XYData defines a 1D (x,y) data set. More...

#include <xydata.h>

Classes
struct	Pair

Public Member Functions
	XYData ()

virtual	~XYData ()

int	read_file (const string &filename)

int	write_file (const string &filename) const

float	calc_correlation (XYData *xy, float minx, float maxx) const

void	update ()

float	get_yatx (float x, bool outzero=true)

float	get_yatx_smooth (float x, int smoothing)

float	get_x (size_t i) const

void	set_x (size_t i, float x)

float	get_y (size_t i) const

void	set_y (size_t i, float y)

void	insort (float x, float y)

void	dedupx ()

vector< float >	get_xlist () const

vector< float >	get_ylist () const

vector< float >	get_state () const

void	set_state (vector< float >)

void	set_xy_list (const vector< float > &xlist, const vector< float > &ylist)

void	make_gauss (int n, float xmax, float width)

size_t	get_size () const

void	set_size (size_t n)

float	get_miny ()

float	get_maxy ()

bool	is_validx (float x) const

Private Attributes
vector< Pair >	data

float	ymin

float	ymax

float	mean_x_spacing

Detailed Description

XYData defines a 1D (x,y) data set.

Definition at line 46 of file xydata.h.

Constructor & Destructor Documentation

◆ XYData()

XYData::XYData ( )

Definition at line 48 of file xydata.cpp.

        : ymin(FLT_MAX), ymax(-FLT_MAX), mean_x_spacing(1.0)
{
}

◆ ~XYData()

virtual EMAN::XYData::~XYData ( )

inlinevirtual

Definition at line 67 of file xydata.h.

68 {

69 }

Member Function Documentation

◆ calc_correlation()

float XYData::calc_correlation	(	XYData *	xy,
		float	minx,
		float	maxx
	)		const

Definition at line 129 of file xydata.cpp.

{
        size_t n = data.size();
        float x0 = data[0].x;
        float xn = data[n - 1].x;
 
        if (maxx <= minx || minx >= xn || maxx <= x0) {
                LOGERR("incorrect minx, maxx=%f,%f for this XYData range [%f,%f]",
                           minx, maxx, x0, xn);
                return 0;
        }
 
        float scc = 0;
        float norm1 = 0;
        float norm2 = 0;
 
        xy->update();
        for (size_t i = 0; i < n; i++) {
                float x = data[i].x;
                if (x >= minx && x <= maxx && xy->is_validx(x)) {
                        float selfy = data[i].y;
                        float xyy = xy->get_yatx(x);
 
                        scc += selfy * xyy;
                        norm1 += selfy * selfy;
                        norm2 += xyy * xyy;
                }
        }
 
        float result = scc / sqrt(norm1 * norm2);
        return result;
}

References data, get_yatx(), is_validx(), LOGERR, sqrt(), update(), and x.

◆ dedupx()

void XYData::dedupx ( )

Definition at line 253 of file xydata.cpp.

                    {
        float acnt=1.0;
        for (std::vector<Pair>::iterator it = data.begin() ; it+1 < data.end(); ++it) {
                while (it+1<data.end() && it->x==(it+1)->x) {
//                      printf("%d\t%d\t%1.0f\t%f\t%f\n",it-data.begin(),data.end()-it,acnt,it->x,(it+1)->x);
                        it->y+=(it+1)->y;
                        acnt+=1.0;
                        data.erase(it+1);
                }
                if (acnt>1.0) {
                        it->y/=acnt;
                        acnt=1.0;
                }
        }
}

References data, and y.

◆ get_maxy()

float EMAN::XYData::get_maxy ( )

inline

Definition at line 140 of file xydata.h.

                {
//                      update();
                        return ymax;
                }

References ymax.

◆ get_miny()

float EMAN::XYData::get_miny ( )

inline

Definition at line 134 of file xydata.h.

                {
//                      update();
                        return ymin;
                }

References ymin.

◆ get_size()

size_t EMAN::XYData::get_size ( ) const

inline

Definition at line 127 of file xydata.h.

                {
                        return data.size();
                }

References data.

Referenced by EMAN::SetSFProcessor::create_radial_func(), EMAN::FSCFourierProcessor::process(), EMAN::SNRProcessor::process_inplace(), EMAN::SetIsoPowProcessor::process_inplace(), and EMAN::TestUtil::to_emobject().

