#include <histogram.h>

Inheritance diagram for Histogram2D:

Collaboration diagram for Histogram2D:

Public Member Functions
	Histogram2D ()

	Histogram2D (const Histogram2D &H)

void	clear ()

Histogram2D &	operator= (const Histogram2D &H)

void	assign (const Histogram2D &H)

void	init (double imin_val, double imax_val, int in_steps, double jmin_val, double jmax_val, int jn_steps)

void	insert_value (double v, double u)

void	write (const FileName &fn)

void	val2index (double v, double u, int &i, int &j) const

void	index2val (double i, double j, double &v, double &u) const

double	Ihist_min () const

double	Ihist_max () const

double	Istep () const

int	IstepNo () const

double	Jhist_min () const

double	Jhist_max () const

double	Jstep () const

int	JstepNo () const

int	sampleNo () const

Public Member Functions inherited from MultidimArray< double >
	MultidimArray ()

	MultidimArray (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim, double *data)

	MultidimArray (size_t Ndim, int Zdim, int Ydim, int Xdim)

	MultidimArray (int Zdim, int Ydim, int Xdim)

	MultidimArray (int Ydim, int Xdim)

	MultidimArray (int Xdim)

	MultidimArray (const MultidimArray< double > &V)

	MultidimArray (MultidimArray< double > &&V) noexcept

	MultidimArray (const Matrix1D< double > &V)

	MultidimArray (const std::vector< double > &vector)

virtual	~MultidimArray ()

void	clear ()

void	coreInit () noexcept

void	swap (MultidimArray< double > &other) noexcept

void	coreAllocate (size_t _ndim, int _zdim, int _ydim, int _xdim)

void	coreAllocate ()

void	coreAllocateReuse ()

FILE *	mmapFile (double *&_data, size_t nzyxDim) const

void	coreDeallocate () noexcept

void	alias (const MultidimArray< double > &m)

void	aliasRow (const MultidimArray< double > &m, size_t select_row)

void	aliasSlice (const MultidimArray< double > &m, size_t select_slice)

void	aliasImageInStack (const MultidimArray< double > &m, size_t select_image)

void	resize (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim, bool copy=true)

void	resize (const MultidimArray< T1 > &v, bool copy=true)

void	resizeNoCopy (const MultidimArray< T1 > &v)

void	checkDimensionWithDebug (int dim, const char *file, int line) const

void	selfWindow (int n0, int z0, int y0, int x0, int nF, int zF, int yF, int xF, double init_value=0)

void	selfWindow (int z0, int y0, int x0, int zF, int yF, int xF, double init_value=0)

void	selfWindow (int y0, int x0, int yF, int xF, double init_value=0)

void	selfWindow (int x0, int xF, double init_value=0)

void	window (MultidimArray< T1 > &result, int n0, int z0, int y0, int x0, int nF, int zF, int yF, int xF, T1 init_value=0) const

void	window (MultidimArray< T1 > &result, int z0, int y0, int x0, int zF, int yF, int xF, T1 init_value=0) const

void	window (MultidimArray< T1 > &result, int y0, int x0, int yF, int xF, T1 init_value=0) const

void	window (MultidimArray< T1 > &result, int x0, int xF, T1 init_value=0) const

void	patch (MultidimArray< double > patchArray, int x, int y)

double &	operator() (const Matrix1D< double > &v) const

double &	operator() (const Matrix1D< int > &v) const

double &	operator() (size_t n, int k, int i, int j) const

double &	operator() (int k, int i, int j) const

double &	operator() (int i, int j) const

double &	operator() (int i) const

double &	operator[] (size_t i) const

void *	getArrayPointer () const

void	getImage (size_t n, MultidimArray< double > &M, size_t n2=0) const

void	getSlice (int k, MultidimArray< T1 > &M, char axis='Z', bool reverse=false, size_t n=0) const

void	getSliceAsMatrix (size_t k, Matrix2D< double > &m) const

void	getAliasAsRowVector (Matrix1D< double > &m) const

void	setSlice (int k, const MultidimArray< T1 > &v, size_t n=0)

void	reslice (MultidimArray< T1 > &out, AxisView face, bool flip=false, size_t n=0) const

