diff --git a/doc/mcx_help.html b/doc/mcx_help.html index 6aaff93a..92d3869d 100644 --- a/doc/mcx_help.html +++ b/doc/mcx_help.html @@ -92,6 +92,7 @@

--bench

  • cube60
  • cube60b
  • cube60planar +
  • cubesph60b
  • skinvessel
  • sphshell
  • spherebox @@ -398,6 +399,10 @@

    -K / --mediabyte

  • 1 or byte: 0-128 tissue labels
  • 2 or short: 0-65535 (max to 4000) tissue labels
  • 4 or integer: integer tissue labels +
  • 96 or asgn_float: mua/mus/g/n 4xfloat format +
  • 97 or svmc: split-voxel MC 8-byte format +
  • 98 or mixlabel: label1+label2+label1_percentage +
  • 99 or labelplus: 32bit composite voxel format
  • 100 or muamus_float: 2x 32bit floats for mua/mus
  • 101 or mua_float: 1 float per voxel for mua
  • 102 or muamus_half: 2x 16bit float for mua/mus @@ -641,6 +646,7 @@

    -d / --savedet

         '-d' or '-d 1' to enable (default) or 
         '-d 0' to disable
    +    '-d 3' terminate simulation when detected
     

    When this option is enabled, a binary file, with a suffix of .mch, will be produced in additional to the '.mc2' output. The .mch file contains the partial path data for all photons enters the apertures of the detectors. @@ -804,10 +810,10 @@

    -F / --outputformat

    the bnii/jnii formats support compression (-Z) and generate small files load jnii (JSON) and bnii (UBJSON) files using below lightweight libraries in MATLAB or Python:

    @@ -930,7 +936,8 @@

    -D / --debug

       1 R  debug RNG
       2 M  store photon trajectory info (saved in a .mct file, can be loaded with loadmch.m)
    -  4 P  print progress bar
    +  4 P  print progress bar 
    +  8 T  save trajectory data only, disable flux/detp
     

    combine multiple items by using a string, or add selected numbers together @@ -1002,7 +1009,7 @@

    2.1. JSON input file format

    "Domain::VolumeFile": "file full path to the volume description file, can be a binary or JSON file", "Domain::Dim": "dimension of the data array stored in the volume file", "Domain::OriginType": "similar to --srcfrom0, 1 if the origin is [0 0 0], 0 if it is [1.0,1.0,1.0]", - "Domain::LengthUnit": "define the voxel length in mm, similar to --unitinmm", + "Domain::LengthUnit": "define the voxel length in mm, similar to --unitinmm", "Domain::Media": "the first medium is always assigned to voxels with a value of 0 or outside of the volume, the second row is for medium type 1, and so on. mua and mus must be in 1/mm unit", @@ -1021,38 +1028,38 @@

    2.1. JSON input file format

    } }, "Domain": { - "VolumeFile": "semi60x60x60.bin", + "VolumeFile": "semi60x60x60.bin", "Dim": [60,60,60], "OriginType": 1, - "LengthUnit": 1, + "LengthUnit": 1, "Media": [ {"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0}, {"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.0} ] }, "Session": { - "Photons": 1000000, - "RNGSeed": 29012392, - "ID": "qtest" + "Photons": 1000000, + "RNGSeed": 29012392, + "ID": "qtest" }, "Forward": { - "T0": 0.0e+00, - "T1": 5.0e-09, - "Dt": 5.0e-09 + "T0": 0.0e+00, + "T1": 5.0e-09, + "Dt": 5.0e-09 }, "Optode": { - "Source": { - "Pos": [29.0, 29.0, 0.0], - "Dir": [0.0, 0.0, 1.0], - "Type": "pencil", - "Param1": [0.0, 0.0, 0.0, 0.0], - "Param2": [0.0, 0.0, 0.0, 0.0] - }, - "Detector": [ - { - "Pos": [29.0, 19.0, 0.0], - "R": 1.0 - }, + "Source": { + "Pos": [29.0, 29.0, 0.0], + "Dir": [0.0, 0.0, 1.0], + "Type": "pencil", + "Param1": [0.0, 0.0, 0.0, 0.0], + "Param2": [0.0, 0.0, 0.0, 0.0] + }, + "Detector": [ + { + "Pos": [29.0, 19.0, 0.0], + "R": 1.0 + }, { "Pos": [29.0, 39.0, 0.0], "R": 1.0 @@ -1065,7 +1072,7 @@

    2.1. JSON input file format

    "Pos": [39.0, 29.0, 0.0], "R": 1.0 } - ] + ] } }