MCX configuration header. More...

#include <stdio.h>
#include <vector_types.h>
#include "cjson/cJSON.h"
#include "float.h"
#include "nifti1.h"

Include dependency graph for mcx_utils.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	MCXMedium

struct	MCXPolarizeMedium

struct	MCXHistoryHeader

struct	PhotonReplay

struct	MCXGPUInfo

struct	MCXConfig

Macros
#define	EPS FLT_EPSILON
	< use multi-threading for running simulation on multiple GPUs More...

#define	VERY_BIG (1.f/FLT_EPSILON)

#define	MAX_FULL_PATH 2048

#define	MAX_PATH_LENGTH 1024

#define	MAX_SESSION_LENGTH 256

#define	MAX_DEVICE 256

#define	MCX_CUDA_ERROR_LAUNCH_FAILED 719

#define	MCX_CUDA_ARCH 100

#define	MCX_ERROR(id, msg) mcx_error(id,msg,__FILE__,__LINE__)

#define	MIN(a, b) ((a)<(b)?(a):(b))

#define	MAX(a, b) ((a)>(b)?(a):(b))

#define	MCX_FPRINTF(fp, ...) fprintf(fp,__VA_ARGS__)

Typedefs
typedef unsigned int	uint

typedef unsigned short	ushort

typedef struct MCXMedium	Medium

typedef struct MCXPolarizeMedium	POLMedium

typedef struct MCXHistoryHeader	History

typedef struct PhotonReplay	Replay

typedef struct MCXGPUInfo	GPUInfo

typedef struct MCXConfig	Config

Enumerations
enum	TOutputType { otFlux, otFluence, otEnergy, otJacobian, otWP, otDCS, otRF, otL }

enum	TMCXParent { mpStandalone, mpMATLAB, mpPython }

enum	TOutputFormat { ofMC2, ofNifti, ofAnalyze, ofUBJSON, ofTX3, ofJNifti, ofBJNifti }

enum	TBoundary { bcUnknown, bcReflect, bcAbsorb, bcMirror, bcCyclic }

enum	TBJData { JDB_mixed, JDB_nulltype, JDB_noop, JDB_true, JDB_false, JDB_char, JDB_string, JDB_hp, JDB_int8, JDB_uint8, JDB_int16, JDB_uint16, JDB_int32, JDB_uint32, JDB_int64, JDB_uint64, JDB_half, JDB_single, JDB_double, JDB_array, JDB_object, JDB_numtypes }

Functions
void	mcx_savedata (float dat, size_t len, Config cfg)
	Save volumetric output (fluence etc) to mc2 format binary file. More...

void	mcx_savenii (float dat, size_t len, char name, int type32bit, int outputformatid, Config *cfg)
	Save volumetric output (fluence etc) to an Nifty format binary file. More...

void	mcx_error (const int id, const char msg, const char file, const int linenum)
	Error reporting function. More...

void	mcx_loadconfig (FILE in, Config cfg)
	Load user inputs from a .inp input file. More...

void	mcx_saveconfig (FILE in, Config cfg)
	Save simulation settings to an inp file. More...

void	mcx_readconfig (char fname, Config cfg)
	Read simulation settings from a configuration file (.inp or .json) More...

void	mcx_writeconfig (char fname, Config cfg)
	Write simulation settings to an inp file. More...

void	mcx_initcfg (Config *cfg)
	Initializing the simulation configuration with default values. More...

void	mcx_clearcfg (Config *cfg)
	Clearing the simulation configuration data structure. More...

void	mcx_preprocess (Config *cfg)
	Preprocess user input and prepare the cfg data structure. More...

void	mcx_parsecmd (int argc, char argv[], Config cfg)
	Main function to read user command line options. More...

void	mcx_usage (Config cfg, char exename)
	Print MCX help information. More...

void	mcx_printheader (Config *cfg)
	Print MCX output header. More...

void	mcx_loadvolume (char filename, Config cfg, int isbuf)
	Load media index data volume (.bin or .vol) to the memory. More...

