reconstructor.cpp

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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
 *
 * */
 
#include "reconstructor.h"
#include "plugins/reconstructor_template.h"
#include "ctf.h"
#include "emassert.h"
#include "symmetry.h"
#include <cstring>
#include <fstream>
#include <iomanip>
 
#include <gsl/gsl_statistics_double.h>
#include <gsl/gsl_fit.h>
 
#ifdef EMAN2_USING_CUDA
#include "cuda/cuda_reconstructor.h"
#endif
 
//#define DEBUG_POINT   1
 
using namespace EMAN;
using std::complex;
 
 
#include <iostream>
using std::cerr;
using std::endl;
using std::cout; // for debug
 
#include <algorithm>
// find, for_each
 
#include <iomanip>
using std::setprecision;
 
template < typename T > void checked_delete( T*& x )
{
    typedef char type_must_be_complete[ sizeof(T)? 1: -1 ];
    (void) sizeof(type_must_be_complete);
    delete x;
    x = NULL;
}
 
const string FourierReconstructor::NAME = "fourier";
const string FourierIterReconstructor::NAME = "fourier_iter";
const string FourierReconstructorSimple2D::NAME = "fouriersimple2D";
const string WienerFourierReconstructor::NAME = "wiener_fourier";
const string BackProjectionReconstructor::NAME = "back_projection";
const string RealMedianReconstructor::NAME = "real_median";
const string nn4Reconstructor::NAME = "nn4";
const string nn4_rectReconstructor::NAME = "nn4_rect";
const string nnSSNR_Reconstructor::NAME = "nnSSNR";
const string nn4_ctfReconstructor::NAME = "nn4_ctf";
const string nn4_ctfwReconstructor::NAME = "nn4_ctfw";
const string nn4_ctfwsReconstructor::NAME = "nn4_ctfws";
const string nn4_ctf_rectReconstructor::NAME = "nn4_ctf_rect";
const string nnSSNR_ctfReconstructor::NAME = "nnSSNR_ctf";
 
template <> Factory < Reconstructor >::Factory()
{
        force_add<FourierReconstructor>();
        force_add<FourierIterReconstructor>();
        force_add<FourierReconstructorSimple2D>();
//      force_add(&BaldwinWoolfordReconstructor::NEW);
        force_add<WienerFourierReconstructor>();
        force_add<RealMedianReconstructor>();
        force_add<BackProjectionReconstructor>();
        force_add<nn4Reconstructor>();
        force_add<nn4_rectReconstructor>();
        force_add<nnSSNR_Reconstructor>();
        force_add<nn4_ctfReconstructor>();
        force_add<nn4_ctfwReconstructor>();
        force_add<nn4_ctfwsReconstructor>();
        force_add<nn4_ctf_rectReconstructor>();
        force_add<nnSSNR_ctfReconstructor>();
//      force_add<XYZReconstructor>();
}
 
class ctf_store_real
{
public:
 
    static void init( int winsize, const Ctf* ctf ) {
                Dict params = ctf->to_dict();
 
                m_winsize = winsize;
 
                m_voltage = params["voltage"];
                m_pixel   = params["apix"];
                m_cs      = params["cs"];
                m_ampcont = params["ampcont"];
                m_bfactor = params["bfactor"];
                m_defocus = params["defocus"];
                m_dza     = params["dfdiff"];
                m_azz     = params["dfang"];
                m_winsize2= m_winsize*m_winsize;
                m_vecsize = m_winsize2/4;
    }
 
    // static float get_ctf( int r2 ,int i, int j) {
        //      float  ak = std::sqrt( r2/float(m_winsize2) )/m_pixel;
        //      if(m_dza == 0.0f)  return Util::tf( m_defocus, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1);
        //      else {
        //              float az = atan2(float(j), float(i));
        //              float dzz = m_defocus - m_dza/2.0f*sin(2*(az+m_azz*M_PI/180.0f));
        //              return Util::tf( dzz, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1);
        //      }
        // }
        
    static EMData* get_ctf_real() {
                return Util::ctf_img_real(m_winsize, m_winsize, 1, m_defocus, m_pixel, m_voltage, m_cs, m_ampcont, m_bfactor, m_dza, m_azz, 1);
        }
 
private:
 
        static int m_winsize, m_winsize2, m_vecsize;
        static float m_cs;
        static float m_voltage;
        static float m_pixel;
        static float m_ampcont;
        static float m_bfactor;
        static float m_defocus;
        static float m_dza;
        static float m_azz;
};
 
int ctf_store_real::m_winsize, ctf_store_real::m_winsize2, ctf_store_real::m_vecsize;
 
float ctf_store_real::m_cs, ctf_store_real::m_voltage, ctf_store_real::m_pixel;
float ctf_store_real::m_ampcont, ctf_store_real::m_bfactor;
float ctf_store_real::m_defocus, ctf_store_real::m_dza, ctf_store_real::m_azz;
 
 
void FourierReconstructorSimple2D::setup()
{
        nx = params.set_default("nx",0);
 
        if ( nx < 0 ) throw InvalidValueException(nx, "nx must be positive");
 
        bool is_fftodd = (nx % 2 == 1);
 
        ny = nx;
        nx += 2-is_fftodd;
 
        image = new EMData();
        image->set_size(nx, ny);
        image->set_complex(true);
        image->set_fftodd(is_fftodd);
        image->set_ri(true);
 
        tmp_data = new EMData();
        tmp_data->set_size(nx/2, nx);
}
 
int FourierReconstructorSimple2D::insert_slice(const EMData* const slice, const Transform & euler, const float)
{
 
        // Are these exceptions really necessary? (d.woolford)
        if (!slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        if ( slice->get_ndim() != 1 ) throw ImageDimensionException("Image dimension must be 1");
 
        // I could also test to make sure the image is the right dimensions...
        if (slice->is_complex()) throw ImageFormatException("The image is complex, expecting real");
 
        EMData* working_slice = slice->process("xform.phaseorigin.tocorner");
 
        // Fourier transform the slice
        working_slice->do_fft_inplace();
 
        float* rdata = image->get_data();
        float* norm = tmp_data->get_data();
        float* dat = working_slice->get_data();
 
        float g[4];
        int offset[4];
        float dt[2];
        offset[0] = 0; offset[1] = 2; offset[2] = nx; offset[3] = nx+2;
 
        float alt = -((float)(euler.get_rotation("2d"))["alpha"])*M_PI/180.0f;
        for (int x = 0; x < working_slice->get_xsize() / 2; x++) {
 
                float rx = (float) x;
 
                float xx = rx*cos(alt);
                float yy = rx*sin(alt);
                float cc = 1.0;
 
                if (xx < 0) {
                        xx = -xx;
                        yy = -yy;
                        cc = -1.0;
                }
 
                yy += ny / 2;
 
 
                dt[0] = dat[2*x];
                dt[1] = cc * dat[2*x+1];
 
                // PHIL IS INTERESTED FROM HERE DOWN
                int x0 = (int) floor(xx);
                int y0 = (int) floor(yy);
 
                int i = 2*x0 + y0*nx;
 
                float dx = xx - x0;
                float dy = yy - y0;
 
                g[0] = Util::agauss(1, dx, dy, 0, EMConsts::I2G);
                g[1] = Util::agauss(1, 1 - dx, dy, 0, EMConsts::I2G);
                g[2] = Util::agauss(1, dx, 1 - dy, 0, EMConsts::I2G);
                g[3] = Util::agauss(1, 1 - dx, 1 - dy, 0, EMConsts::I2G);
 
                // At the extreme we can only do some much...
                if ( x0 == nx-2 ) {
                        int k = i + offset[0];
                        rdata[k] += g[0] * dt[0];
                        rdata[k + 1] += g[0] * dt[1];
                        norm[k/2] += g[0];
 
                        k = i + offset[2];
                        rdata[k] += g[2] * dt[0];
                        rdata[k + 1] += g[2] * dt[1];
                        norm[k/2] += g[2];
                        continue;
 
                }
                // capture and accommodate for periodic boundary conditions in the x direction
                if ( x0 > nx-2 ) {
                        int dif = x0 - (nx-2);
                        x0 -= dif;
                }
                // At the extreme we can only do some much...
                if ( y0 == ny -1 ) {
                        int k = i + offset[0];
                        rdata[k] += g[0] * dt[0];
                        rdata[k + 1] += g[0] * dt[1];
                        norm[k/2] += g[0];
 
                        k = i + offset[1];
                        rdata[k] += g[1] * dt[0];
                        rdata[k + 1] += g[1] * dt[1];
                        norm[k/2] += g[1];
                        continue;
                }
                // capture and accommodate for periodic boundary conditions in the y direction
                if ( y0 > ny-1) {
                        int dif = y0 - (ny-1);
                        y0 -= dif;
                }
 
                if (x0 >= nx - 2 || y0 >= ny - 1) continue;
 
 
 
 
                for (int j = 0; j < 4; j++)
                {
                        int k = i + offset[j];
                        rdata[k] += g[j] * dt[0];
                        rdata[k + 1] += g[j] * dt[1];
                        norm[k/2] += g[j];
 
                }
        }
 
        return 0;
 
}
 
EMData *FourierReconstructorSimple2D::finish(bool)
{
        normalize_threed();
 
        image->process_inplace("xform.fourierorigin.tocorner");
        image->do_ift_inplace();
        image->depad();
        image->process_inplace("xform.phaseorigin.tocenter");
 
        EMData *ret = image;
        image = 0;
        return  ret;
}
 
void ReconstructorVolumeData::normalize_threed(const bool sqrtnorm,const bool wiener)
// normalizes the 3-D Fourier volume. Also imposes appropriate complex conjugate relationships
{
        float* norm = tmp_data->get_data();
        float* rdata = image->get_data();
        
        size_t nnx=tmp_data->get_xsize();
        size_t nnxy=tmp_data->get_ysize()*nnx;
        
//      printf("%d %d %d %d %d %d\n",subnx,subny,subnz,image->get_xsize(),image->get_ysize(),image->get_zsize());
 
        // FIXME should throw a sensible error
        if ( 0 == norm ) throw NullPointerException("The normalization volume was null!");
        if ( 0 == rdata ) throw NullPointerException("The complex reconstruction volume was null!");
 
#ifdef DEBUG_POINT
        std::complex<float> pv = image->get_complex_at(113,0,23);
        float pnv = tmp_data->get_value_at(113,0,23);
        printf("norm: %1.4g\t%1.4g\t%1.4g\n",pv.real()/pnv,pv.imag()/pnv,pnv);
#endif
        
        // add_complex_at handles complex conjugate addition, but the normalization image doesn't
        // take this into account, so we need to sum the appropriate values
        // only works for whole volumes!
        if (subx0==0 && subnx==nx && suby0==0 && subny==ny && subz0==0 && subnz==nz) {
//              printf("cc gain correction\n");
                for (int z=-nz/2; z<nz/2; z++) {
                        for (int y=0; y<=ny/2; y++) {
                                if (z<=0 && (y==0||y==ny/2)) continue;
                                // x=0 plane
                                size_t idx1=(y==0?0:ny-y)*nnx+(z<=0?-z:nz-z)*nnxy;
                                size_t idx2=y*nnx+(z<0?nz+z:z)*nnxy;
                                if (idx1==idx2) continue;
                                float snorm=norm[idx1]+norm[idx2];
                                norm[idx1]=norm[idx2]=snorm;
                                
                                // This is the x=nx-1 plane
                                idx1+=nnx-1;
                                idx2+=nnx-1;
                                snorm=norm[idx1]+norm[idx2];
                                norm[idx1]=norm[idx2]=snorm;
                        }
                }
                // special cases not handled elsewhere
                norm[0     +   0*nnx+nz/2*nnxy]*=2;
                norm[0     +ny/2*nnx+   0*nnxy]*=2;
                norm[0     +ny/2*nnx+nz/2*nnxy]*=2;
                norm[nx/2-1+   0*nnx+nz/2*nnxy]*=2;
                norm[nx/2-1+ny/2*nnx+   0*nnxy]*=2;
        }
//      else printf("Subregion, no CC plane correction\n");
        
        // The math is a bit tricky to explain. Wiener filter is basically SNR/(1+SNR)
        // In this case, data have already been effectively multiplied by SNR (one image at a time),
        // so without Wiener filter, we just divide by total SNR. With Wiener filter, we just add
        // 1.0 to total SNR, and we're done             --steve
        float wfilt=0.0;
        if (wiener) wfilt=1.0;          
                
        // actual normalization
        for (size_t i = 0; i < (size_t)subnx * subny * subnz; i += 2) {
                float d = norm[i/2];
                if (sqrtnorm) d=sqrt(d);
                if (d == 0) {
                        rdata[i] = 0;
                        rdata[i + 1] = 0;
                }
                else {
//                      rdata[i]=1.0/d;
//                      rdata[i+1]=0.0;         // for debugging only
                        rdata[i] /= d+wfilt;
                        rdata[i + 1] /= d+wfilt;
                }
        }
 
        
        // This task should now be handled by use of add_complex_at, which adds both values when appropriate
        
        // enforce complex conj, only works on subvolumes if the complete conjugate plane is in the volume
//      if (subx0==0 && subnx>1 && subny==ny && subnz==nz) {
//              for (int z=0; z<=nz/2; z++) {
//                      for (int y=1; y<=ny; y++) {
//                              if (y==0 && z==0) continue;
//                              // x=0
//                              size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny;
//                              size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny;
//                              float ar=(rdata[i]+rdata[i2])/2.0f;
//                              float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
//                              rdata[i]=ar;
//                              rdata[i2]=ar;
//                              rdata[i+1]=ai;
//                              rdata[i2+1]=-ai;
//                      }
//              }
//      }
 
//      if (subx0+subnx==nx && subnx>1 && subny==ny && subnz==nz) {
//              for (int z=0; z<=nz/2; z++) {
//                      for (int y=1; y<=ny; y++) {
//                              if (y==0 && z==0) continue;
//                              // x=0
//                              size_t i=(size_t)(y%ny)*subnx+(size_t)(z%nz)*subnx*subny+subnx-2;
//                              size_t i2=(size_t)(ny-y)*subnx+(size_t)((nz-z)%nz)*subnx*subny+subnx-2;
//                              float ar=(rdata[i]+rdata[i2])/2.0f;
//                              float ai=(rdata[i+1]-rdata[i2+1])/2.0f;
//                              rdata[i]=ar;
//                              rdata[i2]=ar;
//                              rdata[i+1]=ai;
//                              rdata[i2+1]=-ai;
//                      }
//              }
//      }
}
 
void FourierIterReconstructor::setup() {
        // default setting behavior - does not override if the parameter is already set
        params.set_default("verbose",(int)0);
        
        vector<int> size=params["size"];
 
        nx = size[0]+2;
        ny = size[1];
        nz = size[2];
        nx2=nx/2-2;
        ny2=ny/2;
        nz2=nz/2;
        
        subnx=nx; subny=ny; subnz=nz;
        subx0=suby0=subz0=0;
 
        if (nx%2==1) throw ImageDimensionException("ERROR: FourierIterReconstructor only supports even box sizes");
 
        // The fourier volume where the reconstruction lives
        if (image) delete image;
        image = new EMData(nx,ny,nz);
        image->set_complex(true);
        image->set_fftodd(false);
        image->set_ri(true);
        image->to_zero();
        
        // This is the normalization volume
        if (tmp_data) delete tmp_data;
        tmp_data = new EMData(nx/2,ny,nz);
        tmp_data->to_zero();
        
        // this is the reference volume used to define the interpolation kernel
        // regular "setup" doesn't have one, in which case we default to a local gaussian kernel
        // This should only happen during the first iteration
        if (ref_vol) { delete ref_vol; ref_vol=0; }
//      ref_vol = new EMData(nx,ny,nz);
//      ref_vol->set_complex(true);
//      ref_vol->set_fftodd(false);
//      ref_vol->set_ri(true);
//      ref_vol->to_one();
        
        
        
        if ( (bool) params["verbose"] )
        {
                cout << "3D Fourier dimensions are " << nx << " " << ny << " " << nz << endl;
                cout << "3D Fourier subvolume is " << subnx << " " << subny << " " << subnz << endl;
                printf ("You will require approximately %1.3g GB of memory to reconstruct this volume\n",((float)subnx*subny*subnz*sizeof(float)*2.5)/1000000000.0);
        }
        
}
void FourierIterReconstructor::setup_seed(EMData* seed,float seed_weight) {
        setup();                // ok, a little dumb to initialize ref_vol then immediately delete it
        if (seed->is_complex()) ref_vol=seed->copy();   // we assume tocorner was called properly and dimensions are correct
        else {
                ref_vol=seed->do_fft();
                ref_vol->process_inplace("xform.phaseorigin.tocorner");
        }
}
 
void FourierIterReconstructor::setup_seedandweights(EMData* seed,EMData* weight) {
        setup();                // ok, a little dumb to initialize ref_vol then immediately delete it
        if (seed->is_complex()) ref_vol=seed->copy();   // we assume tocorner was called properly and dimensions are correct
        else {
                ref_vol=seed->do_fft();
                ref_vol->process_inplace("xform.phaseorigin.tocorner");
        }
        printf("Warning: FourierIterReconstructor ignores seed weights");
}
 
// warning: this clears any existing seed volume
void FourierIterReconstructor::clear() {
        setup();
}
 
EMData* FourierIterReconstructor::preprocess_slice( const EMData* const slice,  const Transform& t ) { 
        // Shift the image pixels so the real space origin is now located at the phase origin (at the bottom left of the image)
        EMData* return_slice = 0;
        Transform tmp(t);
        tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly, this way we only do 2d translation,scaling and mirroring
 
        if (tmp.is_identity()) return_slice=slice->copy();
        else return_slice = slice->process("xform",Dict("transform",&tmp));
 
        return_slice->process_inplace("xform.phaseorigin.tocorner");
        return_slice->do_fft_inplace();
        return_slice->mult((float)sqrt(1.0f/(return_slice->get_ysize())*return_slice->get_xsize()));
 
        return_slice->set_attr("reconstruct_preproc",(int)1);
        return return_slice;
}
 
int FourierIterReconstructor::insert_slice(const EMData* const slice, const Transform & arg, const float weight) { 
        Transform * rotation;
        rotation = new Transform(arg); // assignment operator
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        rotation->set_scale(1.0);
        rotation->set_mirror(false);
        rotation->set_trans(0,0,0);
 
//      if (slice->get_attr_default("reconstruct_preproc",(int) 0)) throw ImageDimensionException("ERROR: FourierIterReconstructor requires preprocess_slice() to be called in advance");
 
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
 
        float inx=(float)(slice->get_xsize());          // x/y dimensions of the input image
        float iny=(float)(slice->get_ysize());
        size_t ny2sq=ny*ny/4;
        
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                Transform t3d = (*rotation)*(*it);
                for (int y = -iny/2; y < iny/2; y++) {
                        for (int x = 0; x < inx/2; x++) {
 
                                float rx = (float) x/(inx-2.0f);        // coords relative to Nyquist=.5
                                float ry = (float) y/iny;
                                int r=Util::hypot_fast_int(x,y);
                                if (r>iny/2+3 && abs(inx-iny)<3) continue;      // no filling in Fourier corners...
 
                                Vec3f coord(rx,ry,0);
                                coord = coord*t3d; // transpose multiplication
                                float xx = coord[0]; // transformed coordinates in terms of Nyquist
                                float yy = coord[1];
                                float zz = coord[2];
 
                                // Map back to real pixel coordinates in output volume
                                xx=xx*(nx-2);
                                yy=yy*ny;
                                zz=zz*nz;
                                
                                
                                int x0 = (int) floor(xx-2.5);
                                int y0 = (int) floor(yy-2.5);
                                int z0 = (int) floor(zz-2.5);
 
                                std::complex<float>dt=slice->get_complex_at(x,y);                       // The data value we want to insert
 
                                if (x0<-nx2-4 || y0<-ny2-4 || z0<-nz2-4 || x0>nx2+3 || y0>ny2+3 || z0>nz2+3 ) continue;
 
                                // no error checking on add_complex_fast, so we need to be careful here
                                int x1=x0+5;
                                int y1=y0+5;
                                int z1=z0+5;
                                if (x0<-nx2) x0=-nx2;
                                if (x1>nx2) x1=nx2;
                                if (y0<-ny2) y0=-ny2;
                                if (y1>ny2) y1=ny2;
                                if (z0<-nz2) z0=-nz2;
                                if (z1>nz2) z1=nz2;
 
                                if (ref_vol) {
                                        // The value in the reference volume at the center insertion location (nearest voxel)
//                                      std::complex<float>nodt=ref_vol->get_complex_at(Util::round(xx),Util::round(yy),Util::round(zz));               
 
                                        // Here we trilinear interpolate the point value from the reference volume
                                        float xx0=floor(xx);
                                        float yy0=floor(yy);
                                        float zz0=floor(zz);
                                        std::complex<float>nodt=Util::trilinear_interpolate_complex(
                                                ref_vol->get_complex_at(xx0,yy0,zz0),
                                                ref_vol->get_complex_at(xx0+1,yy0,zz0),
                                                ref_vol->get_complex_at(xx0,yy0+1,zz0),
                                                ref_vol->get_complex_at(xx0+1,yy0+1,zz0),
                                                ref_vol->get_complex_at(xx0,yy0,zz0+1),
                                                ref_vol->get_complex_at(xx0+1,yy0,zz0+1),
                                                ref_vol->get_complex_at(xx0,yy0+1,zz0+1),
                                                ref_vol->get_complex_at(xx0+1,yy0+1,zz0+1),
                                                xx-xx0,yy-yy0,zz-zz0);
                                        
//                                      float h=1.0f/EMConsts::I5G;
                                        float h=1.0f/2.0f;              // This value was optimized empirically for a specific test case
                                        float gg=1.0;   //default no radial weight
                                        for (int k = z0 ; k <= z1; k++) {
                                                for (int j = y0 ; j <= y1; j++) {
                                                        for (int i = x0; i <= x1; i ++) {
                                                                if ((size_t)i*i+j*j+k*k>ny2sq) continue;
                                                                std::complex<float>ntdt=ref_vol->get_complex_at(i,j,k);
                                                                //gg=abs(nodt);                 // we use this as a weight
                                                                //if (gg==0) continue;
                                                                //gg=1.0;                       // turn off local weight
                                                                //std::complex<float>updt=dt*ntdt/nodt;         // This is the unweighted target value for i,j,k
                                                                std::complex<float>updt=dt+ntdt-nodt;
                                                                
                                                                float rl = Util::hypot3sq((float) i - xx, j - yy, k - zz);
                                                                gg = Util::fast_exp(-rl *h);
                                                                
                                                                size_t off;
                                                                off=image->add_complex_at_fast(i,j,k,updt*gg*weight);
                                                                tmp_data->get_data()[off/2]+=gg*weight;
                                                        }
                                                }
                                        }
                                } else {
                                        float h=1.0f/((Util::hypot3sq(xx,yy,zz)/4000)+.15);             // gaussian kernel is used as a weight not a kernel. We increase radius of integration with resolution. Changed away from this on 11/10/17
                                        h=h<0.1?0.1:h;  // new formula has h from 0.2 to 5
 
                                        float rl, gg;
                                        for (int k = z0 ; k <= z1; k++) {
                                                for (int j = y0 ; j <= y1; j++) {
                                                        for (int i = x0; i <= x1; i ++) {
                                                                rl = Util::hypot3sq((float) i - xx, j - yy, k - zz);
                                                                gg = Util::fast_exp(-rl *h);
 
                                                                size_t off;
                                                                off=image->add_complex_at_fast(i,j,k,dt*gg*weight);
                                                                //if (off==image->get_size()) 
                                                                //printf("%d %d %d\t%g %g %g %g\t%ld\n",i,j,k,dt.real(),dt.imag(),gg,weight,off);
                                                                tmp_data->get_data()[off/2]+=gg*weight;         // This is for interpolation rather than gridding
                                                        }
                                                }
                                        }
                                }
                        }
                }
        }
        
        
        delete rotation; rotation=0;
        return 0;
}
 
int FourierIterReconstructor::determine_slice_agreement(EMData*  input_slice, const Transform & arg, const float weight,bool sub) { return 0; }
 
EMData *FourierIterReconstructor::finish(bool doift) {
        normalize_threed(0);
        
        if (doift) {
                image->do_ift_inplace();
                image->depad();
                image->process_inplace("xform.phaseorigin.tocenter");
        }
 
        image->update();
        
        if (params.has_key("savenorm") && strlen((const char *)params["savenorm"])>0) {
                if (tmp_data->get_ysize()%2==0 && tmp_data->get_zsize()%2==0) tmp_data->process_inplace("xform.fourierorigin.tocenter");
                tmp_data->write_image((const char *)params["savenorm"]);
        }
 
        //Since we give up the ownership of the pointer to-be-returned, it's caller's responsibility to delete the returned image.
        //So we wrap this function with return_value_policy< manage_new_object >() in libpyReconstructor2.cpp to hand over ownership to Python.
        EMData *ret=image;
        image=0;
        
        return ret;
}
 
void FourierIterReconstructor::free_memory() {
        if (image) delete image;
        if (tmp_data) delete tmp_data;
        if (ref_vol) delete ref_vol;
        image=tmp_data=ref_vol=0;
}
 
 
void FourierReconstructor::load_default_settings()
{
        inserter=0;
        image=0;
        tmp_data=0;
}
 
void FourierReconstructor::free_memory()
{
        if (image) { delete image; image=0; }
        if (tmp_data) { delete tmp_data; tmp_data=0; }
        if ( inserter != 0 )
        {
                delete inserter;
                inserter = 0;
        }
}
 
#include <sstream>
 
void FourierReconstructor::load_inserter()
{
//      ss
//      string mode = (string)params["mode"];
        Dict parms;
        parms["data"] = image;
        parms["norm"] = tmp_data->get_data();
        // These aren't necessary because we deal with them before calling the inserter
//      parms["subnx"] = nx;
//      parms["subny"] = ny;
//      parms["subnx"] = nz;
//      parms["subx0"] = x0;
//      parms["suby0"] = y0;
//      parms["subz0"] = z0;
 
        if ( inserter != 0 )
        {
                delete inserter;
        }
 
        inserter = Factory<FourierPixelInserter3D>::get((string)params["mode"], parms);
        inserter->init();
}
 
void FourierReconstructor::setup()
{
        // default setting behavior - does not override if the parameter is already set
        params.set_default("mode","gauss_2");
        params.set_default("verbose",(int)0);
        
        vector<int> size=params["size"];
 
        nx = size[0];
        ny = size[1];
        nz = size[2];
        nx2=nx/2-1;
        ny2=ny/2;
        nz2=nz/2;
 
#ifdef RECONDEBUG
        ddata=(double *)malloc(sizeof(double)*250);
        dnorm=(double *)malloc(sizeof(double)*250);
        for (int i=0; i<250; i++) ddata[i]=dnorm[i]=0.0;
#endif
 
        // Adjust nx if for Fourier transform even odd issues
        bool is_fftodd = (nx % 2 == 1);
        // The Fourier transform requires one extra pixel in the x direction,
        // which is two spaces in memory, one each for the complex and the
        // real components
        nx += 2-is_fftodd;
 
        if (params.has_key("subvolume")) {
                vector<int> sub=params["subvolume"];
                subx0=sub[0];
                suby0=sub[1];
                subz0=sub[2];
                subnx=sub[3];
                subny=sub[4];
                subnz=sub[5];
 
                if (subx0<0 || suby0<0 || subz0<0 || subx0+subnx>nx || suby0+subny>ny || subz0+subnz>nz)
                        throw ImageDimensionException("The subvolume cannot extend outside the reconstructed volume");
 
        }
        else {
                subx0=suby0=subz0=0;
                subnx=nx;
                subny=ny;
                subnz=nz;
        }
 
