PTS User Manual v100 - Simon Fraser University
Contents
1. define photon density pos downstream of collimating hole 00 00 00 00 00 00 0 009000 0 00 00 00 00 00 00 00 00 0 009500 0 00 00 00 00 00 00 00 00 0 010000 0 00 00 00 00 00 00 00 00 0 010500 0 00 00 00 00 00 00 00 00 0 011000 0 00 00 00 00 00 00 00 00 0 011500 0 00 00 00 00 00 00 00 00 0 012000 0 00 00 00 00 00 00 00 00 0 012500 type PLANAR type of density map shptype RECTANGLE type of shape for object 1 0000000 1 0000000 10 2710010 point 0 1 0000000 1 0000000 10 2710010 point 1 2 1 0000000 1 0000000 10 2710010 point p3 1 0000000 1 0000000 10 2710010 normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length m 0 if planar row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index col HASH PHOTPOSX 0 000150 0 000150 0 000005 column index 0 000150 0 000115 idxrow idxcol 0 000120 000090 000060 000030 000000 000030 000060 000090 000120 data 00 0 0 0 0 000085 000055 000025 000005 000035 000065 000095 000125 0 00 00 point 32. center for circle 2 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 surface normal 0 000145 0 000140 0 000110 0 000105 0 000080 0 000075 0 000050 0 000045 0 000020 0 000015 0 000010 0 000015 0 000040 0 000045 0 000070 0 000075 0 000100 0 000105 0 000130 0 000135 0 00 0 00 0 00 0 00 123 id of density 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 000135 0 000100 000070 000040 000010 000020 000050 000080 000110 000140 0 00 00 OOOO OGO 0 0 0 0 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00
3. 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 oooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo o 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oooo oOooooooo ooooooo oOooooooo 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00
4. 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 0 0 007500 007000 006500 006000 005500 005000 004500 004000
5. 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 O OG QOO OG QOO Oo oo CE 0 6X3 r4 Oo 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 Ooo O OO OO XO c 0 0 Oc 00 00
6. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 OTO O GO 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00
7. 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 COO Coco COO QUO OG C OO O0 OL OO OUO C Cx 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00
8. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 ooooo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0
9. 0 009000 205 0 705 006000 003000 000000 003000 006000 009000 012000 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 012000 0 008500 0 0 0 OOOO oF 005500 002500 000500 003500 006500 009500 012500 0 00 00 00 00 00 00 00 90 7 8 0 00 00 00 00 00 00 00 00 77 98 0 00 00 00 00 00 00 00 90 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 point 0 point 1 point 2 point 3 oOoooococ oOoooococ oOoooococ 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 surface normal 0 if planar row indexl HASH PHOTPOSY 0 012500 0 012500 0 000500 row index idxcol col HASH PHOTPOSX 0 012500 0 012500 0 000500 column index 0 012500 0 011500 0 008000 0 0 0 012500 012000 011500 011000 010500 005000 002000 001000 004000 007000
10. 25 Test Case 4 Comparison of Quasi Ballistic to Ballistic Photons for a Single Scattering Medium with a Collimating Hole essei eiie seien seien nana natnra nn 26 Test Case 5 A Point Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes 30 Test Case 6 A Uniform Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes 34 PROGRAM THEORY AND STRUCTURE 36 HINTS AND gie ie 36 APPENDIX A STANDARD SETUP INPUT FILE FOR ALL TEST CASES 37 APPENDIX B TEST CASE 1 INPUT 39 APPENDIX C TEST CASE 1 OUTPUT 41 APPENDIX D TEST CASE 2 INPUT FILE 4 eren 46 APPENDIX E TEST CASE 2 OUTPUT FILE eese nennen nnne nnne nnne nnn 48 APPENDIX F TEST CASE INPUT 53 APPENDIX TEST CASE 3 OUTPUT FILE 55 APPENDIX TEST CASE 4 INPUT nennen nnne nnn nnn nn 60 APPENDIX TEST CASE 4 OUTPUT 63
11. 010500 010000 009500 009000 008500 008000 010000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 119 010500 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 011000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00
12. 0 012500 0 012500 0 000500 column index 0 012000 0 idxcol 0 009500 006500 003500 000500 002500 005500 0 012500 0 009000 0 006000 0 003000 0 000000 0 003000 0 006000 9 0 0 00 008500 0 00 350 00 365 00 384 00 368 00 334 00 0 00 009000 0 00 240 00 380 00 395 00 375 00 368 00 0 00 009500 0 00 0 00 387 00 404 00 367 00 359 00 1 00 010000 0 00 0 00 344 00 390 00 357 00 231 00 0 00 010500 0 00 0 00 376 00 374 00 368 00 2 00 0 00 011000 0 00 0 00 196 00 403 00 397 00 0 00 0 00 011500 3 00 0 00 0 00 341 00 164 00 2 00 0 00 012000 0 00 00 00 00 00 00 00 CX oe 012500 0 008500 0 005500 0 002500 0 000500 0 003500 0 006500 0 00 349 00 397 00 375 00 364 00 412 00 381 00 353 00 409 00 352 00 391 00 0 00 0 00 159 00 357 00 375 00 380 00 361 00 0 00 0 00 2 00 304 00 364 00 375 00 40 00 0 00 0 00 0 00 381 00 382 00 356 00 0 00 0 00 324 00 355 00 377 00 1 00 0 00 0 00 0 00 0 00 368 00 63 00 0 00 0 00 0 00 00 00 00 00 00 00 MP OO Ww gt id of density map center for circle 2 surface normal 011500 0 008000 0 005000 0 002000 0 001000 0 004000 0 007000 118 0 011000 0 007500 0 004500 0 001500 0 001500 0 004500 0 007500 0 00 337 00 362 00 365 00 405 0
13. 003500 003000 002500 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 120 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 0
14. z coords of second point p2 11 10 261 x 2 coords of third point 1 1 10 261 z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator hole 1 hole medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100 0 10 261 x z coords of first point pl 0 000100 0 000025 10 261 x z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 2 hole medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium 0 0 10 261 z coords of first point pl 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 3 hole medium for collimator downstream of sample 1 factor of medium mean cosine of forward scatter
15. 0 0 01125 10 012 z coords of second point p3 0 0 10 004 x y z coords of fourth point cutting plane normalvector 0 0 1 normal vector of cut surface plano side on right Medium define a scattering and absorbing medium lens semisphere shape id converging lens g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 2 index of refraction shptype SEMISPHERE shape of medium p000 9 9755 x y z coords of first point pl 0 0 2485 9 9755 x z coords of second point 0 0 10 2235 x y z coords of fourth point normalvector 0 0 1 normal vector of cut surface plano side on left Medium define a scattering and absorbing medium id slit blocking medium blocking medium for slit upstream of sample g 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 10 25 x y z coords of first point pl 1 1 10 25 x y 2 coords of second point 2 11 10 25 x y 2 coords of third point p3 1 1 10 25 x y z coords of fourth point extrudelen 0005 extrusion length of box Medium define a scattering and absorbing medium id slit opening medium blocking medium for slit upstream of sample g 1 g factor of medium mean cosine of forward scattering
16. 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 006000 006500 007000 007500 008000 008500 009000 009500 010000 010500 011000 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 90 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00
17. 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 97 00 00 00 00 00 00 00 00 0 000025 00 00 00 00 00 00 00 00 0 000020 00 00 00 00 00 00 00 00 0 000015 00 00 00 00 00 00 00 00 0 000010 00 00 00 00
18. AW 11 00 6 00 6 00 1 00 0 00 16 00 16 00 13 00 5 00 2 00 5 00 3 00 10 00 8 00 14 00 11 00 2 00 2 00 2 00 9 00 9 00 10 00 1 00 2 00 6 00 2 00 13 00 8 00 17 00 5 00 5 00 3 00 2 00 13 00 2 00 5 00 6 00 2 00 3 00 0 00 4 00 7 00 5 00 5 00 2 00 4 00 5 00 4 00 0 00 5 00 3 00 2 00 7 00 9 00 2 00 7 00 3 00 8 00 21 00 1 00 8 00 3 00 9 00 7 00 X 20 00 9 00 00 00 00 00 00 N 7 00 9 00 00 00 00 00 00 awhe 00 00 00 00 00 00 00 N 3 00 6 00 5 00 1 00 8 00 22 00 3 00 6 00 4 00 7 00 8 00 6 00 2 00 5 00 M OQ NN 4 00 6 00 15 00 13 00 23 00 17 00 11 00 20 00 2 00 3 00 9 00 5 00 8 00 24 00 9 00 2 00 15 00 9 00 1 00 7 00 5 00 19 00 8 00 9 00 9 00 11 00 20 00 10 00 4 00 23 00 21 00 20 00 4 00 9 00 1 00 0 00 8 00 14 00 1 00 16 00 00 00 00 00 00 4 00 00 00 00 00 00 00 00 17 00 6 00 1 00 0 00 1 00 14 00 23 00 23 00 9 00 3 00 6 00 14 00 15 00 21 00 5 00 8 00 dnb gt 5 00 00 2 00 6 00 16 00 2 00 8 00 3 00 6 00 3 00 9 00 20 00 3 00 2 00 11 00 16 00 3 00 9 00 16 00 9 00 4 00 9 00 20 00 0 00 15 00 25 00 0 19 00 7 00 14 00 3 00 7 00 1 00 3 00 23 00 4 00 17 00 6 00 21 00 4 00 3 00 7 00 2
19. 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 125 e O Oo QUO PO cO GO cO C 00 00 0 000005 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 00 0 0 00 00 00 00 000000 000005 000010 000015 000020 000025 000030 000035 000040 0 OOo UO OO Og 0F 0 0 0 OG O
20. 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 83 eoo oto CIC ao 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00
21. followed by three values representing the x and lt absolute coordinates of the point In the sample medium defined above point is 1 1 0 010001 A circle shape is defined by two or three co planar points and optionally Point is the center of the circle and point is a point on the circumference of the circle If the surface normal vector is specified using the normalvector token then no additional points are required If the surface normal vector is not specified then point lying on the circumference of the circle and not co located with point is needed so that the surface normal vector may be calculated by taking the cross product of the vector from to p with the vector from to Three Dimensional Primitive Shapes semi sphere shape a portion of a sphere with a flat edge is defined by two or three co planar points and optionally p in the same manner a circle Point is the center of the sphere and point is a point on the circumference of the sphere If the surface normal vector to the great circle formed by po and p is specified using the normalvector token then point p is not required If the surface normal vector is not specified then point lying on the circumference of the sphere co planar with and and not co located with point is needed so that the surface normal vector of the great circle formed by points and
22. o OOOO lt lt 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 006000 006500 007000 007500 008000 008500 009000 009500 010000 010500 011000 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 85
23. 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 Appendix Test Case 6 Input File A Uniform Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes Input File testcase6 mci 100 RunInfo comment Test Case 6 N Uniform source with two 45 deg mirrors 10 x beam expander 0 2 mm slit collimating holes and three include stdsetup mci include the standard setup for all test cases random number generator and bounding box Medium define a scattering and absorbing medium id mirror 1 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CIRCLE shape of medium pO 0 10 0
24. 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 8 70 81 70 65 7 65 82 82 68 66 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 1 00 00 00 00 00 00 00 9 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 ooooo oOooooooo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00
25. 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 OOO 0 80 72 72 72 18 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 OO 7 04 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 0 0 0 002000 oOoooococ 001500 001000 86 79 49 73 69 000500 83 81 84 75 61 000000 oOoooococ 000500 001000 001500 002000 002500 003000 00 00 00 0 00 00 00 00 00 00 00
26. 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 001000 001500 002000 002500 003000 003500 004000 004500 005000 005500 006000 oOoooococ oOoooococ 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 94 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00
27. 00 00 0 00 00 TO OOTO 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 b 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 X 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00
28. 00 00 0 00 71 00 0 00 0 00 281 00 0 00 0 00 296 00 0 00 1 00 246 00 0 00 1 00 273 00 0 00 0 00 208 00 0 00 0 00 284 00 0 00 0 00 09 00 0 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 420 00 1252 00 419 00 1021 00 1268 00 1260 00 979 00 396 00 1281 00 371 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 00 00 0 00 1 000000 1 000000 0 020001 point 0 center for circle pl 1 000000 1 000000 0 020001 point 1 p2 1 000000 1 000000 0 020001 point 2 p3 1 000000 1 000000 0 020001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTSCATTERCOUNT 0 000000 50 000000 1 000000 row index idxcol col HASH PHOTPOSRSOURCE 0 000000 0 000050 0 000005 column index 0 000000 0 000005 0 000010 0 000015 0 000020 000030 0 000035 0 000040 0 000045 0 000050 data 4007 00 11867 00 19872 00 28263 00 35906 00 00 0 00 0 00 0 00 0 00 0 000000 N 0 00 13 00 12 00 22 00 48 00 00 0 00 0 00 0 00 0 00 1 000000 N 0 00 4 00 1 00 3 00 4 00 00 0 00 0 00 0 00 0 00 2 000000 N 0 00 0 00 0 00 1 00 1 00 00 0 00 0 00 0 00 0 00 3 000000 N 0 00 0 00 0 00 0 00 0 00 00 0
29. 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 CU CY OGOOGO oO eo OOo oo Oo 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 oo oOooooooo oO
30. 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 Oo Cx O0 CO OO oOooooooo o 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 0 0 005000 004500 004000 003500 003000 002500 002000 001500 001000 000500 000000 00 00 0 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00
31. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 ooooooo ooooooo oOooooooo oOooooooo oOooooooo 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 OOo define a photon density map id x y pos of beam after expansion id of density map 0 00 00 00 00 00 00 00 00 0 011500 0 00 00 00 00 00 00 00 00 0 012000 0 00 00 00 00 00 00 00 00 0 012500 type PLANAR type of density map shptype RECTANGLE type of shape for object p0 1 0000000 1 0000000 10 2490000 1 0000000 1 0000000 10 2490000 p2 1 0000000 1 0000000 10 2490000 p3 1 0000000 1 0000000 10 2490000 normalvector 0 0000000 0 0000000 1 0000000 m extrudelen 0 000000 extrusion length idxrow 0 009500 006500 003500 000500 002500 005500 008500 011500 data 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00
32. 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 003500 004000 004500 005000 005500 006000 006500 007000 007500 008000 008500 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00
33. The foundation of optical tomography is the shadowgram a two dimensional image that shows the differences in absorption of ballistic particles traveling through a medium Figure 3 shows the primary components of an apparatus to produce shadowgrams In Figure 3 a photon source produces photons with trajectories that are perpendicular to the scattering medium The photons enter the scattering medium and become one of the following types highly scattered strongly scattered back towards the photon source or away from the detector scattered reach the detector but do not carry information about the internal structure of the scattering medium quasi ballistic slightly scattered but remain on a trajectory very close to the original trajectory ballistic no scattering occurs the photons pass through directly the medium on a ballistic trajectory blocked path is blocked by the object or absorbed photon is absorbed by the medium In a perfectly non absorbing and non scattering medium with no reflection or refraction at the surface and a perfectly absorbing object within the medium the photon detector would register only the ballistic photons and these photons would have a distribution equal to the source distribution in areas of the detector that are not shadowed by the object There would be no photons within the shadow of the object on the detector The accuracy of all optical methods of detecting photons to produce shadowgrams can be compared
34. may be calculated by taking the cross product of the vector from to with the vector from to cutting plane that is perpendicular to the normal vector is defined by point p which lies the cutting plane The portion of the sphere defined by the above points and bisected by the cutting plane that is considered to be the shape of the medium is the portion that has the normal vector passing from inside the medium to outside the medium through the cutting plane as shown in Figure 4 Figure 4 Defining a Semi Sphere mediums must be three dimensional objects not planar This implies that a positive non zero extrusion length must be specified for RECTANGLES and CIRCLES plane shapes otherwise A SEMISPHERE is a three dimensional dimensional object and the extrusion length is not used A4 R T d Pai x ig OMA en m Su 7 Figure 5 Defining A Cube Figure 6 Defining a Cylinder An extruded plane rectangle forms a cube and an extruded plane circle forms a cylinder as shown in Figures 5 and 6 The extrusion is performed in the direction of the surface normal vector to the plane and is of the length specified by the extrudelen value token It should be noted that surface normals as defined by the PTS software always point into a 3D object NURB Primitive Shapes NURB surfaces are parametric surfaces
35. scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 0000000 1000 0000000 1000 0000000 point 0 center for circle 1000 0000000 1000 0000000 1000 0000000 point 1 p2 1000 0000000 1000 0000000 1000 0000000 point 2 p3 1000 0000000 1000 0000000 1000 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 690 875478 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 1000 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 690 875478 extinction coefficient m 1 albedo 1 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object 1 0000000 1 0000000 1 0000000 point 0 center for circle pl 1 0000000 1 0000000
36. type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2710010 point 0 center for circle 1 0000000 1 0000000 10 2710010 point 1 p2 1 0000000 1 0000000 10 2710010 point 2 p3 1 0000000 1 0000000 10 2710010 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index idxcol col HASH PHOTPOSX 0 000150 0 000150 0 000005 column index 0 000150 0 000145 0 000140 0 000135 0 000130 0 000120 0 000115 0 000110 0 000105 0 000100 0 000095 0 000090 0 000085 0 000080 0 000075 0 000070 0 000065 0 000060 0 000055 0 000050 0 000045 0 000040 0 000035 0 000030 0 000025 0 000020 0 000015 0 000010 0 000005 0 000000 0 000005 0 000010 0 000015 0 000020 0 000025 0 000030 0 000035 0 000040 0 000045 0 000050 0 000055 0 000060 0 000065 0 000070 0 000075 0 000080 0 000085 0 000090 0 000095 0 000100 0 000105 0 000110 0 000115 0 000120 0 000125 0 000130 0 000135 0 000140 0 000145 data 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000050 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 0
37. x y z coords of third point p3 1 1 9 9 x y z coords of fourth point idxcol col hash PHOTPOSX 0 002 0 002 0 0001 hash lookup x pos idxrow row hash PHOTPOSY 0 002 0 002 0 0001 hash lookup pos This photon density map is defined to be a plane rectangle of width and height equal to two meters centered on 0 0 9 9 lying parallel to the x y plane All photons that passes through this rectangle are evaluated according to photon calculations defined in the idxcol and idxrow token lines idx is short for index The photon calculations for each index idxrow and idxcol generate a table cell reference equivalent to bin location for the passing photon event and the value of that cell is incremented In this manner a two dimensional map of photon density information is compiled during the simulation run The tables used by photon density maps are arranged in rows and columns which define cells A cell is a bin that extends between a minimum and maximum row index value and a minimum and maximum column index value Index structures for the rows and columns are used to map the floating point values produced by the photon calculations to a particular cell An index structure is defined by the idxcol or idxrow token line This line has the form idxcol id hash photoncalculationtype valmin valmax valdelta where id is the identifier of the index hash is the only lookup type presently implemented photoncalc
38. 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 0 0 010000 009500 009000 008500 008000 007500 007000 006500 006000 005500 005000 00 00 0 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 92 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 0
39. 0 00 0 0 00 0 00 394 00 314 00 362 00 372 00 0 00 0 00 0 0 00 0 00 379 00 389 00 361 00 371 00 0 00 0 00 0 0 00 7 00 356 00 383 00 372 00 352 00 0 00 0 00 0 0 00 291 00 366 00 370 00 361 00 396 00 1 00 0 00 0 0 00 390 00 403 00 403 00 383 00 345 00 16 00 0 00 0 0 00 343 00 389 00 355 00 397 00 368 00 287 00 0 00 0 0 00 401 00 352 00 361 00 388 00 398 00 368 00 0 00 0 0 00 398 00 388 00 e 004000 007000 010000 0 00 0 00 1 00 355 00 176 00 0 00 0 00 012500 0 00 0 00 207 00 409 00 380 00 0 00 0 00 012000 0 00 0 00 356 00 374 00 403 00 0 00 0 00 011500 0 00 0 00 387 00 392 00 375 00 264 00 0 00 011000 0 00 1 00 371 00 359 00 401 00 368 00 0 00 010500 0 00 221 00 368 00 374 00 360 00 363 00 0 00 010000 00 368 00 381 00 373 00 366 00 366 00 00 009500 00 361 00 381 00 388 00 383 00 362 00 0 00 009000 0 00 341 00 392 00 372 00 411 00 373 00 12 00 008500 0 00 354 00 388 00 373 00 368 00 344 00 228 00 008000 0 00 397 00 359 00 114 0 004500 0 007500 0 010500 0 00 0 00 0 00 393 00 56 00 0 00 0 00 0 00 2 00 337 00 358 00 349 00 0 00 0 00 0 00 0 00 376 00 406 00 360 00 0 00 0 00 0 00 0 00 392 00 373 00 354 00 35 00 1 00 0 00 145 00 333 00 379 00 374 00 326 00 0 00 0 00 416 00 379 00 400 00 3
40. 0 00 1 00 350 00 378 00 378 00 385 00 0 00 0 00 0 00 1 00 386 00 373 00 388 00 352 00 1 00 0 00 0 00 0 00 373 00 339 00 372 00 355 00 2 00 1 00 1 00 0 00 258 00 399 00 365 00 261 00 0 00 1 00 0 00 0 00 0 00 367 00 374 00 0 00 0 00 1 00 1 00 0 00 0 00 301 00 291 00 0 00 0 00 0 00 0 00 00 00 00 00 00 00 00 23 00 0 00 0 0 00 263 00 389 00 386 00 382 00 377 00 1 00 0 00 0 0 00 13 00 361 00 344 00 379 00 378 00 2 00 0 00 0 0 00 1 00 355 00 380 00 389 00 345 00 0 00 0 00 0 0 00 0 00 358 00 391 00 348 00 374 00 0 00 1 00 0 0 00 0 00 348 00 357 00 352 00 59 00 0 00 0 00 0 0 00 1 00 52 00 388 00 370 00 0 00 0 00 0 00 0 1 00 0 00 1 00 333 00 209 00 1 00 0 00 1 00 0 0 00 00 00 00 00 00 00 define a photon density id x y pos of beam upstream of collimating hole type PLANAR type of density map shptype RECTANGLE type of shape for object 1 0000000 1 0000000 10 2610000 point 0 pl 1 0000000 1 0000000 10 2610000 point 1 p2 1 0000000 1 0000000 10 2610000 point 1 0000000 1 0000000 10 2610000 point 3 normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length m 0 if planar row HASH PHOTPOSY 0 012500 0 012500 0 000500 row index col HASH
41. 00 00 00 00 25 00 0 00 0 00 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 0 00 1 00 0 00 N oo 0 000050 0 000045 0 000040 0 000035 0 000030 36 0 000025 737 00 658 00 0 00 0 000020 268 231 0 00 238 316 0 00 317 276 0 00 234 303 0 00 244 318 0 00 289 258 0 00 00 00 00 00 00 00 00 00 00 00 00 00 673 00 723 00 0 00 0 00 0 00 0 00 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 oo 0 0 0 0 0 0 0 1 1 000015 41 000020 000025 000030 000035 000040 000045 0 00 0 000050 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 4 00 0 00 0 00 297 00 0 00 0 00 350 00 264 00 0 00 0 00 296 00 215 00 0 00 0 00 269 00 290 00 0 00 0 00 230 00 269 00 0 00 0 00 221 00 296 00 0 00 0 00 317 00 304 00 0 00 0 00 341 00 0 00 0 00 0 00 0 00 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00
42. 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 oooo 00 00 00 00 00
43. 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 Zooo OOGO 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00
44. 00 00 00 00 0 000005 00 00 00 00 00 00 00 00 0 000000 00 00 00 00 00 00 00 00 0 000005 00 00 00 00 00 00 00 00 0 000010 00 00 00 00 00 00 00 00 0 000015 00 00 00 00 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 TOO 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 0
45. 00 00 00 00 00 DUNAUN C 0 00 15 00 2 00 2 00 4 00 00 4 00 23 00 6 00 0 00 4 00 4 00 3 00 1 00 19 00 24 00 7 00 2 00 3 00 4 00 4 00 2 00 24 00 10 00 3 00 4 00 9 00 2 00 5 00 3 00 6 00 13 00 5 00 2 00 6 00 4 00 5 00 5 00 5 00 17 00 8 00 12 00 27 00 18 3 00 4 5 00 16 12 00 0 003000 16 00 3 00 1 00 6 27 00 2 7 00 3 00 3 14 00 11 8 00 0 003500 13 00 2 00 3 00 7 00 10 3 00 3 00 4 8 00 15 7 00 0 004000 9 00 6 00 3 00 2 00 4 00 4 00 16 00 1 12 00 0 004500 12 00 11 00 00 00 00 00 00 2 00 0 005000 12 00 00 00 00 00 00 gt NS 17 00 59 5 00 0 005500 9 00 5 00 3 00 25 7 00 2 00 8 00 2 15 00 14 7 00 0 006000 17 00 2 00 00 2 3 00 2 00 3 3 00 3 00 22 00 0 006500 18 00 6 00 3 00 3 7 00 2 00 8 00 4 6 00 2 00 0 007000 16 00 5 00 4 00 3 3 00 3 00 2 8 00 10 9 00 20 00 0 007500 17 00 9 00 5 00 5 00 0 6 00 2 10 00 13 9 00 18 00 0 008000 11 00 18 00 8 00 9 00 00 00 3 00 00 00 2 00 00 00 00 6 00 4 00 00 00 00 00 00 6 00 4 00 00 00 00 00 00 10 00 8 00 00 00 00 00 00 8 00 00 00 00 00 00 00 9 00 3 00 00 00 00 00 00 13 00 3 00 00 00 00 00 4 00 12
46. 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 OO OO 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 OO OO 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0
47. 00 00 00 00 center for circle surface normal if planar 000050 0 000005 row index 000050 0 000005 column index 0 000035 0 000000 0 000030 43 00 44 00 36 00 40 00 57 00 45 00 66 00 76 00 35 00 55 00 70 00 45 00 44 00 105 00 55 00 46 00 614296 00 50 00 77 00 638384 60 60 00 636713 62 91 00 637064 82 81 00 635237 89 80 00 635580 Tl 73 00 635978 76 87 00 636808 69 49 00 636627 72 00 615567 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 000030 0 000005 0 000035 39 00 50 00 41 00 44 00 54 00 37 00 39 00 59 00 50 00 60 00 70 00 37 00 73 00 76 00 43 00 66 00 484038 00 55 00 82 00 638662 63 92 00 636691 DU 90 00 637554 59 03 00 04 00 02 00 03 00 637370 63 80 00 638549 55 75 00 483498 00 636699 58 636913 68 636835 62 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 48 000025 00 40 00 19 00 48 00 61 00 41 00 46 00 84 00 34 00 59 00 64 00 57 00 TU 00 93 00 51 00 87 201615 00 00 38 00 82 202228 483931 614743 614386 483541 200802 98 82 00 00 00 00 00 00 00 00 00 202567 00 101 00 77 00 70 00 38 00 0 000020 48 00 41 00 101
48. 00 3513 400 353 400 336 00 00 00 00 00 00 00 371 379 388 384 354 00 00 00 00 00 00 00 400 00 354 378 360 344 00 00 00 00 391 385 424 396 425 366 384 370 380 375 383 394 389 366 359 358 394 421 394 371 398 399 366 389 452 393 378 232 360 345 390 408 354 354 Taa 361 361 370 384 369 396 369 36 389 380 353 378 375 38 375 344 3 354 238 397 410 371 391 369 10 389 392 371 355 359 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 388 00 367 347 403 399 00 00 00 00 347 00 0 00 1 00 410 00 378 00 386 00 371 00 281 00 0 00 0 00 384 00 369 00 373 00 383 00 11 00 0 00 2 00 341 00 395 00 382 00 375 00 0 00 0 00 0 00 345 00 398 00 354 00 351 00 1 00 0 00 0 00 82 00 355 00 329 00 358 00 1 00 0 00 0 00 0 00 383 00 355 00 56 00 0 00 0 00 0 00 0 00 233 00 365 00 0 00 0 00 1 00 00 00 00 00 00 00 00 283 00 0 00 0 00 25 00 379 00 342 00 366 00 396 00 26 00 0 00
