constel Namespace Reference

Classes
class	AfficheAntFiberPointBundleListener
struct	Bracket_accessor_PointIndex
class	BundleInteractionReader
	(2022/10/10 reverse engineering, Denis) This class is a BundleReader with an additional protected variable, _listenedFiberInfo, which is entirely manipulated (filled and used) from foreign classes, which are made friends in order for them to access it. More...
class	BundleLoader
class	Connectivity
class	CurvilinearAbscissaBundleListener
class	FiberNameAccordingToMeshIntersectionBundleListener
class	FiberNameAccordingToMeshTextureIntersectionBundleListener
class	FibersWeightsReader
class	FibersWeightsWriter
class	LengthBundleListener
class	ListenedFiberInfo
class	MemAntBundleListener
class	MeshConnectionBundleListener
class	MeshHistoLengthConnectionBundleListener
class	MeshIntersectionBundleListener
class	MeshIntersectionMatrixBundleListener
class	MeshIntersectionMatrixWithLengthBundleListener
class	MeshIntersectionNoSmoothingBundleListener
class	MeshIntersectionNoSmoothingFasterBundleListener
class	SavingMeshIntersectionBundleListener
class	SelectBundlesFromLength
class	SelectBundlesFromNames
class	SelectFiberListenerFromMesh
	Fibers selection by regions on a mesh (plus a label texture). More...
class	SubSamplerFromMeshIntersectionBundleListener

Typedefs
typedef aims::FiberPoint	Point
typedef std::vector< Point >	Fiber
typedef std::vector< Fiber >	Fibers
typedef std::vector< Fibers >	BundlesSet
typedef std::pair< Fiber, double >	WeightedFiber
typedef std::vector< WeightedFiber >	WeightedFibers
typedef std::vector< Connectivity >	Connectivities
typedef std::vector< std::vector< std::size_t > >	CNeighborhoods
typedef std::vector< std::pair< std::size_t, double > >	QuickMap
typedef std::map< std::size_t, float >	DistMap
typedef std::vector< QuickMap >	Connection
typedef std::vector< Connection >	BundleConnections
typedef boost::shared_ptr< BundleConnections >	BundleConnections_shared_ptr
typedef std::vector< unsigned >	ConnectionsLength
typedef std::vector< float >	ConnectionsFloatLength
typedef boost::shared_ptr< ConnectionsLength >	ConnectionsLength_shared_ptr
typedef std::vector< std::set< unsigned > >	PolygonsByVertexIndex
typedef std::vector< PolygonsByVertexIndex >	PolygonsByVertexIndex_collection
typedef std::vector< std::pair< uint, Point3df > >	KDTreeVertices
typedef KDTree::KDTree< 3, std::pair< uint, Point3df >, Bracket_accessor_PointIndex< Point3df > >	KDTree

