slices.h File Reference

#include <iomanip>
#include <cartobase/type/string_conversion.h>
#include <aims/io/process.h>
#include <aims/io/io_g.h>
#include <aims/data/data_g.h>
#include <aims/math/mathelem.h>
#include <aims/morphology/morphology_g.h>
#include <aims/utility/converter_g.h>

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Classes
class	SlicesDetector
class	SlicesStacker
class	RGBSlicesStacker
class	GreyLevelSlicesStacker
struct	Component
struct	Tests
struct	Maxima
class	HistologyScanSlicesDetector

Macros
#define	INCH   25.49
#define	NB_MODES   2
#define	MIN_HISTO   0
#define	MAX_HISTO   64
#define	MAX_INT16_T   32767
#define	MAX_ITER   500
#define	MID_WINDOW   4
#define	FRACTION   3.0
#define	BORDER_LOCAL   10
#define	BORDER_GLOBAL   50
#define	PERCENT_SURFACE   .2
#define	EROSION   1

Typedefs
typedef struct Component *	ComponentPtr
typedef struct Tests *	TestsPtr
typedef struct Maxima *	MaximaPtr
typedef std::vector< Component >::iterator	CompIterator
typedef std::vector< Maxima >::iterator	MaxIterator

Enumerations
enum	ContinuityParameterTested { ComponentSurface , ComponentSize_hz , ComponentSize_vt }
enum	Direction { Horizontal , Vertical }
enum	HistoAnalysisFunction { HistogramMode , ProjectionMode }