49. 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 0 00 0 00 0 00 N 0 0 0 0 0 691 00 690 00 0 00 0 00 0 00 0 00 0 00 260 223 STT 262 283 334 238 270 0 00 00 00 00 00 00 00 00 0 000050 0 000015 0 000015 0 000045 0 00 0 00 0 00 000050 0 00 0 00 0 00 000045 0 00 0 00 0 00 000040 0 00 0 00 0 00 000035 0 00 0 00 0 00 000030 0 00 443 00 0 00 000025 0 00 1271 00 0 00 000020 0 00 232 00 352 00 0 00 0 00 230 00 290 00 0 00 0 00 246 00 264 00 0 00 0 00 302 00 236 00 0 00 0 0 0 0 0 0 963 12 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 scattering medium id of density map center for circle 1 2 3 surface normal 0 if planar 00045 0 000040 0 000010 0 000005 000020 0 000025 000050 0 00 0 00 00 0 00 00 0 00 0 00 0 00 00 0 00 00 0 00 0 00 0 00 00 0 00 00 0 00 0 00 0 00 00 0 00 00 0 00 0 00 0 00 00 0 00 00 0 00 0 00 0 00 00 1206 00 00 0 00 0 00 0 00 25 00 1273 00 0 00 0 00 0 00 0 00 297 00 295 00 432 00 0 00 0 00 0 000015 0 00 0 00 269 00 282 00 974 00 0 00 0 00
50. 010000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 86 oOoooococ 5 center for circle 0 0 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 011000 0 007500 004500 001500 001500 004500 007500 010500 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 Q 0 0 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 010500 0 007000 004000 001000 002000 005000 008000 011000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 oOoooococ 0 00 00 00 00 00 00 00 0 00 00 00 0
51. 365 001000 356 367 383 382 409 415 343 000500 361 00 393 418 432 347 389 411 000000 370 366 358 392 420 398 371 000500 388 385 408 351 372 369 001000 9292 362 393 00 397 393 377 417 001500 358 369 404 402 408 384 405 002000 360 376 393 402 391 403 364 002500 368 415 416 384 387 409 375 003000 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 116 362 419 384 393 352 355 362 366 406 390 431 384 396 394 405 392 412 409 383 374 385 419 408 405 405 351 367 335 441 431 3527 410 430 364 380 380 353 389 375 366 399 381 362 330 389 378 410 383 421 421 37 95 392 421 374 371 00 328 417 390 405 400 387 394 363 359 384 389 407 366 409 367 376 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 411 404 369 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 3
52. 6 00 0 010000 002500 005500 008500 011500 data 0 00 0 00 252 00 335 00 2 00 0 00 0 00 0 00 2 00 363 00 371 00 53 00 1 00 0 00 0 00 74 00 388 00 369 00 344 00 0 00 0 00 0 00 369 00 374 00 407 00 350 00 0 00 0 00 0 00 375 00 360 00 391 00 401 00 0 00 0 00 0 00 343 00 374 00 372 00 380 00 6 00 0 00 0 00 380 00 328 00 373 00 394 00 289 00 0 00 31 00 352 00 387 00 381 00 387 00 384 00 0 00 287 00 362 00 416 00 342 00 389 00 397 00 0 00 350 00 356 00 373 00 353 00 404 00 367 00 0 00 375 00 359 00 oooo 003000 006000 009000 012000 0 00 0 00 2 00 278 00 279 00 1 00 0 00 1 00 0 00 0 00 1 00 377 00 341 00 0 00 1 00 0 00 1 00 0 00 252 00 385 00 343 00 229 00 0 00 1 00 0 00 0 00 356 00 384 00 381 00 397 00 0 00 0 00 0 00 0 00 356 00 388 00 355 00 367 00 0 00 0 00 0 00 0 00 384 00 375 00 390 00 367 00 0 00 0 00 0 00 21 00 374 00 362 00 399 00 368 00 26 00 0 00 0 00 290 00 438 00 391 00 387 00 375 00 305 00 0 00 00 359 00 407 00 364 00 364 00 401 00 354 00 0 00 00 344 00 362 00 384 00 326 00 372 00 375 00 0 00 0 00 360 00 383 00 003500 006500 009500 012500 0 00 0 00 0 00 341 00 234 00 0 00 0 00 0 00 0 0 00 0 00 62 00 377 00 359 00 0 00 0 00 2 00 0 1 00 1 00 391 00 354 00 363 00 89 00 0 00
53. 6 00 18 00 8 00 22 00 5 00 20 00 4 00 13 00 3 00 21 00 8 00 3 00 20 00 19 00 21 00 7 00 0 00 9 00 14 00 9 00 20 00 16 00 1 00 00 00 00 00 00 00 7 00 00 00 00 00 00 00 N CQ F2 O0 O0 I2 0 012000 0 011500 0 008500 0 008000 0 005500 0 005000 0 002500 0 002000 0 000500 0 001000 0 003500 0 004000 0 006500 0 007000 0 009500 0 010000 0 012500 19 00 19 00 4 00 8 00 8 00 5 00 8 00 2 00 17 00 15 00 1 00 6 00 5 00 4 00 4 00 0 012500 19 00 20 00 26 00 1 00 8 00 14 00 4 00 8 00 6 00 5 00 11 00 19 00 20 00 7 00 10 00 0 012000 14 00 20 00 4 00 7 00 6 00 2 00 5 00 2 00 5 00 20 00 14 00 11 00 3 00 20 00 0 00 0 011500 16 00 21 00 7 00 9 00 7 00 8 00 9 00 2 00 5 00 8 00 2 00 0 00 21 00 23 00 8 00 0 011000 5 00 22 00 2 00 0 00 3 00 3 00 00 5 00 0 00 5 00 7 00 2 00 20 00 8 00 2 00 0 010500 8 00 12 00 10 00 7 00 0 00 4 00 9 00 5 00 8 00 2 00 3 00 9 00 1 00 7 00 9 00 0 010000 12 00 17 00 7 00 8 00 6 00 3 00 5 00 00 5 00 10 00 3 00 0 00 0 00 2 00 21 00 0 009500 12 00 19 00 3 00 23 00 1 00 8 00 4 00 2 00 00 4 00 4 00 14 00 7 00 9 00 23 00 0 009000 14 00 15 00 6 00 12 00 6 00 2 00 7 00 3 00 4 00 3 00 3 00 13 00 1 00 14 00 4 00 0 008500 8 00 15 00 11 00 16 00 4 00 2 00 2 00 7 00 2 00 1 00 5 00 15 00 109 0 011000 0 007500 0 004500 0 001500 0 0015
54. 9 1 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1000 1000 1000 x y z coords of first point pl 1000 1000 1000 x y z coords of second point p2 1000 1000 1000 x y z coords of third point p3 1000 1000 1000 x z coords of fourth point extrudelen 2000 extrusion length of box 38 Appendix Test 1 Input File A Single Medium with No Scattering or Absorption Input File testcase mci RunInfo comment Test Case 1 A Single Medium with No Scattering or Absorption include stdsetup mci bounding box Medium define a scatter include the standard setup for all test cases random number generator and ing and absorbing medium id scattering medium sample of scattering medium mean cosine of forward scattering angle g 9 g factor of medium scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 shptype RECTANGLE of refraction shape of medium pO 1 1 1 z coords of first point pl 13 11 y 111 vw extrudelen 01 PhotonSource defi z coords of second point z coords of third point z coords of fourth point extrusion length of box ne a photon source Ma Ma id uniform source 1 type UNIFORM u
55. Q r O source density The Boltzmann equation has been solved analytically for a few simple geometries When the absorption is small compared to the scattering a diffusion theory approximation of the Boltzmann equation is often employed However for arbitrarily complex geometries of the kind found in optical tomography applications the Boltzmann equation cannot be solved analytically In these instances numerical simulation primarily those based upon Monte Carlo modeling is employed to generate highly accurate results For interstellar mediums a phase function 5 2 that describes the experimentally observed distribution of scattering angles of photons was developed by Henyey and Greenstein It has been found by Jacques et al that the Henyey Greenstein phase function 5 also accurately describes the scattering of light in biological tissue The important parameter of this phase function is g the cosine of the forward scattering angle Values of g can vary from 1 to 1 with 0 representing uniform scattering and values close to 1 representing a high degree of forward scattering Many common biological tissues have a high degree of forward scattering with g values ranging from 0 79 to 0 98 for 633 nm wavelength photons At present the PTS software only supports the Henyey Greenstein phase function The Henyey Greenstein HG function is 5 2 sin 24 1 1 1 8 0 4p 2 where S sos 2psin d g
56. The probability density function for the pathlength derived from the Beer Lambert Law is p l probability that length occurs such that 0 lt p lt 1 0 e where L length of single leg of random walk between scattering events From the probability density function the random variable can be directly determined 1 RND random number uniformly distributed between 0 and 1 such In RND that 0 lt RND lt 1 A similar derivation can be used to determine the length of each leg between absorption events based upon the absorption coefficient The change in photon trajectory from O to at each scattering event is calculated by decomposing the trajectory into two components relative to the original trajectory and f as shown in Figure 2 The probability density functions for angles and f are pf l p f probability that angle f occurs such that 2T 0O p f l where p 8 5 8 p 0 probability that angle occurs such that 0 p 1 this is the Henyey Greenstein function x SCATTERING EVENT Figure 2 Change in Photon Trajectory From the probability density functions the random variables and f can be directly determined 24 1 1 cos 2 1 g 28 1 g 2gRND It can be seen that the sampling of distributions by random variables is at the core of all Monte Carlo simulations Optical Tomography
57. albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object 0 0100000 0 0001000 10 2500000 point 0 center for circle pl 0 0100000 0 0001000 10 2500000 point 1 2 0 0100000 0 0001000 10 2500000 point 2 3 0 0100000 0 0001000 10 2500000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000500 extrusion length m 0 if planar Medium define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 400000 index of refraction shptype RECTANGLE type of shape for object 0 0200000 0 0200000 10 2510000 point 0 center for circle pl 0 0200000 0 0200000 10 2510000 point 1 p2 0 0200000 0 0200000 10 2510000 point 2 p3 0 0200000 0 0200000 10 2510000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator block
58. extrudelen 0 002000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id mirror 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 8059 047876 coefficient of absorption m 1 TI scatterratio 0 000000 scattering ratio scattered to ballistic photons direction of extrudelen absorbratio 10000000 004464 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 8059 047876 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 10000 000000 index of refraction shptype CIRCLE type of shape for object p0 0 0000000 0 0000000 9 5000000 point 0 center for circle pl 0 0000000 0 0150000 9 5000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 7071068 0 0000000 0 7071068 surface normal extrudelen 0 002000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id diverging lens 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorpt
59. it has proven useful to reduce the amount of light entering a scattering medium with a slit Such an element is modeled in Test Case 5 by superimposing a cube of ambient medium on a cube of blocking medium The following definitions show how 0 2 mm x 20 mm slit is constructed Medium define a scattering and absorbing medium id slit blocking medium blocking medium for slit upstream of sample g 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium 1 1 10 25 x 2 coords of first point pl 1 1 10 25 x 2 coords of second point 1 1 10 25 x 2 coords of third point 3 1 1 10 25 x 2 coords of fourth point extrudelen 0005 extrusion length of box Medium define a scattering and absorbing medium id slit opening medium blocking medium for slit upstream of sample lt 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium 01 0001 10 25 z coords of first point pl 01 0001 10 25 x y z coords of second point p2 01 0001 10 25 x z coords of third point p3 01 0001 10 25 x y z coords of fourth point extrudelen 0005 extrusion length of box The array of thre
60. movecount 1 position 0 3941447 0 2066050 0 0784892 movecount 2 position 0 2069607 0 1618084 0 0000000 movecount 3 position 0 2430430 0 0541142 0 1886936 movecount 4 position 0 3026797 0 0130430 0 0000000 movecount 5 position 1 5311961 1 3964815 1 1000000 current position end position list end wire body end define uniform source 1 0 22 Test Cases The preceding sections have introduced photon transport through Monte Carlo simulation and described the input and output file formats along with program operation This section is dedicated to describing a number of test cases that showcase particular aspects of the PTS software It is expected that the user will become acquainted with the definition of simulation models and the types of results possible by following these test cases Each test case is comprised of an input file with the mci extension and an output file with the mco extension These files can be found in Appendices A to M The majority of the test cases were run with a limited number of photons in order to demonstrate a particular principle All test cases are capable of being re run by the user with larger numbers of photons Test Case 1 A Single Medium with No Scattering or Absorption A simple test case is to duplicate some of the work of Jacques and Chu by defining a single uniform photon source of radius 25 microns and a single 1 cm thick scattering medium For Test Case 1
61. p2 1 0000000 1 0000000 9 9000000 point 2 3 1 0000000 1 0000000 9 9000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 012500 0 012500 0 000500 row index idxcol col HASH PHOTPOSX 0 012500 0 012500 0 000500 column index 0 012500 0 012000 0 011500 0 011000 0 010500 0 010000 009500 0 009000 0 008500 0 008000 0 007500 0 007000 006500 0 006000 0 005500 0 005000 0 004500 0 004000 003500 0 003000 0 002500 0 002000 0 001500 0 001000 000500 0 000000 0 000500 0 001000 0 001500 0 002000 002500 0 003000 0 003500 0 004000 0 004500 0 005000 005500 0 006000 0 006500 0 007000 0 007500 0 008000 008500 0 009000 0 009500 0 010000 0 010500 0 011000 011500 0 012000 0 012500 data 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 012500 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 012000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0
62. p3 1 1 10 261 x y idxcol col 1 has idxrow row 1 1 has Map define a density ma type planar planar ty shptype RECTANGLE sha 1 1 10 271001 pl 1 1 10 271001 sh I 10 241001 p3 1 1 10 271001 x idxcol col 1 has idxrow row 1 1 has Map define a density ma type planar planar ty shptype RECTANGLE sha pO 1 1 10 271001 x pl 1 1 10 271001 p2 1 1 10 271001 x p3 1 1 10 271001 x idxcol col 1 has idxrow row 1 1 has er type planar planar type shptype RECTANGLE shape N NNN p pe pe N NNN p pe pe h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup expansion of map of medium coords of first point coords of second point coords of third point coords of fourth point h PHOTPOSX 0 0125 0 0125 0 0005 hash lookup h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup id x y pos of beam upstream of collimating hole of map of medium coords of first point coords of second point coords of third point coords of fourth point h PHOTPOSX 0 0125 0 0125 0 0005 hash lookup h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup id x y pos downstream of collimating hole of map of medium 2 coords of first point 2 coords of second point 2 coords of third point 2 coords of fourth point id photon info downstream
63. point 1 p2 1001 0000000 1001 0000000 1001 0000000 point 2 p3 1001 0000000 1001 0000000 1001 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 0000000 1000 0000000 1000 0000000 point 0 center for circle pl 1000 0000000 1000 0000000 1000 0000000 point 1 p2 1000 0000000 1000 0000000 1000 0000000 point 2 p3 1000 0000000 1000 0000000 1000 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 690 875478 coefficient of scattering m 1 mua 0 000000 coefficient
64. radius of circle squared RunInfo runend Sat Dec 28 14 29 59 2002 ending time and date of run Map define a photon density map id x y pos of beam before expansion id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object p0 1 0000000 1 0000000 9 9000000 point 0 center for circle 1 0000000 1 0000000 9 9000000 point 1 p2 1 0000000 1 0000000 9 9000000 point 2 1 0000000 1 0000000 9 9000000 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row indexl HASH PHOTPOSY 0 012500 0 012500 0 000500 row index idxcol col HASH 0 012500 0 012500 0 000500 column index 108 0 009500 006500 003500 000500 002500 005500 008500 011500 data 4 00 3 00 1 00 5 00 4 00 1 00 2 00 3 00 6 00 7 00 0 00 6 00 22 00 9 00 3 00 3 00 4 00 20 00 7 00 3 00 24 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 X 6 00 00 00 00 00 00 00 X 5 00 3 00 5 00 0 00 2 00 6 00 30 00 N 7 00 0 00 4 00 5 00 6 00 1 00 24 00 N 1 00 1 00 3 00 3 00 0 00 21 00 9 00 9 00 4 00 3 00 2 00 5 00 CO 0 012500 0 009000 0 006000 0 003000 0 000000 0 003000 006000 009000 012000 16 00 20 00 1 00
65. z coords of center in m pl 0 0 000025 0 x z coords of point on circumference normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 100000 number of photons to launch from source Map define a density map id x y pos of beam upstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 999999 z coords of first point pl 1 1 999999 x z coords of second point p2 1 1 999999 x z coords of third point p3 1 1 999999 x z coords of fourth point idxcol col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x pos idxrow row hash 0 000050 0 000050 0 000005 hash lookup pos Map define a density map id x y pos of beam downstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 1 010001 x z coords of first point pl 1 1 1 010001 x z coords of second point p2 1 1 1 010001 x y z coords of third point p3 1 1 1 010001 x z coords of fourth point col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x idxrow row hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup pos The output file contains the density map images showing the photon density with columns showing the x coordinate and rows showing the y coordinate of t
66. 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 000500 0 00 00 004500 oOoooococ 004000 003500 003000 002500 002000 001500 001000 000500 000000 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 93 cx 6 Oooo oo Mo 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00
67. 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 000500 001000 001500 002000 002500 003000 003500 004000 004500 005000 005500 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 89 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00
68. 0 Monte Carlo Simulation Monte Carlo simulation is a well established means of modeling the Boltzmann transport equation for photons in a scattering and absorbing medium In this method the path of each photon is simulated according to statistical parameters from the source to the detector Based upon the properties of the scattering medium the photon is moved a distance along its path The photon s trajectory is then altered according to a distribution of scattering angles and it is moved again This sequence repeats until the photon exits the scattering medium or is absorbed The advantage of the Monte Carlo method is that it can be used to simulate arbitrarily complex geometries in absorbing and scattering mediums However this method does require substantial computational resources to simulate enough photons to have a statistically valid distribution The Monte Carlo method is widely used for simulating many types of problems that are difficult to model by other methods Such problems include particle transport for which the Monte Carlo method was originally developed as well as finance and statistics The essence of the Monte Carlo method is that an event which has a specified probability density function is represented by a random number with the same probability density function When sufficiently large numbers of events are simulated in this manner the distribution of probabilities that are randomly generated matches the specified dist
69. 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 121 79 194 82 55 76 83 76 71 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 79 78 84 64 87 88 90 75 oOoooococ 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 1 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00
70. 0 00 00 00 00 00 00 00 00 0 00 00 00 00 0 012000 0 008500 0 0 Qo Oo o 005500 002500 000500 003500 006500 009500 012500 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 point 0 point 1 point 2 point 3 m 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 surface normal 0 if planar row indexl HASH PHOTPOSY 0 012500 0 012500 0 000500 row index col indexl HASH PHOTPOSX 0 012500 0 012500 0 000500 column index 0 012500 0 011500 0 008000 205 0 0 012500 012000 011500 011000 010500 005000 002000 001000 004000 007000 010000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 91 oOoooococ center for circle 0 0 0 oOoooococ o
71. 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 QUO OO cO Od p 0 0 OO OO OOo C Oo OOo O0 Oo 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 TO OGOOGO O O OOG OOG 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0
72. 0 00 00 0 00 0 00 0 00 0 00 27 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 28 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 29 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 30 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 31 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 32 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 33 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 34 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 35 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 36 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 37 000000 68 0 000025 0 T25 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 38 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 39 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 40 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 41 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 42 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 43 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 44 0
73. 0 00 0 00 0 00 0 00 0 00 0 00 0 000015 N 0 00 0 00 0 00 0 00 0 00 317 00 230 00 269 00 282 00 333 00 282 00 262 00 290 00 974 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000010 N 0 00 0 00 0 00 0 00 0 00 283 00 246 00 263 00 304 00 257 00 234 00 334 00 264 00 196 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000005 N 0 00 0 00 0 00 0 00 0 00 238 00 302 00 241 00 259 00 187 00 256 00 270 00 236 00 129 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000000 N 0 00 0 00 0 00 0 00 0 00 333 00 263 00 228 00 284 00 279 00 327 00 286 00 285 00 944 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000005 N 0 00 0 00 0 00 0 00 0 00 291 00 277 00 290 00 294 00 230 00 259 00 299 00 248 00 442 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000010 0 00 0 00 0 00 0 00 0 00 686 00 1290 00 1296 00 1281 00 1273 00 1306 00 710 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000015 0 00 0 00 0 00 0 00 0 00 0 00 407 00 931 00 1246 00 1242 00 1007 00 pos of beam upstream of scattering medium id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 0 9999990 point 0 center for circle 1 0000000 1 0000000 0 9999990 point 1 p2 1 0000000 1 0000000 0 9999990 point 2 p3 1 0000000 1 0000000 0 9999990 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 000050 0 000050 0 000005 row
74. 0 000010 0 00 0 00 263 00 304 00 196 00 0 00 0 00 0 000005 0 00 0 00 241 00 259 00 129 00 0 00 0 00 0 000000 44 0 000035 0 000000 0 000030 0 00 00 0 00 e 0 00 00 00 0 00 00 00 0 00 00 0 00 0 00 00 0 00 0 00 1216 00 0 00 0 00 1247 00 0 00 0 00 233 00 0 00 0 00 333 00 0 00 0 00 257 00 0 00 0 00 187 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 column index 0 000030 0 000005 0 000035 0 00 00 0 00 0 00 00 0 00 0 00 00 0 00 0 00 00 0 00 0 00 00 0 00 0 00 1034 00 0 00 0 00 1251 00 0 00 0 00 267 00 0 00 0 00 282 00 0 00 0 00 234 00 0 00 0 00 256 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000025 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 450 00 1264 00 384 00 1004 00 1225 00 1220 00 1333 1286 0 00 1291 1299 0 00 00 00 00 00 686 00 710 00 0 00 00 00 o o 00 00 o o 00 00 o o 00 00 o o 00 00 o o 00 00 o o 00 00 o 0 0 70 EPIO 0 0 0 ELIO 000015 0 00 1263 00 1285 00 0 00 0 00 12
75. 00 43 00 68 00 41 00 39 00 51 00 27 00 id of density map surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow 0 0000 0 00001 0 00004 data 0 00 20 0 0 row HASH PHOTPOSY 0 000050 0 idxcol col 1 1 HASH PHOTPOSX 0 000050 0 0 000050 0 000015 0 000015 0 000045 0 00 0 00 66 000050 0 000005 row index 000050 0 000005 0 000045 0 000040 0 000035 0 000010 0 000005 0 000000 0 000020 0 000025 0 000030 0 000050 0 00 0 00 0 00 0 00 0 00 0 00 91 00 98 00 75 00 97 00 1242 00 59 00 222 00 1564 00 80 00 99 00 611 00 86 00 85 00 608 00 82 00 243 00 547 00 43 00 235 00 557 00 72 00 228 00 510 00 78 00 234 00 588 00 90 00 216 00 1477 00 52 00 68 00 1221 00 56 00 89 00 216 00 24 00 49 00 76 00 56 00 40 00 94 00 21 00 36 00 62 00 53 00 59 00 32 00 38 00 49 00 40 00 27 00 column index 0 000030 0 000005 0 000035 0 00 0 00 66 72 50 207 655 54 205 1515 38 659 314 506 532 245 614 202 1548 220 622 60 90 210 50 64 63 57 53 61 41 60 62 50 49 28 45 45 64 21 0 0000 0 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
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84. 00 0 00 0 00 0 00 4 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 5 000000 N 0 00 0 00 0 00 0 00 1 00 00 0 00 0 00 0 00 0 00 6 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 7 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 8 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 9 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 10 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 11 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 12 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 13 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 14 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 15 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 16 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 17 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 18 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 19 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 20 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 21 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 22 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 23 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 24 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 25 000000 N 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 26 000000 N 0 00 0 00 0 00 0 00
85. 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000040 98 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 000000 0 00 00 00 0 00 00 00 0 00 00 00 oo oo oo oo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 Li 70 RIED 7905 770 770 0 0 EI 0 10 770 EO 000035 000030 000025 000020 000015 000010 000005 000000 000005 000010 000015 000020 000025 000030 000035 000040 000045 000050 0 0 0 0 0 0 0 0 0 0 0 0 0 0 o o o o o o o o o o o 0 00 00 00 0 00 00 00 0 00
86. 00 2 00 2 00 0 000005 N 2 00 1 00 0 00 1 00 1 00 23 00 9 00 20 00 7 00 8 00 12 00 11 00 20 00 9 00 5 00 1 00 3 00 3 00 00 3 00 3 00 0 000000 51 27 00 15 00 2 00 0 17 00 18 00 1 00 0 00 00 0 00 0 N 00 00 00 N 00 00 00 00 99 00 00 2 00 0 00 0 3 00 0 0 00 0 00 0 3 00 0 00 0 000005 000010 000015 000020 000025 000030 000035 000040 000045 000050 1 1 1 30 2 mn 2 00 7 00 6 00 2 00 3 00 5 00 1 00 00 00 3 00 00 00 1 00 00 00 2 00 00 00 0 00 00 00 2 00 00 00 2 00 00 00 0 00 00 00 1 1 2 00 7 00 0 00 2 00 8 00 1 00 2 00 00 00 1 00 00 00 2 00 00 00 1 00 00 00 2 00 00 00 1 00 00 00 0 00 00 00 1 00 00 00 2 1 N 0 00 3 00 1 00 1 00 6 00 0 00 0 00 00 00 4 00 00 00 0 00 00 00 2 00 00 00 1 00 00 00 0 00 00 00 1 00 00 00 0 00 00 00 52 1 1 N N n 4 00 2 00 1 00 1 00 8 00 1 00 1 00 00 00 2 00 00 00 5 00 00 00 1 00 00 00 2 00 00 00 1 00 00 00 1 00 00 00 2 00 00 00 1 2 3 00 7 00 6 00 2 00 2 00 1 00 1 00 00 00 1 00 00 00 3 0
87. 00 77 00 100 00 81 00 77 00 75 00 39 00 0 000025 42 00 35 00 70 00 73 00 74 00 66 00 56 00 75 00 35 00 0 000030 43 00 52 00 57 00 46 00 65 00 61 00 49 00 45 00 23 00 0 000035 33 00 42 00 55 00 44 00 55 00 65 00 58 00 49 00 31 00 0 000040 38 00 43 00 54 00 56 00 54 00 54 00 41 00 43 00 33 00 0 000045 X 33 00 32 00 44 00 45 00 42 00 45 00 59 00 36 00 31 00 0 000050 Map define a photon density map id x y pos of beam downstream of type PLANAR type of density map shptype RECTANGLE type of shape 1 0000000 1 0000000 1 0100010 pl 1 0000000 1 0000000 1 0100010 p2 1 0000000 1 0000000 1 0100010 p3 1 0000000 1 0000000 1 0100010 normalvector 0 0000000 0 0000000 1 extrudelen 0 000000 extrusion le for object point 0 point 1 53 00 50 00 109 00 44 00 57 00 85 00 51 00 53 00 58 00 45 00 47 00 41 00 43 00 39 00 53 00 42 00 36 00 46 00 37 00 58 00 67 00 80 00 53 00 54 00 81 00 57 00 50 00 68 00 38 00 38 00 55 00 47 00 46 00 55 00 28 00 48 00 54 00 50 00 Scattering medium id of density map center for circle point 2 point 3 0000000 surface normal ngth m 0 if planar idxrow row 1 1 HASH PHOTPOSY 0 000050 0 idxcol col 1 1 HASH PHOTPOSX 0 000050 0 0 000050 0 000045 0 000020 0 000015 0 000010 0 000010 0 000015 0 000020 0 000040 0 000045 0 000050 data 65 00 64 00 69 00 6
