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, float zratio, 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] = zratio*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] = zratio*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         int nxyz = sizeofprojection*npad;
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*zratio;
01264                                 
01265                                 //binlinear interpolation
01266                                 float xp = coordinate_2d_square[0];
01267                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nxyz+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_dza     = params["dfdiff"];
01550         m_azz     = params["dfang"];
01551         m_winsize2= m_winsize*m_winsize;
01552         m_vecsize = m_winsize2/4;
01553     }
01554 
01555     static float get_ctf( int r2 ,int i, int j)
01556     {
01557         float  ak = std::sqrt( r2/float(m_winsize2) )/m_pixel;
01558         if(m_dza == 0.0f)
01559                 return Util::tf( m_defocus, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1);
01560         else {
01561                 float az = atan2(float(j), float(i));
01562                 float dzz = m_defocus + m_dza/2.0f*sin(2*(az-m_azz*M_PI/180.0f - M_PI/2.0f));
01563                 return Util::tf( dzz, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1);
01564         }
01565     }
01566 
01567 private:
01568 
01569     static int m_winsize, m_winsize2, m_vecsize;
01570     static float m_cs;
01571     static float m_voltage;
01572     static float m_pixel;
01573     static float m_ampcont;
01574     static float m_bfactor;
01575     static float m_defocus;
01576     static float m_dza;
01577     static float m_azz;
01578 };
01579 
01580 
01581 int ctf_store::m_winsize, ctf_store::m_winsize2, ctf_store::m_vecsize;
01582 
01583 float ctf_store::m_cs, ctf_store::m_voltage, ctf_store::m_pixel;
01584 float ctf_store::m_ampcont, ctf_store::m_bfactor;
01585 float ctf_store::m_defocus, ctf_store::m_dza, ctf_store::m_azz;
01586 
01587 
01588 class ctf_store_new
01589 {
01590 public:
01591 
01592     static void init( int winsize, const Ctf* ctf )
01593     {
01594         Dict params = ctf->to_dict();
01595 
01596         m_winsize = winsize;
01597 
01598         m_voltage = params["voltage"];
01599         m_pixel   = params["apix"];
01600         m_cs      = params["cs"];
01601         m_ampcont = params["ampcont"];
01602         m_bfactor = params["bfactor"];
01603         m_defocus = params["defocus"];
01604         m_dza     = params["dfdiff"];
01605         m_azz     = params["dfang"];
01606         m_winsize2= m_winsize*m_winsize;
01607         m_vecsize = m_winsize2/4;
01608     }
01609 
01610     static float get_ctf( float r2 )
01611     {
01612         float ak = std::sqrt( r2/float(m_winsize2) )/m_pixel;
01613         return Util::tf( m_defocus, ak, m_voltage, m_cs, m_ampcont, m_bfactor, 1);
01614     }
01615 
01616 private:
01617 
01618     static int m_winsize, m_winsize2, m_vecsize;
01619     static float m_cs;
01620     static float m_voltage;
01621     static float m_pixel;
01622     static float m_ampcont;
01623     static float m_bfactor;
01624     static float m_defocus;
01625     static float m_dza;
01626     static float m_azz;
01627 };
01628 
01629 
01630 int ctf_store_new::m_winsize, ctf_store_new::m_winsize2, ctf_store_new::m_vecsize;
01631 
01632 float ctf_store_new::m_cs, ctf_store_new::m_voltage, ctf_store_new::m_pixel;
01633 float ctf_store_new::m_ampcont, ctf_store_new::m_bfactor;
01634 float ctf_store_new::m_defocus, ctf_store_new::m_dza, ctf_store_new::m_azz;
01635 
01636 
01637 
01638 //  Helper functions for method nn4_ctf
01639 void EMData::onelinenn_ctf(int j, int n, int n2,
01640                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01641 
01642         int remove = bi->get_attr_default( "remove", 0 );
01643 
01644         int jp = (j >= 0) ? j+1 : n+j+1;
01645         // loop over x
01646         for (int i = 0; i <= n2; i++) {
01647                 int r2 = i*i+j*j;
01648                 if ( (r2<n*n/4) && !((0==i) && (j<0)) ) {
01649                         float ctf = ctf_store::get_ctf( r2, i, j ); //This is in 2D projection plane
01650                         float xnew = i*tf[0][0] + j*tf[1][0];
01651                         float ynew = i*tf[0][1] + j*tf[1][1];
01652                         float znew = i*tf[0][2] + j*tf[1][2];
01653                         std::complex<float> btq;
01654                         if (xnew < 0.) {
01655                                 xnew = -xnew;
01656                                 ynew = -ynew;
01657                                 znew = -znew;
01658                                 btq = conj(bi->cmplx(i,jp));
01659                         } else  btq = bi->cmplx(i,jp);
01660                         int ixn = int(xnew + 0.5 + n) - n;
01661                         int iyn = int(ynew + 0.5 + n) - n;
01662                         int izn = int(znew + 0.5 + n) - n;
01663 
01664                         int iza, iya;
01665                         if (izn >= 0)  iza = izn + 1;
01666                         else           iza = n + izn + 1;
01667 
01668                         if (iyn >= 0) iya = iyn + 1;
01669                         else          iya = n + iyn + 1;
01670 
01671                         if(remove > 0 ) {
01672                                 cmplx(ixn,iya,iza) -= btq*ctf*float(mult);
01673                                 (*w)(ixn,iya,iza)  -= ctf*ctf*mult;
01674                         } else {
01675                                 cmplx(ixn,iya,iza) += btq*ctf*float(mult);
01676                                 (*w)(ixn,iya,iza)  += ctf*ctf*mult;
01677                         }
01678 
01679                 }
01680         }
01681 }
01682 
01683 void EMData::onelinenn_ctf_applied(int j, int n, int n2,
01684                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
01685 
01686         int remove = bi->get_attr_default( "remove", 0 );
01687 
01688         int jp = (j >= 0) ? j+1 : n+j+1;
01689         // loop over x
01690         for (int i = 0; i <= n2; i++) {
01691                 int r2 = i*i + j*j;
01692                 if ( (r2< n*n/4) && !((0==i) && (j< 0)) ) {
01693                         float  ctf = ctf_store::get_ctf(r2, i, j);
01694 
01695                          //        if ( !((0 == i) && (j < 0))) {
01696                         float xnew = i*tf[0][0] + j*tf[1][0];
01697                         float ynew = i*tf[0][1] + j*tf[1][1];
01698                         float znew = i*tf[0][2] + j*tf[1][2];
01699                         std::complex<float> btq;
01700                         if (xnew < 0.) {
01701                                 xnew = -xnew;
01702                                 ynew = -ynew;
01703                                 znew = -znew;
01704                                 btq = conj(bi->cmplx(i,jp));
01705                         } else  btq = bi->cmplx(i,jp);
01706                         int ixn = int(xnew + 0.5 + n) - n;
01707                         int iyn = int(ynew + 0.5 + n) - n;
01708                         int izn = int(znew + 0.5 + n) - n;
01709                         
01710                         int iza, iya;
01711                         if (izn >= 0)  iza = izn + 1;
01712                         else           iza = n + izn + 1;
01713 
01714                         if (iyn >= 0) iya = iyn + 1;
01715                         else          iya = n + iyn + 1;
01716 
01717                         if( remove > 0 ) {
01718                                 cmplx(ixn,iya,iza) -= btq*float(mult);
01719                                 (*w)(ixn,iya,iza) -= mult*ctf*ctf;
01720                         } else {
01721                                 cmplx(ixn,iya,iza) += btq*float(mult);
01722                                 (*w)(ixn,iya,iza) += mult*ctf*ctf;
01723                         }
01724 
01725                 }
01726         }
01727 }
01728 
01729 void
01730 EMData::nn_ctf(EMData* w, EMData* myfft, const Transform& tf, int mult) {
01731         ENTERFUNC;
01732         int nxc = attr_dict["nxc"]; // # of complex elements along x
01733         // let's treat nr, bi, and local data as matrices
01734         vector<int> saved_offsets = get_array_offsets();
01735         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01736         set_array_offsets(0,1,1);
01737         myfft->set_array_offsets(0,1);
01738 
01739         Ctf* ctf = myfft->get_attr("ctf");
01740         ctf_store::init( ny, ctf );
01741         if(ctf) {delete ctf; ctf=0;}
01742 
01743         // loop over frequencies in y
01744         for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn_ctf(iy, ny, nxc, w, myfft, tf, mult);
01745         set_array_offsets(saved_offsets);
01746         myfft->set_array_offsets(myfft_saved_offsets);
01747         EXITFUNC;
01748 }
01749 
01750 void
01751 EMData::nn_ctf_applied(EMData* w, EMData* myfft, const Transform& tf, int mult) {
01752         ENTERFUNC;
01753         int nxc = attr_dict["nxc"]; // # of complex elements along x
01754         // let's treat nr, bi, and local data as matrices
01755         vector<int> saved_offsets = get_array_offsets();
01756         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01757         set_array_offsets(0,1,1);
01758         myfft->set_array_offsets(0,1);
01759 
01760         Ctf* ctf = myfft->get_attr( "ctf" );
01761         ctf_store::init( ny, ctf );
01762         if(ctf) {delete ctf; ctf=0;}
01763         //}
01764 
01765         // loop over frequencies in y
01766         for (int iy = -ny/2 + 1; iy <= ny/2; iy++) onelinenn_ctf_applied(iy, ny, nxc, w, myfft, tf, mult);
01767         set_array_offsets(saved_offsets);
01768         myfft->set_array_offsets(myfft_saved_offsets);
01769         EXITFUNC;
01770 }
01771 
01772 
01773 void EMData::insert_rect_slice_ctf(EMData* w, EMData* myfft, const Transform& trans, int sizeofprojection, float xratio, float yratio, float zratio, int npad, int mult)
01774 {
01775         ENTERFUNC;
01776         vector<int> saved_offsets = get_array_offsets();
01777         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01778         set_array_offsets(0,1,1);
01779         myfft->set_array_offsets(0,1);
01780         
01781         // insert rectangular fft from my nn4_rect code
01782 
01783         Vec2f coordinate_2d_square;
01784         Vec3f coordinate_3dnew;
01785         Vec3f axis_newx;
01786         Vec3f axis_newy;
01787         Vec3f tempv;
01788         
01789         //begin of scaling factor calculation
01790         //unit vector x,y of 2D fft transformed to new positon after rotation and scaling
01791         axis_newx[0] = xratio*0.5f*(sizeofprojection*npad)*trans[0][0];
01792         axis_newx[1] = yratio*0.5f*(sizeofprojection*npad)*trans[0][1];
01793         axis_newx[2] = zratio*0.5f*(sizeofprojection*npad)*trans[0][2];
01794 
01795         float ellipse_length_x = std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
01796         
01797         int ellipse_length_x_int = int(ellipse_length_x);
01798         float ellipse_step_x = 0.5f*(sizeofprojection*npad)/float(ellipse_length_x_int);
01799         float xscale = ellipse_step_x;//scal increased
01800 
01801         axis_newy[0] = xratio*0.5f*(sizeofprojection*npad)*trans[1][0];
01802         axis_newy[1] = yratio*0.5f*(sizeofprojection*npad)*trans[1][1];
01803         axis_newy[2] = zratio*0.5f*(sizeofprojection*npad)*trans[1][2];
01804 
01805 
01806 
01807         float ellipse_length_y = std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
01808         int ellipse_length_y_int = int(ellipse_length_y);
01809         float ellipse_step_y = 0.5f*(sizeofprojection*npad)/float(ellipse_length_y_int);
01810         float yscale = ellipse_step_y;
01811         //end of scaling factor calculation
01812         std::complex<float> c1;
01813         int nxyz = sizeofprojection*npad;
01814         Ctf* ctf = myfft->get_attr( "ctf" );
01815         ctf_store_new::init( nxyz, ctf );
01816         if(ctf) {delete ctf; ctf=0;}
01817         int remove = myfft->get_attr_default( "remove", 0 );
01818 
01819         float r2=0.25f*sizeofprojection*npad*sizeofprojection*npad;
01820         float r2_at_point;
01821         
01822         for(int i=0;i<ellipse_length_x_int;i++) {
01823                 for(int j=-1*ellipse_length_y_int+1; j<=ellipse_length_y_int; j++) {
01824                     
01825                         r2_at_point=i*xscale*i*xscale+j*yscale*j*yscale;
01826                         if(r2_at_point<=r2 && ! ((0==i) && (j<0))) {
01827                                 
01828                                 float ctf_value = ctf_store_new::get_ctf( r2_at_point );
01829                                 coordinate_2d_square[0] = xscale*float(i);
01830                                 coordinate_2d_square[1] = yscale*float(j);
01831                                 float xnew = coordinate_2d_square[0]*trans[0][0] + coordinate_2d_square[1]*trans[1][0];
01832                                 float ynew = coordinate_2d_square[0]*trans[0][1] + coordinate_2d_square[1]*trans[1][1];
01833                                 float znew = coordinate_2d_square[0]*trans[0][2] + coordinate_2d_square[1]*trans[1][2];
01834                                 coordinate_3dnew[0] = xnew*xratio;
01835                                 coordinate_3dnew[1] = ynew*yratio;
01836                                 coordinate_3dnew[2] = znew*zratio;
01837                                 
01838                                 //binlinear interpolation
01839                                 float xp = coordinate_2d_square[0];
01840                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nxyz+coordinate_2d_square[1]+1;
01841                                 std::complex<float> lin_interpolated(0,0);
01842                                 int xlow=int(xp),xhigh=int(xp)+1;
01843                                 int ylow=int(yp),yhigh=int(yp)+1;
01844                                 float tx=xp-xlow,ty=yp-ylow;
01845 
01846                                 
01847                                 if(j == -1) {
01848                                         
01849                                         if(ylow<yp)
01850                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01851                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty) + myfft->cmplx(xhigh,yhigh)*tx*ty;
01852                                         else 
01853                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)
01854                                                 + myfft->cmplx(xhigh,ylow)*tx;
01855                                                                         
01856                                         }
01857                                 else {
01858                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01859                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty)+ myfft->cmplx(xhigh,yhigh)*tx*ty;
01860                                         
01861                                         }
01862                                         
01863                                 c1 = lin_interpolated;
01864                                 
01865                                 //now nearest neighborhood interpolation
01866                                 
01867                                 std::complex<float> btq;
01868                                 if ( coordinate_3dnew[0] < 0.) {
01869                                         coordinate_3dnew[0] = -coordinate_3dnew[0];
01870                                         coordinate_3dnew[1] = -coordinate_3dnew[1];
01871                                         coordinate_3dnew[2] = -coordinate_3dnew[2];
01872                                         btq = conj(c1);
01873                                         } else {
01874                                         btq = c1;
01875                                         }
01876                                 int ixn = int(coordinate_3dnew[0] + 0.5 + nx) - nx;
01877                                 int iyn = int(coordinate_3dnew[1] + 0.5 + ny) - ny;
01878                                 int izn = int(coordinate_3dnew[2] + 0.5 + nz) - nz;
01879 
01880                                 int iza, iya;
01881                                 if (izn >= 0)  iza = izn + 1;
01882                                 else           iza = nz + izn + 1;
01883 
01884                                 if (iyn >= 0) iya = iyn + 1;
01885                                 else          iya = ny + iyn + 1;
01886 
01887                                 if(remove > 0 ) {
01888                                         cmplx(ixn,iya,iza) -= btq*ctf_value*float(mult);
01889                                         (*w)(ixn,iya,iza) -= ctf_value*ctf_value*mult;
01890                                         } else {
01891                                         cmplx(ixn,iya,iza) += btq*ctf_value*float(mult);
01892                                         (*w)(ixn,iya,iza) += ctf_value*ctf_value*mult;
01893                                         }
01894                                         
01895                                 }
01896                         }
01897                             
01898                 }
01899 
01900 
01901         //end insert rectanular fft
01902                 
01903         set_array_offsets(saved_offsets);
01904         myfft->set_array_offsets(myfft_saved_offsets);
01905         EXITFUNC;
01906 
01907 }
01908 
01909 
01910 void EMData::insert_rect_slice_ctf_applied(EMData* w, EMData* myfft,const Transform& trans,int sizeofprojection,float xratio,float yratio, float zratio, int npad,int mult)
01911 {
01912         ENTERFUNC;
01913         vector<int> saved_offsets = get_array_offsets();
01914         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
01915         set_array_offsets(0,1,1);
01916         myfft->set_array_offsets(0,1);
01917         
01918         // insert rectangular fft from my nn4_rect code
01919 
01920         Vec2f coordinate_2d_square;
01921         Vec3f coordinate_3dnew;
01922         Vec3f axis_newx;
01923         Vec3f axis_newy;
01924         Vec3f tempv;
01925         
01926         //begin of scaling factor calculation
01927         //unit vector x,y of 2D fft transformed to new positon after rotation and scaling
01928         axis_newx[0] = xratio*0.5f*(sizeofprojection*npad)*trans[0][0];
01929         axis_newx[1] = yratio*0.5f*(sizeofprojection*npad)*trans[0][1];
01930         axis_newx[2] = zratio*0.5f*(sizeofprojection*npad)*trans[0][2];
01931 
01932         float ellipse_length_x = std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
01933         
01934         int ellipse_length_x_int = int(ellipse_length_x);
01935         float ellipse_step_x = 0.5f*(sizeofprojection*npad)/float(ellipse_length_x_int);
01936         float xscale = ellipse_step_x;//scal increased
01937 
01938         axis_newy[0] = xratio*0.5f*(sizeofprojection*npad)*trans[1][0];
01939         axis_newy[1] = yratio*0.5f*(sizeofprojection*npad)*trans[1][1];
01940         axis_newy[2] = zratio*0.5f*(sizeofprojection*npad)*trans[1][2];
01941 
01942 
01943 
01944         float ellipse_length_y = std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
01945         int ellipse_length_y_int = int(ellipse_length_y);
01946         float ellipse_step_y = 0.5f*(sizeofprojection*npad)/float(ellipse_length_y_int);
01947         float yscale = ellipse_step_y;
01948         //end of scaling factor calculation
01949         std::complex<float> c1;
01950         int nxyz = sizeofprojection*npad;
01951         Ctf* ctf = myfft->get_attr( "ctf" );
01952         ctf_store_new::init( nxyz, ctf );
01953         if(ctf) {delete ctf; ctf=0;}
01954         int remove = myfft->get_attr_default( "remove", 0 );
01955 
01956         float r2=0.25f*sizeofprojection*npad*sizeofprojection*npad;
01957         float r2_at_point;
01958         
01959         for(int i=0;i<ellipse_length_x_int;i++) {
01960                 for(int j=-1*ellipse_length_y_int+1; j<=ellipse_length_y_int; j++) {
01961                     
01962                         r2_at_point=i*xscale*i*xscale+j*yscale*j*yscale;
01963                         if(r2_at_point<=r2 && ! ((0==i) && (j<0))) {
01964                                 
01965                                 float ctf_value = ctf_store_new::get_ctf( r2_at_point );
01966                                 coordinate_2d_square[0] = xscale*float(i);
01967                                 coordinate_2d_square[1] = yscale*float(j);
01968                                 float xnew = coordinate_2d_square[0]*trans[0][0] + coordinate_2d_square[1]*trans[1][0];
01969                                 float ynew = coordinate_2d_square[0]*trans[0][1] + coordinate_2d_square[1]*trans[1][1];
01970                                 float znew = coordinate_2d_square[0]*trans[0][2] + coordinate_2d_square[1]*trans[1][2];
01971                                 coordinate_3dnew[0] = xnew*xratio;
01972                                 coordinate_3dnew[1] = ynew*yratio;
01973                                 coordinate_3dnew[2] = znew*zratio;
01974                                 
01975                                 //binlinear interpolation
01976                                 float xp = coordinate_2d_square[0];
01977                                 float yp = ( coordinate_2d_square[1] >= 0) ? coordinate_2d_square[1]+1 : nxyz+coordinate_2d_square[1]+1;
01978                                 std::complex<float> lin_interpolated(0,0);
01979                                 int xlow=int(xp),xhigh=int(xp)+1;
01980                                 int ylow=int(yp),yhigh=int(yp)+1;
01981                                 float tx=xp-xlow,ty=yp-ylow;
01982 
01983                                 
01984                                 if(j == -1) {
01985                                         
01986                                         if(ylow<yp)
01987                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01988                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty) + myfft->cmplx(xhigh,yhigh)*tx*ty;
01989                                         else 
01990                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)
01991                                                 + myfft->cmplx(xhigh,ylow)*tx;
01992                                                                         
01993                                         }
01994                                 else {
01995                                                 lin_interpolated=myfft->cmplx(xlow,ylow)*(1-tx)*(1-ty) + myfft->cmplx(xlow,yhigh)*(1-tx)*ty
01996                                                 + myfft->cmplx(xhigh,ylow)*tx*(1-ty)+ myfft->cmplx(xhigh,yhigh)*tx*ty;
01997                                         
01998                                         }
01999                                         
02000                                 c1 = lin_interpolated;
02001                                 
02002                                 //now nearest neighborhood interpolation
02003                                 
02004                                 std::complex<float> btq;
02005                                 if ( coordinate_3dnew[0] < 0.) {
02006                                         coordinate_3dnew[0] = -coordinate_3dnew[0];
02007                                         coordinate_3dnew[1] = -coordinate_3dnew[1];
02008                                         coordinate_3dnew[2] = -coordinate_3dnew[2];
02009                                         btq = conj(c1);
02010                                         } else {
02011                                         btq = c1;
02012                                         }
02013                                 int ixn = int(coordinate_3dnew[0] + 0.5 + nx) - nx;
02014                                 int iyn = int(coordinate_3dnew[1] + 0.5 + ny) - ny;
02015                                 int izn = int(coordinate_3dnew[2] + 0.5 + nz) - nz;
02016 
02017                                 int iza, iya;
02018                                 if (izn >= 0)  iza = izn + 1;
02019                                 else           iza = nz + izn + 1;
02020 
02021                                 if (iyn >= 0) iya = iyn + 1;
02022                                 else          iya = ny + iyn + 1;
02023 
02024                                 if(remove > 0 ) {
02025                                         cmplx(ixn,iya,iza) -= btq*float(mult);
02026                                         (*w)(ixn,iya,iza) -= ctf_value*ctf_value*mult;
02027                                         } else {
02028                                         cmplx(ixn,iya,iza) += btq*float(mult);
02029                                         (*w)(ixn,iya,iza) += ctf_value*ctf_value*mult;
02030                                         }
02031                                         
02032                                 }
02033                         }
02034                             
02035                 }
02036 
02037 
02038         //end insert rectanular fft
02039                 
02040         set_array_offsets(saved_offsets);
02041         myfft->set_array_offsets(myfft_saved_offsets);
02042         EXITFUNC;
02043 
02044 }
02045 
02046 
02047 /*
02048 Data::onelinenn_ctf(int j, int n, int n2,
02049                           EMData* w, EMData* bi, const Transform& tf, int mult) {//std::cout<<"   onelinenn_ctf  "<<j<<"  "<<n<<"  "<<n2<<"  "<<std::endl;
02050 
02051         int remove = bi->get_attr_default( "remove", 0 );
02052 
02053         int jp = (j >= 0) ? j+1 : n+j+1;
02054         // loop over x
02055         for (int i = 0; i <= n2; i++) {
02056                 int r2 = i*i+j*j;
02057                 if ( (r2<n*n/4) && !( (0==i) && (j<0) ) ) {
02058                         float  ctf = ctf_store::get_ctf( r2 );
02059                         float xnew = i*tf[0][0] + j*tf[1][0];
02060                         float ynew = i*tf[0][1] + j*tf[1][1];
02061                         float znew = i*tf[0][2] + j*tf[1][2];
02062                         std::complex<float> btq;
02063                         if (xnew < 0.) {
02064                                 xnew = -xnew;
02065                                 ynew = -ynew;
02066                                 znew = -znew;
02067                                 btq = conj(bi->cmplx(i,jp));
02068                         } else  btq = bi->cmplx(i,jp);
02069                         int ixn = int(xnew + 0.5 + n) - n;
02070                         int iyn = int(ynew + 0.5 + n) - n;
02071                         int izn = int(znew + 0.5 + n) - n;
02072                         if ((ixn <= n2) && (iyn >= -n2) && (iyn <= n2) && (izn >= -n2) && (izn <= n2)) {
02073                                 if (ixn >= 0) {
02074                                         int iza, iya;
02075                                         if (izn >= 0)  iza = izn + 1;
02076                                         else           iza = n + izn + 1;
02077 
02078                                         if (iyn >= 0) iya = iyn + 1;
02079                                         else          iya = n + iyn + 1;
02080 
02081                                         if(remove > 0 ) {
02082                                             cmplx(ixn,iya,iza) -= btq*ctf*float(mult);
02083                                             (*w)(ixn,iya,iza) -= ctf*ctf*mult;
02084                                         } else {
02085                                             cmplx(ixn,iya,iza) += btq*ctf*float(mult);
02086                                             (*w)(ixn,iya,iza) += ctf*ctf*mult;
02087                                         }
02088 
02089                                        //       std::cout<<"    "<<j<<"  "<<ixn<<"  "<<iya<<"  "<<iza<<"  "<<ctf<<std::endl;
02090                                 } else {
02091                                         int izt, iyt;
02092                                         if (izn > 0) izt = n - izn + 1;
02093                                         else         izt = -izn + 1;
02094 
02095                                         if (iyn > 0) iyt = n - iyn + 1;
02096                                         else         iyt = -iyn + 1;
02097 
02098                                         if( remove > 0 ) {
02099                                             cmplx(-ixn,iyt,izt) -= conj(btq)*ctf*float(mult);
02100                                             (*w)(-ixn,iyt,izt) -= ctf*ctf*float(mult);
02101                                         } else {
02102                                             cmplx(-ixn,iyt,izt) += conj(btq)*ctf*float(mult);
02103                                             (*w)(-ixn,iyt,izt) += ctf*ctf*float(mult);
02104                                         }
02105 
02106                                         //      std::cout<<" *  " << j << "  " <<-ixn << "  " << iyt << "  " << izt << "  " << ctf <<std::endl;
02107                                 }
02108                         }
02109                 }
02110         }
02111 }
02112 */
02113 
02114 
02115 void EMData::nn_SSNR_ctf(EMData* wptr, EMData* wptr2, EMData* wptr3, EMData* myfft, const Transform& tf, int)
02116 {
02117         /***   Preparing terms for SSNR
02118               m_wvolume F^3D Wiener volume
02119              wptr   ctf^2
02120             wptr5  ctf^2*|P^2D->3D(F^3D)|^2
02121            wptr4  2*Real(conj(F_k^2D)*ctf*P^2D->3D(F^3D))
02122           wptr2  F_k^2D*conj(F_k^2D) or |F_k^2D|^2
02123           Kn is counted in the previous routine, and won't be
02124          calculated any more.
