Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

emdata_sparx.cpp

Go to the documentation of this file.
00001 
00005 /*
00006  * Author: Pawel A.Penczek, 09/09/2006 (Pawel.A.Penczek@uth.tmc.edu)
00007  * Copyright (c) 2000-2006 The University of Texas - Houston Medical School
00008  *
00009  * This software is issued under a joint BSD/GNU license. You may use the
00010  * source code in this file under either license. However, note that the
00011  * complete EMAN2 and SPARX software packages have some GPL dependencies,
00012  * so you are responsible for compliance with the licenses of these packages
00013  * if you opt to use BSD licensing. The warranty disclaimer below holds
00014  * in either instance.
00015  *
00016  * This complete copyright notice must be included in any revised version of the
00017  * source code. Additional authorship citations may be added, but existing
00018  * author citations must be preserved.
00019  *
00020  * This program is free software; you can redistribute it and/or modify
00021  * it under the terms of the GNU General Public License as published by
00022  * the Free Software Foundation; either version 2 of the License, or
00023  * (at your option) any later version.
00024  *
00025  * This program is distributed in the hope that it will be useful,
00026  * but WITHOUT ANY WARRANTY; without even the implied warranty of
00027  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
00028  * GNU General Public License for more details.
00029  *
00030  * You should have received a copy of the GNU General Public License
00031  * along with this program; if not, write to the Free Software
00032  * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
00033  *
00034  */
00035 
00036 #include <stack>
00037 #include "ctf.h"
00038 #include "emdata.h"
00039 #include <iostream>
00040 #include <cmath>
00041 #include <cstring>
00042 
00043 #include <gsl/gsl_sf_bessel.h>
00044 #include <gsl/gsl_errno.h>
00045 #include <vector>
00046 #include <boost/shared_ptr.hpp>
00047 
00048 using boost::shared_ptr;
00049 using std::vector;
00050 using std::cout;
00051 using namespace EMAN;
00052 using namespace std;
00053 
00054 EMData *EMData::real2FH(float OverSamplekB) // PRB
00055 {
00056         int nx        = get_xsize();
00057         int ny        = get_ysize();
00058         int nz        = get_zsize();
00059         int Center  = (int) floor( (nx+1.0)/2.0 +.01);
00060 #ifdef DEBUG
00061         printf("nx=%d, ny=%d, nz=%d Center=%d\n", nx,ny,nz, Center);
00062 #endif  //DEBUG
00063         float ScalFactor=4.1f;
00064         gsl_set_error_handler_off();
00065 
00066         if ( (nz==1) && (nx==ny) && (!is_complex())  && (Center*2)==(nx+1)){
00067 #ifdef DEBUG
00068                 printf("entered if \n");fflush(stdout);
00069 #endif  //DEBUG
00070 //              MArray2D ImBW = this ->get_2dview();
00071                 EMData*  ImBW = this ;
00072                 int Size=nx;
00073                 int iMax = (int) floor( (Size-1.0)/2 +.01);
00074                 int CountMax = (iMax+2)*(iMax+1)/2;
00075                 int *PermMatTr  = new int[CountMax];
00076                 float *RValsSorted  = new float[CountMax];
00077                 float *weightofkValsSorted = new float[CountMax];
00078                 int *SizeReturned = new int[1];
00079                 Util::Radialize(PermMatTr, RValsSorted,weightofkValsSorted,Size, SizeReturned);
00080                 int RIntMax= SizeReturned[0];
00081 
00082                 int mMax = (int) floor( ScalFactor*RValsSorted[RIntMax-1]+10.0);
00083 
00084                 int kIntMax=2+ (int) floor( RValsSorted[RIntMax-1]*OverSamplekB);
00085                 float *kVec2Use= new float[kIntMax];
00086                 for (int kk=0; kk<kIntMax; kk++){
00087                         kVec2Use[kk]= ((float) kk)/OverSamplekB;}
00088 
00089                 float *krVec= new float[kIntMax*RIntMax];
00090                 int Count=0;
00091                 for (int jk=0; jk<kIntMax; jk++ ){
00092                         for (int jR=0; jR<RIntMax; jR++ ){
00093                                 krVec[Count]=2.0f*M_PI*RValsSorted[jR]
00094                                         *kVec2Use[jk]/( (float) Size);
00095                                 Count++;
00096 //                              printf("krVec[%d]=%f \n",Count,krVec[Count-1]);fflush(stdout);
00097                 }} // end building up krVec
00098                 float krVecMin= kVec2Use[1]*RValsSorted[1];
00099                 float krVecMax = krVec[kIntMax*RIntMax-1]+krVecMin;
00100                 int Number2Use = (int) floor(OverSamplekB*krVecMax+1.0);
00101                 float *krVec2Use      = new float[Number2Use+1];
00102                 float *sampledBesselJ = new float[Number2Use+1];
00103 #ifdef DEBUG
00104                 printf("Size=%d, iMax=%d, SizeReturned=%d, RIntMax=%d, \n"
00105                       "mMax=%d, kIntMax=%d, krVecMin=%f, krVecMax=%f,  Number2Use=%d  \n\n",
00106                         Size, iMax, SizeReturned[0], RIntMax, mMax, kIntMax,
00107                                krVecMin,krVecMax,Number2Use);fflush(stdout);
00108 #endif  //DEBUG
00109                 for (int jkr=0; jkr<= Number2Use; jkr++) {
00110                         krVec2Use[jkr] =((float)jkr)*krVecMax/
00111                                     ((float)Number2Use);
00112 //                      printf("krVec2Use[%d]=%f \n",jkr+1,krVec2Use[jkr]);fflush(stdout);
00113                 }
00114 
00115 
00116                 EMData* rhoOfkmB = copy(); // glibc detected ** malloc(); memory corruption
00117 //              printf("finished O \n");fflush(stdout);
00118                 rhoOfkmB->set_size(2*(mMax+1),kIntMax);
00119                 rhoOfkmB->to_zero();
00120 //              MArray2D rhoOfkmB = FH->get_2dview();
00121 
00122                 int CenterM= Center-1; // to convert from Matlab to C++
00123                 std::complex <float> *rhoOfRandmTemp = new std::complex <float>[RIntMax];
00124                 std::complex <float> rhoTemp;
00125 
00126                 int PCount=0;
00127 
00128                 for (int m=0; m <=mMax; m++){
00129                 //    if m==mMax, tic, end
00130                         std::complex <float> tempF(0.0f,-1.0f);
00131                         std::complex <float> overallFactor = pow(tempF,m);  //(-i)^m ;  % I dropped off the 2 pi
00132                         std::complex <float> mI(0.0f,static_cast<float>(m));
00133                         for (int ii=0; ii< RIntMax; ii++){ rhoOfRandmTemp[ii]=0;}
00134                         for (int jx=0; jx <Center ; jx++) {
00135                                 for (int jy=0; jy <=jx; jy++){
00136                                         float fjx=float(jx);
00137                                         float fjy= float(jy);
00138                                         Count = (jx*jx+jx)/2 +1 +jy;
00139                                         PCount = PermMatTr[Count-1];
00140 //                                      printf("PCount=%d, Count=%d \n", PCount, Count);
00141                                         rhoTemp =  std::complex <float> ((*ImBW)(CenterM+jx,CenterM+jy)) *exp(mI* std::complex <float> (atan2(+fjy,+fjx)))
00142                                          +   std::complex <float> ((*ImBW)(CenterM+jx,CenterM-jy)) * exp(mI*std::complex <float>(atan2(-fjy,+fjx)))
00143                                          +   std::complex <float> ((*ImBW)(CenterM-jx,CenterM+jy)) * exp(mI*std::complex <float>(atan2(+fjy,-fjx)))
00144                                          +   std::complex <float> ((*ImBW)(CenterM-jx,CenterM-jy)) * exp(mI*std::complex <float>(atan2(-fjy,-fjx)))
00145                                          +   std::complex <float> ((*ImBW)(CenterM+jy,CenterM+jx)) * exp(mI*std::complex <float>(atan2(+fjx,+fjy)))
00146                                          +   std::complex <float> ((*ImBW)(CenterM+jy,CenterM-jx)) * exp(mI*std::complex <float>(atan2(-fjx,+fjy)))
00147                                          +   std::complex <float> ((*ImBW)(CenterM-jy,CenterM+jx)) * exp(mI*std::complex <float>(atan2(+fjx,-fjy)))
00148                                          +   std::complex <float> ((*ImBW)(CenterM-jy,CenterM-jx)) * exp(mI*std::complex <float>(atan2(-fjx,-fjy)));
00149                                         if (((jx+jy)==0)&&(m>0) ){
00150                                                 rhoTemp=0;}
00151 //                      printf("m=%d, jx=%d, jy=%d, rhoTemp= %f+ %f i\n", m,jx,jy,(rhoTemp.real()), (rhoTemp.imag()) );fflush(stdout);
00152 //                      {" %f,%f %f,%f %f,%f %f,%f \n",
00153 //                             ImBW[CenterM+jx][CenterM+jy] ,ImBW[CenterM+jx][CenterM-jy]  , ImBW[CenterM-jx][CenterM+jy] ,ImBW[CenterM-jx][CenterM-jy],
00154 //                             ImBW[CenterM+jy][CenterM+jx] ,ImBW[CenterM+jy][CenterM-jx]  , ImBW[CenterM-jy][CenterM+jx] ,ImBW[CenterM-jy][CenterM-jx]);
00155                                         rhoOfRandmTemp[PCount-1] +=
00156                                             rhoTemp/((float)pow(2.,(int)( (jx==0)  +(jy==0)+ (jy==jx))));
00157 
00158                         }} // end walk through lattice
00159 //                      printf("\n m=%d rhoOfRandmTemp" ,m  );fflush(stdout);
00160 //                      for (int ss=0; ss< RIntMax; ss++){
00161 //                              printf(" %3.1f+ %3.1fi \t",(rhoOfRandmTemp[ss].real()), (rhoOfRandmTemp[ss].imag())   );fflush(stdout);}
00162 
00163 // calculate product
00164 
00165                         float tempp;
00166 //                      printf("\n m=%d sampledBesselJ" ,m  );fflush(stdout);
00167                         for (int st=0; st<= Number2Use; st++){
00168                                 tempp=krVec2Use[st];
00169                                 sampledBesselJ[st] = static_cast<float>(gsl_sf_bessel_Jn(m,tempp));
00170 //                              printf(" %3.2f  \t",sampledBesselJ[st]   );fflush(stdout);
00171                         } // good so far
00172 
00173 //                      sampledBesselJ  = BesselJ(m,krVec2Use);
00174                         float *tempMB = new float [kIntMax*RIntMax];
00175                         Util::spline_mat(krVec2Use, sampledBesselJ, Number2Use+1,krVec,tempMB,kIntMax*RIntMax );
00176 //                      printf("\n tempMB m=%d y2" ,m  );fflush(stdout);
00177                         std::complex <float> *rowV = new std::complex <float> [kIntMax];
00178 
00179 //                      for (int st=0; st< kIntMax*RIntMax; st++){printf(" %3.2f  \t",tempMB[st]   );fflush(stdout);} // good so far
00180 
00181 //   tempMB,krVec is in blocks of RIntMax
00182 //                      printf("\n rowV m=%d \t" ,m  );fflush(stdout);
00183                         for (int st=0; st < kIntMax; st++) {
00184                                         rowV[st]=0;
00185                                         for (int sv=0; sv < RIntMax; sv++) {
00186                                                 rowV[st]+=  rhoOfRandmTemp[sv] *tempMB[sv+st*RIntMax];
00187                                         }
00188                                          rowV[st] *= overallFactor;
00189 //                                      printf(" %1.3f +%1.3fi \t" , rowV[st].real(), rowV[st].imag() );fflush(stdout);
00190                         }
00191                         for (int st=0; st < kIntMax; st++) {
00192                                 (*rhoOfkmB)(2*m  ,st) = rowV[st].real();
00193                                 (*rhoOfkmB)(2*m+1,st) = rowV[st].imag();
00194                         }
00195 //                      rowV = overallFactor*rhoOfRandmTemp*tempMBB;
00196 //                      rhoOfkmB(m+1,1:kIntMax) = rowV ;
00197 
00198 //                      if m==mMax, toc, end
00199 
00200 // %'final interpolation'
00201 // %     rhoOfkm(m+1,:) = spline(kVec2Use,rowV,RValsSorted); ;
00202 
00203 
00204                 } // ends m loop
00205 
00206                 update();
00207                 rhoOfkmB-> update();
00208                 rhoOfkmB->set_complex(true);
00209                 if(rhoOfkmB->get_ysize()==1 && rhoOfkmB->get_zsize()==1) {
00210                         rhoOfkmB->set_complex_x(true);
00211                 }
00212         rhoOfkmB->set_ri(true);
00213         rhoOfkmB->set_FH(true);
00214         rhoOfkmB->set_fftodd(true);
00215                 return rhoOfkmB;
00216         } else {
00217                 LOGERR("2D real square odd image expected.");
00218                 throw ImageFormatException("2D real square odd image expected.");
00219         }
00220 }
00221 
00222 EMData *EMData::copy_empty_head() const
00223 {
00224         ENTERFUNC;
00225         EMData *ret = new EMData();
00226         ret->attr_dict = attr_dict;
00227         ret->flags = flags;
00228         ret->all_translation = all_translation;
00229         ret->path = path;
00230         ret->pathnum = pathnum;
00231 
00232 // should these be here? d.woolford I did not comment them out, merely place them here (commented out) to draw attention
00233 //      ret->xoff = xoff;
00234 //      ret->yoff = yoff;
00235 //      ret->zoff = zoff;
00236 //      ret->changecount = changecount;
00237 
00238         ret->update();
00239 
00240         EXITFUNC;
00241         return ret;
00242 }
00243 
00244 
00245 EMData *EMData::FH2F(int Size, float OverSamplekB, int IntensityFlag)  // PRB
00246 {
00247         int nx=get_xsize();
00248         int ny=get_ysize();
00249         int nz=get_zsize();
00250         float ScalFactor=4.1f;
00251         int Center = (int) floor((Size+1.0)/2.0 +.1);
00252         int CenterM= Center-1;
00253         int CountMax = (Center+1)*Center/2;
00254 
00255         int     *PermMatTr           = new int[CountMax];
00256         float  *RValsSorted         = new float[CountMax];
00257         float  *weightofkValsSorted = new float[CountMax];
00258         int      *SizeReturned        = new int[1];
00259         Util::Radialize(PermMatTr, RValsSorted,weightofkValsSorted,Size, SizeReturned);
00260         int RIntMax= SizeReturned[0];  // replaces CountMax; the latter should now never be used.
00261 //      kVec2Use = (0:1/OverSamplek:RValsSorted(RIntMax)+1/OverSamplek); %   in pixels  (otherwise need *2*pi/Size)
00262 
00263         int   mMax = (int) floor( ScalFactor*RValsSorted[RIntMax-1]+10.0);
00264 
00265         int    kIntMax  = 2+ (int) floor( RValsSorted[RIntMax-1]*OverSamplekB);
00266         float *kVec2Use = new float[kIntMax];
00267         for (int kk=0; kk<kIntMax; kk++){
00268                 kVec2Use[kk]= ((float) kk)/OverSamplekB;}
00269 
00270 
00271 
00272 #ifdef DEBUG
00273         printf("nx=%d, ny=%d, nz=%d Center=%d mMax=%d CountMax=%d kIntMax=%d Centerm1=%d  Size=%d\n\n",
00274             nx,ny,nz, Center, mMax, CountMax, kIntMax,  CenterM, Size);
00275 #endif
00276 
00277         EMData * rhoOfkmB = this;
00278 
00279 //     check mMax's are equal
00280 //     check kIntMax's are equal
00281 
00282         if ( (nx==2*(mMax+1)) && (ny==kIntMax) &&(nz==1) ) {
00283 
00284         EMData *rhoOfkandm = copy();
00285         rhoOfkandm ->set_size(2*(mMax+1),RIntMax);
00286         rhoOfkandm ->to_zero();
00287 //      MArray2D rhoOfkandm = tempCopy->get_2dview();  % Just changed Nov 20 2005
00288 //      printf("rhoOfkandm \n");
00289         for (int mr=0; mr <2*(mMax+1); mr++){
00290                 float *Row= new float[kIntMax];
00291                 float *RowOut= new float[RIntMax];
00292                 for (int ii=0; ii<kIntMax; ii++){ Row[ii]=(*rhoOfkmB)(mr,ii);}
00293                 Util::spline_mat(kVec2Use, Row, kIntMax,  RValsSorted, RowOut, RIntMax );
00294                 for (int ii=0; ii<RIntMax; ii++){
00295                         (*rhoOfkandm)(mr,ii) = RowOut[ii];
00296 //                      printf("%3.3f  ",RowOut[ii]);
00297                 }
00298 //              printf(" \n");
00299 //              rhoOfkandm(m+1,:) = spline(kVec2Use,rhoOfkmBReIm(m+1,1:kIntMax),kIntMax,RValsSorted);
00300         }
00301         rhoOfkandm ->update();
00302 
00303 //          So far so good PRB ....
00304 
00305         EMData* outCopy = rhoOfkandm ->copy();
00306         outCopy->set_size(2*Size,Size,1);
00307         outCopy->to_zero();
00308 //      MArray2D ImBWfftRm = outCopy->get_2dview();
00309 
00310         int Count =0, kInt, kIntm1;
00311         std::complex <float> ImfTemp;
00312         float kValue, thetak;
00313 
00314         for (int jkx=0; jkx <Center; jkx++) { // These index the outputted picture
00315                 for (int jky=0; jky<=jkx; jky++){
00316                         kInt = PermMatTr[Count];
00317                         kIntm1= kInt-1;
00318                         Count++;
00319                         float fjkx = float(jkx);
00320                         float fjky = float(jky);
00321 
00322                         kValue = std::sqrt(fjkx*fjkx +  fjky*fjky )  ;
00323 //                      mMaxR= floor(ScalFactor*kValue +10);
00324 
00325  //                   How many copies
00326 
00327                         thetak = atan2(fjky,fjkx);
00328                         ImfTemp = (*rhoOfkandm)(0, kIntm1) ;
00329                         for (int mm= 1; mm <mMax;mm++) {  // The index for m
00330                                 std::complex <float> fact(0,-mm*thetak);
00331                                 std::complex <float> expfact= exp(fact);
00332                                 std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1),(*rhoOfkandm)(2*mm+1,kIntm1));
00333                                 float mmFac = float(1-2*(mm%2));
00334                                 if (IntensityFlag==1){ mmFac=1;}
00335                                 ImfTemp +=   expfact * tempRho + mmFac  *conj(expfact*tempRho);//pow(float(-1),mm)
00336                         }
00337                         (*outCopy)(2*(CenterM+jkx),CenterM+jky)   = ImfTemp.real();
00338                         (*outCopy)(2*(CenterM+jkx)+1,CenterM+jky) = ImfTemp.imag();
00339 //                      printf("jkx=%d, jky=%d; %f + %f i \n",jkx,jky,ImfTemp.real(), ImfTemp.imag());
00340 
00341                         if (jky>0) {
00342                                 thetak = atan2(-fjky,fjkx);
00343                                 ImfTemp = (*rhoOfkandm)(0,kIntm1);
00344                                 for (int mm= 1; mm<mMax; mm++) { // The index for m
00345                                         std::complex <float> fact(0,-mm*thetak);
00346                                         std::complex <float> expfact= exp(fact);
00347                                         std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1), (*rhoOfkandm)(2*mm+1,kIntm1));
00348                                         float mmFac = float(1-2*(mm%2));
00349                                         if (IntensityFlag==1){ mmFac=1;}
00350                                         ImfTemp +=   expfact * tempRho +  mmFac  *conj(expfact*tempRho);
00351                                 }
00352                                 (*outCopy)(2*(CenterM+jkx),CenterM-jky)  = ImfTemp.real();
00353 
00354                                 (*outCopy)(2*(CenterM+jkx)+1,CenterM-jky) = ImfTemp.imag();
00355                         }
00356 
00357                         if (jkx>0) {
00358                                 thetak = atan2(fjky,-fjkx);
00359                                 ImfTemp = (*rhoOfkandm)(0,kIntm1);
00360                                 for (int mm= 1; mm<mMax; mm++) { // The index for m
00361                                         std::complex <float> fact(0,-mm*thetak);
00362                                         std::complex <float> expfact= exp(fact);
00363                                         std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1), (*rhoOfkandm)(2*mm+1,kIntm1));
00364                                         float mmFac = float(1-2*(mm%2));
00365                                         if (IntensityFlag==1){ mmFac=1;}
00366                                         ImfTemp +=   expfact * tempRho +  mmFac *conj(expfact*tempRho);
00367                                 }
00368                                 (*outCopy)(2*(CenterM-jkx)  ,CenterM+jky) = ImfTemp.real();
00369                                 (*outCopy)(2*(CenterM-jkx)+1,CenterM+jky) = ImfTemp.imag();
00370                         }
00371 
00372                         if (jkx>0 && jky>0) {
00373                                 thetak = atan2(-fjky,-fjkx);
00374                                 ImfTemp = (*rhoOfkandm)(0 , kIntm1);
00375                                 for (int mm= 1; mm<mMax; mm++) {  // The index for m
00376                                         std::complex <float> fact(0,-mm*thetak);
00377                                         std::complex <float> expfact= exp(fact);
00378                                         std::complex <float> tempRho( (*rhoOfkandm)(2*mm,kIntm1),(*rhoOfkandm)(2*mm+1,kIntm1) );
00379                                         float mmFac = float(1-2*(mm%2));
00380                                         if (IntensityFlag==1){ mmFac=1;}
00381                                         ImfTemp +=   expfact * tempRho +  mmFac *conj(expfact*tempRho);
00382                                 }
00383                                 (*outCopy)(2*(CenterM-jkx)  ,CenterM-jky) = ImfTemp.real();
00384                                 (*outCopy)(2*(CenterM-jkx)+1,CenterM-jky) = ImfTemp.imag();
00385                         }
00386 
00387                         if (jky< jkx) {
00388                                 thetak = atan2(fjkx,fjky);
00389                                 ImfTemp = (*rhoOfkandm)(0,kIntm1);
00390                                 for (int mm= 1; mm<mMax; mm++){ // The index for m
00391                                         std::complex <float> fact(0,-mm*thetak);
00392                                         std::complex <float> expfact= exp(fact);
00393                                         std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1),(*rhoOfkandm)(2*mm+1,kIntm1));
00394                                         float mmFac = float(1-2*(mm%2));
00395                                         if (IntensityFlag==1){ mmFac=1;}
00396                                         ImfTemp +=   expfact * tempRho +  mmFac *conj(expfact*tempRho);
00397                                 }
00398                                 (*outCopy)(2*(CenterM+jky)  ,CenterM+jkx) = ImfTemp.real();
00399                                 (*outCopy)(2*(CenterM+jky)+1,CenterM+jkx) = ImfTemp.imag();
00400 
00401                                 if (jky>0){
00402                                         thetak = atan2(fjkx,-fjky);
00403                                         ImfTemp = (*rhoOfkandm)(0, kIntm1);
00404                                         for (int mm= 1; mm <mMax; mm++) { // The index for m
00405                                                 std::complex <float> fact(0,-mm*thetak);
00406                                                 std::complex <float> expfact= exp(fact);
00407                                                 std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1),(*rhoOfkandm)(2*mm+1,kIntm1));
00408                                         float mmFac = float(1-2*(mm%2));
00409                                         if (IntensityFlag==1){ mmFac=1;}
00410                                                 ImfTemp +=  expfact * tempRho +  mmFac *conj(expfact*tempRho);
00411                                         }
00412                                         (*outCopy)(2*(CenterM-jky)  ,CenterM+jkx) = ImfTemp.real();
00413                                         (*outCopy)(2*(CenterM-jky)+1,CenterM+jkx) = ImfTemp.imag();
00414                                 }
00415 
00416                                  if (jkx>0) {
00417                                          thetak = atan2(-fjkx,fjky);
00418                                          ImfTemp = (*rhoOfkandm)(0,kIntm1);
00419                                         for (int mm= 1; mm <mMax; mm++) { // The index for m
00420                                                 std::complex <float> fact(0,-mm*thetak);
00421                                                 std::complex <float> expfact= exp(fact);
00422                                                 std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1),(*rhoOfkandm)(2*mm+1,kIntm1));
00423                                                 float mmFac = float(1-2*(mm%2));
00424                                                 if (IntensityFlag==1){ mmFac=1;}
00425                                                 ImfTemp +=  expfact * tempRho +  mmFac *conj(expfact*tempRho);
00426                                         }
00427                                         (*outCopy)(2*(CenterM+jky)  ,CenterM-jkx) = ImfTemp.real();
00428                                         (*outCopy)(2*(CenterM+jky)+1,CenterM-jkx) = ImfTemp.imag();
00429                                 }
00430 
00431                                 if (jkx>0 && jky>0) {
00432                                         thetak = atan2(-fjkx,-fjky);
00433                                         ImfTemp = (*rhoOfkandm)(0,kIntm1) ;
00434                                         for (int mm= 1; mm <mMax; mm++) { // The index for m
00435                                                 std::complex <float> fact(0,-mm*thetak);
00436                                                 std::complex <float> expfact= exp(fact);
00437                                                 std::complex <float> tempRho((*rhoOfkandm)(2*mm,kIntm1) ,(*rhoOfkandm)(2*mm+1,kIntm1) );
00438                                                 float mmFac = float(1-2*(mm%2));
00439                                                 if (IntensityFlag==1){ mmFac=1;}
00440                                                 ImfTemp +=  expfact * tempRho +  mmFac *conj(expfact*tempRho);
00441                                         }
00442                                         (*outCopy)(2*(CenterM-jky)  ,CenterM-jkx) = ImfTemp.real();
00443                                         (*outCopy)(2*(CenterM-jky)+1,CenterM-jkx) = ImfTemp.imag();
00444                                 }
00445                         } // ends jky <jkx
00446 
00447 
00448                 } // ends jky
00449         } // ends jkx
00450         outCopy->update();
00451         outCopy->set_complex(true);
00452         if(outCopy->get_ysize()==1 && outCopy->get_zsize()==1) outCopy->set_complex_x(true);
00453         outCopy->set_ri(true);
00454         outCopy->set_FH(false);
00455         outCopy->set_fftodd(true);
00456         outCopy->set_shuffled(true);
00457         return outCopy;
00458         } else {
00459                 LOGERR("can't be an FH image not this size");
00460                 throw ImageFormatException("something strange about this image: not a FH");
00461 
00462         }
00463 }  // ends FH2F
00464 
00465 
00466 EMData *EMData::FH2Real(int Size, float OverSamplekB, int)  // PRB
00467 {
00468         EMData* FFT= FH2F(Size,OverSamplekB,0);
00469         FFT->process_inplace("xform.fourierorigin.tocorner");
00470         EMData* eguess= FFT ->do_ift();
00471         return eguess;
00472 }  // ends FH2F
00473 
00474 float dist(int lnlen, const float* line_1, const float* line_2)
00475 {
00476         float dis2=0.0;
00477         for( int i=0; i < lnlen; ++i) {
00478                 float tmp = line_1[i] - line_2[i];
00479                 dis2 += tmp*tmp;
00480         }
00481         //return static_cast<float>(std::sqrt(dis2));
00482         return dis2;
00483 }
00484 
00485 float dist_r(int lnlen, const float* line_1, const float* line_2)
00486 {
00487         double dis2 = 0.0;
00488         for( int i=0; i < lnlen; ++i ) {
00489                 float tmp = line_1[lnlen-1-i] - line_2[i];
00490                 dis2 += tmp*tmp;
00491         }
00492         return static_cast<float>(std::sqrt(dis2));
00493 }
00494 
00495 /*
00496 float EMData::cm_euc(EMData* sinoj, int n1, int n2, float alpha1, float alpha2)
00497 {
00498     int lnlen = get_xsize();
00499 
00500         Assert( n1 >=0 && n1 < get_ysize() );
00501         Assert( n2 >=0 && n2 < get_ysize() );
00502         Assert( alpha1>=0.0 && alpha1 < 360.0 );
00503         Assert( alpha2>=0.0 && alpha2 < 360.0 );
00504 
00505         float* line_1 = get_data() + n1*lnlen;
00506         float* line_2 = sinoj->get_data() + n2*lnlen;
00507         float just = (alpha1-180.0f)*(alpha2-180.0f);
00508         if( just > 0.0 ) return dist(lnlen, line_1, line_2);
00509 
00510         if( just == 0.0 ) {
00511                 float dist_1 = dist(lnlen, line_1, line_2);
00512                 float dist_2 = dist_r(lnlen, line_1, line_2);
00513 #ifdef  _WIN32
00514                 return _cpp_min(dist_1, dist_2);
00515 #else
00516                 return std::min(dist_1, dist_2);
00517 #endif  //_WIN32
00518         }
00519 
00520         Assert( (alpha1-180.0)*(alpha2-180.0) < 0.0 );
00521         return dist_r(lnlen, line_1, line_2);
00522 }
00523 */
00524 
00525 float EMData::cm_euc(EMData* sinoj, int n1, int n2)
00526 {
00527     int lnlen = get_xsize();
00528     float* line_1 = get_data() + n1 * lnlen;
00529     float* line_2 = sinoj->get_data() + n2 * lnlen;
00530     return dist(lnlen, line_1, line_2);
00531 }
00532 
00533 EMData* EMData::rotavg() {
00534 
00535         int rmax;
00536 
00537         ENTERFUNC;
00538 
00539 
00540         if (ny<2 && nz <2) {
00541                 LOGERR("No 1D images.");
00542                 throw ImageDimensionException("No 1D images!");
00543         }
00544         
00545         float apix[3];
00546         apix[0] = get_attr_default("apix_x",1.0);
00547         apix[1] = get_attr_default("apix_y",1.0);
00548         apix[2] = get_attr_default("apix_z",1.0);
00549         float min_apix = *std::min_element(&apix[0],&apix[3]);
00550         //here,only the relative value of apix_x, apix_y, apix_z are considered
00551         float apix_x = apix[0]/min_apix;
00552         float apix_y = apix[1]/min_apix;
00553         float apix_z = 1.0;
00554         if( nz > 1) 
00555                 apix_z=apix[2]/min_apix;
00556         float apix_x2 = apix_x*apix_x;
00557         float apix_y2 = apix_y*apix_y;
00558         float apix_z2 = apix_z*apix_z;
00559         
00560         vector<int> saved_offsets = get_array_offsets();
00561         set_array_offsets(-nx/2,-ny/2,-nz/2);
00562         
00563         
00564 #ifdef _WIN32
00565         //int rmax = _cpp_min(nx/2 + nx%2, ny/2 + ny%2);
00566         if ( nz == 1 ) {
00567                 rmax = _cpp_min( nx/2 + nx%2, ny/2 + ny%2);
00568         } else {
00569                 rmax = _cpp_min(nx/2 + nx%2, _cpp_min(ny/2 + ny%2, nz/2 + nz%2));
00570         }
00571 #else
00572         //int rmax = std::min(nx/2 + nx%2, ny/2 + ny%2);
00573         if ( nz == 1 ) {
00574                 rmax = std::min(nx/2 + nx%2, ny/2 + ny%2);
00575         } else {
00576                 rmax = std::min(nx/2 + nx%2, std::min(ny/2 + ny%2, nz/2 + nz%2));
00577         }
00578 #endif  //_WIN32
00579 
00580         float rmax_ratio = 0.0;
00581         if (rmax == nx/2 + nx%2 )
00582                 rmax_ratio = apix_x;
00583         else if (rmax == ny/2 + ny%2)
00584                 rmax_ratio = apix_y;
00585         else
00586                 rmax_ratio = apix_z;
00587         
00588         EMData* ret = new EMData();
00589         ret->set_size(rmax+1, 1, 1);
00590         ret->to_zero();
00591         vector<float> count(rmax+1);
00592         for (int k = -nz/2; k < nz/2 + nz%2; k++) {
00593                 if (abs( k*apix_z) > rmax*rmax_ratio ) continue;
00594                 for (int j = -ny/2; j < ny/2 + ny%2; j++) {
00595                         if (abs( j*apix_y ) > rmax*rmax_ratio) continue;
00596                         for (int i = -nx/2; i < nx/2 + nx%2; i++) {
00597                                 float r = std::sqrt(float(k*k*apix_z2) + float(j*j*apix_y2) + float(i*i*apix_x2))/rmax_ratio;
00598                                 int ir = int(r);
00599                                 if (ir >= rmax) continue;
00600                                 float frac = r - float(ir);
00601                                 (*ret)(ir) += (*this)(i,j,k)*(1.0f - frac);
00602                                 (*ret)(ir+1) += (*this)(i,j,k)*frac;
00603                                 count[ir] += 1.0f - frac;
00604                                 count[ir+1] += frac;
00605                         }
00606                 }
00607         }
00608         for (int ir = 0; ir <= rmax; ir++) {
00609         #ifdef _WIN32
00610                 (*ret)(ir) /= _cpp_max(count[ir],1.0f);
00611         #else
00612                 (*ret)(ir) /= std::max(count[ir],1.0f);
00613         #endif  //_WIN32
00614         }
00615 
00616         set_array_offsets(saved_offsets);
00617         ret->update();
00618         EXITFUNC;
00619         return ret;
00620 }
00621 
00622 EMData* EMData::rotavg_i() {
00623 
00624         int rmax;
00625         ENTERFUNC;
00626         if ( ny == 1 && nz == 1 ) {
00627                 LOGERR("Input image must be 2-D or 3-D!");
00628                 throw ImageDimensionException("Input image must be 2-D or 3-D!");
00629         }
00630 
00631         EMData* avg1D  = new EMData();
00632         EMData* result = new EMData();
00633 
00634         result->set_size(nx,ny,nz);
00635         result->to_zero();
00636         result->set_array_offsets(-nx/2, -ny/2, -nz/2);
00637 
00638         if ( nz == 1 ) {
00639 #ifdef  _WIN32
00640                 rmax = _cpp_min(nx/2 + nx%2, ny/2 + ny%2);
00641         } else {
00642                 rmax = _cpp_min(nx/2 + nx%2, _cpp_min(ny/2 + ny%2, nz/2 + nz%2));
00643 #else
00644                 rmax = std::min(nx/2 + nx%2, ny/2 + ny%2);
00645         } else {
00646                 rmax = std::min(nx/2 + nx%2, std::min(ny/2 + ny%2, nz/2 + nz%2));
00647 #endif  //_WIN32
00648         }
00649 
00650         avg1D = rotavg();
00651         float padded_value = 0.0, r;
00652         int i, j, k, ir;
00653         size_t number_of_pixels = 0;
00654         for ( k = -nz/2; k < nz/2 + nz%2; k++) {
00655                 if (abs(k) > rmax) continue;
00656                 for ( j = -ny/2; j < ny/2 + ny%2; j++) {
00657                         if (abs(j) > rmax) continue;
00658                         for (i = -nx/2; i < nx/2 + nx%2; i++) {
00659                                 r = std::sqrt(float(k*k) + float(j*j) + float(i*i));
00660                                 ir = int(r);
00661                                 if (ir > rmax || ir < rmax-2 ) continue ;
00662                                 else {
00663                                         padded_value += (*avg1D)(ir) ;
00664                                         number_of_pixels++ ;
00665                                 }
00666                         }
00667                 }
00668         }
00669         padded_value /= number_of_pixels;
00670         for ( k = -nz/2; k < nz/2 + nz%2; k++) {
00671                 for ( j = -ny/2; j < ny/2 + ny%2; j++) {
00672                         for ( i = -nx/2; i < nx/2 + nx%2; i++)  {
00673                                 r = std::sqrt(float(k*k) + float(j*j) + float(i*i));
00674                                 ir = int(r);
00675                                 if (ir >= rmax) (*result)(i,j,k) = padded_value ;
00676                                 else            (*result)(i,j,k) = (*avg1D)(ir)+((*avg1D)(ir+1)-(*avg1D)(ir))*(r - float(ir));
00677 
00678                         }
00679                 }
00680         }
00681         result->update();
00682         result->set_array_offsets(0,0,0);
00683         EXITFUNC;
00684         return result;
00685 }
00686 
00687 
00688 EMData* EMData::mult_radial(EMData* radial) {
00689 
00690         ENTERFUNC;
00691         if ( ny == 1 && nz == 1 ) {
00692                 LOGERR("Input image must be 2-D or 3-D!");
00693                 throw ImageDimensionException("Input image must be 2-D or 3-D!");
00694         }
00695 
00696         EMData* result = this->copy_head();
00697 
00698         result->to_zero();
00699         result->set_array_offsets(-nx/2, -ny/2, -nz/2);
00700         this->set_array_offsets(-nx/2, -ny/2, -nz/2);
00701         int rmax = radial->get_xsize();
00702         int i, j, k, ir;
00703         float r;
00704         for ( k = -nz/2; k < nz/2+nz%2; k++) {
00705                 for ( j = -ny/2; j < ny/2+ny%2; j++) {
00706                         for ( i = -nx/2; i < nx/2+nx%2; i++)  {
00707                                 r = std::sqrt(float(k*k) + float(j*j) + float(i*i));
00708                                 ir = int(r);
00709                                 if(ir < rmax-1)  (*result)(i,j,k) = (*this)(i,j,k) * ((*radial)(ir)+((*radial)(ir+1)-(*radial)(ir))*(r - float(ir)));
00710                         }
00711                 }
00712         }
00713         result->update();
00714         result->set_array_offsets(0,0,0);
00715         this->set_array_offsets(0,0,0);
00716         EXITFUNC;
00717         return result;
00718 }
00719 
00720 #define rdata(i,j,k) rdata[(i-1)+((j-1)+(k-1)*ny)*(size_t)nx]
00721 #define square(x) ((x)*(x))
00722 vector<float> EMData::cog() {
00723 
00724         vector<float> cntog;
00725         int ndim = get_ndim();
00726         int i=1,j=1,k=1;
00727         float val,sum1=0.f,MX=0.f,RG=0.f,MY=0.f,MZ=0.f,r=0.f;
00728 
00729         if (ndim == 1) {
00730                 for ( i = 1;i <= nx; i++) {
00731                         val   = rdata(i,j,k);
00732                         sum1 += val;
00733                         MX   += ((i-1)*val);
00734                 }
00735                 MX=(MX/sum1);
00736                 for ( i = 1;i <= nx; i++) {
00737                         val   = rdata(i,j,k);
00738                         sum1 += val;
00739                         RG   += val*(square(MX - (i-1)));
00740                 }
00741                 RG=std::sqrt(RG/sum1);
00742                 MX=MX-(nx/2);
00743                 cntog.push_back(MX);
00744                 cntog.push_back(RG);
00745 #ifdef _WIN32
00746                 cntog.push_back((float)Util::round(MX));
00747 #else
00748                 cntog.push_back(round(MX));
00749 #endif  //_WIN32
00750         } else if (ndim == 2) {
00751                 for (j=1;j<=ny;j++) {
00752                         for (i=1;i<=nx;i++) {
00753                                 val = rdata(i,j,k);
00754                                 sum1 += val;
00755                                 MX   += ((i-1)*val);
00756                                 MY   += ((j-1)*val);
00757                         }
00758                 }
00759                 MX=(MX/sum1);
00760                 MY=(MY/sum1);
00761                 sum1=0.f;
00762                 RG=0.f;
00763                 for (j=1;j<=ny;j++) {
00764                         r = (square(MY-(j-1)));
00765                         for (i=1;i<=nx;i++) {
00766                                 val = rdata(i,j,k);
00767                                 sum1 += val;
00768                                 RG   += val*(square(MX - (i-1)) + r);
00769                         }
00770                 }
00771                 RG = std::sqrt(RG/sum1);
00772                 MX = MX - nx/2;
00773                 MY = MY - ny/2;
00774                 cntog.push_back(MX);
00775                 cntog.push_back(MY);
00776                 cntog.push_back(RG);
00777 #ifdef _WIN32
00778                 cntog.push_back((float)Util::round(MX));cntog.push_back((float)Util::round(MY));
00779 #else
00780                 cntog.push_back(round(MX));cntog.push_back(round(MY));
00781 #endif  //_WIN32
00782         } else {
00783                 for (k = 1;k <= nz;k++) {
00784                         for (j=1;j<=ny;j++) {
00785                                 for (i=1;i<=nx;i++) {
00786                                         val = rdata(i,j,k);
00787                                         sum1 += val;
00788                                         MX += ((i-1)*val);
00789                                         MY += ((j-1)*val);
00790                                         MZ += ((k-1)*val);
00791                                 }
00792                         }
00793                 }
00794                 MX = MX/sum1;
00795                 MY = MY/sum1;
00796                 MZ = MZ/sum1;
00797                 sum1=0.f;
00798                 RG=0.f;
00799                 for (k = 1;k <= nz;k++) {
00800                         for (j=1;j<=ny;j++) {
00801                                 float r = (square(MY-(j-1)) + square(MZ - (k-1)));
00802                                 for (i=1;i<=nx;i++) {
00803                                         val = rdata(i,j,k);
00804                                         sum1 += val;
00805                                         RG   += val*(square(MX - (i-1)) + r);
00806                                 }
00807                         }
00808                 }
00809                 RG = std::sqrt(RG/sum1);
00810                 MX = MX - nx/2;
00811                 MY = MY - ny/2;
00812                 MZ = MZ - nz/2;
00813                 cntog.push_back(MX);
00814                 cntog.push_back(MY);
00815                 cntog.push_back(MZ);
00816                 cntog.push_back(RG);
00817 #ifdef _WIN32
00818                 cntog.push_back((float)Util::round(MX));cntog.push_back((float)Util::round(MY));cntog.push_back((float)Util::round(MZ));
00819 #else
00820                 cntog.push_back(round(MX));cntog.push_back(round(MY));cntog.push_back(round(MZ));
00821 #endif  //_WIN32
00822         }
00823         return cntog;
00824 }
00825 #undef square
00826 #undef rdata
00827 
00828 
00829 
00830 
00831 
00832 vector < float >EMData::calc_fourier_shell_correlation(EMData * with, float w)
00833 {
00834         ENTERFUNC;
00835 
00836 /*
00837  ******************************************************
00838  *DISCLAIMER
00839  * 08/16/05 P.A.Penczek
00840  * The University of Texas
00841  * Pawel.A.Penczek@uth.tmc.edu
00842  * Please do not modify the content of calc_fourier_shell_correlation
00843  ******************************************************/
00844 /*
00845 Fourier Ring/Shell Correlation
00846 Purpose: Calculate CCF in Fourier space as a function of spatial frequency
00847          between a pair of 2-3D images.
