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

#include <vc/segmentation/LocalResliceParticleSim.hpp>

Inheritance diagram for volcart::segmentation::LocalResliceSegmentation:

Collaboration diagram for volcart::segmentation::LocalResliceSegmentation:

Public Types
using	Pointer = std::shared_ptr< LocalResliceSegmentation >

Public Types inherited from volcart::segmentation::ChainSegmentationAlgorithm
enum class	Status { Success , Failure , ReturnedEarly }

using	Pointer = std::shared_ptr< ChainSegmentationAlgorithm >

using	Chain = std::vector< cv::Vec3d >

using	PointSet = volcart::OrderedPointSet< cv::Vec3d >

using	Bounds = volcart::BoundingBox< double, 3 >

Public Member Functions
	LocalResliceSegmentation ()=default
	Default constructor.

	~LocalResliceSegmentation () override=default

void	setTargetZIndex (int z)
	Set the target z-index. More...

void	setOptimizationIterations (int n)
	Set the number of curve optimization iterations per step. More...

void	setAlpha (double a)
	Set the weight for the Active Contour metric. More...

void	setK1 (double k)
	Set the stretch weight factor. More...

void	setK2 (double k)
	Set the curvature weight factor. More...

void	setBeta (double b)
	Set the weight for the Absolute Curvature Sum metric. More...

void	setDelta (double d)
	Set the weight for the Arc Length metric. More...

void	setMaterialThickness (double m)
	Set the estimated thickness of the substrate (in um) More...

void	setResliceSize (int s)
	Set the reslice window size. More...

void	setDistanceWeightFactor (int f)
	Set the distance weight factor for candidate positions. More...

void	setConsiderPrevious (bool b)
	Set whether to consider previous position as candidate position. More...

auto	compute () -> PointSet override
	Compute the segmentation. More...

void	setVisualize (bool b)

void	setDumpVis (bool b)

auto	progressIterations () const -> std::size_t override
	Returns the maximum progress value. More...

Public Member Functions inherited from volcart::segmentation::ChainSegmentationAlgorithm
virtual	~ChainSegmentationAlgorithm ()=default

auto	progressIterations () const -> std::size_t override
	Returns the maximum progress value. More...

void	setVolume (Volume::Pointer vol)
	Set the input Volume. More...

void	setBounds (Bounds b)
	Set the bounding box for computation. More...

void	setChain (Chain c)
	Set the input chain of seed points. More...

void	setNumberOfSteps (std::size_t n)
	Set the number of propagation steps. More...

void	setStepSize (double s)
	Set the propagation step size. More...

auto	getStatus () const -> Status
	Get the status of the previous computation. More...

auto	getPointSet () const -> const PointSet &
	Get the segmented pointset. More...

auto	getPointSet () -> PointSet &
	Get the segmented pointset. More...

virtual std::size_t	progressIterations () const =0

Static Public Member Functions
template<typename... Args>
static auto	New (Args... args) -> Pointer

Private Member Functions
auto	estimate_normal_at_index_ (const FittedCurve &currentCurve, int index) -> cv::Vec3d
	Estimate the normal to the curve at point index. More...

auto	draw_particle_on_slice_ (const FittedCurve &curve, int sliceIndex, int particleIndex=-1, bool showSpline=false) const -> cv::Mat
	Debug: Draw curve on slice image. More...

auto	create_final_pointset_ (const std::vector< std::vector< Voxel > > &points) -> PointSet
	Convert the internal storage array into a final PointSet.

Private Attributes
int	endIndex_ {0}

double	alpha_ {1.0 / 3.0}

double	k1_ {0.5}

double	k2_ {0.5}

double	beta_ {1.0 / 3.0}

double	delta_ {1.0 / 3.0}

int	peakDistanceWeight_ {50}

bool	considerPrevious_ {false}

bool	dumpVis_ {false}

bool	visualize_ {false}

int	numIters_ {15}

double	materialThickness_ {100}

int	resliceSize_ {32}

Static Private Attributes
static constexpr double	DEFAULT_MIN_ENERGY_GRADIENT = 1e-7

Additional Inherited Members
Public Attributes inherited from volcart::IterationsProgress
Signal	progressStarted

Signal< std::size_t >	progressUpdated

Signal	progressComplete

Protected Member Functions inherited from volcart::segmentation::ChainSegmentationAlgorithm
	ChainSegmentationAlgorithm ()=default

Protected Attributes inherited from volcart::segmentation::ChainSegmentationAlgorithm
Volume::Pointer	vol_

Chain	startingChain_

Bounds	bb_

std::size_t	numSteps_ {0}

double	stepSize_ {1.0}

PointSet	result_

Status	status_ {Status::Success}

Detailed Description

Local Reslice Particle Simulation (LRPS) segmentation.

