#include <aims/mesh/mesher.h>

Public Types
enum	SmoothingType { LAPLACIAN , SIMPLESPRING , POLYGONSPRING , LOWPASS }

Public Member Functions
	Mesher ()

virtual	~Mesher ()

void	getInterface (std::map< size_t, std::list< MapOfFacet > > &interface, const carto::rc_ptr< carto::Volume< short > > &thing)

void	doit (const carto::rc_ptr< carto::Volume< short > > &thing, const std::string &name, const std::string &mode="binar")

void	doit (const aims::BucketMap< Void > &thing, const std::string &name, const std::string &mode="binar")

void	doit (const carto::rc_ptr< carto::Volume< short > > &thing, std::map< size_t, std::list< AimsSurfaceTriangle > > &surface)

void	doit (const aims::BucketMap< Void > &thing, std::map< size_t, std::list< AimsSurfaceTriangle > > &surface)

void	getBrain (const carto::rc_ptr< carto::Volume< short > > &thing, AimsSurfaceTriangle &surface, bool insideinterface=false)

void	getBrain (const aims::BucketMap< Void > &thing, AimsSurfaceTriangle &surface, bool insideinterface=false)

void	getWhite (const carto::rc_ptr< carto::Volume< short > > &thing, AimsSurfaceTriangle &surface)

void	getWhite (const aims::BucketMap< Void > &thing, AimsSurfaceTriangle &surface)

void	getSingleLabel (const carto::rc_ptr< carto::Volume< short > > &thing, AimsSurfaceTriangle &surface)

void	getMeshFromMapOfFacet (const carto::rc_ptr< carto::Volume< short > > &thing, AimsSurfaceTriangle &surface, MapOfFacet &mof)

void	setSmoothing (SmoothingType smoothType, int smoothIt, float smoothRate)
	Smoothing. More...

void	setSmoothingLaplacian (float smoothFeatureAngle)

void	setSmoothingSpring (float smoothForce)

void	unsetSmoothing ()

void	smooth (AimsSurfaceTriangle &surface)

void	setDecimation (float deciReductionRate, float deciMaxClearance, float deciMaxError, float deciFeatureAngle)
	Decimation. More...

void	unsetDecimation ()

float	decimate (AimsSurfaceTriangle &surface)

float	decimate (AimsSurfaceTriangle &surface, const std::vector< float > &precthresholds, const TimeTexture< float > &precisionmap)
	Decimation using a precision texture map. More...

void	doit (const carto::rc_ptr< carto::Volume< short > > &thing, std::map< size_t, std::list< std::map< short, std::list< AimsSurfaceTriangle > > > > &surface)

void	doit (const aims::BucketMap< Void > &thing, std::map< size_t, std::list< std::map< short, std::list< AimsSurfaceTriangle > > > > &surface)

void	setSplitting ()

void	unsetSplitting ()

void	setLabelInf (int labelInf)

void	setLabelSup (int labelSup)

void	setMinSurface (float minSurface)

float	surfaceOfInterface (const AimsSurfaceTriangle &surface)

void	setTriOutputFile () __attribute__((__deprecated__("specify extension in the output filename " "of setMeshOutputFile() or doit()")))
	OBSOLETE - specify extension in the output filename of setMeshOutputFile() or doit() More...

void	setMeshOutputFile ()

void	setMinFacetNumber (uint m)

bool	verbose () const

void	setVerbose (bool x)

Protected Member Functions
void	getReducedNeighOutwardCycles (MapOfFacet &thing)

void	getExtendedNeighOfFacet (MapOfFacet &thing)

void	getVertices (const std::vector< Facet * > &vfac, std::vector< Point3df > &vertex, float sizeX, float sizeY, float sizeZ)

void	getSmoothedVertices (const std::vector< Facet * > &vfac, AimsSurfaceTriangle &surface, float rate)

void	getSmoothedLaplacian (const std::vector< Facet * > &vfac, AimsSurfaceTriangle &surface, float featureAngle, int nIteration, float rate)

void	getSmoothedSimpleSpring (const std::vector< Facet * > &vfac, AimsSurfaceTriangle &surface, float force, int nIteration, float rate)

void	getSmoothedPolygonSpring (const std::vector< Facet * > &vfac, AimsSurfaceTriangle &surface, float force, int nIteration, float rate)