Functions
aims::SparseMatrix *	connectivitiesToSparseMatrix (const Connectivities &conn)
Connectivities *	sparseMatrixToConnectivities (const aims::SparseMatrix &mat)
void	sparseMatrixToConnectivities (const aims::SparseMatrix &mat, Connectivities &conn)
void	sparseMatrixToConnectivities (const aims::boost_sparse_matrix &mat, Connectivities &conn)
void	writeConnectivities (const Connectivities &conn, const std::string &filename, bool ascii=false)
Connectivities *	weightedConnMatrix (const WeightedFibers &fibers, const AimsSurfaceTriangle &inAimsMesh, Motion motion, bool verbose=false)
Connectivities *	connMatrix (const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh, float distthresh, float wthresh, Motion motion, bool verbose=false)
Connectivity *	connMatrixSumRows (Connectivities *matrix_ptr, bool verbose=false)
std::vector< double > *	connMatrixSumRows (const aims::SparseOrDenseMatrix &matrix, bool verbose=false)
Connectivities *	connMatrixTargetsRegroup (Connectivities *connMatrixToAllMesh, const TimeTexture< short > &targetRegionsTexture, int targetRegionsNb, bool verbose=false)
Connectivities *	connMatrixReducedFromRegion (Connectivities *allMeshConnMatrix, const TimeTexture< short > &seedRegionsTexture, int seedRegionLabel, int seedRegionLabelVertexNb, std::vector< std::size_t > **seedVertexIndex=0, bool verbose=false)
Connectivities *	connMatrixRegionExtractTargetsRegroup (Connectivities *allMeshConnMatrix, const TimeTexture< short > &seedRegionsTexture, int seedRegionLabel, const TimeTexture< short > &targetRegionsTexture, int targetRegionsNb, std::size_t seedRegionLabelVertexNb, std::vector< std::size_t > **seedVertexIndex, bool verbose=false)
void	writeAimsFmtConnMatrix (Connectivities *connMatrix_ptr, std::string file_name, bool verbose=false)
void	connMatrixNormalize (aims::SparseOrDenseMatrix &connMatrix, bool verbose=false)
Connectivities *	connMatrixRegionExtract (const aims::SparseOrDenseMatrix &allMeshConnMatrix, const TimeTexture< short > &seedRegionsTexture, int seedRegionLabel, std::size_t seedRegionLabelVertexNb, std::vector< std::size_t > **seedVertexIndex=0, bool verbose=false)
TimeTexture< float >	densityTexture (Connectivities *allMeshConnMatrix, std::vector< std::size_t > VertexIndex, bool verbose=false)
TimeTexture< float >	densityTexture (const aims::SparseOrDenseMatrix &allMeshConnMatrix, std::vector< std::size_t > VertexIndex, bool verbose=false)
TimeTexture< float >	meshDensityTexture (Connectivities *connMatrixToAllMesh_ptr, bool verbose=false)
TimeTexture< float >	meshDensityTexture (const aims::SparseOrDenseMatrix &connMatrixToAllMesh, bool verbose=false)
TimeTexture< float > *	oneTargetDensityTargetsRegroupTexture (const Connectivity *lineMatrixToTargetRegions_ptr, const TimeTexture< short > &targetRegionsTex, int timestep)
TimeTexture< float > *	oneTargetDensityTargetsRegroupTexture (const std::vector< double > *lineMatrixToTargetRegions_ptr, const TimeTexture< short > &targetRegionsTex, int timestep)
TimeTexture< float > *	connMatrixRow_TO_TimeTexture_FLOAT (Connectivity *conn_ptr)
Connectivity *	connMatrixToRois (const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh, float distthresh, float wthresh, Motion motion, bool verbose=false)
Connectivities *	connMatrixSeedMeshToTargetMesh (const Fibers &fibers, const AimsSurfaceTriangle &aimsMesh1, const AimsSurfaceTriangle &aimsMesh2, float distthresh, float wthresh, Motion motion, bool verbose=false)
Connectivities *	connMatrixSeedMesh_to_targetMeshTargets_regroup (const aims::SparseOrDenseMatrix &connMatrixToAllMesh, const TimeTexture< short > &targetRegionsTex, int targetRegionsNb, bool verbose=false)
Connectivities *	connMatrixSeedMeshRegions_to_targetMeshTargets_regroup (Connectivities *connMatrixSeedMeshToTargetMesh_ptr, const TimeTexture< short > &seedRegionsTexture, const TimeTexture< short > &targetRegionsTex, int targetRegionsNb, int seedRegionsNb, bool verbose=false)
aims::SparseOrDenseMatrix *	connectivitiesToSparseOrDenseMatrix (const Connectivities &)
void	fillconnMatrix (Connectivities *conn, QuickMap &fiberExtremity1NeighMeshVertex, QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold, double distanceThreshold, unsigned connectionLength=1)
void	fillconnMatrixNoSmoothing (Connectivities *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex, QuickMap &fiberExtremity2NeighMeshVertex)
void	fillconnMatrix (aims::SparseMatrix *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex, QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold, double distanceThreshold, unsigned connectionLength=1)
void	fillconnMatrix (aims::SparseMatrix *conn_ptr, aims::SparseMatrix *conn_ptr2, QuickMap &fiberExtremity1NeighMeshVertex, QuickMap &fiberExtremity2NeighMeshVertex, double connectivityThreshold, double distanceThreshold, std::size_t rowIndex_min, std::size_t rowIndex_max=0, unsigned connectionLength=1)
void	fillNonSymetricConnMatrix (Connectivities *conn_ptr, QuickMap &fiberExtremity1NeighMeshVertex_rows, QuickMap &fiberExtremity2NeighMeshVertex_cols, double connectivityThreshold, double distanceThreshold)
void	fillconnMatrixWithConnections (Connectivities *conn_ptr, const BundleConnections &connections, std::vector< double > cortexConnectionsWeights, double connectivityThreshold, double distanceThreshold)
void	fillconnMatrixWithConnections (aims::SparseMatrix *conn_ptr, const BundleConnections &connections, double connectivityThreshold, double distanceThreshold, std::size_t rowIndex_min=0, std::size_t rowIndex_max=0, aims::SparseMatrix *conn_ptr2=0)
void	fillconnMatrixWithConnectionsPlusLength (Connectivities *conn_ptr, const BundleConnections &connections, double connectivityThreshold, double distanceThreshold, unsigned length_min, unsigned length_max, ConnectionsLength &connectionsLength)
