This defines a surface. More...

#include <mne_surface.h>

Public Types
typedef std::shared_ptr< MNESurface >	SPtr
typedef std::shared_ptr< const MNESurface >	ConstSPtr
Public Types inherited from MNELIB::MNESurfaceOrVolume
typedef QSharedPointer< MNESurfaceOrVolume >	SPtr
typedef QSharedPointer< const MNESurfaceOrVolume >	ConstSPtr
typedef Eigen::Matrix< float, Eigen::Dynamic, 3, Eigen::RowMajor >	PointsT
typedef Eigen::Matrix< float, Eigen::Dynamic, 3, Eigen::RowMajor >	NormalsT
typedef Eigen::Matrix< int, Eigen::Dynamic, 3, Eigen::RowMajor >	TrianglesT

Public Member Functions
	MNESurface ()
	~MNESurface ()
double	sum_solids (const Eigen::Vector3f &from) const
void	triangle_coords (const Eigen::Vector3f &r, int tri, float &x, float &y, float &z) const
int	nearest_triangle_point (const Eigen::Vector3f &r, const MNEProjData *user, int tri, float &x, float &y, float &z) const
int	nearest_triangle_point (const Eigen::Vector3f &r, int tri, float &x, float &y, float &z) const
Eigen::Vector3f	project_to_triangle (int tri, float p, float q) const
Eigen::Vector3f	project_to_triangle (int best, const Eigen::Vector3f &r) const
int	project_to_surface (const MNEProjData *proj_data, const Eigen::Vector3f &r, float &distp) const
void	find_closest_on_surface_approx (const PointsT &r, int np, Eigen::VectorXi &nearest_tri, Eigen::VectorXf &dist, int nstep) const
void	decide_search_restriction (MNEProjData &p, int approx_best, int nstep, const Eigen::Vector3f &r) const
void	activate_neighbors (int start, Eigen::VectorXi &act, int nstep) const
Public Member Functions inherited from MNELIB::MNESurfaceOrVolume
	MNESurfaceOrVolume ()
	Constructs the MNE Surface or Volume.
virtual	~MNESurfaceOrVolume ()
	Destroys the MNE Surface or Volume description.
	MNESurfaceOrVolume (const MNESurfaceOrVolume &)=default
MNESurfaceOrVolume &	operator= (const MNESurfaceOrVolume &)=default
	MNESurfaceOrVolume (MNESurfaceOrVolume &&)=default
MNESurfaceOrVolume &	operator= (MNESurfaceOrVolume &&)=default
void	add_uniform_curv ()
void	add_triangle_data ()
void	compute_surface_cm ()
void	calculate_vertex_distances ()
int	add_vertex_normals ()
int	add_geometry_info (int do_normals, int check_too_many_neighbors)
int	add_geometry_info (int do_normals)
int	add_geometry_info2 (int do_normals)
Eigen::VectorXi	nearestVertIdx () const
Eigen::VectorXd	nearestDistVec () const
void	setNearestData (const Eigen::VectorXi &nearestIdx, const Eigen::VectorXd &nearestDist)

Static Public Member Functions
static MNESurface *	read_bem_surface (const QString &name, int which, int add_geometry, float *sigmap)
static MNESurface *	read_bem_surface2 (const QString &name, int which, int add_geometry, float *sigmap)
static MNESurface *	read_bem_surface (const QString &name, int which, int add_geometry, float *sigmap, bool check_too_many_neighbors)
Static Public Member Functions inherited from MNELIB::MNESurfaceOrVolume
static double	solid_angle (const Eigen::Vector3f &from, const MNELIB::MNETriangle &tri)
static void	compute_cm (const PointsT &rr, int np, float(&cm)[3])

Additional Inherited Members
Public Attributes inherited from MNELIB::MNESurfaceOrVolume
int	type
QString	subject
int	id
int	coord_frame
std::optional< MNEVolGeom >	vol_geom
std::optional< MNEMghTagGroup >	mgh_tags
int	np
PointsT	rr
NormalsT	nn
float	cm [3]
Eigen::VectorXi	inuse
Eigen::VectorXi	vertno
int	nuse
std::vector< Eigen::VectorXi >	neighbor_vert
Eigen::VectorXi	nneighbor_vert
std::vector< Eigen::VectorXf >	vert_dist
float	sigma
int	ntri
std::vector< MNETriangle >	tris
TrianglesT	itris
float	tot_area
int	nuse_tri
std::vector< MNETriangle >	use_tris
TrianglesT	use_itris
std::vector< Eigen::VectorXi >	neighbor_tri
Eigen::VectorXi	nneighbor_tri
std::vector< MNENearest >	nearest
std::vector< std::optional< MNEPatchInfo > >	patches
FIFFLIB::FiffSparseMatrix	dist
float	dist_limit
Eigen::VectorXf	curv
Eigen::VectorXf	val
std::optional< FIFFLIB::FiffCoordTrans >	voxel_surf_RAS_t
int	vol_dims [3]
float	voxel_size [3]
std::optional< FIFFLIB::FiffSparseMatrix >	interpolator
QString	MRI_volume
std::optional< FIFFLIB::FiffCoordTrans >	MRI_voxel_surf_RAS_t
std::optional< FIFFLIB::FiffCoordTrans >	MRI_surf_RAS_RAS_t
int	MRI_vol_dims [3]

Detailed Description

This defines a surface.