void	getSmoothedLowPassFilter (const std::vector< Facet * > &vfac, AimsSurfaceTriangle &surface, int nIteration, float rate)

void	getDecimatedVertices (std::vector< Facet * > &vfac, std::vector< Point3df > &vertex, float reductionRatePercent, float maxClearanceMm, float maxErrorMm, float minFeatureEdgeAngleDegree)

void	getDecimatedVertices (std::vector< Facet * > &vfac, std::vector< Point3df > &vertex, float reductionRatePercent, float maxClearanceMm, float maxErrorMm, float minFeatureEdgeAngleDegree, const std::vector< float > &thresholds, const TimeTexture< float > *precisionmap=0)

float	decimate (AimsSurfaceTriangle &surface, const std::vector< float > &thresholds, const TimeTexture< float > *precisionmap)

void	getNormals (const std::vector< Facet * > &vfac, const std::vector< Point3df > &vertex, std::vector< Point3df > &normal)

void	getTriangles (const std::vector< Facet * > &vfac, std::vector< AimsVector< uint, 3 > > &triangle)

void	splitting (const carto::rc_ptr< carto::Volume< short > > &thing, const std::vector< Facet * > &vfac, const AimsSurfaceTriangle &surface, std::map< short, std::list< AimsSurfaceTriangle > > &splitted)

void	getFacet (const AimsSurfaceTriangle &surface, std::vector< Facet * > &vfac)

void	clear (std::map< size_t, std::list< MapOfFacet > > &interface)

Static Protected Member Functions
static carto::VolumeRef< int16_t >	reshapedVolume (const carto::VolumeRef< int16_t > in_vol)
	reshape (if needed) the input volume to add a border filled with -1 More...

Protected Attributes
bool	_smoothFlag

int	_smoothIt

float	_smoothRate

float	_smoothFeatureAngle

float	_smoothForce

SmoothingType	_smoothType

bool	_deciFlag

float	_deciReductionRate

float	_deciMaxClearance

float	_deciMaxError

float	_deciFeatureAngle

bool	_splittingFlag

int	_labelInf

int	_labelSup

float	_minSurface

bool	_triOutputFlag

uint	_minFacetNumber

bool	_verbose

Detailed Description

Definition at line 52 of file mesher.h.

Member Enumeration Documentation

◆ SmoothingType

enum Mesher::SmoothingType

Enumerator
LAPLACIAN
SIMPLESPRING
POLYGONSPRING
LOWPASS

Definition at line 55 of file mesher.h.

Constructor & Destructor Documentation

◆ Mesher()

Mesher::Mesher ( )

inline

Definition at line 63 of file mesher.h.

◆ ~Mesher()

virtual Mesher::~Mesher ( )

inlinevirtual

Definition at line 81 of file mesher.h.

Member Function Documentation

◆ clear()

void Mesher::clear ( std::map< size_t, std::list< MapOfFacet > > & interface )

protected

◆ decimate() [1/3]

float Mesher::decimate ( AimsSurfaceTriangle & surface )

◆ decimate() [2/3]

float Mesher::decimate	(	AimsSurfaceTriangle &	surface,
		const std::vector< float > &	precthresholds,
		const TimeTexture< float > &	precisionmap
	)

Decimation using a precision texture map.

In this mode, the texture values are checked according to the precision thresholds, and vertices above the threshold are not removed. A time texture may be provided if a step-by-step evolution is needed. Similarly, the thresholds may evolve with decimation timesteps. precisionmap and thresholds may have differing sizes (they are clamped if overrun).

◆ decimate() [3/3]

float Mesher::decimate	(	AimsSurfaceTriangle &	surface,
		const std::vector< float > &	thresholds,
		const TimeTexture< float > *	precisionmap
	)

protected

◆ doit() [1/6]

void Mesher::doit	(	const aims::BucketMap< Void > &	thing,
		const std::string &	name,
		const std::string &	mode = `"binar"`
	)

◆ doit() [2/6]

void Mesher::doit	(	const aims::BucketMap< Void > &	thing,
		std::map< size_t, std::list< AimsSurfaceTriangle > > &	surface
	)

◆ doit() [3/6]

void Mesher::doit	(	const aims::BucketMap< Void > &	thing,
		std::map< size_t, std::list< std::map< short, std::list< AimsSurfaceTriangle > > > > &	surface
	)

◆ doit() [4/6]

void Mesher::doit	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		const std::string &	name,
		const std::string &	mode = `"binar"`
	)

Referenced by aims::ClusterArgMaker::make().