02125                                                     ***/
02126         ENTERFUNC;
02127         int nxc = attr_dict["nxc"];
02128         vector<int> saved_offsets = get_array_offsets();
02129         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
02130         set_array_offsets(0,1,1);
02131         myfft->set_array_offsets(0,1);
02132 
02133         Ctf* ctf = myfft->get_attr("ctf");
02134         ctf_store::init( ny, ctf );
02135         int iymin = is_fftodd() ? -ny/2 : -ny/2 + 1;
02136         int iymax = ny/2;
02137         int izmin = is_fftodd() ? -nz/2 : -nz/2 + 1;
02138         int izmax = nz/2;
02139 //      std::complex<float> tmpq, tmp2;
02140         for (int iy = iymin; iy <= iymax; iy++) {
02141                 int jp = iy >= 0 ? iy+1 : ny+iy+1; //checked, works for both odd and even
02142                 for (int ix = 0; ix <= nxc; ix++) {
02143                         int r2 = ix*ix+iy*iy;
02144                         if (( 4*r2 < ny*ny ) && !( ix == 0 && iy < 0 ) ) {
02145                                 float  ctf = ctf_store::get_ctf( r2, ix, iy )*10.f;// ???PAP
02146                                 float xnew = ix*tf[0][0] + iy*tf[1][0];
02147                                 float ynew = ix*tf[0][1] + iy*tf[1][1];
02148                                 float znew = ix*tf[0][2] + iy*tf[1][2];
02149                                 std::complex<float> btq;
02150                                 if (xnew < 0.0) {
02151                                         xnew = -xnew; // ensures xnew>=0.0
02152                                         ynew = -ynew;
02153                                         znew = -znew;
02154                                         btq = conj(myfft->cmplx(ix,jp));
02155                                 } else  {
02156                                         btq = myfft->cmplx(ix,jp);
02157                                 }
02158                                 int ixn = int(xnew + 0.5 + nx) - nx; // ensures ixn >= 0
02159                                 int iyn = int(ynew + 0.5 + ny) - ny;
02160                                 int izn = int(znew + 0.5 + nz) - nz;
02161                                 if ((ixn <= nxc) && (iyn >= iymin) && (iyn <= iymax) && (izn >= izmin) && (izn <= izmax)) {
02162                                         if (ixn >= 0) {
02163                                                 int iza, iya;
02164                                                 if (izn >= 0) iza = izn + 1;
02165                                                 else          iza = nz + izn + 1;
02166 
02167                                                 if (iyn >= 0) iya = iyn + 1;
02168                                                 else          iya = ny + iyn + 1;
02169 
02170                                                 cmplx(ixn,iya,iza)    += btq*ctf;
02171                                                 (*wptr)(ixn,iya,iza)  += ctf*ctf;
02172                                                 (*wptr2)(ixn,iya,iza) += std::norm(btq);
02173                                                 (*wptr3)(ixn,iya,iza) += 1;
02174                                         } else {
02175                                                 int izt, iyt;
02176                                                 if (izn > 0)  izt = nz - izn + 1;
02177                                                 else          izt = -izn + 1;
02178 
02179                                                 if (iyn > 0) iyt = ny - iyn + 1;
02180                                                 else         iyt = -iyn + 1;
02181 
02182                                                 cmplx(-ixn,iyt,izt)    += std::conj(btq)*ctf;
02183                                                 (*wptr) (-ixn,iyt,izt) += ctf*ctf;
02184                                                 (*wptr2)(-ixn,iyt,izt) += std::norm(btq);
02185                                                 (*wptr3)(-ixn,iyt,izt) += 1;
02186                                         }
02187                                 }
02188                         }
02189                 }
02190         }
02191         set_array_offsets(saved_offsets);
02192         myfft->set_array_offsets(myfft_saved_offsets);
02193         if(ctf) {delete ctf; ctf=0;}
02194         EXITFUNC;
02195 }
02196 
02197 /*void EMData::nn_wiener(EMData* wptr, EMData* wptr3, EMData* myfft, const Transform& tf, int)
02198 {
02199      // Wiener volume calculating routine Counting Kn
02200 
02201         ENTERFUNC;
02202         int nxc = attr_dict["nxc"];
02203         vector<int> saved_offsets = get_array_offsets();
02204         vector<int> myfft_saved_offsets = myfft->get_array_offsets();
02205         set_array_offsets(0,1,1);
02206         myfft->set_array_offsets(0,1);
02207         // if( ! ctf_store::inited() )
02208         float Cs           = myfft->get_attr( "Cs" );
02209         float pixel        = myfft->get_attr( "Pixel_size" );
02210         float voltage      = myfft->get_attr( "voltage");
02211         float amp_contrast = myfft->get_attr( "amp_contrast" );
02212         float b_factor     = 0.0;
02213         ctf_store::init( ny, voltage, pixel, Cs, amp_contrast, b_factor );
02214         float defocus = myfft->get_attr( "defocus" );
02215         int iymin = is_fftodd() ? -ny/2 : -ny/2 + 1 ;
02216         int iymax = ny/2;
02217         int izmin = is_fftodd() ? -nz/2 : -nz/2 + 1 ;
02218         int izmax = nz/2;
02219         for (int iy = iymin; iy <= iymax; iy++) {
02220                 int jp = iy >= 0 ? iy+1 : ny+iy+1; //checked, works for both odd and even
02221                 for (int ix = 0; ix <= nxc; ix++) {
02222                         int r2 = ix*ix+iy*iy;
02223                         if (( 4*r2 < ny*ny ) && !( ix == 0 && iy < 0 ) )
02224                         {
02225                                 float  ctf = ctf_store::get_ctf( defocus, r2 );
02226                                 float xnew = ix*tf[0][0] + iy*tf[1][0];
02227                                 float ynew = ix*tf[0][1] + iy*tf[1][1];
02228                                 float znew = ix*tf[0][2] + iy*tf[1][2];
02229                                 std::complex<float> btq;
02230                                 if (xnew < 0.0)
02231                                 {
02232                                         xnew = -xnew; // ensures xnew>=0.0
02233                                         ynew = -ynew;
02234                                         znew = -znew;
02235                                         btq = conj(myfft->cmplx(ix,jp));
02236                                 } else
02237                                 {
02238                                         btq = myfft->cmplx(ix,jp);
02239                                 }
02240                                 int ixn = int(xnew + 0.5 + nx) - nx; // ensures ixn >= 0
02241                                 int iyn = int(ynew + 0.5 + ny) - ny;
02242                                 int izn = int(znew + 0.5 + nz) - nz;
02243                                 if ((ixn <= nxc) && (iyn >= iymin) && (iyn <= iymax) && (izn >= izmin) && (izn <= izmax)) {
02244                                         if (ixn >= 0)
02245                                         {
02246                                                 int iza, iya;
02247                                                 if (izn >= 0)
02248                                                 {
02249                                                         iza = izn + 1;
02250                                                 } else
02251                                                 {
02252                                                         iza = nz + izn + 1;
02253                                                 }
02254                                                 if (iyn >= 0)
02255                                                 {
02256                                                         iya = iyn + 1;
02257                                                 } else
02258                                                 {
02259                                                         iya = ny + iyn + 1;
02260                                                 }
02261                                                 cmplx(ixn,iya,iza)    += btq*ctf;
02262                                                 (*wptr)(ixn,iya,iza)  += ctf*ctf;
02263                                                 (*wptr3)(ixn,iya,iza) += 1.0;
02264                                         }
02265                                         else
02266                                         {
02267                                                 int izt, iyt;
02268                                                 if (izn > 0)
02269                                                 {
02270                                                         izt = nz - izn + 1;
02271                                                 } else
02272                                                 {
02273                                                         izt = -izn + 1;
02274                                                 }
02275                                                 if (iyn > 0)
02276                                                 {
02277                                                         iyt = ny - iyn + 1;
02278                                                 } else
02279                                                 {
02280                                                         iyt = -iyn + 1;
02281                                                 }
02282                                                 cmplx(-ixn,iyt,izt)    += conj(btq)*ctf;
02283                                                 (*wptr)(-ixn,iyt,izt)  += ctf*ctf;
02284                                                 (*wptr3)(-ixn,iyt,izt) += 1.0;
02285                                         }
02286                                 }
02287                         }
02288                 }
02289         }
02290         set_array_offsets(saved_offsets);
02291         myfft->set_array_offsets(myfft_saved_offsets);
02292         EXITFUNC;
02293 }*/
02294 
02295 void EMData::symplane0_ctf(EMData* w) {
02296         ENTERFUNC;
02297         int nxc = attr_dict["nxc"];
02298         int n = nxc*2;
02299         // let's treat the local data as a matrix
02300         vector<int> saved_offsets = get_array_offsets();
02301         set_array_offsets(0,1,1);
02302         for (int iza = 2; iza <= nxc; iza++) {
02303                 for (int iya = 2; iya <= nxc; iya++) {
02304                         cmplx(0,iya,iza) += conj(cmplx(0,n-iya+2,n-iza+2));
02305                         (*w)(0,iya,iza) += (*w)(0,n-iya+2,n-iza+2);
02306                         cmplx(0,n-iya+2,n-iza+2) = conj(cmplx(0,iya,iza));
02307                         (*w)(0,n-iya+2,n-iza+2) = (*w)(0,iya,iza);
02308                         cmplx(0,n-iya+2,iza) += conj(cmplx(0,iya,n-iza+2));
02309                         (*w)(0,n-iya+2,iza) += (*w)(0,iya,n-iza+2);
02310                         cmplx(0,iya,n-iza+2) = conj(cmplx(0,n-iya+2,iza));
02311                         (*w)(0,iya,n-iza+2) = (*w)(0,n-iya+2,iza);
02312                 }
02313         }
02314         for (int iya = 2; iya <= nxc; iya++) {
02315                 cmplx(0,iya,1) += conj(cmplx(0,n-iya+2,1));
02316                 (*w)(0,iya,1) += (*w)(0,n-iya+2,1);
02317                 cmplx(0,n-iya+2,1) = conj(cmplx(0,iya,1));
02318                 (*w)(0,n-iya+2,1) = (*w)(0,iya,1);
02319         }
02320         for (int iza = 2; iza <= nxc; iza++) {
02321                 cmplx(0,1,iza) += conj(cmplx(0,1,n-iza+2));
02322                 (*w)(0,1,iza) += (*w)(0,1,n-iza+2);
02323                 cmplx(0,1,n-iza+2) = conj(cmplx(0,1,iza));
02324                 (*w)(0,1,n-iza+2) = (*w)(0,1,iza);
02325         }
02326         EXITFUNC;
02327 }
02328 
02329 void EMData::symplane0_rect(EMData* w) {
02330         ENTERFUNC;
02331         nx=get_xsize();
02332         ny=get_ysize();
02333         nz=get_zsize();
02334         int nzc=nz/2;
02335         int nyc=ny/2;
02336 
02337         
02338         // let's treat the local data as a matrix
02339         vector<int> saved_offsets = get_array_offsets();
02340         set_array_offsets(0,1,1);
02341         for (int iza = 2; iza <= nzc; iza++) {
02342                 for (int iya = 2; iya <= nyc; iya++) {
02343                         cmplx(0,iya,iza) += conj(cmplx(0,ny-iya+2,nz-iza+2));
02344                         (*w)(0,iya,iza) += (*w)(0,ny-iya+2,nz-iza+2);
02345                         cmplx(0,ny-iya+2,nz-iza+2) = conj(cmplx(0,iya,iza));
02346                         (*w)(0,ny-iya+2,nz-iza+2) = (*w)(0,iya,iza);
02347                         cmplx(0,ny-iya+2,iza) += conj(cmplx(0,iya,nz-iza+2));
02348                         (*w)(0,ny-iya+2,iza) += (*w)(0,iya,nz-iza+2);
02349                         cmplx(0,iya,nz-iza+2) = conj(cmplx(0,ny-iya+2,iza));
02350                         (*w)(0,iya,nz-iza+2) = (*w)(0,ny-iya+2,iza);
02351                 }
02352         }
02353         for (int iya = 2; iya <= nyc; iya++) {
02354                 cmplx(0,iya,1) += conj(cmplx(0,ny-iya+2,1));
02355                 (*w)(0,iya,1) += (*w)(0,ny-iya+2,1);
02356                 cmplx(0,ny-iya+2,1) = conj(cmplx(0,iya,1));
02357                 (*w)(0,ny-iya+2,1) = (*w)(0,iya,1);
02358         }
02359         for (int iza = 2; iza <= nzc; iza++) {
02360                 cmplx(0,1,iza) += conj(cmplx(0,1,nz-iza+2));
02361                 (*w)(0,1,iza) += (*w)(0,1,nz-iza+2);
02362                 cmplx(0,1,nz-iza+2) = conj(cmplx(0,1,iza));
02363                 (*w)(0,1,nz-iza+2) = (*w)(0,1,iza);
02364         }
02365         EXITFUNC;
02366 }
02367 
02368 EMData* EMData::rot_scale_trans2D(float angDeg, float delx, float dely, float scale) { // quadratic, no background, 2D
02369         float ang=angDeg*M_PI/180.0f;
02370         if (1 >= ny)
02371                 throw ImageDimensionException("Can't rotate 1D image");
02372         if (nz<2) {
02373                 vector<int> saved_offsets = get_array_offsets();
02374                 set_array_offsets(0,0,0);
02375                 if (0.0f == scale) scale = 1.0f; // silently fix common user error
02376                 EMData* ret = copy_head();
02377                 delx = restrict2(delx, nx);
02378                 dely = restrict2(dely, ny);
02379                 // center of image
02380                 int xc = nx/2;
02381                 int yc = ny/2;
02382                 // shifted center for rotation
02383                 float shiftxc = xc + delx;
02384                 float shiftyc = yc + dely;
02385                 // trig
02386                 float cang = cos(ang);
02387                 float sang = sin(ang);
02388                         for (int iy = 0; iy < ny; iy++) {
02389                                 float y = float(iy) - shiftyc;
02390                                 float ycang = y*cang/scale + yc;
02391                                 float ysang = -y*sang/scale + xc;
02392                                 for (int ix = 0; ix < nx; ix++) {
02393                                         float x = float(ix) - shiftxc;
02394                                         float xold = x*cang/scale + ysang ;
02395                                         float yold = x*sang/scale + ycang ;
02396                                         //  quadri is taking care of cyclic count
02397                                         (*ret)(ix,iy) = Util::quadri(xold+1.0f, yold+1.0f, nx, ny, get_data());
02398                                            //have to add one as quadri uses Fortran counting
02399                                 }
02400                         }
02401                 set_array_offsets(saved_offsets);
02402                 return ret;
02403         } else {
02404                 throw ImageDimensionException("Volume not currently supported");
02405         }
02406 }
02407 
02408 EMData* EMData::rot_scale_trans2D_background(float angDeg, float delx, float dely, float scale) { // quadratic, no background, 2D
02409     float ang=angDeg*M_PI/180.0f;
02410         if (1 >= ny)
02411                 throw ImageDimensionException("Can't rotate 1D image");
02412         if (nz<2) {
02413                 vector<int> saved_offsets = get_array_offsets();
02414                 set_array_offsets(0,0,0);
02415                 if (0.0f == scale) scale = 1.0f; // silently fix common user error
02416                 EMData* ret = copy_head();
02417                 delx = restrict2(delx, nx);
02418                 dely = restrict2(dely, ny);
02419                 // center of image
02420                 int xc = nx/2;
02421                 int yc = ny/2;
02422                 // shifted center for rotation
02423                 float shiftxc = xc + delx;
02424                 float shiftyc = yc + dely;
02425                 // trig
02426                 float cang = cos(ang);
02427                 float sang = sin(ang);
02428                         for (int iy = 0; iy < ny; iy++) {
02429                                 float y = float(iy) - shiftyc;
02430                                 float ycang = y*cang/scale + yc;
02431                                 float ysang = -y*sang/scale + xc;
02432                                 for (int ix = 0; ix < nx; ix++) {
02433                                         float x = float(ix) - shiftxc;
02434                                         float xold = x*cang/scale + ysang ;
02435                                         float yold = x*sang/scale + ycang ;
02436                                         //  in quadri_background, wrap around is not done circulantly; if (xold,yold) is not in the image, then it's replaced by (ix,iy)
02437                                         (*ret)(ix,iy) = Util::quadri_background(xold+1.0f, yold+1.0f, nx, ny, get_data(),ix+1,iy+1);
02438                                            //have to add one as quadri uses Fortran counting
02439                                 }
02440                         }
02441                 set_array_offsets(saved_offsets);
02442                 return ret;
02443         } else {
02444                 throw ImageDimensionException("Volume not currently supported");
02445         }
02446 }
02447 
02448 #define in(i,j,k)          in[i+(j+(k*ny))*(size_t)nx]
02449 EMData*
02450 EMData::rot_scale_trans(const Transform &RA) {
02451 
02452         EMData* ret = copy_head();
02453         float *in = this->get_data();
02454         vector<int> saved_offsets = get_array_offsets();
02455         set_array_offsets(0,0,0);
02456         Vec3f translations = RA.get_trans();
02457         Transform RAinv = RA.inverse();
02458 
02459         if (1 >= ny)  throw ImageDimensionException("Can't rotate 1D image");
02460         if (nz < 2) {
02461         float  p1, p2, p3, p4;
02462         float delx = translations.at(0);
02463         float dely = translations.at(1);
02464         delx = restrict2(delx, nx);
02465         dely = restrict2(dely, ny);
02466         int xc = nx/2;
02467         int yc = ny/2;
02468 //         shifted center for rotation
02469         float shiftxc = xc + delx;
02470         float shiftyc = yc + dely;
02471                 for (int iy = 0; iy < ny; iy++) {
02472                         float y = float(iy) - shiftyc;
02473                         float ysang = y*RAinv[0][1]+xc;
02474                         float ycang = y*RAinv[1][1]+yc;
02475                         for (int ix = 0; ix < nx; ix++) {
02476                                 float x = float(ix) - shiftxc;
02477                                 float xold = x*RAinv[0][0] + ysang;
02478                                 float yold = x*RAinv[1][0] + ycang;
02479 
02480                                 xold = restrict1(xold, nx);
02481                                 yold = restrict1(yold, ny);
02482 
02483                                 int xfloor = int(xold);
02484                                 int yfloor = int(yold);
02485                                 float t = xold-xfloor;
02486                                 float u = yold-yfloor;
02487                                 if(xfloor == nx -1 && yfloor == ny -1) {
02488 
02489                                     p1 =in[xfloor   + yfloor*ny];
02490                                         p2 =in[ yfloor*ny];
02491                                         p3 =in[0];
02492                                         p4 =in[xfloor];
02493                                 } else if(xfloor == nx - 1) {
02494 
02495                                         p1 =in[xfloor   + yfloor*ny];
02496                                         p2 =in[           yfloor*ny];
02497                                         p3 =in[          (yfloor+1)*ny];
02498                                         p4 =in[xfloor   + (yfloor+1)*ny];
02499                                 } else if(yfloor == ny - 1) {
02500 
02501                                         p1 =in[xfloor   + yfloor*ny];
02502                                         p2 =in[xfloor+1 + yfloor*ny];
02503                                         p3 =in[xfloor+1 ];
02504                                         p4 =in[xfloor   ];
02505                                 } else {
02506                                         p1 =in[xfloor   + yfloor*ny];
02507                                         p2 =in[xfloor+1 + yfloor*ny];
02508                                         p3 =in[xfloor+1 + (yfloor+1)*ny];
02509                                         p4 =in[xfloor   + (yfloor+1)*ny];
02510                                 }
02511                                 (*ret)(ix,iy) = p1 + u * ( p4 - p1) + t * ( p2 - p1 + u *(p3-p2-p4+p1));
02512                         } //ends x loop
02513                 } // ends y loop
02514                 set_array_offsets(saved_offsets);
02515                 return ret;
02516         } else {
02517 //               This begins the 3D version trilinear interpolation.
02518 
02519         float delx = translations.at(0);
02520         float dely = translations.at(1);
02521         float delz = translations.at(2);
02522         delx = restrict2(delx, nx);
02523         dely = restrict2(dely, ny);
02524         delz = restrict2(delz, nz);
02525         int xc = nx/2;
02526         int yc = ny/2;
02527         int zc = nz/2;
02528 //         shifted center for rotation
02529         float shiftxc = xc + delx;
02530         float shiftyc = yc + dely;
02531         float shiftzc = zc + delz;
02532 
02533                 for (int iz = 0; iz < nz; iz++) {
02534                         float z = float(iz) - shiftzc;
02535                         float xoldz = z*RAinv[0][2]+xc;
02536                         float yoldz = z*RAinv[1][2]+yc;
02537                         float zoldz = z*RAinv[2][2]+zc;
02538                         for (int iy = 0; iy < ny; iy++) {
02539                                 float y = float(iy) - shiftyc;
02540                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02541                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02542                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02543                                 for (int ix = 0; ix < nx; ix++) {
02544                                         float x = float(ix) - shiftxc;
02545                                         float xold = xoldzy + x*RAinv[0][0] ;
02546                                         float yold = yoldzy + x*RAinv[1][0] ;
02547                                         float zold = zoldzy + x*RAinv[2][0] ;
02548 
02549                                         xold = restrict1(xold, nx);
02550                                         yold = restrict1(yold, ny);
02551                                         zold = restrict1(zold, nz);
02552 
02553 
02554                                         int IOX = int(xold);
02555                                         int IOY = int(yold);
02556                                         int IOZ = int(zold);
02557 
02558                                         #ifdef _WIN32
02559                                         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
02560                                         #else
02561                                         int IOXp1 = std::min( nx-1 ,IOX+1);
02562                                         #endif  //_WIN32
02563 
02564                                         #ifdef _WIN32
02565                                         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
02566                                         #else
02567                                         int IOYp1 = std::min( ny-1 ,IOY+1);
02568                                         #endif  //_WIN32
02569 
02570                                         #ifdef _WIN32
02571                                         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
02572                                         #else
02573                                         int IOZp1 = std::min( nz-1 ,IOZ+1);
02574                                         #endif  //_WIN32
02575 
02576                                         float dx = xold-IOX;
02577                                         float dy = yold-IOY;
02578                                         float dz = zold-IOZ;
02579 
02580                                         float a1 = in(IOX,IOY,IOZ);
02581                                         float a2 = in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZ);
02582                                         float a3 = in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZ);
02583                                         float a4 = in(IOX,IOY,IOZp1) - in(IOX,IOY,IOZ);
02584                                         float a5 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOYp1,IOZ) + in(IOXp1,IOYp1,IOZ);
02585                                         float a6 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZp1) + in(IOXp1,IOY,IOZp1);
02586                                         float a7 = in(IOX,IOY,IOZ) - in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZp1) + in(IOX,IOYp1,IOZp1);
02587                                         float a8 = in(IOXp1,IOY,IOZ) + in(IOX,IOYp1,IOZ)+ in(IOX,IOY,IOZp1)
02588                                                         - in(IOX,IOY,IOZ)- in(IOXp1,IOYp1,IOZ) - in(IOXp1,IOY,IOZp1)
02589                                                         - in(IOX,IOYp1,IOZp1) + in(IOXp1,IOYp1,IOZp1);
02590                                         (*ret)(ix,iy,iz) = a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
02591                                 } //ends x loop
02592                         } // ends y loop
02593                 } // ends z loop
02594 
02595                 set_array_offsets(saved_offsets);
02596                 return ret;
02597 
02598 /*     This entire section has to go somewhere for quadratic 3D interpolation PAP 12/29/07
02599 //               This begins the 3D version triquadratic interpolation.
02600 
02601         float delx = translations.at(0);
02602         float dely = translations.at(1);
02603         float delz = translations.at(2);
02604         if(delx >= 0.0f) { delx = fmod(delx, float(nx));} else {delx = -fmod(-delx, float(nx));}
02605         if(dely >= 0.0f) { dely = fmod(dely, float(ny));} else {dely = -fmod(-dely, float(ny));}
02606         if(dely >= 0.0f) { delz = fmod(delz, float(nz));} else {delz = -fmod(-delz, float(nz));}
02607         int xc = nx/2;
02608         int yc = ny/2;
02609         int zc = nz/2;
02610 //         shifted center for rotation
02611         float shiftxc = xc + delx;
02612         float shiftyc = yc + dely;
02613         float shiftzc = zc + delz;
02614 //                  set up array to use later
02615 //
02616                 int xArr[27];
02617                 int yArr[27];
02618                 int zArr[27];
02619                 float fdata[27];
02620 
02621                 for (int iL=0; iL<27 ; iL++){  // need this indexing array later
02622                         xArr[iL]  =  (int) (fmod((float)iL,3.0f) - 1.0f);
02623                         yArr[iL]  =  (int)( fmod( ((float) (iL/3) ),3.0f)- 1.0f);
02624                         zArr[iL]  = ((int) (iL/9)  ) -1;
02625 //                      printf("iL=%d, \t xArr=%d, \t yArr=%d, \t zArr=%d \n",iL, xArr[iL],yArr[iL],zArr[iL]);
02626                 }
02627 
02628 //              for (int iz = 0; iz < nz; iz++) {for (int iy = 0; iy < ny; iy++) {for (int ix = 0; ix < nx; ix++) {
02629 //                    (*ret)(ix,iy,iz) = 0;}}}   // initialize returned data
02630 
02631                 for (int iz = 0; iz < nz; iz++) {
02632                         float z = float(iz) - shiftzc;
02633                         float xoldz = z*RAinv[0][2]+xc;
02634                         float yoldz = z*RAinv[1][2]+yc;
02635                         float zoldz = z*RAinv[2][2]+zc;
02636                         for (int iy = 0; iy < ny; iy++) {
02637                                 float y = float(iy) - shiftyc;
02638                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02639                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02640                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02641                                 for (int ix = 0; ix < nx; ix++) {
02642                                         float x = float(ix) - shiftxc;
02643                                         float xold = xoldzy + x*RAinv[0][0] ;
02644                                         float yold = yoldzy + x*RAinv[1][0] ;
02645                                         float zold = zoldzy + x*RAinv[2][0] ;
02646 
02647 
02648                                 if (xold < 0.0f) xold = fmod((int(xold/float(nx))+1)*nx-xold, float(nx));
02649                                 else if (xold > (float) (nx-1) ) xold = fmod(xold, float(nx));
02650                                 if (yold < 0.0f) yold =fmod((int(yold/float(ny))+1)*ny-yold, float(ny));
02651                                 else if (yold > (float) (ny-1) ) yold = fmod(yold, float(ny));
02652                                 if (zold < 0.0f) zold =fmod((int(zold/float(nz))+1)*nz-zold, float(nz));
02653                                 else if (zold > (float) (nz-1) ) zold = fmod(zold, float(nz));
02654 
02655                                 //  what follows does not accelerate the code; moreover, I doubt it is correct PAP 12/29/07
02656                                 //while ( xold >= (float)(nx) )  xold -= nx;
02657                                 //while ( xold < 0.0f )         xold += nx;
02658                                 //while ( yold >= (float)(ny) )  yold -= ny;
02659                                 //while ( yold < 0.0f )         yold += ny;
02660                                 //while ( zold >= (float)(nz) )  zold -= nz;
02661                                 //while ( zold < 0.0f )         zold += nz;
02662 
02663 //         This is currently coded the way  SPIDER coded it,
02664 //            changing floor to round  in the next 3 lines below may be better
02665 //                                      int IOX = (int) floor(xold); // This is the center of the array
02666 //                                      int IOY = (int) floor(yold ); // In the next loop we interpolate
02667 //                                      int IOZ = (int) floor(zold ); //  If floor is used dx is positive
02668                                         int IOX = int(xold);
02669                                         int IOY = int(yold);
02670                                         int IOZ = int(zold);
02671 
02672                                         float dx = xold-IOX; //remainder(xold,1);  //  now |dx| <= .5
02673                                         float dy = yold-IOY; //remainder(yold,1);
02674                                         float dz = zold-IOZ; //remainder(zold,1);
02675 
02676 //                                      printf(" IOX=%d \t IOY=%d \t IOZ=%d \n", IOX, IOY, IOZ);
02677 //                                      if (IOX>=0 && IOX<nx  && IOY>=0 && IOY < ny && IOZ >= 0 && IOZ < nz ) {
02678 //                                              ROTATED POSITION IS INSIDE OF VOLUME
02679 //                                              FIND INTENSITIES ON 3x3x3 COORDINATE GRID;
02680 //                                     Solution is wrapped
02681                                                 for  (int iL=0; iL<27 ; iL++){
02682                                                         int xCoor = (int) fmod(IOX+xArr[iL] + nx + .0001f, (float) nx);
02683                                                         int yCoor = (int) fmod(IOY+yArr[iL] + ny + .0001f, (float) ny);
02684                                                         int zCoor = (int) fmod(IOZ+zArr[iL] + nz + .0001f, (float) nz);
02685                                                         fdata[iL] = (*this)( xCoor, yCoor ,zCoor );
02686 //                                                      if (iy==iz && iz==0){printf(" fdata=%f \n", fdata[iL]);}
02687 //                                              }
02688                                         }
02689 
02690                                         (*ret)(ix,iy,iz) = Util::triquad(dx, dy, dz, fdata);
02691 //                                      (*ret)(ix,iy,iz) = Util:: trilinear_interpolate(fdata[13],fdata[14],fdata[16],
02692 //                                                                                      fdata[17],fdata[22],fdata[23],
02693 //                                                                                      fdata[25],fdata[26],dx, dy, dz);
02694 //      p1 iL=13,   xArr= 0,         yArr= 0,         zArr= 0
02695 //      p2 iL=14,   xArr= 1,         yArr= 0,         zArr= 0
02696 //      p3 iL=16,   xArr= 0,         yArr= 1,         zArr= 0
02697 //      p4 iL=17,   xArr= 1,         yArr= 1,         zArr= 0
02698 //      p5 iL=22,   xArr= 0,         yArr= 0,         zArr= 1
02699 //      p6 iL=23,   xArr= 1,         yArr= 0,         zArr= 1
02700 //      p7 iL=25,   xArr= 0,         yArr= 1,         zArr= 1
02701 //      p8 iL=26,   xArr= 1,         yArr= 1,         zArr= 1
02702 
02703 
02704 
02705                                 } //ends x loop
02706                         } // ends y loop
02707                 } // ends z loop
02708 
02709                 set_array_offsets(saved_offsets);
02710                 return ret;
02711 */
02712         }
02713 }
02714 #undef  in
02715 
02716 // new function added for background option
02717 #define in(i,j,k)          in[i+(j+(k*ny))*(size_t)nx]
02718 EMData*
02719 EMData::rot_scale_trans_background(const Transform &RA) {
02720         EMData* ret = copy_head();
02721         float *in = this->get_data();
02722         vector<int> saved_offsets = get_array_offsets();
02723         set_array_offsets(0,0,0);
02724         Vec3f translations = RA.get_trans();
02725         Transform RAinv = RA.inverse();
02726 
02727         if (1 >= ny)  throw ImageDimensionException("Can't rotate 1D image");
02728         if (nz < 2) {
02729         float  p1, p2, p3, p4;
02730         float delx = translations.at(0);
02731         float dely = translations.at(1);
02732         delx = restrict2(delx, nx);
02733         dely = restrict2(dely, ny);
02734         int xc = nx/2;
02735         int yc = ny/2;
02736 //         shifted center for rotation
02737         float shiftxc = xc + delx;
02738         float shiftyc = yc + dely;
02739                 for (int iy = 0; iy < ny; iy++) {
02740                         float y = float(iy) - shiftyc;
02741                         float ysang = y*RAinv[0][1]+xc;
02742                         float ycang = y*RAinv[1][1]+yc;
02743                         for (int ix = 0; ix < nx; ix++) {
02744                                 float x = float(ix) - shiftxc;
02745                                 float xold = x*RAinv[0][0] + ysang;
02746                                 float yold = x*RAinv[1][0] + ycang;
02747 
02748                                 // if (xold,yold) is outside the image, then let xold = ix and yold = iy
02749 
02750                 if ( (xold < 0.0f) || (xold >= (float)(nx)) || (yold < 0.0f) || (yold >= (float)(ny)) ){
02751                                     xold = (float)ix;
02752                                         yold = (float)iy;
02753                                 }
02754 
02755                                 int xfloor = int(xold);
02756                                 int yfloor = int(yold);
02757                                 float t = xold-xfloor;
02758                                 float u = yold-yfloor;
02759                                 if(xfloor == nx -1 && yfloor == ny -1) {
02760 
02761                                     p1 =in[xfloor   + yfloor*ny];
02762                                         p2 =in[ yfloor*ny];
02763                                         p3 =in[0];
02764                                         p4 =in[xfloor];
02765                                 } else if(xfloor == nx - 1) {
02766 
02767                                         p1 =in[xfloor   + yfloor*ny];
02768                                         p2 =in[           yfloor*ny];
02769                                         p3 =in[          (yfloor+1)*ny];
02770                                         p4 =in[xfloor   + (yfloor+1)*ny];
02771                                 } else if(yfloor == ny - 1) {
02772 
02773                                         p1 =in[xfloor   + yfloor*ny];
02774                                         p2 =in[xfloor+1 + yfloor*ny];
02775                                         p3 =in[xfloor+1 ];
02776                                         p4 =in[xfloor   ];
02777                                 } else {
02778 
02779                                         p1 =in[xfloor   + yfloor*ny];
02780                                         p2 =in[xfloor+1 + yfloor*ny];
02781                                         p3 =in[xfloor+1 + (yfloor+1)*ny];
02782                                         p4 =in[xfloor   + (yfloor+1)*ny];
02783                                 }
02784                                 (*ret)(ix,iy) = p1 + u * ( p4 - p1) + t * ( p2 - p1 + u *(p3-p2-p4+p1));
02785                         } //ends x loop
02786                 } // ends y loop
02787                 set_array_offsets(saved_offsets);
02788                 return ret;
02789         } else {
02790 //               This begins the 3D version trilinear interpolation.
