +{ + REAL tmp = raysum / ((REAL)(10 * iter)); + *flag = FALSE; + if(trace >= 1) { + fprintf(output, "\n TOLERANCE IS %19.10f \n", tmp); + } + return tmp; +} diff --git a/examples/b3/b3.in b/examples/b3/b3.in new file mode 100644 index 0000000..3dca79c --- /dev/null +++ b/examples/b3/b3.in @@ -0,0 +1,52 @@ +* EXAMPLE 3 +* CREATION OF HEAD PHANTOM. GENERATION OF POLYCHROMATIC +* PROJECTION DATA. +* +* CREATE A PHANTOM +* GENERATE PROJECTION DATA +CREATE +EXAMPLE 3 HEAD PHANTOM +SPECTRUM POLYCHROMATIC 5 +40 10 50 30 60 30 80 20 100 10 +OBJECTS +SEGM 1.375 -7.5 1.1 0.625 19.2 -0.734 +DENS -0.472 -0.288 -0.116 -0.029 +SEGM 1.375 -7.5 1.1 4.32 19.21 0.734 +DENS 0.472 0.288 0.116 0.029 +ELIP 0.0 0.0 8.625 6.4687 90.0 1.0 +DENS 0.7 0.5 0.3 0.2 +ELIP 0.0 0.0 7.875 5.7187 90.0 -0.737 +DENS -0.475 -0.291 -0.118 -0.029 +ELIP 0.0 1.5 0.375 0.3 90.0 -0.003 +DENS -0.006 -0.002 -0.001 -0.0 +SEGM 0.0 -2.25 1.125 0.375 0.0 -0.003 +DENS -0.006 -0.002 -0.001 -0.0 +SEGM -1.0 3.75 1.0 0.5 135.0 -0.003 +DENS -0.006 -0.002 -0.001 0.0 +SEGM 1.0 3.75 1.0 0.5 225.0 -0.003 +DENS -0.006 -0.002 -0.001 0.0 +ELIP 0.675 -0.75 0.225 0.15 140.0 0.025 +DENS 0.016 0.01 0.008 0.008 +ELIP 0.75 1.5 0.375 0.225 50.0 0.005 +DENS 0.004 0.004 0.006 0.005 +TRIA 5.025 3.75 1.125 0.5 110.75 0.737 +DENS 0.475 0.291 0.118 0.029 +TRIA -5.025 3.75 1.125 0.5 -110.75 0.737 +DENS 0.475 0.291 0.118 0.029 +LAST 1.0 +PHANTOM AVERAGE 1 +23 0.77 +RAYSUM AVERAGE 3 +1 1 1 +GEOMETRY +DIVERGENT ARC 78.0 110.0 +RAYS USER 159 0.213 +ANGLE 1 +0.0 +MEASUREMENT NOISY +QUANTUM 10000000.0 360.0 CALIBRATION 2 +SCATTER 0.24 0.4445 +SEED 1 +BACKGROUND 0.0 0.0 0.0 0.0 0.0 +RUN +END diff --git a/examples/b3/b3r.out b/examples/b3/b3r.out new file mode 100644 index 0000000..3c024a1 --- /dev/null +++ b/examples/b3/b3r.out @@ -0,0 +1,148 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> EXAMPLE 3 + + <*> CREATION OF HEAD PHANTOM. GENERATION OF POLYCHROMATIC + + <*> PROJECTION DATA. + + <*> + + <*> CREATE A PHANTOM + + <*> GENERATE PROJECTION DATA + + <#> CREATE + + EXAMPLE 3 HEAD PHANTOM + + + <#> SPECTRUM POLYCHROMATIC 5 + + energy spectrum is polychromatic with 5 energy levels + with the following photon distribution + energy level percent + 40 10 + 50 30 + 60 30 + 80 20 + 100 10 + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 40 50 60 80 100 + + + 1 segm 1.3750 -7.5000 1.1000 0.6250 19.2000 -0.3275 -0.7340 -0.4720 -0.2880 -0.1160 -0.0290 + + + 2 segm 1.3750 -7.5000 1.1000 4.3200 19.2100 0.3275 0.7340 0.4720 0.2880 0.1160 0.0290 + + + 3 elip 0.0000 0.0000 8.6250 6.4687 90.0000 0.5400 1.0000 0.7000 0.5000 0.3000 0.2000 + + + 4 elip 0.0000 0.0000 7.8750 5.7187 90.0000 -0.3300 -0.7370 -0.4750 -0.2910 -0.1180 -0.0290 + + + 5 elip 0.0000 1.5000 0.3750 0.3000 90.0000 -0.0029 -0.0030 -0.0060 -0.0020 -0.0010 -0.0000 + + + 6 segm 0.0000 -2.2500 1.1250 0.3750 0.0000 -0.0029 -0.0030 -0.0060 -0.0020 -0.0010 -0.0000 + + + 7 segm -1.0000 3.7500 1.0000 0.5000 135.0000 -0.0029 -0.0030 -0.0060 -0.0020 -0.0010 0.0000 + + + 8 segm 1.0000 3.7500 1.0000 0.5000 225.0000 -0.0029 -0.0030 -0.0060 -0.0020 -0.0010 0.0000 + + + 9 elip 0.6750 -0.7500 0.2250 0.1500 140.0000 0.0127 0.0250 0.0160 0.0100 0.0080 0.0080 + + + 10 elip 0.7500 1.5000 0.3750 0.2250 50.0000 0.0046 0.0050 0.0040 0.0040 0.0060 0.0050 + + + 11 tria 5.0250 3.7500 1.1250 0.5000 110.7500 0.3300 0.7370 0.4750 0.2910 0.1180 0.0290 + + + 12 tria -5.0250 3.7500 1.1250 0.5000 -110.7500 0.3300 0.7370 0.4750 0.2910 0.1180 0.0290 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 1 + + this run will generate a phantom + density in each pixel is obtained as the average of 1 x 1 points + + + <#> 23 0.77 + picture size 23 x 23, pixel size 0.7700 + + + <#> RAYSUM AVERAGE 3 + + this run will generate projection data + projection data are calculated by dividing each ray interval into 3 substrips + + with aperture (substrip) weights 1 1 1 + + + <#> GEOMETRY + + + <#> DIVERGENT ARC 78.0 110.0 + rays are divergent from point sources + source to origin distance 78.0000 + the detectors lie on an arc with source to detector distance = 110.0000 + + + <#> RAYS USER 159 0.213 + number of rays per projection 159 + at detector spacing 0.2130 + + + <#> ANGLE 1 + total number of projections 1 + + projection angles 0.0000 + + + <#> MEASUREMENT NOISY + noise characteristics of projection data follow + nature characteristics + + <#> QUANTUM 10000000.0 360.0 CALIBRATION 2 + quantum mean number of photons in actual measurement 1.0000e+07 + mean number of photons in calibration measurement is 360.0000 times above + calibration is constant over all projections for any single ray + mean numbers of photons entering each substrip are + 3.3333e+06 3.3333e+06 3.3333e+06 + + <#> SCATTER 0.24 0.4445 + scatter the fraction scattered in line is 0.2400 + scatter extends to a distance of 0.4445 + dying linearly from the middle + + <#> SEED 1 + seed for random number generator is 1 + + + <#> BACKGROUND 0.0 0.0 0.0 0.0 0.0 + at levels + 40 50 60 80 100 + background absorption 0.0000 0.0000 0.0000 0.0000 0.0000 + + + <#> RUN + 0.001 seconds phantom creation + 0.000 seconds projection data creation + 0.002 seconds used for processing command crea + + + <#> END diff --git a/examples/b3/run b/examples/b3/run new file mode 100755 index 0000000..464de06 --- /dev/null +++ b/examples/b3/run @@ -0,0 +1 @@ +snark14 b3.in diff --git a/examples/b4/b4.in b/examples/b4/b4.in new file mode 100644 index 0000000..f43e8e6 --- /dev/null +++ b/examples/b4/b4.in @@ -0,0 +1,46 @@ +********EXAMPLE 4 +* STAR PATTERN WITH PSEUDO PROJECTION DATA +* RECONSTRUCTION BY ART +* +CREATE +EXAMPLE 4 STAR PATTERN +SPECTRUM MONOCHROMATIC 10 +OBJECTS +SECT 0.0 -24.0 6.0 24.0 0.0 1.0 +SECT 21.0 -12.0 6.0 24.0 60.0 1.0 +SECT 21.0 12.0 6.0 24.0 120.0 1.0 +SECT 0.0 24.0 6.0 24.0 180.0 1.0 +SECT -21.0 12.0 6.0 24.0 240.0 1.0 +SECT -21.0 -12.0 6.0 24.0 300.0 1.0 +LAST 1.0 +PHANTOM AVERAGE 1 +25 PIXELS OF SIZE 2.0 +RAYSUM +* +PICTURE TEST +* +PROJECTION PSEUDO +EXAMPLE 4 PSEUDO PROJECTION DATA FOR TWELVE VIEWS +GEOMETRY +PARALLEL VARIABLE STRIP +RAYS PROGRAM 25 2.0 DETECTOR SPACING AT 2.0 +ANGLES 12 EQUALLY SPACED +0.0 165.0 +MEASUREMENT PERFECT +BACKGROUND 50.0 +* +MODE LOWER CONSTRAINT IS SET TO 0.0 UPPER CONSTRAINT IS 1.0 +* +SELECT SNARK RAYSEQ +STEP 3 1 +* +STOP ITERATION 9 +* +EXECUTE ART CONTOUR +EXAMPLE 4 ART RECONSTRUCTION +0.5 0.0 1.0 +1 +ART3 +CONSTRAINT BOUND STEPS 204 +* +END diff --git a/examples/b4/b4r.out b/examples/b4/b4r.out new file mode 100644 index 0000000..e520f3e --- /dev/null +++ b/examples/b4/b4r.out @@ -0,0 +1,243 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> *******EXAMPLE 4 + + <*> STAR PATTERN WITH PSEUDO PROJECTION DATA + + <*> RECONSTRUCTION BY ART + + <*> + + <#> CREATE + + EXAMPLE 4 STAR PATTERN + + + <#> SPECTRUM MONOCHROMATIC 10 + energy spectrum is monochromatic at energy level 10 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 1 + + this run will generate a phantom + density in each pixel is obtained as the average of 1 x 1 points + + + <#> 25 PIXELS OF SIZE 2.0 + picture size 25 x 25, pixel size 2.0000 + + + <#> RAYSUM + + 0.000 seconds phantom creation + 0.000 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 4 STAR PATTERN + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 1 + + density in each pixel is obtained as the average of 1 x 1 points + + + <#> pixe 25 size 2.0000 + picture size 25 x 25, pixel size 2.0000 + + test picture read + EXAMPLE 4 STAR PATTERN + 0.000 seconds used for processing command pict + + + <*> + + <#> PROJECTION PSEUDO + + EXAMPLE 4 PSEUDO PROJECTION DATA FOR TWELVE VIEWS + + + + <#> GEOMETRY + + + <#> PARALLEL VARIABLE STRIP + rays are parallel with variable spacing between rays + data collected along strips + + + + <#> RAYS PROGRAM 25 2.0 DETECTOR SPACING AT 2.0 + number of rays per projection 53 + snark computed number of rays 53 + at detector spacing 2.0000 + + + <#> ANGLES 12 EQUALLY SPACED + total number of projections 12 + + projection angles 0.0000 15.0000 30.0000 45.0000 60.0000 75.0000 90.0000 105.0000 120.0000 135.0000 + 150.0000 165.0000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 50.0 + at levels + 10 + background absorption 50.0000 + + estimate of totlen = 16985.417500 + estimate of totden = 6066.137812 + estimate of average density = 0.3571 + projection data read + EXAMPLE 4 PSEUDO PROJECTION DATA FOR TWELVE VIEWS + 0.000 seconds used for processing command proj + + + <*> + + <#> MODE LOWER CONSTRAINT IS SET TO 0.0 UPPER CONSTRAINT IS 1.0 + lower constraint set to 0.0000 + upper constraint set to 1.0000 + 0.000 seconds used for processing command mode + + + <*> + + <#> SELECT SNARK RAYSEQ + + <#> STEP 3 1 + sequential ray selection with ray-step 1 and projection-step 3 + 0.000 seconds used for processing command sele + + + <*> + + <#> STOP ITERATION 9 + 9 iterations + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE ART CONTOUR + + EXAMPLE 4 ART RECONSTRUCTION + + <#> 0.5 0.0 1.0 + reconstruction is contoured after + + last iteration + + threshold = 0.50000 w1 = 0.00000 w2 = 1.00000 w3 = 0.00000 + + <#> ART3 + art3 method + relaxation parameter is 1.0 + norm is 2 + tolerance is 0.0 + + <#> CONSTRAINT BOUND STEPS 204 + constraint set to boundaries + picture is not normalized + 204 rays are used for each iteration + lower constraint = 0.0000 + upper constraint = 1.0000 + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iteration 2 completed + 0.000 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iteration 3 completed + 0.000 seconds for this iteration + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.000 seconds for this iteration + algorithm executed in iteration 5 + 0.000 seconds for the execution of the algorithm + iteration 5 completed + 0.000 seconds for this iteration + algorithm executed in iteration 6 + 0.000 seconds for the execution of the algorithm + iteration 6 completed + 0.000 seconds for this iteration + algorithm executed in iteration 7 + 0.000 seconds for the execution of the algorithm + iteration 7 completed + 0.000 seconds for this iteration + algorithm executed in iteration 8 + 0.000 seconds for the execution of the algorithm + iteration 8 completed + 0.000 seconds for this iteration + algorithm executed in iteration 9 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 9 + 0.000 seconds for this iteration + 0.001 seconds for all iterations + 0.002 seconds used for processing command exec + + + <*> + + <#> END diff --git a/examples/b4/run b/examples/b4/run new file mode 100755 index 0000000..49bb488 --- /dev/null +++ b/examples/b4/run @@ -0,0 +1 @@ +snark14 b4.in diff --git a/examples/b5/b5.in b/examples/b5/b5.in new file mode 100644 index 0000000..0b2a1d1 --- /dev/null +++ b/examples/b5/b5.in @@ -0,0 +1,75 @@ +*EXAMPLE 5 +*STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS +*RECONSTRUCTION BY ALL APPROPRIATE ALGORITHMS WITH DEFAULT +*OR EASY OPTIONS. +* +CREATE +EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS +SPECTRUM MONOCHROMATIC 10 +OBJECTS +SECT 0.0 -24.0 6.0 24.0 0.0 1.0 +SECT 21.0 -12.0 6.0 24.0 60.0 1.0 +SECT 21.0 12.0 6.0 24.0 120.0 1.0 +SECT 0.0 24.0 6.0 24.0 180.0 1.0 +SECT -21.0 12.0 6.0 24.0 240.0 1.0 +SECT -21.0 -12.0 6.0 24.0 300.0 1.0 +LAST 1.0 +PHANTOM AVERAGE 5 +25 PIXELS OF SIZE 2.0 +RAYSUM AVERAGE 1 +1 +GEOMETRY +PARALLEL UNIFORM STRIP +RAYS USER 25 DETECTOR SPACING 2.0 +ANGLES 24 EQUAL SPACING +0.0 172.5 +MEASUREMENT PERFECT +BACKGROUND 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +EXECUTE BACKPROJECTION +EXAMPLE 5A CONTINUOUS BACKPROJECTION WITH LINEAR INTERPOLATION +CONTINUOUS 2 MULTIPLICATIVE +* +EXECUTE CONVOLUTION +EXAMPLE 5B CONVOLUTION WITH BANDLIMITING FILTER & LINEAR INTERPOLATION +BANDLIMITING 1.0 2 +* +EXECUTE RFL +EXAMPLE 5C RHO FILTERED LAYERGRAM WITH BANDLIMITING FILTER & LINEAR INTERPOLATION +BANDLIMITING 1.0 2 +* +EXECUTE FOURIER +EXAMPLE 5D FOURIER WITH BANDLIMITING FILTER & LINEAR INTERPOLATION +BANDLIMITING 1.0 3 +* +STOP TERMINATION VARIANCE = 0.1 +* +EXECUTE ART +EXAMPLE 5F ART WITH NO TRICKS +ART3 +CONSTRAINT ART2 STEPS 888 +* +EXECUTE MART +EXAMPLE 5G MULTIPLICATIVE ART A LA LENT +METHOD LENT 888 1.0 0.0 +* +EXECUTE QUADRATIC +EXAMPLE 5H OPTIMIZATION OF LEAST SQUARES FUNCTIONAL USING CONJUGATE +3 3 1 0 1 0.1 0.0 0.0 +1 1 1 0 0 0 1.0 0.1 0 +* +EXECUTE SIRT +EXAMPLE 5I GENERALIZED SIMULTANEOUS ITERATIVE RECONSTRUCTION TECHNOLOGY +METHOD GSIRT +* +EVALUATE +EXAMPLE 5 RECONSTRUCTION OF STAR PATTERN FROM PARALLEL PROJECTIONS +WHOLEPIC +111111111111 +* +END diff --git a/examples/b5/b5r.out b/examples/b5/b5r.out new file mode 100644 index 0000000..92855b2 --- /dev/null +++ b/examples/b5/b5r.out @@ -0,0 +1,503 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> EXAMPLE 5 + + <*> STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + + <*> RECONSTRUCTION BY ALL APPROPRIATE ALGORITHMS WITH DEFAULT + + <*> OR EASY OPTIONS. + + <*> + + <#> CREATE + + EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + + + <#> SPECTRUM MONOCHROMATIC 10 + energy spectrum is monochromatic at energy level 10 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 5 + + this run will generate a phantom + density in each pixel is obtained as the average of 5 x 5 points + + + <#> 25 PIXELS OF SIZE 2.0 + picture size 25 x 25, pixel size 2.0000 + + + <#> 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 + + + <#> PARALLEL UNIFORM STRIP + rays are parallel with uniform spacing between rays + data collected along strips + + + + <#> RAYS USER 25 DETECTOR SPACING 2.0 + number of rays per projection 25 + at detector spacing 2.0000 + + + <#> ANGLES 24 EQUAL SPACING + total number of projections 24 + + projection angles 0.0000 7.5000 15.0000 22.5000 30.0000 37.5000 45.0000 52.5000 60.0000 67.5000 + 75.0000 82.5000 90.0000 97.5000 105.0000 112.5000 120.0000 127.5000 135.0000 142.5000 + 150.0000 157.5000 165.0000 172.5000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 0.0 + at levels + 10 + background absorption 0.0000 + + + <#> RUN + 0.000 seconds phantom creation + 0.000 seconds projection data creation + 0.000 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 5 + + density in each pixel is obtained as the average of 5 x 5 points + + + <#> pixe 25 size 2.0000 + picture size 25 x 25, pixel size 2.0000 + + test picture read + EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + 0.003 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> rays aver 1 + + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> geom + + + <#> para unif stri + rays are parallel with uniform spacing between rays + data collected along strips + + + + <#> rays user 25 spacing 2.0000 + number of rays per projection 25 + snark computed number of rays 37 + at detector spacing 2.0000 + + + <#> angl 24 + total number of projections 24 + + + projection angles 0.0000 7.5000 15.0000 22.5000 30.0000 37.5000 45.0000 52.5000 60.0000 67.5000 + 75.0000 82.5000 90.0000 97.5000 105.0000 112.5000 120.0000 127.5000 135.0000 142.5000 + 150.0000 157.5000 165.0000 172.5000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 10 + background absorption 0.0000 + + estimate of totlen = 28263.966195 + estimate of totden = 10749.116539 + estimate of average density = 0.3803 + projection data read + EXAMPLE 5 STAR PATTERN WITH 24 PARALLEL STRIP PROJECTIONS + 0.000 seconds used for processing command proj + + + <*> + + <#> EXECUTE BACKPROJECTION + + EXAMPLE 5A CONTINUOUS BACKPROJECTION WITH LINEAR INTERPOLATION + + <#> CONTINUOUS 2 MULTIPLICATIVE + continuous back-projection + 2 order lagrange interpolation + multiplicative normalization + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.000 seconds for this iteration + 0.000 seconds used for processing command exec + + + <*> + + <#> EXECUTE CONVOLUTION + + EXAMPLE 5B CONVOLUTION WITH BANDLIMITING FILTER & LINEAR INTERPOLATION + + <#> BANDLIMITING 1.0 2 + convolution reconstruction algorithm + using filter band + cutoff (or alpha) = 1.0000 + 2 point lagrange interpolation + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.000 seconds for this iteration + 0.004 seconds used for processing command exec + + + <*> + + <#> EXECUTE RFL + + EXAMPLE 5C RHO FILTERED LAYERGRAM WITH BANDLIMITING FILTER & LINEAR INTERPOLATIO + + <#> BANDLIMITING 1.0 2 + rho-filtered layergram reconstruction algorithm + using filter band + cutoff (or alpha) = 1.0000 + 2 point lagrange interpolation + backprojection is performed on a 26 x 26 region + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.000 seconds for this iteration + 0.000 seconds used for processing command exec + + + <*> + + <#> EXECUTE FOURIER + + EXAMPLE 5D FOURIER WITH BANDLIMITING FILTER & LINEAR INTERPOLATION +f o u r i e r r e c o n s t r u c t i o n + +strip projections + + <#> BANDLIMITING 1.0 3 +filter= 0 +cutoff= 1.00 +interp= 3 +nsize1= 38 +nsize2= 26 +time for projection transforms : 0.000 seconds +time for interpolations : 0.000 seconds +time for backtransform : 0.000 seconds + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.000 seconds for this iteration + 0.000 seconds used for processing command exec + + + <*> + + <#> STOP TERMINATION VARIANCE = 0.1 + termination test vari + epsilon = 0.100000 + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE ART + + EXAMPLE 5F ART WITH NO TRICKS + + <#> ART3 + art3 method + relaxation parameter is 1.0 + norm is 2 + tolerance is 0.0 + + <#> CONSTRAINT ART2 STEPS 888 + constraint art2 way + picture is not normalized + 888 rays are used for each iteration + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + iteration 1 completed + 0.000 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iteration 2 completed + 0.000 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iterative process stops at iteration 3 + the change in variance is less than 0.006869 of the variance + reconstruction completed after iteration 3 + 0.000 seconds for this iteration + 0.000 seconds for all iterations + 0.004 seconds used for processing command exec + + + <*> + + <#> EXECUTE MART + + EXAMPLE 5G MULTIPLICATIVE ART A LA LENT + + <#> METHOD LENT 888 1.0 0.0 + multiplicative art version lent + no of rays used in each iteration 888 + underrelaxation factor 1.00000 + all projection data with values less than 1.0000000000e-20 are ignored + reconstruction not normalized + entropy functional not calculated + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + iteration 1 completed + 0.000 seconds for this iteration + algorithm executed in iteration 2 + 0.004 seconds for the execution of the algorithm + iterative process stops at iteration 2 + the change in variance is less than 0.009779 of the variance + reconstruction