88. 0000000 0 0000000 point 2 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 000025 radius of circle radius squared 0 000000 radius of circle squared RunInfo runend Fri Dec 27 17 06 40 2002 ending time and date of run Map define a photon density map it 0 000050 0 000045 0 000040 0 000035 0 000030 0 000020 0 000015 0 000010 0 000005 0 000000 0 000005 0 000010 0 000015 0 000020 0 000025 0 000030 0 000035 0 000040 0 000045 0 000050 data 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000050 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000045 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000040 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000035 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000030 N 0 00 0 00 0 00 0 00 0 00 0 00 443 00 963 00 1206 00 1216 00 1034 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000025 N 0 00 0 00 0 00 0 00 0 00 691 00 1271 00 1225 00 1273 00 1247 00 1251 00 690 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000020 N 0 00 0 00 0 00 0 00 0 00 260 00 232 00 297 00 295 00 233 00 267 00 223 00 352 00 432 00
89. 000050 0 000005 hash lookup x pos idxrow row 1 1 hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup Map define a density map id x y pos of beam downstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 1 010001 2 coords of first point pl 1 1 1 010001 x 2 coords of second point 2 1 1 1 010001 x 2 coords of third point p3 1 1 1 010001 x z coords of fourth point col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x idxrow row 1 1 hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup pos 47 Appendix Test Case 2 Output File A Single Medium with Scattering but without Absorption Output File testcase2 mco 48 Runinfo information on this simulation run commentO Test Case 2 commentl A Single Medium with Scattering but without Absorption comment2 comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcase2 mci name of input file for this run outputfile testcase2 mco name of output file for this run photonqty 1000000 total number of photons in all sources runstart Fri Dec 27 20 07 42 2002 starting time and date of run RandomNumberGenerator define t
90. 25 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 2 00 00 1 00 2 00 1 00 2 00 3 00 0 000020 2 00 0 00 2 00 1 00 1 00 0 00 2 00 5 00 2 00 1 00 4 00 2 00 2 00 00 1 00 00 0 00 1 00 0 00 00 0 00 0 000025 N 1 00 1 00 3 00 2 00 2 00 2 00 0 00 1 00 00 1 00 2 00 1 00 00 3 00 1 00 0 00 1 00 0 00 1 00 2 00 00 0 000030 N 0 00 0 00 0 00 1 00 2 00 1 00 00 5 00 2 00 0 00 0 00 4 00 0 00 00 1 00 00 0 00 00 0 00 00 0 00 0 000035 X 2 00 2 00 1 00 0 00 2 00 1 00 00 0 00 2 00 0 00 2 00 0 00 00 2 00 0 00 2 00 0 00 00 4 00 0 00 00 0 000040 N 0 00 1 00 0 00 0 00 0 00 0 00 00 0 00 0 00 2 00 00 1 00 00 0 00 2 00 1 00 2 00 0 00 1 00 00 00 0 000045 N 1 00 0 00 1 00 1 00 0 00 2 00 00 0 00 2 00 1 00 00 0 00 2 00 00 0 00 0 00 1 00 00 1 00 00 0 00 0 000050 Map define a photon density map id x y pos of beam downstream of scattering medium id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object p0 1 0000000 1 0000000 1 0100010 point 0 center for circle pl 1 0000000 1 0000000 1 0100010 point 1 p2 1 0000000 1 0000000 1 0100010 point 2 3 1 0000000 1 0000000 1 0100010 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index idxcol col H
91. 3525 38 0 99 0 9 1000727 718 17 0 999 0 9 100078 102 4 0 9999 0 9 9906 15 5 0 99999 0 9 966 3 0 0 999999 0 9 108 1 0 The base algorithms used by the PTS software are similar to those used by Chu and Pfeiffer and should yield similar results although not exact as reflection refraction and other differences do exist between the software A single simulation model is constructed with the PTS software at a scattering ratio of 1000 equivalent to a scattering level of 0 999 and a g factor of 0 9 using the simulation setup shown in Figure 16 It is expected that the numbers of ballistic quasi ballistic and scattered photons will be similar to the values in the Table 4 for that scattering level and g factor This simulation model consists of a single uniform photon source of radius 25 microns and a single 1 cm thick scattering medium with a scattering ratio of 1000 Downstream of the scattering medium is a 1 cm thick by 25 micron radius collimating hole constructed by embedding a cylinder of air in an absorbing cube Multiple photon density maps downstream of the hole act as detectors 26 COLLIMATING HOLE 00 MICRON DIA x 10 mm SCATTERING MEDIUM _ N 10 mm THK N UNIFORM PHOTON SOURCE RADIUS e5 MICRONS HOTON DENSITY MAPS Figure 16 Model Setup for Test Case 4 Figures 17 and 18 show the images from photon x y density maps 50 photons per bin contour levels located upstream and dow
92. 65 0 000005 0 000035 42 37 46 76 44 39 47 92 208 45 00 86 00 00 00 00 00 00 75 00 00 00 00 00 0 000025 74 47 32 44 D2 68 72 79 74 00 33 20 00 00 00 61 00 00 00 00 00 00 00 00 213 00 84 00 43 00 218 00 221 00 49 00 951 00 903 00 41 00 509 00 536 00 62 00 536 00 610 00 57 00 595 00 608 00 60 00 509 00 572 00 65 00 514 00 614 00 77 00 591 00 545 00 32 00 930 00 000 00 49 00 218 00 212 00 27 00 97 00 86 00 44 00 78 00 80 00 37 00 66 00 74 00 28 00 72 00 71 00 51 00 40 00 58 00 26 00 57 00 45 00 12 00 51 00 207 00 210 00 2 61 00 74 00 0 000030 65 00 51 00 589 00 1236 00 14 87 00 87 00 0 000025 87 00 52 00 1554 00 1609 00 15 210 00 221 00 0 000020 56 00 51 00 652 00 606 00 544 00 697 00 46 00 65 00 0 0000 53 00 62 00 599 00 636 00 478 00 267 00 44 00 70 00 0 0000 48 00 43 00 567 00 590 00 566 00 458 00 68 00 39 00 0 00000 85 00 55 00 526 00 562 00 559 00 419 00 58 00 44 00 0 000000 36 00 46 00 518 00 499 00 608 00 271 00 70 00 44 00 0 000005 52 00 46 00 599 00 526 00 574 00 596 00 47 00 38 00 0 000010 74 00 75 00 1608 00 1581 00 16 247 00 217 00 40 00 0 000015 56 00 52 00 633 00 1160 00 14 224 00 92 00 0 000020 68 00 52 00 95 00 208 00 2 7
93. 94 00 47 00 54 00 91 00 49 00 47 00 55 00 46 00 56 00 55 00 47 00 48 00 44 00 30 00 47 00 44 00 28 00 000030 0 000005 0 000035 70 00 89 00 64 00 73 00 73 00 74 00 74 00 87 00 82 00 88 00 96 00 61 00 83 00 98 00 84 00 93 00 583 00 75 00 85 00 833 00 82 00 97 00 790 00 77 00 110 00 804 00 79 00 91 00 771 00 90 00 93 00 762 00 79 00 47 00 72 00 86 00 29 00 62 00 66 00 46 00 48 00 53 00 35 00 54 00 65 00 41 00 45 00 42 00 44 00 41 00 48 00 29 00 000025 80 00 54 00 77 00 72 00 61 00 62 00 80 00 82 00 69 00 80 00 90 00 78 00 89 00 102 00 75 00 82 00 324 00 84 00 95 00 774 00 75 00 317 00 782 00 79 00 586 00 786 00 87 00 765 00 805 00 96 00 739 00 775 00 90 00 799 00 782 00 86 00 0 786 00 780 00 72 00 0 450 00 518 00 65 00 0 109 00 98 00 83 00 0 93 00 103 00 61 00 0 98 00 87 00 59 00 0 88 00 92 00 71 00 0 79 00 91 00 83 00 0 65 00 78 00 74 00 0 83 00 75 00 76 00 0 72 00 806 00 613 00 000005 81 00 720 00 329 00 000010 82 00 803 00 94 00 000015 67 00 329 00 75 00 000020 68 00 89 00 90 00 000025 83 00 87 00 93 00 000030 75 00 88 00 78 00 000035 78 00 75 00 59 00 000040 55 00 100 00 89 00 000045 67 00 79 00 78 00 000050 76 00 771 00 97 00 83 00
94. Map Located Downstream of Collimating Hole Relating Radial Distance wrt Center of Photon Source to Number of Scattering Events Radial Distance wrt Center of Source microns No of Scatter 0 5 10 15 20 25 Events 0 4007 11867 19872 28263 35906 0 1 0 13 12 22 48 12 2 0 4 1 3 4 0 3 0 0 0 1 1 0 4 0 0 0 0 0 0 5 0 0 0 0 0 0 6 0 0 0 0 1 0 Table 6 Test Case 4 Portion of Density Map Located Downstream of Collimating Hole Relating Radial Distance wrt Photon Starting Position to Number of Scattering Events Radial Distance wrt Center of Source microns No of Scatter 0 5 10 15 20 25 30 35 40 45 50 Events 0 99915 0 0 0 0 0 0 0 0 0 0 1 4 5 21 7 16 17 13 14 6 5 0 2 1 1 1 0 4 2 2 0 1 0 0 3 0 0 0 0 1 0 1 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1 0 0 0 0 0 0 0 0 28 It can be seen that number of ballistic photons is 99 915 in both tables photons that underwent zero scattering events although Table 5 shows these photons radially distributed based upon the uniform source distribution while Table 6 shows all of the ballistic photons binned into one cell It is not possible to determine the number of quasi ballistic photons from Tables 5 or 6 although the total number of photons reaching the density maps can be determined to be 100 038 by summing all cells in either density map The determination of the quantity of quasi ballistic photons depends upon the definition of what constitutes
95. Medium define a scattering and absorbing medium id bounding box id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 100000000 000000 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 0000000 1001 0000000 1001 0000000 point 0 center for circle pl 1001 0000000 1001 0000000 1001 0000000 point 1 p2 1001 0000000 1001 0000000 1001 0000000 point 2 p3 1001 0000000 1001 0000000 1001 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbe
96. Medium with Scattering but without Absorption include stdsetup mci include the standard setup for all test cases random number generator and bounding box Medium define a scattering and absorbing medium id scattering medium sample of scattering medium g 9 g factor of medium mean cosine of forward scattering angle scatterratio 1000 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 1 z coords of first point pl 1 1 1 2 coords of second point 2 1 1 1 z coords of third point p3 1 1 1 2 coords of fourth point extrudelen 01 extrusion length of box PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source pO 0 0 0 z coords of center in m pl 0 0 000025 0 x z coords of point on circumference normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1000000 number of photons to launch from source Map define a density map id x y pos of beam upstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 999999 x y z coords of first point 1 1 999999 x z coords of second point p2 1 1 999999 x y z coords of third point p3 1 1 999999 x z coords of fourth point idxcol col hash PHOTPOSX 0 000050 0
97. Uniform Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes Output File testcase6 mco 104 RunInfo information on this simulation run comment0O Test Case 6 commentl Uniform source with two 45 deg mirrors 10 x beam expander 0 2 mm slit and three collimating holes comment2 comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcase6 mci name of input file for this run outputfile testcase6 mco name of output file for this run photonqty 1000000 total number of photons in all sources runstart Sat Dec 28 14 14 45 2002 starting time and date of run RandomNumberGenerator define the random number generator type MC type of random number generator seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed Medium define a scattering and absorbing medium id bounding box id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption rat
98. a photon passes through a detector then some characteristics of the photon are recorded Media 3D objects are defined as blocks cylinders or semi spheres The order in which objects are defined is important as the last object defined determines the characteristics of the medium In this approach a fish tank would be defined by first defining a block of air then defining a block of glass inside the block of air then defining a block of water inside the block of glass The photon will check its current position at each scattering refraction reflection event and use the optical properties of the last defined medium within which it finds itself This approach allows complex objects diverging lenses collimating holes etc to be defined as combinations of simple primitives blocks cylinders semi spheres The PTS software does not inherently support complex optical devices such as lenses mirrors etc However because it is geometry based creating mediums with a lens shape and the correct optical properties will create a lens Similarly creating a block with high index of refraction will create a mirror due to Fresnel reflection and creating a hole of vacuum through an absorbing medium will create a collimating hole etc Input to the PTS software is done through text file generally with the extension mci for Monte Carlo input A well defined syntax is used to specify mediums photons sources and detectors photon density maps The
99. a quasi ballistic photon The results shown in Table 4 were calculated by considering a quasi ballistic photon to be one that underwent at least one scattering event and did not wander to a position that was outside of a cylinder centered on the photon source with a radius of 30 microns However photons that are launched near the outer edge of the photon source 25 microns do not have to wander very far in the radial direction before leaving the cylinder but must wander up to 50 microns in the opposite direction across the cylinder to exit the cylinder To avoid this asymmetry a quasi ballistic photon can be defined as a photon that does not wander outside of a cylinder centered on its starting position with an axis oriented along the initial photon trajectory Table 7 shows the last density map that implement these two methods of determining quasi ballistic photons Table 7 Test Case 4 Density Map Located Downstream of Collimating Hole Relating Maximum Radial Distance wrt Photon Source to Maximum Radial Distance wrt Photon Starting Position Maximum Radial Distance wrt Center of Source microns Maximum Radial Distance wrt Photon Starting Position 0 5 10 15 20 25 30 35 40 45 50 microns 0 4007 11868 19872 28264 35908 0 0 0 0 0 0 5 0 0 3 1 2 0 0 0 0 0 0 10 0 0 2 9 10 0 0 0 0 0 0 15 0 0 1 1 4 2 0 0 0 0 0 20 0 0 1 7 11 1 0 0 0 0 25 0 0 0 5 12 3 0 0 0 0 30 0 0 0 3 10 3 0 0 1 0 0 35 0 0 0 0 13 1 0 0 0 0 40 0
100. against this ideal model However in a medium that is both scattering and absorbing the photons exiting the medium do not have the same distribution as the source As the scattering level is increased the fraction of ballistic photons decreases At scattering levels needed for biomedical applications the relative fraction of ballistic photons is less than 10 The challenge in optical tomography is to accept the photons that carry information about the internal structure of the scattering medium while rejecting those that do not QUASI BALLISTIC PHOTON DETECTOR PHOTON SCATTERING MEDIUM SHADOW IMAGE OF OBJECT OBJECT IN SCATTERING MEDIUM PHOTON SOURCE BACKSCATTERED PHOTON PHOTON BALLISTIC PHOTON BLOCKED PHOTON ABSORBED PHOTON NN Figure 3 Basic Setup for Producing A Shadowgram In Figure 3 two types of photons carry information about objects within the medium ballistic and quasi ballistic photons Ballistic photons have a pathlength which can be directly related to travel time through the medium that is equal to that of the medium and a trajectory that is unchanged by passage through the scattering medium Quasi ballistic photons have undergone one or more scattering events but have been scattered in such a manner as to have pathlengths that are close to that of the medium and a trajectory that is only slightly changed by passage through the scattering medium Clea
101. and absorbing medium id diverging lens 1 glass part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 45 index of refraction shptype CIRCLE shape of medium p000 10 x y z coords of first point pl 0 0 015 10 x coords of second point normalvector 0 0 1 normal vector for extrude extrudelen 0 004 extrusion length of cylinder Medium define a scattering and absorbing medium lens semisphere shape id diverging lens 2 air part of diverging lens 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype SEMISPHERE shape of medium p000 10 012 x y z coords of first point 0 0 01125 10 012 y z coords of second point 0 0 10 004 x y z coords of fourth point cutting plane normalvector 0 0 1 normal vector of cut surface plano side on right This combination forms a diverging lens with a plano side on the left in Figure 19 and the concave side on the right The points and p were selected to form semi sphere with a radius of 0 011250 m in accordance with the Lensmaker Formula which applies to thin lenses operating in vacuum below f the focal distance m where n the index of refraction of the lens medium the radius of curv
102. criteria for density map absorbcriteria NONE absorption criteria for density map calccount 205653 number of photons that met calccriteria absorbcount 0 number of photons that met absorbcriteria totalcount 205653 number of photons that passed through density map containcount 87777 number of photons contained within density map containmax 10000000000000000000 max number of photons allowed to be contained within density map shptype CIRCLE type of shape for object 0 00000000 0 00000000 0 08600000 point 0 pl 0 00000000 0 00000000 0 00000000 point 1 p2 0 00000000 0 00000000 0 00000000 point 2 p3 0 00000000 0 00000000 0 00000000 point 3 normalvector 0 00000000 0 00000000 1 00000000 surface normal extrudelen 0 00000000 extrusion length m 0 if planar radius 0 00500000 radius of circle m radius2 0 0000250000 radius of circle squared m 2 idxrow image y pos HASH PHOTPOSY 0 00100000 0 00100000 0 00001000 row index idxcol image x pos HASH PHOTPOSX 0 00100000 0 00100000 0 00001000 column index center for circle Text Output File mco The output file contains a complete description of the simulation model as well as the results produced by photon density maps and PHOTINFO calculations The output file is in the same form uses the same language and syntax as the input file allowing the output file to act as the input file to the PTS software if desired useful for recreating simulation runs A
103. default mci default mco mlmainl2 testl test1 mci testl mco mimainl2 testl txt test1 txt testl mco mimainl2 testla in testla out testla in testla out Text Input File mci The input file contains a complete description of the simulation model and is processed by the PTS software prior to the commencement of a simulation run Each simulation run requires a separate input file batch runs are not supported by the current version of the PTS software The input file is written in a human readable ASCII text form It follows many standard ANSI C conventions such as the facility to include other input files using the include statement the ability to add comments using a leading and the capability to split long lines using the line continuation character The level of complexity required to described the simulation model is not high therefore a simple context based language was developed that mirrors the underlying object oriented nature of the software This language is used in both the input file and the output file and indeed an output file may be read as an input file to recreate a simulation run In this language tokens characters separated by white space or enclosed in quotation marks are used as the fundamental syntactical building block A token is evaluated in one of three ways it is used to change the primary context it is used to change the secondary context or it is used to form a value based upon its positio
104. extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object 0 0001000 0 0000000 10 2610000 point 0 center for circle pl 0 0001000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000025 radius of circle m radius squared 0 000000 radius of circle squared PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM type of photon source qty 1000000 initial number of photons in source to launch qtyleft 1000000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object pO 0 1000000 0 0000000 0 0000000 point 0 center for circle 1 0 1000000 0 0012500 0 0000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 001250 radius of circle m radius squared 0 000002
105. of capturing photon information and reporting results In addition the optical characteristics of reflection and refraction at object surfaces are fully supported The program can be thought of as a form of ray tracing with individual photons forming the rays and user defined image planes capturing the results In the PTS software photons are assumed to be discrete particles and only ballistic behaviour is modeled A full description of the software and its underlying modules is beyond the scope of this User Manual The reader is referred to Development of Software Tools for Simulation of Photon Transport in Scattering and Absorbing Media the Photon Transport Simulator for information on the overall program and to Development of NURB Surface and Visualization Extensions to the Photon Transport Simulator for information on the NURB surface and Scheme ACIS extensions Hints and Tricks Use a standard setup file such as stdsetup mci to configure all models in a consistent manner Include this setup file into the actual model input file using the include statement Copy this setup file into the same directory as the other mci input files Set the PATH command to the directory containing the 1 12 file and then set the current directory to be the directory in which the mci input files are located This will shorten the command line Output files mco and scm will be in the current directory unless output file names including
106. p3 1 1 10 249 x idxcol col 1 1 has idxrow row 1 1 has pe of map pe of medium coords of first point coords of second point coords of third point coords of fourth point h PHOTPOSX 0 0125 0 0125 0 0005 hash lookup x pos h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup N NNN Map define a density map id x y pos of beam upstream of collimating hole type planar planar ty shptype RECTANGLE sha 1 1 10 261 pl 1 1 10 261 x p2 1 1 10 261 x y 3 1 1 10 261 idxcol col 1 has idxrow row 1 1 has pe of map pe of medium coords of first point coords of second point coords of third point coords of fourth point h PHOTPOSX 0 0125 0 0125 0 0005 hash lookup x pos h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup pos N NNN Map define a density map id x y pos downstream type planar planar ty shptype RECTANGLE sha 1 1 10 271001 x 1 1 1 10 271001 p2 sl I 10 241001 0 p3 1 1 10 271001 idxcol col 1 1 has idxrow row 1 1 has of collimating hole pe of map pe of medium y z coords of first point y z coords of second point y z coords of third point y z coords of fourth point h PHOTPOSX 0 000150 0 000150 0 000005 hash lookup x pos h PHOTPOSY 0 000050 0 000050 0 000005 hash lookup pos 103 Appendix Test Case 6 Output File A
107. path are specified The Scheme output file contains all of the medium objects including the bounding box and the ambient media Edit the scm text file to delete the definitions for these objects before loading the Scheme file into ACIS These two objects are larger than all other objects and will obscure the view of everything else Photon trajectories are represented in ACIS as wire bodies In order to view the photon trajectory and point photon sources the OpenGL viewport must be configured to display edges and vertices 36 Appendix A Standard Setup Input File for all Test Cases Input File stdsetup mci standard setup file for Test Cases written by Nick Pfeiffer Dec 27 02 RandomNumberGenerator define the random number generator used for the simulation type MC type of random number generator seed 0 initial seed Medium define a scattering and absorbing medium id bounding box 1 factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 100000000 0 coefficient of absorption indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1001 1001 1001 x z coords of first point pl 1001 1001 1001 x y z coords of second point p2 1001 1001 1001 x y z coords of third point 1001 1001 1001 2 coords of fourth point extrudelen 2002 extrusion length of box Medium define a scattering and absorbing medium id ambient
108. photon information posstart 0 1000000 0 0000020 0 0000000 starting position trajstart 0 0000000 0 0000000 1 0000000 starting trajectory poscurrent 0 0000000 0 0000198 10 2710010 current position trajcurrent 0 0000000 0 0000002 1 0000000 current trajectory medium ambient current medium in which photon resides wavelength 514 000000 wavelength of photon nm movecount 12 number of moves made by photon 33 scattercount 0 number of scatter events reflectcount 2 number of reflect events refractcount 10 number of refract events pathlength 10 371001 total pathlength m life 0 000000034610 lifetime of photon secs desireddist 10000000000000000000 000000 current desired distance photposrsource 0 100000 radial component of current position reference to the photon source normal photposrstart 0 100000 radial component of current position reference to the photon start trajectory and pos phottrajdotsource 1 000000 dot product of current trajectory and photon source cosine of forward scattering angle for photons with starting trajectory equal to source normal hottrajdotstart 1 000000 dot product of current trajectory and photon starting trajectory cosine of forward scattering angle photposrmaxsource 0 100000 maximum radial component of any recorded position reference to the photon source normal photposrmaxstart 0 100000 maximum radial component of any recorded position reference to the photon start traject
109. that represent arbitrary surfaces in space In essence NURB surface is a mapping from v parameter space to x z R space A description of NURB surfaces is beyond the scope of this User Manual please see Development of NURB Surface and Visualization Extensions to the Photon Transport Simulator for details Control Points Figure 7 Rendered and Wireframe View of Simple NURB Surface Control points P form a net within which the NURB surface lies the surface lies within the convex hull of the control points The number and location of knots and the degree may be different for the and v directions For the NURB curve and surface software extensions developed for the PTS system the parameters are assumed to lie between 0 and 1 with the endpoints representing the endpoints of open non singular NURB curves and surfaces The simple NURB surface of degree 2 in both the and directions is shown in Figure 7 The PTS software is primarily intended for photon transport simulation of scattering mediums and needs to be able to represent rather simple objects The rationale for developing NURB surface extensions was to be able to accurately model non spherical optical lenses and mirrors as well as soft objects Due to the limitations of the underlying geometry data structure already in place a subset of full NURB surfaces was developed A NURBPLANE shape is defined as the three dimensional shape formed by the
110. the medium is defined to have no scattering or absorption Figure 9 shows the simulation model SCATTERING MEDIUM 10 mm THK UNIFORM PHOTON SOURCE RADIUS 25 MICRONS 4 PHOTON DENSITY MAP_ UPSTREAM OF MEDIUM PHOTON DENSITY DOWNSTREAM OF MEDIUM Figure 9 Model Setup for Test Case 1 In Test Case 1 two photon density maps are defined to capture the x and y coordinates of the photons as they pass through creating an image of the beam One photon density map is located 1 micron upstream of the scattering medium the other photon density map is located 1 micron downstream of the scattering medium Segments of the input file showing the definition of the scattering medium photon source and density maps are shown below Medium define a scattering and absorbing medium id scattering medium sample of scattering medium g 9 g factor of medium mean cosine of forward scattering angle scatterratio 0 1000 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 1 2 coords of first point pl 1 1 1 2 coords of second point 2 1 1 1 z coords of third point p3 1 1 1 z coords of fourth point extrudelen 01 extrusion length of box 23 PhotonSource define photon source id uniform source 1 type UNIFORM uniform type of photon source pO 0 0 0 x
