Renderable cortical surface mesh with per-vertex color, curvature data, and GPU buffer management. More...

#include <brainsurface.h>

Classes
struct	Bvh

Public Types
enum	TissueType { TissueUnknown = 0 , TissueBrain = 1 , TissueSkin = 2 , TissueOuterSkull = 3 , TissueInnerSkull = 4 }
using	VisualizationMode = DISP3DLIB::VisualizationMode

Public Member Functions
	BrainSurface ()
	~BrainSurface ()
void	setVisible (bool visible)
bool	isVisible () const
void	setHemi (int hemi)
void	setTissueType (TissueType type)
TissueType	tissueType () const
int	hemi () const
void	fromSurface (const FSLIB::FsSurface &surf)
void	fromBemSurface (const MNELIB::MNEBemSurface &surf, const QColor &color=Qt::white)
void	createFromData (const Eigen::MatrixX3f &vertices, const Eigen::MatrixX3i &triangles, const QColor &color)
void	createFromData (const Eigen::MatrixX3f &vertices, const Eigen::MatrixX3f &normals, const Eigen::MatrixX3i &triangles, const QColor &color)
bool	loadAnnotation (const QString &path)
void	addAnnotation (const FSLIB::FsAnnotation &annotation)
void	labelElements (int verticesPerElement)
void	setVisualizationMode (VisualizationMode mode)
void	applySourceEstimateColors (const QVector< uint32_t > &colors)
void	clearSourceEstimateColors ()
GpuStream	geometryStream () const
GpuStream	colorStream () const
GpuStream	annotationStream () const
GpuStream	indexStream () const
const RenderKey &	renderKey () const
uint32_t	indexCount () const
uint32_t	vertexCount () const
Eigen::MatrixX3f	vertexPositions () const
Eigen::MatrixX3f	vertexNormals () const
QVector< uint32_t >	triangleIndices () const
const QVector< VertexData > &	vertexDataRef () const
const QVector< uint32_t > &	colorsRef () const
const QVector< uint32_t > &	annotationColorsRef () const
float	minX () const
float	maxX () const
void	boundingBox (QVector3D &min, QVector3D &max) const
bool	intersects (const QVector3D &rayOrigin, const QVector3D &rayDir, float &dist, int &vertexIdx) const
QString	getAnnotationLabel (int vertexIdx) const
int	getAnnotationLabelId (int vertexIdx) const
void	setSelectedRegion (int regionId)
void	translateX (float offset)
void	transform (const QMatrix4x4 &m)
void	applyTransform (const QMatrix4x4 &m)
std::vector< Eigen::VectorXi >	computeNeighbors () const
Eigen::MatrixX3f	verticesAsMatrix () const
void	setUseDefaultColor (bool useDefault)
void	setColor (const QColor &color)
void	setSelected (bool selected)
bool	isSelected () const
int	selectedRegionId () const
int	selectedVertexStart () const
void	setSelectedVertexRange (int start, int count)
std::optional< uint32_t >	selectedLabel () const

Static Public Attributes
static constexpr VisualizationMode	ModeSurface = DISP3DLIB::ModeSurface
static constexpr VisualizationMode	ModeAnnotation = DISP3DLIB::ModeAnnotation
static constexpr VisualizationMode	ModeScientific = DISP3DLIB::ModeScientific
static constexpr VisualizationMode	ModeSourceEstimate = DISP3DLIB::ModeSourceEstimate

Detailed Description

Renderable cortical surface mesh with per-vertex color, curvature data, and GPU buffer management.

BrainSurface manages the geometry and visual properties of a single brain mesh.

Definition at line 81 of file brainsurface.h.

Member Typedef Documentation

◆ VisualizationMode

using DISP3DLIB::BrainSurface::VisualizationMode = DISP3DLIB::VisualizationMode

Definition at line 98 of file brainsurface.h.

Member Enumeration Documentation

◆ TissueType

enum DISP3DLIB::BrainSurface::TissueType

Enumerator
TissueUnknown
TissueBrain
TissueSkin
TissueOuterSkull
TissueInnerSkull

Definition at line 104 of file brainsurface.h.

