Namespaces
	convolutionfilter

	convolutionsubsampler

	DataManip

	internal

	knn

	meshdistance

	RoiDiff

	singlechannel

	SparseOrDenseMatrix

	SparseVolume

	strel

	SurfaceGenerator

	util

Classes
class	_convertedNiftiArrayValue

class	_convertedNiftiArrayValue< AimsVector< U, D > >

class	_convertedNiftiValue

class	_convertedNiftiValue< AimsVector< U, D > >

class	AffineLeastSquareEstimation

class	AffineTransformation3d

class	AimsApplication

class	AimsFastAllocationData

class	AimsGraphReader

class	AimsGraphWriter

struct	AimsGraphWriter_Private

class	AimsRoi

class	AnyTypeReader

class	AnyTypeReaderProcess

class	APCReader

class	ArgFormat

class	ArgHeader

class	ArgReader

class	ArgWriter

class	BarycenterCurvature

class	BaseDiffusionSmoother
	Base class for Heat diffusion. More...

class	BaseMaskedDiffusionSmoother

class	BaseScaleSpace

class	BBBMap

class	BckFormat

class	BckHeader

class	BckMapFormat

class	BckMapReader

class	BckMapWriter

class	BckReader

class	BckWriter

struct	bestPoint3d

class	Bifurcation

class	BlobMeasurements

class	BoixCurvature

class	BoixGaussianCurvature

class	Border

class	BorderFiller

class	BorderIterator

class	BoundingBox

class	BSpline
	Centered and scaled B-Spline function, evaluated at run time. More...

struct	BSplineOrder
	1D B-Spline functions centered on 0, recursively evaluated at run time. More...

struct	BSplineOrder< 0 >
	Specialization for 0 order B-Spline. More...

class	BucketBlobExtractor
	Blobs and watershed. More...

class	BucketMap

class	BucketMapGenerator

class	Bundle

class	BundleFormatReader

class	BundleInfo

class	BundleListener

class	BundleMotion

class	BundleProducer

class	BundleReader

class	BundleRegroup

class	BundleROISelect

class	BundleROISplit

class	Bundles

class	BundleSampler

class	BundlesFeatures

class	BundlesFusion

class	BundleSlicesToMesh

class	BundlesSlicer

class	BundlesSlicerListener

class	BundleToGraph

class	BundleToGraphWriter

class	BundleTransformer
	Apply a spatial transformation to fiber bundles. More...

class	BundleWriter

class	CausalSinglePoleIIRFilter
	Special case of Infinite Impulse Response filter. More...

class	CBFMap

class	CBVMap

class	ChannelReader

class	CiftiTools

class	ClassifStrategy

class	Clock

class	ClusterArgMaker

class	CoarseReader

class	ColorMap

class	ConeSamplable

class	ConnectedComponentEngine

class	ConnectedComponentEngine< AimsData< T >, AimsData< O > >

class	Connectivity

class	ConnectomistBundlesReader

class	ConvolutionFilter
	Convolution Filter. More...

class	ConvolutionSubSampler
	Convolution Filter. More...

class	CoordinatesFieldMeshInterpoler

struct	CoordinatesLess

struct	CoordinatesLess< T, 3 >

class	CoupledDiffusion2DSmoother

class	CoupledSmoother

class	CoupledSmoother< AimsData< T >, AimsData< T > >

class	CubicResampler
	Volume resampler using cubic interpolation. More...

class	Curvature

class	CurvatureFactory

class	CurveOrientation

class	CurveSelection

class	CutMesh

class	CutTexturedMesh

class	DecomposedAffineTransformation3d

class	DefaultAsciiItemReader

class	DefaultAsciiItemReader< AimsBucketItem< T > >

class	DefaultAsciiItemReader< DtiTensor >

class	DefaultAsciiItemReader< SparseMatrix >

class	DefaultAsciiItemReader< std::list< T > >

class	DefaultAsciiItemReader< std::vector< T > >

class	DefaultAsciiItemReader< Tensor >

class	DefaultAsciiItemReader< Trieder >

class	DefaultAsciiItemWriter

class	DefaultAsciiItemWriter< AimsBucketItem< T > >

class	DefaultAsciiItemWriter< DtiTensor >

class	DefaultAsciiItemWriter< SparseMatrix >

class	DefaultAsciiItemWriter< std::list< T > >

class	DefaultAsciiItemWriter< std::vector< T > >

class	DefaultAsciiItemWriter< Tensor >

class	DefaultAsciiItemWriter< Trieder >

class	DefaultBSwapItemReader

class	DefaultBSwapItemReader< AimsBucketItem< T > >

class	DefaultBSwapItemReader< AimsVector< T, D > >

class	DefaultBSwapItemReader< DtiTensor >

class	DefaultBSwapItemReader< SparseMatrix >

class	DefaultBSwapItemReader< std::list< T > >

class	DefaultBSwapItemReader< std::vector< T > >

class	DefaultBSwapItemReader< Tensor >

class	DefaultBSwapItemReader< Trieder >

class	DefaultBSwapItemWriter

class	DefaultBSwapItemWriter< AimsBucketItem< T > >

class	DefaultBSwapItemWriter< AimsVector< T, D > >

class	DefaultBSwapItemWriter< DtiTensor >

class	DefaultBSwapItemWriter< SparseMatrix >

class	DefaultBSwapItemWriter< std::list< T > >

class	DefaultBSwapItemWriter< std::vector< T > >

class	DefaultBSwapItemWriter< Tensor >

class	DefaultBSwapItemWriter< Trieder >

class	DefaultItemReader

class	DefaultItemReader< AimsBucketItem< T > >

class	DefaultItemReader< AimsVector< T, D > >

class	DefaultItemReader< DtiTensor >

class	DefaultItemReader< SparseMatrix >

class	DefaultItemReader< std::list< T > >

class	DefaultItemReader< std::vector< T > >

class	DefaultItemReader< Tensor >

class	DefaultItemReader< Trieder >

class	DefaultItemWriter

class	DefaultItemWriter< AimsBucketItem< T > >

class	DefaultItemWriter< AimsVector< T, D > >

class	DefaultItemWriter< DtiTensor >

class	DefaultItemWriter< SparseMatrix >

class	DefaultItemWriter< std::list< T > >

class	DefaultItemWriter< std::vector< T > >

class	DefaultItemWriter< Tensor >

class	DefaultItemWriter< Trieder >

class	DelayMap

class	DericheSmoother

class	DiffusionSmoother
	Heat diffusion with a volume of given datasource (Dirichlet conditions) More...

class	DirectBSplineFilter
	This filter uses a convolution with Spline basis functions. More...

class	DirectBSplineSubSampler
	Class excuting a spline-based subsampling. More...

class	DiscreteBSpline
	Discrete B-Splines B-Spline pre sampled only on integral values. More...

class	DiscreteU

class	DiscreteUB

class	DiscriminantAnalysis

class	DiscriminantAnalysisElement

class	Distance

class	DynamicStrategy

class	EcatFormat

class	EcatHeader

class	EcatPlugin

class	EcatReader

class	EcatSinoHeader

class	EcatSinoReader

class	EcatSinoWriter

class	EcatWriter

class	ElementFilteringFunction
	Base class for filtering functions applied in a structuring element. More...

class	ElementFilteringFunctionFactory
	Associates a string with a ElementFilteringFunction. More...

class	ElementFilteringImageAlgorithm

class	ExtractGreyLevelBlobs

class	ExtremaDifferenceFilter

class	ExtremaDifferenceSubSampling

class	FastBSpline
	Centered and scaled B-Spline function, evaluated at run time. More...

class	FastMarching
	Fast marching algorithm implementation, for images or buckets. More...

class	FdfFormat

class	FdfHeader

class	FdfParType

class	FdfPlugin

class	FdfProcPar

class	FdfReader

class	FfdTransformation
	FFD vector field deformation transform. More...

class	FiberInfo

class	FiberOversampler

class	FileFormat

class	FileFormatDictionary

class	FilteringFunctionInterface
	Pure virtual class: interface for filtering functions called by aims::FilteringImageAlgorithm and aims::SubSamplingImageAlgorithm. More...

class	FilteringImageAlgorithmInterface

struct	FilterType

class	Finder

class	FinderBckFormat

class	FinderEcatFormat

class	FinderFdfFormat

class	FinderFormat

class	FinderGenesisFormat

class	FinderGiftiFormat

class	FinderGraphFormat

class	FinderHieFormat

class	FinderImasFormat

class	FinderJpegFormat

class	FinderMeshFormat

class	FinderMniObjFormat

class	FinderPlyFormat

class	FinderSpmFormat

class	FinderTexFormat

class	FinderTiffFormat

class	FinderTriFormat

class	FinderTrmFormat

class	FinderVidaFormat

class	FinderWavefrontFormat

class	FiniteElementCurvature

class	FiniteElementSmoother

class	FoldArgOverSegment

class	FoldGraphAttributes
	Creation of cortical folds graph attributes. More...