111. the probability that the photon will be absorbed in where distance In pd the extrusion length of the medium UE a The coefficient of scattering or absorption may also be specified directly mus 0 000000 coefficient of scattering m 1 mua 2993 329531 coefficient of absorption m 1 The indexrefraction secondary context token is used to specify the index of refraction of the medium If no index of refraction is specified an index of refraction of 1 is assumed Similarly if no scattering or absorption coefficient is specified either directly or indirectly a value of zero is assumed The geometry of an object is fully defined by its shape An identical shape definition method with the same secondary context tokens is used for photon sources and photon density maps as well as mediums A shape definition consists of a shape type RECTANGLE CIRCLE or SEMISHERE several defining points an optional normal vector and an optional extrusion length distances coordinates lengths etc are defined in meters Two Dimensional Primitive Shapes A rectangular shape is defined by four co planar points p2 and p representing the corners of the rectangle The surface normal to this rectangle may be specified by the normalvector value token or is calculated by taking the cross product of the vector from to with the vector from to Points are defined by the secondary context token
112. z coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude Medium define a scattering and absorbing medium id mirror 2 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CIRCLE shape of medium p000 9 5 x y z coords of first point 0 0 015 9 5 x z coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude Medium define a scattering and absorbing medium id diverging lens 1 glass part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 45 index of refraction shptype CIRCLE shape of medium p000 10 x y z coords of first point 0 0 015 10 x y 2 coords of second point normalvector 0 0 1 normal vector for extrude extrudelen 0 004 extrusion length of cylinder Medium define a scattering and absorbing medium lens semisphere shape id diverging lens 2 air part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype SEMISPHERE shape of medium pO 0 0 10 012 x y 2 coords of first point
113. 0 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 oOoooococ 010000 oOoooococ 009500 oOoooococ 009000 oOoooococ 008500 oOoooococ 008000 007500 007000 oooooo 006500 006000 oOoooooo 005500 ooooo 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 87 Ooo Q 05 OOO lt QUO 0 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00
114. 0 0 000020 0 00 1 00 3037 00 2680 00 3880 00 6 00 00 0 000015 1 00 2 00 2816 00 2837 00 9630 00 2 00 2 00 0 000010 4 00 2 00 2577 00 2503 00 2220 00 2 00 00 0 000005 1 00 1 00 2786 00 2730 00 2492 00 1 00 2 00 0 000000 4 00 1 00 2703 00 2689 00 9718 00 2 00 0 00 0 000005 1 00 0 00 2547 00 2688 00 4143 00 0 00 2 00 0 000010 0 00 0 00 13004 00 12532 00 1 00 2 00 2 00 0 000015 1 00 2 00 9715 00 12452 00 50 center for circle surface normal if planar 000050 0 000005 row index 000050 0 000005 column index 0 000030 0 000005 0 000035 0 000000 0 000030 2 00 1 00 0 00 2 00 0 00 1 00 0 00 4 00 0 00 0 00 2 00 1 00 0 00 00 2 00 1 00 12324 00 0 00 3 00 12831 00 1 00 1 00 2647 00 1 00 1 00 2550 00 2 00 0 00 2704 00 2 00 0 00 2863 00 1 00 4 00 2648 00 2 00 3 00 2725 00 1 00 0 00 12531 00 0 00 0 00 12239 00 0 000035 0 00 00 4 00 0 00 00 0 00 1 00 00 0 00 0 00 2 00 00 2 00 00 00 3 00 9648 00 5 00 1 00 12878 00 3 00 1 00 2846 00 1 00 2 00 2760 00 1 00 1 00 2552 00 2 00 3 00 2736 00 0 00 3 00 2852 00 4 00 1 00 2719 00 0 00 0 00 12718 00 1 00 2 00 9609 00 0 0000 0 0 0 00 3 00 16 Te 00 N 4 00 00 4139 00 4078 9689 12168 12340 9681 3914 0 4139 00
115. 0 00 00 5 00 00 00 0 00 00 00 2 00 00 00 0 00 00 00 2 00 00 00 13 00 13 00 3 00 4 00 16 00 2 00 4 00 2 00 7 00 3 00 1 00 1 00 1 00 0 00 3 00 0 00 1 00 1 00 3 00 3 00 4 00 2 00 1 00 2 00 3 00 1 00 Appendix Test Case Input File A Single Medium with Scattering Using 50 000 000 Photons Input File testcase3 mci RunInfo comment Test Case 3 N A Single Medium with Scattering but without Absorption N Photon Source with 50 million photons include stdsetup mci include the standard setup for all test cases random number generator bounding box Medium define a scattering and absorbing medium id scattering medium sample of scattering medium 9 g factor of medium mean cosine of forward scattering angle scatterratio 1000 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 1 z coords of first point pl 1 1 1 x y z coords of second point p211 1 x y z coords of third point p3 11 1 x y z coords of fourth point extrudelen 01 extrusion length of box PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source p0000 x z coords of center in m 1 0 0 000025 0 x z coords of point on circumference in m normalvector 0 0 1 launch photons parallel to z axis wavelength 514
116. 0 0 002000 0 001000 113 surface normal 0 if planar 012500 0 000500 row index 012500 0 000500 column index 0 011000 0 007500 0 004500 0 001500 0 001500 2 00 0 00 4 00 8 00 19 00 5 00 8 00 3 00 12 00 9 00 5 00 13 00 3 00 4 00 20 00 5 00 17 00 15 00 0 00 3 00 2 00 10 00 5 00 16 00 15 00 2 00 6 00 9 00 21 00 5 00 6 00 12 00 3 00 9 00 7 00 9 00 5 00 17 00 00 00 00 00 00 00 NN 20 00 4 00 0 00 0 00 4 00 22 00 27 00 15 00 7 00 9 00 14 00 13 00 23 00 8 00 center for circle 3 00 6 00 1 00 2 00 14 00 22 00 2 00 3 00 6 00 8 00 18 00 8 00 2 00 6 00 8 00 20 00 17 00 5 00 3 00 9 00 9 00 3 00 24 00 18 00 5 00 5 00 3 00 3 00 6 00 2 00 14 00 2 00 8 00 2 00 7 00 21 00 14 00 00 00 00 00 00 00 N Da FEN 20 00 4 00 21 00 2 00 3 00 12 00 20 00 16 00 4 00 2 00 10 00 17 00 4 00 20 00 0 010500 0 007000 0 004000 0 001000 0 002000 3 00 9 00 20 00 6 00 9 00 8 00 3 00 3 00 12 00 8 00 2 00 8 00 5 00 6 00 8 00 10 00 9 00 20 00 15 00 9 00 7 00 2 00 10 00 9 00 17 00 20 00 5 00 00 00 00 00 Q 16 00 7 00 4 00 1 00 9 00 23 00 19 00 00 00 00 00 00 00 53 14 00 4 00 2 00 8 00 1 00 13 00 2 00 22 00 3 00 6 00 8 00 16 00 22 00
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119. 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 QC CO CO OOO OOO O 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 006500 007000 007500 008000 008500 009000 00
120. 0 00 00 0 00 00 84 TOO GTO 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 TO OOTO 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 0
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122. 0 00 00 00 0 00 00 00 00 00 00 00 0 010000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 ooooooo oOooooooo oOooooooo ooooooo oOooooooo oOooooooo ooooooo ooooooo oOooooooo ooooooo ooooo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oOooooooo ooooooo oOooooooo oOooooooo oOooooooo ooooooo oOooooooo ooooooo oOooooooo ooooooo ooooo 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 ooooooo ooooooo ooooooo oOooooooo ooooooo ooooooo ooooooo Oooooooo oOooooooo oOooooooo ooooo 0 00 00 00 00 00 00 00 0
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124. 0 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 OOO
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128. 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 tle 378 372 369 395 341 29Ts 354 398 386 390 390 399 215 334 365 349 50 0 0 0 365 366 398 0 0 364 343 389 383 416 346 0 0 390 354 384 374 395 369 0 0 395 354 380 377 367 374 0 0 28 367 364 36 364 367 0 0 24 394 377 390 383 374 372 342 364 357 377 384 345 346 387 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 379 410 415 400 362 367 363 379 373 404 382 399 396 369 374 409 373 369 0 0 394 396 349 382 393 386 0 00 391 343 403 368 368 378 0 00 369 391 398 39d 392 380 0 00 37 350 387 390 37 388 1 00 392 368 39 379 36 359 0 00 383 35 364 392 380 405 1 00 363 370 388 381 360 345 0 00 0 304 0 398 366 353 367 00 00 00 00 00 00 00 00 00 00 00 00 00 0
129. 0 408 00 344 00 338 00 384 00 370 00 355 00 0 00 1 00 331 00 362 00 361 00 350 00 138 00 1 00 0 00 36 00 344 00 346 00 356 00 1 00 0 00 0 00 0 00 399 00 397 00 375 00 1 00 0 00 0 00 0 00 359 00 392 00 313 00 0 00 0 00 0 00 0 00 69 00 385 00 1 00 1 00 0 00 1 00 00 00 00 00 00 00 0 010500 0 007000 0 004000 0 001000 0 002000 0 005000 0 008000 0 00 373 00 373 00 389 00 397 00 397 00 374 00 395 00 388 00 374 00 240 00 0 00 0 00 360 00 385 00 373 00 371 00 0 00 0 00 0 00 280 00 380 00 357 00 359 00 1 00 0 00 0 00 0 00 378 00 362 00 395 00 0 00 0 00 0 00 0 00 369 00 373 00 197 00 0 00 0 00 0 00 1 00 169 00 350 00 0 00 00 00 0 00 00 00 00 00 00 00 oOoooococ 0 010000 008500 011500 data 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00
130. 0 0 0 3 4 0 0 0 0 0 45 0 0 0 0 1 3 1 0 0 0 0 50 0 0 0 0 0 0 0 0 0 0 0 From Table 7 the number of photons that did not leave the 30 micron radius cylinder centered on the photon source is determined by summing all of the table bins in the columns from 0 to 25 microns less than 30 microns and subtracting the number of ballistic photons The number of scattered photons is the difference between the total number of photons passing through the collimating hole and the sum of the ballistic and quasi ballistic photons From Table 7 the number of photons that did not leave the 30 micron radius cylinder centered on the photon starting positions is determined by summing all of the table bins in the rows from 0 to 25 microns less than 30 microns and subtracting the number of ballistic photons Table 8 shows a summary of these derived quantities 29 Table 8 Test Case 4 Summary Ballistic Quasi Ballistic and Scattered Photon Quantities from Tables 4 and 7 No of No of No of Ballistic Photons Quasi Ballistic Scattered Photons Using a Maximum Radial Distance wrt Center of Source of 99915 120 3 30 microns Using a Maximum Radial Distance wrt Center of Starting 99915 79 44 Position of 30 microns Earlier work by Chu Pfeiffer Using a Maximum Radial Distance wrt Center of Source of 30 microns 100078 102 4 It can be seen that the numbers of ballistic quasi ballistic and scattered photons calculated by the PTS software compare
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132. 0 0 0000000 1 0000000 extrudelen 0 000000 extrusion length idxrow 0 000020 0 000010 0 000040 data 0 00 00 1 00 N 00 00 1 00 N 00 00 0 00 N 00 00 0 00 N 00 2 00 n NB NN 3 00 3 00 6949 00 2654 00 00 N 2613 00 2617 00 0 00 N 2909 00 2756 00 0 00 N 2928 00 2923 00 3 00 N 2758 00 2595 00 00 N 2762 00 2969 00 00 N 2508 00 2820 00 0 00 N 6830 00 2916 00 2 00 N 5 00 7 5 0 00 0 WOO 0 0 000050 0 000015 0 000015 0 000045 0 00 1 00 0 00 000050 3 00 3 00 0 00 000045 0 00 0 00 0 00 000040 0 00 1 00 1 00 000035 2 00 2 00 1 00 000030 1 00 3986 00 2 00 000025 0 00 12537 00 6918 00 2 00 2 00 2633 00 2724 00 2 00 1 00 2547 00 2880 00 00 0 00 2861 00 2760 00 3 00 2 00 2680 00 2793 00 2 00 1 00 2820 00 2755 00 00 0 00 2835 00 2709 00 00 1 00 12652 00 6958 00 00 0 00 4060 00 row indexl HASH PHOTPOSY 0 000050 0 idxcol col 1 1 HASH PHOTPOSX 0 000050 0 point 0 point 1 point 2 point 3 m 0 0 000045 0 000040 0 000010 0 000005 0 000020 0 000025 0 000050 1 00 0 00 1 00 3 00 1 00 0 00 0 00 2 00 2 00 3 00 3 00 0 00 1 00 1 00 0 00 0 00 00 2 00 2 00 1 00 00 0 00 00 1 00 1 00 1 00 2 00 1 00 00 3 00 1 00 0 00 9506 00 12417 00 00 0 00 0 00 2 00 12854 00 12947 00 4 00 2 00 0
133. 0 00 00 00 00 00 00 00 00 define a photon density id x y pos of beam upstream of collimating hole 00 00 00 00 00 0 011500 0 00 00 00 00 00 00 00 00 0 012000 0 00 00 00 00 00 00 00 00 0 012500 type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2610000 pl 1 0000000 1 0000000 10 2610000 p2 1 0000000 1 0000000 10 2610000 p3 1 0000000 1 0000000 10 2610000 normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length idxrow idxcol 0 009500 006500 003500 000500 002500 005500 008500 011500 data 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 00 00 00 00 00 N 00 00 0 00 0 009000 0 0 0 0 006000 003000 000000 003000 006000 009000 012000 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00
134. 0 00 23 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 24 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 25 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 26 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 27 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 28 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 29 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 30 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 31 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 32 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 33 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 34 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 35 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 36 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 37 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 38 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 39 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 40 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 41 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 42 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 43 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 44 000000 N 0 00 0 00
135. 0 00 0 00 0 00 0 00 0 00 983 00 1219 00 0 00 0 00 0 00 0 00 1301 00 1304 00 0 00 0 00 0 00 0 00 310 00 197 00 441 00 0 00 0 00 0 000015 0 00 0 00 299 00 311 00 009 00 0 00 0 00 0 000010 0 00 0 00 268 00 253 00 198 00 0 00 0 00 0 000005 0 00 0 00 213 00 211 00 183 00 1 00 0 00 0 000000 0 00 0 00 180 00 271 00 961 00 0 00 0 00 0 000005 0 00 0 00 238 00 297 00 377 00 0 00 0 00 0 000010 0 00 0 00 1284 00 1349 00 0 00 0 00 0 00 0 00 939 00 1226 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 Map define a photon density map id scattercount vs radial position wrt source downstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object 67 1261 12 13 15 99 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 86 00 0 00 0 00 281 00 0 00 0 00 297 00 0 00 0 00 276 00 0 00 0 00 296 00 0 00 0 00 260 00 0 00 0 00 267 00 0 00 0 00 22 00 0 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 989 12 12 924 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00
136. 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000045 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000050 define a photon density id photon info downstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2710010 point 0 center for circle pl 1 0000000 1 0000000 10 2710010 point 1 p2 1 0000000 1 0000000 10 2710010 point 2 p3 1 0000000 1 0000000 10 2710010 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index idxcol col 1 1 HASH PHOTINFO 0 000000 20 000000 1 000000 column index 0 000000 1 000000 2 000000 3 000000 4 000000 6 000000 7 000000 8 000000 9 000000 10 000000 11 000000 12 000000 13 000000 14 000000 15 000000 16 000000 17 000000 18 000000 19 000000 20 000000 data 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000050 X 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000045 0 00 0 00 0 00 0 00 0 00 0
137. 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 45 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 46 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 47 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 48 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 49 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 50 000000 Map define a photon density map id max radial deviation wrt source vs max radial deviation wrt start pos downstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 000000 1 000000 0 020001 point 0 center for circle pl 1 000000 1 000000 0 020001 point 1 p2 1 000000 1 000000 0 020001 point 2 p3 1 000000 1 000000 0 020001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row 1 1 HASH PHOTPOSRMAXSTART 0 000000 0 000050 0 000005 row index idxcol col HASH PHOTPOSRMAXSOURCE 0 000000 0 000050 0 000005 column index 0 000000 0 000005 0 000010 0 000015 0 000020 0 000025 000030 0 000035 0 000040 0 000045 0 000050 data 4007 00 11868 00 19872 00 28264 00 35908 00 0 00 00 0 00 0 00 0 00 0 00 0 000000 N 0 00 0 00 3 00 1 00 2 00 0 00 00 0 00 0 00 0 00 0 00 0 000005 N 0 00 0 00 2 00 9 00 10 00 0 00 00 0 00 0 00 0 00 0 00 0 000010 N 0 00 0 00
138. 0 10 261 x y z coords of first point pl 0 000100 0 000025 10 261 x z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 2 hole medium for collimator downstream of sample 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 0 10 261 x y z coords of first point pl 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 3 hole medium for collimator downstream of sample g 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100 0 10 261 x y z coords of first point pl 0 000100 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole In order to verify the operation of the model a single photon is launched from a point photon source The photon is specified with a start
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141. 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 82 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00
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143. 00 00 00 00 3 3 11 00 3 00 7 00 2 00 2 00 6 00 11 00 9 00 2 00 00 00 00 00 00 9 00 4 00 2 00 15 00 2 00 1 00 13 00 8 00 2 00 7 00 33 00 2 00 4 00 19 00 12 00 2 00 22 00 4 00 4 00 4 00 18 00 20 00 1 00 27 00 5 00 2 00 3 00 16 00 14 00 00 00 00 00 Ov 3 00 4 00 18 00 4 00 5 00 3 00 2 00 3 00 2 00 14 00 1 00 0 00 3 00 7 00 2 00 2 00 16 00 6 00 5 00 5 00 4114 00 13 00 5 00 22 00 6 00 6 00 6 00 22794 00 8 00 8 00 3 00 7 00 4 00 3 00 22804 00 6 00 2 00 1 00 3 00 2 00 3 00 4199 00 7 00 5 00 7 00 4 00 00 5 00 7 00 00 3 00 3 00 N 00 00 00 00 00 00 6 00 N 00 00 00 00 00 00 5 00 N 8 00 5 00 3 00 00 4 00 00 3 00 N 4 00 00 23 00 LS 5 00 4 00 8 00 7 00 00 00 00 00 00 Ww 7 00 10 00 00 6 00 00 1 00 19 00 2 00 2 00 00 3 00 3 00 3 00 5 00 19 00 4 00 2 00 4 00 0 00 0 00 5 00 4 00 10 00 0 00 5 00 3 00 3 00 3 00 1 00 21 00 20 00 4 00 3 00 5 00 2 00 7 00 5 00 16 00 16 00 00 00 00 00 00 00 9 00 13 00 00 00 00 00 00 00 8 00 16 00 gt HOUT 3 00 3 00 3 00 6 00 10 00 11 00 19 00 0 002500 21 00 11 00 17 00 1 00 1 00 2 00 2 00 1 00 27
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146. 00 00 00 oOooooooo oOooooooo oOooooooo oOooooooo Oooooooo Oooooooo Oooooooo oOooooooo oooo 009000 012000 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 o0 OG O0 0 C oooo 009500 012500 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 oOoooococ 012500 oOoooococ 012000 oOoooococ 011500 011000
147. 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo ooooo oOooooooo 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo Oooooooo oOoooooo 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00
148. 00 00 00 126 00 00 00 00 00 0 000045 0 00 00 00 00 00 00 00 00 00 0 000050 00 00 00 00 0 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00
149. 00 00 00 00 ooooo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ooooo 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 CK oO OGOGO 0 00 00 00 00 00 00 00 00 00 0 00
150. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 oOoooococ oOoooococ 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 011500 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 012000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 012500 define a photon density id pos downstream of collimating hole id of density map type PLANAR
151. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 oo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
152. 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 122 TOO GTO 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00
153. 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 000500 001000 001500 002000 002500 003000 003500 004000 004500 005000 005500 TO GOOO 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 0
154. 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 oo 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 0 0 010500 010000 009500 009000 008500 008000 007500 007000 006500 006000 005500 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00
155. 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 OOOO oF OOOO lt lt 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00
156. 00 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 10 261 x y z coords of first point pl 1 1 10 261 x gt coords of second point p211 10 261 x y z coords of third point p3 1 1 10 261 x z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator hole medium hole medium for collimator downstream of sample g 1 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium p000 10 261 x y z coords of first point 1 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole As the purpose of the PTS software is to enable the use of lens systems to be investigated as a means of enhancing the filtering properties of collimator arrays in angular domain imaging systems it was decided that the ability to model lenses accurately was required Initially thin lenses were to be modeled as discrete planar objects which altered the trajectory of photons passing through them However the addition of Fresnel reflection and refraction at the surface of mediums provided a better mechanism for simulating lenses The semi sphere shape was described earlier and was impleme
157. 00 point 0 center for circle pl 0 0000000 0 0112500 10 0120000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 10 0040000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 011250 radius of circle m radius squared 0 000127 radius of circle squared Medium define a scattering and absorbing medium id converging lens id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 2 000000 index of refraction shptype SEMISPHERE type of shape for object p0 0 0000000 0 0000000 9 9755000 point 0 center for circle pl 0 0000000 0 2485000 9 9755000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 10 2235000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 248500 radius of circle m radius squared 0 061752 radius of circle squared Medium define a scattering and ab
158. 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 o o o o o o o o o o o o o o o 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 oo o o 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 99 e 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00
159. 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 376 388 330 286 248 375 00 37 7 00 350 383 245 33 380 381 00 360 00 385 00 45 376 00 00 00 391 347 56 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 421 411 416 426 00 00 420 396 320 00 35 384 401 390 391 390 3577 00 372 SH 3914 377 379 408 359 00 344 345 392 391 425 00 415 00 392 00 381 409 392 371 342 00 365 401 404 361 342 406 344 00 3181 364 383 397 374 353 365 00 380 393 409 405 383 383 352 00 37 9 354 396 389 354 432 367 00 400 ST 393 383 376 376 367 00 351 385 403 405 436 389 391 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 0 plate 0 0 2 0 0 0 0 0 387 394 417 390 365 002000 418 413 387 386 403 39 378 001500 363 362 398 362 431 375
160. 00 3 00 1 00 2 00 6 00 7 00 15 00 2 00 5 00 3 00 1 00 18 00 15 00 9 00 0 002000 12 00 17 00 16 00 2 00 4 00 3 00 6 00 4 00 31 00 3 00 4198 00 22793 00 2 00 5 00 4 00 4 00 1 00 4 00 4 00 11 00 12 00 11 00 0 001500 18 00 16 00 13 00 1 00 1 00 2 00 4 00 15 00 19 00 4174 00 46313 00 52694 00 2 00 2 00 5 00 6 00 2 00 2 00 7 00 3 00 10 00 23 00 8 00 0 001000 18 00 14 00 12 00 4 00 5 00 1 00 3 00 17 00 21 00 23007 00 52402 00 52678 00 5 00 1 00 5 00 4 00 5 00 4 00 6 00 3 00 14 00 15 00 12 00 0 000500 21 00 10 00 17 00 1 00 3 00 3 00 2 00 23 00 22 00 22835 00 52735 00 52643 00 5 00 2 00 3 00 6 00 4 00 1 00 2 00 5 00 10 00 11 00 13 00 0 000000 15 00 7 00 14 00 2 00 3 00 3 00 1 00 10 00 18 00 4195 00 46505 00 52642 00 4 00 2 00 6 00 4 00 5 00 3 00 3 00 2 00 6 00 11 00 13 00 0 000500 13 00 16 00 13 00 3 00 2 00 0 00 4 00 10 00 25 00 4 00 4154 00 22828 00 4 00 4 00 4 00 2 00 4 00 4 00 6 00 9 00 9 00 5 00 0 001000 11 00 11 00 12 00 3 00 4 00 3 00 6 00 3 00 28 00 00 4 00 3 00 00 5 00 17 00 3 00 2 00 5 00 7 00 16 00 10 00 5 00 0 001500 10 00 16 00 13 00 2 00 1 00 4 00 00 0 00 6 00 2 00 5 00 1 00 3 00 6 00 35 00 4 00 3 00 2 00 7 00 14 00 15 00 3 00 0 002000 11 00 13 00 12 00 2 00 1 00 1 00 00 1 00 6 00 2 00 3 00 3 00 3 00 27 00 18 00 4 00 3 00 2 00 10 00 10 00 13 00 5 00 0 002500 15 00 14 00 20 00 8 00 3 00 0 00 7 00 3 00 2 00 9 00 3 00 2 00 111 1 00 11 00 12 00 6 00 20
161. 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 011500 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 011000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 0 00 0 00 81 oo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oo 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00
162. 00 0 00 0 00 0 00 1 00 0 00 1 00 0 00 0 00 0 00 0 00 3 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 4 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 5 000000 N 0 00 0 00 1 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 6 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 7 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 8 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 9 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 10 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 11 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 12 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 13 000000 X 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 14 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 15 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 16 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 17 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 18 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 19 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 20 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 21 000000 69 0 0 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00 0 00 22 000000 N 0 00 0 00 0 00 0 00 0 00 0 00 00 0 00 0 00 0 00
163. 0000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 0000000 1001 0000000 1001 0000000 point 0 center for circle pl 1001 0000000 1001 0000000 1001 0000000 point 1 p2 1001 0000000 1001 0000000 1001 0000000 point 2 p3 1001 0000000 1001 0000000 1001 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 0000000 1000 0000000 1000 0000000 point 0 center for circle pl 1000 0000000 1000 0000000 1000 0000000 point 1 p2 1000 0000000 1000 0000000 1000 0000000 point 2 p3 1000 0000000 1000 0000000 1000 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium
164. 00000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 45 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 46 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 47 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 48 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 49 000000 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 50 000000 define a photon density id scattercount vs radial position wrt start pos downstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object 1 000000 1 000000 0 020001 point 0 center for circle pl 1 000000 1 000000 0 020001 point 1 p2 1 000000 1 000000 0 020001 point 2 p3 1 000000 1 000000 0 020001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTSCATTERCOUNT 0 000000 50 000000 1 000000 row index col HASH PHOTPOSRSTART 0 000000 0 000050 0 000005 column index 0 000000 0 000005 0 000010 0 000015 0 000020 0 000025 0 000030 0 000035 0 000040 0 000045 0 000050 data 99915 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 000000 4 00 5 00 21 00 7 00 16 00 17 00 13 00 14 00 6 00 5 00 0 00 1 000000 X 1 00 1 00 1 00 0 00 4 00 2 00 2 00 0 00 1 00 0 00 0 00 2 000000 N 0
