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emdata.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 "all_imageio.h"
00038 #include "ctf.h"
00039 #include "processor.h"
00040 #include "aligner.h"
00041 #include "cmp.h"
00042 #include "emfft.h"
00043 #include "projector.h"
00044 #include "geometry.h"
00045 
00046 #include <gsl/gsl_sf_bessel.h>
00047 #include <gsl/gsl_errno.h>
00048 
00049 #include <iomanip>
00050 #include <complex>
00051 
00052 #include <algorithm> // fill
00053 #include <cmath>
00054 
00055 #ifdef WIN32
00056         #define M_PI 3.14159265358979323846f
00057 #endif  //WIN32
00058 
00059 #define EMDATA_EMAN2_DEBUG 0
00060 
00061 #ifdef EMAN2_USING_CUDA
00062 //#include <driver_functions.h>
00063 #include "cuda/cuda_processor.h"
00064 #include "cuda/cuda_emfft.h"
00065 #endif // EMAN2_USING_CUDA
00066 
00067 using namespace EMAN;
00068 using namespace std;
00069 using namespace boost;
00070 
00071 int EMData::totalalloc=0;               // mainly used for debugging/memory leak purposes
00072 
00073 EMData::EMData() :
00074 #ifdef EMAN2_USING_CUDA
00075                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0), 
00076 #endif //EMAN2_USING_CUDA
00077                 attr_dict(), rdata(0), supp(0), flags(0), changecount(0), nx(0), ny(0), nz(0), nxy(0), nxyz(0), xoff(0), yoff(0),
00078                 zoff(0), all_translation(),     path(""), pathnum(0), rot_fp(0)
00079 
00080 {
00081         ENTERFUNC;
00082 
00083         attr_dict["apix_x"] = 1.0f;
00084         attr_dict["apix_y"] = 1.0f;
00085         attr_dict["apix_z"] = 1.0f;
00086 
00087         attr_dict["is_complex"] = int(0);
00088         attr_dict["is_complex_x"] = int(0);
00089         attr_dict["is_complex_ri"] = int(1);
00090 
00091         attr_dict["datatype"] = (int)EMUtil::EM_FLOAT;
00092 
00093         EMData::totalalloc++;
00094 #ifdef MEMDEBUG2
00095         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00096 #endif
00097 
00098         EXITFUNC;
00099 }
00100 
00101 EMData::EMData(const string& filename, int image_index) :
00102 #ifdef EMAN2_USING_CUDA
00103                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0),
00104 #endif //EMAN2_USING_CUDA
00105                 attr_dict(), rdata(0), supp(0), flags(0), changecount(0), nx(0), ny(0), nz(0), nxy(0), nxyz(0), xoff(0), yoff(0), zoff(0),
00106                 all_translation(),      path(filename), pathnum(image_index), rot_fp(0)
00107 {
00108         ENTERFUNC;
00109 
00110         attr_dict["apix_x"] = 1.0f;
00111         attr_dict["apix_y"] = 1.0f;
00112         attr_dict["apix_z"] = 1.0f;
00113 
00114         attr_dict["is_complex"] = int(0);
00115         attr_dict["is_complex_x"] = int(0);
00116         attr_dict["is_complex_ri"] = int(1);
00117 
00118         attr_dict["datatype"] = (int)EMUtil::EM_FLOAT;
00119 
00120         this->read_image(filename, image_index);
00121 
00122         update();
00123         EMData::totalalloc++;
00124 #ifdef MEMDEBUG2
00125         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00126 #endif
00127 
00128         EXITFUNC;
00129 }
00130 
00131 EMData::EMData(const EMData& that) :
00132 #ifdef EMAN2_USING_CUDA
00133                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0),
00134 #endif //EMAN2_USING_CUDA
00135                 attr_dict(that.attr_dict), rdata(0), supp(0), flags(that.flags), changecount(that.changecount), nx(that.nx), ny(that.ny), nz(that.nz),
00136                 nxy(that.nx*that.ny), nxyz((size_t)that.nx*that.ny*that.nz), xoff(that.xoff), yoff(that.yoff), zoff(that.zoff),all_translation(that.all_translation),   path(that.path),
00137                 pathnum(that.pathnum), rot_fp(0)
00138 {
00139         ENTERFUNC;
00140         
00141         float* data = that.rdata;
00142         size_t num_bytes = (size_t)nx*ny*nz*sizeof(float);
00143         if (data && num_bytes != 0)
00144         {
00145                 rdata = (float*)EMUtil::em_malloc(num_bytes);
00146                 EMUtil::em_memcpy(rdata, data, num_bytes);
00147         }
00148 #ifdef EMAN2_USING_CUDA
00149         if (num_bytes != 0 && that.cudarwdata != 0) {
00150                 //cout << "That copy constructor" << endl;
00151                 rw_alloc();
00152                 cudaError_t error = cudaMemcpy(cudarwdata,that.cudarwdata,num_bytes,cudaMemcpyDeviceToDevice);
00153                 if ( error != cudaSuccess ) throw UnexpectedBehaviorException("cudaMemcpy failed in EMData copy construction with error: " + string(cudaGetErrorString(error)));
00154         }
00155 #endif //EMAN2_USING_CUDA
00156 
00157         if (that.rot_fp != 0) rot_fp = new EMData(*(that.rot_fp));
00158 
00159         EMData::totalalloc++;
00160 #ifdef MEMDEBUG2
00161         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00162 #endif
00163 
00164         ENTERFUNC;
00165 }
00166 
00167 EMData& EMData::operator=(const EMData& that)
00168 {
00169         ENTERFUNC;
00170 
00171         if ( this != &that )
00172         {
00173                 free_memory(); // Free memory sets nx,ny and nz to 0
00174 
00175                 // Only copy the rdata if it exists, we could be in a scenario where only the header has been read
00176                 float* data = that.rdata;
00177                 size_t num_bytes = that.nx*that.ny*that.nz*sizeof(float);
00178                 if (data && num_bytes != 0)
00179                 {
00180                         nx = 1; // This prevents a memset in set_size
00181                         set_size(that.nx,that.ny,that.nz);
00182                         EMUtil::em_memcpy(rdata, data, num_bytes);
00183                 }
00184 
00185                 flags = that.flags;
00186 
00187                 all_translation = that.all_translation;
00188 
00189                 path = that.path;
00190                 pathnum = that.pathnum;
00191                 attr_dict = that.attr_dict;
00192 
00193                 xoff = that.xoff;
00194                 yoff = that.yoff;
00195                 zoff = that.zoff;
00196 
00197 #ifdef EMAN2_USING_CUDA
00198                 cout << "That copy constructor #2" << endl;
00199                 if (num_bytes != 0 && that.cudarwdata != 0) {
00200                         rw_alloc();
00201                         cudaError_t error = cudaMemcpy(cudarwdata,that.cudarwdata,num_bytes,cudaMemcpyDeviceToDevice);
00202                         if ( error != cudaSuccess ) throw UnexpectedBehaviorException("cudaMemcpy failed in EMData copy construction with error: " + string(cudaGetErrorString(error)));
00203                         
00204                 }
00205 #endif //EMAN2_USING_CUDA
00206 
00207                 changecount = that.changecount;
00208 
00209                 if (that.rot_fp != 0) rot_fp = new EMData(*(that.rot_fp));
00210                 else rot_fp = 0;
00211         }
00212         EXITFUNC;
00213         return *this;
00214 }
00215 
00216 EMData::EMData(int nx, int ny, int nz, bool is_real) :
00217 #ifdef EMAN2_USING_CUDA
00218                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0),
00219 #endif //EMAN2_USING_CUDA
00220                 attr_dict(), rdata(0), supp(0), flags(0), changecount(0), nx(0), ny(0), nz(0), nxy(0), nxyz(0), xoff(0), yoff(0), zoff(0),
00221                 all_translation(),      path(""), pathnum(0), rot_fp(0)
00222 {
00223         ENTERFUNC;
00224 
00225         // used to replace cube 'pixel'
00226         attr_dict["apix_x"] = 1.0f;
00227         attr_dict["apix_y"] = 1.0f;
00228         attr_dict["apix_z"] = 1.0f;
00229 
00230         if(is_real) {   // create a real image [nx, ny, nz]
00231                 attr_dict["is_complex"] = int(0);
00232                 attr_dict["is_complex_x"] = int(0);
00233                 attr_dict["is_complex_ri"] = int(1);
00234                 set_size(nx, ny, nz);
00235         }
00236         else {  //create a complex image which real dimension is [ny, ny, nz]
00237                 int new_nx = nx + 2 - nx%2;
00238                 set_size(new_nx, ny, nz);
00239 
00240                 attr_dict["is_complex"] = int(1);
00241 
00242                 if(ny==1 && nz ==1)     {
00243                         attr_dict["is_complex_x"] = int(1);
00244                 }
00245                 else {
00246                         attr_dict["is_complex_x"] = int(0);
00247                 }
00248 
00249                 attr_dict["is_complex_ri"] = int(1);
00250                 attr_dict["is_fftpad"] = int(1);
00251 
00252                 if(nx%2 == 1) {
00253                         attr_dict["is_fftodd"] = 1;
00254                 }
00255         }
00256 
00257         this->to_zero();
00258         update();
00259         EMData::totalalloc++;
00260 #ifdef MEMDEBUG2
00261         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00262 #endif
00263 
00264         EXITFUNC;
00265 }
00266 
00267 
00268 EMData::EMData(float* data, const int x, const int y, const int z, const Dict& attr_dict) :
00269 #ifdef EMAN2_USING_CUDA
00270                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0),
00271 #endif //EMAN2_USING_CUDA
00272                 attr_dict(attr_dict), rdata(data), supp(0), flags(0), changecount(0), nx(x), ny(y), nz(z), nxy(x*y), nxyz((size_t)x*y*z), xoff(0),
00273                 yoff(0), zoff(0), all_translation(), path(""), pathnum(0), rot_fp(0)
00274 {
00275         ENTERFUNC;
00276         // used to replace cube 'pixel'
00277         attr_dict["apix_x"] = 1.0f;
00278         attr_dict["apix_y"] = 1.0f;
00279         attr_dict["apix_z"] = 1.0f;
00280 
00281         EMData::totalalloc++;
00282 #ifdef MEMDEBUG2
00283         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00284 #endif
00285 
00286         update();
00287         EXITFUNC;
00288 }
00289 
00290 #ifdef EMAN2_USING_CUDA
00291 
00292 EMData::EMData(float* data, float* cudadata, const int x, const int y, const int z, const Dict& attr_dict) :
00293                 cudarwdata(cudadata), cudarodata(0), num_bytes(x*y*z*sizeof(float)), nextlistitem(0), prevlistitem(0), roneedsupdate(0),
00294                 attr_dict(attr_dict), rdata(data), supp(0), flags(0), changecount(0), nx(x), ny(y), nz(z), nxy(x*y), nxyz((size_t)x*y*z), xoff(0),
00295                 yoff(0), zoff(0), all_translation(), path(""), pathnum(0), rot_fp(0)
00296 {
00297         ENTERFUNC;
00298 
00299         // used to replace cube 'pixel'
00300         attr_dict["apix_x"] = 1.0f;
00301         attr_dict["apix_y"] = 1.0f;
00302         attr_dict["apix_z"] = 1.0f;
00303 
00304         EMData::totalalloc++;
00305 #ifdef MEMDEBUG2
00306         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00307 #endif
00308 
00309         update();
00310         EXITFUNC;
00311 }
00312 
00313 #endif //EMAN2_USING_CUDA
00314 
00315 //debug
00316 using std::cout;
00317 using std::endl;
00318 EMData::~EMData()
00319 {
00320         ENTERFUNC;
00321         free_memory();
00322 
00323 #ifdef EMAN2_USING_CUDA
00324         if(cudarwdata){rw_free();}
00325         if(cudarodata){ro_free();}
00326 #endif // EMAN2_USING_CUDA
00327         EMData::totalalloc--;
00328 #ifdef MEMDEBUG2
00329         printf("EMDATA-  %4d    %p\n",EMData::totalalloc,this);
00330 #endif
00331         EXITFUNC;
00332 }
00333 
00334 void EMData::clip_inplace(const Region & area,const float& fill_value)
00335 {
00336         // Added by d.woolford
00337         ENTERFUNC;
00338 
00339 //      printf("cip %d %d %d %d %d %d %f %d %d %d\n",area.origin[0],area.origin[1],area.origin[2],area.size[0],area.size[1],area.size[2],fill_value,nx,ny,nz);
00340         // Store the current dimension values
00341         int prev_nx = nx, prev_ny = ny, prev_nz = nz;
00342         size_t prev_size = (size_t)nx*ny*nz;
00343 
00344         // Get the zsize, ysize and xsize of the final area, these are the new dimension sizes of the pixel data
00345         int new_nz = ( area.size[2]==0 ? 1 : (int)area.size[2]);
00346         int new_ny = ( area.size[1]==0 ? 1 : (int)area.size[1]);
00347         int new_nx = (int)area.size[0];
00348 
00349         if ( new_nz < 0 || new_ny < 0 || new_nx < 0 )
00350         {
00351                 // Negative image dimensions were never tested nor considered when creating this implementation
00352                 throw ImageDimensionException("New image dimensions are negative - this is not supported in the clip_inplace operation");
00353         }
00354 
00355         size_t new_size = (size_t)new_nz*new_ny*new_nx;
00356 
00357         // Get the translation values, they are used to construct the ClipInplaceVariables object
00358         int x0 = (int) area.origin[0];
00359         int y0 = (int) area.origin[1];
00360         int z0 = (int) area.origin[2];
00361 
00362         // Get a object that calculates all the interesting variables associated with the clip inplace operation
00363         ClipInplaceVariables civ(prev_nx, prev_ny, prev_nz, new_nx, new_ny, new_nz, x0, y0, z0);
00364 
00365         get_data(); // Do this here to make sure rdata is up to date, applicable if GPU stuff is occuring
00366         // Double check to see if any memory shifting even has to occur
00367         if ( x0 > prev_nx || y0 > prev_ny || z0 > prev_nz || civ.x_iter == 0 || civ.y_iter == 0 || civ.z_iter == 0)
00368         {
00369                 // In this case the volume has been shifted beyond the location of the pixel rdata and
00370                 // the client should expect to see a volume with nothing in it.
00371 
00372                 // Set size calls realloc,
00373                 set_size(new_nx, new_ny, new_nz);
00374 
00375                 // Set pixel memory to zero - the client should expect to see nothing
00376                 EMUtil::em_memset(rdata, 0, (size_t)new_nx*new_ny*new_nz);
00377 
00378                 return;
00379         }
00380 
00381         // Resize the volume before memory shifting occurs if the new volume is larger than the previous volume
00382         // All of the pixel rdata is guaranteed to be at the start of the new volume because realloc (called in set size)
00383         // guarantees this.
00384         if ( new_size > prev_size )
00385                 set_size(new_nx, new_ny, new_nz);
00386 
00387         // Store the clipped row size.
00388         size_t clipped_row_size = (civ.x_iter) * sizeof(float);
00389 
00390         // Get the new sector sizes to save multiplication later.
00391         size_t new_sec_size = new_nx * new_ny;
00392         size_t prev_sec_size = prev_nx * prev_ny;
00393 
00394         // Determine the memory locations of the source and destination pixels - at the point nearest
00395         // to the beginning of the volume (rdata)
00396         size_t src_it_begin = civ.prv_z_bottom*prev_sec_size + civ.prv_y_front*prev_nx + civ.prv_x_left;
00397         size_t dst_it_begin = civ.new_z_bottom*new_sec_size + civ.new_y_front*new_nx + civ.new_x_left;
00398 
00399         // This loop is in the forward direction (starting at points nearest to the beginning of the volume)
00400         // it copies memory only when the destination pointer is less the source pointer - therefore
00401         // ensuring that no memory "copied to" is yet to be "copied from"
00402         for (int i = 0; i < civ.z_iter; ++i) {
00403                 for (int j = 0; j < civ.y_iter; ++j) {
00404 
00405                         // Determine the memory increments as dependent on i and j
00406                         // This could be optimized so that not so many multiplications are occurring...
00407                         size_t dst_inc = dst_it_begin + j*new_nx + i*new_sec_size;
00408                         size_t src_inc = src_it_begin + j*prev_nx + i*prev_sec_size;
00409                         float* local_dst = rdata + dst_inc;
00410                         float* local_src = rdata + src_inc;
00411 
00412                         if ( dst_inc >= src_inc )
00413                         {
00414                                 // this is fine, it will happen now and then and it will be necessary to continue.
00415                                 // the tempatation is to break, but you can't do that (because the point where memory intersects
00416                                 // could be in this slice - and yes, this aspect could be optimized).
00417                                 continue;
00418                         }
00419 
00420                         // Asserts are compiled only in debug mode
00421                         // This situation not encountered in testing thus far
00422                         Assert( dst_inc < new_size && src_inc < prev_size && dst_inc >= 0 && src_inc >= 0 );
00423 
00424                         // Finally copy the memory
00425                         EMUtil::em_memcpy(local_dst, local_src, clipped_row_size);
00426                 }
00427         }
00428 
00429         // Determine the memory locations of the source and destination pixels - at the point nearest
00430         // to the end of the volume (rdata+new_size)
00431         size_t src_it_end = prev_size - civ.prv_z_top*prev_sec_size - civ.prv_y_back*prev_nx - prev_nx + civ.prv_x_left;
00432         size_t dst_it_end = new_size - civ.new_z_top*new_sec_size - civ.new_y_back*new_nx - new_nx + civ.new_x_left;
00433 
00434         // This loop is in the reverse direction (starting at points nearest to the end of the volume).
00435         // It copies memory only when the destination pointer is greater than  the source pointer therefore
00436         // ensuring that no memory "copied to" is yet to be "copied from"
00437         for (int i = 0; i < civ.z_iter; ++i) {
00438                 for (int j = 0; j < civ.y_iter; ++j) {
00439 
00440                         // Determine the memory increments as dependent on i and j
00441                         size_t dst_inc = dst_it_end - j*new_nx - i*new_sec_size;
00442                         size_t src_inc = src_it_end - j*prev_nx - i*prev_sec_size;
00443                         float* local_dst = rdata + dst_inc;
00444                         float* local_src = rdata + src_inc;
00445 
00446                         if (dst_inc <= (src_inc + civ.x_iter ))
00447                         {
00448                                 // Overlap
00449                                 if ( dst_inc > src_inc )
00450                                 {
00451                                         // Because the memcpy operation is the forward direction, and this "reverse
00452                                         // direction" loop is proceeding in a backwards direction, it is possible
00453                                         // that memory copied to is yet to be copied from (because memcpy goes forward).
00454                                         // In this scenario pixel memory "copied to" is yet to be "copied from"
00455                                         // i.e. there is overlap
00456 
00457                                         // memmove handles overlapping cases.
00458                                         // memmove could use a temporary buffer, or could go just go backwards
00459                                         // the specification doesn't say how the function behaves...
00460                                         // If memmove creates a temporary buffer is clip_inplace no longer inplace?
00461                                         memmove(local_dst, local_src, clipped_row_size);
00462                                 }
00463                                 continue;
00464                         }
00465 
00466                         // This situation not encountered in testing thus far
00467                         Assert( dst_inc < new_size && src_inc < prev_size && dst_inc >= 0 && src_inc >= 0 );
00468 
00469                         // Perform the memory copy
00470                         EMUtil::em_memcpy(local_dst, local_src, clipped_row_size);
00471                 }
00472         }
00473 
00474         // Resize the volume after memory shifting occurs if the new volume is smaller than the previous volume
00475         // set_size calls realloc, guaranteeing that the pixel rdata is in the right location.