void	fillconnMatrixWithConnectionsPlusLengthWeight (Connectivities *conn_ptr, const BundleConnections &connections, double connectivityThreshold, double distanceThreshold, unsigned length_min, unsigned length_max, ConnectionsLength &connectionsLength)
void	fillconnMatrixWithConnectionsPlusFloatLengthWeight (Connectivities *conn_ptr, const BundleConnections &connections, double connectivityThreshold, double distanceThreshold, float length_min, float length_max, ConnectionsFloatLength &connectionsLength)
void	fillNonSymetricConnMatrixWithConnections (Connectivities *conn_ptr, const BundleConnections &connections, double connectivityThreshold, double distanceThreshold)
template<int D, class T>
bool	computeIntersectionPointFiberSegmentAndMesh (const AimsTimeSurface< D, T > &aimsMesh, const std::vector< std::set< unsigned > > &polygonsByVertex_Index, Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint, QuickMap **polygonVerticesDistMap=0)
template<int D, class T>
bool	computeIntersectionPointFiberSegmentAndMesh2 (const AimsTimeSurface< D, T > &aimsMesh, const std::vector< std::set< unsigned > > &polygonsByVertex_Index, Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint, QuickMap **polygonVerticesDistMap=0)
template<int D, class T>
bool	computeIntersectionPointNeighborhoodFiberSegmentAndMesh (const AimsTimeSurface< D, T > &aimsMesh, const std::vector< std::set< unsigned > > &polygonsByVertex_Index, Point3df fiberPoint1, Point3df fiberPoint2, unsigned meshClosestPoint, std::vector< QuickMap > &distanceThresholdNeighborhoodByVertex, QuickMap **polygonVerticesDistMap_2ptr)
void	connMatrixTargetsToTargets (const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh, Motion motion, const TimeTexture< short > &targetRegionsTex, std::string filename)
void	connMatrixSeedRegion (const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh, Motion motion, const TimeTexture< short > &seedRegionsTex, std::size_t seedRegionLabel, std::string connmatrix_filename, std::string connTexture_filename)
void	connMatrixSeedRegionSmoothed (const Fibers &fibers, const AimsSurfaceTriangle &inAimsMesh, Motion motion, const TimeTexture< short > &seedRegionsTex, std::size_t seedRegionLabel, float distthresh, float wthresh, std::string connmatrix_filename, std::string connTexture_filename="", bool logOption=false)
TimeTexture< short > *	fusionMeshROIs_to_Texture_S16 (const AimsSurfaceTriangle &inAimsMesh, const Graph &ROI_graph, float distthresh, std::string vertex_property="aims_roi")
TimeTexture< short > *	fusionMeshFoldGraph_to_Texture (const AimsSurfaceTriangle &inAimsMesh, const Graph &ROI_graph, float distthresh, std::string vertex_property="aims_roi", std::string label_name="roi_label")
Graph *	texMeshAndBundles_to_BundlesGraph (const AimsSurfaceTriangle &inAimsMesh, carto::rc_ptr< TimeTexture< short > > tex, std::string namesMode, std::string bundlesFile_name, Motion motion, const std::string &BundlesNamesfile_name=std::string(), float fibers_filter_proportion=0., int texture_time_step=0)
Graph *	texMeshAndBundles_to_BundlesGraph_WithIntersectionComputing (const AimsSurfaceTriangle &inAimsMesh, const TimeTexture< short > &tex, std::string bundlesFile_name, Motion motion, std::string BundlesNamesfile_name)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< aims::SparseMatrix > matrix, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int32_t > &patches, int32_t patch)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< aims::SparseMatrix > matrix, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int16_t > &patches, int32_t patch)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< aims::SparseOrDenseMatrix > matrix, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int32_t > &patches, int32_t patch)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< aims::SparseOrDenseMatrix > matrix, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int16_t > &patches, int32_t patch)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< Connectivities > conn_ptr, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int32_t > &patches, int32_t patch)
void	sparseMatrixDiffusionSmoothing (carto::rc_ptr< Connectivities > conn_ptr, const AimsTimeSurface< 3, Void > &mesh, double connectivityThreshold, double distanceThreshold, const TimeTexture< int16_t > &patches, int32_t patch)
void	sparseMatrixGaussianSmoothing (aims::SparseMatrix &matrix, const AimsSurfaceTriangle &aimsMesh, float distthresh, float wthresh=0.0)
void	sparseMatrixGaussianSmoothingNormed (aims::SparseMatrix &matrix, const AimsSurfaceTriangle &aimsMesh, float distthresh, float wthresh=0.0)
template<int D, class T>
std::vector< std::set< unsigned > >	surfacePolygonsIndex (const AimsTimeSurface< D, T > &surf)
std::set< unsigned >	surfacePolygonsIndexByVerticesGroup (const std::vector< std::set< unsigned > > &polygonsByVertex_Index, std::vector< unsigned > &vertexIndex)
bool	hasVertexLabel (const TimeTexture< short > &labeled_tex, std::set< unsigned > vertexIndex_set, int label)
bool	connectedCommponent_isInside (const AimsSurfaceTriangle &aimsMesh, const TimeTexture< short > &region_tex, std::vector< std::size_t > connectedCommponent_vertexIndex)
std::size_t	firstBoundaryVertex (const AimsSurfaceTriangle &aimsMesh, const TimeTexture< short > &region_tex, std::vector< std::size_t > connectedCommponent_vertexIndex)
template<typename T>
std::size_t	boundaryVertexBiggestValue (const AimsSurfaceTriangle &aimsMesh, const TimeTexture< short > &region_tex, std::vector< std::size_t > connectedCommponent_vertexIndex, const TimeTexture< T > &values_tex)
bool	computeIntersectionSegmentPolygon (Point3df segmentBeginPoint, Point3df segmentEndPoint, std::vector< Point3df > polygon, Point3df **intersection_point=0)
KDTreeVertices	kdt_vertices (const AimsSurfaceTriangle &mesh)
	get vertices vector with index for each vertex
float	dist2 (const Point3df &p1, const Point3df &p2)