void	mcx_normalize (float field[], float scale, int fieldlen, int option, int pidx, int srcnum)
	Normalize the solution by multiplying a scaling factor. More...

void	mcx_kahanSum (float sum, float kahanc, float input)
	Kahan summation: Add a sequence of finite precision floating point numbers. More...

int	mcx_readarg (int argc, char argv[], int id, void output, const char *type)
	Function to read a single parameter value followed by a command line option. More...

void	mcx_printlog (Config cfg, char str)
	Print a message to the console or a log file. More...

int	mcx_remap (char *opt)
	Test if a long command line option is supported. More...

void	mcx_maskdet (Config *cfg)
	Pre-label the voxel near a detector for easy photon detection. More...

void	mcx_dumpmask (Config *cfg)
	Save the pre-masked volume (with detector ID) to an nii file. More...

void	mcx_version (Config *cfg)
	Print MCX software version. More...

void	mcx_convertrow2col (unsigned int *vol, uint3 dim)
	Convert a row-major (C/C++) array to a column-major (MATLAB/FORTRAN) array. More...

void	mcx_convertrow2col64 (size_t *vol, uint3 dim)
	Convert a row-major (C/C++) array to a column-major (MATLAB/FORTRAN) array. More...

void	mcx_convertcol2row (unsigned int *vol, uint3 dim)
	Convert a column-major (MATLAB/FORTRAN) array to a row-major (C/C++) array. More...

void	mcx_convertcol2row4d (unsigned int *vol, uint4 dim)
	Convert a column-major (MATLAB/FORTRAN) array to a row-major (C/C++) array. More...

int	mcx_loadjson (cJSON root, Config cfg)
	Load user inputs from a .json input file. More...

int	mcx_keylookup (char key, const char table[])
	Look up a string in a string list and return the index. More...

int	mcx_lookupindex (char key, const char index)
	Look up a single character in a string. More...

int	mcx_parsedebugopt (char debugopt, const char debugflag)
	Parse the debug flag in the letter format. More...

void	mcx_savedetphoton (float ppath, void seeds, int count, int seedbyte, Config *cfg)
	Save detected photon data to mch format binary file. More...

void	mcx_loadseedfile (Config *cfg)
	Load previously saved photon seeds from an .mch file for replay. More...

void	mcx_cleargpuinfo (GPUInfo **gpuinfo)
	Reset and clear the GPU information data structure. More...

int	mcx_isbinstr (const char *str)
	Test if a string contains only '0' and '1'. More...

void	mcx_progressbar (float percent, Config *cfg)
	Print a progress bar. More...

void	mcx_flush (Config *cfg)
	Force flush the command line to print the message. More...

int	mcx_run_from_json (char *jsonstr)
	Run MCX simulations from a JSON input in a persistent session. More...

float	mcx_updatemua (unsigned int mediaid, Config *cfg)
	Retrieve mua for different cfg.vol formats to convert fluence back to energy in post-processing. More...

void	mcx_savejdata (char filename, Config cfg)
	Save simulation settings to an inp file. More...

int	mcx_jdataencode (void vol, int ndim, uint dims, char type, int byte, int zipid, void obj, int isubj, Config *cfg)
	Export an ND volumetric image to JSON/JData encoded construct. More...

int	mcx_jdatadecode (void *vol, int ndim, uint dims, int maxdim, char type, cJSON obj, Config *cfg)
	Decode an ND array from JSON/JData construct and output to a volumetric array. More...

void	mcx_savejnii (float vol, int ndim, uint dims, float voxelsize, char name, int isfloat, Config *cfg)
	Save volumetric output (fluence etc) to a JNIfTI/JSON/JData format file. More...

void	mcx_savebnii (float vol, int ndim, uint dims, float voxelsize, char name, int isfloat, Config *cfg)
	Save volumetric output (fluence etc) to a binary JNIfTI/JSON/JData format file. More...

void	mcx_savejdet (float ppath, void seeds, uint count, int doappend, Config *cfg)
	Save detected photon data to mch format binary file. More...

