OpenMEEG Namespace Reference

Namespaces
namespace	maths

Classes
class	analyticD3
class	analyticDipPotDer
class	analyticS
class	BlocksBase
class	BoundingBox
	An Oriented Mesh is a mesh associated with a boolean stating if it is well oriented. More...
class	CommandLine
class	Conductivity
class	DiagonalBlock
class	Dipole
class	Domain
	a Domain is a vector of SimpleDomain A Domain is the intersection of simple domains (of type SimpleDomain). More...
class	Edge
	Edge Edge class. More...
class	FastSparseMatrix
class	Forward
class	GainEEG
class	GainEEGadjoint
class	GainEEGMEGadjoint
class	GainEITInternalPot
class	GainInternalPot
class	GainMEG
class	GainMEGadjoint
class	Geometry
	Geometry contains the electrophysiological model Vertices, meshes and domains are stored in this geometry. More...
class	GeometryIO
class	HeadMatrixBlocks
class	Integrator
class	Interface
	Interface class An interface is a closed-shape composed of oriented meshes (vector of oriented meshes). More...
class	Jacobi
class	LinOp
class	LinOpInfo
struct	LinOpValue
class	Logger
class	Matrix
	Matrix class Matrix class. More...
class	Mesh
class	MeshIO
class	NonDiagonalBlock
class	NullBuffer
class	NullStream
class	OrientedMesh
	An Oriented Mesh is a mesh associated with a boolean stating if it is well oriented. More...
class	PartialBlock
class	ProgressBar
class	Sensors
	Sensors class for EEG and MEG sensors. More...
class	SimpleDomain
	a SimpleDomain is a pair of an Interface and a boolean. More...
class	SparseMatrix
class	SymMatrix
class	Triangle
	Triangle Triangle class. More...
struct	TriangleIndices
class	Vect3
	Vect3. More...
class	Vector
class	Vertex
	Vertex. More...

Typedefs
typedef std::vector< Domain >	Domains
	A vector of Domain is called Domains.
typedef std::vector< Edge >	Edges
typedef std::vector< Interface >	Interfaces
	A vector of Interface is called Interfaces.
typedef std::vector< Mesh >	Meshes
using	Strings = std::vector<std::string>
typedef std::vector< Triangle >	Triangles
typedef std::vector< Triangle * >	TrianglesRefs
typedef std::map< unsigned, unsigned >	IndexMap
typedef Vect3	Normal
typedef std::vector< Normal >	Normals
typedef std::vector< Vertex >	Vertices
typedef std::vector< Vertex * >	VerticesRefs
typedef unsigned	Dimension
typedef unsigned	Index

Enumerations
enum	InfoLevel {   DEBUG , PROGRESS , INFORMATION , WARNING ,   ERROR }
enum	DeepCopy { DEEP_COPY }