02791 
02792         float delx = translations.at(0);
02793         float dely = translations.at(1);
02794         float delz = translations.at(2);
02795         delx = restrict2(delx, nx);
02796         dely = restrict2(dely, ny);
02797         delz = restrict2(delz, nz);
02798         int xc = nx/2;
02799         int yc = ny/2;
02800         int zc = nz/2;
02801 //         shifted center for rotation
02802         float shiftxc = xc + delx;
02803         float shiftyc = yc + dely;
02804         float shiftzc = zc + delz;
02805 
02806                 for (int iz = 0; iz < nz; iz++) {
02807                         float z = float(iz) - shiftzc;
02808                         float xoldz = z*RAinv[0][2]+xc;
02809                         float yoldz = z*RAinv[1][2]+yc;
02810                         float zoldz = z*RAinv[2][2]+zc;
02811                         for (int iy = 0; iy < ny; iy++) {
02812                                 float y = float(iy) - shiftyc;
02813                                 float xoldzy = xoldz + y*RAinv[0][1] ;
02814                                 float yoldzy = yoldz + y*RAinv[1][1] ;
02815                                 float zoldzy = zoldz + y*RAinv[2][1] ;
02816                                 for (int ix = 0; ix < nx; ix++) {
02817                                         float x = float(ix) - shiftxc;
02818                                         float xold = xoldzy + x*RAinv[0][0] ;
02819                                         float yold = yoldzy + x*RAinv[1][0] ;
02820                                         float zold = zoldzy + x*RAinv[2][0] ;
02821 
02822                                         // if (xold,yold,zold) is outside the image, then let xold = ix, yold = iy and zold=iz
02823 
02824                     if ( (xold < 0.0f) || (xold >= (float)(nx)) || (yold < 0.0f) || (yold >= (float)(ny))  || (zold < 0.0f) || (zold >= (float)(nz)) ){
02825                                          xold = (float)ix;
02826                                              yold = (float)iy;
02827                                                  zold = (float)iz;
02828                                         }
02829 
02830                                         int IOX = int(xold);
02831                                         int IOY = int(yold);
02832                                         int IOZ = int(zold);
02833 
02834                                         #ifdef _WIN32
02835                                         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
02836                                         #else
02837                                         int IOXp1 = std::min( nx-1 ,IOX+1);
02838                                         #endif  //_WIN32
02839 
02840                                         #ifdef _WIN32
02841                                         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
02842                                         #else
02843                                         int IOYp1 = std::min( ny-1 ,IOY+1);
02844                                         #endif  //_WIN32
02845 
02846                                         #ifdef _WIN32
02847                                         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
02848                                         #else
02849                                         int IOZp1 = std::min( nz-1 ,IOZ+1);
02850                                         #endif  //_WIN32
02851 
02852                                         float dx = xold-IOX;
02853                                         float dy = yold-IOY;
02854                                         float dz = zold-IOZ;
02855 
02856                                         float a1 = in(IOX,IOY,IOZ);
02857                                         float a2 = in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZ);
02858                                         float a3 = in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZ);
02859                                         float a4 = in(IOX,IOY,IOZp1) - in(IOX,IOY,IOZ);
02860                                         float a5 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOYp1,IOZ) + in(IOXp1,IOYp1,IOZ);
02861                                         float a6 = in(IOX,IOY,IOZ) - in(IOXp1,IOY,IOZ) - in(IOX,IOY,IOZp1) + in(IOXp1,IOY,IOZp1);
02862                                         float a7 = in(IOX,IOY,IOZ) - in(IOX,IOYp1,IOZ) - in(IOX,IOY,IOZp1) + in(IOX,IOYp1,IOZp1);
02863                                         float a8 = in(IOXp1,IOY,IOZ) + in(IOX,IOYp1,IOZ)+ in(IOX,IOY,IOZp1)
02864                                                         - in(IOX,IOY,IOZ)- in(IOXp1,IOYp1,IOZ) - in(IOXp1,IOY,IOZp1)
02865                                                         - in(IOX,IOYp1,IOZp1) + in(IOXp1,IOYp1,IOZp1);
02866                                         (*ret)(ix,iy,iz) = a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
02867                                 } //ends x loop
02868                         } // ends y loop
02869                 } // ends z loop
02870 
02871                 set_array_offsets(saved_offsets);
02872                 return ret;
02873 
02874         }
02875 }
02876 #undef  in
02877 
02878 
02879 /*
02880 EMData*
02881 EMData::rot_scale_conv(float ang, float delx, float dely, Util::KaiserBessel& kb) {
02882         int nxn, nyn, nzn;
02883         const float scale=0.5;
02884         float  sum, w;
02885         if (1 >= ny)
02886                 throw ImageDimensionException("Can't rotate 1D image");
02887         if (1 < nz)
02888                 throw ImageDimensionException("Volume not currently supported");
02889         nxn=nx/2;nyn=ny/2;nzn=nz/2;
02890 
02891         int K = kb.get_window_size();
02892         int kbmin = -K/2;
02893         int kbmax = -kbmin;
02894         int kbc = kbmax+1;
02895         vector<int> saved_offsets = get_array_offsets();
02896         set_array_offsets(0,0,0);
02897         EMData* ret = new EMData();
02898 #ifdef _WIN32
02899         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
02900 #else
02901         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
02902 #endif  //_WIN32
02903         ret->to_zero();  //we will leave margins zeroed.
02904         delx = fmod(delx, float(nxn));
02905         dely = fmod(dely, float(nyn));
02906         // center of big image,
02907         int xc = nxn;
02908         int ixs = nxn%2;  // extra shift on account of odd-sized images
02909         int yc = nyn;
02910         int iys = nyn%2;
02911         // center of small image
02912         int xcn = nxn/2;
02913         int ycn = nyn/2;
02914         // shifted center for rotation
02915         float shiftxc = xcn + delx;
02916         float shiftyc = ycn + dely;
02917         // bounds if origin at center
02918         float ymin = -ny/2.0f;
02919         float xmin = -nx/2.0f;
02920         float ymax = -ymin;
02921         float xmax = -xmin;
02922         if (0 == nx%2) xmax--;
02923         if (0 == ny%2) ymax--;
02924         // trig
02925         float cang = cos(ang);
02926         float sang = sin(ang);
02927                 for (int iy = 0; iy < nyn; iy++) {
02928                         float y = float(iy) - shiftyc;
02929                         float ycang = y*cang/scale + yc;
02930                         float ysang = -y*sang/scale + xc;
02931                         for (int ix = 0; ix < nxn; ix++) {
02932                                 float x = float(ix) - shiftxc;
02933                                 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
02934                                 float yold = x*sang/scale + ycang-iys;
02935                                 int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
02936                                      sum=0.0f;    w=0.0f;
02937                                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
02938                                   for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
02939                                   float q = kb.i0win_tab(xold - inxold-m1)*kb.i0win_tab(yold - inyold-m2);
02940                                   sum += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;}}
02941                                 }else{
02942                                   for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
02943                                   float q =kb.i0win_tab(xold - inxold-m1)*kb.i0win_tab(yold - inyold-m2);
02944                                   sum += (*this)(inxold+m1,inyold+m2)*q;w+=q;}}
02945                                 }
02946                                 (*ret)(ix,iy)=sum/w;
02947                         }
02948                 }
02949         set_array_offsets(saved_offsets);
02950         return ret;
02951 }
02952 */
02953 
02954 EMData* EMData::rot_scale_conv(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
02955         int nxn, nyn, nzn;
02956         if(scale_input == 0.0f) scale_input = 1.0f;
02957         //const float scale=0.5;
02958         float  scale = 0.5f*scale_input;
02959         float  sum, w;
02960         if (1 >= ny)
02961                 throw ImageDimensionException("Can't rotate 1D image");
02962         if (1 < nz)
02963                 throw ImageDimensionException("Volume not currently supported");
02964         nxn=nx/2;nyn=ny/2;nzn=nz/2;
02965 
02966         int K = kb.get_window_size();
02967         int kbmin = -K/2;
02968         int kbmax = -kbmin;
02969         int kbc = kbmax+1;
02970         vector<int> saved_offsets = get_array_offsets();
02971         set_array_offsets(0,0,0);
02972         EMData* ret = this->copy_head();
02973 #ifdef _WIN32
02974         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
02975 #else
02976         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
02977 #endif  //_WIN32
02978         //ret->to_zero();  //we will leave margins zeroed.
02979         delx = restrict2(delx, nx);
02980         dely = restrict2(dely, ny);
02981         // center of big image,
02982         int xc = nxn;
02983         int ixs = nxn%2;  // extra shift on account of odd-sized images
02984         int yc = nyn;
02985         int iys = nyn%2;
02986         // center of small image
02987         int xcn = nxn/2;
02988         int ycn = nyn/2;
02989         // shifted center for rotation
02990         float shiftxc = xcn + delx;
02991         float shiftyc = ycn + dely;
02992         // bounds if origin at center
02993         float ymin = -ny/2.0f;
02994         float xmin = -nx/2.0f;
02995         float ymax = -ymin;
02996         float xmax = -xmin;
02997         if (0 == nx%2) xmax--;
02998         if (0 == ny%2) ymax--;
02999 
03000         float   *t = (float*)calloc(kbmax-kbmin+1, sizeof(float));
03001 
03002         // trig
03003         float cang = cos(ang);
03004         float sang = sin(ang);
03005         for (int iy = 0; iy < nyn; iy++) {
03006                 float y = float(iy) - shiftyc;
03007                 float ycang = y*cang/scale + yc;
03008                 float ysang = -y*sang/scale + xc;
03009                 for (int ix = 0; ix < nxn; ix++) {
03010                         float x = float(ix) - shiftxc;
03011                         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
03012                         float yold = x*sang/scale + ycang-iys;
03013 
03014                         xold = restrict1(xold, nx);
03015                         yold = restrict1(yold, ny);
03016 
03017                         int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
03018                         sum=0.0f;    w=0.0f;
03019                         for (int m1 =kbmin; m1 <=kbmax; m1++) t[m1-kbmin] = kb.i0win_tab(xold - inxold-m1);
03020                         if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03021                                 for (int m2 =kbmin; m2 <=kbmax; m2++) {
03022                                         float qt = kb.i0win_tab(yold - inyold-m2);
03023                                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03024                                                 float q = t[m1-kbmin]*qt;
03025                                                 sum += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;
03026                                         }
03027                                 }
03028                         } else {
03029                                 for (int m2 =kbmin; m2 <=kbmax; m2++) {
03030                                         float qt = kb.i0win_tab(yold - inyold-m2);
03031                                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03032                                                 float q = t[m1-kbmin]*qt;
03033                                                 sum += (*this)(inxold+m1,inyold+m2)*q; w+=q;}
03034                                         }
03035                         }
03036                         (*ret)(ix,iy)=sum/w;
03037                 }
03038         }
03039         if (t) free(t);
03040         set_array_offsets(saved_offsets);
03041         return ret;
03042 }
03043 
03044 // Notes by Yang on 10/02/07
03045 // 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.
03046 EMData* EMData::rot_scale_conv7(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03047         int nxn, nyn, nzn;
03048         float  scale = 0.5f*scale_input;
03049         float  sum, w;
03050         if (1 >= ny)
03051                 throw ImageDimensionException("Can't rotate 1D image");
03052         if (1 < nz)
03053                 throw ImageDimensionException("Volume not currently supported");
03054         nxn = nx/2; nyn=ny/2; nzn=nz/2;
03055 
03056         int K = kb.get_window_size();
03057         int kbmin = -K/2;
03058         int kbmax = -kbmin;
03059         int kbc = kbmax+1;
03060         vector<int> saved_offsets = get_array_offsets();
03061         set_array_offsets(0,0,0);
03062         EMData* ret = this->copy_head();
03063 #ifdef _WIN32
03064         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03065 #else
03066         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03067 #endif  //_WIN32
03068         //ret->to_zero();  //we will leave margins zeroed.
03069         delx = restrict2(delx, nx);
03070         dely = restrict2(dely, ny);
03071         // center of big image,
03072         int xc = nxn;
03073         int ixs = nxn%2;  // extra shift on account of odd-sized images
03074         int yc = nyn;
03075         int iys = nyn%2;
03076         // center of small image
03077         int xcn = nxn/2;
03078         int ycn = nyn/2;
03079         // shifted center for rotation
03080         float shiftxc = xcn + delx;
03081         float shiftyc = ycn + dely;
03082         // bounds if origin at center
03083         float ymin = -ny/2.0f;
03084         float xmin = -nx/2.0f;
03085         float ymax = -ymin;
03086         float xmax = -xmin;
03087         if (0 == nx%2) xmax--;
03088         if (0 == ny%2) ymax--;
03089 
03090         float   *t = (float*)calloc(kbmax-kbmin+1, sizeof(float));
03091 
03092         // trig
03093         float cang = cos(ang);
03094         float sang = sin(ang);
03095         for (int iy = 0; iy < nyn; iy++) {
03096                 float y = float(iy) - shiftyc;
03097                 float ycang = y*cang/scale + yc;
03098                 float ysang = -y*sang/scale + xc;
03099                 for (int ix = 0; ix < nxn; ix++) {
03100                         float x = float(ix) - shiftxc;
03101                         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
03102                         float yold = x*sang/scale + ycang-iys;
03103 
03104                         xold = restrict1(xold, nx);
03105                         yold = restrict1(yold, ny);
03106 
03107                         int inxold = int(Util::round(xold)); int inyold = int(Util::round(yold));
03108                         sum=0.0f;    w=0.0f;
03109 
03110                         float tablex1 = kb.i0win_tab(xold-inxold+3);
03111                         float tablex2 = kb.i0win_tab(xold-inxold+2);
03112                         float tablex3 = kb.i0win_tab(xold-inxold+1);
03113                         float tablex4 = kb.i0win_tab(xold-inxold);
03114                         float tablex5 = kb.i0win_tab(xold-inxold-1);
03115                         float tablex6 = kb.i0win_tab(xold-inxold-2);
03116                         float tablex7 = kb.i0win_tab(xold-inxold-3);
03117 
03118                         float tabley1 = kb.i0win_tab(yold-inyold+3);
03119                         float tabley2 = kb.i0win_tab(yold-inyold+2);
03120                         float tabley3 = kb.i0win_tab(yold-inyold+1);
03121                         float tabley4 = kb.i0win_tab(yold-inyold);
03122                         float tabley5 = kb.i0win_tab(yold-inyold-1);
03123                         float tabley6 = kb.i0win_tab(yold-inyold-2);
03124                         float tabley7 = kb.i0win_tab(yold-inyold-3);
03125 
03126                         int x1, x2, x3, x4, x5, x6, x7, y1, y2, y3, y4, y5, y6, y7;
03127 
03128                         if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03129                                 x1 = (inxold-3+nx)%nx;
03130                                 x2 = (inxold-2+nx)%nx;
03131                                 x3 = (inxold-1+nx)%nx;
03132                                 x4 = (inxold  +nx)%nx;
03133                                 x5 = (inxold+1+nx)%nx;
03134                                 x6 = (inxold+2+nx)%nx;
03135                                 x7 = (inxold+3+nx)%nx;
03136 
03137                                 y1 = (inyold-3+ny)%ny;
03138                                 y2 = (inyold-2+ny)%ny;
03139                                 y3 = (inyold-1+ny)%ny;
03140                                 y4 = (inyold  +ny)%ny;
03141                                 y5 = (inyold+1+ny)%ny;
03142                                 y6 = (inyold+2+ny)%ny;
03143                                 y7 = (inyold+3+ny)%ny;
03144                         } else {
03145                                 x1 = inxold-3;
03146                                 x2 = inxold-2;
03147                                 x3 = inxold-1;
03148                                 x4 = inxold;
03149                                 x5 = inxold+1;
03150                                 x6 = inxold+2;
03151                                 x7 = inxold+3;
03152 
03153                                 y1 = inyold-3;
03154                                 y2 = inyold-2;
03155                                 y3 = inyold-1;
03156                                 y4 = inyold;
03157                                 y5 = inyold+1;
03158                                 y6 = inyold+2;
03159                                 y7 = inyold+3;
03160                         }
03161                         sum    =   ( (*this)(x1,y1)*tablex1 + (*this)(x2,y1)*tablex2 + (*this)(x3,y1)*tablex3 +
03162                                      (*this)(x4,y1)*tablex4 + (*this)(x5,y1)*tablex5 + (*this)(x6,y1)*tablex6 +
03163                                      (*this)(x7,y1)*tablex7 ) * tabley1 +
03164                                    ( (*this)(x1,y2)*tablex1 + (*this)(x2,y2)*tablex2 + (*this)(x3,y2)*tablex3 +
03165                                      (*this)(x4,y2)*tablex4 + (*this)(x5,y2)*tablex5 + (*this)(x6,y2)*tablex6 +
03166                                      (*this)(x7,y2)*tablex7 ) * tabley2 +
03167                                    ( (*this)(x1,y3)*tablex1 + (*this)(x2,y3)*tablex2 + (*this)(x3,y3)*tablex3 +
03168                                      (*this)(x4,y3)*tablex4 + (*this)(x5,y3)*tablex5 + (*this)(x6,y3)*tablex6 +
03169                                      (*this)(x7,y3)*tablex7 ) * tabley3 +
03170                                    ( (*this)(x1,y4)*tablex1 + (*this)(x2,y4)*tablex2 + (*this)(x3,y4)*tablex3 +
03171                                      (*this)(x4,y4)*tablex4 + (*this)(x5,y4)*tablex5 + (*this)(x6,y4)*tablex6 +
03172                                      (*this)(x7,y4)*tablex7 ) * tabley4 +
03173                                    ( (*this)(x1,y5)*tablex1 + (*this)(x2,y5)*tablex2 + (*this)(x3,y5)*tablex3 +
03174                                      (*this)(x4,y5)*tablex4 + (*this)(x5,y5)*tablex5 + (*this)(x6,y5)*tablex6 +
03175                                      (*this)(x7,y5)*tablex7 ) * tabley5 +
03176                                    ( (*this)(x1,y6)*tablex1 + (*this)(x2,y6)*tablex2 + (*this)(x3,y6)*tablex3 +
03177                                      (*this)(x4,y6)*tablex4 + (*this)(x5,y6)*tablex5 + (*this)(x6,y6)*tablex6 +
03178                                      (*this)(x7,y6)*tablex7 ) * tabley6 +
03179                                    ( (*this)(x1,y7)*tablex1 + (*this)(x2,y7)*tablex2 + (*this)(x3,y7)*tablex3 +
03180                                      (*this)(x4,y7)*tablex4 + (*this)(x5,y7)*tablex5 + (*this)(x6,y7)*tablex6 +
03181                                      (*this)(x7,y7)*tablex7 ) * tabley7;
03182 
03183                         w = (tablex1+tablex2+tablex3+tablex4+tablex5+tablex6+tablex7) *
03184                             (tabley1+tabley2+tabley3+tabley4+tabley5+tabley6+tabley7);
03185 
03186                         (*ret)(ix,iy)=sum/w;
03187                 }
03188         }
03189         if (t) free(t);
03190         set_array_offsets(saved_offsets);
03191         return ret;
03192 }
03193 
03194 EMData* EMData::downsample(Util::sincBlackman& kb, float scale) {
03195 
03196         /*int M = kb.get_sB_size();
03197         int kbmin = -M/2;
03198         int kbmax = -kbmin;*/
03199 
03200         int nxn, nyn, nzn;
03201         nxn = (int)(nx*scale); nyn = (int)(ny*scale); nzn = (int)(nz*scale);
03202 
03203         vector<int> saved_offsets = get_array_offsets();
03204         set_array_offsets(0,0,0);
03205         EMData* ret = this->copy_head();
03206 #ifdef _WIN32
03207         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03208 #else
03209         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03210 #endif  //_WIN32
03211         ret->to_zero();  //we will leave margins zeroed.
03212 
03213         // scan new, find pixels in old
03214         if(nz == 1)
03215         {
03216                 for (int iy =0; iy < nyn; iy++) {
03217                         float y = float(iy)/scale;
03218                         for (int ix = 0; ix < nxn; ix++) {
03219                                 float x = float(ix)/scale;
03220                                 (*ret)(ix,iy) = this->get_pixel_filtered(x, y, 1.0f, kb);
03221                         }
03222                 }
03223         }
03224         else{
03225                 
03226                 for (int iz =0; iz < nzn; iz++) {
03227                         float z = float(iz)/scale;
03228                         for (int iy =0; iy < nyn; iy++) {
03229                                 float y = float(iy)/scale;
03230                                 for (int ix = 0; ix < nxn; ix++) {
03231                                         float x = float(ix)/scale;
03232                                         (*ret)(ix,iy,iz) = this->get_pixel_filtered(x, y, z, kb);
03233                                 }
03234                         }
03235                 }
03236         
03237         }
03238         set_array_offsets(saved_offsets);
03239         return ret;
03240 }
03241 
03242 
03243 EMData* EMData::rot_scale_conv_new(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03244 
03245         if (scale_input == 0.0f) scale_input = 1.0f;
03246         float  scale = 0.5f*scale_input;
03247 
03248         if (1 >= ny)
03249                 throw ImageDimensionException("Can't rotate 1D image");
03250         if (1 < nz)
03251                 throw ImageDimensionException("Use rot_scale_conv_new_3D for volumes");
03252         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03253 
03254         vector<int> saved_offsets = get_array_offsets();
03255         set_array_offsets(0,0,0);
03256         EMData* ret = this->copy_head();
03257 #ifdef _WIN32
03258         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03259 #else
03260         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03261 #endif  //_WIN32
03262         //ret->to_zero();  //we will leave margins zeroed.
03263         delx = restrict2(delx, nx);
03264         dely = restrict2(dely, ny);
03265         // center of big image,
03266         int xc = nxn;
03267         int ixs = nxn%2;  // extra shift on account of odd-sized images
03268         int yc = nyn;
03269         int iys = nyn%2;
03270         // center of small image
03271         int xcn = nxn/2;
03272         int ycn = nyn/2;
03273         // shifted center for rotation
03274         float shiftxc = xcn + delx;
03275         float shiftyc = ycn + dely;
03276         // bounds if origin at center
03277         float ymin = -ny/2.0f;
03278         float xmin = -nx/2.0f;
03279         float ymax = -ymin;
03280         float xmax = -xmin;
03281         if (0 == nx%2) xmax--;
03282         if (0 == ny%2) ymax--;
03283 
03284         float* data = this->get_data();
03285 
03286         float cang = cos(ang);
03287         float sang = sin(ang);
03288         for (int iy = 0; iy < nyn; iy++) {
03289                 float y = float(iy) - shiftyc;
03290                 float ycang = y*cang/scale + yc;
03291                 float ysang = -y*sang/scale + xc;
03292                 for (int ix = 0; ix < nxn; ix++) {
03293                         float x = float(ix) - shiftxc;
03294                         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
03295                         float yold = x*sang/scale + ycang-iys;
03296 
03297                         (*ret)(ix,iy) = Util::get_pixel_conv_new(nx, ny, 1, xold, yold, 1, data, kb);
03298                 }
03299         }
03300         set_array_offsets(saved_offsets);
03301         return ret;
03302 }
03303 
03304 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) {
03305 
03306         if (scale_input == 0.0f) scale_input = 1.0f;
03307         float  scale = 0.5f*scale_input;
03308 
03309         if (1 >= ny)
03310                 throw ImageDimensionException("Can't rotate 1D image");
03311         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03312 
03313         vector<int> saved_offsets = get_array_offsets();
03314         set_array_offsets(0,0,0);
03315         EMData* ret = this->copy_head();
03316 #ifdef _WIN32
03317         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03318 #else
03319         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03320 #endif  //_WIN32
03321         //ret->to_zero();  //we will leave margins zeroed.
03322         if(wrap){
03323                 delx = restrict2(delx, nx);
03324                 dely = restrict2(dely, ny);
03325                 delz = restrict2(delz, nz);
03326         }
03327         // center of big image,
03328         int xc = nxn;
03329         int ixs = nxn%2;  // extra shift on account of odd-sized images
03330         int yc = nyn;
03331         int iys = nyn%2;
03332         int zc = nzn;
03333         int izs = nzn%2;
03334         // center of small image
03335         int xcn = nxn/2;
03336         int ycn = nyn/2;
03337         int zcn = nzn/2;
03338         // shifted center for rotation
03339         float shiftxc = xcn + delx;
03340         float shiftyc = ycn + dely;
03341         float shiftzc = zcn + delz;
03342         // bounds if origin at center
03343         float zmin = -nz/2.0f;
03344         float ymin = -ny/2.0f;
03345         float xmin = -nx/2.0f;
03346         float zmax = -zmin;
03347         float ymax = -ymin;
03348         float xmax = -xmin;
03349         if (0 == nx%2) xmax--;
03350         if (0 == ny%2) ymax--;
03351         if (0 == nz%2) zmax--;
03352 
03353         float* data = this->get_data();
03354 
03355         float cf = cos(phi);   float sf = sin(phi);
03356         float ct = cos(theta); float st = sin(theta);
03357         float cp = cos(psi);   float sp = sin(psi);
03358         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
03359         float a11 =  cp*ct*cf-sp*sf; float a12 =  cp*ct*sf+sp*cf; float a13 = -cp*st;
03360         float a21 = -sp*ct*cf-cp*sf; float a22 = -sp*ct*sf+cp*cf; float a23 =  sp*st;
03361         float a31 =  st*cf;          float a32 =  st*sf;          float a33 =  ct;
03362         for (int iz = 0; iz < nzn; iz++) {
03363                 float z = (float(iz) - shiftzc)/scale;
03364                 float zco1 = a31*z+xc;
03365                 float zco2 = a32*z+yc;
03366                 float zco3 = a33*z+zc;
03367                 for (int iy = 0; iy < nyn; iy++) {
03368                         float y = (float(iy) - shiftyc)/scale;
03369                         float yco1 = zco1+a21*y;
03370                         float yco2 = zco2+a22*y;
03371                         float yco3 = zco3+a23*y;
03372                         for (int ix = 0; ix < nxn; ix++) {
03373                                 float x = (float(ix) - shiftxc)/scale;
03374                                 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
03375                                 float yold = yco2+a12*x-iys;
03376                                 float zold = yco3+a13*x-izs;
03377                                 if(!wrap && (xold<0.0 || xold>nx-1 || yold<0.0 || yold>ny-1 || zold<0.0 || zold>nz-1))
03378                                         (*ret)(ix,iy,iz) = 0.0;
03379                                 else
03380                                         (*ret)(ix,iy,iz) = Util::get_pixel_conv_new(nx, ny, nz, xold, yold, zold, data, kb);
03381                         }
03382                 }
03383         }
03384         set_array_offsets(saved_offsets);
03385         return ret;
03386 }
03387 
03388 EMData* EMData::rot_scale_conv_new_background(float ang, float delx, float dely, Util::KaiserBessel& kb, float scale_input) {
03389 
03390         int nxn, nyn, nzn;
03391 
03392         if (scale_input == 0.0f) scale_input = 1.0f;
03393         float  scale = 0.5f*scale_input;
03394 
03395         if (1 >= ny)
03396                 throw ImageDimensionException("Can't rotate 1D image");
03397         if (1 < nz)
03398                 throw ImageDimensionException("Use rot_scale_conv_new_background_3D for volumes");
03399         nxn = nx/2; nyn = ny/2; nzn = nz/2;
03400 
03401         vector<int> saved_offsets = get_array_offsets();
03402         set_array_offsets(0,0,0);
03403         EMData* ret = this->copy_head();
03404 #ifdef _WIN32
03405         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03406 #else
03407         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03408 #endif  //_WIN32
03409         //ret->to_zero();  //we will leave margins zeroed.
03410         delx = restrict2(delx, nx);
03411         dely = restrict2(dely, ny);
03412         // center of big image,
03413         int xc = nxn;
03414         int ixs = nxn%2;  // extra shift on account of odd-sized images
03415         int yc = nyn;
03416         int iys = nyn%2;
03417         // center of small image
03418         int xcn = nxn/2;
03419         int ycn = nyn/2;
03420         // shifted center for rotation
03421         float shiftxc = xcn + delx;
03422         float shiftyc = ycn + dely;
03423         // bounds if origin at center
03424         float ymin = -ny/2.0f;
03425         float xmin = -nx/2.0f;
03426         float ymax = -ymin;
03427         float xmax = -xmin;
03428         if (0 == nx%2) xmax--;
03429         if (0 == ny%2) ymax--;
03430 
03431         float* data = this->get_data();
03432 
03433         // trig
03434         float cang = cos(ang);
03435         float sang = sin(ang);
03436         for (int iy = 0; iy < nyn; iy++) {
03437                 float y = float(iy) - shiftyc;
03438                 float ycang = y*cang/scale + yc;
03439                 float ysang = -y*sang/scale + xc;
03440                 for (int ix = 0; ix < nxn; ix++) {
03441                         float x = float(ix) - shiftxc;
03442                         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
03443                         float yold = x*sang/scale + ycang-iys;
03444 
03445                         (*ret)(ix,iy) = Util::get_pixel_conv_new_background(nx, ny, 1, xold, yold, 1, data, kb, ix, iy);
03446                 }
03447         }
03448         set_array_offsets(saved_offsets);
03449         return ret;
03450 }
03451 
03452 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) {
03453 
03454         if (scale_input == 0.0f) scale_input = 1.0f;
03455         float  scale = 0.5f*scale_input;
03456 
03457         if (1 >= ny)
03458                 throw ImageDimensionException("Can't rotate 1D image");
03459         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
03460 
03461         vector<int> saved_offsets = get_array_offsets();
03462         set_array_offsets(0,0,0);
03463         EMData* ret = this->copy_head();
03464 #ifdef _WIN32
03465         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
03466 #else
03467         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
03468 #endif  //_WIN32
03469         //ret->to_zero();  //we will leave margins zeroed.