165. 1 00 7 00 00 7 00 00 8 00 0 00 0 00 4 00 00 5 00 10 00 7 00 22 00 0 9 00 27 00 9 00 10 00 10 00 27 00 11 00 21 00 0 define a photon density id x y pos of beam after expansion id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2490000 pl 1 0000000 1 0000000 10 2490000 p2 1 0000000 1 0000000 10 2490000 p3 1 0000000 1 0000000 10 2490000 normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length idxrow if 0 009500 0 006500 0 003500 0 000500 row HASH PHOTPOSY 0 012500 0 idxcol col HASH PHOTPOSX 0 012500 0 0 012500 0 009000 0 006000 0 003000 0 000000 0 012000 0 008500 0 005500 0 002500 0 000500 8 00 0 7 00 0 7 00 0 3 00 0 9 00 0 21 00 0 point 0 point 1 point 2 point 3 7 00 3 00 1 00 8 00 008500 17 00 2 00 5 00 5 00 9 00 4 00 0 00 009000 24 00 1 00 8 00 8 00 12 00 0 00 12 00 009500 20 00 1 00 6 00 0 00 12 00 24 00 17 00 010000 13 00 9 00 15 00 00 00 00 00 010500 16 00 1 00 10 00 2 00 4 00 5 00 0 00 011000 17 00 7 00 6 00 8 00 6 00 5 00 9 00 011500 23 00 20 00 4 00 0 00 4 00 12 00 21 00 012000 17 00 18 00 17 00 16 00 11 00 15 00 18 00 012500 0 011500 0 008000 0 00500
166. 1 00 1 00 4 00 2 00 00 0 00 0 00 0 00 0 00 0 000015 N 0 00 0 00 1 00 7 00 11 00 1 00 00 0 00 0 00 0 00 0 00 0 000020 N 0 00 0 00 0 00 5 00 12 00 3 00 00 0 00 0 00 0 00 0 00 0 000025 70 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 0 00 00 71 3 00 00 7 0 0 00 00 0 0 00 00 0 0 00 00 0 0 00 00 0 000030 000035 000040 000045 000050 10 13 00 00 00 00 00 00 00 00 00 00 Appendix J Test 5 Input File A Point Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes Input File testcase5 mci RunInfo comment Test Case 5 N Point source with two 45 deg mirrors 10 x beam expander 0 2 mm slit collimating holes and three include stdsetup mci include the standard setup for all test cases random number generator and bounding box Medium define a scattering and absorbing medium id mirror 1 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CIRCLE shape of medium pO 0 10 0 9 5 x y 2 coords of first point pl 0 10 0 015 9 5 x y
167. 1 00 63 00 71 00 79 00 86 00 66 00 0 000050 67 00 78 00 80 00 83 00 112 00 66 00 84 00 70 00 66 00 0 000045 73 00 67 00 84 00 75 00 87 00 83 00 87 00 76 00 69 00 0 000040 63 00 76 00 102 00 100 00 99 00 89 00 96 00 77 00 68 00 0 000035 71 00 55 00 98 00 103 00 110 00 92 00 95 00 76 00 64 00 0 000030 81 00 80 00 96 00 330 00 617 00 116 00 94 00 90 00 74 00 0 000025 68 00 71 00 476 00 790 00 731 00 449 00 93 00 100 00 73 00 0 000020 88 00 83 00 768 00 814 00 769 00 773 00 323 00 99 00 89 00 0 000015 77 00 86 00 788 00 772 00 811 00 725 00 628 00 107 00 67 00 0 000010 85 00 77 00 805 00 811 00 818 00 783 00 738 00 114 00 83 00 0 000005 91 00 76 00 734 00 797 00 800 00 756 00 764 00 91 00 71 00 0 000000 0 000005 0 000025 78 00 79 00 74 00 76 00 80 00 75 00 6 00 94 00 62 00 69 00 93 00 64 00 70 00 108 00 74 00 66 00 756 00 78 00 62 00 770 00 99 00 83 00 810 00 92 00 95 00 816 00 81 00 88 00 840 00 97 00 85 00 780 00 104 00 58 000050 0 000005 000050 0 000005 0 000040 row index column index 0 000035 0 000000 0 000030 79 00 68 00 57 00 94 00 84 00 62 00 79 00 97 00 87 00 94 00 115 00 75 00 82 00 110 00 64 00 97 00 725 00 67 00 81 00 776 00 98 00 89 00 777 00 95 00 96 00 827 00 74 00 105 00 829 00 96 00 103 00 797 00 77 00 52 00 70 00
168. 1 0000000 point 1 p2 1 0000000 1 0000000 1 0000000 point 2 3 1 0000000 1 0000000 1 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM type of photon source qty 1000000 initial number of photons in source to launch qtyleft 1000000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object 49 0 0000000 0 0000000 0 0000000 point 0 center for circle 0 0000000 0 0000250 0 0000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m radius 0 000025 radius of circle 0 if planar radius squared 0 000000 radius of circle squared RunInfo runend Fri Dec 27 20 15 37 2002 ending time and date of run Map define a photon density map id x y pos of beam upstream of scattering medium id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 0 9999990 pl 1 0000000 1 0000000 0 9999990 p2 1 0000000 1 0000000 0 9999990 p3 1 0000000 1 0000000 0 9999990 normalvector 0 000000
169. 10 x y z coords of second point normalvector 0 0 1 normal vector for extrude extrudelen 0 004 extrusion length of cylinder Medium define a scattering and absorbing medium lens semi sphere shape id diverging lens 2 air part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype SEMISPHERE shape of medium 0 0 10 012 x 2 coords of first point pl 0 0 01125 10 012 x z coords of second point p3 0 0 10 004 x y z coords of fourth point normalvector 0 0 1 normal vector of cut surface plano side on right Boundary and Ambient Media A bounding box is a cube that encompasses the entire model space Its purpose is to absorb all photons that reach its inner surface The PTS software requires that a bounding box be specified A bounding box is used in conjunction with an ambient medium to provide a universe within which the simulation model exists The bounding box is the first medium defined in the input file and extends beyond the entire model A bounding box of length width and height of 2002 meters centered on 0 0 0 is used for all test cases described The ambient medium specifies the properties used whenever the photon does not lie within a user specified medium object The ambient medium usually defined to have the properties of air or vacuum i
170. 15 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 414 380 414 380 349 351 373 358 403 366 395 387 386 382 385 409 394 364 361 380 367 392 406 406 404 405 367 364 399 341 387 00 411 349 417 3574 399 398 00 415 358 382 38 35 374 354 365 8155 00 00 00 359 396 354 00 00 00 00 358 368 364 00 339 358 352 00 393 377 00 358 00 395 392 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 410 376 00 369 00 378 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 396 386 423 385 356 318 S17 369 398 374 412 409 375 332 349 377 379 440 393 385 355 388 361 400 418 377 378 400 368 410 370 364 376 380 387 437 347 370 391 357 409 351 391 373 370 339 351 378 362 386 416 396 351 361 300 328 411 411 42 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
171. 31 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2610000 point 0 center for circle pl 1 0000000 1 0000000 10 2610000 point 1 p2 1 0000000 1 0000000 10 2610000 point 2 p3 1 0000000 1 0000000 10 2610000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator hole 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo 107 indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object pO 0 0001000 0 0000000 10 2610000 point 0 center for circle pl 0 0001000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000025 radius of c
172. 7 00 637399 638248 48 00 49 00 637682 637343 55 00 51 00 637319 638934 50 00 54 00 635403 637263 50 00 71 00 637674 637487 60 00 40 00 636584 636635 44 00 51 00 635524 348040 52 00 46 00 201048 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 poin poi po poi 0 000045 0 000010 0 000020 0 000050 25 00 52 00 45 00 39 00 53 00 58 00 43 00 84 00 46 00 59 00 70 00 58 00 42 00 89 00 56 00 47 00 483492 00 62 00 48 00 636816 00 106 00 44 00 0 47 00 639659 00 202007 00 36 00 7 0 53 00 636662 00 483471 00 47 00 0 67 00 636240 00 615785 00 49 00 0 51 00 636816 00 617142 00 44 00 0 43 00 635273 00 484250 00 44 00 0 55 00 634642 00 202864 00 53 00 0 51 00 637278 00 92 00 43 00 0 60 00 483809 00 m 0 nt 1 int 2 nt 3 0 000040 0 000005 0 000025 40 00 45 00 49 00 41 00 54 00 49 00 48 00 86 00 47 00 54 00 81 00 53 00 64 00 117 00 59 00 59 00 615161 00 60 00 74 00 639634 78 000020 76 00 636614 100 000015 55 00 637267 85 000010 79 00 635696 112 000005 58 00 636046 99 000000 60 00 635342 88 000005 48 00 637046 9l 000010 52 00 634486 89 000015 59 00 613906 00 57 00 00 00 00 00 00 00 00 00 00 00 00
173. 7 00 81 00 0 000025 41 00 53 00 203 00 88 00 76 00 73 00 0 000030 36 00 32 00 70 00 79 00 55 00 44 00 0 000035 44 00 63 00 60 00 67 00 52 00 44 00 0 000040 26 00 49 00 59 00 74 00 47 00 57 00 0 000045 30 00 14 00 39 00 81 00 44 00 42 00 39 00 0 000050 Map define a photon density map id x y pos of beam downstream of collimating h type PLANAR type of density map shptype RECTANGLE type of shape for object point 0 center for circle pl 1 000000 1 000000 0 020001 point 1 p2 1 000000 1 000000 0 020001 point 2 p3 1 000000 1 000000 0 020001 point 3 p0 1 000000 1 000000 0 020001 normalvector 0 000000 0 000000 1 000000 49 00 13 00 75 00 53 00 89 00 55 00 59 00 74 00 85 00 64 00 496 0 200 0 5 84 00 642 0 230 0 0 84 00 578 0 236 0 5 74 00 519 0 239 0 83 00 561 0 222 0 83 00 611 0 187 0 68 00 31 00 170 0 56 00 86 00 72 00 56 00 17 00 75 00 53 00 87 00 51 00 53 00 70 00 42 00 48 00 66 00 38 00 33 00 53 00 32 00 27 00 65 00 42 00 ole 64 00 211 00 63 00 79 00 1515 00 59 00 88 00 1571 00 71 00 89 00 0 572 00 0 181 00 207 00 0 626 00 0 249 00 94 00 0 590 00 0 89 00 91 00 0 606 00 0 99 00 96 00 0 593 00 0 86 00 71 00 0 571 00 0 73 00 69 00 1620 00 0 49 00 81 00 1435 00 79 00 61 00 235 00 40 00 43 00 201 00 43 00 51 00 64 00 78 00 62 00 74 00 48
174. 734 00 91 00 65 00 798 00 112 00 75 00 596 00 82 00 63 00 92 00 82 00 67 00 94 00 90 00 72 00 89 00 78 00 81 00 78 00 68 00 59 00 75 00 71 00 58 00 55 00 72 00 84 00 810 00 91 00 74 00 804 00 86 00 90 00 796 00 95 00 76 00 728 00 94 00 67 00 104 00 86 00 69 00 88 00 73 00 89 00 91 00 85 00 59 00 66 00 68 00 71 00 81 00 73 00 56 00 66 00 73 00 59 101 00 847 00 100 00 97 00 720 00 95 00 89 00 755 00 85 00 83 00 747 00 87 00 95 00 105 00 89 00 64 00 105 00 70 00 92 00 98 00 94 00 85 00 84 00 60 00 58 00 71 00 75 00 75 00 80 00 83 00 102 00 776 00 85 00 128 00 809 00 78 00 77 00 766 00 85 00 80 00 635 00 67 00 83 00 93 00 60 00 96 00 109 00 70 00 78 00 83 00 87 00 78 00 83 00 87 00 79 00 96 00 78 00 75 00 75 00 68 00 621 00 773 00 76 00 318 00 754 00 80 00 109 00 773 00 73 00 106 00 292 00 72 00 92 00 113 00 68 00 84 00 106 00 69 00 98 00 91 00 74 00 73 00 72 00 76 00 79 00 80 00 76 00 60 00 68 00 65 00 Appendix Test Case 4 Input File Comparison of Quasi Ballistic to Ballistic Photons for a Single Scattering Medium with a Collimating Hole Input File testcase4 mci RunInfo comment Test Case 4 N Duplication of Chu and Pfeiffer Simulation Results N to Determine Ratio of Quasi Ballistic to Ballistic Photons inclu
175. 74 00 368 364 00 341 407 00 366 389 00 414 435 00 403 379 00 413 392 00 363 1 00 0 004500 298 00 376 398 00 361 397 00 395 386 00 396 394 00 356 405 00 355 390 00 395 2 00 0 004000 383 00 357 344 00 39315 402 00 409 385 00 3725 380 00 388 383 00 353 354 00 387 0 00 0 003500 388 00 397 352 00 363 376 00 388 367 00 404 401 00 373 358 00 370 393 00 389 0 00 0 003000 370 00 350 385 00 381 429 00 374 412 00 376 405 00 379 407 00 431 356 00 370 0 00 0 002500 359 00 388 389 00 350 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 115 406 385 373 00 142 39 252 363 393 370 380 339 216 355 362 389 402 404 355 350 362 358 IIT 404 00 354 376 417 382 361 371 407 385 353 382 384 361 385 382 387 369 349 366 33155 390 444 387 394 345 429 345 405 408 370 351 334 388 365 384 411 363 381 361 372 379 413 364 380 394 383 373 402 00 00 00 00 00 00 00 00 00 00 00 373 357 366 374 356 385 00 00 00 00 00 00
176. 77 00 1248 00 0 00 0 00 1290 00 0 00 0 00 407 00 000020 000025 000030 000035 000040 000045 000050 0 00 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 00 0 00 o 0 00 0 00 1228 00 1284 00 944 00 0 00 0 00 0 000005 0 00 0 00 1290 00 1294 00 442 00 0 00 0 00 0 000010 0 00 0 00 1296 00 1281 00 0 00 0 00 0 00 0 00 931 00 1246 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 45 1279 00 0 00 1230 00 0 00 0 00 0 00 0 00 1273 00 1242 0 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 1327 00 0 00 1259 00 0 00 0 00 0 00 0 00 1306 00 1007 00 0 00 0 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 961 00 404 00 1316 00 399 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 Appendix D Test Case 2 Input File A Single Medium with Scattering but without Absorption Input File testcase2 mci 46 RunInfo comment Test Case 2 A Single
177. 889 Major Project Apr 10 2003 This User Guide is designed to provide a quick introduction to the PTS software and to act as a command syntax reference Users are referred to the above reports for additional details In this User Guide references have been removed see above reports for original references The PTS software is believed to function as indicated however not all features have been exhaustively tested and no claim is given for absolute reliability or correctness Users are cautioned to check output for reasonableness and to confirm new geometries etc with simple test cases Software Methodology The PTS software uses a ray trace Monte Carlo method to simulate photons The software is geometry based and allows the creation of multiple arbitrary three dimensional 3D media multiple photons sources and multiple photon detectors Briefly a photon is launched from a defined photon source and travels in a straight line until it is scattered or intersects the face of a medium If it is scattered then a new photon direction is determined based upon the phase function If it intersects a medium then a new photon direction is determined based upon Fresnel reflection refraction at the boundary Whenever a photon is scattered or reflected refracted a check is done to determine whether the photon was absorbed If the photon was absorbed then its life is terminated If a photon is not absorbed then it continues until it is absorbed If
178. 9 5 x y 2 coords of first point pl 0 10 0 015 9 5 x y 2 coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude Medium define a scattering and absorbing medium id mirror 2 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CIRCLE shape of medium p000 9 5 x y z coords of first point 0 0 015 9 5 x z coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude Medium define a scattering and absorbing medium id diverging lens 1 glass part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 45 index of refraction shptype CIRCLE shape of medium 0 0 10 y z coords of first point 0 0 015 10 x coords of second point normalvector 0 0 1 normal vector for extrude extrudelen 0 004 extrusion length of cylinder Medium define a scattering and absorbing medium lens semisphere shape id diverging lens 2 air part of diverging lens g 1 0 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype SEMISPHE
179. 92 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 422 402 370 354 367 374 390 412 394 365 366 337 383 395 384 399 386 358 388 362 413 400 396 412 365 390 349 00 435 390 407 390 405 411 386 366 437 383 405 377 348 373 386 391 401 376 367 369 393 399 413 374 386 386 332 354 376 386 418 406 361 360 397 3793 379 398 389 S 336 370 368 385 377 403 368 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 380 00 401 363 382 426 374 392 3795 430 394 374 394 378 380 409 392 382 351 370 401 394 403 391 3923 392 374 349 409 364 361 374 376 381 385 407 405 393 412 362 376 375 429 376 00 365 353 379 427 366 401 396 392 401 377 418 403 403 370 369 407 379 344 386 00 422 419 376 401 367 417 330 408 420 396 389 383 385 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0
180. 94 00 361 00 0 00 00 362 00 351 00 374 00 346 00 407 00 00 0 00 385 00 391 00 405 00 371 00 385 00 00 0 00 353 00 388 00 381 00 360 00 339 00 0 00 0 00 357 00 343 00 348 00 378 00 351 00 0 00 0 00 346 00 370 00 0 005000 0 008000 0 011000 0 00 0 00 1 00 0 00 74 00 145 00 372 00 387 00 1 00 0 00 1 00 1 00 0 00 0 00 0 00 1 00 1 00 0 00 328 00 370 00 372 00 366 00 316 00 193 00 0 00 0 00 0 00 0 00 0 00 0 00 3 00 0 00 363 00 369 00 347 00 381 00 361 00 372 00 0 00 0 00 0 00 0 00 0 00 0 00 48 00 245 00 386 00 392 00 374 00 357 00 367 00 355 00 0 00 0 00 0 00 0 00 2 00 0 00 377 00 399 00 381 00 350 00 404 00 363 00 365 00 406 00 151 00 2 00 0 00 0 00 0 00 0 00 352 00 397 00 382 00 361 00 385 00 362 00 360 00 374 00 392 00 239 00 1 00 0 00 0 00 1 00 356 00 369 00 411 00 381 00 377 00 388 00 381 00 423 00 351 00 359 00 0 00 1 00 1 00 1 00 397 00 375 00 406 00 384 00 368 00 409 00 368 00 383 00 385 00 394 00 0 00 2 00 0 00 4 00 368 00 371 00 358 00 380 00 393 00 375 00 400 00 349 00 382 00 380 00 0 00 1 00 0 00 242 00 370 00 379 00 361 00 396 00 385 00 366 00 374 00 384 00 387 00 388 00 1 00 0 00 139 00 319 00 388 00 355 00 344 00 379 00 385 00 375 00 398 00 00 372 00 375 00 390 00 365 00 374 00 00 366 00 386 00 389 00 374 00 379 00 0 00 361 00 377 00 373 00 411 00 347 00 368 00 0 00 375 00 375 00 381 0
181. 9500 010000 010500 011000 oOoooococ oOoooococ oOoooococ oOoooococ oOoooococ oOoooococ oOooocococ oOoooococ oOoooococ oOoooococ 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 95 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00
182. APPENDIX J TEST CASE 5 INPUT FILE nennen nnne nnne nnn 72 APPENDIX TEST CASE 5 OUTPUT 76 APPENDIX L TEST CASE 6 INPUT FILE creen nennen nnn nnne nnne nnns 100 APPENDIX M TEST CASE 6 OUTPUT FILE 104 Introduction Background This User Manual describes the basic operation of the Photon Transport Simulator PTS program written by Nick Pfeiffer for use in investigating photon transport through scattering and absorbing media It describes the latest version of the PTS software m1 main12 exe June 11 2006 The PTS software is a ray trace Monte Carlo photon simulator It was originally developed in October 2002 and has been steadily modified as required to allow Nick Pfeiffer to investigate photon transport problems It is considered to be a working tool and as such is expected to be changed and extended as needed The PTS software is written in ANSI C and compiled using a Borland C compiler The source code is self documenting and should be self explanatory when used in conjunction with the following reports Nick Pfeiffer Development of Software Tools for Simulation of Photon Transport in Scattering and Absorbing Media the Photon Transport Simulator SFU ENSC 892 Major Project Dec 28 2002 Nick Pfeiffer Development of NURB Surface and Visualization Extensions to the Photon Transport Simulator SFU ENSC
183. ASH PHOTPOSX 0 000050 0 000050 0 000005 column index 0 000050 0 000045 0 000040 0 000035 0 000030 0 000025 0 000020 0 000015 0 000010 0 000005 0 000000 0 000005 0 000010 0 000015 0 000020 0 000025 0 000030 0 000035 0 000040 0 000045 0 000050 data 1 00 0 00 1 00 1 00 6 00 2 00 4 00 1 00 0 00 00 2 00 3 00 0 00 2 00 1 00 0 00 0 00 0 00 0 00 1 00 1 00 0 000050 N 0 00 2 00 3 00 5 00 1 00 2 00 0 00 4 00 7 00 0 00 2 00 2 00 2 00 0 00 1 00 2 00 00 0 00 0 00 0 00 2 00 0 000045 X 3 00 3 00 1 00 0 00 2 00 1 00 1 00 0 00 0 00 0 00 1 00 0 00 1 00 2 00 2 00 00 00 1 00 4 00 2 00 0 00 0 000040 N 1 00 1 00 2 00 2 00 1 00 2 00 3 00 2 00 2 00 00 4 00 3 00 2 00 0 00 0 00 00 0 00 1 00 0 00 0 00 3 00 0 000035 N 5 00 4 00 1 00 1 00 2 00 2 00 1 00 0 00 3 00 2 00 4 00 4 00 1 00 3 00 2 00 00 00 2 00 1 00 3 00 0 00 0 000030 N 1 00 1 00 1 00 1 00 1 00 1 00 0 00 6 00 14 00 11 00 19 00 14 00 5 00 7 00 1 00 00 0 00 0 00 1 00 3 00 3 00 0 000025 N 2 00 4 00 0 00 1 00 2 00 1 00 6 00 16 00 23 00 17 00 14 00 16 00 16 00 6 00 0 00 1 00 3 00 2 00 3 00 00 0 00 0 000020 X 1 00 2 00 4 00 3 00 5 00 8 00 7 00 4 00 6 00 15 00 13 00 22 00 11 00 4 00 5 00 0 00 2 00 2 00 00 00 0 00 0 000015 N 0 00 0 00 3 00 1 00 1 00 1 00 2 00 5 00 4 00 29 00 13 00 13 00 19 00 8 00 1 00 3 00 1 00 0 00 00 2 00 4 00 0 000010 N 3 00 3 00 2 00 1 00 0 00 3 00 5 00 0 00 6 00 16 00 22 00 11 00 22 00 5 00 9 00 3 00 6 00 2 00
184. Ooooococ oOoooococ 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 id of density map 0 011000 0 007500 004500 001500 001500 004500 007500 010500 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 0 0 0 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 010500 0 007000 004000 001000 002000 005000 008000 011000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 010000 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 00 00 00 00 oooo oOooooooo
185. RCLE shape of medium 0 10 0 9 5 z coords of first point pl 0 10 0 015 9 5 x y z coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude Medium define a scattering and absorbing medium id mirror 2 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CIRCLE shape of medium 0 0 9 5 z coords of first point pl 0 0 015 9 5 x y z coords of second point extrudelen 0 002 extrude length normalvector 1 0 1 normal vector for extrude 30 POINT PHOTON ACT SOURCE COLLIMATING ARRAY 3 x 50 MICRON DIA HOLES 10 mm THK SCATTERING MEDIUM 10 mm N 0 2 mm x 20 SLIT 1 MIRROR Y N DIVERGING LENS CONVERGING LENS DENSITY 85 mm F 250 mm b PHOTON DENSITY MAPS Figure 19 Model Setup for Test Case 5 The diverging lens with a focal length of 25 mm is constructed by using two superimposed mediums The first medium is a block of non scattering non absorbing material with an index of refraction of 1 45 The second medium is a semi sphere of non scattering non absorbing material with an index of refraction of 1 identical to the ambient medium Medium define a scattering
186. RE shape of medium 0 0 10 012 x y 2 coords of first point pl 0 0 01125 10 012 x y z coords of second point p30 0 10 004 x y z coords of fourth point cutting plane normalvector 0 0 1 normal vector of cut surface plano side on right Medium define a scattering and absorbing medium lens semisphere shape id converging lens g 1 0 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 2 index of refraction shptype SEMISPHERE shape of medium p000 9 9755 x y z coords of first point pl 0 0 2485 9 9755 x z coords of second point 0 0 10 2235 x y z coords of fourth point normalvector 0 0 1 normal vector of cut surface plano side on left Medium define a scattering and absorbing medium id slit blocking medium blocking medium for slit upstream of sample g 1 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 10 25 x y 2 coords of first point pl 1 1 10 25 x y z coords of second point p211 10 25 x y z coords of third point 1 1 10 25 x y 2 coords of fourth point extrudelen 0005 extrusion length of box Medium define a scattering and absorbing medium id slit opening medium blocking medium for slit upstream of sa
187. User Manual v1 00 Photon Transport Simulator Nick Pfeiffer Simon Fraser University May 6 2008 Table of Contents INTRODUCTION eec 1 a 1 Software Methodology 21 1 Basic 2 Monte Carlo SimulatiOn dentist ptensetasicesuseeesoniy 3 Optical 1 De 1 7 ine iia 5 PROGRAM 7 22 7 Text INCI 7 Information on a Simulation 8 Random Number Generator ML oio ee ce 8 Scattering and Absorbing Mediums Lee esee sese ee seen seen natnra natn nana anna anna sa an rasa anna uana 9 Photon SOULCOS 15 Photon Density 16 Text Output File mco 19 Scheme Output File 20 TEST CASES See 23 Test Case 1 A Single Medium with No Scattering or Absorption 23 Test Case 2 A Single Medium with Scattering but without 24 Test Case 3 A Single Medium with Scattering Using 50 000 000 Photons
188. anar planar ty shptype RECTANGLE sha pO 1 1 0200015 x pl 1 1 0200015 x p2 1 1 0200015 x p3 1 1 0200015 x idxcol col 1 1 has idxrow row 1 1 has Yr Yr Yr id max radial deviation wrt source vs Yr h PHOTSCATTERCOUNT 0 50 1 hash lookup scattercount p ial position wrt start pos downstream of collimating hole pe of map pe of medium z coords of z coords of z coords of third point z coords of fourth point h PHOTPOSRSTART 0 0 000050 0 000005 hash lookup h PHOTSCATTERCOUNT 0 50 1 hash lookup first point second point radial pos wrt start scattercount p max radial deviation wrt start pos downstream of pe of map pe of medium z coords of first point z coords of second point z coords of third point z coords of fourth point h PHOTPOSRMAXSOURCE 0 0 000050 0 000005 hash max radial pos wrt source h PHOTPOSRMAXSTART 0 0 000050 0 000005 hash max radial pos wrt start The first two density maps related the number of times that a photon that passes through the collimating hole has been scattered to the radial position of the photon Two different radial distance measures are used for comparison the first uses the radial distance from the center of the photon source the second uses the radial distance from the starting position of the photon Tables 5 and 6 show portions of these density maps Table 5 Test Case 4 Portion of Density
189. angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction 73 shptype RECTANGLE shape of medium pO 01 0001 10 25 x z coords of first point pl 01 0001 10 25 x z coords of second point p2 01 0001 10 25 x z coords of third point 01 0001 10 25 x 2 coords of fourth point extrudelen 0005 extrusion length of box Medium define a scattering and absorbing medium id scattering medium sample of scattering medium g 9 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 4 index of refraction shptype RECTANGLE shape of medium pO 02 02 10 251 x 2 coords of first point pl 02 02 10 251 x z coords of second point 2 02 02 10 251 x z coords of third point 02 02 10 251 2 coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator blocking medium blocking medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction index of refraction shptype RECTANGLE shape of medium pO 1 1 10 261 x y z coords of first point pl 1 1 10 261 x z coords of second point p2 11 10 261 x 2 coords of
190. ature of the lens m 31 At present the PTS software does not support lens design explicitly rather the user may specify geometry that can be used to model lenses A converging lens with a focal length of 250 mm forms the second optical element in the beam expander and its definition is shown below Medium define a scattering and absorbing medium lens semisphere shape id converging lens g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 2 index of refraction shptype SEMISPHERE shape of medium 0 0 9 9755 z coords of first point pl 0 0 2485 9 9755 x y z coords of second point p3 0 0 10 2235 x y z coords of fourth point normalvector 0 0 1 normal vector of cut surface plano side on left The Gaussian beam expander is formed when the focal points of the diverging and converging lenses are coincident By placing the plano side of the converging lens approximately 225 mm from the plano side of the diverging lens the actual distance used in the model is 223 5 mm photons passing through the converging lens are refracted such that their trajectory is parallel to the z axis The magnification of this beam expander is the ratio of the focal lengths and is equal to 10 Test Case 6 will demonstrate the effect of the beam expander with a uniform photon source When using the silicon micromachined collimator array at SFU
191. comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcase3 mci name of input file for this run outputfile testcase3 mco name of output file for this run photonqty 50000000 total number of photons in all sources runstart Fri Dec 27 22 27 15 2002 starting time and date of run RandomNumberGenerator define the random number generator type MC type of random number generator Seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed Medium define a scattering and absorbing medium id bounding box id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 100000000 000000 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 0000000 1001 0000000 1001 0000000 point 0 center for circle pl 1001 0000000 1001 0000000 1001 0000000
192. cted with a non scattering medium so there is no scattering of the light from the slit to the first density map Figure 22 Test Case 6 Plot of Photon Density Figure 23 Test Case 6 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Beam Expander Downstream of Beam Expander Figure 22 shows a surface contour plot of a square photon x y density map of width and height of 25 mm Figure 23 shows a surface contour plot of a photon x y density map of height 100 microns and width 300 microns centered on the middle collimator hole The low resolution groupings of single photons of the post collimator hole image is due to the combination of small bin size 5 microns x 5 microns and low numbers of photons used of the 1 million photons launched only 6119 passed through the slit at an average intensity of 0 0015 photons per square micron Using a photon source with a larger number of photons will more clearly define the three collimators holes shown in Figure 23 35 Program Theory and Structure Limitations in existing Monte Carlo simulation software for photon transport prompted the development of a completely new software tool the Photon Transport Simulator by the author This tool was designed to perform the same Monte Carlo simulations as existing software by Jacques and extended by Chu and Pfeiffer but with multiple mediums photon sources and more flexible methods