Functions
double	integral_simplified_green (const Vect3 &p0x, const double norm2p0x, const Vect3 &p1x, const double norm2p1x, const Vect3 &p1p0, const double norm2p1p0)
SymMatrix	HeadMat (const Geometry &geo, const Integrator &integrator=Integrator(3, 0, 0.005))
Matrix	SurfSourceMat (const Geometry &geo, Mesh &sources, const Integrator &integrator=Integrator(3, 0, 0.005))
Matrix	DipSourceMat (const Geometry &geo, const Matrix &dipoles, const Integrator &integrator, const std::string &domain_name)
Matrix	DipSourceMat (const Geometry &geo, const Matrix &dipoles, const std::string &domain_name)
Matrix	EITSourceMat (const Geometry &geo, const Sensors &electrodes, const Integrator &integrator=Integrator(3, 0, 0.005))
Matrix	Surf2VolMat (const Geometry &geo, const Matrix &points)
SparseMatrix	Head2EEGMat (const Geometry &geo, const Sensors &electrodes)
SparseMatrix	Head2ECoGMat (const Geometry &geo, const Sensors &electrodes, const Interface &i)
SparseMatrix	Head2ECoGMat (const Geometry &geo, const Sensors &electrodes, const std::string &id)
Matrix	Head2MEGMat (const Geometry &geo, const Sensors &sensors)
Matrix	SurfSource2MEGMat (const Mesh &sources, const Sensors &sensors)
Matrix	DipSource2MEGMat (const Matrix &dipoles, const Sensors &sensors)
Matrix	DipSource2InternalPotMat (const Geometry &geo, const Matrix &dipoles, const Matrix &points, const std::string &domain_name="")
Matrix	CorticalMat (const Geometry &geo, const SparseMatrix &M, const std::string &domain_name="CORTEX", const double alpha=-1.0, const double beta=-1.0, const std::string &filename="", const Integrator &integrator=Integrator(3, 0, 0.005))
Matrix	CorticalMat2 (const Geometry &geo, const SparseMatrix &M, const std::string &domain_name="CORTEX", const double gamma=1.0, const std::string &filename="", const Integrator &integrator=Integrator(3, 0, 0.005))
void	print_version (const char *cmd)
void	assert_non_conflicting_options (const char *command, const unsigned num_options)
double	dist_point_cell (const Vect3 &, const Triangle &, Vect3 &, bool &)
std::tuple< double, const Triangle &, const Mesh & >	dist_point_interface (const Vect3 &, const Interface &, Vect3 &)
std::tuple< double, const Triangle &, const Mesh &, const Interface & >	dist_point_geom (const Vect3 &, const Geometry &, Vect3 &)
std::string	getFilenameExtension (const std::string &name)
std::string	tolower (const std::string &s)
template<typename SelectionMatrix >
Matrix	linsolve (const SymMatrix &H, const SelectionMatrix &S)
void	GeneratePlaneRotation (double &dx, double &dy, double &cs, double &sn)
void	ApplyPlaneRotation (double &dx, double &dy, double &cs, double &sn)
template<class T >
void	Update (Vector &x, int k, T &h, Vector &s, Vector v[])
template<class T , class P >
unsigned	GMRes (const T &A, const P &M, Vector &x, const Vector &b, int max_iter, double tol, unsigned m)
std::ostream &	log_stream (const InfoLevel level)
template<typename T >
bool	almost_equal (const T x, const T y, const double eps=1e3)
void	dispEllapsed (const std::chrono::duration< double > elapsed_seconds)
void	operatorFerguson (const Vect3 &, const Mesh &, Matrix &, const unsigned &, const double)
void	operatorDipolePotDer (const Dipole &, const Mesh &, Vector &, const double, const Integrator &)
void	operatorDipolePot (const Dipole &, const Mesh &, Vector &, const double, const Integrator &)
template<typename REP >
std::istream &	operator>> (std::istream &is, Conductivity< REP > &m)
template<typename REP >
std::ostream &	operator<< (std::ostream &os, const Conductivity< REP > &m)
bool	tri_tri_overlap_test_3d (double p1[3], double q1[3], double r1[3], double p2[3], double q2[3], double r2[3])
bool	coplanar_tri_tri3d (double p1[3], double q1[3], double r1[3], double p2[3], double q2[3], double r2[3], double N1[3], double N2[3])
bool	tri_tri_overlap_test_2d (double p1[2], double q1[2], double r1[2], double p2[2], double q2[2], double r2[2])
bool	tri_tri_intersection_test_3d (double p1[3], double q1[3], double r1[3], double p2[3], double q2[3], double r2[3], int *coplanar, double source[3], double target[3])
double	triangle_area (double p[3], double q[3], double r[3])
bool	ccw_tri_tri_intersection_2d (double p1[2], double q1[2], double r1[2], double p2[2], double q2[2], double r2[2])
double	sqr (const double x)
Vect3	operator* (const double d, const Vect3 &V)
double	dotprod (const Vect3 &V1, const Vect3 &V2)
Vect3	crossprod (const Vect3 &V1, const Vect3 &V2)
double	det (const Vect3 &V1, const Vect3 &V2, const Vect3 &V3)
std::istream &	operator>> (std::istream &is, Vect3 &v)
std::ostream &	operator<< (std::ostream &os, const Vect3 &v)
std::ostream &	operator<< (std::ostream &f, const FastSparseMatrix &M)
BLAS_INT	sizet_to_int (const unsigned &num)
Matrix	nullspace_projector (const Matrix &M)
std::ostream &	operator<< (std::ostream &os, const Matrix &M)
Vector	operator* (const double d, const Vector &v)
std::ostream &	operator<< (std::ostream &f, const Vector &M)
std::istream &	operator>> (std::istream &f, Vector &M)

Typedef Documentation

Domains

typedef std::vector<Domain> OpenMEEG::Domains

A vector of Domain is called Domains.

Definition at line 112 of file domain.h.

