aims Namespace Reference

Namespaces
	convolutionfilter
	convolutionsubsampler
	DataManip
	detail
	internal
	knn
	meshdistance
	meshgraph
	RoiDiff
	singlechannel
	SparseOrDenseMatrix
	SparseVolume
	strel
	SurfaceGenerator
	util

Classes
class	BorderIterator
class	AimsGraphReader
class	AimsGraphWriter
class	BucketMapGenerator
class	PolylinePolynomialInterpolator
class	_convertedNiftiArrayValue
class	_convertedNiftiArrayValue< AimsVector< U, D > >
class	_convertedNiftiValue
class	_convertedNiftiValue< AimsVector< U, D > >
class	AffineTransformation3d
class	AimsApplication
class	AimsFastAllocationData
struct	AimsGraphWriter_Private
class	AimsRoi
class	AnyTypeReader
class	AnyTypeReaderProcess
class	APCReader
class	ArgFormat
class	ArgHeader
class	ArgReader
class	ArgWriter
class	BckFormat
class	BckHeader
class	BckMapFormat
class	BckMapReader
class	BckMapWriter
class	BckReader
class	BckWriter
class	BorderFiller
class	BoundingBox
class	BucketMap
class	BucketUtil
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	BundleWriter
class	ChannelReader
class	CiftiTools
class	Clock
class	CoarseReader
class	ColorMap
class	ConnectedComponentEngine
class	ConnectedComponentEngine< carto::VolumeRef< T >, carto::VolumeRef< O > >
class	Connectivity
class	ConnectomistBundlesReader
class	const_cyclic_iterator
struct	CoordinatesLess
struct	CoordinatesLess< T, 3 >
class	CurveOrientation
class	CurveSelection
class	CutMesh
class	CutTexturedMesh
class	cyclic_iterator
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	EcatFormat
class	EcatHeader
class	EcatPlugin
class	EcatReader
class	EcatSinoHeader
class	EcatSinoReader
class	EcatSinoWriter
class	EcatWriter
class	FdfFormat
class	FdfHeader
class	FdfParType
class	FdfPlugin
class	FdfProcPar
class	FdfReader
class	FiberInfo
class	FiberOversampler
class	FileFormat
class	FileFormatDictionary
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	GenericWriter
class	GenesisFormat
class	GenesisHeader
class	GenesisReader
class	GiftiHeader
class	GiftiMeshFormat
class	GiftiPlugin
class	GiftiTextureFormat
class	GraphBundlesFormat
struct	GraphElementCode
class	GraphManip
class	GraphVolumeFormat
class	Header
class	HieFormat
class	Hierarchy
class	HierarchyReader
class	ImasFormat
class	ImasHeader
class	ImasSorDFormat
class	ImasVolFormat
class	IntegrableOf
class	IntegratorOf
class	Interpolator
class	IOObjectTypesDictionary
class	IOOptions
class	ItemReader
class	ItemWriter
class	JpegFormat
class	JpegHeader
class	JpegPlugin
class	JpegReader
class	JpegWriter
class	LabelNodeFilter
class	LabelReader
class	LinearInterpolator
class	LowLevelArgReader
class	LowLevelArgWriter
class	LowLevelRoiReader
class	LowLevelStandardArgReader
class	LowLevelStandardArgWriter
class	MaskIterator
class	MaskIteratorOf
class	MaskIteratorOf< carto::VolumeRef< T > >
class	MaskIteratorOf< Graph >
class	MathUtil
class	MeshFormat
class	MeshHeader
class	MeshProjection
class	MeshProjectionFactory
class	MeshReader
class	MeshWriter
class	MinfFormat
class	MniObjFormat
class	MniObjHeader
class	MotionedMaskIterator
class	MotionedRoiIterator
class	MotionedVolumeROILabelMap
class	MotionWriter
class	MRTrixBundleReader
class	NameNodeFilter
class	NodeFilter
class	Path
class	PlyFormat
class	PlyHeader
class	PlyPlugin
class	PlyReader
class	PlyWriter
class	PointSetFeatures
class	PointsInImageFeatures
class	Polyline
class	PovFormat
class	PovWriter
class	Process
struct	ProcessInput
class	ProgressInfo
class	PythonHeader
class	Quaternion
class	Reader
class	ReaderAsObject
class	RoiDiff
class	RoiFeatures
class	RoiIterator
class	RoiIteratorOf
class	RoiIteratorOf< carto::VolumeRef< T > >
class	RoiIteratorOf< Graph >
class	ROILabelMap
class	RombergIntegratorOf
class	ScalarFeaturesProvider
class	ScalarSetFeatures
class	ScaledEncoding
class	ScannerConf
class	Selection
class	SelectionExpander
class	SelectionReader
class	SelectionSet
class	SelectionWriter
class	Selector
class	Settings
class	SimpleBundlesSlicer
class	SimpleVoxelSampler
class	Sinogram
class	SliceFormatHeader
class	SomaIOAimsDataFormat
class	SparseMatrix
class	SparseMatrixUtil
class	SparseOrDenseMatrix
class	SparseVolume
class	SparseVolume< BucketMap< T > >
class	SparseVolume< BucketMap< Void > >
class	SparseVolume< carto::Volume< T > >
struct	specifiedLabels
class	SpmFormat
class	SpmHeader
class	SpmReader
class	SpmWriter
class	StandardReferentials
class	StructuredConstVolume
class	StructuredVolume
class	StructuringElement
class	StructuringElementRef
class	StxFormat
class	SurfaceGenerator
class	SurfaceManip
class	Tex2Graph
class	TexFormat
class	TexHeader
class	TexReader
class	TexWriter
class	TiffFormat
class	TiffHeader
class	TiffPlugin
class	TiffReader
class	TiffWriter
class	TrackvisBundleReader
class	TransformationChain3d