Functions
Maxima	affectMaxima (int32_t iter, int32_t num, int32_t val, int32_t pos, int32_t extr)
void	writeComponents (std::vector< Component > &comp)
void	writeVector3int32_t (std::vector< AimsVector< int32_t, 3 > > &vect)
void	writeVectorInt32_t (std::vector< int32_t > &vect)
void	writeAimsInt32_t (carto::VolumeRef< int32_t > &vol)
void	writeAimsFloat (carto::VolumeRef< float > &vol)
void	writeMaxima (std::vector< Maxima > &mxm)
void	writeMaximaIter (std::vector< Maxima > &mxm, int32_t iter)
template<class T>
float	computeHistogramRatio (const carto::VolumeRef< T > &vol, const int32_t bins)
carto::VolumeRef< int32_t >	generateHistogram (const carto::VolumeRef< int16_t > &vol, const int32_t bins=MAX_HISTO)
std::vector< AimsVector< int32_t, 3 > >	updateVDM (std::vector< AimsVector< int32_t, 3 > > &vdm)
carto::VolumeRef< int16_t >	applyThreshold (const carto::VolumeRef< int16_t > &vol, const int16_t threshold_lower_bound, const int16_t threshold_upper_bound, const int16_t new_value=MAX_INT16_T)
carto::VolumeRef< int16_t >	computeConnexComponent (carto::VolumeRef< int16_t > &vol)
std::vector< Component >	removeComponent (std::vector< Component > cpnt, int32_t l)
std::vector< Component >	removeComponents (const std::vector< Component > &cpnt, const std::vector< Component > &to_remove)
std::vector< Component >	insertComponent (std::vector< Component > cpnt, int32_t comp, std::vector< Component > cpnt2slices, int32_t l)
std::vector< int32_t >	getComponentLabels (const std::vector< Component > &cpnt)
std::vector< Component >	extractInformationFromComponent (const carto::VolumeRef< int16_t > &vol)
Tests	testComponents (const std::vector< Component > &cpnt, int32_t number_cpnt)
void	displayComponentsStrategy (const std::vector< Component > &cpnt)
void	displayStatus (const Tests &t)
bool	isValid (const Tests &t)
std::vector< int32_t >	extractVectorFromComponent (std::vector< Component > cpnt, ContinuityParameterTested param)
std::vector< Component >	processMedianConsistencyParameters (std::vector< Component > &cpnt, float variation, int32_t mid_window=0)
carto::VolumeRef< int32_t >	projectData (carto::VolumeRef< int16_t > &X)
carto::VolumeRef< int16_t >	transposeVolume (carto::VolumeRef< int16_t > &vol)
bool	removeComponentsInVolume (carto::VolumeRef< int16_t > &vol, const std::vector< Component > &to_remove)
carto::VolumeRef< int16_t >	extractFromVolume (const carto::VolumeRef< int16_t > &vol, const int32_t x, const int32_t X, const int32_t y, const int32_t Y, const int32_t old_label, const int32_t new_label)
bool	copyToVolume (const carto::VolumeRef< int16_t > &vol, carto::VolumeRef< int16_t > &destvol, const int32_t x, const int32_t X, const int32_t y, const int32_t Y, const int32_t old_label, const int32_t new_label)
std::vector< Component >	openingComponent (std::vector< Component > &cpnt, int32_t comp, carto::VolumeRef< int16_t > vol, float fraction)
std::vector< Component >	separateComponent (std::vector< Component > &cpnt, int32_t comp, carto::VolumeRef< int16_t > vol, int32_t min_surface, Direction dir, float fraction)
std::vector< Component >	getOutliersBySurface (const std::vector< Component > &cpnt, const float min_surface)
std::vector< Component >	getOutliersByWeight (const std::vector< Component > &cpnt, const int32_t slices_number)
std::vector< Component >	filterComponentsBySurface (const std::vector< Component > &cpnt, const float min_surface)
std::vector< Component >	weightedRemoveComponents (std::vector< Component > &cpnt, int32_t slices_number)
std::vector< Component >	processOutlierComponent (std::vector< Component > &cpnt, carto::VolumeRef< int16_t > &vol, int32_t min_surface, int32_t slices_number, float fraction)
int32_t	getDimensionCount (std::vector< int32_t > dimensionsizes)
std::vector< Component >	changeComponentsIndex (std::vector< Component > &components, std::vector< int32_t > dimensionsizes, std::vector< int32_t > dimensionorders, int32_t offset=1, int32_t step=1)
bool	compareComponentsByLabelM (const Component &c1, const Component &c2)
std::vector< Component >	sortComponent (std::vector< Component > &cpnt, std::vector< int32_t > dimensionsizes)
carto::VolumeRef< int16_t >	applyNewLabelling (std::vector< Component > cpnt, carto::VolumeRef< int16_t > vol)
template<class T>
bool	detectSlices (aims::Process &p, const std::string &, aims::Finder &)
int32_t	extractMaxima (std::vector< int32_t > vctr)
template<class T>
void	rescale (carto::VolumeRef< T > &in, carto::RescalerInfo &info)
template<class T>
bool	writeStackedSlices (int32_t dx, int32_t dy, int32_t res, float z, T background, std::vector< Component > &cpnt, carto::VolumeRef< T > &vol, std::string outputfile, std::string format)
template<class T>
bool	writeNumberedSlices (int32_t dx, int32_t dy, int32_t res, float z, T background, std::vector< Component > &cpnt, carto::VolumeRef< T > &vol, std::string outputdir, std::string outputname, std::string format, uint8_t slicemin)
template<class T>
float	getVoxelLebesgue (const carto::VolumeRef< T > &vol)
template<class T>
int32_t	getVoxelCount (const carto::VolumeRef< T > &vol, float value)
template<class T>
T	background (std::vector< Component > &cpnt, carto::VolumeRef< T > &vol)
template<>
AimsRGB	background< AimsRGB > (std::vector< Component > &cpnt, carto::VolumeRef< AimsRGB > &vol)
template<>
AimsRGBA	background< AimsRGBA > (std::vector< Component > &cpnt, carto::VolumeRef< AimsRGBA > &vol)

Macro Definition Documentation

BORDER_GLOBAL

#define BORDER_GLOBAL   50

Definition at line 34 of file slices.h.

Referenced by writeNumberedSlices(), and writeStackedSlices().