void	reslice (AxisView face, bool flip=false, size_t n=0)

void	getCol (size_t j, MultidimArray< double > &v) const

void	setCol (size_t j, const MultidimArray< double > &v)

void	getRow (size_t i, MultidimArray< double > &v) const

void	setRow (int i, const MultidimArray< double > &v)

void	getReal (MultidimArray< double > &realImg) const

void	getImag (MultidimArray< double > &imagImg) const

void	toPhysical (int k_log, int i_log, int j_log, int &k_phys, int &i_phys, int &j_phys) const

void	toPhysical (int i_log, int j_log, int &i_phys, int &j_phys) const

void	toPhysical (int i_log, int &i_phys) const

void	toLogical (int k_phys, int i_phys, int j_phys, int &k_log, int &i_log, int &j_log) const

void	toLogical (int i_phys, int j_phys, int &i_log, int &j_log) const

void	toLogical (int i_phys, int &i_log) const

double	interpolatedElement3D (double x, double y, double z, double outside_value=(double) 0) const

double	interpolatedElement2D (double x, double y, double outside_value=(double) 0) const

double	interpolatedElement2DOutsideZero (double x, double y) const

double	interpolatedElement1D (double x, double outside_value=(double) 0) const

double	interpolatedElementBSpline3D (double x, double y, double z, int SplineDegree=3) const

double	interpolatedElementBSpline2D (double x, double y, int SplineDegree=3) const

double	interpolatedElementBSpline2D_Degree3 (double x, double y) const

double	interpolatedElementBSpline1D (double x, int SplineDegree=3) const

void	printStats (std::ostream &out=std::cout) const

double	computeMax () const

void	maxIndex (int &jmax) const

void	maxIndex (size_t &lmax, int &kmax, int &imax, int &jmax) const

double	computeMin () const

void	minIndex (int &lmin, int &kmin, int &imin, int &jmin) const

void	minIndex (int &kmin, int &imin, int &jmin) const

void	minIndex (int &imin, int &jmin) const

void	minIndex (int &jmin) const

void	computeDoubleMinMax (double &minval, double &maxval) const

void	computeDoubleMinMaxRange (double &minval, double &maxval, size_t offset, size_t size) const

double	computeAvg () const

double	computeStddev () const

void	computeStats (double &avg, double &stddev, double &minval, double &maxval) const

void	computeStats (double &avg, double &stddev, double &min_val, double &max_val, Matrix1D< int > &corner1, Matrix1D< int > &corner2, size_t n=0)

void	computeAvgStdev (U &avg, U &stddev) const

void	computeAvgStdev_within_binary_mask (const MultidimArray< int > &mask, double &avg, double &stddev) const

void	computeMedian_within_binary_mask (const MultidimArray< int > &mask, double &median) const

double	computeMedian () const

void	rangeAdjust (double minF, double maxF)

void	rangeAdjust (double minF, double maxF, MultidimArray< int > &mask)

void	rangeAdjust (const MultidimArray< double > &example, const MultidimArray< int > *mask=NULL)

void	statisticsAdjust (U avgF, U stddevF)

void	initConstant (double val)

void	initZeros (const MultidimArray< T1 > &op)

void	initZeros ()

void	initZeros (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim)

void	initZeros (int Xdim)

void	initZeros (int Ydim, int Xdim)

void	initZeros (int Zdim, int Ydim, int Xdim)

void	initLinear (double minF, double maxF, int n=1, const String &mode="incr")

void	initRandom (double op1, double op2, RandomMode mode=RND_UNIFORM)

void	addNoise (double op1, double op2, const String &mode="uniform", double df=3.) const

MultidimArray< double >	operator+ (const MultidimArray< double > &op1) const

MultidimArray< double >	operator- (const MultidimArray< double > &op1) const

MultidimArray< double >	operator* (const MultidimArray< double > &op1) const

MultidimArray< double >	operator/ (const MultidimArray< double > &op1) const

void	operator+= (const MultidimArray< double > &op1)

void	operator-= (const MultidimArray< double > &op1)

void	operator*= (const MultidimArray< double > &op1)

void	operator/= (const MultidimArray< double > &op1)

double	dotProduct (const MultidimArray< double > &op1)