Constructor & Destructor Documentation

◆ BrainSurface()

DISP3DLIB::BrainSurface::BrainSurface ( )

default

Default Constructor

◆ ~BrainSurface()

DISP3DLIB::BrainSurface::~BrainSurface ( )

default

Destructor

Member Function Documentation

◆ addAnnotation()

void DISP3DLIB::BrainSurface::addAnnotation ( const FSLIB::FsAnnotation & annotation )

Add annotation data directly.

Parameters

[in] annotation Input annotation data.

Definition at line 219 of file brainsurface.cpp.

◆ annotationColorsRef()

const QVector< uint32_t > & DISP3DLIB::BrainSurface::annotationColorsRef ( ) const

inline

Returns: Per-vertex packed ABGR annotation colours, valid while this surface lives.

Definition at line 345 of file brainsurface.h.

◆ annotationStream()

GpuStream DISP3DLIB::BrainSurface::annotationStream ( ) const

Returns: Annotation colour stream (packed ABGR per vertex, 0 where unlabelled).

Definition at line 87 of file brainsurface.cpp.

◆ applySourceEstimateColors()

void DISP3DLIB::BrainSurface::applySourceEstimateColors ( const QVector< uint32_t > & colors )

Apply source estimate colors to vertices.

Parameters

[in] colors Vector of packed ABGR colors, one per vertex.

Definition at line 274 of file brainsurface.cpp.

◆ applyTransform()

void DISP3DLIB::BrainSurface::applyTransform ( const QMatrix4x4 & m )

Apply a transformation to the surface starting from the original data. Note: This prevents transformation accumulation.

Parameters

[in] m Transformation matrix.

Definition at line 396 of file brainsurface.cpp.

◆ boundingBox()

void DISP3DLIB::BrainSurface::boundingBox	(	QVector3D &	min,
		QVector3D &	max ) const

Get bounding box of the surface.

Parameters

[out]	min	Minimum coordinates.
[out]	max	Maximum coordinates.

Definition at line 458 of file brainsurface.cpp.

◆ clearSourceEstimateColors()

void DISP3DLIB::BrainSurface::clearSourceEstimateColors ( )

Clear source estimate overlay colors and restore curvature-based coloring.

Definition at line 290 of file brainsurface.cpp.

◆ colorsRef()

const QVector< uint32_t > & DISP3DLIB::BrainSurface::colorsRef ( ) const

inline

Returns: Per-vertex packed ABGR colours, valid while this surface lives.

Definition at line 337 of file brainsurface.h.

◆ colorStream()

GpuStream DISP3DLIB::BrainSurface::colorStream ( ) const

Returns: Colour stream (packed ABGR per vertex; alpha carries the curvature grey on cortex).

Definition at line 82 of file brainsurface.cpp.

◆ computeNeighbors()

std::vector< Eigen::VectorXi > DISP3DLIB::BrainSurface::computeNeighbors ( ) const

Compute neighbor vertices from triangle connectivity. Required for surface-constrained distance calculations.

Returns: Vector of neighbor indices for each vertex.

Definition at line 408 of file brainsurface.cpp.

◆ createFromData() [1/2]

void DISP3DLIB::BrainSurface::createFromData	(	const Eigen::MatrixX3f &	vertices,
		const Eigen::MatrixX3f &	normals,
		const Eigen::MatrixX3i &	triangles,
		const QColor &	color )

Create surface from raw vertex, normal and triangle data.

Parameters

[in]	vertices	Nx3 matrix of vertex positions.
[in]	normals	Nx3 matrix of vertex normals.
[in]	triangles	Mx3 matrix of triangle indices.
[in]	color	FsSurface color.

Definition at line 166 of file brainsurface.cpp.

◆ createFromData() [2/2]

void DISP3DLIB::BrainSurface::createFromData	(	const Eigen::MatrixX3f &	vertices,
		const Eigen::MatrixX3i &	triangles,
		const QColor &	color )

Create surface from raw vertex and triangle data. Vertex normals are the sums of the adjacent face normals.

Parameters

[in]	vertices	Nx3 matrix of vertex positions.
[in]	triangles	Mx3 matrix of triangle indices.
[in]	color	FsSurface color.

Definition at line 161 of file brainsurface.cpp.