int	mcx_svmc_bgvoxel (int vol)
	Check if a voxel contains background medium(0) More...

void	mcx_loadseedjdat (char filename, Config cfg)
	Load previously saved photon seeds from an .jdat file for replay. More...

void	mcx_prep_polarized (Config *cfg)
	Preprocess media to prepare polarized photon simulation. More...

void	mcx_replayinit (Config cfg, float detps, int dimdetps[2], int seedbyte)
	Initialize the replay data structure from detected photon data - in embedded mode (MATLAB/Python) More...

void	mcx_validatecfg (Config cfg, float detps, int dimdetps[2], int seedbyte)
	Validate all input fields, and warn incompatible inputs. More...

int	mexPrintf (const char *format,...)

int	mexEvalString (const char *command)

Detailed Description

MCX configuration header.

Macro Definition Documentation

◆ EPS

#define EPS FLT_EPSILON

< use multi-threading for running simulation on multiple GPUs

round-off limit

◆ MAX

#define MAX	(	a,
		b
	)	((a)>(b)?(a):(b))

macro to get the max values of two numbers

◆ MAX_DEVICE

#define MAX_DEVICE 256

max number of GPUs to be used

◆ MAX_FULL_PATH

#define MAX_FULL_PATH 2048

max characters in a full file name string

◆ MAX_PATH_LENGTH

#define MAX_PATH_LENGTH 1024

max characters in a full file name string

◆ MAX_SESSION_LENGTH

#define MAX_SESSION_LENGTH 256

max session name length

◆ MCX_CUDA_ARCH

#define MCX_CUDA_ARCH 100

fallback CUDA version

◆ MCX_CUDA_ERROR_LAUNCH_FAILED

#define MCX_CUDA_ERROR_LAUNCH_FAILED 719

CUDA kernel launch error code

◆ MCX_ERROR

#define MCX_ERROR	(	id,
		msg
	)	mcx_error(id,msg,__FILE__,__LINE__)

macro for error handling

◆ MCX_FPRINTF

#define MCX_FPRINTF	(	fp,
		...
	)	fprintf(fp,__VA_ARGS__)

macro to print messages, calls fprintf in command line mode

◆ MIN

#define MIN	(	a,
		b
	)	((a)<(b)?(a):(b))

macro to get the min values of two numbers

◆ VERY_BIG

#define VERY_BIG (1.f/FLT_EPSILON)

a big number

Typedef Documentation

◆ Config

typedef struct MCXConfig Config

Data structure for MCX simulation settings

◆ GPUInfo

typedef struct MCXGPUInfo GPUInfo

Data structure for GPU information

◆ History

typedef struct MCXHistoryHeader History

Header data structure in .mch/.mct files to store detected photon data This header has a total of 256 bytes

◆ Medium

typedef struct MCXMedium Medium

The structure to store optical properties Four relevant optical properties are needed

◆ POLMedium

typedef struct MCXPolarizeMedium POLMedium

The stucture to store medium parameters for polarized photon simulations.

◆ Replay

typedef struct PhotonReplay Replay

Data structure for photon replay

◆ uint

typedef unsigned int uint

use uint for unsigned int

◆ ushort

typedef unsigned short ushort

use ushort for unsigned short

Function Documentation

◆ mcx_clearcfg()

void mcx_clearcfg ( Config * cfg )

Clearing the simulation configuration data structure.

Destructor of the simulation configuration, delete all dynamically allocated members

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◆ mcx_cleargpuinfo()

void mcx_cleargpuinfo ( GPUInfo ** gpuinfo )

Reset and clear the GPU information data structure.

Clearing the GPU information data structure

◆ mcx_convertcol2row()

void mcx_convertcol2row	(	unsigned int **	vol,
		uint3 *	dim
	)

Convert a column-major (MATLAB/FORTRAN) array to a row-major (C/C++) array.