00848 Method: Calculate FFT (if needed), calculate FSC.
00849 Input:  f - real or complex 2-3D image
00850         g - real or complex 2-3D image
00851         w - float ring width
00852 Output: 2D 3xk real image.
00853         k - length of FSC curve, depends on dimensions of the image and ring width
00854         1 column - FSC,
00855         2 column - normalized frequency [0,0.5]
00856         3 column - currently n /error of the FSC = 1/sqrt(n),
00857                      where n is the number of Fourier coefficients within given shell
00858 */
00859         int needfree=0, kz, ky, ii;
00860         float  argx, argy, argz;
00861 
00862         if (!with) {
00863                 throw NullPointerException("NULL input image");
00864         }
00865 
00866 
00867         EMData *f = this;
00868         EMData *g = with;
00869 
00870         int nx  = f->get_xsize();
00871         int ny  = f->get_ysize();
00872         int nz  = f->get_zsize();
00873 
00874         if (ny==0 && nz==0) {
00875                 throw ImageFormatException( "Cannot calculate FSC for 1D images");
00876         }
00877 
00878         if (f->is_complex()) nx = (nx - 2 + f->is_fftodd()); // nx is the real-space size of the input image
00879         int lsd2 = (nx + 2 - nx%2) ; // Extended x-dimension of the complex image
00880 
00881 //  Process f if real
00882         EMData* fpimage = NULL;
00883         if (f->is_complex()) fpimage = f;
00884         else {
00885                 fpimage= f->norm_pad(false, 1); 
00886                 fpimage->do_fft_inplace();
00887                 needfree|=1; // Extend and do the FFT if f is real
00888         } 
00889 
00890 //  Process g if real
00891         EMData* gpimage = NULL;
00892         if (g->is_complex()) gpimage = g;
00893         else {
00894                 gpimage= g->norm_pad(false, 1);
00895                 gpimage->do_fft_inplace();
00896                 needfree|=2;  // Extend and do the FFT if g is real
00897         }
00898 
00899         float *d1 = fpimage->get_data();
00900         float *d2 = gpimage->get_data();
00901 
00902         int nx2 = nx/2;
00903         int ny2 = ny/2;
00904         int nz2 = nz/2;
00905 
00906         float dx2 = 1.0f/float(nx2)/float(nx2);
00907         float dy2 = 1.0f/float(ny2)/float(ny2);
00908 
00909 #ifdef _WIN32
00910         float dz2 = 1.0f / _cpp_max(float(nz2),1.0f)/_cpp_max(float(nz2),1.0f);
00911         int inc = Util::round(float( _cpp_max( _cpp_max(nx2,ny2),nz2) )/w );
00912 #else
00913         float dz2 = 1.0f/std::max(float(nz2),1.0f)/std::max(float(nz2),1.0f);
00914         int inc = Util::round(float(std::max(std::max(nx2,ny2),nz2))/w);
00915 #endif  //_WIN32
00916 
00917         double* ret = new double[inc+1];
00918         double* n1 = new double[inc+1];
00919         double* n2 = new double[inc+1];
00920         float*  lr = new float[inc+1];
00921         for (int i = 0; i <= inc; i++) {
00922                 ret[i] = 0; n1[i] = 0; n2[i] = 0; lr[i]=0;
00923         }
00924 
00925         for (int iz = 0; iz <= nz-1; iz++) {
00926                 if(iz>nz2) kz=iz-nz; else kz=iz; argz = float(kz*kz)*dz2;
00927                 for (int iy = 0; iy <= ny-1; iy++) {
00928                         if(iy>ny2) ky=iy-ny; else ky=iy; argy = argz + float(ky*ky)*dy2;
00929                         for (int ix = 0; ix <= lsd2-1; ix+=2) {
00930                         // Skip Friedel related values
00931                                 if (ix>0 || (kz>=0 && (ky>=0 || kz!=0))) {
00932                                         argx = 0.5f*std::sqrt(argy + float(ix*ix)*0.25f*dx2);
00933                                         int r = Util::round(inc*2*argx);
00934                                         if(r <= inc) {
00935                                                 ii = ix + (iy  + iz * ny)* lsd2;
00936                                                 ret[r] += d1[ii] * double(d2[ii]) + d1[ii + 1] * double(d2[ii + 1]);
00937                                                 n1[r]  += d1[ii] * double(d1[ii]) + d1[ii + 1] * double(d1[ii + 1]);
00938                                                 n2[r]  += d2[ii] * double(d2[ii]) + d2[ii + 1] * double(d2[ii + 1]);
00939                                                 lr[r]  += 2;
00940                                         }
00941                                 }
00942                         }
00943                 }
00944         }
00945 
00946         int  linc = 0;
00947         for (int i = 0; i <= inc; i++) if(lr[i]>0) linc++;
00948 
00949         vector<float> result(linc*3);
00950 
00951         ii = -1;
00952         for (int i = 0; i <= inc; i++) {
00953                 if(lr[i]>0) {
00954                         ii++;
00955                         result[ii]        = float(i)/float(2*inc);
00956                         result[ii+linc]   = float(ret[i] / (std::sqrt(n1[i] * n2[i])));
00957                         result[ii+2*linc] = lr[i]  /*1.0f/sqrt(float(lr[i]))*/;
00958                 }
00959                 /*else {
00960                         result[i]           = 0.0f;
00961                         result[i+inc+1]     = 0.0f;
00962                         result[i+2*(inc+1)] = 0.0f;}*/
00963         }
00964 
00965         if (needfree&1) {
00966                 if (fpimage) {
00967                         delete fpimage;
00968                         fpimage = 0;
00969                 }
00970         }
00971         if (needfree&2) {
00972                 if (gpimage) {
00973                         delete gpimage;
00974                         gpimage = 0;
00975                 }
00976         }
00977         delete[] ret; delete[]  n1; delete[]  n2; delete[]  lr;
00978 
00979         EXITFUNC;
00980         return result;
00981 }
00982 
00983 EMData* EMData::symvol(string symString) {
00984         ENTERFUNC;
00985         int nsym = Transform::get_nsym(symString); // number of symmetries
00986         Transform sym;
00987         // set up output volume
00988         EMData *svol = new EMData;
00989         svol->set_size(nx, ny, nz);
00990         svol->to_zero();
00991         // actual work -- loop over symmetries and symmetrize
00992         for (int isym = 0; isym < nsym; isym++) {
00993                  Transform rm = sym.get_sym(symString, isym);
00994                  EMData* symcopy = this -> rot_scale_trans(rm);
00995                  *svol += (*symcopy);
00996                  delete symcopy;
00997         }
00998         *svol /=  ((float) nsym);
00999         svol->update();
01000         EXITFUNC;
01001         return svol;
01002 }
01003 
01004 #define proj(ix,iy,iz)  proj[ix-1+(iy-1+(iz-1)*ny)*(size_t)nx]
01005 #define pnewimg(ix,iy,iz)  pnewimg[ix-1+(iy-1+(iz-1)*ny)*(size_t)nx]
01006 EMData* EMData::average_circ_sub() const
01007 {
01008 //  this is written as though dimensions could be different, but in fact they should be all equal nx=ny=nz,
01009 //                                                           no check of this
01010         ENTERFUNC;
01011         const EMData* const image = this;
01012         EMData* newimg = copy_head();
01013         float *proj = image->get_data();
01014         float *pnewimg = newimg->get_data();
01015         //  Calculate average outside of a circle
01016         float r2 = static_cast<float>( (nx/2)*(nx/2) );
01017         float qs=0.0f;
01018         int m=0;
01019         int ncz = nz/2 + 1;
01020         int ncy = ny/2 + 1;
01021         int ncx = nx/2 + 1;
01022         for (int iz = 1; iz <= nz; iz++) {
01023                 float yy = static_cast<float>( (iz-ncz)*(iz-ncz) );
01024                 for (int iy = 1; iy <=ny; iy++) { float xx = yy + (iy-ncy)*(iy-ncy);
01025                         for (int ix = 1; ix <= nx; ix++) {
01026                                 if ( xx+float((ix-ncx)*(ix-ncx)) > r2 ) {
01027                                         qs += proj(ix,iy,iz);
01028                                         m++;
01029                                 }
01030                         }
01031                 }
01032         }
01033 
01034 
01035         if( m > 0 ) qs /= m;
01036 
01037         for (int iz = 1; iz <= nz; iz++)
01038                 for (int iy = 1; iy <= ny; iy++)
01039                         for (int ix = 1; ix <= nx; ix++)
01040                                         pnewimg(ix,iy,iz) = proj(ix,iy,iz) - qs;
01041         newimg->update();
01042         return newimg;
01043         EXITFUNC;
01044 }
01045 
01046 
01047 //  Helper functions for method nn
01048 
01049 
01050 void EMData::onelinenn(int j, int n, int n2, EMData* wptr, EMData* bi, const Transform& tf)
01051 {
01052         //std::cout<<"   onelinenn  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01053         int jp = (j >= 0) ? j+1 : n+j+1;
01054         //for(int i = 0; i <= 2; i++){{for(int l = 0; l <= 2; l++) std::cout<<"  "<<tf[l][i];}std::cout<<std::endl;};std::cout<<std::endl;
01055         // loop over x
01056         for (int i = 0; i <= n2; i++) {
01057                 if (((i*i+j*j) < n*n/4) && !((0 == i) && (j < 0))) {
01058 //        if ( !((0 == i) && (j < 0))) {
01059                         float xnew = i*tf[0][0] + j*tf[1][0];
01060                         float ynew = i*tf[0][1] + j*tf[1][1];
01061                         float znew = i*tf[0][2] + j*tf[1][2];
01062                         std::complex<float> btq;
01063                         if (xnew < 0.) {
01064                                 xnew = -xnew;
01065                                 ynew = -ynew;
01066                                 znew = -znew;
01067                                 btq = conj(bi->cmplx(i,jp));
01068                         } else {
01069                                 btq = bi->cmplx(i,jp);
01070                         }
01071                         int ixn = int(xnew + 0.5 + n) - n;
01072                         int iyn = int(ynew + 0.5 + n) - n;
01073                         int izn = int(znew + 0.5 + n) - n;
01074                         
01075                         int iza, iya;
01076                         if (izn >= 0)  iza = izn + 1;
01077                         else           iza = n + izn + 1;
01078 
01079                         if (iyn >= 0) iya = iyn + 1;
01080                         else          iya = n + iyn + 1;
01081 
01082                         cmplx(ixn,iya,iza) += btq;
01083                         //std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<btq<<std::endl;
01084                         (*wptr)(ixn,iya,iza)++;
01085                         
01086                         /*if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2)  && (izn >= -n2) && (izn <= n2)) {
01087                                 if (ixn >= 0) {
01088                                         int iza, iya;
01089                                         if (izn >= 0)  iza = izn + 1;
01090                                         else           iza = n + izn + 1;
01091 
01092                                         if (iyn >= 0) iya = iyn + 1;
01093                                         else          iya = n + iyn + 1;
01094 
01095                                         cmplx(ixn,iya,iza) += btq;
01096                                         //std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<btq<<std::endl;
01097                                         (*wptr)(ixn,iya,iza)++;
01098                                 } else {
01099                                         int izt, iyt;
01100                                         if (izn > 0) izt = n - izn + 1;
01101                                         else         izt = -izn + 1;
01102 
01103                                         if (iyn > 0) iyt = n - iyn + 1;
01104                                         else         iyt = -iyn + 1;
01105 
01106                                         cmplx(-ixn,iyt,izt) += conj(btq);
01107                                         //std::cout<<" *  "<<j<<"  "<<ixn<<"  "<<iyt<<"  "<<izt<<"  "<<btq<<std::endl;
01108                                         (*wptr)(-ixn,iyt,izt)++;
01109                                 }
01110                         }*/
01111                 }
01112         }
01113 }
01114 
01115 
01116 void EMData::onelinenn_mult(int j, int n, int n2, EMData* wptr, EMData* bi, const Transform& tf, int mult)
01117 {
01118         //std::cout<<"   onelinenn  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01119         int jp = (j >= 0) ? j+1 : n+j+1;
01120         //for(int i = 0; i <= 1; i++){for(int l = 0; l <= 2; l++){std::cout<<"  "<<tf[i][l]<<"  "<<std::endl;}}
01121         // loop over x
01122         for (int i = 0; i <= n2; i++) {
01123         if (((i*i+j*j) < n*n/4) && !((0 == i) && (j < 0))) {
01124 //        if ( !((0 == i) && (j < 0))) {
01125                         float xnew = i*tf[0][0] + j*tf[1][0];
01126                         float ynew = i*tf[0][1] + j*tf[1][1];
01127                         float znew = i*tf[0][2] + j*tf[1][2];
01128                         std::complex<float> btq;
01129                         if (xnew < 0.) {
01130                                 xnew = -xnew;
01131                                 ynew = -ynew;
01132                                 znew = -znew;
01133                                 btq = conj(bi->cmplx(i,jp));
01134                         } else {
01135                                 btq = bi->cmplx(i,jp);
01136                         }
01137                         int ixn = int(xnew + 0.5 + n) - n;
01138                         int iyn = int(ynew + 0.5 + n) - n;
01139                         int izn = int(znew + 0.5 + n) - n;
01140                         
01141                         
01142                         int iza, iya;
01143                         if (izn >= 0)  iza = izn + 1;
01144                         else           iza = n + izn + 1;
01145 
01146                         if (iyn >= 0) iya = iyn + 1;
01147                         else          iya = n + iyn + 1;
01148 
01149                         cmplx(ixn,iya,iza) += btq*float(mult);
01150                         (*wptr)(ixn,iya,iza)+=float(mult);
01151                         
01152                         /*if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2)  && (izn >= -n2) && (izn <= n2)) {
01153                                 if (ixn >= 0) {
01154                                         int iza, iya;
01155                                         if (izn >= 0)  iza = izn + 1;
01156                                         else           iza = n + izn + 1;
01157 
01158                                         if (iyn >= 0) iya = iyn + 1;
01159                                         else          iya = n + iyn + 1;
01160 
01161                                         cmplx(ixn,iya,iza) += btq*float(mult);
01162                                         (*wptr)(ixn,iya,iza)+=float(mult);
01163                                 } else {
01164                                         int izt, iyt;
01165                                         if (izn > 0) izt = n - izn + 1;
01166                                         else         izt = -izn + 1;
01167 
01168                                         if (iyn > 0) iyt = n - iyn + 1;
01169                                         else         iyt = -iyn + 1;
01170 
01171                                         cmplx(-ixn,iyt,izt) += conj(btq)*float(mult);
01172                                         (*wptr)(-ixn,iyt,izt)+=float(mult);
01173                                 }
01174                         }*/
01175                 }
01176         }
01177 }
01178 
01179 void EMData::nn(EMData* wptr, EMData* myfft, const Transform& tf, int mult)
01180 {
01181         ENTERFUNC;
01182         int nxc = attr_dict["nxc"]; // # of complex elements along x
01183         // let's treat nr, bi, and local data as matrices
01184         vector<int> saved_offsets = get_array_offsets();
01185         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01186         set_array_offsets(0,1,1);
01187         myfft->set_array_offsets(0,1);
01188         // loop over frequencies in y
01189         //for(int i = 0; i <= 2; i++){{for(int l = 0; l <= 2; l++) std::cout<<"  "<<tf[l][i];}std::cout<<std::endl;};std::cout<<std::endl;
01190         //Dict tt = tf.get_rotation("spider");
01191         //std::cout << static_cast<float>(tt["phi"]) << " " << static_cast<float>(tt["theta"]) << " " << static_cast<float>(tt["psi"]) << std::endl;
01192         if( mult == 1 ) {
01193                 for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn(iy, ny, nxc, wptr, myfft, tf);
01194         } else {
01195                 for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn_mult(iy, ny, nxc, wptr, myfft, tf, mult);
01196         }
01197 
01198         set_array_offsets(saved_offsets);
01199         myfft->set_array_offsets(myfft_saved_offsets);
01200         EXITFUNC;
01201 }
01202 
01203 
01204 void EMData::insert_rect_slice(EMData* w, EMData* myfft, const Transform& trans, int sizeofprojection, float xratio, float yratio, int npad, int mult)
01205 {
01206         ENTERFUNC;
01207         vector<int> saved_offsets = get_array_offsets();
01208         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01209         set_array_offsets(0,1,1);
01210         myfft->set_array_offsets(0,1);
01211         
01212         // insert rectangular fft from my nn4_rect code
01213 
01214         Vec2f coordinate_2d_square;
01215         Vec3f coordinate_3dnew;
01216         Vec3f axis_newx;
01217         Vec3f axis_newy;
01218         Vec3f tempv;
01219         
01220         //begin of scaling factor calculation
01221         //unit vector x,y of 2D fft transformed to new positon after rotation and scaling
01222         axis_newx[0] = xratio*0.5f*(sizeofprojection*npad)*trans[0][0];
01223         axis_newx[1] = yratio*0.5f*(sizeofprojection*npad)*trans[0][1];
01224         axis_newx[2] = 0.5f*(sizeofprojection*npad)*trans[0][2];
01225 
01226         float ellipse_length_x = std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
01227         
01228         int ellipse_length_x_int = int(ellipse_length_x);
01229         float ellipse_step_x = 0.5f*(sizeofprojection*npad)/float(ellipse_length_x_int);
01230         float xscale = ellipse_step_x;//scal increased
01231 
01232         axis_newy[0] = xratio*0.5f*(sizeofprojection*npad)*trans[1][0];
01233         axis_newy[1] = yratio*0.5f*(sizeofprojection*npad)*trans[1][1];
01234         axis_newy[2] = 0.5f*(sizeofprojection*npad)*trans[1][2];
01235 
01236 
01237 
01238         float ellipse_length_y = std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
01239         int ellipse_length_y_int = int(ellipse_length_y);
01240         float ellipse_step_y = 0.5f*(sizeofprojection*npad)/float(ellipse_length_y_int);
01241         float yscale = ellipse_step_y;
01242         //end of scaling factor calculation
01243         std::complex<float> c1;
01244         nz = get_zsize();
01245 
01246         float r2=0.25f*sizeofprojection*npad*sizeofprojection*npad;
01247         float r2_at_point;
01248         
01249         for(int i=0;i<ellipse_length_x_int;i++) {
01250                 for(int j=-1*ellipse_length_y_int+1; j<=ellipse_length_y_int; j++) {
01251                     
01252                         r2_at_point=i*xscale*i*xscale+j*yscale*j*yscale;
01253                         if(r2_at_point<=r2 ) {
01254                                 
01255                                 
01256                                 coordinate_2d_square[0] = xscale*float(i);
01257                                 coordinate_2d_square[1] = yscale*float(j);
01258                                 float xnew = coordinate_2d_square[0]*trans[0][0] + coordinate_2d_square[1]*trans[1][0];
01259                                 float ynew = coordinate_2d_square[0]*trans[0][1] + coordinate_2d_square[1]*trans[1][1];
01260                                 float znew = coordinate_2d_square[0]*trans[0][2] + coordinate_2d_square[1]*trans[1][2];
01261                                 coordinate_3dnew[0] =xnew*xratio;
01262                                 coordinate_3dnew[1] = ynew*yratio;
01263                                 coordinate_3dnew[2] = znew;
01264                                 
01265                                 //binlinear interpolation
01266                                 float xp = coordinate_2d_square[0];
01267                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nz+coordinate_2d_square[1]+1;
01268                                 std::complex<float> lin_interpolated(0,0);
01269                                 int xlow=int(xp),xhigh=int(xp)+1;
01270                                 int ylow=int(yp),yhigh=int(yp)+1;
01271                                 float tx=xp-xlow,ty=yp-ylow;
01272 
01273                                 
01274                                 if(j == -1) {
01275                                         
01276                                         if(ylow<yp)
01277                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01278                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty) + myfft->cmplx(xhigh,yhigh)*tx*ty;
01279                                         else 
01280                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)
01281                                                 + myfft->cmplx(xhigh,ylow)*tx;
01282                                                                         
01283                                         }
01284                                 else {
01285                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01286                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty)+ myfft->cmplx(xhigh,yhigh)*tx*ty;
01287                                         
01288                                         }
01289                                         
01290                                 c1 = lin_interpolated;
01291                                 
01292                                 //now nearest neighborhood interpolation
01293                                 
01294                                 std::complex<float> btq;
01295                                 if ( coordinate_3dnew[0] < 0.) {
01296                                         coordinate_3dnew[0] = -coordinate_3dnew[0];
01297                                         coordinate_3dnew[1] = -coordinate_3dnew[1];
01298                                         coordinate_3dnew[2] = -coordinate_3dnew[2];
01299                                         btq = conj(c1);
01300                                         } else {
01301                                         btq = c1;
01302                                         }
01303                                 int ixn = int(coordinate_3dnew[0] + 0.5 + nx) - nx;
01304                                 int iyn = int(coordinate_3dnew[1] + 0.5 + ny) - ny;
01305                                 int izn = int(coordinate_3dnew[2] + 0.5 + nz) - nz;
01306 
01307                                 int iza, iya;
01308                                 if (izn >= 0)  iza = izn + 1;
01309                                 else           iza = nz + izn + 1;
01310 
01311                                 if (iyn >= 0) iya = iyn + 1;
01312                                 else          iya = ny + iyn + 1;
01313 
01314                                 cmplx(ixn,iya,iza) += btq*float(mult);
01315                                 (*w)(ixn,iya,iza) += mult;
01316                                         
01317                                 }
01318                         }
01319                             
01320                 }
01321 
01322 
01323         //end insert rectanular fft
01324                 
01325         set_array_offsets(saved_offsets);
01326         myfft->set_array_offsets(myfft_saved_offsets);
01327         EXITFUNC;
01328 
01329 }
01330 
01331 
01332 
01333 void EMData::nn_SSNR(EMData* wptr, EMData* wptr2, EMData* myfft, const Transform& tf, int)
01334 {
01335         ENTERFUNC;
01336         int nxc = attr_dict["nxc"];
01337 
01338         vector<int> saved_offsets = get_array_offsets();
01339         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01340 
01341         set_array_offsets(0,1,1);
01342         myfft->set_array_offsets(0,1);
01343 
01344         int iymin = is_fftodd() ? -ny/2 : -ny/2 + 1 ;
01345         int iymax = ny/2;
01346         int izmin = is_fftodd() ? -nz/2 : -nz/2 + 1 ;
01347         int izmax = nz/2;
01348 
01349         for (int iy = iymin; iy <= iymax; iy++) {
01350                 int jp = iy >= 0 ? iy+1 : ny+iy+1; //checked, works for both odd and even
01351                 for (int ix = 0; ix <= nxc; ix++) {
01352                         if (( 4*(ix*ix+iy*iy) < ny*ny ) && !( ix == 0 && iy < 0 ) ) {
01353                                 float xnew = ix*tf[0][0] + iy*tf[1][0];
01354                                 float ynew = ix*tf[0][1] + iy*tf[1][1];
01355                                 float znew = ix*tf[0][2] + iy*tf[1][2];
01356                                 std::complex<float> btq;
01357                                 if (xnew < 0.0) {
01358                                         xnew = -xnew; // ensures xnew>=0.0
01359                                         ynew = -ynew;
01360                                         znew = -znew;
01361                                         btq = conj(myfft->cmplx(ix,jp));
01362                                 } else {
01363                                         btq = myfft->cmplx(ix,jp);
01364                                 }
01365                                 int ixn = int(xnew + 0.5 + nx) - nx; // ensures ixn >= 0
01366                                 int iyn = int(ynew + 0.5 + ny) - ny;
01367                                 int izn = int(znew + 0.5 + nz) - nz;
01368                                 if ((ixn <= nxc) && (iyn >= iymin) && (iyn <= iymax) && (izn >= izmin) && (izn <= izmax)) {
01369                                         if (ixn >= 0) {
01370                                                 int iza, iya;
01371                                                 if (izn >= 0)  iza = izn + 1;
01372                                                 else           iza = nz + izn + 1;
01373 
01374                                                 if (iyn >= 0) iya = iyn + 1;
01375                                                 else          iya = ny + iyn + 1;
01376 
01377                                                 cmplx(ixn,iya,iza) += btq;
01378                                                 (*wptr)(ixn,iya,iza)++;
01379                                                 (*wptr2)(ixn,iya,iza) += norm(btq);
01380                                         } else {
01381                                                 int izt, iyt;
01382                                                 if (izn > 0) izt = nz - izn + 1;
01383                                                 else         izt = -izn + 1;
01384 
01385                                                 if (iyn > 0) iyt = ny - iyn + 1;
01386                                                 else         iyt = -iyn + 1;
01387 
01388                                                 cmplx(-ixn,iyt,izt) += conj(btq);
01389                                                 (*wptr)(-ixn,iyt,izt)++;
01390                                                 (*wptr2)(-ixn,iyt,izt) += norm(btq);
01391                                         }
01392                                 }
01393                         }
01394                 }
01395         }
01396         set_array_offsets(saved_offsets);
01397         myfft->set_array_offsets(myfft_saved_offsets);
01398         EXITFUNC;
01399 }
01400 
01401 
01402 
01403 void EMData::symplane0(EMData* wptr) {
01404         ENTERFUNC;
01405         int nxc = attr_dict["nxc"];
01406         int n = nxc*2;
01407         // let's treat the local data as a matrix
01408         vector<int> saved_offsets = get_array_offsets();
01409         set_array_offsets(0,1,1);
01410         for (int iza = 2; iza <= nxc; iza++) {
01411                 for (int iya = 2; iya <= nxc; iya++) {
01412                         cmplx(0,iya,iza) += conj(cmplx(0,n-iya+2,n-iza+2));
01413                         (*wptr)(0,iya,iza) += (*wptr)(0,n-iya+2,n-iza+2);
01414                         cmplx(0,n-iya+2,n-iza+2) = conj(cmplx(0,iya,iza));
01415                         (*wptr)(0,n-iya+2,n-iza+2) = (*wptr)(0,iya,iza);
01416                         cmplx(0,n-iya+2,iza) += conj(cmplx(0,iya,n-iza+2));
01417                         (*wptr)(0,n-iya+2,iza) += (*wptr)(0,iya,n-iza+2);
01418                         cmplx(0,iya,n-iza+2) = conj(cmplx(0,n-iya+2,iza));
01419                         (*wptr)(0,iya,n-iza+2) = (*wptr)(0,n-iya+2,iza);
01420                 }
01421         }
01422         for (int iya = 2; iya <= nxc; iya++) {
01423                 cmplx(0,iya,1) += conj(cmplx(0,n-iya+2,1));
01424                 (*wptr)(0,iya,1) += (*wptr)(0,n-iya+2,1);
01425                 cmplx(0,n-iya+2,1) = conj(cmplx(0,iya,1));
01426                 (*wptr)(0,n-iya+2,1) = (*wptr)(0,iya,1);
01427         }
01428         for (int iza = 2; iza <= nxc; iza++) {
01429                 cmplx(0,1,iza) += conj(cmplx(0,1,n-iza+2));
01430                 (*wptr)(0,1,iza) += (*wptr)(0,1,n-iza+2);
01431                 cmplx(0,1,n-iza+2) = conj(cmplx(0,1,iza));
01432                 (*wptr)(0,1,n-iza+2) = (*wptr)(0,1,iza);
01433         }
01434         EXITFUNC;
01435 }
01436 
01437 void EMData::symplane1(EMData* wptr, EMData* wptr2) {
01438         ENTERFUNC;
01439         int nxc = attr_dict["nxc"];
01440         int n = nxc*2;
01441         vector<int> saved_offsets = get_array_offsets();
01442         set_array_offsets(0,1,1);
01443         for (int iza = 2; iza <= nxc; iza++) {
01444                 for (int iya = 2; iya <= nxc; iya++) {
01445                         cmplx(0,iya,iza) += conj(cmplx(0,n-iya+2,n-iza+2));
01446                         (*wptr)(0,iya,iza) += (*wptr)(0,n-iya+2,n-iza+2);
01447                         (*wptr2)(0,iya,iza) += (*wptr2)(0,n-iya+2,n-iza+2);
01448                         cmplx(0,n-iya+2,n-iza+2) = conj(cmplx(0,iya,iza));
01449                         (*wptr)(0,n-iya+2,n-iza+2) = (*wptr)(0,iya,iza);
01450                         (*wptr2)(0,n-iya+2,n-iza+2) = (*wptr2)(0,iya,iza);
01451                         cmplx(0,n-iya+2,iza) += conj(cmplx(0,iya,n-iza+2));
01452                         (*wptr)(0,n-iya+2,iza) += (*wptr)(0,iya,n-iza+2);
01453                         (*wptr2)(0,n-iya+2,iza) += (*wptr2)(0,iya,n-iza+2);
01454                         cmplx(0,iya,n-iza+2) = conj(cmplx(0,n-iya+2,iza));
01455                         (*wptr)(0,iya,n-iza+2) = (*wptr)(0,n-iya+2,iza);
01456                         (*wptr2)(0,iya,n-iza+2) = (*wptr2)(0,n-iya+2,iza);
01457                 }
01458         }
01459         for (int iya = 2; iya <= nxc; iya++) {
01460                 cmplx(0,iya,1) += conj(cmplx(0,n-iya+2,1));
01461                 (*wptr)(0,iya,1) += (*wptr)(0,n-iya+2,1);
01462                 (*wptr2)(0,iya,1) += (*wptr2)(0,n-iya+2,1);
01463                 cmplx(0,n-iya+2,1) = conj(cmplx(0,iya,1));
01464                 (*wptr)(0,n-iya+2,1) = (*wptr)(0,iya,1);
01465                 (*wptr2)(0,n-iya+2,1) = (*wptr2)(0,iya,1);
01466         }
01467         for (int iza = 2; iza <= nxc; iza++) {
01468                 cmplx(0,1,iza) += conj(cmplx(0,1,n-iza+2));
01469                 (*wptr)(0,1,iza) += (*wptr)(0,1,n-iza+2);
01470                 (*wptr2)(0,1,iza) += (*wptr2)(0,1,n-iza+2);
01471                 cmplx(0,1,n-iza+2) = conj(cmplx(0,1,iza));
01472                 (*wptr)(0,1,n-iza+2) = (*wptr)(0,1,iza);
01473                 (*wptr2)(0,1,n-iza+2) = (*wptr2)(0,1,iza);
01474         }
01475         EXITFUNC;
01476 }
01477 
01478 void EMData::symplane2(EMData* wptr, EMData* wptr2, EMData* wptr3) {
01479         ENTERFUNC;
01480         int nxc = attr_dict["nxc"];
01481         int n = nxc*2;
01482         vector<int> saved_offsets = get_array_offsets();
01483         set_array_offsets(0,1,1);
01484         for (int iza = 2; iza <= nxc; iza++) {
01485                 for (int iya = 2; iya <= nxc; iya++) {
01486                         cmplx(0,iya,iza) += conj(cmplx(0,n-iya+2,n-iza+2));
01487                         (*wptr)(0,iya,iza) += (*wptr)(0,n-iya+2,n-iza+2);
01488                         (*wptr2)(0,iya,iza) += (*wptr2)(0,n-iya+2,n-iza+2);
01489                         (*wptr3)(0,iya,iza) += (*wptr3)(0,n-iya+2,n-iza+2);
01490 
01491                         cmplx(0,n-iya+2,n-iza+2) = conj(cmplx(0,iya,iza));
01492                         (*wptr)(0,n-iya+2,n-iza+2) = (*wptr)(0,iya,iza);
01493                         (*wptr2)(0,n-iya+2,n-iza+2) = (*wptr2)(0,iya,iza);
01494                         (*wptr3)(0,n-iya+2,n-iza+2) = (*wptr3)(0,iya,iza);
01495 
01496                         cmplx(0,n-iya+2,iza) += conj(cmplx(0,iya,n-iza+2));
01497                         (*wptr)(0,n-iya+2,iza) += (*wptr)(0,iya,n-iza+2);
01498                         (*wptr2)(0,n-iya+2,iza) += (*wptr2)(0,iya,n-iza+2);
01499                         (*wptr3)(0,n-iya+2,iza) += (*wptr3)(0,iya,n-iza+2);
01500 
01501                         cmplx(0,iya,n-iza+2) = conj(cmplx(0,n-iya+2,iza));
01502                         (*wptr)(0,iya,n-iza+2) = (*wptr)(0,n-iya+2,iza);
01503                         (*wptr2)(0,iya,n-iza+2) = (*wptr2)(0,n-iya+2,iza);
01504                         (*wptr3)(0,iya,n-iza+2) = (*wptr3)(0,n-iya+2,iza);
01505                 }
01506         }
01507         for (int iya = 2; iya <= nxc; iya++) {
01508                 cmplx(0,iya,1) += conj(cmplx(0,n-iya+2,1));
01509                 (*wptr)(0,iya,1) += (*wptr)(0,n-iya+2,1);
01510                 (*wptr2)(0,iya,1) += (*wptr2)(0,n-iya+2,1);
01511                 (*wptr3)(0,iya,1) += (*wptr3)(0,n-iya+2,1);
01512 
01513                 cmplx(0,n-iya+2,1) = conj(cmplx(0,iya,1));
01514                 (*wptr)(0,n-iya+2,1) = (*wptr)(0,iya,1);
01515                 (*wptr2)(0,n-iya+2,1) = (*wptr2)(0,iya,1);
01516                 (*wptr3)(0,n-iya+2,1) = (*wptr3)(0,iya,1);
01517         }
01518         for (int iza = 2; iza <= nxc; iza++) {
01519                 cmplx(0,1,iza) += conj(cmplx(0,1,n-iza+2));
01520                 (*wptr)(0,1,iza) += (*wptr)(0,1,n-iza+2);
01521                 (*wptr2)(0,1,iza) += (*wptr2)(0,1,n-iza+2);
01522                 (*wptr3)(0,1,iza) += (*wptr3)(0,1,n-iza+2);
01523 
01524                 cmplx(0,1,n-iza+2) = conj(cmplx(0,1,iza));
01525                 (*wptr)(0,1,n-iza+2) = (*wptr)(0,1,iza);
01526                 (*wptr2)(0,1,n-iza+2) = (*wptr2)(0,1,iza);
01527                 (*wptr3)(0,1,n-iza+2) = (*wptr3)(0,1,iza);
01528         }
01529         EXITFUNC;
01530 }
01531 
01532 
01533 class ctf_store
01534 {
01535 public:
01536 
01537     static void init( int winsize, const Ctf* ctf )
01538     {
01539         Dict params = ctf->to_dict();
01540 
01541         m_winsize = winsize;
01542 
01543         m_voltage = params["voltage"];
01544         m_pixel   = params["apix"];
01545         m_cs      = params["cs"];
01546         m_ampcont = params["ampcont"];
01547         m_bfactor = params["bfactor"];
01548         m_defocus = params["defocus"];
01549         m_winsize2= m_winsize*m_winsize;
01550         m_vecsize = m_winsize2/4;
01551     }
01552 
01553     static float get_ctf( int r2 )
01554     {
01555         float ak = std::sqrt( r2/float(m_winsize2) )/m_pixel;
01556         return Util::tf( m_defocus, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1 );
01557     }
01558 
01559 private:
01560 
01561     static int m_winsize, m_winsize2, m_vecsize;
01562     static float m_cs;
01563     static float m_voltage;
01564     static float m_pixel;
01565     static float m_ampcont;
01566     static float m_bfactor;
01567     static float m_defocus;
01568 };
01569 
01570 
01571 int ctf_store::m_winsize, ctf_store::m_winsize2, ctf_store::m_vecsize;
01572 
01573 float ctf_store::m_cs, ctf_store::m_voltage, ctf_store::m_pixel;
01574 float ctf_store::m_ampcont, ctf_store::m_bfactor;
01575 float ctf_store::m_defocus;
01576 
01577 
01578 class ctf_store_new
01579 {
01580 public:
01581 
01582     static void init( int winsize, const Ctf* ctf )
01583     {
01584         Dict params = ctf->to_dict();
01585 
01586         m_winsize = winsize;
01587 
01588         m_voltage = params["voltage"];
01589         m_pixel   = params["apix"];
01590         m_cs      = params["cs"];
01591         m_ampcont = params["ampcont"];
01592         m_bfactor = params["bfactor"];
01593         m_defocus = params["defocus"];
01594         m_winsize2= m_winsize*m_winsize;
01595         m_vecsize = m_winsize2/4;
01596     }
01597 
01598     static float get_ctf( float r2 )
01599     {
01600         float ak = std::sqrt( r2/float(m_winsize2) )/m_pixel;
01601         return Util::tf( m_defocus, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1 );
01602     }
01603 
01604 private:
01605 
01606     static int m_winsize, m_winsize2, m_vecsize;
01607     static float m_cs;
01608     static float m_voltage;
01609     static float m_pixel;
01610     static float m_ampcont;
01611     static float m_bfactor;
01612     static float m_defocus;
01613 };
01614 
01615 
01616 int ctf_store_new::m_winsize, ctf_store_new::m_winsize2, ctf_store_new::m_vecsize;
01617 
01618 float ctf_store_new::m_cs, ctf_store_new::m_voltage, ctf_store_new::m_pixel;
01619 float ctf_store_new::m_ampcont, ctf_store_new::m_bfactor;
01620 float ctf_store_new::m_defocus;
01621 
01622 
01623 
01624 //  Helper functions for method nn4_ctf
01625 void EMData::onelinenn_ctf(int j, int n, int n2,
01626                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01627 
01628         int remove = bi->get_attr_default( "remove", 0 );
01629 
01630         int jp = (j >= 0) ? j+1 : n+j+1;
01631         // loop over x
01632         for (int i = 0; i <= n2; i++) {
01633                 int r2 = i*i+j*j;
01634                 if ( (r2<n*n/4) && !((0==i) && (j<0)) ) {
01635                         float  ctf = ctf_store::get_ctf( r2 );
01636                         float xnew = i*tf[0][0] + j*tf[1][0];
01637                         float ynew = i*tf[0][1] + j*tf[1][1];
01638                         float znew = i*tf[0][2] + j*tf[1][2];
01639                         std::complex<float> btq;
01640                         if (xnew < 0.) {
01641                                 xnew = -xnew;
01642                                 ynew = -ynew;
01643                                 znew = -znew;
01644                                 btq = conj(bi->cmplx(i,jp));
01645                         } else  btq = bi->cmplx(i,jp);
01646                         int ixn = int(xnew + 0.5 + n) - n;
01647                         int iyn = int(ynew + 0.5 + n) - n;
01648                         int izn = int(znew + 0.5 + n) - n;
01649                         
01650                         int iza, iya;
01651                         if (izn >= 0)  iza = izn + 1;
01652                         else           iza = n + izn + 1;
01653 
01654                         if (iyn >= 0) iya = iyn + 1;
01655                         else          iya = n + iyn + 1;
01656 
01657                         if(remove > 0 ) {
01658                                 cmplx(ixn,iya,iza) -= btq*ctf*float(mult);
01659                                 (*w)(ixn,iya,iza) -= ctf*ctf*mult;
01660                         } else {
01661                                 cmplx(ixn,iya,iza) += btq*ctf*float(mult);
01662                                 (*w)(ixn,iya,iza) += ctf*ctf*mult;
01663                         }
01664 
01665                                        //       std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<ctf<<std::endl;
01666                 
01667                         /*if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
01668                                 if (ixn >= 0) {
01669                                         int iza, iya;
01670                                         if (izn >= 0)  iza = izn + 1;
01671                                         else           iza = n + izn + 1;
01672 
01673                                         if (iyn >= 0) iya = iyn + 1;
01674                                         else          iya = n + iyn + 1;
01675 
01676                                         if(remove > 0 ) {
01677                                             cmplx(ixn,iya,iza) -= btq*ctf*float(mult);
01678                                             (*w)(ixn,iya,iza) -= ctf*ctf*mult;
01679                                         } else {
01680                                             cmplx(ixn,iya,iza) += btq*ctf*float(mult);
01681                                             (*w)(ixn,iya,iza) += ctf*ctf*mult;
01682                                         }
01683 
01684                                        //       std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<ctf<<std::endl;
01685                                 } else {
01686                                         int izt, iyt;
01687                                         if (izn > 0) izt = n - izn + 1;
01688                                         else         izt = -izn + 1;
01689 
01690                                         if (iyn > 0) iyt = n - iyn + 1;
01691                                         else         iyt = -iyn + 1;
01692 
01693                                         if( remove > 0 ) {
01694                                             cmplx(-ixn,iyt,izt) -= conj(btq)*ctf*float(mult);
01695                                             (*w)(-ixn,iyt,izt) -= ctf*ctf*float(mult);
01696                                         } else {
01697                                             cmplx(-ixn,iyt,izt) += conj(btq)*ctf*float(mult);
01698                                             (*w)(-ixn,iyt,izt) += ctf*ctf*float(mult);
01699                                         }
01700 
01701                                         //      std::cout<<" *  " << j << "  " <<-ixn << "  " << iyt << "  " << izt << "  " << ctf <<std::endl;
01702                                 }
01703                         }*/
01704                 }
01705         }
01706 }
01707 
01708 void EMData::onelinenn_ctf_applied(int j, int n, int n2,
01709                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01710 
01711         int remove = bi->get_attr_default( "remove", 0 );
01712 
01713         int jp = (j >= 0) ? j+1 : n+j+1;
01714         // loop over x
01715         for (int i = 0; i <= n2; i++) {
01716                 int r2 = i*i + j*j;
01717                 if ( (r2< n*n/4) && !((0==i) && (j< 0)) ) {
01718                         float  ctf = ctf_store::get_ctf(r2);
01719 
01720                          //        if ( !((0 == i) && (j < 0))) {
01721                         float xnew = i*tf[0][0] + j*tf[1][0];
01722                         float ynew = i*tf[0][1] + j*tf[1][1];
01723                         float znew = i*tf[0][2] + j*tf[1][2];
01724                         std::complex<float> btq;
01725                         if (xnew < 0.) {
01726                                 xnew = -xnew;
01727                                 ynew = -ynew;
01728                                 znew = -znew;
01729                                 btq = conj(bi->cmplx(i,jp));
01730                         } else  btq = bi->cmplx(i,jp);
01731                         int ixn = int(xnew + 0.5 + n) - n;
01732                         int iyn = int(ynew + 0.5 + n) - n;
01733                         int izn = int(znew + 0.5 + n) - n;
01734                         
01735                         int iza, iya;
01736                         if (izn >= 0)  iza = izn + 1;
01737                         else           iza = n + izn + 1;
01738 
01739                         if (iyn >= 0) iya = iyn + 1;
01740                         else          iya = n + iyn + 1;
01741 
01742                         if( remove > 0 ) {
01743                                 cmplx(ixn,iya,iza) -= btq*float(mult);
01744                                 (*w)(ixn,iya,iza) -= mult*ctf*ctf;
01745                         } else {
01746                                 cmplx(ixn,iya,iza) += btq*float(mult);
01747                                 (*w)(ixn,iya,iza) += mult*ctf*ctf;
01748                         }
01749 
01750 
01751                         /*if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
01752                                 if (ixn >= 0) {
01753                                         int iza, iya;
01754                                         if (izn >= 0)  iza = izn + 1;
01755                                         else           iza = n + izn + 1;
01756 
01757                                         if (iyn >= 0) iya = iyn + 1;
01758                                         else          iya = n + iyn + 1;
01759 
01760                                         if( remove > 0 ) {
01761                                                 cmplx(ixn,iya,iza) -= btq*float(mult);