00476         if ( new_size < prev_size )
00477                 set_size(new_nx, new_ny, new_nz);
00478 
00479         // Now set all the edges to zero
00480 
00481         // Set the extra bottom z slices to the fill_value
00482         if (  z0 < 0 )
00483         {
00484                 //EMUtil::em_memset(rdata, 0, (-z0)*new_sec_size*sizeof(float));
00485                 size_t inc = (-z0)*new_sec_size;
00486                 std::fill(rdata,rdata+inc,fill_value);
00487         }
00488 
00489         // Set the extra top z slices to the fill_value
00490         if (  civ.new_z_top > 0 )
00491         {
00492                 float* begin_pointer = rdata + (new_nz-civ.new_z_top)*new_sec_size;
00493                 //EMUtil::em_memset(begin_pointer, 0, (civ.new_z_top)*new_sec_size*sizeof(float));
00494                 float* end_pointer = begin_pointer+(civ.new_z_top)*new_sec_size;
00495                 std::fill(begin_pointer,end_pointer,fill_value);
00496         }
00497 
00498         // Next deal with x and y edges by iterating through each slice
00499         for ( int i = civ.new_z_bottom; i < civ.new_z_bottom + civ.z_iter; ++i )
00500         {
00501                 // Set the extra front y components to the fill_value
00502                 if ( y0 < 0 )
00503                 {
00504                         float* begin_pointer = rdata + i*new_sec_size;
00505                         //EMUtil::em_memset(begin_pointer, 0, (-y0)*new_nx*sizeof(float));
00506                         float* end_pointer = begin_pointer+(-y0)*new_nx;
00507                         std::fill(begin_pointer,end_pointer,fill_value);
00508                 }
00509 
00510                 // Set the extra back y components to the fill_value
00511                 if ( civ.new_y_back > 0 )
00512                 {
00513                         float* begin_pointer = rdata + i*new_sec_size + (new_ny-civ.new_y_back)*new_nx;
00514                         //EMUtil::em_memset(begin_pointer, 0, (civ.new_y_back)*new_nx*sizeof(float));
00515                         float* end_pointer = begin_pointer+(civ.new_y_back)*new_nx;
00516                         std::fill(begin_pointer,end_pointer,fill_value);
00517                 }
00518 
00519                 // Iterate through the y to set each correct x component to the fill_value
00520                 for (int j = civ.new_y_front; j <civ.new_y_front + civ.y_iter; ++j)
00521                 {
00522                         // Set the extra left x components to the fill_value
00523                         if ( x0 < 0 )
00524                         {
00525                                 float* begin_pointer = rdata + i*new_sec_size + j*new_nx;
00526                                 //EMUtil::em_memset(begin_pointer, 0, (-x0)*sizeof(float));
00527                                 float* end_pointer = begin_pointer+(-x0);
00528                                 std::fill(begin_pointer,end_pointer,fill_value);
00529                         }
00530 
00531                         // Set the extra right x components to the fill_value
00532                         if ( civ.new_x_right > 0 )
00533                         {
00534                                 float* begin_pointer = rdata + i*new_sec_size + j*new_nx + (new_nx - civ.new_x_right);
00535                                 //EMUtil::em_memset(begin_pointer, 0, (civ.new_x_right)*sizeof(float));
00536                                 float* end_pointer = begin_pointer+(civ.new_x_right);
00537                                 std::fill(begin_pointer,end_pointer,fill_value);
00538                         }
00539 
00540                 }
00541         }
00542 
00543 // These couts may be useful
00544 //      cout << "start starts " << civ.prv_x_left << " " << civ.prv_y_front << " " << civ.prv_z_bottom << endl;
00545 //      cout << "start ends " << civ.prv_x_right << " " << civ.prv_y_back << " " << civ.prv_z_top << endl;
00546 //      cout << "dst starts " << civ.new_x_left << " " << civ.new_y_front << " " << civ.new_z_bottom << endl;
00547 //      cout << "dst ends " << civ.new_x_right << " " << civ.new_y_back << " " << civ.new_z_top << endl;
00548 //      cout << "total iter z - " << civ.z_iter << " y - " << civ.y_iter << " x - " << civ.x_iter << endl;
00549 //      cout << "=====" << endl;
00550 //      cout << "dst_end is " << dst_it_end << " src end is " << src_it_end << endl;
00551 //      cout << "dst_begin is " << dst_it_begin << " src begin is " << src_it_begin << endl;
00552 
00553         // Update appropriate attributes (Copied and pasted from get_clip)
00554         if( attr_dict.has_key("origin_x") && attr_dict.has_key("origin_y") &&
00555         attr_dict.has_key("origin_z") )
00556         {
00557                 float xorigin = attr_dict["origin_x"];
00558                 float yorigin = attr_dict["origin_y"];
00559                 float zorigin = attr_dict["origin_z"];
00560 
00561                 float apix_x = attr_dict["apix_x"];
00562                 float apix_y = attr_dict["apix_y"];
00563                 float apix_z = attr_dict["apix_z"];
00564 
00565                 set_xyz_origin(xorigin + apix_x * area.origin[0],
00566                         yorigin + apix_y * area.origin[1],
00567                         zorigin + apix_z * area.origin[2]);
00568         }
00569 
00570         // Set the update flag because the size of the image has changed and stats should probably be recalculated if requested.
00571         update();
00572 
00573         EXITFUNC;
00574 }
00575 
00576 EMData *EMData::get_clip(const Region & area, const float fill) const
00577 {
00578         ENTERFUNC;
00579         if (get_ndim() != area.get_ndim()) {
00580                 LOGERR("cannot get %dD clip out of %dD image", area.get_ndim(),get_ndim());
00581                 return 0;
00582         }
00583 
00584         EMData *result = new EMData();
00585 
00586         // Ensure that all of the metadata of this is stored in the new object
00587         // Originally added to ensure that euler angles were retained when preprocessing (zero padding) images
00588         // prior to insertion into the 3D for volume in the reconstruction phase (see reconstructor.cpp/h).
00589         result->attr_dict = this->attr_dict;
00590         int zsize = (int)area.size[2];
00591         if (zsize == 0 && nz <= 1) {
00592                 zsize = 1;
00593         }
00594         int ysize = (ny<=1 && (int)area.size[1]==0 ? 1 : (int)area.size[1]);
00595 
00596         if ( (int)area.size[0] < 0 || ysize < 0 || zsize < 0 )
00597         {
00598                 // Negative image dimensions not supported - added retrospectively by d.woolford (who didn't write get_clip but wrote clip_inplace)
00599                 throw ImageDimensionException("New image dimensions are negative - this is not supported in the the get_clip operation");
00600         }
00601 
00602 //#ifdef EMAN2_USING_CUDA
00603         // Strategy is always to prefer using the GPU if possible
00604 //      bool use_gpu = false;
00605 //      if ( gpu_operation_preferred() ) {
00606 //              result->set_size_cuda((int)area.size[0], ysize, zsize);
00607                 //CudaDataLock lock(this); // Just so we never have to recopy this data to and from the GPU
00608 //              result->get_cuda_data(); // Force the allocation - set_size_cuda is lazy
00609                 // Setting the value is necessary seeing as cuda data is not automatically zeroed
00610 //              result->to_value(fill); // This will automatically use the GPU.
00611 //              use_gpu = true;
00612 //      } else { // cpu == True
00613 //              result->set_size((int)area.size[0], ysize, zsize);
00614 //              if (fill != 0.0) { result->to_value(fill); };
00615 //      }
00616 //#else
00617         result->set_size((int)area.size[0], ysize, zsize);
00618         if (fill != 0.0) { result->to_value(fill); };
00619 //#endif //EMAN2_USING_CUDA
00620 
00621         int x0 = (int) area.origin[0];
00622         x0 = x0 < 0 ? 0 : x0;
00623 
00624         int y0 = (int) area.origin[1];
00625         y0 = y0 < 0 ? 0 : y0;
00626 
00627         int z0 = (int) area.origin[2];
00628         z0 = z0 < 0 ? 0 : z0;
00629 
00630         int x1 = (int) (area.origin[0] + area.size[0]);
00631         x1 = x1 > nx ? nx : x1;
00632 
00633         int y1 = (int) (area.origin[1] + area.size[1]);
00634         y1 = y1 > ny ? ny : y1;
00635 
00636         int z1 = (int) (area.origin[2] + area.size[2]);
00637         z1 = z1 > nz ? nz : z1;
00638         if (z1 <= 0) {
00639                 z1 = 1;
00640         }
00641 
00642         result->insert_clip(this,-((IntPoint)area.origin));
00643 
00644         if( attr_dict.has_key("apix_x") && attr_dict.has_key("apix_y") &&
00645                 attr_dict.has_key("apix_z") )
00646         {
00647                 if( attr_dict.has_key("origin_x") && attr_dict.has_key("origin_y") &&
00648                     attr_dict.has_key("origin_z") )
00649                 {
00650                         float xorigin = attr_dict["origin_x"];
00651                         float yorigin = attr_dict["origin_y"];
00652                         float zorigin = attr_dict["origin_z"];
00653 
00654                         float apix_x = attr_dict["apix_x"];
00655                         float apix_y = attr_dict["apix_y"];
00656                         float apix_z = attr_dict["apix_z"];
00657 
00658                         result->set_xyz_origin(xorigin + apix_x * area.origin[0],
00659                                                                    yorigin + apix_y * area.origin[1],
00660                                                                zorigin + apix_z * area.origin[2]);
00661                 }
00662         }
00663 
00664 //#ifdef EMAN2_USING_CUDA
00665 //      if (use_gpu) result->gpu_update();
00666 //      else result->update();
00667 //#else
00668         result->update();
00669 //#endif // EMAN2_USING_CUDA
00670 
00671 
00672         result->set_path(path);
00673         result->set_pathnum(pathnum);
00674 
00675         EXITFUNC;
00676         return result;
00677 }
00678 
00679 
00680 EMData *EMData::get_top_half() const
00681 {
00682         ENTERFUNC;
00683 
00684         if (get_ndim() != 3) {
00685                 throw ImageDimensionException("3D only");
00686         }
00687 
00688         EMData *half = new EMData();
00689         half->attr_dict = attr_dict;
00690         half->set_size(nx, ny, nz / 2);
00691 
00692         float *half_data = half->get_data();
00693         EMUtil::em_memcpy(half_data, &(get_data()[(size_t)nz / 2 * (size_t)nx * (size_t)ny]), sizeof(float) * (size_t)nx * (size_t)ny * (size_t)nz / 2lu);
00694 
00695         float apix_z = attr_dict["apix_z"];
00696         float origin_z = attr_dict["origin_z"];
00697         origin_z += apix_z * nz / 2;
00698         half->attr_dict["origin_z"] = origin_z;
00699         half->update();
00700 
00701         EXITFUNC;
00702         return half;
00703 }
00704 
00705 
00706 EMData *EMData::get_rotated_clip(const Transform &xform,
00707                                                                  const IntSize &size, float)
00708 {
00709         EMData *result = new EMData();
00710         result->set_size(size[0],size[1],size[2]);
00711 
00712         if (nz==1) {
00713                 for (int y=-size[1]/2; y<(size[1]+1)/2; y++) {
00714                         for (int x=-size[0]/2; x<(size[0]+1)/2; x++) {
00715                                 Vec3f xv=xform.transform(Vec3f((float)x,(float)y,0.0f));
00716                                 float v = 0;
00717 
00718                                 if (xv[0]<0||xv[1]<0||xv[0]>nx-2||xv[1]>ny-2) v=0.;
00719                                 else v=sget_value_at_interp(xv[0],xv[1]);
00720                                 result->set_value_at(x+size[0]/2,y+size[1]/2,v);
00721                         }
00722                 }
00723         }
00724         else {
00725                 for (int z=-size[2]/2; z<(size[2]+1)/2; z++) {
00726                         for (int y=-size[1]/2; y<(size[1]+1)/2; y++) {
00727                                 for (int x=-size[0]/2; x<(size[0]+1)/2; x++) {
00728                                         Vec3f xv=xform.transform(Vec3f((float)x,(float)y,0.0f));
00729                                         float v = 0;
00730 
00731                                         if (xv[0]<0||xv[1]<0||xv[2]<0||xv[0]>nx-2||xv[1]>ny-2||xv[2]>nz-2) v=0.;
00732                                         else v=sget_value_at_interp(xv[0],xv[1],xv[2]);
00733                                         result->set_value_at(x+size[0]/2,y+size[1]/2,z+size[2]/2,v);
00734                                 }
00735                         }
00736                 }
00737         }
00738         result->update();
00739 
00740         return result;
00741 }
00742 
00743 
00744 EMData* EMData::window_center(int l) {
00745         ENTERFUNC;
00746         // sanity checks
00747         int n = nx;
00748         if (is_complex()) {
00749                 LOGERR("Need real-space data for window_center()");
00750                 throw ImageFormatException(
00751                         "Complex input image; real-space expected.");
00752         }
00753         if (is_fftpadded()) {
00754                 // image has been fft-padded, compute the real-space size
00755                 n -= (2 - int(is_fftodd()));
00756         }
00757         int corner = n/2 - l/2;
00758         int ndim = get_ndim();
00759         EMData* ret;
00760         switch (ndim) {
00761                 case 3:
00762                         if ((n != ny) || (n != nz)) {
00763                                 LOGERR("Need the real-space image to be cubic.");
00764                                 throw ImageFormatException(
00765                                                 "Need cubic real-space image.");
00766                         }
00767                         ret = get_clip(Region(corner, corner, corner, l, l, l));
00768                         break;
00769                 case 2:
00770                         if (n != ny) {
00771                                 LOGERR("Need the real-space image to be square.");
00772                                 throw ImageFormatException(
00773                                                 "Need square real-space image.");
00774                         }
00775                         //cout << "Using corner " << corner << endl;
00776                         ret = get_clip(Region(corner, corner, l, l));
00777                         break;
00778                 case 1:
00779                         ret = get_clip(Region(corner, l));
00780                         break;
00781                 default:
00782                         throw ImageDimensionException(
00783                                         "window_center only supports 1-d, 2-d, and 3-d images");
00784         }
00785         return ret;
00786         EXITFUNC;
00787 }
00788 
00789 
00790 float *EMData::setup4slice(bool redo)
00791 {
00792         ENTERFUNC;
00793 
00794         if (!is_complex()) {
00795                 throw ImageFormatException("complex image only");
00796         }
00797 
00798         if (get_ndim() != 3) {
00799                 throw ImageDimensionException("3D only");
00800         }
00801 
00802         if (supp) {
00803                 if (redo) {
00804                         EMUtil::em_free(supp);
00805                         supp = 0;
00806                 }
00807                 else {
00808                         EXITFUNC;
00809                         return supp;
00810                 }
00811         }
00812 
00813         const int SUPP_ROW_SIZE = 8;
00814         const int SUPP_ROW_OFFSET = 4;
00815         const int supp_size = SUPP_ROW_SIZE + SUPP_ROW_OFFSET;
00816 
00817         supp = (float *) EMUtil::em_calloc(supp_size * ny * nz, sizeof(float));
00818         int nxy = nx * ny;
00819         int supp_xy = supp_size * ny;
00820         float * data = get_data();
00821 
00822         for (int z = 0; z < nz; z++) {
00823                 size_t cur_z1 = z * nxy;
00824                 size_t cur_z2 = z * supp_xy;
00825 
00826                 for (int y = 0; y < ny; y++) {
00827                         size_t cur_y1 = y * nx;
00828                         size_t cur_y2 = y * supp_size;
00829 
00830                         for (int x = 0; x < SUPP_ROW_SIZE; x++) {
00831                                 size_t k = (x + SUPP_ROW_OFFSET) + cur_y2 + cur_z2;
00832                                 supp[k] = data[x + cur_y1 + cur_z1];
00833                         }
00834                 }
00835         }
00836 
00837         for (int z = 1, zz = nz - 1; z < nz; z++, zz--) {
00838                 size_t cur_z1 = zz * nxy;
00839                 size_t cur_z2 = z * supp_xy;
00840 
00841                 for (int y = 1, yy = ny - 1; y < ny; y++, yy--) {
00842                         supp[y * 12 + cur_z2] = data[4 + yy * nx + cur_z1];
00843                         supp[1 + y * 12 + cur_z2] = -data[5 + yy * nx + cur_z1];
00844                         supp[2 + y * 12 + cur_z2] = data[2 + yy * nx + cur_z1];
00845                         supp[3 + y * 12 + cur_z2] = -data[3 + yy * nx + cur_z1];
00846                 }
00847         }
00848 
00849         EXITFUNC;
00850         return supp;
00851 }
00852 
00853 
00854 void EMData::scale(float s)
00855 {
00856         ENTERFUNC;
00857         Transform t;
00858         t.set_scale(s);
00859         transform(t);
00860         EXITFUNC;
00861 }
00862 
00863 
00864 void EMData::translate(int dx, int dy, int dz)
00865 {
00866         ENTERFUNC;
00867         translate(Vec3i(dx, dy, dz));
00868         EXITFUNC;
00869 }
00870 
00871 
00872 void EMData::translate(float dx, float dy, float dz)
00873 {
00874         ENTERFUNC;
00875         int dx_ = Util::round(dx);
00876         int dy_ = Util::round(dy);
00877         int dz_ = Util::round(dz);
00878         if( ( (dx-dx_) == 0 ) && ( (dy-dy_) == 0 ) && ( (dz-dz_) == 0 )) {
00879                 translate(dx_, dy_, dz_);
00880         }
00881         else {
00882                 translate(Vec3f(dx, dy, dz));
00883         }
00884         EXITFUNC;
00885 }
00886 
00887 
00888 void EMData::translate(const Vec3i &translation)
00889 {
00890         ENTERFUNC;
00891 
00892         //if traslation is 0, do nothing
00893         if( translation[0] == 0 && translation[1] == 0 && translation[2] == 0) {
00894                 EXITFUNC;
00895                 return;
00896         }
00897 
00898         Dict params("trans",static_cast< vector<int> >(translation));
00899         process_inplace("math.translate.int",params);
00900 
00901         // update() - clip_inplace does the update
00902         all_translation += translation;
00903 
00904         EXITFUNC;
00905 }
00906 
00907 
00908 void EMData::translate(const Vec3f &translation)
00909 {
00910         ENTERFUNC;
00911 
00912         if( translation[0] == 0.0f && translation[1] == 0.0f && translation[2] == 0.0f ) {
00913                 EXITFUNC;
00914                 return;
00915         }
00916 
00917         Transform* t = new Transform();
00918         t->set_trans(translation);
00919         process_inplace("xform",Dict("transform",t));
00920         delete t;
00921 
00922         all_translation += translation;
00923         EXITFUNC;
00924 }
00925 
00926 
00927 void EMData::rotate(float az, float alt, float phi)
00928 {
00929         Dict d("type","eman");
00930         d["az"] = az;
00931         d["alt"] = alt;
00932         d["phi"] = phi;
00933         Transform t(d);
00934         transform(t);
00935 }
00936 
00937 
00938 
00939 void EMData::rotate(const Transform & t)
00940 {
00941         cout << "Deprecation warning in EMData::rotate. Please consider using EMData::transform() instead " << endl;
00942         transform(t);
00943 }
00944 
00945 float EMData::max_3D_pixel_error(const Transform &t1, const Transform & t2, float r) {
00946         
00947         Transform t;
00948         int r0 = (int)r;
00949         float ddmax = 0.0f;
00950 
00951         t = t2*t1.inverse();
00952         for (int i=0; i<int(2*M_PI*r0+0.5); i++) {
00953                 Vec3f v = Vec3f(r0*cos((float)i), r0*sin((float)i), 0);
00954                 Vec3f d = t*v-v;
00955                 float dd = d[0]*d[0]+d[1]*d[1]+d[2]*d[2];
00956                 if (dd > ddmax) ddmax = dd; 
00957         }
00958         return std::sqrt(ddmax);
00959 }
00960 
00961 void EMData::rotate_translate(float az, float alt, float phi, float dx, float dy, float dz)
00962 {
00963         cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00964 //      Transform3D t( az, alt, phi,Vec3f(dx, dy, dz));
00965         Transform t;
00966         t.set_rotation(Dict("type", "eman", "az", az, "alt", alt, "phi", phi));
00967         t.set_trans(dx, dy, dz);
00968         rotate_translate(t);
00969 }
00970 
00971 
00972 void EMData::rotate_translate(float az, float alt, float phi, float dx, float dy,
00973                                                           float dz, float pdx, float pdy, float pdz)
00974 {
00975         cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00976 //      Transform3D t(Vec3f(dx, dy, dz), az, alt, phi, Vec3f(pdx,pdy,pdz));
00977 //      rotate_translate(t);
00978 
00979         Transform t;
00980         t.set_pre_trans(Vec3f(dx, dy, dz));
00981         t.set_rotation(Dict("type", "eman", "az", az, "alt", alt, "phi", phi));
00982         t.set_trans(pdx, pdy, pdz);
00983         rotate_translate(t);
00984 }
00985 
00986 //void EMData::rotate_translate(const Transform3D & RA)
00987 //{
00988 //      cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00989 //      ENTERFUNC;
00990 //
00991 //#if EMDATA_EMAN2_DEBUG
00992 //      std::cout << "start rotate_translate..." << std::endl;
00993 //#endif
00994 //
00995 //      float scale       = RA.get_scale();
00996 //      Vec3f dcenter     = RA.get_center();
00997 //      Vec3f translation = RA.get_posttrans();
00998 //      Dict rotation      = RA.get_rotation(Transform3D::EMAN);
01000 //      Transform3D RAInv = RA.inverse(); // We're rotating the coordinate system, not the data
01002 //#if EMDATA_EMAN2_DEBUG
01003 //      vector<string> keys = rotation.keys();
01004 //      vector<string>::const_iterator it;
01005 //      for(it=keys.begin(); it!=keys.end(); ++it) {
01007 //              std::cout << *it << " : " << (float)rotation.get(*it) << std::endl;
01008 //      }
01009 //#endif
01010 //      float inv_scale = 1.0f;
01011 //
01012 //      if (scale != 0) {
01013 //              inv_scale = 1.0f / scale;
01014 //      }
01015 //
01016 //      float *src_data = 0;
01017 //      float *des_data = 0;
01018 //
01019 //      src_data = get_data();
01020 //      des_data = (float *) EMUtil::em_malloc(nx * ny * nz * sizeof(float));
01021 //
01022 //      if (nz == 1) {
01023 //              float x2c =  nx / 2 - dcenter[0] + RAInv[0][3];
01024 //              float y2c =  ny / 2 - dcenter[1] + RAInv[1][3];
01025 //              float y   = -ny / 2 + dcenter[1]; // changed 0 to 1 in dcenter and below
