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MCX Documentation
1. Command Line Options
Required option
-f / --input
- Format
- String
- Max Length
- 1024 character (including the string ending mark '\0' )
- Description
-f filename.json
or
-f filename.inp
filename may contain absolute or relative path. If the filename has a '.json' extension, this input file is in the JSON format. If the input file name ends with '.inp', it is in the legacy format. If the file name contains space, one must use quotation marks to quote the full file name. In Windows, the quotation must be double quote (""). In Linux or Mac, either single or double quotation mark works.
If this flag is followed by an inline JSON string, such as -f '{...}', the parameter is parsed as an "inline JSON input file".
MC options
-n / --photon
- Format
- an integer or floating point number
- Max Value
- the number can not exceed 2^32-1
- Description
-n N
where N can be either an integer, such as 100000 or a floating point number, such as 1e5. If N is a floating point number, it will be rounded to the largest integer below the current value. If this number is larger than 1e9, we suggest one to use the "-r" option followed by an integer larger than 1.
-r / --repeat
- Format
- an integer
- Max Value
- the number can not exceed 2^32-1
- Description
-r N
where N is a positive integer. When use this option, mcx runs 'total photon number/N' photons in a batch.
This option is useful when one does not have access to a dedicated GPU, i.e. the GPU is used for both display and computation. In such case, the mcx computation time is limited to only 5 to 10 seconds due to the graphics driver. One can use the -r option to make the execution time per batch under the time limit set by the driver.
-b / --reflect
1 to reflect photons at ext. boundary;0 to exit-B / --reflectin
1 to reflect photons at int. boundary; 0 do not-u / --unitinmm
defines the length unit for the grid edge-U / --normalize
1 to normalize flux to unitary; 0 save raw-E / --seed
set random-number-generator seed, -1 to generate if an mch file is followed, MCX "replays" the detected photon; the replay mode can be used to calculate the mua/mus Jacobian matrices-z / --srcfrom0
1 volume origin is [0 0 0]; 0: origin at [1 1 1]-R / --skipradius
-2: use atomics for the entire domain (default) 0: vanilla MCX, no atomic operations >0: radius in which use shared-memory atomics -1: use crop0/crop1 to determine atomic zone-k / --voidtime
when src is outside, 1 enables timer inside void-Y / --replaydet
replay only the detected photons from a given detector (det ID starts from 1), used with -E-P / --shapes
a JSON string for additional shapes in the grid-N / --reseed
number of scattering events before reseeding RNG-F / --faststep
1-use fast 1mm stepping, [0]-precise ray-tracing-e / --minenergy
minimum energy level to terminate a photon-g / --gategroup
number of time gates per run-a / --array
1 for C array (row-major); 0 for Matlab array
GPU options
-L / --listgpu
print GPU information only-t / --thread
total thread number-T / --blocksize
thread number per block-A / --autopilot
auto thread config:1 dedicated GPU;2 non-dedica.-G / --gpu
specify which GPU to use, list GPU by -L; 0 auto or-G / --gpu
using multiple devices (1 enable, 0 disable)-W / --workload
workload for active devices; normalized by sum-I / --printgpu
print GPU information and run program
Output options
-s / --session
a string to label all output file names-d / --savedet
1 to save photon info at detectors; 0 not save-x / --saveexit
1 to save photon exit positions and directions setting -x to 1 also implies setting '-d' to 1-X / --saveref
1 to save diffuse reflectance at the air-voxels right outside of the domain; if non-zero voxels appear at the boundary, pad 0s before using -X-q / --saveseed
1 to save photon RNG seed for replay; 0 not save-M / --dumpmask
1 to dump detector volume masks; 0 do not save-H / --maxdetphoton
max number of detected photons-S / --save2pt
1 to save the flux field; 0 do not save-O / --outputtype
X - output flux, F - fluence, E - energy deposit J - Jacobian (replay mode), P - scattering event counts at each voxel (replay mode only)
User IO options
-h / --help
print this message-v / --version
print MCX revision number-l / --log
print messages to a log file instead-i / --interactive
interactive mode
Debug options
-D / --debug
print debug information (you can use an integer or or a string by combining the following flags)-D [''|RMP]
1 R debug RNG 2 M store photon trajectory info 4 P print progress bar combine multiple items by using a string, or add selected numbers together
Additional options
--gscatter
after a photon completes the specified number of scattering events, mcx then ignores anisotropy g and only performs isotropic scattering for speed--maxvoidstep
maximum distance (in voxel unit) of a photon that can travel before entering the domain, if launched outside (i.e. a widefield source)--maxjumpdebug
when trajectory is requested (i.e. -D M), use this parameter to set the maximum positions stored (default: 1e6)
2. Input file Format
JSON input file format
Starting from version 0.7.9, MCX accepts a JSON-formatted input file in addition to the conventional tMCimg-like input format. JSON (JavaScript Object Notation) is a portable, human-readable and "fat-free" text format to represent complex and hierarchical data. Using the JSON format makes a input file self-explanatory, extensible and easy-to-interface with other applications (like MATLAB).