completed after iteration 2 + 0.004 seconds for this iteration + 0.004 seconds for all iterations + 0.007 seconds used for processing command exec + + + <*> + + <#> EXECUTE QUADRATIC + + EXAMPLE 5H OPTIMIZATION OF LEAST SQUARES FUNCTIONAL USING CONJUGATE + + <#> 3 3 1 0 1 0.1 0.0 0.0 + + <#> 1 1 1 0 0 0 1.0 0.1 0 + the conjugate gradient algorithm + + direct gradient computation + ================================= + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + iteration 1 completed + 0.000 seconds for this iteration + algorithm executed in iteration 2 + 0.003 seconds for the execution of the algorithm + iteration 2 completed + 0.003 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iteration 3 completed + 0.000 seconds for this iteration + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.000 seconds for this iteration + algorithm executed in iteration 5 + 0.004 seconds for the execution of the algorithm + iterative process stops at iteration 5 + the change in variance is less than 0.095803 of the variance + reconstruction completed after iteration 5 + 0.004 seconds for this iteration + 0.007 seconds for all iterations + 0.007 seconds used for processing command exec + + + <*> + + <#> EXECUTE SIRT + + EXAMPLE 5I GENERALIZED SIMULTANEOUS ITERATIVE RECONSTRUCTION TECHNOLOGY + user rays selected + + <#> METHOD GSIRT + gsirt method + sigma = inverse of relaxation = 1.0000 + + this run is unconstrained sirt + this run is unnormalized sirt + starting picture is as in execute command + algorithm executed in iteration 1 + 0.003 seconds for the execution of the algorithm + iteration 1 completed + 0.003 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iteration 2 completed + 0.000 seconds for this iteration + algorithm executed in iteration 3 + 0.000 seconds for the execution of the algorithm + iteration 3 completed + 0.000 seconds for this iteration + algorithm executed in iteration 4 + 0.000 seconds for the execution of the algorithm + iteration 4 completed + 0.000 seconds for this iteration + algorithm executed in iteration 5 + 0.000 seconds for the execution of the algorithm + iteration 5 completed + 0.000 seconds for this iteration + algorithm executed in iteration 6 + 0.002 seconds for the execution of the algorithm + iteration 6 completed + 0.002 seconds for this iteration + algorithm executed in iteration 7 + 0.000 seconds for the execution of the algorithm + iteration 7 completed + 0.000 seconds for this iteration + algorithm executed in iteration 8 + 0.000 seconds for the execution of the algorithm + iteration 8 completed + 0.000 seconds for this iteration + algorithm executed in iteration 9 + 0.000 seconds for the execution of the algorithm + iteration 9 completed + 0.000 seconds for this iteration + algorithm executed in iteration 10 + 0.000 seconds for the execution of the algorithm + iteration 10 completed + 0.000 seconds for this iteration + algorithm executed in iteration 11 + 0.002 seconds for the execution of the algorithm + iteration 11 completed + 0.002 seconds for this iteration + algorithm executed in iteration 12 + 0.000 seconds for the execution of the algorithm + iterative process stops at iteration 12 + the change in variance is less than 0.086811 of the variance + reconstruction completed after iteration 12 + 0.000 seconds for this iteration + 0.008 seconds for all iterations + 0.008 seconds used for processing command exec + + + <*> + + <#> EVALUATE + + EXAMPLE 5 RECONSTRUCTION OF STAR PATTERN FROM PARALLEL PROJECTIONS + + <#> WHOLEPIC + Region cx cy u v ang t1 t2 + + wholepic -1e+20 1e+20 + + iterations 1 2 3 4 5 6 7 8 9 10 + 11 + last iteration + + 0.003 seconds used for processing command eval + + + <*> + + <#> END diff --git a/examples/b5/run b/examples/b5/run new file mode 100755 index 0000000..527f75c --- /dev/null +++ b/examples/b5/run @@ -0,0 +1 @@ +snark14 b5.in diff --git a/examples/b6/b6.in b/examples/b6/b6.in new file mode 100644 index 0000000..7fccbbc --- /dev/null +++ b/examples/b6/b6.in @@ -0,0 +1,60 @@ +*EXAMPLE 6 +*STAR PATTERN WITH 24 DIVERGENT PROJECTIONS +*RECONSTRUCTION BY ALL APPROPRIATE ALGORITHMS WITH DEFAULT +*OR EASY OPTIONS. +* +CREATE +EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS +SPECTRUM MONOCHROMATIC 10 +OBJECTS +SECT 0.0 -24.0 6.0 24.0 0.0 1.0 +SECT 21.0 -12.0 6.0 24.0 60.0 1.0 +SECT 21.0 12.0 6.0 24.0 120.0 1.0 +SECT 0.0 24.0 6.0 24.0 180.0 1.0 +SECT -21.0 12.0 6.0 24.0 240.0 1.0 +SECT -21.0 -12.0 6.0 24.0 300.0 1.0 +LAST 1.0 +PHANTOM AVERAGE 5 +25 PIXELS OF SIZE 2.0 +RAYSUM AVERAGE 1 + 1 +GEOMETRY +DIVERGENT ARC 40.0 40.0 +RAYS PROGRAM 25 2.0 DETECTOR SPACING 2.0 +ANGLES 24 EQUAL SPACING +0.0 345.0 +MEASUREMENT PERFECT +BACKGROUND 0.0 +RUN +* +PICTURE TEST +* +PROJECTION REAL +* +EXECUTE DCONV +EXAMPLE 6A DIVERGENT BEAM CONVOLUTION WITH BANDLIMITING FILTER +2 1 25 1.0 0 +BANDLIMITING +* +STOP TERMINATION VARIANCE = 0.1 +* +EXECUTE ART +EXAMPLE 6C ART WITH NO TRICKS +ART3 +CONSTRAINT ART2 +* +EXECUTE MART +EXAMPLE 6D MULTIPLICATIVE ART A LA LENT +METHOD LENT 0 1.0 0.0 +* +EXECUTE QUADRATIC +EXAMPLE 6E OPTIMIZATION OF LEAST SQUARES FUNCTIONAL USING CONJUGATE GRADIENT +3 3 1 0 1 0.1 0.0 0.0 +1 1 1 0 0 0 1.0 0.1 0 +* +EVALUATE +EXAMPLE 6 RECONSTRUCTION OF STAR PATTERN FROM DIVERGENT PROJECTIONS +WHOLEPIC +11111111111111 +* +END diff --git a/examples/b6/b6r.out b/examples/b6/b6r.out new file mode 100644 index 0000000..4c6f51e --- /dev/null +++ b/examples/b6/b6r.out @@ -0,0 +1,379 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> EXAMPLE 6 + + <*> STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + + <*> RECONSTRUCTION BY ALL APPROPRIATE ALGORITHMS WITH DEFAULT + + <*> OR EASY OPTIONS. + + <*> + + <#> CREATE + + EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + + + <#> SPECTRUM MONOCHROMATIC 10 + energy spectrum is monochromatic at energy level 10 + + + <#> OBJECTS + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> PHANTOM AVERAGE 5 + + this run will generate a phantom + density in each pixel is obtained as the average of 5 x 5 points + + + <#> 25 PIXELS OF SIZE 2.0 + picture size 25 x 25, pixel size 2.0000 + + + <#> 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 40.0 40.0 + rays are divergent from point sources + source to origin distance 40.0000 + the detectors lie on an arc with source to detector distance = 40.0000 + + + <#> RAYS PROGRAM 25 2.0 DETECTOR SPACING 2.0 + number of rays per projection 45 + at detector spacing 2.0000 + + + <#> ANGLES 24 EQUAL SPACING + total number of projections 24 + + projection angles 0.0000 15.0000 30.0000 45.0000 60.0000 75.0000 90.0000 105.0000 120.0000 135.0000 + 150.0000 165.0000 180.0000 195.0000 210.0000 225.0000 240.0000 255.0000 270.0000 285.0000 + 300.0000 315.0000 330.0000 345.0000 + + + <#> MEASUREMENT PERFECT + projection data are noiseless + + + <#> BACKGROUND 0.0 + at levels + 10 + background absorption 0.0000 + + + <#> RUN + 0.000 seconds phantom creation + 0.000 seconds projection data creation + 0.000 seconds used for processing command crea + + + <*> + + <#> PICTURE TEST + + EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 5 + + density in each pixel is obtained as the average of 5 x 5 points + + + <#> pixe 25 size 2.0000 + picture size 25 x 25, pixel size 2.0000 + + test picture read + EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + 0.002 seconds used for processing command pict + + + <*> + + <#> PROJECTION REAL + + EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + + + <#> spec mono 10 + energy spectrum is monochromatic at energy level 10 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 10 + + 1 sect 0.0000 -24.0000 6.0000 24.0000 0.0000 1.0000 1.0000 + + 2 sect 21.0000 -12.0000 6.0000 24.0000 60.0000 1.0000 1.0000 + + 3 sect 21.0000 12.0000 6.0000 24.0000 120.0000 1.0000 1.0000 + + 4 sect 0.0000 24.0000 6.0000 24.0000 180.0000 1.0000 1.0000 + + 5 sect -21.0000 12.0000 6.0000 24.0000 240.0000 1.0000 1.0000 + + 6 sect -21.0000 -12.0000 6.0000 24.0000 300.0000 1.0000 1.0000 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> 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 40.0000 det dist 40.0000 + rays are divergent from point sources + source to origin distance 40.0000 + the detectors lie on an arc with source to detector distance = 40.0000 + + + <#> rays user 45 spacing 2.0000 + number of rays per projection 45 + snark computed number of rays 45 + at detector spacing 2.0000 + + + <#> angl 24 + total number of projections 24 + + + projection angles 0.0000 15.0000 30.0000 45.0000 60.0000 75.0000 90.0000 105.0000 120.0000 135.0000 + 150.0000 165.0000 180.0000 195.0000 210.0000 225.0000 240.0000 255.0000 270.0000 285.0000 + 300.0000 315.0000 330.0000 345.0000 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 10 + background absorption 0.0000 + + estimate of totlen = 32578.803295 + estimate of totden = 11270.139500 + estimate of average density = 0.3459 + projection data read + EXAMPLE 6 STAR PATTERN WITH 24 DIVERGENT PROJECTIONS + 0.000 seconds used for processing command proj + + + <*> + + <#> EXECUTE DCONV + + EXAMPLE 6A DIVERGENT BEAM CONVOLUTION WITH BANDLIMITING FILTER + + <#> 2 1 25 1.0 0 + 2 point lagrange interpolation + one out of every 1 projection(s) used for reconstruction + 25 points used on each side of convolution + pre-smoothing