tools/gtgen_common.cc File Reference

#include <cmath>
#include <i3d/image3d.h>
#include <i3d/regions.h>
#include <i3d/basic.h>
#include "ofRegistration.h"
#include "ofImageTransformation.h"
#include "ofImageStatistic.h"
#include <i3d/LevelSet.h>
#include <i3d/neighbours.h>
#include <i3d/morphology.h>
#include <i3d/DistanceTransform.h>
#include "ofSeparableConvolution.h"
#include <sys/time.h>
#include <ctype.h>
#include <fstream>
#include <iomanip>
#include <list>
#include "gtgen.h"
#include "random.cc"

Classes
struct	V
Defines
#define	FILTER_RADIUS   4
Functions
template<class IT , class OT >
void	CartesianToPolar (IT x, IT y, OT &r, OT &phi)
template<class IT , class OT >
void	PolarToCartesian (IT r, IT phi, OT &x, OT &y)
template<class T >
void	DoRotation (Image3d< T > &XI, Image3d< T > &YI, int xc, int yc, T rangle)
template<class T >
void	DoRotationPseudo3d (Image3d< T > &XI, Image3d< T > &YI, int xc, int yc, T rangle)
template<class T >
void	DoTranslation (Image3d< T > &XI, Image3d< T > &YI, T xc, T yc)
template<class T >
void	DoTranslation3d (Image3d< T > &XI, Image3d< T > &YI, Image3d< T > &ZI, T xc, T yc, T zc)
template<class T >
void	ComputeSimpleGT (Image3d< T > &XI, Image3d< T > &YI, int xc, int yc, T ra, T xt, T yt)
template<class T >
void	ComputeSimpleGT3d (Image3d< T > &XI, Image3d< T > &YI, Image3d< T > &ZI, int xc, int yc, T ra, T xt, T yt, T zt)
template<class FT >
int	AddFlowField (Image3d< FT > &fXI, Image3d< FT > &fYI, Image3d< FT > &fZI, Image3d< FT > const &sXI, Image3d< FT > const &sYI, Image3d< FT > const &sZI)
template<class FT >
int	AddFlowField (Image3d< FT > &fXI, Image3d< FT > &fYI, Image3d< FT > &fZI, const FT sXI, const FT sYI, const FT sZI)
template<class FT >
int	ConcatenateFlowField (Image3d< FT > &fXI, Image3d< FT > &fYI, Image3d< FT > &fZI, Image3d< FT > &sXI, Image3d< FT > &sYI, Image3d< FT > &sZI)
template<class IT , class MT >
int	FindPossibleMovements (LabeledImage3d< size_t, IT > const &sub, const size_t label, Image3d< MT > const &mask, Image3d< MT > &movs, const int distance, const int file_no)
float	VectorsAngle (const float x1, const float y1, const float z1, const float x2, const float y2, const float z2)
float	AngleVariance (const int level)
int	GetLevel (const float x, const float y, const float z)
template<class MT >
char	DetectCollision (struct V const &shift, list< struct V > const &obj, Image3d< MT > const &mask)
template<class IT >
void	ExportShiftList (list< struct V > const &s, const int dim_x, const int dim_y, const int dim_z, Image3d< IT > &img, const IT val=200)
template<class IT , class MT >
int	FindPossibleMovements (Image3d< IT > const &sub, const IT label, const VOI< PIXELS > *voi, Image3d< MT > const &mask, Image3d< MT > &movs, const int distance, const int file_no)
template<class MT >
void	PossibleMovementsInvolveDistance (Image3d< MT > &movs)
template<class MT >
void	PossibleMovementsInvolveDirection (Image3d< MT > &movs, const float vx, const float vy, const float vz)
template<class MT >
int	SelectPossibleMovementVector (Image3d< MT > const &movs, float &rx, float &ry, float &rz, const char equal)
template<class FT >
int	MoveVOI (valarray< Image3d< FT > * > const &res, const int SeqLength, VOI< i3d::PIXELS > const &inVOI, VOI< i3d::PIXELS > &outVOI)
template<class MT , class FT >