BORDER_LOCAL

#define BORDER_LOCAL   10

Definition at line 33 of file slices.h.

Referenced by background(), background< AimsRGB >(), background< AimsRGBA >(), writeNumberedSlices(), and writeStackedSlices().

EROSION

#define EROSION   1

Definition at line 36 of file slices.h.

FRACTION

#define FRACTION   3.0

Definition at line 31 of file slices.h.

Referenced by HistologyScanSlicesDetector::HistologyScanSlicesDetector().

INCH

#define INCH   25.49

Definition at line 23 of file slices.h.

Referenced by writeNumberedSlices(), and writeStackedSlices().

MAX_HISTO

#define MAX_HISTO   64

Definition at line 26 of file slices.h.

Referenced by detectSlices(), generateHistogram(), HistologyScanSlicesDetector::HistologyScanSlicesDetector(), and individStackSlices().

MAX_INT16_T

#define MAX_INT16_T   32767

Definition at line 27 of file slices.h.

Referenced by applyThreshold().

MAX_ITER

#define MAX_ITER   500

Definition at line 28 of file slices.h.

MID_WINDOW

#define MID_WINDOW   4

Definition at line 29 of file slices.h.

MIN_HISTO

#define MIN_HISTO   0

Definition at line 25 of file slices.h.

NB_MODES

#define NB_MODES   2

Definition at line 24 of file slices.h.

Referenced by detectSlices(), HistologyScanSlicesDetector::HistologyScanSlicesDetector(), and individStackSlices().

PERCENT_SURFACE

#define PERCENT_SURFACE   .2

Definition at line 35 of file slices.h.

Typedef Documentation

CompIterator

typedef std::vector<Component>::iterator CompIterator

Definition at line 265 of file slices.h.

ComponentPtr

typedef struct Component * ComponentPtr

MaximaPtr

typedef struct Maxima * MaximaPtr

MaxIterator

typedef std::vector<Maxima>::iterator MaxIterator

Definition at line 266 of file slices.h.

TestsPtr

typedef struct Tests * TestsPtr

Enumeration Type Documentation

ContinuityParameterTested

enum ContinuityParameterTested

Enumerator
ComponentSurface
ComponentSize_hz
ComponentSize_vt

Definition at line 93 of file slices.h.

Direction

enum Direction

Enumerator
Horizontal
Vertical

Definition at line 100 of file slices.h.

HistoAnalysisFunction

enum HistoAnalysisFunction

Enumerator
HistogramMode
ProjectionMode

Definition at line 106 of file slices.h.

Function Documentation

affectMaxima()

Maxima affectMaxima	(	int32_t	iter,
		int32_t	num,
		int32_t	val,
		int32_t	pos,
		int32_t	extr )

applyNewLabelling()

carto::VolumeRef< int16_t > applyNewLabelling	(	std::vector< Component >	cpnt,
		carto::VolumeRef< int16_t >	vol )

applyThreshold()

carto::VolumeRef< int16_t > applyThreshold	(	const carto::VolumeRef< int16_t > &	vol,
		const int16_t	threshold_lower_bound,
		const int16_t	threshold_upper_bound,
		const int16_t	new_value = MAX_INT16_T )

References MAX_INT16_T.

background()

template<class T>

T background ( std::vector< Component > & cpnt, carto::VolumeRef< T > & vol )

inline

Definition at line 489 of file slices.h.

References Component::abscissa_X, Component::abscissa_x, BORDER_LOCAL, Component::bounding_hz, Component::bounding_vt, Component::ordinate_Y, and Component::ordinate_y.

Referenced by HistologyScanSlicesDetector::detectHistogramModes(), individStackSlices(), rescale(), writeNumberedSlices(), and writeStackedSlices().

background< AimsRGB >()

template<>

AimsRGB background< AimsRGB > ( std::vector< Component > & cpnt, carto::VolumeRef< AimsRGB > & vol )

inline

Definition at line 528 of file slices.h.