193. d for the scattering medium Figure 12 Test Case 2 Plot of Photon Density Figure 13 Test Case 2 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Scattering Medium Downstream of Scattering Medium Test Case 3 A Single Medium with Scattering Using 50 000 000 Photons Figures 12 and 13 do not show the expected scattering of the photons very clearly due to the low numbers of photons used 1 million To increase the number of scattered photons per bin Test Case 2 is modified to have a photon source with 50 million photons with all other model definitions being the same as Test Case 2 Figures 14 and 15 show contour plots of the density map data upstream and downstream of the scattering medium with the maximum plotted value limited to 100 photons per bin in order to emphasis low order noise It can be seen that the image of the photon beam upstream of the medium is blurred due to backscattered photons It should be noted that the average number of photons in each bin within the radius of the beam is 636 000 while the average number of backscattered photons captured in bins outside of the beam is approximately 70 B A ee Figure 14 Test Case 3 Plot of Photon Density Figure 15 Test Case 3 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Sca
194. d photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 0000000 1000 0000000 1000 0000000 point 0 center for circle pl 1000 0000000 1000 0000000 1000 0000000 point 1 p2 1000 0000000 1000 0000000 1000 0000000 point 2 p3 1000 0000000 1000 0000000 1000 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id mirror 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 8059 047876 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 10000000 004464 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 8059 047876 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 10000 000000 index of refraction shptype CIRCLE type of shape for object p0 0 1000000 0 0000000 9 5000000 point 0 center for circle pi 0 1000000 0 0150000 9 5000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 7071068 0 0000000 0 7071068 surface normal
195. de stdsetup mci include the standard setup for all test cases random number generator bounding box Medium define a scattering and absorbing medium id scattering medium sample of scattering medium g 9 g factor of medium mean cosine of forward scattering angle scatterratio 1000 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 0 x z coords of first point pl 1 1 0 y z coords of second point p211 0 x y z coords of third point p3 11 0 x y z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator blocking medium blocking medium for collimator downstream of sample g 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 010001 z coords of first point pl 1 1 010001 x y z coords of second point p211 010001 x y z coords of third point p3 11 010001 x y z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator hole medium hole medium for collimator downstream of sample g 1 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering
196. define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 1 0000000 point 0 center for circle pl 1 0000000 1 0000000 1 0000000 point 1 p2 1 0000000 1 0000000 1 0000000 point 2 p3 1 0000000 1 0000000 1 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM type of photon source qty 100000 initial number of photons in source to launch qtyleft 100000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object 42 pO 0 0000000 0 0000000 0 0000000 point 0 center for circle 0 0000000 0 0000250 0 0000000 point 1 p2 0 0000000 0
197. defined by the input file may intersect In this case the medium within which a point is considered to lie is medium which was defined last This characteristic of the PTS software allows complex assemblies of objects to be constructed from simple shapes and mediums Three examples are given a collimating hole within an absorbing medium a diverging lens and a bounding box A collimating hole is constructed by first defining a cube of absorbing medium that is the thickness of the collimator The absorption ratio should be set high enough that no photons will pass through the medium without being absorbed The collimating hole is added by defining a cylinder with the optical properties of air or vacuum after the absorbing medium has been defined Any photons located within the cylinder will use the optical properties of the cylinder air and not those of the absorbing medium If internal reflections are not permitted then the index of refraction of the absorbing medium should be made equal to that of the cylinder This assembly will act as a collimating hole absorbing all photons whose trajectories are not closely aligned with the hole A sample definition of such an assembly is shown below Medium define a scattering and absorbing medium id collimator blocking medium blocking medium for collimator downstream of sample 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 100000000000
198. dius 0 000025 radius of circle m radius squared 0 000000 radius of circle squared Medium define a scattering and absorbing medium id collimator hole 3 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object pO 0 0001000 0 0000000 10 2610000 point 0 center for circle 0 0000000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000103 radius of circle m radius squared 0 000000 radius of circle squared PhotonSource define a photon source id point source 1 id of photon source type POINT type of photon source qty 1 initial number of photons in source to launch qtyleft 1 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of ph
199. e PTS software is expanded Each type of photon calculation returns a single floating point number with the exception of PHOTINFO which not only returns a value equal to the number of time the photon has move but also causes a summary of the information for each photon that triggers the PHOTINFO calculation to be printed in the output file Table 3 shows the allowable types of photon calculations Table 3 Types of Pre defined Photon Calculations Calculation Type Calculation Description PHOTPOSX PHOTPOSY PHOTPOSZ PHOTPOSXSOURCE PHOTPOS YSOURCE PHOTPOSZSOURCE PHOTPOSRSOURCE PHOTPOSRMAXSOURCE PHOTPOSXSTART PHOTPOSYSTART PHOTPOSZSTART PHOTPOSRSTART PHOTPOSRMAXSTART PHOTTRAJX PHOTTRAJY PHOTTRAJZ PHOTTRAJDOTSOURCE PHOTTRAJDOTSTART PHOTMOVECOUNT PHOTSCATTERCOUNT PHOTREFLECTCOUNT PHOTREFRACTCOUNT PHOTWAVELENGTH PHOTPATHLENGTH PHOTLIFE PHOTINFO PHOTPOSRMAXSOURCE PHOTPOSRSTART PHOTPOSXSTART PHOTPOSYSTART PHOTPOSZSTART PHOTPOSRMAXSTART X component of current position m Y component of current position m Z component of current position m X component of current position reference to the photon source Y component of current position reference to the photon source z component of current position reference to the photon source radial component of current position reference to the photon source normal maximum radial component of any recorded position reference to the photon source
200. e collimating holes is constructed by superimposing three cylinders of ambient material upon an absorbing cube In order to eliminate internal reflection inside of the holes the index of refraction of the blocking medium is set to 1 the same as the medium used for the holes It is important to note that when photons are inside of multiple medium the optical properties used are of the last medium defined Hence in the definition of the collimating array the blocking medium is defined before the collimating holes Medium define a scattering and absorbing medium id collimator blocking medium blocking medium for collimator downstream of sample lt 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1 1 10 261 x 2 coords of first point pl 1 1 10 261 gt coords of second point p2 1 1 10 261 z coords of third point 32 p3 1 1 10 261 z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator hole 1 hole medium for collimator downstream of sample g 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100
201. ectory medium test medium 0 ambient current medium in which photon resides wavelength 514 000000 wavelength of photon nm movecount 10 number of moves made by photon scattercount 0 number of scatter events reflectcount 0 number of reflect events refractcount 10 number of refract events pathlength 10 271001 total pathlength m life 0 000000034277 lifetime of photon secs desireddist 10000000000000000000 000000 current desired distance photposrsource 0 000024 radial component of current position wrt to the photon source normal photposrstart 0 000021 radial component of current pos wrt to the photon start traj and pos phottrajdotsource 1 000000 dot product of current traj and photon source cos of fwd sct angle phottrajdotstart 1 000000 dot product of current trajectory and photon starting traj photposrmaxsource 0 000024 max radial component of any recorded pos wrt the phot source normal photposrmaxstart 0 000021 max rad component of any recorded pos wrt the phot start traj and pos poslist 0 000000 0 000002 0 000000 starting position 0 000000 0 000002 10 000000 0 000000 0 000002 10 000750 0 000001 0 000003 10 004000 0 000005 0 000023 10 223500 0 000005 0 000023 10 224000 0 000005 0 000023 10 250000 0 000005 0 000023 10 250500 0 000005 0 000023 10 251000 0 000005 0 000023 10 261000 0 000005 0 000023 10 271000 last recorded position In order to extend the usefulness of pho
202. ensity map of trajectory vs radial position is formed Many different types of photon density maps may be defined and multiple photon density maps may be created Program Operation The PTS software uses a command line interface to specify input and output files A command line interface was chosen along with file based I O in order to allow the PTS software to operate on a wide variety of platforms from PC s to multi processor supercomputers The following sections described the command line interface the input file syntax and the form of the output file containing the simulation results Command Line The current program 12 is started by entering the program name and optional arguments on the command line of an MSDOS window The form of the command is mmainl2 inputfilename outputfilename If the input file name is not specified an input file name of default mci is assumed If the input file name does not contain an extension then the extension Monte Carlo input is assumed If the output file name is not specified then the output file name is assumed to be inputfilenameroot mco where the root of the input file name is the input file name without the extension The current directory is assumed unless the input file name path is specified Some examples are shown in Table 1 Table 1 Examples of Parsing Input and Output File Names from Command Line Command Input File Name Output File Name mlmainl2
203. ent position reference to the photon start ajectory and pos phottrajdotsource 1 000000 dot product of current trajectory and photon source cosine of forward attering angle for photons with starting trajectory equal to source normal phottrajdotstart 1 000000 dot product of current trajectory and photon starting trajectory cosine forward scattering angle photposrmaxsource 0 100000 maximum radial component of any recorded position reference to the oton source normal photposrmaxstart 0 100000 maximum radial component of any recorded position reference to the oton start trajectory and pos poslist 0 1000000 0 0000020 0 0000000 starting position 0 1000000 0 0000020 9 5000000 0 0000000 0 0000020 9 5000000 0 0000000 0 0000020 10 0000000 0 0000000 0 0000020 10 0007500 0 0000000 0 0000023 10 0040000 0 0000000 0 0000198 10 2235000 0 0000000 0 0000198 10 2240000 0 0000000 0 0000198 10 2500000 0 0000000 0 0000198 10 2505000 0 0000000 0 0000198 10 2510000 0 0000000 0 0000198 10 2610000 0 0000000 0 0000198 10 2710000 last recorded position nInfo runend Sat Dec 28 13 27 54 2002 ending time and date of run p define a photon density map id x y pos of beam before expansion id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object p0 1 0000000 1 0000000 9 9000000 point 0 center for circle 1 0000000 1 0000000 9 9000000 point 1
204. enter for circle pl 1 000000 1 000000 0 000000 point 1 p2 1 000000 1 000000 0 000000 point 2 p3 1 000000 1 000000 0 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator blocking medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 2993 329531 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen 64 absorbratio 9996891514694 884766 absorption ratio absorbed to unabsorbed photons of extrudelen mut 2993 329531 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 000000 1 000000 0 010001 point 0 center for circle 1 000000 1 000000 0 010001 point 1 p2 1 000000 1 000000 0 010001 point 2 p3 1 000000 1 000000 0 010001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator hole medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorptio
205. exrefraction 1 000000 of refraction shptype CIRCLE type of shape for object 0 0001000 0 0000000 10 2610000 point 0 center for circle 0 0000000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000103 radius of circle m radius squared 0 000000 radius of circle squared Medium define a scattering and absorbing medium id collimator hole 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object pO 0 0000000 0 0000000 10 2610000 point 0 center for circle 0 0000000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar ra
206. f circle m radius squared 0 000000 radius of circle squared RunInfo runend Tue Dec 24 14 15 28 2002 ending time and date of run Map define a photon density map id x y pos of beam upstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object 1 000000 1 000000 0 010001 point 0 center for circle pl 1 000000 1 000000 0 010001 point 1 p2 1 000000 1 000000 0 010001 point 2 1 000000 1 000000 0 010001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar idxrow row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index in direction in direction of in direction of idxcol col HASH PHOTPOSX 0 000050 0 000050 0 000005 column index 0 000030 0 000050 0 000045 0 000040 0 000035 0 000020 0 000015 0 000010 0 000005 0 000000 0 000010 0 000015 0 000020 0 000025 0 000030 0 000040 0 000045 0 000050 data 36 00 54 00 26 00 42 00 47 00 55 00 54 00 62 00 67 00 47 00 28 00 23 00 39 00 70 00 49 00 0 000050 51 00 29 00 21 00 53 00 73 00 66 00 55 00 84 00 73 00 54 00 49 00 35 00 54 00 46 00 69 00 0 000045 46 00 36 00 53 00 51 00 96 00 74 00 56 00 81 00 70 00 87 00 45 00 30 00 83 00 51 00 41 00 0 000040 62 00 24 00 73 00 64 00 59 00 202 00 91 00 211 00 206 00 93 00 66 00 60 00 61 00 69 00 37 00 0 000035
207. f extrudelen mut 59866 590624 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object 1 0000000 1 0000000 10 2500000 0 center for circle pl 1 0000000 1 0000000 10 2500000 point 1 p2 1 0000000 1 0000000 10 2500000 point 2 p3 1 0000000 1 0000000 10 2500000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000500 extrusion length m 0 if planar Medium define a scattering and absorbing medium id slit opening medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object 0 0100000 0 0001000 10 2500000 point 0 center for circle pl 0 0100000 0 0001000 10 2500000 point 1 2 0 0100000 0 0001000 10 2500000 point 2 3 0 0100000 0 0001000 10 2500000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000500 extrusion length m 0 if pla
208. finition is evaluated in a like manner The use of comments indicated by the leading greatly enhances the readability of the input file The types of primary and secondary contexts and the objects to which they apply are described in the following sections Detailed examples of input and output files are given in the section Test Cases Information on a Simulation Run The RunInfo primary context is used to define comments to describe a simulation run Up to four lines of comments are allowed and the preferred form is shown in the example below RunInfo comment Test Case xx Duplication of Chu and Pfeiffer Simulation Results to determine ratio of quasi Ballistic to ballistic photons using a 1 cm thick scattering medium The line continuation character is used to create four tokens on the same line as the comment token Alternatively each comment line may be specified individually preceded by a commentn token RunInfo commentO0 Test Case xx commentl Duplication of Chu and Pfeiffer Simulation Results comment2 to determine ratio of quasi Ballistic to ballistic photons comment3 using a 1 cm thick scattering medium Random Number Generator Two types of random number generators are currently supported Mersenne Twister MT19937 pseudorandom number generator with period 2 by Takuji Nishimura and Makoto Matsumoto e pseudorandom number generator MC used in program 2 by S Jacques Changing
209. gle Medium with No Scattering or Absorption Output File testcase1 mco 41 RunInfo information on this simulation run commentO Test Case 1 commentl A Single Medium with No Scattering or Absorption comment2 comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcasel mci name of input file for this run outputfile testcasel mco name of output file for this run photongty 100000 total number of photons in all sources runstart Fri Dec 27 17 06 28 2002 starting time and date of run RandomNumberGenerator define the random number generator type MC type of random number generator Seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed Medium define a scattering and absorbing medium id bounding box id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 100000000 000000 extinction coefficient m 1 albedo 0 00
210. he photon position as it passes through the density maps Figures 10 and 11 show contour plots of the density map data created by importing the density map into Microsoft Excel 2000 and graphing the data using the Surface Plot option with a contour interval of 500 It can be seen that the photon beam is indeed uniform and circular and that it is unaffected by the scattering medium Figure 10 Test Case 1 Plot of Photon Density Figure 11 Test Case 1 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Scattering Medium Downstream of Scattering Medium Test Case 2 A Single Medium with Scattering but without Absorption To see the effect of scattering the scattering medium of Test Case is modified to have a scattering ratio of 1000 and a photon source of 1 million photons with all other model definitions being the same as Test Case 1 Figures 12 and 13 show contour plots of the density map data upstream and downstream of the scattering medium contour interval of 5000 for Figure 12 and contour interval of 10 for Figure 13 It can be seen 24 that the photon beam upstream of the medium is still uniform while the downstream image is distorted and is due mainly to the ballistic photons Examination of the density map data shows that the intensity of the downstream image is approximately 1 1000 of the upstream image as expected by the scatter ratio of 1000 use
211. he random number generator type MC type of random number generator seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed Medium define a scattering and absorbing medium id bounding box id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 100000000 000000 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 0000000 1001 0000000 1001 0000000 point 0 center for circle pl 1001 0000000 1001 0000000 1001 0000000 point 1 p2 1001 0000000 1001 0000000 1001 0000000 point 2 p3 1001 0000000 1001 0000000 1001 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1
212. hptype RECTANGLE shape of medium pO 1 1 0200015 x y 2 coords of first point pl 1 1 0200015 x y z coords of second point p2 1 1 0200015 x y z coords of third point p3 1 1 0200015 x y z coords of fourth point idxcol col hash PHOTPOSRSOURCE 0 0 000050 0 000005 hash lookup source 61 col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x pos idxrow row indexl hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup y pos idxcol col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x pos idxrow row hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup y pos id scattercount vs radial position wrt source downstream of collimating hole radial position wrt idxrow row 1 1 has Map define a density ma id scattercount vs rad type planar planar ty shptype RECTANGLE sha pO 1 1 0200015 x pl 1 1 0200015 x p2 1 1 0200015 x p3 1 1 0200015 x idxcol col has idxrow row 1 1 has Map define a density ma max radial deviation id hole type planar planar ty shptype RECTANGLE sha pO 1 1 0200015 x pl 1 1 0200015 x 2 1 1 0200015 p3 1 1 0200015 x idxcol col has wrt source idxrow row 1 1 has start h PHOTSCATTERCOUNT 0 50 1 hash lookup scattercount p ial position wrt start pos downstream of c
213. if planar idxrow row HASH PHOTPOSY 0 000030 0 000024 0 000012 row index idxcol col 1 1 HASH PHOTPOSX 0 000030 0 000024 0 000012 column index 0 000030 0 000018 0 000006 0 000006 0 000018 data 0 00 218 00 453 00 228 00 0 00 0 000030 220 00 702 00 743 00 716 00 212 00 0 000018 406 00 729 00 720 00 717 00 440 00 0 000006 218 00 747 00 691 00 737 00 211 00 0 000006 0 00 229 00 428 00 235 00 0 00 0 000018 The density map output is easily imported into a spreadsheet program by copying the data table to a text file and importing the text file with spaces specified as the token delimiters Only minor editing of the table is required in order to allow numerical post processing The PHOTINFO calculation when triggered by a photon passing through a photon density map causes a summary of the photon s current information to be printed A sample of such a printout is shown in the section Photon Density Map above Care should be taken with the number of photons producing this calculation or the output file can become large Scheme Output File scm The Scheme language output file contains a complete description of the geometry of the simulation model as well as specified photon trajectories The Scheme language output file is intended to be processed by the Scheme language extensions of the ACIS solid modeler Once the Scheme output file has been loaded by the ACIS Scheme extensions the three dime
214. index idxcol col HASH PHOTPOSX 0 000050 0 000050 0 000005 column index 43 0 000025 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 450 00 1264 00 384 00 1004 00 1225 00 1220 00 961 00 404 00 1316 00 399 00 0 00 0 00 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 0 00 N 00 00 oo oo oo oo oo oo 0 0 0 0 0 0 0 00 000020 0 00 0 00 0 00 000025 0 00 0 00 0 00 000030 0 00 0 00 0 00 000035 0 00 00 0 00 000040 0 00 00 0 00 000045 o 0 00 00 0 00 o 0 00 0 000050 define a photon density id x y pos of beam downstream of 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 0 00 00 00 type PLANAR type of density map shptype RECTANGLE type of shape for objec pO 1 0000000 1 0000000 1 0100010 point 0 pl 1 0000000 1 0000000 1 0100010 point p2 1 0000000 1 0000000 1 0100010 point p3 1 0000000 1 0000000 1 0100010 point normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length m row HASH PHOTPOSY 0 000050 0 000050 0 000005 row index idxrow idxcol col HASH PHOTPOSX 0 000050 0 000050 0 000005 0 000020 0 000010 0 000040 data 0 00 0 00 0 00 00 00
215. indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100 0 10 261 x y z coords of first point pl 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole PhotonSource define a photon source id point source 1 type POINT point type of photon source 0 10 0 0 x gt coords of center cm pO 0 10 000002 0 x y z coords of center in cm normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1 number of photons to launch from source Map define a density map id x y pos of beam before expansion type planar planar type of map shptype RECTANGLE shape of medium pO 1 19 9 x z coords of first point pl 1 1 9 9 z coords of second point 2 1 1 9 9 z coords of third point p3 1 1 9 9 x z coords of fourth point col hash PHOTPOSX 0 0125 0 0125 0 0005 hash lookup x pos 74 idxrow row has Map define a density map id x y pos of beam aft 1 1 10 249 x pl 1 1 10 249 x 2 1 1 10 249 x p3 1 1 10 249 x y idxcol col has idxrow row 1 1 has Map define a density ma type planar planar ty shptype RECTANGLE sha 1 4 10 261 y pl 1 1 10 261 x y p2 1 1 10 261 x y
216. ing angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100 0 10 261 x y z coords of first point pl 0 000100 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source 0 10 0 0 z coords of center in cm pl 0 10 0 00125 0 x y z coords of point on circumference in cm normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1000000 number of photons to launch from source Map define a density map id x y pos of beam before expansion type planar planar type of map shptype RECTANGLE shape of medium 1 1 9 9 z coords of first point pl 1 1 9 9 x z coords of second point 1 1 9 9 2 coords of third point p3 1 1 9 9 x z coords of fourth point col hash PHOTPOSX 0 0125 0 0125 0 0005 hash lookup x pos 102 idxrow row has Map define a density ma h PHOTPOSY 0 0125 0 0125 0 0005 hash lookup pos p id x y pos of beam after expansion type planar planar ty shptype RECTANGLE sha 1 1 10 249 pl 1 1 10 249 2 1 1 10 249 x
217. ing medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 2993 329531 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9996891514694 884766 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 2993 329531 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2610000 point 0 center for circle pl 1 0000000 1 0000000 10 2610000 point 1 p2 1 0000000 1 0000000 10 2610000 point 2 p3 1 0000000 1 0000000 10 2610000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator hole 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo 79 ind
218. ing x coordinate of 0 10 m in order to align it with the center of the first mirror and a y coordinate of 2 microns to ensure that it will pass through the 25 micron radius center collimating hole the y coordinate of the photon will become approximately 20 microns after passage through the 10 x beam expander PhotonSource define a photon source id point source 1 type POINT point type of photon source 0 10 0 0 x z coords of center cm 0 10 000002 0 x 2 coords of center cm normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1 number of photons to launch from source A photon density map located after the collimating array with the photon calculation type PHOTINFO is used to print a summary of the photon including a list of its recorded positions to the output file Map define a density map id photon info downstream of collimating hole type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 10 271001 z coords of first point pl 1 1 10 271001 x z coords of second point p2 1 1 10 271001 x y z coords of third point p3 1 1 10 271001 z coords of fourth point idxcol col 1 hash PHOTINFO 0 20 1 hash lookup movecount idxrow row 1 1 hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup y pos The summary for the photon as it passes through that density map is shown below PhotonInfo
219. input text file is in human readable format Output from the PTS software is done through two forms of output text files The first output form with the extension mco for Monte Carlo output is identical to the input form with additional information added Again it is human readable and allows a simple check to confirm that the input file s were processed correctly The second output form with the extension scm for Scheme is designed to create a 3D model of the geometry mediums photon sources detectors and specified photon paths This text file is actually a set of Scheme commands and is designed to be processed by the Scheme editor in ACIS to create the geometry For details on loading the Scheme commands and viewing the resulting model please see the ACIS documentation SFU has a site license for ACIS Basic Scattering Theory The basic equation that governs the steady state scattering of monochromatic light in a homogenous medium is the Boltzmann transport equation photon direction after a scattering event O photon direction before a scattering event 5 radiance at position r in direction U total interaction coefficient also referred to as the extinction coefficient 1 where fu 5 2 O dO O r U scattering coefficient absorption coefficient S phase function normalized angular distribution of scattering