◆ get_state()

vector< float > XYData::get_state ( ) const

Definition at line 285 of file xydata.cpp.

                                       {
        vector<float> list;
        vector<Pair>::const_iterator cit;
        for(cit=data.begin(); cit!=data.end(); ++cit) {
                list.push_back( (*cit).x);
                list.push_back( (*cit).y);
        }
 
        return list;
        
}

References data.

Referenced by EMAN::SetIsoPowProcessor::process_inplace().

◆ get_x()

float EMAN::XYData::get_x ( size_t i ) const

inline

Definition at line 84 of file xydata.h.

                {
                        return data[i].x;
                }

References data.

Referenced by EMAN::SetSFProcessor::create_radial_func(), and EMAN::TestUtil::to_emobject().

◆ get_xlist()

vector< float > XYData::get_xlist ( ) const

Definition at line 310 of file xydata.cpp.

{
        vector<float> xlist;
        vector<Pair>::const_iterator cit;
        for(cit=data.begin(); cit!=data.end(); ++cit) {
                xlist.push_back( (*cit).x);
        }
 
        return xlist;
}

References data.

◆ get_y()

float EMAN::XYData::get_y ( size_t i ) const

inline

Definition at line 95 of file xydata.h.

                {
                        if (i>=data.size()) throw InvalidValueException(i, "Attempt to access XYData out of range");
                        return data[i].y;
                }

References data, and InvalidValueException.

Referenced by EMAN::FSCFourierProcessor::process(), EMAN::SNRProcessor::process_inplace(), EMAN::SetIsoPowProcessor::process_inplace(), and EMAN::TestUtil::to_emobject().

◆ get_yatx()

float XYData::get_yatx	(	float	x,
		bool	outzero = `true`
	)

Definition at line 172 of file xydata.cpp.

{
        if (data.size()==0 || mean_x_spacing==0) return 0.0;
 
        int nx = (int) data.size();
        // Do the range checking up front before we get into trouble
        if (x<data[0].x) return outzero?0.0f:data[0].y;
        if (x>data[nx-1].x) return outzero?0.0f:data[nx-1].y;
        
        int s = (int) floor((x - data[0].x) / mean_x_spacing);
        if (s>nx-1) s=nx-1;
 
        // These deal with possibly nonuniform x values. A btree would be better, but this is simple
        while (s>0 && data[s].x > x) s--;
        while (s<(nx-1) && data[s + 1].x < x ) s++;
        if (s>nx-2) return outzero?0.0f:data[nx-1].y;
        
        float f = (x - data[s].x) / (data[s + 1].x - data[s].x);
        float y = data[s].y * (1 - f) + data[s + 1].y * f;
        return y;
}

References data, mean_x_spacing, x, and y.

Referenced by EMAN::FourierWeightAverager::add_image(), calc_correlation(), EMAN::EMAN1Ctf::compute_1d(), EMAN::EMAN2Ctf::compute_1d(), EMAN::EMAN1Ctf::compute_2d_complex(), EMAN::SetSFProcessor::create_radial_func(), EMAN::FSCFourierProcessor::process(), and EMAN::SetIsoPowProcessor::process_inplace().

◆ get_yatx_smooth()

float XYData::get_yatx_smooth	(	float	x,
		int	smoothing
	)

Definition at line 194 of file xydata.cpp.

{
        if (data.size()==0) return 0.0;
        if (data.size()==1) return data[0].y;
        if (smoothing!=1) throw InvalidParameterException("Only smoothing==1 (linear) currently supported");
        
        int nx = (int) data.size();
        
        int s = nx/2; 
        if (mean_x_spacing>0) s=(int) floor((x - data[0].x) / mean_x_spacing);
        if (s>nx-2) s=nx-2;
        else if (s<0) s=0;
        else {
                // These deal with possibly nonuniform x values. A btree would be better, but this is simple, and there usually won't be THAT many points
                while (s>0 && data[s].x > x) s--;
                while (s<(nx-2) && data[s + 1].x < x ) s++;
        }
        
        float f = 0,y=0;
        if (data[s + 1].x != data[s].x) {
                f= (x - data[s].x) / (data[s + 1].x - data[s].x);
                y = data[s].y * (1 - f) + data[s + 1].y * f;
        }
        else {
                int s2=s;
                while (data[s2].x==data[s].x) {
                        if (s2<nx-1) s2++;
                        if (s>0) s--;
                        if (s==0 &&s2==nx-1) return data[nx/2].y;
                }
                f= (x - data[s].x) / (data[s2].x - data[s].x);
                y = data[s].y * (1 - f) + data[s2].y * f;
                
        }
//      printf("%d %1.2f x %1.2f %1.2f %1.2f y %1.2f %1.2f\n",s,f,x,data[s].x,data[s+1].x,data[s].y,data[s+1].y);
        return y;
}

References data, InvalidParameterException, mean_x_spacing, x, and y.