References Component::abscissa_X, Component::abscissa_x, BORDER_LOCAL, Component::bounding_hz, Component::bounding_vt, Component::ordinate_Y, and Component::ordinate_y.

background< AimsRGBA >()

template<>

AimsRGBA background< AimsRGBA > ( std::vector< Component > & cpnt, carto::VolumeRef< AimsRGBA > & vol )

inline

Definition at line 579 of file slices.h.

References Component::abscissa_X, Component::abscissa_x, BORDER_LOCAL, Component::bounding_hz, Component::bounding_vt, Component::ordinate_Y, and Component::ordinate_y.

changeComponentsIndex()

std::vector< Component > changeComponentsIndex	(	std::vector< Component > &	components,
		std::vector< int32_t >	dimensionsizes,
		std::vector< int32_t >	dimensionorders,
		int32_t	offset = 1,
		int32_t	step = 1 )

Referenced by individStackSlices().

compareComponentsByLabelM()

bool compareComponentsByLabelM	(	const Component &	c1,
		const Component &	c2 )

computeConnexComponent()

carto::VolumeRef< int16_t > computeConnexComponent

(

carto::VolumeRef< int16_t > &

vol

)

computeHistogramRatio()

template<class T>

float computeHistogramRatio	(	const carto::VolumeRef< T > &	vol,
		const int32_t	bins )

copyToVolume()

bool copyToVolume	(	const carto::VolumeRef< int16_t > &	vol,
		carto::VolumeRef< int16_t > &	destvol,
		const int32_t	x,
		const int32_t	X,
		const int32_t	y,
		const int32_t	Y,
		const int32_t	old_label,
		const int32_t	new_label )

detectSlices()

template<class T>

bool detectSlices	(	aims::Process &	p,
		const std::string &	,
		aims::Finder &	)

Definition at line 23 of file slices_d.h.

References HistologyScanSlicesDetector::analyze(), HistologyScanSlicesDetector::boundingBoxes(), SlicesDetector::c, SlicesDetector::disable_checks, SlicesDetector::fileIn, SlicesDetector::fileOut, SlicesDetector::fraction, SlicesDetector::ht, SlicesDetector::lt, MAX_HISTO, SlicesDetector::min_size, SlicesDetector::n, NB_MODES, and SlicesDetector::res.

displayComponentsStrategy()

void displayComponentsStrategy

(

const std::vector< Component > &

cpnt

)

displayStatus()

void displayStatus

(

const Tests &

t

)

extractFromVolume()

carto::VolumeRef< int16_t > extractFromVolume	(	const carto::VolumeRef< int16_t > &	vol,
		const int32_t	x,
		const int32_t	X,
		const int32_t	y,
		const int32_t	Y,
		const int32_t	old_label,
		const int32_t	new_label )

extractInformationFromComponent()

std::vector< Component > extractInformationFromComponent

(

const carto::VolumeRef< int16_t > &

vol

)

extractMaxima()

int32_t extractMaxima

(

std::vector< int32_t >

vctr

)

Referenced by writeNumberedSlices(), and writeStackedSlices().

extractVectorFromComponent()

std::vector< int32_t > extractVectorFromComponent	(	std::vector< Component >	cpnt,
		ContinuityParameterTested	param )

Referenced by writeNumberedSlices(), and writeStackedSlices().

filterComponentsBySurface()

std::vector< Component > filterComponentsBySurface	(	const std::vector< Component > &	cpnt,
		const float	min_surface )

generateHistogram()

carto::VolumeRef< int32_t > generateHistogram	(	const carto::VolumeRef< int16_t > &	vol,
		const int32_t	bins = MAX_HISTO )

References MAX_HISTO.

