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emdata_transform.cpp

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00001 
00005 /*
00006  * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
00007  * Copyright (c) 2000-2006 Baylor College of Medicine
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 "emdata.h"
00037 #include "emfft.h"
00038 
00039 #include <cstring>
00040 #include <cstdio>
00041 
00042 #include  "gsl_sf_result.h"
00043 #include  "gsl_sf_bessel.h"
00044 #include <iostream>
00045 #include <algorithm>
00046 #include <vector>
00047 #include <utility>
00048 #include <cmath>
00049 #include "util.h"
00050 
00051 //#ifdef EMAN2_USING_CUDA
00052 //#include "cuda/cuda_processor.h"
00053 //#endif
00054 
00055 using namespace EMAN;
00056 using namespace std;
00057 typedef vector< pair<float,int> > vp;
00058 
00059 EMData *EMData::do_fft() const
00060 {
00061         ENTERFUNC;
00062 
00063         if (is_complex() ) { // ming add 08/17/2010
00064 #ifdef NATIVE_FFT
00065                 LOGERR(" NATIVE_FFT does not supported complex to complex.");  // PAP
00066                 throw ImageFormatException("real image expected. Input image is complex image.");
00067 #else
00068                 EMData *temp_in=copy();
00069                 EMData *dat= copy_head();
00070                 int offset;
00071                 if(is_fftpadded()) {
00072                         offset = is_fftodd() ? 1 : 2;
00073                 }
00074                 else offset=0;
00075                 //printf("offset=%d\n",offset);
00076                 EMfft::complex_to_complex_nd(temp_in->get_data(),dat->get_data(),nx-offset,ny,nz);
00077 
00078                 if(dat->get_ysize()==1 && dat->get_zsize()==1) dat->set_complex_x(true);
00079 
00080                 dat->update();
00081                 delete temp_in;
00082                 EXITFUNC;
00083                 return dat;
00084 #endif // NATIVE_FFT
00085         } else {
00086                 int nxreal = nx;
00087                 int offset = 2 - nx%2;
00088                 int nx2 = nx + offset;
00089                 EMData* dat = copy_head();
00090                 dat->set_size(nx2, ny, nz);
00091                 //dat->to_zero();  // do not need it, real_to_complex will do it right anyway
00092                 if (offset == 1) dat->set_fftodd(true);
00093                 else             dat->set_fftodd(false);
00094 
00095                 float *d = dat->get_data();
00096                 //std::cout<<" do_fft "<<rdata[5]<<"  "<<d[5]<<std::endl;
00097                 EMfft::real_to_complex_nd(get_data(), d, nxreal, ny, nz);
00098 
00099                 dat->update();
00100                 dat->set_fftpad(true);
00101                 dat->set_complex(true);
00102                 if(dat->get_ysize()==1 && dat->get_zsize()==1) dat->set_complex_x(true);
00103                 dat->set_ri(true);
00104 
00105                 EXITFUNC;
00106                 return dat;
00107         }
00108 }
00109 
00110 EMData *EMData::do_fft_inplace()
00111 {
00112         ENTERFUNC;
00113 
00114         if ( is_complex() ) {
00115                 LOGERR("real image expected. Input image is complex image.");
00116                 throw ImageFormatException("real image expected. Input image is complex image.");
00117         }
00118 
00119         size_t offset;
00120         int nxreal;
00121         get_data(); // Required call if GPU caching is being used. Otherwise harmless
00122         if (!is_fftpadded()) {
00123                 // need to extend the matrix along x
00124                 // meaning nx is the un-fftpadded size
00125                 nxreal = nx;
00126                 offset = 2 - nx%2;
00127                 if (1 == offset) set_fftodd(true);
00128                 else             set_fftodd(false);
00129                 int nxnew = nx + offset;
00130                 set_size(nxnew, ny, nz);
00131                 for (int iz = nz-1; iz >= 0; iz--) {
00132                         for (int iy = ny-1; iy >= 0; iy--) {
00133                                 for (int ix = nxreal-1; ix >= 0; ix--) {
00134                                         size_t oldxpos = ix + (iy + iz*ny)*(size_t)nxreal;
00135                                         size_t newxpos = ix + (iy + iz*ny)*(size_t)nxnew;
00136                                         (*this)(newxpos) = (*this)(oldxpos);
00137                                 }
00138                         }
00139                 }
00140                 set_fftpad(true);
00141         } else {
00142                 offset = is_fftodd() ? 1 : 2;
00143                 nxreal = nx - offset;
00144         }
00145         EMfft::real_to_complex_nd(rdata, rdata, nxreal, ny, nz);
00146 
00147         set_complex(true);
00148         if(ny==1 && nz==1)  set_complex_x(true);
00149         set_ri(true);
00150 
00151         update();
00152 
00153         EXITFUNC;
00154         return this;
00155 }
00156 
00157 #ifdef EMAN2_USING_CUDA
00158 
00159 #include "cuda/cuda_emfft.h"
00160 
00161 EMData *EMData::do_fft_cuda()
00162 {
00163         ENTERFUNC;
00164 
00165         if ( is_complex() ) {
00166                 LOGERR("real image expected. Input image is complex image.");
00167                 throw ImageFormatException("real image expected. Input image is complex image.");
00168         }
00169 
00170         int offset = 2 - nx%2;
00171         EMData* dat = new EMData(0,0,nx+offset,ny,nz,attr_dict);
00172         if(!dat->rw_alloc()) throw UnexpectedBehaviorException("Bad alloc");
00173         //cout << "Doing CUDA FFT " << cudarwdata << endl;
00174         if(cudarwdata == 0){copy_to_cuda();}
00175         cuda_dd_fft_real_to_complex_nd(cudarwdata, dat->cudarwdata, nx, ny,nz, 1);
00176 
00177         if (offset == 1) dat->set_fftodd(true);
00178         else             dat->set_fftodd(false);
00179 
00180         dat->set_fftpad(true);
00181         dat->set_complex(true);
00182         if(dat->get_ysize()==1 && dat->get_zsize()==1) dat->set_complex_x(true);
00183         dat->set_ri(true);
00184         dat->update();
00185 
00186         EXITFUNC;
00187         return dat;
00188 }
00189 
00190 EMData *EMData::do_fft_inplace_cuda()
00191 {
00192         ENTERFUNC;
00193 
00194         if ( is_complex() ) {
00195                 LOGERR("real image expected. Input image is complex image.");
00196                 throw ImageFormatException("real image expected. Input image is complex image.");
00197         }
00198 
00199         int offset = 2 - nx%2;
00200         float* tempcudadata = 0;
00201         cudaError_t error = cudaMalloc((void**)&tempcudadata,(nx + offset)*ny*nz*sizeof(float));
00202         if( error != cudaSuccess) throw ImageFormatException("Couldn't allocate memory.");
00203         
00204         //cout << "Doing CUDA FFT inplace" << cudarwdata << endl;
00205         if(cudarwdata == 0){copy_to_cuda();}
00206         cuda_dd_fft_real_to_complex_nd(cudarwdata, tempcudadata, nx, ny,nz, 1);
00207         // this section is a bit slight of hand it actually does the FFT out of place but this avoids and EMData object creation and detruction...
00208         cudaError_t ferror = cudaFree(cudarwdata);
00209         if ( ferror != cudaSuccess) throw UnexpectedBehaviorException( "CudaFree failed:" + string(cudaGetErrorString(error)));
00210         cudarwdata = tempcudadata;
00211         num_bytes = (nx + offset)*ny*nz*sizeof(float);
00212 
00213         if (offset == 1) set_fftodd(true);
00214         else             set_fftodd(false);
00215 
00216         nx = nx + offset; // don't want to call set_size b/c that will delete my cudadata, remember what I am doing is a bit slignt of hand....
00217         set_fftpad(true);
00218         set_complex(true);
00219         if(get_ysize()==1 && get_zsize()==1) set_complex_x(true);
00220         set_ri(true);
00221         update();
00222 
00223         EXITFUNC;
00224         return this;
00225 }
00226 
00227 EMData *EMData::do_ift_cuda()
00228 {
00229         ENTERFUNC;
00230 
00231         if (!is_complex()) {
00232                 LOGERR("complex image expected. Input image is real image.");
00233                 throw ImageFormatException("complex image expected. Input image is real image.");
00234         }
00235 
00236         if (!is_ri()) {
00237                 throw ImageFormatException("complex ri expected. Got amplitude/phase.");
00238         }
00239 
00240         int offset = is_fftodd() ? 1 : 2;
00241         EMData* dat = new EMData(0,0,nx-offset,ny,nz,attr_dict);
00242         if(!dat->rw_alloc()) throw UnexpectedBehaviorException("Bad alloc");
00243         
00244         if(cudarwdata == 0){copy_to_cuda();}
00245 
00246         
00247         int ndim = get_ndim();
00248         if ( ndim == 1 ) {
00249                 cuda_dd_fft_complex_to_real_nd(cudarwdata,dat->cudarwdata, nx-offset,1,1,1);
00250         } else if (ndim == 2) {
00251                 cuda_dd_fft_complex_to_real_nd(cudarwdata,dat->cudarwdata, ny,nx-offset,1,1);
00252         } else if (ndim == 3) {
00253                 cuda_dd_fft_complex_to_real_nd(cudarwdata,dat->cudarwdata, nz,ny,nx-offset,1);
00254         } else throw ImageDimensionException("No cuda FFT support of images with dimensions exceeding 3");
00255         
00256         // SCALE the inverse FFT
00257         float scale = 1.0f/static_cast<float>((dat->get_size()));
00258         dat->mult(scale); 
00259 
00260         dat->set_fftpad(false);
00261         dat->set_fftodd(false);
00262         dat->set_complex(false);
00263         if(dat->get_ysize()==1 && dat->get_zsize()==1)  dat->set_complex_x(false);
00264         dat->set_ri(false);
00265 //      dat->gpu_update();
00266         dat->update(); 
00267         
00268         EXITFUNC;
00269         return dat;
00270 }
00271 
00272 /*
00273    FFT in place does not depad, hence this routine is of limited use b/c mem operations on the device are quite SLOW, JFF
00274    use
00275 */
00276 
00277 EMData *EMData::do_ift_inplace_cuda()
00278 {
00279         ENTERFUNC;
00280 
00281         if (!is_complex()) {
00282                 LOGERR("complex image expected. Input image is real image.");
00283                 throw ImageFormatException("complex image expected. Input image is real image.");
00284         }
00285 
00286         if (!is_ri()) {
00287                 LOGWARN("run IFT on AP data, only RI should be used. ");
00288         }
00289 
00290         int offset = is_fftodd() ? 1 : 2;
00291         
00292         if(cudarwdata == 0){copy_to_cuda();}
00293         
00294         int ndim = get_ndim();
00295         if ( ndim == 1 ) {
00296                 cuda_dd_fft_complex_to_real_nd(cudarwdata,cudarwdata, nx-offset,1,1,1);
00297         } else if (ndim == 2) {
00298                 cuda_dd_fft_complex_to_real_nd(cudarwdata,cudarwdata, ny,nx-offset,1,1);
00299         } else if (ndim == 3) {
00300                 cuda_dd_fft_complex_to_real_nd(cudarwdata,cudarwdata, nz,ny,nx-offset,1);
00301         } else throw ImageDimensionException("No cuda FFT support of images with dimensions exceeding 3");
00302 #if defined     FFTW2 || defined FFTW3 //native fft and ACML already done normalization
00303         // SCALE the inverse FFT
00304         int nxo = nx - offset;
00305         float scale = 1.0f / (nxo * ny * nz);
00306         mult(scale); //if we are just doing a CCF, this is a waste!