Parameters

[in,out]	vol	a 3D array (wrapped in 1D) to be converted
[in]	dim	the dimensions of the 3D array

◆ mcx_convertcol2row4d()

void mcx_convertcol2row4d	(	unsigned int **	vol,
		uint4 *	dim
	)

Convert a column-major (MATLAB/FORTRAN) array to a row-major (C/C++) array.

Parameters

[in,out]	vol	a 3D array (wrapped in 1D) to be converted
[in]	dim	the dimensions of the 3D array

◆ mcx_convertrow2col()

void mcx_convertrow2col	(	unsigned int **	vol,
		uint3 *	dim
	)

Convert a row-major (C/C++) array to a column-major (MATLAB/FORTRAN) array.

Parameters

[in,out]	vol	a 3D array (wrapped in 1D) to be converted
[in]	dim	the dimensions of the 3D array

◆ mcx_convertrow2col64()

void mcx_convertrow2col64	(	size_t **	vol,
		uint3 *	dim
	)

Convert a row-major (C/C++) array to a column-major (MATLAB/FORTRAN) array.

Parameters

[in,out]	vol	a 3D array (wrapped in 1D) to be converted
[in]	dim	the dimensions of the 3D array

◆ mcx_dumpmask()

void mcx_dumpmask ( Config * cfg )

Save the pre-masked volume (with detector ID) to an nii file.

To test the results, you should use -M to dump the det-mask, load it in matlab, and plot the interface containing the detector with pcolor() (has the matching index), and then draw a circle with the radius and center set in the input file. the pixels should completely cover the circle.

Parameters

[in] cfg simulation configuration

◆ mcx_error()

void mcx_error	(	const int	id,
		const char *	msg,
		const char *	file,
		const int	linenum
	)

Error reporting function.

Parameters

[in]	id	a single integer for the types of the error
[in]	msg	the error message string
[in]	file	the unit file name where this error is raised
[in]	linenum	the line number in the file where this error is raised

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◆ mcx_flush()

void mcx_flush ( Config * cfg )

Force flush the command line to print the message.

Parameters

[in] cfg simulation configuration

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◆ mcx_initcfg()

void mcx_initcfg ( Config * cfg )

Initializing the simulation configuration with default values.

Constructor of the simulation configuration, initializing all field to default values

expect 1-byte per medium index, use –mediabyte to set to 2 or 4

in theory, mcx can use min block size 32 because no communication between threads, but 64 seems to work the best

launch many threads to saturate the device to maximize throughput

default is Matlab array

output detected photon data by default, use -d 0 to disable

use pencil beam as default source type

default RNG seed, a big integer, with a hidden meaning :)

This format is only supported by C99

by default, honor anisotropy for all scattering, use –gscatter to reduce it

use the first GPU device by default

◆ mcx_isbinstr()

int mcx_isbinstr ( const char * str )

Test if a string contains only '0' and '1'.

Parameters

[in] str string to be tested

◆ mcx_jdatadecode()

int mcx_jdatadecode	(	void **	vol,
		int *	ndim,
		uint *	dims,
		int	maxdim,
		char **	type,
		cJSON *	obj,
		Config *	cfg
	)

Decode an ND array from JSON/JData construct and output to a volumetric array.

The JData specification defines a portable way to encode and share volumetric ND arrays and other complex data structures, such as trees, graphs and tables. This function is capable of importing any ND numerical arrays in the JData construct in to a generic array, permitting data decompression and base64 decoding.

Parameters

[in]	vol	a pointer that points to the ND array buffer
[in]	ndim	the number of dimensions
[in]	dims	an integer pointer that points to the dimensional vector
[in]	type	a string of JData data types, such as "uint8" "float32", "int32" etc
[in]	byte	number of byte per voxel
[in]	zipid	zip method: 0:zlib,1:gzip,2:base64,3:lzma,4:lzip,5:lz4,6:lz4hc
[in]	obj	a pre-created cJSON object to store the output JData fields

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◆ mcx_jdataencode()

int mcx_jdataencode	(	void *	vol,
		int	ndim,
		uint *	dims,
		char *	type,
		int	byte,
		int	zipid,
		void *	obj,
		int	isubj,
		Config *	cfg
	)

Export an ND volumetric image to JSON/JData encoded construct.