class	GaborFilter

class	GenericWriter

class	GenesisFormat

class	GenesisHeader

class	GenesisReader

class	GeodesicPath
	Geodesic paths or distance maps, using the Dijkstra algorithm. More...

class	GeometricProperties

class	GiftiHeader

class	GiftiMeshFormat

class	GiftiPlugin

class	GiftiTextureFormat

class	GradientAdvection
	Propagate labels along a vector field. More...

class	GraphBundlesFormat

struct	GraphElementCode

class	GraphIterator

class	GraphManip

class	GraphVolumeFormat

class	GreyLevelBlob

class	GreyLevelBlobTools

class	HarmonicCageMeshResampler

class	Header

class	HieFormat

class	Hierarchy

class	HierarchyReader

class	HMap

class	IIRFilterBase
	Base class for separable infinite impulse response filters. More...

class	ImageAlgorithm
	aims::ImageAlgorithm class used to implement image algorithms More...

class	ImageAlgorithmInterface
	aims::ImageAlgorithmInterface is the interface for an image processing algorithm. More...

class	ImageAlgorithmSwitch
	aims::ImageAlgorithmSwitch switches between multichannel and monochannel `ImageAlgorithmInterface` More...

class	ImageAlgorithmSwitch< T, false >
	aims::ImageAlgorithmSwitch switch specialization for mono-channel `ImageAlgorithmInterface` More...

class	ImageAlgorithmSwitch< T, true >
	aims::ImageAlgorithmSwitch switch specialization for multi-channel `ImageAlgorithmInterface` More...

class	ImasFormat

class	ImasHeader

class	ImasSorDFormat

class	ImasVolFormat

class	Individuals

class	IntegrableOf

class	IntegratorOf

class	InterpolatedVolume
	Spline interpolation of volumes with simple accessors to interpolated values. More...

class	Interpolator

class	InverseBSplineFilter
	This filter uses an inverse B-Spline convolution function to transform a discrete signal to its spline representation. More...

class	IOObjectTypesDictionary

class	IOOptions

class	ItemReader

class	ItemWriter

class	IterativeClassification

class	JpegFormat

class	JpegHeader

class	JpegPlugin

class	JpegReader

class	JpegWriter

class	KmeansStrategy

class	LabelNodeFilter

class	LabelReader

class	LinearFilteringFunction
	Base class for linear filtering functions. More...

class	LinearFilteringFunctionFactory

class	LinearFilteringImageAlgorithm

class	LinearInterpolator

class	LinearResampler
	Volume resampler using linear (order 1) interpolation. More...

class	LowLevelArgReader

class	LowLevelArgWriter

class	LowLevelRoiReader

class	LowLevelStandardArgReader

class	LowLevelStandardArgWriter

struct	ltstr_blob

struct	ltstr_p3d

struct	ltstr_p3d< Point3d >

struct	ltstr_p3d< std::pair< Point3df, uint > >

class	MajorityFilter

class	MajorityLabelResampler
	Volume resampler using linear (order 1) interpolation, then selects the majority label in the neighbouring values. More...

class	MajoritySubSampling

class	MaskedDiffusionSmoother

class	MaskedDiffusionSmoother< T, AimsData< short > >
	Heat diffusion, with Dirichlet and Neumann border conditions. More...

class	MaskedDiffusionSmoother< T, std::vector< Point3df > >
	Heat diffusion, with Dirichlet and Neumann border conditions. More...

class	MaskIterator

class	MaskIteratorOf

class	MaskIteratorOf< AimsData< T > >

class	MaskIteratorOf< Graph >

class	MathUtil

class	MaxFilter

class	MaximumPoint

class	MaxSubSampling

class	MeanFilter

class	MeanSubSampling

class	MedianFilter

class	MedianResampler
	Volume resampler using linear (order 1) interpolation, then selects the median value in the neighbouring values. More...

class	MedianSubSampling

class	MeshFormat

class	MeshHeader

class	MeshInterpoler
	Triangular mesh and texture interpolation. More...

class	MeshProjection

class	MeshProjectionFactory

class	MeshReader

class	MeshToVoxelsResampler
	3D rasterization (voxelization) of a mesh O : AimsData<unsigned int> or BucketMap<Void> More...

class	MeshWriter

class	MinfFormat

class	MinFilter

class	MinSubSampling

class	MixtureOfPPCA

class	MniObjFormat

class	MniObjHeader

class	MorphoGreyLevel
	Grey-level mathematical morphology. More...

class	MotionedMaskIterator

class	MotionedRoiIterator

class	MotionedVolumeROILabelMap

class	MotionWriter

class	MovingAverageCascadeFilter
	Separable Cascade of Moving Average Filter. More...

class	MovingAverageCascadeKernel
	1D Cascade of Moving Average Kernel More...

class	MovingAverageCascadeSubSampler

class	MovingAverageFilter
	Separable Moving Average Filter. More...

class	MovingAverageKernel
	1D Moving Average Kernel More...

class	MovingAverageSubSampler

class	MRTrixBundleReader

class	MTTMap

struct	MultiChannelResamplerSwitch

struct	MultiChannelResamplerSwitch< false, T >

struct	MultiChannelResamplerSwitch< true, T >

class	NameNodeFilter

class	NearestNeighborResampler
	Volume resampler using nearest-neighbour interpolation. More...

class	NodeFilter

class	NotNullMeanFilter

class	NotNullMeanSubSampling

class	NotNullMedianFilter

class	NotNullMedianSubSampling

struct	PairCompare

class	Path

class	PcaStrategy

class	PerfusionAif

class	PerfusionAifAverage

class	PerfusionAifBest

class	PerfusionAifFactory

class	PerfusionAifLinearCorrection

class	PerfusionAifMatrix
	Class PerfusionAifMatrix. More...

class	PerfusionAifMatrixFactory

class	PerfusionAifMatrixStrategy

class	PerfusionAifNoCorrection

class	PerfusionAifPoints
	Class PerfusionAifPoints. More...

class	PerfusionAifSelection

class	PerfusionAifStrategy

class	PerfusionDeconvolution

class	PerfusionDeconvolutionFactory

class	PerfusionDeconvolutionStrategy

class	PerfusionFFTDeconvolution

class	PerfusionFit

class	PerfusionFitFactory

class	PerfusionFitGammaVariate

class	PerfusionFitStrategy

class	PerfusionGammaFit

class	PerfusionLinearFitGammaVariate

class	PerfusionMapBase

class	PerfusionMaps
	Class PerfusionMaps. More...

class	PerfusionMask
	class PerfusionMask More...

class	PerfusionNoFit

class	PerfusionNoSmoothing

class	PerfusionParameters

class	PerfusionPreInjection
	PerfusionPreInjection class. More...

class	PerfusionProcessing

class	PerfusionProcessingCenter

class	PerfusionQuantification
	Class PerfusionQuantification. More...

class	PerfusionSkip
	Class PerfusionSkip. More...

class	PerfusionSmoothing

class	PerfusionSmoothing2D

class	PerfusionSmoothing3D

class	PerfusionSmoothingBase

class	PerfusionSmoothingFactory

class	PerfusionSmoothingStrategy

class	PerfusionSmoothingT

class	PerfusionSplitVolume
	Perfusion class. More...

class	PerfusionSVDDeconvolution

class	PerfusionSVDFactory

class	PerfusionSVDInversion

class	PerfusionSVDStrategy

class	PerfusionSVDTikhonov

class	PerfusionSVDTikhonovGradient

class	PerfusionSVDTruncated

class	PeronaMalikSmoother

class	PlyFormat

class	PlyHeader

class	PlyPlugin

class	PlyReader

class	PlyWriter

struct	Point3dCompare

struct	Point3dfCompare

class	PointsDistribution
	Points repartition using forces in a given geometry (on a sphere for instance). More...

class	PointSetFeatures

class	PointsInImageFeatures

class	Polyline

class	PolylinePolynomialInterpolator

class	PovFormat

class	PovWriter

class	PpcaAnalyserElement

class	PrimalSketch

class	Primalsketch2graph

class	ProbabilisticPca

class	ProbabilisticPcaElement

class	Process

struct	ProcessInput

class	ProgressInfo

class	PythonHeader

class	QuadraticResampler
	Volume resampler using quadratic (order 2) interpolation. More...

class	QuarticResampler
	Volume resampler using quartic (order 4) interpolation. More...

class	Quaternion

class	QuinticResampler
	Volume resampler using quintic (order 5) interpolation. More...

class	Reader

class	ReaderAsObject

class	RealToRealFunctionTabulation

class	RegularBinnedHistogram
	Histogram container class, with a specified number of regular bins. More...

class	Resampler
	Resampling of data from a volume, applying a transformation. More...