00307 #endif //FFTW2 || FFTW3
00308 
00309         set_fftpad(true);
00310         set_complex(false);
00311 
00312         if(ny==1 && nz==1) set_complex_x(false);
00313         set_ri(false);
00314         update();
00315         
00316         EXITFUNC;
00317         return this;
00318 }
00319 
00320 #endif //EMAN2_USING_CUDA
00321 
00322 EMData *EMData::do_ift()
00323 {
00324         ENTERFUNC;
00325 
00326         if (!is_complex()) {
00327                 LOGERR("complex image expected. Input image is real image.");
00328                 throw ImageFormatException("complex image expected. Input image is real image.");
00329         }
00330 
00331         if (!is_ri()) {
00332                 LOGWARN("run IFT on AP data, only RI should be used. Converting.");
00333         }
00334 
00335         get_data(); // Required call if GPU caching is being used. Otherwise harmless
00336         EMData* dat = copy_head();
00337         dat->set_size(nx, ny, nz);
00338         ap2ri();
00339 
00340         float *d = dat->get_data();
00341         int ndim = get_ndim();
00342 
00343         /* Do inplace IFT on a image copy, because the complex to real transform of
00344          * nd will destroy its input array even for out-of-place transforms.
00345          */
00346         memcpy((char *) d, (char *) rdata, (size_t)nx * ny * nz * sizeof(float));
00347 
00348         int offset = is_fftodd() ? 1 : 2;
00349         //cout << "Sending offset " << offset << " " << nx-offset << endl;
00350         if (ndim == 1) {
00351                 EMfft::complex_to_real_nd(d, d, nx - offset, ny, nz);
00352         } else {
00353                 EMfft::complex_to_real_nd(d, d, nx - offset, ny, nz);
00354 
00355                 size_t row_size = (nx - offset) * sizeof(float);
00356                 for (size_t i = 1; i < (size_t)ny * nz; i++) {
00357                         memmove((char *) &d[i * (nx - offset)], (char *) &d[i * nx], row_size);
00358                 }
00359         }
00360 
00361         dat->set_size(nx - offset, ny, nz);     //remove the padding
00362 #if defined     FFTW2 || defined FFTW3 //native fft and ACML already done normalization
00363         // SCALE the inverse FFT
00364         float scale = 1.0f / ((nx - offset) * ny * nz);
00365         dat->mult(scale);
00366 #endif  //FFTW2 || FFTW3
00367         dat->set_fftodd(false);
00368         dat->set_fftpad(false);
00369         dat->set_complex(false);
00370         if(dat->get_ysize()==1 && dat->get_zsize()==1)  dat->set_complex_x(false);
00371         dat->set_ri(false);
00372         dat->update();
00373 
00374 
00375         EXITFUNC;
00376         return dat;
00377 }
00378 
00379 /*
00380    FFT in place does not depad, return real x-extended image (needs to be depadded before use as PAP does in CCF routines)
00381    use
00382 */
00383 EMData *EMData::do_ift_inplace()
00384 {
00385         ENTERFUNC;
00386 
00387         if (!is_complex()) {
00388                 LOGERR("complex image expected. Input image is real image.");
00389                 throw ImageFormatException("complex image expected. Input image is real image.");
00390         }
00391 
00392         if (!is_ri()) {
00393                 LOGWARN("run IFT on AP data, only RI should be used. ");
00394         }
00395         ap2ri();
00396 
00397         int offset = is_fftodd() ? 1 : 2;
00398         float* data = get_data();
00399         EMfft::complex_to_real_nd(data, data, nx - offset, ny, nz);
00400 
00401 #if defined     FFTW2 || defined FFTW3  //native fft and ACML already done normalization
00402         // SCALE the inverse FFT
00403         int nxo = nx - offset;
00404         float scale = 1.0f / ((size_t)nxo * ny * nz);
00405         mult(scale);
00406 #endif //FFTW2 || FFTW3
00407 
00408         set_fftpad(true);
00409         set_complex(false);
00410         if(ny==1 && nz==1) set_complex_x(false);
00411         set_ri(false);
00412         update();
00413 
00414         EXITFUNC;
00415         return this;
00416 }
00417 #undef rdata
00418 
00419 
00420 std::string EMData::render_ap24(int x0, int y0, int ixsize, int iysize,
00421                                                  int bpl, float scale, int mingray, int maxgray,
00422                                                  float render_min, float render_max,float gamma,int flags)
00423 {
00424         ENTERFUNC;
00425 
00426         int asrgb;
00427         int hist=(flags&2)/2;
00428         int invy=(flags&4)?1:0;
00429 
00430         if (!is_complex()) throw ImageDimensionException("complex only");
00431 
00432         if (get_ndim() != 2) {
00433                 throw ImageDimensionException("2D only");
00434         }
00435 
00436         if (is_complex()) ri2ap();
00437 
00438         if (render_max <= render_min) {
00439                 render_max = render_min + 0.01f;
00440         }
00441 
00442         if (gamma<=0) gamma=1.0;
00443 
00444         // Calculating a full floating point gamma for
00445         // each pixel in the image slows rendering unacceptably
00446         // however, applying a gamma-mapping to an 8 bit colorspace
00447         // has unaccepable accuracy. So, we oversample the 8 bit colorspace
00448         // as a 12 bit colorspace and apply the gamma mapping to that
00449         // This should produce good accuracy for gamma values
00450         // larger than 0.5 (and a high upper limit)
00451         static int smg0=0,smg1=0;       // while this destroys threadsafety in the rendering process
00452         static float sgam=0;            // it is necessary for speed when rendering large numbers of small images
00453         static unsigned char gammamap[4096];
00454         if (gamma!=1.0 && (smg0!=mingray || smg1!=maxgray || sgam!=gamma)) {
00455                 for (int i=0; i<4096; i++) {
00456                         if (mingray<maxgray) gammamap[i]=(unsigned char)(mingray+(maxgray-mingray+0.999)*pow(((float)i/4096.0f),gamma));
00457                         else gammamap[4095-i]=(unsigned char)(mingray+(maxgray-mingray+0.999)*pow(((float)i/4096.0f),gamma));
00458                 }
00459         }
00460         smg0=mingray;   // so we don't recompute the map unless something changes
00461         smg1=maxgray;
00462         sgam=gamma;
00463 
00464         if (flags&8) asrgb=4;
00465         else if (flags&1) asrgb=3;
00466         else throw ImageDimensionException("must set flag 1 or 8");
00467 
00468         std::string ret=std::string();
00469 //      ret.resize(iysize*bpl);
00470         ret.assign(iysize*bpl+hist*1024,char(mingray));
00471         unsigned char *data=(unsigned char *)ret.data();
00472         unsigned int *histd=(unsigned int *)(data+iysize*bpl);
00473         if (hist) {
00474                 for (int i=0; i<256; i++) histd[i]=0;
00475         }
00476 
00477         float rm = render_min;
00478         float inv_scale = 1.0f / scale;
00479         int ysize = iysize;
00480         int xsize = ixsize;
00481 
00482         int ymin = 0;
00483         if (iysize * inv_scale > ny) {
00484                 ymin = (int) (iysize - ny / inv_scale);
00485         }
00486 
00487         float gs = (maxgray - mingray) / (render_max - render_min);
00488         float gs2 = 4095.999f / (render_max - render_min);
00489 //      float gs2 = 1.0 / (render_max - render_min);
00490         if (render_max < render_min) {
00491                 gs = 0;
00492                 rm = FLT_MAX;
00493         }
00494 
00495         int dsx = -1;
00496         int dsy = 0;
00497         int remx = 0;
00498         int remy = 0;
00499         const int scale_n = 100000;
00500 
00501         int addi = 0;
00502         int addr = 0;
00503         if (inv_scale == floor(inv_scale)) {
00504                 dsx = (int) inv_scale;
00505                 dsy = (int) (inv_scale * nx);
00506         }
00507         else {
00508                 addi = (int) floor(inv_scale);
00509                 addr = (int) (scale_n * (inv_scale - floor(inv_scale)));
00510         }
00511 
00512         int xmin = 0;
00513         if (x0 < 0) {
00514                 xmin = (int) (-x0 / inv_scale);
00515                 xsize -= (int) floor(x0 / inv_scale);
00516                 x0 = 0;
00517         }
00518 
00519         if ((xsize - xmin) * inv_scale > (nx - x0)) {
00520                 xsize = (int) ((nx - x0) / inv_scale + xmin);
00521         }
00522         int ymax = ysize - 1;
00523         if (y0 < 0) {
00524                 ymax = (int) (ysize + y0 / inv_scale - 1);
00525                 ymin += (int) floor(y0 / inv_scale);
00526                 y0 = 0;
00527         }
00528 
00529         if (xmin < 0) xmin = 0;
00530         if (ymin < 0) ymin = 0;
00531         if (xsize > ixsize) xsize = ixsize;
00532         if (ymax > iysize) ymax = iysize;
00533 
00534         int lmax = nx * ny - 1;
00535 
00536         int mid=nx*ny/2;
00537         float* image_data = get_data();
00538         if (dsx != -1) {
00539                 int l = y0 * nx;
00540                 for (int j = ymax; j >= ymin; j--) {
00541                         int ll = x0;
00542                         for (int i = xmin; i < xsize; i++) {
00543                                 if (l + ll > lmax || ll >= nx - 2) break;
00544 
00545                                 int k = 0;
00546                                 unsigned char p;
00547                                 int ph;
00548                                 if (ll >= nx / 2) {
00549                                         if (l >= (ny - inv_scale) * nx) k = 2 * (ll - nx / 2) + 2;
00550                                         else k = 2 * (ll - nx / 2) + l + 2 + nx;
00551                                         if (k>=mid) k-=mid;             // These 2 lines handle the Fourier origin being in the corner, not the middle
00552                                         else k+=mid;
00553                                         ph = (int)(image_data[k+1]*768/(2.0*M_PI))+384; // complex phase as integer 0-767
00554                                 }
00555                                 else {
00556                                         k = nx * ny - (l + 2 * ll) - 2;
00557                                         ph = (int)(-image_data[k+1]*768/(2.0*M_PI))+384;        // complex phase as integer 0-767
00558                                         if (k>=mid) k-=mid;             // These 2 lines handle the Fourier origin being in the corner, not the middle
00559                                         else k+=mid;
00560                                 }
00561                                 float t = image_data[k];
00562                                 if (t <= rm)  p = mingray;
00563                                 else if (t >= render_max) p = maxgray;
00564                                 else if (gamma!=1.0) {
00565                                         k=(int)(gs2 * (t-render_min));          // map float value to 0-4096 range
00566                                         p = gammamap[k];                                        // apply gamma using precomputed gamma map
00567                                 }
00568                                 else {
00569                                         p = (unsigned char) (gs * (t - render_min));
00570                                         p += mingray;
00571                                 }
00572                                 if (ph<256) {
00573                                         data[i * asrgb + j * bpl] = p*(255-ph)/256;
00574                                         data[i * asrgb + j * bpl+1] = p*ph/256;
00575                                         data[i * asrgb + j * bpl+2] = 0;
00576                                 }
00577                                 else if (ph<512) {
00578                                         data[i * asrgb + j * bpl+1] = p*(511-ph)/256;
00579                                         data[i * asrgb + j * bpl+2] = p*(ph-256)/256;
00580                                         data[i * asrgb + j * bpl] = 0;
00581                                 }
00582                                 else {
00583                                         data[i * asrgb + j * bpl+2] = p*(767-ph)/256;
00584                                         data[i * asrgb + j * bpl] = p*(ph-512)/256;
00585                                         data[i * asrgb + j * bpl+1] = 0;
00586                                 }
00587                                 if (hist) histd[p]++;
00588                                 ll += dsx;
00589                         }
00590                         l += dsy;
00591                 }
00592         }
00593         else {
00594                 remy = 10;
00595                 int l = y0 * nx;
00596                 for (int j = ymax; j >= ymin; j--) {