weight on center ray = 1.0000 + pre-smoothing weight on side rays = 0.0000 + accurate back-projection + + <#> BANDLIMITING + band-limiting filter + total time for obtaining smoothed projection data was 0.000 + total time for convoluting projection data was 0.000 + total time for back-projecting was 0.000 + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.000 seconds for this iteration + 0.002 seconds used for processing command exec + + + <*> + + <#> STOP TERMINATION VARIANCE = 0.1 + termination test vari + epsilon = 0.100000 + 0.000 seconds used for processing command stop + + + <*> + + <#> EXECUTE ART + + EXAMPLE 6C ART WITH NO TRICKS + + <#> ART3 + art3 method + relaxation parameter is 1.0 + norm is 2 + tolerance is 0.0 + + <#> CONSTRAINT ART2 + constraint art2 way + relaxation constraints with cr = 1.0 + picture is not normalized + 1080 rays are used for each iteration + algorithm executed in iteration 1 + 0.000 seconds for the execution of the algorithm + iteration 1 completed + 0.000 seconds for this iteration + algorithm executed in iteration 2 + 0.000 seconds for the execution of the algorithm + iterative process stops at iteration 2 + the change in variance is less than 0.041353 of the variance + reconstruction completed after iteration 2 + 0.000 seconds for this iteration + 0.000 seconds for all iterations + 0.002 seconds used for processing command exec + + + <*> + + <#> EXECUTE MART + + EXAMPLE 6D MULTIPLICATIVE ART A LA LENT + + <#> METHOD LENT 0 1.0 0.0 + multiplicative art version lent + no of rays used in each iteration 1080 + underrelaxation factor 1.00000 + all projection data with values less than 1.0000000000e-20 are ignored + reconstruction not normalized + entropy functional not calculated + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.001 seconds for the execution of the algorithm + iterative process stops at iteration 2 + the change in variance is less than 0.026757 of the variance + reconstruction completed after iteration 2 + 0.001 seconds for this iteration + 0.001 seconds for all iterations + 0.002 seconds used for processing command exec + + + <*> + + <#> EXECUTE QUADRATIC + + EXAMPLE 6E OPTIMIZATION OF LEAST SQUARES FUNCTIONAL USING CONJUGATE GRADIENT + + <#> 3 3 1 0 1 0.1 0.0 0.0 + + <#> 1 1 1 0 0 0 1.0 0.1 0 + the conjugate gradient algorithm + + direct gradient computation + ================================= + algorithm executed in iteration 1 + 0.001 seconds for the execution of the algorithm + iteration 1 completed + 0.001 seconds for this iteration + algorithm executed in iteration 2 + 0.002 seconds for the execution of the algorithm + iteration 2 completed + 0.002 seconds for this iteration + algorithm executed in iteration 3 + 0.001 seconds for the execution of the algorithm + iteration 3 completed + 0.001 seconds for this iteration + algorithm executed in iteration 4 + 0.001 seconds for the execution of the algorithm + iteration 4 completed + 0.001 seconds for this iteration + algorithm executed in iteration 5 + 0.002 seconds for the execution of the algorithm + iterative process stops at iteration 5 + the change in variance is less than 0.046725 of the variance + reconstruction completed after iteration 5 + 0.002 seconds for this iteration + 0.005 seconds for all iterations + 0.006 seconds used for processing command exec + + + <*> + + <#> EVALUATE + + EXAMPLE 6 RECONSTRUCTION OF STAR PATTERN FROM DIVERGENT PROJECTIONS + + <#> WHOLEPIC + Region cx cy u v ang t1 t2 + + wholepic -1e+20 1e+20 + + iterations 1 2 3 4 5 6 7 8 9 10 + 11 12 13 + last iteration + + 0.002 seconds used for processing command eval + + + <*> + + <#> END diff --git a/examples/b6/run b/examples/b6/run new file mode 100755 index 0000000..cc90d6f --- /dev/null +++ b/examples/b6/run @@ -0,0 +1 @@ +snark14 b6.in diff --git a/examples/b7/b7.in b/examples/b7/b7.in new file mode 100644 index 0000000..cf9b982 --- /dev/null +++ b/examples/b7/b7.in @@ -0,0 +1,64 @@ +********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 NOISY +QUANTUM 1.0 1.0 CALIBRATION 4 +SEED 0 +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/b7/b7r.out b/examples/b7/b7r.out new file mode 100644 index 0000000..fec9182 --- /dev/null +++ b/examples/b7/b7r.out @@ -0,0 +1,534 @@ + 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/b7/run b/examples/b7/run new file mode 100755 index 0000000..01e9eb9 --- /dev/null +++ b/examples/b7/run @@ -0,0 +1 @@ +snark14 b7.in diff --git a/examples/b8/b8.in b/examples/b8/b8.in new file mode 100644 index 0000000..204979e --- /dev/null +++ b/examples/b8/b8.in @@ -0,0 +1,43 @@ +********* EXAMPLE 8 +* RECONSTRUCTION OF HEAD PHANTOM USING LINOGRAM AND FILTERED +* BACKPROJECTION METHODS. SINC FILTER FOR LINOGRAM AND COSINE +* FILTER FOR FBP. +* +create +EXAMPLE 8 LINOGRAM RECONSTRUCTION +spectrum monochromatic 75 +objects cx cy u v ang den +elip 0.000 0.000 8.625 6.4687 90.00 0.416 +elip 0.000 0.000 7.875 5.7187 90.00 -0.206 +elip 0.000 1.500 0.375 0.3000 90.00 -0.003 +elip 0.675 -0.750 0.225 0.1500 140.00 0.010 +elip 0.750 1.500 0.375 0.2250 50.00 0.003 +segm 1.375 -7.500 1.100 0.6250 19.20 -0.204 +segm 1.375 -7.500 1.100 4.3200 19.21 0.204 +segm 0.000 -2.250 1.125 0.3750 0.00 -0.003 +segm 0.000 -2.250 1.125 3.0000 0.00 0.003 +segm -1.000 3.750 1.000 0.5000 135.00 -0.003 +segm -1.000 3.750 1.000 3.0000 135.00 0.003 +segm 1.000 3.750 1.000 0.5000 225.00 -0.003 +segm 1.000 3.750 1.000 3.0000 225.00 0.003 +tria 5.025 3.750 1.125 0.5000 110.75 0.206 +tria -5.025 3.750 1.125 0.9000 -110.75 0.206 +last 1.0 +phantom average 5 +115 0.1504 +raysum average 1 +1 +geometry +linogram +measurement perfect +background absorption is 0.0 +run +picture test +projection real +execute lino +EXAMPLE 8a LINOGRAM METHOD +sinc 1.0 +execute conv +EXAMPLE 8b FILTERED BACKPROJECTION +cosine 1.0 2 +end diff --git a/examples/b8/b8r.out b/examples/b8/b8r.out new file mode 100644 index 0000000..18817fd --- /dev/null +++ b/examples/b8/b8r.out @@ -0,0 +1,386 @@ + snark14.s170426 - A PICTURE RECONSTRUCTION PROGRAM + + + <*> ******** EXAMPLE 8 + + <*> RECONSTRUCTION OF HEAD PHANTOM USING LINOGRAM AND FILTERED + + <*> BACKPROJECTION METHODS. SINC FILTER FOR LINOGRAM AND COSINE + + <*> FILTER FOR FBP. + + <*> + + <#> create + + EXAMPLE 8 LINOGRAM RECONSTRUCTION + + + <#> spectrum monochromatic 75 + energy spectrum is monochromatic at energy level 75 + + + <#> objects cx cy u v ang den + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 8.6250 6.4687 90.0000 0.4160 0.4160 + + 2 elip 0.0000 0.0000 7.8750 5.7187 90.0000 -0.2060 -0.2060 + + 3 elip 0.0000 1.5000 0.3750 0.3000 90.0000 -0.0030 -0.0030 + + 4 elip 0.6750 -0.7500 0.2250 0.1500 140.0000 0.0100 0.0100 + + 5 elip 0.7500 1.5000 0.3750 0.2250 50.0000 0.0030 0.0030 + + 6 segm 1.3750 -7.5000 1.1000 0.6250 19.2000 -0.2040 -0.2040 + + 7 segm 1.3750 -7.5000 1.1000 4.3200 19.2100 0.2040 0.2040 + + 8 segm 0.0000 -2.2500 1.1250 0.3750 0.0000 -0.0030 -0.0030 + + 9 segm 0.0000 -2.2500 1.1250 3.0000 0.0000 0.0030 0.0030 + + 10 segm -1.0000 3.7500 1.0000 0.5000 135.0000 -0.0030 -0.0030 + + 11 segm -1.0000 3.7500 1.0000 3.0000 135.0000 0.0030 0.0030 + + 12 segm 1.0000 3.7500 1.0000 0.5000 225.0000 -0.0030 -0.0030 + + 13 segm 1.0000 3.7500 1.0000 3.0000 225.0000 0.0030 0.0030 + + 14 tria 5.0250 3.7500 1.1250 0.5000 110.7500 0.2060 0.2060 + + 15 tria -5.0250 3.7500 1.1250 0.9000 -110.7500 0.2060 0.2060 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phantom average 5 + + this run will generate a phantom + density in each pixel is obtained as the average of 5 x 5 points + + + <#> 115 0.1504 + picture size 115 x 115, pixel size 0.1504 + + + <#> 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 + + + <#> linogram + rays are parallel with variable spacing between rays + data collected along lines + + + number of rays per projection 231 + at detector spacing 0.1504 + + total number of projections 462 + projection angles 45.1243 45.3745 45.6268 45.8814 46.1382 46.3972 46.6584 46.9220 47.1878 47.4559 + 47.7263 47.9991 48.2742 48.5517 48.8316 49.1140 49.3987 49.6859 49.9756 50.2677 + 50.5623 50.8595 51.1592 51.4614 51.7662 52.0735 52.3835 52.6961 53.0112 53.3290 + 53.6495 53.9726 54.2984 54.6269 54.9581 55.2920 55.6285 55.9679 56.3099 56.6547 + 57.0023 57.3526 57.7057 58.0616 58.4202 58.7816 59.1458 59.5128 59.8826 60.2551 + 60.6305 61.0086 61.3895 61.7733 62.1597 62.5490 62.9410 63.3358 63.7334 64.1336 + 64.5367 64.9424 65.3508 65.7619 66.1757 66.5922 67.0113 67.4330 67.8573 68.2842 + 68.7136 69.1455 69.5800 70.0169 70.4562 70.8980 71.3421 71.7886 72.2373 72.6884 + 73.1416 73.5970 74.0546 74.5143 74.9760 75.4397 75.9054 76.3730 76.8425 77.3137 + 77.7867 78.2614 78.7378 79.2157 79.6952 80.1761 80.6584 81.1420 81.6270 82.1131 + 82.6004 83.0888 83.5782 84.0685 84.5597 85.0517 85.5444 86.0378 86.5318 87.0263 + 87.5212 88.0165 88.5121 89.0080 89.5039 90.0000 90.4961 90.9920 91.4879 91.9835 + 92.4788 92.9737 93.4682 93.9622 94.4556 94.9483 95.4403 95.9315 96.4218 96.9112 + 97.3996 97.8869 98.3730 98.8580 99.3416 99.8239 100.3048 100.7843 101.2622 101.7386 + 102.2133 102.6863 103.1575 103.6270 104.0946 104.5603 105.0240 105.4857 105.9454 106.4030 + 106.8584 107.3116 107.7627 108.2114 108.6579 109.1020 109.5438 109.9831 110.4200 110.8545 + 111.2864 111.7158 112.1427 112.5670 112.9887 113.4078 113.8243 114.2381 114.6492 