01762                                                 (*w)(ixn,iya,iza) -= mult*ctf*ctf;
01763                                         } else {
01764                                                 cmplx(ixn,iya,iza) += btq*float(mult);
01765                                                 (*w)(ixn,iya,iza) += mult*ctf*ctf;
01766                                         }
01767 
01768                                 } else {
01769                                         int izt, iyt;
01770                                         if (izn > 0) izt = n - izn + 1;
01771                                         else         izt = -izn + 1;
01772 
01773                                         if (iyn > 0) iyt = n - iyn + 1;
01774                                         else         iyt = -iyn + 1;
01775 
01776 
01777                                         if( remove > 0 ) {
01778                                                 cmplx(-ixn,iyt,izt) -= conj(btq)*float(mult);
01779                                                 (*w)(-ixn,iyt,izt) -= mult*ctf*ctf;
01780                                         } else {
01781                                                 cmplx(-ixn,iyt,izt) += conj(btq)*float(mult);
01782                                                 (*w)(-ixn,iyt,izt) += mult*ctf*ctf;
01783                                         }
01784                                         //std::cout<<" *  "<<j<<"  "<<ixn<<"  "<<iyt<<"  "<<izt<<"  "<<btq<<std::endl;
01785                                 }
01786                         }*/
01787                 }
01788         }
01789 }
01790 
01791 void
01792 EMData::nn_ctf(EMData* w, EMData* myfft, const Transform& tf, int mult) {
01793         ENTERFUNC;
01794         int nxc = attr_dict["nxc"]; // # of complex elements along x
01795         // let's treat nr, bi, and local data as matrices
01796         vector<int> saved_offsets = get_array_offsets();
01797         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01798         set_array_offsets(0,1,1);
01799         myfft->set_array_offsets(0,1);
01800 
01801         Ctf* ctf = myfft->get_attr("ctf");
01802         ctf_store::init( ny, ctf );
01803         if(ctf) {delete ctf; ctf=0;}
01804 
01805         // loop over frequencies in y
01806         for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn_ctf(iy, ny, nxc, w, myfft, tf, mult);
01807         set_array_offsets(saved_offsets);
01808         myfft->set_array_offsets(myfft_saved_offsets);
01809         EXITFUNC;
01810 }
01811 
01812 void
01813 EMData::nn_ctf_applied(EMData* w, EMData* myfft, const Transform& tf, int mult) {
01814         ENTERFUNC;
01815         int nxc = attr_dict["nxc"]; // # of complex elements along x
01816         // let's treat nr, bi, and local data as matrices
01817         vector<int> saved_offsets = get_array_offsets();
01818         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01819         set_array_offsets(0,1,1);
01820         myfft->set_array_offsets(0,1);
01821 
01822         Ctf* ctf = myfft->get_attr( "ctf" );
01823         ctf_store::init( ny, ctf );
01824         if(ctf) {delete ctf; ctf=0;}
01825         //}
01826 
01827         // loop over frequencies in y
01828         for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn_ctf_applied(iy, ny, nxc, w, myfft, tf, mult);
01829         set_array_offsets(saved_offsets);
01830         myfft->set_array_offsets(myfft_saved_offsets);
01831         EXITFUNC;
01832 }
01833 
01834 
01835 void EMData::insert_rect_slice_ctf(EMData* w, EMData* myfft, const Transform& trans, int sizeofprojection, float xratio, float yratio, int npad, int mult)
01836 {
01837         ENTERFUNC;
01838         vector<int> saved_offsets = get_array_offsets();
01839         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01840         set_array_offsets(0,1,1);
01841         myfft->set_array_offsets(0,1);
01842         
01843         // insert rectangular fft from my nn4_rect code
01844 
01845         Vec2f coordinate_2d_square;
01846         Vec3f coordinate_3dnew;
01847         Vec3f axis_newx;
01848         Vec3f axis_newy;
01849         Vec3f tempv;
01850         
01851         //begin of scaling factor calculation
01852         //unit vector x,y of 2D fft transformed to new positon after rotation and scaling
01853         axis_newx[0] = xratio*0.5f*(sizeofprojection*npad)*trans[0][0];
01854         axis_newx[1] = yratio*0.5f*(sizeofprojection*npad)*trans[0][1];
01855         axis_newx[2] = 0.5f*(sizeofprojection*npad)*trans[0][2];
01856 
01857         float ellipse_length_x = std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
01858         
01859         int ellipse_length_x_int = int(ellipse_length_x);
01860         float ellipse_step_x = 0.5f*(sizeofprojection*npad)/float(ellipse_length_x_int);
01861         float xscale = ellipse_step_x;//scal increased
01862 
01863         axis_newy[0] = xratio*0.5f*(sizeofprojection*npad)*trans[1][0];
01864         axis_newy[1] = yratio*0.5f*(sizeofprojection*npad)*trans[1][1];
01865         axis_newy[2] = 0.5f*(sizeofprojection*npad)*trans[1][2];
01866 
01867 
01868 
01869         float ellipse_length_y = std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
01870         int ellipse_length_y_int = int(ellipse_length_y);
01871         float ellipse_step_y = 0.5f*(sizeofprojection*npad)/float(ellipse_length_y_int);
01872         float yscale = ellipse_step_y;
01873         //end of scaling factor calculation
01874         std::complex<float> c1;
01875         nz = get_zsize();
01876         Ctf* ctf = myfft->get_attr( "ctf" );
01877         ctf_store_new::init( nz, ctf );
01878         if(ctf) {delete ctf; ctf=0;}
01879         int remove = myfft->get_attr_default( "remove", 0 );
01880 
01881         float r2=0.25f*sizeofprojection*npad*sizeofprojection*npad;
01882         float r2_at_point;
01883         
01884         for(int i=0;i<ellipse_length_x_int;i++) {
01885                 for(int j=-1*ellipse_length_y_int+1; j<=ellipse_length_y_int; j++) {
01886                     
01887                         r2_at_point=i*xscale*i*xscale+j*yscale*j*yscale;
01888                         if(r2_at_point<=r2 && ! ((0==i) && (j<0))) {
01889                                 
01890                                 float ctf_value = ctf_store_new::get_ctf( r2_at_point );
01891                                 coordinate_2d_square[0] = xscale*float(i);
01892                                 coordinate_2d_square[1] = yscale*float(j);
01893                                 float xnew = coordinate_2d_square[0]*trans[0][0] + coordinate_2d_square[1]*trans[1][0];
01894                                 float ynew = coordinate_2d_square[0]*trans[0][1] + coordinate_2d_square[1]*trans[1][1];
01895                                 float znew = coordinate_2d_square[0]*trans[0][2] + coordinate_2d_square[1]*trans[1][2];
01896                                 coordinate_3dnew[0] =xnew*xratio;
01897                                 coordinate_3dnew[1] = ynew*yratio;
01898                                 coordinate_3dnew[2] = znew;
01899                                 
01900                                 //binlinear interpolation
01901                                 float xp = coordinate_2d_square[0];
01902                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nz+coordinate_2d_square[1]+1;
01903                                 std::complex<float> lin_interpolated(0,0);
01904                                 int xlow=int(xp),xhigh=int(xp)+1;
01905                                 int ylow=int(yp),yhigh=int(yp)+1;
01906                                 float tx=xp-xlow,ty=yp-ylow;
01907 
01908                                 
01909                                 if(j == -1) {
01910                                         
01911                                         if(ylow<yp)
01912                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01913                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty) + myfft->cmplx(xhigh,yhigh)*tx*ty;
01914                                         else 
01915                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)
01916                                                 + myfft->cmplx(xhigh,ylow)*tx;
01917                                                                         
01918                                         }
01919                                 else {
01920                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01921                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty)+ myfft->cmplx(xhigh,yhigh)*tx*ty;
01922                                         
01923                                         }
01924                                         
01925                                 c1 = lin_interpolated;
01926                                 
01927                                 //now nearest neighborhood interpolation
01928                                 
01929                                 std::complex<float> btq;
01930                                 if ( coordinate_3dnew[0] < 0.) {
01931                                         coordinate_3dnew[0] = -coordinate_3dnew[0];
01932                                         coordinate_3dnew[1] = -coordinate_3dnew[1];
01933                                         coordinate_3dnew[2] = -coordinate_3dnew[2];
01934                                         btq = conj(c1);
01935                                         } else {
01936                                         btq = c1;
01937                                         }
01938                                 int ixn = int(coordinate_3dnew[0] + 0.5 + nx) - nx;
01939                                 int iyn = int(coordinate_3dnew[1] + 0.5 + ny) - ny;
01940                                 int izn = int(coordinate_3dnew[2] + 0.5 + nz) - nz;
01941 
01942                                 int iza, iya;
01943                                 if (izn >= 0)  iza = izn + 1;
01944                                 else           iza = nz + izn + 1;
01945 
01946                                 if (iyn >= 0) iya = iyn + 1;
01947                                 else          iya = ny + iyn + 1;
01948 
01949                                 if(remove > 0 ) {
01950                                         cmplx(ixn,iya,iza) -= btq*ctf_value*float(mult);
01951                                         (*w)(ixn,iya,iza) -= ctf_value*ctf_value*mult;
01952                                         } else {
01953                                         cmplx(ixn,iya,iza) += btq*ctf_value*float(mult);
01954                                         (*w)(ixn,iya,iza) += ctf_value*ctf_value*mult;
01955                                         }
01956                                         
01957                                 }
01958                         }
01959                             
01960                 }
01961 
01962 
01963         //end insert rectanular fft
01964                 
01965         set_array_offsets(saved_offsets);
01966         myfft->set_array_offsets(myfft_saved_offsets);
01967         EXITFUNC;
01968 
01969 }
01970 
01971 
01972 void EMData::insert_rect_slice_ctf_applied(EMData* w, EMData* myfft,const Transform& trans,int sizeofprojection,float xratio,float yratio,int npad,int mult)
01973 {
01974         ENTERFUNC;
01975         vector<int> saved_offsets = get_array_offsets();
01976         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01977         set_array_offsets(0,1,1);
01978         myfft->set_array_offsets(0,1);
01979         
01980         // insert rectangular fft from my nn4_rect code
01981 
01982         Vec2f coordinate_2d_square;
01983         Vec3f coordinate_3dnew;
01984         Vec3f axis_newx;
01985         Vec3f axis_newy;
01986         Vec3f tempv;
01987         
01988         //begin of scaling factor calculation
01989         //unit vector x,y of 2D fft transformed to new positon after rotation and scaling
01990         axis_newx[0] = xratio*0.5f*(sizeofprojection*npad)*trans[0][0];
01991         axis_newx[1] = yratio*0.5f*(sizeofprojection*npad)*trans[0][1];
01992         axis_newx[2] = 0.5f*(sizeofprojection*npad)*trans[0][2];
01993 
01994         float ellipse_length_x = std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
01995         
01996         int ellipse_length_x_int = int(ellipse_length_x);
01997         float ellipse_step_x = 0.5f*(sizeofprojection*npad)/float(ellipse_length_x_int);
01998         float xscale = ellipse_step_x;//scal increased
01999 
02000         axis_newy[0] = xratio*0.5f*(sizeofprojection*npad)*trans[1][0];
02001         axis_newy[1] = yratio*0.5f*(sizeofprojection*npad)*trans[1][1];
02002         axis_newy[2] = 0.5f*(sizeofprojection*npad)*trans[1][2];
02003 
02004 
02005 
02006         float ellipse_length_y = std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
02007         int ellipse_length_y_int = int(ellipse_length_y);
02008         float ellipse_step_y = 0.5f*(sizeofprojection*npad)/float(ellipse_length_y_int);
02009         float yscale = ellipse_step_y;
02010         //end of scaling factor calculation
02011         std::complex<float> c1;
02012         nz = get_zsize();
02013         Ctf* ctf = myfft->get_attr( "ctf" );
02014         ctf_store_new::init( nz, ctf );
02015         if(ctf) {delete ctf; ctf=0;}
02016         int remove = myfft->get_attr_default( "remove", 0 );
02017 
02018         float r2=0.25f*sizeofprojection*npad*sizeofprojection*npad;
02019         float r2_at_point;
02020         
02021         for(int i=0;i<ellipse_length_x_int;i++) {
02022                 for(int j=-1*ellipse_length_y_int+1; j<=ellipse_length_y_int; j++) {
02023                     
02024                         r2_at_point=i*xscale*i*xscale+j*yscale*j*yscale;
02025                         if(r2_at_point<=r2 && ! ((0==i) && (j<0))) {
02026                                 
02027                                 float ctf_value = ctf_store_new::get_ctf( r2_at_point );
02028                                 coordinate_2d_square[0] = xscale*float(i);
02029                                 coordinate_2d_square[1] = yscale*float(j);
02030                                 float xnew = coordinate_2d_square[0]*trans[0][0] + coordinate_2d_square[1]*trans[1][0];
02031                                 float ynew = coordinate_2d_square[0]*trans[0][1] + coordinate_2d_square[1]*trans[1][1];
02032                                 float znew = coordinate_2d_square[0]*trans[0][2] + coordinate_2d_square[1]*trans[1][2];
02033                                 coordinate_3dnew[0] =xnew*xratio;
02034                                 coordinate_3dnew[1] = ynew*yratio;
02035                                 coordinate_3dnew[2] = znew;
02036                                 
02037                                 //binlinear interpolation
02038                                 float xp = coordinate_2d_square[0];
02039                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nz+coordinate_2d_square[1]+1;
02040                                 std::complex<float> lin_interpolated(0,0);
02041                                 int xlow=int(xp),xhigh=int(xp)+1;
02042                                 int ylow=int(yp),yhigh=int(yp)+1;
02043                                 float tx=xp-xlow,ty=yp-ylow;
02044 
02045                                 
02046                                 if(j == -1) {
02047                                         
02048                                         if(ylow<yp)
02049                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
02050                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty) + myfft->cmplx(xhigh,yhigh)*tx*ty;
02051                                         else 
02052                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)
02053                                                 + myfft->cmplx(xhigh,ylow)*tx;
02054                                                                         
02055                                         }
02056                                 else {
02057                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
02058                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty)+ myfft->cmplx(xhigh,yhigh)*tx*ty;
02059                                         
02060                                         }
02061                                         
02062                                 c1 = lin_interpolated;
02063                                 
02064                                 //now nearest neighborhood interpolation
02065                                 
02066                                 std::complex<float> btq;
02067                                 if ( coordinate_3dnew[0] < 0.) {
02068                                         coordinate_3dnew[0] = -coordinate_3dnew[0];
02069                                         coordinate_3dnew[1] = -coordinate_3dnew[1];
02070                                         coordinate_3dnew[2] = -coordinate_3dnew[2];
02071                                         btq = conj(c1);
02072                                         } else {
02073                                         btq = c1;
02074                                         }
02075                                 int ixn = int(coordinate_3dnew[0] + 0.5 + nx) - nx;
02076                                 int iyn = int(coordinate_3dnew[1] + 0.5 + ny) - ny;
02077                                 int izn = int(coordinate_3dnew[2] + 0.5 + nz) - nz;
02078 
02079                                 int iza, iya;
02080                                 if (izn >= 0)  iza = izn + 1;
02081                                 else           iza = nz + izn + 1;
02082 
02083                                 if (iyn >= 0) iya = iyn + 1;
02084                                 else          iya = ny + iyn + 1;
02085 
02086                                 if(remove > 0 ) {
02087                                         cmplx(ixn,iya,iza) -= btq*float(mult);
02088                                         (*w)(ixn,iya,iza) -= ctf_value*ctf_value*mult;
02089                                         } else {
02090                                         cmplx(ixn,iya,iza) += btq*float(mult);
02091                                         (*w)(ixn,iya,iza) += ctf_value*ctf_value*mult;
02092                                         }
02093                                         
02094                                 }
02095                         }
02096                             
02097                 }
02098 
02099 
02100         //end insert rectanular fft
02101                 
02102         set_array_offsets(saved_offsets);
02103         myfft->set_array_offsets(myfft_saved_offsets);
02104         EXITFUNC;
02105 
02106 }
02107 
02108 
02109 /*
02110 Data::onelinenn_ctf(int j, int n, int n2,
02111                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
02112 
02113         int remove = bi->get_attr_default( "remove", 0 );
02114 
02115         int jp = (j >= 0) ? j+1 : n+j+1;
02116         // loop over x
02117         for (int i = 0; i <= n2; i++) {
02118                 int r2 = i*i+j*j;
02119                 if ( (r2<n*n/4) && !( (0==i) && (j<0) ) ) {
02120                         float  ctf = ctf_store::get_ctf( r2 );
02121                         float xnew = i*tf[0][0] + j*tf[1][0];
02122                         float ynew = i*tf[0][1] + j*tf[1][1];
02123                         float znew = i*tf[0][2] + j*tf[1][2];
02124                         std::complex<float> btq;
02125                         if (xnew < 0.) {
02126                                 xnew = -xnew;
02127                                 ynew = -ynew;
02128                                 znew = -znew;
02129                                 btq = conj(bi->cmplx(i,jp));
02130                         } else  btq = bi->cmplx(i,jp);
02131                         int ixn = int(xnew + 0.5 + n) - n;
02132                         int iyn = int(ynew + 0.5 + n) - n;
02133                         int izn = int(znew + 0.5 + n) - n;
02134                         if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
02135                                 if (ixn >= 0) {
02136                                         int iza, iya;
02137                                         if (izn >= 0)  iza = izn + 1;
02138                                         else           iza = n + izn + 1;
02139 
02140                                         if (iyn >= 0) iya = iyn + 1;
02141                                         else          iya = n + iyn + 1;
02142 
02143                                         if(remove > 0 ) {
02144                                             cmplx(ixn,iya,iza) -= btq*ctf*float(mult);
02145                                             (*w)(ixn,iya,iza) -= ctf*ctf*mult;
02146                                         } else {
02147                                             cmplx(ixn,iya,iza) += btq*ctf*float(mult);
02148                                             (*w)(ixn,iya,iza) += ctf*ctf*mult;
02149                                         }
02150 
02151                                        //       std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<ctf<<std::endl;
02152                                 } else {
02153                                         int izt, iyt;
02154                                         if (izn > 0) izt = n - izn + 1;
02155                                         else         izt = -izn + 1;
02156 
02157                                         if (iyn > 0) iyt = n - iyn + 1;
02158                                         else         iyt = -iyn + 1;
02159 
02160                                         if( remove > 0 ) {
02161                                             cmplx(-ixn,iyt,izt) -= conj(btq)*ctf*float(mult);
02162                                             (*w)(-ixn,iyt,izt) -= ctf*ctf*float(mult);
02163                                         } else {
02164                                             cmplx(-ixn,iyt,izt) += conj(btq)*ctf*float(mult);
02165                                             (*w)(-ixn,iyt,izt) += ctf*ctf*float(mult);
02166                                         }
02167 
02168                                         //      std::cout<<" *  " << j << "  " <<-ixn << "  " << iyt << "  " << izt << "  " << ctf <<std::endl;
02169                                 }
02170                         }
02171                 }
02172         }
02173 }
02174 */
02175 
02176 
02177 void EMData::nn_SSNR_ctf(EMData* wptr, EMData* wptr2, EMData* wptr3, EMData* myfft, const Transform& tf, int)
02178 {
02179         /***   Preparing terms for SSNR
02180               m_wvolume F^3D Wiener volume
02181              wptr   ctf^2
02182             wptr5  ctf^2*|P^2D->3D(F^3D)|^2
02183            wptr4  2*Real(conj(F_k^2D)*ctf*P^2D->3D(F^3D))
02184           wptr2  F_k^2D*conj(F_k^2D) or |F_k^2D|^2
02185           Kn is counted in the previous routine, and won't be
02186          calculated any more.
02187                                                     ***/
02188         ENTERFUNC;
02189         int nxc = attr_dict["nxc"];
02190         vector<int> saved_offsets = get_array_offsets();
02191         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
02192         set_array_offsets(0,1,1);
02193         myfft->set_array_offsets(0,1);
02194 
02195         Ctf* ctf = myfft->get_attr("ctf");
02196         ctf_store::init( ny, ctf );
02197         int iymin = is_fftodd() ? -ny/2 : -ny/2 + 1;
02198         int iymax = ny/2;
02199         int izmin = is_fftodd() ? -nz/2 : -nz/2 + 1;
02200         int izmax = nz/2;
02201 //      std::complex<float> tmpq, tmp2;
02202         for (int iy = iymin; iy <= iymax; iy++) {
02203                 int jp = iy >= 0 ? iy+1 : ny+iy+1; //checked, works for both odd and even
02204                 for (int ix = 0; ix <= nxc; ix++) {
02205                         int r2 = ix*ix+iy*iy;
02206                         if (( 4*r2 < ny*ny ) && !( ix == 0 && iy < 0 ) ) {
02207                                 float  ctf = ctf_store::get_ctf( r2 )*10.f;
02208                                 float xnew = ix*tf[0][0] + iy*tf[1][0];
02209                                 float ynew = ix*tf[0][1] + iy*tf[1][1];
02210                                 float znew = ix*tf[0][2] + iy*tf[1][2];
02211                                 std::complex<float> btq;
02212                                 if (xnew < 0.0) {
02213                                         xnew = -xnew; // ensures xnew>=0.0
02214                                         ynew = -ynew;
02215                                         znew = -znew;
02216                                         btq = conj(myfft->cmplx(ix,jp));
02217                                 } else  {
02218                                         btq = myfft->cmplx(ix,jp);
02219                                 }
02220                                 int ixn = int(xnew + 0.5 + nx) - nx; // ensures ixn >= 0
02221                                 int iyn = int(ynew + 0.5 + ny) - ny;
02222                                 int izn = int(znew + 0.5 + nz) - nz;
02223                                 if ((ixn <= nxc) && (iyn >= iymin) && (iyn <= iymax) && (izn >= izmin) && (izn <= izmax)) {
02224                                         if (ixn >= 0) {
02225                                                 int iza, iya;
02226                                                 if (izn >= 0) iza = izn + 1;
02227                                                 else          iza = nz + izn + 1;
02228 
02229                                                 if (iyn >= 0) iya = iyn + 1;
02230                                                 else          iya = ny + iyn + 1;
02231 
02232                                                 cmplx(ixn,iya,iza)    += btq*ctf;
02233                                                 (*wptr)(ixn,iya,iza)  += ctf*ctf;
02234                                                 (*wptr2)(ixn,iya,iza) += std::norm(btq);
02235                                                 (*wptr3)(ixn,iya,iza) += 1;
02236                                         } else {
02237                                                 int izt, iyt;
02238                                                 if (izn > 0)  izt = nz - izn + 1;
02239                                                 else          izt = -izn + 1;
02240 
02241                                                 if (iyn > 0) iyt = ny - iyn + 1;
02242                                                 else         iyt = -iyn + 1;
02243 
02244                                                 cmplx(-ixn,iyt,izt)    += std::conj(btq)*ctf;
02245                                                 (*wptr) (-ixn,iyt,izt) += ctf*ctf;
02246                                                 (*wptr2)(-ixn,iyt,izt) += std::norm(btq);
02247                                                 (*wptr3)(-ixn,iyt,izt) += 1;
02248                                         }
02249                                 }
02250                         }
02251                 }
02252         }
02253         set_array_offsets(saved_offsets);
02254         myfft->set_array_offsets(myfft_saved_offsets);
02255         if(ctf) {delete ctf; ctf=0;}
02256         EXITFUNC;
02257 }
02258 
02259 /*void EMData::nn_wiener(EMData* wptr, EMData* wptr3, EMData* myfft, const Transform& tf, int)
02260 {
02261      // Wiener volume calculating routine Counting Kn
02262 
02263         ENTERFUNC;
02264         int nxc = attr_dict["nxc"];
02265         vector<int> saved_offsets = get_array_offsets();
02266         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
02267         set_array_offsets(0,1,1);
02268         myfft->set_array_offsets(0,1);
02269         // if( ! ctf_store::inited() )
02270         float Cs           = myfft->get_attr( "Cs" );
02271         float pixel        = myfft->get_attr( "Pixel_size" );
02272         float voltage      = myfft->get_attr( "voltage");
02273         float amp_contrast = myfft->get_attr( "amp_contrast" );
02274         float b_factor     = 0.0;
02275         ctf_store::init( ny, voltage, pixel, Cs, amp_contrast, b_factor );
02276         float defocus = myfft->get_attr( "defocus" );
02277         int iymin = is_fftodd() ? -ny/2 : -ny/2 + 1 ;
02278         int iymax = ny/2;
02279         int izmin = is_fftodd() ? -nz/2 : -nz/2 + 1 ;
02280         int izmax = nz/2;
02281         for (int iy = iymin; iy <= iymax; iy++) {
02282                 int jp = iy >= 0 ? iy+1 : ny+iy+1; //checked, works for both odd and even
02283                 for (int ix = 0; ix <= nxc; ix++) {
02284                         int r2 = ix*ix+iy*iy;
02285                         if (( 4*r2 < ny*ny ) && !( ix == 0 && iy < 0 ) )
02286                         {
02287                                 float  ctf = ctf_store::get_ctf( defocus, r2 );
02288                                 float xnew = ix*tf[0][0] + iy*tf[1][0];
02289                                 float ynew = ix*tf[0][1] + iy*tf[1][1];
02290                                 float znew = ix*tf[0][2] + iy*tf[1][2];
02291                                 std::complex<float> btq;
02292                                 if (xnew < 0.0)
02293                                 {
02294                                         xnew = -xnew; // ensures xnew>=0.0
02295                                         ynew = -ynew;
02296                                         znew = -znew;
02297                                         btq = conj(myfft->cmplx(ix,jp));
02298                                 } else
02299                                 {
02300                                         btq = myfft->cmplx(ix,jp);
02301                                 }
02302                                 int ixn = int(xnew + 0.5 + nx) - nx; // ensures ixn >= 0
02303                                 int iyn = int(ynew + 0.5 + ny) - ny;
02304                                 int izn = int(znew + 0.5 + nz) - nz;
02305                                 if ((ixn <= nxc) && (iyn >= iymin) && (iyn <= iymax) && (izn >= izmin) && (izn <= izmax)) {
02306                                         if (ixn >= 0)
02307                                         {
02308                                                 int iza, iya;
02309                                                 if (izn >= 0)
02310                                                 {
02311                                                         iza = izn + 1;
02312                                                 } else
02313                                                 {
02314                                                         iza = nz + izn + 1;
02315                                                 }
02316                                                 if (iyn >= 0)
02317                                                 {
02318                                                         iya = iyn + 1;
02319                                                 } else
02320                                                 {
02321                                                         iya = ny + iyn + 1;
02322                                                 }
02323                                                 cmplx(ixn,iya,iza)    += btq*ctf;
02324                                                 (*wptr)(ixn,iya,iza)  += ctf*ctf;
02325                                                 (*wptr3)(ixn,iya,iza) += 1.0;
02326                                         }
02327                                         else
02328                                         {
02329                                                 int izt, iyt;
02330                                                 if (izn > 0)
02331                                                 {
02332                                                         izt = nz - izn + 1;
02333                                                 } else
02334                                                 {
02335                                                         izt = -izn + 1;
02336                                                 }
02337                                                 if (iyn > 0)
02338                                                 {
02339                                                         iyt = ny - iyn + 1;
02340                                                 } else
02341                                                 {
02342                                                         iyt = -iyn + 1;
02343                                                 }
02344                                                 cmplx(-ixn,iyt,izt)    += conj(btq)*ctf;
02345                                                 (*wptr)(-ixn,iyt,izt)  += ctf*ctf;
02346                                                 (*wptr3)(-ixn,iyt,izt) += 1.0;
02347                                         }
02348                                 }
02349                         }
02350                 }
02351         }
02352         set_array_offsets(saved_offsets);
02353         myfft->set_array_offsets(myfft_saved_offsets);
02354         EXITFUNC;
02355 }*/
02356 
02357 void EMData::symplane0_ctf(EMData* w) {
02358         ENTERFUNC;
02359         int nxc = attr_dict["nxc"];
02360         int n = nxc*2;
02361         // let's treat the local data as a matrix
02362         vector<int> saved_offsets = get_array_offsets();
02363         set_array_offsets(0,1,1);
02364         for (int iza = 2; iza <= nxc; iza++) {
02365                 for (int iya = 2; iya <= nxc; iya++) {
02366                         cmplx(0,iya,iza) += conj(cmplx(0,n-iya+2,n-iza+2));
02367                         (*w)(0,iya,iza) += (*w)(0,n-iya+2,n-iza+2);
02368                         cmplx(0,n-iya+2,n-iza+2) = conj(cmplx(0,iya,iza));
02369                         (*w)(0,n-iya+2,n-iza+2) = (*w)(0,iya,iza);
02370                         cmplx(0,n-iya+2,iza) += conj(cmplx(0,iya,n-iza+2));
02371                         (*w)(0,n-iya+2,iza) += (*w)(0,iya,n-iza+2);
02372                         cmplx(0,iya,n-iza+2) = conj(cmplx(0,n-iya+2,iza));
02373                         (*w)(0,iya,n-iza+2) = (*w)(0,n-iya+2,iza);
02374                 }
02375         }
02376         for (int iya = 2; iya <= nxc; iya++) {
02377                 cmplx(0,iya,1) += conj(cmplx(0,n-iya+2,1));
02378                 (*w)(0,iya,1) += (*w)(0,n-iya+2,1);
02379                 cmplx(0,n-iya+2,1) = conj(cmplx(0,iya,1));
02380                 (*w)(0,n-iya+2,1) = (*w)(0,iya,1);
02381         }
02382         for (int iza = 2; iza <= nxc; iza++) {
02383                 cmplx(0,1,iza) += conj(cmplx(0,1,n-iza+2));
02384                 (*w)(0,1,iza) += (*w)(0,1,n-iza+2);
02385                 cmplx(0,1,n-iza+2) = conj(cmplx(0,1,iza));
02386                 (*w)(0,1,n-iza+2) = (*w)(0,1,iza);
02387         }
02388         EXITFUNC;
02389 }
02390 
02391 void EMData::symplane0_rect(EMData* w) {
02392         ENTERFUNC;
02393         nx=get_xsize();
02394         ny=get_ysize();
02395         nz=get_zsize();
02396         int nzc=nz/2;
02397         int nyc=ny/2;
02398 
02399         
02400         // let's treat the local data as a matrix
02401         vector<int> saved_offsets = get_array_offsets();
02402         set_array_offsets(0,1,1);
02403         for (int iza = 2; iza <= nzc; iza++) {
02404                 for (int iya = 2; iya <= nyc; iya++) {
02405                         cmplx(0,iya,iza) += conj(cmplx(0,ny-iya+2,nz-iza+2));
02406                         (*w)(0,iya,iza) += (*w)(0,ny-iya+2,nz-iza+2);
02407                         cmplx(0,ny-iya+2,nz-iza+2) = conj(cmplx(0,iya,iza));
02408                         (*w)(0,ny-iya+2,nz-iza+2) = (*w)(0,iya,iza);
02409                         cmplx(0,ny-iya+2,iza) += conj(cmplx(0,iya,nz-iza+2));
02410                         (*w)(0,ny-iya+2,iza) += (*w)(0,iya,nz-iza+2);
02411                         cmplx(0,iya,nz-iza+2) = conj(cmplx(0,ny-iya+2,iza));
02412                         (*w)(0,iya,nz-iza+2) = (*w)(0,ny-iya+2,iza);
02413                 }
02414         }
02415         for (int iya = 2; iya <= nyc; iya++) {
02416                 cmplx(0,iya,1) += conj(cmplx(0,ny-iya+2,1));
02417                 (*w)(0,iya,1) += (*w)(0,ny-iya+2,1);
02418                 cmplx(0,ny-iya+2,1) = conj(cmplx(0,iya,1));
02419                 (*w)(0,ny-iya+2,1) = (*w)(0,iya,1);
02420         }
02421         for (int iza = 2; iza <= nzc; iza++) {
02422                 cmplx(0,1,iza) += conj(cmplx(0,1,nz-iza+2));
02423                 (*w)(0,1,iza) += (*w)(0,1,nz-iza+2);
02424                 cmplx(0,1,nz-iza+2) = conj(cmplx(0,1,iza));
02425                 (*w)(0,1,nz-iza+2) = (*w)(0,1,iza);
02426         }
02427         EXITFUNC;
02428 }
02429 
02430 EMData* EMData::rot_scale_trans2D(float angDeg, float delx, float dely, float scale) { // quadratic, no background, 2D
02431         float ang=angDeg*M_PI/180.0f;
02432         if (1 >= ny)
02433                 throw ImageDimensionException("Can't rotate 1D image");
02434         if (nz<2) {
02435                 vector<int> saved_offsets = get_array_offsets();
02436                 set_array_offsets(0,0,0);
02437                 if (0.0f == scale) scale = 1.0f; // silently fix common user error
02438                 EMData* ret = copy_head();
02439                 delx = restrict2(delx, nx);
02440                 dely = restrict2(dely, ny);
02441                 // center of image
02442                 int xc = nx/2;
02443                 int yc = ny/2;
02444                 // shifted center for rotation
02445                 float shiftxc = xc + delx;
02446                 float shiftyc = yc + dely;
02447                 // trig
02448                 float cang = cos(ang);
02449                 float sang = sin(ang);
02450                         for (int iy = 0; iy < ny; iy++) {
02451                                 float y = float(iy) - shiftyc;
02452                                 float ycang = y*cang/scale + yc;
02453                                 float ysang = -y*sang/scale + xc;
02454                                 for (int ix = 0; ix < nx; ix++) {
02455                                         float x = float(ix) - shiftxc;
02456                                         float xold = x*cang/scale + ysang ;
02457                                         float yold = x*sang/scale + ycang ;
02458                                         //  quadri is taking care of cyclic count
02459                                         (*ret)(ix,iy) = Util::quadri(xold+1.0f, yold+1.0f, nx, ny, get_data());
02460                                            //have to add one as quadri uses Fortran counting
02461                                 }
02462                         }
02463                 set_array_offsets(saved_offsets);
02464                 return ret;
02465         } else {
02466                 throw ImageDimensionException("Volume not currently supported");
02467         }
02468 }
02469 
02470 EMData* EMData::rot_scale_trans2D_background(float angDeg, float delx, float dely, float scale) { // quadratic, no background, 2D
02471     float ang=angDeg*M_PI/180.0f;
02472         if (1 >= ny)
02473                 throw ImageDimensionException("Can't rotate 1D image");
02474         if (nz<2) {
02475                 vector<int> saved_offsets = get_array_offsets();
02476                 set_array_offsets(0,0,0);
02477                 if (0.0f == scale) scale = 1.0f; // silently fix common user error
02478                 EMData* ret = copy_head();
02479                 delx = restrict2(delx, nx);
02480                 dely = restrict2(dely, ny);
02481                 // center of image
02482                 int xc = nx/2;
02483                 int yc = ny/2;
02484                 // shifted center for rotation
02485                 float shiftxc = xc + delx;
02486                 float shiftyc = yc + dely;
02487                 // trig
02488                 float cang = cos(ang);
02489                 float sang = sin(ang);
02490                         for (int iy = 0; iy < ny; iy++) {
02491                                 float y = float(iy) - shiftyc;
02492                                 float ycang = y*cang/scale + yc;
02493                                 float ysang = -y*sang/scale + xc;
02494                                 for (int ix = 0; ix < nx; ix++) {
02495                                         float x = float(ix) - shiftxc;
02496                                         float xold = x*cang/scale + ysang ;
02497                                         float yold = x*sang/scale + ycang ;
02498                                         //  in quadri_background, wrap around is not done circulantly; if (xold,yold) is not in the image, then it's replaced by (ix,iy)
02499                                         (*ret)(ix,iy) = Util::quadri_background(xold+1.0f, yold+1.0f, nx, ny, get_data(),ix+1,iy+1);
02500                                            //have to add one as quadri uses Fortran counting
02501                                 }
02502                         }
02503                 set_array_offsets(saved_offsets);
02504                 return ret;
02505         } else {
02506                 throw ImageDimensionException("Volume not currently supported");
02507         }
02508 }
02509 
02510 #define in(i,j,k)          in[i+(j+(k*ny))*(size_t)nx]
02511 EMData*
02512 EMData::rot_scale_trans(const Transform &RA) {
02513 
02514         EMData* ret = copy_head();
02515         float *in = this->get_data();
02516         vector<int> saved_offsets = get_array_offsets();
02517         set_array_offsets(0,0,0);
02518         Vec3f translations = RA.get_trans();
02519         Transform RAinv = RA.inverse();
02520 
02521         if (1 >= ny)  throw ImageDimensionException("Can't rotate 1D image");
02522         if (nz < 2) {
02523         float  p1, p2, p3, p4;
02524         float delx = translations.at(0);
02525         float dely = translations.at(1);
02526         delx = restrict2(delx, nx);
02527         dely = restrict2(dely, ny);
02528         int xc = nx/2;
02529         int yc = ny/2;
02530 //         shifted center for rotation
02531         float shiftxc = xc + delx;
02532         float shiftyc = yc + dely;
02533                 for (int iy = 0; iy < ny; iy++) {
02534                         float y = float(iy) - shiftyc;
02535                         float ysang = y*RAinv[0][1]+xc;
02536                         float ycang = y*RAinv[1][1]+yc;
02537                         for (int ix = 0; ix < nx; ix++) {
02538                                 float x = float(ix) - shiftxc;
02539                                 float xold = x*RAinv[0][0] + ysang;
02540                                 float yold = x*RAinv[1][0] + ycang;
02541 
02542                                 xold = restrict1(xold, nx);
02543                                 yold = restrict1(yold, ny);
02544 
02545                                 int xfloor = int(xold);
02546                                 int yfloor = int(yold);
02547                                 float t = xold-xfloor;
02548                                 float u = yold-yfloor;
02549                                 if(xfloor == nx -1 && yfloor == ny -1) {
02550 
02551                                     p1 =in[xfloor   + yfloor*ny];
02552                                         p2 =in[ yfloor*ny];
02553                                         p3 =in[0];
02554                                         p4 =in[xfloor];
02555                                 } else if(xfloor == nx - 1) {
02556 
02557                                         p1 =in[xfloor   + yfloor*ny];
02558                                         p2 =in[           yfloor*ny];
02559                                         p3 =in[          (yfloor+1)*ny];
02560                                         p4 =in[xfloor   + (yfloor+1)*ny];
02561                                 } else if(yfloor == ny - 1) {
02562 
02563                                         p1 =in[xfloor   + yfloor*ny];
02564                                         p2 =in[xfloor+1 + yfloor*ny];
02565                                         p3 =in[xfloor+1 ];
02566                                         p4 =in[xfloor   ];
02567                                 } else {
02568                                         p1 =in[xfloor   + yfloor*ny];
02569                                         p2 =in[xfloor+1 + yfloor*ny];
02570                                         p3 =in[xfloor+1 + (yfloor+1)*ny];
02571                                         p4 =in[xfloor   + (yfloor+1)*ny];
02572                                 }
02573                                 (*ret)(ix,iy) = p1 + u * ( p4 - p1) + t * ( p2 - p1 + u *(p3-p2-p4+p1));
02574                         } //ends x loop
02575                 } // ends y loop
02576                 set_array_offsets(saved_offsets);
02577                 return ret;
02578         } else {
02579 //               This begins the 3D version trilinear interpolation.