00597                         int br = l;
00598                         remx = 10;
00599                         int ll = x0;
00600                         for (int i = xmin; i < xsize - 1; i++) {
00601                                 if (l + ll > lmax || ll >= nx - 2) {
00602                                         break;
00603                                 }
00604                                 int k = 0;
00605                                 unsigned char p;
00606                                 int ph;
00607                                 if (ll >= nx / 2) {
00608                                         if (l >= (ny * nx - nx)) k = 2 * (ll - nx / 2) + 2;
00609                                         else k = 2 * (ll - nx / 2) + l + 2 + nx;
00610                                         if (k>=mid) k-=mid;             // These 2 lines handle the Fourier origin being in the corner, not the middle
00611                                         else k+=mid;
00612                                         ph = (int)(image_data[k+1]*768/(2.0*M_PI))+384; // complex phase as integer 0-767
00613                                 }
00614                                 else {
00615                                         k = nx * ny - (l + 2 * ll) - 2;
00616                                         if (k>=mid) k-=mid;             // These 2 lines handle the Fourier origin being in the corner, not the middle
00617                                         else k+=mid;
00618                                         ph = (int)(-image_data[k+1]*768/(2.0*M_PI))+384;        // complex phase as integer 0-767
00619                                 }
00620 
00621                                 float t = image_data[k];
00622                                 if (t <= rm)
00623                                         p = mingray;
00624                                 else if (t >= render_max) {
00625                                         p = maxgray;
00626                                 }
00627                                 else if (gamma!=1.0) {
00628                                         k=(int)(gs2 * (t-render_min));          // map float value to 0-4096 range
00629                                         p = gammamap[k];                                        // apply gamma using precomputed gamma map
00630                                 }
00631                                 else {
00632                                         p = (unsigned char) (gs * (t - render_min));
00633                                         p += mingray;
00634                                 }
00635                                 if (ph<256) {
00636                                         data[i * asrgb + j * bpl] = p*(255-ph)/256;
00637                                         data[i * asrgb + j * bpl+1] = p*ph/256;
00638                                         data[i * asrgb + j * bpl+2] = 0;
00639                                 }
00640                                 else if (ph<512) {
00641                                         data[i * asrgb + j * bpl+1] = p*(511-ph)/256;
00642                                         data[i * asrgb + j * bpl+2] = p*(ph-256)/256;
00643                                         data[i * asrgb + j * bpl] = 0;
00644                                 }
00645                                 else {
00646                                         data[i * asrgb + j * bpl+2] = p*(767-ph)/256;
00647                                         data[i * asrgb + j * bpl] = p*(ph-512)/256;
00648                                         data[i * asrgb + j * bpl+1] = 0;
00649                                 }
00650                                 if (hist) histd[p]++;
00651                                 ll += addi;
00652                                 remx += addr;
00653                                 if (remx > scale_n) {
00654                                         remx -= scale_n;
00655                                         ll++;
00656                                 }
00657                         }
00658                         l = br + addi * nx;
00659                         remy += addr;
00660                         if (remy > scale_n) {
00661                                 remy -= scale_n;
00662                                 l += nx;
00663                         }
00664                 }
00665         }
00666 
00667         // this replicates r -> g,b
00668         if (asrgb==4) {
00669                 for (int j=ymin*bpl; j<=ymax*bpl; j+=bpl) {
00670                         for (int i=xmin; i<xsize*4; i+=4) {
00671                                 data[i+j+3]=255;
00672                         }
00673                 }
00674         }
00675 
00676         EXITFUNC;
00677 
00678         // ok, ok, not the most efficient place to do this, but it works
00679         if (invy) {
00680                 int x,y;
00681                 char swp;
00682                 for (y=0; y<iysize/2; y++) {
00683                         for (x=0; x<ixsize; x++) {
00684                                 swp=ret[y*bpl+x];
00685                                 ret[y*bpl+x]=ret[(iysize-y-1)*bpl+x];
00686                                 ret[(iysize-y-1)*bpl+x]=swp;
00687                         }
00688                 }
00689         }
00690 
00691     //  return PyString_FromStringAndSize((const char*) data,iysize*bpl);
00692         return ret;
00693 }
00694 
00695 
00696 void EMData::render_amp24( int x0, int y0, int ixsize, int iysize,
00697                                                   int bpl, float scale, int mingray, int maxgray,
00698                                                   float render_min, float render_max, void *ref,
00699                                                   void cmap(void *, int coord, unsigned char *tri))
00700 {
00701         ENTERFUNC;
00702 
00703         if (get_ndim() != 2) {
00704                 throw ImageDimensionException("2D only");
00705         }
00706 
00707         if (is_complex()) {
00708                 ri2ap();
00709         }
00710 
00711         if (render_max <= render_min) {
00712                 render_max = render_min + 0.01f;
00713         }
00714 
00715         std::string ret=std::string();
00716         ret.resize(iysize*bpl);
00717         unsigned char *data=(unsigned char *)ret.data();
00718 
00719         float rm = render_min;
00720         float inv_scale = 1.0f / scale;
00721         int ysize = iysize;
00722         int xsize = ixsize;
00723         const int scale_n = 100000;
00724 
00725         int ymin = 0;
00726         if ( iysize * inv_scale > ny) {
00727                 ymin = (int) (iysize - ny / inv_scale);
00728         }
00729         float gs = (maxgray - mingray) / (render_max - render_min);
00730         if (render_max < render_min) {
00731                 gs = 0;
00732                 rm = FLT_MAX;
00733         }
00734         int dsx = -1;
00735         int dsy = 0;
00736         if (inv_scale == floor(inv_scale)) {
00737                 dsx = (int) inv_scale;
00738                 dsy = (int) (inv_scale * nx);
00739         }
00740         int addi = 0;
00741         int addr = 0;
00742 
00743         if (dsx == -1) {
00744                 addi = (int) floor(inv_scale);
00745                 addr = (int) (scale_n * (inv_scale - floor(inv_scale)));
00746         }
00747 
00748         int remx = 0;
00749         int remy = 0;
00750         int xmin = 0;
00751         if (x0 < 0) {
00752                 xmin = (int) (-x0 / inv_scale);
00753                 xsize -= (int) floor(x0 / inv_scale);
00754                 x0 = 0;
00755         }
00756 
00757         if ((xsize - xmin) * inv_scale > (nx - x0)) {
00758                 xsize = (int) ((nx - x0) / inv_scale + xmin);
00759         }
00760         int ymax = ysize - 1;
00761         if (y0 < 0) {
00762                 ymax = (int) (ysize + y0 / inv_scale - 1);
00763                 ymin += (int) floor(y0 / inv_scale);
00764                 y0 = 0;
00765         }
00766 
00767 
00768         if (xmin < 0) {
00769                 xmin = 0;
00770         }
00771 
00772         if (ymin < 0) {
00773                 ymin = 0;
00774         }
00775         if (xsize > ixsize) {
00776                 xsize = ixsize;
00777         }
00778         if (ymax > iysize) {
00779                 ymax = iysize;
00780         }
00781 
00782         int lmax = nx * ny - 1;
00783         unsigned char tri[3];
00784         float* image_data = get_data();
00785         if (is_complex()) {
00786                 if (dsx != -1) {
00787                         int l = y0 * nx;
00788                         for (int j = ymax; j >= ymin; j--) {
00789                                 int ll = x0;
00790                                 for (int i = xmin; i < xsize; i++, ll += dsx) {
00791                                         if (l + ll > lmax || ll >= nx - 2) {
00792                                                 break;
00793                                         }
00794                                         int kk = 0;
00795                                         if (ll >= nx / 2) {
00796                                                 if (l >= (ny - inv_scale) * nx) {
00797                                                         kk = 2 * (ll - nx / 2) + 2;
00798                                                 }
00799                                                 else {
00800                                                         kk = 2 * (ll - nx / 2) + l + 2 + nx;
00801                                                 }
00802                                         }
00803                                         else {
00804                                                 kk = nx * ny - (l + 2 * ll) - 2;
00805                                         }
00806                                         int k = 0;
00807                                         float t = image_data[kk];
00808                                         if (t <= rm) {
00809                                                 k = mingray;
00810                                         }
00811                                         else if (t >= render_max) {
00812                                                 k = maxgray;
00813                                         }
00814                                         else {
00815                                                 k = (int) (gs * (t - render_min));
00816                                                 k += mingray;
00817                                         }
00818                                         tri[0] = static_cast < unsigned char >(k);
00819                                         cmap(ref, kk, tri);
00820                                         data[i * 3 + j * bpl] = tri[0];
00821                                         data[i * 3 + 1 + j * bpl] = tri[1];
00822                                         data[i * 3 + 2 + j * bpl] = tri[2];
00823                                 }
00824                                 l += dsy;
00825                         }
00826                 }
00827                 else {
00828                         remy = 10;
00829                         for (int j = ymax, l = y0 * nx; j >= ymin; j--) {
00830                                 int br = l;
00831                                 remx = 10;
00832                                 for (int i = xmin, ll = x0; i < xsize - 1; i++) {
00833                                         if (l + ll > lmax || ll >= nx - 2) {
00834                                                 break;
00835                                         }
00836                                         int kk = 0;
00837                                         if (ll >= nx / 2) {
00838                                                 if (l >= (ny * nx - nx)) {
00839                                                         kk = 2 * (ll - nx / 2) + 2;
00840                                                 }
00841                                                 else {
00842                                                         kk = 2 * (ll - nx / 2) + l + 2 + nx;
00843                                                 }
00844                                         }
00845                                         else {
00846                                                 kk = nx * ny - (l + 2 * ll) - 2;
00847                                         }
00848                                         int k = 0;
00849                                         float t = image_data[kk];
00850                                         if (t <= rm) {
00851                                                 k = mingray;
00852                                         }
