#include <vc/segmentation/OpticalFlowSegmentation.hpp>

Inheritance diagram for volcart::segmentation::OpticalFlowSegmentation:

Collaboration diagram for volcart::segmentation::OpticalFlowSegmentation:

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

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
	OpticalFlowSegmentation ()=default
	Default constructor.

	~OpticalFlowSegmentation () override=default

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

void	setOutsideThreshold (std::uint8_t outside)
	Set the threshold of what pixel brightness is considered inside a sheet (higher as threshold) and outside (lower as threshold)

void	setOFThreshold (std::uint8_t ofThr)
	Set the threshold of what pixel brightness is considered while calculating optical flow, darker pixels OF is interpolated from brighter ones in the area.

void	setOFDispThreshold (std::uint32_t ofDispThrs)
	Set the maximum single pixel optical flow displacement before interpolating a pixel region.

void	setSmoothBrightnessThreshold (std::uint8_t brightness)
	Set the threshold for what pixel brightness is considered as being outside the sheet. Pixels above this threshold are considered outside the sheet and are smoothed in an attempt to get them tracking the sheet again.

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

void	setMaxThreads (std::uint32_t t)
	Set the maximum number of threads.

void	resetMaxThreads ()
	Clear the maximum number of threads.

void	setVisualize (bool b)

void	setDumpVis (bool b)

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

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	compute_curve_ (const FittedCurve &currentCurve, int zIndex) -> std::vector< Voxel >
	Compute the curve for z + 1 given a curve on z using the optical flow between the two slices.

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}

std::uint8_t	outsideThreshold_ {80}

std::uint8_t	opticalFlowPixelThreshold_ {80}

std::uint32_t	opticalFlowDisplacementThreshold_ {10}

std::uint8_t	smoothByBrightness_ {180}

double	materialThickness_ {100}

std::optional< std::uint32_t >	maxThreads_

bool	dumpVis_ {false}

bool	visualize_ {false}

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

Optical Flow Segmentation.

Author: Julian Schilliger (May 2023)

This algorithm propagates a chain of points forward through a volume from a starting z-index to an ending z-index (inclusive). It uses optical flow to track the shape of the layer. Each seed point is assumed to be placed within the layer rather than on its surface boundary.

Warning: This algorithm is non-deterministic and yields slightly different results each run.

Definition at line 31 of file OpticalFlowSegmentation.hpp.

Member Typedef Documentation

◆ Pointer

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

Pointer

Definition at line 35 of file OpticalFlowSegmentation.hpp.

Constructor & Destructor Documentation

◆ ~OpticalFlowSegmentation()

volcart::segmentation::OpticalFlowSegmentation::~OpticalFlowSegmentation ( )

overridedefault

Default destructor

Member Function Documentation

◆ compute()

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

overridevirtual

Compute the segmentation.

Implements volcart::segmentation::ChainSegmentationAlgorithm.

◆ draw_particle_on_slice_()

auto volcart::segmentation::OpticalFlowSegmentation::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

◆ New()

template<typename... Args>

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

inlinestatic

Make a new shared instance

Definition at line 45 of file OpticalFlowSegmentation.hpp.

◆ progressIterations()

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

overridevirtual

Returns the maximum progress value.

Reimplemented from volcart::segmentation::ChainSegmentationAlgorithm.

◆ setDumpVis()

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

Debug: Dumps reslices and intensity maps to disk

◆ setMaterialThickness()

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

Set the estimated thickness of the substrate (in um)

Used to generate the radius of the structure tensor calculation

◆ setVisualize()

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

Debug: Shows intensity maps in GUI window

Member Data Documentation

◆ dumpVis_

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

private

Dump visualization to disk flag

Definition at line 170 of file OpticalFlowSegmentation.hpp.

◆ endIndex_

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

private

Target z-index

Definition at line 132 of file OpticalFlowSegmentation.hpp.

◆ materialThickness_

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

private

Estimated material thickness in um

Definition at line 166 of file OpticalFlowSegmentation.hpp.

◆ maxThreads_

std::optional<std::uint32_t> volcart::segmentation::OpticalFlowSegmentation::maxThreads_

private

Maximum number of threads

Definition at line 168 of file OpticalFlowSegmentation.hpp.

◆ opticalFlowDisplacementThreshold_

std::uint32_t volcart::segmentation::OpticalFlowSegmentation::opticalFlowDisplacementThreshold_ {10}

private

Threshold of how many pixel optical flow can displace a point, if higher, recompute optical flow with region's average flow. This parameter sets the maximum single pixel optical flow displacement before interpolating a pixel region. Range minimum: 0. Higher values allow more displacement before interpolation, while lower values trigger interpolation more frequently.

Definition at line 157 of file OpticalFlowSegmentation.hpp.

◆ opticalFlowPixelThreshold_

std::uint8_t volcart::segmentation::OpticalFlowSegmentation::opticalFlowPixelThreshold_ {80}

private

Disregarding pixel that are darker during optical flow computation. This parameter sets the threshold for what pixel brightness is considered while calculating optical flow. Darker pixels' optical flow is interpolated from brighter ones in the area. Range: 0-255. Higher values disregard more dark pixels during computation, while lower values include more dark pixels.

Definition at line 148 of file OpticalFlowSegmentation.hpp.

◆ outsideThreshold_

std::uint8_t volcart::segmentation::OpticalFlowSegmentation::outsideThreshold_ {80}

private

Darker pixels are considered outside the sheet. This parameter sets the threshold of what pixel brightness is considered too deep inside a sheet (higher than the threshold) and then tries to smoothen those points back towards the edge of the sheet. Range: 0-255.

Definition at line 139 of file OpticalFlowSegmentation.hpp.

◆ smoothByBrightness_

std::uint8_t volcart::segmentation::OpticalFlowSegmentation::smoothByBrightness_ {180}

private

This parameter sets the threshold for what pixel brightness is considered as being outside the sheet. Pixels considered outside the sheet are smoothed in an attempt to get them tracking the sheet again. Range: 0-255. Smooth curve at pixels above this threshold.

Definition at line 164 of file OpticalFlowSegmentation.hpp.

◆ visualize_

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

private

Show visualization in GUI flag

Definition at line 172 of file OpticalFlowSegmentation.hpp.

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

vc/segmentation/OpticalFlowSegmentation.hpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Pointer

Constructor & Destructor Documentation

◆ ~OpticalFlowSegmentation()

Member Function Documentation

◆ compute()

◆ draw_particle_on_slice_()

◆ New()

◆ progressIterations()

◆ setDumpVis()

◆ setMaterialThickness()

◆ setVisualize()

Member Data Documentation

◆ dumpVis_

◆ endIndex_

◆ materialThickness_

◆ maxThreads_

◆ opticalFlowDisplacementThreshold_

◆ opticalFlowPixelThreshold_

◆ outsideThreshold_

◆ smoothByBrightness_

◆ visualize_