Namespaces
	BucketBlobExtractor

	convolutionfilter

	convolutionsubsampler

	file

	internal

	io

	knn

	math

	meshdistance

	PointsDistribution

	proba

	ScaleSpace

	singlechannel

	strel

	type

	util

	vol

Classes
class	AffineLeastSquareEstimation

class	BarycenterCurvature

class	BaseDiffusionSmoother

class	BaseMaskedDiffusionSmoother

class	BaseScaleSpace

class	BBBMap

struct	bestPoint3d

class	Bifurcation

class	BlobMeasurements

class	BoixCurvature

class	BoixGaussianCurvature

class	BSpline

struct	BSplineOrder

struct	BSplineOrder< 0 >

class	BucketBlobExtractor

class	BundleTransformer

class	CausalSinglePoleIIRFilter

class	CBFMap

class	CBVMap

class	ClassifStrategy

class	ClusterArgMaker

class	ConeSamplable

class	ConvolutionFilter

class	ConvolutionSubSampler

class	CoordinatesFieldMeshInterpoler

class	CoupledDiffusion2DSmoother

class	CoupledSmoother

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

class	CubicResampler

class	Curvature

class	CurvatureFactory

class	DelayMap

class	DericheSmoother

class	DiffusionSmoother

class	DirectBSplineFilter

class	DirectBSplineSubSampler

class	DiscreteBSpline

class	DiscreteU

class	DiscreteUB

class	DiscriminantAnalysis

class	DiscriminantAnalysisElement

class	Distance

class	DynamicStrategy

class	ElementFilteringFunction

class	ElementFilteringFunctionFactory

class	ElementFilteringImageAlgorithm

struct	EnumInfo

class	ExtractGreyLevelBlobs

class	ExtremaDifferenceFilter

class	ExtremaDifferenceSubSampling

class	FastBSpline

class	FastMarching

class	FfdTransformation

class	FilteringFunctionInterface

class	FilteringImageAlgorithmInterface

struct	FilterType

class	FiniteElementCurvature

class	FiniteElementSmoother

class	FoldArgOverSegment

class	FoldGraphAttributes

class	GaborFilter

class	GeodesicPath

class	GeometricProperties

class	GradientAdvection

class	GradientDescent

class	GreyLevelBlob

class	GreyLevelBlobTools

class	HarmonicCageMeshResampler

class	HMap

class	IIRFilterBase

class	ImageAlgorithm

class	ImageAlgorithmInterface

class	ImageAlgorithmSwitch

class	ImageAlgorithmSwitch< T, false >

class	ImageAlgorithmSwitch< T, true >

class	Individuals

class	InterpolatedVolume

class	InverseBSplineFilter

class	IterativeClassification

class	KmeansStrategy

class	LinearFilteringFunction

class	LinearFilteringFunctionFactory

class	LinearFilteringImageAlgorithm

class	LinearResampler

struct	ltstr_blob

struct	ltstr_p3d

struct	ltstr_p3d< Point3d >

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

class	MajorityFilter

class	MajorityLabelResampler

class	MajoritySubSampling

class	MaskedDiffusionSmoother

class	MaskedDiffusionSmoother< T, AimsData< short > >

class	MaskedDiffusionSmoother< T, std::vector< Point3df > >

class	MaxFilter

class	MaximumPoint

class	MaxSubSampling

class	MeanFilter

class	MeanSubSampling

class	MedianFilter

class	MedianResampler

class	MedianSubSampling

class	MeshInterpoler

class	MeshToVoxelsResampler

class	MinFilter

class	MinSubSampling

class	MixtureOfPPCA

class	MorphoGreyLevel

class	MovingAverageCascadeFilter

class	MovingAverageCascadeKernel

class	MovingAverageCascadeSubSampler

class	MovingAverageFilter

class	MovingAverageKernel

class	MovingAverageSubSampler

class	MTTMap

struct	MultiChannelResamplerSwitch

struct	MultiChannelResamplerSwitch< false, T >

struct	MultiChannelResamplerSwitch< true, T >

class	NearestNeighborResampler

class	Newton
	Newton's Method for optimization. More...

class	NoLineSearch
	Object used by classes that can take a line search tool as template argument but need a default object when no line search is needed. More...