MultidimArray< double >	operator+ (double op1) const

MultidimArray< double >	operator- (double op1) const

MultidimArray< double >	operator* (double op1) const

MultidimArray< double >	operator/ (double op1) const

void	operator+= (const double &op1)

void	operator-= (const double &op1)

void	operator*= (const double &op1)

void	operator/= (const double &op1)

void	equal (double op1, MultidimArray< char > &result) const

MultidimArray< double >	operator- () const

bool	equal (const MultidimArray< double > &op, double accuracy=XMIPP_EQUAL_ACCURACY) const

MultidimArray< double > &	operator= (const MultidimArray< double > &op1)

MultidimArray< double > &	operator= (MultidimArray< double > &&other) noexcept

MultidimArray< double > &	operator= (const Matrix2D< double > &op1)

void	copy (Matrix2D< double > &op1) const

double ***	adaptForNumericalRecipes3D (size_t n=0) const

void	killAdaptationForNumericalRecipes3D (double ***m) const

double **	adaptForNumericalRecipes2D (size_t n=0) const

double *	adaptForNumericalRecipes22D () const

void	loadFromNumericalRecipes2D (double **m, int Ydim, int Xdim)

void	killAdaptationForNumericalRecipes2D (double **m) const

void	killAdaptationForNumericalRecipes22D (double **m) const

double *	adaptForNumericalRecipes1D () const

void	killAdaptationForNumericalRecipes1D (double *m) const

void	centerOfMass (Matrix1D< double > &center, void *mask=NULL, size_t n=0)

void	sort (MultidimArray< double > &result) const

void	indexSort (MultidimArray< int > &indx) const

void	cumlativeDensityFunction (MultidimArray< double > &cdf)

void	threshold (const String &type, double a, double b=0, MultidimArray< int > *mask=NULL)

size_t	countThreshold (const String &type, double a, double b, MultidimArray< int > *mask=NULL)

void	substitute (double oldv, double newv, double accuracy=XMIPP_EQUAL_ACCURACY, MultidimArray< int > *mask=NULL)

void	randomSubstitute (double oldv, double avgv, double sigv, double accuracy=XMIPP_EQUAL_ACCURACY, MultidimArray< int > *mask=NULL)

void	binarize (double val=0, double accuracy=XMIPP_EQUAL_ACCURACY, MultidimArray< int > *mask=NULL)

void	binarizeRange (double valMin=0, double valMax=255, MultidimArray< int > *mask=NULL)

void	selfROUND ()

void	selfCEIL ()

void	selfFLOOR ()

void	selfABS ()

void	selfNormalizeInterval (double minPerc=0.25, double maxPerc=0.75, int Npix=1000)

void	selfSQRT ()

double	sum () const

double	sum2 () const

void	selfLog10 ()

void	selfLog ()

void	selfReverseX ()

void	selfReverseY ()

void	selfReverseZ ()

void	profile (int x0, int y0, int xF, int yF, int N, MultidimArray< double > &profile) const

void	showWithGnuPlot (const String &xlabel, const String &title)

void	edit ()

void	write (const FileName &fn) const

Public Member Functions inherited from MultidimArrayBase
virtual	~MultidimArrayBase ()

int	getDim () const

void	setMmap (bool mmap)

void	maxIndex (ArrayCoord &pos) const

void	maxIndex (int &kmax, int &imax, int &jmax) const

void	maxIndex (int &imax, int &jmax) const

void	maxIndex (int &jmax) const

void	printShape (std::ostream &out=std::cout) const

void	setNdim (int Ndim)

void	setZdim (int Zdim)

void	setYdim (int Ydim)

void	setXdim (int Xdim)

void	setDimensions (int Xdim, int Ydim, int Zdim, size_t Ndim)

void	setDimensions (ArrayDim &newDim)

void	getDimensions (size_t &Xdim, size_t &Ydim, size_t &Zdim, size_t &Ndim) const

void	getDimensions (ArrayDim &idim) const

ArrayDim	getDimensions () const

void	getDimensions (int *size) const

size_t	getSize () const

void	resize (size_t Zdim, size_t Ydim, size_t Xdim)

void	resize (size_t Ydim, size_t Xdim)

void	resize (size_t Xdim)