03470         if (wrap){
03471                 delx = restrict2(delx, nx);
03472                 dely = restrict2(dely, ny);
03473                 delz = restrict2(delz, nz);
03474         }
03475         // center of big image,
03476         int xc = nxn;
03477         int ixs = nxn%2;  // extra shift on account of odd-sized images
03478         int yc = nyn;
03479         int iys = nyn%2;
03480         int zc = nzn;
03481         int izs = nzn%2;
03482         // center of small image
03483         int xcn = nxn/2;
03484         int ycn = nyn/2;
03485         int zcn = nzn/2;
03486         // shifted center for rotation
03487         float shiftxc = xcn + delx;
03488         float shiftyc = ycn + dely;
03489         float shiftzc = zcn + delz;
03490         // bounds if origin at center
03491         float zmin = -nz/2.0f;
03492         float ymin = -ny/2.0f;
03493         float xmin = -nx/2.0f;
03494         float zmax = -zmin;
03495         float ymax = -ymin;
03496         float xmax = -xmin;
03497         if (0 == nx%2) xmax--;
03498         if (0 == ny%2) ymax--;
03499         if (0 == nz%2) zmax--;
03500 
03501         float* data = this->get_data();
03502 
03503         float cf = cos(phi);   float sf = sin(phi);
03504         float ct = cos(theta); float st = sin(theta);
03505         float cp = cos(psi);   float sp = sin(psi);
03506         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
03507         float a11 =  cp*ct*cf-sp*sf; float a12 =  cp*ct*sf+sp*cf; float a13 = -cp*st;
03508         float a21 = -sp*ct*cf-cp*sf; float a22 = -sp*ct*sf+cp*cf; float a23 =  sp*st;
03509         float a31 =  st*cf;          float a32 =  st*sf;          float a33 =  ct;
03510         for (int iz = 0; iz < nzn; iz++) {
03511                 float z = (float(iz) - shiftzc)/scale;
03512                 float zco1 = a31*z+xc;
03513                 float zco2 = a32*z+yc;
03514                 float zco3 = a33*z+zc;
03515                 for (int iy = 0; iy < nyn; iy++) {
03516                         float y = (float(iy) - shiftyc)/scale;
03517                         float yco1 = zco1+a21*y;
03518                         float yco2 = zco2+a22*y;
03519                         float yco3 = zco3+a23*y;
03520                         for (int ix = 0; ix < nxn; ix++) {
03521                                 float x = (float(ix) - shiftxc)/scale;
03522                                 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
03523                                 float yold = yco2+a12*x-iys;
03524                                 float zold = yco3+a13*x-izs;
03525                                 if(!wrap && (xold<0.0 || xold>nx-1 || yold<0.0 || yold>ny-1 || zold<0.0 || zold>nz-1))
03526                                         (*ret)(ix,iy,iz) = 0.0;
03527                                 else
03528                                         (*ret)(ix,iy,iz) = Util::get_pixel_conv_new_background(nx, ny, nz, xold, yold, zold, data, kb, ix, iy);
03529                         }
03530                 }
03531         }
03532         set_array_offsets(saved_offsets);
03533         return ret;
03534 }
03535 
03536 
03537 float  EMData::get_pixel_conv(float delx, float dely, float delz, Util::KaiserBessel& kb) {
03538 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03539 
03540         int K     = kb.get_window_size();
03541         int kbmin = -K/2;
03542         int kbmax = -kbmin;
03543         int kbc   = kbmax+1;
03544 
03545         float pixel =0.0f;
03546         float w=0.0f;
03547 
03548         delx = restrict2(delx, nx);
03549         int inxold = int(Util::round(delx));
03550         if(ny<2) {  //1D
03551                 if(inxold <= kbc || inxold >=nx-kbc-2 )  {
03552                         //  loop for ends
03553                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03554                                 float q = kb.i0win_tab(delx - inxold-m1);
03555                                 pixel += (*this)((inxold+m1+nx)%nx)*q; w+=q;
03556                         }
03557                 } else {
03558                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03559                                 float q = kb.i0win_tab(delx - inxold-m1);
03560                                 pixel += (*this)(inxold+m1)*q; w+=q;
03561                         }
03562                 }
03563 
03564         } else if(nz<2) {  // 2D
03565                 dely = restrict2(dely, ny);
03566                 int inyold = int(Util::round(dely));
03567                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03568                         //  loop for strips
03569                         for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03570                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2);
03571                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q; w+=q;}
03572                         }
03573                 } else {
03574                         for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03575                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2);
03576                                 pixel += (*this)(inxold+m1,inyold+m2)*q; w+=q;}
03577                         }
03578                 }
03579         } else {  //  3D
03580                 dely = restrict2(dely, ny);
03581                 int inyold = int(Util::round(dely));
03582                 delz = restrict2(delz, nz);
03583                 int inzold = int(Util::round(delz));
03584                     //cout << inxold<<"  "<< kbc<<"  "<< nx-kbc-2<<"  "<< endl;
03585                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2  || inzold <= kbc || inzold >=nz-kbc-2 )  {
03586                         //  loop for strips
03587                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03588                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2)*kb.i0win_tab(delz - inzold-m3);
03589                                 //cout << "BB  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)<< endl;
03590                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)*q ;w+=q;}}
03591                         }
03592                 } else {
03593                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03594                                 float q = kb.i0win_tab(delx - inxold-m1)*kb.i0win_tab(dely - inyold-m2)*kb.i0win_tab(delz - inzold-m3);
03595                                 //cout << "OO  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)(inxold+m1,inyold+m2,inzold+m3)<< endl;
03596                                 pixel += (*this)(inxold+m1,inyold+m2,inzold+m3)*q; w+=q;}}
03597                         }
03598                 }
03599         }
03600         return pixel/w;
03601 }
03602 
03603 
03604 float  EMData::get_pixel_filtered(float delx, float dely, float delz, Util::sincBlackman& kb) {
03605 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03606 
03607         int K     = kb.get_sB_size();
03608         int kbmin = -K/2;
03609         int kbmax = -kbmin;
03610         int kbc   = kbmax+1;
03611 
03612         float pixel =0.0f;
03613         float w=0.0f;
03614 
03615         //delx = restrict2(delx, nx);   //  In this function the old location is always within the      image
03616         int inxold = int(Util::round(delx));
03617         /*if(ny<2) {  //1D
03618                 if(inxold <= kbc || inxold >=nx-kbc-2 )  {
03619                         //  loop for ends
03620                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03621                                 float q = kb.sBwin_tab(delx - inxold-m1);
03622                                 pixel += (*this)((inxold+m1+nx)%nx)*q; w+=q;
03623                         }
03624                 } else {
03625                         for (int m1 =kbmin; m1 <=kbmax; m1++) {
03626                                 float q = kb.sBwin_tab(delx - inxold-m1);
03627                                 pixel += (*this)(inxold+m1)*q; w+=q;
03628                         }
03629                 }
03630 
03631         } else */
03632         if(nz<2) {  
03633                 //dely = restrict2(dely, ny);
03634                 int inyold = int(Util::round(dely));
03635                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2 )  {
03636                         //  loop for strips
03637                         for (int m2 =kbmin; m2 <=kbmax; m2++){
03638                                 float t = kb.sBwin_tab(dely - inyold-m2);
03639                                 for (int m1 =kbmin; m1 <=kbmax; m1++) {
03640                                         float q = kb.sBwin_tab(delx - inxold-m1)*t;
03641                                         pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny)*q;
03642                                         w += q;
03643                                 }
03644                         }
03645                 } else {
03646                         for (int m2 =kbmin; m2 <=kbmax; m2++){
03647                                 float t = kb.sBwin_tab(dely - inyold-m2);
03648                                 for (int m1 =kbmin; m1 <=kbmax; m1++) {
03649                                         float q = kb.sBwin_tab(delx - inxold-m1)*t;
03650                                         pixel += (*this)(inxold+m1,inyold+m2)*q;
03651                                         w += q;
03652                                 }
03653                         }
03654                 }
03655         } else {  //  3D
03656                 //std::cout<<"pixel_filtered 3D"<<std::endl;
03657                 dely = restrict2(dely, ny);
03658                 int inyold = int(Util::round(dely));
03659                 delz = restrict2(delz, nz);
03660                 int inzold = int(Util::round(delz));
03661                     //cout << inxold<<"  "<< kbc<<"  "<< nx-kbc-2<<"  "<< endl;
03662                 if(inxold <= kbc || inxold >=nx-kbc-2 || inyold <= kbc || inyold >=ny-kbc-2  || inzold <= kbc || inzold >=nz-kbc-2 )  {
03663                         //  loop for strips
03664                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03665                                 float q = kb.sBwin_tab(delx - inxold-m1)*kb.sBwin_tab(dely - inyold-m2)*kb.sBwin_tab(delz - inzold-m3);
03666                                 //cout << "BB  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)<< endl;
03667                                 pixel += (*this)((inxold+m1+nx)%nx,(inyold+m2+ny)%ny,(inzold+m3+nz)%nz)*q ;w+=q;}}
03668                         }
03669                 } else {
03670                         for (int m3 =kbmin; m3 <=kbmax; m3++){ for (int m2 =kbmin; m2 <=kbmax; m2++){ for (int m1 =kbmin; m1 <=kbmax; m1++) {
03671                                 float q = kb.sBwin_tab(delx - inxold-m1)*kb.sBwin_tab(dely - inyold-m2)*kb.sBwin_tab(delz - inzold-m3);
03672                                 //cout << "OO  "<<m1<<"  "<< m2<<"  "<< m3<<"  "<< q<<"  "<< q<<"  "<<(*this)(inxold+m1,inyold+m2,inzold+m3)<< endl;
03673                                 pixel += (*this)(inxold+m1,inyold+m2,inzold+m3)*q; w+=q;}}
03674                         }
03675                 }
03676         }
03677         return pixel/w;
03678 }
03679 
03680 // Note by Yang on 10/02/07
03681 // 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
03682 // 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.
03683 float  EMData::get_pixel_conv7(float delx, float dely, float delz, Util::KaiserBessel& kb) {
03684 //  here counting is in C style, so coordinates of the pixel delx should be [0-nx-1]
03685 
03686         float *image=(this->get_data());
03687         int nx = this->get_xsize();
03688         int ny = this->get_ysize();
03689         int nz = this->get_zsize();
03690 
03691         float result;
03692 
03693         result = Util::get_pixel_conv_new(nx,ny,nz,delx,dely,delz,image,kb);
03694         return result;
03695 }
03696 
03697 float EMData::getconvpt2d_kbi0(float x, float y, Util::KaiserBessel::kbi0_win win, int size) {
03698         const int nxhalf = nx/2;
03699         const int nyhalf = ny/2;
03700         const int bd = size/2;
03701         float* wxarr = new float[size];
03702         float* wyarr = new float[size];
03703         float* wx = wxarr + bd; // wx[-bd] = wxarr[0]
03704         float* wy = wyarr + bd;
03705         int ixc = int(x + 0.5f*Util::sgn(x));
03706         int iyc = int(y + 0.5f*Util::sgn(y));
03707         if (abs(ixc) > nxhalf)
03708                 throw InvalidValueException(ixc, "getconv: X value out of range");
03709         if (abs(iyc) > nyhalf)
03710                 throw InvalidValueException(ixc, "getconv: Y value out of range");
03711         for (int i = -bd; i <= bd; i++) {
03712                 int iyp = iyc + i;
03713                 wy[i] = win(y - iyp);
03714                 int ixp = ixc + i;
03715                 wx[i] = win(x - ixp);
03716         }
03717         vector<int> saved_offsets = get_array_offsets();
03718         set_array_offsets(-nxhalf, -nyhalf);
03719         float conv = 0.f, wsum = 0.f;
03720         for (int iy = -bd; iy <= bd; iy++) {
03721                 int iyp = iyc + iy;
03722                 for (int ix = -bd; ix <= bd; ix++) {
03723                         int ixp = ixc + ix;
03724                         float wg = wx[ix]*wy[iy];
03725                         conv += (*this)(ixp,iyp)*wg;
03726                         wsum += wg;
03727                 }
03728         }
03729         set_array_offsets(saved_offsets);
03730         delete [] wxarr;
03731         delete [] wyarr;
03732         //return conv/wsum;
03733         return conv;
03734 }
03735 
03736 std::complex<float> EMData::extractpoint(float nuxnew, float nuynew, Util::KaiserBessel& kb) {
03737         if (2 != get_ndim())
03738                 throw ImageDimensionException("extractpoint needs a 2-D image.");
03739         if (!is_complex())
03740                 throw ImageFormatException("extractpoint requires a fourier image");
03741         int nxreal = nx - 2;
03742         if (nxreal != ny)
03743                 throw ImageDimensionException("extractpoint requires ny == nx");
03744         int nhalf = nxreal/2;
03745         int kbsize = kb.get_window_size();
03746         int kbmin = -kbsize/2;
03747         int kbmax = -kbmin;
03748         bool flip = (nuxnew < 0.f);
03749         if (flip) {
03750                 nuxnew *= -1;
03751                 nuynew *= -1;
03752         }
03753         // put (xnew,ynew) on a grid.  The indices will be wrong for
03754         // the Fourier elements in the image, but the grid sizing will
03755         // be correct.
03756         int ixn = int(Util::round(nuxnew));
03757         int iyn = int(Util::round(nuynew));
03758         // set up some temporary weighting arrays
03759         float* wy0 = new float[kbmax - kbmin + 1];
03760         float* wy = wy0 - kbmin; // wy[kbmin:kbmax]
03761         float* wx0 = new float[kbmax - kbmin + 1];
03762         float* wx = wx0 - kbmin;
03763         for (int i = kbmin; i <= kbmax; i++) {
03764                         int iyp = iyn + i;
03765                         wy[i] = kb.i0win_tab(nuynew - iyp);
03766                         int ixp = ixn + i;
03767                         wx[i] = kb.i0win_tab(nuxnew - ixp);
03768         }
03769         // restrict loops to non-zero elements
03770         int iymin = 0;
03771         for (int iy = kbmin; iy <= -1; iy++) {
03772                 if (wy[iy] != 0.f) {
03773                         iymin = iy;
03774                         break;
03775                 }
03776         }
03777         int iymax = 0;
03778         for (int iy = kbmax; iy >= 1; iy--) {
03779                 if (wy[iy] != 0.f) {
03780                         iymax = iy;
03781                         break;
03782                 }
03783         }
03784         int ixmin = 0;
03785         for (int ix = kbmin; ix <= -1; ix++) {
03786                 if (wx[ix] != 0.f) {
03787                         ixmin = ix;
03788                         break;
03789                 }
03790         }
03791         int ixmax = 0;
03792         for (int ix = kbmax; ix >= 1; ix--) {
03793                 if (wx[ix] != 0.f) {
03794                         ixmax = ix;
03795                         break;
03796                 }
03797         }
03798         float wsum = 0.0f;
03799         for (int iy = iymin; iy <= iymax; iy++)
03800                 for (int ix = ixmin; ix <= ixmax; ix++)
03801                         wsum += wx[ix]*wy[iy];
03802         std::complex<float> result(0.f,0.f);
03803         if ((ixn >= -kbmin) && (ixn <= nhalf-1-kbmax) && (iyn >= -nhalf-kbmin) && (iyn <= nhalf-1-kbmax)) {
03804                 // (xin,yin) not within window border from the edge
03805                 for (int iy = iymin; iy <= iymax; iy++) {
03806                         int iyp = iyn + iy;
03807                         for (int ix = ixmin; ix <= ixmax; ix++) {
03808                                 int ixp = ixn + ix;
03809                                 float w = wx[ix]*wy[iy];
03810                                 std::complex<float> val = cmplx(ixp,iyp);
03811                                 result += val*w;
03812                         }
03813                 }
03814         } else {
03815                 // points that "stick out"
03816                 for (int iy = iymin; iy <= iymax; iy++) {
03817                         int iyp = iyn + iy;
03818                         for (int ix = ixmin; ix <= ixmax; ix++) {
03819                                 int ixp = ixn + ix;
03820                                 bool mirror = false;
03821                                 int ixt= ixp, iyt= iyp;
03822                                 if (ixt < 0) {
03823                                         ixt = -ixt;
03824                                         iyt = -iyt;
03825                                         mirror = !mirror;
03826                                 }
03827                                 if (ixt > nhalf) {
03828                                         ixt = nxreal - ixt;
03829                                         iyt = -iyt;
03830                                         mirror = !mirror;
03831                                 }
03832                                 if (iyt > nhalf-1)  iyt -= nxreal;
03833                                 if (iyt < -nhalf)   iyt += nxreal;
03834                                 float w = wx[ix]*wy[iy];
03835                                 std::complex<float> val = this->cmplx(ixt,iyt);
03836                                 if (mirror)  result += conj(val)*w;
03837                                 else         result += val*w;
03838                         }
03839                 }
03840         }
03841         if (flip)  result = conj(result)/wsum;
03842         else       result /= wsum;
03843         delete [] wx0;
03844         delete [] wy0;
03845         return result;
03846 }
03847 
03848 EMData* EMData::extractline(Util::KaiserBessel& kb, float nuxnew, float nuynew)
03849 {
03850         if (!is_complex())
03851                 throw ImageFormatException("extractline requires a fourier image");
03852         if (nx%2 != 0)
03853                 throw ImageDimensionException("extractline requires nx to be even");
03854         int nxreal = nx - 2;
03855         if (nxreal != ny)
03856                 throw ImageDimensionException("extractline requires ny == nx");
03857         // build complex result image
03858         EMData* res = new EMData();
03859         res->set_size(nx,1,1);
03860         res->to_zero();
03861         res->set_complex(true);
03862         res->set_fftodd(false);
03863         res->set_fftpad(true);
03864         res->set_ri(true);
03865         // Array offsets: (0..nhalf,-nhalf..nhalf-1)
03866         int n = nxreal;
03867         int nhalf = n/2;
03868         vector<int> saved_offsets = get_array_offsets();
03869         set_array_offsets(0,-nhalf,-nhalf);
03870 
03871         // set up some temporary weighting arrays
03872         int kbsize = kb.get_window_size();
03873         int kbmin = -kbsize/2;
03874         int kbmax = -kbmin;
03875         float* wy0 = new float[kbmax - kbmin + 1];
03876         float* wy = wy0 - kbmin; // wy[kbmin:kbmax]
03877         float* wx0 = new float[kbmax - kbmin + 1];
03878         float* wx = wx0 - kbmin;
03879 
03880         int   count = 0;
03881         float wsum = 0.f;
03882         bool  flip = (nuxnew < 0.f);
03883 
03884         for (int jx = 0; jx <= nhalf; jx++) {
03885                 float xnew = jx*nuxnew, ynew = jx*nuynew;
03886                 count++;
03887                 std::complex<float> btq(0.f,0.f);
03888                 if (flip) {
03889                         xnew = -xnew;
03890                         ynew = -ynew;
03891                 }
03892                 int ixn = int(Util::round(xnew));
03893                 int iyn = int(Util::round(ynew));
03894                 // populate weight arrays
03895                 for (int i=kbmin; i <= kbmax; i++) {
03896                         int iyp = iyn + i;
03897                         wy[i] = kb.i0win_tab(ynew - iyp);
03898                         int ixp = ixn + i;
03899                         wx[i] = kb.i0win_tab(xnew - ixp);
03900                 }
03901                 // restrict weight arrays to non-zero elements
03902 
03903                 int lnby = 0;
03904                 for (int iy = kbmin; iy <= -1; iy++) {
03905                         if (wy[iy] != 0.f) {
03906                                 lnby = iy;
03907                                 break;
03908                         }
03909                 }
03910                 int lney = 0;
03911                 for (int iy = kbmax; iy >= 1; iy--) {
03912                         if (wy[iy] != 0.f) {
03913                                 lney = iy;
03914                                 break;
03915                         }
03916                 }
03917                 int lnbx = 0;
03918                 for (int ix = kbmin; ix <= -1; ix++) {
03919                         if (wx[ix] != 0.f) {
03920                                 lnbx = ix;
03921                                 break;
03922                         }
03923                 }
03924                 int lnex = 0;
03925                 for (int ix = kbmax; ix >= 1; ix--) {
03926                         if (wx[ix] != 0.f) {
03927                                 lnex = ix;
03928                                 break;
03929                         }
03930                 }
03931                 if (ixn >= -kbmin && ixn <= nhalf-1-kbmax
03932                                 && iyn >= -nhalf-kbmin && iyn <= nhalf-1-kbmax) {
03933                         // interior points
03934                         for (int ly=lnby; ly<=lney; ly++) {
03935                                 int iyp = iyn + ly;
03936                                 for (int lx=lnbx; lx<=lnex; lx++) {
03937                                         int ixp = ixn + lx;
03938                                         float wg = wx[lx]*wy[ly];
03939                                         btq += cmplx(ixp,iyp)*wg;
03940                                         wsum += wg;
03941                                 }
03942                         }
03943                 } else {
03944                         // points "sticking out"
03945                         for (int ly=lnby; ly<=lney; ly++) {
03946                                 int iyp = iyn + ly;
03947                                 for (int lx=lnbx; lx<=lnex; lx++) {
03948                                         int ixp = ixn + lx;
03949                                         float wg = wx[lx]*wy[ly];
03950                                         bool mirror = false;
03951                                         int ixt(ixp), iyt(iyp);
03952                                         if (ixt > nhalf || ixt < -nhalf) {
03953                                                 ixt = Util::sgn(ixt)*(n - abs(ixt));
03954                                                 iyt = -iyt;
03955                                                 mirror = !mirror;
03956                                         }
03957                                         if (iyt >= nhalf || iyt < -nhalf) {
03958                                                 if (ixt != 0) {
03959                                                         ixt = -ixt;
03960                                                         iyt = Util::sgn(iyt)*(n - abs(iyt));
03961                                                         mirror = !mirror;
03962                                                 } else {
03963                                                         iyt -= n*Util::sgn(iyt);
03964                                                 }
03965                                         }
03966                                         if (ixt < 0) {
03967                                                 ixt = -ixt;
03968                                                 iyt = -iyt;
03969                                                 mirror = !mirror;
03970                                         }
03971                                         if (iyt == nhalf) iyt = -nhalf;
03972                                         if (mirror) btq += conj(cmplx(ixt,iyt))*wg;
03973                                         else        btq += cmplx(ixt,iyt)*wg;
03974                                         wsum += wg;
03975                                 }
03976                         }
03977                 }
03978                 if (flip) res->cmplx(jx) = conj(btq);
03979                 else      res->cmplx(jx) = btq;
03980         }
03981         for (int jx = 0; jx <= nhalf; jx++)  res->cmplx(jx) *= count/wsum;
03982 
03983         delete[] wx0; delete[] wy0;
03984         set_array_offsets(saved_offsets);
03985         res->set_array_offsets(0,0,0);
03986         return res;
03987 }
03988 
03989 
03991 inline void swapx(float* a, float* b, float* temp, size_t nbytes) {
03992         memcpy(temp, a, nbytes);
03993         memcpy(a, b, nbytes);
03994         memcpy(b, temp, nbytes);
03995 }
03996 
03997 void EMData::fft_shuffle() {
03998         if (!is_complex())
03999                 throw ImageFormatException("fft_shuffle requires a fourier image");
04000         vector<int> offsets = get_array_offsets();
04001         set_array_offsets(); // clear offsets before shuffling
04002         EMData& self = *this;
04003         int nyhalf = ny/2;
04004         int nzhalf = nz/2;
04005         int nbytes = nx*sizeof(float);
04006         float* temp = new float[nx];
04007         for (int iz=0; iz < nz; iz++)
04008                 for (int iy=0; iy < nyhalf; iy++)
04009                         swapx(&self(0,iy,iz),&self(0,iy+nyhalf,iz),temp,nbytes);
04010         if (nz > 1) {
04011                 for (int iy=0; iy < ny; iy++)
04012                         for (int iz=0; iz < nzhalf; iz++)
04013                                 swapx(&self(0,iy,iz),&self(0,iy,iz+nzhalf),temp,nbytes);
04014         }
04015         set_shuffled(!is_shuffled()); // toggle
04016         set_array_offsets(offsets); // reset offsets
04017         update();
04018         delete[] temp;
04019 }
04020 
04021 void EMData::pad_corner(float *pad_image) {
04022         size_t nbytes = nx*sizeof(float);
04023         for (int iy=0; iy<ny; iy++)
04024                 memcpy(&(*this)(0,iy), pad_image+3+(iy+3)*nx, nbytes);
04025 }
04026 
04027 void EMData::shuffle_pad_corner(float *pad_image) {
04028         int nyhalf = ny/2;
04029         size_t nbytes = nx*sizeof(float);
04030         for (int iy = 0; iy < nyhalf; iy++)
04031                 memcpy(&(*this)(0,iy), pad_image+6+(iy+nyhalf+3)*nx, nbytes);
04032         for (int iy = nyhalf; iy < ny; iy++)
04033                 memcpy(&(*this)(0,iy), pad_image+6+(iy-nyhalf+3)*nx, nbytes);
04034 }
04035 
04036 #define    QUADPI                       3.141592653589793238462643383279502884197
04037 #define    DGR_TO_RAD                   QUADPI/180
04038 
04039 // We tried to pad the Fourier image to reduce the stick out points, howover it is not very efficient.
04040 /*
04041 EMData* EMData::fouriergridrot2d(float ang, float scale, Util::KaiserBessel& kb) {
04042         if (2 != get_ndim())
04043                 throw ImageDimensionException("fouriergridrot2d needs a 2-D image.");
04044         if (!is_complex())
04045                 throw ImageFormatException("fouriergridrot2d requires a fourier image");
04046         int nxreal = nx - 2 + int(is_fftodd());
04047         if (nxreal != ny)
04048                 throw ImageDimensionException("fouriergridrot2d requires ny == nx(real)");
04049         if (0 != nxreal%2)
04050                 throw ImageDimensionException("fouriergridrot2d needs an even image.");
04051         if (scale == 0.0f) scale = 1.0f;
04052         int nxhalf = nxreal/2;
04053         int nyhalf = ny/2;
04054 
04055         EMData *pad_this = new EMData();
04056         pad_this->set_size(nx+12, ny+6);
04057         //pad_this->to_zero();
04058         float* pad_image = pad_this-> get_data();
04059 
04060         if (!is_shuffled()) {
04061                 shuffle_pad_corner(pad_image);
04062         } else {
04063                 pad_corner(pad_image);
04064         }
04065         pad_this -> set_array_offsets(-6, -nyhalf-3);
04066 
04067         EMData* result = copy_head();
04068         set_array_offsets(0,-nyhalf);
04069         result->set_array_offsets(0,-nyhalf);
04070 
04071         ang = ang*DGR_TO_RAD;
04072         float cang = cos(ang);
04073         float sang = sin(ang);
04074         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04075                 float ycang = iy*cang;
04076                 float ysang = iy*sang;
04077                 for (int ix = 0; ix <= nxhalf; ix++) {
04078                         float nuxold = (ix*cang - ysang)*scale;
04079                         float nuyold = (ix*sang + ycang)*scale;
04080                         result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, pad_this, kb);
04081                 }
04082         }
04083         result->set_array_offsets();
04084         result->fft_shuffle(); // reset to an unshuffled result
04085         result->update();
04086         set_array_offsets();
04087         fft_shuffle(); // reset to an unshuffled complex image
04088         return result;
04089 }*/
04090 
04091 
04092 EMData* EMData::fouriergridrot2d(float ang, float scale, Util::KaiserBessel& kb) {
04093         if (2 != get_ndim())
04094                 throw ImageDimensionException("fouriergridrot2d needs a 2-D image.");
04095         if (!is_complex())
04096                 throw ImageFormatException("fouriergridrot2d requires a fourier image");
04097         int nxreal = nx - 2 + int(is_fftodd());
04098         if (nxreal != ny)
04099                 throw ImageDimensionException("fouriergridrot2d requires ny == nx(real)");
04100         if (0 != nxreal%2)
04101                 throw ImageDimensionException("fouriergridrot2d needs an even image.");
04102         if (scale == 0.0f) scale = 1.0f;
04103         int nxhalf = nxreal/2;
04104         int nyhalf = ny/2;
04105         float cir = (float)((nxhalf-1)*(nxhalf-1));
04106 
04107         if (!is_shuffled()) fft_shuffle();
04108 
04109         EMData* result = copy_head();
04110         set_array_offsets(0,-nyhalf);
04111         result->set_array_offsets(0,-nyhalf);
04112 
04113 
04114 
04115         ang = ang*(float)DGR_TO_RAD;
04116         float cang = cos(ang);
04117         float sang = sin(ang);
04118         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04119                 float ycang = iy*cang;
04120                 float ysang = iy*sang;
04121                 for (int ix = 0; ix <= nxhalf; ix++) {
04122                         float nuxold = (ix*cang - ysang)*scale;
04123                         float nuyold = (ix*sang + ycang)*scale;
04124                         if (nuxold*nuxold+nuyold*nuyold<cir) result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, this, kb);
04125                         //result->cmplx(ix,iy) = extractpoint(nuxold, nuyold, kb);
04126                 }
04127         }
04128         result->set_array_offsets();
04129         result->fft_shuffle(); // reset to an unshuffled result
04130         result->update();
04131         set_array_offsets();
04132         fft_shuffle(); // reset to an unshuffled complex image
04133         return result;
04134 }
04135 
04136 EMData* EMData::fouriergridrot_shift2d(float ang, float sx, float sy, Util::KaiserBessel& kb) {
04137         if (2 != get_ndim())
04138                 throw ImageDimensionException("fouriergridrot_shift2d needs a 2-D image.");
04139         if (!is_complex())
04140                 throw ImageFormatException("fouriergridrot_shift2d requires a fourier image");
04141         int nxreal = nx - 2 + int(is_fftodd());
04142         if (nxreal != ny)
04143                 throw ImageDimensionException("fouriergridrot_shift2d requires ny == nx(real)");
04144         if (0 != nxreal%2)
04145                 throw ImageDimensionException("fouriergridrot_shift2d needs an even image.");
04146         int nxhalf = nxreal/2;
04147         int nyhalf = ny/2;
04148 
04149         if (!is_shuffled()) fft_shuffle();
04150 
04151         EMData* result = copy_head();
04152         set_array_offsets(0, -nyhalf);
04153         result->set_array_offsets(0, -nyhalf);
04154 
04155         ang = ang*(float)DGR_TO_RAD;
04156         float cang = cos(ang);
04157         float sang = sin(ang);
04158         float temp = -2.0f*M_PI/nxreal;
04159         for (int iy = -nyhalf; iy < nyhalf; iy++) {
04160                 float ycang = iy*cang;
04161                 float ysang = iy*sang;
04162                 for (int ix = 0; ix <= nxhalf; ix++) {
04163                         float nuxold = ix*cang - ysang;
04164                         float nuyold = ix*sang + ycang;
04165                         result->cmplx(ix,iy) = Util::extractpoint2(nx, ny, nuxold, nuyold, this, kb);
04166                         //result->cmplx(ix,iy) = extractpoint(nuxold, nuyold, kb);
04167                         float phase_ang = temp*(sx*ix+sy*iy);
04168                         result->cmplx(ix,iy) *= complex<float>(cos(phase_ang), sin(phase_ang));
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 #undef QUADPI
04180 #undef DGR_TO_RAD
04181 
04182 void EMData::divkbsinh(const Util::KaiserBessel& kb) {
04183         
04184         if (is_complex())
04185                 throw ImageFormatException("divkbsinh requires a real image.");
04186         vector<int> saved_offsets = get_array_offsets();
04187         set_array_offsets(0,0,0);
04188         // Note that the following loops will work for 1-, 2-, and 3-D
04189         // images, since the "extra" weights will be 1.0.  (For example,
04190         // for a 2-d image iz=0, nz=1, so iz-nz/2 = 0 - 1/2 = 0, since
04191         // the division is an integer division.)
04192         for (int iz=0; iz < nz; iz++) {
04193                 float wz = kb.sinhwin(static_cast<float>(iz-nz/2));
04194                 for (int iy=0; iy < ny; iy++) {
04195                         float wy = kb.sinhwin(static_cast<float>(iy-ny/2));
04196                         for (int ix=0; ix < nx; ix++) {
04197                                 float wx = kb.sinhwin(static_cast<float>(ix-nx/2));
04198                                 float w = wx*wy*wz;
04199                                 (*this)(ix,iy,iz) /= w;
04200                         }
04201                 }
04202         }
04203         set_array_offsets(saved_offsets);
04204 }
04205 
04206 void EMData::divkbsinh_rect(const Util::KaiserBessel& kbx, const Util::KaiserBessel& kby, const Util::KaiserBessel& kbz) {
04207 
04208         if (is_complex())
04209                 throw ImageFormatException("divkbsinh requires a real image.");
04210         vector<int> saved_offsets = get_array_offsets();
04211         set_array_offsets(0,0,0);
04212         // Note that the following loops will work for 1-, 2-, and 3-D
04213         // images, since the "extra" weights will be 1.0.  (For example,
04214         // for a 2-d image iz=0, nz=1, so iz-nz/2 = 0 - 1/2 = 0, since
04215         // the division is an integer division.)