class	TransformationGraph3d
class	TrapezeIntegratorOf
class	TriFormat
class	TriHeader
class	TriReader
class	TriWriter
class	TrmHeader
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	ImageAlgorithmInterface
	aims::ImageAlgorithmInterface is the interface for an image processing algorithm. More...
class	ImageAlgorithm
	aims::ImageAlgorithm class used to implement image algorithms 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	Individuals
class	ClassifStrategy
class	Distance
class	DynamicStrategy
class	IterativeClassification
class	KmeansStrategy
class	PpcaAnalyserElement
class	MixtureOfPPCA
class	PcaStrategy
class	GradientAdvection
	Propagate labels along a vector field. More...
class	FastMarching
	Fast marching algorithm implementation, for images or buckets. More...
struct	Point3dfCompare
struct	Point3dCompare
struct	PairCompare
struct	SetCompare
class	RealToRealFunctionTabulation
class	FoldGraphAttributes
	Creation of cortical folds graph attributes. More...
class	FoldArgOverSegment
class	GeodesicPath
	Geodesic paths or distance maps, using the Dijkstra algorithm. More...
class	RegularBinnedHistogram
	Histogram container class, with a specified number of regular bins. More...
class	InterpolatedVolume
	Spline interpolation of volumes with simple accessors to interpolated values. More...
class	RoiSelectorReader
class	RoiGtmReader
class	RoiGtmWriter
	Class for AimsRoiGtm writing operation. More...
class	DiscriminantAnalysisElement
class	DiscriminantAnalysis
class	BaseHarrisDetector
	Harris Corner Detector. More...
class	HarrisDetector
class	HarrisDetector< T, 2 >
class	ProbabilisticPcaElement
class	ProbabilisticPca
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	BSpline
	Centered and scaled B-Spline function, evaluated at run time. More...
class	FastBSpline
	*Centered and *scaled B-Spline function, evaluated at run time. 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	DiscreteBSpline
	Discrete B-Splines B-Spline pre sampled only on integral values. More...
class	GeometricProperties
class	Curvature
class	CurvatureFactory
class	FiniteElementCurvature
class	BoixCurvature
class	BarycenterCurvature
class	BoixGaussianCurvature
class	GaussianCurvature
class	VertexRemover
	A class to remove a vertex from a mesh, and remeshing the hole. More...
class	MeshInterpoler
	Triangular mesh and texture interpolation. More...
class	CoordinatesFieldMeshInterpoler
class	MorphoGreyLevel
	Grey-level mathematical morphology. More...
class	PointsDistribution
	Points repartition using forces in a given geometry (on a sphere for instance). More...
class	DericheSmoother
class	PeronaMalikSmoother
class	FiniteElementSmoother
struct	ltstr_p3d
struct	ltstr_p3d< Point3d >
struct	ltstr_p3d< std::pair< Point3df, uint > >
class	MaximumPoint
	class for maxima More...
class	SaddlePoint
	class for saddle points More...
class	GreyLevelBlob
	Class for grey-level blobs Templated with respect to the type of points: TypeSite<carto::VolumeRef<T> >::type for images TypeSite<AimsSurface<D, Void> >::type for textures. More...
class	BlobMeasurements
class	ExtractGreyLevelBlobs
	Class that define grey-level blobs algorithm extraction. More...
class	GreyLevelBlobTools
	class that provide some tools for blob management More...
class	BaseScaleSpace
class	ScaleSpace
class	ScaleSpace< carto::VolumeRef< T >, carto::VolumeRef< T > >
class	ScaleSpace< AimsSurface< D, Void >, Texture< T > >
class	ScaleLevel
class	ScaleLevel< carto::VolumeRef< T >, carto::VolumeRef< T > >
class	ScaleLevel< AimsSurface< D, Void >, Texture< T > >
class	Smoother
class	Smoother< carto::VolumeRef< T >, carto::VolumeRef< T > >
class	Smoother< AimsSurface< D, Void >, Texture< T > >
class	PrimalSketch
class	ScaleSpaceBlob
class	Bifurcation
struct	ltstr_blob
class	Primalsketch2graph
class	CoupledSmoother
class	CoupledSmoother< carto::VolumeRef< T >, carto::VolumeRef< T > >
class	CoupledDiffusion2DSmoother
class	ConvolutionSubSampler
	Convolution Filter. More...
class	DirectBSplineSubSampler
	Class excuting a spline-based subsampling. More...
class	MovingAverageSubSampler
class	MovingAverageCascadeSubSampler
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	DiscreteU
class	DiscreteUB
class	SubSamplingPyramidBuilder
class	FfdTransformation
	FFD vector field deformation transform. More...
class	SplineFfd
	FFD vector field deformation transform. More...
class	TrilinearFfd
	FFD vector field deformation transform. More...
class	Writer< aims::FfdTransformation >
	FFD vector field transformation writer. More...
class	CubicResampler
	Volume resampler using cubic interpolation. More...
class	HarmonicCageMeshResampler
class	LinearResampler
	Volume resampler using linear (order 1) interpolation. More...
