Definition of basic mesh data structures and inline vector operations. More...

#include <stdio.h>
#include <math.h>
#include "mmc_utils.h"
#include "mmc_rand_posix.c"

Include dependency graph for mmc_mesh.h:

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Classes
struct	MMC_mesh
	Basic FEM mesh data structrure. More...

struct	MMC_raytracer
	Ray-tracer data structrure for pre-computed data. More...

Macros
#define	MMC_UNDEFINED (3.40282347e+38F)

#define	ID_UNDEFINED 0x7FFFFFFF

#define	R_RAND_MAX (1.f/RAND_MAX)

#define	TWO_PI (M_PI*2.0)

#define	EPS 1e-6f

#define	LOG_MT_MAX 22.1807097779182f

#define	R_MIN_MUS 1e9f

#define	R_C0 3.335640951981520e-12f

#define	DELTA_MUA 1e-4f

#define	VERY_BIG 1e30f

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

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

#define	MESH_ERROR(a) mesh_error((a),__FILE__,__LINE__)

Typedefs
typedef struct MMC_mesh	tetmesh

typedef struct MMC_raytracer	raytracer

Functions
void	mesh_init (tetmesh *mesh)
	Initializing the mesh data structure with default values. More...

void	mesh_init_from_cfg (tetmesh mesh, mcconfig cfg)
	Loading user-specified mesh data. More...

void	mesh_loadnode (tetmesh mesh, mcconfig cfg)
	Load node file and initialize the related mesh properties. More...

void	mesh_loadelem (tetmesh mesh, mcconfig cfg)
	Load element file and initialize the related mesh properties. More...

void	mesh_loadfaceneighbor (tetmesh mesh, mcconfig cfg)
	Load face-neightbor element list and initialize the related mesh properties. More...

void	mesh_loadmedia (tetmesh mesh, mcconfig cfg)
	Load optical property file and initialize the related mesh properties. More...

void	mesh_loadelemvol (tetmesh mesh, mcconfig cfg)
	Load tet element volume file and initialize the related mesh properties. More...

void	mesh_loadseedfile (tetmesh mesh, mcconfig cfg)
	Load previously saved photon seeds from an .mch file for replay. More...

void	mesh_clear (tetmesh *mesh)
	Clearing the mesh data structure. More...

float	mesh_normalize (tetmesh mesh, mcconfig cfg, float Eabsorb, float Etotal, int pair)
	Function to normalize the fluence and remove influence from photon number and volume. More...

void	mesh_build (tetmesh *mesh)

void	mesh_error (const char msg, const char file, const int linenum)
	Error-handling in mesh operations. More...

void	mesh_filenames (const char format, char foutput, mcconfig *cfg)
	Construct a full mesh file name using cfg session and root path. More...

void	mesh_saveweight (tetmesh mesh, mcconfig cfg, int isref)
	Save the fluence output to a file. More...

void	mesh_savedetphoton (float ppath, void seeds, int count, int seedbyte, mcconfig *cfg)
	Save detected photon data into an .mch history file. More...

void	mesh_getdetimage (float detmap, float ppath, int count, mcconfig cfg, tetmesh mesh)
	Save binned detected photon data over an area-detector as time-resolved 2D images. More...

void	mesh_savedetimage (float detmap, mcconfig cfg)
	Save binned detected photon data over an area-detector. More...

float	mesh_getdetweight (int photonid, int colcount, float ppath, mcconfig cfg)
	Recompute the detected photon weight from the partial-pathlengths. More...

void	mesh_srcdetelem (tetmesh mesh, mcconfig cfg)
	Identify wide-field source and detector-related elements (type=-1 for source, type=-2 for det) More...

void	mesh_createdualmesh (tetmesh mesh, mcconfig cfg)

void	mesh_loadroi (tetmesh mesh, mcconfig cfg)
	Load edge/node/face roi for implicit MMC. More...

double	mesh_getreff_approx (double n_in, double n_out)
	Compute the effective reflection coefficient Reff using approximated formula. More...

double	mesh_getreff (double n_in, double n_out)
	Compute the effective reflection coefficient Reff. More...

void	tracer_init (raytracer tracer, tetmesh mesh, char methodid)
	Initialize a data structure storing all pre-computed ray-tracing related data. More...

void	tracer_build (raytracer *tracer)
	Pre-computed ray-tracing related data. More...

void	tracer_prep (raytracer tracer, mcconfig cfg)
	Preparing for the ray-tracing calculations. More...

void	tracer_clear (raytracer *tracer)
	Clear the ray-tracing data structure. More...

float	mc_next_scatter (float g, float3 dir, RandType ran, RandType ran0, mcconfig cfg, float *pmom)
	Performing one scattering event of the photon. More...