04216         for (int iz=0; iz < nz; iz++) {
04217                 float wz = kbz.sinhwin(static_cast<float>(iz-nz/2));
04218                 for (int iy=0; iy < ny; iy++) {
04219                         float wy = kby.sinhwin(static_cast<float>(iy-ny/2));
04220                         for (int ix=0; ix < nx; ix++) {
04221                                 float wx = kbx.sinhwin(static_cast<float>(ix-nx/2));
04222                                 float w = wx*wy*wz;
04223                                 (*this)(ix,iy,iz) /= w;
04224                         }
04225                 }
04226         }
04227         
04228         set_array_offsets(saved_offsets);
04229 }
04230 
04231 /* OBSOLETED  PAP
04232 Dict EMData::masked_stats(const EMData* mask) {
04233         if (is_complex())
04234                 throw ImageFormatException(
04235                                 "Complex images not supported by EMData::masked_stats");
04236         float* ptr = get_data();
04237         float* mptr = mask->get_data();
04238         long double sum1 = 0.L;
04239         long double sum2 = 0.L;
04240         long nmask = 0L;
04241         for (long i = 0; i < nx*ny*nz; i++,ptr++,mptr++) {
04242                 if (*mptr > 0.5f) {
04243                         nmask++;
04244                         sum1 += *ptr;
04245                         sum2 += (*ptr)*(*ptr);
04246                 }
04247         }
04248         float avg = static_cast<float>(sum1/nmask);
04249         float sig2 = static_cast<float>(sum2/nmask - avg*avg);
04250         float sig = sqrt(sig2);
04251         Dict mydict;
04252         mydict["avg"] = avg; mydict["sigma"] = sig; mydict["nmask"] = int(nmask);
04253         return mydict;
04254 }
04255 */
04256 
04257 EMData* EMData::extract_plane(const Transform& tf, Util::KaiserBessel& kb) {
04258         if (!is_complex())
04259                 throw ImageFormatException("extractplane requires a complex image");
04260         if (nx%2 != 0)
04261                 throw ImageDimensionException("extractplane requires nx to be even");
04262         int nxreal = nx - 2;
04263         if (nxreal != ny || nxreal != nz)
04264                 throw ImageDimensionException("extractplane requires ny == nx == nz");
04265         // build complex result image
04266         EMData* res = new EMData();
04267         res->set_size(nx,ny,1);
04268         res->to_zero();
04269         res->set_complex(true);
04270         res->set_fftodd(false);
04271         res->set_fftpad(true);
04272         res->set_ri(true);
04273         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04274         int n = nxreal;
04275         int nhalf = n/2;
04276         vector<int> saved_offsets = get_array_offsets();
04277         set_array_offsets(0,-nhalf,-nhalf);
04278         res->set_array_offsets(0,-nhalf,0);
04279         // set up some temporary weighting arrays
04280         int kbsize =  kb.get_window_size();
04281         int kbmin  = -kbsize/2;
04282         int kbmax  = -kbmin;
04283         float* wy0 = new float[kbmax - kbmin + 1];
04284         float* wy  = wy0 - kbmin; // wy[kbmin:kbmax]
04285         float* wx0 = new float[kbmax - kbmin + 1];
04286         float* wx  = wx0 - kbmin;
04287         float* wz0 = new float[kbmax - kbmin + 1];
04288         float* wz  = wz0 - kbmin;
04289         float rim = nhalf*float(nhalf);
04290         int count = 0;
04291         float wsum = 0.f;
04292         Transform tftrans = tf; // need transpose of tf here for consistency
04293         tftrans.invert();      // with spider
04294         for (int jy = -nhalf; jy < nhalf; jy++) 
04295         {
04296                 for (int jx = 0; jx <= nhalf; jx++) 
04297                 {
04298                         Vec3f nucur((float)jx, (float)jy, 0.f);
04299                         Vec3f nunew = tftrans*nucur;
04300                         float xnew = nunew[0], ynew = nunew[1], znew = nunew[2];
04301                         if (xnew*xnew+ynew*ynew+znew*znew <= rim) 
04302                         {
04303                                 count++;
04304                                 std::complex<float> btq(0.f,0.f);
04305                                 bool flip = false;
04306                                 if (xnew < 0.f) {
04307                                         flip = true;
04308                                         xnew = -xnew;
04309                                         ynew = -ynew;
04310                                         znew = -znew;
04311                                 }
04312                                 int ixn = int(Util::round(xnew));
04313                                 int iyn = int(Util::round(ynew));
04314                                 int izn = int(Util::round(znew));
04315                                 // populate weight arrays
04316                                 for (int i=kbmin; i <= kbmax; i++) {
04317                                         int izp = izn + i;
04318                                         wz[i] = kb.i0win_tab(znew - izp);
04319                                         int iyp = iyn + i;
04320                                         wy[i] = kb.i0win_tab(ynew - iyp);
04321                                         int ixp = ixn + i;
04322                                         wx[i] = kb.i0win_tab(xnew - ixp);
04323 
04324                                 }
04325                                 // restrict weight arrays to non-zero elements
04326                                 int lnbz = 0;
04327                                 for (int iz = kbmin; iz <= -1; iz++) {
04328                                         if (wz[iz] != 0.f) {
04329                                                 lnbz = iz;
04330                                                 break;
04331                                         }
04332                                 }
04333                                 int lnez = 0;
04334                                 for (int iz = kbmax; iz >= 1; iz--) {
04335                                         if (wz[iz] != 0.f) {
04336                                                 lnez = iz;
04337                                                 break;
04338                                         }
04339                                 }
04340                                 int lnby = 0;
04341                                 for (int iy = kbmin; iy <= -1; iy++) {
04342                                         if (wy[iy] != 0.f) {
04343                                                 lnby = iy;
04344                                                 break;
04345                                         }
04346                                 }
04347                                 int lney = 0;
04348                                 for (int iy = kbmax; iy >= 1; iy--) {
04349                                         if (wy[iy] != 0.f) {
04350                                                 lney = iy;
04351                                                 break;
04352                                         }
04353                                 }
04354                                 int lnbx = 0;
04355                                 for (int ix = kbmin; ix <= -1; ix++) {
04356                                         if (wx[ix] != 0.f) {
04357                                                 lnbx = ix;
04358                                                 break;
04359                                         }
04360                                 }
04361                                 int lnex = 0;
04362                                 for (int ix = kbmax; ix >= 1; ix--) {
04363                                         if (wx[ix] != 0.f) {
04364                                                 lnex = ix;
04365                                                 break;
04366                                         }
04367                                 }
04368                                 if    (ixn >= -kbmin      && ixn <= nhalf-1-kbmax
04369                                    && iyn >= -nhalf-kbmin && iyn <= nhalf-1-kbmax
04370                                    && izn >= -nhalf-kbmin && izn <= nhalf-1-kbmax) {
04371                                         // interior points
04372                                         for (int lz = lnbz; lz <= lnez; lz++) {
04373                                                 int izp = izn + lz;
04374                                                 for (int ly=lnby; ly<=lney; ly++) {
04375                                                         int iyp = iyn + ly;
04376                                                         float ty = wz[lz]*wy[ly];
04377                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04378                                                                 int ixp = ixn + lx;
04379                                                                 float wg = wx[lx]*ty;
04380                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04381                                                                 wsum += wg;
04382                                                         }
04383                                                 }
04384                                         }
04385                                 } else {
04386                                         // points "sticking out"
04387                                         for (int lz = lnbz; lz <= lnez; lz++) {
04388                                                 int izp = izn + lz;
04389                                                 for (int ly=lnby; ly<=lney; ly++) {
04390                                                         int iyp = iyn + ly;
04391                                                         float ty = wz[lz]*wy[ly];
04392                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04393                                                                 int ixp = ixn + lx;
04394                                                                 float wg = wx[lx]*ty;
04395                                                                 bool mirror = false;
04396                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04397                                                                 if (ixt > nhalf || ixt < -nhalf) {
04398                                                                         ixt = Util::sgn(ixt)
04399                                                                                   *(n - abs(ixt));
04400                                                                         iyt = -iyt;
04401                                                                         izt = -izt;
04402                                                                         mirror = !mirror;
04403                                                                 }
04404                                                                 if (iyt >= nhalf || iyt < -nhalf) {
04405                                                                         if (ixt != 0) {
04406                                                                                 ixt = -ixt;
04407                                                                                 iyt = Util::sgn(iyt)
04408                                                                                           *(n - abs(iyt));
04409                                                                                 izt = -izt;
04410                                                                                 mirror = !mirror;
04411                                                                         } else {
04412                                                                                 iyt -= n*Util::sgn(iyt);
04413                                                                         }
04414                                                                 }
04415                                                                 if (izt >= nhalf || izt < -nhalf) {
04416                                                                         if (ixt != 0) {
04417                                                                                 ixt = -ixt;
04418                                                                                 iyt = -iyt;
04419                                                                                 izt = Util::sgn(izt)
04420                                                                                           *(n - abs(izt));
04421                                                                                 mirror = !mirror;
04422                                                                         } else {
04423                                                                                 izt -= Util::sgn(izt)*n;
04424                                                                         }
04425                                                                 }
04426                                                                 if (ixt < 0) {
04427                                                                         ixt = -ixt;
04428                                                                         iyt = -iyt;
04429                                                                         izt = -izt;
04430                                                                         mirror = !mirror;
04431                                                                 }
04432                                                                 if (iyt == nhalf) iyt = -nhalf;
04433                                                                 if (izt == nhalf) izt = -nhalf;
04434                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04435                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04436                                                                 wsum += wg;
04437                                                         }
04438                                                 }
04439                                         }
04440                                 }
04441                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04442                                 else       res->cmplx(jx,jy) = btq;
04443                         }
04444                 }
04445         }
04446         for (int jy = -nhalf; jy < nhalf; jy++)
04447                 for (int jx = 0; jx <= nhalf; jx++)
04448                         res->cmplx(jx,jy) *= count/wsum;
04449         delete[] wx0; delete[] wy0; delete[] wz0;
04450         set_array_offsets(saved_offsets);
04451         res->set_array_offsets(0,0,0);
04452         res->set_shuffled(true);
04453         return res;
04454 }
04455 
04456 
04458 
04459 
04460 
04461 EMData* EMData::extract_plane_rect(const Transform& tf, Util::KaiserBessel& kbx,Util::KaiserBessel& kby, Util::KaiserBessel& kbz) {
04462         
04463 
04464         if (!is_complex())
04465                 throw ImageFormatException("extractplane requires a complex image");
04466         if (nx%2 != 0)
04467                 throw ImageDimensionException("extractplane requires nx to be even");
04468 
04469         int nxfromxyz = max( max(nx-2,ny), nz) + 2;
04470         //int nxfromz = nz+2;
04471         //int nxcircal = nxfromz - 2;
04472         int nxcircal = nxfromxyz - 2;
04473         EMData* res = new EMData();
04474         //res->set_size(nxfromz,nz,1);
04475         res->set_size(nxfromxyz,nxcircal,1);
04476         res->to_zero();
04477         res->set_complex(true);
04478         res->set_fftodd(false);
04479         res->set_fftpad(true);
04480         res->set_ri(true);
04481         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04482         int n = nxcircal;
04483         int nhalf = n/2;
04484         int nxhalf = (nx-2)/2;
04485         int nyhalf = ny/2;
04486         int nzhalf = nz/2;
04487         
04488         vector<int> saved_offsets = get_array_offsets();
04489         set_array_offsets(0, -nyhalf, -nzhalf);
04490         res->set_array_offsets(0,-nhalf,0);
04491         // set up some temporary weighting arrays
04492         int kbxsize =  kbx.get_window_size();
04493         int kbxmin  = -kbxsize/2;
04494         int kbxmax  = -kbxmin;
04495 
04496         int kbysize =  kby.get_window_size();
04497         int kbymin  = -kbysize/2;
04498         int kbymax  = -kbymin;
04499 
04500         int kbzsize =  kbz.get_window_size();
04501         int kbzmin  = -kbzsize/2;
04502         int kbzmax  = -kbzmin;
04503 
04504         //std::cout<<"kb size x,y,z=="<<kbxsize<<" "<<kbysize<<" "<<kbzsize<<std::endl;
04505         float* wy0 = new float[kbymax - kbymin + 1];
04506         float* wy  = wy0 - kbymin; // wy[kbmin:kbmax]
04507         float* wx0 = new float[kbxmax - kbxmin + 1];
04508         float* wx  = wx0 - kbxmin;
04509         float* wz0 = new float[kbzmax - kbzmin + 1];
04510         float* wz  = wz0 - kbzmin;
04511         float rim = nhalf*float(nhalf);
04512         int count = 0;
04513         float wsum = 0.f;
04514         Transform tftrans = tf; // need transpose of tf here for consistency
04515         tftrans.invert();      // with spider
04516         float xratio=float(nx-2)/float(nxcircal);
04517         float yratio=float(ny)/float(nxcircal);
04518         float zratio=float(nz)/float(nxcircal);
04519         //std::cout<<"xratio,yratio=="<<xratio<<" "<<yratio<<std::endl;
04520         for (int jy = -nhalf; jy < nhalf; jy++) 
04521         {
04522                 for (int jx = 0; jx <= nhalf; jx++) 
04523                 {
04524                         Vec3f nucur((float)jx, (float)jy, 0.f);
04525                         Vec3f nunew = tftrans*nucur;
04526                         float xnew = nunew[0]*xratio, ynew = nunew[1]*yratio, znew = nunew[2]*zratio;
04527                         
04528                         if (nunew[0]*nunew[0]+nunew[1]*nunew[1]+nunew[2]*nunew[2] <= rim)
04529                         {
04530                                 count++;
04531                                 std::complex<float> btq(0.f,0.f);
04532                                 bool flip = false;
04533                                 if (xnew < 0.f) {
04534                                         flip = true;
04535                                         xnew = -xnew;
04536                                         ynew = -ynew;
04537                                         znew = -znew;
04538                                 }
04539                                 int ixn = int(Util::round(xnew));
04540                                 int iyn = int(Util::round(ynew));
04541                                 int izn = int(Util::round(znew));
04542                                 // populate weight arrays
04543                                 for (int i=kbzmin; i <= kbzmax; i++) {
04544                                         int izp = izn + i;
04545                                         wz[i] = kbz.i0win_tab(znew - izp);
04546                                         }
04547                                 for (int i=kbymin; i <= kbymax; i++) {
04548                                         int iyp = iyn + i;
04549                                         wy[i] = kby.i0win_tab(ynew - iyp);
04550                                         }
04551                                 for (int i=kbxmin; i <= kbxmax; i++) {
04552                                         int ixp = ixn + i;
04553                                         wx[i] = kbx.i0win_tab(xnew - ixp);
04554                                         }
04555                 
04556 
04557                                 
04558                                 // restrict weight arrays to non-zero elements
04559                                 int lnbz = 0;
04560                                 for (int iz = kbzmin; iz <= -1; iz++) {
04561                                         if (wz[iz] != 0.f) {
04562                                                 lnbz = iz;
04563                                                 break;
04564                                         }
04565                                 }
04566                                 int lnez = 0;
04567                                 for (int iz = kbzmax; iz >= 1; iz--) {
04568                                         if (wz[iz] != 0.f) {
04569                                                 lnez = iz;
04570                                                 break;
04571                                         }
04572                                 }
04573                                 int lnby = 0;
04574                                 for (int iy = kbymin; iy <= -1; iy++) {
04575                                         if (wy[iy] != 0.f) {
04576                                                 lnby = iy;
04577                                                 break;
04578                                         }
04579                                 }
04580                                 int lney = 0;
04581                                 for (int iy = kbymax; iy >= 1; iy--) {
04582                                         if (wy[iy] != 0.f) {
04583                                                 lney = iy;
04584                                                 break;
04585                                         }
04586                                 }
04587                                 int lnbx = 0;
04588                                 for (int ix = kbxmin; ix <= -1; ix++) {
04589                                         if (wx[ix] != 0.f) {
04590                                                 lnbx = ix;
04591                                                 break;
04592                                         }
04593                                 }
04594                                 int lnex = 0;
04595                                 for (int ix = kbxmax; ix >= 1; ix--) {
04596                                         if (wx[ix] != 0.f) {
04597                                                 lnex = ix;
04598                                                 break;
04599                                         }
04600                                 }
04601                                 if    (ixn >= -kbxmin      && ixn <= nxhalf-1-kbxmax
04602                                    && iyn >= -nyhalf-kbymin && iyn <= nyhalf-1-kbymax
04603                                    && izn >= -nzhalf-kbzmin && izn <= nzhalf-1-kbzmax) {
04604                                         // interior points
04605                                         for (int lz = lnbz; lz <= lnez; lz++) {
04606                                                 int izp = izn + lz;
04607                                                 for (int ly=lnby; ly<=lney; ly++) {
04608                                                         int iyp = iyn + ly;
04609                                                         float ty = wz[lz]*wy[ly];
04610                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04611                                                                 int ixp = ixn + lx;
04612                                                                 float wg = wx[lx]*ty;
04613                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04614                                                                 wsum += wg;
04615                                                         }
04616                                                 }
04617                                         }
04618                                 } 
04619                                 else {
04620                                         // points "sticking out"
04621                                         for (int lz = lnbz; lz <= lnez; lz++) {
04622                                                 int izp = izn + lz;
04623                                                 for (int ly=lnby; ly<=lney; ly++) {
04624                                                         int iyp = iyn + ly;
04625                                                         float ty = wz[lz]*wy[ly];
04626                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04627                                                                 int ixp = ixn + lx;
04628                                                                 float wg = wx[lx]*ty;
04629                                                                 bool mirror = false;
04630                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04631                                                                 if (ixt > nxhalf || ixt < -nxhalf) {
04632                                                                         ixt = Util::sgn(ixt)
04633                                                                                   *(nx-2-abs(ixt));
04634                                                                         iyt = -iyt;
04635                                                                         izt = -izt;
04636                                                                         mirror = !mirror;
04637                                                                 }
04638                                                                 if (iyt >= nyhalf || iyt < -nyhalf) {
04639                                                                         if (ixt != 0) {
04640                                                                                 ixt = -ixt;
04641                                                                                 iyt = Util::sgn(iyt)
04642                                                                                           *(ny - abs(iyt));
04643                                                                                 izt = -izt;
04644                                                                                 mirror = !mirror;
04645                                                                         } else {
04646                                                                                 iyt -= ny*Util::sgn(iyt);
04647                                                                         }
04648                                                                 }
04649                                                                 if (izt >= nzhalf || izt < -nzhalf) {
04650                                                                         if (ixt != 0) {
04651                                                                                 ixt = -ixt;
04652                                                                                 iyt = -iyt;
04653                                                                                 izt = Util::sgn(izt)
04654                                                                                           *(nz - abs(izt));
04655                                                                                 mirror = !mirror;
04656                                                                         } else {
04657                                                                                 izt -= Util::sgn(izt)*nz;
04658                                                                         }
04659                                                                 }
04660                                                                 if (ixt < 0) {
04661                                                                         ixt = -ixt;
04662                                                                         iyt = -iyt;
04663                                                                         izt = -izt;
04664                                                                         mirror = !mirror;
04665                                                                 }
04666                                                                 if (iyt == nyhalf) iyt = -nyhalf;
04667                                                                 if (izt == nzhalf) izt = -nzhalf;
04668                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04669                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04670                                                                 wsum += wg;
04671                                                         }
04672                                                 }
04673                                         }
04674                                 }
04675                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04676                                 else       res->cmplx(jx,jy) = btq;
04677                         }
04678                 }
04679         }
04680         for (int jy = -nhalf; jy < nhalf; jy++)
04681                 for (int jx = 0; jx <= nhalf; jx++)
04682                         res->cmplx(jx,jy) *= count/wsum;
04683         delete[] wx0; delete[] wy0; delete[] wz0;
04684         set_array_offsets(saved_offsets);
04685         res->set_array_offsets(0,0,0);
04686         res->set_shuffled(true);
04687         return res;
04688 }
04689 
04690 
04691 
04692 EMData* EMData::extract_plane_rect_fast(const Transform& tf, Util::KaiserBessel& kbx,Util::KaiserBessel& kby, Util::KaiserBessel& kbz) {
04693         
04694         
04695 
04696         if (!is_complex())
04697                 throw ImageFormatException("extractplane requires a complex image");
04698         if (nx%2 != 0)
04699                 throw ImageDimensionException("extractplane requires nx to be even");
04700 
04701         int nxfromz=nz+2;
04702         int nxcircal = nxfromz - 2;
04703 
04704         // build complex result image
04705         float xratio=float(nx-2)/float(nz);
04706         float yratio=float(ny)/float(nz);
04707         Vec3f axis_newx,axis_newy;
04708         axis_newx[0] = xratio*0.5f*nz*tf[0][0];
04709         axis_newx[1] = yratio*0.5f*nz*tf[0][1];
04710         axis_newx[2] = 0.5f*nz*tf[0][2];
04711 
04712 
04713         float ellipse_length_x=std::sqrt(axis_newx[0]*axis_newx[0]+axis_newx[1]*axis_newx[1]+axis_newx[2]*axis_newx[2]);
04714         
04715         int ellipse_length_x_int=int(ellipse_length_x);
04716         float ellipse_step_x=0.5f*nz/float(ellipse_length_x_int);
04717         float xscale=ellipse_step_x;//scal increased
04718 
04719         axis_newy[0] = xratio*0.5f*nz*tf[1][0];
04720         axis_newy[1] = yratio*0.5f*nz*tf[1][1];
04721         axis_newy[2] = 0.5f*nz*tf[1][2];
04722 
04723 
04724         float ellipse_length_y=std::sqrt(axis_newy[0]*axis_newy[0]+axis_newy[1]*axis_newy[1]+axis_newy[2]*axis_newy[2]);
04725         int ellipse_length_y_int=int(ellipse_length_y);
04726         float ellipse_step_y=0.5f*nz/float(ellipse_length_y_int);
04727         float yscale=ellipse_step_y;
04728         //end of scaling factor calculation
04729         int nx_e=ellipse_length_x_int*2;
04730         int ny_e=ellipse_length_y_int*2;
04731         int nx_ec=nx_e+2;       
04732 
04733         EMData* res = new EMData();
04734         res->set_size(nx_ec,ny_e,1);
04735         res->to_zero();
04736         res->set_complex(true);
04737         res->set_fftodd(false);
04738         res->set_fftpad(true);
04739         res->set_ri(true);
04740         //std::cout<<"cpp fast extract_plane is called"<<std::endl;
04741         //std::cout<<"nx_e,ny_e===="<<nx_e<<"  "<<ny_e<<std::endl;
04742         // Array offsets: (0..nhalf,-nhalf..nhalf-1,-nhalf..nhalf-1)
04743         int n = nxcircal;
04744         int nhalf = n/2;
04745         int nhalfx_e = nx_e/2;
04746         int nhalfy_e = ny_e/2;
04747         int nxhalf=(nx-2)/2;
04748         int nyhalf=ny/2;
04749         int nzhalf=nz/2;
04750         //std::cout<<"nhalf,nxhalf,nyhalf,nzhalf=="<<nhalf<<" "<<nxhalf<<" "<<nyhalf<<" "<<nzhalf<<std::endl;
04751         vector<int> saved_offsets = get_array_offsets();
04752         set_array_offsets(0,-nyhalf,-nzhalf);
04753         res->set_array_offsets(0,-nhalfy_e,0);
04754         // set up some temporary weighting arrays
04755         int kbxsize =  kbx.get_window_size();
04756         int kbxmin  = -kbxsize/2;
04757         int kbxmax  = -kbxmin;
04758 
04759         int kbysize =  kby.get_window_size();
04760         int kbymin  = -kbysize/2;
04761         int kbymax  = -kbymin;
04762 
04763         int kbzsize =  kbz.get_window_size();
04764         int kbzmin  = -kbzsize/2;
04765         int kbzmax  = -kbzmin;
04766 
04767         //std::cout<<"kb size x,y,z=="<<kbxsize<<" "<<kbysize<<" "<<kbzsize<<std::endl;
04768         float* wy0 = new float[kbymax - kbymin + 1];
04769         float* wy  = wy0 - kbymin; // wy[kbmin:kbmax]
04770         float* wx0 = new float[kbxmax - kbxmin + 1];
04771         float* wx  = wx0 - kbxmin;
04772         float* wz0 = new float[kbzmax - kbzmin + 1];
04773         float* wz  = wz0 - kbzmin;
04774         float rim = nhalf*float(nhalf);
04775         int count = 0;
04776         float wsum = 0.f;
04777         Transform tftrans = tf; // need transpose of tf here for consistency
04778         tftrans.invert();      // with spider
04779 
04780         //std::cout<<"xratio,yratio=="<<xratio<<" "<<yratio<<std::endl;
04781         for (int jy = -nhalfy_e; jy < nhalfy_e; jy++) 
04782         {
04783                 for (int jx = 0; jx <= nhalfx_e; jx++) 
04784                 {
04785                         Vec3f nucur((float)jx, (float)jy, 0.f);
04786                         nucur[0]=nucur[0]*xscale;nucur[1]=nucur[1]*yscale;;
04787                         Vec3f nunew = tftrans*nucur;
04788                         float xnew = nunew[0]*xratio, ynew = nunew[1]*yratio, znew = nunew[2];
04789                         
04790                         if (nunew[0]*nunew[0]+nunew[1]*nunew[1]+nunew[2]*nunew[2] <= rim)
04791                         {
04792                                 count++;
04793                                 std::complex<float> btq(0.f,0.f);
04794                                 bool flip = false;
04795                                 if (xnew < 0.f) {
04796                                         flip = true;
04797                                         xnew = -xnew;
04798                                         ynew = -ynew;
04799                                         znew = -znew;
04800                                 }
04801                                 int ixn = int(Util::round(xnew));
04802                                 int iyn = int(Util::round(ynew));
04803                                 int izn = int(Util::round(znew));
04804                                 // populate weight arrays
04805                                 for (int i=kbzmin; i <= kbzmax; i++) {
04806                                         int izp = izn + i;
04807                                         wz[i] = kbz.i0win_tab(znew - izp);
04808                                         }
04809                                 for (int i=kbymin; i <= kbymax; i++) {
04810                                         int iyp = iyn + i;
04811                                         wy[i] = kby.i0win_tab(ynew - iyp);
04812                                         }
04813                                 for (int i=kbxmin; i <= kbxmax; i++) {
04814                                         int ixp = ixn + i;
04815                                         wx[i] = kbx.i0win_tab(xnew - ixp);
04816                                         }
04817                 
04818 
04819                                 
04820                                 // restrict weight arrays to non-zero elements
04821                                 int lnbz = 0;
04822                                 for (int iz = kbzmin; iz <= -1; iz++) {
04823                                         if (wz[iz] != 0.f) {
04824                                                 lnbz = iz;
04825                                                 break;
04826                                         }
04827                                 }
04828                                 int lnez = 0;
04829                                 for (int iz = kbzmax; iz >= 1; iz--) {
04830                                         if (wz[iz] != 0.f) {
04831                                                 lnez = iz;
04832                                                 break;
04833                                         }
04834                                 }
04835                                 int lnby = 0;
04836                                 for (int iy = kbymin; iy <= -1; iy++) {
04837                                         if (wy[iy] != 0.f) {
04838                                                 lnby = iy;
04839                                                 break;
04840                                         }
04841                                 }
04842                                 int lney = 0;
04843                                 for (int iy = kbymax; iy >= 1; iy--) {
04844                                         if (wy[iy] != 0.f) {
04845                                                 lney = iy;
04846                                                 break;
04847                                         }
04848                                 }
04849                                 int lnbx = 0;
04850                                 for (int ix = kbxmin; ix <= -1; ix++) {
04851                                         if (wx[ix] != 0.f) {
04852                                                 lnbx = ix;
04853                                                 break;
04854                                         }
04855                                 }
04856                                 int lnex = 0;
04857                                 for (int ix = kbxmax; ix >= 1; ix--) {
04858                                         if (wx[ix] != 0.f) {
04859                                                 lnex = ix;
04860                                                 break;
04861                                         }
04862                                 }
04863                                 if    (ixn >= -kbxmin      && ixn <= nxhalf-1-kbxmax
04864                                    && iyn >= -nyhalf-kbymin && iyn <= nyhalf-1-kbymax
04865                                    && izn >= -nzhalf-kbzmin && izn <= nzhalf-1-kbzmax) {
04866                                         // interior points
04867                                         for (int lz = lnbz; lz <= lnez; lz++) {
04868                                                 int izp = izn + lz;
04869                                                 for (int ly=lnby; ly<=lney; ly++) {
04870                                                         int iyp = iyn + ly;
04871                                                         float ty = wz[lz]*wy[ly];
04872                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04873                                                                 int ixp = ixn + lx;
04874                                                                 float wg = wx[lx]*ty;
04875                                                                 btq += cmplx(ixp,iyp,izp)*wg;
04876                                                                 wsum += wg;
04877                                                         }
04878                                                 }
04879                                         }
04880                                 } 
04881                                 else {
04882                                         // points "sticking out"
04883                                         for (int lz = lnbz; lz <= lnez; lz++) {
04884                                                 int izp = izn + lz;
04885                                                 for (int ly=lnby; ly<=lney; ly++) {
04886                                                         int iyp = iyn + ly;
04887                                                         float ty = wz[lz]*wy[ly];
04888                                                         for (int lx=lnbx; lx<=lnex; lx++) {
04889                                                                 int ixp = ixn + lx;
04890                                                                 float wg = wx[lx]*ty;
04891                                                                 bool mirror = false;
04892                                                                 int ixt(ixp), iyt(iyp), izt(izp);
04893                                                                 if (ixt > nxhalf || ixt < -nxhalf) {
04894                                                                         ixt = Util::sgn(ixt)
04895                                                                                   *(nx-2-abs(ixt));
04896                                                                         iyt = -iyt;
04897                                                                         izt = -izt;
04898                                                                         mirror = !mirror;
04899                                                                 }
04900                                                                 if (iyt >= nyhalf || iyt < -nyhalf) {
04901                                                                         if (ixt != 0) {
04902                                                                                 ixt = -ixt;
04903                                                                                 iyt = Util::sgn(iyt)
04904                                                                                           *(ny - abs(iyt));
04905                                                                                 izt = -izt;
04906                                                                                 mirror = !mirror;
04907                                                                         } else {
04908                                                                                 iyt -= ny*Util::sgn(iyt);
04909                                                                         }
04910                                                                 }
04911                                                                 if (izt >= nzhalf || izt < -nzhalf) {
04912                                                                         if (ixt != 0) {
04913                                                                                 ixt = -ixt;
04914                                                                                 iyt = -iyt;
04915                                                                                 izt = Util::sgn(izt)
04916                                                                                           *(nz - abs(izt));
04917                                                                                 mirror = !mirror;
04918                                                                         } else {
04919                                                                                 izt -= Util::sgn(izt)*nz;
04920                                                                         }
04921                                                                 }
04922                                                                 if (ixt < 0) {
04923                                                                         ixt = -ixt;
04924                                                                         iyt = -iyt;
04925                                                                         izt = -izt;
04926                                                                         mirror = !mirror;
04927                                                                 }
04928                                                                 if (iyt == nyhalf) iyt = -nyhalf;
04929                                                                 if (izt == nzhalf) izt = -nzhalf;
04930                                                                 if (mirror)   btq += conj(cmplx(ixt,iyt,izt))*wg;
04931                                                                 else          btq += cmplx(ixt,iyt,izt)*wg;
04932                                                                 wsum += wg;
04933                                                         }
04934                                                 }
04935                                         }
04936                                 }
04937                                 if (flip)  res->cmplx(jx,jy) = conj(btq);
04938                                 else       res->cmplx(jx,jy) = btq;
04939                         }
04940                 }
04941         }
04942         for (int jy = -nhalfy_e; jy < nhalfy_e; jy++)
04943                 for (int jx = 0; jx <= nhalfx_e; jx++)
04944                         res->cmplx(jx,jy) *= count/wsum;
04945         delete[] wx0; delete[] wy0; delete[] wz0;
04946         set_array_offsets(saved_offsets);
04947         res->set_array_offsets(0,0,0);
04948         res->set_shuffled(true);
04949         return res;
04950 }
04951 
04952 
04953 
04954 
04955 bool EMData::peakcmp(const Pixel& p1, const Pixel& p2) {
04956     return (p1.value > p2.value);
04957 }
04958 
04959 ostream& operator<< (ostream& os, const Pixel& peak) {
04960     os <<  peak.x <<  peak.y << peak.z  << peak.value;
04961     return os;
04962 }
04963 
04964 /*vector<float> EMData::max_search() {
04965 
04966         EMData& buf = *this;
04967 
04968         int nx = buf.get_xsize();
04969         int ny = buf.get_ysize();
04970         int nz = buf.get_zsize();
04971 
04972         int dim = buf.get_ndim();
04973 
04974         vector<float> result;
04975 
04976         if (dim == 1) {
04977                 float max = -1e20f;
04978                 int index = -1;
04979                 for (int i=0; i<nx; i++) {
04980                         if (buf(i)>max) {
04981                                 max = buf(i);
04982                                 index = i;
04983                         }
04984                 }
04985                 result.push_back((float)index);
04986                 result.push_back(max);
04987         } else if (dim == 2) {
04988                 float max = -1e20f;
04989                 int index1 = -1;
04990                 int index2 = -1;
04991                 for (int i=0; i<nx; i++) {
04992                         for (int j=0; j<ny; j++) {
04993                                 if (buf(i, j)>max) {
04994                                         max = buf(i, j);
04995                                         index1 = i;
04996                                         index2 = j;
04997                                 }
04998                         }
04999                 }
05000                 result.push_back((float)index1);
05001                 result.push_back((float)index2);
05002                 result.push_back(max);
05003         } else {
05004                 float max = -1e20f;
05005                 int index1 = -1;
05006                 int index2 = -1;
05007                 int index3 = -1;
05008                 for (int i=0; i<nx; i++) {
05009                         for (int j=0; j<ny; j++) {
05010                                 for (int k=0; k<nz; k++) {
05011                                         if (buf(i, j, k)>max) {
05012                                                 max = buf(i, j, k);
05013                                                 index1 = i;
05014                                                 index2 = j;
05015                                                 index3 = k;
05016                                         }
05017                                 }
05018                         }
05019                 }
05020                 result.push_back((float)index1);
05021                 result.push_back((float)index2);
05022                 result.push_back((float)index3);
05023                 result.push_back(max);
05024         }
05025         return result;
05026 }*/
05027 
05028 vector<float> EMData::peak_search(int ml, float invert) {
05029 
05030         EMData& buf = *this;
05031         vector<Pixel> peaks;
05032         int img_dim;
05033         int i, j, k;
05034         int i__1, i__2;
05035         int j__1, j__2;
05036         //int k__1, k__2;
05037         bool peak_check;
05038         img_dim=buf.get_ndim();
05039         vector<int> ix, jy, kz;
05040         vector<float>res;
05041         int nx = buf.get_xsize();
05042         int ny = buf.get_ysize();
05043         int nz = buf.get_zsize();
05044         if(invert <= 0.0f)  invert=-1.0f;
05045         else                invert=1.0f ;
05046         int count = 0;
05047         switch (img_dim)  {
05048         case(1):
05049                 for(i=0;i<=nx-1;++i)  {
05050                         i__1 = (i-1+nx)%nx;
05051                         i__2 = (i+1)%nx;
05052                         // Commented by Yang on 05/14/07
05053                         // 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.
