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MC 1.0 Design Document

Command-line Parameters

infile - the default is infile.xml 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,Delta

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

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

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

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

Possible Inputs

Run the simulation from the application folder without specifying an input file:

C:\MonteCarlo\Application>C:\MonteCarlo\Application\mc

Input File: C:\MonteCarlo\Application\infile.xml
Output Path: C:\MonteCarlo\Application
Results Folder Name: infile

Run the simulation from the Results folder without specifying an input file:

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc

Input File: C:\MonteCarlo\Results\infile.xml
Output Path: C:\MonteCarlo\Results
Results Folder Name: infile

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

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\myinfile.xml

Input File: C:\MonteCarlo\Simulation\myinfile.xml
Output Path: C:\MonteCarlo\Results
Results Folder Name: myinfile

Run the simulation spcifying one of the xml input files and an output folder

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.xml outpath= C:\MonteCarlo\NewResults

Input File: C:\MonteCarlo\Simulation\infile_database.xml
Output Path: C:\MonteCarlo\NewResults
Results Folder Name: infile_database

Run the simulation spcifying one of the xml input files and a relative output folder

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.xml outpath= \Test

Input File: C:\MonteCarlo\Simulation\infile_database.xml
Output Path: C:\MonteCarlo\Results\Test
Results Folder Name: C:\MonteCarlo\Results\Test

Run the simulation from the application folder without specifying an input file:

C:\MonteCarlo\Application>C:\MonteCarlo\Application\mc paramsweep=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Application\infile.xml
Output Path: C:\MonteCarlo\Application
Results Folder Names:
  • infile_mua1_0.01
  • infile_mua1_0.02
  • infile_mua1_0.03
  • infile_mua1_0.04

Run the simulation from the Results folder without specifying an input file:

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc paramsweep=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Application\infile.xml
Output Path: C:\MonteCarlo\Results
Results Folder Names:
  • infile_mua1_0.01
  • infile_mua1_0.02
  • infile_mua1_0.03
  • infile_mua1_0.04

Run the simulation specifying one of the xml input files:

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\myinfile.xml paramsweep=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\myinfile.xml
Output Path: C:\MonteCarlo\Results
Results Folder Names:
  • myinfile_mua1_0.01
  • myinfile_mua1_0.02
  • myinfile_mua1_0.03
  • myinfile_mua1_0.04

Run the simulation spcifying one of the xml input files and an output folder

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.xml outpath= C:\MonteCarlo\NewResults paramsweep=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\infile_database.xml
Output Path: C:\MonteCarlo\NewResults
Results Folder Names:
  • infile_database_mua1_0.01
  • infile_database_mua1_0.02
  • infile_database_mua1_0.03
  • infile_database_mua1_0.04

Run the simulation spcifying one of the xml input files and an output folder and an output tag

C:\MonteCarlo\Results>C:\MonteCarlo\Application\mc infile=C:\MonteCarlo\Simulation\infile_database.xml outpath= C:\MonteCarlo\NewResults outname=myResults paramsweep=mua1,0.01,0.04,0.01

Input File: C:\MonteCarlo\Simulation\infile_database.xml
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


Last edited Jun 6, 2011 at 8:19 PM by lmalenfant, version 16

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