Detailed Description

Definition of basic mesh data structures and inline vector operations.

Function Documentation

◆ mc_next_scatter()

float mc_next_scatter	(	float	g,
		float3 *	dir,
		RandType *	ran,
		RandType *	ran0,
		mcconfig *	cfg,
		float *	pmom
	)

Performing one scattering event of the photon.

This function updates the direction of the photon by performing a scattering calculation

Parameters

[in]	g	anisotropy g
[out]	dir	current ray direction vector
[out]	ran	random number generator states
[out]	ran0	additional random number generator states
[out]	cfg	the simulation configuration
[out]	pmom	buffer to store momentum transfer data if needed

◆ mesh_clear()

void mesh_clear ( tetmesh * mesh )

Clearing the mesh data structure.

Destructor of the mesh data structure, delete all dynamically allocated members

◆ mesh_error()

void mesh_error	(	const char *	msg,
		const char *	file,
		const int	linenum
	)

Error-handling in mesh operations.

Parameters

[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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◆ mesh_filenames()

void mesh_filenames	(	const char *	format,
		char *	foutput,
		mcconfig *	cfg
	)

Construct a full mesh file name using cfg session and root path.

Parameters

[in]	format	a format string to form the file name
[in]	foutput	pointer to the output string buffer
[in]	cfg	the simulation configuration structure

◆ mesh_getdetimage()

void mesh_getdetimage	(	float *	detmap,
		float *	ppath,
		int	count,
		mcconfig *	cfg,
		tetmesh *	mesh
	)

Save binned detected photon data over an area-detector as time-resolved 2D images.

When an area detector is used (such as a CCD), storing all detected photons can generate a huge output file. This can be mitigated by accumulate the data first to a rasterized detector grid, and then save only the integrated data.

Parameters

[out]	detmap	buffer points to the output detector data array
[in]	ppath	buffer points to the detected photon data (partial-path, det id, etc)
[in]	count	how many photons are detected
[in]	cfg	the simulation configuration
[in]	mesh	the mesh object

◆ mesh_getdetweight()

float mesh_getdetweight	(	int	photonid,
		int	colcount,
		float *	ppath,
		mcconfig *	cfg
	)

Recompute the detected photon weight from the partial-pathlengths.

This function currently does not consider the final transmission coeff before the photon being detected.

Parameters

[in]	photonid	index of the detected photon
[in]	colcount	how many 4-byte records per detected photon
[in]	ppath	buffer points to the detected photon data (partial-path, det id, etc)
[in]	cfg	the simulation configuration

◆ mesh_getreff()

double mesh_getreff	(	double	n_in,
		double	n_out
	)

Compute the effective reflection coefficient Reff.

Parameters

[in]	n_in	refractive index of the diffusive medium
[in]	n_out	refractive index of the non-diffusive medium

◆ mesh_getreff_approx()

double mesh_getreff_approx	(	double	n_in,
		double	n_out
	)

Compute the effective reflection coefficient Reff using approximated formula.

accuracy is limited see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482362/

Parameters

[out]	tracer	the ray-tracer data structure
[in]	pmesh	the mesh object
[in]	methodid	the ray-tracing algorithm to be used

◆ mesh_init()

void mesh_init ( tetmesh * mesh )

Initializing the mesh data structure with default values.

Constructor of the mesh object, initializing all field to default values

◆ mesh_init_from_cfg()

void mesh_init_from_cfg	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Loading user-specified mesh data.

Loading node, element etc from files into memory

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◆ mesh_loadelem()

void mesh_loadelem	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load element file and initialize the related mesh properties.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadelemvol()

void mesh_loadelemvol	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load tet element volume file and initialize the related mesh properties.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadfaceneighbor()

void mesh_loadfaceneighbor	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load face-neightbor element list and initialize the related mesh properties.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadmedia()

void mesh_loadmedia	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load optical property file and initialize the related mesh properties.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadnode()

void mesh_loadnode	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load node file and initialize the related mesh properties.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadroi()

void mesh_loadroi	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Load edge/node/face roi for implicit MMC.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

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◆ mesh_loadseedfile()

void mesh_loadseedfile	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

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

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

◆ mesh_normalize()

float mesh_normalize	(	tetmesh *	mesh,
		mcconfig *	cfg,
		float	Eabsorb,
		float	Etotal,
		int	pair
	)

Function to normalize the fluence and remove influence from photon number and volume.

