Comment on “A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation” |
Biomedical Optics Express, Vol. 2, Issue 5, pp. 1258-1264 (2011)
http://dx.doi.org/10.1364/BOE.2.001258
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Abstract
The Monte Carlo (MC) method is a popular approach to modeling photon propagation inside general turbid media, such as human tissue. Progress had been made in the past year with the independent proposals of two mesh-based Monte Carlo methods employing ray-tracing techniques. Both methods have shown improvements in accuracy and efficiency in modeling complex domains. A recent paper by Shen and Wang [Biomed. Opt. Express 2, 44 (2011)] reported preliminary results towards the cross-validation of the two mesh-based MC algorithms and software implementations, showing a 3–6 fold speed difference between the two software packages. In this comment, we share our views on unbiased software comparisons and discuss additional issues such as the use of pre-computed data, interpolation strategies, impact of compiler settings, use of Russian roulette, memory cost and potential pitfalls in measuring algorithm performance. Despite key differences between the two algorithms in handling of non-tetrahedral meshes, we found that they share similar structure and performance for tetrahedral meshes. A significant fraction of the observed speed differences in the mentioned article was the result of inconsistent use of compilers and libraries.
© 2011 OSA
Comment
1. H. Shen and G. Wang, “A tetrahedron-based inhomogeneous Monte Carlo optical simulator,” Phys. Med. Biol. 55(4), 947–962 (2010). [CrossRef] [PubMed]
2. Q. Fang, “Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates,” Biomed. Opt. Express 1(1), 165–175 (2010). [CrossRef] [PubMed]
3. E. Margallo-Balbás and P. J. French, “Shape based Monte Carlo code for light transport in complex heterogeneous Tissues,” Opt. Express 15(21), 14086–14098 (2007). [CrossRef] [PubMed]
5. N. Ren, J. Liang, X. Qu, J. Li, B. Lu, and J. Tian, “GPU-based Monte Carlo simulation for light propagation in complex heterogeneous tissues,” Opt. Express 18(7), 6811–6823 (2010). [CrossRef] [PubMed]
3. E. Margallo-Balbás and P. J. French, “Shape based Monte Carlo code for light transport in complex heterogeneous Tissues,” Opt. Express 15(21), 14086–14098 (2007). [CrossRef] [PubMed]
5. N. Ren, J. Liang, X. Qu, J. Li, B. Lu, and J. Tian, “GPU-based Monte Carlo simulation for light propagation in complex heterogeneous tissues,” Opt. Express 18(7), 6811–6823 (2010). [CrossRef] [PubMed]
10. H. Shen and G. Wang, “TIM-OS Project Site,” https://sites.google.com/a/imaging.sbes.vt.edu/tim-os/.
11. Q. Fang, “Mesh-based Monte Carlo—the software,” http://mcx.sourceforge.net/mmc/.
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
Comparison of the ray-tracing algorithms
13. J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed]
13. J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
13. J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
13. J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
Comparison of interpolation strategies
Impact of compilers and optimization settings
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
10. H. Shen and G. Wang, “TIM-OS Project Site,” https://sites.google.com/a/imaging.sbes.vt.edu/tim-os/.
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
11. Q. Fang, “Mesh-based Monte Carlo—the software,” http://mcx.sourceforge.net/mmc/.
Other related issues
15. Intel Knowledge Base, “New fast basic random number generator SFMT19937 in Intel MKL,” (2010), http://software.intel.com/en-us/articles/new-fast-basic-random-number-generator-sfmt19937-in-intel-mkl/.