class	ResamplerFactory

class	RigidLeastSquareEstimation

class	RigidTransformEstimation

class	RoiDiff

class	RoiFeatures

class	RoiGtm

class	RoiGtmReader

class	RoiGtmWriter
	Class for AimsRoiGtm writing operation. More...

class	RoiIterator

class	RoiIteratorOf

class	RoiIteratorOf< AimsData< T > >

class	RoiIteratorOf< Graph >

class	ROILabelMap

class	RoiSelector

class	RoiSelectorReader

class	RoiStats

class	RombergIntegratorOf

class	SaddlePoint

class	ScalarFeaturesProvider

class	ScalarSetFeatures

class	ScaledEncoding

class	ScaleLevel

class	ScaleLevel< AimsData< T >, AimsData< T > >

class	ScaleLevel< AimsSurface< D, Void >, Texture< T > >

class	ScaleSpace

class	ScaleSpace< AimsData< T >, AimsData< T > >

class	ScaleSpace< AimsSurface< D, Void >, Texture< T > >

class	ScaleSpaceBlob

class	ScannerConf

class	Selection

class	SelectionExpander

class	SelectionReader

class	SelectionSet

class	SelectionWriter

class	Selector

struct	SetCompare

class	Settings

class	SeventhOrderResampler
	Volume resampler using seventh-order interpolation. More...

class	SimiLeastSquareEstimation

class	SimpleBundlesSlicer

class	SimpleVoxelSampler

class	Sinogram

class	SixthOrderResampler
	Volume resampler using sixth-order interpolation. More...

class	SliceFormatHeader

class	Smoother

class	Smoother< AimsData< T >, AimsData< T > >

class	Smoother< AimsSurface< D, Void >, Texture< T > >

class	SomaIOAimsDataFormat

class	Spam

class	SpamBase

class	SpamFromLikelihood

class	SparseMatrix

class	SparseMatrixUtil

class	SparseOrDenseMatrix

class	SparseVolume

class	SparseVolume< BucketMap< T > >

class	SparseVolume< BucketMap< Void > >

class	SparseVolume< carto::Volume< T > >

struct	specifiedLabels

class	SphereSamplable

class	SplineFfd
	FFD vector field deformation transform. More...

class	SplinePyramid
	Pyramid of Interpolated Volumes. More...

class	SplinePyramidBuilder
	The method follows that of Under, Aldroubi & Eden, "The L2 Polynomial Spline Pyramid" in IEEE Transactions on Pattern Analysis and Machine Intelligence (1993) More...

class	SplineResampler
	B-Spline-based resampling. More...

class	SpmFormat

class	SpmHeader

class	SpmReader

class	SpmWriter

class	StandardReferentials

class	StDevFilter

class	StructuredConstVolume

class	StructuredVolume

class	StructuringElement

class	StructuringElementRef

class	StxFormat

class	SubSamplingImageAlgorithm
	aims::SubSamplingImageAlgorithm is the algorithm to subsample image. More...

class	SubSamplingPyramidBuilder

class	SumFilter

class	SumSubSampling

class	SurfaceGenerator

class	SurfaceManip

class	SymAllPoleIIRFilter
	Symmetric, all-pole, infinite impulse response Filter. More...

class	TabulBSpline
	Pre-computed B-Spline values In the "order 0" case, the array is not used (the analytical expression is too simple) More...

class	Tex2Graph

class	TexFormat

class	TexHeader

class	TexReader

class	TextureSmoothing

class	TexWriter

class	TiffFormat

class	TiffHeader

class	TiffPlugin

class	TiffReader

class	TiffWriter

class	TrackvisBundleReader

class	TransformationChain3d

class	TransformLeastSquareEstimation

class	TranslationLeastSquareEstimation

class	TrapezeIntegratorOf

class	TriFormat

class	TriHeader

class	TrilinearFfd
	FFD vector field deformation transform. More...

class	TriReader

class	TriWriter

class	TrmFormat

class	TrmHeader

class	TTPMap

class	VarFilter

class	VidaFormat

class	VidaHeader

class	VidaPlugin

class	VidaReader

class	VidaWriter

class	VolumeFormat

class	VolumeRefFormat

class	VolumeROILabelMap

class	VoxelSampler

class	Vrml1Format

class	WavefrontHeader

class	WavefrontMeshFormat

class	WavefrontMeshReader

class	WavefrontMeshWriter

class	WavefrontMeshWriter< D, Void >

class	Writer

class	Writer< aims::FfdTransformation >
	FFD vector field transformation writer. More...

Typedefs
typedef CoordinatesLess< Point3d, 3 >	BucketMapLess

typedef carto::rc_ptr< Bundle >	RBundle

typedef carto::rc_ptr< BundleListener >	RBundleListener

typedef carto::rc_ptr< BundleProducer >	RBundleProducer

typedef aims::Polyline::Point_t	FiberPoint

typedef std::vector< aims::FiberPoint >	Fiber

typedef std::vector< Fiber >	Fibers

typedef std::vector< Fibers >	BundlesSet

typedef std::map< std::string, std::map< std::string, GraphElementCode > >	GraphElementTable

typedef IntegrableOf< float >	Integrable

typedef IntegratorOf< float >	Integrator

typedef RombergIntegratorOf< float >	RombergIntegrator

typedef TrapezeIntegratorOf< float >	TrapezeIntegrator

typedef carto::AllocatorContext	Allocator

typedef boost::numeric::ublas::sparse_matrix< double >	boost_sparse_matrix

typedef boost::numeric::ublas::sparse_vector< double >	boost_sparse_vector

typedef ProgressInfo< double, double >	Progression

typedef std::set< Point3df, Point3dfCompare >	Point3dfSet

typedef std::map< Point3df, Point3dfSet, Point3dfCompare >	Point3dfNeigh

typedef std::map< unsigned, std::set< std::pair< unsigned, float > > >	LaplacianWeights

Enumerations
enum	DistanceType { NORM1, NORM2, NORM2SQR, INFNORM }

enum	PrimalsketchDataType { SURFACE, IMAGE }

enum	PrimalSketchEvents { APPEAR = 1, DISAPPEAR, MERGE, SPLIT, COMPLEX }

Functions
void	AimsConnectedComponent (AimsData< T > &data, aims::Connectivity::Type connectivity, std::map< T, size_t > &valids, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)

void	AimsConnectedComponent (AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)

void	AimsConnectedComponent (BucketMap< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minSize=0, size_t maxSize=0, size_t numMax=0, bool verbose=true)

void	AimsConnectedComponent (AimsBucket< Void > &component, const AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)

void	AimsConnectedComponent (AimsBucket< Void > &component, const BucketMap< T > &data, Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)

AimsData< int16_t >	AimsLabeledConnectedComponent (AimsBucket< Void > &component, const AimsData< T > &data, aims::Connectivity::Type connectivity, const T &backgrnd=0, bool bin=true, size_t minsize=0, size_t maxSize=0, size_t maxcomp=0, bool verbose=true)

AimsData< T >	diag (const AimsData< T > &thing)

AimsData< T >	undiag (const AimsData< T > &thing)

AimsData< T >	transpose (const AimsData< T > &thing)

void	incSorting (AimsData< T > &thing)

void	decSorting (AimsData< T > &thing)

AimsData< int32_t >	incOrder (const AimsData< T > &thing)

AimsData< int32_t >	decOrder (const AimsData< T > &thing)

bool	hasSameDim (const AimsData< T > &v1, const AimsData< T > &v2)

bool	hasSameSize (const AimsData< T > &v1, const AimsData< T > &v2)

AimsData< T >	triInf (const AimsData< T > &thing)

AimsData< T >	triSup (const AimsData< T > &thing)

std::string	aimsVersion ()

AIMSDATA_API T	byteswap (const T &x)

AIMSDATA_API T	byteswap16 (const T &x)

AIMSDATA_API T	byteswap32 (const T &x)

AIMSDATA_API T	byteswap64 (const T &x)

AIMSDATA_API short	byteswap (const short &x)

AIMSDATA_API unsigned short	byteswap (const unsigned short &x)

AIMSDATA_API int	byteswap (const int &x)

AIMSDATA_API unsigned int	byteswap (unsigned int x)

AIMSDATA_API float	byteswap (const float &x)

GenesisReader< T > &	operator>> (GenesisReader< T > &reader, AimsData< T > &thing)

AIMSDATA_API HierarchyReader &	operator>> (HierarchyReader &, Tree &)

HierarchyReader &	operator>> (HierarchyReader &reader, Hierarchy &thing)

MotionWriter &	operator<< (MotionWriter &writer, const AffineTransformation3d &thing) __attribute__((__deprecated__("OBSOLETE")))