Typedef Documentation

BundleConnections

typedef std::vector<Connection> constel::BundleConnections

Definition at line 72 of file connectivities.h.

BundleConnections_shared_ptr

typedef boost::shared_ptr<BundleConnections> constel::BundleConnections_shared_ptr

Definition at line 73 of file connectivities.h.

BundlesSet

typedef std::vector<Fibers> constel::BundlesSet

Definition at line 10 of file bundleSet.h.

CNeighborhoods

typedef std::vector<std::vector<std::size_t> > constel::CNeighborhoods

Definition at line 68 of file connectivities.h.

Connection

typedef std::vector<QuickMap> constel::Connection

Definition at line 71 of file connectivities.h.

ConnectionsFloatLength

typedef std::vector<float> constel::ConnectionsFloatLength

Definition at line 75 of file connectivities.h.

ConnectionsLength

typedef std::vector<unsigned> constel::ConnectionsLength

Definition at line 74 of file connectivities.h.

ConnectionsLength_shared_ptr

typedef boost::shared_ptr<ConnectionsLength> constel::ConnectionsLength_shared_ptr

Definition at line 76 of file connectivities.h.

Connectivities

typedef std::vector<Connectivity> constel::Connectivities

Definition at line 67 of file connectivities.h.

DistMap

typedef std::map<std::size_t, float> constel::DistMap

Definition at line 70 of file connectivities.h.

Fiber

typedef std::vector<Point> constel::Fiber

Definition at line 8 of file bundleSet.h.

Fibers

typedef std::vector<Fiber> constel::Fibers

Definition at line 9 of file bundleSet.h.

KDTree

typedef KDTree::KDTree<3, std::pair<uint, Point3df>, Bracket_accessor_PointIndex<Point3df> > constel::KDTree

Definition at line 46 of file tildefs.h.

KDTreeVertices

typedef std::vector< std::pair< uint, Point3df > > constel::KDTreeVertices

Definition at line 29 of file tildefs.h.

Point

typedef aims::FiberPoint constel::Point

Definition at line 7 of file bundleSet.h.

PolygonsByVertexIndex

typedef std::vector<std::set<unsigned> > constel::PolygonsByVertexIndex

Definition at line 77 of file connectivities.h.

PolygonsByVertexIndex_collection

typedef std::vector<PolygonsByVertexIndex> constel::PolygonsByVertexIndex_collection

Definition at line 78 of file connectivities.h.

QuickMap

typedef std::vector<std::pair<std::size_t, double> > constel::QuickMap

Definition at line 69 of file connectivities.h.

WeightedFiber

typedef std::pair<Fiber, double> constel::WeightedFiber

Definition at line 11 of file bundleSet.h.

WeightedFibers

typedef std::vector<WeightedFiber> constel::WeightedFibers

Definition at line 12 of file bundleSet.h.