00853                                         else if (t >= render_max) {
00854                                                 k = maxgray;
00855                                         }
00856                                         else {
00857                                                 k = (int) (gs * (t - render_min));
00858                                                 k += mingray;
00859                                         }
00860                                         tri[0] = static_cast < unsigned char >(k);
00861                                         cmap(ref, kk, tri);
00862                                         data[i * 3 + j * bpl] = tri[0];
00863                                         data[i * 3 + 1 + j * bpl] = tri[1];
00864                                         data[i * 3 + 2 + j * bpl] = tri[2];
00865                                         ll += addi;
00866                                         remx += addr;
00867                                         if (remx > scale_n) {
00868                                                 remx -= scale_n;
00869                                                 ll++;
00870                                         }
00871                                 }
00872                                 l = br + addi * nx;
00873                                 remy += addr;
00874                                 if (remy > scale_n) {
00875                                         remy -= scale_n;
00876                                         l += nx;
00877                                 }
00878                         }
00879                 }
00880         }
00881         else {
00882                 if (dsx != -1) {
00883                         for (int j = ymax, l = x0 + y0 * nx; j >= ymin; j--) {
00884                                 int br = l;
00885                                 for (int i = xmin; i < xsize; i++, l += dsx) {
00886                                         if (l > lmax) {
00887                                                 break;
00888                                         }
00889                                         float t = image_data[l];
00890                                         int k = 0;
00891                                         if (t <= rm) {
00892                                                 k = mingray;
00893                                         }
00894                                         else if (t >= render_max) {
00895                                                 k = maxgray;
00896                                         }
00897                                         else {
00898                                                 k = (int) (gs * (t - render_min));
00899                                                 k += mingray;
00900                                         }
00901                                         tri[0] = static_cast < unsigned char >(k);
00902                                         cmap(ref, l, tri);
00903                                         data[i * 3 + j * bpl] = tri[0];
00904                                         data[i * 3 + 1 + j * bpl] = tri[1];
00905                                         data[i * 3 + 2 + j * bpl] = tri[2];
00906                                 }
00907                                 l = br + dsy;
00908                         }
00909                 }
00910                 else {
00911                         remy = 10;
00912                         for (int j = ymax, l = x0 + y0 * nx; j >= ymin; j--) {
00913                                 int br = l;
00914                                 remx = 10;
00915                                 for (int i = xmin; i < xsize; i++) {
00916                                         if (l > lmax) {
00917                                                 break;
00918                                         }
00919                                         float t = image_data[l];
00920                                         int k = 0;
00921                                         if (t <= rm) {
00922                                                 k = mingray;
00923                                         }
00924                                         else if (t >= render_max) {
00925                                                 k = maxgray;
00926                                         }
00927                                         else {
00928                                                 k = (int) (gs * (t - render_min));
00929                                                 k += mingray;
00930                                         }
00931                                         tri[0] = static_cast < unsigned char >(k);
00932                                         cmap(ref, l, tri);
00933                                         data[i * 3 + j * bpl] = tri[0];
00934                                         data[i * 3 + 1 + j * bpl] = tri[1];
00935                                         data[i * 3 + 2 + j * bpl] = tri[2];
00936                                         l += addi;
00937                                         remx += addr;
00938                                         if (remx > scale_n) {
00939                                                 remx -= scale_n;
00940                                                 l++;
00941                                         }
00942                                 }
00943                                 l = br + addi * nx;
00944                                 remy += addr;
00945                                 if (remy > scale_n) {
00946                                         remy -= scale_n;
00947                                         l += nx;
00948                                 }
00949                         }
00950                 }
00951         }
00952 
00953         EXITFUNC;
00954 }
00955 
00956 void EMData::ap2ri()
00957 {
00958         ENTERFUNC;
00959 
00960         if (!is_complex() || is_ri()) {
00961                 return;
00962         }
00963         
00964         Util::ap2ri(get_data(), (size_t)nx * ny * nz);
00965         set_ri(true);
00966         update();
00967         EXITFUNC;
00968 }
00969 
00970 void EMData::ri2inten()
00971 {
00972         ENTERFUNC;
00973 
00974         if (!is_complex()) return;
00975         if (!is_ri()) ap2ri();
00976 
00977         float * data = get_data();
00978         size_t size = (size_t)nx * ny * nz;
00979         for (size_t i = 0; i < size; i += 2) {
00980                 data[i]=data[i]*data[i]+data[i+1]*data[i+1];
00981                 data[i+1]=0;
00982         }
00983 
00984         set_attr("is_intensity", int(1));
00985         update();
00986         EXITFUNC;
00987 }
00988 
00989 
00990 void EMData::ri2ap()
00991 {
00992         ENTERFUNC;
00993 
00994         if (!is_complex() || !is_ri()) {
00995                 return;
00996         }
00997 
00998         float * data = get_data();
00999 
01000         size_t size = (size_t)nx * ny * nz;
01001         for (size_t i = 0; i < size; i += 2) {
01002 #ifdef  _WIN32
01003                 float f = (float)_hypot(data[i], data[i + 1]);
01004 #else
01005                 float f = (float)hypot(data[i], data[i + 1]);
01006 #endif
01007                 if (data[i] == 0 && data[i + 1] == 0) {
01008                         data[i + 1] = 0;
01009                 }
01010                 else {
01011                         data[i + 1] = atan2(data[i + 1], data[i]);
01012                 }
01013                 data[i] = f;
01014         }
01015 
01016         set_ri(false);
01017         update();
01018         EXITFUNC;
01019 }
01020 
01021 
01022 float calc_bessel(const int n, const float& x) {
01023         gsl_sf_result result;
01024 //      int success =
01025         gsl_sf_bessel_Jn_e(n,(double)x, &result);
01026         return (float)result.val;
01027 }
01028 
01029 EMData*   EMData::bispecRotTransInvN(int N, int NK)
01030 {
01031 
01032         int EndP = this -> get_xsize(); // length(fTrueVec);
01033         int Mid  = (int) ((1+EndP)/2);
01034         int End = 2*Mid-1;
01035 
01036         int CountxyMax = End*End;
01037 
01038         int   *SortfkInds       = new    int[CountxyMax];
01039         int   *kVecX            = new    int[CountxyMax];
01040         int   *kVecY            = new    int[CountxyMax];
01041         float *fkVecR           = new  float[CountxyMax];
01042         float *fkVecI           = new  float[CountxyMax];
01043         float *absD1fkVec       = new  float[CountxyMax];
01044         float *absD1fkVecSorted = new  float[CountxyMax];
01045 
01046         float *jxjyatan2         = new  float[End*End]; //  jxjyatan2[jy*End + jx]  = atan2(jy+1-Mid , jx +1 -Mid);
01047 
01048         EMData * ThisCopy = new EMData(End,End);
01049 
01050         for (int jx=0; jx <End ; jx++) {
01051                 for (int jy=0; jy <End ; jy++) {
01052                         float ValNow = this -> get_value_at(jx,jy);
01053                         ThisCopy -> set_value_at(jx,jy,ValNow);
01054 //              cout<< " jxM= " << jx+1<<" jyM= " << jy+1<< "ValNow" << ValNow << endl; //    Works
01055         }}
01056 
01057 
01058         EMData* fk = ThisCopy -> do_fft();
01059         fk          ->process_inplace("xform.fourierorigin.tocenter");
01060 
01061 //      EMData* fk
01062         EMData* fkRCopy = new EMData(End,End);
01063         EMData* fkICopy = new EMData(End,End);
01064         EMData* fkCopy  = new EMData(End,End);
01065 
01066 
01067         for  (int jCount= 0; jCount<End*End; jCount++) {
01068 //              jCount = jy*End + jx;
01069                 int jx             = jCount%End ;
01070                 int jy             = (jCount-jx)/End ;
01071                 jxjyatan2[jCount]  = atan2((float)(jy+1-Mid) , (float)(jx +1-Mid));
01072         }
01073 
01074 
01075         for (int kEx= 0; kEx<2*Mid; kEx=kEx+2) { // kEx twice the value of the Fourier
01076                                                 // x variable: EMAN index for real, imag
01077                 int kx    = kEx/2;              // kx  is  the value of the Fourier variable
01078                 int kIx   = kx+Mid-1; // This is the value of the index for a matlab image (-1)
01079                 int kCx   =  -kx ;
01080                 int kCIx  = kCx+ Mid-1 ;
01081                 for (int kEy= 0 ; kEy<End; kEy++) { // This is the value of the EMAN index
01082                         int kIy              =  kEy       ; //  This is the value of the index for a matlab image (-1)
01083                         int ky               =  kEy+1-Mid; // (kEy+ Mid-1)%End - Mid+1 ;  // This is the actual value of the Fourier variable
01084                         float realVal        =  fk -> get_value_at(kEx  ,kEy) ;
01085                         float imagVal        =  fk -> get_value_at(kEx+1,kEy) ;
01086                         float absVal         =  ::sqrt(realVal*realVal+imagVal*imagVal);
01087                         float fkAng          =  atan2(imagVal,realVal);
01088 
01089                         float NewRealVal   ;
01090                         float NewImagVal   ;
01091                         float AngMatlab    ;
01092 
01093                         if (kIx==Mid-1) {
01094 //                              AngMatlab = -fkAng - 2.*M_PI*(kIy+ 1-Mid)*(Mid)/End;
01095 //                      cout<< "i= " << i << " kIx= " << kIx << " kIy=" << kIy << " fkVecR[i] =" << fkVecR[i]<< " fkVecI[i]="  << fkVecI[i] <<"  angle[i]= "  << AngMatlab << endl;
01096                         }
01097 
01098                         if (kIx>Mid-1){
01099 //                      cout<< "i= " << i << " kIx= " << kIx << " kIy=" << kIy << " fkVecR[i] =" << fkVecR[i]<< " fkVecI[i]="  << fkVecI[i] <<"  angle[i]= "  << AngMatlab << endl;
01100                         }
01101 
01102                         AngMatlab = fkAng - 2.0f*M_PI*(kx +ky)*(Mid)/End;
01103                         NewRealVal  =   absVal*cos(AngMatlab);
01104                         NewImagVal  =   absVal*sin(AngMatlab);
01105 
01106 
01107                         fkVecR[kIy+kIx *End] =  NewRealVal ;
01108                         fkVecR[kIy+kCIx*End] =  NewRealVal ;
01109                         fkVecI[kIy+kIx *End] =  NewImagVal ;
01110                         fkVecI[kIy+kCIx*End] = -NewImagVal ;
01111                         absD1fkVec[kIy + kIx  *End] = absVal;
01112                         absD1fkVec[kIy + kCIx *End] = absVal;
01113                         kVecX[kIy+kIx  *End] =  kx      ;
01114                         kVecX[kIy+kCIx *End] =  kCx    ;
01115                         kVecY[kIy+kIx  *End] =  ky     ;
01116                         kVecY[kIy+kCIx *End] =  ky     ;