02580 
02581         float delx = translations.at(0);
02582         float dely = translations.at(1);
02583         float delz = translations.at(2);
02584         delx = restrict2(delx, nx);
02585         dely = restrict2(dely, ny);
02586         delz = restrict2(delz, nz);
02587         int xc = nx/2;
02588         int yc = ny/2;
02589         int zc = nz/2;
02590 //         shifted center for rotation
02591         float shiftxc = xc + delx;
02592         float shiftyc = yc + dely;
02593         float shiftzc = zc + delz;
02594 
02595                 for (int iz = 0; iz < nz; iz++) {
02596                         float z = float(iz) - shiftzc;
02597                         float xoldz = z*RAinv[0][2]+xc;
02598                         float yoldz = z*RAinv[1][2]+yc;
02599                         float zoldz = z*RAinv[2][2]+zc;
02600                         for (int iy = 0; iy < ny; iy++) {
02601                                 float y = float(iy) - shiftyc;
02602                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02603                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02604                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02605                                 for (int ix = 0; ix < nx; ix++) {
02606                                         float x = float(ix) - shiftxc;
02607                                         float xold = xoldzy + x*RAinv[0][0] ;
02608                                         float yold = yoldzy + x*RAinv[1][0] ;
02609                                         float zold = zoldzy + x*RAinv[2][0] ;
02610 
02611                                         xold = restrict1(xold, nx);
02612                                         yold = restrict1(yold, ny);
02613                                         zold = restrict1(zold, nz);
02614 
02615 
02616                                         int IOX = int(xold);
02617                                         int IOY = int(yold);
02618                                         int IOZ = int(zold);
02619 
02620                                         #ifdef _WIN32
02621                                         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
02622                                         #else
02623                                         int IOXp1 = std::min( nx-1 ,IOX+1);
02624                                         #endif  //_WIN32
02625 
02626                                         #ifdef _WIN32
02627                                         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
02628                                         #else
02629                                         int IOYp1 = std::min( ny-1 ,IOY+1);
02630                                         #endif  //_WIN32
02631 
02632                                         #ifdef _WIN32
02633                                         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
02634                                         #else
02635                                         int IOZp1 = std::min( nz-1 ,IOZ+1);
02636                                         #endif  //_WIN32
02637 
02638                                         float dx = xold-IOX;
02639                                         float dy = yold-IOY;
02640                                         float dz = zold-IOZ;
02641 
02642                                         float a1 = in(IOX,IOY,IOZ);
02643                                         float a2 = in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZ);
02644                                         float a3 = in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZ);
02645                                         float a4 = in(IOX,IOY,IOZp1) - in(IOX,IOY,IOZ);
02646                                         float a5 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOYp1,IOZ) + in(IOXp1,IOYp1,IOZ);
02647                                         float a6 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZp1) + in(IOXp1,IOY,IOZp1);
02648                                         float a7 = in(IOX,IOY,IOZ) - in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZp1) + in(IOX,IOYp1,IOZp1);
02649                                         float a8 = in(IOXp1,IOY,IOZ) + in(IOX,IOYp1,IOZ)+ in(IOX,IOY,IOZp1)
02650                                                         - in(IOX,IOY,IOZ)- in(IOXp1,IOYp1,IOZ) - in(IOXp1,IOY,IOZp1)
02651                                                         - in(IOX,IOYp1,IOZp1) + in(IOXp1,IOYp1,IOZp1);
02652                                         (*ret)(ix,iy,iz) = a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
02653                                 } //ends x loop
02654                         } // ends y loop
02655                 } // ends z loop
02656 
02657                 set_array_offsets(saved_offsets);
02658                 return ret;
02659 
02660 /*     This entire section has to go somewhere for quadratic 3D interpolation PAP 12/29/07
02661 //               This begins the 3D version triquadratic interpolation.
02662 
02663         float delx = translations.at(0);
02664         float dely = translations.at(1);
02665         float delz = translations.at(2);
02666         if(delx >= 0.0f) { delx = fmod(delx, float(nx));} else {delx = -fmod(-delx, float(nx));}
02667         if(dely >= 0.0f) { dely = fmod(dely, float(ny));} else {dely = -fmod(-dely, float(ny));}
02668         if(dely >= 0.0f) { delz = fmod(delz, float(nz));} else {delz = -fmod(-delz, float(nz));}
02669         int xc = nx/2;
02670         int yc = ny/2;
02671         int zc = nz/2;
02672 //         shifted center for rotation
02673         float shiftxc = xc + delx;
02674         float shiftyc = yc + dely;
02675         float shiftzc = zc + delz;
02676 //                  set up array to use later
02677 //
02678                 int xArr[27];
02679                 int yArr[27];
02680                 int zArr[27];
02681                 float fdata[27];
02682 
02683                 for (int iL=0; iL<27 ; iL++){  // need this indexing array later
02684                         xArr[iL]  =  (int) (fmod((float)iL,3.0f) - 1.0f);
02685                         yArr[iL]  =  (int)( fmod( ((float) (iL/3) ),3.0f)- 1.0f);
02686                         zArr[iL]  = ((int) (iL/9)  ) -1;
02687 //                      printf("iL=%d, \t xArr=%d, \t yArr=%d, \t zArr=%d \n",iL, xArr[iL],yArr[iL],zArr[iL]);
02688                 }
02689 
02690 //              for (int iz = 0; iz < nz; iz++) {for (int iy = 0; iy < ny; iy++) {for (int ix = 0; ix < nx; ix++) {
02691 //                    (*ret)(ix,iy,iz) = 0;}}}   // initialize returned data
02692 
02693                 for (int iz = 0; iz < nz; iz++) {
02694                         float z = float(iz) - shiftzc;
02695                         float xoldz = z*RAinv[0][2]+xc;
02696                         float yoldz = z*RAinv[1][2]+yc;
02697                         float zoldz = z*RAinv[2][2]+zc;
02698                         for (int iy = 0; iy < ny; iy++) {
02699                                 float y = float(iy) - shiftyc;
02700                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02701                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02702                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02703                                 for (int ix = 0; ix < nx; ix++) {
02704                                         float x = float(ix) - shiftxc;
02705                                         float xold = xoldzy + x*RAinv[0][0] ;
02706                                         float yold = yoldzy + x*RAinv[1][0] ;
02707                                         float zold = zoldzy + x*RAinv[2][0] ;
02708 
02709 
02710                                 if (xold < 0.0f) xold = fmod((int(xold/float(nx))+1)*nx-xold, float(nx));
02711                                 else if (xold > (float) (nx-1) ) xold = fmod(xold, float(nx));
02712                                 if (yold < 0.0f) yold =fmod((int(yold/float(ny))+1)*ny-yold, float(ny));
02713                                 else if (yold > (float) (ny-1) ) yold = fmod(yold, float(ny));
02714                                 if (zold < 0.0f) zold =fmod((int(zold/float(nz))+1)*nz-zold, float(nz));
02715                                 else if (zold > (float) (nz-1) ) zold = fmod(zold, float(nz));
02716 
02717                                 //  what follows does not accelerate the code; moreover, I doubt it is correct PAP 12/29/07
02718                                 //while ( xold >= (float)(nx) )  xold -= nx;
02719                                 //while ( xold < 0.0f )         xold += nx;
02720                                 //while ( yold >= (float)(ny) )  yold -= ny;
02721                                 //while ( yold < 0.0f )         yold += ny;
02722                                 //while ( zold >= (float)(nz) )  zold -= nz;
02723                                 //while ( zold < 0.0f )         zold += nz;
02724 
02725 //         This is currently coded the way  SPIDER coded it,
02726 //            changing floor to round  in the next 3 lines below may be better
02727 //                                      int IOX = (int) floor(xold); // This is the center of the array
02728 //                                      int IOY = (int) floor(yold ); // In the next loop we interpolate
02729 //                                      int IOZ = (int) floor(zold ); //  If floor is used dx is positive
02730                                         int IOX = int(xold);
02731                                         int IOY = int(yold);
02732                                         int IOZ = int(zold);
02733 
02734                                         float dx = xold-IOX; //remainder(xold,1);  //  now |dx| <= .5
02735                                         float dy = yold-IOY; //remainder(yold,1);
02736                                         float dz = zold-IOZ; //remainder(zold,1);
02737 
02738 //                                      printf(" IOX=%d \t IOY=%d \t IOZ=%d \n", IOX, IOY, IOZ);
02739 //                                      if (IOX>=0 && IOX<nx  && IOY>=0 && IOY < ny && IOZ >= 0 && IOZ < nz ) {
02740 //                                              ROTATED POSITION IS INSIDE OF VOLUME
02741 //                                              FIND INTENSITIES ON 3x3x3 COORDINATE GRID;
02742 //                                     Solution is wrapped
02743                                                 for  (int iL=0; iL<27 ; iL++){
02744                                                         int xCoor = (int) fmod(IOX+xArr[iL] + nx + .0001f, (float) nx);
02745                                                         int yCoor = (int) fmod(IOY+yArr[iL] + ny + .0001f, (float) ny);
02746                                                         int zCoor = (int) fmod(IOZ+zArr[iL] + nz + .0001f, (float) nz);
02747                                                         fdata[iL] = (*this)( xCoor, yCoor ,zCoor );
02748 //                                                      if (iy==iz && iz==0){printf(" fdata=%f \n", fdata[iL]);}
02749 //                                              }
02750                                         }
02751 
02752                                         (*ret)(ix,iy,iz) = Util::triquad(dx, dy, dz, fdata);
02753 //                                      (*ret)(ix,iy,iz) = Util:: trilinear_interpolate(fdata[13],fdata[14],fdata[16],
02754 //                                                                                      fdata[17],fdata[22],fdata[23],
02755 //                                                                                      fdata[25],fdata[26],dx, dy, dz);
02756 //      p1 iL=13,   xArr= 0,         yArr= 0,         zArr= 0
02757 //      p2 iL=14,   xArr= 1,         yArr= 0,         zArr= 0
02758 //      p3 iL=16,   xArr= 0,         yArr= 1,         zArr= 0
02759 //      p4 iL=17,   xArr= 1,         yArr= 1,         zArr= 0
02760 //      p5 iL=22,   xArr= 0,         yArr= 0,         zArr= 1
02761 //      p6 iL=23,   xArr= 1,         yArr= 0,         zArr= 1
02762 //      p7 iL=25,   xArr= 0,         yArr= 1,         zArr= 1
02763 //      p8 iL=26,   xArr= 1,         yArr= 1,         zArr= 1
02764 
02765 
02766 
02767                                 } //ends x loop
02768                         } // ends y loop
02769                 } // ends z loop
02770 
02771                 set_array_offsets(saved_offsets);
02772                 return ret;
02773 */
02774         }
02775 }
02776 #undef  in
02777 
02778 // new function added for background option
02779 #define in(i,j,k)          in[i+(j+(k*ny))*(size_t)nx]
02780 EMData*
02781 EMData::rot_scale_trans_background(const Transform &RA) {
02782         EMData* ret = copy_head();
02783         float *in = this->get_data();
02784         vector<int> saved_offsets = get_array_offsets();
02785         set_array_offsets(0,0,0);
02786         Vec3f translations = RA.get_trans();
02787         Transform RAinv = RA.inverse();
02788 
02789         if (1 >= ny)  throw ImageDimensionException("Can't rotate 1D image");
02790         if (nz < 2) {
02791         float  p1, p2, p3, p4;
02792         float delx = translations.at(0);
02793         float dely = translations.at(1);
02794         delx = restrict2(delx, nx);
02795         dely = restrict2(dely, ny);
02796         int xc = nx/2;
02797         int yc = ny/2;
02798 //         shifted center for rotation
02799         float shiftxc = xc + delx;
02800         float shiftyc = yc + dely;
02801                 for (int iy = 0; iy < ny; iy++) {
02802                         float y = float(iy) - shiftyc;
02803                         float ysang = y*RAinv[0][1]+xc;
02804                         float ycang = y*RAinv[1][1]+yc;
02805                         for (int ix = 0; ix < nx; ix++) {
02806                                 float x = float(ix) - shiftxc;
02807                                 float xold = x*RAinv[0][0] + ysang;
02808                                 float yold = x*RAinv[1][0] + ycang;
02809 
02810                                 // if (xold,yold) is outside the image, then let xold = ix and yold = iy
02811 
02812                 if ( (xold < 0.0f) || (xold >= (float)(nx)) || (yold < 0.0f) || (yold >= (float)(ny)) ){
02813                                     xold = (float)ix;
02814                                         yold = (float)iy;
02815                                 }
02816 
02817                                 int xfloor = int(xold);
02818                                 int yfloor = int(yold);
02819                                 float t = xold-xfloor;
02820                                 float u = yold-yfloor;
02821                                 if(xfloor == nx -1 && yfloor == ny -1) {
02822 
02823                                     p1 =in[xfloor   + yfloor*ny];
02824                                         p2 =in[ yfloor*ny];
02825                                         p3 =in[0];
02826                                         p4 =in[xfloor];
02827                                 } else if(xfloor == nx - 1) {
02828 
02829                                         p1 =in[xfloor   + yfloor*ny];
02830                                         p2 =in[           yfloor*ny];
02831                                         p3 =in[          (yfloor+1)*ny];
02832                                         p4 =in[xfloor   + (yfloor+1)*ny];
02833                                 } else if(yfloor == ny - 1) {
02834 
02835                                         p1 =in[xfloor   + yfloor*ny];
02836                                         p2 =in[xfloor+1 + yfloor*ny];
02837                                         p3 =in[xfloor+1 ];
02838                                         p4 =in[xfloor   ];
02839                                 } else {
02840 
02841                                         p1 =in[xfloor   + yfloor*ny];
02842                                         p2 =in[xfloor+1 + yfloor*ny];
02843                                         p3 =in[xfloor+1 + (yfloor+1)*ny];
02844                                         p4 =in[xfloor   + (yfloor+1)*ny];
02845                                 }
02846                                 (*ret)(ix,iy) = p1 + u * ( p4 - p1) + t * ( p2 - p1 + u *(p3-p2-p4+p1));
02847                         } //ends x loop
02848                 } // ends y loop
02849                 set_array_offsets(saved_offsets);
02850                 return ret;
02851         } else {
02852 //               This begins the 3D version trilinear interpolation.
02853 
02854         float delx = translations.at(0);
02855         float dely = translations.at(1);
02856         float delz = translations.at(2);
02857         delx = restrict2(delx, nx);
02858         dely = restrict2(dely, ny);
02859         delz = restrict2(delz, nz);
02860         int xc = nx/2;
02861         int yc = ny/2;
02862         int zc = nz/2;
02863 //         shifted center for rotation
02864         float shiftxc = xc + delx;
02865         float shiftyc = yc + dely;
02866         float shiftzc = zc + delz;
02867 
02868                 for (int iz = 0; iz < nz; iz++) {
02869                         float z = float(iz) - shiftzc;
02870                         float xoldz = z*RAinv[0][2]+xc;
02871                         float yoldz = z*RAinv[1][2]+yc;
02872                         float zoldz = z*RAinv[2][2]+zc;
02873                         for (int iy = 0; iy < ny; iy++) {
02874                                 float y = float(iy) - shiftyc;
02875                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02876                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02877                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02878                                 for (int ix = 0; ix < nx; ix++) {
02879                                         float x = float(ix) - shiftxc;
02880                                         float xold = xoldzy + x*RAinv[0][0] ;
02881                                         float yold = yoldzy + x*RAinv[1][0] ;
02882                                         float zold = zoldzy + x*RAinv[2][0] ;
02883 
02884                                         // if (xold,yold,zold) is outside the image, then let xold = ix, yold = iy and zold=iz
02885 
02886                     if ( (xold < 0.0f) || (xold >= (float)(nx)) || (yold < 0.0f) || (yold >= (float)(ny))  || (zold < 0.0f) || (zold >= (float)(nz)) ){
02887                                          xold = (float)ix;
02888                                              yold = (float)iy;
02889                                                  zold = (float)iz;
02890                                         }
02891 
02892                                         int IOX = int(xold);
02893                                         int IOY = int(yold);
02894                                         int IOZ = int(zold);
02895 
02896                                         #ifdef _WIN32
02897                                         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
02898                                         #else
02899                                         int IOXp1 = std::min( nx-1 ,IOX+1);
02900                                         #endif  //_WIN32
02901 
02902                                         #ifdef _WIN32
02903                                         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
02904                                         #else
02905                                         int IOYp1 = std::min( ny-1 ,IOY+1);
02906                                         #endif  //_WIN32
02907 
02908                                         #ifdef _WIN32
02909                                         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
02910                                         #else
02911                                         int IOZp1 = std::min( nz-1 ,IOZ+1);
02912                                         #endif  //_WIN32
02913 
02914                                         float dx = xold-IOX;
02915                                         float dy = yold-IOY;
02916                                         float dz = zold-IOZ;
02917 
02918                                         float a1 = in(IOX,IOY,IOZ);
02919                                         float a2 = in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZ);
02920                                         float a3 = in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZ);
02921                                         float a4 = in(IOX,IOY,IOZp1) - in(IOX,IOY,IOZ);
02922                                         float a5 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOYp1,IOZ) + in(IOXp1,IOYp1,IOZ);
02923                                         float a6 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZp1) + in(IOXp1,IOY,IOZp1);
02924                                         float a7 = in(IOX,IOY,IOZ) - in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZp1) + in(IOX,IOYp1,IOZp1);
02925                                         float a8 = in(IOXp1,IOY,IOZ) + in(IOX,IOYp1,IOZ)+ in(IOX,IOY,IOZp1)
02926                                                         - in(IOX,IOY,IOZ)- in(IOXp1,IOYp1,IOZ) - in(IOXp1,IOY,IOZp1)
02927                                                         - in(IOX,IOYp1,IOZp1) + in(IOXp1,IOYp1,IOZp1);
02928                                         (*ret)(ix,iy,iz) = a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
02929                                 } //ends x loop
02930                         } // ends y loop
02931                 } // ends z loop
02932 
02933                 set_array_offsets(saved_offsets);
02934                 return ret;
02935 
02936         }
02937 }
02938 #undef  in
02939 
02940 
02941 /*
02942 EMData*
02943 EMData::rot_scale_conv(float ang, float delx, float dely, Util::KaiserBessel& kb) {
02944         int nxn, nyn, nzn;
02945         const float scale=0.5;
02946         float  sum, w;
02947         if (1 >= ny)
02948                 throw ImageDimensionException("Can't rotate 1D image");
02949         if (1 < nz)
02950                 throw ImageDimensionException("Volume not currently supported");
02951         nxn=nx/2;nyn=ny/2;nzn=nz/2;
02952 
02953         int K = kb.get_window_size();
02954         int kbmin = -K/2;
02955         int kbmax = -kbmin;
02956         int kbc = kbmax+1;
02957         vector<int> saved_offsets = get_array_offsets();
02958         set_array_offsets(0,0,0);
02959         EMData* ret = new EMData();
02960 #ifdef _WIN32
02961         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
02962 #else
02963         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
02964 #endif  //_WIN32
02965         ret->to_zero();  //we will leave margins zeroed.
02966         delx = fmod(delx, float(nxn));
02967         dely = fmod(dely, float(nyn));
02968         // center of big image,
02969         int xc = nxn;
02970         int ixs = nxn%2;  // extra shift on account of odd-sized images
02971         int yc = nyn;
02972         int iys = nyn%2;
02973         // center of small image
02974         int xcn = nxn/2;
02975         int ycn = nyn/2;
02976         // shifted center for rotation
02977         float shiftxc = xcn + delx;
02978         float shiftyc = ycn + dely;
02979         // bounds if origin at center
02980         float ymin = -ny/2.0f;
02981         float xmin = -nx/2.0f;
02982         float ymax = -ymin;
02983         float xmax = -xmin;
02984         if (0 == nx%2) xmax--;
02985         if (0 == ny%2) ymax--;
02986         // trig
02987         float cang = cos(ang);
02988         float sang = sin(ang);
02989                 for (int iy = 0; iy < nyn; iy++) {
02990                         float y = float(iy) - shiftyc;
02991                         float ycang = y*cang/scale + yc;
02992                         float ysang = -y*sang/scale + xc;
02993                         for (int ix = 0; ix < nxn; ix++) {
02994                                 float x = float(ix) - shiftxc;
02995                                 float xold = x*cang/scale + ysang-ixs;// have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
02996                                 float yold = x*sang/scale + ycang-iys;
02997                                 int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
02998                                      sum=0.0f;    w=0.0f;
02999                                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03000                                   for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03001                                   float q = kb.i0win_tab(xold - inxold-m1)*kb.i0win_tab(yold - inyold-m2);
03002                                   sum += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;}}
03003                                 }else{
03004                                   for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03005                                   float q =kb.i0win_tab(xold - inxold-m1)*kb.i0win_tab(yold - inyold-m2);
03006                                   sum += (*this)(inxold+m1,inyold+m2)*q;w+=q;}}
03007                                 }
03008                                 (*ret)(ix,iy)=sum/w;
03009                         }
03010                 }
03011         set_array_offsets(saved_offsets);
03012         return ret;
03013 }
03014 */
03015 
03016 EMData* EMData::rot_scale_conv(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03017         int nxn, nyn, nzn;
03018         if(scale_input == 0.0f) scale_input = 1.0f;
03019         //const float scale=0.5;
03020         float  scale = 0.5f*scale_input;
03021         float  sum, w;
03022         if (1 >= ny)
03023                 throw ImageDimensionException("Can't rotate 1D image");
03024         if (1 < nz)
03025                 throw ImageDimensionException("Volume not currently supported");
03026         nxn=nx/2;nyn=ny/2;nzn=nz/2;
03027 
03028         int K = kb.get_window_size();
03029         int kbmin = -K/2;
03030         int kbmax = -kbmin;
03031         int kbc = kbmax+1;
03032         vector<int> saved_offsets = get_array_offsets();
03033         set_array_offsets(0,0,0);
03034         EMData* ret = this->copy_head();
03035 #ifdef _WIN32
03036         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03037 #else
03038         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03039 #endif  //_WIN32
03040         //ret->to_zero();  //we will leave margins zeroed.
03041         delx = restrict2(delx, nx);
03042         dely = restrict2(dely, ny);
03043         // center of big image,
03044         int xc = nxn;
03045         int ixs = nxn%2;  // extra shift on account of odd-sized images
03046         int yc = nyn;
03047         int iys = nyn%2;
03048         // center of small image
03049         int xcn = nxn/2;
03050         int ycn = nyn/2;
03051         // shifted center for rotation
03052         float shiftxc = xcn + delx;
03053         float shiftyc = ycn + dely;
03054         // bounds if origin at center
03055         float ymin = -ny/2.0f;
03056         float xmin = -nx/2.0f;
03057         float ymax = -ymin;
03058         float xmax = -xmin;
03059         if (0 == nx%2) xmax--;
03060         if (0 == ny%2) ymax--;
03061 
03062         float   *t = (float*)calloc(kbmax-kbmin+1, sizeof(float));
03063 
03064         // trig
03065         float cang = cos(ang);
03066         float sang = sin(ang);
03067         for (int iy = 0; iy < nyn; iy++) {
03068                 float y = float(iy) - shiftyc;
03069                 float ycang = y*cang/scale + yc;
03070                 float ysang = -y*sang/scale + xc;
03071                 for (int ix = 0; ix < nxn; ix++) {
03072                         float x = float(ix) - shiftxc;
03073                         float xold = x*cang/scale + ysang-ixs;// have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
03074                         float yold = x*sang/scale + ycang-iys;
03075 
03076                         xold = restrict1(xold, nx);
03077                         yold = restrict1(yold, ny);
03078 
03079                         int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
03080                         sum=0.0f;    w=0.0f;
03081                         for (int m1 =kbmin; m1 <=kbmax; m1++) t[m1-kbmin] = kb.i0win_tab(xold - inxold-m1);
03082                         if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03083                                 for (int m2 =kbmin; m2 <=kbmax; m2++) {
03084                                         float qt = kb.i0win_tab(yold - inyold-m2);
03085                                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03086                                                 float q = t[m1-kbmin]*qt;
03087                                                 sum += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;
03088                                         }
03089                                 }
03090                         } else {
03091                                 for (int m2 =kbmin; m2 <=kbmax; m2++) {
03092                                         float qt = kb.i0win_tab(yold - inyold-m2);
03093                                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03094                                                 float q = t[m1-kbmin]*qt;
03095                                                 sum += (*this)(inxold+m1,inyold+m2)*q; w+=q;}
03096                                         }
03097                         }
03098                         (*ret)(ix,iy)=sum/w;
03099                 }
03100         }
03101         if (t) free(t);
03102         set_array_offsets(saved_offsets);
03103         return ret;
03104 }
03105 
03106 // Notes by Yang on 10/02/07
03107 // This function is at first just a test, but I found it is slightly faster (about 10%) than rot_scale_conv_new(), so I decided to retain it.
03108 EMData* EMData::rot_scale_conv7(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03109         int nxn, nyn, nzn;
03110         float  scale = 0.5f*scale_input;
03111         float  sum, w;
03112         if (1 >= ny)
03113                 throw ImageDimensionException("Can't rotate 1D image");
03114         if (1 < nz)
03115                 throw ImageDimensionException("Volume not currently supported");
03116         nxn = nx/2; nyn=ny/2; nzn=nz/2;
03117 
03118         int K = kb.get_window_size();
03119         int kbmin = -K/2;
03120         int kbmax = -kbmin;
03121         int kbc = kbmax+1;
03122         vector<int> saved_offsets = get_array_offsets();
03123         set_array_offsets(0,0,0);
03124         EMData* ret = this->copy_head();
03125 #ifdef _WIN32
03126         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03127 #else
03128         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03129 #endif  //_WIN32
03130         //ret->to_zero();  //we will leave margins zeroed.
03131         delx = restrict2(delx, nx);
03132         dely = restrict2(dely, ny);
03133         // center of big image,
03134         int xc = nxn;
03135         int ixs = nxn%2;  // extra shift on account of odd-sized images
03136         int yc = nyn;
03137         int iys = nyn%2;
03138         // center of small image
03139         int xcn = nxn/2;
03140         int ycn = nyn/2;
03141         // shifted center for rotation
03142         float shiftxc = xcn + delx;
03143         float shiftyc = ycn + dely;
03144         // bounds if origin at center
03145         float ymin = -ny/2.0f;
03146         float xmin = -nx/2.0f;
03147         float ymax = -ymin;
03148         float xmax = -xmin;
03149         if (0 == nx%2) xmax--;
03150         if (0 == ny%2) ymax--;
03151 
03152         float   *t = (float*)calloc(kbmax-kbmin+1, sizeof(float));
03153 
03154         // trig
03155         float cang = cos(ang);
03156         float sang = sin(ang);
03157         for (int iy = 0; iy < nyn; iy++) {
03158                 float y = float(iy) - shiftyc;
03159                 float ycang = y*cang/scale + yc;
03160                 float ysang = -y*sang/scale + xc;
03161                 for (int ix = 0; ix < nxn; ix++) {
03162                         float x = float(ix) - shiftxc;
03163                         float xold = x*cang/scale + ysang-ixs;// have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
03164                         float yold = x*sang/scale + ycang-iys;
03165 
03166                         xold = restrict1(xold, nx);
03167                         yold = restrict1(yold, ny);
03168 
03169                         int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
03170                         sum=0.0f;    w=0.0f;
03171 
03172                         float tablex1 = kb.i0win_tab(xold-inxold+3);
03173                         float tablex2 = kb.i0win_tab(xold-inxold+2);
03174                         float tablex3 = kb.i0win_tab(xold-inxold+1);
03175                         float tablex4 = kb.i0win_tab(xold-inxold);
03176                         float tablex5 = kb.i0win_tab(xold-inxold-1);
03177                         float tablex6 = kb.i0win_tab(xold-inxold-2);
03178                         float tablex7 = kb.i0win_tab(xold-inxold-3);
03179 
03180                         float tabley1 = kb.i0win_tab(yold-inyold+3);
03181                         float tabley2 = kb.i0win_tab(yold-inyold+2);
03182                         float tabley3 = kb.i0win_tab(yold-inyold+1);
03183                         float tabley4 = kb.i0win_tab(yold-inyold);
03184                         float tabley5 = kb.i0win_tab(yold-inyold-1);
03185                         float tabley6 = kb.i0win_tab(yold-inyold-2);
03186                         float tabley7 = kb.i0win_tab(yold-inyold-3);
03187 
03188                         int x1, x2, x3, x4, x5, x6, x7, y1, y2, y3, y4, y5, y6, y7;
03189 
03190                         if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03191                                 x1 = (inxold-3+nx)%nx;
03192                                 x2 = (inxold-2+nx)%nx;
03193                                 x3 = (inxold-1+nx)%nx;
03194                                 x4 = (inxold  +nx)%nx;
03195                                 x5 = (inxold+1+nx)%nx;
03196                                 x6 = (inxold+2+nx)%nx;
03197                                 x7 = (inxold+3+nx)%nx;
03198 
03199                                 y1 = (inyold-3+ny)%ny;
03200                                 y2 = (inyold-2+ny)%ny;
03201                                 y3 = (inyold-1+ny)%ny;
03202                                 y4 = (inyold  +ny)%ny;
03203                                 y5 = (inyold+1+ny)%ny;
03204                                 y6 = (inyold+2+ny)%ny;
03205                                 y7 = (inyold+3+ny)%ny;
03206                         } else {
03207                                 x1 = inxold-3;
03208                                 x2 = inxold-2;
03209                                 x3 = inxold-1;
03210                                 x4 = inxold;
03211                                 x5 = inxold+1;
03212                                 x6 = inxold+2;
03213                                 x7 = inxold+3;
03214 
03215                                 y1 = inyold-3;
03216                                 y2 = inyold-2;
03217                                 y3 = inyold-1;
03218                                 y4 = inyold;
03219                                 y5 = inyold+1;
03220                                 y6 = inyold+2;
03221                                 y7 = inyold+3;
03222                         }
03223                         sum    =   ( (*this)(x1,y1)*tablex1 + (*this)(x2,y1)*tablex2 + (*this)(x3,y1)*tablex3 +
03224                                      (*this)(x4,y1)*tablex4 + (*this)(x5,y1)*tablex5 + (*this)(x6,y1)*tablex6 +
03225                                      (*this)(x7,y1)*tablex7 ) * tabley1 +
03226                                    ( (*this)(x1,y2)*tablex1 + (*this)(x2,y2)*tablex2 + (*this)(x3,y2)*tablex3 +
03227                                      (*this)(x4,y2)*tablex4 + (*this)(x5,y2)*tablex5 + (*this)(x6,y2)*tablex6 +
03228                                      (*this)(x7,y2)*tablex7 ) * tabley2 +
03229                                    ( (*this)(x1,y3)*tablex1 + (*this)(x2,y3)*tablex2 + (*this)(x3,y3)*tablex3 +
03230                                      (*this)(x4,y3)*tablex4 + (*this)(x5,y3)*tablex5 + (*this)(x6,y3)*tablex6 +
03231                                      (*this)(x7,y3)*tablex7 ) * tabley3 +
03232                                    ( (*this)(x1,y4)*tablex1 + (*this)(x2,y4)*tablex2 + (*this)(x3,y4)*tablex3 +
03233                                      (*this)(x4,y4)*tablex4 + (*this)(x5,y4)*tablex5 + (*this)(x6,y4)*tablex6 +
03234                                      (*this)(x7,y4)*tablex7 ) * tabley4 +
03235                                    ( (*this)(x1,y5)*tablex1 + (*this)(x2,y5)*tablex2 + (*this)(x3,y5)*tablex3 +
03236                                      (*this)(x4,y5)*tablex4 + (*this)(x5,y5)*tablex5 + (*this)(x6,y5)*tablex6 +
03237                                      (*this)(x7,y5)*tablex7 ) * tabley5 +
03238                                    ( (*this)(x1,y6)*tablex1 + (*this)(x2,y6)*tablex2 + (*this)(x3,y6)*tablex3 +
03239                                      (*this)(x4,y6)*tablex4 + (*this)(x5,y6)*tablex5 + (*this)(x6,y6)*tablex6 +
03240                                      (*this)(x7,y6)*tablex7 ) * tabley6 +
03241                                    ( (*this)(x1,y7)*tablex1 + (*this)(x2,y7)*tablex2 + (*this)(x3,y7)*tablex3 +
03242                                      (*this)(x4,y7)*tablex4 + (*this)(x5,y7)*tablex5 + (*this)(x6,y7)*tablex6 +
03243                                      (*this)(x7,y7)*tablex7 ) * tabley7;
03244 
03245                         w = (tablex1+tablex2+tablex3+tablex4+tablex5+tablex6+tablex7) *
03246                             (tabley1+tabley2+tabley3+tabley4+tabley5+tabley6+tabley7);
03247 
03248                         (*ret)(ix,iy)=sum/w;
03249                 }
03250         }
03251         if (t) free(t);
03252         set_array_offsets(saved_offsets);
03253         return ret;
03254 }
03255 
03256 EMData* EMData::downsample(Util::sincBlackman& kb, float scale) {
03257 
03258         /*int M = kb.get_sB_size();
03259         int kbmin = -M/2;
03260         int kbmax = -kbmin;*/
03261 
03262         int nxn, nyn, nzn;
03263         nxn = (int)(nx*scale); nyn = (int)(ny*scale); nzn = (int)(nz*scale);
03264 
03265         vector<int> saved_offsets = get_array_offsets();
03266         set_array_offsets(0,0,0);
03267         EMData* ret = this->copy_head();
03268 #ifdef _WIN32
03269         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03270 #else
03271         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03272 #endif  //_WIN32
03273         ret->to_zero();  //we will leave margins zeroed.
03274 
03275         // scan new, find pixels in old
03276         for (int iy =0; iy < nyn; iy++) {
03277                 float y = float(iy)/scale;
03278                 for (int ix = 0; ix < nxn; ix++) {
03279                         float x = float(ix)/scale;
03280                         (*ret)(ix,iy) = this->get_pixel_filtered(x, y, 1.0f, kb);
03281                 }
03282         }
03283         set_array_offsets(saved_offsets);
03284         return ret;
03285 }
03286 
03287 
03288 EMData* EMData::rot_scale_conv_new(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03289 
03290         if (scale_input == 0.0f) scale_input = 1.0f;
03291         float  scale = 0.5f*scale_input;
03292 
03293         if (1 >= ny)
03294                 throw ImageDimensionException("Can't rotate 1D image");
03295         if (1 < nz)
03296                 throw ImageDimensionException("Use rot_scale_conv_new_3D for volumes");
03297         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03298 
03299         vector<int> saved_offsets = get_array_offsets();
03300         set_array_offsets(0,0,0);
03301         EMData* ret = this->copy_head();
03302 #ifdef _WIN32
03303         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03304 #else
03305         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03306 #endif  //_WIN32
03307         //ret->to_zero();  //we will leave margins zeroed.
03308         delx = restrict2(delx, nx);
03309         dely = restrict2(dely, ny);
03310         // center of big image,
03311         int xc = nxn;
03312         int ixs = nxn%2;  // extra shift on account of odd-sized images
03313         int yc = nyn;
03314         int iys = nyn%2;
03315         // center of small image
03316         int xcn = nxn/2;
03317         int ycn = nyn/2;
03318         // shifted center for rotation
03319         float shiftxc = xcn + delx;
03320         float shiftyc = ycn + dely;
03321         // bounds if origin at center
03322         float ymin = -ny/2.0f;
03323         float xmin = -nx/2.0f;
03324         float ymax = -ymin;
03325         float xmax = -xmin;
03326         if (0 == nx%2) xmax--;
03327         if (0 == ny%2) ymax--;
03328 
03329         float* data = this->get_data();
03330 
03331         float cang = cos(ang);
03332         float sang = sin(ang);
03333         for (int iy = 0; iy < nyn; iy++) {
03334                 float y = float(iy) - shiftyc;
03335                 float ycang = y*cang/scale + yc;
03336                 float ysang = -y*sang/scale + xc;
03337                 for (int ix = 0; ix < nxn; ix++) {
03338                         float x = float(ix) - shiftxc;
03339                         float xold = x*cang/scale + ysang-ixs;// have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
03340                         float yold = x*sang/scale + ycang-iys;
03341 
03342                         (*ret)(ix,iy) = Util::get_pixel_conv_new(nx, ny, 1, xold, yold, 1, data, kb);
03343                 }
03344         }
03345         set_array_offsets(saved_offsets);
03346         return ret;
03347 }
03348 
03349 EMData* EMData::rot_scale_conv_new_3D(float phi, float theta, float psi, float delx, float dely, float delz, Util::KaiserBessel& kb, float scale_input, bool wrap) {
03350 
03351         if (scale_input == 0.0f) scale_input = 1.0f;
03352         float  scale = 0.5f*scale_input;
03353 
03354         if (1 >= ny)
03355                 throw ImageDimensionException("Can't rotate 1D image");
03356         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03357 
03358         vector<int> saved_offsets = get_array_offsets();
03359         set_array_offsets(0,0,0);
03360         EMData* ret = this->copy_head();
03361 #ifdef _WIN32
03362         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03363 #else
03364         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03365 #endif  //_WIN32
03366         //ret->to_zero();  //we will leave margins zeroed.