A sample JSON input file can be found under the examples/quicktest folder. The same file, qtest.json, is also shown below:
{
"Help": {
"[en]": {
"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::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",
"Session::Photons": "if -n is not specified in the command line, this defines the total photon number",
"Session::ID": "if -s is not specified in the command line, this defines the output file name stub",
"Forward::T0": "the start time of the simulation, in seconds",
"Forward::T1": "the end time of the simulation, in seconds",
"Forward::Dt": "the width of each time window, in seconds",
"Optode::Source::Pos": "the grid position of the source, can be non-integers, in grid unit",
"Optode::Detector::Pos": "the grid position of a detector, can be non-integers, in grid unit",
"Optode::Source::Dir": "the unitary directional vector of the photon at launch",
"Optode::Source::Type": "source types, must be one of the following:
pencil,isotropic,cone,gaussian,planar,pattern,fourier,arcsine,disk,fourierx,fourierx2d",
"Optode::Source::Param1": "source parameters, 4 floating-point numbers",
"Optode::Source::Param2": "additional source parameters, 4 floating-point numbers"
}
},
"Domain": {
"VolumeFile": "semi60x60x60.bin",
"Dim": [60,60,60],
"OriginType": 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"
},
"Forward": {
"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
},
{
"Pos": [29.0, 39.0, 0.0],
"R": 1.0
},
{
"Pos": [19.0, 29.0, 0.0],
"R": 1.0
},
{
"Pos": [39.0, 29.0, 0.0],
"R": 1.0
}
]
}
}
A JSON input file requiers several root objects, namely "Domain", "Session", "Forward" and "Optode". Other root sections, like "Help", will be ignored. Each object is a data structure providing information indicated by its name. Each object can contain various sub-fields. The orders of the fields in the same level are flexible. For each field, you can always find the equivalent fields in the *.inp input files. For example, The "VolumeFile" field under the "Domain" object is the same as Line#6 in qtest.inp; the "RNGSeed" under "Session" is the same as Line#2; the "Optode.Source.Pos" is the same as the triplet in Line#3; the "Forward.T0" is the same as the first number in Line#5, etc.
An MCX JSON input file must be a valid JSON text file. You can validate your input file by running a JSON validator, for example http://jsonlint.com/ You should always use "" to quote a "name" and separate parallel items by ",".
MCX accepts an alternative form of JSON input, but using it is not recommended. In the alternative format, you can use
"rootobj_name.field_name": valueto represent any parameter directly in the root level. For example
{
"Domain.VolumeFile": "semi60x60x60.json",
"Session.Photons": 10000000,
...
}
You can even mix the alternative format with the standard format. If any input parameter has values in both formats in a single input file, the standard-formatted value has higher priority.
To invoke the JSON-formatted input file in your simulations, you can use the "-f" command line option with MCX, just like using an .inp file. For example:
mcx -A -n 20 -f onecube.json -s onecubejson
The input file must have a ".json" suffix in order for MCX to recognize. If the input information is set in both command line, and input file, the command line value has higher priority (this is the same for .inp input files). For example, when using "-n 20", the value set in "Session"/"Photons" is overwritten to 20; when using "-s onecubejson", the "Session"/"ID" value is modified. If your JSON input file is invalid, MCX will quit and point out where the format is incorrect.
inp input file format
Historically, MCX supports an extended version of the input file format used by tMCimg. The difference is that MCX allows comments in the input file. A typical MCX input file looks like this:
1000000 # total photon, use -n to overwrite in the command line
29012392 # RNG seed, negative to generate
30.0 30.0 0.0 1 # source position (in grid unit), the last num (optional) sets srcfrom0 (-z)
0 0 1 # initial directional vector
0.e+00 1.e-09 1.e-10 # time-gates(s): start, end, step
semi60x60x60.bin # volume ('unsigned char' binary format)
1 60 1 60 # x voxel size in mm (isotropic only), dim, start/end indices
1 60 1 60 # y voxel size, must be same as x, dim, start/end indices
1 60 1 60 # y voxel size, must be same as x, dim, start/end indices
1 # num of media
1.010101 0.01 0.005 1.37 # scat. mus (1/mm), g, mua (1/mm), n
4 1.0 # detector number and default radius (in grid unit)
30.0 20.0 0.0 2.0 # detector 1 position (real numbers in grid unit) and individual radius (optional)
30.0 40.0 0.0 # ..., if individual radius is ignored, MCX will use the default radius
20.0 30.0 0.0 #
40.0 30.0 0.0 #
pencil # source type (optional)
0 0 0 0 # parameters (4 floats) for the selected source
0 0 0 0 # additional source parameters
Note that the scattering coefficient mus=musp/(1-g).