Implements the MNE Surface (Replaces typedef mneSurfaceOrVolume mneSurface; struct of MNE-C mne_types.h).

Definition at line 78 of file mne_surface.h.

Inheritance diagram for MNELIB::MNESurface:

Member Typedef Documentation

◆ ConstSPtr

typedef std::shared_ptr<const MNESurface> MNELIB::MNESurface::ConstSPtr

Const shared pointer type for MNESurface.

Definition at line 82 of file mne_surface.h.

◆ SPtr

typedef std::shared_ptr<MNESurface> MNELIB::MNESurface::SPtr

Shared pointer type for MNESurface.

Definition at line 81 of file mne_surface.h.

Constructor & Destructor Documentation

◆ MNESurface()

MNESurface::MNESurface ( )

Constructs the MNE Surface

Definition at line 103 of file mne_surface.cpp.

◆ ~MNESurface()

MNESurface::~MNESurface ( )

Destroys the MNE Surface

Definition at line 109 of file mne_surface.cpp.

Member Function Documentation

◆ activate_neighbors()

void MNESurface::activate_neighbors	(	int	start,
		Eigen::VectorXi &	act,
		int	nstep ) const

Recursively mark neighboring triangles as active.

Parameters

[in]	start	Starting vertex index.
[in,out]	act	Triangle activation array.
[in]	nstep	Recursive expansion steps.

Definition at line 388 of file mne_surface.cpp.

◆ decide_search_restriction()

void MNESurface::decide_search_restriction	(	MNEProjData &	p,
		int	approx_best,
		int	nstep,
		const Eigen::Vector3f &	r ) const

Set up the triangle activation mask for a restricted surface search.

Parameters

[in,out]	p	The projection data whose mask is set.
[in]	approx_best	Approximate best triangle, or negative for brute-force.
[in]	nstep	Neighborhood expansion levels.
[in]	r	The query point.

Definition at line 335 of file mne_surface.cpp.

◆ find_closest_on_surface_approx()

void MNESurface::find_closest_on_surface_approx	(	const PointsT &	r,
		int	np,
		Eigen::VectorXi &	nearest_tri,
		Eigen::VectorXf &	dist,
		int	nstep ) const

For each point, find the closest point on the surface using neighborhood-restricted search.

Parameters

[in]	r	Array of np point coordinates.
[in]	np	Number of points.
[in,out]	nearest_tri	Best triangle index for each point.
[out]	dist	Distance to the surface for each point.
[in]	nstep	Number of neighborhood expansion steps.

Definition at line 308 of file mne_surface.cpp.

◆ nearest_triangle_point() [1/2]

int MNESurface::nearest_triangle_point	(	const Eigen::Vector3f &	r,
		const MNEProjData *	user,
		int	tri,
		float &	x,
		float &	y,
		float &	z ) const

Find the nearest point on a triangle to a given point.

Parameters

[in]	r	The point.
[in]	user	Optional MNEProjData restricting active triangles (may be NULL).
[in]	tri	Triangle index.
[out]	x	Coordinate along first edge.
[out]	y	Coordinate along second edge.
[out]	z	Distance from the triangle.

Returns: TRUE if the triangle is active, FALSE if inactive.

Definition at line 156 of file mne_surface.cpp.

◆ nearest_triangle_point() [2/2]

int MNESurface::nearest_triangle_point	(	const Eigen::Vector3f &	r,
		int	tri,
		float &	x,
		float &	y,
		float &	z ) const

Find the nearest point on a triangle (simplified, no projection data).

Parameters

[in]	r	The point.
[in]	tri	Triangle index.
[out]	x	Coordinate along first edge.
[out]	y	Coordinate along second edge.
[out]	z	Distance from the triangle.

Returns: TRUE always.

Definition at line 253 of file mne_surface.cpp.

◆ project_to_surface()

int MNESurface::project_to_surface	(	const MNEProjData *	proj_data,
		const Eigen::Vector3f &	r,
		float &	distp ) const

Project a point onto the nearest triangle of the surface.