void	resize (ArrayDim &adim, bool copy=true)

void	resizeNoCopy (size_t Ndim, size_t Zdim, size_t Ydim, size_t Xdim)

void	resizeNoCopy (size_t Zdim, size_t Ydim, size_t Xdim)

void	resizeNoCopy (size_t Ydim, size_t Xdim)

void	resizeNoCopy (size_t Xdim)

size_t	rowNumber () const

size_t	colNumber () const

void	copyShape (const MultidimArrayBase &m)

bool	sameShape (const MultidimArrayBase &op) const

void	setXmippOrigin ()

void	resetOrigin ()

void	moveOriginTo (int k, int i, int j)

void	moveOriginTo (int i, int j)

int	startingZ () const

int	finishingZ () const

int	startingY () const

int	finishingY () const

int	startingX () const

int	finishingX () const

bool	isCorner (const Matrix1D< double > &v) const

bool	outside (int k, int i, int j) const

bool	outside (int i, int j) const

bool	outside (int i) const

bool	outside (const Matrix1D< double > &r) const

Public Attributes
double	imin

double	imax

double	istep_size

double	jmin

double	jmax

double	jstep_size

int	no_samples

Public Attributes inherited from MultidimArray< double >
double *	data

Public Attributes inherited from MultidimArrayBase
bool	destroyData

size_t	ndim

size_t	zdim

size_t	ydim

size_t	xdim

size_t	yxdim

size_t	zyxdim

size_t	nzyxdim

int	zinit

int	yinit

int	xinit

bool	mmapOn

FILE *	mFd

size_t	nzyxdimAlloc

Friends
std::ostream &	operator<< (std::ostream &o, const Histogram2D &hist)

Detailed Description

Histograms with 2 parameters

The histogram with 2 parameters can be regarded as an approximation to the joint probability density function of two variables (just dividing the histogram by its total mass). Ie, the 2D histogram is the count of times that a certain combination of values in two variables has occurred. For example, this 2D histograms can be used to plot the projection distribution over the topological sphere, in such situation only the first two Euler angles are interesting and we could plot how many projections are there with first angle equal to 45 degrees and second equal to 0 degrees, and so on covering the whole range for each angle.

The 2D histogram is defined, as in the 1D case, by the respective ranges for the two variables and the number of intervals on each range. The distribution and limits of intervals are just the 2D extension of the graph shown in histograms 1D.

Definition at line 699 of file histogram.h.

Constructor & Destructor Documentation

◆ Histogram2D() [1/2]

Histogram2D::Histogram2D ( )

inline

Empty constructor

Creates an empty histogram. Before using it you must initialise it with init

Histogram2D hist;

Definition at line 720 of file histogram.h.

     {
         clear();
     }

◆ Histogram2D() [2/2]

Histogram2D::Histogram2D ( const Histogram2D & H )

inline

Copy constructor

Makes an exact copy of the given histogram into another histogram.

Histogram2D hist2(hist1);

Definition at line 733 of file histogram.h.

     {
         *this = H;
     }

Member Function Documentation

◆ assign()

void Histogram2D::assign ( const Histogram2D & H )

Another function for assigment.

Definition at line 506 of file histogram.cpp.

 {
     *this = H;
 }

◆ clear()

void Histogram2D::clear ( )

virtual

Empties an histogram

Remember to initialise it before using it again.

hist.clear();

Implements MultidimArrayBase.

Definition at line 476 of file histogram.cpp.

 {
     imin = 0;
     imax = 0;
     istep_size = 0;
     jmin = 0;
     jmax = 0;
     jstep_size = 0;
     no_samples = 0;
     MultidimArray<double>::clear();
 }

◆ Ihist_max()

double Histogram2D::Ihist_max ( ) const

inline

Maximum i value where the histogram is defined

std::cout << "Maximum value for histogram " << hist.Imax() << std::endl;

Definition at line 866 of file histogram.h.

     {
         return imax;
     }

◆ Ihist_min()

double Histogram2D::Ihist_min ( ) const

inline

Minimum i value where the histogram is defined

std::cout << "Minimum value for histogram " << hist.Imin() << std::endl;

Definition at line 855 of file histogram.h.