 
        // Odd dimension support is here atm, but not above.
        if (image) delete image;
        image = new EMData();
        image->set_size(subnx, subny, subnz);
        image->set_complex(true);
        image->set_fftodd(is_fftodd);
        image->set_ri(true);
//      printf("%d %d %d\n\n",subnx,subny,subnz);
        image->to_zero();
 
        if (params.has_key("subvolume")) {
                image->set_attr("subvolume_x0",subx0);
                image->set_attr("subvolume_y0",suby0);
                image->set_attr("subvolume_z0",subz0);
                image->set_attr("subvolume_full_nx",nx);
                image->set_attr("subvolume_full_ny",ny);
                image->set_attr("subvolume_full_nz",nz);
        }
        
        if (tmp_data) delete tmp_data;
        tmp_data = new EMData();
        tmp_data->set_size(subnx/2, subny, subnz);
        tmp_data->to_zero();
        tmp_data->update();
 
        load_inserter();
 
#ifdef RECONDEBUG
        printf("copied\n");
        inserter->ddata=ddata;
        inserter->dnorm=dnorm;
#endif
        
        if ( (bool) params["verbose"] )
        {
                cout << "3D Fourier dimensions are " << nx << " " << ny << " " << nz << endl;
                cout << "3D Fourier subvolume is " << subnx << " " << subny << " " << subnz << endl;
                printf ("You will require approximately %1.3g GB of memory to reconstruct this volume\n",((float)subnx*subny*subnz*sizeof(float)*1.5)/1000000000.0);
        }
}
 
void FourierReconstructor::setup_seed(EMData* seed,float seed_weight) {
        // default setting behavior - does not override if the parameter is already set
        params.set_default("mode","gauss_2");
 
        vector<int> size=params["size"];
 
        nx = size[0];
        ny = size[1];
        nz = size[2];
        nx2=nx/2-1;
        ny2=ny/2;
        nz2=nz/2;
 
 
        // Adjust nx if for Fourier transform even odd issues
        bool is_fftodd = (nx % 2 == 1);
        // The Fourier transform requires one extra pixel in the x direction,
        // which is two spaces in memory, one each for the complex and the
        // real components
        nx += 2-is_fftodd;
 
        if (params.has_key("subvolume")) {
                vector<int> sub=params["subvolume"];
                subx0=sub[0];
                suby0=sub[1];
                subz0=sub[2];
                subnx=sub[3];
                subny=sub[4];
                subnz=sub[5];
 
                if (subx0<0 || suby0<0 || subz0<0 || subx0+subnx>nx || suby0+subny>ny || subz0+subnz>nz)
                        throw ImageDimensionException("The subvolume cannot extend outside the reconstructed volume");
 
        }
        else {
                subx0=suby0=subz0=0;
                subnx=nx;
                subny=ny;
                subnz=nz;
        }
 
        if (seed->get_xsize()!=subnx || seed->get_ysize()!=subny || seed->get_zsize()!=subnz || !seed->is_complex())
                throw ImageDimensionException("The dimensions of the seed volume do not match the reconstruction size");
 
        // Odd dimension support is here atm, but not above.
        image = seed->copy();
        image->mult(seed_weight);               // The lack of this line was what was causing all of the strange normalization issues
 
        
 
        if (params.has_key("subvolume")) {
                image->set_attr("subvolume_x0",subx0);
                image->set_attr("subvolume_y0",suby0);
                image->set_attr("subvolume_z0",subz0);
                image->set_attr("subvolume_full_nx",nx);
                image->set_attr("subvolume_full_ny",ny);
                image->set_attr("subvolume_full_nz",nz);
        }
 
        if (tmp_data) delete tmp_data;
        tmp_data = new EMData();
        tmp_data->set_size(subnx/2, subny, subnz);
        tmp_data->to_value(seed_weight);
        
        // The values at x=0 and x=nyquist are added twice in the map normally, but the normalization is only added once
        // This is compensated in the final normalization. In the seed volume we accomodate this by reducing the seed
        // alternatively we could double the actual values. Impact is similar, if not 100% identical
        if (subx0==0) {
                for (int k=0; k<subnz; k++) {
                        for (int j=0; j<subny; j++) {
                                tmp_data->set_value_at(0,j,k,seed_weight/2.0);
                        }
                }
                tmp_data->set_value_at(0,subny/2,0,seed_weight);
                tmp_data->set_value_at(0,0,subnz/2,seed_weight);
        }
        if (subnx+subx0==nx) {
                for (int k=0; k<subnz; k++) {
                        for (int j=0; j<subny; j++) {
                                tmp_data->set_value_at(subnx/2-1,j,k,seed_weight/2.0);
                        }
                }
                tmp_data->set_value_at(subnx/2-1,subny/2,0,seed_weight);
                tmp_data->set_value_at(subnx/2-1,0,subnz/2,seed_weight);
        }
        
 
        
        load_inserter();
        
#ifdef DEBUG_POINT
        std::complex<float> pv = image->get_complex_at(113,0,23);
        float pnv = tmp_data->get_value_at(113,0,23);
        printf("seed: %1.4g\t%1.4g\t%1.4g\n",pv.real()/pnv,pv.imag()/pnv,pnv);
#endif
 
 
        if ( (bool) params["quiet"] == false )
        {
                cout << "Seeded direct Fourier inversion";
                cout << "3D Fourier dimensions are " << nx << " " << ny << " " << nz << endl;
                cout << "3D Fourier subvolume is " << subnx << " " << subny << " " << subnz << endl;
                cout << "You will require approximately " << setprecision(3) << (subnx*subny*subnz*sizeof(float)*1.5)/1000000000.0 << "GB of memory to reconstruct this volume" << endl;
        }
}
 
void FourierReconstructor::setup_seedandweights(EMData* seed,EMData* seed_weight) {
        // default setting behavior - does not override if the parameter is already set
        
        // WARNING - when seed_weight is provided it must already be compensated at x=0 and x=nx-1 (should be 1/2 the actual value)
        params.set_default("mode","gauss_2");
 
        vector<int> size=params["size"];
 
        nx = size[0];
        ny = size[1];
        nz = size[2];
        nx2=nx/2-1;
        ny2=ny/2;
        nz2=nz/2;
 
 
        // Adjust nx if for Fourier transform even odd issues
        bool is_fftodd = (nx % 2 == 1);
        // The Fourier transform requires one extra pixel in the x direction,
        // which is two spaces in memory, one each for the complex and the
        // real components
        nx += 2-is_fftodd;
 
        if (params.has_key("subvolume")) {
                vector<int> sub=params["subvolume"];
                subx0=sub[0];
                suby0=sub[1];
                subz0=sub[2];
                subnx=sub[3];
                subny=sub[4];
                subnz=sub[5];
 
                if (subx0<0 || suby0<0 || subz0<0 || subx0+subnx>nx || suby0+subny>ny || subz0+subnz>nz)
                        throw ImageDimensionException("The subvolume cannot extend outside the reconstructed volume");
 
        }
        else {
                subx0=suby0=subz0=0;
                subnx=nx;
                subny=ny;
                subnz=nz;
        }
 
        if (seed->get_xsize()!=subnx || seed->get_ysize()!=subny || seed->get_zsize()!=subnz || !seed->is_complex())
                throw ImageDimensionException("The dimensions of the seed volume do not match the reconstruction size");
 
        // Odd dimension support is here atm, but not above.
        image = seed->copy();   // note that if the provided seed has not been 'premultiplied' by the weights, bad things may result!
        
        if (params.has_key("subvolume")) {
                image->set_attr("subvolume_x0",subx0);
                image->set_attr("subvolume_y0",suby0);
                image->set_attr("subvolume_z0",subz0);
                image->set_attr("subvolume_full_nx",nx);
                image->set_attr("subvolume_full_ny",ny);
                image->set_attr("subvolume_full_nz",nz);
        }
 
        if (tmp_data) delete tmp_data;
        tmp_data=seed_weight->copy();
 
        load_inserter();
 
        if ( (bool) params["quiet"] == false )
        {
                cout << "Seeded direct Fourier inversion";
                cout << "3D Fourier dimensions are " << nx << " " << ny << " " << nz << endl;
                cout << "3D Fourier subvolume is " << subnx << " " << subny << " " << subnz << endl;
                cout << "You will require approximately " << setprecision(3) << (subnx*subny*subnz*sizeof(float)*1.5)/1000000000.0 << "GB of memory to reconstruct this volume" << endl;
        }
}
 
 
void FourierReconstructor::clear()
{
        bool zeroimage = true;
        bool zerotmpimg = true;
        
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(image->getcudarwdata()) {
                        to_zero_cuda(image->getcudarwdata(),image->get_xsize(),image->get_ysize(),image->get_zsize());
                        zeroimage = false;
                }
                if(tmp_data->getcudarwdata()) {
                        //to_zero_cuda(tmp_data->getcudarwdata(),image->get_xsize(),image->get_ysize(),image->get_zsize());
                        zerotmpimg = false;
                }
        }
#endif
 
        if(zeroimage) image->to_zero();
        if(zerotmpimg) tmp_data->to_zero();
        
}
 
EMData* FourierReconstructor::preprocess_slice( const EMData* const slice,  const Transform& t )
{
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(!slice->getcudarwdata()) slice->copy_to_cuda(); //copy slice to cuda using the const version
        }
#endif
        // Shift the image pixels so the real space origin is now located at the phase origin (at the bottom left of the image)
        EMData* return_slice = 0;
        Transform tmp(t);
        tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly, this way we only do 2d translation,scaling and mirroring
 
        if (tmp.is_identity()) return_slice=slice->copy();
        else return_slice = slice->process("xform",Dict("transform",&tmp));
 
        return_slice->process_inplace("xform.phaseorigin.tocorner");
 
//      printf("@@@ %d\n",(int)return_slice->get_attr("nx"));
        // Fourier transform the slice
        
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1 && return_slice->getcudarwdata()) {
                return_slice->do_fft_inplace_cuda(); //a CUDA FFT inplace is quite slow as there is a lot of mem copying.
        }else{
                return_slice->do_fft_inplace();
        }
#else
        return_slice->do_fft_inplace();
#endif
 
//      printf("%d\n",(int)return_slice->get_attr("nx"));
 
        return_slice->mult((float)sqrt(1.0f/(return_slice->get_ysize())*return_slice->get_xsize()));
 
        // Shift the Fourier transform so that it's origin is in the center (bottom) of the image.
//      return_slice->process_inplace("xform.fourierorigin.tocenter");
 
        return_slice->set_attr("reconstruct_preproc",(int)1);
        return return_slice;
}
 
 
int FourierReconstructor::insert_slice(const EMData* const input_slice, const Transform & arg, const float oweight)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        
//      image->set_attr("apix_x",input_slice->get_attr("apix_x"));
//      image->set_attr("apix_y",input_slice->get_attr("apix_y"));
//      image->set_attr("apix_z",input_slice->get_attr("apix_z"));
 
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(!input_slice->getcudarwdata()) input_slice->copy_to_cuda(); //copy slice to cuda using the const version
        }
#endif
 
        bool usessnr=params.set_default("usessnr",false);
        bool corners=params.set_default("corners",false);
        float weight=oweight;
        if (usessnr) {
                if (input_slice->has_attr("class_ssnr")) weight=-1.0;   // negative weight is a flag for using SSNR
                else weight=0;
        }
 
        if (weight==0) return -1;
        
Transform * rotation;
/*      if ( input_slice->has_attr("xform.projection") ) {
                rotation = (Transform*) (input_slice->get_attr("xform.projection")); // assignment operator
        } else {*/
        rotation = new Transform(arg); // assignment operator
//      }
 
        EMData *slice;
        if (input_slice->get_attr_default("reconstruct_preproc",(int) 0)) slice=input_slice->copy();
        else slice = preprocess_slice( input_slice, *rotation);
 
 
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        rotation->set_scale(1.0);
        rotation->set_mirror(false);
        rotation->set_trans(0,0,0);
 
        // Finally to the pixel wise slice insertion
        //slice->copy_to_cuda();
//      EMData *s2=slice->do_ift();
//      s2->write_image("is.hdf",-1);
        do_insert_slice_work(slice, *rotation, weight, corners);
        
        delete rotation; rotation=0;
        delete slice;
 
//      image->update();
        return 0;
}
 
// note that negative weight is a prompt for using SSNR from header
void FourierReconstructor::do_insert_slice_work(const EMData* const input_slice, const Transform & arg,const float weight,const bool corners)
{
        // Reload the inserter if the mode has changed
//      string mode = (string) params["mode"];
//      if ( mode != inserter->get_name() )     load_inserter();
 
//      int y_in = input_slice->get_ysize();
//      int x_in = input_slice->get_xsize();
//      // Adjust the dimensions to account for odd and even ffts
//      if (input_slice->is_fftodd()) x_in -= 1;
//      else x_in -= 2;
 
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
 
        float inx=(float)(input_slice->get_xsize());            // x/y dimensions of the input image
        float iny=(float)(input_slice->get_ysize());
        
        if (abs(inx-iny)>2 && weight<0) printf("WARNING: Fourier Reconstruction failure. SSNR flag set with asymmetric dimensions on input image\n");
        
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(!image->getcudarwdata()){
                        image->copy_to_cuda();
                        tmp_data->copy_to_cuda();
                }
                float * m = new float[12];
                for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                        Transform t3d = arg*(*it);
                        t3d.copy_matrix_into_array(m);
                        //cout << "using CUDA " << image->getcudarwdata() << endl;
                        insert_slice_cuda(m,input_slice->getcudarwdata(),image->getcudarwdata(),tmp_data->getcudarwdata(),inx,iny,image->get_xsize(),image->get_ysize(),image->get_zsize(), weight);
                }
                delete m;
                return;
        }
#endif
        vector<float> ssnr;
        float sscale = 1.0f;
        if (weight<0) {
                ssnr=input_slice->get_attr("class_ssnr");
                sscale=2.0*(ssnr.size()-1)/iny;
        }
        
        float rweight=weight;
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                Transform t3d = arg*(*it);
                for (int y = -iny/2; y < iny/2; y++) {
                        for (int x = 0; x < inx/2; x++) {
 
                                float rx = (float) x/(inx-2.0f);        // coords relative to Nyquist=.5
                                float ry = (float) y/iny;
                                if (corners) {
                                        if (weight<0) {
                                                int r=Util::hypot_fast_int(x,y);
                                                rweight=Util::get_max(0.0f,ssnr[int(r*sscale)]);
                                        }
                                }
                                else {
                                        int r=Util::hypot_fast_int(x,y);
                                        if (r>iny/2 && abs(inx-iny)<3) continue;        // no filling in Fourier corners...
 
                                        if (weight<0) rweight=Util::get_max(0.0f,ssnr[int(r*sscale)]);
                                }
//                              printf("%d\t%f\n",int(r*sscale),rweight);
 
                                Vec3f coord(rx,ry,0);
                                coord = coord*t3d; // transpose multiplication
                                float xx = coord[0]; // transformed coordinates in terms of Nyquist
                                float yy = coord[1];
                                float zz = coord[2];
 
                                // Map back to real pixel coordinates in output volume
                                xx=xx*(nx-2);
                                yy=yy*ny;
                                zz=zz*nz;
                                
//                              if (x==10 && y==0) printf("10,0 -> %1.2f,%1.2f,%1.2f\t(%5.2f %5.2f %5.2f   %5.2f %5.2f %5.2f   %5.2f %5.2f %5.2f) %1.0f %d\n",
//                                      xx,yy,zz,t3d.at(0,0),t3d.at(0,1),t3d.at(0,2),t3d.at(1,0),t3d.at(1,1),t3d.at(1,2),t3d.at(2,0),t3d.at(2,1),t3d.at(2,2),inx,nx);
//                              if (x==0 && y==10 FourierReconstructor:) printf("0,10 -> %1.2f,%1.2f,%1.2f\t(%5.2f %5.2f %5.2f   %5.2f %5.2f %5.2f   %5.2f %5.2f %5.2f)\n",
//                                      xx,yy,zz,t3d.at(0,0),t3d.at(0,1),t3d.at(0,2),t3d.at(1,0),t3d.at(1,1),t3d.at(1,2),t3d.at(2,0),t3d.at(2,1),t3d.at(2,2));
 
                                //printf("%3.1f %3.1f %3.1f\t %1.4f %1.4f\t%1.4f\n",xx,yy,zz,input_slice->get_complex_at(x,y).real(),input_slice->get_complex_at(x,y).imag(),weight);
//                              if (floor(xx)==45 && floor(yy)==45 &&floor(zz)==0) printf("%d. 45 45 0\t %d %d\t %1.4f %1.4f\t%1.4f\n",(int)input_slice->get_attr("n"),x,y,input_slice->get_complex_at(x,y).real(),input_slice->get_complex_at(x,y).imag(),weight);
//                              if (floor(xx)==21 && floor(yy)==21 &&floor(zz)==0) printf("%d. 21 21 0\t %d %d\t %1.4f %1.4f\t%1.4f\n",(int)input_slice->get_attr("n"),x,y,input_slice->get_complex_at(x,y).real(),input_slice->get_complex_at(x,y).imag(),weight);
                                inserter->insert_pixel(xx,yy,zz,input_slice->get_complex_at(x,y),rweight);
                        }
                }
        }
}
 
int FourierReconstructor::determine_slice_agreement(EMData*  input_slice, const Transform & arg, const float weight,bool sub)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(!input_slice->getcudarwdata()) input_slice->copy_to_cuda(); //copy slice to cuda using the const version
        }
#endif
 
        Transform * rotation;
        rotation = new Transform(arg); // assignment operator
 
        EMData *slice;
        if (input_slice->get_attr_default("reconstruct_preproc",(int) 0)) slice=input_slice->copy();
        else slice = preprocess_slice( input_slice, *rotation);
 
 
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        rotation->set_scale(1.0);
        rotation->set_mirror(false);
        rotation->set_trans(0,0,0);
        if (sub) do_insert_slice_work(slice, *rotation, -weight);
        // Remove the current slice first (not threadsafe, but otherwise performance would be awful)
        
        // Compare
        do_compare_slice_work(slice, *rotation,weight);
 
        input_slice->set_attr("reconstruct_norm",slice->get_attr("reconstruct_norm"));
        input_slice->set_attr("reconstruct_absqual",slice->get_attr("reconstruct_absqual"));
        input_slice->set_attr("reconstruct_absqual_lowres",slice->get_attr("reconstruct_absqual_lowres"));
//      input_slice->set_attr("reconstruct_qual",slice->get_attr("reconstruct_qual"));
        input_slice->set_attr("reconstruct_weight",slice->get_attr("reconstruct_weight"));
 
        // Now put the slice back
        if (sub) do_insert_slice_work(slice, *rotation, weight);
 
        delete rotation;
        delete slice;
 
//      image->update();
        return 0;
 
}
 
void FourierReconstructor::do_compare_slice_work(EMData* input_slice, const Transform & arg,float weight)
{
 
        float dt[3];    // This stores the complex and weight from the volume
        float dt2[2];   // This stores the local image complex
        float *dat = input_slice->get_data();
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
 
        float inx=(float)(input_slice->get_xsize());            // x/y dimensions of the input image
        float iny=(float)(input_slice->get_ysize());
        float apix=input_slice->get_attr("apix_x");
        float rmax=iny*apix/12.0;               // radius at 12 A, use as cutoff for low res insertion quality
        if (rmax>iny/2.0-1.0) rmax=iny/2.0-1.0;         // in case of large A/pix
        if (rmax<5.0) rmax=5.0;         // can't imagine this will happen
        
        double dotlow=0;        // low resolution dot product
        double dlpow=0;
        double dlpow2=0;
        
        double dot=0;           // summed pixel*weight dot product
        double vweight=0;               // sum of weights
        double power=0;         // sum of inten*weight from volume
        double power2=0;                // sum of inten*weight from image
//      double amp=0,amp2=0;    // used for normalization, weighted amplitude averages under specific conditions
        bool use_cpu = true;
        
        int nval=0;
 
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1) {
                if(!input_slice->getcudarwdata()) input_slice->copy_to_cuda();
                if(!image->getcudarwdata()){
                        image->copy_to_cuda();
                        tmp_data->copy_to_cuda();
                }
                for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                        Transform t3d = arg*(*it);
                        float * m = new float[12];
                        t3d.copy_matrix_into_array(m);
                        float4 stats = determine_slice_agreement_cuda(m,input_slice->getcudarwdata(),image->getcudarwdata(),tmp_data->getcudarwdata(),inx,iny,image->get_xsize(),image->get_ysize(),image->get_zsize(), weight);
                        dot = stats.x;
                        vweight = stats.y;
                        power = stats.z;
                        power2 = stats.w;
                        //cout << "CUDA stats " << stats.x << " " << stats.y << " " << stats.z << " " << stats.w << endl;
                        use_cpu = false;
                }
        }
#endif
        if(use_cpu) {
                for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                        Transform t3d = arg*(*it);
                        for (int y = -iny/2; y < iny/2; y++) {
                                for (int x = 0; x <=  inx/2; x++) {
                                        if (x==0 && y==0) continue;             // We don't want to use the Fourier origin
 
                                        float rx = (float) x/(inx-2);   // coords relative to Nyquist=.5
                                        float ry = (float) y/iny;
 
//                                      if ((rx * rx + Util::square(ry - max_input_dim "xform.projection"/ 2)) > rl)
//                                      continue;
 
                                        Vec3f coord(rx,ry,0);
                                        coord = coord*t3d; // transpose multiplication
                                        float xx = coord[0]; // transformed coordinates in terms of Nyquist
                                        float yy = coord[1];
                                        float zz = coord[2];
 
 
                                        if (fabs(xx)>0.5 || fabs(yy)>=0.5 || fabs(zz)>=0.5) continue;
 
                                        // Map back to actual pixel coordinates in output volume
                                        xx=xx*(nx-2);
                                        yy=yy*ny;
                                        zz=zz*nz;
 
 
                                        int idx = (int)(x * 2 + inx*(y<0?iny+y:y));
                                        dt2[0] = dat[idx];
                                        dt2[1] = dat[idx+1];
 
                                        // value returned indirectly in dt
                                        if (!pixel_at(xx,yy,zz,dt) || dt[2]==0) continue;
 
//                                      printf("%f\t%f\t%f\t%f\t%f\n",dt[0],dt[1],dt[2],dt2[0],dt2[1]);
                                        float r=(float)Util::hypot_fast(x,y);
                                        if (r>3 && r<rmax) {
                                                dotlow+=(dt[0]*dt2[0]+dt[1]*dt2[1])*dt[2];
                                                dlpow+=(dt[0]*dt[0]+dt[1]*dt[1])*dt[2];
                                                dlpow2+=(dt2[0]*dt2[0]+dt2[1]*dt2[1])*dt[2];
                                        }
                                        
                                        
//                                      if (r<6) continue; 
                                        vweight+=dt[2];
                                        dot+=(dt[0]*dt2[0]+dt[1]*dt2[1])*dt[2];
                                        power+=(dt[0]*dt[0]+dt[1]*dt[1])*dt[2];
                                        power2+=(dt2[0]*dt2[0]+dt2[1]*dt2[1])*dt[2];
//                                      printf("%d\t%d\t%f\t%f\t%f\n",x,y,dt[0],dt[1],dt[2]);
//                                      if (r>2 && dt[2]>=0.5) {
//                                              amp+=hypot(dt[0]*dt[0],dt[1]*dt[1])*dt[2];
//                                              amp2+=hypot(dt2[0]*dt2[0],dt2[1]*dt2[1])*dt[2];
//                                      }
                                        nval++;
                                }
                        }
                        //cout << dot << " " << vweight << " " << power << " " << power2 << endl;
                }
        }
        
        dot/=sqrt(power*power2);                // normalize the dot product
        if (dlpow*dlpow2>0) dotlow/=sqrt(dlpow*dlpow2);
//      input_slice->set_attr("reconstruct_norm",(float)(power2<=0?1.0:sqrt(power/power2)/(inx*iny)));
        input_slice->set_attr("reconstruct_norm",(float)(power2<=0?1.0:sqrt(power/power2)));
//      input_slice->set_attr("reconstruct_norm",(float)(amp2<=0?1.0:amp/amp2));
        input_slice->set_attr("reconstruct_absqual",(float)dot);
        input_slice->set_attr("reconstruct_absqual_lowres",(float)dotlow);
        float rw=weight<=0?1.0f:1.0f/weight;
        input_slice->set_attr("reconstruct_qual",(float)(dot*rw/((rw-1.0)*dot+1.0)));   // here weight is a proxy for SNR
        input_slice->set_attr("reconstruct_weight",(float)(vweight/(float)(nval)));
//      printf("** %g\t%g\t%g\t%g ##\n",dot,vweight,power,power2);
        //printf("** %f %f %f ##\n",(float)(power2<=0?1.0:sqrt(power/power2)/(inx*iny)),(float)dot,(float)(dot*weight/((weight-1.0)*dot+1.0)));
}
 
EMData* FourierReconstructor::projection(const Transform &euler, int ret_fourier) {
        
        if (subx0!=0 || suby0!=0 || subz0!=0 || subnx!=nx || subny!=ny ||subnz!=nz) 
                throw ImageDimensionException("ERROR: Reconstructor->projection() does not work with subvolumes");
        
        EMData *ret = new EMData(nx,ny,1);
        ret->set_complex(1);
        ret->set_ri(1);
        ret->set_attr("apix_x",image->get_attr("apix_x"));
        ret->set_attr("apix_y",image->get_attr("apix_y"));
        ret->set_attr("apix_z",image->get_attr("apix_z"));
        
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        Transform rotation(euler);
        rotation.set_scale(1.0);
        rotation.set_mirror(false);
        rotation.set_trans(0,0,0);
        
        float dt[3];    // This stores the complex and weight from the volume
 
//      float apix=input_slice->get_attr("apix_x");
//      float rmax=iny*apix/12.0;               // radius at 12 A, use as cutoff for low res insertion quality
        
        for (int y = -ny/2; y < ny/2; y++) {
                for (int x = 0; x <=  nx/2; x++) {
 
                        float rx = (float) x/(nx-2);    // coords relative to Nyquist=.5
                        float ry = (float) y/ny;
 
 
                        Vec3f coord(rx,ry,0);
                        coord = coord*rotation; // transpose multiplication
                        float xx = coord[0]; // transformed coordinates in terms of Nyquist
                        float yy = coord[1];
                        float zz = coord[2];
 
 
                        if (fabs(xx)>0.5 || fabs(yy)>=0.5 || fabs(zz)>=0.5) continue;
 
                        // Map back to actual pixel coordinates in output volume
                        xx=xx*(nx-2);
                        yy=yy*ny;
                        zz=zz*nz;
 
                        if (!pixel_at(xx,yy,zz,dt) || dt[2]<0.005) continue;
//                      if (x==0) printf("%d %d %g %g %g\n",x,y,dt[0],dt[1],dt[2]);
                        if ((x==0 ||x==nx/2) && (y!=0 && y!=-ny/2)) { dt[0]/=2; dt[1]/=2; }
                        ret->set_complex_at(x,y,std::complex<float>(dt[0],dt[1]));      // division by dt[2] already handled in pixel_at
                }
        }
        
        Transform translation;
        translation.set_trans(euler.get_trans());
        ret->process_inplace("xform",Dict("transform",&translation));
        if (!ret_fourier) {
                ret->process_inplace("xform.phaseorigin.tocenter");
                EMData *tmp=ret->do_ift();
                delete ret;
                ret=tmp;
        }
        return ret;
}
 
 
bool FourierReconstructor::pixel_at(const float& xx, const float& yy, const float& zz, float *dt)
{
        int x0 = (int) Util::round(xx);
        int y0 = (int) Util::round(yy);
        int z0 = (int) Util::round(zz);
 
        std::complex<float> val=image->get_complex_at(x0,y0,z0);
        size_t idx=image->get_complex_index_fast(x0,y0,z0)/2;
        float norm=tmp_data->get_value_at_index(idx);
        dt[0]=val.real()/norm;
        dt[1]=val.imag()/norm;
        dt[2]=norm;
//      printf("%d %d %d    %g %g %g\n",x0,y0,z0,dt[0],dt[1],dt[2]);
        return true;
        
        //Trilinear interpolation version caused prominent interpolation artifacts due to high noise levels
        // between 1/2 Nyquist and Nyquist. While the nearest neighbor interpolation used above still has
        // artifacts, it seems better for this puprose.
        
