CIFTI-2 shaped matrices manipulation tools. More...

#include <aims/sparsematrix/ciftitools.h>

Public Types
typedef std::map< std::string, int >	BrainStuctureToMeshMap

typedef std::vector< carto::rc_ptr< TimeTexture< int > > >	RoiTextureList

typedef std::vector< carto::rc_ptr< TimeTexture< float > > >	TextureList

Public Member Functions
	CiftiTools (carto::rc_ptr< SparseOrDenseMatrix > matrix, const BrainStuctureToMeshMap &smap=BrainStuctureToMeshMap())

	~CiftiTools ()

const carto::rc_ptr< SparseOrDenseMatrix >	matrix () const

carto::rc_ptr< SparseOrDenseMatrix >	matrix ()

void	setMatrix (carto::rc_ptr< SparseOrDenseMatrix > matrix)

const BrainStuctureToMeshMap &	brainStructureMap () const

BrainStuctureToMeshMap &	brainStructureMap ()

void	setBrainStructureMap (const BrainStuctureToMeshMap &smap)

RoiTextureList *	roiTextureFromDimension (int dim) const
	Get ROI information for a given matrix dimension. More...

TextureList *	expandedValueTextureFromDimension (int dim, const std::vector< int > &dim_indices_pos, TextureList *existing_tex_list=0) const
	Get matrix data in textures, possibly expanded to regions if needed. More...

int	valuesDimNum () const

std::string	dimensionType (int dim) const

carto::Object	getDimensionObject (int dim) const

template<typename T >
void	buildDimensionObjectFromLabelsTexture (int dim, const TimeTexture< T > &tex)
	buid a dimension object in a simple case where the matrix (probably non-cifti) is a reduced matrix over regions of a single mesh More...

void	getParcelsInfo (carto::Object cifti_info, RoiTextureList &) const

void	getBrainModelsInfo (carto::Object cifti_info, RoiTextureList &) const

void	getBrainModelsTexture (carto::Object cifti_info, TextureList &texlist, int dim, const std::vector< int > &dim_indices_pos) const

void	getParcelsTexture (carto::Object cifti_info, TextureList &texlist, int dim, const std::vector< int > &dim_indices_pos) const

std::list< std::string >	getBrainStructures (int dim, bool keepSurfaces=true, bool keepVoxels=true) const

std::vector< int >	getIndicesForBrainStructure (int dim, const std::string &struct_name) const
	Get the list of matrix indices corresponding to a given brain structure, on a given dimension. More...

std::vector< int >	getIndicesForSurfaceIndices (int dim, int surface_num, const std::vector< int > &roi_indices) const
	Get the list of matrix indices corresponding to a given region on a mesh, for a given dimension. More...

size_t	getBrainStructureMeshNumberOfNodes (int dim, const std::string &struct_name) const

bool	isMatchingSurface (int dim, const AimsTimeSurface< 3, Void > &mesh, std::list< std::string > &brainmodels, int &surf_index, int surf_hint=0) const
	checks if the given mesh matches a surface description in the given dimension of the Cifti matrix. More...

template<typename T >
bool	isMatchingTexture (int dim, const TimeTexture< T > &tex, std::list< std::string > &brainmodels, int &surf_index, int surf_hint=0) const
	checks if the given texture matches a surface description in the given dimension of the Cifti matrix. More...

bool	isMatchingSurfaceOrTexture (int dim, size_t nvertices, const carto::Object header, std::list< std::string > &brainmodels, int &surf_index, int surf_hint=0) const

Static Public Member Functions
static BrainStuctureToMeshMap	defaultBrainStructureToMeshMap ()
	Define the brain structure to mesh mapping: several meshes may be involved in CIFTI data mapping (typically a left hemisphere mesh and a right) More...

static int	valuesDimNum (carto::Object cifti_info)

static size_t	valuesDimSize (const SparseOrDenseMatrix &mat, int value_dim)

static std::string	dimensionType (carto::Object cifti_info, int dim)

static void	getLabelsInfo (carto::Object cifti_info, RoiTextureList &)

static void	getSeriesInfo (carto::Object cifti_info, RoiTextureList &)

Detailed Description

CIFTI-2 shaped matrices manipulation tools.

This class eases manipulation of matrices (SparseOrDenseMatrix) with CIFTI information in their header. CIFTI information specify the nature of data contained in the matrix, and can bring ROIs or parcellations information.

Mainly one can obtain textures to map matrix information onto meshes. Textures may be ROI information (label textures, TimeTexture<int>), or matrix values textures, possibly expanded onto brain regions (TimeTexture<float> in this case).

Definition at line 69 of file ciftitools.h.

Member Typedef Documentation

◆ BrainStuctureToMeshMap

typedef std::map<std::string, int> aims::CiftiTools::BrainStuctureToMeshMap

Definition at line 72 of file ciftitools.h.