getComponentLabels()

std::vector< int32_t > getComponentLabels

(

const std::vector< Component > &

cpnt

)

getDimensionCount()

int32_t getDimensionCount

(

std::vector< int32_t >

dimensionsizes

)

getOutliersBySurface()

std::vector< Component > getOutliersBySurface	(	const std::vector< Component > &	cpnt,
		const float	min_surface )

getOutliersByWeight()

std::vector< Component > getOutliersByWeight	(	const std::vector< Component > &	cpnt,
		const int32_t	slices_number )

getVoxelCount()

template<class T>

int32_t getVoxelCount	(	const carto::VolumeRef< T > &	vol,
		float	value )

getVoxelLebesgue()

template<class T>

float getVoxelLebesgue

(

const carto::VolumeRef< T > &

vol

)

insertComponent()

std::vector< Component > insertComponent	(	std::vector< Component >	cpnt,
		int32_t	comp,
		std::vector< Component >	cpnt2slices,
		int32_t	l )

isValid()

bool isValid

(

const Tests &

t

)

openingComponent()

std::vector< Component > openingComponent	(	std::vector< Component > &	cpnt,
		int32_t	comp,
		carto::VolumeRef< int16_t >	vol,
		float	fraction )

processMedianConsistencyParameters()

std::vector< Component > processMedianConsistencyParameters	(	std::vector< Component > &	cpnt,
		float	variation,
		int32_t	mid_window = 0 )

processOutlierComponent()

std::vector< Component > processOutlierComponent	(	std::vector< Component > &	cpnt,
		carto::VolumeRef< int16_t > &	vol,
		int32_t	min_surface,
		int32_t	slices_number,
		float	fraction )

projectData()

carto::VolumeRef< int32_t > projectData

(

carto::VolumeRef< int16_t > &

X

)

removeComponent()

std::vector< Component > removeComponent	(	std::vector< Component >	cpnt,
		int32_t	l )

removeComponents()

std::vector< Component > removeComponents	(	const std::vector< Component > &	cpnt,
		const std::vector< Component > &	to_remove )

removeComponentsInVolume()

bool removeComponentsInVolume	(	carto::VolumeRef< int16_t > &	vol,
		const std::vector< Component > &	to_remove )

rescale()

template<class T>

void rescale	(	carto::VolumeRef< T > &	in,
		carto::RescalerInfo &	info )

References background().

Referenced by bio::ChannelExtractor< AimsHSV, C >::getChannela(), bio::ChannelExtractor< AimsRGB, C >::getChannela(), bio::ChannelExtractor< AimsRGBA, C >::getChannela(), bio::ChannelExtractor< AimsHSV, C >::getChannelB(), bio::ChannelExtractor< AimsHSV, C >::getChannelb(), bio::ChannelExtractor< AimsRGB, C >::getChannelb(), bio::ChannelExtractor< AimsRGBA, C >::getChannelb(), bio::ChannelExtractor< AimsHSV, C >::getChannelCb(), bio::ChannelExtractor< AimsRGB, C >::getChannelCb(), bio::ChannelExtractor< AimsRGBA, C >::getChannelCb(), bio::ChannelExtractor< AimsHSV, C >::getChannelCr(), bio::ChannelExtractor< AimsRGB, C >::getChannelCr(), bio::ChannelExtractor< AimsRGBA, C >::getChannelCr(), bio::ChannelExtractor< AimsHSV, C >::getChannelG(), bio::ChannelExtractor< AimsRGB, C >::getChannelH(), bio::ChannelExtractor< AimsRGBA, C >::getChannelH(), bio::ChannelExtractor< AimsHSV, C >::getChannelL(), bio::ChannelExtractor< AimsRGB, C >::getChannelL(), bio::ChannelExtractor< AimsRGBA, C >::getChannelL(), bio::ChannelExtractor< AimsHSV, C >::getChannelR(), bio::ChannelExtractor< AimsHSV, C >::getChannelRGBNorm(), bio::ChannelExtractor< AimsRGB, C >::getChannelRGBNorm(), bio::ChannelExtractor< AimsRGBA, C >::getChannelRGBNorm(), bio::ChannelExtractor< AimsRGB, C >::getChannelS(), bio::ChannelExtractor< AimsRGBA, C >::getChannelS(), bio::ChannelExtractor< AimsRGB, C >::getChannelV(), bio::ChannelExtractor< AimsRGBA, C >::getChannelV(), bio::ChannelExtractor< AimsHSV, C >::getChannelX(), bio::ChannelExtractor< AimsRGB, C >::getChannelX(), bio::ChannelExtractor< AimsRGBA, C >::getChannelX(), bio::ChannelExtractor< AimsHSV, C >::getChannelY(), bio::ChannelExtractor< AimsRGB, C >::getChannelY(), bio::ChannelExtractor< AimsRGBA, C >::getChannelY(), bio::ChannelExtractor< AimsHSV, C >::getChannelYl(), bio::ChannelExtractor< AimsRGB, C >::getChannelYl(), bio::ChannelExtractor< AimsRGBA, C >::getChannelYl(), bio::ChannelExtractor< AimsHSV, C >::getChannelZ(), bio::ChannelExtractor< AimsRGB, C >::getChannelZ(), and bio::ChannelExtractor< AimsRGBA, C >::getChannelZ().