//      int x0 = (int) floor(xx);
//      int y0 = (int) floor(yy);
//      int z0 = (int) floor(zz);
//      
//      float *rdata=image->get_data();
//      float *norm=tmp_data->get_data();
//      float normsum=0,normsum2=0;
// 
//      dt[0]=dt[1]=dt[2]=0.0;
// 
//      if (nx==subnx) {                        // normal full reconstruction
//              if (x0<-nx2-1 || y0<-ny2-1 || z0<-nz2-1 || x0>nx2 || y0>ny2 || z0>nz2 ) return false;
// 
//              
//              
//              int x1=x0+1;
//              int y1=y0+1;
//              int z1=z0+1;
//              if (x0<-nx2) x0=-nx2;
//              if (x1>nx2) x1=nx2;
//              if (y0<-ny2) y0=-ny2;
//              if (y1>ny2) y1=ny2;
//              if (z0<-nz2) z0=-nz2;
//              if (z1>nz2) z1=nz2;
//              
//              size_t idx=0;
//              float r, gg;
//              for (int k = z0 ; k <= z1; k++) {
//                      for (int j = y0 ; j <= y1; j++) {
//                              for (int i = x0; i <= x1; i ++) {
//                                      idx=image->get_complex_index_fast(i,j,k);
// //                                   r = Util::hypot3sq((float) i - xx, j - yy, k - zz);
// //                                   gg = Util::fast_exp(-r / EMConsts::I2G);
//                                      gg=(1.0-fabs(i-xx))*(1.0-fabs(j-yy))*(1.0-fabs(k-zz));  // Change from Gaussian to trilinear, 6/7/20
//                                      
//                                      dt[0]+=gg*rdata[idx];
//                                      dt[1]+=(i<0?-1.0f:1.0f)*gg*rdata[idx+1];
//                                      //dt[2]+=norm[idx/2]*gg;
//                                      normsum2+=gg;
//                                      normsum+=gg*norm[idx/2];
//                                      if (i==0) {
//                                              normsum2+=gg;
//                                              normsum+=gg*norm[idx/2];                                
//                                      }
//                              }
//                      }
//              }
//              if (normsum==0) return false;
//              dt[0]/=normsum;
//              dt[1]/=normsum;
//              dt[2]=normsum/normsum2;
// #ifdef DEBUG_POINT
//              if (z0==23 && y0==0 && x0==113) {
//                      std::complex<float> pv = image->get_complex_at(113,0,23);
//                      float pnv = tmp_data->get_value_at(113,0,23);
//                      printf("pixat: %1.4g\t%1.4g\t%1.4g\t%1.4g\t%1.4g\t%1.4g\n",pv.real()/pnv,pv.imag()/pnv,pnv,dt[0],dt[1],dt[2]);
//              }
// #endif
// //           printf("%1.2f,%1.2f,%1.2f\t%1.3f\t%1.3f\t%1.3f\t%1.3f\t%1.3f\n",xx,yy,zz,dt[0],dt[1],dt[2],rdata[idx],rdata[idx+1]);
//              return true;
//      } 
//      else {                                  // for subvolumes, not optimized yet
//              size_t idx;
//              float r, gg;
//              for (int k = z0 ; k <= z0 + 1; k++) {
//                      for (int j = y0 ; j <= y0 + 1; j++) {
//                              for (int i = x0; i <= x0 + 1; i ++) {
//                                      r = Util::hypot3sq((float) i - xx, j - yy, k - zz);
//                                      idx=image->get_complex_index(i,j,k,subx0,suby0,subz0,nx,ny,nz);
//                                      gg = Util::fast_exp(-r / EMConsts::I2G)*norm[idx/2];
//                                      
//                                      dt[0]+=gg*rdata[idx];
//                                      dt[1]+=(i<0?-1.0f:1.0f)*gg*rdata[idx+1];
//                                      dt[2]+=norm[idx/2];
//                                      normsum+=gg;
//                              }
//                      }
//              }
//              
//              if (normsum==0)  return false;
//              return true;
//      }
}
 
 
EMData *FourierReconstructor::finish(bool doift)
{
//      float *norm = tmp_data->get_data();
//      float *rdata = image->get_data();
#ifdef EMAN2_USING_CUDA
        if(EMData::usecuda == 1 && image->getcudarwdata()){
                cout << "copy back from CUDA" << endl;
                image->copy_from_device();
                tmp_data->copy_from_device();
        }
#endif
        
        bool sqrtnorm=params.set_default("sqrtnorm",false);
        normalize_threed(sqrtnorm);
//      printf("%f\t%f\t%f\n",tmp_data->get_value_at(67,19,1),image->get_value_at(135,19,1),image->get_value_at(134,19,1));
        
// This compares single precision sum to double precision sum near the origin
#ifdef RECONDEBUG
        for (int k=0; k<5; k++) {
                for (int j=0; j<5; j++) {
                        for (int i=0; i<5; i++) {
                                int idx=i*2+j*10+k*50;
                                std::complex <double> a(ddata[idx],ddata[idx+1]);
                                double b=dnorm[idx];
                                a/=b;
                                printf("%d %d %d   %1.4lg\t%1.4g     %1.4lg\t%1.4g\n",i,j,k,a.real(),image->get_value_at(i*2,j,k),a.imag(),image->get_value_at(i*2+1,j,k));
                        }
                }
        }
#endif
        
//      tmp_data->write_image("density.mrc");
 
        // we may as well delete the tmp data now... it saves memory and the calling program might
        // need memory after it gets the return volume.
        // If this delete didn't happen now, it would happen when the deconstructor was called --david
        // no longer a good idea with the new iterative scheme -- steve
//      if ( tmp_data != 0 )
//      {
//              delete tmp_data;
//              tmp_data = 0;
//      }
 
/*      image->process_inplace("xform.fourierorigin.tocorner");*/
 
        if (doift) {
                image->do_ift_inplace();
                image->depad();
                image->process_inplace("xform.phaseorigin.tocenter");
        }
        // If the image was padded it should be the original size, as the client would expect
        //  I blocked the rest, it is almost certainly incorrect  PAP 07/31/08
        // No, it's not incorrect. You are wrong. You have the meaning of nx mixed up. DSAW 09/23/cd
        // This should now be handled in the calling program --steve 11/03/09
//      bool is_fftodd = (nx % 2 == 1);
//      if ( (nx-2*(!is_fftodd)) != output_x || ny != output_y || nz != output_z )
//      {
//              FloatPoint origin( (nx-output_x)/2, (ny-output_y)/2, (nz-output_z)/2 );
//              FloatSize region_size( output_x, output_y, output_z);
//              Region clip_region( origin, region_size );
//              image->clip_inplace( clip_region );
//      }
 
        // Should be an "if (verbose)" here or something
        //print_stats(quality_scores);
 
        image->update();
        
        
        if (params.has_key("normout")) {
//              if (tmp_data->get_ysize()%2==0 && tmp_data->get_zsize()%2==0) tmp_data->process_inplace("xform.fourierorigin.tocenter");
                EMData *normout=(EMData*) params["normout"];
                normout->set_data(tmp_data->copy()->get_data());
                normout->update();
        }
        
        if (params.has_key("savenorm") && strlen((const char *)params["savenorm"])>0) {
                if (tmp_data->get_ysize()%2==0 && tmp_data->get_zsize()%2==0) tmp_data->process_inplace("xform.fourierorigin.tocenter");
                tmp_data->write_image((const char *)params["savenorm"]);
        }
 
        delete tmp_data;
        tmp_data=0;
        //Since we give up the ownership of the pointer to-be-returned, it's caller's responsibility to delete the returned image.
        //So we wrap this function with return_value_policy< manage_new_object >() in libpyReconstructor2.cpp to hand over ownership to Python.
        EMData *ret=image;
        image=0;
        
        return ret;
}
 
int WienerFourierReconstructor::insert_slice(const EMData* const input_slice, const Transform & arg, const float weight)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        Transform * rotation;
/*      if ( input_slice->has_attr("xform.projection") ) {
                rotation = (Transform*) (input_slice->get_attr("xform.projection")); // assignment operator
        } else {*/
        rotation = new Transform(arg); // assignment operator
//      }
 
        if (!input_slice->has_attr("ctf_snr_total")) 
                throw NotExistingObjectException("ctf_snr_total","No SNR information present in class-average. Must use the ctf.auto or ctfw.auto averager.");
 
        EMData *slice;
        if (input_slice->get_attr_default("reconstruct_preproc",(int) 0)) slice=input_slice->copy();
        else slice = preprocess_slice( input_slice, *rotation);
 
 
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        rotation->set_scale(1.0);
        rotation->set_mirror(false);
        rotation->set_trans(0,0,0);
 
        // Finally to the pixel wise slice insertion
        do_insert_slice_work(slice, *rotation, weight);
 
        delete rotation; rotation=0;
        delete slice;
 
//      image->update();
        return 0;
}
 
void WienerFourierReconstructor::do_insert_slice_work(const EMData* const input_slice, const Transform & arg,const float inweight)
{
 
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
 
        float inx=(float)(input_slice->get_xsize());            // x/y dimensions of the input image
        float iny=(float)(input_slice->get_ysize());
        
        int undo_wiener=(int)input_slice->get_attr_default("ctf_wiener_filtered",0);    // indicates whether we need to undo a wiener filter before insertion
//      if (undo_wiener) throw UnexpectedBehaviorException("wiener_fourier does not yet accept already Wiener filtered class-averages. Suggest using ctf.auto averager for now.");
        
        vector<float> snr=input_slice->get_attr("ctf_snr_total");
        float sub=1.0;
        if (inweight<0) sub=-1.0;
        float weight;
        
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                Transform t3d = arg*(*it);
                for (int y = -iny/2; y < iny/2; y++) {
                        for (int x = 0; x <=  inx/2; x++) {
 
                                float rx = (float) x/(inx-2.0f);        // coords relative to Nyquist=.5
                                float ry = (float) y/iny;
 
                                // This deals with the SNR weight
                                float rn = (float)hypot(rx,ry);
                                if (rn>=.5) continue;           // no SNR in the corners, and we're going to mask them later anyway
                                rn*=snr.size()*2.0f;
                                int rni=(int)floor(rn);
                                if ((unsigned int)rni>=snr.size()-1) weight=snr[snr.size()-1]*sub;
                                else {
                                        rn-=rni;
                                        weight=Util::linear_interpolate(snr[rni],snr[rni+1],rn);
                                }
//                              if (weight>500.0) printf("%f %d %d %f %f %d %f\n",weight,x,y,rx,ry,rni);
                                
                                Vec3f coord(rx,ry,0);
                                coord = coord*t3d; // transpose multiplication
                                float xx = coord[0]; // transformed coordinates in terms of Nyquist
                                float yy = coord[1];
                                float zz = coord[2];
 
                                // Map back to real pixel coordinates in output volume
                                xx=xx*(nx-2);
                                yy=yy*ny;
                                zz=zz*nz;
 
//                              printf("%f\n",weight);
                                if (undo_wiener) inserter->insert_pixel(xx,yy,zz,(input_slice->get_complex_at(x,y))*((weight+1.0f)/weight),weight*sub);
                                else inserter->insert_pixel(xx,yy,zz,input_slice->get_complex_at(x,y),weight*sub);
                        }
                }
        }
}
 
int WienerFourierReconstructor::determine_slice_agreement(EMData*  input_slice, const Transform & arg, const float weight,bool sub)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        Transform * rotation;
        rotation = new Transform(arg); // assignment operator
 
        EMData *slice;
        if (input_slice->get_attr_default("reconstruct_preproc",(int) 0)) slice=input_slice->copy();
        else slice = preprocess_slice( input_slice, *rotation);
 
 
        // We must use only the rotational component of the transform, scaling, translation and mirroring
        // are not implemented in Fourier space, but are in preprocess_slice
        rotation->set_scale(1.0);
        rotation->set_mirror(false);
        rotation->set_trans(0,0,0);
 
//      tmp_data->write_image("dbug.hdf",0);
        
        // Remove the current slice first (not threadsafe, but otherwise performance would be awful)
        if (sub) do_insert_slice_work(slice, *rotation, -weight);
 
        // Compare
        do_compare_slice_work(slice, *rotation,weight);
 
        input_slice->set_attr("reconstruct_norm",slice->get_attr("reconstruct_norm"));
        input_slice->set_attr("reconstruct_absqual",slice->get_attr("reconstruct_absqual"));
//      input_slice->set_attr("reconstruct_qual",slice->get_attr("reconstruct_qual"));
        input_slice->set_attr("reconstruct_weight",slice->get_attr("reconstruct_weight"));
 
        // Now put the slice back
        if (sub) do_insert_slice_work(slice, *rotation, weight);
 
 
        delete rotation;
        delete slice;
 
//      image->update();
        return 0;
 
}
 
void WienerFourierReconstructor::do_compare_slice_work(EMData* input_slice, const Transform & arg,float weight)
{
 
        float dt[3];    // This stores the complex and weight from the volume
        float dt2[2];   // This stores the local image complex
        float *dat = input_slice->get_data();
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
 
        float inx=(float)(input_slice->get_xsize());            // x/y dimensions of the input image
        float iny=(float)(input_slice->get_ysize());
 
        double dot=0;           // summed pixel*weight dot product
        double vweight=0;               // sum of weights
        double power=0;         // sum of inten*weight from volume
        double power2=0;                // sum of inten*weight from image
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                Transform t3d = arg*(*it);
                for (int y = -iny/2; y < iny/2; y++) {
                        for (int x = 0; x <=  inx/2; x++) {
                                if (x==0 && y==0) continue;             // We don't want to use the Fourier origin
 
                                float rx = (float) x/(inx-2);   // coords relative to Nyquist=.5
                                float ry = (float) y/iny;
 
//                              if ((rx * rx + Util::square(ry - max_input_dim / 2)) > rl)
//                                      continue;
 
                                Vec3f coord(rx,ry,0);
                                coord = coord*t3d; // transpose multiplication
                                float xx = coord[0]; // transformed coordinates in terms of Nyquist
                                float yy = coord[1];
                                float zz = coord[2];
 
 
                                if (fabs(xx)>0.5 || fabs(yy)>=0.5 || fabs(zz)>=0.5) continue;
 
                                // Map back to actual pixel coordinates in output volume
                                xx=xx*(nx-2);
                                yy=yy*ny;
                                zz=zz*nz;
 
 
                                int idx = (int)(x * 2 + inx*(y<0?iny+y:y));
                                dt2[0] = dat[idx];
                                dt2[1] = dat[idx+1];
 
                                // value returned indirectly in dt
                                if (!pixel_at(xx,yy,zz,dt) || dt[2]<=0) continue;
 
//                              printf("%f\t%f\t%f\t%f\t%f\n",dt[0],dt[1],dt[2],dt2[0],dt2[1]);
                                dot+=(dt[0]*dt2[0]+dt[1]*dt2[1])*dt[2];
                                vweight+=dt[2];
                                power+=(dt[0]*dt[0]+dt[1]*dt[1])*dt[2];
                                power2+=(dt2[0]*dt2[0]+dt2[1]*dt2[1])*dt[2];
                        }
                }
        }
 
        dot/=sqrt(power*power2);                // normalize the dot product
//      input_slice->set_attr("reconstruct_norm",(float)(power2<=0?1.0:sqrt(power/power2)/(inx*iny)));
        input_slice->set_attr("reconstruct_norm",(float)(power2<=0?1.0:sqrt(power/power2)));
        input_slice->set_attr("reconstruct_absqual",(float)dot);
        float rw=weight<=0?1.0f:1.0f/weight;
        input_slice->set_attr("reconstruct_qual",(float)(dot*rw/((rw-1.0)*dot+1.0)));   // here weight is a proxy for SNR
        input_slice->set_attr("reconstruct_weight",(float)vweight/(float)(subnx*subny*subnz));
//      printf("** %g\t%g\t%g\t%g ##\n",dot,vweight,power,power2);
        //printf("** %f %f %f ##\n",(float)(power2<=0?1.0:sqrt(power/power2)/(inx*iny)),(float)dot,(float)(dot*weight/((weight-1.0)*dot+1.0)));
}
 
bool WienerFourierReconstructor::pixel_at(const float& xx, const float& yy, const float& zz, float *dt)
{
        int x0 = (int) floor(xx);
        int y0 = (int) floor(yy);
        int z0 = (int) floor(zz);
        
        float *rdata=image->get_data();
        float *norm=tmp_data->get_data();
        float normsum=0,normsum2=0;
 
        dt[0]=dt[1]=dt[2]=0.0;
 
        if (nx==subnx) {                        // normal full reconstruction
                if (x0<-nx2-1 || y0<-ny2-1 || z0<-nz2-1 || x0>nx2 || y0>ny2 || z0>nz2 ) return false;
 
                // no error checking on add_complex_fast, so we need to be careful here
                int x1=x0+1;
                int y1=y0+1;
                int z1=z0+1;
                if (x0<-nx2) x0=-nx2;
                if (x1>nx2) x1=nx2;
                if (y0<-ny2) y0=-ny2;
                if (y1>ny2) y1=ny2;
                if (z0<-nz2) z0=-nz2;
                if (z1>nz2) z1=nz2;
                
                size_t idx=0;
                float r, gg;
                for (int k = z0 ; k <= z1; k++) {
                        for (int j = y0 ; j <= y1; j++) {
                                for (int i = x0; i <= x1; i ++) {
                                        r = Util::hypot3sq((float) i - xx, j - yy, k - zz);
                                        idx=image->get_complex_index_fast(i,j,k);
                                        gg = Util::fast_exp(-r / EMConsts::I2G);
                                        
                                        dt[0]+=gg*rdata[idx];
                                        dt[1]+=(i<0?-1.0f:1.0f)*gg*rdata[idx+1];
                                        dt[2]+=norm[idx/2]*gg;
                                        normsum2+=gg;
                                        normsum+=gg*norm[idx/2];                                
                                }
                        }
                }
                if (normsum==0) return false;
                dt[0]/=normsum;
                dt[1]/=normsum;
                dt[2]/=normsum2;
//              printf("%1.2f,%1.2f,%1.2f\t%1.3f\t%1.3f\t%1.3f\t%1.3f\t%1.3f\n",xx,yy,zz,dt[0],dt[1],dt[2],rdata[idx],rdata[idx+1]);
                return true;
        } 
        else {                                  // for subvolumes, not optimized yet
                size_t idx;
                float r, gg;
                for (int k = z0 ; k <= z0 + 1; k++) {
                        for (int j = y0 ; j <= y0 + 1; j++) {
                                for (int i = x0; i <= x0 + 1; i ++) {
                                        r = Util::hypot3sq((float) i - xx, j - yy, k - zz);
                                        idx=image->get_complex_index(i,j,k,subx0,suby0,subz0,nx,ny,nz);
                                        gg = Util::fast_exp(-r / EMConsts::I2G)*norm[idx/2];
                                        
                                        dt[0]+=gg*rdata[idx];
                                        dt[1]+=(i<0?-1.0f:1.0f)*gg*rdata[idx+1];
                                        dt[2]+=norm[idx/2];
                                        normsum+=gg;                            
                                }
                        }
                }
                
                if (normsum==0)  return false;
                return true;
        }
}
 
 
EMData *WienerFourierReconstructor::finish(bool doift)
{
 
        bool sqrtnorm=params.set_default("sqrtnorm",false);
        normalize_threed(sqrtnorm,true);                // true is the wiener filter
 
        if (doift) {
                image->do_ift_inplace();
                image->depad();
                image->process_inplace("xform.phaseorigin.tocenter");
        }
 
        image->update();
        
        if (params.has_key("savenorm") && strlen((const char *)params["savenorm"])>0) {
                if (tmp_data->get_ysize()%2==0 && tmp_data->get_zsize()%2==0) tmp_data->process_inplace("xform.fourierorigin.tocenter");
                tmp_data->write_image((const char *)params["savenorm"]);
        }
 
        delete tmp_data;
        tmp_data=0;
        EMData *ret=image;
        image=0;
        
        return ret;
}
 
/*
void BaldwinWoolfordReconstructor::setup()
{
        //This is a bit of a hack - but for now it suffices
        params.set_default("mode","nearest_neighbor");
        WienerFourierReconstructor::setup();
        // Set up the Baldwin Kernel
        int P = (int)((1.0+0.25)*max_input_dim+1);
        float r = (float)(max_input_dim+1)/(float)P;
        dfreq = 0.2f;
        if (W != 0) delete [] W;
        int maskwidth = params.set_default("maskwidth",2);
        W = Util::getBaldwinGridWeights(maskwidth, (float)P, r,dfreq,0.5f,0.2f);
}
 
EMData* BaldwinWoolfordReconstructor::finish(bool doift)
{
        tmp_data->write_image("density.mrc");
        image->process_inplace("xform.fourierorigin.tocorner");
        image->do_ift_inplace();
        image->depad();
        image->process_inplace("xform.phaseorigin.tocenter");
 
        if ( (bool) params.set_default("postmultiply", false) )
        {
                cout << "POST MULTIPLYING" << endl;
        // now undo the Fourier convolution with real space division
                float* d = image->get_data();
                float N = (float) image->get_xsize()/2.0f;
                N *= N;
                size_t rnx = image->get_xsize();
                size_t rny = image->get_ysize();
                size_t rnxy = rnx*rny;
                int cx = image->get_xsize()/2;
                int cy = image->get_ysize()/2;
                int cz = image->get_zsize()/2;
                size_t idx;
                for (int k = 0; k < image->get_zsize(); ++k ){
                        for (int j = 0; j < image->get_ysize(); ++j ) {
                                for (int i =0; i < image->get_xsize(); ++i ) {
                                        float xd = (float)(i-cx); xd *= xd;
                                        float yd = (float)(j-cy); yd *= yd;
                                        float zd = (float)(k-cz); zd *= zd;
                                        float weight = exp((xd+yd+zd)/N);
                                        idx = k*rnxy + j*rnx + i;
                                        d[idx] *=  weight;
                                }
                        }
                }
        }
        image->update();
        return  image;
}
 
#include <iomanip>
 
// int BaldwinWoolfordReconstructor::insert_slice_weights(const Transform& t3d)
// {
//      bool fftodd = image->is_fftodd();
//      int rnx = nx-2*!fftodd;
//
//      float y_scale = 1.0, x_scale = 1.0;
//
//      if ( ny != rnx  )
//      {
//              if ( rnx > ny ) y_scale = (float) rnx / (float) ny;
//              else x_scale = (float) ny / (float) rnx;
//      }
//
//      int tnx = tmp_data->get_xsize();
//      int tny = tmp_data->get_ysize();
//      int tnz = tmp_data->get_zsize();
//
//      vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
//      for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
//              Transform n3d = t3d*(*it);
//
//              for (int y = 0; y < tny; y++) {
//                      for (int x = 0; x < tnx; x++) {
//
//                              float rx = (float) x;
//                              float ry = (float) y;
//
//                              if ( ny != rnx )
//                              {
//                                      if ( rnx > ny ) ry *= y_scale;
//                                      else rx *= x_scale;
//                              }
// //                           float xx = rx * n3d[0][0] + (ry - tny/2) * n3d[1][0];
// //                           float yy = rx * n3d[0][1] + (ry - tny/2) * n3d[1][1];
// //                           float zz = rx * n3d[0][2] + (ry - tny/2) * n3d[1][2];
//
//                              Vec3f coord(rx,(ry - tny/2),0);
//                              coord = coord*n3d; // transpose multiplication
//                              float xx = coord[0];
//                              float yy = coord[1];
//                              float zz = coord[2];
//
//                              if (xx < 0 ){
//                                      xx = -xx;
//                                      yy = -yy;
//                                      zz = -zz;
//                              }
//
//                              yy += tny/2;
//                              zz += tnz/2;
//                              insert_density_at(xx,yy,zz);
//                      }
//              }
//      }
//
//      return 0;
// }
 
void BaldwinWoolfordReconstructor::insert_density_at(const float& x, const float& y, const float& z)
{
        int xl = Util::fast_floor(x);
        int yl = Util::fast_floor(y);
        int zl = Util::fast_floor(z);
 
        // w is the windowing width
        int w = params.set_default("maskwidth",2);
        float wsquared = (float) w*w;
        float dw = 1.0f/w;
        dw *= dw;
 
        // w minus one - this control the number of
        // pixels/voxels to the left of the main pixel
        // that will have density
        int wmox = w-1;
        int wmoy = w-1;
        int wmoz = w-1;
 
        // If any coordinate is incedental with a vertex, then
        // make sure there is symmetry in density accruing.
        // i.e. the window width must be equal in both directions
        if ( ((float) xl) == x ) wmox = w;
        if ( ((float) yl) == y ) wmoy = w;
        if ( ((float) zl) == z ) wmoz = w;
 
        float* d = tmp_data->get_data();
        int tnx = tmp_data->get_xsize();
        int tny = tmp_data->get_ysize();
        int tnz = tmp_data->get_zsize();
        size_t tnxy = tnx*tny;
 
        int mode = params.set_default("mode","nearest_neighbor");
 
        for(int k = zl-wmoz; k <= zl+w; ++k ) {
                for(int j = yl-wmoy; j <= yl+w; ++j) {
                        for( int i = xl-wmox; i <= xl+w; ++i) {
                                float fac = 1.0;
                                int ic = i, jc = j, kc = k;
 
                                // Fourier space is periodic, which is enforced
                                // by the next 6 if statements. These if statements
                                // assume that the Fourier DC components is at
                                // (0,ny/2,nz/2).
                                if ( i <= 0 ) {
 
                                        if ( x != 0 && i == 0 ) fac = 1.0;
                                        else if ( x == 0 && i < 0) continue;
//                                      if (i < 0 ) ic = -i;
                                        if (i < 0 ) {
                                                continue;
                                                ic = -i;
                                                jc = tny-jc;
                                                kc = tnz-kc;
                                        }
                                }
                                if ( ic >= tnx ) ic = 2*tnx-ic-1;
                                if ( jc < 0 ) jc = tny+jc;
                                if ( jc >= tny ) jc = jc-tny;
                                if ( kc < 0 ) kc = tnz+kc;
                                if ( kc >= tnz ) kc = kc-tnz;
//                              if ( ic >= tnx ) continue;
//                              if ( jc < 0 ) continue;
//                              if ( jc >= tny ) continue;
//                              if ( kc < 0 ) continue;
//                              if ( kc >= tnz ) continue;
                                // This shouldn't happen
                                // Debug remove later
                                if ( ic < 0 ) { cout << "wo 1" << endl; }
                                if ( ic >= tnx  ){ cout << "wo 2" << endl; }
                                if ( jc < 0 ) { cout << "wo 3" << endl; }
                                if ( jc >= tny ) { cout << "wo 4" << endl; }
                                if ( kc < 0 ) { cout << "wo 5" << endl; }
                                if ( kc >= tnz ) { cout << "wo 6" << endl; }
 
 
                                float zd = (z-(float)k);
                                float yd = (y-(float)j);
                                float xd = (x-(float)i);
                                zd *= zd; yd *= yd; xd *= xd;
                                float distsquared = xd+yd+zd;
                                // We enforce a spherical kernel
                                if ( mode == 1 && distsquared > wsquared ) continue;
 
//                              float f = fac*exp(-dw*(distsquared));
                                float f = fac*exp(-2.467f*(distsquared));
                                // Debug - this error should never occur.
                                if ( (kc*tnxy+jc*tnx+ic) >= tnxy*tnz ) throw OutofRangeException(0,tnxy*tnz,kc*tnxy+jc*tnx+ic, "in density insertion" );
                                d[kc*tnxy+jc*tnx+ic] += f;
                        }
                }
        }
}
 
int BaldwinWoolfordReconstructor::insert_slice(const EMData* const input_slice, const Transform & t, const float weight)
{
        Transform * rotation;
        if ( input_slice->has_attr("xform.projection") ) {
                rotation = (Transform*) (input_slice->get_attr("xform.projection")); // assignment operator
        } else {
                rotation = new Transform(t); // assignment operator
        }
        Transform tmp(*rotation);
        tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly
 