Function Documentation

boundaryVertexBiggestValue()

template<typename T>

std::size_t constel::boundaryVertexBiggestValue	(	const AimsSurfaceTriangle &	aimsMesh,
		const TimeTexture< short > &	region_tex,
		std::vector< std::size_t >	connectedCommponent_vertexIndex,
		const TimeTexture< T > &	values_tex )

computeIntersectionPointFiberSegmentAndMesh()

template<int D, class T>

bool constel::computeIntersectionPointFiberSegmentAndMesh	(	const AimsTimeSurface< D, T > &	aimsMesh,
		const std::vector< std::set< unsigned > > &	polygonsByVertex_Index,
		Point3df	fiberPoint1,
		Point3df	fiberPoint2,
		unsigned	meshClosestPoint,
		QuickMap **	polygonVerticesDistMap = 0 )

computeIntersectionPointFiberSegmentAndMesh2()

template<int D, class T>

bool constel::computeIntersectionPointFiberSegmentAndMesh2	(	const AimsTimeSurface< D, T > &	aimsMesh,
		const std::vector< std::set< unsigned > > &	polygonsByVertex_Index,
		Point3df	fiberPoint1,
		Point3df	fiberPoint2,
		unsigned	meshClosestPoint,
		QuickMap **	polygonVerticesDistMap = 0 )

computeIntersectionPointNeighborhoodFiberSegmentAndMesh()

template<int D, class T>

bool constel::computeIntersectionPointNeighborhoodFiberSegmentAndMesh	(	const AimsTimeSurface< D, T > &	aimsMesh,
		const std::vector< std::set< unsigned > > &	polygonsByVertex_Index,
		Point3df	fiberPoint1,
		Point3df	fiberPoint2,
		unsigned	meshClosestPoint,
		std::vector< QuickMap > &	distanceThresholdNeighborhoodByVertex,
		QuickMap **	polygonVerticesDistMap_2ptr )

computeIntersectionSegmentPolygon()

bool constel::computeIntersectionSegmentPolygon	(	Point3df	segmentBeginPoint,
		Point3df	segmentEndPoint,
		std::vector< Point3df >	polygon,
		Point3df **	intersection_point = 0 )

connectedCommponent_isInside()

bool constel::connectedCommponent_isInside	(	const AimsSurfaceTriangle &	aimsMesh,
		const TimeTexture< short > &	region_tex,
		std::vector< std::size_t >	connectedCommponent_vertexIndex )

connectivitiesToSparseMatrix()

aims::SparseMatrix * constel::connectivitiesToSparseMatrix

(

const Connectivities &

conn

)

connectivitiesToSparseOrDenseMatrix()

aims::SparseOrDenseMatrix * constel::connectivitiesToSparseOrDenseMatrix

(

const Connectivities &

)

connMatrix()

Connectivities * constel::connMatrix	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		float	distthresh,
		float	wthresh,
		Motion	motion,
		bool	verbose = false )

Referenced by connMatrixNormalize().

connMatrixNormalize()

void constel::connMatrixNormalize	(	aims::SparseOrDenseMatrix &	connMatrix,
		bool	verbose = false )

References connMatrix().

connMatrixReducedFromRegion()

Connectivities * constel::connMatrixReducedFromRegion	(	Connectivities *	allMeshConnMatrix,
		const TimeTexture< short > &	seedRegionsTexture,
		int	seedRegionLabel,
		int	seedRegionLabelVertexNb,
		std::vector< std::size_t > **	seedVertexIndex = 0,
		bool	verbose = false )

connMatrixRegionExtract()

Connectivities * constel::connMatrixRegionExtract	(	const aims::SparseOrDenseMatrix &	allMeshConnMatrix,
		const TimeTexture< short > &	seedRegionsTexture,
		int	seedRegionLabel,
		std::size_t	seedRegionLabelVertexNb,
		std::vector< std::size_t > **	seedVertexIndex = 0,
		bool	verbose = false )

connMatrixRegionExtractTargetsRegroup()

Connectivities * constel::connMatrixRegionExtractTargetsRegroup	(	Connectivities *	allMeshConnMatrix,
		const TimeTexture< short > &	seedRegionsTexture,
		int	seedRegionLabel,
		const TimeTexture< short > &	targetRegionsTexture,
		int	targetRegionsNb,
		std::size_t	seedRegionLabelVertexNb,
		std::vector< std::size_t > **	seedVertexIndex,
		bool	verbose = false )

connMatrixRow_TO_TimeTexture_FLOAT()

TimeTexture< float > * constel::connMatrixRow_TO_TimeTexture_FLOAT

(

Connectivity *

conn_ptr

)

connMatrixSeedMesh_to_targetMeshTargets_regroup()