     {
         return imin;
     }

◆ index2val()

void Histogram2D::index2val	(	double	i,
		double	j,
		double &	v,
		double &	u
	)		const

inline

Index –> Value

Given the code of one interval, this function returns the value of its starting point (its left-top border point, ie, its lowest corner). If the intervals are defined as [v0,vF) and [u0,uF), this function returns the point (v0,u0)

hist.index2val(5, 1, v, u);

Definition at line 843 of file histogram.h.

     {
         v = imin + i * istep_size;
         u = jmin + j * jstep_size;
     }

◆ init()

void Histogram2D::init	(	double	imin_val,
		double	imax_val,
		int	in_steps,
		double	jmin_val,
		double	jmax_val,
		int	jn_steps
	)

Initialisation of the histogram

This is the operation which allows the histogram to be used. This should be performed before inserting any value in it. The information given to this initialisation is the range for each variable within which the values will be counted, and the number of steps (discrete bars) in these ranges.If the value is outside the defined ranges it will not be taken into account although we have asked for its insertion in the histogram.

hist.init(0, 90, 100, 0, 360, 200);

// 100 steps in the range V=0...90 and 200 steps for U=0...360

Definition at line 512 of file histogram.cpp.

 {
     // V axis
     imin = imin_val;
     imax = imax_val;
     istep_size = (double) (imax_val - imin_val) / (double) in_steps;
 
     // U axis
     jmin = jmin_val;
     jmax = jmax_val;
     jstep_size = (double) (jmax_val - jmin_val) / (double) jn_steps;
 
     initZeros(in_steps, jn_steps);
     no_samples = 0;
 }

◆ insert_value()

void Histogram2D::insert_value	(	double	v,
		double	u
	)

Insert a value within histogram

The right interval is chosen according to the initialisation of the histogram and the count of elements in that interval is incremented by 1. If the value lies outside the global range of the histogram nothing is done. Notice that two values are needed, these are the two values of the two variables in our example of the projection at with first Euler angle=45 and second=0, the insertion of this projection in the 2D histogram would be like in the following example.

hist.insert_value(45, 0);

Definition at line 530 of file histogram.cpp.

 {
     int i, j;
     val2index(v, u, i, j);
     if (i == -1 || j == -1)
         return; // it is outside our scope
     int Xdim=(int)XSIZE(*this);
     int Ydim=(int)YSIZE(*this);
     i = CLIP(i, 0, Ydim);
     j = CLIP(j, 0, Xdim);
     A2D_ELEM(*this, i, j)++;
     no_samples++;
 }

◆ Istep()

double Histogram2D::Istep ( ) const

inline

Step size in i for the histogram

std::cout << "Step size of the histogram " << hist.Istep() << std::endl;

Definition at line 877 of file histogram.h.

     {
         return istep_size;
     }

◆ IstepNo()

int Histogram2D::IstepNo ( ) const

inline

Number of steps in i in the histogram

std::cout << "No. Steps in the histogram " << hist.IstepNo() << std::endl;

Definition at line 888 of file histogram.h.

     {
         return YSIZE(*this);
     }

◆ Jhist_max()

double Histogram2D::Jhist_max ( ) const

inline

Maximum j value where the histogram is defined

std::cout << "Maximum value for histogram " << hist.Jmax() << std::endl;

Definition at line 910 of file histogram.h.

     {
         return jmax;
     }

◆ Jhist_min()

double Histogram2D::Jhist_min ( ) const

inline

Minimum j value where the histogram is defined

std::cout << "Minimum value for histogram " << hist.Jmin() << std::endl;

Definition at line 899 of file histogram.h.

     {
         return jmin;
     }

◆ Jstep()

double Histogram2D::Jstep ( ) const

inline

Step size in j for the histogram

std::cout << "Step size of the histogram " << hist.Jstep() << std::endl;

Definition at line 921 of file histogram.h.

     {
         return jstep_size;
     }

◆ JstepNo()

int Histogram2D::JstepNo ( ) const

inline

Number of steps in j in the histogram

std::cout << "No. Steps in the histogram " << hist.JstepNo() << std::endl;

Definition at line 932 of file histogram.h.

     {
         return XSIZE(*this);
     }

◆ operator=()

Histogram2D & Histogram2D::operator= ( const Histogram2D & H )

Assignment.