        Vec2f trans = tmp.get_trans_2d();
        float scale = tmp.get_scale();
        bool mirror = tmp.get_mirror();
        EMData* slice = 0;
        if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) {
                slice = input_slice->process("xform",Dict("transform",&tmp));
        } else if ( mirror == true ) {
                slice = input_slice->process("xform.flip",Dict("axis","x"));
        }
        if ( slice == 0 ) {
                slice = input_slice->process("xform.phaseorigin.tocorner");
        } else {
                slice->process_inplace("xform.phaseorigin.tocorner");
        }
 
        slice->do_fft_inplace();
        slice->process_inplace("xform.fourierorigin.tocenter");
        float *dat = slice->get_data();
        float dt[2];
 
        bool fftodd = image->is_fftodd();
        int rnx = nx-2*!fftodd;
 
        float y_scale = 1.0, x_scale = 1.0;
 
        if ( ny != rnx  )
        {
                if ( rnx > ny ) y_scale = (float) rnx / (float) ny;
                else x_scale = (float) ny / (float) rnx;
        }
 
        int tnx = tmp_data->get_xsize();
        int tny = tmp_data->get_ysize();
        int tnz = tmp_data->get_zsize();
 
        vector<Transform> syms = Symmetry3D::get_symmetries((string)params["sym"]);
//      float weight = params.set_default("weight",1.0f);
 
        rotation->set_scale(1.0); rotation->set_mirror(false); rotation->set_trans(0,0,0);
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
                Transform t3d = (*rotation)*(*it);
 
                for (int y = 0; y < tny; y++) {
                        for (int x = 0; x < tnx; x++) {
                                float rx = (float) x;
                                float ry = (float) y;
 
                                if ( ny != rnx )
                                {
                                        if ( rnx > ny ) ry *= y_scale;
                                        else rx *= x_scale;
                                }
 
//                              float xx = rx * n3d[0][0] + (ry - tny/2) * n3d[1][0];
//                              float yy = rx * n3d[0][1] + (ry - tny/2) * n3d[1][1];
//                              float zz = rx * n3d[0][2] + (ry - tny/2) * n3d[1][2];
 
                                Vec3f coord(rx,(ry - tny/2),0);
                                coord = coord*t3d; // transpose multiplication
                                float xx = coord[0];
                                float yy = coord[1];
                                float zz = coord[2];
 
 
                                float cc = 1;
                                if (xx < 0 ){
                                        xx = -xx;
                                        yy = -yy;
                                        zz = -zz;
                                        cc = -1;
                                }
 
                                yy += tny/2;
                                zz += tnz/2;
 
                                int idx = x * 2 + y * (slice->get_xsize());
                                dt[0] = dat[idx];
                                dt[1] = cc * dat[idx+1];
 
                                insert_pixel(xx,yy,zz,dt);
                        }
                }
        }
 
        if(rotation) {delete rotation; rotation=0;}
        delete slice;
 
        return 0;
}
 
void BaldwinWoolfordReconstructor::insert_pixel(const float& x, const float& y, const float& z, const float dt[2])
{
        int xl = Util::fast_floor(x);
        int yl = Util::fast_floor(y);
        int zl = Util::fast_floor(z);
 
        // w is the windowing width
        int w = params.set_default("maskwidth",2);
        float wsquared = (float) w*w;
        float dw = 1.0f/w;
        dw *= dw;
 
        int wmox = w-1;
        int wmoy = w-1;
        int wmoz = w-1;
 
        // If any coordinate is incedental with a vertex, then
        // make sure there is symmetry in density accruing.
        // i.e. the window width must be equal in both directions
        if ( ((float) xl) == x ) wmox = w;
        if ( ((float) yl) == y ) wmoy = w;
        if ( ((float) zl) == z ) wmoz = w;
 
        float* we = tmp_data->get_data();
        int tnx = tmp_data->get_xsize();
        int tny = tmp_data->get_ysize();
        int tnz = tmp_data->get_zsize();
        int tnxy = tnx*tny;
 
        int rnx = 2*tnx;
        int rnxy = 2*tnxy;
 
        int mode = params.set_default("mode","nearest_neighbor");
 
        float* d = image->get_data();
        for(int k = zl-wmoz; k <= zl+w; ++k ) {
                for(int j = yl-wmoy; j <= yl+w; ++j) {
                        for( int i = xl-wmox; i <= xl+w; ++i) {
                                float fac = 1.0;
                                int ic = i, jc = j, kc = k;
 
                                // Fourier space is periodic, which is enforced
                                // by the next 6 if statements. These if statements
                                // assume that the Fourier DC component is at
                                // (0,ny/2,nz/2).
                                float negfac=1.0;
                                if ( i <= 0 ) {
                                        if ( x != 0 && i == 0 ) fac = 1.0;
                                        else if ( x == 0 && i < 0) continue;
                                        if (i < 0 ) {
                                                continue;
                                                ic = -i;
                                                jc = tny-jc;
                                                kc = tnz-kc;
                                                negfac=-1.0;
                                        }
                                }
                                if ( ic >= tnx ) ic = 2*tnx-ic-1;
                                if ( jc < 0 ) jc = tny+jc;
                                if ( jc >= tny ) jc = jc-tny;
                                if ( kc < 0 ) kc = tnz+kc;
                                if ( kc >= tnz ) kc = kc-tnz;
//                              if ( ic >= tnx ) continue;
//                              if ( jc < 0 ) continue;
//                              if ( jc >= tny ) continue;
//                              if ( kc < 0 ) continue;
//                              if ( kc >= tnz ) continue;
 
                                float zd = (z-(float)k);
                                float yd = (y-(float)j);
                                float xd = (x-(float)i);
                                zd *= zd; yd *= yd; xd *= xd;
                                float distsquared = xd+yd+zd;
//                              float f = fac*exp(-dw*(distsquared));
                                float f = fac*exp(-2.467f*(distsquared));
                                float weight = f/we[kc*tnxy+jc*tnx+ic];
                                // debug - this error should never occur
                                if ( (kc*rnxy+jc*rnx+2*ic+1) >= rnxy*tnz ) throw OutofRangeException(0,rnxy*tnz,kc*rnxy+jc*rnx+2*ic+1, "in pixel insertion" );
                                size_t k = kc*rnxy+jc*rnx+2*ic;
 
                                float factor, dist,residual;
                                int sizeW,sizeWmid,idx;
                                switch (mode) {
                                        case 0:
                                                d[k] += weight*f*dt[0];
                                                d[k+1] += negfac*weight*f*dt[1];
                                                cout << "hello" << endl;
                                        break;
 
                                        case 1:
                                                // We enforce a spherical kernel
                                                if ( distsquared > wsquared ) continue;
 
                                                sizeW = (int)(1+2*w/dfreq);
                                                sizeWmid = sizeW/2;
 
                                                dist = sqrtf(distsquared);
                                                idx = (int)(sizeWmid + dist/dfreq);
                                                if (idx >= sizeW) throw InvalidValueException(idx, "idx was greater than or equal to sizeW");
                                                residual = dist/dfreq - (int)(dist/dfreq);
                                                if ( fabs(residual) > 1) throw InvalidValueException(residual, "Residual was too big");
 
                                                factor = (W[idx]*(1.0f-residual)+W[idx+1]*residual)*weight;
 
                                                d[k] += dt[0]*factor;
                                                d[k+1] += dt[1]*factor;
                                        break;
 
                                        default:
                                                throw InvalidValueException(mode, "The mode was unsupported in BaldwinWoolfordReconstructor::insert_pixel");
                                        break;
                                }
                        }
                }
        }
}
 
// void BaldwinWoolfordReconstructor::insert_pixel(const float& x, const float& y, const float& z, const float dt[2])
// {
//      int xl = Util::fast_floor(x);
//      int yl = Util::fast_floor(y);
//      int zl = Util::fast_floor(z);
//
//      // w is the windowing width
//      int w = params.set_default("maskwidth",2);
//      float dw = 1.0/w;
//      dw *= dw;
// //   dw = 2;
// //   cout << w << endl;
//      //      int w = 3;
//      // w minus one - this control the number of
//      // pixels/voxels to the left of the main pixel
//      // that will have density
//      int wmox = w-1;
//      int wmoy = w-1;
//      int wmoz = w-1;
//
//      // If any coordinate is incedental with a vertex, then
//      // make sure there is symmetry in density accruing.
//      // i.e. the window width must be equal in both directions
//      if ( ((float) xl) == x ) wmox = w;
//      if ( ((float) yl) == y ) wmoy = w;
//      if ( ((float) zl) == z ) wmoz = w;
//
//      float* d = tmp_data->get_data();
//      int tnx = tmp_data->get_xsize();
//      int tny = tmp_data->get_ysize();
//      int tnz = tmp_data->get_zsize();
//      int tnxy = tnx*tny;
//
//      float weight = 1.0;
// //
//      for(int k = zl-wmoz; k <= zl+w; ++k ) {
//              for(int j = yl-wmoy; j <= yl+w; ++j) {
//                      for( int i = xl-wmox; i <= xl+w; ++i) {
//                              float fac = 1.0;
//                              int ic = i, jc = j, kc = k;
//
//                              // Fourier space is periodic, which is enforced
//                              // by the next 6 if statements. These if statements
//                              // assume that the Fourier DC components is at
//                              // (0,ny/2,nz/2).
//                              if ( i <= 0 ) {
//                                      if ( x != 0 && i == 0 ) fac = 1.0;
//                                      else if ( x == 0 && i < 0) continue;
// //                                   if (i < 0 ) ic = -i;
//                                      if (i < 0 ) {
//                                              ic = -i;
//                                              jc = tny-jc;
//                                              kc = tnz-kc;
//                                      }
//                              }
//                              if ( ic >= tnx ) ic = 2*tnx-ic-1;
//                              if ( jc < 0 ) jc = tny+jc;
//                              if ( jc >= tny ) jc = jc-tny;
//                              if ( kc < 0 ) kc = tnz+kc;
//                              if ( kc >= tnz ) kc = kc-tnz;
//                              // This shouldn't happen
//                              // Debug remove later
//                              if ( ic < 0 ) { cout << "wo 1" << endl; }
//                              if ( ic >= tnx  ){ cout << "wo 2" << endl; }
//                              if ( jc < 0 ) { cout << "wo 3" << endl; }
//                              if ( jc >= tny ) { cout << "wo 4" << endl; }
//                              if ( kc < 0 ) { cout << "wo 5" << endl; }
//                              if ( kc >= tnz ) { cout << "wo 6" << endl; }
//
//
//                              float zd = (z-(float)k);
//                              float yd = (y-(float)j);
//                              float xd = (x-(float)i);
//                              zd *= zd; yd *= yd; xd *= xd;
//                              // Debug - this error should never occur.
//                              if ( (kc*tnxy+jc*tnx+ic) >= tnxy*tnz ) throw OutofRangeException(0,tnxy*tnz,kc*tnxy+jc*tnx+ic, "in weight determination insertion" );
// //                           float f = fac*exp(-dw*(xd+yd+zd)*0.5);
//                              float f = exp(-2.467*(xd+yd+zd));
//                              weight += f*(d[kc*tnxy+jc*tnx+ic] - f);
//                      }
//              }
//      }
//      weight = 1.0/weight;
//      int rnx = 2*tnx;
//      int rnxy = 2*tnxy;
//      d = image->get_data();
//      for(int k = zl-wmoz; k <= zl+w; ++k ) {
//              for(int j = yl-wmoy; j <= yl+w; ++j) {
//                      for( int i = xl-wmox; i <= xl+w; ++i) {
//                              float fac = 1.0;
//                              int ic = i, jc = j, kc = k;
//
//                              // Fourier space is periodic, which is enforced
//                              // by the next 6 if statements. These if statements
//                              // assume that the Fourier DC components is at
//                              // (0,ny/2,nz/2).
//                              float negfac=1.0;
//                              if ( i <= 0 ) {
//                                      if ( x != 0 && i == 0 ) fac = 1.0;
//                                      else if ( x == 0 && i < 0) continue;
//                                      if (i < 0 ) {
//                                              continue;
//                                              ic = -i;
//                                              jc = tny-jc;
//                                              kc = tnz-kc;
//                                              negfac=-1.0;
//                                      }
//                              }
//                              if ( ic >= tnx ) ic = 2*tnx-ic-1;
//                              if ( jc < 0 ) jc = tny+jc;
//                              if ( jc >= tny ) jc = jc-tny;
//                              if ( kc < 0 ) kc = tnz+kc;
//                              if ( kc >= tnz ) kc = kc-tnz;
//                              // This shouldn't happen
//                              // Debug remove later
//
//
//                              float zd = (z-(float)k);
//                              float yd = (y-(float)j);
//                              float xd = (x-(float)i);
//                              zd *= zd; yd *= yd; xd *= xd;
// //                           float f = fac*exp(-dw*(xd+yd+zd));
//                              float f = exp(-4.934*(xd+yd+zd));
//                              // Debug - this error should never occur.
//                              if ( (kc*rnxy+jc*rnx+2*ic+1) >= rnxy*tnz ) throw OutofRangeException(0,rnxy*tnz,kc*rnxy+jc*rnx+2*ic+1, "in pixel insertion" );
//
//                              d[kc*rnxy+jc*rnx+2*ic] += weight*f*dt[0];
//                              d[kc*rnxy+jc*rnx+2*ic+1] += negfac*weight*f*dt[1];
//                      }
//              }
//      }
// }
*/
 
void RealMedianReconstructor::setup()
{
        vector<int> size=params["size"];
        nx = size[0];
        ny = size[1];
        nz = size[2];
        image = new EMData(nx,ny,nz);
        image->to_zero();
        
        if (!slices.empty()) {
                for (std::vector<EMData *>::iterator it = slices.begin() ; it != slices.end(); ++it) delete *it;
                slices.clear();
        }
        xforms.clear();
}
 
EMData* RealMedianReconstructor::preprocess_slice(const EMData* const slice, const Transform& t)
{
 
//      EMData* return_slice = slice->process("normalize.edgemean");
//      return_slice->process_inplace("filter.linearfourier");
 
        EMData* return_slice;
 
//      return_slice = slice->process("filter.linearfourier");
        return_slice = slice->copy();
        
//      Transform tmp(t);
//      tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly
//      Vec2f trans = tmp.get_trans_2d();
//      float scale = tmp.get_scale();
//      bool mirror = tmp.get_mirror();
//      if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) {
//              return_slice->transform(tmp);
//      } 
//      if ( mirror == true ) {
//              return_slice->process_inplace("xform.flip",Dict("axis","x"));
//      }
 
        return return_slice;
}
 
int RealMedianReconstructor::insert_slice(const EMData* const input, const Transform &t, const float weight)
{
        if (!input) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        if (input->get_xsize() != input->get_ysize() || input->get_xsize() != nx) {
                LOGERR("tried to insert image that was not correction dimensions");
                return 1;
        }
        
        slices.push_back(input->copy());
        xforms.push_back(t);
 
        return 0;
}
 
// This is just a dummy function. It does not return meaningful numbers
int RealMedianReconstructor::determine_slice_agreement(EMData*  input_slice, const Transform & arg, const float weight,bool sub)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        input_slice->set_attr("reconstruct_norm",1.0f);
        input_slice->set_attr("reconstruct_absqual",1.0f);
        input_slice->set_attr("reconstruct_weight",1.0f);
 
        return 0;
 
}
 
EMData *RealMedianReconstructor::finish(bool doift)
{
        
        int mode = params.set_default("mode",0);        // confusing, mode means mode of operation
 
        // We do the actual reconstruction here from all of the slices
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nx; x++) {
                                std::vector<float> vals;
                                std::vector<Transform>::iterator itt = xforms.begin();
                                for (std::vector<EMData *>::iterator it = slices.begin() ; it != slices.end(); ++it,++itt) {
                                        Vec3f imvec = itt->transform(x-nx/2.0f,y-ny/2.0f,z-nz/2.0f);
                                        
                                        // single interpolated value from 2-D
                                        float val=(*it)->sget_value_at_interp(imvec[0]+nx/2,imvec[1]+ny/2);
                                        if (val!=0) vals.push_back(val);
                                        
                                        // uses all 4 of the nearest values from the 2-D image
//                                      int xx=floor(imvec[0]+nx/2);
//                                      int yy=floor(imvec[1]+ny/2);
//                                      float val=(*it)->sget_value_at(xx,yy);
//                                      if (val!=0) vals.push_back(val);
//                                      val=(*it)->sget_value_at(xx+1,yy);
//                                      if (val!=0) vals.push_back(val);
//                                      val=(*it)->sget_value_at(xx+1,yy+1);
//                                      if (val!=0) vals.push_back(val);
//                                      val=(*it)->sget_value_at(xx,yy+1);
//                                      if (val!=0) vals.push_back(val);
                                }
                                if (vals.size()==0) continue;
                                
//                              // debugging, save all values for specific voxels to look at statistics
//                              if ((x==515&&y==461&&z==281) ||
//                              (x==516&&y==462&&z==299) ||
//                              (x==516&&y==461&&z==262) ||
//                              (x==212&&y==409&&z==304)) {
//                                      char fsp[80];
//                                      sprintf(fsp,"stat_%d_%d_%d.txt",x,y,z);
//                                      FILE *out=fopen(fsp,"w");
//                                      for (std::vector<float>::iterator v = vals.begin(); v!=vals.end(); ++v) fprintf(out,"%f\n",*v);
//                                      fclose(out);
//                              }
                                
                                switch(mode) {
                                // median, the namesake of the reconstructor
                                case 0:
                                        std::sort(vals.begin(),vals.end());
                                        //printf("%d %d %d    %d\n",x,y,z,vals.size());
                                        image->set_value_at(x,y,z,vals[vals.size()/2]);         // for even sizes, not quite right, and should include possibility of local average
                                        break;
 
                                // This is something like a mode. It progressively subdivides the numeric axis in halves
                                // until reaching a small number of values which are then averaged
                                case 1:
                                        {
                                        // We only use this method if we have at least 6 possible values for the voxel, otherwise we just average
                                        if (vals.size()<6) {
                                                float val=0;
                                                for (int i=0; i<vals.size(); i++) val+=vals[i];
                                                image->set_value_at(x,y,z,val/vals.size());
                                                break;
                                        }
                                        // Sort the list to simplify the remaining logic
                                        std::sort(vals.begin(),vals.end());
                                        int v0=0,v1=vals.size(),vs=v1/2;                // bracket values, v0 first, v1 last+1, vs is first value in second zone
                                        
                                        // we continue until we have a zone containing 4 or fewer values
                                        //int count=0;
                                        while (v1-v0>8) {
                                                float cen=(vals[v0]+vals[v1-1])/2.0f;           // value halfway between the extremes
                                                for (vs=v0; vs<v1; vs++) { if (vals[vs]>=cen) break; }          // find the first value in the upper zone
                                                // shift to the zone containing more values
                                                if (v1-vs>vs-v0) v0=vs;
                                                else v1=vs;
                                                //printf("%d %d %d %d\t%g\t%g\t%g\t%g\t%g\t%g\t%g\n",v0,vs,v1,vals.size(),cen,vals[0],vals[v0],vals[vs-1],vals[vs],vals[v1],vals[vals.size()-1]);
                                                //count++;
                                                //if (count>20) exit(1);
                                        }
                                        float val=0;
                                        for (int i=v0; i<v1; i++) val+=vals[i];
                                        image->set_value_at(x,y,z,val/(v1-v0));
                                        break;
                                        }
                                // median with a bias towards zero (positive and negative), using 1/3 or 2/3 position in the sorted array
                                case 2:
                                {
                                        if (vals.size()<6) {
                                                float val=0;
                                                for (int i=0; i<vals.size(); i++) val+=vals[i];
                                                image->set_value_at(x,y,z,val/vals.size());
                                                break;
                                        }
                                        std::sort(vals.begin(),vals.end());
                                        //printf("%d %d %d    %d\n",x,y,z,vals.size());
                                        int p1=vals.size()/3-1;
                                        int p2=vals.size()*2/3;
                                        float v=(fabs(vals[p1])<fabs(vals[p2]))?(vals[p1]+vals[p1-1]+vals[p1+1])/3.0f:(vals[p2]+vals[p2-1]+vals[p2+1])/3.0f;
                                        image->set_value_at(x,y,z,v);           // for even sizes, not quite right, and should include possibility of local average
                                        break;
                                }
                                // bias the median towards the half of the points spanning the narrower range
                                case 3:
                                {
                                        if (vals.size()<6) {
                                                float val=0;
                                                for (int i=0; i<vals.size(); i++) val+=vals[i];
                                                image->set_value_at(x,y,z,val/vals.size());
                                                break;
                                        }
                                        std::sort(vals.begin(),vals.end());
                                        //printf("%d %d %d    %d\n",x,y,z,vals.size());
                                        int p1=vals.size()/3-1;
                                        int p2=vals.size()/2;
                                        int p3=vals.size()*2/3;
                                        float v=(vals[p2]-vals[0]<vals[vals.size()-1]-vals[p2])?(vals[p1]+vals[p1-1]+vals[p1+1])/3.0f:(vals[p3]+vals[p3-1]+vals[p3+1])/3.0f;
                                        image->set_value_at(x,y,z,v);           // for even sizes, not quite right, and should include possibility of local average
                                        break;
                                }
                                case 4:
                                {
                                        // too few values, return median
                                        if (vals.size()<10) {
                                                std::sort(vals.begin(),vals.end());
                                                image->set_value_at(x,y,z,vals[vals.size()/2]);         // for even sizes, not quite right, and should include possibility of local average
                                                break;
                                        }
                                        
                                        //compute stats
                                        int n=vals.size();
                                        float mean=0,sigma=0;
                                        for (int i=0; i<n; i++) { mean+=vals[i]; sigma+=vals[i]*vals[i]; }
                                        mean/=n;
                                        sigma=sqrt(sigma/n-mean);
                                        // low & high refer to angle not value
                                        float low=(vals[0]+vals[1]+vals[2]+vals[3])/4.0f;
                                        float high=(vals[n-1]+vals[n-2]+vals[n-3]+vals[n-4])/4.0f;
                                        
                                        // If both extreme tilts roughly agree, then we assume that's the right range to use and we average values near that
                                        // by computing the mean of all values within 1 sigma of all values
                                        if (fabs(low-high)<sigma) {
                                                mean=(low+high)*4.0f;
                                                int c=8;
                                                for (int i=4; i<n-4; i++) { 
                                                        if (fabs(vals[i]-mean/c)<sigma) { mean+=vals[i]; c++; } 
                                                }
                                                image->set_value_at(x,y,z,mean/c);
                                        }
                                        // This means the extremes disagree and we have to pick which value is best, we go with min(fabs)
                                        else {
                                                if (fabs(low)<fabs(high)) mean=low*4.0;
                                                else mean=high*4.0;
                                                int c=4;
                                                for (int i=4; i<n-4; i++) { 
                                                        if (fabs(vals[i]-mean/c)<sigma) { mean+=vals[i]; c++; } 
                                                }
                                                image->set_value_at(x,y,z,mean/c);
                                        }
                                        break;
                                }
                                }
                        }
                }
        } 
 
 
//      transform->set_scale(1.0);
//      transform->set_mirror(false);
//      transform->set_trans(0,0,0);
//      transform->invert();
 
//      tmp->transform(t.inverse());            // This was incorrect. inverse() was missing
//      image->add(*tmp);
 
//      if(transform) {delete transform; transform=0;}
 
        // apply symmetry if requested
        Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
        vector<Transform> syms = sym->get_syms();
 
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
 
//              it->printme();
                Transform t=*it;
                EMData *tmpcopy = image->process("xform",Dict("transform",(EMObject)&t));
                image->add(*tmpcopy);
                delete tmpcopy;
        }
 
        image->mult(1.0f/(float)sym->get_nsym());
        delete sym;
//      if (image->get_xsize()==image->get_ysize() && image->get_ysize()==image->get_zsize()) {
//              image->process_inplace("mask.sharp",Dict("outer_radius",image->get_xsize()/2-1));
//      }
//      else printf("No masking %d %d %d\n",image->get_xsize(),image->get_ysize(),image->get_zsize());
        
        // erase out copy of the projection data
        if (!slices.empty()) {
                for (std::vector<EMData *>::iterator it = slices.begin() ; it != slices.end(); ++it) delete *it;
                slices.clear();
        }
        xforms.clear();
        
        EMData *ret = image;
        if (!doift) {
                ret=image->do_fft();
                ret->process_inplace("xform.phaseorigin.tocorner");
                delete image;
        }
        image = 0 ;
        return ret;
}
 
 
void BackProjectionReconstructor::setup()
{
        image = new EMData();
        vector<int> size=params["size"];
        nx = size[0];
        ny = size[1];
        nz = size[2];
        image->set_size(nx, ny, nz);
}
 
EMData* BackProjectionReconstructor::preprocess_slice(const EMData* const slice, const Transform& t)
{
 
//      EMData* return_slice = slice->process("normalize.edgemean");
//      return_slice->process_inplace("filter.linearfourier");
 
        EMData* return_slice;
 
        return_slice = slice->process("filter.linearfourier");
//      return_slice = slice->copy();
        
//      Transform tmp(t);
//      tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly
//      Vec2f trans = tmp.get_trans_2d();
//      float scale = tmp.get_scale();
//      bool mirror = tmp.get_mirror();
//      if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) {
//              return_slice->transform(tmp);
//      } 
//      if ( mirror == true ) {
//              return_slice->process_inplace("xform.flip",Dict("axis","x"));
//      }
 
        return return_slice;
}
 
int BackProjectionReconstructor::insert_slice(const EMData* const input, const Transform &t, const float)
{
        if (!input) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        if (input->get_xsize() != input->get_ysize() || input->get_xsize() != nx) {
                LOGERR("tried to insert image that was not correction dimensions");
                return 1;
        }
 
//      Transform * transform;
//      if ( input->has_attr("xform.projection") ) {
//              transform = (Transform*) (input->get_attr("xform.projection")); // assignment operator
//      } else {
//              transform = new Transform(t); // assignment operator
//      }
        EMData* slice = preprocess_slice(input, t);
 
        // Clearly weight isn't a useful concept in back-projection without compensating with an exact-filter
//      float weight = params["weight"];
//      slice->mult(weight);
 
        EMData *tmp = new EMData();
        tmp->set_size(nx, ny, nz);
 
        float *slice_data = slice->get_data();
        float *tmp_data = tmp->get_data();
 
        size_t nxy = nx * ny;
        size_t nxy_size = nxy * sizeof(float);;
        for (int i = 0; i < nz; ++i) {
                memcpy(&tmp_data[nxy * i], slice_data, nxy_size);
        }
        tmp->update();
 
//      transform->set_scale(1.0);
//      transform->set_mirror(false);
//      transform->set_trans(0,0,0);
//      transform->invert();
 
        tmp->transform(t.inverse());            // This was incorrect. inverse() was missing
        image->add(*tmp);
 
//      if(transform) {delete transform; transform=0;}
        delete tmp;
        delete slice;
 
        return 0;
}
 
int BackProjectionReconstructor::determine_slice_agreement(EMData*  input_slice, const Transform & arg, const float weight,bool sub)
{
        // Are these exceptions really necessary? (d.woolford)
        if (!input_slice) throw NullPointerException("EMData pointer (input image) is NULL");
 
        input_slice->set_attr("reconstruct_norm",1.0f);
        input_slice->set_attr("reconstruct_absqual",1.0f);
        input_slice->set_attr("reconstruct_weight",1.0f);
 
        return 0;
 
}
 
EMData *BackProjectionReconstructor::finish(bool)
{
 
        Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]);
        vector<Transform> syms = sym->get_syms();
 
        for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) {
 
//              it->printme();
                Transform t=*it;
                EMData *tmpcopy = image->process("xform",Dict("transform",(EMObject)&t));
                image->add(*tmpcopy);
                delete tmpcopy;
        }
 
        image->mult(1.0f/(float)sym->get_nsym());
        delete sym;
        if (image->get_xsize()==image->get_ysize() && image->get_ysize()==image->get_zsize()) {
                image->process_inplace("mask.sharp",Dict("outer_radius",image->get_xsize()/2-1));
        }
        else printf("No masking %d %d %d\n",image->get_xsize(),image->get_ysize(),image->get_zsize());
                