Parameters

[in]	proj_data	Optional MNEProjData restricting active triangles (may be NULL).
[in]	r	The 3D point to project.
[out]	distp	Receives the signed distance to the surface.

Returns: Index of the closest triangle, or -1 if none found.

Definition at line 282 of file mne_surface.cpp.

◆ project_to_triangle() [1/2]

Eigen::Vector3f MNESurface::project_to_triangle	(	int	best,
		const Eigen::Vector3f &	r ) const

Find the nearest point on a given triangle and return the projected 3D coordinates.

Parameters

[in]	best	Triangle index.
[in]	r	The source point.

Returns: The projected 3D point.

Definition at line 273 of file mne_surface.cpp.

◆ project_to_triangle() [2/2]

Eigen::Vector3f MNESurface::project_to_triangle	(	int	tri,
		float	p,
		float	q ) const

Compute 3D position on a triangle from barycentric coordinates.

Parameters

[in]	tri	Triangle index.
[in]	p	Barycentric coordinate along first edge.
[in]	q	Barycentric coordinate along second edge.

Returns: The 3D point on the triangle.

Definition at line 260 of file mne_surface.cpp.

◆ read_bem_surface() [1/2]

MNESurface * MNESurface::read_bem_surface	(	const QString &	name,
		int	which,
		int	add_geometry,
		float *	sigmap )

static

Read a BEM surface from a FIFF file (excess-neighbor checking enabled).

Parameters

[in]	name	Path to the BEM FIFF file.
[in]	which	Surface ID to load (-1 loads the first found).
[in]	add_geometry	If non-zero, compute full geometry info.
[out]	sigmap	If non-null, receives the surface conductivity.

Returns: The loaded surface, or NULL on failure. Caller takes ownership.

Definition at line 405 of file mne_surface.cpp.

◆ read_bem_surface() [2/2]

MNESurface * MNESurface::read_bem_surface	(	const QString &	name,
		int	which,
		int	add_geometry,
		float *	sigmap,
		bool	check_too_many_neighbors )

static

Read a BEM surface from a FIFF file.

Parameters

[in]	name	Path to the BEM FIFF file.
[in]	which	Surface ID to load (-1 loads the first found).
[in]	add_geometry	If non-zero, compute full geometry info.
[out]	sigmap	If non-null, receives the surface conductivity.
[in]	check_too_many_neighbors	Fail on excess neighbor count.

Returns: The loaded surface, or NULL on failure. Caller takes ownership.

Definition at line 419 of file mne_surface.cpp.

◆ read_bem_surface2()

MNESurface * MNESurface::read_bem_surface2	(	const QString &	name,
		int	which,
		int	add_geometry,
		float *	sigmap )

static

Read a BEM surface from a FIFF file (excess-neighbor checking disabled).

Parameters

[in]	name	Path to the BEM FIFF file.
[in]	which	Surface ID to load (-1 loads the first found).
[in]	add_geometry	If non-zero, compute full geometry info.
[out]	sigmap	If non-null, receives the surface conductivity.

Returns: The loaded surface, or NULL on failure. Caller takes ownership.

Definition at line 412 of file mne_surface.cpp.

◆ sum_solids()

double MNESurface::sum_solids ( const Eigen::Vector3f & from ) const

Sum the solid angles of all triangles as seen from a given point. ~4pi if inside, ~0 if outside.

Parameters

[in] from The test point.

Returns: Total solid angle in steradians.

Definition at line 117 of file mne_surface.cpp.

◆ triangle_coords()

void MNESurface::triangle_coords	(	const Eigen::Vector3f &	r,
		int	tri,
		float &	x,
		float &	y,
		float &	z ) const

Compute barycentric-like coordinates of a point relative to a triangle.

Parameters

[in]	r	The point.
[in]	tri	Triangle index.
[out]	x	Barycentric coordinate along first edge.
[out]	y	Barycentric coordinate along second edge.
[out]	z	Signed perpendicular distance from the plane.

Definition at line 130 of file mne_surface.cpp.

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

src/libraries/mne/mne_surface.h
src/libraries/mne/mne_surface.cpp

Public Types

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstSPtr

◆ SPtr

Constructor & Destructor Documentation

◆ MNESurface()

◆ ~MNESurface()

Member Function Documentation

◆ activate_neighbors()

◆ decide_search_restriction()

◆ find_closest_on_surface_approx()

◆ nearest_triangle_point() [1/2]

◆ nearest_triangle_point() [2/2]

◆ project_to_surface()

◆ project_to_triangle() [1/2]

◆ project_to_triangle() [2/2]

◆ read_bem_surface() [1/2]

◆ read_bem_surface() [2/2]

◆ read_bem_surface2()

◆ sum_solids()

◆ triangle_coords()