115.0576 + 115.4633 115.8664 116.2666 116.6642 117.0590 117.4510 117.8403 118.2267 118.6105 118.9914 + 119.3695 119.7449 120.1174 120.4872 120.8542 121.2184 121.5798 121.9384 122.2943 122.6474 + 122.9977 123.3453 123.6901 124.0321 124.3715 124.7080 125.0419 125.3731 125.7016 126.0274 + 126.3505 126.6710 126.9888 127.3039 127.6165 127.9265 128.2338 128.5386 128.8408 129.1405 + 129.4377 129.7323 130.0244 130.3141 130.6013 130.8860 131.1684 131.4483 131.7258 132.0009 + 132.2737 132.5441 132.8122 133.0780 133.3416 133.6028 133.8618 134.1186 134.3732 134.6255 + 134.8757 135.1243 135.3745 135.6268 135.8814 136.1382 136.3972 136.6584 136.9220 137.1878 + 137.4559 137.7263 137.9991 138.2742 138.5517 138.8316 139.1140 139.3987 139.6859 139.9756 + 140.2677 140.5623 140.8595 141.1592 141.4614 141.7662 142.0735 142.3835 142.6961 143.0112 + 143.3290 143.6495 143.9726 144.2984 144.6269 144.9581 145.2920 145.6285 145.9679 146.3099 + 146.6547 147.0023 147.3526 147.7057 148.0616 148.4202 148.7816 149.1458 149.5128 149.8826 + 150.2551 150.6305 151.0086 151.3895 151.7733 152.1597 152.5490 152.9410 153.3358 153.7334 + 154.1336 154.5367 154.9424 155.3508 155.7619 156.1757 156.5922 157.0113 157.4330 157.8573 + 158.2842 158.7136 159.1455 159.5800 160.0169 160.4562 160.8980 161.3421 161.7886 162.2373 + 162.6884 163.1416 163.5970 164.0546 164.5143 164.9760 165.4397 165.9054 166.3730 166.8425 + 167.3137 167.7867 168.2614 168.7378 169.2157 169.6952 170.1761 170.6584 171.1420 171.6270 + 172.1131 172.6004 173.0888 173.5782 174.0685 174.5597 175.0517 175.5444 176.0378 176.5318 + 177.0263 177.5212 178.0165 178.5121 179.0080 179.5039 180.0000 180.4961 180.9920 181.4879 + 181.9835 182.4788 182.9737 183.4682 183.9622 184.4556 184.9483 185.4403 185.9315 186.4218 + 186.9112 187.3996 187.8869 188.3730 188.8580 189.3416 189.8239 190.3048 190.7843 191.2622 + 191.7386 192.2133 192.6863 193.1575 193.6270 194.0946 194.5603 195.0240 195.4857 195.9454 + 196.4030 196.8584 197.3116 197.7627 198.2114 198.6579 199.1020 199.5438 199.9831 200.4200 + 200.8545 201.2864 201.7158 202.1427 202.5670 202.9887 203.4078 203.8243 204.2381 204.6492 + 205.0576 205.4633 205.8664 206.2666 206.6642 207.0590 207.4510 207.8403 208.2267 208.6105 + 208.9914 209.3695 209.7449 210.1174 210.4872 210.8542 211.2184 211.5798 211.9384 212.2943 + 212.6474 212.9977 213.3453 213.6901 214.0321 214.3715 214.7080 215.0419 215.3731 215.7016 + 216.0274 216.3505 216.6710 216.9888 217.3039 217.6165 217.9265 218.2338 218.5386 218.8408 + 219.1405 219.4377 219.7323 220.0244 220.3141 220.6013 220.8860 221.1684 221.4483 221.7258 + 222.0009 222.2737 222.5441 222.8122 223.0780 223.3416 223.6028 223.8618 224.1186 224.3732 + 224.6255 224.8757 + + + <#> measurement perfect + projection data are noiseless + + + <#> background absorption is 0.0 + at levels + 75 + background absorption 0.0000 + + + <#> run + 0.024 seconds phantom creation + 0.109 seconds projection data creation + 0.135 seconds used for processing command crea + + + <#> picture test + + EXAMPLE 8 LINOGRAM RECONSTRUCTION + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 8.6250 6.4687 90.0000 0.4160 0.4160 + + 2 elip 0.0000 0.0000 7.8750 5.7187 90.0000 -0.2060 -0.2060 + + 3 elip 0.0000 1.5000 0.3750 0.3000 90.0000 -0.0030 -0.0030 + + 4 elip 0.6750 -0.7500 0.2250 0.1500 140.0000 0.0100 0.0100 + + 5 elip 0.7500 1.5000 0.3750 0.2250 50.0000 0.0030 0.0030 + + 6 segm 1.3750 -7.5000 1.1000 0.6250 19.2000 -0.2040 -0.2040 + + 7 segm 1.3750 -7.5000 1.1000 4.3200 19.2100 0.2040 0.2040 + + 8 segm 0.0000 -2.2500 1.1250 0.3750 0.0000 -0.0030 -0.0030 + + 9 segm 0.0000 -2.2500 1.1250 3.0000 0.0000 0.0030 0.0030 + + 10 segm -1.0000 3.7500 1.0000 0.5000 135.0000 -0.0030 -0.0030 + + 11 segm -1.0000 3.7500 1.0000 3.0000 135.0000 0.0030 0.0030 + + 12 segm 1.0000 3.7500 1.0000 0.5000 225.0000 -0.0030 -0.0030 + + 13 segm 1.0000 3.7500 1.0000 3.0000 225.0000 0.0030 0.0030 + + 14 tria 5.0250 3.7500 1.1250 0.5000 110.7500 0.2060 0.2060 + + 15 tria -5.0250 3.7500 1.1250 0.9000 -110.7500 0.2060 0.2060 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> phan aver 5 + + density in each pixel is obtained as the average of 5 x 5 points + + + <#> pixe 115 size 0.1504 + picture size 115 x 115, pixel size 0.1504 + + test picture read + EXAMPLE 8 LINOGRAM RECONSTRUCTION + 0.004 seconds used for processing command pict + + + <#> projection real + + EXAMPLE 8 LINOGRAM RECONSTRUCTION + + + <#> spec mono 75 + energy spectrum is monochromatic at energy level 75 + + + <#> obje + description of objects + density at levels + numb type x-coord y-coord x-length y-length angle av dens 75 + + 1 elip 0.0000 0.0000 8.6250 6.4687 90.0000 0.4160 0.4160 + + 2 elip 0.0000 0.0000 7.8750 5.7187 90.0000 -0.2060 -0.2060 + + 3 elip 0.0000 1.5000 0.3750 0.3000 90.0000 -0.0030 -0.0030 + + 4 elip 0.6750 -0.7500 0.2250 0.1500 140.0000 0.0100 0.0100 + + 5 elip 0.7500 1.5000 0.3750 0.2250 50.0000 0.0030 0.0030 + + 6 segm 1.3750 -7.5000 1.1000 0.6250 19.2000 -0.2040 -0.2040 + + 7 segm 1.3750 -7.5000 1.1000 4.3200 19.2100 0.2040 0.2040 + + 8 segm 0.0000 -2.2500 1.1250 0.3750 0.0000 -0.0030 -0.0030 + + 9 segm 0.0000 -2.2500 1.1250 3.0000 0.0000 0.0030 0.0030 + + 10 segm -1.0000 3.7500 1.0000 0.5000 135.0000 -0.0030 -0.0030 + + 11 segm -1.0000 3.7500 1.0000 3.0000 135.0000 0.0030 0.0030 + + 12 segm 1.0000 3.7500 1.0000 0.5000 225.0000 -0.0030 -0.0030 + + 13 segm 1.0000 3.7500 1.0000 3.0000 225.0000 0.0030 0.0030 + + 14 tria 5.0250 3.7500 1.1250 0.5000 110.7500 0.2060 0.2060 + + 15 tria -5.0250 3.7500 1.1250 0.9000 -110.7500 0.2060 0.2060 + + scale factor multiplying object densities 1.0000 + + seed set to 0 + inhomogeneity set to 0.0000 + + <#> rays aver 1 + + projection data are calculated by dividing each ray interval into 1 substrips + + with aperture (substrip) weights 1 + + + <#> geom + + + <#> lino + rays are parallel with variable spacing between rays + data collected along lines + + + number of rays per projection 231 + snark computed number of rays 233 + at detector spacing 0.1504 + + total number of projections 462 + projection angles 45.1243 45.3745 45.6268 45.8814 46.1382 46.3972 46.6584 46.9220 47.1878 47.4559 + 47.7263 47.9991 48.2742 48.5517 48.8316 49.1140 49.3987 49.6859 49.9756 50.2677 + 50.5623 50.8595 51.1592 51.4614 51.7662 52.0735 52.3835 52.6961 53.0112 53.3290 + 53.6495 53.9726 54.2984 54.6269 54.9581 55.2920 55.6285 55.9679 56.3099 56.6547 + 57.0023 57.3526 57.7057 58.0616 58.4202 58.7816 59.1458 59.5128 59.8826 60.2551 + 60.6305 61.0086 61.3895 61.7733 62.1597 62.5490 62.9410 63.3358 63.7334 64.1336 + 64.5367 64.9424 65.3508 65.7619 66.1757 66.5922 67.0113 67.4330 67.8573 68.2842 + 68.7136 69.1455 69.5800 70.0169 70.4562 70.8980 71.3421 71.7886 72.2373 72.6884 + 73.1416 73.5970 74.0546 74.5143 74.9760 75.4397 75.9054 76.3730 76.8425 77.3137 + 77.7867 78.2614 78.7378 79.2157 79.6952 80.1761 80.6584 81.1420 81.6270 82.1131 + 82.6004 83.0888 83.5782 84.0685 84.5597 85.0517 85.5444 86.0378 86.5318 87.0263 + 87.5212 88.0165 88.5121 89.0080 89.5039 90.0000 90.4961 90.9920 91.4879 91.9835 + 92.4788 92.9737 93.4682 93.9622 94.4556 94.9483 95.4403 95.9315 96.4218 96.9112 + 97.3996 97.8869 98.3730 98.8580 99.3416 99.8239 100.3048 100.7843 101.2622 101.7386 + 102.2133 102.6863 103.1575 103.6270 104.0946 104.5603 105.0240 105.4857 105.9454 106.4030 + 106.8584 107.3116 107.7627 108.2114 108.6579 109.1020 109.5438 109.9831 110.4200 110.8545 + 111.2864 111.7158 112.1427 112.5670 112.9887 113.4078 113.8243 114.2381 114.6492 115.0576 + 115.4633 115.8664 116.2666 116.6642 117.0590 117.4510 117.8403 118.2267 118.6105 118.9914 + 119.3695 119.7449 120.1174 120.4872 120.8542 121.2184 121.5798 121.9384 122.2943 122.6474 + 122.9977 123.3453 123.6901 124.0321 124.3715 124.7080 125.0419 125.3731 125.7016 126.0274 + 126.3505 126.6710 126.9888 127.3039 127.6165 127.9265 128.2338 128.5386 128.8408 129.1405 + 129.4377 129.7323 130.0244 130.3141 130.6013 130.8860 131.1684 131.4483 131.7258 132.0009 + 132.2737 132.5441 132.8122 133.0780 133.3416 133.6028 133.8618 134.1186 134.3732 134.6255 + 134.8757 135.1243 135.3745 135.6268 135.8814 136.1382 136.3972 136.6584 136.9220 137.1878 + 137.4559 137.7263 137.9991 138.2742 138.5517 138.8316 139.1140 139.3987 139.6859 139.9756 + 140.2677 140.5623 140.8595 141.1592 141.4614 141.7662 142.0735 142.3835 142.6961 143.0112 + 143.3290 143.6495 143.9726 144.2984 144.6269 144.9581 145.2920 145.6285 145.9679 146.3099 + 146.6547 147.0023 147.3526 147.7057 148.0616 148.4202 148.7816 149.1458 149.5128 149.8826 + 150.2551 150.6305 151.0086 151.3895 151.7733 152.1597 152.5490 152.9410 153.3358 153.7334 + 154.1336 154.5367 154.9424 155.3508 155.7619 156.1757 156.5922 157.0113 157.4330 157.8573 + 158.2842 158.7136 159.1455 159.5800 160.0169 160.4562 160.8980 161.3421 161.7886 162.2373 + 162.6884 163.1416 163.5970 164.0546 164.5143 164.9760 165.4397 165.9054 166.3730 166.8425 + 167.3137 167.7867 168.2614 168.7378 169.2157 169.6952 170.1761 170.6584 171.1420 171.6270 + 172.1131 172.6004 173.0888 173.5782 174.0685 174.5597 175.0517 175.5444 176.0378 176.5318 + 177.0263 177.5212 178.0165 178.5121 179.0080 179.5039 180.0000 180.4961 180.9920 181.4879 + 181.9835 182.4788 182.9737 183.4682 183.9622 184.4556 184.9483 185.4403 185.9315 186.4218 + 186.9112 187.3996 187.8869 188.3730 188.8580 189.3416 189.8239 190.3048 