◆ fromBemSurface()

void DISP3DLIB::BrainSurface::fromBemSurface	(	const MNELIB::MNEBemSurface &	surf,
		const QColor &	color = Qt::white )

Load geometry from a MNE BEM surface.

Parameters

[in]	surf	Input BEM surface.
[in]	color	Base color for the surface.

Definition at line 142 of file brainsurface.cpp.

◆ fromSurface()

void DISP3DLIB::BrainSurface::fromSurface ( const FSLIB::FsSurface & surf )

Load geometry from a FreeSurfer surface.

Parameters

[in] surf Input FreeSurfer surface.

Definition at line 120 of file brainsurface.cpp.

◆ geometryStream()

GpuStream DISP3DLIB::BrainSurface::geometryStream ( ) const

Returns: Geometry stream (DISP3DLIB::VertexData per vertex).

Definition at line 77 of file brainsurface.cpp.

◆ getAnnotationLabel()

QString DISP3DLIB::BrainSurface::getAnnotationLabel ( int vertexIdx ) const

Get the annotation label name for a given vertex.

Parameters

[in] vertexIdx Index of the vertex.

Returns: FsLabel name.

Definition at line 742 of file brainsurface.cpp.

◆ getAnnotationLabelId()

int DISP3DLIB::BrainSurface::getAnnotationLabelId ( int vertexIdx ) const

Definition at line 766 of file brainsurface.cpp.

◆ hemi()

int DISP3DLIB::BrainSurface::hemi ( ) const

inline

Get the hemisphere index.

Returns: Hemisphere index (0=LH, 1=RH).

Definition at line 171 of file brainsurface.h.

◆ indexCount()

uint32_t DISP3DLIB::BrainSurface::indexCount ( ) const

inline

Definition at line 290 of file brainsurface.h.

◆ indexStream()

GpuStream DISP3DLIB::BrainSurface::indexStream ( ) const

Returns: Triangle index stream (three uint32 per triangle).

Definition at line 92 of file brainsurface.cpp.

◆ intersects()

bool DISP3DLIB::BrainSurface::intersects	(	const QVector3D &	rayOrigin,
		const QVector3D &	rayDir,
		float &	dist,
		int &	vertexIdx ) const

Test ray intersection with this surface.

Parameters

[in]	rayOrigin	Ray origin in world/local space (object is assumed at 0,0,0 usually unless transformed externally). Note: The BrainSurface vertices are typically already transformed (e.g. by View3D model matrix logic? No, BrainView applies matrix in shader. The vertices here are raw. So ray must be transformed to local space OR vertices transformed to world.
[in]	rayDir	Ray direction (normalized).
[out]	dist	Distance to intersection.
[in,out]	vertexIdx	Index of the vertex closest to the intersection.

Returns: True if intersected.

Definition at line 640 of file brainsurface.cpp.

◆ isSelected()

bool DISP3DLIB::BrainSurface::isSelected ( ) const

inline

Definition at line 465 of file brainsurface.h.

◆ isVisible()

bool DISP3DLIB::BrainSurface::isVisible ( ) const

inline

Check if the surface is visible.

Returns: True if visible.

Definition at line 127 of file brainsurface.h.

◆ labelElements()

void DISP3DLIB::BrainSurface::labelElements ( int verticesPerElement )

Give each run of vertices its own label key, so one element of a batched mesh (e.g. one digitizer sphere) can be highlighted on its own.

Parameters

[in] verticesPerElement Number of consecutive vertices per element.

Definition at line 245 of file brainsurface.cpp.

◆ loadAnnotation()

bool DISP3DLIB::BrainSurface::loadAnnotation ( const QString & path )

Load annotation data from file.

Parameters

[in] path Path to the .annot file.

Returns: True if successful.

Definition at line 208 of file brainsurface.cpp.

◆ maxX()

float DISP3DLIB::BrainSurface::maxX ( ) const

Get maximum X coordinate.

Returns: Maximum X value.

Definition at line 344 of file brainsurface.cpp.

◆ minX()

float DISP3DLIB::BrainSurface::minX ( ) const

Get minimum X coordinate.

Returns: Minimum X value.