This algorithm propagates a chain of points forward through a volume from a starting z-index to an ending z-index. Each point is assumed to start within a "channel" of maximum intensity, that is, the bright voxels of a page layer. As the chain propagates forward, each point produces a reslice image that is locally orthogonal to the layer. Using this view, the algorithm finds the weighted set of maxima local to the point. These are assumed to be layer voxels on the current or a nearby layer. Using the sorted maxima for each point, the algorithm then selects the propagated positions for all points in the chain that minimize the energy loss of the chain curvature.

The ending index is inclusive.

Definition at line 34 of file LocalResliceParticleSim.hpp.

Member Typedef Documentation

◆ Pointer

using volcart::segmentation::LocalResliceSegmentation::Pointer = std::shared_ptr<LocalResliceSegmentation>

Pointer

Definition at line 38 of file LocalResliceParticleSim.hpp.

Constructor & Destructor Documentation

◆ ~LocalResliceSegmentation()

volcart::segmentation::LocalResliceSegmentation::~LocalResliceSegmentation ( )

overridedefault

Default destructor

Member Function Documentation

◆ compute()

auto volcart::segmentation::LocalResliceSegmentation::compute ( ) -> PointSet

overridevirtual

Compute the segmentation.

Implements volcart::segmentation::ChainSegmentationAlgorithm.

◆ draw_particle_on_slice_()

auto volcart::segmentation::LocalResliceSegmentation::draw_particle_on_slice_	(	const FittedCurve &	curve,
		int	sliceIndex,
		int	particleIndex = `-1`,
		bool	showSpline = `false`
	)		const -> cv::Mat

private

Debug: Draw curve on slice image.

Parameters

curve	Input curve
sliceIndex	Slice on which to draw
particleIndex	Highlight point at particleIndex
showSpline	Draw interpolated curve. Default only draws points

◆ estimate_normal_at_index_()

auto volcart::segmentation::LocalResliceSegmentation::estimate_normal_at_index_	(	const FittedCurve &	currentCurve,
		int	index
	)		-> cv::Vec3d

private

Estimate the normal to the curve at point index.

Parameters

currentCurve	Input curve
index	Index of point on curve

◆ New()

template<typename... Args>

static auto volcart::segmentation::LocalResliceSegmentation::New ( Args... args ) -> Pointer

inlinestatic

Make a new shared instance

Definition at line 48 of file LocalResliceParticleSim.hpp.

◆ progressIterations()

auto volcart::segmentation::LocalResliceSegmentation::progressIterations ( ) const -> std::size_t

overridevirtual

Returns the maximum progress value.

Reimplemented from volcart::segmentation::ChainSegmentationAlgorithm.

◆ setAlpha()

void volcart::segmentation::LocalResliceSegmentation::setAlpha ( double a )

inline

Set the weight for the Active Contour metric.

See also: double ActiveContourInternal()

Definition at line 64 of file LocalResliceParticleSim.hpp.

◆ setBeta()

void volcart::segmentation::LocalResliceSegmentation::setBeta ( double b )

inline

Set the weight for the Absolute Curvature Sum metric.

See also: double AbsCurvatureSum()

Definition at line 82 of file LocalResliceParticleSim.hpp.

◆ setConsiderPrevious()

void volcart::segmentation::LocalResliceSegmentation::setConsiderPrevious ( bool b )

inline

Set whether to consider previous position as candidate position.

Definition at line 105 of file LocalResliceParticleSim.hpp.

◆ setDelta()

void volcart::segmentation::LocalResliceSegmentation::setDelta ( double d )

inline

Set the weight for the Arc Length metric.

See also: double WindowedArcLength()

Definition at line 88 of file LocalResliceParticleSim.hpp.

◆ setDistanceWeightFactor()

void volcart::segmentation::LocalResliceSegmentation::setDistanceWeightFactor ( int f )

inline

Set the distance weight factor for candidate positions.

Definition at line 101 of file LocalResliceParticleSim.hpp.

◆ setDumpVis()

void volcart::segmentation::LocalResliceSegmentation::setDumpVis ( bool b )

inline

Debug: Dumps reslices and intensity maps to disk

Definition at line 114 of file LocalResliceParticleSim.hpp.

◆ setK1()

void volcart::segmentation::LocalResliceSegmentation::setK1 ( double k )

inline

Set the stretch weight factor.

See also: double ActiveContourInternal()

Definition at line 70 of file LocalResliceParticleSim.hpp.

◆ setK2()

void volcart::segmentation::LocalResliceSegmentation::setK2 ( double k )

inline

Set the curvature weight factor.

See also: double ActiveContourInternal()

Definition at line 76 of file LocalResliceParticleSim.hpp.

◆ setMaterialThickness()

void volcart::segmentation::LocalResliceSegmentation::setMaterialThickness ( double m )

inline

Set the estimated thickness of the substrate (in um)

Used to generate the radius of the structure tensor calculation

Definition at line 95 of file LocalResliceParticleSim.hpp.

◆ setOptimizationIterations()

void volcart::segmentation::LocalResliceSegmentation::setOptimizationIterations ( int n )

inline

Set the number of curve optimization iterations per step.

