A Voxelized Human Phantom (VHP) geometry. More...

#include <egs_vhp_geometry.h>

Inheritance diagram for EGS_VHPGeometry:

Public Member Functions
	EGS_VHPGeometry (const char phantom_file, const char media_file, int slice_min=0, int slice_max=1000000, const string &Name="")

bool	isInside (const EGS_Vector &x)

int	isWhere (const EGS_Vector &x)

int	inside (const EGS_Vector &x)

int	medium (int ireg) const

int	computeIntersections (int ireg, int n, const EGS_Vector &X, const EGS_Vector &u, EGS_GeometryIntersections *isections)

EGS_Float	howfarToOutside (int ireg, const EGS_Vector &x, const EGS_Vector &u)

int	howfar (int ireg, const EGS_Vector &x, const EGS_Vector &u, EGS_Float &t, int newmed=0, EGS_Vector normal=0)

EGS_Float	hownear (int ireg, const EGS_Vector &x)

int	getMaxStep () const

bool	isOK () const

int	getNx () const

int	getNy () const

int	getNz () const

const string &	getType () const

void	printInfo () const

void	setMicros (EGS_Input *)

Public Member Functions inherited from EGS_BaseGeometry
	EGS_BaseGeometry (const string &Name)
	Construct a geometry named Name. More...

virtual	~EGS_BaseGeometry ()
	Destructor. More...

bool	isConvex () const
	Is the geometry convex? More...

virtual EGS_Float	getVolume (int ireg)
	Calculates the volume of region ireg. More...

virtual EGS_Float	getBound (int idir, int ind)
	Returns region boundaries in direction determined by idir. More...

virtual int	getNRegDir (int idir)

int	regions () const
	Returns the number of local regions in this geometry. More...

virtual bool	isRealRegion (int ireg) const
	Returnes true if ireg is a real region, false otherwise. More...

void	setMedium (const string &Name)
	Set all regions to a medium with name Name. More...

void	setMedium (int start, int end, const string &Name, int delta=1)
	Set every delta'th region between start and end to the medium named Name. More...

void	setMedium (int imed)
	Set all regions to a medium with index imed. More...

void	setMedium (int istart, int iend, int imed, int delta=1)
	Set every delta'th region between start and end (inclusive) to imed. More...

void	setMedia (EGS_Input *inp)
	Set the media in the geometry from the input pointed to by inp. More...

bool	hasRhoScaling () const
	Does this geometry object have a mass density scaling feature? More...

virtual EGS_Float	getRelativeRho (int ireg) const
	Get the relative mass density in region ireg. More...

virtual void	setRelativeRho (int start, int end, EGS_Float rho)
	Set the relative mass density in regions. More...

virtual void	setRelativeRho (EGS_Input *)
	Set the relative mass density from an user input. More...

EGS_Float	getMediumRho (int ind) const

virtual void	setApplication (EGS_Application *app)

bool	hasBScaling () const
	Does this geometry object have a B field scaling feature?

virtual EGS_Float	getBScaling (int ireg) const
	Get the B field scaling factor in region ireg.

virtual void	setBScaling (int start, int end, EGS_Float bf)
	Set the B field scaling factor in regions. More...

virtual void	setBScaling (EGS_Input *)
	Set the B field scaling factor from an user input. More...

const string &	getName () const
	Get the name of this geometry. More...

void	setDebug (bool deb)
	Turn debugging on. More...

void	setName (EGS_Input *inp)
	Set the name of the geometry from the input inp. More...

void	setBoundaryTolerance (EGS_Input *inp)
	Set the value of the boundary tolerance from the input inp. More...

void	setBoundaryTolerance (EGS_Float tol)
	Set the value of the boundary tolerance from argument.

virtual bool	hasBooleanProperty (int ireg, EGS_BPType prop) const
	Is the boolean property prop set for region ireg ?

virtual void	setBooleanProperty (EGS_BPType prop)
	Set the boolean properties of the entire geometry to prop. More...

virtual void	addBooleanProperty (int bit)
	Add a boolean property for the entire geometry by setting the bit'th bit. More...

virtual void	setBooleanProperty (EGS_BPType prop, int start, int end, int step=1)
	Set the boolean properties of every step'th region between start and end (inclusive) to prop. More...

virtual void	addBooleanProperty (int bit, int start, int end, int step=1)
	Add a boolean property to every step'th region between start and end (inclusive) by setting the bit'th bit. More...

int	ref ()
	Increase the reference count to this geometry. More...

int	deref ()
	Decrease the reference count to this geometry. More...