Edges

typedef std::vector<Edge> OpenMEEG::Edges

Definition at line 41 of file edge.h.

Interfaces

typedef std::vector<Interface> OpenMEEG::Interfaces

A vector of Interface is called Interfaces.

Definition at line 116 of file interface.h.

Meshes

typedef std::vector<Mesh> OpenMEEG::Meshes

Definition at line 276 of file mesh.h.

Strings

using OpenMEEG::Strings = std::vector<std::string>

Definition at line 20 of file om_common.h.

Triangles

typedef std::vector<Triangle> OpenMEEG::Triangles

Definition at line 145 of file triangle.h.

TrianglesRefs

typedef std::vector<Triangle*> OpenMEEG::TrianglesRefs

Definition at line 146 of file triangle.h.

IndexMap

typedef std::map<unsigned,unsigned> OpenMEEG::IndexMap

Definition at line 148 of file triangle.h.

Normal

typedef Vect3 OpenMEEG::Normal

Definition at line 131 of file vect3.h.

Normals

typedef std::vector<Normal> OpenMEEG::Normals

Definition at line 132 of file vect3.h.

Vertices

typedef std::vector<Vertex> OpenMEEG::Vertices

Definition at line 37 of file vertex.h.

VerticesRefs

typedef std::vector<Vertex*> OpenMEEG::VerticesRefs

Definition at line 38 of file vertex.h.

Dimension

typedef unsigned OpenMEEG::Dimension

Definition at line 32 of file linop.h.

Index

typedef unsigned OpenMEEG::Index

Definition at line 33 of file linop.h.

Enumeration Type Documentation

InfoLevel

enum OpenMEEG::InfoLevel

Enumerator
DEBUG
PROGRESS
INFORMATION
WARNING
ERROR

Definition at line 15 of file logger.h.

DeepCopy

enum OpenMEEG::DeepCopy

Enumerator
DEEP_COPY

Definition at line 84 of file linop.h.

Function Documentation

integral_simplified_green()

double OpenMEEG::integral_simplified_green ( const Vect3 & p0x, const double norm2p0x, const Vect3 & p1x, const double norm2p1x, const Vect3 & p1p0, const double norm2p1p0 )

inline

Definition at line 16 of file analytics.h.

HeadMat()

SymMatrix OpenMEEG::HeadMat	(	const Geometry &	geo,
		const Integrator &	integrator = Integrator(3, 0, 0.005) )

SurfSourceMat()

Matrix OpenMEEG::SurfSourceMat	(	const Geometry &	geo,
		Mesh &	sources,
		const Integrator &	integrator = Integrator(3, 0, 0.005) )

DipSourceMat() [1/2]

Matrix OpenMEEG::DipSourceMat	(	const Geometry &	geo,
		const Matrix &	dipoles,
		const Integrator &	integrator,
		const std::string &	domain_name )

DipSourceMat() [2/2]

Matrix OpenMEEG::DipSourceMat	(	const Geometry &	geo,
		const Matrix &	dipoles,
		const std::string &	domain_name )

EITSourceMat()

Matrix OpenMEEG::EITSourceMat	(	const Geometry &	geo,
		const Sensors &	electrodes,
		const Integrator &	integrator = Integrator(3, 0, 0.005) )

Surf2VolMat()

Matrix OpenMEEG::Surf2VolMat	(	const Geometry &	geo,
		const Matrix &	points )

Head2EEGMat()

SparseMatrix OpenMEEG::Head2EEGMat	(	const Geometry &	geo,
		const Sensors &	electrodes )

Head2ECoGMat() [1/2]

SparseMatrix OpenMEEG::Head2ECoGMat	(	const Geometry &	geo,
		const Sensors &	electrodes,
		const Interface &	i )

Head2ECoGMat() [2/2]

SparseMatrix OpenMEEG::Head2ECoGMat ( const Geometry & geo, const Sensors & electrodes, const std::string & id )

inline

Definition at line 45 of file assemble.h.