Definition at line 58 of file LocalResliceParticleSim.hpp.

◆ setResliceSize()

void volcart::segmentation::LocalResliceSegmentation::setResliceSize ( int s )

inline

Set the reslice window size.

Definition at line 98 of file LocalResliceParticleSim.hpp.

◆ setTargetZIndex()

void volcart::segmentation::LocalResliceSegmentation::setTargetZIndex ( int z )

inline

Set the target z-index.

Definition at line 55 of file LocalResliceParticleSim.hpp.

◆ setVisualize()

void volcart::segmentation::LocalResliceSegmentation::setVisualize ( bool b )

inline

Debug: Shows intensity maps in GUI window

Definition at line 111 of file LocalResliceParticleSim.hpp.

Member Data Documentation

◆ alpha_

double volcart::segmentation::LocalResliceSegmentation::alpha_ {1.0 / 3.0}

private

Active Contour weight parameter

Definition at line 151 of file LocalResliceParticleSim.hpp.

◆ beta_

double volcart::segmentation::LocalResliceSegmentation::beta_ {1.0 / 3.0}

private

Abs. Curvature Sum weight parameter

Definition at line 157 of file LocalResliceParticleSim.hpp.

◆ considerPrevious_

bool volcart::segmentation::LocalResliceSegmentation::considerPrevious_ {false}

private

Reconsider previous position flag

Definition at line 163 of file LocalResliceParticleSim.hpp.

◆ DEFAULT_MIN_ENERGY_GRADIENT

constexpr double volcart::segmentation::LocalResliceSegmentation::DEFAULT_MIN_ENERGY_GRADIENT = 1e-7

staticconstexprprivate

Default minimum energy gradient

Definition at line 146 of file LocalResliceParticleSim.hpp.

◆ delta_

double volcart::segmentation::LocalResliceSegmentation::delta_ {1.0 / 3.0}

private

Arc Length weight parameter

Definition at line 159 of file LocalResliceParticleSim.hpp.

◆ dumpVis_

bool volcart::segmentation::LocalResliceSegmentation::dumpVis_ {false}

private

Dump visualization to disk flag

Definition at line 165 of file LocalResliceParticleSim.hpp.

◆ endIndex_

int volcart::segmentation::LocalResliceSegmentation::endIndex_ {0}

private

Target z-index

Definition at line 149 of file LocalResliceParticleSim.hpp.

◆ k1_

double volcart::segmentation::LocalResliceSegmentation::k1_ {0.5}

private

Active Contour stretch parameter

Definition at line 153 of file LocalResliceParticleSim.hpp.

◆ k2_

double volcart::segmentation::LocalResliceSegmentation::k2_ {0.5}

private

Active Contour curvature parameter

Definition at line 155 of file LocalResliceParticleSim.hpp.

◆ materialThickness_

double volcart::segmentation::LocalResliceSegmentation::materialThickness_ {100}

private

Estimated material thickness in um

Definition at line 171 of file LocalResliceParticleSim.hpp.

◆ numIters_

int volcart::segmentation::LocalResliceSegmentation::numIters_ {15}

private

Number of curve optimization iterations

Definition at line 169 of file LocalResliceParticleSim.hpp.

◆ peakDistanceWeight_

int volcart::segmentation::LocalResliceSegmentation::peakDistanceWeight_ {50}

private

Distance weight factor for candidate positions

Definition at line 161 of file LocalResliceParticleSim.hpp.

◆ resliceSize_

int volcart::segmentation::LocalResliceSegmentation::resliceSize_ {32}

private

Window size for reslice

Definition at line 173 of file LocalResliceParticleSim.hpp.

◆ visualize_

bool volcart::segmentation::LocalResliceSegmentation::visualize_ {false}

private

Show visualization in GUI flag

Definition at line 167 of file LocalResliceParticleSim.hpp.

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

vc/segmentation/LocalResliceParticleSim.hpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Pointer

Constructor & Destructor Documentation

◆ ~LocalResliceSegmentation()

Member Function Documentation

◆ compute()

◆ draw_particle_on_slice_()

◆ estimate_normal_at_index_()

◆ New()

◆ progressIterations()

◆ setAlpha()

◆ setBeta()

◆ setConsiderPrevious()

◆ setDelta()

◆ setDistanceWeightFactor()

◆ setDumpVis()

◆ setK1()

◆ setK2()

◆ setMaterialThickness()

◆ setOptimizationIterations()

◆ setResliceSize()

◆ setTargetZIndex()

◆ setVisualize()

Member Data Documentation

◆ alpha_

◆ beta_

◆ considerPrevious_

◆ DEFAULT_MIN_ENERGY_GRADIENT

◆ delta_

◆ dumpVis_

◆ endIndex_

◆ k1_

◆ k2_

◆ materialThickness_

◆ numIters_

◆ peakDistanceWeight_

◆ resliceSize_

◆ visualize_