        EMData *ret = image;
        image = 0 ;
        return ret;
}
 
EMData* EMAN::padfft_slice( const EMData* const slice, const Transform& t, int npad )
{
        int nx = slice->get_xsize();
        int ny = slice->get_ysize();
        int padffted= slice->get_attr_default("padffted", 0);
        int ndim = (ny==1) ? 1 : 2;
        int iext = slice->is_fftodd();
        int extension = (2-iext)*padffted;  //  If 2, it means it is a Fourier file.
 
        if( ndim==2 && (nx-extension)!=ny ) {
                LOGERR("Input image must be square!");
                throw ImageDimensionException("Input image must be square!");
        }
 
        EMData* padfftslice = NULL;
        if( padffted == 0) {
                // process 2D slice or 1D line -- subtract the average outside of the circle, zero-pad, fft extend, and fft
                EMData* temp = slice->average_circ_sub();
 
                padfftslice = temp->norm_pad( false, npad );
                checked_delete( temp );
 
                padfftslice->do_fft_inplace();
        } else {
                padfftslice = new EMData(*slice);
        }
 
        // shift the projection
        Vec2f trans = t.get_trans_2d();
        float sx = -trans[0];
        float sy = -trans[1];
        if(sx != 0.0f || sy != 0.0) padfftslice->process_inplace("filter.shift", Dict("x_shift", sx, "y_shift", sy, "z_shift", 0.0f));
 
        int remove = slice->get_attr_default("remove", 0);
        padfftslice->set_attr( "remove", remove );
        padfftslice->center_origin_fft();
        return padfftslice;
}
 
 
//####################################################################################
 
 
enum weighting_method { NONE, ESTIMATE, VORONOI };
 
float max2d( int kc, const vector<float>& pow_a )
{
        float max = 0.0;
        for( int i=-kc; i <= kc; ++i ) {
                for( int j=-kc; j <= kc; ++j ) {
                        if( i==0 && j==0 ) continue;
                        {
                                int c = 2*kc+1 - std::abs(i) - std::abs(j);
                                max = max + pow_a[c];
                        }
                }
        }
        return max;
}
 
float max3d( int kc, const vector<float>& pow_a )
{
        float max = 0.0;
        for( int i=-kc; i <= kc; ++i ) {
                for( int j=-kc; j <= kc; ++j ) {
                        for( int k=-kc; k <= kc; ++k ) {
                                if( i==0 && j==0 && k==0 ) continue;
                                // if( i!=0 )
                                {
                                        int c = 3*kc+1 - std::abs(i) - std::abs(j) - std::abs(k);
                                        max = max + pow_a[c];
                                        // max = max + c * c;
                                        // max = max + c;
                                }
                        }
                }
        }
        return max;
}
 
 
#define  tw(i,j,k)      tw[ i-1 + (j-1+(k-1)*iy)*ix ]
 
void circumfnn( EMData* win , int npad)
{
        float *tw = win->get_data();
        //  correct for the fall-off of NN interpolation using sinc functions
        //  mask and subtract circumference average
        int ix = win->get_xsize();
        int iy = win->get_ysize();
        int iz = win->get_zsize();
        int L2 = (ix/2)*(ix/2);
        int L2P = (ix/2-1)*(ix/2-1);
 
        int IP = ix/2+1;
        int JP = iy/2+1;
        int KP = iz/2+1;
 
        //  sinc functions tabulated for fall-off
        float* sincx = new float[IP+1];
        float* sincy = new float[JP+1];
        float* sincz = new float[KP+1];
 
        sincx[0] = 1.0f;
        sincy[0] = 1.0f;
        sincz[0] = 1.0f;
 
        float cor;
        if( npad == 1 )  cor = 1.0;
        else  cor = 4.0;
 
        float cdf = M_PI/(cor*ix);
        for (int i = 1; i <= IP; ++i)  sincx[i] = sin(i*cdf)/(i*cdf);
        cdf = M_PI/(cor*iy);
        for (int i = 1; i <= JP; ++i)  sincy[i] = sin(i*cdf)/(i*cdf);
        cdf = M_PI/(cor*iz);
        for (int i = 1; i <= KP; ++i)  sincz[i] = sin(i*cdf)/(i*cdf);
        for (int k = 1; k <= iz; ++k) {
                int kkp = abs(k-KP);
                for (int j = 1; j <= iy; ++j) {
                        cdf = sincy[abs(j- JP)]*sincz[kkp];
                        for (int i = 1; i <= ix; ++i)  tw(i,j,k) /= (sincx[abs(i-IP)]*cdf);
                }
        }
 
        delete[] sincx;
        delete[] sincy;
        delete[] sincz;
 
        float  TNR = 0.0f;
        size_t m = 0;
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                size_t LR = (k-KP)*(k-KP)+(j-JP)*(j-JP)+(i-IP)*(i-IP);
                                if (LR >= (size_t)L2P && LR<=(size_t)L2) {
                                        TNR += tw(i,j,k);
                                        ++m;
                                }
                        }
                }
        }
 
        TNR /=float(m);
        
        
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                size_t LR = (k-KP)*(k-KP)+(j-JP)*(j-JP)+(i-IP)*(i-IP);
                                if (LR<=(size_t)L2) tw(i,j,k) -= TNR;
                                else                tw(i,j,k)  = 0.0f;
                        }
                }
        }
 
}
 
 
void circumftrl( EMData* win , int npad)
{
        float *tw = win->get_data();
        //  correct for the fall-off of tri-linear interpolation using sinc^2 functions
        //  mask and subtract circumference average
        int ix = win->get_xsize();
        int iy = win->get_ysize();
        int iz = win->get_zsize();
        int L2 = (ix/2)*(ix/2);
        int L2P = (ix/2-1)*(ix/2-1);
 
        int IP = ix/2+1;
        int JP = iy/2+1;
        int KP = iz/2+1;
 
        //  sinc functions tabulated for fall-off
        float* sincx = new float[IP+1];
        float* sincy = new float[JP+1];
        float* sincz = new float[KP+1];
 
        sincx[0] = 1.0f;
        sincy[0] = 1.0f;
        sincz[0] = 1.0f;
 
        float cor;
        if( npad == 1 )  cor = 1.0;
        else  cor = 4.0;
 
        float cdf = M_PI/(cor*ix);
        for (int i = 1; i <= IP; ++i)  sincx[i] = pow(sin(i*cdf)/(i*cdf),2);
        cdf = M_PI/(cor*iy);
        for (int i = 1; i <= JP; ++i)  sincy[i] = pow(sin(i*cdf)/(i*cdf),2);
        cdf = M_PI/(cor*iz);
        for (int i = 1; i <= KP; ++i)  sincz[i] = pow(sin(i*cdf)/(i*cdf),2);
        for (int k = 1; k <= iz; ++k) {
                int kkp = abs(k-KP);
                for (int j = 1; j <= iy; ++j) {
                        cdf = sincy[abs(j- JP)]*sincz[kkp];
                        for (int i = 1; i <= ix; ++i)  tw(i,j,k) /= (sincx[abs(i-IP)]*cdf);
                }
        }
 
        delete[] sincx;
        delete[] sincy;
        delete[] sincz;
 
        float  TNR = 0.0f;
        size_t m = 0;
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                size_t LR = (k-KP)*(k-KP)+(j-JP)*(j-JP)+(i-IP)*(i-IP);
                                if (LR >= (size_t)L2P && LR<=(size_t)L2) {
                                        TNR += tw(i,j,k);
                                        ++m;
                                }
                        }
                }
        }
 
        TNR /=float(m);
        
        
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                size_t LR = (k-KP)*(k-KP)+(j-JP)*(j-JP)+(i-IP)*(i-IP);
                                if (LR<=(size_t)L2) tw(i,j,k) -= TNR;
                                else                tw(i,j,k)  = 0.0f;
                        }
                }
        }
 
}
 
 
 
//####################################################################################
 
//** nn4 reconstructor
 
nn4Reconstructor::nn4Reconstructor()
{
        m_volume = NULL;
        m_wptr   = NULL;
}
 
nn4Reconstructor::nn4Reconstructor( const string& symmetry, int size, int npad )
{
        setup( symmetry, size, npad );
        load_default_settings();
        //print_params();
}
 
nn4Reconstructor::~nn4Reconstructor()
{
        //if( m_delete_volume ) checked_delete(m_volume); 
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
 
void nn4Reconstructor::setup()
{
 
        int size = params["size"];
        int npad = params["npad"];
 
        string symmetry;
        if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
        else                               symmetry = "c1";
 
        if( params.has_key("ndim") )  m_ndim = params["ndim"];
        else                          m_ndim = 3;
 
        if( params.has_key( "snr" ) )  m_osnr = 1.0f/float( params["snr"] );
        else                           m_osnr = 0.0;
 
        setup( symmetry, size, npad );
}
 
void nn4Reconstructor::setup( const string& symmetry, int size, int npad )
{
        m_weighting = ESTIMATE;
        m_wghta = 0.2f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        m_vnx = size;
        m_vny = size;
        m_vnz = (m_ndim==3) ? size : 1;
 
        m_vnxp = size*npad;
        m_vnyp = size*npad;
        m_vnzp = (m_ndim==3) ? size*npad : 1;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
 
        buildFFTVolume();
        buildNormVolume();
 
}
 
 
void nn4Reconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
        // ----------------------------------------------------------------
        // Added by Zhengfan Yang on 03/15/07
        // Original author: please check whether my revision is correct and
        // other Reconstructor need similiar revision.
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        // ----------------------------------------------------------------
 
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nn4Reconstructor::buildNormVolume() {
 
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 &&
                m_wptr->get_ysize() != m_vnyp &&
                m_wptr->get_zsize() != m_vnzp ) {
                m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
                m_wptr->to_zero();
        }
        m_wptr->set_array_offsets(0,1,1);
}
 
void printImage( const EMData* line )
{
        Assert( line->get_zsize()==1 );
 
 
        int nx = line->get_xsize();
        int ny = line->get_ysize();
        for( int j=0; j < ny; ++j ) {
                for( int i=0; i < nx; ++i )  printf( "%10.3f ", line->get_value_at(i,j) );
                printf( "\n" );
        }
}
 
 
 
int nn4Reconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight) {
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        int padffted= slice->get_attr_default( "padffted", 0 );
        if( m_ndim==3 ) {
                if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
        } else {
                Assert( m_ndim==2 );
                if( slice->get_ysize() !=1 ) {
                        LOGERR( "for 2D reconstruction, a line is excepted" );
                        return 1;
                }
        }
        if( weight > 0.0f )  {
 
                EMData* padfft = padfft_slice( slice, t,  m_npad );
 
                if( m_ndim==3 ) {
                        insert_padfft_slice( padfft, t, weight );
                } else {
                        float alpha = padfft->get_attr( "alpha" );
                        alpha = alpha/180.0f*M_PI;
                        for(int i=0; i < m_vnxc+1; ++i ) {
                                float xnew = i*cos(alpha);
                                float ynew = -i*sin(alpha);
                                float btqr = padfft->get_value_at( 2*i, 0, 0 );
                                float btqi = padfft->get_value_at( 2*i+1, 0, 0 );
                                if( xnew < 0.0 ) {
                                        xnew *= -1;
                                        ynew *= -1;
                                        btqi *= -1;
                                }
 
                                int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
                                int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
 
                                if(iyn < 0 ) iyn += m_vnyp;
 
                                (*m_volume)( 2*ixn, iyn+1, 1 )   += btqr * weight;
                                (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * weight;
                                (*m_wptr)(ixn,iyn+1, 1) += weight;
                        }
 
                }
                checked_delete( padfft );
        }
        return 0;
}
 
int nn4Reconstructor::insert_padfft_slice( EMData* padfft, const Transform& t, float weight )
{
        Assert( padfft != NULL );
 
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++)  m_volume->nn( m_wptr, padfft, tsym[isym], weight);
        
        return 0;
}
 
 
EMData* nn4Reconstructor::finish(bool) {
 
        if( m_ndim == 3 ) {
                m_volume->symplane0(m_wptr);
        } else {
                for( int i=1; i <= m_vnyp; ++i ) {
 
                        if( (*m_wptr)(0, i, 1)==0.0 ) {
                                int j = m_vnyp + 1 - i;
                                (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
                                (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
                                (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
                        }
                }
        }
 
 
        int box = 7;
        int kc = (box-1)/2;
        vector< float > pow_a( m_ndim*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a.back()=0.0;
 
        float alpha = 0.0;
        if( m_ndim==3) {
                int vol = box*box*box;
                float max = max3d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        } else {
                int ara = box*box;
                float max = max2d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)ara ) / max;
        }
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
                                        float tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
                                        if( m_weighting == ESTIMATE && false) {  // HERE
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
 
                                                                int kcz = (m_ndim==3) ? kc : 0;
                                                                for( int kk = -kcz; kk <= kcz; ++kk ) {
                                                                        int nbrcz = cz + kk;
                                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
                                                                                int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                        }
                                                                }
                                                        }
                                                }
                                                float wght = 1.0f / ( 1.0f - alpha * sum );
                                                tmp = tmp * wght;
                                        }
//cout<<" mvol "<<ix<<"  "<<iy<<"  "<<iz<<"  "<<(*m_volume)(2*ix,iy,iz)<<"  "<<(*m_volume)(2*ix+1,iy,iz)<<"  "<<tmp<<"  "<<m_osnr<<endl;
                                        (*m_volume)(2*ix,iy,iz)   *= tmp;
                                        (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        //if(m_ndim==2) printImage( m_volume );
 
        // back fft
        m_volume->do_ift_inplace();
 
        // EMData* win = m_volume->window_center(m_vnx);
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
#undef  tw
 
 
nn4_rectReconstructor::nn4_rectReconstructor()
{
        m_volume = NULL;
        m_wptr   = NULL;
}
 
nn4_rectReconstructor::nn4_rectReconstructor( const string& symmetry, int size, int npad )
{
        m_volume = NULL;
        m_wptr   = NULL;
        setup( symmetry, size, npad );
        load_default_settings();
        print_params();
}
 
nn4_rectReconstructor::~nn4_rectReconstructor()
{
        //if( m_delete_volume ) checked_delete(m_volume);
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
 
void nn4_rectReconstructor::setup()
{
        m_sizeofprojection = params["sizeprojection"];
        int npad = params["npad"];
        m_count=0;
 
        string symmetry;
        if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
        else                               symmetry = "c1";
 
        if( params.has_key("ndim") )  m_ndim = params["ndim"];             
        else                            m_ndim = 3;
    
        if( params.has_key( "snr" ) )  m_osnr = 1.0f/float( params["snr"] );
        else                           m_osnr = 0.0;
 
        setup( symmetry, m_sizeofprojection, npad );
}
 
void nn4_rectReconstructor::setup( const string& symmetry, int sizeprojection, int npad )
{
        m_weighting = ESTIMATE;
        m_wghta = 0.2f;
        m_symmetry = symmetry;
        m_npad = npad;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        if( params.has_key("sizex") )  m_vnx = params["sizex"];
        else if(params.has_key("xratio")) 
                {
                float temp=params["xratio"];
                m_vnx=int(float(sizeprojection)*temp);
                }
        else                           m_vnx=sizeprojection;
 
        if( params.has_key("sizey") )  m_vny = params["sizey"];
        else if (params.has_key("yratio"))  
               {
                float temp=params["yratio"];
                 m_vny=int(float(sizeprojection)*temp);
                }
        else m_vny=sizeprojection;
 
        if( params.has_key("sizez") ) 
                m_vnz = params["sizez"];
        else 
                if (params.has_key("zratio"))
                {
                        float temp=params["zratio"];
                        m_vnz=int(float(sizeprojection)*temp);
                }
                else                          
                        m_vnz = (m_ndim==3) ? sizeprojection : 1;
        
        m_xratio=float(m_vnx)/float(sizeprojection);    
        m_yratio=float(m_vny)/float(sizeprojection);
        m_zratio=float(m_vnz)/float(sizeprojection);
 
        m_vnxp = m_vnx*npad;
        m_vnyp = m_vny*npad;
        m_vnzp = (m_ndim==3) ? m_vnz*npad : 1;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = (m_ndim==3) ? m_vnzp/2 : 1;
 
        buildFFTVolume();
        buildNormVolume();
}
 
 
void nn4_rectReconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
        // ----------------------------------------------------------------
        // Added by Zhengfan Yang on 03/15/07
        // Original author: please check whether my revision is correct and
        // other Reconstructor need similiar revision.
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        // ----------------------------------------------------------------
 
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nn4_rectReconstructor::buildNormVolume() {
 
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 &&
                m_wptr->get_ysize() != m_vnyp &&
                m_wptr->get_zsize() != m_vnzp ) {
                m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
                m_wptr->to_zero();
        }
 
        m_wptr->set_array_offsets(0,1,1);
}
 
int nn4_rectReconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight) {
        // sanity checks
 
 
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
 
        int padffted= slice->get_attr_default( "padffted", 0 );
        if( m_ndim==3 ) {
                if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_sizeofprojection)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
        } 
        if (m_ndim==2) {
                if( slice->get_ysize() !=1 ) {
                        LOGERR( "for 2D reconstruction, a line is excepted" );
                        return 1;
                }
        }
        if( weight > 0.0f )  {
 
                EMData* padfft = padfft_slice( slice, t,  m_npad );
                
                //Assert( mult > 0 );
 
                if( m_ndim==3 ) {
                        insert_padfft_slice( padfft, t, weight );               
                } else {
                        float ellipse_length,ellipse_step,cos_alpha,sin_alpha;
                        int ellipse_length_int;
                        float alpha = padfft->get_attr( "alpha" );
                        alpha = alpha/180.0f*M_PI;
                        int loop_range;
                        float temp1,temp2;
                                        temp1=m_xratio*cos(alpha)*float(m_sizeofprojection*m_npad)/2;
                        temp2=m_yratio*sin(alpha)*float(m_sizeofprojection*m_npad)/2;
                        ellipse_length=sqrt(temp1*temp1+temp2*temp2);
                        ellipse_length_int=int(ellipse_length);
                        ellipse_step=0.5f*(m_sizeofprojection*m_npad)/float(ellipse_length_int);
                        loop_range=ellipse_length_int;
                        cos_alpha=temp1/ellipse_length;
                        sin_alpha=temp2/ellipse_length;
                        if(m_count%100==0) {
                                std::cout<<"#############################################################"<<std::endl;
                                std::cout<<"line insert start=="<<m_count<<std::endl;
                                std::cout<<"ellipse length=="<<ellipse_length_int<<"ellips step=="<<ellipse_step<<std::endl;
                                std::cout<<"loop_range"<<loop_range<<std::endl;
                                                        std::cout<<"x and y ratio=="<<m_xratio<<"  "<<m_yratio<<std::endl;
                                std::cout<<"cos sin of alpha=="<<cos(alpha)<<"   "<<sin(alpha)<<std::endl;
                                std::cout<<"cos sin of alpha_new==="<<cos_alpha<<sin_alpha<<std::endl;
                                std::cout<<"alpah dig==="<<cos_alpha<<sin_alpha<<std::endl;
                                std::cout<<"prjection maximum==="<<loop_range*ellipse_step<<"ideal maximum"<<m_sizeofprojection*m_npad/2<<std::endl;
                                std::cout<<"x_size=="<<m_volume->get_xsize()<<"y_size=="<<m_volume->get_ysize()<<std::endl;
                                std::cout<<"#############################################################"<<std::endl;
                        }
                        for(int i=0; i <=loop_range; ++i ) {
                                float xnew = i*cos_alpha;
                                float ynew = -i*sin_alpha;
                                if(m_count%100==0&&i==loop_range)
                                        std::cout<<"x_new=="<<xnew<<"Y_new=="<<ynew<<std::endl;
                                float btqr=0,btqi=0;
                                float xprj=i*ellipse_step;
                                float t=xprj-int(xprj);
                                btqr = (1-t)*padfft->get_value_at( 2*int(xprj), 0, 0 )+t*padfft->get_value_at( 2*(1+int(xprj)), 0, 0 );
                                btqi = (1-t)*padfft->get_value_at( 2*int(xprj)+1, 0, 0 )+t*padfft->get_value_at( 2*(1+int(xprj))+1, 0, 0 );
                                if( xnew < 0.0 ) {
                                        xnew *= -1;
                                        ynew *= -1;
                                        btqi *= -1;
                                }
 
                                int ixn = int(xnew+0.5+m_vnxp) - m_vnxp;
                                int iyn = int(ynew+0.5+m_vnyp) - m_vnyp;
 
                                if(iyn < 0 ) iyn += m_vnyp;
                                if(m_count%100==0&&i==loop_range)
                                        std::cout<<"xnn=="<<ixn<<"ynn=="<<iyn<<std::endl;
                                (*m_volume)( 2*ixn, iyn+1, 1 )   += btqr * weight;
                                (*m_volume)( 2*ixn+1, iyn+1, 1 ) += btqi * weight;
                                (*m_wptr)(ixn,iyn+1, 1) += weight;
                        }
 
 
                }
                checked_delete( padfft );
                return 0;
        } else return 0;
}
 
 
 
 
int nn4_rectReconstructor::insert_padfft_slice( EMData* padded, const Transform& t, float weight )
{
        Assert( padded != NULL );
                
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++)
                m_volume->insert_rect_slice(m_wptr, padded, tsym[isym], m_sizeofprojection, m_xratio, m_yratio, m_zratio, m_npad, weight);
 
        return 0;
 
}
 
#define  tw(i,j,k)      tw[ i-1 + (j-1+(k-1)*iy)*ix ]
void circumfnn_rect( EMData* win , int npad)
{
        float *tw = win->get_data();
        //  correct for the fall-off
        //  mask and subtract circumfnnerence average
        int ix = win->get_xsize();
        int iy = win->get_ysize();
        int iz = win->get_zsize();
 
        int IP = ix/2+1;
        int JP = iy/2+1;
        int KP = iz/2+1;
        
        //  sinc functions tabulated for fall-off
        float* sincx = new float[IP+1];
        float* sincy = new float[JP+1];
        float* sincz = new float[KP+1];
 
        sincx[0] = 1.0f;
        sincy[0] = 1.0f;
        sincz[0] = 1.0f;
 
        float cdf = M_PI/float(npad*2*ix);
        for (int i = 1; i <= IP; ++i)  sincx[i] = sin(i*cdf)/(i*cdf);
        cdf = M_PI/float(npad*2*iy);
        for (int i = 1; i <= JP; ++i)  sincy[i] = sin(i*cdf)/(i*cdf);
        cdf = M_PI/float(npad*2*iz);
        for (int i = 1; i <= KP; ++i)  sincz[i] = sin(i*cdf)/(i*cdf);
        for (int k = 1; k <= iz; ++k) {
                int kkp = abs(k-KP);
                for (int j = 1; j <= iy; ++j) {
                        cdf = sincy[abs(j- JP)]*sincz[kkp];
                        for (int i = 1; i <= ix; ++i)  tw(i,j,k) /= (sincx[abs(i-IP)]*cdf);
                }
        }
 
        delete[] sincx;
        delete[] sincy;
        delete[] sincz;
        
        
        
        float dxx = 1.0f/float(0.25*ix*ix);
        float dyy = 1.0f/float(0.25*iy*iy);
        
        
        
        float LR2=(float(ix)/2-1)*(float(ix)/2-1)*dxx;
 
        float  TNR = 0.0f;
        size_t m = 0;
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                float LR = (j-JP)*(j-JP)*dyy+(i-IP)*(i-IP)*dxx;
                                if (LR<=1.0f && LR >= LR2) {
                                        TNR += tw(i,j,k);
                                        ++m;
                                }
                        }
                }
        }
 
        TNR /=float(m);
        
 
        for (int k = 1; k <= iz; ++k) {
                for (int j = 1; j <= iy; ++j) {
                        for (int i = 1; i <= ix; ++i) {
                                float LR = (j-JP)*(j-JP)*dyy+(i-IP)*(i-IP)*dxx;
                                if (LR<=1.0f)  tw(i,j,k)=tw(i,j,k)-TNR;
                                else            tw(i,j,k) = 0.0f;       
                        }
                }
        }
 
}
#undef tw 
 
EMData* nn4_rectReconstructor::finish(bool)
{
        
        if( m_ndim==3 ) {
                m_volume->symplane0_rect(m_wptr);
        } else {
                for( int i=1; i <= m_vnyp; ++i ) {
 
                        if( (*m_wptr)(0, i, 1)==0.0 ) {
                                int j = m_vnyp + 1 - i;
                                (*m_wptr)(0, i, 1) = (*m_wptr)(0, j, 1);
                                (*m_volume)(0, i, 1) = (*m_volume)(0, j, 1);
                                (*m_volume)(1, i, 1) = (*m_volume)(1, j, 1);
                        }
                }
        }
 
 
        int box = 7;
        int kc = (box-1)/2;
        vector< float > pow_a( m_ndim*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a.back()=0.0;
 
        float alpha = 0.0;
        if( m_ndim==3) {
                int vol = box*box*box;
                float max = max3d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        } else {
                int ara = box*box;
                float max = max2d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)ara ) / max;
        }
 
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0) {//(*v) should be treated as complex!!
                                        float tmp;
                                        tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+m_osnr);
                                        
                                        if( m_weighting == ESTIMATE ) {
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
 
                                                                int kcz = (m_ndim==3) ? kc : 0;
                                                                for( int kk = -kcz; kk <= kcz; ++kk ) {
                                                                        int nbrcz = cz + kk;
                                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
                                                                                int c = m_ndim*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                        }
                                                                }
                                                        }
                                                }
                                                float wght = 1.0f / ( 1.0f - alpha * sum );
                                                tmp = tmp * wght;
                                        }
                                        (*m_volume)(2*ix,iy,iz)   *= tmp;
                                        (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        //if(m_ndim==2) printImage( m_volume );
 
        // back fft
        m_volume->do_ift_inplace();
 
        
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn_rect( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
 
 
// Added By Zhengfan Yang on 03/16/07
// Beginning of the addition
// --------------------------------------------------------------------------------
 
nnSSNR_Reconstructor::nnSSNR_Reconstructor()
{
        m_volume = NULL;
        m_wptr   = NULL;
        m_wptr2  = NULL;
}
 
nnSSNR_Reconstructor::nnSSNR_Reconstructor( const string& symmetry, int size, int npad)
{
        m_volume = NULL;
        m_wptr   = NULL;
        m_wptr2  = NULL;
 
        setup( symmetry, size, npad );
}
 
nnSSNR_Reconstructor::~nnSSNR_Reconstructor()
{
        //if( m_delete_volume ) checked_delete(m_volume);
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //if( m_delete_weight2 ) checked_delete( m_wptr2 );
 
        //checked_delete( m_result );
}
 
void nnSSNR_Reconstructor::setup()
{
        int size = params["size"];
        int npad = params["npad"];
 
        string symmetry;
        if( params.has_key("symmetry") ) symmetry = params["symmetry"].to_str();
        else                             symmetry = "c1";
 
        setup( symmetry, size, npad );
}
 
void nnSSNR_Reconstructor::setup( const string& symmetry, int size, int npad )
{
 
        m_weighting = ESTIMATE;
        m_wghta = 0.2f;
        m_wghtb = 0.004f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        m_vnx = size;
        m_vny = size;
        m_vnz = size;
 
        m_vnxp = size*npad;
        m_vnyp = size*npad;
        m_vnzp = size*npad;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
        buildNorm2Volume();
 