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
Conclusions
12. H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
Acknowledgment
References and links
1. | H. Shen and G. Wang, “A tetrahedron-based inhomogeneous Monte Carlo optical simulator,” Phys. Med. Biol. 55(4), 947–962 (2010). [CrossRef] [PubMed] |
2. | Q. Fang, “Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates,” Biomed. Opt. Express 1(1), 165–175 (2010). [CrossRef] [PubMed] |
3. | E. Margallo-Balbás and P. J. French, “Shape based Monte Carlo code for light transport in complex heterogeneous Tissues,” Opt. Express 15(21), 14086–14098 (2007). [CrossRef] [PubMed] |
4. | C. Wächter, “Quasi-Monte Carlo light transport simulation by efficient ray tracing,” Ph.D. dissertation (Ulm University, 2007) |
5. | N. Ren, J. Liang, X. Qu, J. Li, B. Lu, and J. Tian, “GPU-based Monte Carlo simulation for light propagation in complex heterogeneous tissues,” Opt. Express 18(7), 6811–6823 (2010). [CrossRef] [PubMed] |
6. | I. Wald, “Realtime ray tracing and interactive global illumination,” Ph.D. dissertation (Saarland University, 2004). |
7. | D. Badouel, “An efficient ray-polygon intersection,” Graphics Gems, S.A. Glassner, ed. (Academic Press Professional, 1990), pp. 390–393. |
8. | N. Platis and T. Theoharis, “Fast ray-tetrahedron intersection using Plücker coordinates,” J. Graph. Tools 8(4), 37–48 (2003). |
9. | M. Shevtsov, A. Soupikov, and A. Kapustin, “Ray-triangle intersection algorithm for modern CPU architectures,” in Proceedings of GraphiCon 2007, (2007), pp. 33–39. |
10. | H. Shen and G. Wang, “TIM-OS Project Site,” https://sites.google.com/a/imaging.sbes.vt.edu/tim-os/. |
11. | Q. Fang, “Mesh-based Monte Carlo—the software,” http://mcx.sourceforge.net/mmc/. |
12. | H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed] |
13. | J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed] |
14. | K. H. Huebner, The Finite Element Method for Engineers (Wiley, 2001), Section 10.6.4. |
15. | Intel Knowledge Base, “New fast basic random number generator SFMT19937 in Intel MKL,” (2010), http://software.intel.com/en-us/articles/new-fast-basic-random-number-generator-sfmt19937-in-intel-mkl/. |
OCIS Codes
(170.3660) Medical optics and biotechnology : Light propagation in tissues
(170.5280) Medical optics and biotechnology : Photon migration
(170.7050) Medical optics and biotechnology : Turbid media
ToC Category:
Optics of Tissue and Turbid Media
History
Original Manuscript: December 13, 2010
Manuscript Accepted: December 29, 2010
Published: April 19, 2011
Citation
Qianqian Fang, "Comment on “A study on tetrahedron-based inhomogeneous Monte-Carlo optical simulation”," Biomed. Opt. Express 2, 1258-1264 (2011)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-2-5-1258
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References
- H. Shen and G. Wang, “A tetrahedron-based inhomogeneous Monte Carlo optical simulator,” Phys. Med. Biol. 55(4), 947–962 (2010). [CrossRef] [PubMed]
- Q. Fang, “Mesh-based Monte Carlo method using fast ray-tracing in Plücker coordinates,” Biomed. Opt. Express 1(1), 165–175 (2010). [CrossRef] [PubMed]
- E. Margallo-Balbás and P. J. French, “Shape based Monte Carlo code for light transport in complex heterogeneous Tissues,” Opt. Express 15(21), 14086–14098 (2007). [CrossRef] [PubMed]
- C. Wächter, “Quasi-Monte Carlo light transport simulation by efficient ray tracing,” Ph.D. dissertation (Ulm University, 2007)
- N. Ren, J. Liang, X. Qu, J. Li, B. Lu, and J. Tian, “GPU-based Monte Carlo simulation for light propagation in complex heterogeneous tissues,” Opt. Express 18(7), 6811–6823 (2010). [CrossRef] [PubMed]
- I. Wald, “Realtime ray tracing and interactive global illumination,” Ph.D. dissertation (Saarland University, 2004).
- D. Badouel, “An efficient ray-polygon intersection,” Graphics Gems, S.A. Glassner, ed. (Academic Press Professional, 1990), pp. 390–393.
- N. Platis and T. Theoharis, “Fast ray-tetrahedron intersection using Plücker coordinates,” J. Graph. Tools 8(4), 37–48 (2003).
- M. Shevtsov, A. Soupikov, and A. Kapustin, “Ray-triangle intersection algorithm for modern CPU architectures,” in Proceedings of GraphiCon 2007, (2007), pp. 33–39.
- H. Shen and G. Wang, “TIM-OS Project Site,” https://sites.google.com/a/imaging.sbes.vt.edu/tim-os/ .
- Q. Fang, “Mesh-based Monte Carlo—the software,” http://mcx.sourceforge.net/mmc/ .
- H. Shen and G. Wang, “A study on tetrahedron-based inhomogeneous Monte Carlo optical simulation,” Biomed. Opt. Express 2(1), 44–57 (2011). [CrossRef] [PubMed]
- J. Havel and A. Herout, “Yet faster ray-triangle intersection (using SSE4),” IEEE Trans. Vis. Comput. Graph. 16(3), 434–438 (2010). [CrossRef] [PubMed]
- K. H. Huebner, The Finite Element Method for Engineers (Wiley, 2001), Section 10.6.4.
- Intel Knowledge Base, “New fast basic random number generator SFMT19937 in Intel MKL,” (2010), http://software.intel.com/en-us/articles/new-fast-basic-random-number-generator-sfmt19937-in-intel-mkl/ .
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