#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.

◆ 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(), and individStackSlices().

◆ MAX_INT16_T

#define MAX_INT16_T 32767

Definition at line 27 of file slices.h.

◆ 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(), 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`
	)

◆ 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, SlicesDetector::c, Component::ordinate_y, and Component::ordinate_Y.

Referenced by 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, SlicesDetector::c, 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, SlicesDetector::c, 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`
	)

◆ 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
	)

◆ 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 )

Classes

Macros

Typedefs

Enumerations

Functions

Macro Definition Documentation

◆ BORDER_GLOBAL

◆ BORDER_LOCAL

◆ EROSION

◆ FRACTION

◆ INCH

◆ MAX_HISTO

◆ MAX_INT16_T

◆ MAX_ITER

◆ MID_WINDOW

◆ MIN_HISTO

◆ NB_MODES

◆ PERCENT_SURFACE

Typedef Documentation

◆ CompIterator

◆ ComponentPtr

◆ MaximaPtr

◆ MaxIterator

◆ TestsPtr

Enumeration Type Documentation

◆ ContinuityParameterTested

◆ Direction

◆ HistoAnalysisFunction

Function Documentation

◆ affectMaxima()

◆ applyNewLabelling()

◆ applyThreshold()

◆ background()

◆ background< AimsRGB >()

◆ background< AimsRGBA >()

◆ changeComponentsIndex()

◆ compareComponentsByLabelM()

◆ computeConnexComponent()

◆ computeHistogramRatio()

◆ copyToVolume()

◆ detectSlices()

◆ displayComponentsStrategy()

◆ displayStatus()

◆ extractFromVolume()

◆ extractInformationFromComponent()

◆ extractMaxima()

◆ extractVectorFromComponent()

◆ filterComponentsBySurface()

◆ generateHistogram()

◆ getComponentLabels()

◆ getDimensionCount()

◆ getOutliersBySurface()

◆ getOutliersByWeight()

◆ getVoxelCount()

◆ getVoxelLebesgue()

◆ insertComponent()

◆ isValid()

◆ openingComponent()

◆ processMedianConsistencyParameters()

◆ processOutlierComponent()

◆ projectData()

◆ removeComponent()

◆ removeComponents()

◆ removeComponentsInVolume()

◆ rescale()

◆ separateComponent()

◆ sortComponent()

◆ testComponents()

◆ transposeVolume()

◆ updateVDM()

◆ weightedRemoveComponents()

◆ writeAimsFloat()

◆ writeAimsInt32_t()

◆ writeComponents()

◆ writeMaxima()

◆ writeMaximaIter()

◆ writeNumberedSlices()

◆ writeStackedSlices()

◆ writeVector3int32_t()

◆ writeVectorInt32_t()