◆ doit() [5/6]

void Mesher::doit	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		std::map< size_t, std::list< AimsSurfaceTriangle > > &	surface
	)

◆ doit() [6/6]

void Mesher::doit	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		std::map< size_t, std::list< std::map< short, std::list< AimsSurfaceTriangle > > > > &	surface
	)

◆ getBrain() [1/2]

void Mesher::getBrain	(	const aims::BucketMap< Void > &	thing,
		AimsSurfaceTriangle &	surface,
		bool	insideinterface = `false`
	)

◆ getBrain() [2/2]

void Mesher::getBrain	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		AimsSurfaceTriangle &	surface,
		bool	insideinterface = `false`
	)

◆ getDecimatedVertices() [1/2]

void Mesher::getDecimatedVertices	(	std::vector< Facet * > &	vfac,
		std::vector< Point3df > &	vertex,
		float	reductionRatePercent,
		float	maxClearanceMm,
		float	maxErrorMm,
		float	minFeatureEdgeAngleDegree
	)

protected

◆ getDecimatedVertices() [2/2]

void Mesher::getDecimatedVertices	(	std::vector< Facet * > &	vfac,
		std::vector< Point3df > &	vertex,
		float	reductionRatePercent,
		float	maxClearanceMm,
		float	maxErrorMm,
		float	minFeatureEdgeAngleDegree,
		const std::vector< float > &	thresholds,
		const TimeTexture< float > *	precisionmap = `0`
	)

protected

◆ getExtendedNeighOfFacet()

void Mesher::getExtendedNeighOfFacet ( MapOfFacet & thing )

protected

◆ getFacet()

void Mesher::getFacet	(	const AimsSurfaceTriangle &	surface,
		std::vector< Facet * > &	vfac
	)

protected

◆ getInterface()

void Mesher::getInterface	(	std::map< size_t, std::list< MapOfFacet > > &	interface,
		const carto::rc_ptr< carto::Volume< short > > &	thing
	)

◆ getMeshFromMapOfFacet()

void Mesher::getMeshFromMapOfFacet	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		AimsSurfaceTriangle &	surface,
		MapOfFacet &	mof
	)

◆ getNormals()

void Mesher::getNormals	(	const std::vector< Facet * > &	vfac,
		const std::vector< Point3df > &	vertex,
		std::vector< Point3df > &	normal
	)

protected

◆ getReducedNeighOutwardCycles()

void Mesher::getReducedNeighOutwardCycles ( MapOfFacet & thing )

protected

◆ getSingleLabel()

void Mesher::getSingleLabel	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		AimsSurfaceTriangle &	surface
	)

◆ getSmoothedLaplacian()

void Mesher::getSmoothedLaplacian	(	const std::vector< Facet * > &	vfac,
		AimsSurfaceTriangle &	surface,
		float	featureAngle,
		int	nIteration,
		float	rate
	)

protected

◆ getSmoothedLowPassFilter()

void Mesher::getSmoothedLowPassFilter	(	const std::vector< Facet * > &	vfac,
		AimsSurfaceTriangle &	surface,
		int	nIteration,
		float	rate
	)

protected

◆ getSmoothedPolygonSpring()

void Mesher::getSmoothedPolygonSpring	(	const std::vector< Facet * > &	vfac,
		AimsSurfaceTriangle &	surface,
		float	force,
		int	nIteration,
		float	rate
	)

protected

◆ getSmoothedSimpleSpring()

void Mesher::getSmoothedSimpleSpring	(	const std::vector< Facet * > &	vfac,
		AimsSurfaceTriangle &	surface,
		float	force,
		int	nIteration,
		float	rate
	)

protected

◆ getSmoothedVertices()

void Mesher::getSmoothedVertices	(	const std::vector< Facet * > &	vfac,
		AimsSurfaceTriangle &	surface,
		float	rate
	)

protected

◆ getTriangles()

void Mesher::getTriangles	(	const std::vector< Facet * > &	vfac,
		std::vector< AimsVector< uint, 3 > > &	triangle
	)

protected

◆ getVertices()

void Mesher::getVertices	(	const std::vector< Facet * > &	vfac,
		std::vector< Point3df > &	vertex,
		float	sizeX,
		float	sizeY,
		float	sizeZ
	)

protected

◆ getWhite() [1/2]

void Mesher::getWhite	(	const aims::BucketMap< Void > &	thing,
		AimsSurfaceTriangle &	surface
	)