This function outputs the Green's function from the raw simulation data. This needs to divide the total simulated photon energy, normalize the volumes of each node/elem, and consider the length unit and time-gates

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration
[in]	Eabsorb	total absorbed energy from ray-tracing accummulation
[in]	Etotal	total launched energy, equal to photon number if not pattern-source

mesh->med[mesh->type[i]].n;

◆ mesh_savedetimage()

void mesh_savedetimage	(	float *	detmap,
		mcconfig *	cfg
	)

Save binned detected photon data over an area-detector.

function for saving binned detected photon data into time-resolved 2D images

Parameters

[in]	detmap	buffer points to the output detector data array
[in]	cfg	the simulation configuration

◆ mesh_savedetphoton()

void mesh_savedetphoton	(	float *	ppath,
		void *	seeds,
		int	count,
		int	seedbyte,
		mcconfig *	cfg
	)

Save detected photon data into an .mch history file.

Parameters

[in]	ppath	buffer points to the detected photon data (partial-path, det id, etc)
[in]	seeds	buffer points to the detected photon seeds
[in]	count	how many photons are detected
[in]	seedbyte	how many bytes per detected photon seed
[in]	cfg	the simulation configuration

◆ mesh_saveweight()

void mesh_saveweight	(	tetmesh *	mesh,
		mcconfig *	cfg,
		int	isref
	)

Save the fluence output to a file.

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration

◆ mesh_srcdetelem()

void mesh_srcdetelem	(	tetmesh *	mesh,
		mcconfig *	cfg
	)

Identify wide-field source and detector-related elements (type=-1 for source, type=-2 for det)

Parameters

[in]	mesh	the mesh object
[in]	cfg	the simulation configuration structure

◆ tracer_build()

void tracer_build ( raytracer * tracer )

Pre-computed ray-tracing related data.

the pre-computed ray-tracing data include d: the vector of the 6 edges: edge[i]=[ni1,ni2]: d[i]=ni2 - ni1 m: the cross-product of the end-nodes of the 6-edges: edge[i]=[ni1,ni2]: m[i]=ni1 x ni2 n: the normal vector of the 4 facets, pointing outwards

Parameters

[out] tracer the ray-tracer data structure

◆ tracer_clear()

void tracer_clear ( raytracer * tracer )

Clear the ray-tracing data structure.

Deconstructor of the ray-tracing data structure

Parameters

[out] tracer the ray-tracer data structure

◆ tracer_init()

void tracer_init	(	raytracer *	tracer,
		tetmesh *	pmesh,
		char	methodid
	)

Initialize a data structure storing all pre-computed ray-tracing related data.

the pre-computed ray-tracing data include d: the vector of the 6 edges m: the cross-product of the end-nodes of the 6-edges n1 x n2 n: the normal vector of the 4 facets, pointing outwards

Parameters

[out]	tracer	the ray-tracer data structure
[in]	pmesh	the mesh object
[in]	methodid	the ray-tracing algorithm to be used

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◆ tracer_prep()

void tracer_prep	(	raytracer *	tracer,
		mcconfig *	cfg
	)

Preparing for the ray-tracing calculations.

This function build the ray-tracing precomputed data and test if the initial element (e0) encloses the photon launch position.

Parameters

[out]	tracer	the ray-tracer data structure
[in]	cfg	the simulation configuration structure

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Classes

Macros

Typedefs

Functions

Detailed Description

Function Documentation

◆ mc_next_scatter()

◆ mesh_clear()

◆ mesh_error()

◆ mesh_filenames()

◆ mesh_getdetimage()

◆ mesh_getdetweight()

◆ mesh_getreff()

◆ mesh_getreff_approx()

◆ mesh_init()

◆ mesh_init_from_cfg()

◆ mesh_loadelem()

◆ mesh_loadelemvol()

◆ mesh_loadfaceneighbor()

◆ mesh_loadmedia()

◆ mesh_loadnode()

◆ mesh_loadroi()

◆ mesh_loadseedfile()

◆ mesh_normalize()

◆ mesh_savedetimage()

◆ mesh_savedetphoton()

◆ mesh_saveweight()

◆ mesh_srcdetelem()

◆ tracer_build()

◆ tracer_clear()

◆ tracer_init()

◆ tracer_prep()