class	NormalDistribution

class	NormalEstimation

class	NotNullMeanFilter

class	NotNullMeanSubSampling

class	NotNullMedianFilter

class	NotNullMedianSubSampling

struct	PairCompare

class	PcaStrategy

class	PerfusionAif

class	PerfusionAifAverage

class	PerfusionAifBest

class	PerfusionAifFactory

class	PerfusionAifLinearCorrection

class	PerfusionAifMatrix

class	PerfusionAifMatrixFactory

class	PerfusionAifMatrixStrategy

class	PerfusionAifNoCorrection

class	PerfusionAifPoints

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	PerfusionMask

class	PerfusionNoFit

class	PerfusionNoSmoothing

class	PerfusionParameters

class	PerfusionPreInjection

class	PerfusionProcessing

class	PerfusionProcessingCenter

class	PerfusionQuantification

class	PerfusionSkip

class	PerfusionSmoothing

class	PerfusionSmoothing2D

class	PerfusionSmoothing3D

class	PerfusionSmoothingBase

class	PerfusionSmoothingFactory

class	PerfusionSmoothingStrategy

class	PerfusionSmoothingT

class	PerfusionSplitVolume

class	PerfusionSVDDeconvolution

class	PerfusionSVDFactory

class	PerfusionSVDInversion

class	PerfusionSVDStrategy

class	PerfusionSVDTikhonov

class	PerfusionSVDTikhonovGradient

class	PerfusionSVDTruncated

class	PeronaMalikSmoother

struct	Point3dCompare

struct	Point3dfCompare

class	PointsDistribution

class	PpcaAnalyserElement

class	PrimalSketch

class	Primalsketch2graph

class	ProbabilisticPca

class	ProbabilisticPcaElement

class	QuadraticResampler

class	QuarticResampler

class	QuinticResampler

class	RealToRealFunctionTabulation

class	RegularBinnedHistogram

class	Resampler

class	ResamplerFactory

class	RigidLeastSquareEstimation

class	RigidTransformEstimation

class	RoiGtm

class	RoiGtmReader

class	RoiGtmWriter

class	RoiSelector

class	RoiSelectorReader

class	RoiStats

class	SaddlePoint

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

struct	SetCompare

class	SeventhOrderResampler

class	SimiLeastSquareEstimation

class	SixthOrderResampler

class	Smoother

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

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

class	Spam

class	SpamBase

class	SpamFromLikelihood

class	SphereSamplable

class	SplineFfd

class	SplinePyramid

class	SplinePyramidBuilder

class	SplineResampler

class	StDevFilter

class	SubSamplingImageAlgorithm

class	SubSamplingPyramidBuilder

class	SumFilter

class	SumSubSampling

class	SymAllPoleIIRFilter

class	TabulBSpline

class	TextureSmoothing

class	TransformLeastSquareEstimation

class	TranslationLeastSquareEstimation

class	TrilinearFfd

class	TTPMap

class	VarFilter

class	WolfeLineSearch
	Once an ascent direction is given, this class performs a line search that respects wolfe conditions. More...

class	Writer< aims::FfdTransformation >

Typedefs
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

enum	PrimalsketchDataType

enum	PrimalSketchEvents

Functions
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)

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)

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)

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)

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)

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

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

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

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

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

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

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

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

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

AimsBucket< Void > *	GetSSBlobMeshBucket (AimsSurfaceTriangle *mesh)

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

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

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

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

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

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

class	__attribute__ ((__deprecated__)) MaskLinearResampler

int	mirrorCoeff (int i, int size)

	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)

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

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

void	setKernel ()

	AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE (GaborFilterFunc, AimsRGB)

	AIMS_LIN_FILTERFUNC_MULTICHANNEL_DECLARE (GaborFilterFunc, AimsRGBA)

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

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

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

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)

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

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

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

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

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

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

template<typename T >
std::ostream &	operator<< (std::ostream &out, const std::vector< T > &v)

void	message (const std::string &message, bool header, bool doit=true)

void	setOutColor (const std::string &color="black", bool light=false)

void	resetOutColor ()

Variables
	NORM1

	NORM2

	NORM2SQR

	INFNORM

	SURFACE

	IMAGE

	APPEAR

	DISAPPEAR

	MERGE

	SPLIT

	COMPLEX

const int	BACKGROUND

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

Function Documentation

◆ message()

void aims::message	(	const std::string &	message,
		bool	header,
		bool	doit = `true`
	)

Definition at line 42 of file trace.h.

References resetOutColor(), and setOutColor().

◆ operator<<()

template<typename T >

std::ostream& aims::operator<<	(	std::ostream &	out,
		const std::vector< T > &	v
	)

Definition at line 32 of file trace.h.

◆ resetOutColor()

void aims::resetOutColor ( )

Referenced by message().

◆ setOutColor()

void aims::setOutColor	(	const std::string &	color = `"black"`,
		bool	light = `false`
	)

Referenced by message().

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Function Documentation

◆ message()

◆ operator<<()

◆ resetOutColor()

◆ setOutColor()