int	CreateSeparateFlowFields (Image3d< MT > const &mask, Image3d< MT > const &movs_mask, valarray< Image3d< FT > * > const &res, const unsigned int SeqLength, const unsigned int Sigma, vector< Image3d< MT > * > &fg_masks, vector< Image3d< FT > * > &X_FF, vector< Image3d< FT > * > &Y_FF, vector< Image3d< FT > * > &Z_FF, int &NumberOfComponents)
void	ShowLocalPaths (vector< Image3d< GRAY8 > * > const &fg_masks, map< size_t, int > &thresholds, const GRAY8 val, Image3d< GRAY8 > const &movs_mask, Image3d< GRAY8 > &debug_image)
void	LocalFFsDebug (vector< Image3d< GRAY8 > * > const &fg_masks, vector< Image3d< float > * > const &X_FF, vector< Image3d< float > * > const &Y_FF, vector< Image3d< float > * > const &Z_FF, const char *basename, const int SeqNo)
template<class T >
void	EnlargeMask (Image3d< T > const &in, Image3d< T > &out, int count)
template<class VOXEL >
int	EstimateThreshold (Image3d< VOXEL > const &img, const int size)
void	FloatToGray8Threshold (const Image3d< float > &fimg, Image3d< GRAY8 > &gimg, float thres, const GRAY8 gmin, const GRAY8 gmax)
template<class T >
void	ApplyLODGaussianBlur (Image3d< T > *XI, Image3d< T > *YI, Image3d< T > *ZI, T sigma)
template<class MT >
float	SumUpImage (Image3d< MT > const &i)
template<class MT >
void	EnhanceImage (Image3d< MT > &i)
template<class T , class MT >
double	MeanFromCellBackground (Image3d< T > &input, Image3d< MT > &mask, Image3d< MT > &Mask, int slice)
template<class T >
T	GenerateMoreBackground (Image3d< T > &input, Image3d< T > &mask, Image3d< T > &Mask, size_t slice, char init)
template<class T >
T	GenerateMoreBackground_nonPerSlices (Image3d< T > &input, Image3d< T > &mask, Image3d< T > &Mask, char init)
template<class IN , class OUT >
void	FillInHoles (Image3d< IN > &input, Image3d< OUT > &out, Image3d< IN > &mask, OUT bg_value)
template<class IN , class OUT >
void	FillInCell (Image3d< IN > &input, Image3d< OUT > &out, Image3d< IN > &mask, Image3d< IN > &Mask)
template<class IN , class OUT , class MT >
void	ExtractComponents (Image3d< IN > &input, Image3d< OUT > &out, Image3d< MT > &mask)
template<class IN , class OUT , class MT >
void	InsertComponents (Image3d< IN > &input, Image3d< OUT > &out, Image3d< MT > &mask, float alter)
template<class IN , class OUT , class MT >
void	InsertComponents_nonInterleaved (Image3d< IN > &input, Image3d< OUT > &out, Image3d< MT > &mask, float alter)
template<class MT , class VT >
void	ApplyMask (Image3d< MT > *Mask, Image3d< VT > *XI, Image3d< VT > *YI, Image3d< VT > *ZI, VT val)
template<class VOXEL >
void	SaveResults (char *FName, Image3d< VOXEL > *XI, Image3d< VOXEL > *YI, Image3d< VOXEL > *ZI)
void	ShowStats (Image3d< float > &orig, Image3d< float > &created, Image3d< GRAY8 > &Mask)
template void	DoTranslation (Image3d< float > &XI, Image3d< float > &YI, float xc, float yc)
template void	DoTranslation3d (Image3d< float > &XI, Image3d< float > &YI, Image3d< float > &ZI, float xc, float yc, float zc)
template void	ComputeSimpleGT (Image3d< float > &XI, Image3d< float > &YI, int xc, int yc, float ra, float xt, float yt)
template void	ComputeSimpleGT3d (Image3d< float > &XI, Image3d< float > &YI, Image3d< float > &ZI, int xc, int yc, float ra, float xt, float yt, float zt)
template int	AddFlowField (Image3d< float > &fXI, Image3d< float > &fYI, Image3d< float > &fZI, Image3d< float > const &sXI, Image3d< float > const &sYI, Image3d< float > const &sZI)
template int	AddFlowField (Image3d< float > &fXI, Image3d< float > &fYI, Image3d< float > &fZI, const float sXI, const float sYI, const float sZI)