Connectivities * constel::connMatrixSeedMesh_to_targetMeshTargets_regroup	(	const aims::SparseOrDenseMatrix &	connMatrixToAllMesh,
		const TimeTexture< short > &	targetRegionsTex,
		int	targetRegionsNb,
		bool	verbose = false )

connMatrixSeedMeshRegions_to_targetMeshTargets_regroup()

Connectivities * constel::connMatrixSeedMeshRegions_to_targetMeshTargets_regroup	(	Connectivities *	connMatrixSeedMeshToTargetMesh_ptr,
		const TimeTexture< short > &	seedRegionsTexture,
		const TimeTexture< short > &	targetRegionsTex,
		int	targetRegionsNb,
		int	seedRegionsNb,
		bool	verbose = false )

connMatrixSeedMeshToTargetMesh()

Connectivities * constel::connMatrixSeedMeshToTargetMesh	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	aimsMesh1,
		const AimsSurfaceTriangle &	aimsMesh2,
		float	distthresh,
		float	wthresh,
		Motion	motion,
		bool	verbose = false )

connMatrixSeedRegion()

void constel::connMatrixSeedRegion	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		Motion	motion,
		const TimeTexture< short > &	seedRegionsTex,
		std::size_t	seedRegionLabel,
		std::string	connmatrix_filename,
		std::string	connTexture_filename )

connMatrixSeedRegionSmoothed()

void constel::connMatrixSeedRegionSmoothed	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		Motion	motion,
		const TimeTexture< short > &	seedRegionsTex,
		std::size_t	seedRegionLabel,
		float	distthresh,
		float	wthresh,
		std::string	connmatrix_filename,
		std::string	connTexture_filename = "",
		bool	logOption = false )

connMatrixSumRows() [1/2]

Connectivity * constel::connMatrixSumRows	(	Connectivities *	matrix_ptr,
		bool	verbose = false )

connMatrixSumRows() [2/2]

std::vector< double > * constel::connMatrixSumRows	(	const aims::SparseOrDenseMatrix &	matrix,
		bool	verbose = false )

connMatrixTargetsRegroup()

Connectivities * constel::connMatrixTargetsRegroup	(	Connectivities *	connMatrixToAllMesh,
		const TimeTexture< short > &	targetRegionsTexture,
		int	targetRegionsNb,
		bool	verbose = false )

connMatrixTargetsToTargets()

void constel::connMatrixTargetsToTargets	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		Motion	motion,
		const TimeTexture< short > &	targetRegionsTex,
		std::string	filename )

connMatrixToRois()

Connectivity * constel::connMatrixToRois	(	const Fibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		float	distthresh,
		float	wthresh,
		Motion	motion,
		bool	verbose = false )

densityTexture() [1/2]

TimeTexture< float > constel::densityTexture	(	Connectivities *	allMeshConnMatrix,
		std::vector< std::size_t >	VertexIndex,
		bool	verbose = false )

densityTexture() [2/2]

TimeTexture< float > constel::densityTexture	(	const aims::SparseOrDenseMatrix &	allMeshConnMatrix,
		std::vector< std::size_t >	VertexIndex,
		bool	verbose = false )

dist2()

float constel::dist2 ( const Point3df & p1, const Point3df & p2 )

inline

Definition at line 49 of file tildefs.h.

fillconnMatrix() [1/3]

void constel::fillconnMatrix	(	aims::SparseMatrix *	conn_ptr,
		aims::SparseMatrix *	conn_ptr2,
		QuickMap &	fiberExtremity1NeighMeshVertex,
		QuickMap &	fiberExtremity2NeighMeshVertex,
		double	connectivityThreshold,
		double	distanceThreshold,
		std::size_t	rowIndex_min,
		std::size_t	rowIndex_max = 0,
		unsigned	connectionLength = 1 )

fillconnMatrix() [2/3]

void constel::fillconnMatrix	(	aims::SparseMatrix *	conn_ptr,
		QuickMap &	fiberExtremity1NeighMeshVertex,
		QuickMap &	fiberExtremity2NeighMeshVertex,
		double	connectivityThreshold,
		double	distanceThreshold,
		unsigned	connectionLength = 1 )

fillconnMatrix() [3/3]

void constel::fillconnMatrix	(	Connectivities *	conn,
		QuickMap &	fiberExtremity1NeighMeshVertex,
		QuickMap &	fiberExtremity2NeighMeshVertex,
		double	connectivityThreshold,
		double	distanceThreshold,
		unsigned	connectionLength = 1 )