01117 //                      printf("kx=%d,ky=%d,tempVal =%f+ i %4.2f \n",kx,ky,realVal,imagVal );
01118 //                      cout << "kx = " << kx << "; ky = "<< ky << "; val is" << realVal<<"+ i "<<imagVal<< endl;
01119 
01120 //                      cout << "kIMx = "<< kIx+1 << "; kIMy = "<< kIy+1 <<"; fkAng*9/ 2pi is " << fkAng*9/2/M_PI<<  endl;
01121 //                      cout << "kIMx = "<< kIx+1 << "; kIMy = "<< kIy+1 <<"; absval is " << absVal<<  "; realval is " << NewRealVal<< "; imagval is " << NewImagVal<< endl;
01122                         fkCopy  -> set_value_at(kIx ,kIy, absVal);
01123                         fkCopy  -> set_value_at(kCIx,kIy, absVal);
01124                         fkRCopy -> set_value_at(kIx, kIy, NewRealVal);
01125                         fkRCopy -> set_value_at(kCIx,kIy, NewRealVal);
01126                         fkICopy -> set_value_at(kIx, kIy, NewImagVal);
01127                         fkICopy -> set_value_at(kCIx,kIy,-NewImagVal);
01128 
01129                 }
01130         }
01131 #ifdef _WIN32
01132         _unlink("fkCopy.???");
01133         _unlink("fk?Copy.???");
01134 #else
01135         system("rm -f fkCopy.???");
01136         system("rm -f fk?Copy.???");
01137 #endif  //_WIN32
01138         fkCopy  -> write_image("fkCopy.img");
01139         fkRCopy -> write_image("fkRCopy.img");
01140         fkICopy -> write_image("fkICopy.img");
01141 
01142         cout << "Starting the sort "<< endl;
01143 
01144         vector< pair<float, int> > absInds;
01145         for(int i  = 0; i < CountxyMax; ++i ) {
01146                 pair<float,int> p;
01147                 p = make_pair(absD1fkVec[i],i); // p = make_pair(rand(),i);
01148                 absInds.push_back( p);
01149         }
01150 
01151         std::sort(absInds.begin(),absInds.end());
01152 
01153         for(int i  = 0; i < CountxyMax; ++i ) {
01154                 pair<float,int> p   ;
01155                 p = absInds[i]         ;
01156                 absD1fkVecSorted[CountxyMax-1-i] =  p.first ;
01157                 SortfkInds[CountxyMax-1-i]       =  p.second ;
01158         }
01159 
01160         cout << "Ending the sort "<< endl;
01161 
01162 // float AngsMat[] ={2.8448, -0.3677,-0.2801,-1.0494,-1.7836,-2.5179, 2.9959, 3.0835,-0.1290,-0.8876,2.1829, 2.2705,1.5011,0.7669,0.0327,-0.7366,-0.6489,2.4215,-1.6029,1.4676,1.5552,0.7859,0.0517,-0.6825,-1.4518,-1.3642,1.7063,-1.7845,1.2859,1.3736,0.6043,-0.1299,-0.8642,-1.6335,-1.5459,1.5247,-1.6546,1.4159,1.5036,0.7342,0,-0.7342,-1.5036,-1.4159,1.6546,-1.5247,1.5459,1.6335,0.8642,0.1299,-0.6043,-1.3736,-1.286,1.7846,-1.7063,1.3642,1.4519,0.6825,-0.0517,-0.7859,-1.5553,-1.4676,1.6029,-2.4216,0.649,0.7366,-0.0327,-0.767,-1.5012,-2.2705,-2.1829,0.8877,0.1291,-3.0836,-2.9959,2.5179,1.7837,1.0495,0.2801,0.3677,-2.8449};
01163 
01164 
01165         for(int i  = 0; i < CountxyMax; ++i ) {  // creates a new fkVec
01166                 int Si  = SortfkInds[i];
01167                 int kIx = (int)  Si/End;  kIx = (int)  i/End; // i = kIx*End+kIy
01168 //              int kIy = Si  - kIx*End;  kIy = i  - kIx*End;
01169 //              int iC = (End-1-kIx)*End + (End-1-kIy);
01170 //              if (i<30) { cout<< "i= " << i << " kIx= " << kIx << " kIy=" << kIy << " valAft=" << absD1fkVecSorted[i]<< " valBef="  <<     absD1fkVec[Si] << "  SortfkInds = " << Si <<endl; }// This worked
01171 //              cout<< "i= " << i << " kIx= " << kIx << " kIy=" << kIy << " fkVecR[i] =" << fkVecR[i]<< " fkVecI[i]="  << fkVecI[i] <<"  angle[i]= "  << fkAng << endl;
01172         }
01173         cout<< "Ratio of Last Amplitude to First Amplitude= " << absD1fkVecSorted[NK] /absD1fkVecSorted[0]  << endl;
01174 
01175 //      pause;
01176 
01177 //      for(int i  = 0; i < NK; ++i ) { // Prints out the new fkVec ,  CountxyMax
01178 //              int Si= SortfkInds[i];
01179 //              int kIx = (int)  Si/End; // i = kIx*End+kIy
01180 //              int kIy = Si  - kIx*End;
01181 //              cout << " kIxM= " << kIx+1 << " kIyM=" << kIy+1 << " fkVecAbs=" << ::sqrt(fkVecR[Si]*fkVecR[Si] +  fkVecI[Si]* fkVecI[Si]) << " fkVecAbs=" << absD1fkVecSorted[i] << " kx= " << kVecX[Si] <<  " ky=" << kVecY[Si] <<  endl;
01182 //      }
01183 
01184 //       angEMAN+angMat+angDiff    =0  mod 2 pi
01185 
01186 //      angDiff=  2*pi*((-4):4)*(Mid)/End; angEMAN+angMat+angDiff= integer*2 *pi
01187 //              [  absD1fkVecSorted, SortfkInds] =sort( absD1fkVec,'descend') ;
01188 //      Util::sort_mat(&absD1fkVec[0],&absD1fkVec[Countxy],&SortfkInds[0],&SortfkInds[Countxy]);
01189 
01190 
01191 //      Let radial sampling be 0:0.5:(Mid-1)
01192 
01193  //     int NK=  min(12,CountxyMax) ;
01194 
01195 
01196 
01197         cout << "NK = " << NK << endl;
01198         float frR= 3.0/4.0;
01199         int LradRange= (int) (floor(Mid/frR)) ;
01200 
01201         float *radRange = new float[LradRange]; //= 0:.75:(Mid-1);
01202         radRange[0]=0;
01203         for (int irad=1; irad < LradRange; irad++){
01204                         radRange[irad] = radRange[irad-1] + frR; }
01205 
01206 
01207 
01208          // should equal to (2*Mid-1)
01209         cout << "Starting the calculation of invariants for N= " << N << endl;
01210 
01211 /*      int NMax=5;            */
01212 
01213         EMData* RotTransInv = new EMData();
01214         RotTransInv -> set_size(LradRange,LradRange);
01215 
01216 
01217 //      float  *RotTransInv       = new float[LradRange*LradRange ] ;
01218 //      float  *RotTransInvN      = new float[LradRange*LradRange*(NMax+1) ] ;
01219 
01220 //      for (int N=0 ; N<NMax; N++) {
01221 
01222         for (int jr1=0; jr1 < LradRange ; jr1++ ) { // LradRange
01223                 float r1= radRange[jr1];
01224 //              cout << "Pre jr2 "<< endl;
01225                 for (int jr2=0;  jr2<LradRange;  jr2++ ) { //LradRange
01226                         float r2= radRange[jr2];
01227                         float RotTransInvTemp=0;
01228                         for (int jCountkxy =0; jCountkxy<NK; jCountkxy++){
01229                                 int Countkxy =SortfkInds[jCountkxy] ;   // 1: CountxyMax
01230                                 int kx = kVecX[Countkxy] ;
01231                                 int ky = kVecY[Countkxy] ;
01232                                 float k2 = (float)(kx*kx+ky*ky);
01233                                 if (k2==0) { continue;}
01234                                 float phiK =0;
01235                                 if (k2>0) phiK= jxjyatan2[ (ky+Mid-1)*End + kx+Mid-1];  phiK= atan2((float)ky,(float)kx);
01236 
01237                                 float fkR     = fkVecR[Countkxy] ;
01238                                 float fkI     = fkVecI[Countkxy]  ;
01239 /*                              printf("jCountkxy=%d, Countkxy=%d,absD1fkVec(Countkxy)=%f,\t\t kx=%d, ky=%d \n", jCountkxy, Countkxy, absD1fkVec[Countkxy], kx, ky);*/
01240 
01241                                 for (int jCountqxy =0; jCountqxy<NK; jCountqxy++){
01242                                         int Countqxy =SortfkInds[jCountqxy] ;   // Countqxy is the index for absD1fkVec
01243                                         int qx   = kVecX[Countqxy] ;
01244                                         int qy   = kVecY[Countqxy] ;
01245                                         int q2   = qx*qx+qy*qy;
01246                                         if (q2==0) {continue;}
01247                                         float phiQ =0;
01248                                         if (q2>0) phiQ = jxjyatan2[ (qy+Mid-1)*End + qx+Mid-1];   phiQ=atan2((float)qy,(float)qx);
01249                                         float fqR     = fkVecR[Countqxy]  ;
01250                                         float fqI     = fkVecI[Countqxy]  ;
01251                                         int kCx  = (-kx-qx);
01252                                         int kCy  = (-ky-qy);
01253                                         int kCIx = ((kCx+Mid+2*End)%End);// labels of the image in C
01254                                         int kCIy = ((kCy+Mid+2*End)%End);
01255                                         kCx  = kCIx-Mid; // correct
01256                                         kCy  = kCIy-Mid; // correct
01257                                         int CountCxy = kCIx*End+kCIy;
01258                                         float fCR     = fkVecR[CountCxy];
01259                                         float fCI     = fkVecI[CountCxy];
01260                                         if (jr1+jr2==-1) {
01261                                         printf("jCountqxy=%d , Countqxy=%d, absD1fkVec(Countqxy)=%f,qx=%d, qy=%d \n", jCountqxy, Countqxy, absD1fkVec[Countqxy],qx, qy);
01262                                         printf(" CountCxy=%d,absD1fkVec[CountCxy]=%f,  kCx=%d,     kCy=%d \n",CountCxy, absD1fkVec[CountCxy], kCx, kCy );
01263                                         }
01264                                         for (int p=0; p<NK; p++){
01265 //                                              printf("p=%d, SortfkInds[p]=%d, CountCxy =%d \n", p,SortfkInds[p], CountCxy);
01266                                                 if (SortfkInds[p]==CountCxy){
01267                                                         float Arg1 = 2.0f*M_PI*r1*::sqrt((float) q2)/End;
01268                                                         float Arg2 = 2.0f*M_PI*r2*::sqrt((float) k2)/End;
01269 //                                                      printf("Arg1=%4.2f, Arg2=%4.2f,  \n",Arg1, Arg2 );
01270 //                                                      if (Arg1+ Arg2<15) {
01271                                                                 float bispectemp  = (fkR*(fqR*fCR -fqI*fCI) -fkI*(fqI*fCR  +fqR*fCI))
01272                                                                 * cos(N*(phiK-phiQ+M_PI));
01273                                                                 bispectemp  -= (fkR*(fqR*fCI + fqI*fCR) +fkI*(fqR*fCR - fqI*fCI))
01274                                                                 * sin(N*(phiK-phiQ+M_PI));
01275                                                                 float bess1 = calc_bessel(N, Arg1 );
01276                                                                 float bess2 = calc_bessel(N, Arg2 );
01277 //                      printf("fkr=%4.2f, fqr=%4.2f, bess1=%4.2f,bess2=%4.2f \n",fkR, fqR, bess1, bess2);
01278 /*                      printf("p =%d, SortfkInds[p]=%d, CountCxy=%d, Arg1 =%4.2f, bess1=%4.2f,  \n",
01279                                 p, SortfkInds[p],CountCxy, Arg1, bess1);*/
01280                                                                 RotTransInvTemp   = RotTransInvTemp  + bispectemp  * bess1*bess2 ;
01281 //                                                      }
01282                                                 }
01283                                         }
01284                                 } // jCountqxy
01285                         } // jCountkxy
01286                         RotTransInv -> set_value_at(jr1,jr2, RotTransInvTemp)   ;
01287 /*              RotTransInvN[jr1 + LradRange*jr2+LradRange*LradRange*N] = RotTransInvTemp  ;*/
01288                 } //jr2
01289         } //jr1
01290 // }//N
01291 
01292         return  RotTransInv ;
01293 
01294 
01295 }
01296 
01297 
01298 
01299 /*
01300 // find example
01301 #include <iostream>
01302 #include <algorithm>
01303 #include <vector>
01304 using namespace std;
01305 
01306 int main () {
01307   int myints[] = { 10, 20, 30 ,40 };
01308   int * p;
01309 
01310   // pointer to array element:
01311   p = find(myints,myints+4,30);
01312   ++p;
01313   cout << "The element following 30 is " << *p << endl;
01314 
01315   vector<int> myvector (myints,myints+4);
01316   vector<int>::iterator it;
01317 
01318   // iterator to vector element:
01319   it = find (myvector.begin(), myvector.end(), 30);
01320   ++it;
01321   cout << "The element following 30 is " << *it << endl;
01322 
01323   return 0;
01324 }*/
01325 
01326 EMData*   EMData::bispecRotTransInvDirect(int type)
01327 {
01328 
01329         int EndP = this -> get_xsize(); // length(fTrueVec);
01330         int Mid  = (int) ((1+EndP)/2);
01331         int End = 2*Mid-1;
01332 
01333         int CountxyMax = End*End;
01334 
01335 //      int   *SortfkInds       = new    int[CountxyMax];
01336         int   *kVecX            = new    int[CountxyMax];
01337         int   *kVecY            = new    int[CountxyMax];
01338         float *fkVecR           = new  float[CountxyMax];
01339         float *fkVecI           = new  float[CountxyMax];
01340         float *absD1fkVec       = new  float[CountxyMax];
01341 //      float *absD1fkVecSorted = new  float[CountxyMax];
01342 