template int	ConcatenateFlowField (Image3d< float > &fXI, Image3d< float > &fYI, Image3d< float > &fZI, Image3d< float > &sXI, Image3d< float > &sYI, Image3d< float > &sZI)
template int	FindPossibleMovements (LabeledImage3d< size_t, GRAY8 > const &sub, const size_t label, Image3d< GRAY8 > const &mask, Image3d< GRAY8 > &movs, const int distance, const int file_no)
template int	FindPossibleMovements (Image3d< size_t > const &sub, const size_t label, const VOI< PIXELS > *voi, Image3d< GRAY8 > const &mask, Image3d< GRAY8 > &movs, const int distance, const int file_no)
template int	FindPossibleMovements (Image3d< GRAY8 > const &sub, const GRAY8 label, const VOI< PIXELS > *voi, Image3d< GRAY8 > const &mask, Image3d< GRAY8 > &movs, const int distance, const int file_no)
template int	SelectPossibleMovementVector (Image3d< GRAY8 > const &movs, float &rx, float &ry, float &rz, const char equal)
template void	PossibleMovementsInvolveDistance (Image3d< GRAY8 > &movs)
template void	PossibleMovementsInvolveDirection (Image3d< GRAY8 > &movs, const float vx, const float vy, const float vz)
template int	CreateSeparateFlowFields (Image3d< GRAY8 > const &mask, Image3d< GRAY8 > const &movs_mask, valarray< Image3d< float > * > const &res, const unsigned int SeqLength, const unsigned int Sigma, vector< Image3d< GRAY8 > * > &fg_masks, vector< Image3d< float > * > &X_FF, vector< Image3d< float > * > &Y_FF, vector< Image3d< float > * > &Z_FF, int &NumberOfComponents)
template void	EnlargeMask (Image3d< GRAY8 > const &in, Image3d< GRAY8 > &out, int count)
template int	EstimateThreshold (Image3d< GRAY8 > const &img, const int size)
template int	EstimateThreshold (Image3d< float > const &img, const int size)
template void	ApplyLODGaussianBlur (Image3d< float > *XI, Image3d< float > *YI, Image3d< float > *ZI, float sigma)
template float	SumUpImage (Image3d< GRAY8 > const &i)
template float	SumUpImage (Image3d< float > const &i)
template void	EnhanceImage (Image3d< GRAY8 > &i)
template GRAY8	GenerateMoreBackground (Image3d< GRAY8 > &input, Image3d< GRAY8 > &mask, Image3d< GRAY8 > &Mask, size_t slice, char init)
template GRAY8	GenerateMoreBackground_nonPerSlices (Image3d< GRAY8 > &input, Image3d< GRAY8 > &mask, Image3d< GRAY8 > &Mask, char init)
template void	FillInCell (Image3d< GRAY8 > &input, Image3d< float > &out, Image3d< GRAY8 > &mask, Image3d< GRAY8 > &Mask)
template void	ExtractComponents (Image3d< GRAY8 > &input, Image3d< GRAY8 > &out, Image3d< GRAY8 > &mask)
template void	ExtractComponents (Image3d< float > &input, Image3d< GRAY8 > &out, Image3d< GRAY8 > &mask)
template void	ExtractComponents (Image3d< float > &input, Image3d< float > &out, Image3d< GRAY8 > &mask)
template void	InsertComponents (Image3d< GRAY8 > &input, Image3d< float > &out, Image3d< GRAY8 > &mask, float alter)
template void	InsertComponents (Image3d< float > &input, Image3d< float > &out, Image3d< GRAY8 > &mask, float alter)
template void	InsertComponents_nonInterleaved (Image3d< GRAY8 > &input, Image3d< float > &out, Image3d< GRAY8 > &mask, float alter)
template void	InsertComponents_nonInterleaved (Image3d< float > &input, Image3d< float > &out, Image3d< GRAY8 > &mask, float alter)
template void	SaveResults (char *FName, Image3d< float > *XI, Image3d< float > *YI, Image3d< float > *ZI)
template void	ApplyMask (Image3d< GRAY8 > *Mask, Image3d< float > *XI, Image3d< float > *YI, Image3d< float > *ZI, float val)
Variables
vector< GRAY8 >	slice_means