The JData specification defines a portable way to encode and share volumetric ND arrays and other complex data structures, such as trees, graphs and tables. This function is capable of exporting any ND numerical arrays into a JData construct, permitting data compression and base64 encoding.

Parameters

[in]	vol	a pointer that points to the ND array buffer
[in]	ndim	the number of dimensions
[in]	dims	an integer pointer that points to the dimensional vector
[in]	type	a string of JData data types, such as "uint8" "float32", "int32" etc
[in]	byte	number of byte per voxel
[in]	zipid	zip method: 0:zlib,1:gzip,2:base64,3:lzma,4:lzip,5:lz4,6:lz4hc
[in]	obj	a pre-created cJSON object to store the output JData fields

◆ mcx_kahanSum()

void mcx_kahanSum	(	float *	sum,
		float *	kahanc,
		float	input
	)

Kahan summation: Add a sequence of finite precision floating point numbers.

Source: https://en.wikipedia.org/wiki/Kahan_summation_algorithm

Parameters

[in,out]	sum	sum of the squence before and after adding the next element
[in,out]	kahanc	a running compensation for lost low-order bits
[in]	input	the next element of the sequence

◆ mcx_keylookup()

int mcx_keylookup	(	char *	origkey,
		const char *	table[]
	)

Look up a string in a string list and return the index.

Parameters

[in]	origkey	string to be looked up
[out]	table	the dictionary where the string is searched

Returns: if found, return the index of the string in the dictionary, otherwise -1.

◆ mcx_loadconfig()

void mcx_loadconfig	(	FILE *	in,
		Config *	cfg
	)

Load user inputs from a .inp input file.

This function loads user input from a simple text input format in a .inp extension

Parameters

[in]	in	file handle to the .inp file
[in]	cfg	simulation configuration

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◆ mcx_loadjson()

int mcx_loadjson	(	cJSON *	root,
		Config *	cfg
	)

Load user inputs from a .json input file.

This function loads user input from a JSON format in a .json extension

Parameters

[out]	root	json data structure pointer
[in]	cfg	simulation configuration

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◆ mcx_loadseedfile()

void mcx_loadseedfile ( Config * cfg )

Load previously saved photon seeds from an .mch file for replay.

Parameters

[in,out] cfg simulation configuration

◆ mcx_loadseedjdat()

void mcx_loadseedjdat	(	char *	filename,
		Config *	cfg
	)

Load previously saved photon seeds from an .jdat file for replay.

Parameters

[in]	filename	the name/path of the .jdat file produced from the baseline simulation
[in,out]	cfg	simulation configuration

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◆ mcx_loadvolume()

void mcx_loadvolume	(	char *	filename,
		Config *	cfg,
		int	isbuf
	)

Load media index data volume (.bin or .vol) to the memory.

Parameters

[in]	filename	file name to the binary volume data (support 1,2 and 4 bytes per voxel)
[in]	cfg	simulation configuration

float to half conversion https://stackoverflow.com/questions/3026441/float32-to-float16/5587983#5587983 https://gamedev.stackexchange.com/a/17410 (for denorms)

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◆ mcx_lookupindex()

int mcx_lookupindex	(	char *	key,
		const char *	index
	)

Look up a single character in a string.

Parameters

[in]	key	character to be looked up
[out]	index	the dictionary string where the char is searched

Returns: if found, return 0; otherwise, return 1

◆ mcx_maskdet()

void mcx_maskdet ( Config * cfg )

Pre-label the voxel near a detector for easy photon detection.

This function preprocess the volume and detector data and add the detector ID to the upper 16bits of the voxel that the detector encompasses. If two detectors cover the same voxel, the later one will overwrite the ID of the 1st one. In MCX kernel, the detector coverage is tested for all detectors despite the label written (only used as a binary mask)

Parameters

[in] cfg simulation configuration

The goal here is to find a set of voxels for each detector so that the intersection between a sphere of R=cfg->detradius,c0=cfg->detpos[d] and the object surface (or bounding box) is fully covered.