JSON shape file format
Starting from v0.7.9, MCX can also use a shape description file in the place of the volume file. Using a shape-description file can save you from making a binary .bin volume. A shape file uses more descriptive syntax and can be easily understood and shared with others.
Samples on how to use the shape files are included under the example/shapetest folder.
The sample shape file, shapes.json, is shown below:
{
"MCX_Shape_Command_Help":{
"Shapes::Common Rules": "Shapes is an array object. The Tag field sets the voxel value for each
region; if Tag is missing, use 0. Tag must be smaller than the maximum media number in the
input file.Most parameters are in floating-point (FP). If a parameter is a coordinate, it
assumes the origin is defined at the lowest corner of the first voxel, unless user overwrite
with an Origin object. The default origin of all shapes is initialized by user's --srcfrom0
setting: if srcfrom0=1, the lowest corner of the 1st voxel is [0,0,0]; otherwise, it is [1,1,1]",
"Shapes::Name": "Just for documentation purposes, not parsed in MCX",
"Shapes::Origin": "A floating-point (FP) triplet, set coordinate origin for the subsequent objects",
"Shapes::Grid": "Recreate the background grid with the given dimension (Size) and fill-value (Tag)",
"Shapes::Sphere": "A 3D sphere, centered at C0 with radius R, both have FP values",
"Shapes::Box": "A 3D box, with lower corner O and edge length Size, both have FP values",
"Shapes::SubGrid": "A sub-section of the grid, integer O- and Size-triplet, inclusive of both ends",
"Shapes::XLayers/YLayers/ZLayers": "Layered structures, defined by an array of integer triples:
[start,end,tag]. Ends are inclusive in MATLAB array indices. XLayers are perpendicular to x-axis, and so on",
"Shapes::XSlabs/YSlabs/ZSlabs": "Slab structures, consisted of a list of FP pairs [start,end]
both ends are inclusive in MATLAB array indices, all XSlabs are perpendicular to x-axis, and so on",
"Shapes::Cylinder": "A finite cylinder, defined by the two ends, C0 and C1, along the axis and a radius R",
"Shapes::UpperSpace": "A semi-space defined by inequality A*x+B*y+C*z>D, Coef is required, but not Equ"
},
"Shapes": [
{"Name": "Test"},
{"Origin": [0,0,0]},
{"Grid": {"Tag":1, "Size":[40,60,50]}},
{"Sphere": {"Tag":2, "O":[30,30,30],"R":20}},
{"Box": {"Tag":0, "O":[10,10,10],"Size":[10,10,10]}},
{"Subgrid": {"Tag":1, "O":[13,13,13],"Size":[5,5,5]}},
{"UpperSpace":{"Tag":3,"Coef":[1,-1,0,0],"Equ":"A*x+B*y+C*z>D"}},
{"XSlabs": {"Tag":4, "Bound":[[5,15],[35,40]]}},
{"Cylinder": {"Tag":2, "C0": [0.0,0.0,0.0], "C1": [15.0,8.0,10.0], "R": 4.0}},
{"ZLayers": [[1,10,1],[11,30,2],[31,50,3]]}
]
}
A shape file must contain a "Shapes" object in the root level. Other root-level fields are ignored. The "Shapes" object is a JSON array, with each element representing a 3D object or setting. The object-class commands include "Grid", "Sphere", "Box" etc. Each of these object include a number of sub-fields to specify the parameters of the object. For example, the "Sphere" object has 3 subfields, "O", "R" and "Tag". Field "O" has a value of 1x3 array, representing the center of the sphere; "R" is a scalar for the radius; "Tag" is the voxel values. The most useful command is "[XYZ]Layers". It contains a series of integer triplets, specifying the starting index, ending index and voxel value of a layered structure. If multiple objects are included, the subsequent objects always overwrite the overlapping regions covered by the previous objects.
There are a few ways for you to use shape description records in your MCX simulations. You can save it to a JSON shape file, and put the file name in Line#6 of yoru .inp file, or set as the value for Domain.VolumeFile field in a .json input file. In these cases, a shape file must have a suffix of .json.
You can also merge the Shapes section with a .json input file by simply appending the Shapes section to the root-level object. You can find an example, jsonshape_allinone.json, under examples/shapetest. In this case, you no longer need to define the "VolumeFile" field in the input.
Another way to use Shapes is to specify it using the -P (or --shapes) command line flag. For example:
mcx -f input.json -P '{"Shapes":[{"ZLayers":[[1,10,1],[11,30,2],[31,60,3]]}]}'
This will first initialize a volume based on the settings in the input .json file, and then rasterize new objects to the domain and overwrite regions that are overlapping.
For both JSON-formatted input and shape files, you can use the JSONlab toolbox [4] to load and process in MATLAB.