01343 
01344         float *jxjyatan2         = new  float[End*End];
01345 
01346 
01347         EMData * ThisCopy = new EMData(End,End);
01348 
01349         for (int jx=0; jx <End ; jx++) {  // create jxjyatan2
01350                 for (int jy=0; jy <End ; jy++) {
01351                         float ValNow = this -> get_value_at(jx,jy);
01352                         ThisCopy -> set_value_at(jx,jy,ValNow);
01353                         jxjyatan2[jy*End + jx]  = atan2((float)(jy+1-Mid) , (float)(jx +1 -Mid));
01354 //              cout<< " jxM= " << jx+1<<" jyM= " << jy+1<< "ValNow" << ValNow << endl; //    Works
01355         }}
01356 
01357 
01358         EMData* fk = ThisCopy -> do_fft();
01359         fk          ->process_inplace("xform.fourierorigin.tocenter");
01360 
01361 //      Create kVecX , kVecy etc
01362 
01363         for (int kEx= 0; kEx<2*Mid; kEx=kEx+2) { // kEx twice the value of the Fourier
01364                                                 // x variable: EMAN index for real, imag
01365                 int kx    = kEx/2;              // kx  is  the value of the Fourier variable
01366                 int kIx   = kx+Mid-1; // This is the value of the index for a matlab image (-1)
01367                 int kCx   = -kx ;
01368                 int kCIx  = kCx+ Mid-1 ;
01369                 for (int kEy= 0 ; kEy<End; kEy++) { // This is the value of the EMAN index
01370                         int kIy              =  kEy       ; //  This is the value of the index for a matlab image (-1)
01371                         int ky               =  kEy+1-Mid; // (kEy+ Mid-1)%End - Mid+1 ;  // This is the actual value of the Fourier variable
01372                         float realVal        =  fk -> get_value_at(kEx  ,kEy) ;
01373                         float imagVal        =  fk -> get_value_at(kEx+1,kEy) ;
01374                         float absVal         =  ::sqrt(realVal*realVal+imagVal*imagVal);
01375                         float fkAng          =  atan2(imagVal,realVal);
01376 
01377                         float NewRealVal   ;
01378                         float NewImagVal   ;
01379                         float AngMatlab    ;
01380 
01381                         if (kIx==Mid-1) {
01382 //                              AngMatlab = -fkAng - 2.*M_PI*(kIy+ 1-Mid)*(Mid)/End;
01383                         }
01384 
01385                         if (kIx>Mid-1){
01386 //                      cout<< "i= " << i << " kIx= " << kIx << " kIy=" << kIy << " fkVecR[i] =" << fkVecR[i]<< " fkVecI[i]="  << fkVecI[i] <<"  angle[i]= "  << AngMatlab << endl;
01387                         }
01388 
01389                         AngMatlab = fkAng - 2.0f*M_PI*(kx +ky)*(Mid)/End;
01390                         NewRealVal  =   absVal*cos(AngMatlab);
01391                         NewImagVal  =   absVal*sin(AngMatlab);
01392 
01393 
01394                         fkVecR[ kIy +kIx *End] =  NewRealVal ;
01395                         fkVecR[(End-1-kIy)+kCIx*End] =  NewRealVal ;
01396                         fkVecI[ kIy +kIx *End] =  NewImagVal ;
01397                         fkVecI[(End-1-kIy)+kCIx*End] = -NewImagVal ;
01398                         absD1fkVec[(End-1-kIy) + kIx  *End] = absVal;
01399                         absD1fkVec[(End-1-kIy) + kCIx *End] = absVal;
01400                         kVecX[kIy+kIx  *End] =  kx      ;
01401                         kVecX[kIy+kCIx *End] =  kCx    ;
01402                         kVecY[kIy+kIx  *End] =  ky     ;
01403                         kVecY[kIy+kCIx *End] =  ky     ;
01404 
01405  //                     cout << " kIxM= " << kIx+1 << " kIy=" << kIy+1 << " fkVecR[i] =" << NewRealVal << " fkVecI[i]="  << NewImagVal <<"  angle[i]= "  << AngMatlab << " Total Index" << kIy+kIx *End << endl;
01406 
01407 //                      printf("kx=%d,ky=%d,tempVal =%f+ i %4.2f \n",kx,ky,realVal,imagVal );
01408 //                      cout << "kx = " << kx << "; ky = "<< ky << "; val is" << realVal<<"+ i "<<imagVal<< endl;
01409 
01410 //                      cout << "kIMx = "<< kIx+1 << "; kIMy = "<< kIy+1 <<"; fkAng*9/ 2pi is " << fkAng*9/2/M_PI<<  endl;
01411 //                      cout << "kIMx = "<< kIx+1 << "; kIMy = "<< kIy+1 <<"; absval is " << absVal<<  "; realval is " << NewRealVal<< "; imagval is " << NewImagVal<< endl;
01412                 }
01413         }
01414 
01415 
01416 //      for (int TotalInd = 0 ;  TotalInd < CountxyMax ; TotalInd++){
01417 //              int kx     = kVecX[TotalInd]; // This is the value of the index for a matlab image (-1)
01418 //              int kIx    = kx+Mid-1; // This is the value of the index for a matlab image (-1)
01419 //              int ky     = kVecY[TotalInd];
01420 //              int kIy    = ky+Mid-1; // This is the value of the index for a matlab image (-1)
01421                 //float fkR  = fkVecR[kIy+kIx *End]  ;
01422                 //float fkI  = fkVecI[kIy+kIx *End]  ;
01423 //      }
01424 
01425         float frR= 3.0/4.0;
01426         frR= 1;
01427         int LradRange= (int) (1+floor(Mid/frR -.1)) ;
01428 
01429         float *radRange = new float[LradRange]; //= 0:.75:(Mid-1);
01430         for (int irad=0; irad < LradRange; irad++){
01431                         radRange[irad] =  frR*irad;
01432 //                      cout << " irad = " << irad << " radRange[irad]= " <<  radRange[irad] <<  " LradRange= " << LradRange << endl;
01433         }
01434 
01435         cout << "Starting the calculation of invariants" << endl;
01436 
01437 
01438         if (type==0) {
01439                 int LthetaRange  = 59;
01440                 float ftR        = (2.0f*M_PI/LthetaRange );
01441                 float *thetaRange = new float[LthetaRange]; //= 0:.75:(Mid-1);
01442 
01443                 for (int ith=0; ith < LthetaRange; ith++){
01444                                 thetaRange[ith] =  ftR*ith; }
01445 
01446                 int TotalVol = LradRange*LradRange*LthetaRange;
01447 
01448                 float *RotTransInv   = new  float[TotalVol];
01449                 float *WeightInv     = new  float[TotalVol];
01450 
01451                 for (int jW=0; jW<TotalVol; jW++) {
01452                         RotTransInv[jW] = 0;
01453                         WeightInv[jW]   = 0;
01454                 }
01455 
01456                 for (int jW=0; jW<TotalVol; jW++) {
01457                         RotTransInv[jW] = 0;
01458                         WeightInv[jW]   = 0;
01459                 }
01460         //      float  *RotTransInv       = new float[LradRange*LradRange ] ;
01461         //      float  *RotTransInvN      = new float[LradRange*LradRange*(NMax+1) ] ;
01462 
01463                 for (int Countkxy =0; Countkxy<CountxyMax; Countkxy++){  // Main Section for type 0
01464                         int kx = kVecX[Countkxy] ;
01465                         int ky = kVecY[Countkxy] ;
01466                         float k2 = ::sqrt((float)(kx*kx+ky*ky));
01467                         float phiK =0;
01468                         if (k2>0)    phiK = jxjyatan2[ (ky+Mid-1)*End + kx+Mid-1]; //  phiK=atan2(ky,kx);
01469                         float fkR     = fkVecR[(ky+Mid-1) + (kx+Mid-1) *End] ;
01470                         float fkI     = fkVecI[(ky+Mid-1) + (kx+Mid-1) *End]  ;
01471         //              printf("Countkxy=%d,\t kx=%d, ky=%d, fkR=%3.2f,fkI=%3.2f \n", Countkxy, kx, ky, fkR, fkI);
01472 
01473                         if ((k2==0)|| (k2>Mid) ) { continue;}
01474 
01475                         for (int Countqxy =0; Countqxy<CountxyMax; Countqxy++){   // This is the innermost loop
01476                                 int qx   = kVecX[Countqxy] ;
01477                                 int qy   = kVecY[Countqxy] ;
01478                                 float q2   = ::sqrt((float)(qx*qx+qy*qy));
01479                                 if ((q2==0)|| (q2>Mid) ) {continue;}
01480                                 float phiQ =0;
01481                                 if (q2>0)   phiQ = jxjyatan2[ (qy+Mid-1)*End + qx+Mid-1]; // phiQ=atan2(qy,qx);
01482                                 float fqR     = fkVecR[(qy+Mid-1) + (qx+Mid-1) *End] ;
01483                                 float fqI     = fkVecI[(qy+Mid-1) + (qx+Mid-1) *End]  ;
01484                                 int kCx  = (-kx-qx);
01485                                 int kCy  = (-ky-qy);
01486                                 int kCIx = ((kCx+Mid+2*End)%End);// labels of the image in C
01487                                 int kCIy = ((kCy+Mid+2*End)%End);
01488                                 kCx  = ((kCIx+End-1)%End)+1-Mid; // correct
01489                                 kCy  = ((kCIy+End-1)%End)+1-Mid ; // correct
01490 
01491 //                              float C2   = ::sqrt((float)(kCx*kCx+ kCy*kCy));
01492                                 int CountCxy  = (kCx+Mid-1)*End+(kCy+Mid-1);
01493                                 float fCR     = fkVecR[CountCxy];
01494                                 float fCI     = fkVecI[CountCxy];
01495         /*                      if (Countkxy==1) {
01496                                         printf(" Countqxy=%d, absD1fkVec(Countqxy)=%f,qx=%d, qy=%d \n", Countqxy, absD1fkVec[Countqxy],qx, qy);
01497                                         printf(" CountCxy=%d, absD1fkVec[CountCxy]=%f,kCx=%d,kCy=%d \n",CountCxy, absD1fkVec[CountCxy], kCx, kCy );
01498                                 }*/
01499 //                              float   phiC = jxjyatan2[ (kCy+Mid-1)*End + kCx+Mid-1];
01500                                 float   phiQK = (4*M_PI+phiQ-phiK);
01501                                 while (phiQK> (2*M_PI)) phiQK -= (2*M_PI);
01502 
01503 
01504 
01505                                 float bispectemp  = (fkR*(fqR*fCR -fqI*fCI) -fkI*(fqI*fCR  +fqR*fCI));
01506 
01507                                 if  ((q2<k2) )  continue;
01508 //                              if  ((q2<k2) || (C2<k2) || (C2<q2))  continue;
01509 
01510         //                              printf(" CountCxy=%d, absD1fkVec[CountCxy]=%f,kCx=%d,kCy=%d \n",CountCxy, absD1fkVec[CountCxy], kCx, kCy );
01511 
01512         //                      up to here, matched perfectly with Matlab
01513 
01514                                 int k2IndLo  = 0; while ((k2>=radRange[k2IndLo+1]) && (k2IndLo+1 < LradRange ) ) k2IndLo +=1;
01515                                 int k2IndHi = k2IndLo;
01516                                 float k2Lo= radRange[k2IndLo];
01517                                 if (k2IndLo+1< LradRange) {
01518                                         k2IndHi   = k2IndLo+1;
01519                                 }
01520 //                              float k2Hi= radRange[k2IndHi];
01521 
01522                                 float kCof =k2-k2Lo;
01523 
01524                                 int q2IndLo  = 0; while ((q2>=radRange[q2IndLo+1]) && (q2IndLo+1 < LradRange ) ) q2IndLo +=1;
01525                                 int q2IndHi=q2IndLo;
01526                                 float q2Lo= radRange[q2IndLo];
01527                                 if (q2IndLo+1 < LradRange)  {
01528                                         q2IndHi   = q2IndLo+1 ;
01529                                 }
01530                                 float qCof = q2-q2Lo;
01531 
01532                                 if ((qCof<0) || (qCof >1) ) {
01533                                         cout<< "Weird! qCof="<< qCof <<  " q2="<< q2 << " q2IndLo="<< q2IndLo << endl ;
01534                                         int x    ;
01535                                         cin >> x ;
01536                                 }
01537 
01538                                 int thetaIndLo = 0; while ((phiQK>=thetaRange[thetaIndLo+1])&& (thetaIndLo+1<LthetaRange)) thetaIndLo +=1;
01539                                 int thetaIndHi = thetaIndLo;
01540 
01541                                 float thetaLo  = thetaRange[thetaIndLo];
01542                                 float thetaHi = thetaLo;
01543                                 float thetaCof = 0;
01544 
01545                                 if (thetaIndLo+1< LthetaRange) {
01546                                         thetaIndHi = thetaIndLo +1;
01547                                 }else{
01548                                         thetaIndHi=0;
01549                                 }
01550 
01551                                 thetaHi    = thetaRange[thetaIndHi];
01552 
01553                                 if (thetaHi==thetaLo) {
01554                                         thetaCof =0 ;
01555                                 } else {
01556                                         thetaCof   = (phiQK-thetaLo)/(thetaHi-thetaLo);
01557                                 }
01558 