◆ RoiTextureList

typedef std::vector<carto::rc_ptr<TimeTexture<int> > > aims::CiftiTools::RoiTextureList

Definition at line 73 of file ciftitools.h.

◆ TextureList

typedef std::vector<carto::rc_ptr<TimeTexture<float> > > aims::CiftiTools::TextureList

Definition at line 74 of file ciftitools.h.

Constructor & Destructor Documentation

◆ CiftiTools()

aims::CiftiTools::CiftiTools	(	carto::rc_ptr< SparseOrDenseMatrix >	matrix,
		const BrainStuctureToMeshMap &	smap = `BrainStuctureToMeshMap()`
	)

◆ ~CiftiTools()

aims::CiftiTools::~CiftiTools ( )

Member Function Documentation

◆ brainStructureMap() [1/2]

const BrainStuctureToMeshMap& aims::CiftiTools::brainStructureMap ( ) const

inline

Definition at line 86 of file ciftitools.h.

◆ brainStructureMap() [2/2]

BrainStuctureToMeshMap& aims::CiftiTools::brainStructureMap ( )

inline

Definition at line 88 of file ciftitools.h.

◆ buildDimensionObjectFromLabelsTexture()

template<typename T >

void aims::CiftiTools::buildDimensionObjectFromLabelsTexture	(	int	dim,
		const TimeTexture< T > &	tex
	)

buid a dimension object in a simple case where the matrix (probably non-cifti) is a reduced matrix over regions of a single mesh

◆ defaultBrainStructureToMeshMap()

static BrainStuctureToMeshMap aims::CiftiTools::defaultBrainStructureToMeshMap ( )

static

Define the brain structure to mesh mapping: several meshes may be involved in CIFTI data mapping (typically a left hemisphere mesh and a right)

◆ dimensionType() [1/2]

static std::string aims::CiftiTools::dimensionType	(	carto::Object	cifti_info,
		int	dim
	)

static

◆ dimensionType() [2/2]

std::string aims::CiftiTools::dimensionType ( int dim ) const

◆ expandedValueTextureFromDimension()

TextureList* aims::CiftiTools::expandedValueTextureFromDimension	(	int	dim,
		const std::vector< int > &	dim_indices_pos,
		TextureList *	existing_tex_list = `0`
	)		const

Get matrix data in textures, possibly expanded to regions if needed.

Parcels data will be expanded to all vertices of each parcel, etc. The resulting textures can be mapped on appropriate brain meshes.

Scalar or time series data will be stored in texture timepoints.

Labels data will be stored in separate textures because they provide possibly different colormaps. In this case the returned list will have the size meshes_number * labels_number, and will be stored in this order:

[ mesh0_label0, mesh1_label0, .. meshN_label0, mesh0_label1, .. meshN_label1, .. mesh0_label0, .. meshN_labelM ]

◆ getBrainModelsInfo()

void aims::CiftiTools::getBrainModelsInfo	(	carto::Object	cifti_info,
		RoiTextureList &
	)		const

◆ getBrainModelsTexture()

void aims::CiftiTools::getBrainModelsTexture	(	carto::Object	cifti_info,
		TextureList &	texlist,
		int	dim,
		const std::vector< int > &	dim_indices_pos
	)		const

◆ getBrainStructureMeshNumberOfNodes()

size_t aims::CiftiTools::getBrainStructureMeshNumberOfNodes	(	int	dim,
		const std::string &	struct_name
	)		const

◆ getBrainStructures()

std::list<std::string> aims::CiftiTools::getBrainStructures	(	int	dim,
		bool	keepSurfaces = `true`,
		bool	keepVoxels = `true`
	)		const

◆ getDimensionObject()

carto::Object aims::CiftiTools::getDimensionObject ( int dim ) const

◆ getIndicesForBrainStructure()

std::vector<int> aims::CiftiTools::getIndicesForBrainStructure	(	int	dim,
		const std::string &	struct_name
	)		const

Get the list of matrix indices corresponding to a given brain structure, on a given dimension.

◆ getIndicesForSurfaceIndices()

std::vector<int> aims::CiftiTools::getIndicesForSurfaceIndices	(	int	dim,
		int	surface_num,
		const std::vector< int > &	roi_indices
	)		const

Get the list of matrix indices corresponding to a given region on a mesh, for a given dimension.