01026 //              for (int j = 0; j < ny; j++, y += 1.0f) {
01027 //                      float x = -nx / 2 + dcenter[0];
01028 //                      for (int i = 0; i < nx; i++, x += 1.0f) {
01029 //                              float x2 = RAInv[0][0]*x + RAInv[0][1]*y + x2c;
01030 //                              float y2 = RAInv[1][0]*x + RAInv[1][1]*y + y2c;
01031 //
01032 //                              if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
01033 //                                      des_data[i + j * nx] = 0; // It may be tempting to set this value to the
01034 //                                      // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
01035 //                              }
01036 //                              else {
01037 //                                      int ii = Util::fast_floor(x2);
01038 //                                      int jj = Util::fast_floor(y2);
01039 //                                      int k0 = ii + jj * nx;
01040 //                                      int k1 = k0 + 1;
01041 //                                      int k2 = k0 + nx;
01042 //                                      int k3 = k0 + nx + 1;
01043 //
01044 //                                      if (ii == nx - 1) {
01045 //                                              k1--;
01046 //                                              k3--;
01047 //                                      }
01048 //                                      if (jj == ny - 1) {
01049 //                                              k2 -= nx;
01050 //                                              k3 -= nx;
01051 //                                      }
01052 //
01053 //                                      float t = x2 - ii;
01054 //                                      float u = y2 - jj;
01055 //
01056 //                                      des_data[i + j * nx] = Util::bilinear_interpolate(src_data[k0],src_data[k1], src_data[k2], src_data[k3],t,u); // This is essentially basic interpolation
01057 //                              }
01058 //                      }
01059 //              }
01060 //      }
01061 //      else {
01062 //#if EMDATA_EMAN2_DEBUG
01063 //              std::cout << "This is the 3D case." << std::endl    ;
01064 //#endif
01065 //
01066 //              Transform3D mx = RA;
01067 //              mx.set_scale(inv_scale);
01068 //
01069 //#if EMDATA_EMAN2_DEBUG
01072 //#endif
01073 //
01074 //              int nxy = nx * ny;
01075 //              int l = 0;
01076 //
01077 //              float x2c =  nx / 2 - dcenter[0] + RAInv[0][3];;
01078 //              float y2c =  ny / 2 - dcenter[1] + RAInv[1][3];;
01079 //              float z2c =  nz / 2 - dcenter[2] + RAInv[2][3];;
01080 //
01081 //              float z   = -nz / 2 + dcenter[2]; //
01082 //
01083 //              size_t ii, k0, k1, k2, k3, k4, k5, k6, k7;
01084 //              for (int k = 0; k < nz; k++, z += 1.0f) {
01085 //                      float y   = -ny / 2 + dcenter[1]; //
01086 //                      for (int j = 0; j < ny; j++,   y += 1.0f) {
01087 //                              float x = -nx / 2 + dcenter[0];
01088 //                              for (int i = 0; i < nx; i++, l++ ,  x += 1.0f) {
01089 //                                      float x2 = RAInv[0][0] * x + RAInv[0][1] * y + RAInv[0][2] * z + x2c;
01090 //                                      float y2 = RAInv[1][0] * x + RAInv[1][1] * y + RAInv[1][2] * z + y2c;
01091 //                                      float z2 = RAInv[2][0] * x + RAInv[2][1] * y + RAInv[2][2] * z + z2c;
01092 //
01093 //
01094 //                                      if (x2 < 0 || y2 < 0 || z2 < 0 ||
01095 //                                              x2 >= nx  || y2 >= ny  || z2>= nz ) {
01096 //                                              des_data[l] = 0;
01097 //                                      }
01098 //                                      else {
01099 //                                              int ix = Util::fast_floor(x2);
01100 //                                              int iy = Util::fast_floor(y2);
01101 //                                              int iz = Util::fast_floor(z2);
01102 //                                              float tuvx = x2-ix;
01103 //                                              float tuvy = y2-iy;
01104 //                                              float tuvz = z2-iz;
01105 //                                              ii = ix + iy * nx + iz * nxy;
01106 //
01107 //                                              k0 = ii;
01108 //                                              k1 = k0 + 1;
01109 //                                              k2 = k0 + nx;
01110 //                                              k3 = k0 + nx+1;
01111 //                                              k4 = k0 + nxy;
01112 //                                              k5 = k1 + nxy;
01113 //                                              k6 = k2 + nxy;
01114 //                                              k7 = k3 + nxy;
01115 //
01116 //                                              if (ix == nx - 1) {
01117 //                                                      k1--;
01118 //                                                      k3--;
01119 //                                                      k5--;
01120 //                                                      k7--;
01121 //                                              }
01122 //                                              if (iy == ny - 1) {
01123 //                                                      k2 -= nx;
01124 //                                                      k3 -= nx;
01125 //                                                      k6 -= nx;
01126 //                                                      k7 -= nx;
01127 //                                              }
01128 //                                              if (iz == nz - 1) {
01129 //                                                      k4 -= nxy;
01130 //                                                      k5 -= nxy;
01131 //                                                      k6 -= nxy;
01132 //                                                      k7 -= nxy;
01133 //                                              }
01134 //
01135 //                                              des_data[l] = Util::trilinear_interpolate(src_data[k0],
01136 //                                                        src_data[k1],
01137 //                                                        src_data[k2],
01138 //                                                        src_data[k3],
01139 //                                                        src_data[k4],
01140 //                                                        src_data[k5],
01141 //                                                        src_data[k6],
01142 //                                                        src_data[k7],
01143 //                                                        tuvx, tuvy, tuvz);
01144 //#if EMDATA_EMAN2_DEBUG
01145 //                                              printf(" ix=%d \t iy=%d \t iz=%d \t value=%f \n", ix ,iy, iz, des_data[l] );
01146 //                                              std::cout << src_data[ii] << std::endl;
01147 //#endif
01148 //                                      }
01149 //                              }
01150 //                      }
01151 //              }
01152 //      }
01153 //
01154 //      if( rdata )
01155 //      {
01156 //              EMUtil::em_free(rdata);
01157 //              rdata = 0;
01158 //      }
01159 //      rdata = des_data;
01160 //
01161 //      scale_pixel(inv_scale);
01162 //
01163 //      attr_dict["origin_x"] = (float) attr_dict["origin_x"] * inv_scale;
01164 //      attr_dict["origin_y"] = (float) attr_dict["origin_y"] * inv_scale;
01165 //      attr_dict["origin_z"] = (float) attr_dict["origin_z"] * inv_scale;
01166 //
01167 //      update();
01168 //      all_translation += translation;
01169 //      EXITFUNC;
01170 //}
01171 
01172 
01173 
01174 
01175 void EMData::rotate_x(int dx)
01176 {
01177         ENTERFUNC;
01178 
01179         if (get_ndim() > 2) {
01180                 throw ImageDimensionException("no 3D image");
01181         }
01182 
01183 
01184         size_t row_size = nx * sizeof(float);
01185         float *tmp = (float*)EMUtil::em_malloc(row_size);
01186         float * data = get_data();
01187 
01188         for (int y = 0; y < ny; y++) {
01189                 int y_nx = y * nx;
01190                 for (int x = 0; x < nx; x++) {
01191                         tmp[x] = data[y_nx + (x + dx) % nx];
01192                 }
01193                 EMUtil::em_memcpy(&data[y_nx], tmp, row_size);
01194         }
01195 
01196         update();
01197         if( tmp )
01198         {
01199                 delete[]tmp;
01200                 tmp = 0;
01201         }
01202         EXITFUNC;
01203 }
01204 
01205 double EMData::dot_rotate_translate(EMData * with, float dx, float dy, float da, const bool mirror)
01206 {
01207         ENTERFUNC;
01208 
01209         if (!EMUtil::is_same_size(this, with)) {
01210                 LOGERR("images not same size");
01211                 throw ImageFormatException("images not same size");
01212         }
01213 
01214         if (get_ndim() == 3) {
01215                 LOGERR("1D/2D Images only");
01216                 throw ImageDimensionException("1D/2D only");
01217         }
01218 
01219         float *this_data = 0;
01220 
01221         this_data = get_data();
01222 
01223         float da_rad = da*(float)M_PI/180.0f;
01224 
01225         float *with_data = with->get_data();
01226         float mx0 = cos(da_rad);
01227         float mx1 = sin(da_rad);
01228         float y = -ny / 2.0f;
01229         float my0 = mx0 * (-nx / 2.0f - 1.0f) + nx / 2.0f - dx;
01230         float my1 = -mx1 * (-nx / 2.0f - 1.0f) + ny / 2.0f - dy;
01231         double result = 0;
01232 
01233         for (int j = 0; j < ny; j++) {
01234                 float x2 = my0 + mx1 * y;
01235                 float y2 = my1 + mx0 * y;
01236 
01237                 int ii = Util::fast_floor(x2);
01238                 int jj = Util::fast_floor(y2);
01239                 float t = x2 - ii;
01240                 float u = y2 - jj;
01241 
01242                 for (int i = 0; i < nx; i++) {
01243                         t += mx0;
01244                         u -= mx1;
01245 
01246                         if (t >= 1.0f) {
01247                                 ii++;
01248                                 t -= 1.0f;
01249                         }
01250 
01251                         if (u >= 1.0f) {
01252                                 jj++;
01253                                 u -= 1.0f;
01254                         }
01255 
01256                         if (t < 0) {
01257                                 ii--;
01258                                 t += 1.0f;
01259                         }
01260 
01261                         if (u < 0) {
01262                                 jj--;
01263                                 u += 1.0f;
01264                         }
01265 
01266                         if (ii >= 0 && ii <= nx - 2 && jj >= 0 && jj <= ny - 2) {
01267                                 int k0 = ii + jj * nx;
01268                                 int k1 = k0 + 1;
01269                                 int k2 = k0 + nx + 1;
01270                                 int k3 = k0 + nx;
01271 
01272                                 float tt = 1 - t;
01273                                 float uu = 1 - u;
01274                                 int idx = i + j * nx;
01275                                 if (mirror) idx = nx-1-i+j*nx; // mirroring of Transforms is always about the y axis
01276                                 result += (this_data[k0] * tt * uu + this_data[k1] * t * uu +
01277                                                    this_data[k2] * t * u + this_data[k3] * tt * u) * with_data[idx];
01278                         }
01279                 }
01280                 y += 1.0f;
01281         }
01282 
01283         EXITFUNC;
01284         return result;
01285 }
01286 
01287 
01288 EMData *EMData::little_big_dot(EMData * with, bool do_sigma)
01289 {
01290         ENTERFUNC;
01291 
01292         if (get_ndim() > 2) {
01293                 throw ImageDimensionException("1D/2D only");
01294         }
01295 
01296         EMData *ret = copy_head();
01297         ret->set_size(nx,ny,nz);
01298         ret->to_zero();
01299 
01300         int nx2 = with->get_xsize();
01301         int ny2 = with->get_ysize();
01302         float em = with->get_edge_mean();
01303 
01304         float *data = get_data();
01305         float *with_data = with->get_data();
01306         float *ret_data = ret->get_data();
01307 
01308         float sum2 = (Util::square((float)with->get_attr("sigma")) +
01309                                   Util::square((float)with->get_attr("mean")));
01310         if (do_sigma) {
01311                 for (int j = ny2 / 2; j < ny - ny2 / 2; j++) {
01312                         for (int i = nx2 / 2; i < nx - nx2 / 2; i++) {
01313                                 float sum = 0;
01314                                 float sum1 = 0;
01315                                 float summ = 0;
01316                                 int k = 0;
01317 
01318                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01319                                         for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01320                                                 int l = ii + jj * nx;
01321                                                 sum1 += Util::square(data[l]);
01322                                                 summ += data[l];
01323                                                 sum += data[l] * with_data[k];
01324                                                 k++;
01325                                         }
01326                                 }
01327                                 float tmp_f1 = (sum1 / 2.0f - sum) / (nx2 * ny2);
01328                                 float tmp_f2 = Util::square((float)with->get_attr("mean") -
01329                                                                                         summ / (nx2 * ny2));
01330                                 ret_data[i + j * nx] = sum2 + tmp_f1 - tmp_f2;
01331                         }
01332                 }
01333         }
01334         else {
01335                 for (int j = ny2 / 2; j < ny - ny2 / 2; j++) {
01336                         for (int i = nx2 / 2; i < nx - nx2 / 2; i++) {
01337                                 float eml = 0;
01338                                 float dot = 0;
01339                                 float dot2 = 0;
01340 
01341                                 for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01342                                         eml += data[ii + (j - ny2 / 2) * nx] + data[ii + (j + ny2 / 2 - 1) * nx];
01343                                 }
01344 
01345                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01346                                         eml += data[i - nx2 / 2 + jj * nx] + data[i + nx2 / 2 - 1 + jj * nx];
01347                                 }
01348 
01349                                 eml /= (nx2 + ny2) * 2.0f;
01350                                 int k = 0;
01351 
01352                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01353                                         for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01354                                                 dot += (data[ii + jj * nx] - eml) * (with_data[k] - em);
01355                                                 dot2 += Util::square(data[ii + jj * nx] - eml);
01356                                                 k++;
01357                                         }
01358                                 }
01359 
01360                                 dot2 = std::sqrt(dot2);
01361 
01362                                 if (dot2 == 0) {
01363                                         ret_data[i + j * nx] = 0;
01364                                 }
01365                                 else {
01366                                         ret_data[i + j * nx] = dot / (nx2 * ny2 * dot2 * (float)with->get_attr("sigma"));
01367                                 }
01368                         }
01369                 }
01370         }
01371 
01372         ret->update();
01373 
01374         EXITFUNC;
01375         return ret;
01376 }
01377 
01378 
01379 EMData *EMData::do_radon()
01380 {
01381         ENTERFUNC;
01382 
01383         if (get_ndim() != 2) {
01384                 throw ImageDimensionException("2D only");
01385         }
01386 
01387         if (nx != ny) {
01388                 throw ImageFormatException("square image only");
01389         }
01390 
01391         EMData *result = new EMData();
01392         result->set_size(nx, ny, 1);
01393         result->to_zero();
01394         float *result_data = result->get_data();
01395 
01396         EMData *this_copy = this;
01397         this_copy = copy();
01398 
01399         for (int i = 0; i < nx; i++) {
01400                 Transform t(Dict("type","2d","alpha",(float) M_PI * 2.0f * i / nx));
01401                 this_copy->transform(t);
01402 
01403                 float *copy_data = this_copy->get_data();
01404 
01405                 for (int y = 0; y < nx; y++) {
01406                         for (int x = 0; x < nx; x++) {
01407                                 if (Util::square(x - nx / 2) + Util::square(y - nx / 2) <= nx * nx / 4) {
01408                                         result_data[i + y * nx] += copy_data[x + y * nx];
01409                                 }
01410                         }
01411                 }
01412 
01413                 this_copy->update();
01414         }
01415 
01416         result->update();
01417 
01418         if( this_copy )
01419         {
01420                 delete this_copy;
01421                 this_copy = 0;
01422         }
01423 
01424         EXITFUNC;
01425         return result;
01426 }
01427 
01428 void EMData::zero_corner_circulant(const int radius)
01429 {
01430         if ( nz > 1 && nz < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - nz is too small");
01431         if ( ny > 1 && ny < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - ny is too small");
01432         if ( nx > 1 && nx < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - nx is too small");
01433 
01434         int it_z = radius;
01435         int it_y = radius;
01436         int it_x = radius;
01437 
01438         if ( nz == 1 ) it_z = 0;
01439         if ( ny == 1 ) it_y = 0;
01440         if ( nx == 1 ) it_z = 0;
01441 
01442         if ( nz == 1 && ny == 1 )
01443         {
01444                 for ( int x = -it_x; x <= it_x; ++x )
01445                         get_value_at_wrap(x) = 0;
01446 
01447         }
01448         else if ( nz == 1 )
01449         {
01450                 for ( int y = -it_y; y <= it_y; ++y)
01451                         for ( int x = -it_x; x <= it_x; ++x )
01452                                 get_value_at_wrap(x,y) = 0;
01453         }
01454         else
01455         {
01456                 for( int z = -it_z; z <= it_z; ++z )
01457                         for ( int y = -it_y; y <= it_y; ++y)
01458                                 for ( int x = -it_x; x < it_x; ++x )
01459                                         get_value_at_wrap(x,y,z) = 0;
01460 
01461         }
01462 
01463 }
01464 
01465 EMData *EMData::calc_ccf(EMData * with, fp_flag fpflag,bool center)
01466 {
01467         ENTERFUNC;
01468 
01469         if( with == 0 ) {
01470 #ifdef EMAN2_USING_CUDA //CUDA 
01471         if(cudarwdata) {
01472                 EMData* ifft = 0;
01473                 bool delifft = false;
01474                 int offset = 0;
01475                 
01476                 //do fft if not alreay done
01477                 if(!is_complex()){
01478                         ifft = do_fft_cuda();
01479                         delifft = true;
01480                         offset = 2 - nx%2;
01481                 }else{
01482                         ifft = this;
01483                 }
01484                 calc_conv_cuda(ifft->cudarwdata,ifft->cudarwdata,nx + offset, ny, nz); //this is the business end, results go in afft
01485                 
01486                 EMData * conv = ifft->do_ift_cuda();
01487                 if(delifft) delete ifft;
01488                         
01489                 return conv;
01490         }
01491 #endif
01492                 EXITFUNC;
01493                 return convolution(this,this,fpflag, center);
01494         }
01495         else if ( with == this ){ // this if statement is not necessary, the correlation function tests to see if with == this
01496                 EXITFUNC;
01497                 return correlation(this, this, fpflag,center);
01498         }
01499         else {
01500 
01501 #ifdef EMAN2_USING_CUDA //CUDA 
01502                 // assume always get rw data (makes life a lot easier!!! 
01503                 // also assume that both images are the same size. When using CUDA we are only interested in speed, not flexibility!!
01504                 // P.S. (I feel like I am pounding square pegs into a round holes with CUDA)
01505                 if(cudarwdata && with->cudarwdata) {
01506                         //cout << "using CUDA for ccf" << endl;
01507                         EMData* afft = 0;
01508                         EMData* bfft = 0;
01509                         bool delafft = false, delbfft = false;
01510                         int offset = 0;
01511                         
01512                         //do ffts if not alreay done
01513                         if(!is_complex()){
01514                                 afft = do_fft_cuda();
01515                                 delafft = true;
01516                                 offset = 2 - nx%2;
01517                                 //cout << "Do cuda FFT A" << endl;
01518                         }else{
01519                                 afft = this;
01520                         }
01521                         if(!with->is_complex()){
01522                                 bfft = with->do_fft_cuda();
01523                                 //cout << "Do cuda FFT B" << endl;
01524                                 delbfft = true;
01525                         }else{
01526                                 bfft = with;
01527                         }
01528 
01529                         calc_ccf_cuda(afft->cudarwdata,bfft->cudarwdata,nx + offset, ny, nz); //this is the business end, results go in afft
01530                         
01531                         if(delbfft) delete bfft;
01532                         
01533                         EMData * corr = afft->do_ift_cuda();
01534                         if(delafft) delete afft;
01535                         //cor->do_ift_inplace_cuda();//a bit faster, but I'll alos need to rearrnage the mem structure for it to work, BUT this is very SLOW.
