MCCL Examples

Monte Carlo Command Line Options

Command-line Parameters

help - displays brief description of parameters described below
infile - the default is infile.txt in the root of the application, accepts relative and absolute paths
outpath - default is the root of the application, accepts relative and absolute paths
outname - default is the infile name, this value is appended if there is a parameter sweep
paramsweep - takes the sweep parameter name and values in the format:
paramsweep=<SweepParameterType>,Start,Stop,Count
paramsweepdelta - takes the sweep parameter name and values in the format:
paramsweepdelta=<SweepParameterType>,Start,Stop,Delta
paramsweeplist - takes the sweep parameter name and values in the format:
paramsweeplist=<SweepParameterType>,number of values,val1,val2,...,valn
geninfiles - generates sample infiles and names them infile_XXX.txt

Values for SweepParameterType

mua1 - absorption coefficient for tissue layer 1
mus1 - scattering coefficient for tissue layer 1
n1 - refractive index for tissue layer 1
g1 - anisotropy for tissue layer 1
d1 - thickness for tissue layer 1

mua2 - absorption coefficient for tissue layer 2
mus2 - scattering coefficient for tissue layer 2
n2 - refractive index for tissue layer 2
g2 - anisotropy for tissue layer 2
d2 - thickness for tissue layer 2

muai - absorption coefficient for tissue layer i
musi - scattering coefficient for tissue layer i
ni - refractive index for tissue layer i
gi - anisotropy for tissue layer i
di - thickness for tissue layer i

nphot - number of photons to launch from the source

Program Structure

Example: Create a folder called MonteCarlo with 2 sub-folders “Application” and “Simulation”. In Application place all the files needed to run mc.exe (Same files as the zip file). In Simulation place any input files, myinfile.txt.

• MonteCarlo (folder)
  • Application (folder)
  • Simulation (folder)
  • Results (folder)

Possible Inputs for Windows (examples for Linux or Mac given below)

Run the simulation from the Results folder specifying one of the txt input files:

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\myinfile.txt

Input File: C:\MonteCarlo\Simulation\myinfile.txt with OutputName="results" specified in myinfile.txt
Output Path: C:\MonteCarlo\Results
Results Folder Name: results

Run the simulation specifying one of the txt input files and an output folder

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.txt outpath=C:\MonteCarlo\NewResults

Input File: C:\MonteCarlo\Simulation\infile_database.txt with OutputName="results" specified in infile_database.txt
Output Path: C:\MonteCarlo\NewResults
Results Folder Name: results

Run the simulation specifying one of the txt input files:

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\myinfile.txt paramsweepdelta=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\myinfile.txt with OutputName="results" specified in myinfile.txt
Output Path: C:\MonteCarlo\Results
Results Folder Names:

• results_mua1_0.01
• results_mua1_0.02
• results_mua1_0.03
• results_mua1_0.04

Run the simulation specifying one of the txt input files and an output folder

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.txt outpath=C:\MonteCarlo\NewResults paramsweepdelta=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\infile_database.txt with OutputName="results" specified in infile_database.txt
Output Path: C:\MonteCarlo\NewResults
Results Folder Names:

• results_mua1_0.01
• results_mua1_0.02
• results_mua1_0.03
• results_mua1_0.04

Run the simulation specifying one of the txt input files and an output folder and an output tag

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.txt outpath=C:\MonteCarlo\NewResults outname=myResults paramsweepdelta=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\infile_database.txt
Output Path: C:\MonteCarlo\NewResults
Output tag: myResults
Results Folder Names:

• myResults_mua1_0.01
• myResults_mua1_0.02
• myResults_mua1_0.03
• myResults_mua1_0.04

Run the simulation specifying one of the txt input files and an output folder and a 3D parameter sweep

Note: if g and mus are in the parameter sweep, make sure to specify the mus sweep after the g sweep

C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.txt outpath=C:\MonteCarlo\NewResults outname=myResults paramsweep=mua1,0.01,0.03,2 paramsweep=g1,0.8,0.9,2 paramsweep=mus1,5.0,6.0,2 

Input File: C:\MonteCarlo\Simulation\infile_database.txt
Output Path: C:\MonteCarlo\NewResults
Output tag: myResults
Results Folder Names:

• myResults_mua1_0.01_g1_0.80_mus1_5.00
• myResults_mua1_0.01_g1_0.80_mus1_6.00
• myResults_mua1_0.01_g1_0.90_mus1_5.00
• myResults_mua1_0.01_g1_0.90_mus1_6.00
• myResults_mua1_0.03_g1_0.80_mus1_5.00
• myResults_mua1_0.03_g1_0.80_mus1_6.00
• myResults_mua1_0.03_g1_0.90_mus1_5.00
• myResults_mua1_0.03_g1_0.90_mus1_6.00

Possible Inputs for Linux or Mac

All of the above commands described for Windows will also work on linux or Mac by replacing C:\MonteCarlo\Simulation with /home/user/MonteCarlo/Simulation.

Run the simulation from the directory (e.g. /home/user/MonteCarlo/) where the zip file was unzipped:

./mc infile=myinfile.txt

Input File: /home/user/MonteCarlo/myinfile.txt with OutputName="results" specified in myinfile.txt
Output Path: /home/user/MonteCarlo/
Results Folder Name: results

Run the simulation from some other directory:

/home/user/MonteCarlo/mc infile=/home/user/MonteCarlo/Simulation/myinfile.txt

Input File: /home/user/MonteCarlo/Simulation/myinfile.txt with OutputName="results" specified in myinfile.txt
Output Path: /home/user/MonteCarlo/
Results Folder Name: results