05054                         //  03/07/08  I undid the change.  If you change the comparison, it changes the meaning of peak definition.
05055                         float qbf = buf(i)*invert;
05056                         peak_check = qbf > buf(i__1)*invert && qbf > buf(i__2)*invert;
05057                         if(peak_check) {
05058                                 if(count < ml) {
05059                                         count++;
05060                                         peaks.push_back( Pixel(i, 0, 0, qbf) );
05061                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05062                                 } else {
05063                                         if( qbf > (peaks.back()).value ) {
05064                                                 //  do the switch and sort again
05065                                                 peaks.pop_back();
05066                                                 peaks.push_back( Pixel(i, 0, 0, qbf) );
05067                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05068                                         }
05069                                 }
05070                         }
05071                 }
05072         break;
05073         case(2):
05074         /*  Removed boundary conditions, PAP 03/10/08
05075                 for(j=0;j<=ny-1;++j)  {
05076                         j__1 = (j-1+ny)%ny;
05077                         j__2 = (j+1)%ny;
05078                         for(i=0;i<=nx-1;++i) {
05079                                 i__1 = (i-1+nx)%nx;
05080                                 i__2 = (i+1)%nx;
05081         */
05082                 for(j=1;j<=ny-2;++j)  {
05083                         j__1 = j-1;
05084                         j__2 = j+1;
05085                         for(i=1;i<=nx-2;++i) {
05086                                 i__1 = i-1;
05087                                 i__2 = i+1;
05088                                 float qbf = buf(i,j)*invert;
05089                                 peak_check = (qbf > buf(i,j__1)*invert) && (qbf > buf(i,j__2)*invert);
05090                                 if(peak_check) {
05091                                         peak_check = (qbf > buf(i__1,j)*invert) && (qbf > buf(i__2,j)*invert);
05092                                         if(peak_check) {
05093                                                 peak_check = (qbf > buf(i__1,j__1)*invert) && (qbf > buf(i__1,j__2)*invert);
05094                                                 if(peak_check) {
05095                                                         peak_check = (qbf > buf(i__2,j__1)*invert) && (qbf > buf(i__2,j__2)*invert);
05096                                                         if(peak_check) {
05097                                                                 if(count < ml) {
05098                                                                         count++;
05099                                                                         peaks.push_back( Pixel(i, j, 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, j, 0, qbf) );
05106                                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05107                                                                         }
05108                                                                 }
05109                                                         }
05110                                                 }
05111                                         }
05112                                 }
05113                         }
05114                 }
05115         break;
05116         case(3):  //looks ugly, but it is the best I can do,  PAP 03/07/08
05117         /*  Removed boundary conditions, PAP 03/10/08
05118                 for(k=0;k<=nz-1;++k) {
05119                         kz.clear();
05120                         k__1 = (k-1+nz)%nz;
05121                         k__2 = (k+1)%nz;
05122                         kz.push_back(k__1);
05123                         kz.push_back(k);
05124                         kz.push_back(k__2);
05125                         for(j=0;j<=ny-1;++j) {
05126                                 jy.clear();
05127                                 j__1 = (j-1+ny)%ny;
05128                                 j__2 = (j+1)%ny;
05129                                 jy.push_back(j__1);
05130                                 jy.push_back(j);
05131                                 jy.push_back(j__2);
05132                                 for(i=0;i<=nx-1;++i) {
05133                                         ix.clear();
05134                                         i__1 = (i-1+nx)%nx;
05135                                         i__2 = (i+1)%nx;
05136         */
05137                 for(k=1; k<=nz-2; ++k) {
05138                         kz.clear();
05139                         kz.push_back(k-1);
05140                         kz.push_back(k);
05141                         kz.push_back(k+1);
05142                         for(j=1; j<=ny-2; ++j) {
05143                                 jy.clear();
05144                                 jy.push_back(j-1);
05145                                 jy.push_back(j);
05146                                 jy.push_back(j+1);
05147                                 for(i=1; i<=nx-2; ++i) {
05148                                         ix.clear();
05149                                         ix.push_back(i-1);
05150                                         ix.push_back(i);
05151                                         ix.push_back(i+1);
05152                                         float qbf = buf(i,j,k)*invert;
05153                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05154                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05155                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05156                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05157                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05158                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05159                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05160                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05161                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05162                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05163                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05164                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05165                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05166                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05167                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05168                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05169                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05170                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05171                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05172                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05173                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05174                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05175                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05176                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05177                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05178                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05179                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05180                                         if(peak_check) {
05181                                                 if(count < ml) {
05182                                                         count++;
05183                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05184                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05185                                                 } else {
05186                                                         if( qbf > (peaks.back()).value ) {
05187                                                                 //  do the switch and sort again
05188                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05189                                                                 peaks.pop_back();
05190                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05191                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05192                                                         }
05193                                                 }
05194                                         }
05195                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05196                                 }
05197                         }
05198                 }
05199                 //  Add circular closure for x direction: needed for circular ccf,
05200                 //  should not have adverse impact on other code.  PAP -7/22/08
05201                 for(k=1; k<=nz-2; ++k) {
05202                         kz.clear();
05203                         kz.push_back(k-1);
05204                         kz.push_back(k);
05205                         kz.push_back(k+1);
05206                         for(j=1; j<=ny-2; ++j) {
05207                                 jy.clear();
05208                                 jy.push_back(j-1);
05209                                 jy.push_back(j);
05210                                 jy.push_back(j+1);
05211                                 for(i=0; i<=0; ++i) {
05212                                         ix.clear();
05213                                         ix.push_back(nx-1);
05214                                         ix.push_back(i);
05215                                         ix.push_back(i+1);
05216                                         float qbf = buf(i,j,k)*invert;
05217                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05218                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05219                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05220                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05221                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05222                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05223                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05224                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05225                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05226                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05227                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05228                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05229                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05230                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05231                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05232                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05233                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05234                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05235                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05236                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05237                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05238                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05239                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05240                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05241                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05242                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05243                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05244                                         if(peak_check) {
05245                                                 if(count < ml) {
05246                                                         count++;
05247                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05248                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05249                                                 } else {
05250                                                         if( qbf > (peaks.back()).value ) {
05251                                                                 //  do the switch and sort again
05252                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05253                                                                 peaks.pop_back();
05254                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05255                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05256                                                         }
05257                                                 }
05258                                         }
05259                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05260                                 }
05261                                 for(i=nx-1; i<=nx-1; ++i) {
05262                                         ix.clear();
05263                                         ix.push_back(i-1);
05264                                         ix.push_back(i);
05265                                         ix.push_back(0);
05266                                         float qbf = buf(i,j,k)*invert;
05267                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05268                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05269                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05270                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05271                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05272                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05273                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05274                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05275                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05276                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05277                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05278                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05279                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05280                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05281                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05282                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05283                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05284                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05285                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05286                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05287                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05288                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05289                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05290                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05291                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05292                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05293                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05294                                         if(peak_check) {
05295                                                 if(count < ml) {
05296                                                         count++;
05297                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05298                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05299                                                 } else {
05300                                                         if( qbf > (peaks.back()).value ) {
05301                                                                 //  do the switch and sort again
05302                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05303                                                                 peaks.pop_back();
05304                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05305                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05306                                                         }
05307                                                 }
05308                                         }
05309                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05310                                 }
05311                         }
05312                 }
05313         break;
05314 /*      case(5):  //looks ugly, but it is the best I can do,  PAP 03/07/08
05315         int nu = buf.get_usize();
05316         int nv = buf.get_vsize();
05317         vector<int> lu, mv;
05318                 for(m=1; m<=nv-2; ++m) {
05319                         mv.clear();
05320                         mv.push_back(m-1);
05321                         mv.push_back(m);
05322                         mv.push_back(m+1);
05323                 for(l=1; l<=nu-2; ++l) {
05324                         lu.clear();
05325                         lu.push_back(l-1);
05326                         lu.push_back(l);
05327                         lu.push_back(l+1);
05328                 for(k=1; k<=nz-2; ++k) {
05329                         kz.clear();
05330                         kz.push_back(k-1);
05331                         kz.push_back(k);
05332                         kz.push_back(k+1);
05333                         for(j=1; j<=ny-2; ++j) {
05334                                 jy.clear();
05335                                 jy.push_back(j-1);
05336                                 jy.push_back(j);
05337                                 jy.push_back(j+1);
05338                                 for(i=1; i<=nx-2; ++i) {
05339                                         ix.clear();
05340                                         ix.push_back(i-1);
05341                                         ix.push_back(i);
05342                                         ix.push_back(i+1);
05343                                         float qbf = buf(i,j,k,l,m)*invert;
05344                                         peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[0])*invert;
05345                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[0])*invert;
05346                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[0])*invert;
05347                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[0])*invert;
05348                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[0])*invert;
05349                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[0])*invert;
05350                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[0])*invert;
05351                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[0])*invert;
05352                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[0])*invert;
05353                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[0])*invert;
05354                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[0])*invert;
05355                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[0])*invert;
05356                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[0])*invert;
05357                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[0])*invert;
05358                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[0])*invert;
05359                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[0])*invert;
05360                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[0])*invert;
05361                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[0])*invert;
05362                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[0])*invert;
05363                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[0])*invert;
05364                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[0])*invert;
05365                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[0])*invert;
05366                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[0])*invert;
05367                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[0])*invert;
05368                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[0])*invert;
05369                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[0])*invert;
05370                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[0])*invert;
05371 
05372                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[0])*invert;
05373                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[0])*invert;
05374                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[0])*invert;
05375                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[0])*invert;
05376                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[0])*invert;
05377                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[0])*invert;
05378                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[0])*invert;
05379                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[0])*invert;
05380                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[0])*invert;
05381                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[0])*invert;
05382                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[0])*invert;
05383                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[0])*invert;
05384                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[0])*invert;
05385                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[0])*invert;
05386                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[0])*invert;
05387                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[0])*invert;
05388                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[0])*invert;
05389                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[0])*invert;
05390                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[0])*invert;
05391                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[0])*invert;
05392                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[0])*invert;
05393                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[0])*invert;
05394                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[0])*invert;
05395                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[0])*invert;
05396                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[0])*invert;
05397                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[0])*invert;
05398                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[0])*invert;
05399 
05400                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[0])*invert;
05401                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[0])*invert;
05402                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[0])*invert;
05403                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[0])*invert;
05404                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[0])*invert;
05405                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[0])*invert;
05406                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[0])*invert;
05407                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[0])*invert;
05408                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[0])*invert;
05409                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[0])*invert;
05410                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[0])*invert;
05411                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[0])*invert;
05412                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[0])*invert;
05413                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[0])*invert;
05414                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[0])*invert;
05415                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[0])*invert;
05416                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[0])*invert;
05417                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[0])*invert;
05418                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[0])*invert;
05419                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[0])*invert;
05420                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[0])*invert;
05421                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[0])*invert;
05422                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[0])*invert;
05423                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[0])*invert;
05424                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[0])*invert;
05425                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[0])*invert;
05426                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[0])*invert;
05427 
05428 
05429                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[1])*invert;
05430                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[1])*invert;
05431                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[1])*invert;
05432                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[1])*invert;
05433                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[1])*invert;
05434                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[1])*invert;
05435                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[1])*invert;
05436                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[1])*invert;
05437                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[1])*invert;
05438                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[1])*invert;
05439                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[1])*invert;
05440                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[1])*invert;
05441                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[1])*invert;
05442                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[1])*invert;
05443                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[1])*invert;
05444                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[1])*invert;
05445                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[1])*invert;
05446                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[1])*invert;
05447                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[1])*invert;
05448                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[1])*invert;
05449                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[1])*invert;
05450                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[1])*invert;
05451                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[1])*invert;
05452                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[1])*invert;
05453                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[1])*invert;
05454                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[1])*invert;
05455                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[1])*invert;
05456 
05457                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[1])*invert;
05458                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[1])*invert;
05459                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[1])*invert;
05460                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[1])*invert;
05461                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[1])*invert;
05462                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[1])*invert;
05463                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[1])*invert;
05464                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[1])*invert;
05465                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[1])*invert;
05466                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[1])*invert;
05467                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[1])*invert;
05468                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[1])*invert;
05469                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[1])*invert;
05470                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[1])*invert;
05471                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[1])*invert;
05472                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[1])*invert;
05473                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[1])*invert;
05474                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[1])*invert;
05475                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[1])*invert;
05476                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[1])*invert;
05477                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[1])*invert;
05478                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[1])*invert;
05479                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[1])*invert;
05480                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[1])*invert;
05481                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[1])*invert;
05482                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[1])*invert;
05483                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[1])*invert;
05484 
05485                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[1])*invert;
05486                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[1])*invert;
05487                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[1])*invert;
05488                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[1])*invert;
05489                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[1])*invert;
05490                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[1])*invert;
05491                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[1])*invert;
05492                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[1])*invert;
05493                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[1])*invert;
05494                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[1])*invert;
05495                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[1])*invert;
05496                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[1])*invert;
05497                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[1])*invert;
05498                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[1])*invert;
05499                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[1])*invert;
05500                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[1])*invert;
05501                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[1])*invert;
05502                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[1])*invert;
05503                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[1])*invert;
05504                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[1])*invert;
05505                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[1])*invert;
05506                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[1])*invert;
05507                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[1])*invert;
05508                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[1])*invert;
05509                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[1])*invert;
05510                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[1])*invert;
05511                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[1])*invert;
05512 
05513 
05514                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[0],mv[2])*invert;
05515                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[0],mv[2])*invert;
05516                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[0],mv[2])*invert;
05517                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[0],mv[2])*invert;
05518                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[0],mv[2])*invert;
05519                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[0],mv[2])*invert;
05520                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[0],mv[2])*invert;
05521                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[0],mv[2])*invert;
05522                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[0],mv[2])*invert;
05523                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[0],mv[2])*invert;
05524                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[0],mv[2])*invert;
05525                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[0],mv[2])*invert;
05526                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[0],mv[2])*invert;
05527                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[0],mv[2])*invert;
05528                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[0],mv[2])*invert;
05529                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[0],mv[2])*invert;
05530                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[0],mv[2])*invert;
05531                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[0],mv[2])*invert;
05532                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[0],mv[2])*invert;
05533                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[0],mv[2])*invert;
05534                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[0],mv[2])*invert;
05535                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[0],mv[2])*invert;
05536                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[0],mv[2])*invert;
05537                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[0],mv[2])*invert;
05538                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[0],mv[2])*invert;
05539                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[0],mv[2])*invert;
05540                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[0],mv[2])*invert;
05541 
05542                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[1],mv[2])*invert;
05543                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[1],mv[2])*invert;
05544                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[1],mv[2])*invert;
05545                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[1],mv[2])*invert;
05546                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[1],mv[2])*invert;
05547                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[1],mv[2])*invert;
05548                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[1],mv[2])*invert;
05549                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[1],mv[2])*invert;
05550                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[1],mv[2])*invert;
05551                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[1],mv[2])*invert;
05552                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[1],mv[2])*invert;
05553                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[1],mv[2])*invert;
05554                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[1],mv[2])*invert;
05555                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[1],mv[2])*invert;
05556                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[1],mv[2])*invert;
05557                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[1],mv[2])*invert;
05558                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[1],mv[2])*invert;
05559                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[1],mv[2])*invert;
05560                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[1],mv[2])*invert;
05561                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[1],mv[2])*invert;
05562                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[1],mv[2])*invert;
05563                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[1],mv[2])*invert;
05564                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[1],mv[2])*invert;
05565                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[1],mv[2])*invert;
05566                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[1],mv[2])*invert;
05567                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[1],mv[2])*invert;
05568                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[1],mv[2])*invert;
05569 
05570                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[0],lu[2],mv[2])*invert;
05571                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0],lu[2],mv[2])*invert;
05572                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0],lu[2],mv[2])*invert;
05573                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0],lu[2],mv[2])*invert;
05574                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0],lu[2],mv[2])*invert;
05575                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0],lu[2],mv[2])*invert;
05576                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0],lu[2],mv[2])*invert;
05577                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0],lu[2],mv[2])*invert;
05578                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0],lu[2],mv[2])*invert;
05579                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1],lu[2],mv[2])*invert;
05580                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1],lu[2],mv[2])*invert;
05581                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1],lu[2],mv[2])*invert;
05582                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1],lu[2],mv[2])*invert;
05583                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1],lu[2],mv[2])*invert;
05584                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1],lu[2],mv[2])*invert;
05585                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1],lu[2],mv[2])*invert;
05586                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1],lu[2],mv[2])*invert;
05587                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1],lu[2],mv[2])*invert;
05588                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2],lu[2],mv[2])*invert;
05589                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2],lu[2],mv[2])*invert;
05590                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2],lu[2],mv[2])*invert;
05591                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2],lu[2],mv[2])*invert;
05592                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2],lu[2],mv[2])*invert;
05593                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2],lu[2],mv[2])*invert;
05594                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2],lu[2],mv[2])*invert;
05595                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2],lu[2],mv[2])*invert;
05596                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],lu[2],mv[2])*invert;
05597                                         if(peak_check) {
05598                                                 if(count < ml) {
05599                                                         count++;
05600                                                         //peaks.push_back( Pixel(i, j, k, l, m, qbf) );
05601                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05602                                                 } else {
05603                                                         if( qbf > (peaks.back()).value ) {
05604                                                                 //  do the switch and sort again
05605                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05606                                                                 peaks.pop_back();
05607                                                                 //peaks.push_back( Pixel(i, j, k, l, m, qbf) );
05608                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05609                                                         }
05610                                                 }
05611                                         }
05612                                         }}}}}}}}}}}}}}}}}}}}}}}}}}
05613                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05614                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05615                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05616                                         }}}}}}}}}}}}}}}}}}}}}}}}}}
05617                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05618                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05619                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05620                                         }}}}}}}}}}}}}}}}}}}}}}}}}}}
05621                                 }
05622                         }
05623                 }
05624                 }
05625                 }
05626                 //  Add circular closure for x, y, and z directions: needed for circular ccf,
05627                 //  should not have adverse impact on other code.  PAP 11/7/08
05628                 for(m=1; m<=nv-2; ++m) {
05629                         mv.clear();
05630                         mv.push_back(m-1);
05631                         mv.push_back(m);
05632                         mv.push_back(m+1);
05633                 for(l=1; l<=nu-2; ++l) {
05634                         lu.clear();
05635                         lu.push_back(l-1);
05636                         lu.push_back(l);
05637                         lu.push_back(l+1);
05638                 for(k=1; k<=nz-2; ++k) {
05639                         kz.clear();
05640                         kz.push_back(k-1);
05641                         kz.push_back(k);
05642                         kz.push_back(k+1);
05643                         for(j=1; j<=ny-2; ++j) {
05644                                 jy.clear();
05645                                 jy.push_back(j-1);
05646                                 jy.push_back(j);
05647                                 jy.push_back(j+1);
05648                                 for(i=0; i<=0; ++i) {
05649                                         ix.clear();
05650                                         ix.push_back(nx-1);
05651                                         ix.push_back(i);
05652                                         ix.push_back(i+1);
05653                                         float qbf = buf(i,j,k)*invert;
05654                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05655                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05656                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05657                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05658                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05659                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05660                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05661                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05662                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05663                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05664                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05665                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05666                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05667                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05668                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05669                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05670                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05671                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05672                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05673                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05674                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05675                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05676                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05677                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05678                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05679                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05680                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2])*invert;
05681                                         if(peak_check) {
05682                                                 if(count < ml) {
05683                                                         count++;
05684                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05685                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05686                                                 } else {
05687                                                         if( qbf > (peaks.back()).value ) {
05688                                                                 //  do the switch and sort again
05689                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05690                                                                 peaks.pop_back();
05691                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05692                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05693                                                         }
05694                                                 }
05695                                         }
05696                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05697                                 }
05698                                 for(i=nx-1; i<=nx-1; ++i) {
05699                                         ix.clear();
05700                                         ix.push_back(i-1);
05701                                         ix.push_back(i);
05702                                         ix.push_back(0);
05703                                         float qbf = buf(i,j,k)*invert;
05704                                         peak_check = qbf > buf(ix[0],jy[0],kz[0])*invert;
05705                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[0])*invert;
05706                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[0])*invert;
05707                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[0])*invert;
05708                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[0])*invert;
05709                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[0])*invert;
05710                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[0])*invert;
05711                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[0])*invert;
05712                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[0])*invert;
05713                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[1])*invert;
05714                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[1])*invert;
05715                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[1])*invert;
05716                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[1])*invert;
05717                                         //if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[1])*invert;
05718                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[1])*invert;
05719                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[1])*invert;
05720                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[1])*invert;
05721                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[1])*invert;
05722                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[0],kz[2])*invert;
05723                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[0],kz[2])*invert;
05724                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[0],kz[2])*invert;
05725                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[1],kz[2])*invert;
05726                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[1],kz[2])*invert;
05727                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[1],kz[2])*invert;
05728                                         if( peak_check ) {peak_check = qbf > buf(ix[0],jy[2],kz[2])*invert;
05729                                         if( peak_check ) {peak_check = qbf > buf(ix[1],jy[2],kz[2])*invert;
05730                                         if( peak_check ) {peak_check = qbf > buf(ix[2],jy[2],kz[2],3,3)*invert;
05731                                         if(peak_check) {
05732                                                 if(count < ml) {
05733                                                         count++;
05734                                                         peaks.push_back( Pixel(i, j, k, qbf) );
05735                                                         if(count == ml-1) sort(peaks.begin(), peaks.end(), peakcmp);
05736                                                 } else {
05737                                                         if( qbf > (peaks.back()).value ) {
05738                                                                 //  do the switch and sort again
05739                                                                 //cout << qbf<<"   "<< (peaks.back()).value <<"   "<< (*peaks.begin()).value <<endl;
05740                                                                 peaks.pop_back();
05741                                                                 peaks.push_back( Pixel(i, j, k, qbf) );
05742                                                                 if(ml > 1) sort(peaks.begin(), peaks.end(), peakcmp);
05743                                                         }
05744                                                 }
05745                                         }
05746                                         }}}}}}}}}}}}}}}}}}}}}}}}}
05747                                 }
05748                         }
05749                 }
05750                 }
05751                 }
05752         break;*/
05753         }
05754         // do we have a peak list yet?
05755         if (peaks.begin() != peaks.end()) {
05756           // yes. sort it
05757           sort(peaks.begin(), peaks.end(), peakcmp);
05758 
05759           int count = 0;
05760 
05761           float xval = (*peaks.begin()).value;
05762           // loop over all peaks
05763           for (vector<Pixel>::iterator it = peaks.begin(); it != peaks.end(); it++)  {
05764             // current peak count
05765             count++;
05766             // is current peak count below max?