Definition at line 489 of file histogram.cpp.

 {
     if (this != &H)
     {
         this->MultidimArray<double>::operator =(H);
         imin = H.imin;
         imax = H.imax;
         istep_size = H.istep_size;
         jmin = H.jmin;
         jmax = H.jmax;
         jstep_size = H.jstep_size;
         no_samples = H.no_samples;
     }
     return *this;
 }

◆ sampleNo()

int Histogram2D::sampleNo ( ) const

inline

Number of samples introduced in the histogram

std::cout << "No. Samples in the histogram " << hist.sampleNo() << std::endl;

Definition at line 943 of file histogram.h.

     {
         return no_samples;
     }

◆ val2index()

void Histogram2D::val2index	(	double	v,
		double	u,
		int &	i,
		int &	j
	)		const

inline

Value –> Index

Given two values for the two variables it returns the code of the interval where it should be counted. If it is outside the global range of the histogram it returns -1 for that variable (i or j). The following example tells you that the interval corresponding to (45,0) is that with code (i,j), i.e, you could access to hist()(i,j) to know how many projections are there in the same interval as this projection.

hist.val2index(45, 0, i, j);

Definition at line 813 of file histogram.h.

     {
         if (v == imax)
             i = IstepNo() - 1;
         else
             i = (int) FLOOR((v - imin) / istep_size);
 
         if (u == jmax)
             j = JstepNo() - 1;
 
         j = (int) FLOOR((u - jmin) / jstep_size);
 
         if (i < 0 || i >= IstepNo())
             i = -1;
 
         if (j < 0 || j >= JstepNo())
             j = -1;
     }

◆ write()

void Histogram2D::write ( const FileName & fn )

Write an histogram to disk

Definition at line 561 of file histogram.cpp.

 {
     std::ofstream fh;
     fh.open(fn.c_str(), std::ios::out);
     if (!fh)
         REPORT_ERROR(ERR_IO_NOTOPEN, (std::string)"histogram2D::write: File " + fn + " cannot be openned for output");
     fh << *this;
     fh.close();
 }

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	o,
		const Histogram2D &	hist
	)

friend

Show an histogram

The first column and second column are the (X,Y) coordinates of each histogram measure. The third one is the histogram measure.

Definition at line 545 of file histogram.cpp.

 {
     MultidimArray<double> aux;
     aux.resize(hist.IstepNo() * hist.JstepNo(), 3);
     int n = 0;
     FOR_ALL_ELEMENTS_IN_ARRAY2D(hist)
     {
         hist.index2val(i, j, A2D_ELEM(aux, n, 0), A2D_ELEM(aux, n, 1));
         A2D_ELEM(aux, n, 2) = A2D_ELEM(hist, i, j);
         n++;
     }
     o << aux;
     return o;
 }

Member Data Documentation

◆ imax

double Histogram2D::imax

Definition at line 704 of file histogram.h.

◆ imin

double Histogram2D::imin

Definition at line 703 of file histogram.h.

◆ istep_size

double Histogram2D::istep_size

Definition at line 705 of file histogram.h.

◆ jmax

double Histogram2D::jmax

Definition at line 707 of file histogram.h.

◆ jmin

double Histogram2D::jmin

Definition at line 706 of file histogram.h.

◆ jstep_size

double Histogram2D::jstep_size

Definition at line 708 of file histogram.h.

◆ no_samples

int Histogram2D::no_samples

Definition at line 709 of file histogram.h.

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

xmippCore/core/histogram.h
xmippCore/core/histogram.cpp

Public Member Functions

Public Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Histogram2D() [1/2]

◆ Histogram2D() [2/2]

Member Function Documentation

◆ assign()

◆ clear()

◆ Ihist_max()

◆ Ihist_min()

◆ index2val()

◆ init()

◆ insert_value()

◆ Istep()

◆ IstepNo()

◆ Jhist_max()

◆ Jhist_min()

◆ Jstep()

◆ JstepNo()

◆ operator=()

◆ sampleNo()

◆ val2index()

◆ write()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ imax

◆ imin

◆ istep_size

◆ jmax

◆ jmin

◆ jstep_size

◆ no_samples