01536                         
01537                         return corr;
01538                 }
01539 #endif
01540                 
01541                 // If the argument EMData pointer is not the same size we automatically resize it
01542                 bool undoresize = false;
01543                 int wnx = with->get_xsize(); int wny = with->get_ysize(); int wnz = with->get_zsize(); // obviously is one image is complex and the other real they won't be the same size and we DONT! want to clip JFF
01544                 if (!(is_complex() ^ with->is_complex()) && (wnx != nx || wny != ny || wnz != nz)) {
01545                         cout << "Warning!!! resizing image before CCF calculation" << endl;
01546                         Region r((wnx-nx)/2, (wny-ny)/2, (wnz-nz)/2,nx,ny,nz);
01547                         with->clip_inplace(r);
01548                         undoresize = true;
01549                 }
01550 
01551                 EMData* cor = correlation(this, with, fpflag, center);
01552 
01553                 // If the argument EMData pointer was resized, it is returned to its original dimensions
01554                 if ( undoresize ) {
01555                         Region r((nx-wnx)/2, (ny-wny)/2,(nz-wnz)/2,wnx,wny,wnz);
01556                         with->clip_inplace(r);
01557                 }
01558 
01559                 EXITFUNC;
01560                 return cor;
01561         }
01562 }
01563 
01564 EMData *EMData::calc_ccfx( EMData * const with, int y0, int y1, bool no_sum, bool flip)
01565 {
01566         ENTERFUNC;
01567 
01568         if (!with) {
01569                 LOGERR("NULL 'with' image. ");
01570                 throw NullPointerException("NULL input image");
01571         }
01572 
01573         if (!EMUtil::is_same_size(this, with)) {
01574                 LOGERR("images not same size: (%d,%d,%d) != (%d,%d,%d)",
01575                            nx, ny, nz,
01576                            with->get_xsize(), with->get_ysize(), with->get_zsize());
01577                 throw ImageFormatException("images not same size");
01578         }
01579         if (get_ndim() > 2) {
01580                 LOGERR("2D images only");
01581                 throw ImageDimensionException("2D images only");
01582         }
01583 
01584         if (y1 <= y0) {
01585                 y1 = ny;
01586         }
01587 
01588         if (y0 >= y1) {
01589                 y0 = 0;
01590         }
01591 
01592         if (y0 < 0) {
01593                 y0 = 0;
01594         }
01595 
01596         if (y1 > ny) {
01597                 y1 = ny;
01598         }
01599         if (is_complex_x() || with->is_complex_x() ) throw; // Woops don't support this anymore!
01600 
01601         static int nx_fft = 0;
01602         static int ny_fft = 0;
01603         static EMData f1;
01604         static EMData f2;
01605         static EMData rslt;
01606 
01607         int height = y1-y0;
01608         int width = (nx+2-(nx%2));
01609         if (width != nx_fft || height != ny_fft ) {
01610                 f1.set_size(width,height);
01611                 f2.set_size(width,height);
01612                 rslt.set_size(nx,height);
01613                 nx_fft = width;
01614                 ny_fft = height;
01615         }
01616 
01617 #ifdef EMAN2_USING_CUDA
01618         if (cudarwdata && with->cudarwdata) {
01619                 //cout << "calc_ccfx CUDA" << endl;
01620                 if(!f1.cudarwdata) f1.rw_alloc();
01621                 if(!f2.cudarwdata) f2.rw_alloc();
01622                 if(!rslt.cudarwdata) rslt.rw_alloc();
01623                 cuda_dd_fft_real_to_complex_nd(cudarwdata, f1.cudarwdata, nx, 1, 1, height);
01624                 cuda_dd_fft_real_to_complex_nd(with->cudarwdata, f2.cudarwdata, nx, 1, 1, height);
01625                 calc_ccf_cuda(f1.cudarwdata, f2.cudarwdata, nx, ny, nz);
01626                 cuda_dd_fft_complex_to_real_nd(f1.cudarwdata, rslt.cudarwdata, nx, 1, 1, height);
01627                 if(no_sum){
01628                         EMData* result = new EMData(rslt);
01629                         return result;
01630                 }
01631                 EMData* cf = new EMData(0,0,nx,1,1); //cuda constructor
01632                 cf->runcuda(emdata_column_sum(rslt.cudarwdata, nx, ny));
01633 
01634                 EXITFUNC;
01635                 return cf;
01636         }
01637 #endif
01638 
01639         float *d1 = get_data();
01640         float *d2 = with->get_data();
01641         float *f1d = f1.get_data();
01642         float *f2d = f2.get_data();
01643         for (int j = 0; j < height; j++) {
01644                 EMfft::real_to_complex_1d(d1 + j * nx, f1d+j*width, nx);
01645                 EMfft::real_to_complex_1d(d2 + j * nx, f2d+j*width, nx);
01646         }
01647 
01648         if(flip == false) {
01649                 for (int j = 0; j < height; j++) {
01650                         float *f1a = f1d + j * width;
01651                         float *f2a = f2d + j * width;
01652 
01653                         for (int i = 0; i < width / 2; i++) {
01654                                 float re1 = f1a[2*i];
01655                                 float re2 = f2a[2*i];
01656                                 float im1 = f1a[2*i+1];
01657                                 float im2 = f2a[2*i+1];
01658 
01659                                 f1d[j*width+i*2] = re1 * re2 + im1 * im2;
01660                                 f1d[j*width+i*2+1] = im1 * re2 - re1 * im2;
01661                         }
01662                 }
01663         } else {
01664                 for (int j = 0; j < height; j++) {
01665                         float *f1a = f1d + j * width;
01666                         float *f2a = f2d + j * width;
01667 
01668                         for (int i = 0; i < width / 2; i++) {
01669                                 float re1 = f1a[2*i];
01670                                 float re2 = f2a[2*i];
01671                                 float im1 = f1a[2*i+1];
01672                                 float im2 = f2a[2*i+1];
01673 
01674                                 f1d[j*width+i*2] = re1 * re2 - im1 * im2;
01675                                 f1d[j*width+i*2+1] = im1 * re2 + re1 * im2;
01676                         }
01677                 }
01678         }
01679 
01680         float* rd = rslt.get_data();
01681         for (int j = y0; j < y1; j++) {
01682                 EMfft::complex_to_real_1d(f1d+j*width, rd+j*nx, nx);
01683         }
01684 
01685         if (no_sum) {
01686                 rslt.update(); // This is important in terms of the copy - the returned object won't have the correct flags unless we do this
01687                 EXITFUNC;
01688                 return new EMData(rslt);
01689         } else {
01690                 EMData *cf = new EMData(nx,1,1);
01691                 cf->to_zero();
01692                 float *c = cf->get_data();
01693                 for (int j = 0; j < height; j++) {
01694                         for(int i = 0; i < nx; ++i) {
01695                                 c[i] += rd[i+j*nx];
01696                         }
01697                 }
01698                 cf->update();
01699                 EXITFUNC;
01700                 return cf;
01701         }
01702 }
01703 
01704 EMData *EMData::make_rotational_footprint_cmc( bool unwrap) {
01705         ENTERFUNC;
01706         update_stat();
01707         // Note that rotational_footprint caching saves a large amount of time
01708         // but this is at the expense of memory. Note that a policy is hardcoded here,
01709         // that is that caching is only employed when premasked is false and unwrap
01710         // is true - this is probably going to be what is used in most scenarios
01711         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01712         // generated by e2speedtest.
01713         if ( rot_fp != 0 && unwrap == true) {
01714                 return new EMData(*rot_fp);
01715         }
01716 
01717         static EMData obj_filt;
01718         EMData* filt = &obj_filt;
01719         filt->set_complex(true);
01720 
01721 
01722         // The filter object is nothing more than a cached high pass filter
01723         // Ultimately it is used an argument to the EMData::mult(EMData,prevent_complex_multiplication (bool))
01724         // function in calc_mutual_correlation. Note that in the function the prevent_complex_multiplication
01725         // set to true, which is used for speed reasons.
01726         if (filt->get_xsize() != nx+2-(nx%2) || filt->get_ysize() != ny ||
01727                    filt->get_zsize() != nz ) {
01728                 filt->set_size(nx+2-(nx%2), ny, nz);
01729                 filt->to_one();
01730 
01731                 filt->process_inplace("filter.highpass.gauss", Dict("cutoff_abs", 1.5f/nx));
01732         }
01733 
01734         EMData *ccf = this->calc_mutual_correlation(this, true,filt);
01735         ccf->sub(ccf->get_edge_mean());
01736         EMData *result = ccf->unwrap();
01737         delete ccf; ccf = 0;
01738 
01739         EXITFUNC;
01740         if ( unwrap == true)
01741         {
01742         // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01743 
01744 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01745 // to throw any exception
01746 // if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01747 
01748 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01749 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01750                 rot_fp = result;
01751                 return new EMData(*rot_fp);
01752         }
01753         else return result;
01754 }
01755 
01756 EMData *EMData::make_rotational_footprint( bool unwrap) {
01757         ENTERFUNC;
01758         update_stat();
01759         // Note that rotational_footprint caching saves a large amount of time
01760         // but this is at the expense of memory. Note that a policy is hardcoded here,
01761         // that is that caching is only employed when premasked is false and unwrap
01762         // is true - this is probably going to be what is used in most scenarios
01763         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01764         // generated by e2speedtest.
01765         if ( rot_fp != 0 && unwrap == true) {
01766                 return new EMData(*rot_fp);
01767         }
01768 
01769         EMData* ccf = this->calc_ccf(this,CIRCULANT,true);
01770         ccf->sub(ccf->get_edge_mean());
01771         //ccf->process_inplace("xform.phaseorigin.tocenter"); ccf did the centering
01772         EMData *result = ccf->unwrap();
01773         delete ccf; ccf = 0;
01774 
01775         EXITFUNC;
01776         if ( unwrap == true)
01777         { // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01778 
01779 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01780 // to throw any exception
01781 // if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01782 
01783 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01784 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01785                 rot_fp = result;
01786                 return new EMData(*rot_fp);
01787         }
01788         else return result;
01789 }
01790 
01791 EMData *EMData::make_rotational_footprint_e1( bool unwrap)
01792 {
01793         ENTERFUNC;
01794 
01795         update_stat();
01796         // Note that rotational_footprint caching saves a large amount of time
01797         // but this is at the expense of memory. Note that a policy is hardcoded here,
01798         // that is that caching is only employed when premasked is false and unwrap
01799         // is true - this is probably going to be what is used in most scenarios
01800         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01801         // generated by e2speedtest.
01802         if ( rot_fp != 0 && unwrap == true) {
01803                 return new EMData(*rot_fp);
01804         }
01805 
01806         static EMData obj_filt;
01807         EMData* filt = &obj_filt;
01808         filt->set_complex(true);
01809 //      Region filt_region;
01810 
01811 //      if (nx & 1) {
01812 //              LOGERR("even image xsize only");                throw ImageFormatException("even image xsize only");
01813 //      }
01814 
01815         int cs = (((nx * 7 / 4) & 0xfffff8) - nx) / 2; // this pads the image to 1 3/4 * size with result divis. by 8
01816 
01817         static EMData big_clip;
01818         int big_x = nx+2*cs;
01819         int big_y = ny+2*cs;
01820         int big_z = 1;
01821         if ( nz != 1 ) {
01822                 big_z = nz+2*cs;
01823         }
01824 
01825 
01826         if ( big_clip.get_xsize() != big_x || big_clip.get_ysize() != big_y || big_clip.get_zsize() != big_z ) {
01827                 big_clip.set_size(big_x,big_y,big_z);
01828         }
01829         // It is important to set all newly established pixels around the boundaries to the mean
01830         // If this is not done then the associated rotational alignment routine breaks, in fact
01831         // everythin just goes foo.
01832 
01833         big_clip.to_value(get_edge_mean());
01834 
01835         if (nz != 1) {
01836                 big_clip.insert_clip(this,IntPoint(cs,cs,cs));
01837         } else  {
01838                 big_clip.insert_clip(this,IntPoint(cs,cs,0));
01839         }
01840         
01841         // The filter object is nothing more than a cached high pass filter
01842         // Ultimately it is used an argument to the EMData::mult(EMData,prevent_complex_multiplication (bool))
01843         // function in calc_mutual_correlation. Note that in the function the prevent_complex_multiplication
01844         // set to true, which is used for speed reasons.
01845         if (filt->get_xsize() != big_clip.get_xsize() +2-(big_clip.get_xsize()%2) || filt->get_ysize() != big_clip.get_ysize() ||
01846                    filt->get_zsize() != big_clip.get_zsize()) {
01847                 filt->set_size(big_clip.get_xsize() + 2-(big_clip.get_xsize()%2), big_clip.get_ysize(), big_clip.get_zsize());
01848                 filt->to_one();
01849                 filt->process_inplace("filter.highpass.gauss", Dict("cutoff_abs", 1.5f/nx));
01850 #ifdef EMAN2_USING_CUDA
01851                 if(big_clip.cudarwdata)
01852                 {
01853                         filt->copy_to_cuda(); // since this occurs just once for many images, we don't pay much of a speed pentalty here, and we avoid the hassel of messing with sparx
01854                 }
01855 #endif
01856         }
01857 #ifdef EMAN2_USING_CUDA
01858         if(big_clip.cudarwdata && !filt->cudarwdata)
01859         {
01860                 filt->copy_to_cuda(); // since this occurs just once for many images, we don't pay much of a speed pentalty here, and we avoid the hassel of messing with sparx
01861         }
01862 #endif
01863         
01864         EMData *mc = big_clip.calc_mutual_correlation(&big_clip, true,filt);
01865         mc->sub(mc->get_edge_mean());
01866 
01867         static EMData sml_clip;
01868         int sml_x = nx * 3 / 2;
01869         int sml_y = ny * 3 / 2;
01870         int sml_z = 1;
01871         if ( nz != 1 ) {
01872                 sml_z = nz * 3 / 2;
01873         }
01874 
01875         if ( sml_clip.get_xsize() != sml_x || sml_clip.get_ysize() != sml_y || sml_clip.get_zsize() != sml_z ) {
01876                 sml_clip.set_size(sml_x,sml_y,sml_z);   }
01877         if (nz != 1) {
01878                 sml_clip.insert_clip(mc,IntPoint(-cs+nx/4,-cs+ny/4,-cs+nz/4));
01879         } else {
01880                 sml_clip.insert_clip(mc,IntPoint(-cs+nx/4,-cs+ny/4,0));
01881         }
01882                 
01883         delete mc; mc = 0;
01884         EMData * result = NULL;
01885         
01886         if (nz == 1) {
01887                 if (!unwrap) {
01888 #ifdef EMAN2_USING_CUDA
01889                         if(sml_clip.cudarwdata) throw UnexpectedBehaviorException("shap masking is not yet supported by CUDA");
01890 #endif
01891                         result = sml_clip.process("mask.sharp", Dict("outer_radius", -1, "value", 0));
01892 
01893                 }
01894                 else {
01895                         result = sml_clip.unwrap();
01896                 }
01897         }
01898         else {
01899                 // I am not sure why there is any consideration of non 2D images, but it was here
01900                 // in the first port so I kept when I cleaned this function up (d.woolford)
01901 //              result = clipped_mc;
01902                 result = new EMData(sml_clip);
01903         }
01904         
01905 #ifdef EMAN2_USING_CUDA
01906         sml_clip.roneedsanupdate(); //If we didn't do this then unwrap would use data from the previous call of this function, happens b/c sml_clip is static
01907 #endif
01908         EXITFUNC;
01909         if ( unwrap == true)
01910         { // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01911 
01912                 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01913                 // to throw any exception
01914                 if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01915 
01916                 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01917                 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01918                 rot_fp = result;
01919                 return new EMData(*rot_fp);
01920         }
01921         else return result;
01922 }
01923 
01924 EMData *EMData::make_footprint(int type)
01925 {
01926 //      printf("Make fp %d\n",type);
01927         if (type==0) {
01928                 EMData *un=make_rotational_footprint_e1(); // Use EMAN1's footprint strategy
01929                 if (un->get_ysize() <= 6) {
01930                         throw UnexpectedBehaviorException("In EMData::make_footprint. The rotational footprint is too small");
01931                 }
01932                 EMData *tmp=un->get_clip(Region(0,4,un->get_xsize(),un->get_ysize()-6));        // 4 and 6 are empirical
01933                 EMData *cx=tmp->calc_ccfx(tmp,0,-1,1);
01934                 EMData *fp=cx->get_clip(Region(0,0,cx->get_xsize()/2,cx->get_ysize()));
01935                 delete un;
01936                 delete tmp;
01937                 delete cx;
01938                 return fp;
01939         }
01940         else if (type==1 || type==2 ||type==5 || type==6) {
01941                 int i,j,kx,ky,lx,ly;
01942 
01943                 EMData *fft=do_fft();
01944 
01945                 // map for x,y -> radius for speed
01946                 int rmax=(get_xsize()+1)/2;
01947                 float *rmap=(float *)malloc(rmax*rmax*sizeof(float));
01948                 for (i=0; i<rmax; i++) {
01949                         for (j=0; j<rmax; j++) {
01950 #ifdef _WIN32
01951                                 rmap[i+j*rmax]=_hypotf((float)i,(float)j);
01952 #else
01953                                 rmap[i+j*rmax]=hypot((float)i,(float)j);
01954 #endif  //_WIN32
01955 //                              printf("%d\t%d\t%f\n",i,j,rmap[i+j*rmax]);
01956                         }
01957                 }
01958 
01959                 EMData *fp=new EMData(rmax*2+2,rmax*2,1);
01960                 fp->set_complex(1);
01961                 fp->to_zero();
01962 
01963                 // Two vectors in to complex space (kx,ky) and (lx,ly)
01964                 // We are computing the bispectrum, f(k).f(l).f*(k+l)
01965                 // but integrating out two dimensions, leaving |k|,|l|
01966                 for (kx=-rmax+1; kx<rmax; kx++) {
01967                         for (ky=-rmax+1; ky<rmax; ky++) {
01968                                 for (lx=-rmax+1; lx<rmax; lx++) {
01969                                         for (ly=-rmax+1; ly<rmax; ly++) {
01970                                                 int ax=kx+lx;
01971                                                 int ay=ky+ly;
01972                                                 if (abs(ax)>=rmax || abs(ay)>=rmax) continue;
01973                                                 int r1=(int)floor(.5+rmap[abs(kx)+rmax*abs(ky)]);
01974                                                 int r2=(int)floor(.5+rmap[abs(lx)+rmax*abs(ly)]);
01975 //                                              if (r1>500 ||r2>500) printf("%d\t%d\t%d\t%d\t%d\t%d\n",kx,ky,lx,ly,r1,r2);
01976 //                                              float r3=rmap[ax+rmax*ay];
01977                                                 if (r1+r2>=rmax) continue;
01978 
01979                                                 std::complex<float> p=fft->get_complex_at(kx,ky)*fft->get_complex_at(lx,ly)*conj(fft->get_complex_at(ax,ay));
01980                                                 fp->set_value_at(r1*2,r2,p.real()+fp->get_value_at(r1*2,r2));           // We keep only the real component in anticipation of zero phase sum
01981 //                                              fp->set_value_at(r1*2,rmax*2-r2-1,  fp->get_value_at(r1*2,r2));         // We keep only the real component in anticipation of zero phase sum
01982 //                                              fp->set_value_at(r1*2+1,r2,p.real()+fp->get_value_at(r1*2+1,r2));               // We keep only the real component in anticipation of zero phase sum
01983                                                 fp->set_value_at(r1*2+1,r2,fp->get_value_at(r1*2+1,r2)+1);                      // a normalization counter
01984                                         }
01985                                 }
01986                         }
01987                 }
01988 
01989                 // Normalizes the pixels based on the accumulated counts then sets the imaginary components back to zero
01990                 if (type==5 || type==6) {
01991                         for (i=0; i<rmax*2; i+=2) {
01992                                 for (j=0; j<rmax; j++) {
01993                                         float norm=fp->get_value_at(i+1,j);
01994 #ifdef _WIN32
01995                                         fp->set_value_at(i,rmax*2-j-1,pow(fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm), 1.0f/3.0f));
01996                                         fp->set_value_at(i,j,pow(fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm), 1.0f/3.0f));
01997 #else
01998                                         fp->set_value_at(i,rmax*2-j-1,cbrt(fp->get_value_at(i,j)/(norm==0?1.0:norm)));
01999                                         fp->set_value_at(i,j,cbrt(fp->get_value_at(i,j)/(norm==0?1.0:norm)));
02000 #endif  //_WIN32
02001                                         fp->set_value_at(i+1,j,0.0);
02002                                 }
02003                         }
02004                 }
02005                 else {
02006                         for (i=0; i<rmax*2; i+=2) {
02007                                 for (j=0; j<rmax; j++) {
02008                                         float norm=fp->get_value_at(i+1,j);
02009                                         fp->set_value_at(i,rmax*2-j-1,fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm));
02010                                         fp->set_value_at(i,j,fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm));
02011                                         fp->set_value_at(i+1,j,0.0);
02012                                 }