AIMSDATA_API PovWriter< D, T > &	operator<< (PovWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)

bool	canEncodeAsScaledS16 (const carto::Volume< T > &vol, float &slope, float &offset, bool enableoffset=true, double *maxerr=0)

bool	canEncodeAsScaledS16 (const carto::Volume< float > &vol, float &slope, float &offset, bool enableoffset, double *)

bool	canEncodeAsScaledS16 (const carto::Volume< double > &vol, float &slope, float &offset, bool enableoffset, double *)

SpmReader< T > &	operator>> (SpmReader< T > &reader, AimsData< T > &thing)

SpmWriter< T > &	operator<< (SpmWriter< T > &writer, const AimsData< T > &thing)

void	spmAttributesConverter (carto::Object header)

void	spmAttributesConverter (carto::GenericObject &header)

aims::GenericWriter &	operator<< (aims::GenericWriter &writer, const T &thing)

aims::Writer< T > &	operator<< (aims::Writer< T > &writer, const T &thing)

AIMSDATA_API MeshReader< D, T > &	operator>> (MeshReader< D, T > &reader, AimsTimeSurface< D, T > &thing)

AIMSDATA_API MeshWriter< D, T > &	operator<< (MeshWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)

TriReader &	operator>> (TriReader &reader, AimsSurfaceTriangle &thing)

TriWriter &	operator<< (TriWriter &writer, AimsSurfaceTriangle &thing)

AIMSDATA_API TexReader< T > &	operator>> (TexReader< T > &r, TimeTexture< T > &thing)

AIMSDATA_API ItemWriter< T > &	operator>> (ItemWriter< T > &w, TimeTexture< T > &thing)

WavefrontMeshWriter< D, T > &	operator<< (WavefrontMeshWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)

WavefrontMeshReader< D, T > &	operator>> (WavefrontMeshReader< D, T > &reader, AimsTimeSurface< D, T > &thing)

int	textureMax (const TimeTexture< short > &intex)

int	textureMin (const TimeTexture< short > &intex)

std::map< short, size_t > *	labelsHistogram (const TimeTexture< short > &intex, int maxlabel=32767, int minlabel=-32768, bool verbose=false)

carto::VolumeRef< AimsRGBA >	giftiColormap (const carto::Object header)

carto::VolumeRef< AimsRGBA >	giftiColormap (const TimeTexture< T > &texture)

BucketMap< Void > *	mask (const BucketMap< Void > &src, const BucketMap< Void > &m, bool intersect=true)

BucketMap< Void > *	maskWithVolume (const BucketMap< Void > &src, const carto::rc_ptr< carto::Volume< T > > m, const T &val=0, bool insideval=false)

carto::rc_ptr< Interpolator >	getLinearInterpolator (const std::string &)

carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< T > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint8_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int8_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint16_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int16_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< short > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< uint32_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< int32_t > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< float > &)

template carto::rc_ptr< Interpolator >	getLinearInterpolator (const AimsData< double > &)

Quaternion	operator* (const Quaternion &a, const Quaternion &b)

void	floodFill (carto::Volume< T > &vol, const Point3d &pos, T value, Connectivity::Type connectivity=Connectivity::CONNECTIVITY_18_XYZ, T tolerence=0, bool verbose=false)

carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName)

carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler)

carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data)

carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler)

carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, const Motion &motion)

carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)

carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, const Motion &motion)

carto::rc_ptr< MaskIterator >	getMaskIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)

carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())

carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())

carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())

carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, const Motion &)

carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &)

carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, const Motion &motion)

carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, const Motion &motion)

carto::rc_ptr< RoiIterator >	getRoiIterator (const AimsData< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)

carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, carto::rc_ptr< VoxelSampler > voxelSampler, const Motion &motion)

aims::SparseMatrix	operator+ (const aims::SparseMatrix &thing)

aims::SparseMatrix	operator- (const aims::SparseMatrix &thing)

aims::SparseMatrix	operator+ (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)

aims::SparseMatrix	operator- (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)

aims::SparseMatrix	operator* (const aims::SparseMatrix &thing1, const aims::SparseMatrix &thing2)

std::vector< double >	operator* (const aims::SparseMatrix &thing1, const std::vector< double > &thing2)

aims::SparseMatrix	operator* (const aims::SparseMatrix &thing1, const double &thing2)

aims::SparseMatrix	operator/ (const aims::SparseMatrix &thing1, const double &thing2)

aims::SparseOrDenseMatrix	operator- (const aims::SparseOrDenseMatrix &thing)

aims::SparseOrDenseMatrix	operator+ (const aims::SparseOrDenseMatrix &thing1, const aims::SparseOrDenseMatrix &thing2)

aims::SparseOrDenseMatrix	operator- (const aims::SparseOrDenseMatrix &thing1, const aims::SparseOrDenseMatrix &thing2)

aims::SparseOrDenseMatrix	operator* (const aims::SparseOrDenseMatrix &thing1, const double &thing2)

aims::SparseOrDenseMatrix	operator/ (const aims::SparseOrDenseMatrix &thing1, const double &thing2)

void	transformBoundingBox (const AffineTransformation3d &AffineTransformation3d, const Point3df &pmin1, const Point3df &pmax1, Point3df &pmin2, Point3df &pmax2)

AffineTransformation3d	operator* (const AffineTransformation3d &affineTransformation3d1, const AffineTransformation3d &affineTransformation3d2)

void	minmax (const ObjectType &, ValueType &min, ValueType &max)

void	minmax (const AimsData< ValueType > &volume, ValueType &min, ValueType &max)

void	minmax (const carto::Volume< ValueType > &volume, ValueType &min, ValueType &max)

void	minmax (const carto::rc_ptr< carto::Volume< ValueType > > &volume, ValueType &min, ValueType &max)

void	minmax (const carto::VolumeRef< ValueType > &volume, ValueType &min, ValueType &max)

std::ostream &	operator<< (std::ostream &out, aims::ProgressInfo< T1, T2 > &progression)

EcatReader< T > &	operator>> (EcatReader< T > &reader, AimsData< T > &thing)

EcatSinoReader< T > &	operator>> (EcatSinoReader< T > &reader, std::vector< Sinogram< T > > &thing)

EcatSinoWriter< T > &	operator<< (EcatSinoWriter< T > &writer, Sinogram< T > &thing)

EcatSinoWriter< T > &	operator<< (EcatSinoWriter< T > &writer, const std::vector< Sinogram< T > > &thing)

EcatWriter &	operator<< (EcatWriter &writer, const AimsData< short > &thing)

EcatWriter &	operator<< (EcatWriter &writer, const AimsData< float > &thing)

VidaReader< T > &	operator>> (VidaReader< T > &reader, AimsData< T > &thing)

VidaWriter &	operator<< (VidaWriter &writer, const AimsData< short > &thing)

VidaWriter &	operator<< (VidaWriter &writer, const AimsData< float > &thing)

PlyReader< D, T > &	operator>> (PlyReader< D, T > &reader, AimsTimeSurface< D, T > &thing)

PlyWriter< D, T > &	operator<< (PlyWriter< D, T > &writer, const AimsTimeSurface< D, T > &thing)

AIMSDATA_API FdfReader< T > &	operator>> (FdfReader< T > &, AimsData< T > &)

JpegReader< T > &	operator>> (JpegReader< T > &reader, AimsData< T > &thing)

JpegWriter< T > &	operator<< (JpegWriter< T > &writer, const AimsData< T > &thing)

TiffReader< T > &	operator>> (TiffReader< T > &reader, AimsData< T > &thing)

TiffWriter< T > &	operator<< (TiffWriter< T > &writer, const AimsData< T > &thing)

U	convertedNiftiValue (void *data, int index, int dtype)

U	convertedNiftiArrayValue (void *data, int index, int dtype, size_t size)

std::string	niftiDataType (int dt)

int	niftiIntDataType (const std::string &typecode)

std::string	giftiTextureDataType (int dtype, int &ndim, int *dims, int intent, int &ntime)

AIMSDATA_API REAL	AimsLagrangeInterpolationOf (const AimsData< REAL > &xa, const AimsData< REAL > &ya, REAL x, REAL *dy)

float	AimsLagrangeInterpolation (const AimsData< float > &xa, const AimsData< float > &ya, float x, float *dy)

T	sqr (const T &x)

T	cub (const T &x)

float	sgn (const T &x)

T	absdiff (const T &x, const T &y)

AimsRGB	absdiff (const AimsRGB &x, const AimsRGB &y)