03367         if(wrap){
03368                 delx = restrict2(delx, nx);
03369                 dely = restrict2(dely, ny);
03370                 delz = restrict2(delz, nz);
03371         }
03372         // center of big image,
03373         int xc = nxn;
03374         int ixs = nxn%2;  // extra shift on account of odd-sized images
03375         int yc = nyn;
03376         int iys = nyn%2;
03377         int zc = nzn;
03378         int izs = nzn%2;
03379         // center of small image
03380         int xcn = nxn/2;
03381         int ycn = nyn/2;
03382         int zcn = nzn/2;
03383         // shifted center for rotation
03384         float shiftxc = xcn + delx;
03385         float shiftyc = ycn + dely;
03386         float shiftzc = zcn + delz;
03387         // bounds if origin at center
03388         float zmin = -nz/2.0f;
03389         float ymin = -ny/2.0f;
03390         float xmin = -nx/2.0f;
03391         float zmax = -zmin;
03392         float ymax = -ymin;
03393         float xmax = -xmin;
03394         if (0 == nx%2) xmax--;
03395         if (0 == ny%2) ymax--;
03396         if (0 == nz%2) zmax--;
03397 
03398         float* data = this->get_data();
03399 
03400         float cf = cos(phi);   float sf = sin(phi);
03401         float ct = cos(theta); float st = sin(theta);
03402         float cp = cos(psi);   float sp = sin(psi);
03403         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
03404         float a11 =  cp*ct*cf-sp*sf; float a12 =  cp*ct*sf+sp*cf; float a13 = -cp*st;
03405         float a21 = -sp*ct*cf-cp*sf; float a22 = -sp*ct*sf+cp*cf; float a23 =  sp*st;
03406         float a31 =  st*cf;          float a32 =  st*sf;          float a33 =  ct;
03407         for (int iz = 0; iz < nzn; iz++) {
03408                 float z = (float(iz) - shiftzc)/scale;
03409                 float zco1 = a31*z+xc;
03410                 float zco2 = a32*z+yc;
03411                 float zco3 = a33*z+zc;
03412                 for (int iy = 0; iy < nyn; iy++) {
03413                         float y = (float(iy) - shiftyc)/scale;
03414                         float yco1 = zco1+a21*y;
03415                         float yco2 = zco2+a22*y;
03416                         float yco3 = zco3+a23*y;
03417                         for (int ix = 0; ix < nxn; ix++) {
03418                                 float x = (float(ix) - shiftxc)/scale;
03419                                 float xold = yco1+a11*x-ixs; //have to add the fraction on account of odd-sized images for which Fourier zero-padding changes the center location
03420                                 float yold = yco2+a12*x-iys;
03421                                 float zold = yco3+a13*x-izs;
03422                                 if(!wrap && (xold<0.0 || xold>nx-1 || yold<0.0 || yold>ny-1 || zold<0.0 || zold>nz-1))
03423                                         (*ret)(ix,iy,iz) = 0.0;
03424                                 else
03425                                         (*ret)(ix,iy,iz) = Util::get_pixel_conv_new(nx, ny, nz, xold, yold, zold, data, kb);
03426                         }
03427                 }
03428         }
03429         set_array_offsets(saved_offsets);
03430         return ret;
03431 }
03432 
03433 EMData* EMData::rot_scale_conv_new_background(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03434 
03435         int nxn, nyn, nzn;
03436 
03437         if (scale_input == 0.0f) scale_input = 1.0f;
03438         float  scale = 0.5f*scale_input;
03439 
03440         if (1 >= ny)
03441                 throw ImageDimensionException("Can't rotate 1D image");
03442         if (1 < nz)
03443                 throw ImageDimensionException("Use rot_scale_conv_new_background_3D for volumes");
03444         nxn = nx/2; nyn = ny/2; nzn = nz/2;
03445 
03446         vector<int> saved_offsets = get_array_offsets();
03447         set_array_offsets(0,0,0);
03448         EMData* ret = this->copy_head();
03449 #ifdef _WIN32
03450         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03451 #else
03452         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03453 #endif  //_WIN32
03454         //ret->to_zero();  //we will leave margins zeroed.
03455         delx = restrict2(delx, nx);
03456         dely = restrict2(dely, ny);
03457         // center of big image,
03458         int xc = nxn;
03459         int ixs = nxn%2;  // extra shift on account of odd-sized images
03460         int yc = nyn;
03461         int iys = nyn%2;
03462         // center of small image
03463         int xcn = nxn/2;
03464         int ycn = nyn/2;
03465         // shifted center for rotation
03466         float shiftxc = xcn + delx;
03467         float shiftyc = ycn + dely;
03468         // bounds if origin at center
03469         float ymin = -ny/2.0f;
03470         float xmin = -nx/2.0f;
03471         float ymax = -ymin;
03472         float xmax = -xmin;
03473         if (0 == nx%2) xmax--;
03474         if (0 == ny%2) ymax--;
03475 
03476         float* data = this->get_data();
03477 
03478         // trig
03479         float cang = cos(ang);
03480         float sang = sin(ang);
03481         for (int iy = 0; iy < nyn; iy++) {
03482                 float y = float(iy) - shiftyc;
03483                 float ycang = y*cang/scale + yc;
03484                 float ysang = -y*sang/scale + xc;
03485                 for (int ix = 0; ix < nxn; ix++) {
03486                         float x = float(ix) - shiftxc;
03487                         float xold = x*cang/scale + ysang-ixs;// have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
03488                         float yold = x*sang/scale + ycang-iys;
03489 
03490                         (*ret)(ix,iy) = Util::get_pixel_conv_new_background(nx, ny, 1, xold, yold, 1, data, kb, ix, iy);
03491                 }
03492         }
03493         set_array_offsets(saved_offsets);
03494         return ret;
03495 }
03496 
03497 EMData* EMData::rot_scale_conv_new_background_3D(float phi, float theta, float psi, float delx, float dely, float delz, Util::KaiserBessel& kb, float scale_input, bool wrap) {
03498 
03499         if (scale_input == 0.0f) scale_input = 1.0f;
03500         float  scale = 0.5f*scale_input;
03501 
03502         if (1 >= ny)
03503                 throw ImageDimensionException("Can't rotate 1D image");
03504         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03505 
03506         vector<int> saved_offsets = get_array_offsets();
03507         set_array_offsets(0,0,0);
03508         EMData* ret = this->copy_head();
03509 #ifdef _WIN32
03510         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03511 #else
03512         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03513 #endif  //_WIN32
03514         //ret->to_zero();  //we will leave margins zeroed.
03515         if (wrap){
03516                 delx = restrict2(delx, nx);
03517                 dely = restrict2(dely, ny);
03518                 delz = restrict2(delz, nz);
03519         }
03520         // center of big image,
03521         int xc = nxn;
03522         int ixs = nxn%2;  // extra shift on account of odd-sized images
03523         int yc = nyn;
03524         int iys = nyn%2;
03525         int zc = nzn;
03526         int izs = nzn%2;
03527         // center of small image
03528         int xcn = nxn/2;
03529         int ycn = nyn/2;
03530         int zcn = nzn/2;
03531         // shifted center for rotation
03532         float shiftxc = xcn + delx;
03533         float shiftyc = ycn + dely;
03534         float shiftzc = zcn + delz;
03535         // bounds if origin at center
03536         float zmin = -nz/2.0f;
03537         float ymin = -ny/2.0f;
03538         float xmin = -nx/2.0f;
03539         float zmax = -zmin;
03540         float ymax = -ymin;
03541         float xmax = -xmin;
03542         if (0 == nx%2) xmax--;
03543         if (0 == ny%2) ymax--;
03544         if (0 == nz%2) zmax--;
03545 
03546         float* data = this->get_data();
03547 
03548         float cf = cos(phi);   float sf = sin(phi);
03549         float ct = cos(theta); float st = sin(theta);
03550         float cp = cos(psi);   float sp = sin(psi);
03551         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
03552         float a11 =  cp*ct*cf-sp*sf; float a12 =  cp*ct*sf+sp*cf; float a13 = -cp*st;
03553         float a21 = -sp*ct*cf-cp*sf; float a22 = -sp*ct*sf+cp*cf; float a23 =  sp*st;
03554         float a31 =  st*cf;          float a32 =  st*sf;          float a33 =  ct;
03555         for (int iz = 0; iz < nzn; iz++) {
03556                 float z = (float(iz) - shiftzc)/scale;
03557                 float zco1 = a31*z+xc;
03558                 float zco2 = a32*z+yc;
03559                 float zco3 = a33*z+zc;
03560                 for (int iy = 0; iy < nyn; iy++) {
03561                         float y = (float(iy) - shiftyc)/scale;
03562                         float yco1 = zco1+a21*y;
03563                         float yco2 = zco2+a22*y;
03564                         float yco3 = zco3+a23*y;
03565                         for (int ix = 0; ix < nxn; ix++) {
03566                                 float x = (float(ix) - shiftxc)/scale;
03567                                 float xold = yco1+a11*x-ixs; //have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
03568                                 float yold = yco2+a12*x-iys;
03569                                 float zold = yco3+a13*x-izs;
03570                                 if(!wrap && (xold<0.0 || xold>nx-1 || yold<0.0 || yold>ny-1 || zold<0.0 || zold>nz-1))
03571                                         (*ret)(ix,iy,iz) = 0.0;
03572                                 else
03573                                         (*ret)(ix,iy,iz) = Util::get_pixel_conv_new_background(nx, ny, nz, xold, yold, zold, data, kb, ix, iy);
03574                         }
03575                 }
03576         }
03577         set_array_offsets(saved_offsets);
03578         return ret;
03579 }
03580 
03581 
03582 float  EMData::get_pixel_conv(float delx, float dely, float delz, Util::KaiserBessel& kb) {
03583 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03584 
03585         int K     = kb.get_window_size();
03586         int kbmin = -K/2;
03587         int kbmax = -kbmin;
03588         int kbc   = kbmax+1;
03589 
03590         float pixel =0.0f;
03591         float w=0.0f;
03592 
03593         delx = restrict2(delx, nx);
03594         int inxold = int(Util::round(delx));
03595         if(ny<2) {  //1D
03596                 if(inxold <= kbc || inxold >=nx-kbc-2 )  {
03597                         //  loop for ends
03598                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03599                                 float q = kb.i0win_tab(delx - inxold-m1);
03600                                 pixel += (*this)((inxold+m1+nx)%nx)*q; w+=q;
03601                         }
03602                 } else {
03603                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03604                                 float q = kb.i0win_tab(delx - inxold-m1);
03605                                 pixel += (*this)(inxold+m1)*q; w+=q;
03606                         }
03607                 }
03608 
03609         } else if(nz<2) {  // 2D
03610                 dely = restrict2(dely, ny);
03611                 int inyold = int(Util::round(dely));
03612                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03613                         //  loop for strips
03614                         for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03615                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2);
03616                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;}
03617                         }
03618                 } else {
03619                         for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03620                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2);
03621                                 pixel += (*this)(inxold+m1,inyold+m2)*q; w+=q;}
03622                         }
03623                 }
03624         } else {  //  3D
03625                 dely = restrict2(dely, ny);
03626                 int inyold = int(Util::round(dely));
03627                 delz = restrict2(delz, nz);
03628                 int inzold = int(Util::round(delz));
03629                     //cout << inxold<<"  "<< kbc<<"  "<< nx-kbc-2<<"  "<< endl;
03630                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2  || inzold <= kbc || inzold >=nz-kbc-2 )  {
03631                         //  loop for strips
03632                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03633                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2)*kb.i0win_tab(delz - inzold-m3);
03634                                 //cout << "BB  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)<< endl;
03635                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)*q ;w+=q;}}
03636                         }
03637                 } else {
03638                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03639                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2)*kb.i0win_tab(delz - inzold-m3);
03640                                 //cout << "OO  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)(inxold+m1,inyold+m2,inzold+m3)<< endl;
03641                                 pixel += (*this)(inxold+m1,inyold+m2,inzold+m3)*q; w+=q;}}
03642                         }
03643                 }
03644         }
03645         return pixel/w;
03646 }
03647 
03648 
03649 float  EMData::get_pixel_filtered(float delx, float dely, float, Util::sincBlackman& kb) {
03650 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03651 
03652         int K     = kb.get_sB_size();
03653         int kbmin = -K/2;
03654         int kbmax = -kbmin;
03655         int kbc   = kbmax+1;
03656 
03657         float pixel =0.0f;
03658         float w=0.0f;
03659 
03660         //delx = restrict2(delx, nx);   //  In this function the old location is always within the      image
03661         int inxold = int(Util::round(delx));
03662         /*if(ny<2) {  //1D
03663                 if(inxold <= kbc || inxold >=nx-kbc-2 )  {
03664                         //  loop for ends
03665                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03666                                 float q = kb.sBwin_tab(delx - inxold-m1);
03667                                 pixel += (*this)((inxold+m1+nx)%nx)*q; w+=q;
03668                         }
03669                 } else {
03670                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03671                                 float q = kb.sBwin_tab(delx - inxold-m1);
03672                                 pixel += (*this)(inxold+m1)*q; w+=q;
03673                         }
03674                 }
03675 
03676         } else if(nz<2) {  // 2D*/
03677                 //dely = restrict2(dely, ny);
03678                 int inyold = int(Util::round(dely));
03679                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03680                         //  loop for strips
03681                         for (int m2 =kbmin; m2 <=kbmax; m2++){
03682                                 float t = kb.sBwin_tab(dely - inyold-m2);
03683                                 for (int m1 =kbmin; m1 <=kbmax; m1++) {
03684                                         float q = kb.sBwin_tab(delx - inxold-m1)*t;
03685                                         pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q;
03686                                         w += q;
03687                                 }
03688                         }
03689                 } else {
03690                         for (int m2 =kbmin; m2 <=kbmax; m2++){
03691                                 float t = kb.sBwin_tab(dely - inyold-m2);
03692                                 for (int m1 =kbmin; m1 <=kbmax; m1++) {
03693                                         float q = kb.sBwin_tab(delx - inxold-m1)*t;
03694                                         pixel += (*this)(inxold+m1,inyold+m2)*q;
03695                                         w += q;
03696                                 }
03697                         }
03698                 }
03699         /*} else {  //  3D
03700                 dely = restrict2(dely, ny);
03701                 int inyold = int(Util::round(dely));
03702                 delz = restrict2(delz, nz);
03703                 int inzold = int(Util::round(delz));
03704                     //cout << inxold<<"  "<< kbc<<"  "<< nx-kbc-2<<"  "<< endl;
03705                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2  || inzold <= kbc || inzold >=nz-kbc-2 )  {
03706                         //  loop for strips
03707                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03708                                 float q = kb.sBwin_tab(delx - inxold-m1)*kb.sBwin_tab(dely - inyold-m2)*kb.sBwin_tab(delz - inzold-m3);
03709                                 //cout << "BB  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)<< endl;
03710                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)*q ;w+=q;}}
03711                         }
03712                 } else {
03713                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03714                                 float q = kb.sBwin_tab(delx - inxold-m1)*kb.sBwin_tab(dely - inyold-m2)*kb.sBwin_tab(delz - inzold-m3);
03715                                 //cout << "OO  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)(inxold+m1,inyold+m2,inzold+m3)<< endl;
03716                                 pixel += (*this)(inxold+m1,inyold+m2,inzold+m3)*q; w+=q;}}
03717                         }
03718                 }
03719         }*/
03720         return pixel/w;
03721 }
03722 
03723 // Note by Yang on 10/02/07
03724 // get_pixel_conv7() is equivalent to get_pixel_conv_new(), however, it is written in this way such that it can be used in python directly
03725 // By the way, get_pixel_conv_new() is a faster version of get_pixel_conv(), I have done a lot of testing and show that their results are the same.
03726 float  EMData::get_pixel_conv7(float delx, float dely, float delz, Util::KaiserBessel& kb) {
03727 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03728 
03729         float *image=(this->get_data());
03730         int nx = this->get_xsize();
03731         int ny = this->get_ysize();
03732         int nz = this->get_zsize();
03733 
03734         float result;
03735 
03736         result = Util::get_pixel_conv_new(nx,ny,nz,delx,dely,delz,image,kb);
03737         return result;
03738 }
03739 
03740 float EMData::getconvpt2d_kbi0(float x, float y, Util::KaiserBessel::kbi0_win win, int size) {
03741         const int nxhalf = nx/2;
03742         const int nyhalf = ny/2;
03743         const int bd = size/2;
03744         float* wxarr = new float[size];
03745         float* wyarr = new float[size];
03746         float* wx = wxarr + bd; // wx[-bd] = wxarr[0]
03747         float* wy = wyarr + bd;
03748         int ixc = int(x + 0.5f*Util::sgn(x));
03749         int iyc = int(y + 0.5f*Util::sgn(y));
03750         if (abs(ixc) > nxhalf)
03751                 throw InvalidValueException(ixc, "getconv: X value out of range");
03752         if (abs(iyc) > nyhalf)
03753                 throw InvalidValueException(ixc, "getconv: Y value out of range");
03754         for (int i = -bd; i <= bd; i++) {
03755                 int iyp = iyc + i;
03756                 wy[i] = win(y - iyp);
03757                 int ixp = ixc + i;
03758                 wx[i] = win(x - ixp);
03759         }
03760         vector<int> saved_offsets = get_array_offsets();
03761         set_array_offsets(-nxhalf, -nyhalf);
03762         float conv = 0.f, wsum = 0.f;
03763         for (int iy = -bd; iy <= bd; iy++) {
03764                 int iyp = iyc + iy;
03765                 for (int ix = -bd; ix <= bd; ix++) {
03766                         int ixp = ixc + ix;
03767                         float wg = wx[ix]*wy[iy];
03768                         conv += (*this)(ixp,iyp)*wg;
03769                         wsum += wg;
03770                 }
03771         }
03772         set_array_offsets(saved_offsets);
03773         delete [] wxarr;
03774         delete [] wyarr;
03775         //return conv/wsum;
03776         return conv;
03777 }
03778 
03779 std::complex<float> EMData::extractpoint(float nuxnew, float nuynew, Util::KaiserBessel& kb) {
03780         if (2 != get_ndim())
03781                 throw ImageDimensionException("extractpoint needs a 2-D image.");
03782         if (!is_complex())
03783                 throw ImageFormatException("extractpoint requires a fourier image");
03784         int nxreal = nx - 2;
03785         if (nxreal != ny)
03786                 throw ImageDimensionException("extractpoint requires ny == nx");
03787         int nhalf = nxreal/2;
03788         int kbsize = kb.get_window_size();
03789         int kbmin = -kbsize/2;
03790         int kbmax = -kbmin;
03791         bool flip = (nuxnew < 0.f);
03792         if (flip) {
03793                 nuxnew *= -1;
03794                 nuynew *= -1;
03795         }
03796         // put (xnew,ynew) on a grid.  The indices will be wrong for
03797         // the Fourier elements in the image, but the grid sizing will
03798         // be correct.
03799         int ixn = int(Util::round(nuxnew));
03800         int iyn = int(Util::round(nuynew));
03801         // set up some temporary weighting arrays
03802         float* wy0 = new float[kbmax - kbmin + 1];
03803         float* wy = wy0 - kbmin; // wy[kbmin:kbmax]
03804         float* wx0 = new float[kbmax - kbmin + 1];
03805         float* wx = wx0 - kbmin;
03806         for (int i = kbmin; i <= kbmax; i++) {
03807                         int iyp = iyn + i;
03808                         wy[i] = kb.i0win_tab(nuynew - iyp);
03809                         int ixp = ixn + i;
03810                         wx[i] = kb.i0win_tab(nuxnew - ixp);
03811         }
03812         // restrict loops to non-zero elements
03813         int iymin = 0;
03814         for (int iy = kbmin; iy <= -1; iy++) {
03815                 if (wy[iy] != 0.f) {
03816                         iymin = iy;
03817                         break;
03818                 }
03819         }
03820         int iymax = 0;
03821         for (int iy = kbmax; iy >= 1; iy--) {
03822                 if (wy[iy] != 0.f) {
03823                         iymax = iy;
03824                         break;
03825                 }
03826         }
03827         int ixmin = 0;
03828         for (int ix = kbmin; ix <= -1; ix++) {
03829                 if (wx[ix] != 0.f) {
03830                         ixmin = ix;
03831                         break;
03832                 }
03833         }
03834         int ixmax = 0;
03835         for (int ix = kbmax; ix >= 1; ix--) {
03836                 if (wx[ix] != 0.f) {
03837                         ixmax = ix;
03838                         break;
03839                 }
03840         }
03841         float wsum = 0.0f;
03842         for (int iy = iymin; iy <= iymax; iy++)
03843                 for (int ix = ixmin; ix <= ixmax; ix++)
03844                         wsum += wx[ix]*wy[iy];
03845         std::complex<float> result(0.f,0.f);
03846         if ((ixn >= -kbmin) && (ixn <= nhalf-1-kbmax) && (iyn >= -nhalf-kbmin) && (iyn <= nhalf-1-kbmax)) {
03847                 // (xin,yin) not within window border from the edge
03848                 for (int iy = iymin; iy <= iymax; iy++) {
03849                         int iyp = iyn + iy;
03850                         for (int ix = ixmin; ix <= ixmax; ix++) {
03851                                 int ixp = ixn + ix;
03852                                 float w = wx[ix]*wy[iy];
03853                                 std::complex<float> val = cmplx(ixp,iyp);
03854                                 result += val*w;
03855                         }
03856                 }
03857         } else {
03858                 // points that "stick out"
03859                 for (int iy = iymin; iy <= iymax; iy++) {
03860                         int iyp = iyn + iy;
03861                         for (int ix = ixmin; ix <= ixmax; ix++) {
03862                                 int ixp = ixn + ix;
03863                                 bool mirror = false;
03864                                 int ixt= ixp, iyt= iyp;
03865                                 if (ixt < 0) {
03866                                         ixt = -ixt;
03867                                         iyt = -iyt;
03868                                         mirror = !mirror;
03869                                 }
03870                                 if (ixt > nhalf) {
03871                                         ixt = nxreal - ixt;
03872                                         iyt = -iyt;
03873                                         mirror = !mirror;
03874                                 }
03875                                 if (iyt > nhalf-1)  iyt -= nxreal;
03876                                 if (iyt < -nhalf)   iyt += nxreal;
03877                                 float w = wx[ix]*wy[iy];
03878                                 std::complex<float> val = this->cmplx(ixt,iyt);
03879                                 if (mirror)  result += conj(val)*w;
03880                                 else         result += val*w;
03881                         }
03882                 }
03883         }
03884         if (flip)  result = conj(result)/wsum;
03885         else       result /= wsum;
03886         delete [] wx0;
03887         delete [] wy0;
03888         return result;
03889 }
03890 
03891 EMData* EMData::extractline(Util::KaiserBessel& kb, float nuxnew, float nuynew)
03892 {
03893         if (!is_complex())
03894                 throw ImageFormatException("extractline requires a fourier image");
03895         if (nx%2 != 0)
03896                 throw ImageDimensionException("extractline requires nx to be even");
03897         int nxreal = nx - 2;
03898         if (nxreal != ny)
03899                 throw ImageDimensionException("extractline requires ny == nx");
03900         // build complex result image
03901         EMData* res = new EMData();
03902         res->set_size(nx,1,1);
03903         res->to_zero();
03904         res->set_complex(true);
03905         res->set_fftodd(false);
03906         res->set_fftpad(true);
03907         res->set_ri(true);
03908         // Array offsets: (0..nhalf,-nhalf..nhalf-1)
03909         int n = nxreal;
03910         int nhalf = n/2;
03911         vector<int> saved_offsets = get_array_offsets();
03912         set_array_offsets(0,-nhalf,-nhalf);
03913 
03914         // set up some temporary weighting arrays
03915         int kbsize = kb.get_window_size();
03916         int kbmin = -kbsize/2;
03917         int kbmax = -kbmin;
03918         float* wy0 = new float[kbmax - kbmin + 1];
03919         float* wy = wy0 - kbmin; // wy[kbmin:kbmax]
03920         float* wx0 = new float[kbmax - kbmin + 1];
03921         float* wx = wx0 - kbmin;
03922 
03923         int   count = 0;
03924         float wsum = 0.f;
03925         bool  flip = (nuxnew < 0.f);
03926 
03927         for (int jx = 0; jx <= nhalf; jx++) {
03928                 float xnew = jx*nuxnew, ynew = jx*nuynew;
03929                 count++;
03930                 std::complex<float> btq(0.f,0.f);
03931                 if (flip) {
03932                         xnew = -xnew;
03933                         ynew = -ynew;
03934                 }
03935                 int ixn = int(Util::round(xnew));
03936                 int iyn = int(Util::round(ynew));
03937                 // populate weight arrays
03938                 for (int i=kbmin; i <= kbmax; i++) {
03939                         int iyp = iyn + i;
03940                         wy[i] = kb.i0win_tab(ynew - iyp);
03941                         int ixp = ixn + i;
03942                         wx[i] = kb.i0win_tab(xnew - ixp);
03943                 }
03944                 // restrict weight arrays to non-zero elements
03945 
03946                 int lnby = 0;
03947                 for (int iy = kbmin; iy <= -1; iy++) {
03948                         if (wy[iy] != 0.f) {
03949                                 lnby = iy;
03950                                 break;
03951                         }
03952                 }
03953                 int lney = 0;
03954                 for (int iy = kbmax; iy >= 1; iy--) {
03955                         if (wy[iy] != 0.f) {
03956                                 lney = iy;
03957                                 break;
03958                         }
03959                 }
03960                 int lnbx = 0;
03961                 for (int ix = kbmin; ix <= -1; ix++) {
03962                         if (wx[ix] != 0.f) {
03963                                 lnbx = ix;
03964                                 break;
03965                         }
03966                 }
03967                 int lnex = 0;
03968                 for (int ix = kbmax; ix >= 1; ix--) {
03969                         if (wx[ix] != 0.f) {
03970                                 lnex = ix;
03971                                 break;
03972                         }
03973                 }
03974                 if (ixn >= -kbmin && ixn <= nhalf-1-kbmax
03975                                 && iyn >= -nhalf-kbmin && iyn <= nhalf-1-kbmax) {
03976                         // interior points
03977                         for (int ly=lnby; ly<=lney; ly++) {
03978                                 int iyp = iyn + ly;
03979                                 for (int lx=lnbx; lx<=lnex; lx++) {
03980                                         int ixp = ixn + lx;
03981                                         float wg = wx[lx]*wy[ly];
03982                                         btq += cmplx(ixp,iyp)*wg;
03983                                         wsum += wg;
03984                                 }
03985                         }
03986                 } else {
03987                         // points "sticking out"
03988                         for (int ly=lnby; ly<=lney; ly++) {
03989                                 int iyp = iyn + ly;
03990                                 for (int lx=lnbx; lx<=lnex; lx++) {
03991                                         int ixp = ixn + lx;
03992                                         float wg = wx[lx]*wy[ly];
03993                                         bool mirror = false;
03994                                         int ixt(ixp), iyt(iyp);
03995                                         if (ixt > nhalf || ixt < -nhalf) {
03996                                                 ixt = Util::sgn(ixt)*(n - abs(ixt));
03997                                                 iyt = -iyt;
03998                                                 mirror = !mirror;
03999                                         }
04000                                         if (iyt >= nhalf || iyt < -nhalf) {
04001                                                 if (ixt != 0) {
04002                                                         ixt = -ixt;
04003                                                         iyt = Util::sgn(iyt)*(n - abs(iyt));
04004                                                         mirror = !mirror;
04005                                                 } else {
04006                                                         iyt -= n*Util::sgn(iyt);
04007                                                 }
04008                                         }
04009                                         if (ixt < 0) {
04010                                                 ixt = -ixt;
04011                                                 iyt = -iyt;
04012                                                 mirror = !mirror;
04013                                         }
04014                                         if (iyt == nhalf) iyt = -nhalf;
04015                                         if (mirror) btq += conj(cmplx(ixt,iyt))*wg;
04016                                         else        btq += cmplx(ixt,iyt)*wg;
04017                                         wsum += wg;
04018                                 }
04019                         }
04020                 }
04021                 if (flip) res->cmplx(jx) = conj(btq);
04022                 else      res->cmplx(jx) = btq;
04023         }
04024         for (int jx = 0; jx <= nhalf; jx++)  res->cmplx(jx) *= count/wsum;
04025 
04026         delete[] wx0; delete[] wy0;
04027         set_array_offsets(saved_offsets);
04028         res->set_array_offsets(0,0,0);
04029         return res;
04030 }
04031 
04032 
04034 inline void swapx(float* a, float* b, float* temp, size_t nbytes) {
04035         memcpy(temp, a, nbytes);
04036         memcpy(a, b, nbytes);
04037         memcpy(b, temp, nbytes);
04038 }
04039 
04040 void EMData::fft_shuffle() {
04041         if (!is_complex())
04042                 throw ImageFormatException("fft_shuffle requires a fourier image");
04043         vector<int> offsets = get_array_offsets();
04044         set_array_offsets(); // clear offsets before shuffling
04045         EMData& self = *this;
04046         int nyhalf = ny/2;
04047         int nzhalf = nz/2;
04048         int nbytes = nx*sizeof(float);
04049         float* temp = new float[nx];
04050         for (int iz=0; iz < nz; iz++)
04051                 for (int iy=0; iy < nyhalf; iy++)
04052                         swapx(&self(0,iy,iz),&self(0,iy+nyhalf,iz),temp,nbytes);
04053         if (nz > 1) {
04054                 for (int iy=0; iy < ny; iy++)
04055                         for (int iz=0; iz < nzhalf; iz++)
04056                                 swapx(&self(0,iy,iz),&self(0,iy,iz+nzhalf),temp,nbytes);
04057         }
04058         set_shuffled(!is_shuffled()); // toggle
04059         set_array_offsets(offsets); // reset offsets
04060         update();
04061         delete[] temp;
04062 }
04063 
04064 void EMData::pad_corner(float *pad_image) {
04065         size_t nbytes = nx*sizeof(float);
04066         for (int iy=0; iy<ny; iy++)
04067                 memcpy(&(*this)(0,iy), pad_image+3+(iy+3)*nx, nbytes);
04068 }
04069 
04070 void EMData::shuffle_pad_corner(float *pad_image) {
04071         int nyhalf = ny/2;
04072         size_t nbytes = nx*sizeof(float);
04073         for (int iy = 0; iy < nyhalf; iy++)
04074                 memcpy(&(*this)(0,iy), pad_image+6+(iy+nyhalf+3)*nx, nbytes);
04075         for (int iy = nyhalf; iy < ny; iy++)
04076                 memcpy(&(*this)(0,iy), pad_image+6+(iy-nyhalf+3)*nx, nbytes);
04077 }
04078 
04079 #define    QUADPI                       3.141592653589793238462643383279502884197
04080 #define    DGR_TO_RAD                   QUADPI/180
04081 
04082 // We tried to pad the Fourier image to reduce the stick out points, howover it is not very efficient.
04083 /*
04084 EMData* EMData::fouriergridrot2d(float ang, float scale, Util::KaiserBessel& kb) {
04085         if (2 != get_ndim())
04086                 throw ImageDimensionException("fouriergridrot2d needs a 2-D image.");
04087         if (!is_complex())
04088                 throw ImageFormatException("fouriergridrot2d requires a fourier image");
04089         int nxreal = nx - 2 + int(is_fftodd());
04090         if (nxreal != ny)
04091                 throw ImageDimensionException("fouriergridrot2d requires ny == nx(real)");
04092         if (0 != nxreal%2)
04093                 throw ImageDimensionException("fouriergridrot2d needs an even image.");
04094         if (scale == 0.0f) scale = 1.0f;
04095         int nxhalf = nxreal/2;
04096         int nyhalf = ny/2;
04097 
04098         EMData *pad_this = new EMData();
04099         pad_this->set_size(nx+12, ny+6);
04100         //pad_this->to_zero();
04101         float* pad_image = pad_this-> get_data();
04102 
04103         if (!is_shuffled()) {
04104                 shuffle_pad_corner(pad_image);
04105         } else {
04106                 pad_corner(pad_image);
04107         }
04108         pad_this -> set_array_offsets(-6, -nyhalf-3);
04109 
04110         EMData* result = copy_head();
04111         set_array_offsets(0,-nyhalf);
04112         result->set_array_offsets(0,-nyhalf);
04113 
04114         ang = ang*DGR_TO_RAD;
04115         float cang = cos(ang);
04116         float sang = sin(ang);
04117         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04118                 float ycang = iy*cang;
04119                 float ysang = iy*sang;
04120                 for (int ix = 0; ix <= nxhalf; ix++) {
04121                         float nuxold = (ix*cang - ysang)*scale;
04122                         float nuyold = (ix*sang + ycang)*scale;
04123                         result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, pad_this, kb);
04124                 }
04125         }
04126         result->set_array_offsets();
04127         result->fft_shuffle(); // reset to an unshuffled result
04128         result->update();
04129         set_array_offsets();
04130         fft_shuffle(); // reset to an unshuffled complex image
04131         return result;
04132 }*/
04133 
04134 
04135 EMData* EMData::fouriergridrot2d(float ang, float scale, Util::KaiserBessel& kb) {
04136         if (2 != get_ndim())
04137                 throw ImageDimensionException("fouriergridrot2d needs a 2-D image.");
04138         if (!is_complex())
04139                 throw ImageFormatException("fouriergridrot2d requires a fourier image");
04140         int nxreal = nx - 2 + int(is_fftodd());
04141         if (nxreal != ny)
04142                 throw ImageDimensionException("fouriergridrot2d requires ny == nx(real)");
04143         if (0 != nxreal%2)
04144                 throw ImageDimensionException("fouriergridrot2d needs an even image.");
04145         if (scale == 0.0f) scale = 1.0f;
04146         int nxhalf = nxreal/2;
04147         int nyhalf = ny/2;
04148         float cir = (float)((nxhalf-1)*(nxhalf-1));
04149 
04150         if (!is_shuffled()) fft_shuffle();
04151 
04152         EMData* result = copy_head();
04153         set_array_offsets(0,-nyhalf);
04154         result->set_array_offsets(0,-nyhalf);
04155 
04156 
04157 
04158         ang = ang*(float)DGR_TO_RAD;
04159         float cang = cos(ang);
04160         float sang = sin(ang);
04161         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04162                 float ycang = iy*cang;
04163                 float ysang = iy*sang;
04164                 for (int ix = 0; ix <= nxhalf; ix++) {
04165                         float nuxold = (ix*cang - ysang)*scale;
04166                         float nuyold = (ix*sang + ycang)*scale;
04167                         if (nuxold*nuxold+nuyold*nuyold<cir) result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, this, kb);
04168                         //result->cmplx(ix,iy) = extractpoint(nuxold, nuyold, kb);
04169                 }
04170         }
04171         result->set_array_offsets();
04172         result->fft_shuffle(); // reset to an unshuffled result
04173         result->update();
04174         set_array_offsets();
04175         fft_shuffle(); // reset to an unshuffled complex image
04176         return result;
04177 }
04178 
04179 EMData* EMData::fouriergridrot_shift2d(float ang, float sx, float sy, Util::KaiserBessel& kb) {
04180         if (2 != get_ndim())
04181                 throw ImageDimensionException("fouriergridrot_shift2d needs a 2-D image.");
04182         if (!is_complex())
04183                 throw ImageFormatException("fouriergridrot_shift2d requires a fourier image");
04184         int nxreal = nx - 2 + int(is_fftodd());
04185         if (nxreal != ny)
04186                 throw ImageDimensionException("fouriergridrot_shift2d requires ny == nx(real)");
04187         if (0 != nxreal%2)
04188                 throw ImageDimensionException("fouriergridrot_shift2d needs an even image.");
04189         int nxhalf = nxreal/2;
04190         int nyhalf = ny/2;
04191 
04192         if (!is_shuffled()) fft_shuffle();
04193 
04194         EMData* result = copy_head();
04195         set_array_offsets(0, -nyhalf);
04196         result->set_array_offsets(0, -nyhalf);
04197 
04198         ang = ang*(float)DGR_TO_RAD;
04199         float cang = cos(ang);
04200         float sang = sin(ang);
04201         float temp = -2.0f*M_PI/nxreal;
04202         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04203                 float ycang = iy*cang;
04204                 float ysang = iy*sang;
04205                 for (int ix = 0; ix <= nxhalf; ix++) {
04206                         float nuxold = ix*cang - ysang;
04207                         float nuyold = ix*sang + ycang;
04208                         result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, this, kb);
04209                         //result->cmplx(ix,iy) = extractpoint(nuxold, nuyold, kb);
04210                         float phase_ang = temp*(sx*ix+sy*iy);
04211                         result->cmplx(ix,iy) *= complex<float>(cos(phase_ang), sin(phase_ang));
04212                 }
04213         }
04214         result->set_array_offsets();
04215         result->fft_shuffle(); // reset to an unshuffled result
04216         result->update();
04217         set_array_offsets();
04218         fft_shuffle(); // reset to an unshuffled complex image
04219         return result;
04220 }
04221 
04222 #undef QUADPI
04223 #undef DGR_TO_RAD
04224 
04225 void EMData::divkbsinh(const Util::KaiserBessel& kb) {
04226         
04227         if (is_complex())
04228                 throw ImageFormatException("divkbsinh requires a real image.");
04229         vector<int> saved_offsets = get_array_offsets();
04230         set_array_offsets(0,0,0);
04231         // Note that the following loops will work for 1-, 2-, and 3-D
04232         // images, since the "extra" weights will be 1.0.  (For example,
04233         // for a 2-d image iz=0, nz=1, so iz-nz/2 = 0 - 1/2 = 0, since
04234         // the division is an integer division.)
04235         for (int iz=0; iz < nz; iz++) {
04236                 float wz = kb.sinhwin(static_cast<float>(iz-nz/2));
04237                 for (int iy=0; iy < ny; iy++) {
04238                         float wy = kb.sinhwin(static_cast<float>(iy-ny/2));
04239                         for (int ix=0; ix < nx; ix++) {
04240                                 float wx = kb.sinhwin(static_cast<float>(ix-nx/2));
04241                                 float w = wx*wy*wz;
04242                                 (*this)(ix,iy,iz) /= w;
04243                         }
04244                 }
04245         }
04246         set_array_offsets(saved_offsets);
04247 }
04248 
04249 void EMData::divkbsinh_rect(const Util::KaiserBessel& kbx, const Util::KaiserBessel& kby, const Util::KaiserBessel& kbz) {
04250 
04251         if (is_complex())
04252                 throw ImageFormatException("divkbsinh requires a real image.");
04253         vector<int> saved_offsets = get_array_offsets();
04254         set_array_offsets(0,0,0);
04255         // Note that the following loops will work for 1-, 2-, and 3-D
04256         // images, since the "extra" weights will be 1.0.  (For example,
04257         // for a 2-d image iz=0, nz=1, so iz-nz/2 = 0 - 1/2 = 0, since
04258         // the division is an integer division.)
