#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 = OrderedPointSet< cv::Vec3d >

using	Bounds = BoundingBox< double, 3 >

Public Member Functions
	OpticalFlowSegmentation ()=default
	Default constructor.

	~OpticalFlowSegmentation () override=default

void	setStartZIndex (int z)
	Set the start z-index.

auto	getStartZIndex () const -> int
	Get the start z-index.

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

auto	getTargetZIndex () const -> int
	Get 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	setEnableSmoothOutliers (bool enable)
	Set whether to enable outlier points smoothening.

void	setEnableEdgeDetection (bool enable)
	Set whether to enable edge detection.

void	setEdgeJumpDistance (std::uint32_t distance)
	Set the minimum jump distance for edge detection.

void	setEdgeBounceDistance (std::uint32_t distance)
	Set the maximum bounce distance for edge detection.

void	setInterpolate (bool b)
	Set whether to interpolate against the master cloud.

void	setInterpolationWindow (std::uint32_t window)
	Set how wide the interpolation window should be.

auto	getInterpolationWindow () const -> std::uint32_t
	Get how wide the interpolation window should be.

void	setInterpolationDistance (std::uint32_t distance)
	Set how many slices the interpolation center is away from the start slice.

auto	getInterpolationDistance () const -> std::uint32_t
	Get how many slices the interpolation center is away from the start slice.

void	setMasterCloud (PointSet masterCloud)
	Set the already computed masterCloud OrderedPointSet.

void	setReSegmentationChain (Chain c)
	Set the input chain of re-segmentation points.

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
	~ChainSegmentationAlgorithm () override=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) const -> std::vector< Voxel >
	Compute the curve for z + 1 given a curve on z using the optical flow between the two slices.

auto	interpolate_ (int interpStart, int interpEnd, int startChain, int startResegChain) -> std::vector< std::vector< Voxel > >
	Blend the re-segmentation run into the forward run over an interpolation window. More...

auto	run_ofs_ (Chain currentVs, int startChainIndex, int anchorEndIdx, int targetIndex, int stepAdjustment, std::size_t &iteration, bool backwards, const filesystem::path &debugDir) -> std::tuple< std::vector< std::vector< Voxel > >, Status >
	Run the optical flow segmentation in one direction. More...

Private Attributes
int	startIndex_ {0}

int	endIndex_ {0}

std::uint8_t	outsideThreshold_ {80}

std::uint8_t	opticalFlowPixelThreshold_ {80}

std::uint32_t	opticalFlowDisplacementThreshold_ {10}

std::uint8_t	smoothByBrightness_ {180}

bool	enableSmoothenOutlier_ {true}

bool	enableEdge_ {false}

std::uint32_t	edgeJumpDistance_ {6}

std::uint32_t	edgeBounceDistance_ {3}

bool	requestInterp_ {false}

std::uint32_t	interpWindow_ {5}

std::uint32_t	interpDist_ {25}

Chain	resegStartingChain_

PointSet	masterCloud_

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

Date: 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 32 of file OpticalFlowSegmentation.hpp.

Member Typedef Documentation

◆ Pointer

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

Pointer

Definition at line 36 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.

◆ interpolate_()

auto volcart::segmentation::OpticalFlowSegmentation::interpolate_	(	int	interpStart,
		int	interpEnd,
		int	startChain,
		int	startResegChain
	)		-> std::vector< std::vector< Voxel > >

private

Blend the re-segmentation run into the forward run over an interpolation window.

Parameters

interpStart	First z-slice of the interpolation window
interpEnd	Last z-slice of the interpolation window
startChain	Z-index of the primary starting chain
startResegChain	Z-index of the re-segmentation starting chain

◆ New()

template<typename... Args>

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

inlinestatic

Make a new shared instance

Definition at line 46 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.

◆ run_ofs_()

auto volcart::segmentation::OpticalFlowSegmentation::run_ofs_	(	Chain	currentVs,
		int	startChainIndex,
		int	anchorEndIdx,
		int	targetIndex,
		int	stepAdjustment,
		std::size_t &	iteration,
		bool	backwards,
		const filesystem::path &	debugDir
	)		-> std::tuple< std::vector< std::vector< Voxel > >, Status >

private

Run the optical flow segmentation in one direction.