}
 
void nnSSNR_Reconstructor::buildFFTVolume() {
 
        m_volume = params["fftvol"]; 
        m_volume->set_size(m_vnxp+ 2 - m_vnxp%2,m_vnyp,m_vnzp);
        m_volume->to_zero();
        if ( m_vnxp % 2 == 0 ) m_volume->set_fftodd(0);
        else                   m_volume->set_fftodd(1);
 
        m_volume->set_nxc(m_vnxc);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nnSSNR_Reconstructor::buildNormVolume() {
 
        m_wptr = params["weight"];
        m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
        m_wptr->to_zero();
        m_wptr->set_array_offsets(0,1,1);
}
 
void nnSSNR_Reconstructor::buildNorm2Volume() {
 
        m_wptr2 = params["weight2"];
        m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp);
        m_wptr2->to_zero();
        m_wptr2->set_array_offsets(0,1,1);
}
 
 
int nnSSNR_Reconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight) {
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if( weight > 0.0f )  {
                int padffted=slice->get_attr_default( "padffted", 0 );
 
                if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that has wrong size.");
                        return 1;
                }
 
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                insert_padfft_slice( padfft, t, weight );
 
                checked_delete( padfft );
                return 0;
        } else return 0;
}
 
int nnSSNR_Reconstructor::insert_padfft_slice( EMData* padfft, const Transform& t, float weight )
{
        Assert( padfft != NULL );
        // insert slice for all symmetry related positions
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (int isym=0; isym < m_nsym; isym++) m_volume->nn_SSNR( m_wptr, m_wptr2, padfft, tsym[isym], weight);
 
        return 0;
}
 
 
EMData* nnSSNR_Reconstructor::finish(bool)
{
/*
  I changed the code on 05/15/2008 so it only returns variance.
  Lines commented out are marked by //#
  The version prior to the currect changes is r1.190
  PAP
*/
        int kz, ky;
        //#int iix, iiy, iiz;
        int box = 7;
        int kc = (box-1)/2;
        float alpha = 0.0;
        float argx, argy, argz;
        vector< float > pow_a( 3*kc+1, 1.0 );
        float w = params["w"];
        EMData* SSNR = params["SSNR"];
        //#EMData* vol_ssnr = new EMData();
        //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp);
        //#vol_ssnr->to_zero();
        //#  new line follow
        EMData* vol_ssnr = params["vol_ssnr"];
        vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp);
        vol_ssnr->to_zero();
        if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0);
        else                   vol_ssnr->set_fftodd(1);
        vol_ssnr->set_nxc(m_vnxc);
        vol_ssnr->set_complex(true);
        vol_ssnr->set_ri(true);
        vol_ssnr->set_fftpad(false);
        //#
 
        float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc);
        float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc);
        float dz2 = 1.0f/Util::get_max(float(m_vnzc),1.0f)/Util::get_max(float(m_vnzc),1.0f);
        int   inc = Util::round(float(Util::get_max(m_vnxc,m_vnyc,m_vnzc))/w);
 
        SSNR->set_size(inc+1,4,1);
 
        float *nom    = new float[inc+1];
        float *denom  = new float[inc+1];
        int  *nn     = new int[inc+1];
        int  *ka     = new int[inc+1];
        float wght = 1.0f;
        for (int i = 0; i <= inc; i++) {
                nom[i] = 0.0f;
                denom[i] = 0.0f;
                nn[i] = 0;
                ka[i] = 0;
        }
 
        m_volume->symplane1(m_wptr, m_wptr2);
 
        if ( m_weighting == ESTIMATE ) {
                int vol = box*box*box;
                for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
                pow_a[3*kc] = 0.0;
                float max = max3d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        }
 
        for (int iz = 1; iz <= m_vnzp; iz++) {
                if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1;
                argz = float(kz*kz)*dz2;
                for (int iy = 1; iy <= m_vnyp; iy++) {
                        if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1;
                        argy = argz + float(ky*ky)*dy2;
                        for (int ix = 0; ix <= m_vnxc; ix++) {
                                float Kn = (*m_wptr)(ix,iy,iz);
                                argx = std::sqrt(argy + float(ix*ix)*dx2);
                                int r = Util::round(float(inc)*argx);
                                if ( r >= 0 && Kn > 4.5f ) {
                                        if ( m_weighting == ESTIMATE ) {
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
 
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                    for ( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                                        int nbrcz = cz + jj;
                                                                        if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
                                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                        }
                                                                }
                                                        }
                                                }
                                                wght = 1.0f / ( 1.0f - alpha * sum );
                                        } // end of ( m_weighting == ESTIMATE )
                                        float nominator = std::norm(m_volume->cmplx(ix,iy,iz)/Kn);
                                        float denominator = ((*m_wptr2)(ix,iy,iz)-nominator)/(Kn-1.0f);
                                        // Skip Friedel related values
                                        if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) {
                                                if ( r <= inc ) {
                                                        nom[r]   += nominator*wght;
                                                        denom[r] += denominator/Kn*wght;
                                                        nn[r]    += 2;
                                                        ka[r]    += int(Kn);
                                                }
/*
                                                //#float  tmp = Util::get_max(nominator/denominator/Kn-1.0f,0.0f);
                                                //  Create SSNR as a 3D array (-n/2:n/2+n%2-1)
                                                iix = m_vnxc + ix; iiy = m_vnyc + ky; iiz = m_vnzc + kz;
                                                if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
                                                        (*vol_ssnr)(iix, iiy, iiz) = tmp;
                                                // Friedel part
                                                iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz;
                                                if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
                                                        (*vol_ssnr)(iix, iiy, iiz) = tmp;
*/
 
                                        }
                                        (*vol_ssnr)(2*ix, iy-1, iz-1) = nominator*wght;//Kn;//denominator*wght;//
                                        //(*vol_ssnr)(2*ix, iy-1, iz-1) =  real(m_volume->cmplx(ix,iy,iz))*wght/Kn;
                                        //(*vol_ssnr)(2*ix+1, iy-1, iz-1) = imag(m_volume->cmplx(ix,iy,iz))*wght/Kn;
                                } // end of Kn>4.5
                        }
                }
        }
 
        for (int i = 0; i <= inc; i++)  {
                (*SSNR)(i,0,0) = nom[i];  
                (*SSNR)(i,1,0) = denom[i];    // variance
                (*SSNR)(i,2,0) = static_cast<float>(nn[i]);
                (*SSNR)(i,3,0) = static_cast<float>(ka[i]);
        }
        vol_ssnr->update();
        
        delete[] nom;
        delete[] denom;
        delete[] nn;
        delete[] ka;
 
        return 0;
}
 
// -----------------------------------------------------------------------------------
// End of this addition
 
//####################################################################################
//** nn4 ctf reconstructor
 
nn4_ctfReconstructor::nn4_ctfReconstructor()
{
        m_volume  = NULL;
        m_wptr    = NULL;
}
 
nn4_ctfReconstructor::nn4_ctfReconstructor( const string& symmetry, int size, int npad, float snr, int sign )
{
        setup( symmetry, size, npad, snr, sign );
}
 
nn4_ctfReconstructor::~nn4_ctfReconstructor()
{
        //if( m_delete_volume ) checked_delete(m_volume);
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
void nn4_ctfReconstructor::setup()
{
        if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given");
 
        int size = params["size"];
        int npad = params.has_key("npad") ? int(params["npad"]) : 2;
        // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
        int sign = 1;
        string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
 
        float snr = params["snr"];
 
        m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0;
        setup( symmetry, size, npad, snr, sign );
 
}
 
void nn4_ctfReconstructor::setup( const string& symmetry, int size, int npad, float snr, int sign )
{
        m_weighting = ESTIMATE;
        if( params.has_key("weighting") ) {
                if( int( params["weighting"])==0 ) m_weighting = NONE;
        }
 
 
 
        m_wghta = 0.2f;
        m_wghtb = 0.004f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_sign = sign;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        m_snr = snr;
 
        m_vnx = size;
        m_vny = size;
        m_vnz = size;
 
        m_vnxp = size*npad;
        m_vnyp = size*npad;
        m_vnzp = size*npad;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
}
 
void nn4_ctfReconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
 
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nn4_ctfReconstructor::buildNormVolume()
{
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) {
               m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
               m_wptr->to_zero();
        }
 
        m_wptr->set_array_offsets(0,1,1);
 
}
 
int nn4_ctfReconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight)
{
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if( weight > 0.0f )  {
                int buffed = slice->get_attr_default( "buffed", 0 );
                        if( buffed > 0 ) {
                                insert_buffed_slice( slice, weight );
                                return 0;
                        }
 
                int padffted= slice->get_attr_default("padffted", 0);
                if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
 
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                float tmp = padfft->get_attr_default("ctf_applied", 0);
                int   ctf_applied = (int) tmp;
 
                // Generate 2D CTF (EMData object)
        //ctf_store_real::init( padfft->get_ysize(), padfft->get_attr( "ctf" ) );
        //EMData* ctf2d = ctf_store_real::get_ctf_real(); //This is in 2D projection plane
        int winsize = padfft->get_ysize();
                Ctf* ctf = padfft->get_attr( "ctf" );
                Dict params = ctf->to_dict();   
                EMData* ctf2d = Util::ctf_img_real(winsize , winsize, 1, params["defocus"], params["apix"],params["voltage"], params["cs"], \
                params["ampcont"], params["bfactor"], params["dfdiff"], params["dfang"], 1);
                params.clear();
                if(ctf) {delete ctf; ctf=0;}
                int nx=ctf2d->get_xsize(),ny=ctf2d->get_ysize(),nz=ctf2d->get_zsize();
                float *ctf2d_ptr  = ctf2d->get_data();
 
                size_t size = (size_t)nx*ny*nz;
                if (!ctf_applied) {
                        for (int i = 0; i < size; ++i) padfft->cmplx(i) *= ctf2d_ptr[i]; // Multiply padfft by CTF
                }
 
                for (int i = 0; i < size; ++i) ctf2d_ptr[i] *= ctf2d_ptr[i];     // Square 2D CTF
                
                insert_padfft_slice(padfft, ctf2d, t, weight);
 
                checked_delete( ctf2d );  
                checked_delete( padfft );
 
        }
        return 0;
}
 
int nn4_ctfReconstructor::insert_buffed_slice( const EMData* buffed, float weight )
{
        const float* bufdata = buffed->get_data();
        float* cdata = m_volume->get_data();
        float* wdata = m_wptr->get_data();
 
        int npoint = buffed->get_xsize()/4;
        for( int i=0; i < npoint; ++i ) {
 
                int pos2 = int( bufdata[4*i] );
                int pos1 = pos2 * 2;
                cdata[pos1  ] += bufdata[4*i+1]*weight;
                cdata[pos1+1] += bufdata[4*i+2]*weight;
                wdata[pos2  ] += bufdata[4*i+3]*weight;
/*
        std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: ";
        std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " ";
        std::cout << pos2 << " " << bufdata[5*i+4] << std::endl;
 */
        }
        return 0;
}
 
int nn4_ctfReconstructor::insert_padfft_slice( EMData* padfft, EMData* ctf2d2, const Transform& t, float weight)
{
        Assert( padfft != NULL );
        
        vector<float> abc_list;
        int abc_list_len = 0;   
        if (m_volume->has_attr("smear"))
        {
                abc_list = m_volume->get_attr("smear");
                abc_list_len = abc_list.size();
        }
                                
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++) {
                if (abc_list_len == 0)
                        m_volume->nn_ctf_exists(m_wptr, padfft, ctf2d2, tsym[isym], weight);
                else
                        for (int i = 0; i < abc_list_len; i += 4) {
                                m_volume->nn_ctf_exists(m_wptr, padfft, ctf2d2, tsym[isym] * Transform(Dict("type", "SPIDER", "phi",  abc_list[i], "theta", abc_list[i+1], "psi", abc_list[i+2])), weight * abc_list[i+3]);
                        }
        }
        return 0;
}
 
EMData* nn4_ctfReconstructor::finish(bool)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_ctf(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
        // normalize
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                                        float tmp=0.0f;
                                        if( m_varsnr )  {
                                            int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                            int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                                float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr);//*m_sign;
                                        } else  {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr);//*m_sign;
                                        }
 
                        if( m_weighting == ESTIMATE ) {
                                int cx = ix;
                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                float sum = 0.0;
                                for( int ii = -kc; ii <= kc; ++ii ) {
                                        int nbrcx = cx + ii;
                                        if( nbrcx >= m_vnxc ) continue;
                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                int nbrcy = cy + jj;
                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                        int nbrcz = cz + jj;
                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                        if( nbrcx < 0 ) {
                                                                nbrcx = -nbrcx;
                                                                nbrcy = -nbrcy;
                                                                nbrcz = -nbrcz;
                                                        }
 
                                                        int nbrix = nbrcx;
                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                sum = sum + pow_a[c];
                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                        }
                                                }
                                        }
                                }
                                float wght = 1.0f / ( 1.0f - alpha * sum );
/*
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 */
                                tmp = tmp * wght;
                                }
                                (*m_volume)(2*ix,iy,iz) *= tmp;
                                (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
 
 
//####################################################################################
//** nn4 ctfw reconstructor
 
nn4_ctfwReconstructor::nn4_ctfwReconstructor()
{
        m_volume  = NULL;
        m_wptr    = NULL;
}
 
nn4_ctfwReconstructor::nn4_ctfwReconstructor( const string& symmetry, int size, int npad, float snr, int sign, int do_ctf )
{
        setup( symmetry, size, npad, snr, sign, do_ctf );
}
 
nn4_ctfwReconstructor::~nn4_ctfwReconstructor()
{
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
void nn4_ctfwReconstructor::setup()
{
        if( ! params.has_key("size") ) throw std::logic_error("Error: image size is not given");
 
        int size = params["size"];
        int npad = params.has_key("npad") ? int(params["npad"]) : 2;
        // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
        int sign = 1;
        string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
 
        float  snr = params["snr"];
        int do_ctf = params["do_ctf"];
 
        setup( symmetry, size, npad, snr, sign, do_ctf );
 
}
 
void nn4_ctfwReconstructor::setup( const string& symmetry, int size, int npad, float snr, int sign, int do_ctf )
{
        m_weighting = ESTIMATE;
        if( params.has_key("weighting") ) {
                if( int( params["weighting"])==0 ) m_weighting = NONE;
        }
 
        m_wghta = 0.2f;
        m_wghtb = 0.004f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_sign = sign;
        m_nsym = Transform::get_nsym(m_symmetry);
        m_do_ctf = do_ctf;
 
        m_snr = snr;
 
        m_vnx = size;
        m_vny = size;
        m_vnz = size;
 
        //m_vnxp = size*npad;
        //m_vnyp = size*npad;
        //m_vnzp = size*npad;
        m_vnxp = size;
        m_vnyp = size;
        m_vnzp = size;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
        m_refvol = params["refvol"];
 
}
 
void nn4_ctfwReconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
 
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nn4_ctfwReconstructor::buildNormVolume()
{
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) {
               m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
               m_wptr->to_zero();
        }
 
        m_wptr->set_array_offsets(0,1,1);
 
}
 
int nn4_ctfwReconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight)
{
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if(weight >0.0f) {
                /*
                int buffed = slice->get_attr_default( "buffed", 0 );
                        if( buffed > 0 ) {
                                insert_buffed_slice( slice, weight );
                                return 0;
                        }
                */
 
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                EMData* ctf2d = NULL;
                if( m_do_ctf == 1 ) {
                        float tmp = padfft->get_attr_default("ctf_applied", 0);
                        int   ctf_applied = (int) tmp;
 
                        // Generate 2D CTF (EMData object)
                        //ctf_store_real::init( padfft->get_ysize(), padfft->get_attr( "ctf" ) );
                   int winsize = padfft->get_ysize();
                   Ctf* ctf = padfft->get_attr( "ctf" );
                   Dict params = ctf->to_dict();        
                   ctf2d = Util::ctf_img_real(winsize , winsize, 1, params["defocus"], params["apix"],params["voltage"], params["cs"], \
                           params["ampcont"], params["bfactor"], params["dfdiff"], params["dfang"], 1);
                        params.clear();
                        if(ctf) {delete ctf; ctf=0;}
                        //ctf2d = ctf_store_real::get_ctf_real(); //This is in 2D projection plane
                        int nx=ctf2d->get_xsize(),ny=ctf2d->get_ysize(),nz=ctf2d->get_zsize();
                        float *ctf2d_ptr  = ctf2d->get_data();
 
                        size_t size = (size_t)nx*ny*nz;
                        if (!ctf_applied) {
                                for (int i = 0; i < size; ++i) padfft->cmplx(i) *= ctf2d_ptr[i]; // Multiply padfft by CTF
                        }
 
                        for (int i = 0; i < size; ++i) ctf2d_ptr[i] *= ctf2d_ptr[i];     // Squared 2D CTF
                } else {
                        int nx=padfft->get_xsize(),ny=padfft->get_ysize(),nz=padfft->get_zsize();
                        ctf2d = new EMData();
                        ctf2d->set_size(nx/2,ny,nz);
                        float *ctf2d_ptr  = ctf2d->get_data();
                        size_t size = (size_t)nx*ny*nz/2;
                        for (int i = 0; i < size; ++i) ctf2d_ptr[i] = 1.0;
                }
 
                vector<float> bckgnoise;
                bckgnoise = slice->get_attr("bckgnoise");
 
                insert_padfft_slice_weighted(padfft, ctf2d, bckgnoise, t, weight);
 
                checked_delete( ctf2d );
                checked_delete( padfft );
                bckgnoise.clear();
 
        }
        return 0;
}
 
int nn4_ctfwReconstructor::insert_padfft_slice_weighted( EMData* padfft, EMData* ctf2d2, vector<float> bckgnoise, const Transform& t, float weight )
{
        Assert( padfft != NULL );
 
        vector<float> abc_list;
        int abc_list_len = 0;   
        if (m_volume->has_attr("smear")) {
                abc_list = m_volume->get_attr("smear");
                abc_list_len = abc_list.size();
        }
 
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++) {
                if (abc_list_len == 0)
                        m_volume->nn_ctfw(m_wptr, padfft, ctf2d2, m_npad, bckgnoise, tsym[isym], weight);
                else
                        for (int i = 0; i < abc_list_len; i += 4) 
                                m_volume->nn_ctfw(m_wptr, padfft, ctf2d2, m_npad, bckgnoise, tsym[isym] * Transform(Dict("type", "SPIDER", "phi",  abc_list[i], "theta", abc_list[i+1], "psi", abc_list[i+2])), weight * abc_list[i+3]);
        }
        return 0;
}
 
 
EMData* nn4_ctfwReconstructor::finish(bool compensate)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_refvol->set_array_offsets(0, 1, 1);
        if(m_volume->is_fftodd())       m_volume->symplane0_odd(m_wptr);
        else                                            m_volume->symplane0_ctf(m_wptr);
        bool do_invert = false;
        bool refvol_present = (*m_refvol)(0) > 0.0f ;
        /*
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
        */
 
 
        int ix,iy,iz;
        //  refvol carries fsc
        int  limitres = m_vnyc-1;
        if( refvol_present )  { // If fsc is set to zero, it will be straightforward reconstruction with snr = 1
                for (ix = 0; ix < m_vnyc; ix++) {
                                //cout<<"  fsc  "<< m_vnyc-ix-1 <<"   "<<m_vnyc<<"   "<<(*m_refvol)(m_vnyc-ix-1)<<endl;
                          if( (*m_refvol)(m_vnyc-ix-1) == 0.0f )  limitres = m_vnyc-ix-2;
                }
        } else {
//cout<<"   limitres   "<<limitres<<endl;
 
                vector<float> count(m_vnyc+1, 0.0f);
                vector<float> sigma2(m_vnyc+1, 0.0f);
 
                //  compute sigma2
                for (iz = 1; iz <= m_vnzp; iz++) {
                        int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                        float argz = float(izp*izp);
                        for (iy = 1; iy <= m_vnyp; iy++) {
                                int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                float argy = argz + float(iyp*iyp);
                                for (ix = 0; ix <= m_vnxc; ix++) {
                                        if(ix>0 || (izp>=0 && (iyp>=0 || izp!=0))) {  //Skip Friedel related values
                                                float r = std::sqrt(argy + float(ix*ix));
                                                int  ir = int(r);
                                                if (ir <= limitres) {
                                                        float frac = r - float(ir);
                                                        float qres = 1.0f - frac;
                                                        float temp = (*m_wptr)(ix,iy,iz);
                                                        //cout<<" WEIGHTS "<<jx<<"  "<<jy<<"  "<<ir<<"  "<<temp<<"  "<<frac<<endl;
                                                        //cout<<" WEIGHTS "<<ix<<"  "<<iy-1<<"  "<<iz-1<<"  "<<temp<<"  "<<endl;
                                                        sigma2[ir]   += temp*qres;
                                                        sigma2[ir+1] += temp*frac;
                                                        count[ir]    += qres;
                                                        count[ir+1]  += frac;
                                                }
                                        }
                                }
                        }
                }
                for (ix = 0; ix <= m_vnyc; ix++) {
                        if( count[ix] > 0.0f )  (*m_refvol)(ix) = sigma2[ix]/count[ix];
                        //cout<<"  sigma2  "<< ix <<"   "<<sigma2[ix]<<endl;
                }
                /*
                #  This part will have to be done on python level.
                float fudge = m_refvol->get_attr("fudge");
                // now counter will serve to keep fsc-derived stuff
                for (ix = 0; ix <= limitres; ix++)  count[ix] = fudge * sigma2[ix] * (1.0f - (*m_refvol)(ix))/(*m_refvol)(ix);  //fudge?
                count[limitres+1] = count[limitres];
                //for (ix = 0; ix <= limitres+1; ix++)  cout<<"  tau2  "<< ix <<"   "<<count[ix]<<endl;
                */
        
        }
 
 
        // normalize
        float osnr = 0.0f;
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                        float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                float r = std::sqrt(argy + float(ix*ix));
                                int  ir = int(r);
                                if (ir <= limitres) {
                                        if ( (*m_wptr)(ix,iy,iz) > 0.0f) {
                                                if( refvol_present) {
                                                        float frac = r - float(ir);
                                                        float qres = 1.0f - frac;
                                                        osnr = qres*(*m_refvol)(ir) + frac*(*m_refvol)(ir+1);
                                                        //if(osnr == 0.0f)  osnr = 1.0f/(0.001*(*m_wptr)(ix,iy,iz));
                                                        //cout<<"  "<<iz<<"   "<<iy<<"   "<<"   "<<ix<<"   "<<ir<<"   "<<(*m_wptr)(ix,iy,iz)<<"   "<<osnr<<"      "<<(*m_volume)(2*ix,iy,iz)<<"      "<<(*m_volume)(2*ix+1,iy,iz)<<endl;
                                                }  else osnr = 0.0f;
 
                                                float tmp = ((*m_wptr)(ix,iy,iz)+osnr);
 
                                                if(do_invert){
                                                        if(tmp>0.0f) {
                                                        //cout<<" mvol "<<ix<<"  "<<iy<<"  "<<iz<<"  "<<(*m_volume)(2*ix,iy,iz)<<"  "<<(*m_volume)(2*ix+1,iy,iz)<<"  "<<tmp<<"  "<<osnr<<endl;
                                                                (*m_volume)(2*ix,iy,iz)   /= tmp;
                                                                (*m_volume)(2*ix+1,iy,iz) /= tmp;
                                                        } else {
                                                                (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                                                (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                                        }
                                                }  else (*m_wptr)(ix,iy,iz) = tmp;
                                        }
                                } else {
                                        (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                        (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                }
                        }
                }
        }
 
        if(do_invert)  {
                m_volume->center_origin_fft();
                // back fft
                m_volume->do_ift_inplace();
                int npad = m_volume->get_attr("npad");
                m_volume->depad();
                if( compensate )  circumftrl( m_volume, npad );
                m_volume->set_array_offsets( 0, 0, 0 );
        }
 
        return 0;
}
 
 
 
#ifdef False
EMData* nn4_ctfwReconstructor::finish(bool)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_ctf(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
        // normalize
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                                        float tmp=0.0f;
                                        if( m_varsnr )  {
                                            int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                            int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                                float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr);//*m_sign;
                                        } else  {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr);//*m_sign;
                                        }
 
                        if( m_weighting == ESTIMATE ) {
                                int cx = ix;
                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                float sum = 0.0;
                                for( int ii = -kc; ii <= kc; ++ii ) {
                                        int nbrcx = cx + ii;
                                        if( nbrcx >= m_vnxc ) continue;
                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                int nbrcy = cy + jj;
                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                        int nbrcz = cz + jj;
                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                        if( nbrcx < 0 ) {
                                                                nbrcx = -nbrcx;
                                                                nbrcy = -nbrcy;
                                                                nbrcz = -nbrcz;
                                                        }
 
                                                        int nbrix = nbrcx;
                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                sum = sum + pow_a[c];
                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                        }
                                                }
                                        }
                                }
                                float wght = 1.0f / ( 1.0f - alpha * sum );
/*
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 */
                                tmp = tmp * wght;
                                }
                                (*m_volume)(2*ix,iy,iz) *= tmp;
                                (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
 
 
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_ctf(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        //float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
    vector<float> sigma2(m_vnyc+1, 0.0f);
    vector<float> count(m_vnyc+1, 0.0f);
 
        int ix,iy,iz;
        // compute sigma2
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
            float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                            if(ix>0 || (izp>=0 && (iyp>=0 || izp!=0))) {  //Skip Friedel related values
                    float r = std::sqrt(argy + float(ix*ix));
                    int  ir = int(r);
                    if (ir <= m_vnyc) {
                        float frac = r - float(ir);
                        float qres = 1.0f - frac;
                        float temp = (*m_wptr)(ix,iy,iz);
                        //cout<<" WEIGHTS "<<jx<<"  "<<jy<<"  "<<ir<<"  "<<temp<<"  "<<frac<<endl;
                        //cout<<" WEIGHTS "<<ix<<"  "<<iy-1<<"  "<<iz-1<<"  "<<temp<<"  "<<endl;
                        sigma2[ir]   += temp*qres;
                        sigma2[ir+1] += temp*frac;
                        count[ir]    += qres;
                        count[ir+1]  += frac;
                    }
                }
            }
        }
    }
    for (ix = 0; ix <= m_vnyc+1; ix++) {
        if( sigma2[ix] > 0.0f )  sigma2[ix] = count[ix]/sigma2[ix];
        //cout<<"  1/sigma2  "<< ix <<"   "<<sigma2[ix]<<endl;
    }
    // now counter will serve to keep fsc-derived stuff
        //  refvol carries fsc
        float fudge = m_refvol->get_attr("fudge");
    for (ix = 0; ix <= m_vnyc+1; ix++)
                  count[ix] = Util::get_max(0.0f, Util::get_min( 0.999f, (*m_refvol)(ix) ) );
    for (ix = 0; ix <= m_vnyc+1; ix++)  count[ix] = count[ix]/(1.0f - count[ix]) * sigma2[ix];
    for (ix = 0; ix <= m_vnyc+1; ix++)  {
        if ( count[ix] >0.0f) count[ix] = fudge/count[ix];  //fudge?
    }
//for (ix = 0; ix <= m_vnyc+1; ix++)  cout<<"  tau2  "<< ix <<"   "<<count[ix]<<"  m_wptr  "<<(*m_wptr)(ix,1,1)<<endl;
 
        // normalize
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
            float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                    float r = std::sqrt(argy + float(ix*ix));
                    int  ir = int(r);
                        //cout<<"  m_wptr  "<<(*m_wptr)(ix,iy,iz)<<endl;
                    if (ir <= m_vnyc) {
                        float frac = r - float(ir);
                        float qres = 1.0f - frac;
                        osnr = qres*count[ir] + frac*count[ir+1];
                        if(osnr == 0.0f)  osnr = 1.0f/(0.001*(*m_wptr)(ix,iy,iz));
                        //cout<<"  "<<iz<<"   "<<iy<<"   "<<"   "<<ix<<"   "<<(*m_wptr)(ix,iy,iz)<<"   "<<osnr<<"      "<<(*m_volume)(2*ix,iy,iz)<<"      "<<(*m_volume)(2*ix+1,iy,iz)<<endl;
                                            float tmp=((*m_wptr)(ix,iy,iz)+osnr);
                                            //if( m_varsnr )  tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign;
                                            //else {
                                            //cout<<"  "<<iz<<"  "<<iy<<"  "<<"  "<<ix<<"  "<<iz<<"  "<<"  "<<(*m_wptr)(ix,iy,iz)<<"  "<<osnr<<"  "<<endl;
                                            if(tmp>0.0f) {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/tmp;
 