class	MajorityLabelResampler
	Volume resampler using linear (order 1) interpolation, then selects the majority label in the neighbouring values. More...
class	MeshToVoxelsResampler
	3D rasterization (voxelization) of a mesh O : VolumeRef<unsigned int> or BucketMap<Void> More...
class	NearestNeighborResampler
	Volume resampler using nearest-neighbour interpolation. More...
class	QuadraticResampler
	Volume resampler using quadratic (order 2) interpolation. More...
class	QuarticResampler
	Volume resampler using quartic (order 4) interpolation. More...
class	QuinticResampler
	Volume resampler using quintic (order 5) interpolation. More...
class	Resampler
	Resampling of data from a volume, applying a transformation. More...
class	ResamplerFactory
class	ExtremaDifferenceSubSampling
class	MajoritySubSampling
class	MaxSubSampling
class	MeanSubSampling
class	MedianResampler
	Volume resampler using linear (order 1) interpolation, then selects the median value in the neighbouring values. More...
class	MedianSubSampling
class	MinSubSampling
class	NotNullMeanSubSampling
class	NotNullMedianSubSampling
class	SumSubSampling
class	ConeSamplable
class	SphereSamplable
class	SixthOrderResampler
	Volume resampler using sixth-order interpolation. More...
class	SeventhOrderResampler
	Volume resampler using seventh-order interpolation. More...
struct	MultiChannelResamplerSwitch
class	SplineResampler
	B-Spline-based resampling. More...
struct	MultiChannelResamplerSwitch< false, T >
struct	MultiChannelResamplerSwitch< true, T >
class	SubSamplingImageAlgorithm
	aims::SubSamplingImageAlgorithm is the algorithm to subsample image. More...
class	ClusterArgMaker
class	RoiGtm
class	RoiStats
class	RoiSelector
class	BucketBlobExtractor
	Blobs and watershed. More...
class	TextureSmoothing
class	ConvolutionFilter
	Convolution Filter. More...
class	ExtremaDifferenceFilter
class	BaseDiffusionSmoother
	Base class for Heat diffusion. More...
class	DiffusionSmoother
	Heat diffusion with a volume of given datasource (Dirichlet conditions) More...
class	BaseMaskedDiffusionSmoother
class	MaskedDiffusionSmoother
class	MaskedDiffusionSmoother< T, std::vector< Point3df > >
	Heat diffusion, with Dirichlet and Neumann border conditions. More...
class	MaskedDiffusionSmoother< T, carto::VolumeRef< short > >
	Heat diffusion, with Dirichlet and Neumann border conditions. More...
class	FilteringFunctionInterface
	Pure virtual class: interface for filtering functions called by aims::FilteringImageAlgorithm and aims::SubSamplingImageAlgorithm. More...
class	ElementFilteringFunction
	Base class for filtering functions applied in a structuring element. More...
class	ElementFilteringFunctionFactory
	Associates a string with a ElementFilteringFunction. More...
class	LinearFilteringFunction
	Base class for linear filtering functions. More...
class	LinearFilteringFunctionFactory
class	FilteringImageAlgorithmInterface
class	LinearFilteringImageAlgorithm
class	ElementFilteringImageAlgorithm
class	GaborFilter
class	MedianFilter
class	NotNullMedianFilter
class	MeanFilter
class	NotNullMeanFilter
class	MinFilter
class	MaxFilter
class	MajorityFilter
class	NotNullMajorityFilter
class	MovingAverageKernel
	1D Moving Average Kernel More...
class	MovingAverageCascadeKernel
	1D Cascade of Moving Average Kernel More...
class	MovingAverageFilter
	Separable Moving Average Filter. More...
class	MovingAverageCascadeFilter
	Separable Cascade of Moving Average Filter. More...
class	SumFilter
class	VarFilter
class	StDevFilter
class	IIRFilterBase
	Base class for separable infinite impulse response filters. More...
class	CausalSinglePoleIIRFilter
	Special case of Infinite Impulse Response filter. More...
class	SymAllPoleIIRFilter
	Symmetric, all-pole, infinite impulse response Filter. More...
class	InverseBSplineFilter
	This filter uses an inverse B-Spline convolution function to transform a discrete signal to its spline representation. More...
class	DirectBSplineFilter
	This filter uses a convolution with Spline basis functions. More...
struct	FilterType
class	SpamBase
class	SpamFromLikelihood
class	Spam
class	TransformLeastSquareEstimation
class	AffineLeastSquareEstimation
class	RigidLeastSquareEstimation
class	TranslationLeastSquareEstimation
class	SimiLeastSquareEstimation
class	RigidTransformEstimation
class	BundleTransformer
	Apply a spatial transformation to fiber bundles. 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 (carto::VolumeRef< 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 (carto::VolumeRef< 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 carto::VolumeRef< 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)