01559                                 if ((thetaCof>2*M_PI)  ) {
01560                                         cout<< "Weird! thetaCof="<< thetaCof <<endl ;
01561                                         thetaCof=0;
01562                                 }
01563 
01564 
01565         //                      if ((thetaIndLo>=58) || (k2IndLo >= LradRange-1) || (q2IndLo >= LradRange-1) ) {
01566 
01567 
01568                                 for (int jk =1; jk<=2; jk++){
01569                                 for (int jq =1; jq<=2; jq++){
01570                                 for (int jtheta =1; jtheta<=2; jtheta++){
01571 
01572                                         float Weight = (kCof+(1-2*kCof)*(jk==1))*(qCof+(1-2*qCof)*(jq==1))
01573                                                         * (thetaCof+(1-2*thetaCof)*(jtheta==1));
01574 
01575 
01576                                         int k2Ind      =  k2IndLo*(jk==1)      +   k2IndHi*(jk==2);
01577                                         int q2Ind      =  q2IndLo*(jq==1)      +   q2IndHi*(jq==2);
01578                                         int thetaInd   =  thetaIndLo*(jtheta==1)  + thetaIndHi*(jtheta ==2);
01579                                         int TotalInd   = thetaInd*LradRange*LradRange+q2Ind*LradRange+k2Ind;
01580         /*                              if (TotalInd+1 >=  LthetaRange*LradRange*LradRange) {
01581                                                 cout << "Weird!!! TotalInd="<< TotalInd << " IndMax" << LthetaRange*LradRange*LradRange << " LradRange=" << LradRange << endl;
01582                                                 cout << "k2Ind= "<< k2Ind  << " q2Ind="<< q2Ind  << " thetaInd="<< thetaInd  << " q2IndLo="<< q2IndLo  << " q2IndHi="<< q2IndHi  <<  endl;
01583                                                 cout << "k2=" << k2 << "q2=" << q2 << " phiQK=" << phiQK*180.0/M_PI<< endl;
01584                                         }*/
01585 
01586                                         RotTransInv[TotalInd] += Weight*bispectemp;
01587                                         WeightInv[TotalInd]   +=  Weight;
01588         //                              cout << "k2Ind= "<< k2Ind  << " q2Ind="<< q2Ind  << "Weight=" << Weight << endl;
01589                                 }}}
01590                         } // Countqxy
01591                 } // Countkxy
01592 
01593                 cout << "Finished Main Section " << endl;
01594 
01595         /*              RotTransInvN[jr1 + LradRange*jr2+LradRange*LradRange*N] = RotTransInvTemp  ;*/
01596 
01597                 cout << " LradRange " <<LradRange <<" LthetaRange " << LthetaRange << endl;
01598                 EMData *RotTransInvF  = new  EMData(LradRange,LradRange,LthetaRange);
01599                 EMData *WeightImage   = new  EMData(LradRange,LradRange,LthetaRange);
01600 
01601         //      cout << "FFFFFFF" << endl;
01602         //
01603         //      RotTransInvF -> set_size(LradRange,LradRange,LthetaRange);
01604         //
01605         //      cout << "GGGG" << endl;
01606 
01607                 for (int jtheta =0; jtheta < LthetaRange; jtheta++){    // write out to RotTransInvF
01608                 for (int jq =0; jq<LradRange; jq++){ // LradRange
01609                 for (int jk =0; jk<LradRange ; jk++){// LradRange
01610         //              cout << "Hi There" << endl;
01611                         int TotalInd   = jtheta*LradRange*LradRange+jq*LradRange+jk;
01612                         float Weight = WeightInv[TotalInd];
01613                         WeightImage    -> set_value_at(jk,jq,jtheta,Weight);
01614                         RotTransInvF   -> set_value_at(jk,jq,jtheta,0);
01615                         if (Weight <= 0) continue;
01616                         RotTransInvF -> set_value_at(jk,jq,jtheta,RotTransInv[TotalInd] / Weight);//  include /Weight
01617                         int newjtheta = (LthetaRange- jtheta)%LthetaRange;
01618                         RotTransInvF -> set_value_at(jq,jk,newjtheta,RotTransInv[TotalInd]/Weight );//  include /Weight
01619                                 }
01620                         }
01621                 }
01622 
01623                 cout << " Almost Done " << endl;
01624 #ifdef  _WIN32
01625                 _unlink("WeightImage.???");
01626 #else
01627                 system("rm -f WeightImage.???");
01628 #endif  //_WIN32
01629                 WeightImage  -> write_image("WeightImage.img");
01630 
01631                 return  RotTransInvF ;
01632         } // Finish type 0
01633 
01634         if (type==1) {
01635                 int TotalVol = LradRange*LradRange;
01636 
01637                 float *RotTransInv   = new  float[TotalVol];
01638                 float *WeightInv     = new  float[TotalVol];
01639 
01640                 for (int jW=0; jW<TotalVol; jW++) {
01641                         RotTransInv[jW] = 0;
01642                         WeightInv[jW]   = 0;
01643                 }
01644 
01645 
01646                 for (int Countkxy =0; Countkxy<CountxyMax; Countkxy++){
01647                         int kx = kVecX[Countkxy] ;
01648                         int ky = kVecY[Countkxy] ;
01649                         float k2 = ::sqrt((float)(kx*kx+ky*ky));
01650                         float fkR     = fkVecR[(ky+Mid-1) + (kx+Mid-1) *End] ;
01651                         float fkI     = fkVecI[(ky+Mid-1) + (kx+Mid-1) *End]  ;
01652         //              printf("Countkxy=%d,\t kx=%d, ky=%d, fkR=%3.2f,fkI=%3.2f \n", Countkxy, kx, ky, fkR, fkI);
01653 
01654                         if ((k2==0)|| (k2>Mid) ) { continue;}
01655 
01656                         for (int Countqxy =0; Countqxy<CountxyMax; Countqxy++){   // This is the innermost loop
01657 
01658 //                      up to here, matched perfectly with Matlab
01659                                 int qx   = kVecX[Countqxy] ;
01660                                 int qy   = kVecY[Countqxy] ;
01661                                 float q2   = ::sqrt((float)(qx*qx+qy*qy));
01662                                 if ((q2==0)|| (q2>Mid) ) {continue;}
01663                                 if  ((q2<k2) )   continue;
01664 
01665                                 float fqR     = fkVecR[(qy+Mid-1) + (qx+Mid-1) *End] ;
01666                                 float fqI     = fkVecI[(qy+Mid-1) + (qx+Mid-1) *End]  ;
01667 
01668                                 int kCx  = (-kx-qx);
01669                                 int kCy  = (-ky-qy);
01670                                 int kCIx = ((kCx+Mid+2*End)%End);// labels of the image in C
01671                                 int kCIy = ((kCy+Mid+2*End)%End);
01672                                 kCx  = ((kCIx+End-1)%End)+1-Mid; // correct
01673                                 kCy  = ((kCIy+End-1)%End)+1-Mid ; // correct
01674 
01675 //                              float C2   = ::sqrt((float)(kCx*kCx+ kCy*kCy));
01676                                 int CountCxy  = (kCx+Mid-1)*End+(kCy+Mid-1);
01677                                 float fCR     = fkVecR[CountCxy];
01678                                 float fCI     = fkVecI[CountCxy];
01679 
01680 
01681                                 float bispectemp  = (fkR*(fqR*fCR -fqI*fCI) -fkI*(fqI*fCR  +fqR*fCI));
01682 
01683 
01684                                 int k2IndLo  = 0; while ((k2>=radRange[k2IndLo+1]) && (k2IndLo+1 < LradRange ) ) k2IndLo +=1;
01685                                 int k2IndHi = k2IndLo;
01686                                 float k2Lo= radRange[k2IndLo];
01687                                 if (k2IndLo+1< LradRange) {
01688                                         k2IndHi   = k2IndLo+1;
01689                                 }
01690 //                              float k2Hi= radRange[k2IndHi];
01691 
01692                                 float kCof =k2-k2Lo;
01693 
01694                                 int q2IndLo  = 0; while ((q2>=radRange[q2IndLo+1]) && (q2IndLo+1 < LradRange ) ) q2IndLo +=1;
01695                                 int q2IndHi=q2IndLo;
01696                                 float q2Lo= radRange[q2IndLo];
01697                                 if (q2IndLo+1 < LradRange)  {
01698                                         q2IndHi   = q2IndLo+1 ;
01699                                 }
01700                                 float qCof = q2-q2Lo;
01701 
01702 
01703                                 for (int jk =1; jk<=2; jk++){
01704                                 for (int jq =1; jq<=2; jq++){
01705 
01706                                         float Weight = (kCof+(1-2*kCof)*(jk==1))*(qCof+(1-2*qCof)*(jq==1));
01707 
01708                                         int k2Ind      =  k2IndLo*(jk==1)      +   k2IndHi*(jk==2);
01709                                         int q2Ind      =  q2IndLo*(jq==1)      +   q2IndHi*(jq==2);
01710                                         int TotalInd   = q2Ind*LradRange+k2Ind;
01711                                         RotTransInv[TotalInd] += Weight*bispectemp;
01712                                         WeightInv[TotalInd]   +=  Weight;
01713         //                              cout << "k2Ind= "<< k2Ind  << " q2Ind="<< q2Ind  << "Weight=" << Weight << endl;
01714                                 }}
01715                         } // Countqxy
01716                 } // Countkxy
01717 
01718 //              cout << "Finished Main Section " << endl;
01719 //              cout << " LradRange " <<LradRange <<  endl;
01720 
01721 
01722                 EMData *RotTransInvF  = new  EMData(LradRange,LradRange);
01723                 EMData *WeightImage   = new  EMData(LradRange,LradRange);
01724 
01725                 for (int jk =0; jk<LradRange ; jk++){// LradRange
01726                 for (int jq =jk; jq<LradRange; jq++){ // LradRange
01727                         int TotalInd      = jq*LradRange+jk;
01728                         int TotalIndBar   = jq*LradRange+jk;
01729                         float Weight = WeightInv[TotalInd] + WeightInv[TotalIndBar];
01730                         if (Weight <=0) continue;
01731                         WeightImage    -> set_value_at(jk,jq,Weight);
01732                         WeightImage    -> set_value_at(jq,jk,Weight);
01733 #ifdef _WIN32
01734                         float ValNow  = pow( (RotTransInv[TotalInd] + RotTransInv[TotalIndBar]) / Weight, 1.0f/3.0f )  ;
01735 #else
01736                         float ValNow  = cbrt( (RotTransInv[TotalInd] + RotTransInv[TotalIndBar]) / Weight )  ;
01737 #endif  //_WIN32
01738                         RotTransInvF -> set_value_at(jk,jq,ValNow);//  include /Weight
01739                         RotTransInvF -> set_value_at(jq,jk,ValNow );//  include /Weight
01740                 }}
01741 
01742 #ifdef  _WIN32
01743                 _unlink("WeightImage.???");
01744 #else
01745                 system("rm -f WeightImage.???");
01746 #endif  //_WIN32
01747                 WeightImage  -> write_image("WeightImage.img");
01748 
01749                 return  RotTransInvF ;
01750         }
01751         return 0;
01752 }
01753 
01754 
01755 void EMData::insert_clip(const EMData * const block, const IntPoint &origin) {
01756         int nx1 = block->get_xsize();
01757         int ny1 = block->get_ysize();
01758         int nz1 = block->get_zsize();
01759 
01760         Region area(origin[0], origin[1], origin[2],nx1, ny1, nz1);
01761 
01762         //make sure the block fits in EMData 
01763         int x0 = (int) area.origin[0];
01764         x0 = x0 < 0 ? 0 : x0;
01765 
01766         int y0 = (int) area.origin[1];
01767         y0 = y0 < 0 ? 0 : y0;
01768 
01769         int z0 = (int) area.origin[2];
01770         z0 = z0 < 0 ? 0 : z0;
01771 
01772         int x1 = (int) (area.origin[0] + area.size[0]);
01773         x1 = x1 > nx ? nx : x1;
01774 
01775         int y1 = (int) (area.origin[1] + area.size[1]);
01776         y1 = y1 > ny ? ny : y1;
01777 
01778         int z1 = (int) (area.origin[2] + area.size[2]);
01779         z1 = z1 > nz ? nz : z1;
01780         if (z1 <= 0) {
01781                 z1 = 1;
01782         }
01783 
01784         int xd0 = (int) (area.origin[0] < 0 ? -area.origin[0] : 0);
01785         int yd0 = (int) (area.origin[1] < 0 ? -area.origin[1] : 0);
01786         int zd0 = (int) (area.origin[2] < 0 ? -area.origin[2] : 0);
01787 
01788         if (x1 < x0 || y1 < y0 || z1 < z0) return; // out of bounds, this is fine, nothing happens
01789 
01790         size_t clipped_row_size = (x1-x0) * sizeof(float);
01791         size_t src_secsize =  (size_t)(nx1 * ny1);
01792         size_t dst_secsize = (size_t)(nx * ny);
01793 
01794 /*
01795 #ifdef EMAN2_USING_CUDA
01796         if(block->cudarwdata){
01797                 // this is VERY slow.....