 
                                /*if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                                        float tmp=0.0f;
                                        if( m_varsnr )  {
                                            int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                            int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                                float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr);//   *m_sign;
                                        } else  {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr);//   *m_sign;
                                        }
                                */
 
                        /*if( m_weighting == ESTIMATE ) {
                                int cx = ix;
                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                float sum = 0.0;
                                for( int ii = -kc; ii <= kc; ++ii ) {
                                        int nbrcx = cx + ii;
                                        if( nbrcx >= m_vnxc ) continue;
                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                int nbrcy = cy + jj;
                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                        int nbrcz = cz + jj;
                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                        if( nbrcx < 0 ) {
                                                                nbrcx = -nbrcx;
                                                                nbrcy = -nbrcy;
                                                                nbrcz = -nbrcz;
                                                        }
 
                                                        int nbrix = nbrcx;
                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                sum = sum + pow_a[c];
                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                        }
                                                }
                                        }
                                }
                                float wght = 1.0f / ( 1.0f - alpha * sum );
/
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 /
                                tmp = tmp * wght;
                                }*/
                                (*m_volume)(2*ix,iy,iz) *= tmp;
                                (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                } else {
                                (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                }
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
#endif
 
//####################nn4_ctfws reconstructor########################################
 
nn4_ctfwsReconstructor::nn4_ctfwsReconstructor()
{
        m_volume  = NULL;
        m_wptr    = NULL;
}
 
nn4_ctfwsReconstructor::nn4_ctfwsReconstructor( const string& symmetry, int size, int npad, float snr, int sign, int do_ctf )
{
        setup( symmetry, size, npad, snr, sign, do_ctf );
}
 
nn4_ctfwsReconstructor::~nn4_ctfwsReconstructor()
{
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
void nn4_ctfwsReconstructor::setup()
{
        //if(!params.has_key("size")) throw std::logic_error("Error: image size is not given");
        int size = params.has_key("size")? int(params["size"]): 0;
        int npad = params.has_key("npad")? int(params["npad"]): 2;
        // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
        int sign = 1;
        string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
        float  snr = params["snr"];
        int do_ctf = params["do_ctf"];
        setup( symmetry, size, npad, snr, sign, do_ctf );
}
 
void nn4_ctfwsReconstructor::setup( const string& symmetry, int size, int npad, float snr, int sign, int do_ctf )
{
        m_weighting = ESTIMATE;
        
                 /*     if( params.has_key("weighting") ) {
                                if( int( params["weighting"])==0) m_weighting = NONE;
                        } */
 
        m_wghta = 0.2f;
        m_wghtb = 0.004f;
 
        m_symmetry = symmetry;
        if (npad!=0) m_npad = npad;
        else m_npad = 0;
        m_sign = sign;
        m_nsym = Transform::get_nsym(m_symmetry);
        m_do_ctf = do_ctf;
 
        m_snr = snr;
 
        m_vnx = size;
        m_vny = size;
        m_vnz = size;
 
        //m_vnxp = size*npad;
        //m_vnyp = size*npad;
        //m_vnzp = size*npad;
        m_vnxp = size;
        m_vnyp = size;
        m_vnzp = size;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
        m_refvol = params["refvol"];
        m_refvol->get_data();
}
 
void nn4_ctfwsReconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
        m_volume->get_data();
        /*
        if (m_npad ==0) m_npad = m_volume->get_attr("npad");
        else { 
            int tmp_npad = m_volume->get_attr("npad");
            if (m_npad != tmp_npad)  m_npad = m_volume->get_attr("npad");
                }
        */
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_array_offsets(0,1,1);
 
/*
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
 
        if ( m_vnxp % 2 == 0 )  m_volume->set_fftodd(0);
        else                    m_volume->set_fftodd(1);
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
        
        */
}
 
void nn4_ctfwsReconstructor::buildNormVolume()
{
        m_wptr = params["weight"];
        m_wptr->get_data();
        m_wptr->set_array_offsets(0,1,1);
/*
        if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) {
               m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
               m_wptr->to_zero();
        }
 
        m_wptr->set_array_offsets(0,1,1);
*/
}
 
int nn4_ctfwsReconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight)
{
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if(weight !=0.0f) {
                /*
                int buffed = slice->get_attr_default( "buffed", 0 );
                        if( buffed > 0 ) {
                                insert_buffed_slice( slice, weight );
                                return 0;
                        }
                */
 
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                EMData* ctf2d = NULL;
                if( m_do_ctf == 1 ) {
                        float tmp = padfft->get_attr_default("ctf_applied", 0);
                        int   ctf_applied = (int) tmp;
 
                        // Generate 2D CTF (EMData object)
                        //ctf_store_real::init( padfft->get_ysize(), padfft->get_attr( "ctf" ) );
                   int winsize = padfft->get_ysize();
                   Ctf* ctf = padfft->get_attr( "ctf" );
                   Dict params = ctf->to_dict();        
                   ctf2d = Util::ctf_img_real(winsize , winsize, 1, params["defocus"], params["apix"],params["voltage"], params["cs"], \
                           params["ampcont"], params["bfactor"], params["dfdiff"], params["dfang"], 1);
                        params.clear();
                        if(ctf) {delete ctf; ctf=0;}
                        //ctf2d = ctf_store_real::get_ctf_real(); //This is in 2D projection plane
                        int nx=ctf2d->get_xsize(),ny=ctf2d->get_ysize(),nz=ctf2d->get_zsize();
                        float *ctf2d_ptr  = ctf2d->get_data();
 
                        size_t size = (size_t)nx*ny*nz;
                        if (!ctf_applied) {
                                for (int i = 0; i < size; ++i) padfft->cmplx(i) *= ctf2d_ptr[i]; // Multiply padfft by CTF
                        }
 
                        for (int i = 0; i < size; ++i) ctf2d_ptr[i] *= ctf2d_ptr[i];     // Squared 2D CTF
                } else {
                        int nx=padfft->get_xsize(),ny=padfft->get_ysize(),nz=padfft->get_zsize();
                        ctf2d = new EMData();
                        ctf2d->set_size(nx/2,ny,nz);
                        float *ctf2d_ptr  = ctf2d->get_data();
                        size_t size = (size_t)nx*ny*nz/2;
                        for (int i = 0; i < size; ++i) ctf2d_ptr[i] = 1.0;
                }
 
                vector<float> bckgnoise;
                bckgnoise = slice->get_attr("bckgnoise");
 
                insert_padfft_slice_weighted(padfft, ctf2d, bckgnoise, t, weight);
 
                checked_delete( ctf2d );
                checked_delete( padfft );
                bckgnoise.clear();
 
        }
        return 0;
}
 
int nn4_ctfwsReconstructor::insert_padfft_slice_weighted( EMData* padfft, EMData* ctf2d2, vector<float> bckgnoise, const Transform& t, float weight )
{
        Assert( padfft != NULL );
 
        vector<float> abc_list;
        int abc_list_len = 0;   
        if (m_volume->has_attr("smear")) {
                abc_list = m_volume->get_attr("smear");
                abc_list_len = abc_list.size();
        }
 
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++) {
                if (abc_list_len == 0)
                        m_volume->nn_ctfw(m_wptr, padfft, ctf2d2, m_npad, bckgnoise, tsym[isym], weight);
                else
                        for (int i = 0; i < abc_list_len; i += 4) 
                                m_volume->nn_ctfw(m_wptr, padfft, ctf2d2, m_npad, bckgnoise, tsym[isym] * Transform(Dict("type", "SPIDER", "phi",  abc_list[i], "theta", abc_list[i+1], "psi", abc_list[i+2])), weight * abc_list[i+3]);
        }
        return 0;
}
 
 
EMData* nn4_ctfwsReconstructor::finish(bool compensate)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_refvol->set_array_offsets(0, 1, 1);
        if(m_volume->is_fftodd())       m_volume->symplane0_odd(m_wptr);
        else                                            m_volume->symplane0_ctf(m_wptr);
        bool do_invert = false;
        bool refvol_present = (*m_refvol)(0) > 0.0f ;
        /*
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
        */
 
 
        int ix,iy,iz;
        //  refvol carries fsc
        int  limitres = m_vnyc-1;
        if( refvol_present )  { // If fsc is set to zero, it will be straightforward reconstruction with snr = 1
                for (ix = 0; ix < m_vnyc; ix++) {
                                //cout<<"  fsc  "<< m_vnyc-ix-1 <<"   "<<m_vnyc<<"   "<<(*m_refvol)(m_vnyc-ix-1)<<endl;
                          if( (*m_refvol)(m_vnyc-ix-1) == 0.0f )  limitres = m_vnyc-ix-2;
                }
        } else {
//cout<<"   limitres   "<<limitres<<endl;
 
                vector<float> count(m_vnyc+1, 0.0f);
                vector<float> sigma2(m_vnyc+1, 0.0f);
 
                //  compute sigma2
                for (iz = 1; iz <= m_vnzp; iz++) {
                        int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                        float argz = float(izp*izp);
                        for (iy = 1; iy <= m_vnyp; iy++) {
                                int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                float argy = argz + float(iyp*iyp);
                                for (ix = 0; ix <= m_vnxc; ix++) {
                                        if(ix>0 || (izp>=0 && (iyp>=0 || izp!=0))) {  //Skip Friedel related values
                                                float r = std::sqrt(argy + float(ix*ix));
                                                int  ir = int(r);
                                                if (ir <= limitres) {
                                                        float frac = r - float(ir);
                                                        float qres = 1.0f - frac;
                                                        float temp = (*m_wptr)(ix,iy,iz);
                                                        //cout<<" WEIGHTS "<<jx<<"  "<<jy<<"  "<<ir<<"  "<<temp<<"  "<<frac<<endl;
                                                        //cout<<" WEIGHTS "<<ix<<"  "<<iy-1<<"  "<<iz-1<<"  "<<temp<<"  "<<endl;
                                                        sigma2[ir]   += temp*qres;
                                                        sigma2[ir+1] += temp*frac;
                                                        count[ir]    += qres;
                                                        count[ir+1]  += frac;
                                                }
                                        }
                                }
                        }
                }
                for (ix = 0; ix <= m_vnyc; ix++) {
                        if( count[ix] > 0.0f )  (*m_refvol)(ix) = sigma2[ix]/count[ix];
                        //cout<<"  sigma2  "<< ix <<"   "<<sigma2[ix]<<endl;
                }
                /*
                #  This part will have to be done on python level.
                float fudge = m_refvol->get_attr("fudge");
                // now counter will serve to keep fsc-derived stuff
                for (ix = 0; ix <= limitres; ix++)  count[ix] = fudge * sigma2[ix] * (1.0f - (*m_refvol)(ix))/(*m_refvol)(ix);  //fudge?
                count[limitres+1] = count[limitres];
                //for (ix = 0; ix <= limitres+1; ix++)  cout<<"  tau2  "<< ix <<"   "<<count[ix]<<endl;
                */
        
        }
 
 
        // normalize
        float osnr = 0.0f;
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                        float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                float r = std::sqrt(argy + float(ix*ix));
                                int  ir = int(r);
                                if (ir <= limitres) {
                                        if ( (*m_wptr)(ix,iy,iz) > 0.0f) {
                                                if( refvol_present) {
                                                        float frac = r - float(ir);
                                                        float qres = 1.0f - frac;
                                                        osnr = qres*(*m_refvol)(ir) + frac*(*m_refvol)(ir+1);
                                                        //if(osnr == 0.0f)  osnr = 1.0f/(0.001*(*m_wptr)(ix,iy,iz));
                                                        //cout<<"  "<<iz<<"   "<<iy<<"   "<<"   "<<ix<<"   "<<ir<<"   "<<(*m_wptr)(ix,iy,iz)<<"   "<<osnr<<"      "<<(*m_volume)(2*ix,iy,iz)<<"      "<<(*m_volume)(2*ix+1,iy,iz)<<endl;
                                                }  else osnr = 0.0f;
 
                                                float tmp = ((*m_wptr)(ix,iy,iz)+osnr);
 
                                                if(do_invert){
                                                        if(tmp>0.0f) {
                                                        //cout<<" mvol "<<ix<<"  "<<iy<<"  "<<iz<<"  "<<(*m_volume)(2*ix,iy,iz)<<"  "<<(*m_volume)(2*ix+1,iy,iz)<<"  "<<tmp<<"  "<<osnr<<endl;
                                                                (*m_volume)(2*ix,iy,iz)   /= tmp;
                                                                (*m_volume)(2*ix+1,iy,iz) /= tmp;
                                                        } else {
                                                                (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                                                (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                                        }
                                                }  else (*m_wptr)(ix,iy,iz) = tmp;
                                        }
                                } else {
                                        (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                        (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                }
                        }
                }
        }
 
        if(do_invert)  {
                m_volume->center_origin_fft();
                // back fft
                m_volume->do_ift_inplace();
                int npad = m_volume->get_attr("npad");
                m_volume->depad();
                if( compensate )  circumftrl( m_volume, npad );
                m_volume->set_array_offsets( 0, 0, 0 );
        }
 
        return 0;
}
 
#ifdef False
EMData* nn4_ctfwsReconstructor::finish(bool)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_ctf(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
        // normalize
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                                        float tmp=0.0f;
                                        if( m_varsnr )  {
                                            int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                            int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                                float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr);//*m_sign;
                                        } else  {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr);//*m_sign;
                                        }
 
                        if( m_weighting == ESTIMATE ) {
                                int cx = ix;
                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                float sum = 0.0;
                                for( int ii = -kc; ii <= kc; ++ii ) {
                                        int nbrcx = cx + ii;
                                        if( nbrcx >= m_vnxc ) continue;
                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                int nbrcy = cy + jj;
                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                        int nbrcz = cz + jj;
                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                        if( nbrcx < 0 ) {
                                                                nbrcx = -nbrcx;
                                                                nbrcy = -nbrcy;
                                                                nbrcz = -nbrcz;
                                                        }
 
                                                        int nbrix = nbrcx;
                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                sum = sum + pow_a[c];
                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                        }
                                                }
                                        }
                                }
                                float wght = 1.0f / ( 1.0f - alpha * sum );
/*
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 */
                                tmp = tmp * wght;
                                }
                                (*m_volume)(2*ix,iy,iz) *= tmp;
                                (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
 
 
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_ctf(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        //float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
    vector<float> sigma2(m_vnyc+1, 0.0f);
    vector<float> count(m_vnyc+1, 0.0f);
 
        int ix,iy,iz;
        // compute sigma2
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
            float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                            if(ix>0 || (izp>=0 && (iyp>=0 || izp!=0))) {  //Skip Friedel related values
                    float r = std::sqrt(argy + float(ix*ix));
                    int  ir = int(r);
                    if (ir <= m_vnyc) {
                        float frac = r - float(ir);
                        float qres = 1.0f - frac;
                        float temp = (*m_wptr)(ix,iy,iz);
                        //cout<<" WEIGHTS "<<jx<<"  "<<jy<<"  "<<ir<<"  "<<temp<<"  "<<frac<<endl;
                        //cout<<" WEIGHTS "<<ix<<"  "<<iy-1<<"  "<<iz-1<<"  "<<temp<<"  "<<endl;
                        sigma2[ir]   += temp*qres;
                        sigma2[ir+1] += temp*frac;
                        count[ir]    += qres;
                        count[ir+1]  += frac;
                    }
                }
            }
        }
    }
    for (ix = 0; ix <= m_vnyc+1; ix++) {
        if( sigma2[ix] > 0.0f )  sigma2[ix] = count[ix]/sigma2[ix];
        //cout<<"  1/sigma2  "<< ix <<"   "<<sigma2[ix]<<endl;
    }
    // now counter will serve to keep fsc-derived stuff
        //  refvol carries fsc
        float fudge = m_refvol->get_attr("fudge");
    for (ix = 0; ix <= m_vnyc+1; ix++)
                  count[ix] = Util::get_max(0.0f, Util::get_min( 0.999f, (*m_refvol)(ix) ) );
    for (ix = 0; ix <= m_vnyc+1; ix++)  count[ix] = count[ix]/(1.0f - count[ix]) * sigma2[ix];
    for (ix = 0; ix <= m_vnyc+1; ix++)  {
        if ( count[ix] >0.0f) count[ix] = fudge/count[ix];  //fudge?
    }
//for (ix = 0; ix <= m_vnyc+1; ix++)  cout<<"  tau2  "<< ix <<"   "<<count[ix]<<"  m_wptr  "<<(*m_wptr)(ix,1,1)<<endl;
 
        // normalize
        for (iz = 1; iz <= m_vnzp; iz++) {
                int   izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                float argz = float(izp*izp);
                for (iy = 1; iy <= m_vnyp; iy++) {
                        int   iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
            float argy = argz + float(iyp*iyp);
                        for (ix = 0; ix <= m_vnxc; ix++) {
                    float r = std::sqrt(argy + float(ix*ix));
                    int  ir = int(r);
                        //cout<<"  m_wptr  "<<(*m_wptr)(ix,iy,iz)<<endl;
                    if (ir <= m_vnyc) {
                        float frac = r - float(ir);
                        float qres = 1.0f - frac;
                        osnr = qres*count[ir] + frac*count[ir+1];
                        if(osnr == 0.0f)  osnr = 1.0f/(0.001*(*m_wptr)(ix,iy,iz));
                        //cout<<"  "<<iz<<"   "<<iy<<"   "<<"   "<<ix<<"   "<<(*m_wptr)(ix,iy,iz)<<"   "<<osnr<<"      "<<(*m_volume)(2*ix,iy,iz)<<"      "<<(*m_volume)(2*ix+1,iy,iz)<<endl;
                                            float tmp=((*m_wptr)(ix,iy,iz)+osnr);
                                            //if( m_varsnr )  tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign;
                                            //else {
                                            //cout<<"  "<<iz<<"  "<<iy<<"  "<<"  "<<ix<<"  "<<iz<<"  "<<"  "<<(*m_wptr)(ix,iy,iz)<<"  "<<osnr<<"  "<<endl;
                                            if(tmp>0.0f) {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/tmp;
 
 
                                /*if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                                        float tmp=0.0f;
                                        if( m_varsnr )  {
                                            int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                                            int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                                float freq = sqrt( (float)(ix*ix+iyp*iyp+izp*izp) );
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr);//   *m_sign;
                                        } else  {
                                                tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr);//   *m_sign;
                                        }
                                */
 
                        /*if( m_weighting == ESTIMATE ) {
                                int cx = ix;
                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                float sum = 0.0;
                                for( int ii = -kc; ii <= kc; ++ii ) {
                                        int nbrcx = cx + ii;
                                        if( nbrcx >= m_vnxc ) continue;
                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                int nbrcy = cy + jj;
                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                        int nbrcz = cz + jj;
                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                        if( nbrcx < 0 ) {
                                                                nbrcx = -nbrcx;
                                                                nbrcy = -nbrcy;
                                                                nbrcz = -nbrcz;
                                                        }
 
                                                        int nbrix = nbrcx;
                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                sum = sum + pow_a[c];
                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                        }
                                                }
                                        }
                                }
                                float wght = 1.0f / ( 1.0f - alpha * sum );
/
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 /
                                tmp = tmp * wght;
                                }*/
                                (*m_volume)(2*ix,iy,iz) *= tmp;
                                (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                } else {
                                (*m_volume)(2*ix,iy,iz)   = 0.0f;
                                (*m_volume)(2*ix+1,iy,iz) = 0.0f;
                                }
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
 
        return 0;
}
#endif
//*** end of nn4_ctfws
 
 
//####################################################################################
//** nn4 ctf rect reconstructor
 
nn4_ctf_rectReconstructor::nn4_ctf_rectReconstructor()
{
        m_volume  = NULL;
        m_wptr    = NULL;
}
 
nn4_ctf_rectReconstructor::nn4_ctf_rectReconstructor( const string& symmetry, int size, int npad, float snr, int sign )
{
        setup( symmetry, size, npad, snr, sign );
}
 
nn4_ctf_rectReconstructor::~nn4_ctf_rectReconstructor()
{
        //if( m_delete_volume ) checked_delete(m_volume);
 
        //if( m_delete_weight ) checked_delete( m_wptr );
 
        //checked_delete( m_result );
}
 
void nn4_ctf_rectReconstructor::setup()
{
        if( ! params.has_key("sizeprojection") ) throw std::logic_error("Error: projection size is not given");
        m_sizeofprojection = params["sizeprojection"];
        int npad = params.has_key("npad") ? int(params["npad"]) : 4;
        // int sign = params.has_key("sign") ? int(params["sign"]) : 1;
        int sign = 1;
        string symmetry = params.has_key("symmetry")? params["symmetry"].to_str() : "c1";
 
        float snr = params["snr"];
 
        m_varsnr = params.has_key("varsnr") ? int(params["varsnr"]) : 0;
        setup( symmetry, m_sizeofprojection, npad, snr, sign );
 
}
 
void nn4_ctf_rectReconstructor::setup( const string& symmetry, int sizeprojection, int npad, float snr, int sign )
{
        m_weighting = ESTIMATE;
        if( params.has_key("weighting") ) {
                int tmp = int( params["weighting"] );
                if( tmp==0 ) m_weighting = NONE;
        }
 
        m_wghta = 0.2f;
        m_wghtb = 0.004f;
 
        m_symmetry = symmetry;
        m_npad = npad;
        m_sign = sign;
        m_nsym = Transform::get_nsym(m_symmetry);
 
        m_snr = snr;
        if (params.has_key("sizex"))  m_vnx = params["sizex"];
        else if (params.has_key("xratio")) {
                float temp=params["xratio"];
                m_vnx=int(float(sizeprojection)*temp);
        } else  m_vnx=sizeprojection;
 
        if (params.has_key("sizey"))  m_vny = params["sizey"];
        else if (params.has_key("yratio")) {
                float temp=params["yratio"];
                m_vny=int(float(sizeprojection)*temp);
        }
        else m_vny=sizeprojection;
        
        if (params.has_key("sizez"))  m_vnz = params["sizez"];
        else if (params.has_key("zratio")) {
                float temp=params["zratio"];
                m_vnz=int(float(sizeprojection)*temp);
        }
        else m_vnz=sizeprojection;
 
        
        m_xratio=float(m_vnx)/float(sizeprojection);    
        m_yratio=float(m_vny)/float(sizeprojection);
        m_zratio=float(m_vnz)/float(sizeprojection);
 
        //std::cout<<"xratio=="<<m_xratio<<"yratio=="<<m_yratio<<std::endl;
        //std::cout<<"sx=="<<m_vnx<<"sy=="<<m_vny<<"sz=="<<m_vnz<<std::endl;
 
        m_vnxp = m_vnx*npad;
        m_vnyp = m_vny*npad;
        m_vnzp = m_vnz*npad;
 
        m_vnxc = m_vnxp/2;
        m_vnyc = m_vnyp/2;
        m_vnzc = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
}
 
void nn4_ctf_rectReconstructor::buildFFTVolume() {
        int offset = 2 - m_vnxp%2;
 
        m_volume = params["fftvol"];
 
        if( m_volume->get_xsize() != m_vnxp+offset && m_volume->get_ysize() != m_vnyp && m_volume->get_zsize() != m_vnzp ) {
                m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
                m_volume->to_zero();
        }
 
        m_volume->set_nxc(m_vnxp/2);
        m_volume->set_complex(true);
        m_volume->set_ri(true);
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
void nn4_ctf_rectReconstructor::buildNormVolume()
{
        m_wptr = params["weight"];
 
        if( m_wptr->get_xsize() != m_vnxc+1 && m_wptr->get_ysize() != m_vnyp && m_wptr->get_zsize() != m_vnzp ) {
               m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
               m_wptr->to_zero();
        }
 
        m_wptr->set_array_offsets(0,1,1);
 
}
 
int nn4_ctf_rectReconstructor::insert_slice(const EMData* const slice, const Transform& t, const float weight)
{
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if(weight >0.0f )  {
                int buffed = slice->get_attr_default( "buffed", 0 );
                if( buffed > 0 ) {
                        insert_buffed_slice( slice, weight );
                        return 0;
                }
 
                int padffted= slice->get_attr_default("padffted", 0);
                //if( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  )
                if( padffted==0 && (slice->get_xsize()!=slice->get_ysize())  )
                {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
 
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                insert_padfft_slice( padfft, t, weight );
 
                checked_delete( padfft );
        }
        return 0;
}
 
int nn4_ctf_rectReconstructor::insert_buffed_slice( const EMData* buffed, float weight )
{
        const float* bufdata = buffed->get_data();
        float* cdata = m_volume->get_data();
        float* wdata = m_wptr->get_data();
 
        int npoint = buffed->get_xsize()/4;
        for( int i=0; i < npoint; ++i ) {
 
                int pos2 = int( bufdata[4*i] );
                int pos1 = pos2 * 2;
                cdata[pos1  ] += bufdata[4*i+1]*weight;
                cdata[pos1+1] += bufdata[4*i+2]*weight;
                wdata[pos2  ] += bufdata[4*i+3]*weight;
/*
        std::cout << "pos1, pos2, ctfv1, ctfv2, ctf2: ";
        std::cout << pos1 << " " << bufdata[5*i+1] << " " << bufdata[5*i+2] << " ";
        std::cout << pos2 << " " << bufdata[5*i+4] << std::endl;
 */
        }
        return 0;
}
 
 
int nn4_ctf_rectReconstructor::insert_padfft_slice( EMData* padfft, const Transform& t, float weight )
{
        float tmp = padfft->get_attr("ctf_applied");
        int   ctf_applied = (int) tmp;
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (unsigned int isym=0; isym < tsym.size(); isym++) {
                if(ctf_applied) m_volume->insert_rect_slice_ctf_applied(m_wptr, padfft, tsym[isym], m_sizeofprojection, m_xratio,m_yratio, m_zratio, m_npad, weight);                   
                else            m_volume->insert_rect_slice_ctf(m_wptr, padfft, tsym[isym], m_sizeofprojection, m_xratio, m_yratio, m_zratio, m_npad, weight);  
        }
 
        return 0;
}
 
EMData* nn4_ctf_rectReconstructor::finish(bool)
{
        m_volume->set_array_offsets(0, 1, 1);
        m_wptr->set_array_offsets(0, 1, 1);
        m_volume->symplane0_rect(m_wptr);
 
        int box = 7;
        int vol = box*box*box;
        int kc = (box-1)/2;
        vector< float > pow_a( 3*kc+1, 1.0 );
        for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
        pow_a[3*kc]=0.0;
 
 
        float max = max3d( kc, pow_a );
        float alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        float osnr = 1.0f/m_snr;
 
        // normalize
        int ix,iy,iz;
        for (iz = 1; iz <= m_vnzp; iz++) {
                for (iy = 1; iy <= m_vnyp; iy++) {
                        for (ix = 0; ix <= m_vnxc; ix++) {
                                if ( (*m_wptr)(ix,iy,iz) > 0.0f) {//(*v) should be treated as complex!!
                    float tmp=0.0f;
                    if( m_varsnr ) {
                        int iyp = (iy<=m_vnyc) ? iy - 1 : iy-m_vnyp-1;
                        int izp = (iz<=m_vnzc) ? iz - 1 : iz-m_vnzp-1;
                                    float freq = sqrt( (float)(ix*ix/(m_xratio*m_xratio)+iyp*iyp/(m_zratio*m_yratio)+izp*izp) );
                        tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+freq*osnr)*m_sign;
                    } else {
                        tmp = (-2*((ix+iy+iz)%2)+1)/((*m_wptr)(ix,iy,iz)+osnr)*m_sign;
                    }
 
                                        if( m_weighting == ESTIMATE ) {
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                        for( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                                        int nbrcz = cz + jj;
                                                                        if( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
 