AimsRGBA	absdiff (const AimsRGBA &x, const AimsRGBA &y)

template<typename T >
BucketMap< Void > *	downPath (const BucketMap< T > &region, const Point3d &pos)

template BucketMap< Void > *	downPath (const BucketMap< float > &region, const Point3d &pos)

float	fiberDistance (FiberPoint f1, FiberPoint f2, int &fiberSize1, int &fiberSize2)

float	fiberDistanceMax (FiberPoint f1, FiberPoint f2, int &fiberSize1, int &fiberSize2)

float	fiberDistance (std::vector< Point3df > &f1, std::vector< Point3df > &f2)

float	fiberDistanceMax (std::vector< Point3df > &f1, std::vector< Point3df > &f2)

float	getClosestFiberPointDist (Point3df &p1, FiberPoint *f2, Point3df &pMin, int &fiberSize2)

float	getClosestFiberPointDist (Point3df &p1, std::vector< Point3df > &f2, Point3df &pMin)

float	fiberDistanceMaxDistCorrespPoints (FiberPoint f1, FiberPoint f2, int &fiberSize1)

float	fiberDistanceMaxDistCorrespPoints (std::vector< Point3df > &f1, std::vector< Point3df > &f2)

float	calculateMinFibersLength (FiberPoint f1, FiberPoint f2, int &fiberSize1, int &fiberSize2)

float	calculateMinFibersLength (std::vector< Point3df > &f1, std::vector< Point3df > &f2)

float	fiberDistanceMaxDistCorrespPointsNormByMinLength (FiberPoint f1, FiberPoint f2, float normFactor, int &fiberSize1, int &fiberSize2)

float	fiberDistanceMaxDistCorrespPointsNormByMinLength (std::vector< Point3df > &f1, std::vector< Point3df > &f2, float normFactor)

float	fiberAffinity (std::vector< Point3df > &f1, std::vector< Point3df > &f2, float var)

float	fiberAffinityMax (std::vector< Point3df > &f1, std::vector< Point3df > &f2, float var)

float	fiberAffinityMaxDistCorrespPoints (std::vector< Point3df > &f1, std::vector< Point3df > &f2, float var)

float	fiberAffinityMaxDistCorrespPointsNormByMinLength (std::vector< Point3df > &f1, std::vector< Point3df > &f2, float var, float normFactor)

float	fiberAffinity (FiberPoint f1, FiberPoint f2, float var, int &fiberSize1, int &fiberSize2)

float	fiberAffinityMax (FiberPoint f1, FiberPoint f2, float var, int &fiberSize1, int &fiberSize2)

float	fiberAffinityMaxDistCorrespPoints (FiberPoint f1, FiberPoint f2, float var, int &fiberSize1, int &fiberSize2)

float	fiberAffinityMaxDistCorrespPointsNormByMinLength (FiberPoint f1, FiberPoint f2, float var, float normFactor, int &fiberSize1, int &fiberSize2)

RoiSelectorReader &	operator>> (RoiSelectorReader &, Tree &)

RoiSelectorReader &	operator>> (RoiSelectorReader &reader, RoiSelector &thing)

RoiGtmReader &	operator>> (RoiGtmReader &, RoiGtm &)

void	makeLaplacianMatrix (const LaplacianWeights &weights, LaplacianWeights &lmat, float dt)

LaplacianWeights *	sparseMult (const LaplacianWeights &in1, const LaplacianWeights &in2, float sparseThresh=0)

template<typename T >
void	applyLaplacianMatrix (const std::vector< T > &inittex, std::vector< T > &outtex, const LaplacianWeights &lapl)

void	laplacianMatrixThreshold (LaplacianWeights &lmat, float threshold)

LaplacianWeights *	makeLaplacianSmoothingCoefficients (const LaplacianWeights &weights, unsigned niter, float dt, float sparseThresh=0)
	Compute Laplacian smoothing coefficients matrix for niter smoothing iterations. More...

void	distancesFromMesh (const AimsSurfaceTriangle &mesh, std::vector< AimsVector< uint, 2 > > &edges, std::vector< double > &weights)

int	meshWatershed (const AimsSurfaceTriangle &mesh, const std::vector< double > &field, std::vector< int > &idx, std::vector< int > &depth, std::vector< int > &major, std::vector< int > &label, double threshold)
	If I understand: More...

int	meshWatershed (const AimsSurfaceTriangle &mesh, const TimeTexture< double > &field, TimeTexture< int > &idx, TimeTexture< int > &depth, TimeTexture< int > &major, TimeTexture< int > &label, double threshold)

int	meshBlobsBifurcation (const AimsSurfaceTriangle &mesh, const std::vector< double > &field, std::vector< int > &idx, std::vector< double > &height, std::vector< int > &father, std::vector< int > &label, double th)
	Blobs labeling and bifurcations. More...

int	meshBlobsBifurcation (const AimsSurfaceTriangle &mesh, const TimeTexture< double > &field, TimeTexture< int > &idx, TimeTexture< double > &height, TimeTexture< int > &father, TimeTexture< int > &label, double th)

void	blobsHeights (const AimsSurfaceTriangle &mesh, const std::vector< double > &field, const std::vector< int > &watershedlabels, std::vector< int > &junctions)

template<typename T >
AimsData< short > *	GetSSBlobImage (PrimalSketch< AimsData< T >, AimsData< T > > *sketch)

template<int D, class T >
TimeTexture< float >	GetSSBlobTexture (PrimalSketch< AimsSurface< D, Void >, Texture< T > > *sketch)

template<int D, class T >
AimsSurfaceTriangle *	GetSSBlobMesh (PrimalSketch< AimsSurface< D, Void >, Texture< T > > *sketch)

template<typename T >
AimsBucket< Void > *	GetSSBlobBucket (PrimalSketch< AimsData< T >, AimsData< T > > *sketch)

template<int D, class T >
AimsSurfaceTriangle *	GetSSBlobTore (PrimalSketch< AimsSurface< D, Void >, Texture< T > > *sketch)

template<typename Geom , typename Text >
void	AddBlobsToPSGraph (PrimalSketch< Geom, Text > sketch, Graph graph)

template<typename T >
void	AddBlobsToPSGraph (PrimalSketch< AimsData< T >, AimsData< T > > sketch, Graph graph)

template<int D, class T >
void	AddBlobsToPSGraph (PrimalSketch< AimsSurface< D, Void >, Texture< T > > sketch, Graph graph)

template<int D, class T >
AimsSurfaceTriangle *	GetSSBlobMesh (PrimalSketch< AimsSurface< D, Void >, Texture< T > > sketch, AimsSurfaceTriangle mesh)

template<typename T >
AimsBucket< Void > *	GetSSBlobMeshBucket (AimsSurfaceTriangle *mesh)

template<typename T >
SplinePyramid	buildSplinePyramid (const carto::VolumeRef< T > &vol, unsigned order, unsigned factor=2)
	FUNCTORS. More...

template<typename T >
SplinePyramid	buildSplinePyramid (const carto::VolumeRef< T > &vol, unsigned order, const Point4du &factor)

template<typename T >
SplinePyramid	buildSplinePyramid (const carto::VolumeRef< T > &vol, unsigned order, const std::vector< Point4du > &factor)

template<typename T >
SplinePyramid	cubicSplinePyramid (const carto::VolumeRef< T > &vol, unsigned factor=2)

template<typename T >
SplinePyramid	cubicSplinePyramid (const carto::VolumeRef< T > &vol, const Point4du &factor)

template<typename T >
SplinePyramid	cubicSplinePyramid (const carto::VolumeRef< T > &vol, const std::vector< Point4du > &factor)

template<class T >
class	__attribute__ ((__deprecated__)) MaskLinearResampler
	Volume resampler using linear (order 1) interpolation. More...

int	mirrorCoeff (int i, int size)
	This method returns a mirror index when needed. More...

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MedianFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MedianFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (NotNullMedianFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (NotNullMedianFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MeanFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MeanFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (NotNullMeanFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (NotNullMeanFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MinFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MinFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MaxFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MaxFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MajorityFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (MajorityFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (ExtremaDifferenceFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (ExtremaDifferenceFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (SumFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (SumFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (VarFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (VarFilterFunc, AimsRGBA)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (StDevFilterFunc, AimsRGB)

	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (StDevFilterFunc, AimsRGBA)

template<typename VoxelType >
VoxelType	multichannelfiltervalues_nonlin (const ElementFilteringFunction< typename VoxelType::ChannelType > &f, const carto::VolumeRef< VoxelType > &volume)
	Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...) More...

template<typename VoxelType >
VoxelType	multichannelfiltervalues_nonlin (const ElementFilteringFunction< typename VoxelType::ChannelType > &f, const carto::VolumeRef< VoxelType > &volume, const carto::rc_ptr< StructuringElement > &se)
	Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...) More...

void	setKernel ()

	AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE (GaborFilterFunc, AimsRGB)

	AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE (GaborFilterFunc, AimsRGBA)

template<typename VoxelType >
VoxelType	multichannelfiltervalues_lin (const LinearFilteringFunction< typename VoxelType::ChannelType > &f, const carto::VolumeRef< VoxelType > &volume)
	Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...) More...

template<int D>
void	transformMesh (AimsTimeSurface< D, Void > &mesh, const soma::Transformation3d &direct_transformation)
	Apply a spatial transformation to a mesh (AimsTimeSurface) More...