EGS_Float	getBoundaryTolerance ()
	Get the value of the boundary tolerance.

virtual void	getNumberRegions (const string &str, vector< int > &regs)
	Get a list of all the regions labeled with a number.

virtual void	getLabelRegions (const string &str, vector< int > &regs)
	Get the list of all regions labeled with str.

virtual const string &	getLabelName (const int i)
	Get the name of the i-th explicit label in the geometry.

virtual int	getLabelCount ()
	Get the number of explicit labels in the geometry.

int	setLabels (EGS_Input *input)
	Set the labels from an input block.

int	setLabels (const string &inp)
	Set the labels from an input string.

Protected Member Functions
void	setup ()

void	setMedia (EGS_Input inp, int nmed, const int med_ind)

Protected Attributes
EGS_VoxelGeometry *	vg

VHP_OrganData *	organs

int	organ_media [256]

int	organ_micro [256]

string	organ_names [256]

EGS_MicroMatrixCluster **	micros

int	nmicro

int	nmax

int	nmacro

Protected Attributes inherited from EGS_BaseGeometry
int	nreg
	Number of local regions in this geometry. More...

string	name
	Name of this geometry. More...

short *	region_media
	Array of media indeces. More...

int	med
	Medium index. More...

bool	has_rho_scaling
	Does this geometry have relative mass density scvaling? More...

EGS_Float *	rhor
	Array with relative mass densities. More...

bool	has_B_scaling
	Does this geometry has B field scaling factor? More...

bool	has_Ref_rho

EGS_Float *	bfactor
	Array with B field scaling factors. More...

EGS_Float	rhoRef
	Reference density for B field scaling. More...

int	nref
	Number of references to this geometry. More...

bool	debug
	Debugging flag. More...

bool	is_convex
	Is this geometry convex? More...

EGS_BPType	bproperty
	A bit mask of boolean properties for the entire geometry. More...

EGS_BPType *	bp_array
	An array of boolean properties on a region by region basis. More...

EGS_Float	boundaryTolerance
	Boundary tolerance for geometries that need it.

EGS_Float	halfBoundaryTolerance

vector< label >	labels
	Labels. More...

EGS_Application *	app
	The application this object belongs to.

Static Protected Attributes
static string	type = "EGS_VHPGeometry"

Static Protected Attributes inherited from EGS_BaseGeometry
static int	error_flag = 0
	Set to non-zero status if a geometry problem is encountered.

Additional Inherited Members
Static Public Member Functions inherited from EGS_BaseGeometry
static int	findRegion (EGS_Float xp, int np, const EGS_Float *p)
	Find the bin to which xp belongs, given np bin edges p. More...

static int	nMedia ()
	Get the number of media registered so far by all geometries. More...

static const char *	getMediumName (int ind)
	Get the name of medium with index ind. More...

static int	addMedium (const string &medname)
	Add a medium or get the index of an existing medium. More...

static int	getMediumIndex (const string &medname)
	Get the index of a medium named medname. More...

static EGS_BaseGeometry *	createGeometry (EGS_Input *)
	Create a geometry (or geometries) from a given input. More...

static EGS_BaseGeometry *	createSingleGeometry (EGS_Input *inp)
	Create a single geometry from the input inp. More...

static void	clearGeometries ()
	Clears (deletes) all geometries in the currently active geometry list. More...

static EGS_BaseGeometry *	getGeometry (const string &Name)
	Get a pointer to the geometry named Name. More...

static EGS_BaseGeometry **	getGeometries ()

static int	getNGeometries ()

static string	getUniqueName ()
	Get a unique geometry name. More...

static void	describeGeometries ()
	Describes all existing geometries. More...

static void	setActiveGeometryList (int list)
	Set the currently active geometry list. More...

static int	getLastError ()

static void	resetErrorFlag ()

Detailed Description

A Voxelized Human Phantom (VHP) geometry.