fillconnMatrixNoSmoothing()

void constel::fillconnMatrixNoSmoothing	(	Connectivities *	conn_ptr,
		QuickMap &	fiberExtremity1NeighMeshVertex,
		QuickMap &	fiberExtremity2NeighMeshVertex )

fillconnMatrixWithConnections() [1/2]

void constel::fillconnMatrixWithConnections	(	aims::SparseMatrix *	conn_ptr,
		const BundleConnections &	connections,
		double	connectivityThreshold,
		double	distanceThreshold,
		std::size_t	rowIndex_min = 0,
		std::size_t	rowIndex_max = 0,
		aims::SparseMatrix *	conn_ptr2 = 0 )

fillconnMatrixWithConnections() [2/2]

void constel::fillconnMatrixWithConnections	(	Connectivities *	conn_ptr,
		const BundleConnections &	connections,
		std::vector< double >	cortexConnectionsWeights,
		double	connectivityThreshold,
		double	distanceThreshold )

fillconnMatrixWithConnectionsPlusFloatLengthWeight()

void constel::fillconnMatrixWithConnectionsPlusFloatLengthWeight	(	Connectivities *	conn_ptr,
		const BundleConnections &	connections,
		double	connectivityThreshold,
		double	distanceThreshold,
		float	length_min,
		float	length_max,
		ConnectionsFloatLength &	connectionsLength )

fillconnMatrixWithConnectionsPlusLength()

void constel::fillconnMatrixWithConnectionsPlusLength	(	Connectivities *	conn_ptr,
		const BundleConnections &	connections,
		double	connectivityThreshold,
		double	distanceThreshold,
		unsigned	length_min,
		unsigned	length_max,
		ConnectionsLength &	connectionsLength )

fillconnMatrixWithConnectionsPlusLengthWeight()

void constel::fillconnMatrixWithConnectionsPlusLengthWeight	(	Connectivities *	conn_ptr,
		const BundleConnections &	connections,
		double	connectivityThreshold,
		double	distanceThreshold,
		unsigned	length_min,
		unsigned	length_max,
		ConnectionsLength &	connectionsLength )

fillNonSymetricConnMatrix()

void constel::fillNonSymetricConnMatrix	(	Connectivities *	conn_ptr,
		QuickMap &	fiberExtremity1NeighMeshVertex_rows,
		QuickMap &	fiberExtremity2NeighMeshVertex_cols,
		double	connectivityThreshold,
		double	distanceThreshold )

fillNonSymetricConnMatrixWithConnections()

void constel::fillNonSymetricConnMatrixWithConnections	(	Connectivities *	conn_ptr,
		const BundleConnections &	connections,
		double	connectivityThreshold,
		double	distanceThreshold )

firstBoundaryVertex()

std::size_t constel::firstBoundaryVertex	(	const AimsSurfaceTriangle &	aimsMesh,
		const TimeTexture< short > &	region_tex,
		std::vector< std::size_t >	connectedCommponent_vertexIndex )

fusionMeshFoldGraph_to_Texture()

TimeTexture< short > * constel::fusionMeshFoldGraph_to_Texture	(	const AimsSurfaceTriangle &	inAimsMesh,
		const Graph &	ROI_graph,
		float	distthresh,
		std::string	vertex_property = "aims_roi",
		std::string	label_name = "roi_label" )

fusionMeshROIs_to_Texture_S16()

TimeTexture< short > * constel::fusionMeshROIs_to_Texture_S16	(	const AimsSurfaceTriangle &	inAimsMesh,
		const Graph &	ROI_graph,
		float	distthresh,
		std::string	vertex_property = "aims_roi" )

hasVertexLabel()

bool constel::hasVertexLabel	(	const TimeTexture< short > &	labeled_tex,
		std::set< unsigned >	vertexIndex_set,
		int	label )

kdt_vertices()

KDTreeVertices constel::kdt_vertices ( const AimsSurfaceTriangle & mesh )

inline

get vertices vector with index for each vertex

Definition at line 33 of file tildefs.h.

meshDensityTexture() [1/2]

TimeTexture< float > constel::meshDensityTexture	(	Connectivities *	connMatrixToAllMesh_ptr,
		bool	verbose = false )

meshDensityTexture() [2/2]

TimeTexture< float > constel::meshDensityTexture	(	const aims::SparseOrDenseMatrix &	connMatrixToAllMesh,
		bool	verbose = false )

oneTargetDensityTargetsRegroupTexture() [1/2]