Definition at line 334 of file brainsurface.cpp.

◆ renderKey()

const RenderKey & DISP3DLIB::BrainSurface::renderKey ( ) const

inline

Returns: Identity of this surface in the renderer's GPU cache.

Definition at line 285 of file brainsurface.h.

◆ selectedLabel()

std::optional< uint32_t > DISP3DLIB::BrainSurface::selectedLabel ( ) const

Returns: Annotation-stream value of the highlighted vertices (selected region or vertex range), or nothing when no part of the surface is highlighted.

Definition at line 789 of file brainsurface.cpp.

◆ selectedRegionId()

int DISP3DLIB::BrainSurface::selectedRegionId ( ) const

inline

Definition at line 469 of file brainsurface.h.

◆ selectedVertexStart()

int DISP3DLIB::BrainSurface::selectedVertexStart ( ) const

inline

Definition at line 473 of file brainsurface.h.

◆ setColor()

void DISP3DLIB::BrainSurface::setColor ( const QColor & color )

Set the colour of a surface without curvature (BEM, sensors, digitizers, source spaces).

Parameters

[in] color New colour; its alpha is the opacity of the holographic shader.

Definition at line 307 of file brainsurface.cpp.

◆ setHemi()

void DISP3DLIB::BrainSurface::setHemi ( int hemi )

inline

Set the hemisphere index.

Parameters

[in] hemi 0 for Left, 1 for Right.

Definition at line 138 of file brainsurface.h.

◆ setSelected()

void DISP3DLIB::BrainSurface::setSelected ( bool selected )

Definition at line 778 of file brainsurface.cpp.

◆ setSelectedRegion()

void DISP3DLIB::BrainSurface::setSelectedRegion ( int regionId )

Set the selected region for highlighting.

Parameters

[in] regionId The ID of the region to highlight.

Definition at line 773 of file brainsurface.cpp.

◆ setSelectedVertexRange()

void DISP3DLIB::BrainSurface::setSelectedVertexRange	(	int	start,
		int	count )

Highlight a contiguous range of vertices (e.g. a single sphere in a batched mesh). Pass start=-1 to clear the vertex range highlight.

Parameters

[in]	start	First vertex index to highlight (-1 to clear).
[in]	count	Number of vertices to highlight.

Definition at line 783 of file brainsurface.cpp.

◆ setTissueType()

void DISP3DLIB::BrainSurface::setTissueType ( TissueType type )

inline

Set the tissue type (Brain, Skin, Skull, etc.).

Parameters

[in] type TissueType enum value.

Definition at line 149 of file brainsurface.h.

◆ setUseDefaultColor()

void DISP3DLIB::BrainSurface::setUseDefaultColor ( bool useDefault )

Set/Get whether to use the default surface color.

Parameters

[in] useDefault True to use the surface's default color as base, false for white.

Definition at line 299 of file brainsurface.cpp.

◆ setVisible()

void DISP3DLIB::BrainSurface::setVisible ( bool visible )

Set the visibility of the surface.

Parameters

[in] visible True if visible.

Definition at line 259 of file brainsurface.cpp.

◆ setVisualizationMode()

void DISP3DLIB::BrainSurface::setVisualizationMode ( VisualizationMode mode )

Set the visualization mode (FsSurface, FsAnnotation, Scientific).

Parameters

[in] mode VisualizationMode enum.

Definition at line 266 of file brainsurface.cpp.

◆ tissueType()

TissueType DISP3DLIB::BrainSurface::tissueType ( ) const

inline

Get the tissue type.

Returns: TissueType enum value.

Definition at line 160 of file brainsurface.h.

◆ transform()

void DISP3DLIB::BrainSurface::transform ( const QMatrix4x4 & m )

Apply a generic 4x4 transformation matrix to all vertices and normals.

Parameters

[in] m Transformation matrix.

Definition at line 364 of file brainsurface.cpp.

◆ translateX()

void DISP3DLIB::BrainSurface::translateX ( float offset )

Translate all vertices along the X axis.

Parameters

[in] offset Amount to translate.

Definition at line 354 of file brainsurface.cpp.

◆ triangleIndices()

QVector< uint32_t > DISP3DLIB::BrainSurface::triangleIndices ( ) const

inline

Get the triangle index buffer.