carto::VolumeRef< int16_t >	AimsLabeledConnectedComponent (AimsBucket< Void > &component, const carto::VolumeRef< 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 >	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)
bool	write (const T &obj, const std::string &filename, carto::Object options=carto::none(), const std::string *format=0)
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 carto::rc_ptr< carto::Volume< T > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< uint8_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< int8_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< uint16_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< int16_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< short > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< uint32_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< int32_t > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< float > > &)
template carto::rc_ptr< Interpolator >	getLinearInterpolator (const carto::rc_ptr< carto::Volume< 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 carto::rc_ptr< carto::Volume< T > > &data)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::VolumeRef< T > &data)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::VolumeRef< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::rc_ptr< carto::Volume< T > > &data, carto::rc_ptr< VoxelSampler > voxelSampler)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, const AffineTransformation3d &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::VolumeRef< T > &data, const AffineTransformation3d &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::rc_ptr< carto::Volume< T > > &data, const AffineTransformation3d &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::VolumeRef< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &motion)
carto::rc_ptr< MaskIterator >	getMaskIterator (const carto::rc_ptr< carto::Volume< T > > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &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 carto::VolumeRef< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler=carto::rc_ptr< VoxelSampler >())
carto::rc_ptr< RoiIterator >	getRoiIterator (const carto::rc_ptr< carto::Volume< 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 AffineTransformation3d &)
carto::rc_ptr< RoiIterator >	getRoiIterator (const std::string &fileName, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &)
carto::rc_ptr< RoiIterator >	getRoiIterator (const carto::VolumeRef< T > &data, const AffineTransformation3d &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const carto::rc_ptr< carto::Volume< T > > &data, const AffineTransformation3d &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, const AffineTransformation3d &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const carto::VolumeRef< T > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const carto::rc_ptr< carto::Volume< T > > &data, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &motion)
carto::rc_ptr< RoiIterator >	getRoiIterator (const Graph &data, carto::rc_ptr< VoxelSampler > voxelSampler, const AffineTransformation3d &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)
carto::rc_ptr< soma::Transformation3d >	operator* (const carto::rc_ptr< soma::Transformation3d > &transformation3d1, const carto::rc_ptr< soma::Transformation3d > &transformation3d2)
TIterator	cyclic_advance (TIterator i, TContainer &c)
void	minmax (const ObjectType &, 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)
void	toMap (const Vector &vector, std::map< IndexType, typename Vector::value_type > &map, const typename Vector::value_type &background=Vector::value_type(0))
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	AimsLagrangeInterpolation (const std::vector< REAL > &xa, const std::vector< REAL > &ya, REAL x, REAL *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...
std::list< AimsVector< uint, 3 > >	simple_delaunay_triangulation (const std::vector< Point2df > &points)
	SimpleDelaunayTriangulation. 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 >
carto::VolumeRef< short > *	GetSSBlobImage (PrimalSketch< carto::VolumeRef< T >, carto::VolumeRef< 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< carto::VolumeRef< T >, carto::VolumeRef< 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< carto::VolumeRef< T >, carto::VolumeRef< 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)
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 (NotNullMajorityFilterFunc, AimsRGB)
	AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE (NotNullMajorityFilterFunc, 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.)
	\function 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)
	\function 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 142 of file curv.h.

