Thursday, August 20, 2015

using MCML - Monte Carlo light transport in multi-layered scattering media

is referenced in Wang and Wu's Biomedical Optics. Some points I noted for its usage are given below, in addition to the documentation available in the book as well as the included paper in the download.

  • I used Fabrice Bellard's Tiny C compiler to re-compile the code on Windows. It's only a 386 kB standalone download, as against gcc's MinGW and CygWin options which are installers which download more files.
  • After extracting the zip file, you can add its location to the path variable - Control Panel -> System ->  Advanced -> Environment Variables, and then restart the system, or add it to the commandline for a temporary session.
  • Compile, link and create executable with just
    tcc -o mcml.exe mcmlmain.c mcmlgo.c mcmlio.c mcmlnr.c
    Done in less than a second.
  • Incident light angle has direction cosines (0,0,1) by default, can change in mcmlgo.c
  • The output 2-D arrays of Tt_ra, Rd_ra, A_rz are formatted in the ASCII output file as 5 numbers per line(!) and not as lines and columns related to the 2-D array. This can be modified in mcmlio.c - or, of course, when the array is imported into something like Matlab, it needs further processing.
  • Large txt files are created by mcml in case large numbers are specified for dz, dr and da - these will need txt file editors which can handle large files. Files upto a few hundred MB were OK with PsPad, other options are gVim etc as noted here.
  • Section 3.5 of the Biomedical Optics book talks about overflow in the grid - we have to note this - that the last grid element in the direction of the overflow collects the weight - and have to discard that point. In reconstruction Fig 3.4, for eg, the first grid element reading has to be discarded - T_t(0). - or perhaps this is because the measured value is T_t (total transmittance) and what we need is T_d (diffuse transmittance). The angle a (or alpha) in R_d(a) is angle of reflection, so it goes from 0 to pi/2.
  • Section 3.5 also talks about how we should choose the grid size - numbers of da, dz and dr along with values of dz and dr - as a rule of thumb, each grid element should measure about 10% of penetration depth or transport mean free path.

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