TimeTexture< float > * constel::oneTargetDensityTargetsRegroupTexture	(	const Connectivity *	lineMatrixToTargetRegions_ptr,
		const TimeTexture< short > &	targetRegionsTex,
		int	timestep )

oneTargetDensityTargetsRegroupTexture() [2/2]

TimeTexture< float > * constel::oneTargetDensityTargetsRegroupTexture	(	const std::vector< double > *	lineMatrixToTargetRegions_ptr,
		const TimeTexture< short > &	targetRegionsTex,
		int	timestep )

sparseMatrixDiffusionSmoothing() [1/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< aims::SparseMatrix >	matrix,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int16_t > &	patches,
		int32_t	patch )

sparseMatrixDiffusionSmoothing() [2/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< aims::SparseMatrix >	matrix,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int32_t > &	patches,
		int32_t	patch )

sparseMatrixDiffusionSmoothing() [3/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< aims::SparseOrDenseMatrix >	matrix,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int16_t > &	patches,
		int32_t	patch )

sparseMatrixDiffusionSmoothing() [4/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< aims::SparseOrDenseMatrix >	matrix,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int32_t > &	patches,
		int32_t	patch )

sparseMatrixDiffusionSmoothing() [5/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< Connectivities >	conn_ptr,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int16_t > &	patches,
		int32_t	patch )

sparseMatrixDiffusionSmoothing() [6/6]

void constel::sparseMatrixDiffusionSmoothing	(	carto::rc_ptr< Connectivities >	conn_ptr,
		const AimsTimeSurface< 3, Void > &	mesh,
		double	connectivityThreshold,
		double	distanceThreshold,
		const TimeTexture< int32_t > &	patches,
		int32_t	patch )

sparseMatrixGaussianSmoothing()

void constel::sparseMatrixGaussianSmoothing	(	aims::SparseMatrix &	matrix,
		const AimsSurfaceTriangle &	aimsMesh,
		float	distthresh,
		float	wthresh = 0.0 )

sparseMatrixGaussianSmoothingNormed()

void constel::sparseMatrixGaussianSmoothingNormed	(	aims::SparseMatrix &	matrix,
		const AimsSurfaceTriangle &	aimsMesh,
		float	distthresh,
		float	wthresh = 0.0 )

sparseMatrixToConnectivities() [1/3]

void constel::sparseMatrixToConnectivities	(	const aims::boost_sparse_matrix &	mat,
		Connectivities &	conn )

sparseMatrixToConnectivities() [2/3]

Connectivities * constel::sparseMatrixToConnectivities

(

const aims::SparseMatrix &

mat

)

sparseMatrixToConnectivities() [3/3]

void constel::sparseMatrixToConnectivities	(	const aims::SparseMatrix &	mat,
		Connectivities &	conn )

surfacePolygonsIndex()

template<int D, class T>

std::vector< std::set< unsigned > > constel::surfacePolygonsIndex

(

const AimsTimeSurface< D, T > &

surf

)

surfacePolygonsIndexByVerticesGroup()

std::set< unsigned > constel::surfacePolygonsIndexByVerticesGroup	(	const std::vector< std::set< unsigned > > &	polygonsByVertex_Index,
		std::vector< unsigned > &	vertexIndex )

texMeshAndBundles_to_BundlesGraph()

Graph * constel::texMeshAndBundles_to_BundlesGraph	(	const AimsSurfaceTriangle &	inAimsMesh,
		carto::rc_ptr< TimeTexture< short > >	tex,
		std::string	namesMode,
		std::string	bundlesFile_name,
		Motion	motion,
		const std::string &	BundlesNamesfile_name = std::string(),
		float	fibers_filter_proportion = 0.,
		int	texture_time_step = 0 )

texMeshAndBundles_to_BundlesGraph_WithIntersectionComputing()

Graph * constel::texMeshAndBundles_to_BundlesGraph_WithIntersectionComputing	(	const AimsSurfaceTriangle &	inAimsMesh,
		const TimeTexture< short > &	tex,
		std::string	bundlesFile_name,
		Motion	motion,
		std::string	BundlesNamesfile_name )

weightedConnMatrix()

Connectivities * constel::weightedConnMatrix	(	const WeightedFibers &	fibers,
		const AimsSurfaceTriangle &	inAimsMesh,
		Motion	motion,
		bool	verbose = false )

writeAimsFmtConnMatrix()

void constel::writeAimsFmtConnMatrix	(	Connectivities *	connMatrix_ptr,
		std::string	file_name,
		bool	verbose = false )

writeConnectivities()

void constel::writeConnectivities	(	const Connectivities &	conn,
		const std::string &	filename,
		bool	ascii = false )