◆ getLabelsInfo()

static void aims::CiftiTools::getLabelsInfo	(	carto::Object	cifti_info,
		RoiTextureList &
	)

static

◆ getParcelsInfo()

void aims::CiftiTools::getParcelsInfo	(	carto::Object	cifti_info,
		RoiTextureList &
	)		const

◆ getParcelsTexture()

void aims::CiftiTools::getParcelsTexture	(	carto::Object	cifti_info,
		TextureList &	texlist,
		int	dim,
		const std::vector< int > &	dim_indices_pos
	)		const

◆ getSeriesInfo()

static void aims::CiftiTools::getSeriesInfo	(	carto::Object	cifti_info,
		RoiTextureList &
	)

static

◆ isMatchingSurface()

bool aims::CiftiTools::isMatchingSurface	(	int	dim,
		const AimsTimeSurface< 3, Void > &	mesh,
		std::list< std::string > &	brainmodels,
		int &	surf_index,
		int	surf_hint = `0`
	)		const

inline

checks if the given mesh matches a surface description in the given dimension of the Cifti matrix.

Returns true if it matches, and in this case, brainmodels and surf_index are filled in accordingly. surf_hint specifies which surface (index) is tested first.

Definition at line 177 of file ciftitools.h.

◆ isMatchingSurfaceOrTexture()

bool aims::CiftiTools::isMatchingSurfaceOrTexture	(	int	dim,
		size_t	nvertices,
		const carto::Object	header,
		std::list< std::string > &	brainmodels,
		int &	surf_index,
		int	surf_hint = `0`
	)		const

◆ isMatchingTexture()

template<typename T >

bool aims::CiftiTools::isMatchingTexture	(	int	dim,
		const TimeTexture< T > &	tex,
		std::list< std::string > &	brainmodels,
		int &	surf_index,
		int	surf_hint = `0`
	)		const

inline

checks if the given texture matches a surface description in the given dimension of the Cifti matrix.

Returns true if it matches, and in this case, brainmodels and surf_index are filled in accordingly. surf_hint specifies which surface (index) is tested first.

Definition at line 191 of file ciftitools.h.

◆ matrix() [1/2]

const carto::rc_ptr<SparseOrDenseMatrix> aims::CiftiTools::matrix ( ) const

inline

Definition at line 81 of file ciftitools.h.

◆ matrix() [2/2]

carto::rc_ptr<SparseOrDenseMatrix> aims::CiftiTools::matrix ( )

inline

Definition at line 83 of file ciftitools.h.

◆ roiTextureFromDimension()

RoiTextureList* aims::CiftiTools::roiTextureFromDimension ( int dim ) const

Get ROI information for a given matrix dimension.

If the matrix dimension defines ROIs (parcels, brain regions), textures defining these regions are built.

If the matrix dimension defines labels, an empty texture will be created, with appropriate colormap information

If the matrix dimensions defines scalars or series, this function will probably not be useful.

◆ setBrainStructureMap()

void aims::CiftiTools::setBrainStructureMap ( const BrainStuctureToMeshMap & smap )

inline

Definition at line 90 of file ciftitools.h.

◆ setMatrix()

void aims::CiftiTools::setMatrix ( carto::rc_ptr< SparseOrDenseMatrix > matrix )

◆ valuesDimNum() [1/2]

int aims::CiftiTools::valuesDimNum ( ) const

◆ valuesDimNum() [2/2]

static int aims::CiftiTools::valuesDimNum ( carto::Object cifti_info )

static

◆ valuesDimSize()

static size_t aims::CiftiTools::valuesDimSize	(	const SparseOrDenseMatrix &	mat,
		int	value_dim
	)

static

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

aims/sparsematrix/ciftitools.h

Public Types

Public Member Functions

Static Public Member Functions

Detailed Description

Member Typedef Documentation

◆ BrainStuctureToMeshMap

◆ RoiTextureList

◆ TextureList

Constructor & Destructor Documentation

◆ CiftiTools()

◆ ~CiftiTools()

Member Function Documentation

◆ brainStructureMap() [1/2]

◆ brainStructureMap() [2/2]

◆ buildDimensionObjectFromLabelsTexture()

◆ defaultBrainStructureToMeshMap()

◆ dimensionType() [1/2]

◆ dimensionType() [2/2]

◆ expandedValueTextureFromDimension()

◆ getBrainModelsInfo()

◆ getBrainModelsTexture()

◆ getBrainStructureMeshNumberOfNodes()

◆ getBrainStructures()

◆ getDimensionObject()

◆ getIndicesForBrainStructure()

◆ getIndicesForSurfaceIndices()

◆ getLabelsInfo()

◆ getParcelsInfo()

◆ getParcelsTexture()

◆ getSeriesInfo()

◆ isMatchingSurface()

◆ isMatchingSurfaceOrTexture()

◆ isMatchingTexture()

◆ matrix() [1/2]

◆ matrix() [2/2]

◆ roiTextureFromDimension()

◆ setBrainStructureMap()

◆ setMatrix()

◆ valuesDimNum() [1/2]

◆ valuesDimNum() [2/2]

◆ valuesDimSize()