02013                         }
02014                 }
02015 
02016                 free(rmap);
02017                 if (type==2||type==6) {
02018                         EMData *f2=fp->do_ift();
02019                         if (f2->get_value_at(0,0)<0) f2->mult(-1.0f);
02020                         f2->process_inplace("xform.phaseorigin.tocorner");
02021                         delete fp;
02022                         return f2;
02023                 }
02024                 return fp;
02025         }
02026         else if (type==3 || type==4) {
02027                 int h,i,j,kx,ky,lx,ly;
02028 
02029                 EMData *fft=do_fft();
02030 
02031                 // map for x,y -> radius for speed
02032                 int rmax=(get_xsize()+1)/2;
02033                 float *rmap=(float *)malloc(rmax*rmax*sizeof(float));
02034                 for (i=0; i<rmax; i++) {
02035                         for (j=0; j<rmax; j++) {
02036 #ifdef _WIN32
02037                                 rmap[i+j*rmax]=_hypotf((float)i,(float)j);
02038 #else
02039                                 rmap[i+j*rmax]=hypot((float)i,(float)j);
02040 #endif  //_WIN32
02041 //                              printf("%d\t%d\t%f\n",i,j,rmap[i+j*rmax]);
02042                         }
02043                 }
02044 
02045                 EMData *fp=new EMData(rmax*2+2,rmax*2,16);
02046 
02047                 fp->set_complex(1);
02048                 fp->to_zero();
02049 
02050                 // Two vectors in to complex space (kx,ky) and (lx,ly)
02051                 // We are computing the bispectrum, f(k).f(l).f*(k+l)
02052                 // but integrating out two dimensions, leaving |k|,|l|
02053                 for (kx=-rmax+1; kx<rmax; kx++) {
02054                         for (ky=-rmax+1; ky<rmax; ky++) {
02055                                 for (lx=-rmax+1; lx<rmax; lx++) {
02056                                         for (ly=-rmax+1; ly<rmax; ly++) {
02057                                                 int ax=kx+lx;
02058                                                 int ay=ky+ly;
02059                                                 if (abs(ax)>=rmax || abs(ay)>=rmax) continue;
02060                                                 float rr1=rmap[abs(kx)+rmax*abs(ky)];
02061                                                 float rr2=rmap[abs(lx)+rmax*abs(ly)];
02062                                                 int r1=(int)floor(.5+rr1);
02063                                                 int r2=(int)floor(.5+rr2);
02064 //                                              if (r1>500 ||r2>500) printf("%d\t%d\t%d\t%d\t%d\t%d\n",kx,ky,lx,ly,r1,r2);
02065 //                                              float r3=rmap[ax+rmax*ay];
02066                                                 if (r1+r2>=rmax || rr1==0 ||rr2==0) continue;
02067 
02068                                                 std::complex<float> p=fft->get_complex_at(kx,ky)*fft->get_complex_at(lx,ly)*conj(fft->get_complex_at(ax,ay));
02069                                                 int dot=(int)floor((kx*lx+ky*ly)/(rr1*rr2)*7.5);                                        // projection of k on l 0-31
02070                                                 if (dot<0) dot=16+dot;
02071 //                                              int dot=(int)floor((kx*lx+ky*ly)/(rr1*rr2)*7.5+8.0);                                    // projection of k on l 0-15
02072                                                 fp->set_value_at(r1*2,r2,dot,p.real()+fp->get_value_at(r1*2,r2,dot));           // We keep only the real component in anticipation of zero phase sum
02073 //                                              fp->set_value_at(r1*2,rmax*2-r2-1,  fp->get_value_at(r1*2,r2));         // We keep only the real component in anticipation of zero phase sum
02074 //                                              fp->set_value_at(r1*2+1,r2,p.real()+fp->get_value_at(r1*2+1,r2));               // We keep only the real component in anticipation of zero phase sum
02075                                                 fp->set_value_at(r1*2+1,r2,dot,fp->get_value_at(r1*2+1,r2,dot)+1);                      // a normalization counter
02076                                         }
02077                                 }
02078                         }
02079                 }
02080 
02081                 // Normalizes the pixels based on the accumulated counts then sets the imaginary components back to zero
02082                 for (i=0; i<rmax*2; i+=2) {
02083                         for (j=0; j<rmax; j++) {
02084                                 for (h=0; h<16; h++) {
02085                                         float norm=fp->get_value_at(i+1,j,h);
02086 //                                      fp->set_value_at(i,rmax*2-j-1,h,cbrt(fp->get_value_at(i,j,h)/(norm==0?1.0:norm)));
02087 //                                      fp->set_value_at(i,j,h,cbrt(fp->get_value_at(i,j,h)/(norm==0?1.0:norm)));
02088                                         fp->set_value_at(i,rmax*2-j-1,h,(fp->get_value_at(i,j,h)/(norm==0.0f?1.0f:norm)));
02089                                         fp->set_value_at(i,j,h,(fp->get_value_at(i,j,h)/(norm==0.0f?1.0f:norm)));
02090         //                              fp->set_value_at(i,rmax*2-j-1,fp->get_value_at(i,j)/(norm==0?1.0:norm));
02091         //                              fp->set_value_at(i,j,fp->get_value_at(i,j)/(norm==0?1.0:norm));
02092                                         fp->set_value_at(i+1,j,h,0.0);
02093                                 }
02094                         }
02095                 }
02096 
02097                 free(rmap);
02098                 if (type==4) {
02099                         EMData *f2=fp->do_ift();
02100                         if (f2->get_value_at(0,0,0)<0) f2->mult(-1.0f);
02101                         f2->process_inplace("xform.phaseorigin.tocorner");
02102                         delete fp;
02103                         return f2;
02104                 }
02105                 return fp;
02106         }
02107         throw UnexpectedBehaviorException("There is not implementation for the parameters you specified");
02108 }
02109 
02110 
02111 EMData *EMData::calc_mutual_correlation(EMData * with, bool tocenter, EMData * filter)
02112 {
02113         ENTERFUNC;
02114 
02115         if (with && !EMUtil::is_same_size(this, with)) {
02116                 LOGERR("images not same size");
02117                 throw ImageFormatException( "images not same size");
02118         }
02119 
02120 #ifdef EMAN2_USING_CUDA
02121         if(cudarwdata && with->cudarwdata)
02122         {       
02123 
02124                 EMData* this_fft = do_fft_cuda();
02125 
02126                 EMData *cf = 0;
02127                 if (with && with != this) {
02128                         cf = with->do_fft_cuda();
02129                 }else{
02130                         cf = this_fft->copy();
02131                 }
02132                 
02133                 if (filter) {
02134                         if (!EMUtil::is_same_size(filter, cf)) {
02135                                 LOGERR("improperly sized filter");
02136                                 throw ImageFormatException("improperly sized filter");
02137                         }
02138                         mult_complex_efficient_cuda(cf->cudarwdata, filter->cudarwdata, cf->get_xsize(), cf->get_ysize(), cf->get_zsize(), 1);
02139                         mult_complex_efficient_cuda(this_fft->cudarwdata, filter->cudarwdata, this_fft->get_xsize(), this_fft->get_ysize(), this_fft->get_zsize(), 1);
02140                 }
02141                 
02142                 mcf_cuda(this_fft->cudarwdata, cf->cudarwdata, this_fft->get_xsize(), this_fft->get_ysize(), this_fft->get_zsize());
02143                 
02144                 EMData *f2 = cf->do_ift_cuda();
02145 
02146                 if (tocenter) {
02147                         f2->process_inplace("xform.phaseorigin.tocenter");
02148                 }
02149 
02150                 if( cf )
02151                 {
02152                         delete cf;
02153                         cf = 0;
02154                 }
02155 
02156                 if( this_fft )
02157                 {
02158                         delete this_fft;
02159                         this_fft = 0;
02160                 }
02161 
02162                 f2->set_attr("label", "MCF");
02163                 f2->set_path("/tmp/eman.mcf");
02164 
02165                 EXITFUNC;
02166                 return f2;
02167         }
02168 #endif
02169 
02170         EMData *this_fft = 0;
02171         this_fft = do_fft();
02172 
02173         if (!this_fft) {
02174 
02175                 LOGERR("FFT returns NULL image");
02176                 throw NullPointerException("FFT returns NULL image");
02177         }
02178 
02179         this_fft->ap2ri(); //this is not needed!
02180         EMData *cf = 0;
02181 
02182         if (with && with != this) {
02183                 cf = with->do_fft();
02184                 if (!cf) {
02185                         LOGERR("FFT returns NULL image");
02186                         throw NullPointerException("FFT returns NULL image");
02187                 }
02188                 cf->ap2ri(); //nor is this!
02189         }
02190         else {
02191                 cf = this_fft->copy();
02192         }
02193         
02194         if (filter) {
02195                 if (!EMUtil::is_same_size(filter, cf)) {
02196                         LOGERR("improperly sized filter");
02197                         throw ImageFormatException("improperly sized filter");
02198                 }
02199                 
02200                 cf->mult_complex_efficient(*filter,true); //insanely this is required....
02201                 this_fft->mult(*filter,true);
02202                 //cf->mult_complex_efficient(*filter,7); // takes advantage of the fact that the filter is 1 everywhere but near the origin
02203                 //this_fft->mult_complex_efficient(*filter,7);
02204                 /*cf->mult_complex_efficient(*filter,5);
02205                 this_fft->mult_complex_efficient(*filter,5);*/
02206         }
02207 
02208         float *rdata1 = this_fft->get_data();
02209         float *rdata2 = cf->get_data();
02210         size_t this_fft_size = (size_t)this_fft->get_xsize() * this_fft->get_ysize() * this_fft->get_zsize();
02211 
02212         if (with == this) {
02213                 for (size_t i = 0; i < this_fft_size; i += 2) {
02214                         rdata2[i] = std::sqrt(rdata1[i] * rdata2[i] + rdata1[i + 1] * rdata2[i + 1]);
02215                         rdata2[i + 1] = 0;
02216                 }
02217 
02218                 this_fft->update();
02219                 cf->update();
02220         }
02221         else {
02222                 for (size_t i = 0; i < this_fft_size; i += 2) {
02223                         rdata2[i] = (rdata1[i] * rdata2[i] + rdata1[i + 1] * rdata2[i + 1]);
02224                         rdata2[i + 1] = (rdata1[i + 1] * rdata2[i] - rdata1[i] * rdata2[i + 1]);
02225                 }
02226                 
02227                 //This seems like a bug, but it probably is never used....
02228                 for (size_t i = 0; i < this_fft_size; i += 2) {
02229                         float t = Util::square(rdata2[i]) + Util::square(rdata2[i + 1]);
02230                         if (t != 0) {
02231                                 t = pow(t, 0.25f);
02232                                 rdata2[i] /= t;
02233                                 rdata2[i + 1] /= t;
02234                         }
02235                 }
02236                 this_fft->update();
02237                 cf->update();
02238         }
02239 
02240         EMData *f2 = cf->do_ift();
02241 
02242         if (tocenter) {
02243                 f2->process_inplace("xform.phaseorigin.tocenter");
02244         }
02245 
02246         if( cf )
02247         {
02248                 delete cf;
02249                 cf = 0;
02250         }
02251 
02252         if( this_fft )
02253         {
02254                 delete this_fft;
02255                 this_fft = 0;
02256         }
02257 
02258         f2->set_attr("label", "MCF");
02259         f2->set_path("/tmp/eman.mcf");
02260 
02261         EXITFUNC;
02262         return f2;
02263 }
02264 
02265 
02266 vector < float > EMData::calc_hist(int hist_size, float histmin, float histmax,const float& brt, const float& cont)
02267 {
02268         ENTERFUNC;
02269 
02270         static size_t prime[] = { 1, 3, 7, 11, 17, 23, 37, 59, 127, 253, 511 };
02271 
02272         if (histmin == histmax) {
02273                 histmin = get_attr("minimum");
02274                 histmax = get_attr("maximum");
02275         }
02276 
02277         vector <float> hist(hist_size, 0.0);
02278 
02279         int p0 = 0;
02280         int p1 = 0;
02281         size_t size = (size_t)nx * ny * nz;
02282         if (size < 300000) {
02283                 p0 = 0;
02284                 p1 = 0;
02285         }
02286         else if (size < 2000000) {
02287                 p0 = 2;
02288                 p1 = 3;
02289         }
02290         else if (size < 8000000) {
02291                 p0 = 4;
02292                 p1 = 6;
02293         }
02294         else {
02295                 p0 = 7;
02296                 p1 = 9;
02297         }
02298 
02299         if (is_complex() && p0 > 0) {
02300                 p0++;
02301                 p1++;
02302         }
02303 
02304         size_t di = 0;
02305 //      float norm = 0;
02306         size_t n = hist.size();
02307 
02308         float * data = get_data();
02309         for (int k = p0; k <= p1; ++k) {
02310                 if (is_complex()) {
02311                         di = prime[k] * 2;
02312                 }
02313                 else {
02314                         di = prime[k];
02315                 }
02316 
02317 //              norm += (float)size / (float) di;
02318                 float w = (float)n / (histmax - histmin);
02319 
02320                 for(size_t i=0; i<=size-di; i += di) {
02321                         float val;
02322                         if (cont != 1.0f || brt != 0)val = cont*(data[i]+brt);
02323                         else val = data[i];
02324                         int j = Util::round((val - histmin) * w);
02325                         if (j >= 0 && j < (int) n) {
02326                                 hist[j] += 1;
02327                         }
02328                 }
02329         }
02330 /*
02331         for (size_t i = 0; i < hist.size(); ++i) {
02332                 if (norm != 0) {
02333                         hist[i] = hist[i] / norm;
02334                 }
02335         }
02336 */
02337         return hist;
02338 
02339         EXITFUNC;
02340 }
02341 
02342 
02343 
02344 
02345 
02346 vector<float> EMData::calc_az_dist(int n, float a0, float da, float rmin, float rmax)
02347 {
02348         ENTERFUNC;
02349 
02350         a0=a0*M_PI/180.0f;
02351         da=da*M_PI/180.0f;
02352 
02353         if (get_ndim() > 2) {
02354                 throw ImageDimensionException("no 3D image");
02355         }
02356 
02357         float *yc = new float[n];
02358 
02359         vector<float>   vd(n);
02360         for (int i = 0; i < n; i++) {
02361                 yc[i] = 0.00001f;
02362         }
02363 
02364         float * data = get_data();
02365         if (is_complex()) {
02366                 int c = 0;
02367                 for (int y = 0; y < ny; y++) {
02368                         for (int x = 0; x < nx; x += 2, c += 2) {
02369                                 int x1 = x / 2;
02370                                 int y1 = y<ny/2?y:y-ny;
02371                                 float r = (float)Util::hypot_fast(x1,y1);
02372 
02373                                 if (r >= rmin && r <= rmax) {
02374                                         float a = 0;
02375 
02376                                         if (y != ny / 2 || x != 0) {
02377                                                 a = (atan2((float)y1, (float)x1) - a0) / da;
02378                                         }
02379 
02380                                         int i = (int)(floor(a));
02381                                         a -= i;
02382 
02383                                         if (i == 0) {
02384                                                 vd[0] += data[c] * (1.0f - a);
02385                                                 yc[0] += (1.0f - a);
02386                                         }
02387                                         else if (i == n - 1) {
02388                                                 vd[n - 1] += data[c] * a;
02389                                                 yc[n - 1] += a;
02390                                         }
02391                                         else if (i > 0 && i < (n - 1)) {
02392                                                 float h = 0;
02393                                                 if (is_ri()) {
02394 #ifdef  _WIN32
02395                                                         h = (float)_hypot(data[c], data[c + 1]);
02396 #else
02397                                                         h = (float)hypot(data[c], data[c + 1]);
02398 #endif  //_WIN32
02399                                                 }
02400                                                 else {
02401                                                         h = data[c];
02402                                                 }
02403 
02404                                                 vd[i] += h * (1.0f - a);
02405                                                 yc[i] += (1.0f - a);
02406                                                 vd[i + 1] += h * a;
02407                                                 yc[i + 1] += a;
02408                                         }
02409                                 }
02410                         }
02411                 }
02412         }
02413         else {
02414                 int c = 0;
02415                 float half_nx = (nx - 1) / 2.0f;
02416                 float half_ny = (ny - 1) / 2.0f;
02417 
02418                 for (int y = 0; y < ny; y++) {
02419                         for (int x = 0; x < nx; x++, c++) {
02420                                 float y1 = y - half_ny;
02421                                 float x1 = x - half_nx;
02422 #ifdef  _WIN32
02423                                 float r = (float)_hypot(x1, y1);
02424 #else
02425                                 float r = (float)hypot(x1, y1);
02426 #endif
02427 
02428                                 if (r >= rmin && r <= rmax) {
02429                                         float a = 0;
02430                                         if (x1 != 0 || y1 != 0) {
02431                                                 a = atan2(y1, x1);
02432                                                 if (a < 0) {
02433                                                         a += M_PI * 2;
02434                                                 }
02435                                         }
02436 
02437                                         a = (a - a0) / da;
02438                                         int i = static_cast < int >(floor(a));
02439                                         a -= i;
02440 
02441                                         if (i == 0) {
02442                                                 vd[0] += data[c] * (1.0f - a);
02443                                                 yc[0] += (1.0f - a);
02444                                         }
02445                                         else if (i == n - 1) {
02446                                                 vd[n - 1] += data[c] * a;
02447                                                 yc[n - 1] += (a);
02448                                         }
02449                                         else if (i > 0 && i < (n - 1)) {
02450                                                 vd[i] += data[c] * (1.0f - a);
02451                                                 yc[i] += (1.0f - a);
02452                                                 vd[i + 1] += data[c] * a;
02453                                                 yc[i + 1] += a;
02454                                         }
02455                                 }
02456                         }
02457                 }
02458         }
02459 
02460 
02461         for (int i = 0; i < n; i++) {
02462                 vd[i] /= yc[i];
02463         }
02464 
02465         if( yc )
02466         {
02467                 delete[]yc;
02468                 yc = 0;
02469         }
02470 
02471         return vd;
02472 
02473         EXITFUNC;
02474 }
02475 
02476 
02477 EMData *EMData::unwrap(int r1, int r2, int xs, int dx, int dy, bool do360, bool weight_radial) const
02478 {
02479         ENTERFUNC;
02480 
02481         if (get_ndim() != 2) {
02482                 throw ImageDimensionException("2D image only");
02483         }
02484 
02485         int p = 1;
02486         if (do360) {
02487                 p = 2;
02488         }
02489 
02490         if (xs < 1) {
02491                 xs = (int) Util::fast_floor(p * M_PI * ny / 4);
02492                 xs -= xs % 8;
02493                 if (xs<=8) xs=16;
02494         }
02495 
02496         if (r1 < 0) {
02497                 r1 = 4;
02498         }
02499 
02500 #ifdef  _WIN32
02501         int rr = ny / 2 - 2 - (int) Util::fast_floor(static_cast<float>(_hypot(dx, dy)));
02502 #else
02503         int rr = ny / 2 - 2 - (int) Util::fast_floor(static_cast<float>(hypot(dx, dy)));
02504 #endif  //_WIN32
02505         rr-=rr%2;
02506         if (r2 <= r1 || r2 > rr) {
02507                 r2 = rr;
02508         }
02509 
02510         if ( (r2-r1) < 0 ) throw UnexpectedBehaviorException("The combination of function the arguments and the image dimensions causes unexpected behavior internally. Use a larger image, or a smaller value of r1, or a combination of both");
02511 
02512 #ifdef EMAN2_USING_CUDA
02513         if (isrodataongpu()){
02514                 //cout << " CUDA unwrap" << endl;
02515                 EMData* result = new EMData(0,0,xs,(r2-r1),1);
02516                 result->rw_alloc();
02517                 bindcudaarrayA(true);
02518                 emdata_unwrap(result->cudarwdata, r1, r2, xs, p, dx, dy, weight_radial, nx, ny);
02519                 unbindcudaarryA();
02520                 return result;
02521         }
02522 #endif
02523 
02524         EMData *ret = new EMData();
02525         ret->set_size(xs, r2 - r1, 1);
02526         const float *const d = get_const_data();
02527         float *dd = ret->get_data();
02528         float pfac = (float)p/(float)xs;
02529 
02530         int nxon2 = nx/2;
02531         int nyon2 = ny/2;
02532         for (int x = 0; x < xs; x++) {
02533                 float ang = x * M_PI * pfac;
02534                 float si = sin(ang);
02535                 float co = cos(ang);
02536 
02537                 for (int y = 0; y < r2 - r1; y++) {
02538                         float ypr1 = (float)y + r1;
02539                         float xx = ypr1 * co + nxon2 + dx;
02540                         float yy = ypr1 * si + nyon2 + dy;
02541 //                      float t = xx - Util::fast_floor(xx);