Returns: Copy of the index data, three vertex indices per triangle.

Definition at line 321 of file brainsurface.h.

◆ vertexCount()

uint32_t DISP3DLIB::BrainSurface::vertexCount ( ) const

inline

Definition at line 294 of file brainsurface.h.

◆ vertexDataRef()

const QVector< VertexData > & DISP3DLIB::BrainSurface::vertexDataRef ( ) const

inline

Returns: Current vertex geometry, valid while this surface lives.

Definition at line 329 of file brainsurface.h.

◆ vertexNormals()

Eigen::MatrixX3f DISP3DLIB::BrainSurface::vertexNormals ( ) const

Get a copy of the current vertex normals.

Returns: Nx3 matrix of the current vertex normals.

Definition at line 195 of file brainsurface.cpp.

◆ vertexPositions()

Eigen::MatrixX3f DISP3DLIB::BrainSurface::vertexPositions ( ) const

Get a copy of the current vertex positions.

Returns: Nx3 matrix of the current (possibly transformed) vertex positions.

Definition at line 182 of file brainsurface.cpp.

◆ verticesAsMatrix()

Eigen::MatrixX3f DISP3DLIB::BrainSurface::verticesAsMatrix ( ) const

Get vertex positions as Eigen matrix.

Returns: Nx3 matrix of vertex positions.

Definition at line 444 of file brainsurface.cpp.

Member Data Documentation

◆ ModeAnnotation

VisualizationMode DISP3DLIB::BrainSurface::ModeAnnotation = DISP3DLIB::ModeAnnotation

staticconstexpr

Definition at line 100 of file brainsurface.h.

◆ ModeScientific

VisualizationMode DISP3DLIB::BrainSurface::ModeScientific = DISP3DLIB::ModeScientific

staticconstexpr

Definition at line 101 of file brainsurface.h.

◆ ModeSourceEstimate

VisualizationMode DISP3DLIB::BrainSurface::ModeSourceEstimate = DISP3DLIB::ModeSourceEstimate

staticconstexpr

Definition at line 102 of file brainsurface.h.

◆ ModeSurface

VisualizationMode DISP3DLIB::BrainSurface::ModeSurface = DISP3DLIB::ModeSurface

staticconstexpr

Definition at line 99 of file brainsurface.h.

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

src/libraries/disp3D/renderable/brainsurface.h
src/libraries/disp3D/renderable/brainsurface.cpp

Classes

Public Types

Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ VisualizationMode

Member Enumeration Documentation

◆ TissueType

Constructor & Destructor Documentation

◆ BrainSurface()

◆ ~BrainSurface()

Member Function Documentation

◆ addAnnotation()

◆ annotationColorsRef()

◆ annotationStream()

◆ applySourceEstimateColors()

◆ applyTransform()

◆ boundingBox()

◆ clearSourceEstimateColors()

◆ colorsRef()

◆ colorStream()

◆ computeNeighbors()

◆ createFromData() [1/2]

◆ createFromData() [2/2]

◆ fromBemSurface()

◆ fromSurface()

◆ geometryStream()

◆ getAnnotationLabel()

◆ getAnnotationLabelId()

◆ hemi()

◆ indexCount()

◆ indexStream()

◆ intersects()

◆ isSelected()

◆ isVisible()

◆ labelElements()

◆ loadAnnotation()

◆ maxX()

◆ minX()

◆ renderKey()

◆ selectedLabel()

◆ selectedRegionId()

◆ selectedVertexStart()

◆ setColor()

◆ setHemi()

◆ setSelected()

◆ setSelectedRegion()

◆ setSelectedVertexRange()

◆ setTissueType()

◆ setUseDefaultColor()

◆ setVisible()

◆ setVisualizationMode()

◆ tissueType()

◆ transform()

◆ translateX()

◆ triangleIndices()

◆ vertexCount()

◆ vertexDataRef()

◆ vertexNormals()

◆ vertexPositions()

◆ verticesAsMatrix()

Member Data Documentation

◆ ModeAnnotation

◆ ModeScientific

◆ ModeSourceEstimate

◆ ModeSurface