Head2MEGMat()

Matrix OpenMEEG::Head2MEGMat	(	const Geometry &	geo,
		const Sensors &	sensors )

SurfSource2MEGMat()

Matrix OpenMEEG::SurfSource2MEGMat	(	const Mesh &	sources,
		const Sensors &	sensors )

DipSource2MEGMat()

Matrix OpenMEEG::DipSource2MEGMat	(	const Matrix &	dipoles,
		const Sensors &	sensors )

DipSource2InternalPotMat()

Matrix OpenMEEG::DipSource2InternalPotMat	(	const Geometry &	geo,
		const Matrix &	dipoles,
		const Matrix &	points,
		const std::string &	domain_name = "" )

CorticalMat()

Matrix OpenMEEG::CorticalMat	(	const Geometry &	geo,
		const SparseMatrix &	M,
		const std::string &	domain_name = "CORTEX",
		const double	alpha = -1.0,
		const double	beta = -1.0,
		const std::string &	filename = "",
		const Integrator &	integrator = Integrator(3, 0, 0.005) )

CorticalMat2()

Matrix OpenMEEG::CorticalMat2	(	const Geometry &	geo,
		const SparseMatrix &	M,
		const std::string &	domain_name = "CORTEX",
		const double	gamma = 1.0,
		const std::string &	filename = "",
		const Integrator &	integrator = Integrator(3, 0, 0.005) )

print_version()

void OpenMEEG::print_version ( const char * cmd )

inline

Definition at line 194 of file commandline.h.

assert_non_conflicting_options()

void OpenMEEG::assert_non_conflicting_options ( const char * command, const unsigned num_options )

inline

Definition at line 213 of file commandline.h.

dist_point_cell()

double OpenMEEG::dist_point_cell	(	const Vect3 &	,
		const Triangle &	,
		Vect3 &	,
		bool &	)

dist_point_interface()

std::tuple< double, const Triangle &, const Mesh & > OpenMEEG::dist_point_interface	(	const Vect3 &	,
		const Interface &	,
		Vect3 &	)

dist_point_geom()

std::tuple< double, const Triangle &, const Mesh &, const Interface & > OpenMEEG::dist_point_geom	(	const Vect3 &	,
		const Geometry &	,
		Vect3 &	)

getFilenameExtension()

std::string OpenMEEG::getFilenameExtension ( const std::string & name )

inline

Definition at line 18 of file filenames.h.

tolower()

std::string OpenMEEG::tolower ( const std::string & s )

inline

Definition at line 26 of file filenames.h.

linsolve()

template<typename SelectionMatrix >

Matrix OpenMEEG::linsolve	(	const SymMatrix &	H,
		const SelectionMatrix &	S )

Definition at line 52 of file gain.h.

GeneratePlaneRotation()

void OpenMEEG::GeneratePlaneRotation	(	double &	dx,
		double &	dy,
		double &	cs,
		double &	sn )

Definition at line 43 of file gmres.h.

ApplyPlaneRotation()

void OpenMEEG::ApplyPlaneRotation	(	double &	dx,
		double &	dy,
		double &	cs,
		double &	sn )

Definition at line 59 of file gmres.h.

Update()

template<class T >

void OpenMEEG::Update	(	Vector &	x,
		int	k,
		T &	h,
		Vector &	s,
		Vector	v[] )

Definition at line 67 of file gmres.h.

GMRes()

template<class T , class P >

unsigned OpenMEEG::GMRes	(	const T &	A,
		const P &	M,
		Vector &	x,
		const Vector &	b,
		int	max_iter,
		double	tol,
		unsigned	m )

Definition at line 83 of file gmres.h.

log_stream()

std::ostream & OpenMEEG::log_stream ( const InfoLevel level )

inline

Definition at line 39 of file logger.h.

almost_equal()

template<typename T >

bool OpenMEEG::almost_equal	(	const T	x,
		const T	y,
		const double	eps = 1e3 )

Definition at line 24 of file om_common.h.

dispEllapsed()

void OpenMEEG::dispEllapsed ( const std::chrono::duration< double > elapsed_seconds )

inline

Definition at line 23 of file om_utils.h.

operatorFerguson()

void OpenMEEG::operatorFerguson	(	const Vect3 &	,
		const Mesh &	,
		Matrix &	,
		const unsigned &	,
		const double	)

operatorDipolePotDer()

void OpenMEEG::operatorDipolePotDer	(	const Dipole &	,
		const Mesh &	,
		Vector &	,
		const double	,
		const Integrator &	)

operatorDipolePot()

void OpenMEEG::operatorDipolePot	(	const Dipole &	,
		const Mesh &	,
		Vector &	,
		const double	,
		const Integrator &	)

operator>>() [1/3]

template<typename REP >

std::istream & OpenMEEG::operator>> ( std::istream & is, Conductivity< REP > & m )

inline

Definition at line 28 of file PropertiesSpecialized.h.

