| | JSON Input | Short | Long command | MATLAB/Octave | Value | Meaning | MCX | MCXLAB | MCXCL | MCXLABCL | MMC | MMCLAB | MMCL | MMCLABCL |
|---|
| Optical Parameters | Domain.VolumeFile | | | cfg.vol | 2D or 3D array | Domain volume | Y | Y | Y | Y | | | | |
| Mesh.ID | | | cfg.{node,elem} | mesh data | Domain mesh | | | | | Y | Y | Y | Y |
| Mesh.InitElem | | | cfg.e0 | integer | Initial element index (>0) | | | | | Y | Y | Y | Y |
| Domain.Media | | | cfg.prop | (media count+1)x4 array | Optical properties | Y | Y | Y | Y | Y | Y | Y | Y |
| Forward.T0 | | | cfg.tstart | float | Start time in second | Y | Y | Y | Y | Y | Y | Y | Y |
| Forward.T1 | | | cfg.tend | float | End time in second | Y | Y | Y | Y | Y | Y | Y | Y |
| Forward.Dt | | | cfg.tstep | float | Time gate width in second | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Type | | | cfg.srctype | string ('pencil') | Source type | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Pos | | | cfg.srcpos | 1x4 float | Source position in grid unit | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Dir | | | cfg.srcdir | 1x4 float | Source direction (vx,vy,vz) and focal length | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Param1 | | | cfg.srcparam1 | 1x4 float | Source parameters set 1 | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Param2 | | | cfg.srcparam2 | 1x4 float | Source parameters set 2 | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Source.Pattern | | | cfg.srcpattern | 2D or 3D array | Source pattern data | Y | Y | Y | Y | Y | Y | Y | Y |
| Optode.Detector.{Pos/R} | | | cfg.detpos | Nx4 array | Detector positions and radii | Y | Y | Y | Y | Y | Y | Y | Y |
| Forward.N0 | | | cfg.n0 | float | Background refractive index | | | | | Y | Y | Y | Y |
| MC Settings | | -f | --input | - | string | Input file (.json or .inp) | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.Photons | -n | --photon | cfg.nphoton | integer (0) | Total photon number | Y | Y | Y | Y | Y | Y | Y | Y |
| | -r | --repeat | cfg.repeat | integer (1) | Repeat count (positive int) | Y | Y | Y | Y | | | | |
| Session.DoMismatch | -b | --reflect | cfg.isreflect | bool (1) | Whether to do reflection/transmission | Y | Y | Y | Y | Y | Y | Y | Y |
| | -B | --bc | cfg.bc | 6-char-string (______) | Boundary conditions at 6 directions | Y | Y | Y | Y | | | | |
| Domain.LengthUnit | -u | --unitinmm | cfg.unitinmm | float (1) | Voxel edge length in mm | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoNormalize | -U | --normalize | cfg.isnormalize | bool (1) | Whether to normalize the solutions | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.RNGSeed | -E | --seed | cfg.seed | integer (0) | RNG seed (or a .mch file if replay) | Y | Y | Y | Y | Y | Y | Y | Y |
| Domain.OriginType | -z | --srcfrom0 | cfg.issrcfrom0 | bool (0) | Whether the lower-corner of the domain is 0,0,0 | Y | Y | Y | Y | | | | |
| | -R | --skipradius | cfg.skipradius | float (-2) | Whether to use atomic operations | Y | Y | Y | Y | | | | |
| | -k | --voidtime | cfg.voidtime | bool (1) | Whether to count the time-of-flight before entry | Y | Y | Y | Y | Y | Y | Y | Y |
| | -Y | --replaydet | cfg.replaydet | integer (-1) | Which detetor to be replayed | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoSpecular | -V | --specular | cfg.isspecular | bool (1) | Whether to do specular reflection upon entry | Y | Y | Y | Y | Y | Y | Y | Y |
| | -e | --minenergy | cfg.minenergy | float (0) | Minimum energy to trigger Russian Roulette | Y | Y | Y | Y | Y | Y | Y | Y |
| | -g | --gategroup | cfg.maxgate | integer (1) | Maximum time gate to be simulated together | Y | Y | Y | Y | | | Y | Y |
| GPU Settings | | -L | --listgpu | mcxlab('gpuinfo') | | List available GPUs | Y | Y | Y | Y | Y | Y | Y | Y |
| | -t | --thread | cfg.nthread | integer (16384) | Number of total threads | Y | Y | Y | Y | | | Y | Y |