02542 //                      float u = yy - Util::fast_floor(yy);
02543                         float t = xx - (int)xx;
02544                         float u = yy - (int)yy;
02545 //                      int k = (int) Util::fast_floor(xx) + (int) (Util::fast_floor(yy)) * nx;
02546                         int k = (int) xx + ((int) yy) * nx;
02547                         float val = Util::bilinear_interpolate(d[k], d[k + 1], d[k + nx], d[k + nx+1], t,u);
02548                         if (weight_radial) val *=  ypr1;
02549                         dd[x + y * xs] = val;
02550                 }
02551 
02552         }
02553         ret->update();
02554 
02555         EXITFUNC;
02556         return ret;
02557 }
02558 
02559 // NOTE : x axis is from 0 to 0.5  (Nyquist), and thus properly handles non-square images
02560 // complex only
02561 void EMData::apply_radial_func(float x0, float step, vector < float >array, bool interp)
02562 {
02563         ENTERFUNC;
02564 
02565         if (!is_complex()) throw ImageFormatException("apply_radial_func requires a complex image");
02566 
02567         int n = static_cast < int >(array.size());
02568 
02569         if (n*step>2.0) printf("Warning, apply_radial_func takes x0 and step with respect to Nyquist (0.5)\n");
02570 
02571 //      printf("%f %f %f\n",array[0],array[25],array[50]);
02572 
02573         ap2ri();
02574 
02575         size_t ndims = get_ndim();
02576         float * data = get_data();
02577         if (ndims == 2) {
02578                 int k = 0;
02579                 for (int j = 0; j < ny; j++) {
02580                         for (int i = 0; i < nx; i += 2, k += 2) {
02581                                 float r;
02582 #ifdef  _WIN32
02583                                 if (j<ny/2) r = (float)_hypot(i/(float)(nx*2), j/(float)ny);
02584                                 else r = (float)_hypot(i/(float)(nx*2), (ny-j)/(float)ny);
02585 #else
02586                                 if (j<ny/2) r = (float)hypot(i/(float)(nx*2), j/(float)ny);
02587                                 else r = (float)hypot(i/(float)(nx*2), (ny-j)/(float)ny);
02588 #endif  //_WIN32
02589                                 r = (r - x0) / step;
02590 
02591                                 int l = 0;
02592                                 if (interp) {
02593                                         l = (int) floor(r);
02594                                 }
02595                                 else {
02596                                         l = (int) floor(r + 1);
02597                                 }
02598 
02599 
02600                                 float f = 0;
02601                                 if (l >= n - 2) {
02602                                         f = array[n - 1];
02603                                 }
02604                                 else {
02605                                         if (interp) {
02606                                                 r -= l;
02607                                                 f = (array[l] * (1.0f - r) + array[l + 1] * r);
02608                                         }
02609                                         else {
02610                                                 f = array[l];
02611                                         }
02612                                 }
02613 
02614                                 data[k] *= f;
02615                                 data[k + 1] *= f;
02616                         }
02617                 }
02618         }
02619         else if (ndims == 3) {
02620                 int k = 0;
02621                 for (int m = 0; m < nz; m++) {
02622                         float mnz;
02623                         if (m<nz/2) mnz=m*m/(float)(nz*nz);
02624                         else { mnz=(nz-m)/(float)nz; mnz*=mnz; }
02625 
02626                         for (int j = 0; j < ny; j++) {
02627                                 float jny;
02628                                 if (j<ny/2) jny= j*j/(float)(ny*ny);
02629                                 else { jny=(ny-j)/(float)ny; jny*=jny; }
02630 
02631                                 for (int i = 0; i < nx; i += 2, k += 2) {
02632                                         float r = std::sqrt((i * i / (nx*nx*4.0f)) + jny + mnz);
02633                                         r = (r - x0) / step;
02634 
02635                                         int l = 0;
02636                                         if (interp) {
02637                                                 l = (int) floor(r);
02638                                         }
02639                                         else {
02640                                                 l = (int) floor(r + 1);
02641                                         }
02642 
02643 
02644                                         float f = 0;
02645                                         if (l >= n - 2) {
02646                                                 f = array[n - 1];
02647                                         }
02648                                         else {
02649                                                 if (interp) {
02650                                                         r -= l;
02651                                                         f = (array[l] * (1.0f - r) + array[l + 1] * r);
02652                                                 }
02653                                                 else {
02654                                                         f = array[l];
02655                                                 }
02656                                         }
02657 
02658                                         data[k] *= f;
02659                                         data[k + 1] *= f;
02660                                 }
02661                         }
02662                 }
02663 
02664         }
02665 
02666         update();
02667         EXITFUNC;
02668 }
02669 
02670 vector<float> EMData::calc_radial_dist(int n, float x0, float dx, bool inten)
02671 {
02672         ENTERFUNC;
02673 
02674         vector<float>ret(n);
02675         vector<float>norm(n);
02676 
02677         int x,y,z,i;
02678         int step=is_complex()?2:1;
02679         int isinten=get_attr_default("is_intensity",0);
02680 
02681         if (isinten&&!inten) { throw InvalidParameterException("Must set inten for calc_radial_dist with intensity image"); }
02682 
02683         for (i=0; i<n; i++) ret[i]=norm[i]=0.0;
02684         float * data = get_data();
02685 
02686         // We do 2D separately to avoid the hypot3 call
02687         if (nz==1) {
02688                 for (y=i=0; y<ny; y++) {
02689                         for (x=0; x<nx; x+=step,i+=step) {
02690                                 float r,v;
02691                                 if (step==2) {          //complex
02692                                         if (x==0 && y>ny/2) continue;
02693                                         r=(float)(Util::hypot_fast(x/2,y<ny/2?y:ny-y));         // origin at 0,0; periodic
02694                                         if (!inten) {
02695 #ifdef  _WIN32
02696                                                 if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02697 #else
02698                                                 if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02699 #endif
02700                                                 else v=data[i];                                                 // amp/phase, just get amp
02701                                         } else {
02702                                                 if (isinten) v=data[i];
02703                                                 else if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02704                                                 else v=data[i]*data[i];
02705                                         }
02706                                 }
02707                                 else {
02708                                         r=(float)(Util::hypot_fast(x-nx/2,y-ny/2));
02709                                         if (inten) v=data[i]*data[i];
02710                                         else v=data[i];
02711                                 }
02712                                 r=(r-x0)/dx;
02713                                 int f=int(r);   // safe truncation, so floor isn't needed
02714                                 r-=float(f);    // r is now the fractional spacing between bins
02715 //                              printf("%d\t%d\t%d\t%1.3f\t%d\t%1.3f\t%1.4g\n",x,y,f,r,step,Util::hypot_fast(x/2,y<ny/2?y:ny-y),v);
02716                                 if (f>=0 && f<n) {
02717                                         ret[f]+=v*(1.0f-r);
02718                                         norm[f]+=(1.0f-r);
02719                                         if (f<n-1) {
02720                                                 ret[f+1]+=v*r;
02721                                                 norm[f+1]+=r;
02722                                         }
02723                                 }
02724                         }
02725                 }
02726         }
02727         else {
02728                 size_t i;       //3D file may have >2G size
02729                 for (z=i=0; z<nz; ++z) {
02730                         for (y=0; y<ny; ++y) {
02731                                 for (x=0; x<nx; x+=step,i+=step) {
02732                                         float r,v;
02733                                         if (step==2) {  //complex
02734                                                 if (x==0 && z<nz/2) continue;
02735                                                 if (x==0 && z==nz/2 && y<ny/2) continue;
02736                                                 r=Util::hypot3(x/2,y<ny/2?y:ny-y,z<nz/2?z:nz-z);        // origin at 0,0; periodic
02737                                                 if (!inten) {
02738 #ifdef  _WIN32
02739                                                         if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02740 #else
02741                                                         if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02742 #endif  //_WIN32
02743                                                         else v=data[i];                                                 // amp/phase, just get amp
02744                                                 } else {
02745                                                         if (isinten) v=data[i];
02746                                                         else if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02747                                                         else v=data[i]*data[i];
02748                                                 }
02749                                         }
02750                                         else {
02751                                                 r=Util::hypot3(x-nx/2,y-ny/2,z-nz/2);
02752                                                 if (inten) v=data[i]*data[i];
02753                                                 else v=data[i];
02754                                         }
02755                                         r=(r-x0)/dx;
02756                                         int f=int(r);   // safe truncation, so floor isn't needed
02757                                         r-=float(f);    // r is now the fractional spacing between bins
02758                                         if (f>=0 && f<n) {
02759                                                 ret[f]+=v*(1.0f-r);
02760                                                 norm[f]+=(1.0f-r);
02761                                                 if (f<n-1) {
02762                                                         ret[f+1]+=v*r;
02763                                                         norm[f+1]+=r;
02764                                                 }
02765                                         }
02766                                 }
02767                         }
02768                 }
02769         }
02770 
02771         for (i=0; i<n; i++) ret[i]/=norm[i]?norm[i]:1.0f;       // Normalize
02772 
02773         EXITFUNC;
02774 
02775         return ret;
02776 }
02777 
02778 vector<float> EMData::calc_radial_dist(int n, float x0, float dx, int nwedge, bool inten)
02779 {
02780         ENTERFUNC;
02781 
02782         if (nz > 1) {
02783                 LOGERR("2D images only.");
02784                 throw ImageDimensionException("2D images only");
02785         }
02786 
02787         vector<float>ret(n*nwedge);
02788         vector<float>norm(n*nwedge);
02789 
02790         int x,y,i;
02791         int step=is_complex()?2:1;
02792         float astep=static_cast<float>(M_PI*2.0/nwedge);
02793         float* data = get_data();
02794         for (i=0; i<n*nwedge; i++) ret[i]=norm[i]=0.0;
02795 
02796         // We do 2D separately to avoid the hypot3 call
02797         for (y=i=0; y<ny; y++) {
02798                 for (x=0; x<nx; x+=step,i+=step) {
02799                         float r,v,a;
02800                         if (is_complex()) {
02801 #ifdef  _WIN32
02802                                 r=static_cast<float>(_hypot(x/2.0,y<ny/2?y:ny-y));              // origin at 0,0; periodic
02803 #else
02804                                 r=static_cast<float>(hypot(x/2.0,y<ny/2?y:ny-y));               // origin at 0,0; periodic
02805 #endif
02806                                 a=atan2(float(y<ny/2?y:ny-y),x/2.0f);
02807                                 if (!inten) {
02808 #ifdef  _WIN32
02809                                         if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02810 #else
02811                                         if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02812 #endif  //_WIN32
02813                                         else v=data[i];                                                 // amp/phase, just get amp
02814                                 } else {
02815                                         if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02816                                         else v=data[i]*data[i];
02817                                 }
02818                         }
02819                         else {
02820 #ifdef  _WIN32
02821                                 r=static_cast<float>(_hypot(x-nx/2,y-ny/2));
02822 #else
02823                                 r=static_cast<float>(hypot(x-nx/2,y-ny/2));
02824 #endif  //_WIN32
02825                                 a=atan2(float(y-ny/2),float(x-nx/2));
02826                                 if (inten) v=data[i]*data[i];
02827                                 else v=data[i];
02828                         }
02829                         int bin=n*int((a+M_PI)/astep);
02830                         if (bin>=nwedge) bin=nwedge-1;
02831                         r=(r-x0)/dx;
02832                         int f=int(r);   // safe truncation, so floor isn't needed
02833                         r-=float(f);    // r is now the fractional spacing between bins
02834                         if (f>=0 && f<n) {
02835                                 ret[f+bin]+=v*(1.0f-r);
02836                                 norm[f+bin]+=(1.0f-r);
02837                                 if (f<n-1) {
02838                                         ret[f+1+bin]+=v*r;
02839                                         norm[f+1+bin]+=r;
02840                                 }
02841                         }
02842                 }
02843         }
02844 
02845         for (i=0; i<n*nwedge; i++) ret[i]/=norm[i]?norm[i]:1.0f;        // Normalize
02846         EXITFUNC;
02847 
02848         return ret;
02849 }
02850 
02851 void EMData::cconj() {
02852         ENTERFUNC;
02853         if (!is_complex() || !is_ri())
02854                 throw ImageFormatException("EMData::conj requires a complex, ri image");
02855         int nxreal = nx -2 + int(is_fftodd());
02856         int nxhalf = nxreal/2;
02857         for (int iz = 0; iz < nz; iz++)
02858                 for (int iy = 0; iy < ny; iy++)
02859                         for (int ix = 0; ix <= nxhalf; ix++)
02860                                 cmplx(ix,iy,iz) = conj(cmplx(ix,iy,iz));
02861         EXITFUNC;
02862 }
02863 
02864 //#ifdef EMAN2_USING_CUDA
02865 //void EMData::update_stat_cuda() const
02866 //{
02867 //      float* stats = update_stats_cuda(cudarwdata);
02868         
02869 //      attr_dict["mean"] = stats[0];
02870 //      attr_dict["sigma"] = stats[1];
02871         
02872 //      free(stats);
02873 //}
02874 //#endif
02875 
02876 void EMData::update_stat() const
02877 {
02878         ENTERFUNC;
02879 //      printf("update stat %f %d\n",(float)attr_dict["mean"],flags);
02880         if (!(flags & EMDATA_NEEDUPD))
02881         {
02882                 EXITFUNC;
02883                 return;
02884         }
02885 
02886         float* data = get_data();
02887         float max = -FLT_MAX;
02888         float min = -max;
02889 
02890         double sum = 0;
02891         double square_sum = 0;
02892 
02893         int step = 1;
02894         if (is_complex() && !is_ri()) {
02895                 step = 2;
02896         }
02897 
02898         int n_nonzero = 0;
02899 
02900         size_t size = (size_t)nx*ny*nz;
02901         for (size_t i = 0; i < size; i += step) {
02902                 float v = data[i];
02903         #ifdef _WIN32
02904                 max = _cpp_max(max,v);
02905                 min = _cpp_min(min,v);
02906         #else
02907                 max=std::max<float>(max,v);
02908                 min=std::min<float>(min,v);
02909         #endif  //_WIN32
02910                 sum += v;
02911                 square_sum += v * (double)(v);
02912                 if (v != 0) n_nonzero++;
02913         }
02914 
02915         size_t n = size / step;
02916         double mean = sum / n;
02917 
02918 #ifdef _WIN32
02919         float sigma = (float)std::sqrt( _cpp_max(0.0,(square_sum - sum*sum / n)/(n-1)));
02920         n_nonzero = _cpp_max(1,n_nonzero);
02921         double sigma_nonzero = std::sqrt( _cpp_max(0,(square_sum  - sum*sum/n_nonzero)/(n_nonzero-1)));
02922 #else
02923         float sigma = (float)std::sqrt(std::max<double>(0.0,(square_sum - sum*sum / n)/(n-1)));
02924         n_nonzero = std::max<int>(1,n_nonzero);
02925         double sigma_nonzero = std::sqrt(std::max<double>(0,(square_sum  - sum*sum/n_nonzero)/(n_nonzero-1)));
02926 #endif  //_WIN32
02927         double mean_nonzero = sum / n_nonzero; // previous version overcounted! G2
02928 
02929         attr_dict["minimum"] = min;
02930         attr_dict["maximum"] = max;
02931         attr_dict["mean"] = (float)(mean);
02932         attr_dict["sigma"] = (float)(sigma);
02933         attr_dict["square_sum"] = (float)(square_sum);
02934         attr_dict["mean_nonzero"] = (float)(mean_nonzero);
02935         attr_dict["sigma_nonzero"] = (float)(sigma_nonzero);
02936         attr_dict["is_complex"] = (int) is_complex();
02937         attr_dict["is_complex_ri"] = (int) is_ri();
02938 
02939         flags &= ~EMDATA_NEEDUPD;
02940 
02941         if (rot_fp != 0)
02942         {
02943                 delete rot_fp; rot_fp = 0;
02944         }
02945 
02946         EXITFUNC;
02947 //      printf("done stat %f %f %f\n",(float)mean,(float)max,(float)sigma);
02948 }
02949 
02950 bool EMData::operator==(const EMData& that) const {
02951         if (that.get_xsize() != nx || that.get_ysize() != ny || that.get_zsize() != nz ) return false;
02952 
02953         const float*  d1 = that.get_const_data();
02954         float* d2 = get_data();
02955 
02956         for(size_t i =0; i < get_size(); ++i,++d1,++d2) {
02957                 if ((*d1) != (*d2)) return false;
02958         }
02959         return true;
02960 
02961 }
02962 
02963 EMData * EMAN::operator+(const EMData & em, float n)
02964 {
02965         EMData * r = em.copy();
02966         r->add(n);
02967         return r;
02968 }
02969 
02970 EMData * EMAN::operator-(const EMData & em, float n)
02971 {
02972         EMData* r = em.copy();
02973         r->sub(n);
02974         return r;
02975 }
02976 
02977 EMData * EMAN::operator*(const EMData & em, float n)
02978 {
02979         EMData* r = em.copy();
02980         r ->mult(n);
02981         return r;
02982 }
02983 
02984 EMData * EMAN::operator/(const EMData & em, float n)
02985 {
02986         EMData * r = em.copy();
02987         r->div(n);
02988         return r;
02989 }
02990 
02991 
02992 EMData * EMAN::operator+(float n, const EMData & em)
02993 {
02994         EMData * r = em.copy();
02995         r->add(n);
02996         return r;
02997 }
02998 
02999 EMData * EMAN::operator-(float n, const EMData & em)
03000 {
03001         EMData * r = em.copy();
03002         r->mult(-1.0f);
03003         r->add(n);
03004         return r;
03005 }
03006 
03007 EMData * EMAN::operator*(float n, const EMData & em)
03008 {
03009         EMData * r = em.copy();
03010         r->mult(n);
03011         return r;
03012 }
03013 
03014 EMData * EMAN::operator/(float n, const EMData & em)
03015 {
03016         EMData * r = em.copy();
03017         r->to_one();
03018         r->mult(n);
03019         r->div(em);
03020 
03021         return r;
03022 }
03023 
03024 EMData * EMAN::rsub(const EMData & em, float n)
03025 {
03026         return EMAN::operator-(n, em);
03027 }
03028 
03029 EMData * EMAN::rdiv(const EMData & em, float n)
03030 {
03031         return EMAN::operator/(n, em);
03032 }
03033 
03034 EMData * EMAN::operator+(const EMData & a, const EMData & b)
03035 {
03036         EMData * r = a.copy();
03037         r->add(b);
03038         return r;
03039 }
03040 
03041 EMData * EMAN::operator-(const EMData & a, const EMData & b)
03042 {
03043         EMData * r = a.copy();
03044         r->sub(b);
03045         return r;
03046 }
03047 
03048 EMData * EMAN::operator*(const EMData & a, const EMData & b)
03049 {
03050         EMData * r = a.copy();
03051         r->mult(b);
03052         return r;
03053 }
03054 
03055 EMData * EMAN::operator/(const EMData & a, const EMData & b)
03056 {
03057         EMData * r = a.copy();
03058         r->div(b);
03059         return r;
03060 }
03061 
03062 void EMData::set_xyz_origin(float origin_x, float origin_y, float origin_z)
03063 {
03064         attr_dict["origin_x"] = origin_x;
03065         attr_dict["origin_y"] = origin_y;
03066         attr_dict["origin_z"] = origin_z;
03067 }
03068 
03069 #if 0
03070 void EMData::calc_rcf(EMData * with, vector < float >&sum_array)
03071 {
03072         ENTERFUNC;
03073 
03074         int array_size = sum_array.size();
03075         float da = 2 * M_PI / array_size;
03076         float *dat = new float[array_size + 2];
03077         float *dat2 = new float[array_size + 2];
03078         int nx2 = nx * 9 / 20;
03079 
03080         float lim = 0;
03081         if (fabs(translation[0]) < fabs(translation[1])) {
03082                 lim = fabs(translation[1]);
03083         }
03084         else {
03085                 lim = fabs(translation[0]);
03086         }
03087 
03088         nx2 -= static_cast < int >(floor(lim));
03089 
03090         for (int i = 0; i < array_size; i++) {
03091                 sum_array[i] = 0;
03092         }
03093 
03094         float sigma = attr_dict["sigma"];
