Mesher Class Reference

#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.
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.
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.
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()
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

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.

References _deciFeatureAngle, _deciFlag, _deciMaxClearance, _deciMaxError, _deciReductionRate, _labelInf, _labelSup, _minFacetNumber, _minSurface, _smoothFeatureAngle, _smoothFlag, _smoothForce, _smoothIt, _smoothRate, _smoothType, _splittingFlag, _triOutputFlag, _verbose, and LOWPASS.

~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] (instance : 0.4) smoothForce in [0.0;1.0] (instance : 0.2)

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.

Referenced by Mesher().

_deciFlag

bool Mesher::_deciFlag

protected

Definition at line 203 of file mesher.h.

Referenced by Mesher().

_deciMaxClearance

float Mesher::_deciMaxClearance

protected

Definition at line 205 of file mesher.h.

Referenced by Mesher().

_deciMaxError

float Mesher::_deciMaxError

protected

Definition at line 206 of file mesher.h.

Referenced by Mesher().

_deciReductionRate

float Mesher::_deciReductionRate

protected

Definition at line 204 of file mesher.h.

Referenced by Mesher().

_labelInf

int Mesher::_labelInf

protected

Definition at line 211 of file mesher.h.

Referenced by Mesher(), and setLabelInf().

_labelSup

int Mesher::_labelSup

protected

Definition at line 212 of file mesher.h.

Referenced by Mesher(), and setLabelSup().

_minFacetNumber

uint Mesher::_minFacetNumber

protected

Definition at line 218 of file mesher.h.

Referenced by Mesher(), and setMinFacetNumber().

_minSurface

float Mesher::_minSurface

protected

Definition at line 214 of file mesher.h.

Referenced by Mesher(), and setMinSurface().

_smoothFeatureAngle

float Mesher::_smoothFeatureAngle

protected

Definition at line 199 of file mesher.h.

Referenced by Mesher().

_smoothFlag

bool Mesher::_smoothFlag

protected

Definition at line 196 of file mesher.h.

Referenced by Mesher().

_smoothForce

float Mesher::_smoothForce

protected

Definition at line 200 of file mesher.h.

Referenced by Mesher().

_smoothIt

int Mesher::_smoothIt

protected

Definition at line 197 of file mesher.h.

Referenced by Mesher().

_smoothRate

float Mesher::_smoothRate

protected

Definition at line 198 of file mesher.h.

Referenced by Mesher().

_smoothType

SmoothingType Mesher::_smoothType

protected

Definition at line 201 of file mesher.h.

Referenced by Mesher().

_splittingFlag

bool Mesher::_splittingFlag

protected

Definition at line 209 of file mesher.h.

Referenced by Mesher().

_triOutputFlag

bool Mesher::_triOutputFlag

protected

Definition at line 216 of file mesher.h.

Referenced by Mesher(), setMeshOutputFile(), and setTriOutputFile().

_verbose

bool Mesher::_verbose

protected

Definition at line 220 of file mesher.h.

Referenced by Mesher(), setVerbose(), and verbose().

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

• aims/mesh/mesher.h