Segmentation algorithms and utilities library More...

Classes
class	ChainSegmentationAlgorithm
	Base class for segmentation algorithms that propagate a collected chain of points. More...

class	ComputeVolumetricMask
	Compute a VolumetricMask from a PointSet. More...

class	EnergyMetrics
	A collection of energy metrics for evaluating a FittedCurve. More...

class	FittedCurve
	Fits a curve to a set of points for resampling. More...

class	ForceChain
	A simple class for tracking a list of offset vectors ("forces") More...

class	IntensityMap
	A class representing the intensity map generated from a row of a matrix, normalized to the range [0, 1]. More...

class	LocalResliceSegmentation
	Local Reslice Particle Simulation (LRPS) segmentation. More...

class	OpticalFlowSegmentation
	Optical Flow Segmentation. More...

class	Particle
	A simple particle class. More...

class	ParticleChain
	A simple class for keeping track of a connected chain of Particle objects. More...

class	RegionGrowingSegmentationAlgorithmBaseClass
	Base class for segmentation algorithms that create a segmentation by growing from a set of seed points. More...

class	Spline
	Simple spline wrapper around Eigen::Spline. More...

class	StructureTensorParticleSim
	Structure Tensor Particle Simulation (STPS) segmentation. More...

class	ThinnedFloodFillSegmentation
	ThinnedFloodFillSegmentation. More...

Typedefs
template<typename Scalar >
using	CubicSpline = Spline< Scalar, 3 >

using	Force = cv::Vec3d

Functions
template<typename T1 , typename T2 >
std::vector< std::pair< T1, T2 > >	Zip (const std::vector< T1 > &v1, const std::vector< T2 > &v2)
	Combine two equal-sized vectors into a single vector of paired elements. More...

template<typename T , int Length>
std::pair< std::vector< T >, std::vector< T > >	Unzip (const std::vector< cv::Vec< T, Length > > &vs)
	Separate single vector of paired elements into two vectors of single elements. More...

template<typename T >
std::vector< double >	NormalizeVector (const std::vector< T > &v, double newMin=0, double newMax=1)
	Normalize vector elements to within the range [newMin, newMax]. More...

template<typename T , int Len>
std::vector< cv::Vec< double, Len > >	NormalizeVector (const std::vector< cv::Vec< T, Len > > vs)
	Normalize vector of cv::Vec using cv::norm. More...

template<typename T >
T	D1Forward (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the first derivative for a sampled point. More...

template<typename T >
T	D1Backward (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the first derivative for a sampled point. More...

template<typename T >
T	D1Central (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the first derivative for a sampled point. More...

template<typename T >
T	D1FivePointStencil (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the first derivative for a sampled point using a five-point stencil. More...

template<typename T >
T	D1At (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the first derivative for a sampled point. More...

template<typename T >
std::vector< T >	D1 (const std::vector< T > &vs, int hstep=1)
	Calculate the first derivative for a vector of sampled points. More...

template<typename T >
T	D2Forward (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the second derivative for a sampled point. More...

template<typename T >
T	D2Backward (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the second derivative for a sampled point. More...

template<typename T >
T	D2Central (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the second derivative for a sampled point. More...

template<typename T >
T	D2FivePointStencil (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the second derivative for a sampled point using a five-point stencil. More...

template<typename T >
T	D2At (const std::vector< T > &vs, int index, int hstep=1)
	Calculate the second derivative for a sampled point. More...

template<typename T >
std::vector< T >	D2 (const std::vector< T > &vs, int hstep=1)
	Calculate the second derivative for a vector of sampled points. More...

auto	operator+ (ForceChain lhs, const ForceChain &rhs) -> ForceChain

auto	operator* (ForceChain lhs, const double &rhs) -> ForceChain

auto	operator* (const double &rhs, ForceChain lhs) -> ForceChain

Particle	operator+ (Particle lhs, const cv::Vec3d &rhs)

Particle	operator* (Particle lhs, const double &rhs)

auto	operator+ (ParticleChain lhs, const ForceChain &rhs) -> ParticleChain

auto	operator+ (const ForceChain &rhs, ParticleChain lhs) -> ParticleChain

auto	operator* (ParticleChain lhs, const double &rhs) -> ParticleChain

auto	operator* (const double &rhs, ParticleChain lhs) -> ParticleChain

std::vector< cv::Vec3i >	GetNeighbors (const cv::Vec3i &v)

int	EuclideanDistance (const cv::Vec3i &start, const cv::Vec3i &end)

std::size_t	MeasureThickness (const cv::Vec3i &seed, const cv::Mat &slice, std::uint16_t low, std::uint16_t high, bool measureVert, std::size_t maxRadius)

template<class Container >
auto	Median (Container c)

std::vector< cv::Vec3i >	DoFloodFill (const std::vector< cv::Vec3i > &pts, int bound, cv::Mat img, std::uint16_t low, std::uint16_t high)