Point3dfNeigh

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

Definition at line 119 of file stlsort.h.

Point3dfSet

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

Definition at line 118 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

AddBlobsToPSGraph() [1/3]

template<int D, class T >

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

Definition at line 404 of file primalSketchUtil.h.

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

AddBlobsToPSGraph() [2/3]

template<typename T >

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

Definition at line 362 of file primalSketchUtil.h.

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

AddBlobsToPSGraph() [3/3]

template<typename Geom , typename Text >

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

Definition at line 356 of file primalSketchUtil.h.

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

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [1/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	ExtremaDifferenceFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [2/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	ExtremaDifferenceFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [3/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MajorityFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [4/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MajorityFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [5/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MaxFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [6/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MaxFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [7/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MeanFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [8/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MeanFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [9/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MedianFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [10/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MedianFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [11/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MinFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [12/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	MinFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [13/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMajorityFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [14/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMajorityFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [15/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMeanFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [16/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMeanFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [17/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMedianFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [18/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	NotNullMedianFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [19/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	StDevFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [20/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	StDevFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [21/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	SumFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [22/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	SumFilterFunc	,
		AimsRGBA
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [23/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	VarFilterFunc	,
		AimsRGB
	)

AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE() [24/24]

aims::AIMS_ELEMENT_FILTERFUNC_MULTICHANNEL_DECLARE	(	VarFilterFunc	,
		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,
		const Point4du &	factor
	)

Definition at line 187 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 std::vector< Point4du > &	factor
	)

Definition at line 194 of file splinepyramid.h.

References aims::SplinePyramidBuilder::execute().

buildSplinePyramid() [3/3]

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().

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

clip() [2/2]

template<typename T >

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

\function clip

Clip values outside [min, max]

Definition at line 84 of file dynamic_d.h.

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

Referenced by clipDynamic().

clipDynamic() [1/2]

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

clipDynamic() [2/2]

template<typename T >

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

\function 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< class >::deepcopy().

cubicSplinePyramid() [1/3]

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() [2/3]

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().

cubicSplinePyramid() [3/3]

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().

distancesFromMesh()

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

downPath() [1/2]

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

downPath() [2/2]

template<typename T >

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

fiberAffinity() [1/2]

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

fiberAffinity() [2/2]

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

fiberAffinityMax() [1/2]

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

fiberAffinityMax() [2/2]

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

fiberAffinityMaxDistCorrespPoints() [1/2]

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

fiberAffinityMaxDistCorrespPoints() [2/2]

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

fiberAffinityMaxDistCorrespPointsNormByMinLength() [1/2]

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

fiberAffinityMaxDistCorrespPointsNormByMinLength() [2/2]

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

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< carto::VolumeRef< T >, carto::VolumeRef< T > > *

sketch

)

Definition at line 188 of file primalSketchUtil.h.