| | -T | --blocksize | cfg.nblocksize | integer (64) | Size of thread block | Y | Y | Y | Y | | | Y | Y |
| Session.DoAutoThread | -A | --autopilot | cfg.autopilot | bool (1) | Choosing thread/block automatically | Y | Y | Y | Y | | | Y | Y |
| | -G | --gpu | cfg.gpuid | integer (1) or 01 string | Specify which GPUs to use | Y | Y | Y | Y | | | Y | Y |
| | -W | --workload | cfg.workload | float,float,... | Workload split between GPUs | Y | Y | Y | Y | | | Y | Y |
| | -I | --printgpu | - | | Print GPU information then run simulation | Y | | Y | | | | | |
| Input | Shapes | -P | --shapes | cfg.shapes | JSON string '{...}' | JSON-based domain descriptors | Y | Y | Y | Y | | | | |
| Domain.MediaFormat | -K | --mediabyte | array types in cfg.vol | 1,2,4,101,... (1) | Volume data voxel format | Y | Y | Y | Y | | | | |
| | -a | --array | - | bool (0) | Whether the array is in row-major | Y | | Y | | | | | |
| Output Settings | Session.ID | -s | --session | - | a sring ('default') | Output file stub | Y | | Y | | Y | | Y | |
| Session.OutputType | -O | --outputtype | cfg.outputtype | XFEJPM (X) | Output data type | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoPartialPath | -d | --savedet | 2nd output of mcxlab | bool (1) | Whether to save detected photons | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.SaveDataMask | -w | --savedetflag | cfg.savedetflag | DSPMXVW (DP) | What fields to save per detected photon | Y | Y | Y | Y | | | | |
| Session.DoSaveExit | -x | --saveexit | cfg.issaveexit | bool (0) | Whether to save exit positions and dir | Y | Y | Y | Y | Y | Y | Y | Y |
| | -X | --saveref | cfg.issaveref | bool (0) | Whether to save diffuse reflectance | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoDCS | -m | --momentum | cfg.ismomentum | bool (0) | Whether to save momentum transfer | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoSaveSeed | -q | --saveseed | cfg.issaveseed | bool (0) | Whether to save RNG seeds for replay | Y | Y | Y | Y | Y | Y | Y | Y |
| | -M | --dumpmask | 3rd output of mcxlab | bool (0) | Return the preprocessed volume | Y | Y | Y | Y | | | | |
| | -H | --maxdetphoton | cfg.maxdetphoton | integer (1000000) | Maximum count of detected photon | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.DoSaveVolume | -S | --save2pt | 1st output of mcxlab | bool (1) | Whether to save fluence | Y | Y | Y | Y | Y | Y | Y | Y |
| Session.OutputFormat | -F | --outputformat | - | mc2,nii,hdr (mc2) | Output file format | Y | | Y | | Y | | Y | |
| User IO | | -h | --help | help mcxlab | | Print help info | Y | Y | Y | Y | Y | Y | Y | Y |
| | -v | --version | - | | Print version info | Y | | Y | | | | | |
| | -l | --log | - | bool (0) | Print info to a file | Y | | Y | | Y | | Y | |
| | -i | --interactive | - | | Interactive mode | Y | | Y | | Y | | Y | |
| Advanced Settings | Session.Debug | -D | --debug | cfg.debuglevel | RMP ('') | Debug flags | Y | Y | Y | Y | Y | Y | Y | Y |
| | -k | --kernel | - | string ('') | Path to a user-specified kernel file | | | Y | | | | | |
| | -o | --optlevel | cfg.optlevel | 0,1,2,3 (3) | OpenCL optimization level | | | Y | Y | | | | |
| | -J | --compileropt | - | string ('') | OpenCL JIT compiler flags | | | Y | Y | | | | |
| Session.RootPath | | --root | cfg.root | string ('') | Root path of the output files | Y | | Y | | Y | | Y | |
| | | --gscatter | cfg.gscatter | integer (1e9) | Number of scatter events before isotropic scattering | Y | Y | Y | Y | Y | Y | Y | Y |
| | | --maxvoidstep | cfg.maxvoidstep | integer (1000) | Maximum steps in the background | Y | Y | Y | Y | | | | |
| | | --maxjumpdebug | cfg.maxjumpdebug | integer (10000000) | Maximum trajectory points | Y | Y | Y | Y | | | | |
| | | --internalsrc | cfg.internalsrc | bool (0) | A point source inside the non-zero voxel | | | Y | Y | | | | |
![[Home]](/img/mcx_wiki_banner.png)