carto::rc_ptr< BucketMap< Void > >	transformBucketDirect (const BucketMap< Void > &bck, const soma::Transformation3d &direct_transformation, Point3df vs=Point3df(0., 0., 0.))
	Apply a spatial transformation to a BucketMap. More...

carto::rc_ptr< BucketMap< Void > >	resampleBucket (const BucketMap< Void > &bck, const soma::Transformation3d &direct_transformation, const soma::Transformation3d &inverse_transformation, Point3df vs=Point3df(0., 0., 0.), bool also_pushforward=true)
	Apply a spatial transformation to a BucketMap. More...

void	transformGraph (Graph &graph, const soma::Transformation3d &direct_transformation, const soma::Transformation3d *inverse_transformation, Point3df vs=Point3df(0., 0., 0.))
	Apply a spatial transformation to all objects contained in a Graph. More...

template<int D>
void	transformMesh (AimsTimeSurface< D, Void > &mesh, const Transformation3d &direct_transformation)

template<typename T >
carto::VolumeRef< T >	clipDynamic (const carto::VolumeRef< T > &in, bool flatten_mask=true, float pct_kept=1.)
	clipDynamic More...

template<typename T >
carto::VolumeRef< T >	clipDynamic (carto::VolumeRef< T > &in, bool flatten_mask=true, float pct_kept=1., bool in_place=true)

template<typename T >
carto::VolumeRef< T >	clip (const carto::VolumeRef< T > &in, const T &min, const T &max)
	clip More...

template<typename T >
carto::VolumeRef< T >	clip (carto::VolumeRef< T > &in, const T &min, const T &max, bool in_place=false)

Variables
const int	BACKGROUND = 0

double	_sigma

double	_theta

double	_lambda

double	_psi

double	_gamma

bool	_real

int	_nstd

bool	_init

std::vector< int >	_amplitude

std::vector< float >	_voxelsize

carto::VolumeRef< double >	_kernel

Typedef Documentation

◆ LaplacianWeights

typedef std::map<unsigned, std::set< std::pair<unsigned,float> > > aims::LaplacianWeights

Definition at line 131 of file curv.h.

◆ Point3dfNeigh

typedef std::map<Point3df,Point3dfSet,Point3dfCompare> aims::Point3dfNeigh

Definition at line 120 of file stlsort.h.

◆ Point3dfSet

typedef std::set<Point3df,Point3dfCompare> aims::Point3dfSet

Definition at line 119 of file stlsort.h.

Enumeration Type Documentation

◆ DistanceType

enum aims::DistanceType

Enumerator
NORM1
NORM2
NORM2SQR
INFNORM

Definition at line 47 of file kmeansstrategy.h.

◆ PrimalsketchDataType

enum aims::PrimalsketchDataType

Enumerator
SURFACE
IMAGE

Definition at line 52 of file primalSketch.h.

◆ PrimalSketchEvents

enum aims::PrimalSketchEvents

Enumerator
APPEAR
DISAPPEAR
MERGE
SPLIT
COMPLEX

Definition at line 47 of file scaleSpaceBlob.h.

Function Documentation

◆ attribute()

template<class T >

class aims::__attribute__ ( (__deprecated__) )

Volume resampler using linear (order 1) interpolation.

Deprecated:: {This resampler shows unreliable behaviour: depending of the platform it does not always resample the last element along each axis correctly. Also, it uses some clever optimizations that do not check for overflow. If you need such a masked resampler, please consider contributing a fixed version.}

This resampler will consider input voxels that are equal to -32768 (hard-coded) as masked. The mask value (-32768) will always be returned for any interpolation involving a masked voxel.

The default background value for this resampler is -32768 (same as the mask value).

The resampling API is described in the base class, Resampler.

Definition at line 64 of file masklinresampler.h.

References CARTO_OVERRIDE, static_assert, and verbose.

◆ AddBlobsToPSGraph() [1/3]

template<typename Geom , typename Text >

void aims::AddBlobsToPSGraph	(	PrimalSketch< Geom, Text > *	sketch,
		Graph *	graph
	)

Definition at line 359 of file primalSketchUtil.h.

Referenced by aims::Primalsketch2graph< Geom, Text >::DoIt().

◆ AddBlobsToPSGraph() [2/3]

template<typename T >

void aims::AddBlobsToPSGraph	(	PrimalSketch< AimsData< T >, AimsData< T > > *	sketch,
		Graph *	graph
	)

Definition at line 365 of file primalSketchUtil.h.

References GetSSBlobBucket(), aims::BucketMap< T >::setSizeX(), aims::BucketMap< T >::setSizeY(), aims::BucketMap< T >::setSizeZ(), aims::GraphManip::storeAims(), and Graph::vertices().

◆ AddBlobsToPSGraph() [3/3]

template<int D, class T >

void aims::AddBlobsToPSGraph	(	PrimalSketch< AimsSurface< D, Void >, Texture< T > > *	sketch,
		Graph *	graph
	)

Definition at line 409 of file primalSketchUtil.h.

References GetSSBlobMesh(), aims::meshdistance::max(), aims::meshdistance::min(), aims::BucketMap< T >::setSizeX(), aims::BucketMap< T >::setSizeY(), aims::BucketMap< T >::setSizeZ(), aims::GraphManip::storeAims(), and Graph::vertices().

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [1/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MedianFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [2/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MedianFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [3/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMedianFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [4/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMedianFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [5/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MeanFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [6/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MeanFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [7/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMeanFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [8/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMeanFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [9/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MinFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [10/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MinFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [11/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MaxFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [12/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MaxFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [13/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MajorityFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [14/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MajorityFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [15/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	ExtremaDifferenceFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [16/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	ExtremaDifferenceFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [17/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	SumFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [18/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	SumFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [19/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	VarFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [20/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	VarFilterFunc	,
		AimsRGBA
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [21/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	StDevFilterFunc	,
		AimsRGB
	)

◆ AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [22/22]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	StDevFilterFunc	,
		AimsRGBA
	)

◆ AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE() [1/2]

aims::AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE	(	GaborFilterFunc	,
		AimsRGB
	)

◆ AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE() [2/2]

aims::AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE	(	GaborFilterFunc	,
		AimsRGBA
	)

◆ applyLaplacianMatrix()

template<typename T >

void aims::applyLaplacianMatrix	(	const std::vector< T > &	inittex,
		std::vector< T > &	outtex,
		const LaplacianWeights &	lapl
	)

◆ blobsHeights()

void aims::blobsHeights	(	const AimsSurfaceTriangle &	mesh,
		const std::vector< double > &	field,
		const std::vector< int > &	watershedlabels,
		std::vector< int > &	junctions
	)

◆ buildSplinePyramid() [1/3]

template<typename T >

SplinePyramid aims::buildSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		unsigned	order,
		unsigned	factor = `2`
	)

FUNCTORS.

Definition at line 179 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ buildSplinePyramid() [2/3]

template<typename T >

SplinePyramid aims::buildSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		unsigned	order,
		const Point4du &	factor
	)

Definition at line 187 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ buildSplinePyramid() [3/3]

template<typename T >

SplinePyramid aims::buildSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		unsigned	order,
		const std::vector< Point4du > &	factor
	)

Definition at line 194 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ calculateMinFibersLength() [1/2]

float aims::calculateMinFibersLength	(	FiberPoint *	f1,
		FiberPoint *	f2,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ calculateMinFibersLength() [2/2]

float aims::calculateMinFibersLength	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2
	)

◆ clip() [1/2]

template<typename T >

carto::VolumeRef< T > aims::clip	(	const carto::VolumeRef< T > &	in,
		const T &	min,
		const T &	max
	)

clip

Clip values outside [min, max]

Definition at line 84 of file dynamic_d.h.

References carto::VolumeRef< T >::deepcopy(), aims::meshdistance::max(), and aims::meshdistance::min().

Referenced by clipDynamic().

◆ clip() [2/2]

template<typename T >

carto::VolumeRef< T > aims::clip	(	carto::VolumeRef< T > &	in,
		const T &	min,
		const T &	max,
		bool	in_place = `false`
	)

Definition at line 63 of file dynamic_d.h.

References carto::VolumeRef< T >::deepcopy(), carto::VolumeRef< T >::getSizeT(), carto::VolumeRef< T >::getSizeX(), carto::VolumeRef< T >::getSizeY(), carto::VolumeRef< T >::getSizeZ(), aims::meshdistance::max(), and aims::meshdistance::min().

◆ clipDynamic() [1/2]

template<typename T >

carto::VolumeRef< T > aims::clipDynamic	(	const carto::VolumeRef< T > &	in,
		bool	flatten_mask = `true`,
		float	pct_kept = `1.`
	)

clipDynamic

This method allows preprocessing of images to avoid squeezed histograms due to mask or outlier values.