This geometry type can be used to model a voxelized representation of a phantom. In principle a VHP geometry is the same as a XYZ geometry. The main reason for providing a separate implementation is the huge number of voxels needed to represent a whole body human phantom using 1-2 mm resolution, which necessitates a more careful memory use. In addition, this implementation provides the possibility to include a micro-voxel representation of the human spongiosa obtained from micro-CT images. A VHP geometry is defined as follows:

* library      = egs_vhp_geometry
* name         = some_name
* phantom data = phantom_data_file
* media data   = media_data_file
* slice range  = min_slice max_slice
*

In the above, the slice range input, which is optional, can be used to select a given slice range instead of using the entire phantom. The file phantom_data_file is a binary file containing the definition of the phantom. The format of this file is as follows:

one byte indicating the endianess of the machine where the data was created (0=big endian, 1=little endian).
three 64 bit floating point values defining voxel size in x-, y- and z-direction
number of slices nslice (16 bit unsigned integer value). Note that increasing slice number corresponds to increasing z coordinate.
followed by the data for the nslice slices. The data for a slice consists of
first and last row (16 bit usigned integers)
followed by the last-first+1 data for a row The data for a row consists of
number nreg of regions (16 bit usigned integer)
followed by nreg+1 pixel indeces (16 bit usigned integers)
followed by nreg organ indeces (8 bit unsigned integers) so that all voxels between and $p_{j+1}$ are set to organ . This data structure, also used at run time, provides a significant compression compared to simply using an array of organ indeces (e.g., one needs about 12 MB to represent Richard Kramer's FAX phantom compared to about 150 MB that would be needed for the 1361 x 474 x 224 voxels of this phantom). Its disadvantage is the slighly slower ( $\sim$ 10-15%) access to the organ index of a voxel.

The file media_data_file is an ASCII file that defines the organ names and the materials to be used for each organ. Its format is as follows:

number of different organs
followed by lines consisting of organ index, medium index and organ name.
followed by number of media nmed
followed by nmed lines with a single medium name per line (media names are the actual medium names in the PEGS file to be used for the simulation).

To add a micro-voxel representation of spongiosa, one includes in the geometry definition the following inputs:

* BSC thickness = thickness in cm
* TB medium = medium name
* BM medium = medium name
* micro matrix = micro_data_file1 organ1 organ2 ...
* micro matrix = micro_data_file2 organ1 organ2 ...
* ...
*

The TB medium and BM medium inputs define the PEGS medium names of trabecular bone and bone marrow. The BSC thickness sets the thickness of the bone surface cells (BSC) layer. Note that in the current implementation the BSC thickness can not exceed the micro-voxel size. The binary files micro_data_file_i define micro matrix clusters to replace macro voxels that have organ indeces organ1 organ2 .... A micro matrix cluster consists of $M_x \times M_y \times M_z$ micro matrices of dimension $N_x \times N_y \times N_z$ . This cluster is repeated periodically in spongiosa organs set to use this cluster. Note that the micro-matrix voxel size is automatically determned from the macro voxel size and the number of micro-voxels in a micro matrix. The format of the micro matrix file is as follows:

(8 bit unsigned integers)
followed by (8 bit unsigned integers)
followed by $M_x \times M_y \times M_z \times N_x \times N_y \times N_z$ 8 bit integers defining the micro matrix medium (0 corresponds to trabecular bone, 1 to bone marrow). Note that bone marrow voxels neighboring trabecular bone are automatically marked to contain a BSC sub-volume.

Definition at line 1303 of file egs_vhp_geometry.h.

The documentation for this class was generated from the following files:

/home/rwtownson/EGSnrc/HEN_HOUSE/egs++/geometry/egs_vhp_geometry/egs_vhp_geometry.h
/home/rwtownson/EGSnrc/HEN_HOUSE/egs++/geometry/egs_vhp_geometry/egs_vhp_geometry.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Additional Inherited Members

Detailed Description