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Define Documentation

#define FILTER_RADIUS   4

---

Function Documentation

float VectorsAngle	(	const float	x1,
		const float	y1,
		const float	z1,
		const float	x2,
		const float	y2,
		const float	z2
	)			[inline]

float AngleVariance

(

const int

level

)

[inline]

int GetLevel	(	const float	x,
		const float	y,
		const float	z
	)			[inline]

template<class MT >

char DetectCollision	(	struct V const &	shift,
		list< struct V > const &	obj,
		Image3d< MT > const &	mask
	)

template<class IT >

void ExportShiftList	(	list< struct V > const &	s,
		const int	dim_x,
		const int	dim_y,
		const int	dim_z,
		Image3d< IT > &	img,
		const IT	val = 200
	)

template void DoTranslation	(	Image3d< float > &	XI,
		Image3d< float > &	YI,
		float	xc,
		float	yc
	)

template void DoTranslation3d	(	Image3d< float > &	XI,
		Image3d< float > &	YI,
		Image3d< float > &	ZI,
		float	xc,
		float	yc,
		float	zc
	)

template void ComputeSimpleGT	(	Image3d< float > &	XI,
		Image3d< float > &	YI,
		int	xc,
		int	yc,
		float	ra,
		float	xt,
		float	yt
	)

template void ComputeSimpleGT3d	(	Image3d< float > &	XI,
		Image3d< float > &	YI,
		Image3d< float > &	ZI,
		int	xc,
		int	yc,
		float	ra,
		float	xt,
		float	yt,
		float	zt
	)

template int AddFlowField	(	Image3d< float > &	fXI,
		Image3d< float > &	fYI,
		Image3d< float > &	fZI,
		Image3d< float > const &	sXI,
		Image3d< float > const &	sYI,
		Image3d< float > const &	sZI
	)

template int AddFlowField	(	Image3d< float > &	fXI,
		Image3d< float > &	fYI,
		Image3d< float > &	fZI,
		const float	sXI,
		const float	sYI,
		const float	sZI
	)

template int ConcatenateFlowField	(	Image3d< float > &	fXI,
		Image3d< float > &	fYI,
		Image3d< float > &	fZI,
		Image3d< float > &	sXI,
		Image3d< float > &	sYI,
		Image3d< float > &	sZI
	)

template int FindPossibleMovements	(	LabeledImage3d< size_t, GRAY8 > const &	sub,
		const size_t	label,
		Image3d< GRAY8 > const &	mask,
		Image3d< GRAY8 > &	movs,
		const int	distance,
		const int	file_no
	)

template int FindPossibleMovements	(	Image3d< size_t > const &	sub,
		const size_t	label,
		const VOI< PIXELS > *	voi,
		Image3d< GRAY8 > const &	mask,
		Image3d< GRAY8 > &	movs,
		const int	distance,
		const int	file_no
	)