◆ get_ylist()

vector< float > XYData::get_ylist ( ) const

Definition at line 321 of file xydata.cpp.

{
        vector<float> ylist;
        vector<Pair>::const_iterator cit;
        for(cit=data.begin(); cit!=data.end(); ++cit) {
                ylist.push_back( (*cit).y);
        }
 
        return ylist;
}

References data.

◆ insort()

void XYData::insort	(	float	x,
		float	y
	)

Definition at line 233 of file xydata.cpp.

                                    {
        data.push_back(Pair(x,y));
        update();
        
        
        //      int nx = (int) data.size();
//      if (nx==0) { data.push_back(Pair(x,y)); return; }
//      
//      int s = (int) floor((x - data[0].x) / mean_x_spacing);
//      if (s>nx) s=nx;
//      else if (s<0) s=0;
//      else {
//      // These deal with possibly nonuniform x values. A btree would be better, but this is simple, and there usually won't be THAT many points
//              while (s>0 && data[s-1].x > x) s--;
//              while (s<nx && data[s].x <= x ) s++;
//      }
//      data.insert(data.begin()+s,Pair(x,y));
}       

References data, update(), x, and y.

◆ is_validx()

bool EMAN::XYData::is_validx ( float x ) const

inline

Definition at line 146 of file xydata.h.

                {
                        if (x < data[0].x || x > data[data.size() - 1].x)
                        {
                                return false;
                        }
                        return true;
                }

References data, and x.

Referenced by calc_correlation().

◆ make_gauss()

void XYData::make_gauss	(	int	n,
		float	xmax,
		float	width
	)

Definition at line 162 of file xydata.cpp.

{
        set_size(n);
        for (int i=0; i<n; i++) {
                float x=i*xmax/n;
                data[i].x=x;
                data[i].y=exp(-x*x/(width*width));
        }
}

References data, set_size(), and x.

Referenced by EMAN::GaussSegmentProcessor::process().

◆ read_file()

int XYData::read_file ( const string & filename )

Definition at line 77 of file xydata.cpp.

{
        FILE *in = fopen(filename.c_str(), "rb");
        if (!in) {
                throw FileAccessException(filename.c_str());
//              LOGERR("cannot open xydata file '%s'", filename.c_str());
//              return 1;
        }
 
        char buf[MAXPATHLEN];
        char tmp_str[MAXPATHLEN];
 
        while (fgets(buf, MAXPATHLEN, in)) {
                if (buf[0] != '#') {
                        float x = 0;
                        float y = 0;
 
                        if (sscanf(buf, " %f%[^.0-9-]%f", &x, tmp_str, &y) != 3) {
                                break;
                        }
                        data.push_back(Pair(x, y));
                }
        }
 
        fclose(in);
        in = 0;
 
        update();
 
        return 0;
}

References data, FileAccessException, update(), x, and y.

Referenced by EMAN::SetSFProcessor::create_radial_func(), EMAN::FSCFourierProcessor::process(), and EMAN::SNRProcessor::process_inplace().

◆ set_size()

void XYData::set_size ( size_t n )

Definition at line 280 of file xydata.cpp.

{
        data.resize(n, Pair(0.0f, 0.0f));
}

References data.

Referenced by make_gauss().

◆ set_state()

void XYData::set_state ( vector< float > list )

Definition at line 297 of file xydata.cpp.

                                          {
        if(list.size()%2==1) {
                throw InvalidParameterException("Invalid pickled data");
        }
 
        data.clear();
        for(unsigned int i=0; i<list.size(); i+=2) {
                data.push_back(Pair(list[i], list[i+1]));
        }
 
        update();
}

References data, InvalidParameterException, and update().

Referenced by EMAN::SetIsoPowProcessor::process_inplace().