05767             if(count <= ml) {
05768               // yes, so append it
05769               res.push_back((*it).value);
05770               res.push_back(static_cast<float>((*it).x));
05771 
05772               if(img_dim > 1) {
05773                 res.push_back(static_cast<float>((*it).y));
05774                 if(nz > 1) res.push_back(static_cast<float>((*it).z));
05775               }
05776 
05777               if(xval != 0.0) res.push_back((*it).value/xval);
05778               else            res.push_back((*it).value);
05779               res.push_back((*it).x-float(int(nx/2)));
05780               if(img_dim >1) {
05781                 res.push_back((*it).y-float(int(ny/2)));
05782                 if(nz>1)   res.push_back((*it).z-float(nz/2));
05783               }
05784             }
05785           }
05786           res.insert(res.begin(),1,img_dim);
05787         } else {
05788           // no peak list. build empty list
05789           res.push_back(buf(0,0,0));
05790           res.insert(res.begin(),1,0.0);
05791         }
05792 
05793         // return results list
05794         return res;
05795 }
05796 
05797 #define rdata(i,j,k) rdata[(i-1)+((j-1)+(k-1)*ny)*(size_t)nx]
05798 #define X(i) X[i-1]
05799 #define Y(j) Y[j-1]
05800 #define Z(k) Z[k-1]
05801 vector<float> EMData::phase_cog()
05802 {
05803         vector<float> ph_cntog;
05804         int i=1,j=1,k=1;
05805         float C=0.f,S=0.f,P=0.f,F1=0.f,SNX;
05806         if (get_ndim()==1) {
05807                 P = 8*atan(1.0f)/nx;
05808                 for (i=1;i<=nx;i++) {
05809                         C += cos(P * (i-1)) * rdata(i,j,k);
05810                         S += sin(P * (i-1)) * rdata(i,j,k);
05811                 }
05812                 F1 = atan2(S,C);
05813                 if (F1 < 0.0)  F1 += 8*atan(1.0f);
05814                 SNX = F1/P +1.0f;
05815                 SNX = SNX - ((nx/2)+1);
05816                 ph_cntog.push_back(SNX);
05817 #ifdef _WIN32
05818                 ph_cntog.push_back((float)Util::round(SNX));
05819 #else
05820                 ph_cntog.push_back(round(SNX));
05821 #endif //_WIN32
05822         } else if (get_ndim()==2)  {
05823 #ifdef _WIN32
05824                 float SNY;
05825                 float T=0.0f;
05826                 vector<float> X;
05827                 X.resize(nx);
05828 #else
05829                 float SNY,X[nx],T=0.f;
05830 #endif  //_WIN32
05831                 for ( i=1;i<=nx;i++) X(i)=0.0;
05832                 P = 8*atan(1.0f)/ny;
05833                 for(j=1;j<=ny;j++) {
05834                         T=0.f;
05835                         for(i=1;i<=nx;i++) {
05836                                 T += rdata(i,j,k);
05837                                 X(i)+=rdata(i,j,k);
05838                         }
05839                         C += cos(P*(j-1))*T;
05840                         S += sin(P*(j-1))*T;
05841                 }
05842                 F1=atan2(S,C);
05843                 if(F1<0.0)  F1 += 8*atan(1.0f);
05844                 SNY = F1/P +1.0f;
05845                 C=0.f;  S=0.f;
05846                 P = 8*atan(1.0f)/nx;
05847                 for(i=1;i<=nx;i++) {
05848                         C += cos(P*(i-1))*X(i);
05849                         S += sin(P*(i-1))*X(i);
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                 SNY = SNY - ((ny/2)+1);
05856                 ph_cntog.push_back(SNX); ph_cntog.push_back(SNY);
05857 #ifdef _WIN32
05858                  ph_cntog.push_back((float)Util::round(SNX)); ph_cntog.push_back((float)Util::round(SNY));
05859 #else
05860                  ph_cntog.push_back(round(SNX)); ph_cntog.push_back(round(SNY));
05861 #endif  //_WIN32
05862         } else {
05863 #ifdef _WIN32
05864                 float val=0.f,sum1=0.f, SNY,SNZ;
05865                 vector<float> X;
05866                 X.resize(nx);
05867                 vector<float> Y;
05868                 Y.resize(ny);
05869                 vector<float> Z;
05870                 Z.resize(nz);
05871 #else
05872                 float val=0.f, sum1=0.f, X[nx], Y[ny], Z[nz], SNY, SNZ;
05873 #endif  //_WIN32
05874                  for (i=1;i<=nx;i++)  X(i)=0.0;
05875                  for (j=1;j<=ny;j++)  Y(j)=0.0;
05876                  for (k=1;k<=nz;k++)  Z(k)=0.0;
05877                  for(k=1;k<=nz;k++)  {
05878                         for(j=1;j<=ny;j++) {
05879                                 sum1=0.f;
05880                                 for(i=1;i<=nx;i++)  {
05881                                         val = rdata(i,j,k);
05882                                         sum1 += val;
05883                                         X(i) += val;
05884                                 }
05885                                 Y(j) += sum1;
05886                                 Z(k) += sum1;
05887                         }
05888                 }
05889                 P = 8*atan(1.0f)/nx;
05890                 for (i=1;i<=nx;i++) {
05891                         C += cos(P*(i-1))*X(i);
05892                         S += sin(P*(i-1))*X(i);
05893                 }
05894                 F1=atan2(S,C);
05895                 if(F1<0.0) F1 += 8*atan(1.0f);
05896                 SNX = F1/P +1.0f;
05897                 C=0.f;  S=0.f;
05898                 P = 8*atan(1.0f)/ny;
05899                 for(j=1;j<=ny;j++) {
05900                         C += cos(P*(j-1))*Y(j);
05901                         S += sin(P*(j-1))*Y(j);
05902                 }
05903                 F1=atan2(S,C);
05904                 if(F1<0.0)  F1 += 8*atan(1.0f);
05905                 SNY = F1/P +1.0f;
05906                 C=0.f;  S=0.f;
05907                 P = 8*atan(1.0f)/nz;
05908                 for(k=1;k<=nz;k++) {
05909                         C += cos(P*(k-1))*Z(k);
05910                         S += sin(P*(k-1))*Z(k);
05911                 }
05912                 F1=atan2(S,C);
05913                 if(F1<0.0)  F1 += 8*atan(1.0f);
05914                 SNZ = F1/P +1.0f;
05915                 SNX = SNX - ((nx/2)+1);
05916                 SNY = SNY - ((ny/2)+1);
05917                 SNZ = SNZ - ((nz/2)+1);
05918                 ph_cntog.push_back(SNX); ph_cntog.push_back(SNY); ph_cntog.push_back(SNZ);
05919 #ifdef _WIN32
05920                 ph_cntog.push_back((float)Util::round(SNX)); ph_cntog.push_back((float)Util::round(SNY)); ph_cntog.push_back((float)Util::round(SNZ));
05921 #else
05922                 ph_cntog.push_back(round(SNX)); ph_cntog.push_back(round(SNY));ph_cntog.push_back(round(SNZ));
05923 #endif
05924         }
05925         return ph_cntog;
05926 }
05927 #undef rdata
05928 #undef X
05929 #undef Y
05930 #undef Z
05931 
05932 #define avagadro (6.023*(double)pow(10.0,23.0))
05933 #define density_protein (1.36)
05934 #define R (0.61803399f)
05935 #define C (1.f-R)
05936 float EMData::find_3d_threshold(float mass, float pixel_size)
05937 {
05938         /* Exception Handle */
05939         if(get_ndim()!=3)
05940                 throw ImageDimensionException("The image should be 3D");
05941         /* ===============================================================*/
05942 
05943         /* Calculation of the volume of the voxels */
05944         float density_1_mole, vol_1_mole, vol_angstrom;
05945         int  vol_voxels;
05946         density_1_mole = static_cast<float>( (mass*1000.0f)/avagadro );
05947         vol_1_mole =  static_cast<float>( density_1_mole/density_protein );
05948         vol_angstrom =  static_cast<float>( vol_1_mole*(double)pow((double)pow(10.0,8),3) );
05949         vol_voxels = static_cast<int> (vol_angstrom/(double)pow(pixel_size,3));
05950         /* ===============================================================*/
05951 
05952 
05953         float thr1 = get_attr("maximum");
05954         float thr3 = get_attr("minimum");
05955         float thr2 = (thr1-thr3)/2 + thr3;
05956         size_t size = (size_t)nx*ny*nz;
05957         float x0 = thr1,x3 = thr3,x1,x2,THR=0;
05958 
05959         #ifdef _WIN32
05960                 int ILE = _cpp_min(nx*ny*nx,_cpp_max(1,vol_voxels));
05961         #else
05962                 int ILE = std::min(nx*ny*nx,std::max(1,vol_voxels));
05963         #endif  //_WIN32
05964 
05965         if (abs(thr3-thr2)>abs(thr2-thr1)) {
05966                 x1=thr2;
05967                 x2=thr2+C*(thr3-thr2);
05968         } else {
05969                 x2=thr2;
05970                 x1=thr2-C*(thr2-thr1);
05971         }
05972 
05973         int cnt1=0,cnt2=0;
05974         for (size_t i=0;i<size;++i) {
05975                 if(rdata[i]>=x1)  cnt1++;
05976                 if(rdata[i]>=x2)  cnt2++;
05977         }
05978         float LF1 = static_cast<float>( cnt1 - ILE );
05979         float F1 = LF1*LF1;
05980         float LF2 = static_cast<float>( cnt2 - ILE );
05981         float F2 = LF2*LF2;
05982 
05983         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)))
05984         {
05985                 if(F2 < F1) {
05986                         x0=x1;
05987                         x1=x2;
05988                         x2 = R*x1 + C*x3;
05989                         F1=F2;
05990                         int cnt=0;
05991                         for(size_t i=0;i<size;++i)
05992                                 if(rdata[i]>=x2)
05993                                         cnt++;
05994                         LF2 = static_cast<float>( cnt - ILE );
05995                         F2 = LF2*LF2;
05996                 } else {
05997                         x3=x2;
05998                         x2=x1;
05999                         x1=R*x2 + C*x0;
06000                         F2=F1;
06001                         int cnt=0;
06002                         for(size_t i=0;i<size;++i)
06003                                 if(rdata[i]>=x1)
06004                                         cnt++;
06005                         LF1 = static_cast<float>( cnt - ILE );
06006                         F1 = LF1*LF1;
06007                 }
06008         }
06009 
06010         if(F1 < F2) {
06011                 ILE = static_cast<int> (LF1 + ILE);
06012                 THR = x1;
06013         } else {
06014                 ILE = static_cast<int> (LF2 + ILE);
06015                 THR = x2;
06016         }
06017         return THR;
06018 
06019 }
06020 #undef avagadro
06021 #undef density_protein
06022 #undef R
06023 #undef C
06024 
06025 
06026 // reworked peak_ccf uses max queue lenght for peak objects, i.e. lowest
06027 //    peaks are deleted if queue length is exceeded and a new peak is inserted
06028 //    instead.
06029 
06030 
06031 vector<float> EMData::peak_ccf(float hf_p)
06032 {
06033 
06034   // cout << "peak ccf starting up" << endl;
06035 
06036   EMData & buf = *this;
06037   vector<Pixel> peaks;
06038   int half=int(hf_p);
06039   float hf_p2 = hf_p*hf_p;
06040   int i,j;
06041   int i__1,i__2;
06042   int j__1,j__2;
06043   vector<float>res;
06044   int nx = buf.get_xsize()-half;
06045   int ny = buf.get_ysize()-half;
06046   // iterate over image
06047   for(i=half; i<=nx; ++i) {
06048     // static assignment so we don't have to re-evaluate
06049     i__1 = i-1;
06050     i__2 = i+1;
06051     for (j=half;j<=ny;++j) {
06052       j__1 = j-1;
06053       j__2 = j+1;
06054 
06055       if((buf(i,j)>0.0f)&&buf(i,j)>buf(i,j__1)) {
06056         if(buf(i,j)>buf(i,j__2)) {
06057           if(buf(i,j)>buf(i__1,j)) {
06058             if(buf(i,j)>buf(i__2,j)) {
06059               if(buf(i,j)>buf(i__1,j__1)) {
06060                 if((buf(i,j))> buf(i__1,j__2)) {
06061                   if(buf(i,j)>buf(i__2,j__1)) {
06062                     if(buf(i,j)> buf(i__2,j__2)) {
06063 
06064                       // found a peak
06065                       // empty list?
06066                       if (peaks.size()==0) {
06067                         // yes, so just push the peak onto the list
06068                         peaks.push_back(Pixel(i,j,0,buf(i,j)));
06069 
06070                       } else {
06071                         // not empty list. check neighbourhood for peaks
06072                         // logical not in the name is awkward. renamed to overlap
06073                         bool overlap = false;
06074                         //int  size = peaks.size();
06075 
06076                         // list of peaks to be deleted, if the current peak is the largest (see below).
06077                         //    list contains iterators to the original list, which will have to be processed
06078                         //    back to front (i.e. LIFO: stl::stack)
06079                         std::stack <vector<Pixel>::iterator> delete_stack;
06080 
06081                         // loop over all peaks found so far. this would be nicer with iterators
06082                         for (vector<Pixel>::iterator it=peaks.begin();it!=peaks.end();++it) {
06083                         // for ( int kk= 0; kk< size; kk++) {
06084                         //  vector<Pixel>::iterator it = peaks.begin()+kk;
06085 
06086                           // calc L2 distance
06087                           float radius=((*it).x-float(i))*((*it).x-float(i))+((*it).y-float(j))*((*it).y-float(j));
06088                           if (radius <= hf_p2 ) {
06089                             // peaks overlap
06090                             if( buf(i,j) > (*it).value) {
06091                               // this peak (indexed by (i,j)) is larger, mark the old for deletion
06092                               //    however, we have to be careful. if there is a larger peak within the vicinity of
06093                               //    the new one, this new peak is not marked as such, and the deletion of prior low
06094                               //    peaks should not continued. to make sure this deletion does not happen, we have
06095                               //    to make sure we cycle through all peaks within the vicinity, and only delete smaller
06096                               //    peaks if this new one is the largest in the vicinity.
06097                               delete_stack.push(it);
06098 
06099                               //(*it).x = -half; // this marks entry to be deleted, since it's smaller than the new one
06100 
06101 
06102                             } else {
06103                               overlap = true;
06104                               // old peak is larger, ignore this one. since it's enough to know there is some peak larger
06105                               //    than this one, we can break out of the peak list loop, instead of continuing.
06106                               break;
06107                             }
06108                           }
06109                         }
06110 
06111                         // check whether we need to delete anything. this is marked by the flag overlap == false
06112                         // loop over all peaks and clean out redundant ones
06113                         if (false == overlap) {
06114                           vector<Pixel>::iterator delete_iterator;
06115                           while (!delete_stack.empty()) {
06116                             // pop empties the stack from the back. since we are dealing with iterators, we need to delete
06117                             //    from the back, so as to keep the rest stack intact upon deletion.
06118                             delete_iterator = delete_stack.top();
06119                             peaks.erase(delete_iterator);
06120                             delete_stack.pop();
06121                           }
06122                           // before pushing the peak, we need to check whether max queue length is exceeded and delete
06123                           //     peaks if necessary.
06124                           // XXX: remove hardcoded value!
06125                           if (! (peaks.size() < 2000 )) {
06126 
06127                             //cout << ".";
06128                             // we need to delete a peak first.
06129                             // - resort list to get lowest peak at the back
06130                             sort(peaks.begin(), peaks.end(), peakcmp);
06131 
06132                             // - remove lowest peak
06133                             peaks.pop_back();
06134                           }
06135 
06136                           // push the new peak onto the list of peaks
06137                           peaks.push_back(Pixel(i,j,0,buf(i,j)));
06138                           //cout << "done." << endl;
06139 
06140                         } else {
06141                           // this peak too small and is ignored, so delete_list is ignored as well. make sure delete_list
06142                           //    is empty. probably redundant because of scope, but better safe than sorry.....
06143                           while (!delete_stack.empty()) delete_stack.pop();
06144                         }
06145                       }
06146                     }
06147                   }}}}}}}
06148     }
06149   }
06150 
06151   // we have peaks, so build a results vector.
06152   if(peaks.size()>0) {
06153     // sort peaks by size
06154     sort(peaks.begin(),peaks.end(), peakcmp);
06155     // and push all peaks to the results vector
06156     for (vector<Pixel>::iterator it = peaks.begin(); it != peaks.end(); it++) {
06157       // XXX: this format is necessary for Boost to work???
06158       res.push_back((*it).value);
06159       res.push_back(static_cast<float>((*it).x));
06160       res.push_back(static_cast<float>((*it).y));
06161     }
06162   } else {
06163     // only one or zero (?) entries
06164     res.push_back(buf(0,0,0));
06165     res.insert(res.begin(),1,0.0);
06166   }
06167   return res;
06168 }
06169 
06170 EMData* EMData::get_pow(float n_pow)
06171 {
06172         EMData* buf_new = this->copy_head();
06173         float *in  = this->get_data();
06174         float *out = buf_new->get_data();
06175         for(size_t i=0; i<(size_t)nx*ny*nz; ++i) out[i] = pow(in[i],n_pow);
06176         return buf_new;
06177 }
06178 
06179 EMData* EMData::conjg()
06180 {
06181         if(this->is_complex()) {
06182                 EMData* buf_new = this->copy_head();
06183                 float *in  = this->get_data();
06184                 float *out = buf_new->get_data();
06185                 for(size_t i=0; i<(size_t)nx*ny*nz; i+=2) {out[i] = in[i]; out[i+1] = -in[i+1];}
06186                 return buf_new;
06187         } else throw ImageFormatException("image has to be complex");
06188 }
06189 
06190 EMData* EMData::delete_disconnected_regions(int ix, int iy, int iz) {
06191         if (3 != get_ndim())
06192                 throw ImageDimensionException("delete_disconnected_regions needs a 3-D image.");
06193         if (is_complex())
06194                 throw ImageFormatException("delete_disconnected_regions requires a real image");
06195         if ((*this)(ix+nx/2,iy+ny/2,iz+nz/2) == 0)
06196                 throw ImageDimensionException("delete_disconnected_regions starting point is zero.");
06197 
06198         EMData* result = this->copy_head();
06199         result->to_zero();
06200         (*result)(ix+nx/2,iy+ny/2,iz+nz/2) = (*this)(ix+nx/2,iy+ny/2,iz+nz/2);
06201         bool kpt = true;
06202         //cout << "  delete   "<<(*result)(ix+nx/2,iy+ny/2,iz+nz/2)<<endl;
06203         while(kpt) {
06204                 kpt = false;
06205                 for (int cz = 1; cz < nz-1; cz++) {
06206                         for (int cy = 1; cy < ny-1; cy++) {
06207                                 for (int cx = 1; cx < nx-1; cx++) {
06208                                         if((*result)(cx,cy,cz) == 1) {
06209                                                 for (int lz = -1; lz <= 1; lz++) {
06210                                                         for (int ly = -1; ly <= 1; ly++) {
06211                                                                 for (int lx = -1; lx <= 1; lx++) {
06212                                                                         if(((*this)(cx+lx,cy+ly,cz+lz) == 1) && ((*result)(cx+lx,cy+ly,cz+lz) == 0))  {
06213                                                                                 (*result)(cx+lx,cy+ly,cz+lz) = 1;
06214                                                                                 kpt = true;
06215                                                                         }
06216                                                                 }
06217                                                         }
06218                                                 }
06219                                         }
06220                                 }
06221                         }
06222                 }
06223         }
06224         result->update();
06225         return result;
06226 }
06227 
06228 #define    QUADPI                       3.141592653589793238462643383279502884197
06229 #define    DGR_TO_RAD                   QUADPI/180
06230 
06231 EMData* EMData::helicise(float pixel_size, float dp, float dphi, float section_use, float radius, float minrad) {
06232         if (3 != get_ndim())
06233                 throw ImageDimensionException("helicise needs a 3-D image.");
06234         if (is_complex())
06235                 throw ImageFormatException("helicise requires a real image");
06236         EMData* result = this->copy_head();
06237         result->to_zero();
06238         int nyc = ny/2;
06239         int nxc = nx/2;
06240         int vl = nz-1; //lengh of the volume in pixel
06241         if ( section_use < dp/int(vl*pixel_size) )      
06242                 section_use = (dp)/int(vl*pixel_size);
06243                 
06244         float nb = vl*(1.0f - section_use)/2.0f;
06245 
06246         float ne =  nb+vl*section_use;
06247         int numst = int( (ne-nb)*pixel_size/dp );
06248         
06249         
06250         float r2, ir;
06251         if(radius < 0.0f) r2 = (float)((nxc-1)*(nxc-1));
06252         else r2 = radius*radius;
06253         if(minrad < 0.0f) ir = 0.0f;
06254         else ir = minrad*minrad;
06255         for (int k = 0; k<nz; k++) {
06256                 int nst1 = int ( (nb-k)*pixel_size/dp) -1;
06257                 int nst2 = int ( (ne-k)*pixel_size/dp) +1;
06258                 for (int j = 0; j<ny; j++) {
06259                         int jy = j - nyc;
06260                         int jj = jy*jy;
06261                         for (int i = 0; i<nx; i++) {
06262                                 int ix = i - nxc;
06263                                 float d2 = (float)(ix*ix + jj);
06264                                 if(d2 <= r2 && d2>=ir) {
06265                                         int nq = 0;
06266                                         for ( int ist = nst1; ist < nst2; ist++) {
06267                                                 float zold = (k*pixel_size + ist*dp)/pixel_size;
06268                                                 
06269                                                 if(zold >= nb && zold <= ne) {
06270                                                         // now x-y position
06271                                                         float cphi = ist*dphi*(float)DGR_TO_RAD;
06272                                                         float ca = cos(cphi);
06273                                                         float sa = sin(cphi);
06274                                                         float xold = ix*ca - jy*sa + nxc;
06275                                                         float yold = ix*sa + jy*ca + nyc;
06276                                                         nq++;
06277 
06278         int IOZ = int(zold);
06279         //  Do tri-linear interpolation
06280         int IOX = int(xold);
06281         int IOY = int(yold);
06282         //int IOZ = int(zold);
06283 
06284         #ifdef _WIN32
06285         int IOXp1 = _cpp_min( nx-1 ,IOX+1);
06286         #else
06287         int IOXp1 = std::min( nx-1 ,IOX+1);
06288         #endif  //_WIN32
06289 
06290         #ifdef _WIN32
06291         int IOYp1 = _cpp_min( ny-1 ,IOY+1);
06292         #else
06293         int IOYp1 = std::min( ny-1 ,IOY+1);
06294         #endif  //_WIN32
06295 
06296         #ifdef _WIN32
06297         int IOZp1 = _cpp_min( nz-1 ,IOZ+1);
06298         #else
06299         int IOZp1 = std::min( nz-1 ,IOZ+1);
06300         #endif  //_WIN32
06301 
06302         float dx = xold-IOX;
06303         float dy = yold-IOY;
06304         float dz = zold-IOZ;
06305 
06306         float a1 = (*this)(IOX,IOY,IOZ);
06307         float a2 = (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOY,IOZ);
06308         float a3 = (*this)(IOX,IOYp1,IOZ) - (*this)(IOX,IOY,IOZ);
06309         float a4 = (*this)(IOX,IOY,IOZp1) - (*this)(IOX,IOY,IOZ);
06310         float a5 = (*this)(IOX,IOY,IOZ) - (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOYp1,IOZ) + (*this)(IOXp1,IOYp1,IOZ);
06311         float a6 = (*this)(IOX,IOY,IOZ) - (*this)(IOXp1,IOY,IOZ) - (*this)(IOX,IOY,IOZp1) + (*this)(IOXp1,IOY,IOZp1);
06312         float a7 = (*this)(IOX,IOY,IOZ) - (*this)(IOX,IOYp1,IOZ) - (*this)(IOX,IOY,IOZp1) + (*this)(IOX,IOYp1,IOZp1);
06313         float a8 = (*this)(IOXp1,IOY,IOZ) + (*this)(IOX,IOYp1,IOZ)+ (*this)(IOX,IOY,IOZp1)
06314                         - (*this)(IOX,IOY,IOZ)- (*this)(IOXp1,IOYp1,IOZ) - (*this)(IOXp1,IOY,IOZp1)
06315                         - (*this)(IOX,IOYp1,IOZp1) + (*this)(IOXp1,IOYp1,IOZp1);
06316 
06317 
06318 
06319                                                         (*result)(i,j,k) += a1 + dz*(a4 + a6*dx + (a7 + a8*dx)*dy) + a3*dy + dx*(a2 + a5*dy);
06320                                                         if(nq == numst) break;
06321                                                 }
06322                                         }
06323                                         if(nq != numst)
06324                                                 throw InvalidValueException(nq, "Helicise: incorrect number of repeats encoutered.");
06325                                 }
06326                         }
06327                 }
06328         }
06329         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 ;
06330 
06331         result->update();
06332         return result;
06333 }
06334 
06335 
06336 
06337 EMData* EMData::helicise_grid(float pixel_size, float dp, float dphi, Util::KaiserBessel& kb, float section_use, float radius, float minrad) {
06338         std::cout<<"111111"<<std::endl;
06339         if (3 != get_ndim())
06340                 throw ImageDimensionException("helicise needs a 3-D image.");
06341         if (is_complex())
06342                 throw ImageFormatException("helicise requires a real image");
06343         //begin griding
06344         //if (scale_input == 0.0f) scale_input = 1.0f;
06345         float  scale = 0.5f;//*scale_input;
06346 
06347         
06348         int nxn = nx/2; int nyn = ny/2; int nzn = nz/2;
06349 
06350         vector<int> saved_offsets = get_array_offsets();
06351         set_array_offsets(0,0,0);
06352         EMData* ret = this->copy_head();
06353 #ifdef _WIN32
06354         ret->set_size(nxn, _cpp_max(nyn,1), _cpp_max(nzn,1));
06355 #else
06356         ret->set_size(nxn, std::max(nyn,1), std::max(nzn,1));
06357 #endif  //_WIN32
06358         ret->to_zero();  //we will leave margins zeroed.
06359 
06360         // center of big image,
06361         int xc = nxn;
06362         int ixs = nxn%2;  // extra shift on account of odd-sized images
06363         int yc = nyn;
06364         int iys = nyn%2;
06365         int zc = nzn;
06366         int izs = nzn%2;
06367         // center of small image
06368         int xcn = nxn/2;
06369         int ycn = nyn/2;
06370         int zcn = nzn/2;
06371         // shifted center for rotation
06372         float shiftxc = xcn; // + delx;
06373         float shiftyc = ycn; // + dely;
06374         float shiftzc = zcn; // + delz;
06375         // bounds if origin at center
06376         float zmin = -nz/2.0f;
06377         float ymin = -ny/2.0f;
06378         float xmin = -nx/2.0f;
06379         float zmax = -zmin;
06380         float ymax = -ymin;
06381         float xmax = -xmin;
06382         if (0 == nx%2) xmax--;
06383         if (0 == ny%2) ymax--;
06384         if (0 == nz%2) zmax--;
06385 
06386         float* data = this->get_data();
06387 
06388         
06389         // rotation matrix (the transpose is used in the loop to get (xold,yold,zold)):
06390          
06391         //float a13 = -0.0f;    float a23 =  0.0f;
06392         //float a31 =  0.0f;          float a32 =  0.0f;          float a33 =  1.0f;
06393                 
06394         //end gridding
06395 
06396         
06397         int nyc = nyn/2;
06398         int nxc = nxn/2;
06399         int nb = int(nzn*(1.0f - section_use)/2.);
06400         int ne = nzn - nb -1;
06401         int numst = int(nzn*section_use*pixel_size/dp);
06402         // how many steps needed total, fewer will be used, only those that fall between nb and ne
06403         int nst = int(nzn*pixel_size/dp);
06404         float r2, ir;
06405         if(radius < 0.0f) r2 = (float)((nxc-1)*(nxc-1));
06406         else r2 = radius*radius;
06407         if(minrad < 0.0f) ir = 0.0f;
06408         else ir = minrad*minrad;
06409         
06410         for (int k = 0; k<nzn; k++) {
06411                 for (int j = 0; j<nyn; j++) {
06412                         int jy = j - nyc;
06413                         int jj = jy*jy;
06414                         for (int i = 0; i<nxn; i++) {
06415                                 int ix = i - nxc;
06416                                 float d2 = (float)(ix*ix + jj);
06417                                 if(d2 <= r2 && d2>=ir) {
06418                                         int nq = 0;
06419                                         for ( int ist = -nst; ist <= nst; ist++) {
06420                                                 float zold = (k*pixel_size + ist*dp)/pixel_size;
06421                                                 int IOZ = int(zold);
06422                                                 if(IOZ >= nb && IOZ <= ne) {
06423                                                 
06424                                                         float cphi = ist*dphi*(float)DGR_TO_RAD;
06425                                                         float ca = cos(cphi);
06426                                                         float sa = sin(cphi);
06427                                                         
06428                                                         float xold = ix*ca - jy*sa + nxc;
06429                                                         float yold = ix*sa + jy*ca + nyc;
06430                                                         
06431                                                         float xold_big = (xold-shiftxc)/scale - ixs + xc;
06432                                                         float yold_big = (yold-shiftyc)/scale - iys + yc;
06433                                                         float zold_big = (zold-shiftzc)/scale - izs + zc;
06434                                                         
06435                                                         /*float a11 =  ca; float a12 =  sa;
06436                                                         float a21 = -sa; float a22 = ca;
06437                                                         
06438                                                         float z = (zold - shiftzc)/scale;
06439                                                         float zco1 = a31*z+xc;
06440                                                         float zco2 = a32*z+yc;
06441                                                         float zco3 = a33*z+zc;
06442                                                                                                                 
06443                                                         float y = (float(j) - shiftyc)/scale;
06444                                                         float yco1 = zco1+a21*y;
06445                                                         float yco2 = zco2+a22*y;
06446                                                         float yco3 = zco3+a23*y;
06447                                                         
06448                                                         float x = (float(i) - shiftxc)/scale;
06449                                                         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
06450                                                         float yold_big = yco2+a12*x-iys;
06451                                                         float zold_big = yco3+a13*x-izs;*/
06452                                                         
06453                                                                                                 
06454                                                         nq++;
06455                                                         
06456                                                                 
06457                                                         (*ret)(i,j,k) += Util::get_pixel_conv_new(nx, ny, nz, xold_big, yold_big, zold_big, data, kb);
06458                                                         
06459                                                         
06460                                                         if(nq == numst) break;
06461                                                 }
06462                                         }
06463                                         if(nq != numst)
06464                                                 throw InvalidValueException(nq, "Helicise: incorrect number of repeats encoutered.");
06465                                 }
06466                         }
06467                 }
06468         }
06469         
06470         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 ;
06471         set_array_offsets(saved_offsets);
06472         ret->update();
06473         return ret;
06474 }
06475 
06476 
06477 /*
06478 Purpose: Depad and remove FT extension from a real image.
06479 Method: Depad and remove FT extension from a real image.
06480 return new image.
06481 Input: f real n-dimensional image
06482 Output: depadded image
06483  */
06484 void EMData::depad() {
06485         if (is_complex())
06486                 throw ImageFormatException("Depadding of complex images not supported");
06487         vector<int> saved_offsets = get_array_offsets();
06488         set_array_offsets(0,0,0);
06489         int npad = attr_dict["npad"];
06490         if (0 == npad) npad = 1;
06491         int offset = is_fftodd() ? 1 : 2;
06492         int nxold = (nx - offset)/npad;
06493 #ifdef _WIN32
06494         int nyold = _cpp_max(ny/npad, 1);
06495         int nzold = _cpp_max(nz/npad, 1);
06496 #else
06497         int nyold = std::max<int>(ny/npad, 1);
06498         int nzold = std::max<int>(nz/npad, 1);
06499 #endif  //_WIN32
06500         int xstart = 0, ystart = 0, zstart = 0;
06501         if( npad > 1) {
06502                 xstart = (nx - offset - nxold)/2 + nxold%2;
06503                 if(ny > 1) {
06504                         ystart = (ny - nyold)/2 + nyold%2;
06505                         if(nz > 1) {
06506                                 zstart = (nz - nzold)/2 + nzold%2;
06507                         }
06508                 }
06509         }
06510         int bytes = nxold*sizeof(float);
06511         float* dest = get_data();
06512         for (int iz=0; iz < nzold; iz++) {
06513                 for (int iy = 0; iy < nyold; iy++) {
06514                         memmove(dest, &(*this)(xstart,iy+ystart,iz+zstart), bytes);
06515                         dest += nxold;
06516                 }
06517         }
06518         set_size(nxold, nyold, nzold);
06519         set_attr("npad", 1);
06520         set_fftpad(false);
06521         set_fftodd(false);
06522         set_complex(false);
06523         if(ny==1 && nz==1) set_complex_x(false);
06524         set_array_offsets(saved_offsets);
06525         update();
06526         EXITFUNC;
06527 }
06528 
06529 /*
06530 Purpose: Depad and remove FT extension from a real image.
06531 Method: Depad and remove FT extension from a real image.
06532 return new image.
06533 Input: f real n-dimensional image
06534 Output: depadded image
06535  */
06536 void EMData::depad_corner() {
06537         if(is_complex())
06538                 throw ImageFormatException("Depadding of complex images not allowed");
06539         vector<int> saved_offsets = get_array_offsets();
06540         set_array_offsets(0,0,0);
06541         int npad = attr_dict["npad"];
06542         if(0 == npad) npad = 1;
06543         int offset = is_fftodd() ? 1 : 2;
06544         int nxold = (nx - offset)/npad;
06545 #ifdef _WIN32
06546         int nyold = _cpp_max(ny/npad, 1);
06547         int nzold = _cpp_max(nz/npad, 1);
06548 #else
06549         int nyold = std::max<int>(ny/npad, 1);
06550         int nzold = std::max<int>(nz/npad, 1);
06551 #endif  //_WIN32
06552         size_t bytes = nxold*sizeof(float);
06553         float* dest = get_data();
06554         for (int iz=0; iz < nzold; iz++) {
06555                 for (int iy = 0; iy < nyold; iy++) {
06556                         memmove(dest, &(*this)(0,iy,iz), bytes);
06557                         dest += nxold;
06558                 }
06559         }
06560         set_size(nxold, nyold, nzold);
06561         set_attr("npad", 1);
06562         set_fftpad(false);
06563         set_fftodd(false);
06564         set_complex(false);
06565         if(ny==1 && nz==1) set_complex_x(false);
06566         set_array_offsets(saved_offsets);
06567         update();
06568         EXITFUNC;
06569 }
06570 
06571 
06572 // calculate circumference of the surrounding 1 pixel.
06573 float circumference( EMData* emdata, int npixel )
06574 {
06575         int nx = emdata->get_xsize();
06576         int ny = emdata->get_ysize();
06577         int nz = emdata->get_zsize();
06578 
06579         float* data = emdata->get_data();
06580         if( ny==1 && nz==1 ) {
06581                 // 1d case
06582                 float sumf=0.0;
06583                 int   sumn=0;
06584                 for( int i=0; i < npixel; ++i ) {
06585                         sumf += data[i];
06586                         sumf += data[nx-1-i];
06587                         sumn += 2;
06588                 }
06589                 return sumf/sumn;
06590         }
06591 
06592         if( nz==1 ) {
06593                 float sumf=0.0;
06594                 int   sumn=0;
06595                 int   id=0;
06596                 for( int iy=0; iy < ny; ++iy ) {
06597                         for( int ix=0; ix < nx; ++ix ) {
06598                                 if( iy<npixel || iy>ny-1-npixel || ix<npixel || ix>nx-1-npixel ) {
06599                                     sumf += data[id];
06600                                     sumn += 1;
06601                                 }
06602                                 id++;
06603                         }
06604                 }
06605 
06606                 Assert( id==nx*ny  );
06607                 Assert( sumn == nx*ny - (nx-2*npixel)*(ny-2*npixel) );
06608                 return sumf/sumn;
06609         }
06610 
06611         // 3d cases;
06612 
06613         float sumf = 0.0;
06614         size_t   sumn = 0;
06615         size_t   id = 0;
06616         for( int iz=0; iz < nz; ++iz) {
06617                 for( int iy=0; iy < ny; ++iy) {
06618                         for( int ix=0; ix < nx; ++ix ) {
06619                                 if( iz<npixel||iz>nz-1-npixel||iy<npixel||iy>ny-1-npixel||ix<npixel||ix>nx-1-npixel) {
06620                                         sumf += data[id];
06621                                         sumn += 1;
06622                                 }
06623                                 id++;
06624                         }
06625                 }
06626         }
06627 
06628 
06629         Assert( id==(size_t)nx*ny*nz);
06630         Assert( sumn==(size_t)nx*ny*nz-(size_t)(nx-2*npixel)*(ny-2*npixel)*(nz-2*npixel) );
06631         return sumf/sumn;
06632 }
06633 /*
06634 Purpose: Create a new [normalized] [zero-padded]  image.
06635 Method: Normalize, pad with zero or circumference, extend for fft,
06636 return new image.