04259         for (int iz=0; iz < nz; iz++) {
04260                 float wz = kbz.sinhwin(static_cast<float>(iz-nz/2));
04261                 for (int iy=0; iy < ny; iy++) {
04262                         float wy = kby.sinhwin(static_cast<float>(iy-ny/2));
04263                         for (int ix=0; ix < nx; ix++) {
04264                                 float wx = kbx.sinhwin(static_cast<float>(ix-nx/2));
04265                                 float w = wx*wy*wz;
04266                                 (*this)(ix,iy,iz) /= w;
04267                         }
04268                 }
04269         }
04270         
04271         set_array_offsets(saved_offsets);
04272 }
04273 
04274 /* OBSOLETED  PAP
04275 Dict EMData::masked_stats(const EMData* mask) {
04276         if (is_complex())
04277                 throw ImageFormatException(
04278                                 "Complex images not supported by EMData::masked_stats");
04279         float* ptr = get_data();
04280         float* mptr = mask->get_data();
04281         long double sum1 = 0.L;
04282         long double sum2 = 0.L;
04283         long nmask = 0L;
04284         for (long i = 0; i < nx*ny*nz; i++,ptr++,mptr++) {
04285                 if (*mptr > 0.5f) {
04286                         nmask++;
04287                         sum1 += *ptr;
04288                         sum2 += (*ptr)*(*ptr);
04289                 }
04290         }
04291         float avg = static_cast<float>(sum1/nmask);
04292         float sig2 = static_cast<float>(sum2/nmask - avg*avg);
04293         float sig = sqrt(sig2);
04294         Dict mydict;
04295         mydict["avg"] = avg; mydict["sigma"] = sig; mydict["nmask"] = int(nmask);
04296         return mydict;
04297 }
04298 */
04299 
04300 EMData* EMData::extract_plane(const Transform& tf, Util::KaiserBessel& kb) {
04301         if (!is_complex())
04302                 throw ImageFormatException("extractplane requires a complex image");
04303         if (nx%2 != 0)
04304                 throw ImageDimensionException("extractplane requires nx to be even");
04305         int nxreal = nx - 2;
04306         if (nxreal != ny || nxreal != nz)
04307                 throw ImageDimensionException("extractplane requires ny == nx == nz");
04308         // build complex result image
04309         EMData* res = new EMData();
04310         res->set_size(nx,ny,1);
04311         res->to_zero();
04312         res->set_complex(true);
04313         res->set_fftodd(false);
04314         res->set_fftpad(true);
04315         res->set_ri(true);
04316         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04317         int n = nxreal;
04318         int nhalf = n/2;
04319         vector<int> saved_offsets = get_array_offsets();
04320         set_array_offsets(0,-nhalf,-nhalf);
04321         res->set_array_offsets(0,-nhalf,0);
04322         // set up some temporary weighting arrays
04323         int kbsize =  kb.get_window_size();
04324         int kbmin  = -kbsize/2;
04325         int kbmax  = -kbmin;
04326         float* wy0 = new float[kbmax - kbmin + 1];
04327         float* wy  = wy0 - kbmin; // wy[kbmin:kbmax]
04328         float* wx0 = new float[kbmax - kbmin + 1];
04329         float* wx  = wx0 - kbmin;
04330         float* wz0 = new float[kbmax - kbmin + 1];
04331         float* wz  = wz0 - kbmin;
04332         float rim = nhalf*float(nhalf);
04333         int count = 0;
04334         float wsum = 0.f;
04335         Transform tftrans = tf; // need transpose of tf here for consistency
04336         tftrans.invert();      // with spider
04337         for (int jy = -nhalf; jy < nhalf; jy++) 
04338         {
04339                 for (int jx = 0; jx <= nhalf; jx++) 
04340                 {
04341                         Vec3f nucur((float)jx, (float)jy, 0.f);
04342                         Vec3f nunew = tftrans*nucur;
04343                         float xnew = nunew[0], ynew = nunew[1], znew = nunew[2];
04344                         if (xnew*xnew+ynew*ynew+znew*znew <= rim) 
04345                         {
04346                                 count++;
04347                                 std::complex<float> btq(0.f,0.f);
04348                                 bool flip = false;
04349                                 if (xnew < 0.f) {
04350                                         flip = true;
04351                                         xnew = -xnew;
04352                                         ynew = -ynew;
04353                                         znew = -znew;
04354                                 }
04355                                 int ixn = int(Util::round(xnew));
04356                                 int iyn = int(Util::round(ynew));
04357                                 int izn = int(Util::round(znew));
04358                                 // populate weight arrays
04359                                 for (int i=kbmin; i <= kbmax; i++) {
04360                                         int izp = izn + i;
04361                                         wz[i] = kb.i0win_tab(znew - izp);
04362                                         int iyp = iyn + i;
04363                                         wy[i] = kb.i0win_tab(ynew - iyp);
04364                                         int ixp = ixn + i;
04365                                         wx[i] = kb.i0win_tab(xnew - ixp);
04366 
04367                                 }
04368                                 // restrict weight arrays to non-zero elements
04369                                 int lnbz = 0;
04370                                 for (int iz = kbmin; iz <= -1; iz++) {
04371                                         if (wz[iz] != 0.f) {
04372                                                 lnbz = iz;
04373                                                 break;
04374                                         }
04375                                 }
04376                                 int lnez = 0;
04377                                 for (int iz = kbmax; iz >= 1; iz--) {
04378                                         if (wz[iz] != 0.f) {
04379                                                 lnez = iz;
04380                                                 break;
04381                                         }
04382                                 }
04383                                 int lnby = 0;
04384                                 for (int iy = kbmin; iy <= -1; iy++) {
04385                                         if (wy[iy] != 0.f) {
04386                                                 lnby = iy;
04387                                                 break;
04388                                         }
04389                                 }
04390                                 int lney = 0;
04391                                 for (int iy = kbmax; iy >= 1; iy--) {
04392                                         if (wy[iy] != 0.f) {
04393                                                 lney = iy;
04394                                                 break;
04395                                         }
04396                                 }
04397                                 int lnbx = 0;
04398                                 for (int ix = kbmin; ix <= -1; ix++) {
04399                                         if (wx[ix] != 0.f) {
04400                                                 lnbx = ix;
04401                                                 break;
04402                                         }
04403                                 }
04404                                 int lnex = 0;
04405                                 for (int ix = kbmax; ix >= 1; ix--) {
04406                                         if (wx[ix] != 0.f) {
04407                                                 lnex = ix;
04408                                                 break;
04409                                         }
04410                                 }
04411                                 if    (ixn >= -kbmin      && ixn <= nhalf-1-kbmax
04412                                    && iyn >= -nhalf-kbmin && iyn <= nhalf-1-kbmax
04413                                    && izn >= -nhalf-kbmin && izn <= nhalf-1-kbmax) {
04414                                         // interior points
04415                                         for (int lz = lnbz; lz <= lnez; lz++) {
04416                                                 int izp = izn + lz;
04417                                                 for (int ly=lnby; ly<=lney; ly++) {
04418                                                         int iyp = iyn + ly;
04419                                                         float ty = wz[lz]*wy[ly];
04420                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04421                                                                 int ixp = ixn + lx;
04422                                                                 float wg = wx[lx]*ty;
04423                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04424                                                                 wsum += wg;
04425                                                         }
04426                                                 }
04427                                         }
04428                                 } else {
04429                                         // points "sticking out"
04430                                         for (int lz = lnbz; lz <= lnez; lz++) {
04431                                                 int izp = izn + lz;
04432                                                 for (int ly=lnby; ly<=lney; ly++) {
04433                                                         int iyp = iyn + ly;
04434                                                         float ty = wz[lz]*wy[ly];
04435                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04436                                                                 int ixp = ixn + lx;
04437                                                                 float wg = wx[lx]*ty;
04438                                                                 bool mirror = false;
04439                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04440                                                                 if (ixt > nhalf || ixt < -nhalf) {
04441                                                                         ixt = Util::sgn(ixt)
04442                                                                                   *(n - abs(ixt));
04443                                                                         iyt = -iyt;
04444                                                                         izt = -izt;
04445                                                                         mirror = !mirror;
04446                                                                 }
04447                                                                 if (iyt >= nhalf || iyt < -nhalf) {
04448                                                                         if (ixt != 0) {
04449                                                                                 ixt = -ixt;
04450                                                                                 iyt = Util::sgn(iyt)
04451                                                                                           *(n - abs(iyt));
04452                                                                                 izt = -izt;
04453                                                                                 mirror = !mirror;
04454                                                                         } else {
04455                                                                                 iyt -= n*Util::sgn(iyt);
04456                                                                         }
04457                                                                 }
04458                                                                 if (izt >= nhalf || izt < -nhalf) {
04459                                                                         if (ixt != 0) {
04460                                                                                 ixt = -ixt;
04461                                                                                 iyt = -iyt;
04462                                                                                 izt = Util::sgn(izt)
04463                                                                                           *(n - abs(izt));
04464                                                                                 mirror = !mirror;
04465                                                                         } else {
04466                                                                                 izt -= Util::sgn(izt)*n;
04467                                                                         }
04468                                                                 }
04469                                                                 if (ixt < 0) {
04470                                                                         ixt = -ixt;
04471                                                                         iyt = -iyt;
04472                                                                         izt = -izt;
04473                                                                         mirror = !mirror;
04474                                                                 }
04475                                                                 if (iyt == nhalf) iyt = -nhalf;
04476                                                                 if (izt == nhalf) izt = -nhalf;
04477                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04478                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04479                                                                 wsum += wg;
04480                                                         }
04481                                                 }
04482                                         }
04483                                 }
04484                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04485                                 else       res->cmplx(jx,jy) = btq;
04486                         }
04487                 }
04488         }
04489         for (int jy = -nhalf; jy < nhalf; jy++)
04490                 for (int jx = 0; jx <= nhalf; jx++)
04491                         res->cmplx(jx,jy) *= count/wsum;
04492         delete[] wx0; delete[] wy0; delete[] wz0;
04493         set_array_offsets(saved_offsets);
04494         res->set_array_offsets(0,0,0);
04495         res->set_shuffled(true);
04496         return res;
04497 }
04498 
04499 
04501 
04502 
04503 
04504 EMData* EMData::extract_plane_rect(const Transform& tf, Util::KaiserBessel& kbx,Util::KaiserBessel& kby, Util::KaiserBessel& kbz) {
04505         
04506 
04507         if (!is_complex())
04508                 throw ImageFormatException("extractplane requires a complex image");
04509         if (nx%2 != 0)
04510                 throw ImageDimensionException("extractplane requires nx to be even");
04511 
04512         int nxfromz = nz+2;
04513         int nxcircal = nxfromz - 2;
04514         EMData* res = new EMData();
04515         res->set_size(nxfromz,nz,1);
04516         res->to_zero();
04517         res->set_complex(true);
04518         res->set_fftodd(false);
04519         res->set_fftpad(true);
04520         res->set_ri(true);
04521         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04522         int n = nxcircal;
04523         int nhalf = n/2;
04524         int nxhalf = (nx-2)/2;
04525         int nyhalf = ny/2;
04526         int nzhalf = nz/2;
04527         
04528         vector<int> saved_offsets = get_array_offsets();
04529         set_array_offsets(0, -nyhalf, -nzhalf);
04530         res->set_array_offsets(0,-nhalf,0);
04531         // set up some temporary weighting arrays
04532         int kbxsize =  kbx.get_window_size();
04533         int kbxmin  = -kbxsize/2;
04534         int kbxmax  = -kbxmin;
04535 
04536         int kbysize =  kby.get_window_size();
04537         int kbymin  = -kbysize/2;
04538         int kbymax  = -kbymin;
04539 
04540         int kbzsize =  kbz.get_window_size();
04541         int kbzmin  = -kbzsize/2;
04542         int kbzmax  = -kbzmin;
04543 
04544         //std::cout<<"kb size x,y,z=="<<kbxsize<<" "<<kbysize<<" "<<kbzsize<<std::endl;
04545         float* wy0 = new float[kbymax - kbymin + 1];
04546         float* wy  = wy0 - kbymin; // wy[kbmin:kbmax]
04547         float* wx0 = new float[kbxmax - kbxmin + 1];
04548         float* wx  = wx0 - kbxmin;
04549         float* wz0 = new float[kbzmax - kbzmin + 1];
04550         float* wz  = wz0 - kbzmin;
04551         float rim = nhalf*float(nhalf);
04552         int count = 0;
04553         float wsum = 0.f;
04554         Transform tftrans = tf; // need transpose of tf here for consistency
04555         tftrans.invert();      // with spider
04556         float xratio=float(nx-2)/float(nz);
04557         float yratio=float(ny)/float(nz);
04558         //std::cout<<"xratio,yratio=="<<xratio<<" "<<yratio<<std::endl;
04559         for (int jy = -nhalf; jy < nhalf; jy++) 
04560         {
04561                 for (int jx = 0; jx <= nhalf; jx++) 
04562                 {
04563                         Vec3f nucur((float)jx, (float)jy, 0.f);
04564                         Vec3f nunew = tftrans*nucur;
04565                         float xnew = nunew[0]*xratio, ynew = nunew[1]*yratio, znew = nunew[2];
04566                         
04567                         if (nunew[0]*nunew[0]+nunew[1]*nunew[1]+nunew[2]*nunew[2] <= rim)
04568                         {
04569                                 count++;
04570                                 std::complex<float> btq(0.f,0.f);
04571                                 bool flip = false;
04572                                 if (xnew < 0.f) {
04573                                         flip = true;
04574                                         xnew = -xnew;
04575                                         ynew = -ynew;
04576                                         znew = -znew;
04577                                 }
04578                                 int ixn = int(Util::round(xnew));
04579                                 int iyn = int(Util::round(ynew));
04580                                 int izn = int(Util::round(znew));
04581                                 // populate weight arrays
04582                                 for (int i=kbzmin; i <= kbzmax; i++) {
04583                                         int izp = izn + i;
04584                                         wz[i] = kbz.i0win_tab(znew - izp);
04585                                         }
04586                                 for (int i=kbymin; i <= kbymax; i++) {
04587                                         int iyp = iyn + i;
04588                                         wy[i] = kby.i0win_tab(ynew - iyp);
04589                                         }
04590                                 for (int i=kbxmin; i <= kbxmax; i++) {
04591                                         int ixp = ixn + i;
04592                                         wx[i] = kbx.i0win_tab(xnew - ixp);
04593                                         }
04594                 
04595 
04596                                 
04597                                 // restrict weight arrays to non-zero elements
04598                                 int lnbz = 0;
04599                                 for (int iz = kbzmin; iz <= -1; iz++) {
04600                                         if (wz[iz] != 0.f) {
04601                                                 lnbz = iz;
04602                                                 break;
04603                                         }
04604                                 }
04605                                 int lnez = 0;
04606                                 for (int iz = kbzmax; iz >= 1; iz--) {
04607                                         if (wz[iz] != 0.f) {
04608                                                 lnez = iz;
04609                                                 break;
04610                                         }
04611                                 }
04612                                 int lnby = 0;
04613                                 for (int iy = kbymin; iy <= -1; iy++) {
04614                                         if (wy[iy] != 0.f) {
04615                                                 lnby = iy;
04616                                                 break;
04617                                         }
04618                                 }
04619                                 int lney = 0;
04620                                 for (int iy = kbymax; iy >= 1; iy--) {
04621                                         if (wy[iy] != 0.f) {
04622                                                 lney = iy;
04623                                                 break;
04624                                         }
04625                                 }
04626                                 int lnbx = 0;
04627                                 for (int ix = kbxmin; ix <= -1; ix++) {
04628                                         if (wx[ix] != 0.f) {
04629                                                 lnbx = ix;
04630                                                 break;
04631                                         }
04632                                 }
04633                                 int lnex = 0;
04634                                 for (int ix = kbxmax; ix >= 1; ix--) {
04635                                         if (wx[ix] != 0.f) {
04636                                                 lnex = ix;
04637                                                 break;
04638                                         }
04639                                 }
04640                                 if    (ixn >= -kbxmin      && ixn <= nxhalf-1-kbxmax
04641                                    && iyn >= -nyhalf-kbymin && iyn <= nyhalf-1-kbymax
04642                                    && izn >= -nzhalf-kbzmin && izn <= nzhalf-1-kbzmax) {
04643                                         // interior points
04644                                         for (int lz = lnbz; lz <= lnez; lz++) {
04645                                                 int izp = izn + lz;
04646                                                 for (int ly=lnby; ly<=lney; ly++) {
04647                                                         int iyp = iyn + ly;
04648                                                         float ty = wz[lz]*wy[ly];
04649                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04650                                                                 int ixp = ixn + lx;
04651                                                                 float wg = wx[lx]*ty;
04652                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04653                                                                 wsum += wg;
04654                                                         }
04655                                                 }
04656                                         }
04657                                 } 
04658                                 else {
04659                                         // points "sticking out"
04660                                         for (int lz = lnbz; lz <= lnez; lz++) {
04661                                                 int izp = izn + lz;
04662                                                 for (int ly=lnby; ly<=lney; ly++) {
04663                                                         int iyp = iyn + ly;
04664                                                         float ty = wz[lz]*wy[ly];
04665                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04666                                                                 int ixp = ixn + lx;
04667                                                                 float wg = wx[lx]*ty;
04668                                                                 bool mirror = false;
04669                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04670                                                                 if (ixt > nxhalf || ixt < -nxhalf) {
04671                                                                         ixt = Util::sgn(ixt)
04672                                                                                   *(nx-2-abs(ixt));
04673                                                                         iyt = -iyt;
04674                                                                         izt = -izt;
04675                                                                         mirror = !mirror;
04676                                                                 }
04677                                                                 if (iyt >= nyhalf || iyt < -nyhalf) {
04678                                                                         if (ixt != 0) {
04679                                                                                 ixt = -ixt;
04680                                                                                 iyt = Util::sgn(iyt)
04681                                                                                           *(ny - abs(iyt));
04682                                                                                 izt = -izt;
04683                                                                                 mirror = !mirror;
04684                                                                         } else {
04685                                                                                 iyt -= ny*Util::sgn(iyt);
04686                                                                         }
04687                                                                 }
04688                                                                 if (izt >= nzhalf || izt < -nzhalf) {
04689                                                                         if (ixt != 0) {
04690                                                                                 ixt = -ixt;
04691                                                                                 iyt = -iyt;
04692                                                                                 izt = Util::sgn(izt)
04693                                                                                           *(nz - abs(izt));
04694                                                                                 mirror = !mirror;
04695                                                                         } else {
04696                                                                                 izt -= Util::sgn(izt)*nz;
04697                                                                         }
04698                                                                 }
04699                                                                 if (ixt < 0) {
04700                                                                         ixt = -ixt;
04701                                                                         iyt = -iyt;
04702                                                                         izt = -izt;
04703                                                                         mirror = !mirror;
04704                                                                 }
04705                                                                 if (iyt == nyhalf) iyt = -nyhalf;
04706                                                                 if (izt == nzhalf) izt = -nzhalf;
04707                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04708                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04709                                                                 wsum += wg;
04710                                                         }
04711                                                 }
04712                                         }
04713                                 }
04714                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04715                                 else       res->cmplx(jx,jy) = btq;
04716                         }
04717                 }
04718         }
04719         for (int jy = -nhalf; jy < nhalf; jy++)
04720                 for (int jx = 0; jx <= nhalf; jx++)
04721                         res->cmplx(jx,jy) *= count/wsum;
04722         delete[] wx0; delete[] wy0; delete[] wz0;
04723         set_array_offsets(saved_offsets);
04724         res->set_array_offsets(0,0,0);
04725         res->set_shuffled(true);
04726         return res;
04727 }
04728 
04729 
04730 
04731 EMData* EMData::extract_plane_rect_fast(const Transform& tf, Util::KaiserBessel& kbx,Util::KaiserBessel& kby, Util::KaiserBessel& kbz) {
04732         
04733         
04734 
04735         if (!is_complex())
04736                 throw ImageFormatException("extractplane requires a complex image");
04737         if (nx%2 != 0)
04738                 throw ImageDimensionException("extractplane requires nx to be even");
04739 
04740         int nxfromz=nz+2;
04741         int nxcircal = nxfromz - 2;
04742 
04743         // build complex result image
04744         float xratio=float(nx-2)/float(nz);
04745         float yratio=float(ny)/float(nz);
04746         Vec3f axis_newx,axis_newy;
04747         axis_newx[0] = xratio*0.5f*nz*tf[0][0];
04748         axis_newx[1] = yratio*0.5f*nz*tf[0][1];
04749         axis_newx[2] = 0.5f*nz*tf[0][2];
04750 
04751 
04752         float ellipse_length_x=std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
04753         
04754         int ellipse_length_x_int=int(ellipse_length_x);
04755         float ellipse_step_x=0.5f*nz/float(ellipse_length_x_int);
04756         float xscale=ellipse_step_x;//scal increased
04757 
04758         axis_newy[0] = xratio*0.5f*nz*tf[1][0];
04759         axis_newy[1] = yratio*0.5f*nz*tf[1][1];
04760         axis_newy[2] = 0.5f*nz*tf[1][2];
04761 
04762 
04763         float ellipse_length_y=std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
04764         int ellipse_length_y_int=int(ellipse_length_y);
04765         float ellipse_step_y=0.5f*nz/float(ellipse_length_y_int);
04766         float yscale=ellipse_step_y;
04767         //end of scaling factor calculation
04768         int nx_e=ellipse_length_x_int*2;
04769         int ny_e=ellipse_length_y_int*2;
04770         int nx_ec=nx_e+2;       
04771 
04772         EMData* res = new EMData();
04773         res->set_size(nx_ec,ny_e,1);
04774         res->to_zero();
04775         res->set_complex(true);
04776         res->set_fftodd(false);
04777         res->set_fftpad(true);
04778         res->set_ri(true);
04779         //std::cout<<"cpp fast extract_plane is called"<<std::endl;
04780         //std::cout<<"nx_e,ny_e===="<<nx_e<<"  "<<ny_e<<std::endl;
04781         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04782         int n = nxcircal;
04783         int nhalf = n/2;
04784         int nhalfx_e = nx_e/2;
04785         int nhalfy_e = ny_e/2;
04786         int nxhalf=(nx-2)/2;
04787         int nyhalf=ny/2;
04788         int nzhalf=nz/2;
04789         //std::cout<<"nhalf,nxhalf,nyhalf,nzhalf=="<<nhalf<<" "<<nxhalf<<" "<<nyhalf<<" "<<nzhalf<<std::endl;
04790         vector<int> saved_offsets = get_array_offsets();
04791         set_array_offsets(0,-nyhalf,-nzhalf);
04792         res->set_array_offsets(0,-nhalfy_e,0);
04793         // set up some temporary weighting arrays
04794         int kbxsize =  kbx.get_window_size();
04795         int kbxmin  = -kbxsize/2;
04796         int kbxmax  = -kbxmin;
04797 
04798         int kbysize =  kby.get_window_size();
04799         int kbymin  = -kbysize/2;
04800         int kbymax  = -kbymin;
04801 
04802         int kbzsize =  kbz.get_window_size();
04803         int kbzmin  = -kbzsize/2;
04804         int kbzmax  = -kbzmin;
04805 
04806         //std::cout<<"kb size x,y,z=="<<kbxsize<<" "<<kbysize<<" "<<kbzsize<<std::endl;
04807         float* wy0 = new float[kbymax - kbymin + 1];
04808         float* wy  = wy0 - kbymin; // wy[kbmin:kbmax]
04809         float* wx0 = new float[kbxmax - kbxmin + 1];
04810         float* wx  = wx0 - kbxmin;
04811         float* wz0 = new float[kbzmax - kbzmin + 1];
04812         float* wz  = wz0 - kbzmin;
04813         float rim = nhalf*float(nhalf);
04814         int count = 0;
04815         float wsum = 0.f;
04816         Transform tftrans = tf; // need transpose of tf here for consistency
04817         tftrans.invert();      // with spider
04818 
04819         //std::cout<<"xratio,yratio=="<<xratio<<" "<<yratio<<std::endl;
04820         for (int jy = -nhalfy_e; jy < nhalfy_e; jy++) 
04821         {
04822                 for (int jx = 0; jx <= nhalfx_e; jx++) 
04823                 {
04824                         Vec3f nucur((float)jx, (float)jy, 0.f);
04825                         nucur[0]=nucur[0]*xscale;nucur[1]=nucur[1]*yscale;;
04826                         Vec3f nunew = tftrans*nucur;
04827                         float xnew = nunew[0]*xratio, ynew = nunew[1]*yratio, znew = nunew[2];
04828                         
04829                         if (nunew[0]*nunew[0]+nunew[1]*nunew[1]+nunew[2]*nunew[2] <= rim)
04830                         {
04831                                 count++;
04832                                 std::complex<float> btq(0.f,0.f);
04833                                 bool flip = false;
04834                                 if (xnew < 0.f) {
04835                                         flip = true;
04836                                         xnew = -xnew;
04837                                         ynew = -ynew;
04838                                         znew = -znew;
04839                                 }
04840                                 int ixn = int(Util::round(xnew));
04841                                 int iyn = int(Util::round(ynew));
04842                                 int izn = int(Util::round(znew));
04843                                 // populate weight arrays
04844                                 for (int i=kbzmin; i <= kbzmax; i++) {
04845                                         int izp = izn + i;
04846                                         wz[i] = kbz.i0win_tab(znew - izp);
04847                                         }
04848                                 for (int i=kbymin; i <= kbymax; i++) {
04849                                         int iyp = iyn + i;
04850                                         wy[i] = kby.i0win_tab(ynew - iyp);
04851                                         }
04852                                 for (int i=kbxmin; i <= kbxmax; i++) {
04853                                         int ixp = ixn + i;
04854                                         wx[i] = kbx.i0win_tab(xnew - ixp);
04855                                         }
04856                 
04857 
04858                                 
04859                                 // restrict weight arrays to non-zero elements
04860                                 int lnbz = 0;
04861                                 for (int iz = kbzmin; iz <= -1; iz++) {
04862                                         if (wz[iz] != 0.f) {
04863                                                 lnbz = iz;
04864                                                 break;
04865                                         }
04866                                 }
04867                                 int lnez = 0;
04868                                 for (int iz = kbzmax; iz >= 1; iz--) {
04869                                         if (wz[iz] != 0.f) {
04870                                                 lnez = iz;
04871                                                 break;
04872                                         }
04873                                 }
04874                                 int lnby = 0;
04875                                 for (int iy = kbymin; iy <= -1; iy++) {
04876                                         if (wy[iy] != 0.f) {
04877                                                 lnby = iy;
04878                                                 break;
04879                                         }
04880                                 }
04881                                 int lney = 0;
04882                                 for (int iy = kbymax; iy >= 1; iy--) {
04883                                         if (wy[iy] != 0.f) {
04884                                                 lney = iy;
04885                                                 break;
04886                                         }
04887                                 }
04888                                 int lnbx = 0;
04889                                 for (int ix = kbxmin; ix <= -1; ix++) {
04890                                         if (wx[ix] != 0.f) {
04891                                                 lnbx = ix;
04892                                                 break;
04893                                         }
04894                                 }
04895                                 int lnex = 0;
04896                                 for (int ix = kbxmax; ix >= 1; ix--) {
04897                                         if (wx[ix] != 0.f) {
04898                                                 lnex = ix;
04899                                                 break;
04900                                         }
04901                                 }
04902                                 if    (ixn >= -kbxmin      && ixn <= nxhalf-1-kbxmax
04903                                    && iyn >= -nyhalf-kbymin && iyn <= nyhalf-1-kbymax
04904                                    && izn >= -nzhalf-kbzmin && izn <= nzhalf-1-kbzmax) {
04905                                         // interior points
04906                                         for (int lz = lnbz; lz <= lnez; lz++) {
04907                                                 int izp = izn + lz;
04908                                                 for (int ly=lnby; ly<=lney; ly++) {
04909                                                         int iyp = iyn + ly;
04910                                                         float ty = wz[lz]*wy[ly];
04911                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04912                                                                 int ixp = ixn + lx;
04913                                                                 float wg = wx[lx]*ty;
04914                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04915                                                                 wsum += wg;
04916                                                         }
04917                                                 }
04918                                         }
04919                                 } 
04920                                 else {
04921                                         // points "sticking out"
04922                                         for (int lz = lnbz; lz <= lnez; lz++) {
04923                                                 int izp = izn + lz;
04924                                                 for (int ly=lnby; ly<=lney; ly++) {
04925                                                         int iyp = iyn + ly;
04926                                                         float ty = wz[lz]*wy[ly];
04927                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04928                                                                 int ixp = ixn + lx;
04929                                                                 float wg = wx[lx]*ty;
04930                                                                 bool mirror = false;
04931                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04932                                                                 if (ixt > nxhalf || ixt < -nxhalf) {
04933                                                                         ixt = Util::sgn(ixt)
04934                                                                                   *(nx-2-abs(ixt));
04935                                                                         iyt = -iyt;
04936                                                                         izt = -izt;
04937                                                                         mirror = !mirror;
04938                                                                 }
04939                                                                 if (iyt >= nyhalf || iyt < -nyhalf) {
04940                                                                         if (ixt != 0) {
04941                                                                                 ixt = -ixt;
04942                                                                                 iyt = Util::sgn(iyt)
04943                                                                                           *(ny - abs(iyt));
04944                                                                                 izt = -izt;
04945                                                                                 mirror = !mirror;
04946                                                                         } else {
04947                                                                                 iyt -= ny*Util::sgn(iyt);
04948                                                                         }
04949                                                                 }
04950                                                                 if (izt >= nzhalf || izt < -nzhalf) {
04951                                                                         if (ixt != 0) {
04952                                                                                 ixt = -ixt;
04953                                                                                 iyt = -iyt;
04954                                                                                 izt = Util::sgn(izt)
04955                                                                                           *(nz - abs(izt));
04956                                                                                 mirror = !mirror;
04957                                                                         } else {
04958                                                                                 izt -= Util::sgn(izt)*nz;
04959                                                                         }
04960                                                                 }
04961                                                                 if (ixt < 0) {
04962                                                                         ixt = -ixt;
04963                                                                         iyt = -iyt;
04964                                                                         izt = -izt;
04965                                                                         mirror = !mirror;
04966                                                                 }
04967                                                                 if (iyt == nyhalf) iyt = -nyhalf;
04968                                                                 if (izt == nzhalf) izt = -nzhalf;
04969                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04970                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04971                                                                 wsum += wg;
04972                                                         }
04973                                                 }
04974                                         }
04975                                 }
04976                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04977                                 else       res->cmplx(jx,jy) = btq;
04978                         }
04979                 }
04980         }
04981         for (int jy = -nhalfy_e; jy < nhalfy_e; jy++)
04982                 for (int jx = 0; jx <= nhalfx_e; jx++)
04983                         res->cmplx(jx,jy) *= count/wsum;
04984         delete[] wx0; delete[] wy0; delete[] wz0;
04985         set_array_offsets(saved_offsets);
04986         res->set_array_offsets(0,0,0);
04987         res->set_shuffled(true);
04988         return res;
04989 }
04990 
04991 
04992 
04993 
04994 bool EMData::peakcmp(const Pixel& p1, const Pixel& p2) {
04995     return (p1.value > p2.value);
04996 }
04997 
04998 ostream& operator<< (ostream& os, const Pixel& peak) {
04999     os <<  peak.x <<  peak.y << peak.z  << peak.value;
05000     return os;
05001 }
05002 
05003 /*vector<float> EMData::max_search() {
05004 
05005         EMData& buf = *this;
05006 
05007         int nx = buf.get_xsize();
05008         int ny = buf.get_ysize();
05009         int nz = buf.get_zsize();
05010 
05011         int dim = buf.get_ndim();
05012 
05013         vector<float> result;
05014 
05015         if (dim == 1) {
05016                 float max = -1e20f;
05017                 int index = -1;
05018                 for (int i=0; i<nx; i++) {
05019                         if (buf(i)>max) {
05020                                 max = buf(i);
05021                                 index = i;
05022                         }
05023                 }
05024                 result.push_back((float)index);
05025                 result.push_back(max);
05026         } else if (dim == 2) {
05027                 float max = -1e20f;
05028                 int index1 = -1;
05029                 int index2 = -1;
05030                 for (int i=0; i<nx; i++) {
05031                         for (int j=0; j<ny; j++) {
05032                                 if (buf(i, j)>max) {
05033                                         max = buf(i, j);
05034                                         index1 = i;
05035                                         index2 = j;
05036                                 }
05037                         }
05038                 }
05039                 result.push_back((float)index1);
05040                 result.push_back((float)index2);
05041                 result.push_back(max);
05042         } else {
05043                 float max = -1e20f;
05044                 int index1 = -1;
05045                 int index2 = -1;
05046                 int index3 = -1;
05047                 for (int i=0; i<nx; i++) {
05048                         for (int j=0; j<ny; j++) {
05049                                 for (int k=0; k<nz; k++) {
05050                                         if (buf(i, j, k)>max) {
05051                                                 max = buf(i, j, k);
05052                                                 index1 = i;
05053                                                 index2 = j;
05054                                                 index3 = k;
05055                                         }
05056                                 }
05057                         }
05058                 }
05059                 result.push_back((float)index1);
05060                 result.push_back((float)index2);
05061                 result.push_back((float)index3);
05062                 result.push_back(max);
05063         }
05064         return result;
05065 }*/
05066 
05067 vector<float> EMData::peak_search(int ml, float invert) {
05068 
05069         EMData& buf = *this;
05070         vector<Pixel> peaks;
05071         int img_dim;
05072         int i, j, k;
05073         int i__1, i__2;
05074         int j__1, j__2;
05075         //int k__1, k__2;
05076         bool peak_check;
05077         img_dim=buf.get_ndim();
05078         vector<int> ix, jy, kz;
05079         vector<float>res;
05080         int nx = buf.get_xsize();
05081         int ny = buf.get_ysize();
05082         int nz = buf.get_zsize();
05083         if(invert <= 0.0f)  invert=-1.0f;
05084         else                invert=1.0f ;
05085         int count = 0;
05086         switch (img_dim)  {
05087         case(1):
05088                 for(i=0;i<=nx-1;++i)  {
05089                         i__1 = (i-1+nx)%nx;
05090                         i__2 = (i+1)%nx;
05091                         // Commented by Yang on 05/14/07
05092                         // I changed the following line from > to >=, or in some rare cases (the peak happens to be flat), it will fail to find the peak.
05093                         //  03/07/08  I undid the change.  If you change the comparison, it changes the meaning of peak definition.