◆ getWhite() [2/2]

void Mesher::getWhite	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		AimsSurfaceTriangle &	surface
	)

◆ reshapedVolume()

static carto::VolumeRef<int16_t> Mesher::reshapedVolume ( const carto::VolumeRef< int16_t > in_vol )

staticprotected

reshape (if needed) the input volume to add a border filled with -1

◆ setDecimation()

void Mesher::setDecimation	(	float	deciReductionRate,
		float	deciMaxClearance,
		float	deciMaxError,
		float	deciFeatureAngle
	)

Decimation.

default : deciReductionRate = 99.0 % deciMaxClearance = 3.0 deciMaxError = 0.2 deciFeatureAngle = 180.0 deg

Referenced by aims::ClusterArgMaker::make().

◆ setLabelInf()

void Mesher::setLabelInf ( int labelInf )

inline

Definition at line 169 of file mesher.h.

References _labelInf.

◆ setLabelSup()

void Mesher::setLabelSup ( int labelSup )

inline

Definition at line 170 of file mesher.h.

References _labelSup.

◆ setMeshOutputFile()

void Mesher::setMeshOutputFile ( )

inline

Definition at line 185 of file mesher.h.

References _triOutputFlag.

◆ setMinFacetNumber()

void Mesher::setMinFacetNumber ( uint m )

inline

Definition at line 189 of file mesher.h.

References _minFacetNumber.

Referenced by aims::ClusterArgMaker::make().

◆ setMinSurface()

void Mesher::setMinSurface ( float minSurface )

inline

Definition at line 174 of file mesher.h.

References _minSurface.

◆ setSmoothing()

void Mesher::setSmoothing	(	SmoothingType	smoothType,
		int	smoothIt,
		float	smoothRate
	)

Smoothing.

default : smoothType = LOWPASS (other values are LAPLACIAN, SIMPLESPRING, POLYGONSPRING) smoothIt = 30 smoothRate in 0.0;1.0 smoothForce in 0.0;1.0

Referenced by aims::ClusterArgMaker::make().

◆ setSmoothingLaplacian()

void Mesher::setSmoothingLaplacian ( float smoothFeatureAngle )

Referenced by aims::ClusterArgMaker::make().

◆ setSmoothingSpring()

void Mesher::setSmoothingSpring ( float smoothForce )

◆ setSplitting()

void Mesher::setSplitting ( )

◆ setTriOutputFile()

void Mesher::setTriOutputFile ( )

inline

OBSOLETE - specify extension in the output filename of setMeshOutputFile() or doit()

Definition at line 181 of file mesher.h.

References _triOutputFlag.

◆ setVerbose()

void Mesher::setVerbose ( bool x )

inline

Definition at line 192 of file mesher.h.

References _verbose.

◆ smooth()

void Mesher::smooth ( AimsSurfaceTriangle & surface )

◆ splitting()

void Mesher::splitting	(	const carto::rc_ptr< carto::Volume< short > > &	thing,
		const std::vector< Facet * > &	vfac,
		const AimsSurfaceTriangle &	surface,
		std::map< short, std::list< AimsSurfaceTriangle > > &	splitted
	)

protected

◆ surfaceOfInterface()

float Mesher::surfaceOfInterface ( const AimsSurfaceTriangle & surface )

◆ unsetDecimation()

void Mesher::unsetDecimation ( )

◆ unsetSmoothing()

void Mesher::unsetSmoothing ( )

◆ unsetSplitting()

void Mesher::unsetSplitting ( )

◆ verbose()

bool Mesher::verbose ( ) const

inline

Definition at line 191 of file mesher.h.

References _verbose.

Member Data Documentation

◆ _deciFeatureAngle

float Mesher::_deciFeatureAngle

protected

Definition at line 207 of file mesher.h.

◆ _deciFlag

bool Mesher::_deciFlag

protected

Definition at line 203 of file mesher.h.