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◆ mcx_normalize()

void mcx_normalize	(	float	field[],
		float	scale,
		int	fieldlen,
		int	option,
		int	pidx,
		int	srcnum
	)

Normalize the solution by multiplying a scaling factor.

Parameters

[in,out]	field	volumetric data before normalization
[in]	scale	the scaling factor (or normalization factor) to be applied
[in]	fieldlen	the length (floating point) of elements in the volume
[in]	option	if set to 2, only normalize positive values (negative values for diffuse reflectance calculations)

◆ mcx_parsecmd()

void mcx_parsecmd	(	int	argc,
		char *	argv[],
		Config *	cfg
	)

Main function to read user command line options.

This function process user command line inputs and parse all short and long options.

Parameters

[in]	argc	the number of total command line parameters
[in]	argv	the pointer to all command line options
[in]	cfg	simulation configuration

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◆ mcx_parsedebugopt()

int mcx_parsedebugopt	(	char *	debugopt,
		const char *	debugflag
	)

Parse the debug flag in the letter format.

The debug flag following the -D can be either a string format, or numerical format. This function converts the string debug flags into number format

Parameters

[in]	debugopt	string following the -D parameter
[out]	debugflag	the numerical format of the debug flag

◆ mcx_prep_polarized()

void mcx_prep_polarized ( Config * cfg )

Preprocess media to prepare polarized photon simulation.

This function precompute the scattering coefficent and smatrix for different sphere-medium combinations.

Parameters

[in] cfg simulation configuration

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◆ mcx_preprocess()

void mcx_preprocess ( Config * cfg )

Preprocess user input and prepare the cfg data structure.

This function preprocess the user input and prepare the domain for the simulation. It loads the media index array from file, add detector masks for easy detection, and check inconsistency between the user specified inputs.

Parameters

[in] cfg simulation configuration

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◆ mcx_printheader()

void mcx_printheader ( Config * cfg )

Print MCX output header.

Parameters

[in] cfg simulation configuration

◆ mcx_printlog()

void mcx_printlog	(	Config *	cfg,
		char *	str
	)

Print a message to the console or a log file.

Parameters

[in]	cfg	simulation configuration
[in]	str	a string to be printed

◆ mcx_progressbar()

void mcx_progressbar	(	float	percent,
		Config *	cfg
	)

Print a progress bar.

When -D P is specified, this function prints and update a progress bar.

Parameters

[in]	percent	the percentage value from 1 to 100
[in]	cfg	simulation configuration

◆ mcx_readarg()

int mcx_readarg	(	int	argc,
		char *	argv[],
		int	id,
		void *	output,
		const char *	type
	)

Function to read a single parameter value followed by a command line option.

This function reads different types of parameter values following a command line option.

Parameters

[in]	argc	the number of total command line parameters
[in]	argv	the pointer to all command line options
[in]	id	which parameter to be parsed
[out]	output	the pointer to which the parsed value to be written
[in]	type	the type of data support char, int, float, string, bytenumlist, floatlist

◆ mcx_readconfig()

void mcx_readconfig	(	char *	fname,
		Config *	cfg
	)

Read simulation settings from a configuration file (.inp or .json)

Parameters

[in]	fname	the name of the input file (.inp or .json)
[in]	cfg	simulation configuration

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◆ mcx_remap()

int mcx_remap ( char * opt )

Test if a long command line option is supported.

This function returns 1 if a long option is found, and 0 otherwise

Parameters

[in] opt the long command line option string

◆ mcx_replayinit()

void mcx_replayinit	(	Config *	cfg,
		float *	detps,
		int	dimdetps[2],
		int	seedbyte
	)

Initialize the replay data structure from detected photon data - in embedded mode (MATLAB/Python)

Parameters

[in,out]	cfg	simulation configuration
[in]	detps	detected photon data
[in]	dimdetps	the dimension vector of the detected photon data
[in]	seedbyte	the number of bytes per RNG seed

◆ mcx_run_from_json()

int mcx_run_from_json ( char * jsonstr )

Run MCX simulations from a JSON input in a persistent session.