If flatten_mask is set, the minimum value is replaced by the second minimum minus 1 (or epsilon for floats). This way, if the image was masked, the mask value is closer to the actual data range, else, the data is almost unchanged.
If pct_kept differs from 1, it is used to find a threshold under which at least that percentage of the histogram is kept. All values above are thresholded out and clipped.
Finally, if in place is true (when the input volume is non const), the result is returned in the input volume, else a new volume is allocated.

Definition at line 95 of file dynamic_d.h.

References carto::VolumeRef< T >::deepcopy().

◆ clipDynamic() [2/2]

template<typename T >

carto::VolumeRef< T > aims::clipDynamic	(	carto::VolumeRef< T > &	in,
		bool	flatten_mask = `true`,
		float	pct_kept = `1.`,
		bool	in_place = `true`
	)

Definition at line 104 of file dynamic_d.h.

References accumulate(), carto::VolumeRef< T >::begin(), clip(), carto::deepcopy(), carto::VolumeRef< T >::end(), carto::VolumeRef< T >::getSizeX(), carto::VolumeRef< T >::getSizeY(), carto::VolumeRef< T >::getSizeZ(), aims::meshdistance::max(), aims::meshdistance::min(), and aims::MathUtil< T >::sum().

◆ cubicSplinePyramid() [1/3]

template<typename T >

SplinePyramid aims::cubicSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		unsigned	factor = `2`
	)

Definition at line 203 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ cubicSplinePyramid() [2/3]

template<typename T >

SplinePyramid aims::cubicSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		const Point4du &	factor
	)

Definition at line 211 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ cubicSplinePyramid() [3/3]

template<typename T >

SplinePyramid aims::cubicSplinePyramid	(	const carto::VolumeRef< T > &	vol,
		const std::vector< Point4du > &	factor
	)

Definition at line 219 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

◆ distancesFromMesh()

void aims::distancesFromMesh	(	const AimsSurfaceTriangle &	mesh,
		std::vector< AimsVector< uint, 2 > > &	edges,
		std::vector< double > &	weights
	)

◆ downPath() [1/2]

template<typename T >

BucketMap<Void>* aims::downPath	(	const BucketMap< T > &	region,
		const Point3d &	pos
	)

◆ downPath() [2/2]

template BucketMap<Void>* aims::downPath	(	const BucketMap< float > &	region,
		const Point3d &	pos
	)

◆ fiberAffinity() [1/2]

float aims::fiberAffinity	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2,
		float	var
	)

◆ fiberAffinity() [2/2]

float aims::fiberAffinity	(	FiberPoint *	f1,
		FiberPoint *	f2,
		float	var,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberAffinityMax() [1/2]

float aims::fiberAffinityMax	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2,
		float	var
	)

◆ fiberAffinityMax() [2/2]

float aims::fiberAffinityMax	(	FiberPoint *	f1,
		FiberPoint *	f2,
		float	var,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberAffinityMaxDistCorrespPoints() [1/2]

float aims::fiberAffinityMaxDistCorrespPoints	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2,
		float	var
	)

◆ fiberAffinityMaxDistCorrespPoints() [2/2]

float aims::fiberAffinityMaxDistCorrespPoints	(	FiberPoint *	f1,
		FiberPoint *	f2,
		float	var,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberAffinityMaxDistCorrespPointsNormByMinLength() [1/2]

float aims::fiberAffinityMaxDistCorrespPointsNormByMinLength	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2,
		float	var,
		float	normFactor
	)

◆ fiberAffinityMaxDistCorrespPointsNormByMinLength() [2/2]

float aims::fiberAffinityMaxDistCorrespPointsNormByMinLength	(	FiberPoint *	f1,
		FiberPoint *	f2,
		float	var,
		float	normFactor,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberDistance() [1/2]

float aims::fiberDistance	(	FiberPoint *	f1,
		FiberPoint *	f2,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberDistance() [2/2]

float aims::fiberDistance	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2
	)

◆ fiberDistanceMax() [1/2]

float aims::fiberDistanceMax	(	FiberPoint *	f1,
		FiberPoint *	f2,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberDistanceMax() [2/2]

float aims::fiberDistanceMax	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2
	)

◆ fiberDistanceMaxDistCorrespPoints() [1/2]

float aims::fiberDistanceMaxDistCorrespPoints	(	FiberPoint *	f1,
		FiberPoint *	f2,
		int &	fiberSize1
	)

◆ fiberDistanceMaxDistCorrespPoints() [2/2]

float aims::fiberDistanceMaxDistCorrespPoints	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2
	)

◆ fiberDistanceMaxDistCorrespPointsNormByMinLength() [1/2]

float aims::fiberDistanceMaxDistCorrespPointsNormByMinLength	(	FiberPoint *	f1,
		FiberPoint *	f2,
		float	normFactor,
		int &	fiberSize1,
		int &	fiberSize2
	)

◆ fiberDistanceMaxDistCorrespPointsNormByMinLength() [2/2]

float aims::fiberDistanceMaxDistCorrespPointsNormByMinLength	(	std::vector< Point3df > &	f1,
		std::vector< Point3df > &	f2,
		float	normFactor
	)

◆ getClosestFiberPointDist() [1/2]

float aims::getClosestFiberPointDist	(	Point3df &	p1,
		FiberPoint *	f2,
		Point3df &	pMin,
		int &	fiberSize2
	)

◆ getClosestFiberPointDist() [2/2]

float aims::getClosestFiberPointDist	(	Point3df &	p1,
		std::vector< Point3df > &	f2,
		Point3df &	pMin
	)

◆ GetSSBlobBucket()

template<typename T >

AimsBucket< Void > * aims::GetSSBlobBucket ( PrimalSketch< AimsData< T >, AimsData< T > > * sketch )

Definition at line 191 of file primalSketchUtil.h.

References aims::GreyLevelBlob< T >::GetListePoints(), AimsBucketItem< T >::location(), AimsBucket< T >::setSizeX(), AimsBucket< T >::setSizeY(), and AimsBucket< T >::setSizeZ().

Referenced by AddBlobsToPSGraph().

◆ GetSSBlobImage()

template<typename T >

AimsData< short > * aims::GetSSBlobImage ( PrimalSketch< AimsData< T >, AimsData< T > > * sketch )

Definition at line 72 of file primalSketchUtil.h.

References aims::GreyLevelBlob< T >::GetListePoints(), and AimsData< T >::setSizeXYZT().

◆ GetSSBlobMesh() [1/2]

template<int D, class T >

AimsSurfaceTriangle* aims::GetSSBlobMesh ( PrimalSketch< AimsSurface< D, Void >, Texture< T > > * sketch )

Referenced by AddBlobsToPSGraph(), and GetSSBlobTore().

◆ GetSSBlobMesh() [2/2]

template<int D, class T >

AimsSurfaceTriangle* aims::GetSSBlobMesh	(	PrimalSketch< AimsSurface< D, Void >, Texture< T > > *	sketch,
		AimsSurfaceTriangle *	mesh
	)

Definition at line 227 of file primalSketchUtil.h.

References aims::SurfaceManip::meshMerge(), norm(), AimsSurface< D, T >::polygon(), AimsTimeSurface< D, T >::polygon(), aims::SurfaceGenerator::sphere(), and AimsTimeSurface< D, T >::vertex().

◆ GetSSBlobMeshBucket()

template<typename T >

AimsBucket<Void>* aims::GetSSBlobMeshBucket ( AimsSurfaceTriangle * mesh )

Definition at line 337 of file primalSketchUtil.h.

References AimsBucketItem< T >::location(), AimsBucket< T >::setSizeX(), AimsBucket< T >::setSizeY(), and AimsBucket< T >::setSizeZ().

◆ GetSSBlobTexture()

template<int D, class T >

TimeTexture< float > aims::GetSSBlobTexture ( PrimalSketch< AimsSurface< D, Void >, Texture< T > > * sketch )

Definition at line 121 of file primalSketchUtil.h.

References aims::GreyLevelBlob< T >::GetListePoints().

◆ GetSSBlobTore()

template<int D, class T >

AimsSurfaceTriangle * aims::GetSSBlobTore ( PrimalSketch< AimsSurface< D, Void >, Texture< T > > * sketch )

Definition at line 492 of file primalSketchUtil.h.

References aims::SurfaceGenerator::cylinder(), GetSSBlobMesh(), and aims::SurfaceManip::meshMerge().

◆ laplacianMatrixThreshold()

void aims::laplacianMatrixThreshold	(	LaplacianWeights &	lmat,
		float	threshold
	)

◆ makeLaplacianMatrix()

void aims::makeLaplacianMatrix	(	const LaplacianWeights &	weights,
		LaplacianWeights &	lmat,
		float	dt
	)

◆ makeLaplacianSmoothingCoefficients()

LaplacianWeights* aims::makeLaplacianSmoothingCoefficients	(	const LaplacianWeights &	weights,
		unsigned	niter,
		float	dt,
		float	sparseThresh = `0`
	)

Compute Laplacian smoothing coefficients matrix for niter smoothing iterations.