03095         float with_sigma = with->get_attr_dict().get("sigma");
03096 
03097         vector<float> vdata, vdata2;
03098         for (int i = 8; i < nx2; i += 6) {
03099                 vdata = calc_az_dist(array_size, 0, da, i, i + 6);
03100                 vdata2 = with->calc_az_dist(array_size, 0, da, i, i + 6);
03101                 Assert(vdata.size() <= array_size + 2);
03102                 Assert(cdata2.size() <= array_size + 2);
03103                 std::copy(vdata.begin(), vdata.end(), dat);
03104                 std::copy(vdata2.begin(), vdata2.end(), dat2);
03105 
03106                 EMfft::real_to_complex_1d(dat, dat, array_size);
03107                 EMfft::real_to_complex_1d(dat2, dat2, array_size);
03108 
03109                 for (int j = 0; j < array_size + 2; j += 2) {
03110                         float max = dat[j] * dat2[j] + dat[j + 1] * dat2[j + 1];
03111                         float max2 = dat[j + 1] * dat2[j] - dat2[j + 1] * dat[j];
03112                         dat[j] = max;
03113                         dat[j + 1] = max2;
03114                 }
03115 
03116                 EMfft::complex_to_real_1d(dat, dat, array_size);
03117                 float norm = array_size * array_size * (4.0f * sigma) * (4.0f * with_sigma);
03118 
03119                 for (int j = 0; j < array_size; j++) {
03120                         sum_array[j] += dat[j] * (float) i / norm;
03121                 }
03122         }
03123 
03124         if( dat )
03125         {
03126                 delete[]dat;
03127                 dat = 0;
03128         }
03129 
03130         if( dat2 )
03131         {
03132                 delete[]dat2;
03133                 dat2 = 0;
03134         }
03135         EXITFUNC;
03136 }
03137 
03138 #endif
03139 
03140 void EMData::add_incoherent(EMData * obj)
03141 {
03142         ENTERFUNC;
03143 
03144         if (!obj) {
03145                 LOGERR("NULL image");
03146                 throw NullPointerException("NULL image");
03147         }
03148 
03149         if (!obj->is_complex() || !is_complex()) {
03150                 throw ImageFormatException("complex images only");
03151         }
03152 
03153         if (!EMUtil::is_same_size(this, obj)) {
03154                 throw ImageFormatException("images not same size");
03155         }
03156 
03157         ri2ap();
03158         obj->ri2ap();
03159 
03160         float *dest = get_data();
03161         float *src = obj->get_data();
03162         size_t size = (size_t)nx * ny * nz;
03163         for (size_t j = 0; j < size; j += 2) {
03164 #ifdef  _WIN32
03165                 dest[j] = (float) _hypot(src[j], dest[j]);
03166 #else
03167                 dest[j] = (float) hypot(src[j], dest[j]);
03168 #endif  //_WIN32
03169                 dest[j + 1] = 0;
03170         }
03171 
03172         obj->update();
03173         update();
03174         EXITFUNC;
03175 }
03176 
03177 
03178 float EMData::calc_dist(EMData * second_img, int y_index) const
03179 {
03180         ENTERFUNC;
03181 
03182         if (get_ndim() != 1) {
03183                 throw ImageDimensionException("'this' image is 1D only");
03184         }
03185 
03186         if (second_img->get_xsize() != nx || ny != 1) {
03187                 throw ImageFormatException("image xsize not same");
03188         }
03189 
03190         if (y_index > second_img->get_ysize() || y_index < 0) {
03191                 return -1;
03192         }
03193 
03194         float ret = 0;
03195         float *d1 = get_data();
03196         float *d2 = second_img->get_data() + second_img->get_xsize() * y_index;
03197 
03198         for (int i = 0; i < nx; i++) {
03199                 ret += Util::square(d1[i] - d2[i]);
03200         }
03201         EXITFUNC;
03202         return std::sqrt(ret);
03203 }
03204 
03205 
03206 EMData * EMData::calc_fast_sigma_image( EMData* mask)
03207 {
03208         ENTERFUNC;
03209 
03210         bool maskflag = false;
03211         if (mask == 0) {
03212                 mask = new EMData(nx,ny,nz);
03213                 mask->process_inplace("testimage.circlesphere");
03214                 maskflag = true;
03215         }
03216 
03217         if (get_ndim() != mask->get_ndim() ) throw ImageDimensionException("The dimensions do not match");
03218 
03219         int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
03220 
03221         if ( mnx > nx || mny > ny || mnz > nz)
03222                 throw ImageDimensionException("Can not calculate variance map using an image that is larger than this image");
03223 
03224         size_t P = 0;
03225         for(size_t i = 0; i < mask->get_size(); ++i){
03226                 if (mask->get_value_at(i) != 0){
03227                         ++P;
03228                 }
03229         }
03230         float normfac = 1.0f/(float)P;
03231 
03232 //      bool undoclip = false;
03233 
03234         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
03235 //      if ( mnx < nx || mny < ny || mnz < nz) {
03236         Region r;
03237         if (ny == 1) r = Region((mnx-nxc)/2,nxc);
03238         else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
03239         else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03240         mask->clip_inplace(r,0.0);
03241         //Region r((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03242         //mask->clip_inplace(r);
03243         //undoclip = true;
03244         //}
03245 
03246         // Here we generate the local average of the squares
03247         Region r2;
03248         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
03249         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
03250         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
03251         EMData* squared = get_clip(r2,get_edge_mean());
03252 
03253         EMData* tmp = squared->copy();
03254         Dict pow;
03255         pow["pow"] = 2.0f;
03256         squared->process_inplace("math.pow",pow);
03257         EMData* s = mask->convolute(squared);//ming, mask squared exchange
03258         squared->mult(normfac);
03259 
03260         EMData* m = mask->convolute(tmp);//ming, tmp mask exchange
03261         m->mult(normfac);
03262         m->process_inplace("math.pow",pow);
03263         delete tmp; tmp = 0;
03264         s->sub(*m);
03265         // Here we finally generate the standard deviation image
03266         s->process_inplace("math.sqrt");
03267 
03268 //      if ( undoclip ) {
03269 //              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
03270 //              mask->clip_inplace(r);
03271 //      }
03272 
03273         if (maskflag) {
03274                 delete mask;
03275                 mask = 0;
03276         } else {
03277                 Region r;
03278                 if (ny == 1) r = Region((nxc-mnx)/2,mnx);
03279                 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
03280                 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
03281                 mask->clip_inplace(r);
03282         }
03283 
03284         delete squared;
03285         delete m;
03286 
03287         s->process_inplace("xform.phaseorigin.tocenter");
03288         Region r3;
03289         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
03290         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
03291         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
03292         s->clip_inplace(r3);
03293         EXITFUNC;
03294         return s;
03295 }
03296 
03297 //  The following code looks strange - does anybody know it?  Please let me know, pawel.a.penczek@uth.tmc.edu  04/09/06.
03298 // This is just an implementation of "Roseman's" fast normalized cross-correlation (Ultramicroscopy, 2003). But the contents of this function have changed dramatically since you wrote that comment (d.woolford).
03299 EMData *EMData::calc_flcf(EMData * with)
03300 {
03301         ENTERFUNC;
03302         EMData *this_copy=this;
03303         this_copy=copy();
03304 
03305         int mnx = with->get_xsize(); int mny = with->get_ysize(); int mnz = with->get_zsize();
03306         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
03307 
03308         // Ones is a circular/spherical mask, consisting of 1s.
03309         EMData* ones = new EMData(mnx,mny,mnz);
03310         ones->process_inplace("testimage.circlesphere");
03311 
03312         // Get a copy of with, we will eventually resize it
03313         EMData* with_resized = with->copy();
03314         with_resized->process_inplace("normalize");
03315         with_resized->mult(*ones);
03316 
03317         EMData* s = calc_fast_sigma_image(ones);// Get the local sigma image
03318 
03319         Region r1;
03320         if (ny == 1) r1 = Region((mnx-nxc)/2,nxc);
03321         else if (nz == 1) r1 = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
03322         else r1 = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03323         with_resized->clip_inplace(r1,0.0);
03324 
03325         Region r2;
03326         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
03327         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
03328         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
03329         this_copy->clip_inplace(r2,0.0);
03330 
03331         EMData* corr = this_copy->calc_ccf(with_resized); // the ccf results should have same size as sigma
03332 
03333         corr->process_inplace("xform.phaseorigin.tocenter");
03334         Region r3;
03335         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
03336         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
03337         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
03338         corr->clip_inplace(r3);
03339 
03340         corr->div(*s);
03341 
03342         delete with_resized; delete ones; delete this_copy; delete s;
03343         EXITFUNC;
03344         return corr;
03345 }
03346 
03347 EMData *EMData::convolute(EMData * with)
03348 {
03349         ENTERFUNC;
03350 
03351         EMData *f1 = do_fft();
03352         if (!f1) {
03353                 LOGERR("FFT returns NULL image");
03354                 throw NullPointerException("FFT returns NULL image");
03355         }
03356 
03357         f1->ap2ri();
03358 
03359         EMData *cf = 0;
03360         if (with) {
03361                 cf = with->do_fft();
03362                 if (!cf) {
03363                         LOGERR("FFT returns NULL image");
03364                         throw NullPointerException("FFT returns NULL image");
03365                 }
03366                 cf->ap2ri();
03367         }
03368         else {
03369                 cf = f1->copy();
03370         }
03371         //printf("cf_x=%d, f1y=%d, thisx=%d, withx=%d\n",cf->get_xsize(),f1->get_ysize(),this->get_xsize(),with->get_xsize());
03372         if (with && !EMUtil::is_same_size(f1, cf)) {
03373                 LOGERR("images not same size");
03374                 throw ImageFormatException("images not same size");
03375         }
03376 
03377         float *rdata1 = f1->get_data();
03378         float *rdata2 = cf->get_data();
03379         size_t cf_size = (size_t)cf->get_xsize() * cf->get_ysize() * cf->get_zsize();
03380 
03381         float re,im;
03382 
03383         for (size_t i = 0; i < cf_size; i += 2) {
03384                 re = rdata1[i] * rdata2[i] - rdata1[i + 1] * rdata2[i + 1];
03385                 im = rdata1[i + 1] * rdata2[i] + rdata1[i] * rdata2[i + 1];
03386                 rdata2[i]=re;
03387                 rdata2[i+1]=im;
03388         }
03389         cf->update();
03390         EMData *f2 = cf->do_ift();//ming change cf to cf_temp
03391         //printf("cf_x=%d, f2x=%d, thisx=%d, withx=%d\n",cf->get_xsize(),f2->get_xsize(),this->get_xsize(),with->get_xsize());
03392         if( cf )
03393         {
03394                 delete cf;
03395                 cf = 0;
03396         }
03397 
03398         if( f1 )
03399         {
03400                 delete f1;
03401                 f1=0;
03402         }
03403 
03404         EXITFUNC;
03405         return f2;
03406 }
03407 
03408 
03409 void EMData::common_lines(EMData * image1, EMData * image2,
03410                                                   int mode, int steps, bool horizontal)
03411 {
03412         ENTERFUNC;
03413 
03414         if (!image1 || !image2) {
03415                 throw NullPointerException("NULL image");
03416         }
03417 
03418         if (mode < 0 || mode > 2) {
03419                 throw OutofRangeException(0, 2, mode, "invalid mode");
03420         }
03421 
03422         if (!image1->is_complex()) {
03423                 image1 = image1->do_fft();
03424         }
03425         if (!image2->is_complex()) {
03426                 image2 = image2->do_fft();
03427         }
03428 
03429         image1->ap2ri();
03430         image2->ap2ri();
03431 
03432         if (!EMUtil::is_same_size(image1, image2)) {
03433                 throw ImageFormatException("images not same sizes");
03434         }
03435 
03436         int image2_nx = image2->get_xsize();
03437         int image2_ny = image2->get_ysize();
03438 
03439         int rmax = image2_ny / 4 - 1;
03440         int array_size = steps * rmax * 2;
03441         float *im1 = new float[array_size];
03442         float *im2 = new float[array_size];
03443         for (int i = 0; i < array_size; i++) {
03444                 im1[i] = 0;
03445                 im2[i] = 0;
03446         }
03447 
03448         set_size(steps * 2, steps * 2, 1);
03449 
03450         float *image1_data = image1->get_data();
03451         float *image2_data = image2->get_data();
03452 
03453         float da = M_PI / steps;
03454         float a = -M_PI / 2.0f + da / 2.0f;
03455         int jmax = 0;
03456 
03457         for (int i = 0; i < steps * 2; i += 2, a += da) {
03458                 float s1 = 0;
03459                 float s2 = 0;
03460                 int i2 = i * rmax;
03461                 int j = 0;
03462 
03463                 for (float r = 3.0f; r < rmax - 3.0f; j += 2, r += 1.0f) {
03464                         float x = r * cos(a);
03465                         float y = r * sin(a);
03466 
03467                         if (x < 0) {
03468                                 x = -x;
03469                                 y = -y;
03470                                 LOGERR("CCL ERROR %d, %f !\n", i, -x);
03471                         }
03472 
03473                         int k = (int) (floor(x) * 2 + floor(y + image2_ny / 2) * image2_nx);
03474                         int l = i2 + j;
03475                         float x2 = x - floor(x);
03476                         float y2 = y - floor(y);
03477 
03478                         im1[l] = Util::bilinear_interpolate(image1_data[k],
03479                                                                                                 image1_data[k + 2],
03480                                                                                                 image1_data[k + image2_nx],
03481                                                                                                 image1_data[k + 2 + image2_nx], x2, y2);
03482 
03483                         im2[l] = Util::bilinear_interpolate(image2_data[k],
03484                                                                                                 image2_data[k + 2],
03485                                                                                                 image2_data[k + image2_nx],
03486                                                                                                 image2_data[k + 2 + image2_nx], x2, y2);
03487 
03488                         k++;
03489 
03490                         im1[l + 1] = Util::bilinear_interpolate(image1_data[k],
03491                                                                                                         image1_data[k + 2],
03492                                                                                                         image1_data[k + image2_nx],
03493                                                                                                         image1_data[k + 2 + image2_nx], x2, y2);
03494 
03495                         im2[l + 1] = Util::bilinear_interpolate(image2_data[k],
03496                                                                                                         image2_data[k + 2],
03497                                                                                                         image2_data[k + image2_nx],
03498                                                                                                         image2_data[k + 2 + image2_nx], x2, y2);
03499 
03500                         s1 += Util::square_sum(im1[l], im1[l + 1]);
03501                         s2 += Util::square_sum(im2[l], im2[l + 1]);
03502                 }
03503 
03504                 jmax = j - 1;
03505                 float sqrt_s1 = std::sqrt(s1);
03506                 float sqrt_s2 = std::sqrt(s2);
03507 
03508                 int l = 0;
03509                 for (float r = 1; r < rmax; r += 1.0f) {
03510                         int i3 = i2 + l;
03511                         im1[i3] /= sqrt_s1;
03512                         im1[i3 + 1] /= sqrt_s1;
03513                         im2[i3] /= sqrt_s2;
03514                         im2[i3 + 1] /= sqrt_s2;
03515                         l += 2;
03516                 }
03517         }
03518         float * data = get_data();
03519 
03520         switch (mode) {
03521         case 0:
03522                 for (int m1 = 0; m1 < 2; m1++) {
03523                         for (int m2 = 0; m2 < 2; m2++) {
03524 
03525                                 if (m1 == 0 && m2 == 0) {
03526                                         for (int i = 0; i < steps; i++) {
03527                                                 int i2 = i * rmax * 2;
03528                                                 for (int j = 0; j < steps; j++) {
03529                                                         int l = i + j * steps * 2;
03530                                                         int j2 = j * rmax * 2;
03531                                                         data[l] = 0;
03532                                                         for (int k = 0; k < jmax; k++) {
03533                                                                 data[l] += im1[i2 + k] * im2[j2 + k];
03534                                                         }
03535                                                 }
03536                                         }
03537                                 }
03538                                 else {
03539                                         int steps2 = steps * m2 + steps * steps * 2 * m1;
03540 
03541                                         for (int i = 0; i < steps; i++) {
03542                                                 int i2 = i * rmax * 2;
03543                                                 for (int j = 0; j < steps; j++) {
03544                                                         int j2 = j * rmax * 2;
03545                                                         int l = i + j * steps * 2 + steps2;
03546                                                         data[l] = 0;
03547 
03548                                                         for (int k = 0; k < jmax; k += 2) {
03549                                                                 i2 += k;
03550                                                                 j2 += k;
03551                                                                 data[l] += im1[i2] * im2[j2];
03552                                                                 data[l] += -im1[i2 + 1] * im2[j2 + 1];
03553                                                         }
03554                                                 }
03555                                         }
03556                                 }
03557                         }
03558                 }
03559 
03560                 break;
03561         case 1:
03562                 for (int m1 = 0; m1 < 2; m1++) {
03563                         for (int m2 = 0; m2 < 2; m2++) {
03564                                 int steps2 = steps * m2 + steps * steps * 2 * m1;
03565                                 int p1_sign = 1;
03566                                 if (m1 != m2) {
03567                                         p1_sign = -1;
03568                                 }
03569 
03570                                 for (int i = 0; i < steps; i++) {
03571                                         int i2 = i * rmax * 2;
03572 
03573                                         for (int j = 0; j < steps; j++) {
03574                                                 int j2 = j * rmax * 2;
03575 
03576                                                 int l = i + j * steps * 2 + steps2;
03577                                                 data[l] = 0;
03578                                                 float a = 0;
03579 
03580                                                 for (int k = 0; k < jmax; k += 2) {
03581                                                         i2 += k;
03582                                                         j2 += k;
03583 
03584 #ifdef  _WIN32
03585                                                         float a1 = (float) _hypot(im1[i2], im1[i2 + 1]);
03586 #else
03587                                                         float a1 = (float) hypot(im1[i2], im1[i2 + 1]);
03588 #endif  //_WIN32
03589                                                         float p1 = atan2(im1[i2 + 1], im1[i2]);
03590                                                         float p2 = atan2(im2[j2 + 1], im2[j2]);
03591 
03592                                                         data[l] += Util::angle_sub_2pi(p1_sign * p1, p2) * a1;
03593                                                         a += a1;
03594                                                 }
03595 
03596                                                 data[l] /= (float)(a * M_PI / 180.0f);
03597                                         }
03598                                 }
03599                         }
03600                 }
03601 
03602                 break;
03603         case 2:
03604                 for (int m1 = 0; m1 < 2; m1++) {
03605                         for (int m2 = 0; m2 < 2; m2++) {
03606                                 int steps2 = steps * m2 + steps * steps * 2 * m1;
03607 
03608                                 for (int i = 0; i < steps; i++) {
03609                                         int i2 = i * rmax * 2;
03610 
03611                                         for (int j = 0; j < steps; j++) {
03612                                                 int j2 = j * rmax * 2;
03613                                                 int l = i + j * steps * 2 + steps2;
03614                                                 data[l] = 0;
03615 
03616                                                 for (int k = 0; k < jmax; k += 2) {
03617                                                         i2 += k;
03618                                                         j2 += k;
03619 #ifdef  _WIN32
03620                                                         data[l] += (float) (_hypot(im1[i2], im1[i2 + 1]) * _hypot(im2[j2], im2[j2 + 1]));
03621 #else