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

Referenced by AddBlobsToPSGraph().

GetSSBlobImage()

template<typename T >

carto::VolumeRef< short > * aims::GetSSBlobImage

(

PrimalSketch< carto::VolumeRef< T >, carto::VolumeRef< T > > *

sketch

)

Definition at line 72 of file primalSketchUtil.h.

References carto::VolumeRef< class >::begin(), aims::GreyLevelBlob< T >::GetListePoints(), and carto::VolumeRef< class >::setVoxelSize().

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 224 of file primalSketchUtil.h.

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

GetSSBlobMeshBucket()

template<typename T >

AimsBucket<Void>* aims::GetSSBlobMeshBucket

(

AimsSurfaceTriangle *

mesh

)

Definition at line 334 of file primalSketchUtil.h.

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

GetSSBlobTexture()

template<int D, class T >

TimeTexture< float > aims::GetSSBlobTexture

(

PrimalSketch< AimsSurface< D, Void >, Texture< T > > *

sketch

)

Definition at line 118 of file primalSketchUtil.h.

References aims::GreyLevelBlob< T >::GetListePoints(), and TimeTexture< class >::item().

GetSSBlobTore()

template<int D, class T >

AimsSurfaceTriangle * aims::GetSSBlobTore

(

PrimalSketch< AimsSurface< D, Void >, Texture< T > > *

sketch

)

Definition at line 487 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.

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.

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::setKernel ( )

protected

simple_delaunay_triangulation()

std::list<AimsVector<uint, 3> > aims::simple_delaunay_triangulation

(

const std::vector< Point2df > &

points

)

SimpleDelaunayTriangulation.

Get a Delaunay triangulation for a polygon. Poitns in the polygon should be ordered in a clockwise or counterclockwise order.

Note that it is different from a classical Delaunay algorithm wich meshes a cloud point (and its convex hull), not a polygon as here.

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.}

transformMesh() [1/2]

template<int D>

void aims::transformMesh	(	AimsTimeSurface< D, Void > &	mesh,
		const soma::Transformation3d &	direct_transformation
	)

Apply a spatial transformation to a mesh (AimsTimeSurface)

Each vertex of the mesh is transformed according to the supplied transformation. Normals are re-calculated from the new vertex positions.

transformMesh() [2/2]

template<int D>

void aims::transformMesh	(	AimsTimeSurface< D, Void > &	mesh,
		const Transformation3d &	direct_transformation
	)

Definition at line 45 of file transform_objects_d.h.

References AimsTimeSurface< D, class >::updateNormals(), and AimsTimeSurface< D, class >::vertex().

Variable Documentation

_amplitude

std::vector<int> aims::_amplitude

protected

Definition at line 159 of file filteringfunction_linear.h.

_gamma

double aims::_gamma

protected

Definition at line 155 of file filteringfunction_linear.h.

Referenced by aims::CoupledDiffusion2DSmoother< T >::CoupledDiffusion2DSmoother(), and aims::CoupledDiffusion2DSmoother< T >::doSmoothing().

_init

bool aims::_init

protected

Definition at line 158 of file filteringfunction_linear.h.

_kernel

carto::VolumeRef<double> aims::_kernel

protected

Definition at line 161 of file filteringfunction_linear.h.

_lambda

double aims::_lambda

protected

Definition at line 153 of file filteringfunction_linear.h.

_nstd

int aims::_nstd

protected

Definition at line 157 of file filteringfunction_linear.h.

_psi

double aims::_psi

protected

Definition at line 154 of file filteringfunction_linear.h.

_real

bool aims::_real

protected

Definition at line 156 of file filteringfunction_linear.h.

_sigma

double aims::_sigma

protected

Definition at line 151 of file filteringfunction_linear.h.

Referenced by aims::PeronaMalikSmoother< T >::doSmoothing(), and aims::PeronaMalikSmoother< T >::PeronaMalikSmoother().

_theta

double aims::_theta

protected

Definition at line 152 of file filteringfunction_linear.h.

_voxelsize

std::vector<float> aims::_voxelsize

protected

Definition at line 160 of file filteringfunction_linear.h.

BACKGROUND

const int aims::BACKGROUND = 0

Definition at line 46 of file greyLevelBlob.h.

Referenced by aims::GreyLevelBlob< T >::GreyLevelBlob(), and aims::ExtractGreyLevelBlobs< Geom, Text >::Run().