190.7843 191.2622 + 191.7386 192.2133 192.6863 193.1575 193.6270 194.0946 194.5603 195.0240 195.4857 195.9454 + 196.4030 196.8584 197.3116 197.7627 198.2114 198.6579 199.1020 199.5438 199.9831 200.4200 + 200.8545 201.2864 201.7158 202.1427 202.5670 202.9887 203.4078 203.8243 204.2381 204.6492 + 205.0576 205.4633 205.8664 206.2666 206.6642 207.0590 207.4510 207.8403 208.2267 208.6105 + 208.9914 209.3695 209.7449 210.1174 210.4872 210.8542 211.2184 211.5798 211.9384 212.2943 + 212.6474 212.9977 213.3453 213.6901 214.0321 214.3715 214.7080 215.0419 215.3731 215.7016 + 216.0274 216.3505 216.6710 216.9888 217.3039 217.6165 217.9265 218.2338 218.5386 218.8408 + 219.1405 219.4377 219.7323 220.0244 220.3141 220.6013 220.8860 221.1684 221.4483 221.7258 + 222.0009 222.2737 222.5441 222.8122 223.0780 223.3416 223.6028 223.8618 224.1186 224.3732 + 224.6255 224.8757 + + + <#> meas perf + projection data are noiseless + + + <#> back 0.0000 + at levels + 75 + background absorption 0.0000 + + estimate of totlen = 1054747.357766 + estimate of totden = 154874.529107 + estimate of average density = 0.1468 + projection data read + EXAMPLE 8 LINOGRAM RECONSTRUCTION + 0.048 seconds used for processing command proj + + + <#> execute lino + + EXAMPLE 8a LINOGRAM METHOD + + <#> sinc 1.0 + linogram reconstruction algorithm + using filter sinc + cutoff = 1.0000 + algorithm executed in iteration 1 + 0.066 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.066 seconds for this iteration + 0.203 seconds used for processing command exec + + + <#> execute conv + + EXAMPLE 8b FILTERED BACKPROJECTION + + <#> cosine 1.0 2 + convolution reconstruction algorithm + using filter cosi + cutoff (or alpha) = 1.0000 + 2 point lagrange interpolation + algorithm executed in iteration 1 + 0.113 seconds for the execution of the algorithm + reconstruction completed after iteration 1 + 0.113 seconds for this iteration + 0.246 seconds used for processing command exec + + + <#> end diff --git a/examples/b8/run b/examples/b8/run new file mode 100755 index 0000000..f77dc2f --- /dev/null +++ b/examples/b8/run @@ -0,0 +1 @@ +snark14 b8.in diff --git a/examples/b9/b.9.compare.ss b/examples/b9/b.9.compare.ss new file mode 100644 index 0000000..04f00d1 --- /dev/null +++ b/examples/b9/b.9.compare.ss @@ -0,0 +1,9 @@ +testem +COMPARE alg1 alg2 HITR USR1 + 1 1 + 3 3 + 6 6 + 9 9 + 12 12 + 15 15 +END diff --git a/examples/b9/b.9.experimenter.in b/examples/b9/b.9.experimenter.in new file mode 100644 index 0000000..b8837e1 --- /dev/null +++ b/examples/b9/b.9.experimenter.in @@ -0,0 +1,7 @@ +SEED -1 +ENSEMBLE b.9.virus.ens +EXPERIMENT 1 0 95 1.6 7 18 30 +DATA b.9.projection.ss +RECONSTRUCTION b.9.recon.ss +ANALYSIS b.9.compare.ss +END diff --git a/examples/b9/b.9.projection.ss b/examples/b9/b.9.projection.ss new file mode 100644 index 0000000..e1f3894 --- /dev/null +++ b/examples/b9/b.9.projection.ss @@ -0,0 +1,15 @@ +raysum average 1 +1 +geometry +divergent arc 153 306 +rays user 101 detector spacing 3.2 +angles 300 equally spaced +0 358.8 +measurement noisy +quantum 0.0 0.0 calibr 4 +multiplicative 1.0 0.1 +seed +background 0.0 +run +picture test +projection real diff --git a/examples/b9/b.9.recon.ss b/examples/b9/b.9.recon.ss new file mode 100644 index 0000000..23e29fd --- /dev/null +++ b/examples/b9/b.9.recon.ss @@ -0,0 +1,7 @@ +stop iteration 15 +execute average emap +alg1: testing super snark with ML +gamma is 0.0 +execute average emap +alg2: testing super snark with MAP +gamma is 10.0 diff --git a/examples/b9/b.9.virus.ens b/examples/b9/b.9.virus.ens new file mode 100644 index 0000000..5c3ccf2 --- /dev/null +++ b/examples/b9/b.9.virus.ens @@ -0,0 +1,18 @@ +virus_24_1_0.96_0.6.atl +virus_24_1_0.96_0.7.atl +virus_24_1_0.96_0.8.atl +virus_24_1_0.97_0.6.atl +virus_24_1_0.97_0.7.atl +virus_24_1_0.97_0.8.atl +virus_26_1_0.96_0.6.atl +virus_26_1_0.96_0.7.atl +virus_26_1_0.96_0.8.atl +virus_26_1_0.97_0.6.atl +virus_26_1_0.97_0.7.atl +virus_26_1_0.97_0.8.atl +virus_28_1_0.96_0.6.atl +virus_28_1_0.96_0.7.atl +virus_28_1_0.96_0.8.atl +virus_28_1_0.97_0.6.atl +virus_28_1_0.97_0.7.atl +virus_28_1_0.97_0.8.atl diff --git a/examples/b9/b9r.out b/examples/b9/b9r.out new file mode 100644 index 0000000..35ff8d7 --- /dev/null +++ b/examples/b9/b9r.out @@ -0,0 +1,32 @@ +snark14Experimenter.s170426 +experiment 1 +run 1 +run 2 +run 3 +run 4 +run 5 +run 6 +run 7 +run 8 +run 9 +run 10 +run 11 +run 12 +run 13 +run 14 +run 15 +run 16 +run 17 +run 18 +run 19 +run 20 +run 21 +run 22 +run 23 +run 24 +run 25 +run 26 +run 27 +run 28 +run 29 +run 30 diff --git a/examples/b9/bin/.donotdeletedir b/examples/b9/bin/.donotdeletedir new file mode 100644 index 0000000..e69de29 diff --git a/examples/b9/build b/examples/b9/build new file mode 100755 index 0000000..cae628b --- /dev/null +++ b/examples/b9/build @@ -0,0 +1,4 @@ +#!/bin/bash + +cd src +make install diff --git a/examples/b9/run b/examples/b9/run new file mode 100755 index 0000000..b36e754 --- /dev/null +++ b/examples/b9/run @@ -0,0 +1,2 @@ +./build >&2 +./bin/snark14 -e b.9.experimenter.in diff --git a/examples/b9/src/Makefile b/examples/b9/src/Makefile new file mode 100644 index 0000000..d0a1c0f --- /dev/null +++ b/examples/b9/src/Makefile @@ -0,0 +1,69 @@ +# + +ifndef SNARKINCLUDE +SNARKINCLUDE=/usr/local/snark14/src/snark14/snark +endif + +ifndef SNARKLIBDIR +SNARKLIBDIR=/usr/local/snark14/lib +endif + +ifndef SNARKLIBINCLUDEDIR +SNARKLIBINCLUDEDIR=/usr/local/snark14/include +endif + +ifndef DIGFILEINCLUDE +DIGFILEINCLUDE=/usr/local/snark14/include/DIGFile +endif + +ifndef DIGFILESNARKINCLUDE +DIGFILESNARKINCLUDE=/usr/local/snark14/include/DIGFileSnark +endif + +ifndef DIGRANDINCLUDE +DIGRANDINCLUDE=/usr/local/snark14/include/DIGRand +endif + +OUTDIR=../bin + +INCLUDEDIR = -I/usr/include -I$(XERCESINCLUDE)/.. \ +-I$(DIGFILEINCLUDE) -I$(DIGFILESNARKINCLUDE) -I$(DIGRANDINCLUDE) -I$(SNARKINCLUDE) \ +-I$(SNARKLIBINCLUDEDIR) + +OBJ = \ + user_fom1.o + +LIBS= -L$(SNARKLIBDIR) -lsnark14 -lDIGFile -lDIGFileSnark -lDIGRand -lxerces-c -lm + + +#ifndef CC +CC=gcc +#endif + +#ifndef CFLAGS +CFLAGS=-g -std=c99 -D_GNU_SOURCE +#endif + +###################################### +# setings for testing +#LIBS=/usr/lib/libm.a +#FLAGS= -ffloat-store -O0 -DFFCOMPARE +###################################### + +ALL: snark14 + +snark14: $(OBJ) + $(CXX) $(OBJ) $(CXXFLAGS) -o snark14 $(LIBS) + +clean: + rm -f $(OBJ) + rm -f snark14 + +install: ALL + mv snark14 $(OUTDIR) + +uninstall: + rm -f $(OUTDIR)/snark14 + +%.o: %.c + $(CC) -c -I $(CFLAGS) $(INCLUDEDIR) $< -o $@ diff --git a/examples/b9/src/user_fom1.c b/examples/b9/src/user_fom1.c new file mode 100644 index 0000000..22cc22a --- /dev/null +++ b/examples/b9/src/user_fom1.c @@ -0,0 +1,69 @@ +#include +#include "experimenter.h" +#include "read_eval_phantom1.h" +#include "read_eval_recon3.h" +#include "user_fom1.h" + +/* ----------------------------- user_fom1.c -------------- + + This function illustrates the use of a user-defined figure +of merit. + +INPUTS: + itr1 - array of length niters containing the iteration numbers for the + first algorithm. + itr2 - array of length niters containing the iteration numbers for the + second algorithm. + niters - number of iterations to be compared + keywrd1 - string containing the keyword which defines the first algorithm. + keywrd2 - string containing the keyword which defines the second algorithm. + +OUTPUTS: + user1 - array of length niters containing the user defined figure of + merit for the first algorithm. + user2 - array of length niters containing the user defined figure of + merit for the second algorithm. + +*/ + +void user_fom1(int* itr1, int* itr2, int niters, char* keywrd1, char* keywrd2, double* user1, double* user2) + //int *itr1,*itr2,niters; + //char *keywrd1,*keywrd2; + //double *user1,*user2; +{ + double *phantom,*recon1,*recon2; + int *regions,numstr,i,j,*strarea; + float totarea=0.0,avgarea; + + /* Read in abnormality index and area for phantom structures. + The program which does this is read_eval_phantom1.c. + NOTE: the only information to be used is the value + 'numstr' (which is the number of structures in the phantom) */ + read_eval_phantom1(®ions,&numstr,&phantom,&strarea); + + /* allocate memory to store abnormality indexes and area + (i.e number of pixels) for structures in the + reconstructions */ + recon1 = (double *) malloc(numstr*sizeof(double)); + recon2 = (double *) malloc(numstr*sizeof(double)); + + for(i=0;i < niters;i++) { + /* read in variance for structures in + the reconstructions. Initialize the arrays + which will store the user FOM */ + + //printf("*** about to read variance\n"); /* TEST (JD) */ + read_eval_recon3(itr1[i],keywrd1,numstr,recon1); + read_eval_recon3(itr2[i],keywrd2,numstr,recon2); + /* the varaince of the 'SINGLE' structure to be + used is the first in the array. The FOM value + is 1-variance */ + user1[i]=1-recon1[0]; + user2[i]=1-recon2[0]; + } + + free(phantom); /* free memory for next function call */ + free(recon1); + free(recon2); + free(strarea); +} diff --git a/examples/b9/virus_24_1_0.96_0.6.atl b/examples/b9/virus_24_1_0.96_0.6.atl new file mode 100644 index 0000000..4cb0a96 --- /dev/null +++ b/examples/b9/virus_24_1_0.96_0.6.