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0.0 ) {
                                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                                  // if(ix%20==0 && iy%20==0 && iz%20==0)
                                                                                 //   std::cout << boost::format( "%4d %4d %4d %4d %10.3f" ) % nbrix % nbriy % nbriz % c % sum << std::endl;
                                                                        }
                                                                }
                                                        }
                                                }
                                                float wght = 1.0f / ( 1.0f - alpha * sum );
/*
                        if(ix%10==0 && iy%10==0)
                        {
                            std::cout << boost::format( "%4d %4d %4d " ) % ix % iy %iz;
                            std::cout << boost::format( "%10.3f %10.3f %10.3f " )  % tmp % wght % sum;
                            std::  << boost::format( "%10.3f %10.3e " ) % pow_b[r] % alpha;
                            std::cout << std::endl;
                        }
 */
                                                tmp = tmp * wght;
                                        }
                                        (*m_volume)(2*ix,iy,iz) *= tmp;
                                        (*m_volume)(2*ix+1,iy,iz) *= tmp;
                                }
                        }
                }
        }
 
        // back fft
        m_volume->do_ift_inplace();
        int npad = m_volume->get_attr("npad");
        m_volume->depad();
        circumfnn_rect( m_volume, npad );
        m_volume->set_array_offsets( 0, 0, 0 );
        return 0;
}
 
 
 
// Added By Zhengfan Yang on 04/11/07
// Beginning of the addition
// --------------------------------------------------------------------------------
 
nnSSNR_ctfReconstructor::nnSSNR_ctfReconstructor()
{
        m_volume  = NULL;
        m_wptr    = NULL;
        m_wptr2   = NULL;
        m_wptr3   = NULL;
}
 
nnSSNR_ctfReconstructor::nnSSNR_ctfReconstructor( const string& symmetry, int size, int npad, float snr, int sign)
{
        m_volume  = NULL;
        m_wptr    = NULL;
        m_wptr2   = NULL;
        m_wptr3   = NULL;
 
        setup( symmetry, size, npad, snr, sign );
}
 
nnSSNR_ctfReconstructor::~nnSSNR_ctfReconstructor()
{
 
        //if( m_delete_volume )  checked_delete(m_volume);
        //if( m_delete_weight )  checked_delete( m_wptr );
        //if( m_delete_weight2 ) checked_delete( m_wptr2 );
        //if( m_delete_weight3 ) checked_delete( m_wptr3 );
        //checked_delete( m_result );
}
 
void nnSSNR_ctfReconstructor::setup()
{
        int  size = params["size"];
        int  npad = params["npad"];
        int  sign = params["sign"];
        float snr = params["snr"];
        string symmetry;
        if( params.has_key("symmetry") )  symmetry = params["symmetry"].to_str();
        else                              symmetry = "c1";
        
        setup( symmetry, size, npad, snr, sign );
}
void nnSSNR_ctfReconstructor::setup( const string& symmetry, int size, int npad, float snr, int sign )
{
 
        m_weighting = ESTIMATE;
        m_wghta     = 0.2f;
        m_wghtb     = 0.004f;
        wiener      = 1;
 
        m_symmetry  = symmetry;
        m_npad      = npad;
        m_nsym      = Transform::get_nsym(m_symmetry);
 
        m_sign      = sign;
        m_snr       = snr;
 
        m_vnx       = size;
        m_vny       = size;
        m_vnz       = size;
 
        m_vnxp      = size*npad;
        m_vnyp      = size*npad;
        m_vnzp      = size*npad;
 
        m_vnxc      = m_vnxp/2;
        m_vnyc      = m_vnyp/2;
        m_vnzc      = m_vnzp/2;
 
        buildFFTVolume();
        buildNormVolume();
        buildNorm2Volume();
        buildNorm3Volume();
}
 
void nnSSNR_ctfReconstructor::buildFFTVolume() {
 
        int offset = 2 - m_vnxp%2;
        m_volume = params["fftvol"];
 
        m_volume->set_size(m_vnxp+offset,m_vnyp,m_vnzp);
        m_volume->to_zero();
 
        m_volume->set_fftodd(m_vnxp % 2);
 
        m_volume->set_nxc(m_vnxc);
        m_volume->set_complex(true);
        m_volume->set_ri(true); //(real, imaginary) instead of polar coordinate
        m_volume->set_fftpad(true);
        m_volume->set_attr("npad", m_npad);
        m_volume->set_array_offsets(0,1,1);
}
 
 
void nnSSNR_ctfReconstructor::buildNormVolume()
{
        m_wptr = params["weight"];
        m_wptr->set_size(m_vnxc+1,m_vnyp,m_vnzp);
        m_wptr->to_zero();
        m_wptr->set_array_offsets(0,1,1);
}
 
void nnSSNR_ctfReconstructor::buildNorm2Volume() {
 
        m_wptr2 = params["weight2"];
        m_wptr2->set_size(m_vnxc+1,m_vnyp,m_vnzp);
        m_wptr2->to_zero();
        m_wptr2->set_array_offsets(0,1,1);
}
 
void nnSSNR_ctfReconstructor::buildNorm3Volume() {
 
        m_wptr3 = params["weight3"];
        m_wptr3->set_size(m_vnxc+1,m_vnyp,m_vnzp);
        m_wptr3->to_zero();
        m_wptr3->set_array_offsets(0,1,1);
}
 
int nnSSNR_ctfReconstructor::insert_slice(const EMData *const  slice, const Transform& t, const float weight) {
        // sanity checks
        if (!slice) {
                LOGERR("try to insert NULL slice");
                return 1;
        }
        if( weight > 0.0f ) {
                int padffted= slice->get_attr_default("padffted", 0);
                if ( padffted==0 && (slice->get_xsize()!=slice->get_ysize() || slice->get_xsize()!=m_vnx)  ) {
                        // FIXME: Why doesn't this throw an exception?
                        LOGERR("Tried to insert a slice that is the wrong size.");
                        return 1;
                }
                EMData* padfft = padfft_slice( slice, t, m_npad );
 
                insert_padfft_slice( padfft, t, weight );
 
                checked_delete( padfft );
        }
        return 0;
}
int nnSSNR_ctfReconstructor::insert_padfft_slice( EMData* padfft, const Transform& t, float weight )
{
 
        // insert slice for all symmetry related positions
        vector<Transform> tsym = t.get_sym_proj(m_symmetry);
        for (int isym=0; isym < m_nsym; isym++) m_volume->nn_SSNR_ctf(m_wptr, m_wptr2, m_wptr3, padfft, tsym[isym], weight);
        return 0;
}
 
EMData* nnSSNR_ctfReconstructor::finish(bool)
{
/*
  I changed the code on 05/15/2008 so it only returns variance.
  Lines commented out are marked by //#
  The version prior to the currect changes is r1.190
  PAP
*/
        /***
            m_volume ctf*(P^2D->3D(F^3D))
            m_wptr   ctf^2
            m_wptr2  |P^2D->3D(F^3D)|^2
            m_wptr3  Kn
            nominator = sum_rot [ wght*signal ]
            denominator  = sum_rot[ wght*variance ]
                                                      ***/
        int kz, ky;
        int box = 7;
        int kc  = (box-1)/2;
        float alpha = 0.0;
        float argx, argy, argz;
        vector< float > pow_a( 3*kc+1, 1.0 );
        float w = params["w"];
        float dx2 = 1.0f/float(m_vnxc)/float(m_vnxc);
        float dy2 = 1.0f/float(m_vnyc)/float(m_vnyc);
        float dz2 = 1.0f/Util::get_max(float(m_vnzc),1.0f)/Util::get_max(float(m_vnzc),1.0f);
        int inc = Util::round(float(Util::get_max(m_vnxc,m_vnyc,m_vnzc))/w);
 
        EMData* SSNR = params["SSNR"];
        SSNR->set_size(inc+1,4,1);
        //#EMData* vol_ssnr = new EMData();
        //#vol_ssnr->set_size(m_vnxp, m_vnyp, m_vnzp);
        //#vol_ssnr->to_zero();
        //#  new linea follow
        EMData* vol_ssnr = params["vol_ssnr"];
        vol_ssnr->set_size(m_vnxp+ 2 - m_vnxp%2, m_vnyp ,m_vnzp);
        vol_ssnr->to_zero();
        if ( m_vnxp % 2 == 0 ) vol_ssnr->set_fftodd(0);
        else                   vol_ssnr->set_fftodd(1);
        vol_ssnr->set_nxc(m_vnxc);
        vol_ssnr->set_complex(true);
        vol_ssnr->set_ri(true);
        vol_ssnr->set_fftpad(false);
        //#
        float *nom    = new float[inc+1];
        float *denom  = new float[inc+1];
        int  *ka     = new int[inc+1];
        int  *nn     = new int[inc+1];
        float wght = 1.f;
        for (int i = 0; i <= inc; i++) {
                nom[i]   = 0.0f;
                denom[i] = 0.0f;
                nn[i]    = 0;
                ka[i]    = 0;
        }
        m_volume->symplane2(m_wptr, m_wptr2, m_wptr3);
        if ( m_weighting == ESTIMATE ) {
                int vol = box*box*box;
                for( unsigned int i=1; i < pow_a.size(); ++i ) pow_a[i] = pow_a[i-1] * exp(m_wghta);
                pow_a[3*kc] = 0.0;
                float max = max3d( kc, pow_a );
                alpha = ( 1.0f - 1.0f/(float)vol ) / max;
        }
        for (int iz = 1; iz <= m_vnzp; iz++) {
                if ( iz-1 > m_vnzc ) kz = iz-1-m_vnzp; else kz = iz-1;
                argz = float(kz*kz)*dz2;
                for (int iy = 1; iy <= m_vnyp; iy++) {
                        if ( iy-1 > m_vnyc ) ky = iy-1-m_vnyp; else ky = iy-1;
                        argy = argz + float(ky*ky)*dy2;
                        for (int ix = 0; ix <= m_vnxc; ix++) {
                                float Kn = (*m_wptr3)(ix,iy,iz);
                                argx = std::sqrt(argy + float(ix*ix)*dx2);
                                int r = Util::round(float(inc)*argx);
                                if ( r >= 0 && Kn > 4.5f ) {
                                        if ( m_weighting == ESTIMATE ) {
                                                int cx = ix;
                                                int cy = (iy<=m_vnyc) ? iy - 1 : iy - 1 - m_vnyp;
                                                int cz = (iz<=m_vnzc) ? iz - 1 : iz - 1 - m_vnzp;
                                                float sum = 0.0;
                                                for( int ii = -kc; ii <= kc; ++ii ) {
                                                        int nbrcx = cx + ii;
                                                        if( nbrcx >= m_vnxc ) continue;
                                                        for ( int jj= -kc; jj <= kc; ++jj ) {
                                                                int nbrcy = cy + jj;
                                                                if( nbrcy <= -m_vnyc || nbrcy >= m_vnyc ) continue;
                                                                for( int kk = -kc; kk <= kc; ++kk ) {
                                                                        int nbrcz = cz + jj;
                                                                        if ( nbrcz <= -m_vnyc || nbrcz >= m_vnyc ) continue;
                                                                        if( nbrcx < 0 ) {
                                                                                nbrcx = -nbrcx;
                                                                                nbrcy = -nbrcy;
                                                                                nbrcz = -nbrcz;
                                                                        }
                                                                        int nbrix = nbrcx;
                                                                        int nbriy = nbrcy >= 0 ? nbrcy + 1 : nbrcy + 1 + m_vnyp;
                                                                        int nbriz = nbrcz >= 0 ? nbrcz + 1 : nbrcz + 1 + m_vnzp;
                                                                        if( (*m_wptr)( nbrix, nbriy, nbriz ) == 0 ) {
                                                                                int c = 3*kc+1 - std::abs(ii) - std::abs(jj) - std::abs(kk);
                                                                                sum = sum + pow_a[c];
                                                                        }
                                                                }
                                                        }
                                                }
//                                              int r = std::abs(cx) + std::abs(cy) + std::abs(cz);
                                                wght = 1.0f / ( 1.0f - alpha * sum );
                                        } // end of ( m_weighting == ESTIMATE )
                                        float nominator   = std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz);
                                        float denominator = ((*m_wptr2)(ix,iy,iz)-std::norm(m_volume->cmplx(ix,iy,iz))/(*m_wptr)(ix,iy,iz))/(Kn-1.0f);
                                        // Skip Friedel related values
                                        if( (ix>0 || (kz>=0 && (ky>=0 || kz!=0)))) {
                                                if ( r <= inc ) {
                                                        nom[r]   += nominator*wght;
                                                        denom[r] += denominator/(*m_wptr)(ix,iy,iz)*wght;
                                                        nn[r]    += 2;
                                                        ka[r]    += int(Kn);
                                                }
/*
                                                float  tmp = Util::get_max(nominator/denominator/(*m_wptr)(ix,iy,iz)-1.0f,0.0f);
                                                //  Create SSNR as a 3D array (-n/2:n/2+n%2-1)
                                                int iix = m_vnxc + ix; int iiy = m_vnyc + ky; int iiz = m_vnzc + kz;
                                                if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
                                                        (*vol_ssnr)(iix, iiy, iiz) = tmp;
                                                // Friedel part
                                                iix = m_vnxc - ix; iiy = m_vnyc - ky; iiz = m_vnzc - kz;
                                                if( iix >= 0 && iix < m_vnxp && iiy >= 0 && iiy < m_vnyp && iiz >= 0 && iiz < m_vnzp )
                                                        (*vol_ssnr)(iix, iiy, iiz) = tmp;
*/
                                        }
                                        (*vol_ssnr)(2*ix, iy-1, iz-1) = denominator*wght;
                                } // end of Kn>4.5 or whatever
                        }
                }
        }
        for (int i = 0; i <= inc; i++) {
                (*SSNR)(i,0,0) = nom[i];
                (*SSNR)(i,1,0) = denom[i];
                (*SSNR)(i,2,0) = static_cast<float>(nn[i]);
                (*SSNR)(i,3,0) = static_cast<float>(ka[i]);
        }
        vol_ssnr->update();
 
        delete[] nom;
        delete[] denom;
        delete[] nn;
        delete[] ka;
 
        return 0;
}
 
// -----------------------------------------------------------------------------------
// End of this addition
 
 
void EMAN::dump_reconstructors()
{
        dump_factory < Reconstructor > ();
}
 
map<string, vector<string> > EMAN::dump_reconstructors_list()
{
        return dump_factory_list < Reconstructor > ();
}
 
 
 
 
 
using std::ofstream;
using std::ifstream;
 
 
newfile_store::newfile_store( const string& filename, int npad, bool ctf )
    : m_bin_file( filename + ".bin" ),
      m_txt_file( filename + ".txt" )
{
        m_npad = npad;
        m_ctf = ctf;
}
 
newfile_store::~newfile_store( )
{
}
 
void newfile_store::add_image( EMData* emdata, const Transform& tf )
{
        if( m_bin_of == NULL ) {
            m_bin_of = shared_ptr<ofstream>( new ofstream(m_bin_file.c_str(), std::ios::out|std::ios::binary) );
            m_txt_of = shared_ptr<ofstream>( new ofstream(m_txt_file.c_str()) );
        }
 
 
        EMData* padfft = padfft_slice( emdata, tf, m_npad );
 
        int nx = padfft->get_xsize();
        int ny = padfft->get_ysize();
        int n2 = ny / 2;
        int n = ny;
 
        float voltage=0.0f, pixel=0.0f, Cs=0.0f, ampcont=0.0f, bfactor=0.0f, defocus=0.0f;
 
        if( m_ctf ) {
                Ctf* ctf = emdata->get_attr( "ctf" );
                Dict params = ctf->to_dict();
                voltage = params["voltage"];
                pixel   = params["apix"];
                Cs      = params["cs"];
                ampcont = params["ampcont"];
                bfactor = params["bfactor"];
                defocus = params["defocus"];
                if(ctf) {delete ctf; ctf=0;}
        }
 
        vector<point_t> points;
        for( int j=-ny/2+1; j <= ny/2; j++ ) {
                int jp = (j>=0) ? j+1 : ny+j+1;
                for( int i=0; i <= n2; ++i ) {
                        int r2 = i*i + j*j;
                        if( (r2<ny*ny/4) && !( (i==0) && (j<0) ) ) {
                                float ctf;
                                if( m_ctf ) {
                                        float ak = std::sqrt( r2/float(ny*ny) )/pixel;
                                        ctf = Util::tf( defocus, ak, voltage, Cs, ampcont, bfactor, 1);
                                } else {
                                        ctf = 1.0;
                                }
 
                                float xnew = i*tf[0][0] + j*tf[1][0];
                                float ynew = i*tf[0][1] + j*tf[1][1];
                                float znew = i*tf[0][2] + j*tf[1][2];
                                std::complex<float> btq;
                                if (xnew < 0.) {
                                        xnew = -xnew;
                                        ynew = -ynew;
                                        znew = -znew;
                                        btq = conj(padfft->cmplx(i,jp-1));
                                } else {
                                        btq = padfft->cmplx(i,jp-1);
                                }
 
                                int ixn = int(xnew + 0.5 + n) - n;
                                int iyn = int(ynew + 0.5 + n) - n;
                                int izn = int(znew + 0.5 + n) - n;
                                if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
                                        int ixf, iyf, izf;
                                        if (ixn >= 0) {
                                                int iza, iya;
                                                if (izn >= 0)
                                                    iza = izn + 1;
                                                else
                                                    iza = n + izn + 1;
 
                                                if (iyn >= 0)
                                                    iya = iyn + 1;
                                                else
                                                    iya = n + iyn + 1;
 
                                                ixf = ixn;
                                                iyf = iya;
                                                izf = iza;
                                        } else {
                                                int izt, iyt;
                                                if (izn > 0)
                                                    izt = n - izn + 1;
                                                else
                                                    izt = -izn + 1;
 
                                                if (iyn > 0)
                                                    iyt = n - iyn + 1;
                                                else
                                                    iyt = -iyn + 1;
 
                                                ixf = -ixn;
                                                iyf = iyt;
                                                izf = izt;
                                        }
 
 
                                        int pos2 = ixf + (iyf-1)*nx/2 + (izf-1)*ny*nx/2;
                                        float ctfv1 = btq.real() * ctf;
                                        float ctfv2 = btq.imag() * ctf;
                                        float ctf2 = ctf*ctf;
 
                                        point_t p;
                                        p.pos2 = pos2;
                                        p.real = ctfv1;
                                        p.imag = ctfv2;
                                        p.ctf2 = ctf2;
 
                                        points.push_back( p );
                                }
                        }
                }
        }
 
 
        int npoint = points.size();
        std::istream::off_type offset = (m_offsets.size()==0) ? 0 : m_offsets.back();
        offset += npoint*sizeof(point_t);
        m_offsets.push_back( offset );
 
        *m_txt_of << m_offsets.back() << std::endl;
        m_bin_of->write( (char*)(&points[0]), sizeof(point_t)*npoint );
        checked_delete( padfft );
}
 
void newfile_store::get_image( int id, EMData* buf )
{
        if( m_offsets.size()==0 ) {
                ifstream is( m_txt_file.c_str() );
                std::istream::off_type off;
                while( is >> off ) {
                    m_offsets.push_back( off );
                }
 
                m_bin_if = shared_ptr<std::ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
        }
 
        Assert( m_bin_if != NULL );
 
        std::istream::off_type offset = (id==0) ? 0 : m_offsets[id-1];
        Assert( offset >= 0 );
        m_bin_if->seekg( offset, std::ios::beg );
 
 
        if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() ) {
                std::cout << "bad or fail or eof while fetching id, offset: " << id << " " << offset << std::endl;
                throw std::logic_error( "bad happen" );
        }
 
        int bufsize = (m_offsets[id] - offset)/sizeof(float);
        if( buf->get_xsize() != bufsize ) {
                buf->set_size( bufsize, 1, 1 );
        }
 
        char* data = (char*)(buf->get_data());
        m_bin_if->read( data, sizeof(float)*bufsize );
        buf->update();
}
 
void newfile_store::read( int nprj )
{
        if( m_offsets.size()==0 ) {
            ifstream is( m_txt_file.c_str() );
            std::istream::off_type off;
            while( is >> off ) {
                m_offsets.push_back( off );
            }
        }
 
        if( m_bin_if==NULL ) {
            m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
        }
 
 
        int npoint = m_offsets[0]/sizeof(point_t);
        std::ios::off_type prjsize = m_offsets[0];
 
        try {
            m_points.resize(nprj * npoint);
        }
        catch( std::exception& e ) {
            std::cout << "Error: " << e.what() << std::endl;
        }
 
        int ip = 0;
        for( int i=0; i < nprj; ++i ) {
                m_bin_if->read( (char*)(&m_points[ip]), prjsize );
                if( m_bin_if->bad() || m_bin_if->fail() || m_bin_if->eof() )  {
                        std::cout << "Error: file hander bad or fail or eof" << std::endl;
                        return;
                }
                ip += npoint;
        }
}
 
void newfile_store::add_tovol( EMData* fftvol, EMData* wgtvol, const vector<int>& mults, int pbegin, int pend )
{
        float* vdata = fftvol->get_data();
        float* wdata = wgtvol->get_data();
 
        int npoint = m_offsets[0]/sizeof(point_t);
//    Assert( int(mults.size())==nprj );
        Assert( int(m_points.size())== (pend - pbegin)*npoint );
 
        for( int iprj=pbegin; iprj < pend; ++iprj ) {
                int m = mults[iprj];
                if( m==0 ) continue;
 
                int ipt = (iprj-pbegin)*npoint;
                for( int i=0; i < npoint; ++i )  {
                    int pos2 = m_points[ipt].pos2;
                    int pos1 = pos2*2;
 
                    wdata[pos2]   += m_points[ipt].ctf2*m;
                    vdata[pos1]   += m_points[ipt].real*m;
                    vdata[pos1+1] += m_points[ipt].imag*m;
                    ++ipt;
                }
        }
}
 
void newfile_store::restart()
{
    m_bin_if = shared_ptr< ifstream>( new ifstream(m_bin_file.c_str(), std::ios::in|std::ios::binary) );
}
 
file_store::file_store(const string& filename, int npad, int write, bool ctf)
    : m_bin_file(filename + ".bin"),
      m_txt_file(filename + ".txt")
{
    m_ctf = ctf;
    m_prev = -1;
    m_npad = npad;
    m_write = write;
}
 
file_store::~file_store()
{
}
 
void file_store::add_image( EMData* emdata, const Transform& tf )
{
 
    EMData* padfft = padfft_slice( emdata, tf, m_npad );
 
    float* data = padfft->get_data();
 
    if( m_write && m_bin_ohandle == NULL )
    {
        m_bin_ohandle = shared_ptr< ofstream >( new ofstream(m_bin_file.c_str(), std::ios::out | std::ios::binary) );
        m_txt_ohandle = shared_ptr< ofstream >( new ofstream(m_txt_file.c_str() ) );
        if( m_ctf )
                 *m_txt_ohandle << "Cs pixel voltage ctf_applied amp_contrast defocus ";
 
        *m_txt_ohandle << "phi theta psi" << std::endl;
    }
 
    m_x_out = padfft->get_xsize();
    m_y_out = padfft->get_ysize();
    m_z_out = padfft->get_zsize();
    m_totsize = m_x_out*m_y_out*m_z_out;
 
    if( m_ctf )
    {
        Ctf* ctf = padfft->get_attr( "ctf" );
        Dict ctf_params = ctf->to_dict();
 
        m_ctf_applied = padfft->get_attr( "ctf_applied" );
 
        m_Cs = ctf_params["cs"];
        m_pixel = ctf_params["apix"];
        m_voltage = ctf_params["voltage"];
        m_amp_contrast = ctf_params["ampcont"];
        m_defocuses.push_back( ctf_params["defocus"] );
        if(ctf) {delete ctf; ctf=0;}
    }
 
    Dict params = tf.get_rotation( "spider" );
    float phi = params.get( "phi" );
    float tht = params.get( "theta" );
    float psi = params.get( "psi" );
 
 
    m_phis.push_back( phi );
    m_thetas.push_back( tht );
    m_psis.push_back( psi );
 
    if( m_write )
    {
        m_bin_ohandle->write( (char*)data, sizeof(float)*m_totsize );
 
        if( m_ctf )
        {
            *m_txt_ohandle << m_Cs << " ";
            *m_txt_ohandle << m_pixel << " ";
            *m_txt_ohandle << m_voltage << " ";
            *m_txt_ohandle << m_ctf_applied << " ";
            *m_txt_ohandle << m_amp_contrast << " ";
            *m_txt_ohandle << m_defocuses.back() << " ";
        }
        *m_txt_ohandle << m_phis.back() << " ";
        *m_txt_ohandle << m_thetas.back() << " ";
        *m_txt_ohandle << m_psis.back() << " ";
        *m_txt_ohandle << m_x_out << " ";
        *m_txt_ohandle << m_y_out << " ";
        *m_txt_ohandle << m_z_out << " ";
        *m_txt_ohandle << m_totsize << std::endl;
    }
 
    checked_delete(padfft);
 
}
 
void file_store::get_image( int id, EMData* padfft )
{
 
    if( m_phis.size() == 0 ) {
        ifstream m_txt_ifs( m_txt_file.c_str() );
 
                if( !m_txt_ifs ) std::cerr << "Error: file " << m_txt_file << " does not exist" << std::endl;
 
 
                string line;
                std::getline( m_txt_ifs, line );
 
                float first, defocus, phi, theta, psi;
 
 
 
                while( m_txt_ifs >> first ) {
 
                        if( m_ctf ) {
                                m_Cs = first;
                                m_txt_ifs >> m_pixel >> m_voltage;
                                m_txt_ifs >> m_ctf_applied >> m_amp_contrast;
                                m_txt_ifs >> defocus >> phi >> theta >> psi;
                                m_defocuses.push_back( defocus );
                        } else {
                                phi = first;
                                m_txt_ifs >> theta >> psi;
                        }
 
                        m_txt_ifs >> m_x_out >> m_y_out >> m_z_out >> m_totsize;
                        m_phis.push_back( phi );
                        m_thetas.push_back( theta );
                        m_psis.push_back( psi );
                }
        }
 
        Assert( m_ihandle != NULL );
 
        std::istream::off_type offset = id*sizeof(float)*m_totsize;
        Assert( offset >= 0 );
 
        if( offset > 0 ) m_ihandle->seekg(offset, std::ios::beg);
 
 
        if( m_ihandle->bad() )
        {
                std::cout << "bad while fetching id, offset: " << id << " " << offset << std::endl;
                throw std::logic_error( "bad happen" );
        }
 
        if( m_ihandle->fail() )
        {
                std::cout << "fail while fetching id, offset, curoff: " << id << " " << offset << std::endl;
                throw std::logic_error( "fail happen" );
        }
 
        if( m_ihandle->eof() )
        {
                std::cout << "eof while fetching id, offset: " << id << " " << offset << std::endl;
                throw std::logic_error( "eof happen" );
        }
 
        if( padfft->get_xsize() != m_x_out ||
                padfft->get_ysize() != m_y_out ||
                padfft->get_zsize() != m_z_out )
        {
                padfft->set_size(m_x_out, m_y_out, m_z_out);
        }
 
        char* data = (char*)(padfft->get_data());
        m_ihandle->read( data, sizeof(float)*m_totsize );
        padfft->update();
 
        if( m_ctf ) {
                padfft->set_attr( "Cs", m_Cs );
                padfft->set_attr( "Pixel_size", m_pixel );
                padfft->set_attr( "voltage", m_voltage );
                padfft->set_attr( "ctf_applied", m_ctf_applied );
                padfft->set_attr( "amp_contrast", m_amp_contrast );
                padfft->set_attr( "defocus", m_defocuses[id] );
        }
 
        padfft->set_attr( "padffted", 1 );
        padfft->set_attr( "phi", m_phis[id] );
        padfft->set_attr( "theta", m_thetas[id] );
        padfft->set_attr( "psi", m_psis[id] );
 
}
 
void file_store::restart( )
{
    if( m_ihandle == NULL ) m_ihandle = shared_ptr< ifstream >( new ifstream(m_bin_file.c_str(), std::ios::in | std::ios::binary) );
 
 
    if( m_ihandle->bad() || m_ihandle->fail() || m_ihandle->eof() ) m_ihandle->open( m_bin_file.c_str(), std::ios::binary );
 
    m_ihandle->seekg( 0, std::ios::beg );
}