Parameters

currentVs	Starting chain of points
startChainIndex	Z-index of the starting chain
anchorEndIdx	Z-index at which to stop and return
targetIndex	Final target z-index (used for bounds checking)
stepAdjustment	Initial step offset to align with the grid
iteration	Running progress counter (updated in place)
backwards	True to propagate toward lower z-indices
debugDir	Root directory for debug visualizations

◆ 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 259 of file OpticalFlowSegmentation.hpp.

◆ edgeBounceDistance_

std::uint32_t volcart::segmentation::OpticalFlowSegmentation::edgeBounceDistance_ {3}

private

Maximum displacement (voxels) allowed as a bounce from an edge

Definition at line 243 of file OpticalFlowSegmentation.hpp.

◆ edgeJumpDistance_

std::uint32_t volcart::segmentation::OpticalFlowSegmentation::edgeJumpDistance_ {6}

private

Minimum displacement (voxels) considered an edge jump

Definition at line 241 of file OpticalFlowSegmentation.hpp.

◆ enableEdge_

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

private

Enable edge detection to constrain point movement

Definition at line 239 of file OpticalFlowSegmentation.hpp.

◆ enableSmoothenOutlier_

bool volcart::segmentation::OpticalFlowSegmentation::enableSmoothenOutlier_ {true}

private

Enable smoothing of detected outlier points

Definition at line 237 of file OpticalFlowSegmentation.hpp.

◆ endIndex_

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

private

Target z-index

Definition at line 203 of file OpticalFlowSegmentation.hpp.

◆ interpDist_

std::uint32_t volcart::segmentation::OpticalFlowSegmentation::interpDist_ {25}

private

Distance in slices from the start slice to the interpolation center

Definition at line 249 of file OpticalFlowSegmentation.hpp.

◆ interpWindow_

std::uint32_t volcart::segmentation::OpticalFlowSegmentation::interpWindow_ {5}

private

Half-width of the interpolation window in slices (must be positive)

Definition at line 247 of file OpticalFlowSegmentation.hpp.

◆ masterCloud_

PointSet volcart::segmentation::OpticalFlowSegmentation::masterCloud_

private

Pre-computed master cloud used for interpolation blending

Definition at line 253 of file OpticalFlowSegmentation.hpp.

◆ materialThickness_

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

private

Estimated material thickness in um

Definition at line 255 of file OpticalFlowSegmentation.hpp.

◆ maxThreads_

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

private

Maximum number of threads

Definition at line 257 of file OpticalFlowSegmentation.hpp.

◆ opticalFlowDisplacementThreshold_

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

private

Threshold of how many pixels 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 228 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 219 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 210 of file OpticalFlowSegmentation.hpp.

◆ requestInterp_

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

private

Enable blending of OFS output against the master cloud

Definition at line 245 of file OpticalFlowSegmentation.hpp.

◆ resegStartingChain_

Chain volcart::segmentation::OpticalFlowSegmentation::resegStartingChain_

private

Re-segmentation starting chain provided by the caller

Definition at line 251 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 235 of file OpticalFlowSegmentation.hpp.

◆ startIndex_

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

private

Start z-index

Definition at line 201 of file OpticalFlowSegmentation.hpp.

◆ visualize_

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

private

Show visualization in GUI flag

Definition at line 261 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()

◆ interpolate_()

◆ New()

◆ progressIterations()

◆ run_ofs_()

◆ setDumpVis()

◆ setMaterialThickness()

◆ setVisualize()

Member Data Documentation

◆ dumpVis_

◆ edgeBounceDistance_

◆ edgeJumpDistance_

◆ enableEdge_

◆ enableSmoothenOutlier_

◆ endIndex_

◆ interpDist_

◆ interpWindow_

◆ masterCloud_

◆ materialThickness_

◆ maxThreads_

◆ opticalFlowDisplacementThreshold_

◆ opticalFlowPixelThreshold_

◆ outsideThreshold_

◆ requestInterp_

◆ resegStartingChain_

◆ smoothByBrightness_

◆ startIndex_

◆ visualize_