05094                         float qbf = buf(i)*invert;
05095                         peak_check = qbf > buf(i__1)*invert && qbf > buf(i__2)*invert;
05096                         if(peak_check) {
05097                                 if(count < ml) {
05098                                         count++;
05099                                         peaks.push_back( Pixel(i, 0, 0, qbf) );
05100                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05101                                 } else {
05102                                         if( qbf > (peaks.back()).value ) {
05103                                                 //  do the switch and sort again
05104                                                 peaks.pop_back();
05105                                                 peaks.push_back( Pixel(i, 0, 0, qbf) );
05106                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05107                                         }
05108                                 }
05109                         }
05110                 }
05111         break;
05112         case(2):
05113         /*  Removed boundary conditions, PAP 03/10/08
05114                 for(j=0;j<=ny-1;++j)  {
05115                         j__1 = (j-1+ny)%ny;
05116                         j__2 = (j+1)%ny;
05117                         for(i=0;i<=nx-1;++i) {
05118                                 i__1 = (i-1+nx)%nx;
05119                                 i__2 = (i+1)%nx;
05120         */
05121                 for(j=1;j<=ny-2;++j)  {
05122                         j__1 = j-1;
05123                         j__2 = j+1;
05124                         for(i=1;i<=nx-2;++i) {
05125                                 i__1 = i-1;
05126                                 i__2 = i+1;
05127                                 float qbf = buf(i,j)*invert;
05128                                 peak_check = (qbf > buf(i,j__1)*invert) && (qbf > buf(i,j__2)*invert);
05129                                 if(peak_check) {
05130                                         peak_check = (qbf > buf(i__1,j)*invert) && (qbf > buf(i__2,j)*invert);
05131                                         if(peak_check) {
05132                                                 peak_check = (qbf > buf(i__1,j__1)*invert) && (qbf > buf(i__1,j__2)*invert);
05133                                                 if(peak_check) {
05134                                                         peak_check = (qbf > buf(i__2,j__1)*invert) && (qbf > buf(i__2,j__2)*invert);
05135                                                         if(peak_check) {
05136                                                                 if(count < ml) {
05137                                                                         count++;
05138                                                                         peaks.push_back( Pixel(i, j, 0, qbf) );
05139                                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05140                                                                 } else {
05141                                                                         if( qbf > (peaks.back()).value ) {
05142                                                                                 //  do the switch and sort again
05143                                                                                 peaks.pop_back();
05144                                                                                 peaks.push_back( Pixel(i, j, 0, qbf) );
05145                                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05146                                                                         }
05147                                                                 }
05148                                                         }
05149                                                 }
05150                                         }
05151                                 }
05152                         }
05153                 }
05154         break;
05155         case(3):  //looks ugly, but it is the best I can do,  PAP 03/07/08
05156         /*  Removed boundary conditions, PAP 03/10/08
05157                 for(k=0;k<=nz-1;++k) {
05158                         kz.clear();
05159                         k__1 = (k-1+nz)%nz;
05160                         k__2 = (k+1)%nz;
05161                         kz.push_back(k__1);
05162                         kz.push_back(k);
05163                         kz.push_back(k__2);
05164                         for(j=0;j<=ny-1;++j) {
05165                                 jy.clear();
05166                                 j__1 = (j-1+ny)%ny;
05167                                 j__2 = (j+1)%ny;
05168                                 jy.push_back(j__1);
05169                                 jy.push_back(j);
05170                                 jy.push_back(j__2);
05171                                 for(i=0;i<=nx-1;++i) {
05172                                         ix.clear();
05173                                         i__1 = (i-1+nx)%nx;
05174                                         i__2 = (i+1)%nx;
05175         */
05176                 for(k=1; k<=nz-2; ++k) {
05177                         kz.clear();
05178                         kz.push_back(k-1);
05179                         kz.push_back(k);
05180                         kz.push_back(k+1);
05181                         for(j=1; j<=ny-2; ++j) {
05182                                 jy.clear();
05183                                 jy.push_back(j-1);
05184                                 jy.push_back(j);
05185                                 jy.push_back(j+1);
05186                                 for(i=1; i<=nx-2; ++i) {
05187                                         ix.clear();
05188                                         ix.push_back(i-1);
05189                                         ix.push_back(i);
05190                                         ix.push_back(i+1);
05191                                         float qbf = buf(i,j,k)*invert;
05192                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05193                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05194                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05195                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05196                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05197                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05198                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05199                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05200                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05201                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05202                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05203                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05204                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05205                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05206                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05207                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05208                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05209                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05210                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05211                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05212                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05213                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05214                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05215                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05216                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05217                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05218                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05219                                         if(peak_check) {
05220                                                 if(count < ml) {
05221                                                         count++;
05222                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05223                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05224                                                 } else {
05225                                                         if( qbf > (peaks.back()).value ) {
05226                                                                 //  do the switch and sort again
05227                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05228                                                                 peaks.pop_back();
05229                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05230                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05231                                                         }
05232                                                 }
05233                                         }
05234                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05235                                 }
05236                         }
05237                 }
05238                 //  Add circular closure for x direction: needed for circular ccf,
05239                 //  should not have adverse impact on other code.  PAP -7/22/08
05240                 for(k=1; k<=nz-2; ++k) {
05241                         kz.clear();
05242                         kz.push_back(k-1);
05243                         kz.push_back(k);
05244                         kz.push_back(k+1);
05245                         for(j=1; j<=ny-2; ++j) {
05246                                 jy.clear();
05247                                 jy.push_back(j-1);
05248                                 jy.push_back(j);
05249                                 jy.push_back(j+1);
05250                                 for(i=0; i<=0; ++i) {
05251                                         ix.clear();
05252                                         ix.push_back(nx-1);
05253                                         ix.push_back(i);
05254                                         ix.push_back(i+1);
05255                                         float qbf = buf(i,j,k)*invert;
05256                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05257                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05258                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05259                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05260                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05261                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05262                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05263                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05264                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05265                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05266                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05267                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05268                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05269                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05270                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05271                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05272                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05273                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05274                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05275                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05276                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05277                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05278                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05279                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05280                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05281                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05282                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05283                                         if(peak_check) {
05284                                                 if(count < ml) {
05285                                                         count++;
05286                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05287                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05288                                                 } else {
05289                                                         if( qbf > (peaks.back()).value ) {
05290                                                                 //  do the switch and sort again
05291                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05292                                                                 peaks.pop_back();
05293                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05294                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05295                                                         }
05296                                                 }
05297                                         }
05298                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05299                                 }
05300                                 for(i=nx-1; i<=nx-1; ++i) {
05301                                         ix.clear();
05302                                         ix.push_back(i-1);
05303                                         ix.push_back(i);
05304                                         ix.push_back(0);
05305                                         float qbf = buf(i,j,k)*invert;
05306                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05307                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05308                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05309                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05310                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05311                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05312                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05313                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05314                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05315                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05316                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05317                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05318                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05319                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05320                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05321                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05322                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05323                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05324                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05325                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05326                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05327                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05328                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05329                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05330                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05331                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05332                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05333                                         if(peak_check) {
05334                                                 if(count < ml) {
05335                                                         count++;
05336                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05337                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05338                                                 } else {
05339                                                         if( qbf > (peaks.back()).value ) {
05340                                                                 //  do the switch and sort again
05341                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05342                                                                 peaks.pop_back();
05343                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05344                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05345                                                         }
05346                                                 }
05347                                         }
05348                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05349                                 }
05350                         }
05351                 }
05352         break;
05353 /*      case(5):  //looks ugly, but it is the best I can do,  PAP 03/07/08
05354         int nu = buf.get_usize();
05355         int nv = buf.get_vsize();
05356         vector<int> lu, mv;
05357                 for(m=1; m<=nv-2; ++m) {
05358                         mv.clear();
05359                         mv.push_back(m-1);
05360                         mv.push_back(m);
05361                         mv.push_back(m+1);
05362                 for(l=1; l<=nu-2; ++l) {
05363                         lu.clear();
05364                         lu.push_back(l-1);
05365                         lu.push_back(l);
05366                         lu.push_back(l+1);
05367                 for(k=1; k<=nz-2; ++k) {
05368                         kz.clear();
05369                         kz.push_back(k-1);
05370                         kz.push_back(k);
05371                         kz.push_back(k+1);
05372                         for(j=1; j<=ny-2; ++j) {
05373                                 jy.clear();
05374                                 jy.push_back(j-1);
05375                                 jy.push_back(j);
05376                                 jy.push_back(j+1);
05377                                 for(i=1; i<=nx-2; ++i) {
05378                                         ix.clear();
05379                                         ix.push_back(i-1);
05380                                         ix.push_back(i);
05381                                         ix.push_back(i+1);
05382                                         float qbf = buf(i,j,k,l,m)*invert;
05383                                         peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[0])*invert;
05384                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[0])*invert;
05385                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[0])*invert;
05386                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[0])*invert;
05387                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[0])*invert;
05388                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[0])*invert;
05389                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[0])*invert;
05390                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[0])*invert;
05391                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[0])*invert;
05392                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[0])*invert;
05393                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[0])*invert;
05394                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[0])*invert;
05395                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[0])*invert;
05396                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[0])*invert;
05397                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[0])*invert;
05398                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[0])*invert;
05399                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[0])*invert;
05400                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[0])*invert;
05401                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[0])*invert;
05402                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[0])*invert;
05403                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[0])*invert;
05404                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[0])*invert;
05405                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[0])*invert;
05406                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[0])*invert;
05407                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[0])*invert;
05408                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[0])*invert;
05409                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[0])*invert;
05410 
05411                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[0])*invert;
05412                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[0])*invert;
05413                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[0])*invert;
05414                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[0])*invert;
05415                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[0])*invert;
05416                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[0])*invert;
05417                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[0])*invert;
05418                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[0])*invert;
05419                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[0])*invert;
05420                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[0])*invert;
05421                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[0])*invert;
05422                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[0])*invert;
05423                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[0])*invert;
05424                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[0])*invert;
05425                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[0])*invert;
05426                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[0])*invert;
05427                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[0])*invert;
05428                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[0])*invert;
05429                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[0])*invert;
05430                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[0])*invert;
05431                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[0])*invert;
05432                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[0])*invert;
05433                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[0])*invert;
05434                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[0])*invert;
05435                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[0])*invert;
05436                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[0])*invert;
05437                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[0])*invert;
05438 
05439                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[0])*invert;
05440                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[0])*invert;
05441                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[0])*invert;
05442                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[0])*invert;
05443                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[0])*invert;
05444                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[0])*invert;
05445                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[0])*invert;
05446                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[0])*invert;
05447                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[0])*invert;
05448                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[0])*invert;
05449                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[0])*invert;
05450                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[0])*invert;
05451                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[0])*invert;
05452                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[0])*invert;
05453                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[0])*invert;
05454                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[0])*invert;
05455                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[0])*invert;
05456                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[0])*invert;
05457                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[0])*invert;
05458                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[0])*invert;
05459                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[0])*invert;
05460                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[0])*invert;
05461                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[0])*invert;
05462                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[0])*invert;
05463                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[0])*invert;
05464                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[0])*invert;
05465                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[0])*invert;
05466 
05467 
05468                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[1])*invert;
05469                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[1])*invert;
05470                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[1])*invert;
05471                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[1])*invert;
05472                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[1])*invert;
05473                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[1])*invert;
05474                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[1])*invert;
05475                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[1])*invert;
05476                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[1])*invert;
05477                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[1])*invert;
05478                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[1])*invert;
05479                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[1])*invert;
05480                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[1])*invert;
05481                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[1])*invert;
05482                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[1])*invert;
05483                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[1])*invert;
05484                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[1])*invert;
05485                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[1])*invert;
05486                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[1])*invert;
05487                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[1])*invert;
05488                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[1])*invert;
05489                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[1])*invert;
05490                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[1])*invert;
05491                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[1])*invert;
05492                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[1])*invert;
05493                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[1])*invert;
05494                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[1])*invert;
05495 
05496                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[1])*invert;
05497                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[1])*invert;
05498                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[1])*invert;
05499                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[1])*invert;
05500                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[1])*invert;
05501                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[1])*invert;
05502                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[1])*invert;
05503                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[1])*invert;
05504                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[1])*invert;
05505                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[1])*invert;
05506                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[1])*invert;
05507                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[1])*invert;
05508                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[1])*invert;
05509                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[1])*invert;
05510                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[1])*invert;
05511                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[1])*invert;
05512                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[1])*invert;
05513                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[1])*invert;
05514                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[1])*invert;
05515                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[1])*invert;
05516                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[1])*invert;
05517                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[1])*invert;
05518                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[1])*invert;
05519                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[1])*invert;
05520                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[1])*invert;
05521                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[1])*invert;
05522                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[1])*invert;
05523 
05524                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[1])*invert;
05525                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[1])*invert;
05526                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[1])*invert;
05527                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[1])*invert;
05528                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[1])*invert;
05529                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[1])*invert;
05530                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[1])*invert;
05531                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[1])*invert;
05532                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[1])*invert;
05533                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[1])*invert;
05534                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[1])*invert;
05535                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[1])*invert;
05536                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[1])*invert;
05537                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[1])*invert;
05538                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[1])*invert;
05539                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[1])*invert;
05540                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[1])*invert;
05541                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[1])*invert;
05542                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[1])*invert;
05543                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[1])*invert;
05544                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[1])*invert;
05545                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[1])*invert;
05546                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[1])*invert;
05547                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[1])*invert;
05548                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[1])*invert;
05549                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[1])*invert;
05550                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[1])*invert;
05551 
05552 
05553                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[2])*invert;
05554                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[2])*invert;
05555                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[2])*invert;
05556                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[2])*invert;
05557                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[2])*invert;
05558                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[2])*invert;
05559                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[2])*invert;
05560                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[2])*invert;
05561                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[2])*invert;
05562                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[2])*invert;
05563                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[2])*invert;
05564                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[2])*invert;
05565                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[2])*invert;
05566                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[2])*invert;
05567                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[2])*invert;
05568                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[2])*invert;
05569                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[2])*invert;
05570                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[2])*invert;
05571                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[2])*invert;
05572                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[2])*invert;
05573                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[2])*invert;
05574                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[2])*invert;
05575                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[2])*invert;
05576                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[2])*invert;
05577                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[2])*invert;
05578                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[2])*invert;
05579                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[2])*invert;
05580 
05581                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[2])*invert;
05582                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[2])*invert;
05583                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[2])*invert;
05584                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[2])*invert;
05585                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[2])*invert;
05586                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[2])*invert;
05587                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[2])*invert;
05588                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[2])*invert;
05589                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[2])*invert;
05590                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[2])*invert;
05591                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[2])*invert;
05592                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[2])*invert;
05593                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[2])*invert;
05594                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[2])*invert;
05595                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[2])*invert;
05596                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[2])*invert;
05597                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[2])*invert;
05598                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[2])*invert;
05599                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[2])*invert;
05600                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[2])*invert;
05601                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[2])*invert;
05602                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[2])*invert;
05603                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[2])*invert;
05604                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[2])*invert;
05605                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[2])*invert;
05606                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[2])*invert;
05607                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[2])*invert;
05608 
05609                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[2])*invert;
05610                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[2])*invert;
05611                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[2])*invert;
05612                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[2])*invert;
05613                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[2])*invert;
05614                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[2])*invert;
05615                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[2])*invert;
05616                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[2])*invert;
05617                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[2])*invert;
05618                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[2])*invert;
05619                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[2])*invert;
05620                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[2])*invert;
05621                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[2])*invert;
05622                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[2])*invert;
05623                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[2])*invert;
05624                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[2])*invert;
05625                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[2])*invert;
05626                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[2])*invert;
05627                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[2])*invert;
05628                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[2])*invert;
05629                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[2])*invert;
05630                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[2])*invert;
05631                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[2])*invert;
05632                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[2])*invert;
05633                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[2])*invert;
05634                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[2])*invert;
05635                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[2])*invert;
05636                                         if(peak_check) {
05637                                                 if(count < ml) {
05638                                                         count++;
05639                                                         //peaks.push_back( Pixel(i, j, k, l, m, qbf) );
05640                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05641                                                 } else {
05642                                                         if( qbf > (peaks.back()).value ) {
05643                                                                 //  do the switch and sort again
05644                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05645                                                                 peaks.pop_back();
05646                                                                 //peaks.push_back( Pixel(i, j, k, l, m, qbf) );
05647                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05648                                                         }
05649                                                 }
05650                                         }
05651                                         }}}}}}}}}}}}}}}}}}}}}}}}}}
05652                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05653                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05654                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05655                                         }}}}}}}}}}}}}}}}}}}}}}}}}}
05656                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05657                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05658                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05659                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05660                                 }
05661                         }
05662                 }
05663                 }
05664                 }
05665                 //  Add circular closure for x, y, and z directions: needed for circular ccf,
05666                 //  should not have adverse impact on other code.  PAP 11/7/08
05667                 for(m=1; m<=nv-2; ++m) {
05668                         mv.clear();
05669                         mv.push_back(m-1);
05670                         mv.push_back(m);
05671                         mv.push_back(m+1);
05672                 for(l=1; l<=nu-2; ++l) {
05673                         lu.clear();
05674                         lu.push_back(l-1);
05675                         lu.push_back(l);
05676                         lu.push_back(l+1);
05677                 for(k=1; k<=nz-2; ++k) {
05678                         kz.clear();
05679                         kz.push_back(k-1);
05680                         kz.push_back(k);
05681                         kz.push_back(k+1);
05682                         for(j=1; j<=ny-2; ++j) {
05683                                 jy.clear();
05684                                 jy.push_back(j-1);
05685                                 jy.push_back(j);
05686                                 jy.push_back(j+1);
05687                                 for(i=0; i<=0; ++i) {
05688                                         ix.clear();
05689                                         ix.push_back(nx-1);
05690                                         ix.push_back(i);
05691                                         ix.push_back(i+1);
05692                                         float qbf = buf(i,j,k)*invert;
05693                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05694                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05695                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05696                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05697                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05698                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05699                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05700                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05701                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05702                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05703                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05704                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05705                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05706                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05707                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05708                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05709                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05710                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05711                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05712                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05713                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05714                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05715                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05716                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05717                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05718                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05719                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05720                                         if(peak_check) {
05721                                                 if(count < ml) {
05722                                                         count++;
05723                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05724                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05725                                                 } else {
05726                                                         if( qbf > (peaks.back()).value ) {
05727                                                                 //  do the switch and sort again
05728                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05729                                                                 peaks.pop_back();
05730                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05731                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05732                                                         }
05733                                                 }
05734                                         }
05735                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05736                                 }
05737                                 for(i=nx-1; i<=nx-1; ++i) {
05738                                         ix.clear();
05739                                         ix.push_back(i-1);
05740                                         ix.push_back(i);
05741                                         ix.push_back(0);
05742                                         float qbf = buf(i,j,k)*invert;
05743                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05744                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05745                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05746                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05747                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05748                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05749                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05750                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05751                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05752                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05753                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05754                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05755                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05756                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05757                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05758                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05759                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05760                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05761                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05762                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05763                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05764                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05765                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05766                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05767                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05768                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05769                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],3,3)*invert;
05770                                         if(peak_check) {
05771                                                 if(count < ml) {
05772                                                         count++;
05773                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05774                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05775                                                 } else {
05776                                                         if( qbf > (peaks.back()).value ) {
05777                                                                 //  do the switch and sort again
05778                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05779                                                                 peaks.pop_back();
05780                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05781                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05782                                                         }
05783                                                 }
05784                                         }
05785                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05786                                 }
05787                         }
05788                 }
05789                 }
05790                 }
05791         break;*/
05792         }
05793         // do we have a peak list yet?
05794         if (peaks.begin() != peaks.end()) {
05795           // yes. sort it
05796           sort(peaks.begin(), peaks.end(), peakcmp);
05797 
05798           int count = 0;
05799 
05800           float xval = (*peaks.begin()).value;
05801           // loop over all peaks
05802           for (vector<Pixel>::iterator it = peaks.begin(); it != peaks.end(); it++)  {
05803             // current peak count
05804             count++;
05805             // is current peak count below max?
05806             if(count <= ml) {
05807               // yes, so append it
05808               res.push_back((*it).value);
05809               res.push_back(static_cast<float>((*it).x));
05810 
05811               if(img_dim > 1) {
05812                 res.push_back(static_cast<float>((*it).y));
05813                 if(nz > 1) res.push_back(static_cast<float>((*it).z));
05814               }
05815 
05816               if(xval != 0.0) res.push_back((*it).value/xval);
05817               else            res.push_back((*it).value);
05818               res.push_back((*it).x-float(int(nx/2)));
05819               if(img_dim >1) {
05820                 res.push_back((*it).y-float(int(ny/2)));
05821                 if(nz>1)   res.push_back((*it).z-float(nz/2));
05822               }
05823             }
05824           }
05825           res.insert(res.begin(),1,img_dim);
05826         } else {
05827           // no peak list. build empty list
05828           res.push_back(buf(0,0,0));
05829           res.insert(res.begin(),1,0.0);
05830         }
05831 
05832         // return results list
05833         return res;
05834 }
05835 
05836 #define rdata(i,j,k) rdata[(i-1)+((j-1)+(k-1)*ny)*(size_t)nx]
05837 #define X(i) X[i-1]
05838 #define Y(j) Y[j-1]
05839 #define Z(k) Z[k-1]
05840 vector<float> EMData::phase_cog()
05841 {
05842         vector<float> ph_cntog;
05843         int i=1,j=1,k=1;
05844         float C=0.f,S=0.f,P=0.f,F1=0.f,SNX;
05845         if (get_ndim()==1) {
05846                 P = 8*atan(1.0f)/nx;
05847                 for (i=1;i<=nx;i++) {
05848                         C += cos(P * (i-1)) * rdata(i,j,k);
05849                         S += sin(P * (i-1)) * rdata(i,j,k);
05850                 }
05851                 F1 = atan2(S,C);
05852                 if (F1 < 0.0)  F1 += 8*atan(1.0f);
05853                 SNX = F1/P +1.0f;
05854                 SNX = SNX - ((nx/2)+1);
05855                 ph_cntog.push_back(SNX);
05856 #ifdef _WIN32
05857                 ph_cntog.push_back((float)Util::round(SNX));
05858 #else
05859                 ph_cntog.push_back(round(SNX));
05860 #endif //_WIN32
05861         } else if (get_ndim()==2)  {
05862 #ifdef _WIN32
05863                 float SNY;
05864                 float T=0.0f;
05865                 vector<float> X;
05866                 X.resize(nx);
05867 #else
05868                 float SNY,X[nx],T=0.f;
05869 #endif  //_WIN32
05870                 for ( i=1;i<=nx;i++) X(i)=0.0;
05871                 P = 8*atan(1.0f)/ny;
05872                 for(j=1;j<=ny;j++) {
05873                         T=0.f;
05874                         for(i=1;i<=nx;i++) {
05875                                 T += rdata(i,j,k);
05876                                 X(i)+=rdata(i,j,k);
05877                         }
05878                         C += cos(P*(j-1))*T;
05879                         S += sin(P*(j-1))*T;
05880                 }
05881                 F1=atan2(S,C);
05882                 if(F1<0.0)  F1 += 8*atan(1.0f);
05883                 SNY = F1/P +1.0f;
05884                 C=0.f;  S=0.f;
05885                 P = 8*atan(1.0f)/nx;
05886                 for(i=1;i<=nx;i++) {
05887                         C += cos(P*(i-1))*X(i);
05888                         S += sin(P*(i-1))*X(i);
05889                 }
05890                 F1=atan2(S,C);
05891                 if(F1<0.0) F1 += 8*atan(1.0f);
05892                 SNX = F1/P +1.0f;
05893                 SNX = SNX - ((nx/2)+1);
05894                 SNY = SNY - ((ny/2)+1);
05895                 ph_cntog.push_back(SNX); ph_cntog.push_back(SNY);
05896 #ifdef _WIN32
05897                  ph_cntog.push_back((float)Util::round(SNX)); ph_cntog.push_back((float)Util::round(SNY));
05898 #else
05899                  ph_cntog.push_back(round(SNX)); ph_cntog.push_back(round(SNY));
05900 #endif  //_WIN32
05901         } else {
05902 #ifdef _WIN32
05903                 float val=0.f,sum1=0.f, SNY,SNZ;
05904                 vector<float> X;
05905                 X.resize(nx);
05906                 vector<float> Y;
05907                 Y.resize(ny);
05908                 vector<float> Z;
05909                 Z.resize(nz);
05910 #else
05911                 float val=0.f, sum1=0.f, X[nx], Y[ny], Z[nz], SNY, SNZ;
05912 #endif  //_WIN32
05913                  for (i=1;i<=nx;i++)  X(i)=0.0;
05914                  for (j=1;j<=ny;j++)  Y(j)=0.0;
05915                  for (k=1;k<=nz;k++)  Z(k)=0.0;
05916                  for(k=1;k<=nz;k++)  {
05917                         for(j=1;j<=ny;j++) {
05918                                 sum1=0.f;
05919                                 for(i=1;i<=nx;i++)  {
05920                                         val = rdata(i,j,k);
05921                                         sum1 += val;
05922                                         X(i) += val;
05923                                 }
05924                                 Y(j) += sum1;
05925                                 Z(k) += sum1;
05926                         }
05927                 }
05928                 P = 8*atan(1.0f)/nx;
05929                 for (i=1;i<=nx;i++) {
05930                         C += cos(P*(i-1))*X(i);
05931                         S += sin(P*(i-1))*X(i);
05932                 }
05933                 F1=atan2(S,C);
05934                 if(F1<0.0) F1 += 8*atan(1.0f);
05935                 SNX = F1/P +1.0f;
05936                 C=0.f;  S=0.f;
05937                 P = 8*atan(1.0f)/ny;
05938                 for(j=1;j<=ny;j++) {
05939                         C += cos(P*(j-1))*Y(j);
05940                         S += sin(P*(j-1))*Y(j);
05941                 }
05942                 F1=atan2(S,C);
05943                 if(F1<0.0)  F1 += 8*atan(1.0f);
05944                 SNY = F1/P +1.0f;
05945                 C=0.f;  S=0.f;
05946                 P = 8*atan(1.0f)/nz;
05947                 for(k=1;k<=nz;k++) {
05948                         C += cos(P*(k-1))*Z(k);
05949                         S += sin(P*(k-1))*Z(k);
05950                 }
05951                 F1=atan2(S,C);
05952                 if(F1<0.0)  F1 += 8*atan(1.0f);
05953                 SNZ = F1/P +1.0f;
05954                 SNX = SNX - ((nx/2)+1);
05955                 SNY = SNY - ((ny/2)+1);
05956                 SNZ = SNZ - ((nz/2)+1);
05957                 ph_cntog.push_back(SNX); ph_cntog.push_back(SNY); ph_cntog.push_back(SNZ);
05958 #ifdef _WIN32
05959                 ph_cntog.push_back((float)Util::round(SNX)); ph_cntog.push_back((float)Util::round(SNY)); ph_cntog.push_back((float)Util::round(SNZ));
05960 #else
05961                 ph_cntog.push_back(round(SNX)); ph_cntog.push_back(round(SNY));ph_cntog.push_back(round(SNZ));
05962 #endif
05963         }
05964         return ph_cntog;
05965 }
05966 #undef rdata
05967 #undef X
05968 #undef Y
05969 #undef Z
05970 
05971 #define avagadro (6.023*(double)pow(10.0,23.0))
05972 #define density_protein (1.36)
05973 #define R (0.61803399f)
05974 #define C (1.f-R)
05975 float EMData::find_3d_threshold(float mass, float pixel_size)
05976 {
05977         /* Exception Handle */
05978         if(get_ndim()!=3)
05979                 throw ImageDimensionException("The image should be 3D");
05980         /* ===============================================================*/
05981 
05982         /* Calculation of the volume of the voxels */
05983         float density_1_mole, vol_1_mole, vol_angstrom;
05984         int  vol_voxels;
05985         density_1_mole = static_cast<float>( (mass*1000.0f)/avagadro );
05986         vol_1_mole =  static_cast<float>( density_1_mole/density_protein );
05987         vol_angstrom =  static_cast<float>( vol_1_mole*(double)pow((double)pow(10.0,8),3) );
05988         vol_voxels = static_cast<int> (vol_angstrom/(double)pow(pixel_size,3));
05989         /* ===============================================================*/
05990 
05991 
05992         float thr1 = get_attr("maximum");
05993         float thr3 = get_attr("minimum");
05994         float thr2 = (thr1-thr3)/2 + thr3;
05995         size_t size = (size_t)nx*ny*nz;
05996         float x0 = thr1,x3 = thr3,x1,x2,THR=0;
05997 
05998         #ifdef _WIN32
05999                 int ILE = _cpp_min(nx*ny*nx,_cpp_max(1,vol_voxels));
06000         #else
06001                 int ILE = std::min(nx*ny*nx,std::max(1,vol_voxels));
06002         #endif  //_WIN32
06003 
06004         if (abs(thr3-thr2)>abs(thr2-thr1)) {
06005                 x1=thr2;
06006                 x2=thr2+C*(thr3-thr2);
06007         } else {
06008                 x2=thr2;
06009                 x1=thr2-C*(thr2-thr1);
06010         }
06011 
06012         int cnt1=0,cnt2=0;
06013         for (size_t i=0;i<size;++i) {
06014                 if(rdata[i]>=x1)  cnt1++;
06015                 if(rdata[i]>=x2)  cnt2++;
06016         }
06017         float LF1 = static_cast<float>( cnt1 - ILE );
06018         float F1 = LF1*LF1;
06019         float LF2 = static_cast<float>( cnt2 - ILE );
06020         float F2 = LF2*LF2;
06021 
06022         while ((LF1 != 0 || LF2 != 0) && (fabs(LF1-LF2) >= 1.f) && (abs(x1-x2) > (double)pow(10.0,-5) && abs(x1-x3) > (double)pow(10.0,-5) && abs(x2-x3) > (double)pow(10.0,-5)))
06023         {
06024                 if(F2 < F1) {
06025                         x0=x1;
06026                         x1=x2;
06027                         x2 = R*x1 + C*x3;
06028                         F1=F2;
06029                         int cnt=0;
06030                         for(size_t i=0;i<size;++i)
06031                                 if(rdata[i]>=x2)
06032                                         cnt++;
06033                         LF2 = static_cast<float>( cnt - ILE );
06034                         F2 = LF2*LF2;
06035                 } else {
06036                         x3=x2;
06037                         x2=x1;
06038                         x1=R*x2 + C*x0;
06039                         F2=F1;
06040                         int cnt=0;
06041                         for(size_t i=0;i<size;++i)
06042                                 if(rdata[i]>=x1)
06043                                         cnt++;
06044                         LF1 = static_cast<float>( cnt - ILE );
06045                         F1 = LF1*LF1;
06046                 }
06047         }
06048 
06049         if(F1 < F2) {
06050                 ILE = static_cast<int> (LF1 + ILE);
06051                 THR = x1;
06052         } else {
06053                 ILE = static_cast<int> (LF2 + ILE);
06054                 THR = x2;
06055         }
06056         return THR;
06057 
06058 }
06059 #undef avagadro
06060 #undef density_protein
06061 #undef R
06062 #undef C
06063 
06064 
06065 // reworked peak_ccf uses max queue lenght for peak objects, i.e. lowest
06066 //    peaks are deleted if queue length is exceeded and a new peak is inserted
06067 //    instead.
06068 
06069 
06070 vector<float> EMData::peak_ccf(float hf_p)
06071 {
06072 
06073   // cout << "peak ccf starting up" << endl;
06074 
06075   EMData & buf = *this;
06076   vector<Pixel> peaks;
06077   int half=int(hf_p);
06078   float hf_p2 = hf_p*hf_p;
06079   int i,j;
06080   int i__1,i__2;
06081   int j__1,j__2;
06082   vector<float>res;
06083   int nx = buf.get_xsize()-half;
06084   int ny = buf.get_ysize()-half;
06085   // iterate over image
06086   for(i=half; i<=nx; ++i) {
06087     // static assignment so we don't have to re-evaluate
06088     i__1 = i-1;
06089     i__2 = i+1;
06090     for (j=half;j<=ny;++j) {
06091       j__1 = j-1;
06092       j__2 = j+1;
06093 
06094       if((buf(i,j)>0.0f)&&buf(i,j)>buf(i,j__1)) {
06095         if(buf(i,j)>buf(i,j__2)) {
06096           if(buf(i,j)>buf(i__1,j)) {
06097             if(buf(i,j)>buf(i__2,j)) {
06098               if(buf(i,j)>buf(i__1,j__1)) {
06099                 if((buf(i,j))> buf(i__1,j__2)) {
06100                   if(buf(i,j)>buf(i__2,j__1)) {
06101                     if(buf(i,j)> buf(i__2,j__2)) {
06102 
06103                       // found a peak
06104                       // empty list?
06105                       if (peaks.size()==0) {
06106                         // yes, so just push the peak onto the list
06107                         peaks.push_back(Pixel(i,j,0,buf(i,j)));
06108 
06109                       } else {
06110                         // not empty list. check neighbourhood for peaks
06111                         // logical not in the name is awkward. renamed to overlap
06112                         bool overlap = false;
06113                         //int  size = peaks.size();
06114 
06115                         // list of peaks to be deleted, if the current peak is the largest (see below).
06116                         //    list contains iterators to the original list, which will have to be processed
06117                         //    back to front (i.e. LIFO: stl::stack)
06118                         std::stack <vector<Pixel>::iterator> delete_stack;
06119 
06120                         // loop over all peaks found so far. this would be nicer with iterators
06121                         for (vector<Pixel>::iterator it=peaks.begin();it!=peaks.end();++it) {
06122                         // for ( int kk= 0; kk< size; kk++) {
06123                         //  vector<Pixel>::iterator it = peaks.begin()+kk;
06124 
06125                           // calc L2 distance
06126                           float radius=((*it).x-float(i))*((*it).x-float(i))+((*it).y-float(j))*((*it).y-float(j));
06127                           if (radius <= hf_p2 ) {
06128                             // peaks overlap
06129                             if( buf(i,j) > (*it).value) {
06130                               // this peak (indexed by (i,j)) is larger, mark the old for deletion
06131                               //    however, we have to be careful. if there is a larger peak within the vicinity of
06132                               //    the new one, this new peak is not marked as such, and the deletion of prior low
06133                               //    peaks should not continued. to make sure this deletion does not happen, we have
06134                               //    to make sure we cycle through all peaks within the vicinity, and only delete smaller
06135                               //    peaks if this new one is the largest in the vicinity.
06136                               delete_stack.push(it);
06137 
06138                               //(*it).x = -half; // this marks entry to be deleted, since it's smaller than the new one
06139 
06140 
06141                             } else {
06142                               overlap = true;
06143                               // old peak is larger, ignore this one. since it's enough to know there is some peak larger
06144                               //    than this one, we can break out of the peak list loop, instead of continuing.
06145                               break;
06146                             }
06147                           }
06148                         }
06149 
06150                         // check whether we need to delete anything. this is marked by the flag overlap == false
06151                         // loop over all peaks and clean out redundant ones
06152                         if (false == overlap) {
06153                           vector<Pixel>::iterator delete_iterator;
06154                           while (!delete_stack.empty()) {
06155                             // pop empties the stack from the back. since we are dealing with iterators, we need to delete
06156                             //    from the back, so as to keep the rest stack intact upon deletion.
06157                             delete_iterator = delete_stack.top();
06158                             peaks.erase(delete_iterator);
06159                             delete_stack.pop();
06160                           }
06161                           // before pushing the peak, we need to check whether max queue length is exceeded and delete
06162                           //     peaks if necessary.
06163                           // XXX: remove hardcoded value!
06164                           if (! (peaks.size() < 2000 )) {
06165 
06166                             //cout << ".";
06167                             // we need to delete a peak first.
06168                             // - resort list to get lowest peak at the back
06169                             sort(peaks.begin(), peaks.end(), peakcmp);
06170 
06171                             // - remove lowest peak
06172                             peaks.pop_back();
06173                           }
06174 
06175                           // push the new peak onto the list of peaks
06176                           peaks.push_back(Pixel(i,j,0,buf(i,j)));
06177                           //cout << "done." << endl;
06178 
06179                         } else {
06180                           // this peak too small and is ignored, so delete_list is ignored as well. make sure delete_list
06181                           //    is empty. probably redundant because of scope, but better safe than sorry.....
06182                           while (!delete_stack.empty()) delete_stack.pop();
06183                         }
06184                       }
06185                     }
06186                   }}}}}}}
06187     }
06188   }
06189 
06190   // we have peaks, so build a results vector.
06191   if(peaks.size()>0) {
06192     // sort peaks by size
06193     sort(peaks.begin(),peaks.end(), peakcmp);
06194     // and push all peaks to the results vector
06195     for (vector<Pixel>::iterator it = peaks.begin(); it != peaks.end(); it++) {
06196       // XXX: this format is necessary for Boost to work???
06197       res.push_back((*it).value);
06198       res.push_back(static_cast<float>((*it).x));
06199       res.push_back(static_cast<float>((*it).y));
06200     }
06201   } else {
06202     // only one or zero (?) entries
06203     res.push_back(buf(0,0,0));
06204     res.insert(res.begin(),1,0.0);
06205   }
06206   return res;
06207 }
06208 
06209 EMData* EMData::get_pow(float n_pow)
06210 {
06211         EMData* buf_new = this->copy_head();
06212         float *in  = this->get_data();
06213         float *out = buf_new->get_data();
06214         for(size_t i=0; i<(size_t)nx*ny*nz; ++i) out[i] = pow(in[i],n_pow);
06215         return buf_new;
06216 }
06217 
06218 EMData* EMData::conjg()
06219 {
06220         if(this->is_complex()) {
06221                 EMData* buf_new = this->copy_head();
06222                 float *in  = this->get_data();
06223                 float *out = buf_new->get_data();
06224                 for(size_t i=0; i<(size_t)nx*ny*nz; i+=2) {out[i] = in[i]; out[i+1] = -in[i+1];}
06225                 return buf_new;
06226         } else throw ImageFormatException("image has to be complex");
06227 }
06228 
06229 EMData* EMData::delete_disconnected_regions(int ix, int iy, int iz) {
06230         if (3 != get_ndim())
06231                 throw ImageDimensionException("delete_disconnected_regions needs a 3-D image.");
06232         if (is_complex())
06233                 throw ImageFormatException("delete_disconnected_regions requires a real image");
06234         if ((*this)(ix+nx/2,iy+ny/2,iz+nz/2) == 0)
06235                 throw ImageDimensionException("delete_disconnected_regions starting point is zero.");
06236 
06237         EMData* result = this->copy_head();
06238         result->to_zero();
06239         (*result)(ix+nx/2,iy+ny/2,iz+nz/2) = (*this)(ix+nx/2,iy+ny/2,iz+nz/2);
06240         bool kpt = true;
06241         //cout << "  delete   "<<(*result)(ix+nx/2,iy+ny/2,iz+nz/2)<<endl;
06242         while(kpt) {
06243                 kpt = false;
06244                 for (int cz = 1; cz < nz-1; cz++) {
06245                         for (int cy = 1; cy < ny-1; cy++) {
06246                                 for (int cx = 1; cx < nx-1; cx++) {
06247                                         if((*result)(cx,cy,cz) == 1) {
06248                                                 for (int lz = -1; lz <= 1; lz++) {
06249                                                         for (int ly = -1; ly <= 1; ly++) {
06250                                                                 for (int lx = -1; lx <= 1; lx++) {
06251                                                                         if(((*this)(cx+lx,cy+ly,cz+lz) == 1) && ((*result)(cx+lx,cy+ly,cz+lz) == 0))  {
06252                                                                                 (*result)(cx+lx,cy+ly,cz+lz) = 1;
06253                                                                                 kpt = true;
06254                                                                         }
06255                                                                 }
06256                                                         }
06257                                                 }
06258                                         }
06259                                 }
06260                         }
06261                 }
06262         }
06263         result->update();
06264         return result;
06265 }
06266 
06267 #define    QUADPI                       3.141592653589793238462643383279502884197
06268 #define    DGR_TO_RAD                   QUADPI/180
06269 
06270 EMData* EMData::helicise(float pixel_size, float dp, float dphi, float section_use, float radius, float minrad) {
06271         if (3 != get_ndim())
06272                 throw ImageDimensionException("helicise needs a 3-D image.");
06273         if (is_complex())
06274                 throw ImageFormatException("helicise requires a real image");
06275         EMData* result = this->copy_head();
06276         result->to_zero();
06277         int nyc = ny/2;
06278         int nxc = nx/2;
06279         int vl = nz-1; //lengh of the volume in pixel
06280         if ( section_use < dp/int(vl*pixel_size) )      
06281                 section_use = (dp)/int(vl*pixel_size);
06282                 
06283         float nb = vl*(1.0f - section_use)/2.0f;
06284 
06285         float ne =  nb+vl*section_use;
06286         int numst = int( (ne-nb)*pixel_size/dp );
06287         
06288         
06289         float r2, ir;
06290         if(radius < 0.0f) r2 = (float)((nxc-1)*(nxc-1));
06291         else r2 = radius*radius;
06292         if(minrad < 0.0f) ir = 0.0f;
06293         else ir = minrad*minrad;
06294         for (int k = 0; k<nz; k++) {
06295                 int nst1 = int ( (nb-k)*pixel_size/dp) -1;
06296                 int nst2 = int ( (ne-k)*pixel_size/dp) +1;
06297                 for (int j = 0; j<ny; j++) {
06298                         int jy = j - nyc;
06299                         int jj = jy*jy;
06300                         for (int i = 0; i<nx; i++) {
06301                                 int ix = i - nxc;
06302                                 float d2 = (float)(ix*ix + jj);
06303                                 if(d2 <= r2 && d2>=ir) {
06304                                         int nq = 0;
06305                                         for ( int ist = nst1; ist < nst2; ist++) {
06306                                                 float zold = (k*pixel_size + ist*dp)/pixel_size;
06307                                                 
06308                                                 if(zold >= nb && zold <= ne) {
06309                                                         // now x-y position
06310                                                         float cphi = ist*dphi*(float)DGR_TO_RAD;
06311                                                         float ca = cos(cphi);
06312                                                         float sa = sin(cphi);
06313                                                         float xold = ix*ca - jy*sa + nxc;
06314                                                         float yold = ix*sa + jy*ca + nyc;
06315                                                         nq++;
06316 
06317         int IOZ = int(zold);
06318         //  Do tri-linear interpolation
06319         int IOX = int(xold);
06320         int IOY = int(yold);
06321         //int IOZ = int(zold);
06322 
06323         #ifdef _WIN32
06324         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
06325         #else
06326         int IOXp1 = std::min( nx-1 ,IOX+1);
06327         #endif  //_WIN32
06328 
06329         #ifdef _WIN32
06330         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
06331         #else
06332         int IOYp1 = std::min( ny-1 ,IOY+1);
06333         #endif  //_WIN32
06334 
06335         #ifdef _WIN32
06336         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
06337         #else
06338         int IOZp1 = std::min( nz-1 ,IOZ+1);
06339         #endif  //_WIN32
06340 
06341         float dx = xold-IOX;
06342         float dy = yold-IOY;
06343         float dz = zold-IOZ;
06344 
06345         float a1 = (*this)(IOX,IOY,IOZ);
06346         float a2 = (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOY,IOZ);
06347         float a3 = (*this)(IOX,IOYp1,IOZ) - (*this)(IOX,IOY,IOZ);
06348         float a4 = (*this)(IOX,IOY,IOZp1) - (*this)(IOX,IOY,IOZ);
06349         float a5 = (*this)(IOX,IOY,IOZ) - (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOYp1,IOZ) + (*this)(IOXp1,IOYp1,IOZ);
06350         float a6 = (*this)(IOX,IOY,IOZ) - (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOY,IOZp1) + (*this)(IOXp1,IOY,IOZp1);
06351         float a7 = (*this)(IOX,IOY,IOZ) - (*this)(IOX,IOYp1,IOZ) - (*this)(IOX,IOY,IOZp1) + (*this)(IOX,IOYp1,IOZp1);
06352         float a8 = (*this)(IOXp1,IOY,IOZ) + (*this)(IOX,IOYp1,IOZ)+ (*this)(IOX,IOY,IOZp1)
06353                         - (*this)(IOX,IOY,IOZ)- (*this)(IOXp1,IOYp1,IOZ) - (*this)(IOXp1,IOY,IOZp1)
06354                         - (*this)(IOX,IOYp1,IOZp1) + (*this)(IOXp1,IOYp1,IOZp1);
06355 
06356 
06357 
06358                                                         (*result)(i,j,k) += a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
06359                                                         if(nq == numst) break;
06360                                                 }
06361                                         }
06362                                         if(nq != numst)
06363                                                 throw InvalidValueException(nq, "Helicise: incorrect number of repeats encoutered.");
06364                                 }
06365                         }
06366                 }
06367         }
06368         for (int k = 0; k<nz; k++) for (int j = 0; j<ny; j++) for (int i = 0; i<nx; i++) (*result)(i,j,k) /= numst ;
06369 
06370         result->update();
06371         return result;
06372 }
06373 
06374 
06375 
06376 EMData* EMData::helicise_grid(float pixel_size, float dp, float dphi, Util::KaiserBessel& kb, float section_use, float radius, float minrad) {
06377         std::cout<<"111111"<<std::endl;
06378         if (3 != get_ndim())
06379                 throw ImageDimensionException("helicise needs a 3-D image.");
06380         if (is_complex())
06381                 throw ImageFormatException("helicise requires a real image");
06382         //begin griding
06383         //if (scale_input == 0.0f) scale_input = 1.0f;
06384         float  scale = 0.5f;//*scale_input;
06385 
06386         
06387         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
06388 
06389         vector<int> saved_offsets = get_array_offsets();
06390         set_array_offsets(0,0,0);
06391         EMData* ret = this->copy_head();
06392 #ifdef _WIN32
06393         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
06394 #else
06395         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
06396 #endif  //_WIN32
06397         ret->to_zero();  //we will leave margins zeroed.