220. intersection of a NURB surface and a plane This shape is sufficient within the context of the PTS system to represent a wide range of lens and mirror geometries Double sided NURB surfaces may be formed by combining two NURBPLANE objects in such a manner as to align their planes The syntax fora NURBPLANE shape is described below shptype NURBPLANE po point through which cutting plane passes cutting plane is perpendicular to reference vector and intersects the NURB surface refvector a normal vector to the cutting plane the NURB surface in the direction of this vector is kept the NURB surface in the direction opposite to this vector is discarded controlpointsu number of control points in the u direction controlpointsv number of control points in the v direction degreeu degree of curve in direction between knots degreev degree of curve in v direction between knots knotu knot for direction multiple knots may be listed on a single line knotv knot for v direction multiple knots may be listed on a single line knotsu number of knots in direction optional if omitted is determined by the number of knots in the knot vector knotsv number of knots in v direction optional if omitted is determined by the number of knots in the knot vector controlpoint an individual control point of the form x y z w multiple control points may be listed on a single line A NURBPLANE shape is defined in a manner similar to other
221. io absorbed to unabsorbed photons in direction of extrudelen mut 100000000 000000 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 0000000 1001 0000000 1001 0000000 point 0 center for circle pl 1001 0000000 1001 0000000 1001 0000000 point 1 p2 1001 0000000 1001 0000000 1001 0000000 point 2 p3 1001 0000000 1001 0000000 1001 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define scattering and absorbing medium id ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 0000000 1000 0000000 1000 0000000 point 0 center for circle 1000 0000000 1000 0000000 1000 0000000 point 1 p2 1000 0000000 1000 0000000 1000 0000000 point 2 p3 1000 0000000 1000 0000000 1000 0000000 poin
222. ion m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 450000 index of refraction shptype CIRCLE type of shape for object p0 0 0000000 0 0000000 10 0000000 point 0 center for circle pl 0 0000000 0 0150000 10 0000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 004000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id diverging lens 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype SEMISPHERE type of shape for object p0 0 0000000 0 0000000 10 01200
223. ircle m radius squared 0 000000 radius of circle squared Medium define a scattering and absorbing medium id collimator hole 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object p0 0 0000000 0 0000000 10 2610000 point 0 center for circle pl 0 0000000 0 0000250 10 2610000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000025 radius of circle m radius squared 0 000000 radius of circle squared Medium define a scattering and absorbing medium id collimator hole 3 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of
224. mediums An example of a medium with a NURBPLANE shape that incorporates the NURB surface shown in Figure 7 is shown in the input file fragment below Medium id nurb plane 1 sample of test nurb plane scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 2 index of refraction shptype NURBPLANE shape of medium pO 0 0000000 0 0000000 0 point on plane the cutting plane passes through this point normalvector 0 0000000 0 0000000 1 0000000 surface normal for plane controlpointsu 3 the number of control points in the u direction controlpointsv 3 the number of control points in the v direction degreeu 2 the degree of the curve in the u direction degreev 2 the degree of the curve in the v direction knotu 0 0 0 1 1 1 the knot vector for the direction knotv 0 0 0 1 1 1 the knot vector for the v direction controlpoint 0 5 0 5 0 0 1 0 the first control point 0 0 controlpoint 0 0 0 5 0 0 1 0 the second control point P i 1 350 controlpoint 0 5 0 5 0 0 1 0 the third control point P i 2 50 controlpoint 0 5 0 0 0 0 1 0 0 5 1 controlpoint 0 0 0 0 1 0 1 0 P i 1 1 note that the z coordinate is non zero 12 controlpoint 0 5 0 0 0 0 1 0 P i 2 351 controlpoint 0 5 0 5 0 0 1 0 P i 0 5 2 controlpoint 0 0 0 5 0 0 1 0 P i 1 3752 controlpoint 0 5 0 5 0 0 1 0 the last control point P i 2 132 Complex Shapes Scattering and absorbing medium objects
225. mple g 1 g factor of medium mean cosine of forward scattering angle Scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction 101 shptype RECTANGLE shape of medium pO 01 0001 10 25 x 2 coords of first point pl 01 0001 10 25 x z coords of second point p2 01 0001 10 25 x z coords of third point 01 0001 10 25 x 2 coords of fourth point extrudelen 0005 extrusion length of box Medium define a scattering and absorbing medium id scattering medium sample of scattering medium g 9 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 4 index of refraction shptype RECTANGLE shape of medium pO 02 02 10 251 x 2 coords of first point pl 02 02 10 251 x z coords of second point 2 02 02 10 251 x z coords of third point 02 02 10 251 x z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator blocking medium blocking medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction index of refraction shptype RECTANGLE shape of medium pO 1 1 10 261 x y z coords of first point pl 1 1 10 261 x
226. n m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype CIRCLE type of shape for object pO 0 000000 0 000000 0 010001 point 0 center for circle pl 0 000000 0 000025 0 010000 point 1 p2 0 000000 0 000000 0 000000 point 2 p3 0 000000 0 000000 0 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar radius 0 000025 radius of circle m radius squared 0 000000 radius of circle squared PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM type of photon source qty 100000000 initial number of photons in source to launch qtyleft 100000000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object pO 0 000000 0 000000 0 000000 point 0 center for circle pl 0 000000 0 000025 0 000000 point 1 p2 0 000000 0 000000 0 000000 point 2 p3 0 000000 0 000000 0 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 000025 radius o
227. n in a line i e second token in the line third token etc and the current primary and secondary syntax An example of this input syntax is shown in the input file fragment below describing photon source PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source pO 0 0 0 x z coords of center in m pl 0 0 000025 0 x z coords of point on circumference normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 100000000 number of photons to launch from source In the definition of the photon source the first line PhotonSource is a primary context and causes a new photon source to be created All subsequent tokens are evaluated assuming that they apply to this new photon source The second line id token is a secondary context and causes subsequent tokens to be evaluated in the context of an identifier for the photon source The token uniform source 1 in the second line becomes the identifier for the photon source The token type in the third line changes the secondary context from id to type and the token UNIFORM is evaluated as the type of the photon source The token pO in the fourth line changes the secondary context to be that of point pO of the geometry associated with the photon source The subsequent tokens 0 0 and 0 on the fourth line are evaluated as the x y and z coordinates of point The remainder of the photon source de
228. nar Medium define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 400000 index of refraction shptype RECTANGLE type of shape for object 0 0200000 0 0200000 10 2510000 point 0 center for circle pl 0 0200000 0 0200000 10 2510000 point 1 p2 0 0200000 0 0200000 10 2510000 point 2 p3 0 0200000 0 0200000 10 2510000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id collimator blocking medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 2993 329531 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9996891514694 884766 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 2993 3295
229. niform type of photon source pO 0 0 0 z coords of center m pl 0 0 000025 0 x y z coords of point on circumference in m normalvector 0 0 1 launch photons parallel to z axis wavelength 514 waveleng th in nm qty 100000 number of photons to launch from source p define a density map type planar planar type shptype RECTANGLE shape po 1 1 999999 x y pl 1 1 999999 x 1 21 999999 f x p3 1 1 999999 x idxcol col 1 1 hash idxrow row 1 1 hash p define a density map type planar planar type shptype RECTANGLE shape po 1 1 1 010001 y pl 1 1 1 010001 x p2 1 1 1 010001 x y p3 1 1 1 010001 of map of medium z coords of z coords of z coords of z coords of PHOTPOSX 0 PHOTPOSY 0 of map of medium z coords of z coords of z coords of z coords of id x y pos of beam upstream of scattering medium first point second point third point fourth point 000050 0 000050 0 000005 hash lookup 000050 0 000050 0 000005 hash lookup id x y pos of beam downstream of scattering medium first point second point third point fourth point col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup idxrow row hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup 40 pos y pos pos y pos Appendix Test Case 1 Output File A Sin
230. normal component of current position reference to the photon start pos y component of current position reference to the photon start pos z component of current position reference to the photon start pos radial component of current position reference to the photon start trajectory and pos maximum radial component of any recorded position reference to the photon start trajectory and pos X component of current trajectory y component of current trajectory z component of current trajectory dot product of current trajectory and photon source cosine of forward scattering angle for photons with starting trajectory equal to source normal dot product of current trajectory and photon starting trajectory cosine of forward scattering angle Number of times that photon is moved Number of scattering events Number of reflect events Number of refract events Wavelength nm pathlength m life seconds prints photon information including position list to outfile but returns the number of photon moves movecount maximum radial component of any recorded position reference to the photon source normal radial component of current position reference to the photon start trajectory and pos component of current position reference to the photon start pos y component of current position reference to the photon start pos 7 component of current position reference to the photon start pos maximum radial component of an
231. nsional results may be viewed scaled rotated and otherwise displayed Several examples of ACIS 3D models produced by loading the Scheme file with minor editing are shown in Figure 8 The PTS system builds complex objects from simple primitives such as blocks cylinders spheres and simple forms of NURB surfaces True solid models are not maintained by the PTS system rather a method is employed whereby when primitives intersect the primitive which was defined last occupies the 20 intersection volume The Scheme output file contains ACIS Scheme descriptions of the primitives only complex objects will appear as superimposed primitives When a photon strikes a photon density map which has PHOTINFO as one of the calculations a list of all photon positions trajectory history is printed to the output file At the same time a Scheme description of the photon s trajectory is created as an ACIS wire body entity When the Scheme file is loaded into ACIS the trajectories of such photons may be viewed viewing of edges and vertices should be enabled for the OpenGL window The Scheme output from a sample photon source is shown below define uniform source 1 sheet 2d sheet face face planar disk position 0 000000 0 000000 0 000000 gvector 0 000000 0 000000 1 000000 0 001250 uniform source 1 is a planar disk It can be seen that the identifier assigned to the object in the input file is used with spaces replaced by underscore charac
232. nstream of the collimating hole It can be seen that the collimating hole assembly comprised of a blocking medium and a cylinder of air effectively blocks all photons that do not pass through the hole Figure 17 Test Case 4 Plot of Photon Density Figure 18 Test Case 4 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Collimating Hole Downstream of Collimating Hole In order to determine the number of ballistic quasi ballistic and scattered photons passing through the collimating hole additional density maps are defined define a density map id scattercount vs radial position wrt source downstream of collimating hole type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 0200015 x z coords of first point pl 1 1 0200015 z coords of second point 2 1 1 0200015 2 coords of third point p3 1 1 0200015 x z coords of fourth point idxcol col hash PHOTPOSRSOURCE 0 0 000050 0 000005 hash lookup radial pos wrt source 27 idxrow row 1 1 has p define a density ma id scattercount vs rad type planar planar ty shptype RECTANGLE sha 1 1 0200015 x pl 1 1 0200015 x p2 1 1 0200015 x p3 1 1 0200015 x idxcol col 1 1 has idxrow row 1 1 has p define a density ma llimating hole type pl
233. nted to allow simple lens systems to be modeled A lens is constructed of one or more mediums with the desired shape This shape is a function of the desired optical properties and is used in conjunction with the index of refraction to determine the lens characteristics At present there is no facility for defining lenses using magnification ratios or focal distances rather the reader is referred to basic optics texts for the relevant formulas However once the shape of the lens is determined it can be specified through the use of medium objects and the optical characteristics of the lens will be faithfully modeled by the PTS software A diverging lens is the first element of a Gaussian beam expander and may also be used in beam shrinkers A plano diverging lens is modeled by superimposing a semi sphere of air on a cube of glass A sample definition of a diverging lens with a focal distance of 25 mm used as the first element of a 10 x Gaussian beam expander is shown below The complete beam expander of which this lens is a part is described in section Test Case 5 Medium define a scattering and absorbing medium id diverging lens 1 glass part of diverging lens g 1 0 factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 45 index of refraction shptype CIRCLE shape of medium 0 0 10 x z coords of first point pl 0 0 015
234. ny include statements in the original input files are eliminated in the output file rather the actual included text is printed at the location of the include statement In the output file additional information is added to the RunInfo primary context such as shown in the sample below RunInfo information on this simulation run commentO0 Run to test basic photon transport uniform photon source commentl1 Test 10 x beam expander with slit comment2 comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmainl2 c programauthor Nick Pfeiffer programversiondate February 2005 inputfile default mci name of input file for this run outputfile default mco name of output file for this run photonqty 1000000 total number of photons in all sources runstart Sat Dec 21 17 00 42 2005 starting time and date of run runend Sat Dec 21 17 08 32 2005 ending time and date of run 19 The output file not only prints the definition of each object from the input file it also provides some additional calculated values in the form of comments Review of such calculated values such as the radius of a circle or the normal vector of a shape is useful for ensuring that the input model was properly specified The output from a sample photon source is shown below PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM ty
235. oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo o 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oooo oOooooooo ooooooo oOooooooo 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 ooooooo oOooooooo oOooooooo oOooooooo ooooooo oOooooooo Oooooooo oOoooooo oOooooooo o 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0
236. of absorption m 1 scatterratio 1000 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 690 875478 extinction coefficient m 1 albedo 1 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 1 0000000 point 0 center for circle pl 1 0000000 1 0000000 1 0000000 point 1 p2 1 0000000 1 0000000 1 0000000 point 2 3 1 0000000 1 0000000 1 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 010000 extrusion length m 0 if planar PhotonSource define a photon source id uniform source 1 id of photon source type UNIFORM type of photon source qty 50000000 initial number of photons in source to launch qtyleft 50000000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object 56 0 0000000 0 0000000 0 0000000 point 0 center for circle pl 0 0000000 0 0000250 0 0000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m radius 0 000025 radius of circle m radi
237. of collimating hole of map of medium 2 coords of first point 2 coords of second point 2 coords of third point 2 coords of fourth point h PHOTINFO 0 20 1 hash lookup movecount h PHOTPOSY 0 000050 40 000050 0 000005 hash lookup y pos 75 y pos x pos y pos x pos y pos h PHOTPOSX 0 000150 40 000150 0 000005 hash lookup x pos h PHOTPOSY 0 000050 40 000050 0 000005 hash lookup y pos Appendix Test Case 5 Output File A Point Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes Output File testcase5 mco Runinfo information on this simulation run comment0O Test Case 5 commentl Point source with two 45 deg mirrors 10 x beam expander 0 2 mm slit and three collimating holes comment2 comment3 programdescription Photon Transport Simulator Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcase5 mci name of input file for this run outputfile testcase5 mco name of output file for this run photonqty 1 total number of photons in all sources runstart Sat Dec 28 13 27 54 2002 starting time and date of run RandomNumberGenerator define the random number generator type MC type of random number generator seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed
238. of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1000 000000 1000 000000 1000 000000 point 0 center for circle 1000 000000 1000 000000 1000 000000 point 1 p2 1000 000000 1000 000000 1000 000000 point 2 p3 1000 000000 1000 000000 1000 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id scattering medium id of medium g 0 900000 g factor of medium mean cosine of forward scattering angle mus 690 875478 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 1000 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 690 875478 extinction coefficient m 1 albedo 1 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object 1 000000 1 000000 0 000000 point 0 c
239. ollimating hole pe of map pe of medium y z coords of y z coords of y z coords of third point y z coords of fourth point h PHOTPOSRSTART 0 0 000050 0 000005 hash lookup radial position wrt start h PHOTSCATTERCOUNT 0 50 1 hash lookup scattercount first point second point p wrt source vs max radial deviation wrt start pos downstream of collimating pe of map pe of medium y z coords of first point y z coords of second point y z coords of third point y z coords of fourth point h PHOTPOSRMAXSOURCE 0 0 000050 0 000005 hash lookup max radial position h PHOTPOSRMAXSTART 0 0 000050 0 000005 hash lookup max radial position wrt 62 Appendix Test Case 4 Output File Comparison of Quasi Ballistic to Ballistic Photons for a Single Scattering Medium with a Collimating Hole Output File testcase4 mco RunInfo information on this simulation run commentO0 Test Case 4 commentl Duplication of Chu and Pfeiffer Simulation Results comment2 to Determine Ratio of Quasi Ballistic to Ballistic Photons comment3 programdescription Monte Carlo Simulation of Photon Transport in Media programname ptsl exe mlmain04 c programauthor Nick Pfeiffer programversiondate December 2002 inputfile testcase4 mci name of input file for this run outputfile testcase4 mco name of output file for this run photonqty 100000000 total number of photons in all sources runstart Mon Dec 23 20 59 32 2002
240. ooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oo 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 oo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oOooooooo oo 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 00 0 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00 0 0 00 00 00 00 00 00 00 00
241. ory and pos poslist 0 1000000 0 0000020 0 0000000 starting position 0 1000000 0 0000020 9 5000000 0 0000000 0 0000020 9 5000000 X 0 0000000 0 0000020 10 0000000 0 0000000 0 0000020 10 0007500 0 0000000 0 0000023 10 0040000 0 0000000 0 0000198 10 2235000 0 0000000 0 0000198 10 2240000 X 0 0000000 0 0000198 10 2500000 N 0 0000000 0 0000198 10 2505000 N 0 0000000 0 0000198 10 2510000 0 0000000 0 0000198 10 2610000 0 0000000 0 0000198 10 2710000 1 recorded position It can be seen from the list of recorded positions that photon was reflected by the two 45 degree mirrors and through the beam expander The y coordinate of the photon exiting the beam expander was approximately 10 times that of the y coordinate of the photon entering the beam expander 19 8 vs 2 microns The photon passed through the collimator hole with a trajectory almost parallel to the z axis dx 0 0000000 dy 0 0000002 dz 1 0000000 with the small errors due to alignment of the optics and the small circle of confusion of spherical lenses Test Case 6 A Uniform Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes While Test Case 5 demonstrated the definition of a complex model only a point photon source with a single photon was used Test Case 6 uses the definition of Test Case 5 but substitutes a uniform photon source of 1 25 mm beam radius 2 5 mm diameter in place of
242. otons nm shptype CIRCLE type of shape for object p0 0 1000000 0 0000020 0 0000000 point 0 center for circle pl 0 1000000 0 0000020 0 0000000 point 1 p2 0 1000000 0 0000020 0 0000000 point 2 p3 0 1000000 0 0000020 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 000000 radius of circle m radius squared 0 000000 radius of circle squared PhotonInfo photon information posstart 0 1000000 0 0000020 0 0000000 starting position trajstart 0 0000000 0 0000000 1 0000000 starting trajectory poscurrent 0 0000000 0 0000198 10 2710010 current position trajcurrent 0 0000000 0 0000002 1 0000000 current trajectory medium ambient current medium in which photon resides wavelength 514 000000 wavelength of photon nm movecount 12 number of moves made by photon scattercount 0 number of scatter events reflectcount 2 number of reflect events refractcount 10 number of refract events pathlength 10 371001 total pathlength m life 0 000000034610 lifetime of photon secs desireddist 10000000000000000000 000000 current desired distance 80 tr sc of ph ph Ru Ma 0 OS O O00 C OOOO 0 gt c C OOo photposrsource 0 100000 radial component of current position reference to the photon source rmal photposrstart 0 100000 radial component of curr
243. pe of photon source qty 1000000 initial number of photons in source to launch qtyleft 1000000 number of photons left in source to launch count 0 number of photons already launched from source wavelength 514 000000 wavelength of photons nm shptype CIRCLE type of shape for object p0 0 000000 0 000000 0 000000 point 0 center for circle pi 0 000000 0 001250 0 000000 point 1 p2 0 000000 0 000000 0 000000 point 2 p3 0 000000 0 000000 0 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 001250 radius of circle m radius squared 0 000002 radius of circle squared The output from photon density maps include a data section the secondary context data followed by a single line of token values formatted as multiple lines through the use of the line continuation character as shown in the small sample map below The row and column bin values are indicated by comments Map define a photon density map id x y pos of beam upstream of collimating hole id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object pO 1 000000 1 000000 0 010001 point 0 center for circle pl 1 000000 1 000000 0 010001 point 1 p2 1 000000 1 000000 0 010001 point 2 p3 1 000000 1 000000 0 010001 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 0 000000 extrusion length m 0
244. ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium p000 010001 x y 2 coords of first point 1 0 0 000025 01 x y 2 coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source 0 0 0 x z coords of center in m 1 0 0 000025 0 x z coords of point on circumference in m normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 100000000 number of photons to launch from source Map define a density map id x y pos of beam upstream of collimating hole type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 0100005 x y z coords of first point 1 1 0100005 x y z coords of second point p2 1 1 0100005 x y z coords of third point p3 1 1 0100005 x y z coords of fourth point Map define a density map id x y pos of beam downstream of collimating hole type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 0200015 x y z coords of first point 1 1 0200015 x z coords of second point p2 1 1 0200015 x y z coords of third point p3 1 1 0200015 x y z coords of fourth point Map define a density map type planar planar type of map s
245. rcle pl 0 0000000 0 0150000 10 0000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 004000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id diverging lens 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 000000 index of refraction shptype SEMISPHERE type of shape for object p0 0 0000000 0 0000000 10 0120000 point 0 center for circle pl 0 0000000 0 0112500 10 0120000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 10 0040000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 011250 radius of circle m radius squared 0 000127 radius of circle squared Medium define a scattering and absorbing medium id conve
246. rging lens id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 2 000000 index of refraction shptype SEMISPHERE type of shape for object p0 0 0000000 0 0000000 9 9755000 point 0 center for circle pl 0 0000000 0 2485000 9 9755000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 10 2235000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000000 extrusion length m 0 if planar radius 0 248500 radius of circle m radius squared 0 061752 radius of circle squared Medium define a scattering and absorbing medium id slit blocking medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 106 mua 59866 590624 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9996891514694 884766 absorption ratio absorbed to unabsorbed photons in direction o