Parameters

[in] jsonstr a string in the JSON format, the content of the .json input file

mcxconfig: structure to store all simulation parameters

gpuinfo: structure to store GPU information

activedev: count of total active GPUs to be used

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◆ mcx_savebnii()

void mcx_savebnii	(	float *	vol,
		int	ndim,
		uint *	dims,
		float *	voxelsize,
		char *	name,
		int	isfloat,
		Config *	cfg
	)

Save volumetric output (fluence etc) to a binary JNIfTI/JSON/JData format file.

Parameters

[in]	dat	volumetric data to be saved
[in]	len	total byte length of the data to be saved
[in]	name	output file name (will append '.nii')
[in]	type32bit	type of the data, only support 32bit per record
[in]	outputformatid	decide if save as nii or analyze format
[in]	cfg	simulation configuration

◆ mcx_saveconfig()

void mcx_saveconfig	(	FILE *	out,
		Config *	cfg
	)

Save simulation settings to an inp file.

Parameters

[in]	out	handle to the output file
[in]	cfg	simulation configuration

◆ mcx_savedata()

void mcx_savedata	(	float *	dat,
		size_t	len,
		Config *	cfg
	)

Save volumetric output (fluence etc) to mc2 format binary file.

Parameters

[in]	dat	volumetric data to be saved
[in]	len	total byte length of the data to be saved
[in]	cfg	simulation configuration

◆ mcx_savedetphoton()

void mcx_savedetphoton	(	float *	ppath,
		void *	seeds,
		int	count,
		int	doappend,
		Config *	cfg
	)

Save detected photon data to mch format binary file.

Parameters

[in]	ppath	buffer pointing to the detected photon data (partial path etc)
[in]	seeds	buffer pointing to the detected photon seed data
[in]	count	number of detected photons
[in]	doappend	flag if the new data is appended or write from the begining
[in]	cfg	simulation configuration

◆ mcx_savejdata()

void mcx_savejdata	(	char *	filename,
		Config *	cfg
	)

Save simulation settings to an inp file.

Parameters

[in]	out	handle to the output file
[in]	cfg	simulation configuration

◆ mcx_savejdet()

void mcx_savejdet	(	float *	ppath,
		void *	seeds,
		uint	count,
		int	doappend,
		Config *	cfg
	)

Save detected photon data to mch format binary file.

Parameters

[in]	ppath	buffer pointing to the detected photon data (partial path etc)
[in]	seeds	buffer pointing to the detected photon seed data
[in]	count	number of detected photons
[in]	doappend	flag if the new data is appended or write from the begining
[in]	cfg	simulation configuration

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◆ mcx_savejnii()

void mcx_savejnii	(	float *	vol,
		int	ndim,
		uint *	dims,
		float *	voxelsize,
		char *	name,
		int	isfloat,
		Config *	cfg
	)

Save volumetric output (fluence etc) to a JNIfTI/JSON/JData format file.

Parameters

[in]	dat	volumetric data to be saved
[in]	len	total byte length of the data to be saved
[in]	name	output file name (will append '.nii')
[in]	type32bit	type of the data, only support 32bit per record
[in]	outputformatid	decide if save as nii or analyze format
[in]	cfg	simulation configuration

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◆ mcx_savenii()

void mcx_savenii	(	float *	dat,
		size_t	len,
		char *	name,
		int	type32bit,
		int	outputformatid,
		Config *	cfg
	)

Save volumetric output (fluence etc) to an Nifty format binary file.

Parameters

[in]	dat	volumetric data to be saved
[in]	len	total byte length of the data to be saved
[in]	name	output file name (will append '.nii')
[in]	type32bit	type of the data, only support 32bit per record
[in]	outputformatid	decide if save as nii or analyze format
[in]	cfg	simulation configuration

◆ mcx_svmc_bgvoxel()

int mcx_svmc_bgvoxel ( int vol )

Check if a voxel contains background medium(0)

This function check if a voxel contains background medium, under SVMC mode

Parameters

[in] vol high 32 bit of the input volume under SVMC mdoe

◆ mcx_updatemua()

float mcx_updatemua	(	unsigned int	mediaid,
		Config *	cfg
	)

Retrieve mua for different cfg.vol formats to convert fluence back to energy in post-processing.