VectorMath
std::vector< double >	SquareDiff (const std::vector< Voxel > &v1, const std::vector< Voxel > &v2)
	Computes the difference of Squares on two vectors. More...

double	SumSquareDiff (const std::vector< double > &v1, const std::vector< double > &v2)
	Sums the square differences between two vectors. More...

Variables
static constexpr std::array< std::array< double, 9 >, 4 >	D1_CENTRAL_DIFF_COEFFS

static constexpr std::array< std::array< double, 9 >, 4 >	D2_CENTRAL_DIFF_COEFFS

Detailed Description

Segmentation algorithms and utilities library

Typedef Documentation

◆ Force

using volcart::segmentation::Force = typedef cv::Vec3d

Force type

Definition at line 13 of file ForceChain.hpp.

Function Documentation

◆ DoFloodFill()

std::vector< cv::Vec3i > volcart::segmentation::DoFloodFill	(	const std::vector< cv::Vec3i > &	pts,
		int	bound,
		cv::Mat	img,
		std::uint16_t	low,
		std::uint16_t	high
	)

Run flood fill using the provided set of seed points

Returns the contiguous set of points which fall within the range [low, high] and which are no more than bound distance from an initial seed.

◆ EuclideanDistance()

int volcart::segmentation::EuclideanDistance	(	const cv::Vec3i &	start,
		const cv::Vec3i &	end
	)

Calculate the Euclidean distance between two voxels

◆ GetNeighbors()

std::vector< cv::Vec3i > volcart::segmentation::GetNeighbors ( const cv::Vec3i & v )

Get the list of a voxel's eight neighbors

◆ MeasureThickness()

std::size_t volcart::segmentation::MeasureThickness	(	const cv::Vec3i &	seed,
		const cv::Mat &	slice,
		std::uint16_t	low,
		std::uint16_t	high,
		bool	measureVert,
		std::size_t	maxRadius
	)

Estimate the thickness of page from every seed point.

Projects bidirectionally from the seed until it finds voxels not in the range [low, high] or until maxRadius is reached. If measureVert is true, projects vertically from seed. Otherwise, projects horizontally.

◆ Median()

template<class Container >

auto volcart::segmentation::Median ( Container c )

Find the median element in a container

Definition at line 39 of file FloodFill.hpp.

◆ operator*() [1/5]

auto volcart::segmentation::operator*	(	const double &	rhs,
		ForceChain	lhs
	)		-> ForceChain

Free function operator for multiplying a ForceChain by a scalar

◆ operator*() [2/5]

auto volcart::segmentation::operator*	(	const double &	rhs,
		ParticleChain	lhs
	)		-> ParticleChain

Free function operator for multiplying a ParticleChain by a scalar

◆ operator*() [3/5]

auto volcart::segmentation::operator*	(	ForceChain	lhs,
		const double &	rhs
	)		-> ForceChain

Free function operator for multiplying a ForceChain by a scalar

◆ operator*() [4/5]

Particle volcart::segmentation::operator*	(	Particle	lhs,
		const double &	rhs
	)

Free function operator for Particle and scale factor multiplication

◆ operator*() [5/5]

auto volcart::segmentation::operator*	(	ParticleChain	lhs,
		const double &	rhs
	)		-> ParticleChain

Free function operator for multiplying a ParticleChain by a scalar

◆ operator+() [1/4]

auto volcart::segmentation::operator+	(	const ForceChain &	rhs,
		ParticleChain	lhs
	)		-> ParticleChain

Free function operator for ParticleChain and ForceChain addition

◆ operator+() [2/4]

auto volcart::segmentation::operator+	(	ForceChain	lhs,
		const ForceChain &	rhs
	)		-> ForceChain

Free function operator for per-element ForceChain addition

◆ operator+() [3/4]

Particle volcart::segmentation::operator+	(	Particle	lhs,
		const cv::Vec3d &	rhs
	)

Free function operator for Particle and vector offset addition

◆ operator+() [4/4]

auto volcart::segmentation::operator+	(	ParticleChain	lhs,
		const ForceChain &	rhs
	)		-> ParticleChain