247. ribution The Monte Carlo method is named for the manner in which the random numbers are generated in essence the Monte Carlo method is a form of roulette strategy The Monte Carlo method is applied to photon transport in a homogenous medium as follows 1 aphoton is created with a specified location and trajectory 2 the photon is moved along its trajectory a random distance based upon the properties of the medium absorption and scattering coefficients the photon trajectory is randomly changed step 2 is repeated until the photon exits the scattering medium or is absorbed properties of the photon are recorded Oye vom c step 1 is repeated until a sufficient number of photons have been simulated 7 recorded results distributions of photon properties are post processed and analyzed Figure 1 shows a single photon making a random walk as it is modeled by the Monte Carlo method The random walk observed in Figure 1 represents the simulated path of the photon through the medium When many photons are simulated in the same manner the cumulative results approaches that of experimentally observed photon distributions The length of each leg that the photon travels between scattering events is determined by the scattering coefficient SCATTERING MEDIUM RANDOM LENGTH LAUNCH PHOTON RANDOM RECORD ra PHOTON PROPERTIES SCATTERING EVENTS Figure 1 Random Walk of Single Photon
248. rly the definition of what constitutes a quasi ballistic photon is application dependent For the purposes of this discussion a quasi ballistic photon is defined as a photon that carries information about objects within the medium such that if it is blocked by the object the object s shadow will projected on a shadowgram with some specified degree of accuracy The problem of detecting objects using quasi ballistic photons sometimes referred to in the literature as snake photons is made easier by the fact that for many biological tissues the phase function S is highly peaked towards scattering photons in a forward direction and the absorption coefficient u4 is low for photons with infra red wavelengths This results in a relatively large number of quasi ballistic photons available for use The photon detector shown in Figure 3 is used to create a photon density map This is a map of photon quantities binned in a specific manner Each time a photon passes through the detector the quantity of a specific bin is incremented Many different types of photon properties may be used to define the bins If the bins are defined based on the x y coordinates of the photon as it passes through the detector then a 2D intensity image is formed However if the bins are defined using the trajectory of the photon angular deviation from original trajectory and the radial position of the photon distance perpendicular to original trajectory from source then a d
249. s closely when the same criteria is used to select quasi ballistic photons Test Case 5 A Point Source with Two Mirrors a Beam Expander a Slit a Single Medium and an Array of Three Collimating Holes Many of the features of the PST software are shown in Test Case 5 Figure 19 shows the model setup which consists of two 45 degree reflecting mirrors a 10 x Gaussian beam expander a 0 2 mm x 20 mm slit a scattering medium an array of three collimating holes and appropriate photon density maps This model emulates the experimental setup in use in the Clean Room at SFU While not particularly practical as an model setup a uniform photon source located upstream of the slit would provide a less computational intensive supply of photons this test case does show how mirrors lenses slits and arrays of collimating holes may be combined to create complex simulations The mirrors are defined as cylindrical mediums with high index of refraction and are oriented by specifying the surface normal vector Note that a non unit normal vector is permitted as the PTS software normalizes the vector prior to commencing the simulation run The output file shows this normalized unit vector Medium define a scattering and absorbing medium id mirror 1 first mirror g 1 0 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000 absorb ratio indexrefraction 10000 index of refraction shptype CI
250. s the second medium defined in the input file and is superimposed on the bounding box An ambient medium of length width and height of 2000 meters centered on 0 0 0 is used for all test cases described This combination of ambient medium and bounding box gives a simulation space from 1000 1000 1000 to 1000 1000 1000 Any photons that travel through the ambient medium without reaching a user defined medium encounter the bounding box and are absorbed A definition of bounding box and ambient medium used for all of the test cases is shown below Medium define a scattering and absorbing medium id bounding box medium 0 g 1 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 100000000 0 coefficient of absorption indexrefraction 1 index of refraction shptype RECTANGLE shape of medium pO 1001 1001 1001 2 coords of first point pl 1001 1001 1001 x y z coords of second point p2 1001 1001 1001 x y z coords of third point p3 1001 1001 1001 x y z coords of fourth point extrudelen 2002 extrusion length of box Medium define a scattering and absorbing medium id test medium 0 ambient g 1 g factor of medium mean cosine of forward scattering angle mus 0 0 coefficient of scattering mua 0 0 coefficient of absorption indexrefraction 1 index of refraction shptype RECTANGLE shape of medium 1000 1000 1000 2 coords of first poin
251. scattering ratio scattered to ballistic photons direction of extrudelen absorbratio 10000000 004464 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 8059 047876 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 10000 000000 index of refraction shptype CIRCLE type of shape for object p0 0 0000000 0 0000000 9 5000000 point 0 center for circle pl 0 0000000 0 0150000 9 5000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 7071068 0 0000000 0 7071068 surface normal extrudelen 0 002000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id diverging lens 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1 albedo 0 500000 albedo indexrefraction 1 450000 index of refraction shptype CIRCLE type of shape for object p0 0 0000000 0 0000000 10 0000000 point 0 center for ci
252. sorbing medium id slit blocking medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 78 mua 59866 590624 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9996891514694 884766 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 59866 590624 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1 0000000 1 0000000 10 2500000 point 0 center for circle pl 1 0000000 1 0000000 10 2500000 point 1 p2 1 0000000 1 0000000 10 2500000 point 2 p3 1 0000000 1 0000000 10 2500000 point 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 0 000500 extrusion length m 0 if planar Medium define a scattering and absorbing medium id slit opening medium id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 0 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 0 000000 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 0 000000 extinction coefficient m 1
253. starting time and date of run RandomNumberGenerator define the random number generator type MC type of random number generator Seed 0 000000 initial seed count 0 000000 quantity of numbers generated since initial seed Medium define a scattering and absorbing medium id bounding box medium 0 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 100000000 000000 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 9 999999999999999673000000000000000000000 98 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mut 100000000 000000 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 1 000000 index of refraction shptype RECTANGLE type of shape for object pO 1001 000000 1001 000000 1001 000000 point 0 center for circle pl 1001 000000 1001 000000 1001 000000 point 1 p2 1001 000000 1001 000000 1001 000000 point 2 p3 1001 000000 1001 000000 1001 000000 point 3 normalvector 0 000000 0 000000 1 000000 surface normal extrudelen 2002 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id test medium 0 ambient id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient
254. t pl 1000 1000 1000 x z coords of second point p2 1000 1000 1000 x y z coords of third point p3 1000 1000 1000 x z coords of fourth point extrudelen 2000 extrusion length of box In summary a medium object is used by the PTS software as a flexible mechanism for representing physical objects of arbitrary shapes The combination of the absorption scattering reflection and refraction properties of mediums allows not only scattering objects to be simulated but also embedded objects collimating holes lenses bounding boxes shadow masks and more 14 Photon Sources A photon source is a source of photons used in the simulation Multiple photon sources are allowed A photon source has a physical structure position orientation and geometrical shape a distribution of photons and a quantity of photons to launch In addition the wavelength of photons may be specified although wavelength dependent behaviour is not supported by the PTS software at this time A sample photon source defined using the PhotonSource primary context is shown below PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source 0 0 0 z coords of center in cm pl 0 0 00125 0 x y z coords of point on circumference in cm normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1000000 number of photons to launch from source The initial trajec
255. t 3 normalvector 0 0000000 0 0000000 1 0000000 surface normal extrudelen 2000 000000 extrusion length m 0 if planar Medium define a scattering and absorbing medium id mirror 1 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 8059 047876 coefficient of absorption m 1 scatterratio 0 000000 scattering ratio scattered to ballistic photons in direction of extrudelen absorbratio 10000000 004464 absorption ratio absorbed to unabsorbed photons in direction of extrudelen mat 8059 047876 extinction coefficient m 1 albedo 0 000000 albedo indexrefraction 10000 000000 index of refraction shptype CIRCLE type of shape for object pO 0 1000000 0 0000000 9 5000000 point 0 center for circle pi 0 1000000 0 0150000 9 5000000 point 1 p2 0 0000000 0 0000000 0 0000000 point 2 p3 0 0000000 0 0000000 0 0000000 point 3 normalvector 0 7071068 0 0000000 0 7071068 surface normal extrudelen 0 002000 extrusion length m 0 if planar radius 0 015000 radius of circle m radius squared 0 000225 radius of circle squared Medium define a scattering and absorbing medium id mirror 2 id of medium g 1 000000 g factor of medium mean cosine of forward scattering angle mus 0 000000 coefficient of scattering m 1 mua 8059 047876 coefficient of absorption m 1 105 scatterratio 0 000000
256. ters as the entity name in Scheme d Figure 8 Examples of ACIS Solid Models a reflection refraction from NURBPLANE with a uniform photon source b Cylindrical Spherical Cylindrical Beam Expander c scattering within a medium from a point photon source d side view of scattering within a medium from a point photon source The current version of the PTS parser does only rudimentary checking primarily syntax checking on geometric data It is quite possible to generate a non manifold shape The Scheme visualization output files for ACIS aid in detecting these errors after the fact as non manifold geometry can be viewed by the user 21 The ACIS Scheme language translator exhibits occasional problems in loading Scheme output files These errors are usually the result of a mismatch between the geometric tolerances used by the PTS software and those of the ACIS system Such errors are caused by specifying points that are too close together in a wire body of a photon trajectory Future work may be needed to identify the proper tolerances to use when translating geometries to Scheme The Scheme output of a photon trajectory is shown below Comments are automatically created to aid Scheme program readability create a wire body of photon trajectory for photon uniform source 1 0 define uniform source 1 0 wire body points list position 0 3941447 0 2066050 0 5000000 movecount 0 position 0 3941447 0 2066050 0 0000000
257. the point source PhotonSource define a photon source id uniform source 1 type UNIFORM uniform type of photon source 0 10 0 0 z coords of center in cm pl 0 10 0 00125 0 x y z coords of point on circumference in cm normalvector 0 0 1 launch photons parallel to z axis wavelength 514 wavelength in nm qty 1000000 number of photons to launch from source The effect of the beam expander can be seen in Figures 20 and 21 These figures plotted as surface contour plots on a square photon x y density map of width 25 mm clearly show how the beam size is increased by the Gaussian beam expander The intensity variations in the expanded beam are due to the low numbers of photons used too few photons per density map bin 34 Figure 20 Test Case 6 Plot of Photon Density Figure 21 Test Case 6 Plot of Photon Density as a Function of x Coordinate and y Coordinate as a Function of x Coordinate and y Coordinate Upstream of Beam Expander Downstream of Beam Expander The slit acts to restrict the amount of light entering the scattering medium The 0 2 mm high by 20 mm wide slit upstream of the scattering medium allows ballistic photons through to the linear collimator array but blocks light that would otherwise contribute only to the scattered noise Figures 22 and 23 show the images collected by x y photon density maps located upstream and downstream of the collimating array It should be noted that this simulation is condu
258. the type of random number generator is useful for cross checking simulation results if there exists the possibility that the results were influenced by the sequence of pseudorandom numbers The random number generator may have two types MT for Mersenne Twister and MC for Monte Carlo used by Jacques The initial seed used by the generator may be specified The random number generator must be defined prior to a simulation run An example input file specification for the random number generator defined using the RandomNumberGenerator primary context is shown below RandomNumberGenerator define the random number generator used for the simulation type MC type of random number generator seed 0 initial seed Scattering and Absorbing Mediums Three types of objects are supported by the PTS software scattering and absorbing mediums photon sources and photon density maps The geometry definitions used for all of these objects are the same and will be described in this section only A medium is a general purpose object that is used to represent real i e physical objects Multiple mediums are allowed A medium has a physical structure position orientation and geometrical shape and optical properties absorption and scattering coefficients index of refraction and anisotropy factor g A sample medium defined using the Medium primary context is shown below Medium define a scattering and absorbing medium id collimator blocking medi
259. third point 1 1 10 261 z coords of fourth point extrudelen 01 extrusion length of box Medium define a scattering and absorbing medium id collimator hole 1 hole medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium pO 0 000100 0 10 261 x z coords of first point pl 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 2 hole medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio indexrefraction 1 index of refraction shptype CIRCLE shape of medium 0 0 10 261 z coords of first point pl 0 0 000025 10 261 x y z coords of second point normalvector 0 0 1 direction of hole is in dir n of and parallel to z axis extrudelen 01 extrusion length of hole Medium define a scattering and absorbing medium id collimator hole 3 hole medium for collimator downstream of sample 9 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 0 absorb ratio
260. ton density maps three optional commands secondary contexts are defined The calccriteria determines the eligibility of photons to be considered for calculations adding to the binned density The absorbcriteria determines under what conditions photons are absorbed by the density map and allows the density map to act as a perfect absorbing plane in some situations The containmax command determines the maximum number of photons that the density map will contain useful for limiting the number of photon trajectory histories recorded with the PHOTINFO command 18 The calccriteria and absorbcriteria may have the following values NONE no photons meet criteria NORMAL photons in normal direction meet criteria ANTINORMAL photons in anti normal direction meet criteria ALL all photons meet criteria CALC photons meet criteria if they meet calc limits for table ANTICALC photons meet criteria if they do not meet calc limits for table By default calccriteria is defined as ALL absorbcriteria is defined as NONE and containmax is approximately infinite for a photon density map As a post processing aid a number of values are calculated calccount absorbcount totalcount containcount and displayed as comments An example output excluding the data section of a photon density map is shown below Map define a photon density map id image pixel map id of density map type PLANAR type of density map calccriteria ALL calculation
261. tory of all photons is that of the unit normal vector of the photon source shape unless a spherical or HG angular distribution is specified in which case the distribution is centered on the unit normal vector of the photon source shape Table 2 shows the seven types of photon sources that are implemented Table 2 Types of Photon Sources Source Type Source Description POINT photon source launches all photons from point UNIFORM photon sources launches photons from within the plane circle defined by the shape with a photon intensity distribution that is constant across the circle GAUSSIAN photon source launches photons with a photon intensity distribution that follows a Gaussian distribution centered on the plane circle with a spot size equal to the circle diameter SPHERICAL point source type with spherical distribution POINTHG point source type with Henyey Greenstein distribution specified by g POINTSPHERICALUZ point source type with spherical distribution confined to a solid angle specified by uz or alpha around source reference vector UNIFORMSPHERICALUZ uniform source type with spherical distribution confined to a solid angle specified by uz or cos alpha around source reference vector A sample photon source with uniform spherical distribution is shown below This photon source is a planar disc of radius 200 microns emitting photons that are uniformly distributed over angles from 0 81 of the photon so
262. ttering Medium Downstream of Scattering Medium 25 The image downstream of the medium clearly shows signs of scattering The circular beam is still visible due primarily to ballistic photons while the edges have been blurred The average number of photons in each bin within the radius of the beam is approximately 800 while the average number of scattered photons captured in bins outside of the beam is approximately 80 This image shows the expected behaviour of becoming more uniform as the scattering level is increased It would be expected that if the scattering level was increased further and the number of photons increased also to maintain a reasonable number of photons per bin then the beam would eventually become indistinguishable from the background noise of the scattered photons Test Case 4 Comparison of Quasi Ballistic to Ballistic Photons for a Single Scattering Medium with a Collimating Hole In earlier work Chu and Pfeiffer compared the number of quasi ballistic photons to ballistic photons for a range of scattering ratios and anisotropy factors using Monte Carlo simulation A portion of those results are shown in Table 4 Table 4 Simulation Results for Uniform Source 100 000 000 photons per run no absorption collimating array in place 50 micron diameter holes 1 cm long directly against sample No of No of No of Ballistic Quasi Ballistic Scattered Scattering Level g Photons Photons Photons 09 0 9 9950944
263. ulationtype is the type of photon calculation for the index valmin valmax and valdelta are the minimum maximum and delta values for column index bins In the map above the column index is defined by the idxcol token line to be a hash lookup function with a minimum column index value of 0 0020 m a maximum column index value of 0 0020 m and a column bin width of 0 0001 m This forms a column index with values 0 0020 0 0019 0 0018 0 0018 0 0019 0 0020 There 41 columns in this index with the first column consisting of values from 0 0020 up to but not including 0 0019 and the last column consisting of values from 40 0020 up to but not including 0 0021 The photoncalculationtype token specifies what information is extracted from the passing photon Using the rows and columns of a single table two items of photon information may be correlated by each photon density map In the map above the PHOTPOSX and PHOTPOSY tokens specify that the x coordinate and the y coordinate absolute of the photon position as it passes through the density map are used to create the density map This results in an image of the photon flow with the intensity of the image being relative to the number of photons passing through a particular bin Figure 10 in section Test Case 1 shows the image produced by such an density map A number of types of photon calculations are defined It is expected that additional calculation types will be added as th
264. um blocking medium for collimator downstream of sample 1 g factor of medium mean cosine of forward scattering angle scatterratio 0 scattering ratio absorbratio 10000000000000 absorb ratio indexrefraction 1 index of refraction shptype RECTANGLE shape of medium I 1 010001 x z coords of first point pl 1 1 010001 x z coords of second point p2 11 010001 x y z coords of third point 3 1 1 010001 x 2 coords of fourth point extrudelen 01 extrusion length of box The id token is used to assign an identifier to the medium object it is good practice to identify all objects The anisotropy factor g is specified by the g token It may have a value from 1 to 1 with 1 indicating that photons are scattered fully in the direction of their travel The scatterratio and absorbratio secondary context tokens are used to define the coefficient of scattering or absorption respectively These ratios represent the predicted number of photons scattered or absorbed in transiting through the medium along the extrusion path of the medium to those that are not scattered or absorbed For example a scatterratio of 9 would indicate that 9 photons are scattered for each unscattered photon or the probability of scattering in distance is 90 The relationship between absorbratio and coefficient of absorption u is shown below A similar relationship holds for scattering bus absorbratio absorbratio 1 p
265. urce normal The uz parameter of 0 9999 specifies the cosine of the limit angle for the uniform angular distribution It is most useful for ensuring that photons are randomly emitted in the primary direction of interest PhotonSource define a photon source id Uniform spherical uz source 2 on z axis type UNIFORMSPHERICALUZ uniform spherical distribution confined to traj uz shptype CIRCLE shape of source is a circle pO 0 000000 0 010000 0 000000 x y z coords of center m radius 0 000200 radius of circular map normalvector 0 0 1 launch photons parallel to z axis uz 0 9999 max forward trajectory for uniformly distributed photon angles qty 1000000 number of photons to launch from source Photon Density Maps A photon density map is a planar photon detector object that is used to capture information from photons as they pass through its surface Multiple photon density maps are allowed A photon density map has a physical structure position orientation and geometrical shape and a data table of photon information At present only rectangular and circular density maps are supported 2D only not 3D A sample photon density map defined using the Map primary context is shown below Map define a density map id x y pos of beam before expansion type planar planar type of map shptype RECTANGLE shape of medium 1 1 9 9 z coords of first point pl 1 1 9 9 x z coords of second point p2 1 1 9 9
266. us squared 0 000000 radius of circle squared 0 if planar RunInfo runend Sat Dec 28 03 51 35 2002 ending time and date of run Map define a photon density map id x y pos of beam upstream of scattering medium id of density map type PLANAR type of density map shptype RECTANGLE type of shape for object 1 0000000 1 0000000 0 9999990 pl 1 0000000 1 0000000 0 9999990 p2 1 0000000 1 0000000 0 9999990 p3 1 0000000 1 0000000 0 9999990 normalvector 0 0000000 0 0000000 1 0000000 extrudelen 0 000000 extrusion length row HASH PHOTPOSY 0 000050 0 idxrow idxcol col 1 1 HASH PHOTPOSX 0 000050 0 0 000020 0 000010 0 000040 data 49 00 43 00 31 00 56 00 49 00 24 00 67 00 51 00 37 00 57 00 67 00 35 00 85 00 82 00 33 00 100 00 96 00 42 00 0 346731 637897 50 00 636799 637967 46 00 631913 636346 54 00 637274 636935 66 00 636640 638575 56 00 637380 637036 51 00 634739 637301 52 00 346743 637034 56 00 86 00 740 0 0 0 0 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0 000050 0 000015 0 000015 0 000045 35 00 57 00 51 00 000050 49 00 51 00 50 00 000045 33 00 55 00 49 00 000040 45 00 48 00 54 00 000035 44 00 91 00 70 00 000030 53 00 201550 00 87 00 000025 52 00 636874 348044 57 00 5
267. wavelength in nm qty 50000000 number of photons to launch from source Map define a density map id x y pos of beam upstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium 1 1 999999 y z coords of first point 1 1 999999 x y z coords of second point p2 1 1 999999 x y 2 coords of third point p3 1 1 999999 x z coords of fourth point idxcol col 1 1 hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x pos idxrow row indexl hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup y pos Map define a density map id x y pos of beam downstream of scattering medium type planar planar type of map shptype RECTANGLE shape of medium pO 1 1 1 010001 x y 2 coords of first point pl 1 1 1 010001 x y 2 coords of second point 1 1 1 010001 x y 2 coords of third point p3 1 1 1 010001 x y z coords of fourth point col hash PHOTPOSX 0 000050 0 000050 0 000005 hash lookup x pos idxrow row hash PHOTPOSY 0 000050 0 000050 0 000005 hash lookup y pos 54 Appendix Test Case 3 Output File A Single Medium with Scattering Using 50 000 000 Photons Output File testcase3 mco RunInfo information on this simulation run commentO Test Case 3 commentl A Single Medium with Scattering but without Absorption comment2 Photon Source with 50 million photons
268. y recorded position reference to the photon start trajectory and pos Table 3 Types of Pre defined Photon Calculations cont Calculation Type Calculation Description PHOTPATHLENGTHFRAC fraction formed by dividing pathlength by distance from photon launch to current position PHOTQTYCOUNT photon id quantity count of photons so far PHOTTRAJSTARTDOTSOURCE starting trajectory wrt source PHOTPOSRSTARTSOURCE starting radial position wrt source PHOTTRAJDEVMAX dot product of maximum trajectory deviation and photon source trajectory deviation for each photon location is the angle from the current location to the historical location wrt source trajectory If PHOTINFO is used to define one of the photon calculations in a density map then each photon that passes through the map will cause the photon s trajectory history point by point to be written to the output file This is useful for visualizing photon distributions and paths However as the file size can quickly become very large some care should be taken in limiting the number of photons passing through the map A sample of the photon information in the output file produced by the PHOTINFO calculation is shown below PhotonInfo photon information posstart 0 000000 0 000002 0 000000 starting position trajstart 0 000000 0 000000 1 000000 starting trajectory poscurrent 0 000005 0 000023 10 271001 current position trajcurrent 0 000000 0 000000 1 000000 current traj
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