06398 
06399         // center of big image,
06400         int xc = nxn;
06401         int ixs = nxn%2;  // extra shift on account of odd-sized images
06402         int yc = nyn;
06403         int iys = nyn%2;
06404         int zc = nzn;
06405         int izs = nzn%2;
06406         // center of small image
06407         int xcn = nxn/2;
06408         int ycn = nyn/2;
06409         int zcn = nzn/2;
06410         // shifted center for rotation
06411         float shiftxc = xcn; // + delx;
06412         float shiftyc = ycn; // + dely;
06413         float shiftzc = zcn; // + delz;
06414         // bounds if origin at center
06415         float zmin = -nz/2.0f;
06416         float ymin = -ny/2.0f;
06417         float xmin = -nx/2.0f;
06418         float zmax = -zmin;
06419         float ymax = -ymin;
06420         float xmax = -xmin;
06421         if (0 == nx%2) xmax--;
06422         if (0 == ny%2) ymax--;
06423         if (0 == nz%2) zmax--;
06424 
06425         float* data = this->get_data();
06426 
06427         
06428         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
06429          
06430         //float a13 = -0.0f;    float a23 =  0.0f;
06431         //float a31 =  0.0f;          float a32 =  0.0f;          float a33 =  1.0f;
06432                 
06433         //end gridding
06434 
06435         
06436         int nyc = nyn/2;
06437         int nxc = nxn/2;
06438         int nb = int(nzn*(1.0f - section_use)/2.);
06439         int ne = nzn - nb -1;
06440         int numst = int(nzn*section_use*pixel_size/dp);
06441         // how many steps needed total, fewer will be used, only those that fall between nb and ne
06442         int nst = int(nzn*pixel_size/dp);
06443         float r2, ir;
06444         if(radius < 0.0f) r2 = (float)((nxc-1)*(nxc-1));
06445         else r2 = radius*radius;
06446         if(minrad < 0.0f) ir = 0.0f;
06447         else ir = minrad*minrad;
06448         
06449         for (int k = 0; k<nzn; k++) {
06450                 for (int j = 0; j<nyn; j++) {
06451                         int jy = j - nyc;
06452                         int jj = jy*jy;
06453                         for (int i = 0; i<nxn; i++) {
06454                                 int ix = i - nxc;
06455                                 float d2 = (float)(ix*ix + jj);
06456                                 if(d2 <= r2 && d2>=ir) {
06457                                         int nq = 0;
06458                                         for ( int ist = -nst; ist <= nst; ist++) {
06459                                                 float zold = (k*pixel_size + ist*dp)/pixel_size;
06460                                                 int IOZ = int(zold);
06461                                                 if(IOZ >= nb && IOZ <= ne) {
06462                                                 
06463                                                         float cphi = ist*dphi*(float)DGR_TO_RAD;
06464                                                         float ca = cos(cphi);
06465                                                         float sa = sin(cphi);
06466                                                         
06467                                                         float xold = ix*ca - jy*sa + nxc;
06468                                                         float yold = ix*sa + jy*ca + nyc;
06469                                                         
06470                                                         float xold_big = (xold-shiftxc)/scale - ixs + xc;
06471                                                         float yold_big = (yold-shiftyc)/scale - iys + yc;
06472                                                         float zold_big = (zold-shiftzc)/scale - izs + zc;
06473                                                         
06474                                                         /*float a11 =  ca; float a12 =  sa;
06475                                                         float a21 = -sa; float a22 = ca;
06476                                                         
06477                                                         float z = (zold - shiftzc)/scale;
06478                                                         float zco1 = a31*z+xc;
06479                                                         float zco2 = a32*z+yc;
06480                                                         float zco3 = a33*z+zc;
06481                                                                                                                 
06482                                                         float y = (float(j) - shiftyc)/scale;
06483                                                         float yco1 = zco1+a21*y;
06484                                                         float yco2 = zco2+a22*y;
06485                                                         float yco3 = zco3+a23*y;
06486                                                         
06487                                                         float x = (float(i) - shiftxc)/scale;
06488                                                         float xold_big = yco1+a11*x-ixs; //have to add the fraction on account on odd-sized images for which Fourier zero-padding changes the center location
06489                                                         float yold_big = yco2+a12*x-iys;
06490                                                         float zold_big = yco3+a13*x-izs;*/
06491                                                         
06492                                                                                                 
06493                                                         nq++;
06494                                                         
06495                                                                 
06496                                                         (*ret)(i,j,k) += Util::get_pixel_conv_new(nx, ny, nz, xold_big, yold_big, zold_big, data, kb);
06497                                                         
06498                                                         
06499                                                         if(nq == numst) break;
06500                                                 }
06501                                         }
06502                                         if(nq != numst)
06503                                                 throw InvalidValueException(nq, "Helicise: incorrect number of repeats encoutered.");
06504                                 }
06505                         }
06506                 }
06507         }
06508         
06509         for (int k = 0; k<nzn; k++) for (int j = 0; j<nyn; j++) for (int i = 0; i<nxn; i++) (*ret)(i,j,k) /= numst ;
06510         set_array_offsets(saved_offsets);
06511         ret->update();
06512         return ret;
06513 }
06514 
06515 
06516 /*
06517 Purpose: Depad and remove FT extension from a real image.
06518 Method: Depad and remove FT extension from a real image.
06519 return new image.
06520 Input: f real n-dimensional image
06521 Output: depadded image
06522  */
06523 void EMData::depad() {
06524         if (is_complex())
06525                 throw ImageFormatException("Depadding of complex images not supported");
06526         vector<int> saved_offsets = get_array_offsets();
06527         set_array_offsets(0,0,0);
06528         int npad = attr_dict["npad"];
06529         if (0 == npad) npad = 1;
06530         int offset = is_fftodd() ? 1 : 2;
06531         int nxold = (nx - offset)/npad;
06532 #ifdef _WIN32
06533         int nyold = _cpp_max(ny/npad, 1);
06534         int nzold = _cpp_max(nz/npad, 1);
06535 #else
06536         int nyold = std::max<int>(ny/npad, 1);
06537         int nzold = std::max<int>(nz/npad, 1);
06538 #endif  //_WIN32
06539         int xstart = 0, ystart = 0, zstart = 0;
06540         if( npad > 1) {
06541                 xstart = (nx - offset - nxold)/2 + nxold%2;
06542                 if(ny > 1) {
06543                         ystart = (ny - nyold)/2 + nyold%2;
06544                         if(nz > 1) {
06545                                 zstart = (nz - nzold)/2 + nzold%2;
06546                         }
06547                 }
06548         }
06549         int bytes = nxold*sizeof(float);
06550         float* dest = get_data();
06551         for (int iz=0; iz < nzold; iz++) {
06552                 for (int iy = 0; iy < nyold; iy++) {
06553                         memmove(dest, &(*this)(xstart,iy+ystart,iz+zstart), bytes);
06554                         dest += nxold;
06555                 }
06556         }
06557         set_size(nxold, nyold, nzold);
06558         set_attr("npad", 1);
06559         set_fftpad(false);
06560         set_fftodd(false);
06561         set_complex(false);
06562         if(ny==1 && nz==1) set_complex_x(false);
06563         set_array_offsets(saved_offsets);
06564         update();
06565         EXITFUNC;
06566 }
06567 
06568 /*
06569 Purpose: Depad and remove FT extension from a real image.
06570 Method: Depad and remove FT extension from a real image.
06571 return new image.
06572 Input: f real n-dimensional image
06573 Output: depadded image
06574  */
06575 void EMData::depad_corner() {
06576         if(is_complex())
06577                 throw ImageFormatException("Depadding of complex images not allowed");
06578         vector<int> saved_offsets = get_array_offsets();
06579         set_array_offsets(0,0,0);
06580         int npad = attr_dict["npad"];
06581         if(0 == npad) npad = 1;
06582         int offset = is_fftodd() ? 1 : 2;
06583         int nxold = (nx - offset)/npad;
06584 #ifdef _WIN32
06585         int nyold = _cpp_max(ny/npad, 1);
06586         int nzold = _cpp_max(nz/npad, 1);
06587 #else
06588         int nyold = std::max<int>(ny/npad, 1);
06589         int nzold = std::max<int>(nz/npad, 1);
06590 #endif  //_WIN32
06591         size_t bytes = nxold*sizeof(float);
06592         float* dest = get_data();
06593         for (int iz=0; iz < nzold; iz++) {
06594                 for (int iy = 0; iy < nyold; iy++) {
06595                         memmove(dest, &(*this)(0,iy,iz), bytes);
06596                         dest += nxold;
06597                 }
06598         }
06599         set_size(nxold, nyold, nzold);
06600         set_attr("npad", 1);
06601         set_fftpad(false);
06602         set_fftodd(false);
06603         set_complex(false);
06604         if(ny==1 && nz==1) set_complex_x(false);
06605         set_array_offsets(saved_offsets);
06606         update();
06607         EXITFUNC;
06608 }
06609 
06610 
06611 // calculate circumference of the surrounding 1 pixel.
06612 float circumference( EMData* emdata, int npixel )
06613 {
06614         int nx = emdata->get_xsize();
06615         int ny = emdata->get_ysize();
06616         int nz = emdata->get_zsize();
06617 
06618         float* data = emdata->get_data();
06619         if( ny==1 && nz==1 ) {
06620                 // 1d case
06621                 float sumf=0.0;
06622                 int   sumn=0;
06623                 for( int i=0; i < npixel; ++i ) {
06624                         sumf += data[i];
06625                         sumf += data[nx-1-i];
06626                         sumn += 2;
06627                 }
06628                 return sumf/sumn;
06629         }
06630 
06631         if( nz==1 ) {
06632                 float sumf=0.0;
06633                 int   sumn=0;
06634                 int   id=0;
06635                 for( int iy=0; iy < ny; ++iy ) {
06636                         for( int ix=0; ix < nx; ++ix ) {
06637                                 if( iy<npixel || iy>ny-1-npixel || ix<npixel || ix>nx-1-npixel ) {
06638                                     sumf += data[id];
06639                                     sumn += 1;
06640                                 }
06641                                 id++;
06642                         }
06643                 }
06644 
06645                 Assert( id==nx*ny  );
06646                 Assert( sumn == nx*ny - (nx-2*npixel)*(ny-2*npixel) );
06647                 return sumf/sumn;
06648         }
06649 
06650         // 3d cases;
06651 
06652         float sumf = 0.0;
06653         size_t   sumn = 0;
06654         size_t   id = 0;
06655         for( int iz=0; iz < nz; ++iz) {
06656                 for( int iy=0; iy < ny; ++iy) {
06657                         for( int ix=0; ix < nx; ++ix ) {
06658                                 if( iz<npixel||iz>nz-1-npixel||iy<npixel||iy>ny-1-npixel||ix<npixel||ix>nx-1-npixel) {
06659                                         sumf += data[id];
06660                                         sumn += 1;
06661                                 }
06662                                 id++;
06663                         }
06664                 }
06665         }
06666 
06667 
06668         Assert( id==(size_t)nx*ny*nz);
06669         Assert( sumn==(size_t)nx*ny*nz-(size_t)(nx-2*npixel)*(ny-2*npixel)*(nz-2*npixel) );
06670         return sumf/sumn;
06671 }
06672 /*
06673 Purpose: Create a new [normalized] [zero-padded]  image.
06674 Method: Normalize, pad with zero or circumference, extend for fft,
06675 return new image.
06676 Input: f real n-dimensional image
06677 flag specify normalize, pad, and/or extend
06678 Output: zero-padded, ft-extended, normalized input image
06679  */
06680 EMData* EMData::norm_pad(bool donorm, int npad, int valtype) {
06681         if (this->is_complex())
06682                 throw ImageFormatException("Padding of complex images not supported");
06683         int nx = this->get_xsize();
06684         int ny = this->get_ysize();
06685         int nz = this->get_zsize();
06686         float mean = 0., stddev = 1.;
06687         if(donorm) { // Normalization requested
06688                 mean = this->get_attr("mean");
06689                 stddev = this->get_attr("sigma");
06690         }
06691         // sanity check
06692         if (npad < 1) npad = 1;
06693         int nxpad = npad*nx;
06694         int nypad = npad*ny;
06695         int nzpad = npad*nz;
06696         if (1 == ny) {
06697                 // 1-d image, don't want to pad along y or z
06698                 // Also, assuming that we can't have an image sized as nx=5, ny=1, nz=5.
06699                 nypad = ny;
06700                 nzpad = nz;
06701         } else if (nz == 1) {
06702                 // 2-d image, don't want to pad along z
06703                 nzpad = nz;
06704         }
06705         size_t bytes;
06706         size_t offset;
06707         // Not currently fft-extended, so we want to extend for ffts
06708         offset = 2 - nxpad%2;
06709         bytes = nx*sizeof(float);
06710         EMData* fpimage = copy_head();
06711         fpimage->set_size(nxpad+offset, nypad, nzpad);
06712         int xstart = 0, ystart = 0, zstart = 0;
06713         if( npad > 1) {
06714                 if( valtype==0 ) {
06715                         fpimage->to_zero();
06716                 } else {
06717                         float val = circumference(this, 1);
06718                         float* data = fpimage->get_data();
06719                         int nxyz = (nxpad+offset)*nypad*nzpad;
06720                         for( int i=0; i < nxyz; ++i )  data[i] = val;
06721                 }
06722 
06723                 xstart = (nxpad - nx)/2 + nx%2;
06724                 if(ny > 1) {
06725                         ystart = (nypad - ny)/2 + ny%2;
06726                         if(nz > 1) {
06727                                 zstart = (nzpad - nz)/2 + nz%2;
06728                         }
06729                 }
06730         }
06731 
06732 
06733         vector<int> saved_offsets = this->get_array_offsets();
06734         this->set_array_offsets( 0, 0, 0 );
06735         for (int iz = 0; iz < nz; iz++) {
06736                 for (int iy = 0; iy < ny; iy++) {
06737                         memcpy(&(*fpimage)(xstart,iy+ystart,iz+zstart), &(*this)(0,iy,iz), bytes);
06738                 }
06739         }
06740         this->set_array_offsets( saved_offsets );
06741 
06742 
06743         //  Perform the actual normalization (only on the
06744         //  non-zero section of the image)
06745         if (donorm) { // Normalization requested
06746                 for (int iz = zstart; iz < nz+zstart; iz++)
06747                         for (int iy = ystart; iy < ny+ystart; iy++)
06748                                 for (int ix = xstart; ix < nx+xstart; ix++)
06749                                         (*fpimage)(ix,iy,iz) = ((*fpimage)(ix,iy,iz)-mean)/stddev;
06750         }
06751 
06752         fpimage->set_fftpad(true);
06753         fpimage->set_attr("npad", npad);
06754         if (offset == 1) fpimage->set_fftodd(true);
06755         else             fpimage->set_fftodd(false);
06756         return fpimage;
06757 }
06758 
06759 void EMData::center_origin()
06760 {
06761         ENTERFUNC;
06762         if (is_complex()) {
06763                 LOGERR("Real image expected. Input image is complex.");
06764                 throw ImageFormatException("Real image expected. Input image is complex.");
06765         }
06766         for (int iz = 0; iz < nz; iz++) {
06767                 for (int iy = 0; iy < ny; iy++) {
06768                         for (int ix = 0; ix < nx; ix++) {
06769                                 // next line multiplies by +/- 1
06770                                 (*this)(ix,iy,iz) *= -2*((ix+iy+iz)%2) + 1;
06771                         }
06772                 }
06773         }
06774         update();
06775         EXITFUNC;
06776 }
06777 
06778 void EMData::center_origin_yz()
06779 {
06780         ENTERFUNC;
06781         if (is_complex()) {
06782                 LOGERR("Real image expected. Input image is complex.");
06783                 throw ImageFormatException("Real image expected. Input image is complex.");
06784         }
06785         for (int iz = 0; iz < nz; iz++) {
06786                 for (int iy = (iz+1)%2; iy < ny; iy+=2) {
06787                         for (int ix = 0; ix < nx; ix++) {
06788                                 (*this)(ix,iy,iz) *= -1;
06789                         }
06790                 }
06791         }
06792         update();
06793         EXITFUNC;
06794 }
06795 
06796 void EMData::center_origin_fft()
06797 {
06798         ENTERFUNC;
06799         if (!is_complex()) {
06800                 LOGERR("complex image expected. Input image is real image.");
06801                 throw ImageFormatException("complex image expected. Input image is real image.");
06802         }
06803 
06804         if (!is_ri()) {
06805                 LOGWARN("Only RI should be used. ");
06806         }
06807         vector<int> saved_offsets = get_array_offsets();
06808         // iz in [1,nz], iy in [1,ny], ix in [0,nx/2], but nx comes in as extended and is the same for odd
06809         //                                                 and even, so we can ignore the difference...
06810         //                         in short, as nx is extended, it should be  ix in [0,(nx-2)/2],  corrected PAP 05/20
06811         set_array_offsets(0,1,1);
06812         int nxc = nx/2;
06813 
06814         if (is_fftodd()) {
06815                 for (int iz = 1; iz <= nz; iz++) {
06816                         for (int iy = 1; iy <= ny; iy++) {
06817                                 for (int ix = 0; ix < nxc; ix++) {
06818                                         cmplx(ix,iy,iz) *= float(-2*((ix+iy+iz)%2) + 1);
06819                                         float temp = float(iz-1+iy-1+ix)/float(ny)*M_PI;
06820                                         complex<float> temp2 = complex<float>(cos(temp), -sin(temp));
06821                                         cmplx(ix,iy,iz) *= temp2;
06822                                 }
06823                         }
06824                 }
06825         } else {
06826                 for (int iz = 1; iz <= nz; iz++) {
06827                         for (int iy = 1; iy <= ny; iy++) {
06828                                 for (int ix = 0; ix < nxc; ix++) {
06829                                         // next line multiplies by +/- 1
06830                                         cmplx(ix,iy,iz) *= float(-2*((ix+iy+iz)%2) + 1);
06831                                 }
06832                         }
06833                 }
06834         }
06835         set_array_offsets(saved_offsets);
06836         update();
06837         EXITFUNC;
06838 }
06839 
06840 
06841 #define  fint(i,j,k)  fint[(i-1) + ((j-1) + (k-1)*ny)*(size_t)lsd]
06842 #define  fout(i,j,k)  fout[(i-1) + ((j-1) + (k-1)*nyn)*(size_t)lsdn]
06843 EMData *EMData::FourInterpol(int nxn, int nyni, int nzni, bool RetReal) {
06844 
06845         int nyn, nzn, lsd, lsdn, inx, iny, inz;
06846         int i, j, k;
06847         if (is_complex())
06848                 throw ImageFormatException("Input image has to be real");
06849 
06850         if(ny > 1) {
06851                 nyn = nyni;
06852                 if(nz > 1) {
06853                         nzn = nzni;
06854                 }  else {
06855                         nzn = 1;
06856                 }
06857         } else {
06858                 nyn = 1; nzn = 1;
06859         }
06860         if(nxn<nx || nyn<ny || nzn<nz)  throw ImageDimensionException("Cannot reduce the image size");
06861         lsd = nx + 2 - nx%2;
06862         lsdn = nxn + 2 - nxn%2;
06863 //  do out of place ft
06864         EMData *temp_ft = do_fft();
06865         EMData *ret = this->copy();
06866         ret->set_size(lsdn, nyn, nzn);
06867         ret->to_zero();
06868         float *fout = ret->get_data();
06869         float *fint = temp_ft->get_data();
06870 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
06871 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
06872         float  sq2 = 1.0f/std::sqrt(2.0f);
06873         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
06874         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
06875         inx = nxn-nx; iny = nyn - ny; inz = nzn - nz;
06876         for (k=1; k<=nz/2+1; k++) for (j=1; j<=ny/2+1; j++) for (i=1; i<=lsd; i++) fout(i,j,k)=fint(i,j,k);
06877         if(nyn>1) {
06878         //cout << "  " <<nxn<<"  " <<nyn<<" A " <<nzn<<endl;
06879                 for (k=1; k<=nz/2+1; k++) for (j=ny/2+2+iny; j<=nyn; j++) for (i=1; i<=lsd; i++) fout(i,j,k)=fint(i,j-iny,k);
06880                 if(nzn>1) {
06881                         for (k=nz/2+2+inz; k<=nzn; k++) {
06882                                 for (j=1; j<=ny/2+1; j++) {
06883                                         for (i=1; i<=lsd; i++) {
06884                                                 fout(i,j,k)=fint(i,j,k-inz);
06885                                         }
06886                                 }
06887                                 for (j=ny/2+2+iny; j<=nyn; j++) {
06888                                         for (i=1; i<=lsd; i++) {
06889                                                 fout(i,j,k)=fint(i,j-iny,k-inz);
06890                                         }
06891                                 }
06892                         }
06893                 }
06894         }
06895 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
06896 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
06897 //       ELEMENT.
06898         if(nx%2 == 0 && inx !=0) {
06899                 for (k=1; k<=nzn; k++) {
06900                         for (j=1; j<=nyn; j++) {
06901                                 fout(nx+1,j,k) *= sq2;
06902                                 fout(nx+2,j,k) *= sq2;
06903                         }
06904                 }
06905                 if(nyn>1) {
06906                         for (k=1; k<=nzn; k++) {
06907                           for (i=1; i<=lsd; i++) {
06908                             fout(i,ny/2+1+iny,k) = sq2*fout(i,ny/2+1,k);
06909                             fout(i,ny/2+1,k) *= sq2;
06910                           }
06911                         }
06912                         if(nzn>1) {
06913                                 for (j=1; j<=nyn; j++) {
06914                                         for (i=1; i<=lsd; i++) {
06915                                                 fout(i,j,nz/2+1+inz) = sq2*fout(i,j,nz/2+1);
06916                                                 fout(i,j,nz/2+1) *= sq2;
06917                                         }
06918                                 }
06919                         }
06920                 }
06921         }
06922         ret->set_complex(true);
06923 /*
06924 //  For padding from odd to even dimension additional shift by 1 pixel is necessary.
06925         float  xshift = 0.f, yshift = 0.f, zshift = 0.f;
06926         int nyn2, nzn2;
06927         if(nxn > nx && nx%2 == 1)  xshift = 1.0f;
06928         if(ny > 1) {
06929                 if(nyn > ny && ny%2 == 1)  yshift = 1.0f;
06930                 nyn2 = nyn/2;
06931                 if(nz > 1) {
06932                         if(nzn > nz && nz%2 == 1)  zshift = 1.0f;
06933                         nzn2 = nzn/2;
06934                 }  else {
06935                         nzn2 = 0;
06936                 }
06937         } else {
06938                 nyn2 = 0; nzn2 = 0;
06939         }
06940         if(xshift == 1.0 || yshift == 1.0 || zshift == 1.0)  {
06941                 ret->set_array_offsets(1,1,1);
06942                 int  lsdn2 = lsd/2;
06943                 for (int iz = 1; iz <= nzn; iz++) {
06944                         int jz=iz-1; if(jz>nzn2) jz=jz-nzn;
06945                         for (int iy = 1; iy <= nyn; iy++) {
06946                                 int jy=iy-1; if(jy>nyn2) jy=jy-nyn;
06947                                 for (int ix = 1; ix <= lsdn2; ix++) {
06948                                         int jx=ix-1;
06949                                         ret->cmplx(ix,iy,iz) *=
06950                                         exp(-float(twopi)*iimag*(xshift*jx/nxn + yshift*jy/nyn+ zshift*jz/nzn));
06951                                 }
06952                         }
06953                 }
06954                 ret->set_array_offsets(0,0,0);
06955         }*/
06956         ret->set_ri(1);
06957         ret->set_fftpad(true);
06958         ret->set_attr("npad", 1);
06959         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
06960         if(RetReal) {
06961                 ret->do_ift_inplace();
06962                 ret->depad();
06963         }
06964         ret->update();
06965 
06966         /*Dict d1 = temp_ft->get_attr_dict();
06967         Dict d2 = ret->get_attr_dict();
06968         printf("-----------------Attribute Dict for temp_ft--------------\n");
06969         EMUtil::dump_dict(d1);
06970         printf("-----------------Attribute Dict for ret--------------\n");
06971         EMUtil::dump_dict(d2);*/
06972         delete temp_ft;
06973         temp_ft = 0;
06974         return ret;
06975 }
06976 
06977 EMData *EMData::FourTruncate(int nxn, int nyni, int nzni, bool RetReal) {
06978 
06979         int nyn, nzn, lsd, lsdn, inx, iny, inz;
06980         int i, j, k;
06981         float  *fint;
06982         EMData *temp_ft = NULL;
06983         //if (is_complex())
06984         //      throw ImageFormatException("Input image has to be real");
06985 
06986         if(ny > 1) {
06987                 nyn = nyni;
06988                 if(nz > 1) {
06989                         nzn = nzni;
06990                 }  else {
06991                         nzn = 1;
06992                 }
06993         } else {
06994                 nyn = 1; nzn = 1;
06995         }
06996         if (is_complex()) {
06997                 nx = nx - 2 + nx%2;
06998                 fint = get_data();
06999         } else {
07000                 //  do out of place ft
07001                 temp_ft = do_fft();
07002                 fint = temp_ft->get_data();
07003         }
07004         if(nxn>nx || nyn>ny || nzn>nz)  throw ImageDimensionException("Cannot increase the image size");
07005         lsd = nx + 2 - nx%2;
07006         lsdn = nxn + 2 - nxn%2;
07007         EMData *ret = this->copy_head();
07008         ret->set_size(lsdn, nyn, nzn);
07009         float *fout = ret->get_data();
07010 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07011 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07012         //float  sq2 = std::sqrt(2.0f);
07013         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
07014         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
07015         inx = nx - nxn;  iny = ny - nyn;  inz = nz - nzn;
07016         for (k=1; k<=nzn/2+1; k++) for (j=1; j<=nyn/2+1; j++) for (i=1; i<=lsdn; i++) fout(i,j,k)=fint(i,j,k);
07017         if(nyn>1) {
07018                 for (k=1; k<=nzn/2+1; k++) for (j=nyn/2+2; j<=nyn; j++) for (i=1; i<=lsdn; i++) fout(i,j,k)=fint(i,j+iny,k);
07019                 if(nzn>1) {
07020                         for (k=nzn/2+2; k<=nzn; k++) {
07021                                 for (j=1; j<=nyn/2+1; j++) {
07022                                         for (i=1; i<=lsdn; i++) {
07023                                                 fout(i,j,k)=fint(i,j,k+inz);
07024                                         }
07025                                 }
07026                                 for (j=nyn/2+2; j<=nyn; j++) {
07027                                         for (i=1; i<=lsdn; i++) {
07028                                                 fout(i,j,k)=fint(i,j+iny,k+inz);
07029                                         }
07030                                 }
07031                         }
07032                 }
07033         }
07034 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
07035 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
07036 //       ELEMENT.
07037         /*
07038         if(nxn%2 == 0 && inx !=0) {
07039                 for (k=1; k<=nzn; k++) {
07040                         for (j=1; j<=nyn; j++) {
07041                                 fout(nxn+1,j,k) *= sq2;
07042                                 fout(nxn+2,j,k) *= sq2;
07043                         }
07044                 }
07045                 if(nyn>1) {
07046                         for (k=1; k<=nzn; k++) {
07047                           for (i=1; i<=lsdn; i++) {
07048                             fout(i,nyn/2+1+iny,k) = sq2*fout(i,nyn/2+1,k);
07049                             fout(i,nyn/2+1,k) *= sq2;
07050                           }
07051                         }
07052                         if(nzn>1) {
07053                                 for (j=1; j<=nyn; j++) {
07054                                         for (i=1; i<=lsdn; i++) {
07055                                                 fout(i,j,nzn/2+1+inz) = sq2*fout(i,j,nzn/2+1);
07056                                                 fout(i,j,nzn/2+1) *= sq2;
07057                                         }
07058                                 }
07059                         }
07060                 }
07061         }*/
07062         ret->set_complex(true);
07063         ret->set_ri(1);
07064         ret->set_fftpad(true);
07065         ret->set_attr("npad", 1);
07066         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07067         if(RetReal) {
07068                 ret->do_ift_inplace();
07069                 ret->depad();
07070         }
07071         ret->update();
07072 
07073         /*Dict d1 = temp_ft->get_attr_dict();
07074         Dict d2 = ret->get_attr_dict();
07075         printf("-----------------Attribute Dict for temp_ft--------------\n");
07076         EMUtil::dump_dict(d1);
07077         printf("-----------------Attribute Dict for ret--------------\n");
07078         EMUtil::dump_dict(d2);*/
07079         if (!is_complex()) {
07080                 delete temp_ft;
07081                 temp_ft = 0;
07082         }
07083         return ret;
07084 }
07085 /*
07086 EMData *EMData::FourInterpol_i(int nxn, int nyni, int nzni, bool RetReal) {
07087 
07088         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07089         int i, j, k;
07090 
07091         if(ny > 1) {
07092                 nyn = nyni;
07093                 if(nz > 1) {
07094                         nzn = nzni;
07095                 }  else {
07096                         nzn = 1;
07097                 }
07098         } else {
07099                 nyn = 1; nzn = 1;
07100         }
07101         if(nxn<nx || nyn<ny || nzn<nz)  throw ImageDimensionException("Cannot reduce the image size");
07102         lsd = nx-2 + 2 - nx%2;
07103         lsdn = nxn + 2 - nxn%2;
07104 //  do out of place ft
07105         EMData *temp_ft = this->copy();
07106         EMData *ret = this->copy();
07107         ret->set_size(lsdn, nyn, nzn);
07108         ret->to_zero();
07109         float *fout = ret->get_data();
07110         float *fint = temp_ft->get_data();
07111 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07112 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07113         float  sq2 = 1.0f/std::sqrt(2.0f);
07114         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
07115         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
07116         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07117         for (k=1; k<=nz/2+1; k++) for (j=1; j<=ny/2+1; j++) for (i=1; i<=lsd; i++) fout(i,j,k)=fint(i,j,k);
07118         if(nyn>1) {
07119         //cout << "  " <<nxn<<"  " <<nyn<<" A " <<nzn<<endl;
07120                 for (k=1; k<=nz/2+1; k++) for (j=ny/2+2+iny; j<=nyn; j++) for (i=1; i<=lsd; i++) fout(i,j,k)=fint(i,j-iny,k);
07121                 if(nzn>1) {
07122                         for (k=nz/2+2+inz; k<=nzn; k++) {
07123                                 for (j=1; j<=ny/2+1; j++) {
07124                                         for (i=1; i<=lsd; i++) {
07125                                                 fout(i,j,k)=fint(i,j,k-inz);
07126                                         }
07127                                 }
07128                                 for (j=ny/2+2+iny; j<=nyn; j++) {
07129                                         for (i=1; i<=lsd; i++) {
07130                                                 fout(i,j,k)=fint(i,j-iny,k-inz);
07131                                         }
07132                                 }
07133                         }
07134                 }
07135         }
07136 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
07137 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
07138 //       ELEMENT.
07139         if(nx%2 == 0 && inx !=0) {
07140                 for (k=1; k<=nzn; k++) {
07141                         for (j=1; j<=nyn; j++) {
07142                                 fout(nx-2+1,j,k) *= sq2;
07143                                 fout(nx-2+2,j,k) *= sq2;
07144                         }
07145                 }
07146                 if(nyn>1) {
07147                         for (k=1; k<=nzn; k++) {
07148                           for (i=1; i<=lsd; i++) {
07149                             fout(i,ny/2+1+iny,k) = sq2*fout(i,ny/2+1,k);
07150                             fout(i,ny/2+1,k) *= sq2;
07151                           }
07152                         }
07153                         if(nzn>1) {
07154                                 for (j=1; j<=nyn; j++) {
07155                                         for (i=1; i<=lsd; i++) {
07156                                                 fout(i,j,nz/2+1+inz) = sq2*fout(i,j,nz/2+1);
07157                                                 fout(i,j,nz/2+1) *= sq2;
07158                                         }
07159                                 }
07160                         }
07161                 }
07162         }
07163         ret->set_complex(true);
07164         ret->set_ri(1);
07165         ret->set_fftpad(true);
07166         ret->set_attr("npad", 1);
07167         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07168         if(RetReal) {
07169                 ret->do_ift_inplace();
07170                 ret->depad();
07171         }
07172         ret->update();
07173 
07174         delete temp_ft;
07175         temp_ft = 0;
07176         return ret;
07177 }
07178 */
07179 
07180 EMData *EMData::Four_ds(int nxn, int nyni, int nzni, bool RetReal) {
07181 
07182         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07183         int i, j;
07184 
07185         if(ny > 1) {
07186                 nyn = nyni;
07187                 if(nz > 1) {
07188                         nzn = nzni;
07189                 }  else {
07190                         nzn = 1;
07191                 }
07192         } else {
07193                 nyn = 1; nzn = 1;
07194         }
07195         lsd = nx-2 + 2 - nx%2;
07196         lsdn = nxn + 2 - nxn%2;
07197 //  do out of place ft
07198         EMData *temp_ft = this->copy();
07199         EMData *ret = this->copy();
07200         ret->set_size(lsdn, nyn, nzn);
07201         ret->to_zero();
07202         float *fout = ret->get_data();
07203         float *fint = temp_ft->get_data();
07204 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07205 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07206 //      float  sq2 = 1.0f/std::sqrt(2.0f);
07207         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
07208         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
07209         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07210         for (j=1; j<=nyn; j++)
07211                 for (i=1; i<=lsdn; i++)
07212                         fout(i,j,1)=fint((i-1)/2*4+2-i%2,j*2-1,1);
07213         ret->set_complex(true);
07214         ret->set_ri(1);
07215         //ret->set_fftpad(true);
07216         //ret->set_attr("npad", 1);
07217         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07218         if(RetReal) {
07219                 ret->do_ift_inplace();
07220                 ret->depad();
07221         }
07222         ret->update();
07223 
07224         delete temp_ft;
07225         temp_ft = 0;
07226         return ret;
07227 }
07228 
07229 EMData *EMData::Four_shuf_ds_cen_us(int nxn, int nyni, int, bool RetReal) {
07230 
07231         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07232         int i, j;
07233 
07234         nyn = nyni;
07235         nzn = 1;
07236         lsd = nx;
07237         lsdn = nxn + 2 - nxn%2;
07238 
07239         EMData *temp_ft = this->copy();
07240         EMData *ret = this->copy();
07241         ret->set_size(lsdn, nyn, nzn);
07242         ret->to_zero();
07243         float *fout = ret->get_data();
07244         float *fint = temp_ft->get_data();
07245 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07246 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07247         float  sq2 = 1.0f/std::sqrt(2.0f);
07248 
07249         for (size_t i = 0; i < (size_t)lsd*ny*nz; i++)  fint[i] *= 4;
07250 
07251         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07252         for (j=1; j<=ny/4; j++)
07253                 for (i=1; i<=(nx-2)/2+2; i++) {
07254                         int g = (i-1)/2+1;
07255                         if ((g+j)%2 == 0) {
07256                                 fout(i,j,1)=fint(g*4-2-i%2,j*2-1+ny/2,1);
07257                         } else {
07258                                 fout(i,j,1)=-fint(g*4-2-i%2,j*2-1+ny/2,1);
07259                         }
07260                 }
07261 
07262         for (j=ny/4+1; j<=ny/4+1; j++)
07263                 for (i=1; i<=(nx-2)/2+2; i++) {
07264                         int g = (i-1)/2+1;
07265                         if ((g+j)%2 == 0) {
07266                                 fout(i,j,1)=fint(g*4-2-i%2,j*2-1-ny/2,1);
07267                         } else {
07268                                 fout(i,j,1)=-fint(g*4-2-i%2,j*2-1-ny/2,1);
07269                         }
07270                 }
07271 
07272         for (j=ny/4+2; j<=ny/2; j++)
07273                 for (i=1; i<=(nx-2)/2+2; i++) {
07274                         int g = (i-1)/2+1;
07275                         if ((g+j)%2 == 0) {
07276                                 fout(i,j+ny/2,1)=fint(g*4-2-i%2,j*2-1-ny/2,1);
07277                         } else {
07278                                 fout(i,j+ny/2,1)=-fint(g*4-2-i%2,j*2-1-ny/2,1);
07279                         }
07280                 }
07281 
07282         if (nx%2 == 0) {
07283                 for (j=1; j<=nyn; j++) {
07284                         fout((nx-2)/2+1,j,1) *= sq2;
07285                         fout((nx-2)/2+2,j,1) *= sq2;
07286                 }
07287                 for (i=1; i<=lsd/2+1; i++) {
07288                         fout(i,ny/4+1+ny/2,1) = sq2*fout(i,ny/4+1,1);
07289                         fout(i,ny/4+1,1) *= sq2;
07290                 }
07291         }
07292 
07293         ret->set_complex(true);
07294         ret->set_ri(1);
07295 
07296         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07297         if(RetReal) {
07298                 ret->do_ift_inplace();
07299                 ret->depad();
07300         }
07301         ret->update();
07302 
07303         delete temp_ft;
07304         temp_ft = 0;
07305         return ret;
07306 }
07307 
07308 #undef fint
07309 #undef fout
07310 
07311 #define  fint(jx,jy,jz)  fint[jx + (jy + jz*ny)*(size_t)nox]
07312 EMData *EMData::filter_by_image(EMData* image, bool RetReal) {
07313 
07314 
07315         bool   complex_input = this->is_complex();
07316         nx  = this->get_xsize();
07317         ny  = this->get_ysize();
07318         nz  = this->get_zsize();
07319         int nox;
07320         if (complex_input) nox = (nx - 2 + this->is_fftodd()); else nox = nx;
07321 
07322         int lsd2 = (nox + 2 - nox%2) / 2; // Extended x-dimension of the complex image
07323 
07324         EMData* fp = NULL; // output image
07325         if(complex_input) {
07326                 // fimage must remain pristine
07327                 fp = this->copy();
07328         } else {
07329                 fp = this->norm_pad( false, 1);
07330                 fp->do_fft_inplace();
07331         }
07332         fp->set_array_offsets(1,1,1);
07333         int nx2 = nox/2;
07334         int ny2 = ny/2;
07335         int nz2 = nz/2;
07336         float *fint = image->get_data();
07337         for ( int iz = 1; iz <= nz; iz++) {
07338                 int jz=nz2-iz+1; if(jz<0) jz += nz;
07339                 for ( int iy = 1; iy <= ny; iy++) {
07340                         int jy=ny2-iy+1; if(jy<0) jy += ny;
07341                         for ( int ix = 1; ix <= lsd2; ix++) {
07342                                 int jx = nx2-ix+1;
07343                                 fp->cmplx(ix,iy,iz) *= fint(jx,jy,jz);
07344                         }
07345                 }
07346         }
07347 
07348         fp->set_ri(1);
07349         fp->set_fftpad(true);
07350         fp->set_attr("npad", 1);
07351         if (nx%2 == 1) fp->set_fftodd(true);
07352         else fp->set_fftodd(false);
07353         if(RetReal) {
07354                 fp->do_ift_inplace();
07355                 fp->depad();
07356         }
07357         fp->set_array_offsets(0,0,0);
07358         fp->update();
07359 
07360         return fp;
07361 }
07362 #undef   fint
07363 #define  fint(jx,jy,jz)  fint[jx + (jy + jz*ny)*(size_t)nx]
07364 #define  fout(jx,jy,jz)  fout[jx + (jy + jz*ny)*(size_t)nx]
07365 EMData *EMData::replace_amplitudes(EMData* image, bool RetReal) {
07366 
07367 
07368         bool   complex_input = this->is_complex();
07369         nx  = this->get_xsize();
07370         ny  = this->get_ysize();
07371         nz  = this->get_zsize();
07372         int nox;
07373         if (complex_input) nox = (nx - 2 + this->is_fftodd()); else nox = nx;
07374 
07375         EMData* fp = NULL; // output image
07376         if(complex_input) {
07377                 // fimage must remain pristine
07378                 fp = this->copy();
07379         } else {
07380                 fp = this->norm_pad( false, 1);
07381                 fp->do_fft_inplace();
07382         }
07383         float *fout = fp->get_data();
07384         float *fint = image->get_data();
07385         for ( int iz = 0; iz < nz; iz++) {
07386                 for ( int iy = 0; iy < ny; iy++) {
07387                         for ( int ix = 0; ix < nx; ix+=2) {
07388                                 float qt = fint(ix,iy,iz)*fint(ix,iy,iz)+fint(ix+1,iy,iz)*fint(ix+1,iy,iz);
07389                                 float rt = fout(ix,iy,iz)*fout(ix,iy,iz)+fout(ix+1,iy,iz)*fout(ix+1,iy,iz);
07390                                 if(rt > 1.0e-20) {
07391                                                 fout(ix,iy,iz) *= (qt/rt);
07392                                                 fout(ix+1,iy,iz) *= (qt/rt);
07393                                 } else {
07394                                                 qt = std::sqrt(qt/2.0f);
07395                                                 fout(ix,iy,iz) = qt;
07396                                                 fout(ix+1,iy,iz) = qt;
07397                                 }
07398                         }
07399                 }
07400         }
07401 
07402         fp->set_ri(1);
07403         fp->set_fftpad(true);
07404         fp->set_attr("npad", 1);
07405         if (nx%2 == 1) fp->set_fftodd(true);
07406         else fp->set_fftodd(false);
07407         if(RetReal) {
07408                 fp->do_ift_inplace();
07409                 fp->depad();
07410         }
07411         fp->set_array_offsets(0,0,0);
07412         fp->update();
07413 
07414         return fp;
07415 }
07416 #undef fint
07417 #undef fout
07418 
07419 
07420 #undef QUADPI
07421 #undef DGR_TO_RAD

Generated on Tue Jul 12 13:48:57 2011 for EMAN2 by  doxygen 1.3.9.1