01798                 float *cudasrc = block->cudarwdata + zd0 * src_secsize + yd0 * nx1 + xd0;
01799                 if(!cudarwdata) rw_alloc();
01800                 float *cudadst = cudarwdata + z0 * dst_secsize + y0 * nx + x0;
01801                 for (int i = z0; i < z1; i++) {
01802                         for (int j = y0; j < y1; j++) {
01803                                 //printf("%x %x %d\n", cudadst, cudasrc, clipped_row_size);
01804                                 cudaMemcpy(cudadst,cudasrc,clipped_row_size,cudaMemcpyDeviceToDevice);
01805                                 cudasrc += nx1;
01806                                 cudadst += nx;
01807                         }
01808                         cudasrc += src_gap;
01809                         cudadst += dst_gap;
01810                 }
01811                 return;
01812         }
01813 #endif
01814 */
01815         float *src = block->get_data() + zd0 * src_secsize + yd0 * nx1 + xd0;
01816         float *dst = get_data() + z0 * dst_secsize + y0 * nx + x0;
01817         
01818         size_t src_gap = src_secsize - (y1-y0) * nx1;
01819         size_t dst_gap = dst_secsize - (y1-y0) * nx;
01820         
01821         for (int i = z0; i < z1; i++) {
01822                 for (int j = y0; j < y1; j++) {
01823                         EMUtil::em_memcpy(dst, src, clipped_row_size);
01824                         src += nx1;
01825                         dst += nx;
01826                 }
01827                 src += src_gap;
01828                 dst += dst_gap;
01829         }
01830         
01831 #ifdef EMAN2_USING_CUDA 
01832         if(block->cudarwdata){
01833                 copy_to_cuda(); // copy back to device as padding is faster on the host
01834         }
01835 #endif
01836 
01837         update();
01838         EXITFUNC;
01839 }
01840 
01841 
01842 void EMData::insert_scaled_sum(EMData *block, const FloatPoint &center,
01843                                                    float scale, float)
01844 {
01845         ENTERFUNC;
01846         float * data = get_data();
01847         if (get_ndim()==3) {
01848                 // Start by determining the region to operate on
01849                 int xs=(int)floor(block->get_xsize()*scale/2.0);
01850                 int ys=(int)floor(block->get_ysize()*scale/2.0);
01851                 int zs=(int)floor(block->get_zsize()*scale/2.0);
01852                 int x0=(int)center[0]-xs;
01853                 int x1=(int)center[0]+xs;
01854                 int y0=(int)center[1]-ys;
01855                 int y1=(int)center[1]+ys;
01856                 int z0=(int)center[2]-zs;
01857                 int z1=(int)center[2]+zs;
01858 
01859                 if (x1<0||y1<0||z1<0||x0>get_xsize()||y0>get_ysize()||z0>get_zsize()) return;   // object is completely outside the target volume
01860 
01861                 // make sure we stay inside the volume
01862                 if (x0<0) x0=0;
01863                 if (y0<0) y0=0;
01864                 if (z0<0) z0=0;
01865                 if (x1>=get_xsize()) x1=get_xsize()-1;
01866                 if (y1>=get_ysize()) y1=get_ysize()-1;
01867                 if (z1>=get_zsize()) z1=get_zsize()-1;
01868 
01869                 float bx=block->get_xsize()/2.0f;
01870                 float by=block->get_ysize()/2.0f;
01871                 float bz=block->get_zsize()/2.0f;
01872 
01873                 size_t idx;
01874                 for (int x=x0; x<=x1; x++) {
01875                         for (int y=y0; y<=y1; y++) {
01876                                 for (int z=z0; z<=z1; z++) {
01877                                         idx = x + y * nx + (size_t)z * nx * ny;
01878                                         data[idx] +=
01879                                                 block->sget_value_at_interp((x-center[0])/scale+bx,(y-center[1])/scale+by,(z-center[2])/scale+bz);
01880                                 }
01881                         }
01882                 }
01883                 update();
01884         }
01885         else if (get_ndim()==2) {
01886                 // Start by determining the region to operate on
01887                 int xs=(int)floor(block->get_xsize()*scale/2.0);
01888                 int ys=(int)floor(block->get_ysize()*scale/2.0);
01889                 int x0=(int)center[0]-xs;
01890                 int x1=(int)center[0]+xs;
01891                 int y0=(int)center[1]-ys;
01892                 int y1=(int)center[1]+ys;
01893 
01894                 if (x1<0||y1<0||x0>get_xsize()||y0>get_ysize()) return; // object is completely outside the target volume
01895 
01896                 // make sure we stay inside the volume
01897                 if (x0<0) x0=0;
01898                 if (y0<0) y0=0;
01899                 if (x1>=get_xsize()) x1=get_xsize()-1;
01900                 if (y1>=get_ysize()) y1=get_ysize()-1;
01901 
01902                 float bx=block->get_xsize()/2.0f;
01903                 float by=block->get_ysize()/2.0f;
01904 
01905                 for (int x=x0; x<=x1; x++) {
01906                         for (int y=y0; y<=y1; y++) {
01907                                 data[x + y * nx] +=
01908                                         block->sget_value_at_interp((x-center[0])/scale+bx,(y-center[1])/scale+by);
01909                         }
01910                 }
01911                 update();
01912         }
01913         else {
01914                 LOGERR("insert_scaled_sum supports only 2D and 3D data");
01915                 throw ImageDimensionException("2D/3D only");
01916         }
01917 
01918         EXITFUNC;
01919 }
01920 //                      else if ( m == 0 )
01921 //                      {
01922 //                              if ( n_f == -ny/2 )
01923 //                              {
01924 //                                      t2++;
01925 // //                                   continue;
01926 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01927 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01928 //                                                      double cur_val = return_slice->get_value_at(x,y);
01929 //                                                      return_slice->set_value_at(x,y,cur_val+dat[idx]*std::pow(-1.0f,y));
01930 //                                              }
01931 //                                      }
01932 //                                      if (phase > 0.01 ) cout << "foo 2 " << phase << " " << amp << " " << dat[idx] << endl;
01933 //                              }
01934 //                              else
01935 //                              {
01936 //                                      if ( n_f < 1 ) continue;
01937 //                                      t3++;
01938 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01939 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01940 //                                                      double cur_val = return_slice->get_value_at(x,y);
01941 //                                                      return_slice->set_value_at(x,y,cur_val+2*amp*cos(ndash*y+phase));
01942 //                                              }
01943 //                                      }
01944 //                              }
01945 //                      }
01946 //                      else if ( n_f == -ny/2 )
01947 //                      {
01948 //                              if ( m == ((nx-2)/2) )
01949 //                              {
01950 //                                      t4++;
01951 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01952 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01953 //                                                      double cur_val = return_slice->get_value_at(x,y);
01954 //                                                      return_slice->set_value_at(x,y,cur_val+dat[idx]*std::pow(-1.0f,x+y));
01955 //                                              }
01956 //                                      }
01957 //                                      if (phase > 0.01 ) cout << "foo 4 " << phase << " " << amp << " " << dat[idx] << endl;
01958 //                              }
01959 //                              else
01960 //                              {
01961 //                                      t5++;
01962 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01963 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01964 //                                                      double cur_val = return_slice->get_value_at(x,y);
01965 //                                                      return_slice->set_value_at(x,y,cur_val+2*amp*cos(mdash*x+phase));
01966 //                                              }
01967 //                                      }
01968 //                              }
01969 //                      }
01970 //                      else if ( n_f == 0 )
01971 //                      {
01972 //                              if ( m == ((nx-2)/2) )
01973 //                              {
01974 //                                      t6++;
01975 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01976 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01977 //                                                      double cur_val = return_slice->get_value_at(x,y);
01978 //                                                      return_slice->set_value_at(x,y,cur_val+dat[idx]*std::pow(-1.0f,x));
01979 //                                              }
01980 //                                      }
01981 //                                      if (phase > 0.01 ) cout << "foo 3 " << phase << " " << amp << " " << dat[idx] << endl;
01982 //                              }
01983 //                              else
01984 //                              {
01985 //                                      t7++;
01986 //                                      for (int y = 0; y < return_slice->get_ysize(); ++y) {
01987 //                                              for (int x = 0; x < return_slice->get_xsize(); ++x) {
01988 //                                                      double cur_val = return_slice->get_value_at(x,y);
01989 //                                                      return_slice->set_value_at(x,y,cur_val+2*amp*cos(mdash*x+M_PI*y + phase));
01990 //                                              }
01991 //                                      }
01992 //                              }
01993 //                      }
01994 //                      else if ( m == ((nx-2)/2) )
01995 //                      {
01996 //                              if ( n_f < 1 ) continue;
01997 //                              t8++;
01998 //                              for (int y = 0; y < return_slice->get_ysize(); ++y) {
01999 //                                      for (int x = 0; x < return_slice->get_xsize(); ++x) {
02000 //                                              double cur_val = return_slice->get_value_at(x,y);
02001 //                                              return_slice->set_value_at(x,y,cur_val+2*amp*cos(ndash*y+M_PI*x+phase));
02002 //                                      }
02003 //                              }
02004 //                      }
02005 // }

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