template int FindPossibleMovements	(	Image3d< GRAY8 > const &	sub,
		const GRAY8	label,
		const VOI< PIXELS > *	voi,
		Image3d< GRAY8 > const &	mask,
		Image3d< GRAY8 > &	movs,
		const int	distance,
		const int	file_no
	)

template int SelectPossibleMovementVector	(	Image3d< GRAY8 > const &	movs,
		float &	rx,
		float &	ry,
		float &	rz,
		const char	equal
	)

template void PossibleMovementsInvolveDistance

(

Image3d< GRAY8 > &

movs

)

template void PossibleMovementsInvolveDirection	(	Image3d< GRAY8 > &	movs,
		const float	vx,
		const float	vy,
		const float	vz
	)

template int CreateSeparateFlowFields	(	Image3d< GRAY8 > const &	mask,
		Image3d< GRAY8 > const &	movs_mask,
		valarray< Image3d< float > * > const &	res,
		const unsigned int	SeqLength,
		const unsigned int	Sigma,
		vector< Image3d< GRAY8 > * > &	fg_masks,
		vector< Image3d< float > * > &	X_FF,
		vector< Image3d< float > * > &	Y_FF,
		vector< Image3d< float > * > &	Z_FF,
		int &	NumberOfComponents
	)

template void EnlargeMask	(	Image3d< GRAY8 > const &	in,
		Image3d< GRAY8 > &	out,
		int	count
	)

template int EstimateThreshold	(	Image3d< GRAY8 > const &	img,
		const int	size
	)

template int EstimateThreshold	(	Image3d< float > const &	img,
		const int	size
	)

template void ApplyLODGaussianBlur	(	Image3d< float > *	XI,
		Image3d< float > *	YI,
		Image3d< float > *	ZI,
		float	sigma
	)

template float SumUpImage

(

Image3d< GRAY8 > const &

i

)

template float SumUpImage

(

Image3d< float > const &

i

)

template void EnhanceImage

(

Image3d< GRAY8 > &

i

)

template GRAY8 GenerateMoreBackground	(	Image3d< GRAY8 > &	input,
		Image3d< GRAY8 > &	mask,
		Image3d< GRAY8 > &	Mask,
		size_t	slice,
		char	init
	)

template GRAY8 GenerateMoreBackground_nonPerSlices	(	Image3d< GRAY8 > &	input,
		Image3d< GRAY8 > &	mask,
		Image3d< GRAY8 > &	Mask,
		char	init
	)

template void FillInCell	(	Image3d< GRAY8 > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask,
		Image3d< GRAY8 > &	Mask
	)

template void ExtractComponents	(	Image3d< GRAY8 > &	input,
		Image3d< GRAY8 > &	out,
		Image3d< GRAY8 > &	mask
	)

template void ExtractComponents	(	Image3d< float > &	input,
		Image3d< GRAY8 > &	out,
		Image3d< GRAY8 > &	mask
	)

template void ExtractComponents	(	Image3d< float > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask
	)

template void InsertComponents	(	Image3d< GRAY8 > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask,
		float	alter
	)

template void InsertComponents	(	Image3d< float > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask,
		float	alter
	)

template void InsertComponents_nonInterleaved	(	Image3d< GRAY8 > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask,
		float	alter
	)

template void InsertComponents_nonInterleaved	(	Image3d< float > &	input,
		Image3d< float > &	out,
		Image3d< GRAY8 > &	mask,
		float	alter
	)

template void SaveResults	(	char *	FName,
		Image3d< float > *	XI,
		Image3d< float > *	YI,
		Image3d< float > *	ZI
	)

template void ApplyMask	(	Image3d< GRAY8 > *	Mask,
		Image3d< float > *	XI,
		Image3d< float > *	YI,
		Image3d< float > *	ZI,
		float	val
	)

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Variable Documentation

vector<GRAY8> slice_means