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.96 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.96 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.96 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.96 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.96 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.96 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.96 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.96 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.96 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.96 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.96 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.96 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.96 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.96 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.96 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.96 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.96 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.96 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.96 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.96 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.96 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.96 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.96 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.96 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.6 +SCALE +1 diff --git a/examples/b9/virus_24_1_0.96_0.7.atl b/examples/b9/virus_24_1_0.96_0.7.atl new file mode 100644 index 0000000..054fa1f --- /dev/null +++ b/examples/b9/virus_24_1_0.96_0.7.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.96 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.96 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.96 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.96 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.96 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.96 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.96 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.96 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.96 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.96 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.96 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.96 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.96 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.96 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.96 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.96 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.96 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.96 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.96 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.96 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.96 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.96 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.96 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.96 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.7 +SCALE +1 diff --git a/examples/b9/virus_24_1_0.96_0.8.atl b/examples/b9/virus_24_1_0.96_0.8.atl new file mode 100644 index 0000000..9c9132a --- /dev/null +++ b/examples/b9/virus_24_1_0.96_0.8.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.96 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.96 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.96 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.96 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.96 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.96 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.96 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.96 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.96 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.96 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.96 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.96 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.96 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.96 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.96 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.96 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.96 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.96 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.96 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.96 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.96 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.96 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.96 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.96 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.8 +SCALE +1 diff --git a/examples/b9/virus_24_1_0.97_0.6.atl b/examples/b9/virus_24_1_0.97_0.6.atl new file mode 100644 index 0000000..48d1cc6 --- /dev/null +++ b/examples/b9/virus_24_1_0.97_0.6.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.97 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.97 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.97 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.97 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.97 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.97 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.97 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.97 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.97 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.97 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.97 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.97 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.97 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.97 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.97 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.97 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.97 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.97 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.97 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.97 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.97 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.97 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.97 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.97 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.6 +SCALE +1 diff --git a/examples/b9/virus_24_1_0.97_0.7.atl b/examples/b9/virus_24_1_0.97_0.7.atl new file mode 100644 index 0000000..f208f60 --- /dev/null +++ b/examples/b9/virus_24_1_0.97_0.7.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.97 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.97 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.97 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.97 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.97 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.97 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.97 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.97 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.97 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.97 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.97 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.97 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.97 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.97 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.97 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.97 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.97 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.97 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.97 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.97 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.97 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.97 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.97 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.97 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.7 +SCALE +1 diff --git a/examples/b9/virus_24_1_0.97_0.8.atl b/examples/b9/virus_24_1_0.97_0.8.atl new file mode 100644 index 0000000..752506b --- /dev/null +++ b/examples/b9/virus_24_1_0.97_0.8.atl @@ -0,0 +1,32 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 29.72 29.72 0 0 +PAIR +elip 4.14 63.19 3.89 3.89 0 1 0.97 0.5 +elip 12.36 62.11 3.89 3.89 0 1 0.97 0.5 +elip 20.36 59.97 3.89 3.89 0 1 0.97 0.5 +elip 28.01 56.80 3.89 3.89 0 1 0.97 0.5 +elip 35.18 52.66 3.89 3.89 0 1 0.97 0.5 +elip 41.76 47.61 3.89 3.89 0 1 0.97 0.5 +elip 47.61 41.76 3.89 3.89 0 1 0.97 0.5 +elip 52.66 35.18 3.89 3.89 0 1 0.97 0.5 +elip 56.80 28.01 3.89 3.89 0 1 0.97 0.5 +elip 59.97 20.36 3.89 3.89 0 1 0.97 0.5 +elip 62.11 12.36 3.89 3.89 0 1 0.97 0.5 +elip 63.19 4.14 3.89 3.89 0 1 0.97 0.5 +elip 63.19 -4.14 3.89 3.89 0 1 0.97 0.5 +elip 62.11 -12.36 3.89 3.89 0 1 0.97 0.5 +elip 59.97 -20.36 3.89 3.89 0 1 0.97 0.5 +elip 56.80 -28.01 3.89 3.89 0 1 0.97 0.5 +elip 52.66 -35.18 3.89 3.89 0 1 0.97 0.5 +elip 47.61 -41.76 3.89 3.89 0 1 0.97 0.5 +elip 41.76 -47.61 3.89 3.89 0 1 0.97 0.5 +elip 35.18 -52.66 3.89 3.89 0 1 0.97 0.5 +elip 28.01 -56.80 3.89 3.89 0 1 0.97 0.5 +elip 20.36 -59.97 3.89 3.89 0 1 0.97 0.5 +elip 12.36 -62.11 3.89 3.89 0 1 0.97 0.5 +elip 4.14 -63.19 3.89 3.89 0 1 0.97 0.5 +DUMMY +elip 0 0 59.44 59.44 0 0.8 +SCALE +1 diff --git a/examples/b9/virus_26_1_0.96_0.6.atl b/examples/b9/virus_26_1_0.96_0.6.atl new file mode 100644 index 0000000..428df0b --- /dev/null +++ b/examples/b9/virus_26_1_0.96_0.6.atl @@ -0,0 +1,34 