operator<<() [1/5]

template<typename REP >

std::ostream & OpenMEEG::operator<< ( std::ostream & os, const Conductivity< REP > & m )

inline

Definition at line 31 of file PropertiesSpecialized.h.

tri_tri_overlap_test_3d()

bool OpenMEEG::tri_tri_overlap_test_3d	(	double	p1[3],
		double	q1[3],
		double	r1[3],
		double	p2[3],
		double	q2[3],
		double	r2[3] )

Definition at line 152 of file Triangle_triangle_intersection.h.

coplanar_tri_tri3d()

bool OpenMEEG::coplanar_tri_tri3d	(	double	p1[3],
		double	q1[3],
		double	r1[3],
		double	p2[3],
		double	q2[3],
		double	r2[3],
		double	N1[3],
		double	N2[3] )

Definition at line 216 of file Triangle_triangle_intersection.h.

tri_tri_overlap_test_2d()

bool OpenMEEG::tri_tri_overlap_test_2d	(	double	p1[2],
		double	q1[2],
		double	r1[2],
		double	p2[2],
		double	q2[2],
		double	r2[2] )

Definition at line 536 of file Triangle_triangle_intersection.h.

tri_tri_intersection_test_3d()

bool OpenMEEG::tri_tri_intersection_test_3d	(	double	p1[3],
		double	q1[3],
		double	r1[3],
		double	p2[3],
		double	q2[3],
		double	r2[3],
		int *	coplanar,
		double	source[3],
		double	target[3] )

Definition at line 387 of file Triangle_triangle_intersection.h.

triangle_area()

double OpenMEEG::triangle_area	(	double	p[3],
		double	q[3],
		double	r[3] )

Definition at line 551 of file Triangle_triangle_intersection.h.

ccw_tri_tri_intersection_2d()

bool OpenMEEG::ccw_tri_tri_intersection_2d	(	double	p1[2],
		double	q1[2],
		double	r1[2],
		double	p2[2],
		double	q2[2],
		double	r2[2] )

Definition at line 520 of file Triangle_triangle_intersection.h.

sqr()

double OpenMEEG::sqr ( const double x )

inline

Definition at line 24 of file vect3.h.

operator*() [1/2]

Vect3 OpenMEEG::operator* ( const double d, const Vect3 & V )

inline

Definition at line 105 of file vect3.h.

dotprod()

double OpenMEEG::dotprod ( const Vect3 & V1, const Vect3 & V2 )

inline

Definition at line 106 of file vect3.h.

crossprod()

Vect3 OpenMEEG::crossprod ( const Vect3 & V1, const Vect3 & V2 )

inline

Definition at line 107 of file vect3.h.

det()

double OpenMEEG::det ( const Vect3 & V1, const Vect3 & V2, const Vect3 & V3 )

inline

Definition at line 108 of file vect3.h.

operator>>() [2/3]

std::istream & OpenMEEG::operator>> ( std::istream & is, Vect3 & v )

inline

Definition at line 123 of file vect3.h.

operator<<() [2/5]

std::ostream & OpenMEEG::operator<< ( std::ostream & os, const Vect3 & v )

inline

Definition at line 127 of file vect3.h.

operator<<() [3/5]

std::ostream & OpenMEEG::operator<< ( std::ostream & f, const FastSparseMatrix & M )

inline

Definition at line 55 of file fast_sparse_matrix.h.

sizet_to_int()

BLAS_INT OpenMEEG::sizet_to_int ( const unsigned & num )

inline

Definition at line 26 of file linop.h.

nullspace_projector()

Matrix OpenMEEG::nullspace_projector ( const Matrix & M )

inline

Definition at line 16 of file matop.h.

operator<<() [4/5]

std::ostream & OpenMEEG::operator<< ( std::ostream & os, const Matrix & M )

inline

Definition at line 164 of file matrix.h.

operator*() [2/2]

Vector OpenMEEG::operator* ( const double d, const Vector & v )

inline

Definition at line 236 of file vector.h.

operator<<() [5/5]

std::ostream & OpenMEEG::operator<<	(	std::ostream &	f,
		const Vector &	M )

operator>>() [3/3]

std::istream & OpenMEEG::operator>>	(	std::istream &	f,
		Vector &	M )