◆ set_x()

void EMAN::XYData::set_x	(	size_t	i,
		float	x
	)

inline

Definition at line 89 of file xydata.h.

                {
                        if (i>=data.size()) data.resize(i+1,Pair(0,0));
                        data[i].x = x;
                }

References data, and x.

Referenced by EMAN::FSCFourierProcessor::process().

◆ set_xy_list()

void XYData::set_xy_list	(	const vector< float > &	xlist,
		const vector< float > &	ylist
	)

Definition at line 269 of file xydata.cpp.

{
        if(xlist.size() != ylist.size()) {
                throw InvalidParameterException("xlist and ylist size does not match!");
        }
 
        for(unsigned int i=0; i<xlist.size(); ++i) {
                data.push_back(Pair(xlist[i], ylist[i]));
        }
}

References data, and InvalidParameterException.

◆ set_y()

void EMAN::XYData::set_y	(	size_t	i,
		float	y
	)

inline

Definition at line 101 of file xydata.h.

                {
                        if (i>=data.size()) data.resize(i+1,Pair(0,0));
                        data[i].y = y;
                }

References data, and y.

Referenced by EMAN::FSCFourierProcessor::process(), EMAN::SNRProcessor::process_inplace(), and EMAN::SetIsoPowProcessor::process_inplace().

◆ update()

void XYData::update ( )

Definition at line 53 of file xydata.cpp.

{
        if (data.size()==0) return;
        
        std::sort(data.begin(), data.end());
 
        ymin = FLT_MAX;
        ymax = -FLT_MAX;
 
        typedef vector < Pair >::const_iterator Ptype;
        for (Ptype p = data.begin(); p != data.end(); p++) {
                if (p->y > ymax) {
                        ymax = p->y;
                }
                if (p->y < ymin) {
                        ymin = p->y;
                }
        }
 
        size_t n = data.size();
        mean_x_spacing = (data[n - 1].x - data[0].x) / (float) n;
}

References data, mean_x_spacing, ymax, and ymin.

Referenced by calc_correlation(), insort(), EMAN::SNRProcessor::process_inplace(), read_file(), and set_state().

◆ write_file()

int XYData::write_file ( const string & filename ) const

Definition at line 109 of file xydata.cpp.

{
        FILE *out = fopen(filename.c_str(), "wb");
        if (!out) {
                LOGERR("cannot open xydata file '%s' to write", filename.c_str());
                return 1;
        }
 
        typedef vector < Pair >::const_iterator Ptype;
        for (Ptype p = data.begin(); p != data.end(); p++) {
                fprintf(out, "%1.6g\t%1.6g\n", p->x, p->y);
        }
 
        fclose(out);
        out = 0;
 
        return 0;
}

References data, and LOGERR.

Member Data Documentation

◆ data

vector< Pair > EMAN::XYData::data

private

Definition at line 156 of file xydata.h.

Referenced by calc_correlation(), dedupx(), get_size(), get_state(), get_x(), get_xlist(), get_y(), get_yatx(), get_yatx_smooth(), get_ylist(), insort(), is_validx(), make_gauss(), read_file(), set_size(), set_state(), set_x(), set_xy_list(), set_y(), update(), and write_file().

◆ mean_x_spacing

float EMAN::XYData::mean_x_spacing

private

Definition at line 159 of file xydata.h.

Referenced by get_yatx(), get_yatx_smooth(), and update().

◆ ymax

float EMAN::XYData::ymax

private

Definition at line 158 of file xydata.h.

Referenced by get_maxy(), and update().

◆ ymin

float EMAN::XYData::ymin

private

Definition at line 157 of file xydata.h.

Referenced by get_miny(), and update().

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

Classes

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ XYData()

◆ ~XYData()

Member Function Documentation

◆ calc_correlation()

◆ dedupx()

◆ get_maxy()

◆ get_miny()

◆ get_size()

◆ get_state()

◆ get_x()

◆ get_xlist()

◆ get_y()

◆ get_yatx()

◆ get_yatx_smooth()

◆ get_ylist()

◆ insort()

◆ is_validx()

◆ make_gauss()

◆ read_file()

◆ set_size()

◆ set_state()

◆ set_x()

◆ set_xy_list()

◆ set_y()

◆ update()

◆ write_file()

Member Data Documentation

◆ data

◆ mean_x_spacing

◆ ymax

◆ ymin