emdata_core.h

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/*
 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 *
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 * */

#ifndef emdata__core_h__
#define emdata__core_h__

public:
EMData *copy() const;


EMData *copy_head() const;


void add(float f,int keepzero=0);


void add(const EMData & image);

void addsquare(const EMData & image);


void sub(float f);


void sub(const EMData & image);

void subsquare(const EMData & image);


void mult(int n)
{
        mult((float)n);
}


void mult(float f);


void mult(const EMData & image, bool prevent_complex_multiplication=false);

void mult_complex_efficient(const EMData & em, const int radius);

void div(float f);


void div(const EMData & image);

void to_zero();


void to_one();

void to_value(const float& value);

float dot(EMData * with);


EMData *get_row(int row_index) const;


void set_row(const EMData * data, int row_index);


EMData *get_col(int col_index) const;


void set_col(const EMData * data, int col_index);


inline float get_value_at(int x, int y, int z) const
{
        return get_data()[x + y * nx + z * nxy];
}


inline float get_value_at(int x, int y) const
{
        return get_data()[x + y * nx];
}


inline float get_value_at(size_t i) const
{
        return get_data()[i];
}

std::complex<float> get_complex_at(int x,int y);

float get_value_at_wrap(int x, int y, int z) const;
float& get_value_at_wrap(int x, int y, int z);

float get_value_at_wrap(int x, int y) const;
float& get_value_at_wrap(int x, int y);

float get_value_at_wrap(int x) const;
float& get_value_at_wrap(int x);

float sget_value_at(int x, int y, int z) const;


float sget_value_at(int x, int y) const;


float sget_value_at(size_t i) const;


float sget_value_at_interp(float x, float y) const;


float sget_value_at_interp(float x, float y, float z) const;


inline void set_value_at(int x, int y, int z, float v)
{
        if( x>=nx || x<0 )
        {
                throw OutofRangeException(0, nx-1, x, "x dimension index");
        }
        else if( y>=ny || y<0 )
        {
                throw OutofRangeException(0, ny-1, y, "y dimension index");
        }
        else if( z>=nz || z<0 )
        {
                throw OutofRangeException(0, nz-1, z, "z dimension index");
        }
        else
        {
                get_data()[x + y * nx + z * nxy] = v;
                flags |= EMDATA_NEEDUPD;
                changecount++;
        }
}


inline void set_value_at_fast(int x, int y, int z, float v)
{
        get_data()[x + y * nx + z * nxy] = v;
        flags |= EMDATA_NEEDUPD;
        changecount++;
}


inline void set_value_at(int x, int y, float v)
{
        if( x>=nx || x<0 )
        {
                throw OutofRangeException(0, nx-1, x, "x dimension index");
        }
        else if( y>=ny || y<0 )
        {
                throw OutofRangeException(0, ny-1, y, "y dimension index");
        }
        else
        {
                get_data()[x + y * nx] = v;
                flags |= EMDATA_NEEDUPD;
                changecount++;
        }
}


inline void set_value_at_fast(int x, int y, float v)
{
        get_data()[x + y * nx] = v;
        flags |= EMDATA_NEEDUPD;
        changecount++;
}


inline void set_value_at(int x, float v)
{
        if( x>=nx || x<0 )
        {
                throw OutofRangeException(0, nx-1, x, "x dimension index");
        }
        else
        {
                get_data()[x] = v;
                flags |= EMDATA_NEEDUPD;
                changecount++;
        }
}

inline void set_value_at_fast(int x, float v)
{
        get_data()[x] = v;
        flags |= EMDATA_NEEDUPD;
        changecount++;
}


void free_memory();

EMData & operator+=(float n);
EMData & operator-=(float n);
EMData & operator*=(float n);
EMData & operator/=(float n);

EMData & operator+=(const EMData & em);
EMData & operator-=(const EMData & em);
EMData & operator*=(const EMData & em);
EMData & operator/=(const EMData & em);

bool operator==(const EMData& that) const;

inline float& operator()(const int ix, const int iy, const int iz) const {
        ptrdiff_t pos = (ix-xoff) + ((iy-yoff) + (iz-zoff)*ny)*nx;
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz) {
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
        }
#endif // BOUNDS_CHECKING
        return *(get_data() + pos);
}

inline float& operator()(const int ix, const int iy) const {
        ptrdiff_t pos = (ix - xoff) + (iy-yoff)*nx;
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz)
        {
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
        }
#endif // BOUNDS_CHECKING
        return *(get_data() + pos);
}


inline float& operator()(const int ix) const {
        ptrdiff_t pos = ix - xoff;
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz)
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
#endif // BOUNDS_CHECKING
        return *(get_data() + pos);
}


void set_array_offsets(const int xoff_=0, const int yoff_=0,
                               const int zoff_=0) {
        xoff=xoff_; yoff=yoff_; zoff=zoff_;
}


void set_array_offsets(vector<int> offsets) {
        set_array_offsets(offsets[0],offsets[1],offsets[2]);
}


vector<int> get_array_offsets() {
        vector<int> offsets;
        offsets.push_back(xoff);
        offsets.push_back(yoff);
        offsets.push_back(zoff);
        return offsets;
}


std::complex<float>& cmplx(const int ix, const int iy, const int iz) {
        ptrdiff_t pos = 2*(ix-xoff)+((iy-yoff)+(iz-zoff)*ny)*nx;
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz)
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
#endif // BOUNDS_CHECKING
        float* begin = get_data() + pos;
        return *(reinterpret_cast<std::complex<float>* >(begin));
}


std::complex<float>& cmplx(const int ix, const int iy) {
        ptrdiff_t pos = 2*(ix-xoff)+(iy-yoff)*nx;
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz)
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
#endif // BOUNDS_CHECKING
        float* begin = get_data() + pos;
        return *(reinterpret_cast<std::complex<float>* >(begin));
}


std::complex<float>& cmplx(const int ix) {
        ptrdiff_t pos = 2*(ix-xoff);
#ifdef BOUNDS_CHECKING
        if (pos < 0 || pos >= nx*ny*nz)
                throw OutofRangeException(0, nx*ny*nz-1, pos, "EMData");
#endif // BOUNDS_CHECKING
        float* begin = get_data() + pos;
        return *(reinterpret_cast<std::complex<float>* >(begin));
}


EMData * power(int n) const;

EMData * sqrt() const;


EMData * log() const;


EMData * log10() const;


EMData * real() const;


EMData * imag() const;

EMData * absi() const;


EMData * amplitude() const;


EMData * phase() const;


EMData * real2complex(float img = 0.0f) const;

#endif  //emdata__core_h__