◆ _deciMaxClearance

float Mesher::_deciMaxClearance

protected

Definition at line 205 of file mesher.h.

◆ _deciMaxError

float Mesher::_deciMaxError

protected

Definition at line 206 of file mesher.h.

◆ _deciReductionRate

float Mesher::_deciReductionRate

protected

Definition at line 204 of file mesher.h.

◆ _labelInf

int Mesher::_labelInf

protected

Definition at line 211 of file mesher.h.

Referenced by setLabelInf().

◆ _labelSup

int Mesher::_labelSup

protected

Definition at line 212 of file mesher.h.

Referenced by setLabelSup().

◆ _minFacetNumber

uint Mesher::_minFacetNumber

protected

Definition at line 218 of file mesher.h.

Referenced by setMinFacetNumber().

◆ _minSurface

float Mesher::_minSurface

protected

Definition at line 214 of file mesher.h.

Referenced by setMinSurface().

◆ _smoothFeatureAngle

float Mesher::_smoothFeatureAngle

protected

Definition at line 199 of file mesher.h.

◆ _smoothFlag

bool Mesher::_smoothFlag

protected

Definition at line 196 of file mesher.h.

◆ _smoothForce

float Mesher::_smoothForce

protected

Definition at line 200 of file mesher.h.

◆ _smoothIt

int Mesher::_smoothIt

protected

Definition at line 197 of file mesher.h.

◆ _smoothRate

float Mesher::_smoothRate

protected

Definition at line 198 of file mesher.h.

◆ _smoothType

SmoothingType Mesher::_smoothType

protected

Definition at line 201 of file mesher.h.

◆ _splittingFlag

bool Mesher::_splittingFlag

protected

Definition at line 209 of file mesher.h.

◆ _triOutputFlag

bool Mesher::_triOutputFlag

protected

Definition at line 216 of file mesher.h.

Referenced by setMeshOutputFile(), and setTriOutputFile().

◆ _verbose

bool Mesher::_verbose

protected

Definition at line 220 of file mesher.h.

Referenced by setVerbose(), and verbose().

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

aims/mesh/mesher.h

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ SmoothingType

Constructor & Destructor Documentation

◆ Mesher()

◆ ~Mesher()

Member Function Documentation

◆ clear()

◆ decimate() [1/3]

◆ decimate() [2/3]

◆ decimate() [3/3]

◆ doit() [1/6]

◆ doit() [2/6]

◆ doit() [3/6]

◆ doit() [4/6]

◆ doit() [5/6]

◆ doit() [6/6]

◆ getBrain() [1/2]

◆ getBrain() [2/2]

◆ getDecimatedVertices() [1/2]

◆ getDecimatedVertices() [2/2]

◆ getExtendedNeighOfFacet()

◆ getFacet()

◆ getInterface()

◆ getMeshFromMapOfFacet()

◆ getNormals()

◆ getReducedNeighOutwardCycles()

◆ getSingleLabel()

◆ getSmoothedLaplacian()

◆ getSmoothedLowPassFilter()

◆ getSmoothedPolygonSpring()

◆ getSmoothedSimpleSpring()

◆ getSmoothedVertices()

◆ getTriangles()

◆ getVertices()

◆ getWhite() [1/2]

◆ getWhite() [2/2]

◆ reshapedVolume()

◆ setDecimation()

◆ setLabelInf()

◆ setLabelSup()

◆ setMeshOutputFile()

◆ setMinFacetNumber()

◆ setMinSurface()

◆ setSmoothing()

◆ setSmoothingLaplacian()

◆ setSmoothingSpring()

◆ setSplitting()

◆ setTriOutputFile()

◆ setVerbose()

◆ smooth()

◆ splitting()

◆ surfaceOfInterface()

◆ unsetDecimation()

◆ unsetSmoothing()

◆ unsetSplitting()

◆ verbose()

Member Data Documentation

◆ _deciFeatureAngle

◆ _deciFlag

◆ _deciMaxClearance

◆ _deciMaxError

◆ _deciReductionRate

◆ _labelInf

◆ _labelSup

◆ _minFacetNumber

◆ _minSurface

◆ _smoothFeatureAngle

◆ _smoothFlag

◆ _smoothForce

◆ _smoothIt

◆ _smoothRate

◆ _smoothType

◆ _splittingFlag

◆ _triOutputFlag