Parameters

[out]	output	medium absorption coefficient for the current voxel
[in]	mediaid	medium index of the current voxel
[in]	cfg	simulation configuration

◆ mcx_usage()

void mcx_usage	(	Config *	cfg,
		char *	exename
	)

Print MCX help information.

Parameters

[in]	cfg	simulation configuration structure
[in]	exename	path and name of the mcx executable

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◆ mcx_validatecfg()

void mcx_validatecfg	(	Config *	cfg,
		float *	detps,
		int	dimdetps[2],
		int	seedbyte
	)

Validate all input fields, and warn incompatible inputs.

Perform self-checking and raise exceptions or warnings when input error is detected

Parameters

[in,out]	cfg	simulation configuration
[in]	detps	detected photon data
[in]	dimdetps	the dimension vector of the detected photon data
[in]	seedbyte	the number of bytes per RNG seed

◆ mcx_version()

void mcx_version ( Config * cfg )

Print MCX software version.

Parameters

[in] cfg simulation configuration

◆ mcx_writeconfig()

void mcx_writeconfig	(	char *	fname,
		Config *	cfg
	)

Write simulation settings to an inp file.

Parameters

[in]	fname	the name of the output file
[in]	cfg	simulation configuration

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Classes

Macros

Typedefs

Enumerations

Functions

Detailed Description

Macro Definition Documentation

◆ EPS

◆ MAX

◆ MAX_DEVICE

◆ MAX_FULL_PATH

◆ MAX_PATH_LENGTH

◆ MAX_SESSION_LENGTH

◆ MCX_CUDA_ARCH

◆ MCX_CUDA_ERROR_LAUNCH_FAILED

◆ MCX_ERROR

◆ MCX_FPRINTF

◆ MIN

◆ VERY_BIG

Typedef Documentation

◆ Config

◆ GPUInfo

◆ History

◆ Medium

◆ POLMedium

◆ Replay

◆ uint

◆ ushort

Function Documentation

◆ mcx_clearcfg()

◆ mcx_cleargpuinfo()

◆ mcx_convertcol2row()

◆ mcx_convertcol2row4d()

◆ mcx_convertrow2col()

◆ mcx_convertrow2col64()

◆ mcx_dumpmask()

◆ mcx_error()

◆ mcx_flush()

◆ mcx_initcfg()

◆ mcx_isbinstr()

◆ mcx_jdatadecode()

◆ mcx_jdataencode()

◆ mcx_kahanSum()

◆ mcx_keylookup()

◆ mcx_loadconfig()

◆ mcx_loadjson()

◆ mcx_loadseedfile()

◆ mcx_loadseedjdat()

◆ mcx_loadvolume()

◆ mcx_lookupindex()

◆ mcx_maskdet()

◆ mcx_normalize()

◆ mcx_parsecmd()

◆ mcx_parsedebugopt()

◆ mcx_prep_polarized()

◆ mcx_preprocess()

◆ mcx_printheader()

◆ mcx_printlog()

◆ mcx_progressbar()

◆ mcx_readarg()

◆ mcx_readconfig()

◆ mcx_remap()

◆ mcx_replayinit()

◆ mcx_run_from_json()

◆ mcx_savebnii()

◆ mcx_saveconfig()

◆ mcx_savedata()

◆ mcx_savedetphoton()

◆ mcx_savejdata()

◆ mcx_savejdet()

◆ mcx_savejnii()

◆ mcx_savenii()

◆ mcx_svmc_bgvoxel()

◆ mcx_updatemua()

◆ mcx_usage()

◆ mcx_validatecfg()

◆ mcx_version()

◆ mcx_writeconfig()