separateComponent()

std::vector< Component > separateComponent	(	std::vector< Component > &	cpnt,
		int32_t	comp,
		carto::VolumeRef< int16_t >	vol,
		int32_t	min_surface,
		Direction	dir,
		float	fraction )

sortComponent()

std::vector< Component > sortComponent	(	std::vector< Component > &	cpnt,
		std::vector< int32_t >	dimensionsizes )

Referenced by individStackSlices().

testComponents()

Tests testComponents	(	const std::vector< Component > &	cpnt,
		int32_t	number_cpnt )

transposeVolume()

carto::VolumeRef< int16_t > transposeVolume

(

carto::VolumeRef< int16_t > &

vol

)

updateVDM()

std::vector< AimsVector< int32_t, 3 > > updateVDM

(

std::vector< AimsVector< int32_t, 3 > > &

vdm

)

weightedRemoveComponents()

std::vector< Component > weightedRemoveComponents	(	std::vector< Component > &	cpnt,
		int32_t	slices_number )

writeAimsFloat()

void writeAimsFloat

(

carto::VolumeRef< float > &

vol

)

writeAimsInt32_t()

void writeAimsInt32_t

(

carto::VolumeRef< int32_t > &

vol

)

writeComponents()

void writeComponents

(

std::vector< Component > &

comp

)

Referenced by individStackSlices().

writeMaxima()

void writeMaxima

(

std::vector< Maxima > &

mxm

)

writeMaximaIter()

void writeMaximaIter	(	std::vector< Maxima > &	mxm,
		int32_t	iter )

writeNumberedSlices()

template<class T>

bool writeNumberedSlices	(	int32_t	dx,
		int32_t	dy,
		int32_t	res,
		float	z,
		T	background,
		std::vector< Component > &	cpnt,
		carto::VolumeRef< T > &	vol,
		std::string	outputdir,
		std::string	outputname,
		std::string	format,
		uint8_t	slicemin )

Definition at line 361 of file slices_d.h.

References background(), BORDER_GLOBAL, BORDER_LOCAL, ComponentSize_hz, ComponentSize_vt, extractMaxima(), extractVectorFromComponent(), and INCH.

Referenced by individStackSlices().

writeStackedSlices()

template<class T>

bool writeStackedSlices	(	int32_t	dx,
		int32_t	dy,
		int32_t	res,
		float	z,
		T	background,
		std::vector< Component > &	cpnt,
		carto::VolumeRef< T > &	vol,
		std::string	outputfile,
		std::string	format )

Definition at line 273 of file slices_d.h.

References background(), BORDER_GLOBAL, BORDER_LOCAL, ComponentSize_hz, ComponentSize_vt, extractMaxima(), extractVectorFromComponent(), and INCH.

Referenced by individStackSlices().

writeVector3int32_t()

void writeVector3int32_t

(

std::vector< AimsVector< int32_t, 3 > > &

vect

)

writeVectorInt32_t()

void writeVectorInt32_t

(

std::vector< int32_t > &

vect

)