03622                                                         data[l] += (float) (hypot(im1[i2], im1[i2 + 1]) * hypot(im2[j2], im2[j2 + 1]));
03623 #endif  //_WIN32
03624                                                 }
03625                                         }
03626                                 }
03627                         }
03628                 }
03629 
03630                 break;
03631         default:
03632                 break;
03633         }
03634 
03635         if (horizontal) {
03636                 float *tmp_array = new float[ny];
03637                 for (int i = 1; i < nx; i++) {
03638                         for (int j = 0; j < ny; j++) {
03639                                 tmp_array[j] = get_value_at(i, j);
03640                         }
03641                         for (int j = 0; j < ny; j++) {
03642                                 set_value_at(i, j, 0, tmp_array[(j + i) % ny]);
03643                         }
03644                 }
03645                 if( tmp_array )
03646                 {
03647                         delete[]tmp_array;
03648                         tmp_array = 0;
03649                 }
03650         }
03651 
03652         if( im1 )
03653         {
03654                 delete[]im1;
03655                 im1 = 0;
03656         }
03657 
03658         if( im2 )
03659         {
03660                 delete im2;
03661                 im2 = 0;
03662         }
03663 
03664 
03665         image1->update();
03666         image2->update();
03667         if( image1 )
03668         {
03669                 delete image1;
03670                 image1 = 0;
03671         }
03672         if( image2 )
03673         {
03674                 delete image2;
03675                 image2 = 0;
03676         }
03677         update();
03678         EXITFUNC;
03679 }
03680 
03681 
03682 
03683 void EMData::common_lines_real(EMData * image1, EMData * image2,
03684                                                            int steps, bool horiz)
03685 {
03686         ENTERFUNC;
03687 
03688         if (!image1 || !image2) {
03689                 throw NullPointerException("NULL image");
03690         }
03691 
03692         if (!EMUtil::is_same_size(image1, image2)) {
03693                 throw ImageFormatException("images not same size");
03694         }
03695 
03696         int steps2 = steps * 2;
03697         int image_ny = image1->get_ysize();
03698         EMData *image1_copy = image1->copy();
03699         EMData *image2_copy = image2->copy();
03700 
03701         float *im1 = new float[steps2 * image_ny];
03702         float *im2 = new float[steps2 * image_ny];
03703 
03704         EMData *images[] = { image1_copy, image2_copy };
03705         float *ims[] = { im1, im2 };
03706 
03707         for (int m = 0; m < 2; m++) {
03708                 float *im = ims[m];
03709                 float a = M_PI / steps2;
03710                 Transform t(Dict("type","2d","alpha",-a));
03711                 for (int i = 0; i < steps2; i++) {
03712                         images[i]->transform(t);
03713                         float *data = images[i]->get_data();
03714 
03715                         for (int j = 0; j < image_ny; j++) {
03716                                 float sum = 0;
03717                                 for (int k = 0; k < image_ny; k++) {
03718                                         sum += data[j * image_ny + k];
03719                                 }
03720                                 im[i * image_ny + j] = sum;
03721                         }
03722 
03723                         float sum1 = 0;
03724                         float sum2 = 0;
03725                         for (int j = 0; j < image_ny; j++) {
03726                                 int l = i * image_ny + j;
03727                                 sum1 += im[l];
03728                                 sum2 += im[l] * im[l];
03729                         }
03730 
03731                         float mean = sum1 / image_ny;
03732                         float sigma = std::sqrt(sum2 / image_ny - sum1 * sum1);
03733 
03734                         for (int j = 0; j < image_ny; j++) {
03735                                 int l = i * image_ny + j;
03736                                 im[l] = (im[l] - mean) / sigma;
03737                         }
03738 
03739                         images[i]->update();
03740                         a += M_PI / steps;
03741                 }
03742         }
03743 
03744         set_size(steps2, steps2, 1);
03745         float *data1 = get_data();
03746 
03747         if (horiz) {
03748                 for (int i = 0; i < steps2; i++) {
03749                         for (int j = 0, l = i; j < steps2; j++, l++) {
03750                                 if (l == steps2) {
03751                                         l = 0;
03752                                 }
03753 
03754                                 float sum = 0;
03755                                 for (int k = 0; k < image_ny; k++) {
03756                                         sum += im1[i * image_ny + k] * im2[l * image_ny + k];
03757                                 }
03758                                 data1[i + j * steps2] = sum;
03759                         }
03760                 }
03761         }
03762         else {
03763                 for (int i = 0; i < steps2; i++) {
03764                         for (int j = 0; j < steps2; j++) {
03765                                 float sum = 0;
03766                                 for (int k = 0; k < image_ny; k++) {
03767                                         sum += im1[i * image_ny + k] * im2[j * image_ny + k];
03768                                 }
03769                                 data1[i + j * steps2] = sum;
03770                         }
03771                 }
03772         }
03773 
03774         update();
03775 
03776         if( image1_copy )
03777         {
03778                 delete image1_copy;
03779                 image1_copy = 0;
03780         }
03781 
03782         if( image2_copy )
03783         {
03784                 delete image2_copy;
03785                 image2_copy = 0;
03786         }
03787 
03788         if( im1 )
03789         {
03790                 delete[]im1;
03791                 im1 = 0;
03792         }
03793 
03794         if( im2 )
03795         {
03796                 delete[]im2;
03797                 im2 = 0;
03798         }
03799         EXITFUNC;
03800 }
03801 
03802 
03803 void EMData::cut_slice(const EMData *const map, const Transform& transform, bool interpolate)
03804 {
03805         ENTERFUNC;
03806 
03807         if (!map) throw NullPointerException("NULL image");
03808         // These restrictions should be ultimately restricted so that all that matters is get_ndim() = (map->get_ndim() -1)
03809         if ( get_ndim() != 2 ) throw ImageDimensionException("Can not call cut slice on an image that is not 2D");
03810         if ( map->get_ndim() != 3 ) throw ImageDimensionException("Can not cut slice from an image that is not 3D");
03811         // Now check for complex images - this is really just being thorough
03812         if ( is_complex() ) throw ImageFormatException("Can not call cut slice on an image that is complex");
03813         if ( map->is_complex() ) throw ImageFormatException("Can not cut slice from a complex image");
03814 
03815 
03816         float *sdata = map->get_data();
03817         float *ddata = get_data();
03818 
03819         int map_nx = map->get_xsize();
03820         int map_ny = map->get_ysize();
03821         int map_nz = map->get_zsize();
03822         int map_nxy = map_nx * map_ny;
03823 
03824         int ymax = ny/2;
03825         if ( ny % 2 == 1 ) ymax += 1;
03826         int xmax = nx/2;
03827         if ( nx % 2 == 1 ) xmax += 1;
03828         for (int y = -ny/2; y < ymax; y++) {
03829                 for (int x = -nx/2; x < xmax; x++) {
03830                         Vec3f coord(x,y,0);
03831                         Vec3f soln = transform*coord;
03832 
03833 //                      float xx = (x+pretrans[0]) * (*ort)[0][0] +  (y+pretrans[1]) * (*ort)[0][1] + pretrans[2] * (*ort)[0][2] + posttrans[0];
03834 //                      float yy = (x+pretrans[0]) * (*ort)[1][0] +  (y+pretrans[1]) * (*ort)[1][1] + pretrans[2] * (*ort)[1][2] + posttrans[1];
03835 //                      float zz = (x+pretrans[0]) * (*ort)[2][0] +  (y+pretrans[1]) * (*ort)[2][1] + pretrans[2] * (*ort)[2][2] + posttrans[2];
03836 
03837 
03838 //                      xx += map_nx/2;
03839 //                      yy += map_ny/2;
03840 //                      zz += map_nz/2;
03841 
03842                         float xx = soln[0]+map_nx/2;
03843                         float yy = soln[1]+map_ny/2;
03844                         float zz = soln[2]+map_nz/2;
03845 
03846                         int l = (x+nx/2) + (y+ny/2) * nx;
03847 
03848                         float t = xx - floor(xx);
03849                         float u = yy - floor(yy);
03850                         float v = zz - floor(zz);
03851 
03852                         if (xx < 0 || yy < 0 || zz < 0 ) {
03853                                 ddata[l] = 0;
03854                                 continue;
03855                         }
03856                         if (interpolate) {
03857                                 if ( xx > map_nx - 1 || yy > map_ny - 1 || zz > map_nz - 1) {
03858                                         ddata[l] = 0;
03859                                         continue;
03860                                 }
03861                                 int k = (int) (Util::fast_floor(xx) + Util::fast_floor(yy) * map_nx + Util::fast_floor(zz) * map_nxy);
03862 
03863 
03864                                 if (xx < (map_nx - 1) && yy < (map_ny - 1) && zz < (map_nz - 1)) {
03865                                         ddata[l] = Util::trilinear_interpolate(sdata[k],
03866                                                                 sdata[k + 1], sdata[k + map_nx],sdata[k + map_nx + 1],
03867                                                                 sdata[k + map_nxy], sdata[k + map_nxy + 1], sdata[k + map_nx + map_nxy],
03868                                                                 sdata[k + map_nx + map_nxy + 1],t, u, v);
03869                                 }
03870                                 else if ( xx == (map_nx - 1) && yy == (map_ny - 1) && zz == (map_nz - 1) ) {
03871                                         ddata[l] += sdata[k];
03872                                 }
03873                                 else if ( xx == (map_nx - 1) && yy == (map_ny - 1) ) {
03874                                         ddata[l] +=     Util::linear_interpolate(sdata[k], sdata[k + map_nxy],v);
03875                                 }
03876                                 else if ( xx == (map_nx - 1) && zz == (map_nz - 1) ) {
03877                                         ddata[l] += Util::linear_interpolate(sdata[k], sdata[k + map_nx],u);
03878                                 }
03879                                 else if ( yy == (map_ny - 1) && zz == (map_nz - 1) ) {
03880                                         ddata[l] += Util::linear_interpolate(sdata[k], sdata[k + 1],t);
03881                                 }
03882                                 else if ( xx == (map_nx - 1) ) {
03883                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + map_nx], sdata[k + map_nxy], sdata[k + map_nxy + map_nx],u,v);
03884                                 }
03885                                 else if ( yy == (map_ny - 1) ) {
03886                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + 1], sdata[k + map_nxy], sdata[k + map_nxy + 1],t,v);
03887                                 }
03888                                 else if ( zz == (map_nz - 1) ) {
03889                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + 1], sdata[k + map_nx], sdata[k + map_nx + 1],t,u);
03890                                 }
03891 
03892 //                              if (k >= map->get_size()) {
03893 //                                      cout << xx << " " << yy << " " <<  zz << " " << endl;
03894 //                                      cout << k << " " << get_size() << endl;
03895 //                                      cout << get_xsize() << " " << get_ysize() << " " << get_zsize() << endl;
03896 //                                      throw;
03897 //                                      }
03898 //
03899 //                              ddata[l] = Util::trilinear_interpolate(sdata[k],
03900 //                                              sdata[k + 1], sdata[k + map_nx],sdata[k + map_nx + 1],
03901 //                                              sdata[k + map_nxy], sdata[k + map_nxy + 1], sdata[k + map_nx + map_nxy],
03902 //                                              sdata[k + map_nx + map_nxy + 1],t, u, v);
03903                         }
03904                         else {
03905                                 if ( xx > map_nx - 1 || yy > map_ny - 1 || zz > map_nz - 1) {
03906                                         ddata[l] = 0;
03907                                         continue;
03908                                 }
03909                                 size_t k = Util::round(xx) + Util::round(yy) * map_nx + Util::round(zz) * (size_t)map_nxy;
03910                                 ddata[l] = sdata[k];
03911                         }
03912 
03913                 }
03914         }
03915 
03916         update();
03917 
03918         EXITFUNC;
03919 }
03920 
03921 EMData *EMData::unwrap_largerR(int r1,int r2,int xs, float rmax_f) {
03922         float *d,*dd;
03923         int do360=2;
03924         int rmax = (int)(rmax_f+0.5f);
03925         unsigned long i;
03926         unsigned int nvox=get_xsize()*get_ysize();//ming
03927         float maxmap=0.0f, minmap=0.0f;
03928         float temp=0.0f, diff_den=0.0f, norm=0.0f;
03929         float cut_off_va =0.0f;
03930 
03931         d=get_data();
03932         maxmap=-1000000.0f;
03933         minmap=1000000.0f;
03934         for (i=0;i<nvox;i++){
03935                 if(d[i]>maxmap) maxmap=d[i];
03936                 if(d[i]<minmap) minmap=d[i];
03937         }
03938         diff_den = maxmap-minmap;
03939         for(i=0;i<nvox;i++) {
03940                 temp = (d[i]-minmap)/diff_den;
03941                 if(cut_off_va != 0.0) {               // cut off the lowerset ?% noisy information
03942                         if(temp < cut_off_va)
03943                                 d[i] = 0.0f;                   // set the empty part density=0.0
03944                         else
03945                                 d[i] = temp-cut_off_va;
03946                 }
03947                 else    d[i] = temp;
03948         }
03949 
03950         for(i=0;i<nvox;i++) {
03951                 temp=d[i];
03952                 norm += temp*temp;
03953         }
03954         for(i=0;i<nvox;i++)             d[i] /= norm;                      //  y' = y/norm(y)
03955 
03956         if (xs<1) {
03957                 xs = (int) floor(do360*M_PI*get_ysize()/4); // ming
03958                 xs=Util::calc_best_fft_size(xs); // ming
03959         }
03960         if (r1<0) r1=0;
03961         float maxext=ceil(0.6f*std::sqrt((float)(get_xsize()*get_xsize()+get_ysize()*get_ysize())));// ming add std::
03962 
03963         if (r2<r1) r2=(int)maxext;
03964         EMData *ret = new EMData;
03965 
03966         ret->set_size(xs,r2+1,1);
03967 
03968         dd=ret->get_data();
03969 
03970         for (int i=0; i<xs; i++) {
03971                 float si=sin(i*M_PI*2/xs);
03972                 float co=cos(i*M_PI*2/xs);
03973                 for (int r=0; r<=maxext; r++) {
03974                         float x=(r+r1)*co+get_xsize()/2; // ming
03975                         float y=(r+r1)*si+get_ysize()/2; // ming
03976                         if(x<0.0 || x>=get_xsize()-1.0 || y<0.0 || y>=get_ysize()-1.0 || r>rmax){    //Ming , ~~~~ rmax need pass here
03977                                 for(;r<=r2;r++)                                   // here r2=MAXR
03978                                         dd[i+r*xs]=0.0;
03979                         break;
03980                     }
03981                         int x1=(int)floor(x);
03982                         int y1=(int)floor(y);
03983                         float t=x-x1;
03984                         float u=y-y1;
03985                         float f11= d[x1+y1*get_xsize()]; // ming
03986                         float f21= d[(x1+1)+y1*get_xsize()]; // ming
03987                         float f12= d[x1+(y1+1)*get_xsize()]; // ming
03988                         float f22= d[(x1+1)+(y1+1)*get_xsize()]; // ming
03989                         dd[i+r*xs] = (1-t)*(1-u)*f11+t*(1-u)*f21+t*u*f22+(1-t)*u*f12;
03990                 }
03991         }
03992         update();
03993         ret->update();
03994         return ret;
03995 }
03996 
03997 
03998 EMData *EMData::oneDfftPolar(int size, float rmax, float MAXR){         // sent MAXR value here later!!
03999         float *pcs=get_data();
04000         EMData *imagepcsfft = new EMData;
04001         imagepcsfft->set_size((size+2), (int)MAXR+1, 1);
04002         float *d=imagepcsfft->get_data();
04003 
04004         EMData *data_in=new EMData;
04005         data_in->set_size(size,1,1);
04006         float *in=data_in->get_data();
04007 
04008         for(int row=0; row<=(int)MAXR; ++row){
04009                 if(row<=(int)rmax) {
04010                         for(int i=0; i<size;++i)        in[i] = pcs[i+row*size]; // ming
04011                         data_in->set_complex(false);
04012                         data_in->do_fft_inplace();
04013                         for(int j=0;j<size+2;j++)  d[j+row*(size+2)]=in[j];
04014                 }
04015                 else for(int j=0;j<size+2;j++) d[j+row*(size+2)]=0.0;
04016         }
04017         imagepcsfft->update();
04018         delete data_in;
04019         return imagepcsfft;
04020 }
04021 
04022 
04023 
04024 //#ifdef EMAN2_USING_CUDA
04025 //EMData* EMData::cut_slice_cuda(const Transform& transform)
04026 //{
04027 //      ENTERFUNC;
04028 //
04029         // These restrictions should be ultimately restricted so that all that matters is get_ndim() = (map->get_ndim() -1)
04030 //      if ( get_ndim() != 3 ) throw ImageDimensionException("Can not cut slice from an image that is not 3D");
04031         // Now check for complex images - this is really just being thorough
04032 //      if ( is_complex() ) throw ImageFormatException("Can not call cut slice an image that is complex");
04033 //
04034 
04035 //      EMData* ret = new EMData();
04036 //      ret->set_size_cuda(nx,ny,1);
04037 
04038 //      float * m = new float[12];
04039 //      transform.copy_matrix_into_array(m);
04040 
04041 //      EMDataForCuda tmp = ret->get_data_struct_for_cuda();
04042 //      bind_cuda_texture(); // Binds this image to the global texture
04043 //      cut_slice_cuda_(&tmp,m);
04044 
04045 //      ret->gpu_update();
04046 //      delete [] m;
04047 
04048 //      EXITFUNC;
04049 //      return ret;
04050 //}
04051 
04052 //#endif // EMAN2_USING_CUDA
04053 
04054 
04055 void EMData::uncut_slice(EMData * const map, const Transform& transform) const
04056 {
04057         ENTERFUNC;
04058 
04059         if (!map) throw NullPointerException("NULL image");
04060         // These restrictions should be ultimately restricted so that all that matters is get_ndim() = (map->get_ndim() -1)
04061         if ( get_ndim() != 2 ) throw ImageDimensionException("Can not call cut slice on an image that is not 2D");
04062         if ( map->get_ndim() != 3 ) throw ImageDimensionException("Can not cut slice from an image that is not 3D");
04063         // Now check for complex images - this is really just being thorough
04064         if ( is_complex() ) throw ImageFormatException("Can not call cut slice on an image that is complex");
04065         if ( map->is_complex() ) throw ImageFormatException("Can not cut slice from a complex image");
04066 
04067 //      Transform3D r( 0, 0, 0); // EMAN by default
04068 //      if (!ort) {
04069 //              ort = &r;
04070 //      }
04071 
04072         float *ddata = map->get_data();
04073         float *sdata = get_data();
04074 
04075         int map_nx = map->get_xsize();
04076         int map_ny = map->get_ysize();
04077         int map_nz = map->get_zsize();
04078         int map_nxy = map_nx * map_ny;
04079         float map_nz_round_limit = (float) map_nz-0.5f;
04080         float map_ny_round_limit = (float) map_ny-0.5f;
04081         float map_nx_round_limit = (float) map_nx-0.5f;
04082 /*
04083         Vec3f posttrans = ort->get_posttrans();
04084         Vec3f pretrans = ort->get_pretrans();*/
04085 
04086         int ymax = ny/2;
04087         if ( ny % 2 == 1 ) ymax += 1;
04088         int xmax = nx/2;
04089         if ( nx % 2 == 1 ) xmax += 1;
04090         for (int y = -ny/2; y < ymax; y++) {
04091                 for (int x = -nx/2; x < xmax; x++) {
04092                         Vec3f coord(x,y,0);
04093                         Vec3f soln = transform*coord;
04094 //                      float xx = (x+pretrans[0]) * (*ort)[0][0] +  (y+pretrans[1]) * (*ort)[0][1] + pretrans[2] * (*ort)[0][2] + posttrans[0];
04095 //                      float yy = (x+pretrans[0]) * (*ort)[1][0] +  (y+pretrans[1]) * (*ort)[1][1] + pretrans[2] * (*ort)[1][2] + posttrans[1];
04096 //                      float zz = (x+pretrans[0]) * (*ort)[2][0] +  (y+pretrans[1]) * (*ort)[2][1] + pretrans[2] * (*ort)[2][2] + posttrans[2];
04097 //
04098 //                      xx += map_nx/2;
04099 //                      yy += map_ny/2;
04100 //                      zz += map_nz/2;
04101 //
04102                         float xx = soln[0]+map_nx/2;
04103                         float yy = soln[1]+map_ny/2;
04104                         float zz = soln[2]+map_nz/2;
04105 
04106                         // These 0.5 offsets are here because the round function rounds to the nearest whole number.
04107                         if (xx < -0.5 || yy < -0.5 || zz < -0.5 || xx >= map_nx_round_limit || yy >= map_ny_round_limit || zz >= map_nz_round_limit) continue;
04108 
04109                         size_t k = Util::round(xx) + Util::round(yy) * map_nx + Util::round(zz) * (size_t)map_nxy;
04110                         int l = (x+nx/2) + (y+ny/2) * nx;
04111                         ddata[k] = sdata[l];
04112                 }
04113         }
04114 
04115         map->update();
04116         EXITFUNC;
04117 }
04118 
04119 
04120 void EMData::save_byteorder_to_dict(ImageIO * imageio)
04121 {
04122         string image_endian = "ImageEndian";
04123         string host_endian = "HostEndian";
04124 
04125         if (imageio->is_image_big_endian()) {
04126                 attr_dict[image_endian] = "big";
04127         }
04128         else {
04129                 attr_dict[image_endian] = "little";
04130         }
04131 
04132         if (ByteOrder::is_host_big_endian()) {
04133                 attr_dict[host_endian] = "big";
04134         }
04135         else {
04136                 attr_dict[host_endian] = "little";
04137         }
04138 }
04139 

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