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.20 30.20 0 0 +PAIR +elip 3.87 63.93 3.65 3.65 0 1 0.96 0.5 +elip 11.55 63.00 3.65 3.65 0 1 0.96 0.5 +elip 19.06 61.15 3.65 3.65 0 1 0.96 0.5 +elip 26.29 58.41 3.65 3.65 0 1 0.96 0.5 +elip 33.14 54.81 3.65 3.65 0 1 0.96 0.5 +elip 39.50 50.42 3.65 3.65 0 1 0.96 0.5 +elip 45.29 45.29 3.65 3.65 0 1 0.96 0.5 +elip 50.42 39.50 3.65 3.65 0 1 0.96 0.5 +elip 54.81 33.14 3.65 3.65 0 1 0.96 0.5 +elip 58.41 26.29 3.65 3.65 0 1 0.96 0.5 +elip 61.15 19.06 3.65 3.65 0 1 0.96 0.5 +elip 63.00 11.55 3.65 3.65 0 1 0.96 0.5 +elip 63.93 3.87 3.65 3.65 0 1 0.96 0.5 +elip 63.93 -3.87 3.65 3.65 0 1 0.96 0.5 +elip 63.00 -11.55 3.65 3.65 0 1 0.96 0.5 +elip 61.15 -19.06 3.65 3.65 0 1 0.96 0.5 +elip 58.41 -26.29 3.65 3.65 0 1 0.96 0.5 +elip 54.81 -33.14 3.65 3.65 0 1 0.96 0.5 +elip 50.42 -39.50 3.65 3.65 0 1 0.96 0.5 +elip 45.29 -45.29 3.65 3.65 0 1 0.96 0.5 +elip 39.50 -50.42 3.65 3.65 0 1 0.96 0.5 +elip 33.14 -54.81 3.65 3.65 0 1 0.96 0.5 +elip 26.29 -58.41 3.65 3.65 0 1 0.96 0.5 +elip 19.06 -61.15 3.65 3.65 0 1 0.96 0.5 +elip 11.55 -63.00 3.65 3.65 0 1 0.96 0.5 +elip 3.87 -63.93 3.65 3.65 0 1 0.96 0.5 +DUMMY +elip 0 0 60.40 60.40 0 0.6 +SCALE +1 diff --git a/examples/b9/virus_26_1_0.96_0.7.atl b/examples/b9/virus_26_1_0.96_0.7.atl new file mode 100644 index 0000000..b32d26e --- /dev/null +++ b/examples/b9/virus_26_1_0.96_0.7.atl @@ -0,0 +1,34 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.20 30.20 0 0 +PAIR +elip 3.87 63.93 3.65 3.65 0 1 0.96 0.5 +elip 11.55 63.00 3.65 3.65 0 1 0.96 0.5 +elip 19.06 61.15 3.65 3.65 0 1 0.96 0.5 +elip 26.29 58.41 3.65 3.65 0 1 0.96 0.5 +elip 33.14 54.81 3.65 3.65 0 1 0.96 0.5 +elip 39.50 50.42 3.65 3.65 0 1 0.96 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3.65 0 1 0.97 0.5 +DUMMY +elip 0 0 60.40 60.40 0 0.7 +SCALE +1 diff --git a/examples/b9/virus_26_1_0.97_0.8.atl b/examples/b9/virus_26_1_0.97_0.8.atl new file mode 100644 index 0000000..93bfed6 --- /dev/null +++ b/examples/b9/virus_26_1_0.97_0.8.atl @@ -0,0 +1,34 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.20 30.20 0 0 +PAIR +elip 3.87 63.93 3.65 3.65 0 1 0.97 0.5 +elip 11.55 63.00 3.65 3.65 0 1 0.97 0.5 +elip 19.06 61.15 3.65 3.65 0 1 0.97 0.5 +elip 26.29 58.41 3.65 3.65 0 1 0.97 0.5 +elip 33.14 54.81 3.65 3.65 0 1 0.97 0.5 +elip 39.50 50.42 3.65 3.65 0 1 0.97 0.5 +elip 45.29 45.29 3.65 3.65 0 1 0.97 0.5 +elip 50.42 39.50 3.65 3.65 0 1 0.97 0.5 +elip 54.81 33.14 3.65 3.65 0 1 0.97 0.5 +elip 58.41 26.29 3.65 3.65 0 1 0.97 0.5 +elip 61.15 19.06 3.65 3.65 0 1 0.97 0.5 +elip 63.00 11.55 3.65 3.65 0 1 0.97 0.5 +elip 63.93 3.87 3.65 3.65 0 1 0.97 0.5 +elip 63.93 -3.87 3.65 3.65 0 1 0.97 0.5 +elip 63.00 -11.55 3.65 3.65 0 1 0.97 0.5 +elip 61.15 -19.06 3.65 3.65 0 1 0.97 0.5 +elip 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3.44 3.44 0 1 0.96 0.5 +elip 52.76 37.43 3.44 3.44 0 1 0.96 0.5 +elip 56.62 31.29 3.44 3.44 0 1 0.96 0.5 +elip 59.77 24.76 3.44 3.44 0 1 0.96 0.5 +elip 62.16 17.91 3.44 3.44 0 1 0.96 0.5 +elip 63.78 10.84 3.44 3.44 0 1 0.96 0.5 +elip 64.59 3.63 3.44 3.44 0 1 0.96 0.5 +elip 64.59 -3.63 3.44 3.44 0 1 0.96 0.5 +elip 63.78 -10.84 3.44 3.44 0 1 0.96 0.5 +elip 62.16 -17.91 3.44 3.44 0 1 0.96 0.5 +elip 59.77 -24.76 3.44 3.44 0 1 0.96 0.5 +elip 56.62 -31.29 3.44 3.44 0 1 0.96 0.5 +elip 52.76 -37.43 3.44 3.44 0 1 0.96 0.5 +elip 48.24 -43.11 3.44 3.44 0 1 0.96 0.5 +elip 43.11 -48.24 3.44 3.44 0 1 0.96 0.5 +elip 37.43 -52.76 3.44 3.44 0 1 0.96 0.5 +elip 31.29 -56.62 3.44 3.44 0 1 0.96 0.5 +elip 24.76 -59.77 3.44 3.44 0 1 0.96 0.5 +elip 17.91 -62.16 3.44 3.44 0 1 0.96 0.5 +elip 10.84 -63.78 3.44 3.44 0 1 0.96 0.5 +elip 3.63 -64.59 3.44 3.44 0 1 0.96 0.5 +DUMMY +elip 0 0 61.25 61.25 0 0.8 +SCALE +1 diff --git a/examples/b9/virus_28_1_0.97_0.6.atl b/examples/b9/virus_28_1_0.97_0.6.atl new file mode 100644 index 0000000..e6357a4 --- /dev/null +++ b/examples/b9/virus_28_1_0.97_0.6.atl @@ -0,0 +1,36 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.63 30.63 0 0 +PAIR +elip 3.63 64.59 3.44 3.44 0 1 0.97 0.5 +elip 10.84 63.78 3.44 3.44 0 1 0.97 0.5 +elip 17.91 62.16 3.44 3.44 0 1 0.97 0.5 +elip 24.76 59.77 3.44 3.44 0 1 0.97 0.5 +elip 31.29 56.62 3.44 3.44 0 1 0.97 0.5 +elip 37.43 52.76 3.44 3.44 0 1 0.97 0.5 +elip 43.11 48.24 3.44 3.44 0 1 0.97 0.5 +elip 48.24 43.11 3.44 3.44 0 1 0.97 0.5 +elip 52.76 37.43 3.44 3.44 0 1 0.97 0.5 +elip 56.62 31.29 3.44 3.44 0 1 0.97 0.5 +elip 59.77 24.76 3.44 3.44 0 1 0.97 0.5 +elip 62.16 17.91 3.44 3.44 0 1 0.97 0.5 +elip 63.78 10.84 3.44 3.44 0 1 0.97 0.5 +elip 64.59 3.63 3.44 3.44 0 1 0.97 0.5 +elip 64.59 -3.63 3.44 3.44 0 1 0.97 0.5 +elip 63.78 -10.84 3.44 3.44 0 1 0.97 0.5 +elip 62.16 -17.91 3.44 3.44 0 1 0.97 0.5 +elip 59.77 -24.76 3.44 3.44 0 1 0.97 0.5 +elip 56.62 -31.29 3.44 3.44 0 1 0.97 0.5 +elip 52.76 -37.43 3.44 3.44 0 1 0.97 0.5 +elip 48.24 -43.11 3.44 3.44 0 1 0.97 0.5 +elip 43.11 -48.24 3.44 3.44 0 1 0.97 0.5 +elip 37.43 -52.76 3.44 3.44 0 1 0.97 0.5 +elip 31.29 -56.62 3.44 3.44 0 1 0.97 0.5 +elip 24.76 -59.77 3.44 3.44 0 1 0.97 0.5 +elip 17.91 -62.16 3.44 3.44 0 1 0.97 0.5 +elip 10.84 -63.78 3.44 3.44 0 1 0.97 0.5 +elip 3.63 -64.59 3.44 3.44 0 1 0.97 0.5 +DUMMY +elip 0 0 61.25 61.25 0 0.6 +SCALE +1 diff --git a/examples/b9/virus_28_1_0.97_0.7.atl b/examples/b9/virus_28_1_0.97_0.7.atl new file mode 100644 index 0000000..78daddf --- /dev/null +++ b/examples/b9/virus_28_1_0.97_0.7.atl @@ -0,0 +1,36 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.63 30.63 0 0 +PAIR +elip 3.63 64.59 3.44 3.44 0 1 0.97 0.5 +elip 10.84 63.78 3.44 3.44 0 1 0.97 0.5 +elip 17.91 62.16 3.44 3.44 0 1 0.97 0.5 +elip 24.76 59.77 3.44 3.44 0 1 0.97 0.5 +elip 31.29 56.62 3.44 3.44 0 1 0.97 0.5 +elip 37.43 52.76 3.44 3.44 0 1 0.97 0.5 +elip 43.11 48.24 3.44 3.44 0 1 0.97 0.5 +elip 48.24 43.11 3.44 3.44 0 1 0.97 0.5 +elip 52.76 37.43 3.44 3.44 0 1 0.97 0.5 +elip 56.62 31.29 3.44 3.44 0 1 0.97 0.5 +elip 59.77 24.76 3.44 3.44 0 1 0.97 0.5 +elip 62.16 17.91 3.44 3.44 0 1 0.97 0.5 +elip 63.78 10.84 3.44 3.44 0 1 0.97 0.5 +elip 64.59 3.63 3.44 3.44 0 1 0.97 0.5 +elip 64.59 -3.63 3.44 3.44 0 1 0.97 0.5 +elip 63.78 -10.84 3.44 3.44 0 1 0.97 0.5 +elip 62.16 -17.91 3.44 3.44 0 1 0.97 0.5 +elip 59.77 -24.76 3.44 3.44 0 1 0.97 0.5 +elip 56.62 -31.29 3.44 3.44 0 1 0.97 0.5 +elip 52.76 -37.43 3.44 3.44 0 1 0.97 0.5 +elip 48.24 -43.11 3.44 3.44 0 1 0.97 0.5 +elip 43.11 -48.24 3.44 3.44 0 1 0.97 0.5 +elip 37.43 -52.76 3.44 3.44 0 1 0.97 0.5 +elip 31.29 -56.62 3.44 3.44 0 1 0.97 0.5 +elip 24.76 -59.77 3.44 3.44 0 1 0.97 0.5 +elip 17.91 -62.16 3.44 3.44 0 1 0.97 0.5 +elip 10.84 -63.78 3.44 3.44 0 1 0.97 0.5 +elip 3.63 -64.59 3.44 3.44 0 1 0.97 0.5 +DUMMY +elip 0 0 61.25 61.25 0 0.7 +SCALE +1 diff --git a/examples/b9/virus_28_1_0.97_0.8.atl b/examples/b9/virus_28_1_0.97_0.8.atl new file mode 100644 index 0000000..0193e5a --- /dev/null +++ b/examples/b9/virus_28_1_0.97_0.8.atl @@ -0,0 +1,36 @@ +SPECTRUM MONOCHROMATIC 60 +SINGLE +elip 0 0 30.63 30.63 0 0 +PAIR +elip 3.63 64.59 3.44 3.44 0 1 0.97 0.5 +elip 10.84 63.78 3.44 3.44 0 1 0.97 0.5 +elip 17.91 62.16 3.44 3.44 0 1 0.97 0.5 +elip 24.76 59.77 3.44 3.44 0 1 0.97 0.5 +elip 31.29 56.62 3.44 3.44 0 1 0.97 0.5 +elip 37.43 52.76 3.44 3.44 0 1 0.97 0.5 +elip 43.11 48.24 3.44 3.44 0 1 0.97 0.5 +elip 48.24 43.11 3.44 3.44 0 1 0.97 0.5 +elip 52.76 37.43 3.44 3.44 0 1 0.97 0.5 +elip 56.62 31.29 3.44 3.44 0 1 0.97 0.5 +elip 59.77 24.76 3.44 3.44 0 1 0.97 0.5 +elip 62.16 17.91 3.44 3.44 0 1 0.97 0.5 +elip 63.78 10.84 3.44 3.44 0 1 0.97 0.5 +elip 64.59 3.63 3.44 3.44 0 1 0.97 0.5 +elip 64.59 -3.63 3.44 3.44 0 1 0.97 0.5 +elip 63.78 -10.84 3.44 3.44 0 1 0.97 0.5 +elip 62.16 -17.91 3.44 3.44 0 1 0.97 0.5 +elip 59.77 -24.76 3.44 3.44 0 1 0.97 0.5 +elip 56.62 -31.29 3.44 3.44 0 1 0.97 0.5 +elip 52.76 -37.43 3.44 3.44 0 1 0.97 0.5 +elip 48.24 -43.11 3.44 3.44 0 1 0.97 0.5 +elip 43.11 -48.24 3.44 3.44 0 1 0.97 0.5 +elip 37.43 -52.76 3.44 3.44 0 1 0.97 0.5 +elip 31.29 -56.62 3.44 3.44 0 1 0.97 0.5 +elip 24.76 -59.77 3.44 3.44 0 1 0.97 0.5 +elip 17.91 -62.16 3.44 3.44 0 1 0.97 0.5 +elip 10.84 -63.78 3.44 3.44 0 1 0.97 0.5 +elip 3.63 -64.59 3.44 3.44 0 1 0.97 0.5 +DUMMY +elip 0 0 61.25 61.25 0 0.8 +SCALE +1 diff --git a/examples/regression b/examples/regression new file mode 100755 index 0000000..281ebe7 --- /dev/null +++ b/examples/regression @@ -0,0 +1,15 @@ +#!/bin/bash +for i in `seq 1 11`; +do + echo Computing the diff for example b"$i". + cd b"$i" + if [ `diff -b -B -I '[0-9*.0-9*].*second.*' -I "time for" -I "A PICTURE RECONSTRUCTION" -I "snark14Experimenter" b"$i"r.out b"$i".out | wc -l` == 0 ] + then + echo "No differences found." + else + echo "Some differences were found, you can examine them below." + echo " " + diff -b -B -I '[0-9*.0-9*].*second.*' -I "time for" -I "A PICTURE RECONSTRUCTION" -I "snark14Experimenter" b"$i"r.out b"$i".out | more + fi + cd .. +done diff --git a/examples/run_all b/examples/run_all new file mode 100755 index 0000000..713c9a7 --- /dev/null +++ b/examples/run_all @@ -0,0 +1,19 @@ +#!/bin/bash +#now need to modify run scripts in examples directory +echo "Running all ten examples. This may take a few minutes." +for i in 1 3 4 5 6 7 8 10 11; + do + cd b$i + snark14 b"$i".in > b"$i".out + cd .. +done + +cd b2 +./build +./bin/snark14UserDefined b2.in > b2.out +cd .. + +cd b9 +./build +./bin/snark14 -e b.9.experimenter.in > b9.out +cd .. -- 2.34.1