Input weights should be the output of AimsMeshWeightFiniteElementLaplacian(). sparseThresh can be used to threshold the weights of the sparse matrix at each smoothing iteration, to reduce the sparse matrix size.

◆ meshBlobsBifurcation() [1/2]

int aims::meshBlobsBifurcation	(	const AimsSurfaceTriangle &	mesh,
		const std::vector< double > &	field,
		std::vector< int > &	idx,
		std::vector< double > &	height,
		std::vector< int > &	father,
		std::vector< int > &	label,
		double	th
	)

Blobs labeling and bifurcations.

Parameters

idx	output table of seed node of each blob
father	blob number which merges two (or more) others
height	field value of the peak (seed) node in a blob
label	blob number for each vertex

◆ meshBlobsBifurcation() [2/2]

int aims::meshBlobsBifurcation	(	const AimsSurfaceTriangle &	mesh,
		const TimeTexture< double > &	field,
		TimeTexture< int > &	idx,
		TimeTexture< double > &	height,
		TimeTexture< int > &	father,
		TimeTexture< int > &	label,
		double	th
	)

◆ meshWatershed() [1/2]

int aims::meshWatershed	(	const AimsSurfaceTriangle &	mesh,
		const std::vector< double > &	field,
		std::vector< int > &	idx,
		std::vector< int > &	depth,
		std::vector< int > &	major,
		std::vector< int > &	label,
		double	threshold
	)

If I understand:

Parameters

lidx	will contain the vertex index of each local maximum.
ldepth	will contain the lifetime (number of iterations before death) of each maximum.
label	will contain the basin label, for each vertex.
lmajor	will contain the label of the parent of each basin: label of the highest basin which grew over it.

◆ meshWatershed() [2/2]

int aims::meshWatershed	(	const AimsSurfaceTriangle &	mesh,
		const TimeTexture< double > &	field,
		TimeTexture< int > &	idx,
		TimeTexture< int > &	depth,
		TimeTexture< int > &	major,
		TimeTexture< int > &	label,
		double	threshold
	)

◆ mirrorCoeff()

int aims::mirrorCoeff	(	int	i,
		int	size
	)

inline

This method returns a mirror index when needed.

Only inVolume's size spline coefficient are computed since "outside" coefficients are equal to their mirror inside the image domain. This method computes this mirror correspondance.

If i is in [0, size-1]: returns i
If i is in [size, 2 * size - 2]: returns size - (i - size) - 2
Else: |i| is wrapped modulo 2 * size - 2, then one of the above conditions applies.

Definition at line 209 of file splineresampler.h.

Referenced by aims::SplineResampler< T >::getFold().

◆ multichannelfiltervalues_lin()

template<typename VoxelType >

VoxelType aims::multichannelfiltervalues_lin	(	const LinearFilteringFunction< typename VoxelType::ChannelType > &	f,
		const carto::VolumeRef< VoxelType > &	volume
	)

inline

Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...)

This function does not filter image but only apply filter on set of multichannel data, commonly the neighborhood of a voxel.

Parameters

f	function to use (must derive from `LinearFilteringFunction`)
volume	data to evaluate filter on

Returns: result of the filter on data

Definition at line 36 of file filteringfunction_linear_rgb_d.h.

References aims::LinearFilteringFunction< T >::execute(), and DataTypeInfo< class >::samples().

◆ multichannelfiltervalues_nonlin() [1/2]

template<typename VoxelType >

VoxelType aims::multichannelfiltervalues_nonlin	(	const ElementFilteringFunction< typename VoxelType::ChannelType > &	f,
		const carto::VolumeRef< VoxelType > &	volume
	)

inline

Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...)

This function does not filter image but only apply filter on set of multichannel data, commonly the neighborhood of a voxel.

Parameters

f	function to use (must derive from `ElementFilteringFunction`)
volume	data to evaluate filter on

Returns: result of the filter on data

Definition at line 36 of file filteringfunction_element_rgb_d.h.

References aims::ElementFilteringFunction< T >::execute(), and DataTypeInfo< class >::samples().

◆ multichannelfiltervalues_nonlin() [2/2]

template<typename VoxelType >

VoxelType aims::multichannelfiltervalues_nonlin	(	const ElementFilteringFunction< typename VoxelType::ChannelType > &	f,
		const carto::VolumeRef< VoxelType > &	volume,
		const carto::rc_ptr< StructuringElement > &	se
	)

inline

Templated function to process filter on multichannel data (AimsRGB, AimsRGBA, ...)

This function does not filter image but only apply filter on set of multichannel data, commonly the neighborhood of a voxel.

Parameters

f	function to use (must derive from `ElementFilteringFunction`)
volume	data to evaluate filter on
se	structuring element to evaluate filter on

Returns: result of the filter on data

Definition at line 67 of file filteringfunction_element_rgb_d.h.

References aims::ElementFilteringFunction< T >::execute(), and DataTypeInfo< class >::samples().

◆ operator>>() [1/3]

RoiGtmReader & aims::operator>>	(	RoiGtmReader &	reader,
		RoiGtm &	thing
	)

inline

Definition at line 80 of file roigtmR.h.

References aims::RoiGtmReader::read().

◆ operator>>() [2/3]

RoiSelectorReader& aims::operator>>	(	RoiSelectorReader &	,
		Tree &
	)

◆ operator>>() [3/3]

RoiSelectorReader& aims::operator>>	(	RoiSelectorReader &	reader,
		RoiSelector &	thing
	)

inline

Definition at line 72 of file roiselectorR.h.

References aims::RoiSelectorReader::read().

◆ resampleBucket()

carto::rc_ptr<BucketMap<Void> > aims::resampleBucket	(	const BucketMap< Void > &	bck,
		const soma::Transformation3d &	direct_transformation,
		const soma::Transformation3d &	inverse_transformation,
		Point3df	vs = `Point3df(0., 0., 0.)`,
		bool	also_pushforward = `true`
	)

Apply a spatial transformation to a BucketMap.

The bucket is transformed by resampling, using a pull-back method in the same way as nearest neighbour resampling of a Volume.

Pure pull-back resampling does not behave well when downsampling (it introduces holes), so by default this function returns the union of voxels transformed using the pushforward and pullback methods. Set

also_pushforward to false to disable this behaviour and only perform pure pullback.

The voxel size of the output bucket can optionally be specified in

vs. By default, the same voxel size as the input bucket is used.

Warning: {Alhtough this method is more reliable than transformBucketDirect, it still provides no guarantees of topology preservation.}

◆ setKernel()

void aims::GaborFilterFunc::setKernel ( )

inlineprotected

Definition at line 297 of file filteringfunction_linear_d.h.

References _amplitude, _gamma, _init, _kernel, _lambda, _nstd, _psi, _real, _sigma, _theta, _voxelsize, ASSERT, carto::VolumeRef< T >::getSizeT(), carto::VolumeRef< T >::getSizeX(), carto::VolumeRef< T >::getSizeY(), carto::VolumeRef< T >::getSizeZ(), aims::meshdistance::max(), and carto::verbose.

Referenced by aims::LinearFilteringFunctionFactory< T >::create().

◆ sparseMult()

LaplacianWeights* aims::sparseMult	(	const LaplacianWeights &	in1,
		const LaplacianWeights &	in2,
		float	sparseThresh = `0`
	)

◆ transformBucketDirect()

carto::rc_ptr<BucketMap<Void> > aims::transformBucketDirect	(	const BucketMap< Void > &	bck,
		const soma::Transformation3d &	direct_transformation,
		Point3df	vs = `Point3df(0., 0., 0.)`
	)

Apply a spatial transformation to a BucketMap.

Each voxel of the input bucket is transformed with

direct_transformation, and the closest voxel of the output bucket is set. The voxel size of the output bucket can optionally be specified in
vs. By default, the same voxel size as the input bucket is used.

Warning: {This method provides no guarantees of topology preservation; in fact it will create holes in the resulting bucket, particularly when upsampling. When possible, you should use resampleBucket() instead, which performs nearest-neighbour resampling.}

◆ transformGraph()

void aims::transformGraph	(	Graph &	graph,
		const soma::Transformation3d &	direct_transformation,
		const soma::Transformation3d *	inverse_transformation,
		Point3df	vs = `Point3df(0., 0., 0.)`
	)

Apply a spatial transformation to all objects contained in a Graph.

The graph is modified in-place.

An inverse transformation is necessary for correctly transforming Buckets (see resampleBucket). If inverse_transformation is NULL, buckets will be transformed with the push-forward method only (transformBucketDirect).

Warning: {Volumes are not transformed, neither are graph attributes. Please run AimsFoldArgAtt to fix the values of basic attributes, or the CorticalFoldsGraphUpgradeFromOld BrainVisa process, which can be found under Morphologist/Sulci/graphmanipulation, for a complete update.}