06637 Input: f real n-dimensional image
06638 flag specify normalize, pad, and/or extend
06639 Output: zero-padded, ft-extended, normalized input image
06640  */
06641 EMData* EMData::norm_pad(bool donorm, int npad, int valtype) {
06642         if (this->is_complex())
06643                 throw ImageFormatException("Padding of complex images not supported");
06644         int nx = this->get_xsize();
06645         int ny = this->get_ysize();
06646         int nz = this->get_zsize();
06647         float mean = 0., stddev = 1.;
06648         if(donorm) { // Normalization requested
06649                 mean = this->get_attr("mean");
06650                 stddev = this->get_attr("sigma");
06651         }
06652         // sanity check
06653         if (npad < 1) npad = 1;
06654         int nxpad = npad*nx;
06655         int nypad = npad*ny;
06656         int nzpad = npad*nz;
06657         if (1 == ny) {
06658                 // 1-d image, don't want to pad along y or z
06659                 // Also, assuming that we can't have an image sized as nx=5, ny=1, nz=5.
06660                 nypad = ny;
06661                 nzpad = nz;
06662         } else if (nz == 1) {
06663                 // 2-d image, don't want to pad along z
06664                 nzpad = nz;
06665         }
06666         size_t bytes;
06667         size_t offset;
06668         // Not currently fft-extended, so we want to extend for ffts
06669         offset = 2 - nxpad%2;
06670         bytes = nx*sizeof(float);
06671         EMData* fpimage = copy_head();
06672         fpimage->set_size(nxpad+offset, nypad, nzpad);
06673         int xstart = 0, ystart = 0, zstart = 0;
06674         if( npad > 1) {
06675                 if( valtype==0 ) {
06676                         fpimage->to_zero();
06677                 } else {
06678                         float val = circumference(this, 1);
06679                         float* data = fpimage->get_data();
06680                         int nxyz = (nxpad+offset)*nypad*nzpad;
06681                         for( int i=0; i < nxyz; ++i )  data[i] = val;
06682                 }
06683 
06684                 xstart = (nxpad - nx)/2 + nx%2;
06685                 if(ny > 1) {
06686                         ystart = (nypad - ny)/2 + ny%2;
06687                         if(nz > 1) {
06688                                 zstart = (nzpad - nz)/2 + nz%2;
06689                         }
06690                 }
06691         }
06692 
06693 
06694         vector<int> saved_offsets = this->get_array_offsets();
06695         this->set_array_offsets( 0, 0, 0 );
06696         for (int iz = 0; iz < nz; iz++) {
06697                 for (int iy = 0; iy < ny; iy++) {
06698                         memcpy(&(*fpimage)(xstart,iy+ystart,iz+zstart), &(*this)(0,iy,iz), bytes);
06699                 }
06700         }
06701         this->set_array_offsets( saved_offsets );
06702 
06703 
06704         //  Perform the actual normalization (only on the
06705         //  non-zero section of the image)
06706         if (donorm) { // Normalization requested
06707                 for (int iz = zstart; iz < nz+zstart; iz++)
06708                         for (int iy = ystart; iy < ny+ystart; iy++)
06709                                 for (int ix = xstart; ix < nx+xstart; ix++)
06710                                         (*fpimage)(ix,iy,iz) = ((*fpimage)(ix,iy,iz)-mean)/stddev;
06711         }
06712 
06713         fpimage->set_fftpad(true);
06714         fpimage->set_attr("npad", npad);
06715         if (offset == 1) fpimage->set_fftodd(true);
06716         else             fpimage->set_fftodd(false);
06717         return fpimage;
06718 }
06719 
06720 void EMData::center_origin()
06721 {
06722         ENTERFUNC;
06723         if (is_complex()) {
06724                 LOGERR("Real image expected. Input image is complex.");
06725                 throw ImageFormatException("Real image expected. Input image is complex.");
06726         }
06727         for (int iz = 0; iz < nz; iz++) {
06728                 for (int iy = 0; iy < ny; iy++) {
06729                         for (int ix = 0; ix < nx; ix++) {
06730                                 // next line multiplies by +/- 1
06731                                 (*this)(ix,iy,iz) *= -2*((ix+iy+iz)%2) + 1;
06732                         }
06733                 }
06734         }
06735         update();
06736         EXITFUNC;
06737 }
06738 
06739 void EMData::center_origin_yz()
06740 {
06741         ENTERFUNC;
06742         if (is_complex()) {
06743                 LOGERR("Real image expected. Input image is complex.");
06744                 throw ImageFormatException("Real image expected. Input image is complex.");
06745         }
06746         for (int iz = 0; iz < nz; iz++) {
06747                 for (int iy = (iz+1)%2; iy < ny; iy+=2) {
06748                         for (int ix = 0; ix < nx; ix++) {
06749                                 (*this)(ix,iy,iz) *= -1;
06750                         }
06751                 }
06752         }
06753         update();
06754         EXITFUNC;
06755 }
06756 
06757 void EMData::center_origin_fft()
06758 {
06759         ENTERFUNC;
06760         if (!is_complex()) {
06761                 LOGERR("complex image expected. Input image is real image.");
06762                 throw ImageFormatException("complex image expected. Input image is real image.");
06763         }
06764 
06765         if (!is_ri()) {
06766                 LOGWARN("Only RI should be used. ");
06767         }
06768         vector<int> saved_offsets = get_array_offsets();
06769         // 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
06770         //                                                 and even, so we can ignore the difference...
06771         //                         in short, as nx is extended, it should be  ix in [0,(nx-2)/2],  corrected PAP 05/20
06772         set_array_offsets(0,1,1);
06773         int nxc = nx/2;
06774 
06775         if (is_fftodd()) {
06776                 for (int iz = 1; iz <= nz; iz++) {
06777                         for (int iy = 1; iy <= ny; iy++) {
06778                                 for (int ix = 0; ix < nxc; ix++) {
06779                                         cmplx(ix,iy,iz) *= float(-2*((ix+iy+iz)%2) + 1);
06780                                         float temp = float(iz-1+iy-1+ix)/float(ny)*M_PI;
06781                                         complex<float> temp2 = complex<float>(cos(temp), -sin(temp));
06782                                         cmplx(ix,iy,iz) *= temp2;
06783                                 }
06784                         }
06785                 }
06786         } else {
06787                 for (int iz = 1; iz <= nz; iz++) {
06788                         for (int iy = 1; iy <= ny; iy++) {
06789                                 for (int ix = 0; ix < nxc; ix++) {
06790                                         // next line multiplies by +/- 1
06791                                         cmplx(ix,iy,iz) *= float(-2*((ix+iy+iz)%2) + 1);
06792                                 }
06793                         }
06794                 }
06795         }
06796         set_array_offsets(saved_offsets);
06797         update();
06798         EXITFUNC;
06799 }
06800 
06801 
06802 #define  fint(i,j,k)  fint[(i-1) + ((j-1) + (k-1)*ny)*(size_t)lsd]
06803 #define  fout(i,j,k)  fout[(i-1) + ((j-1) + (k-1)*nyn)*(size_t)lsdn]
06804 EMData *EMData::FourInterpol(int nxn, int nyni, int nzni, bool RetReal) {
06805 
06806         int nyn, nzn, lsd, lsdn, inx, iny, inz;
06807         int i, j, k;
06808         if (is_complex())
06809                 throw ImageFormatException("Input image has to be real");
06810 
06811         if(ny > 1) {
06812                 nyn = nyni;
06813                 if(nz > 1) {
06814                         nzn = nzni;
06815                 }  else {
06816                         nzn = 1;
06817                 }
06818         } else {
06819                 nyn = 1; nzn = 1;
06820         }
06821         if(nxn<nx || nyn<ny || nzn<nz)  throw ImageDimensionException("Cannot reduce the image size");
06822         lsd = nx + 2 - nx%2;
06823         lsdn = nxn + 2 - nxn%2;
06824 //  do out of place ft
06825         EMData *temp_ft = do_fft();
06826         EMData *ret = this->copy();
06827         ret->set_size(lsdn, nyn, nzn);
06828         ret->to_zero();
06829         float *fout = ret->get_data();
06830         float *fint = temp_ft->get_data();
06831 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
06832 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
06833         float  sq2 = 1.0f/std::sqrt(2.0f);
06834         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
06835         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
06836         inx = nxn-nx; iny = nyn - ny; inz = nzn - nz;
06837         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);
06838         if(nyn>1) {
06839         //cout << "  " <<nxn<<"  " <<nyn<<" A " <<nzn<<endl;
06840                 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);
06841                 if(nzn>1) {
06842                         for (k=nz/2+2+inz; k<=nzn; k++) {
06843                                 for (j=1; j<=ny/2+1; j++) {
06844                                         for (i=1; i<=lsd; i++) {
06845                                                 fout(i,j,k)=fint(i,j,k-inz);
06846                                         }
06847                                 }
06848                                 for (j=ny/2+2+iny; j<=nyn; j++) {
06849                                         for (i=1; i<=lsd; i++) {
06850                                                 fout(i,j,k)=fint(i,j-iny,k-inz);
06851                                         }
06852                                 }
06853                         }
06854                 }
06855         }
06856 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
06857 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
06858 //       ELEMENT.
06859         if(nx%2 == 0 && inx !=0) {
06860                 for (k=1; k<=nzn; k++) {
06861                         for (j=1; j<=nyn; j++) {
06862                                 fout(nx+1,j,k) *= sq2;
06863                                 fout(nx+2,j,k) *= sq2;
06864                         }
06865                 }
06866                 if(nyn>1) {
06867                         for (k=1; k<=nzn; k++) {
06868                           for (i=1; i<=lsd; i++) {
06869                             fout(i,ny/2+1+iny,k) = sq2*fout(i,ny/2+1,k);
06870                             fout(i,ny/2+1,k) *= sq2;
06871                           }
06872                         }
06873                         if(nzn>1) {
06874                                 for (j=1; j<=nyn; j++) {
06875                                         for (i=1; i<=lsd; i++) {
06876                                                 fout(i,j,nz/2+1+inz) = sq2*fout(i,j,nz/2+1);
06877                                                 fout(i,j,nz/2+1) *= sq2;
06878                                         }
06879                                 }
06880                         }
06881                 }
06882         }
06883         ret->set_complex(true);
06884 /*
06885 //  For padding from odd to even dimension additional shift by 1 pixel is necessary.
06886         float  xshift = 0.f, yshift = 0.f, zshift = 0.f;
06887         int nyn2, nzn2;
06888         if(nxn > nx && nx%2 == 1)  xshift = 1.0f;
06889         if(ny > 1) {
06890                 if(nyn > ny && ny%2 == 1)  yshift = 1.0f;
06891                 nyn2 = nyn/2;
06892                 if(nz > 1) {
06893                         if(nzn > nz && nz%2 == 1)  zshift = 1.0f;
06894                         nzn2 = nzn/2;
06895                 }  else {
06896                         nzn2 = 0;
06897                 }
06898         } else {
06899                 nyn2 = 0; nzn2 = 0;
06900         }
06901         if(xshift == 1.0 || yshift == 1.0 || zshift == 1.0)  {
06902                 ret->set_array_offsets(1,1,1);
06903                 int  lsdn2 = lsd/2;
06904                 for (int iz = 1; iz <= nzn; iz++) {
06905                         int jz=iz-1; if(jz>nzn2) jz=jz-nzn;
06906                         for (int iy = 1; iy <= nyn; iy++) {
06907                                 int jy=iy-1; if(jy>nyn2) jy=jy-nyn;
06908                                 for (int ix = 1; ix <= lsdn2; ix++) {
06909                                         int jx=ix-1;
06910                                         ret->cmplx(ix,iy,iz) *=
06911                                         exp(-float(twopi)*iimag*(xshift*jx/nxn + yshift*jy/nyn+ zshift*jz/nzn));
06912                                 }
06913                         }
06914                 }
06915                 ret->set_array_offsets(0,0,0);
06916         }*/
06917         ret->set_ri(1);
06918         ret->set_fftpad(true);
06919         ret->set_attr("npad", 1);
06920         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
06921         if(RetReal) {
06922                 ret->do_ift_inplace();
06923                 ret->depad();
06924         }
06925         ret->update();
06926 
06927         /*Dict d1 = temp_ft->get_attr_dict();
06928         Dict d2 = ret->get_attr_dict();
06929         printf("-----------------Attribute Dict for temp_ft--------------\n");
06930         EMUtil::dump_dict(d1);
06931         printf("-----------------Attribute Dict for ret--------------\n");
06932         EMUtil::dump_dict(d2);*/
06933         delete temp_ft;
06934         temp_ft = 0;
06935         return ret;
06936 }
06937 
06938 EMData *EMData::FourTruncate(int nxn, int nyni, int nzni, bool RetReal) {
06939 
06940         int nyn, nzn, lsd, lsdn, inx, iny, inz;
06941         int i, j, k;
06942         float  *fint;
06943         EMData *temp_ft = NULL;
06944         //if (is_complex())
06945         //      throw ImageFormatException("Input image has to be real");
06946 
06947         if(ny > 1) {
06948                 nyn = nyni;
06949                 if(nz > 1) {
06950                         nzn = nzni;
06951                 }  else {
06952                         nzn = 1;
06953                 }
06954         } else {
06955                 nyn = 1; nzn = 1;
06956         }
06957         if (is_complex()) {
06958                 nx = nx - 2 + nx%2;
06959                 fint = get_data();
06960         } else {
06961                 //  do out of place ft
06962                 temp_ft = do_fft();
06963                 fint = temp_ft->get_data();
06964         }
06965         if(nxn>nx || nyn>ny || nzn>nz)  throw ImageDimensionException("Cannot increase the image size");
06966         lsd = nx + 2 - nx%2;
06967         lsdn = nxn + 2 - nxn%2;
06968         EMData *ret = this->copy_head();
06969         ret->set_size(lsdn, nyn, nzn);
06970         float *fout = ret->get_data();
06971 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
06972 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
06973         //float  sq2 = std::sqrt(2.0f);
06974         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
06975         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
06976         inx = nx - nxn;  iny = ny - nyn;  inz = nz - nzn;
06977         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);
06978         if(nyn>1) {
06979                 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);
06980                 if(nzn>1) {
06981                         for (k=nzn/2+2; k<=nzn; k++) {
06982                                 for (j=1; j<=nyn/2+1; j++) {
06983                                         for (i=1; i<=lsdn; i++) {
06984                                                 fout(i,j,k)=fint(i,j,k+inz);
06985                                         }
06986                                 }
06987                                 for (j=nyn/2+2; j<=nyn; j++) {
06988                                         for (i=1; i<=lsdn; i++) {
06989                                                 fout(i,j,k)=fint(i,j+iny,k+inz);
06990                                         }
06991                                 }
06992                         }
06993                 }
06994         }
06995 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
06996 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
06997 //       ELEMENT.
06998         /*
06999         if(nxn%2 == 0 && inx !=0) {
07000                 for (k=1; k<=nzn; k++) {
07001                         for (j=1; j<=nyn; j++) {
07002                                 fout(nxn+1,j,k) *= sq2;
07003                                 fout(nxn+2,j,k) *= sq2;
07004                         }
07005                 }
07006                 if(nyn>1) {
07007                         for (k=1; k<=nzn; k++) {
07008                           for (i=1; i<=lsdn; i++) {
07009                             fout(i,nyn/2+1+iny,k) = sq2*fout(i,nyn/2+1,k);
07010                             fout(i,nyn/2+1,k) *= sq2;
07011                           }
07012                         }
07013                         if(nzn>1) {
07014                                 for (j=1; j<=nyn; j++) {
07015                                         for (i=1; i<=lsdn; i++) {
07016                                                 fout(i,j,nzn/2+1+inz) = sq2*fout(i,j,nzn/2+1);
07017                                                 fout(i,j,nzn/2+1) *= sq2;
07018                                         }
07019                                 }
07020                         }
07021                 }
07022         }*/
07023         ret->set_complex(true);
07024         ret->set_ri(1);
07025         ret->set_fftpad(true);
07026         ret->set_attr("npad", 1);
07027         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07028         if(RetReal) {
07029                 ret->do_ift_inplace();
07030                 ret->depad();
07031         }
07032         ret->update();
07033 
07034         /*Dict d1 = temp_ft->get_attr_dict();
07035         Dict d2 = ret->get_attr_dict();
07036         printf("-----------------Attribute Dict for temp_ft--------------\n");
07037         EMUtil::dump_dict(d1);
07038         printf("-----------------Attribute Dict for ret--------------\n");
07039         EMUtil::dump_dict(d2);*/
07040         if (!is_complex()) {
07041                 delete temp_ft;
07042                 temp_ft = 0;
07043         }
07044         return ret;
07045 }
07046 /*
07047 EMData *EMData::FourInterpol_i(int nxn, int nyni, int nzni, bool RetReal) {
07048 
07049         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07050         int i, j, k;
07051 
07052         if(ny > 1) {
07053                 nyn = nyni;
07054                 if(nz > 1) {
07055                         nzn = nzni;
07056                 }  else {
07057                         nzn = 1;
07058                 }
07059         } else {
07060                 nyn = 1; nzn = 1;
07061         }
07062         if(nxn<nx || nyn<ny || nzn<nz)  throw ImageDimensionException("Cannot reduce the image size");
07063         lsd = nx-2 + 2 - nx%2;
07064         lsdn = nxn + 2 - nxn%2;
07065 //  do out of place ft
07066         EMData *temp_ft = this->copy();
07067         EMData *ret = this->copy();
07068         ret->set_size(lsdn, nyn, nzn);
07069         ret->to_zero();
07070         float *fout = ret->get_data();
07071         float *fint = temp_ft->get_data();
07072 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07073 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07074         float  sq2 = 1.0f/std::sqrt(2.0f);
07075         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
07076         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
07077         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07078         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);
07079         if(nyn>1) {
07080         //cout << "  " <<nxn<<"  " <<nyn<<" A " <<nzn<<endl;
07081                 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);
07082                 if(nzn>1) {
07083                         for (k=nz/2+2+inz; k<=nzn; k++) {
07084                                 for (j=1; j<=ny/2+1; j++) {
07085                                         for (i=1; i<=lsd; i++) {
07086                                                 fout(i,j,k)=fint(i,j,k-inz);
07087                                         }
07088                                 }
07089                                 for (j=ny/2+2+iny; j<=nyn; j++) {
07090                                         for (i=1; i<=lsd; i++) {
07091                                                 fout(i,j,k)=fint(i,j-iny,k-inz);
07092                                         }
07093                                 }
07094                         }
07095                 }
07096         }
07097 //       WEIGHTING FACTOR USED FOR EVEN NSAM. REQUIRED SINCE ADDING ZERO FOR
07098 //       INTERPOLATION WILL INTRODUCE A COMPLEX CONJUGATE FOR NSAM/2'TH
07099 //       ELEMENT.
07100         if(nx%2 == 0 && inx !=0) {
07101                 for (k=1; k<=nzn; k++) {
07102                         for (j=1; j<=nyn; j++) {
07103                                 fout(nx-2+1,j,k) *= sq2;
07104                                 fout(nx-2+2,j,k) *= sq2;
07105                         }
07106                 }
07107                 if(nyn>1) {
07108                         for (k=1; k<=nzn; k++) {
07109                           for (i=1; i<=lsd; i++) {
07110                             fout(i,ny/2+1+iny,k) = sq2*fout(i,ny/2+1,k);
07111                             fout(i,ny/2+1,k) *= sq2;
07112                           }
07113                         }
07114                         if(nzn>1) {
07115                                 for (j=1; j<=nyn; j++) {
07116                                         for (i=1; i<=lsd; i++) {
07117                                                 fout(i,j,nz/2+1+inz) = sq2*fout(i,j,nz/2+1);
07118                                                 fout(i,j,nz/2+1) *= sq2;
07119                                         }
07120                                 }
07121                         }
07122                 }
07123         }
07124         ret->set_complex(true);
07125         ret->set_ri(1);
07126         ret->set_fftpad(true);
07127         ret->set_attr("npad", 1);
07128         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07129         if(RetReal) {
07130                 ret->do_ift_inplace();
07131                 ret->depad();
07132         }
07133         ret->update();
07134 
07135         delete temp_ft;
07136         temp_ft = 0;
07137         return ret;
07138 }
07139 */
07140 
07141 EMData *EMData::Four_ds(int nxn, int nyni, int nzni, bool RetReal) {
07142 
07143         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07144         int i, j;
07145 
07146         if(ny > 1) {
07147                 nyn = nyni;
07148                 if(nz > 1) {
07149                         nzn = nzni;
07150                 }  else {
07151                         nzn = 1;
07152                 }
07153         } else {
07154                 nyn = 1; nzn = 1;
07155         }
07156         lsd = nx-2 + 2 - nx%2;
07157         lsdn = nxn + 2 - nxn%2;
07158 //  do out of place ft
07159         EMData *temp_ft = this->copy();
07160         EMData *ret = this->copy();
07161         ret->set_size(lsdn, nyn, nzn);
07162         ret->to_zero();
07163         float *fout = ret->get_data();
07164         float *fint = temp_ft->get_data();
07165 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07166 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07167 //      float  sq2 = 1.0f/std::sqrt(2.0f);
07168         float  anorm = (float) nxn* (float) nyn* (float) nzn/(float) nx/ (float) ny/ (float) nz;
07169         for (i = 0; i < lsd*ny*nz; i++)  fint[i] *= anorm;
07170         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07171         for (j=1; j<=nyn; j++)
07172                 for (i=1; i<=lsdn; i++)
07173                         fout(i,j,1)=fint((i-1)/2*4+2-i%2,j*2-1,1);
07174         ret->set_complex(true);
07175         ret->set_ri(1);
07176         //ret->set_fftpad(true);
07177         //ret->set_attr("npad", 1);
07178         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07179         if(RetReal) {
07180                 ret->do_ift_inplace();
07181                 ret->depad();
07182         }
07183         ret->update();
07184 
07185         delete temp_ft;
07186         temp_ft = 0;
07187         return ret;
07188 }
07189 
07190 EMData *EMData::Four_shuf_ds_cen_us(int nxn, int nyni, int, bool RetReal) {
07191 
07192         int nyn, nzn, lsd, lsdn, inx, iny, inz;
07193         int i, j;
07194 
07195         nyn = nyni;
07196         nzn = 1;
07197         lsd = nx;
07198         lsdn = nxn + 2 - nxn%2;
07199 
07200         EMData *temp_ft = this->copy();
07201         EMData *ret = this->copy();
07202         ret->set_size(lsdn, nyn, nzn);
07203         ret->to_zero();
07204         float *fout = ret->get_data();
07205         float *fint = temp_ft->get_data();
07206 //  TO KEEP EXACT VALUES ON THE ORIGINAL GRID ONE SHOULD USE
07207 //  SQ2     = 2.0. HOWEVER, TOTAL ENERGY WILL NOT BE CONSERVED
07208         float  sq2 = 1.0f/std::sqrt(2.0f);
07209 
07210         for (size_t i = 0; i < (size_t)lsd*ny*nz; i++)  fint[i] *= 4;
07211 
07212         inx = nxn-(nx-2); iny = nyn - ny; inz = nzn - nz;
07213         for (j=1; j<=ny/4; j++)
07214                 for (i=1; i<=(nx-2)/2+2; i++) {
07215                         int g = (i-1)/2+1;
07216                         if ((g+j)%2 == 0) {
07217                                 fout(i,j,1)=fint(g*4-2-i%2,j*2-1+ny/2,1);
07218                         } else {
07219                                 fout(i,j,1)=-fint(g*4-2-i%2,j*2-1+ny/2,1);
07220                         }
07221                 }
07222 
07223         for (j=ny/4+1; j<=ny/4+1; j++)
07224                 for (i=1; i<=(nx-2)/2+2; i++) {
07225                         int g = (i-1)/2+1;
07226                         if ((g+j)%2 == 0) {
07227                                 fout(i,j,1)=fint(g*4-2-i%2,j*2-1-ny/2,1);
07228                         } else {
07229                                 fout(i,j,1)=-fint(g*4-2-i%2,j*2-1-ny/2,1);
07230                         }
07231                 }
07232 
07233         for (j=ny/4+2; j<=ny/2; j++)
07234                 for (i=1; i<=(nx-2)/2+2; i++) {
07235                         int g = (i-1)/2+1;
07236                         if ((g+j)%2 == 0) {
07237                                 fout(i,j+ny/2,1)=fint(g*4-2-i%2,j*2-1-ny/2,1);
07238                         } else {
07239                                 fout(i,j+ny/2,1)=-fint(g*4-2-i%2,j*2-1-ny/2,1);
07240                         }
07241                 }
07242 
07243         if (nx%2 == 0) {
07244                 for (j=1; j<=nyn; j++) {
07245                         fout((nx-2)/2+1,j,1) *= sq2;
07246                         fout((nx-2)/2+2,j,1) *= sq2;
07247                 }
07248                 for (i=1; i<=lsd/2+1; i++) {
07249                         fout(i,ny/4+1+ny/2,1) = sq2*fout(i,ny/4+1,1);
07250                         fout(i,ny/4+1,1) *= sq2;
07251                 }
07252         }
07253 
07254         ret->set_complex(true);
07255         ret->set_ri(1);
07256 
07257         if (nxn%2 == 1) {ret->set_fftodd(true);} else {ret->set_fftodd(false);}
07258         if(RetReal) {
07259                 ret->do_ift_inplace();
07260                 ret->depad();
07261         }
07262         ret->update();
07263 
07264         delete temp_ft;
07265         temp_ft = 0;
07266         return ret;
07267 }
07268 
07269 #undef fint
07270 #undef fout
07271 
07272 #define  fint(jx,jy,jz)  fint[jx + (jy + jz*ny)*(size_t)nox]
07273 EMData *EMData::filter_by_image(EMData* image, bool RetReal) {
07274 
07275 
07276         bool   complex_input = this->is_complex();
07277         nx  = this->get_xsize();
07278         ny  = this->get_ysize();
07279         nz  = this->get_zsize();
07280         int nox;
07281         if (complex_input) nox = (nx - 2 + this->is_fftodd()); else nox = nx;
07282 
07283         int lsd2 = (nox + 2 - nox%2) / 2; // Extended x-dimension of the complex image
07284 
07285         EMData* fp = NULL; // output image
07286         if(complex_input) {
07287                 // fimage must remain pristine
07288                 fp = this->copy();
07289         } else {
07290                 fp = this->norm_pad( false, 1);
07291                 fp->do_fft_inplace();
07292         }
07293         fp->set_array_offsets(1,1,1);
07294         int nx2 = nox/2;
07295         int ny2 = ny/2;
07296         int nz2 = nz/2;
07297         float *fint = image->get_data();
07298         for ( int iz = 1; iz <= nz; iz++) {
07299                 int jz=nz2-iz+1; if(jz<0) jz += nz;
07300                 for ( int iy = 1; iy <= ny; iy++) {
07301                         int jy=ny2-iy+1; if(jy<0) jy += ny;
07302                         for ( int ix = 1; ix <= lsd2; ix++) {
07303                                 int jx = nx2-ix+1;
07304                                 fp->cmplx(ix,iy,iz) *= fint(jx,jy,jz);
07305                         }
07306                 }
07307         }
07308 
07309         fp->set_ri(1);
07310         fp->set_fftpad(true);
07311         fp->set_attr("npad", 1);
07312         if (nx%2 == 1) fp->set_fftodd(true);
07313         else fp->set_fftodd(false);
07314         if(RetReal) {
07315                 fp->do_ift_inplace();
07316                 fp->depad();
07317         }
07318         fp->set_array_offsets(0,0,0);
07319         fp->update();
07320 
07321         return fp;
07322 }
07323 #undef   fint
07324 #define  fint(jx,jy,jz)  fint[jx + (jy + jz*ny)*(size_t)nx]
07325 #define  fout(jx,jy,jz)  fout[jx + (jy + jz*ny)*(size_t)nx]
07326 EMData *EMData::replace_amplitudes(EMData* image, bool RetReal) {
07327 
07328 
07329         bool   complex_input = this->is_complex();
07330         nx  = this->get_xsize();
07331         ny  = this->get_ysize();
07332         nz  = this->get_zsize();
07333         int nox;
07334         if (complex_input) nox = (nx - 2 + this->is_fftodd()); else nox = nx;
07335 
07336         EMData* fp = NULL; // output image
07337         if(complex_input) {
07338                 // fimage must remain pristine
07339                 fp = this->copy();
07340         } else {
07341                 fp = this->norm_pad( false, 1);
07342                 fp->do_fft_inplace();
07343         }
07344         float *fout = fp->get_data();
07345         float *fint = image->get_data();
07346         for ( int iz = 0; iz < nz; iz++) {
07347                 for ( int iy = 0; iy < ny; iy++) {
07348                         for ( int ix = 0; ix < nx; ix+=2) {
07349                                 float qt = fint(ix,iy,iz)*fint(ix,iy,iz)+fint(ix+1,iy,iz)*fint(ix+1,iy,iz);
07350                                 float rt = fout(ix,iy,iz)*fout(ix,iy,iz)+fout(ix+1,iy,iz)*fout(ix+1,iy,iz);
07351                                 if(rt > 1.0e-20) {
07352                                                 fout(ix,iy,iz) *= (qt/rt);
07353                                                 fout(ix+1,iy,iz) *= (qt/rt);
07354                                 } else {
07355                                                 qt = std::sqrt(qt/2.0f);
07356                                                 fout(ix,iy,iz) = qt;
07357                                                 fout(ix+1,iy,iz) = qt;
07358                                 }
07359                         }
07360                 }
07361         }
07362 
07363         fp->set_ri(1);
07364         fp->set_fftpad(true);
07365         fp->set_attr("npad", 1);
07366         if (nx%2 == 1) fp->set_fftodd(true);
07367         else fp->set_fftodd(false);
07368         if(RetReal) {
07369                 fp->do_ift_inplace();
07370                 fp->depad();
07371         }
07372         fp->set_array_offsets(0,0,0);
07373         fp->update();
07374 
07375         return fp;
07376 }
07377 #undef fint
07378 #undef fout
07379 
07380 
07381 #undef QUADPI
07382 #undef DGR_TO_RAD

Generated on Thu Nov 17 12:43:45 2011 for EMAN2 by  doxygen 1.3.9.1