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), cudadirtybit(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), cudadirtybit(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), cudadirtybit(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 (EMData::usecuda == 1 && num_bytes != 0 && that.cudarwdata != 0) {
00150                 //cout << "That copy constructor" << endl;
00151                 if(!rw_alloc()) throw UnexpectedBehaviorException("Bad 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                 if (EMData::usecuda == 1 && num_bytes != 0 && that.cudarwdata != 0) {
00199                         if(cudarwdata){rw_free();}
00200                         if(!rw_alloc()) throw UnexpectedBehaviorException("Bad 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 #endif //EMAN2_USING_CUDA
00205 
00206                 changecount = that.changecount;
00207 
00208                 if (that.rot_fp != 0) rot_fp = new EMData(*(that.rot_fp));
00209                 else rot_fp = 0;
00210         }
00211         EXITFUNC;
00212         return *this;
00213 }
00214 
00215 EMData::EMData(int nx, int ny, int nz, bool is_real) :
00216 #ifdef EMAN2_USING_CUDA
00217                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0), cudadirtybit(0),
00218 #endif //EMAN2_USING_CUDA
00219                 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),
00220                 all_translation(),      path(""), pathnum(0), rot_fp(0)
00221 {
00222         ENTERFUNC;
00223 
00224         // used to replace cube 'pixel'
00225         attr_dict["apix_x"] = 1.0f;
00226         attr_dict["apix_y"] = 1.0f;
00227         attr_dict["apix_z"] = 1.0f;
00228 
00229         if(is_real) {   // create a real image [nx, ny, nz]
00230                 attr_dict["is_complex"] = int(0);
00231                 attr_dict["is_complex_x"] = int(0);
00232                 attr_dict["is_complex_ri"] = int(1);
00233                 set_size(nx, ny, nz);
00234         }
00235         else {  //create a complex image which real dimension is [ny, ny, nz]
00236                 int new_nx = nx + 2 - nx%2;
00237                 set_size(new_nx, ny, nz);
00238 
00239                 attr_dict["is_complex"] = int(1);
00240 
00241                 if(ny==1 && nz ==1)     {
00242                         attr_dict["is_complex_x"] = int(1);
00243                 }
00244                 else {
00245                         attr_dict["is_complex_x"] = int(0);
00246                 }
00247 
00248                 attr_dict["is_complex_ri"] = int(1);
00249                 attr_dict["is_fftpad"] = int(1);
00250 
00251                 if(nx%2 == 1) {
00252                         attr_dict["is_fftodd"] = 1;
00253                 }
00254         }
00255 
00256         this->to_zero();
00257         update();
00258         EMData::totalalloc++;
00259 #ifdef MEMDEBUG2
00260         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00261 #endif
00262 
00263         EXITFUNC;
00264 }
00265 
00266 
00267 EMData::EMData(float* data, const int x, const int y, const int z, const Dict& attr_dict) :
00268 #ifdef EMAN2_USING_CUDA
00269                 cudarwdata(0), cudarodata(0), num_bytes(0), nextlistitem(0), prevlistitem(0), roneedsupdate(0), cudadirtybit(0),
00270 #endif //EMAN2_USING_CUDA
00271                 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),
00272                 yoff(0), zoff(0), all_translation(), path(""), pathnum(0), rot_fp(0)
00273 {
00274         ENTERFUNC;
00275         // used to replace cube 'pixel'
00276         attr_dict["apix_x"] = 1.0f;
00277         attr_dict["apix_y"] = 1.0f;
00278         attr_dict["apix_z"] = 1.0f;
00279 
00280         EMData::totalalloc++;
00281 #ifdef MEMDEBUG2
00282         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00283 #endif
00284 
00285         update();
00286         EXITFUNC;
00287 }
00288 
00289 #ifdef EMAN2_USING_CUDA
00290 
00291 EMData::EMData(float* data, float* cudadata, const int x, const int y, const int z, const Dict& attr_dict) :
00292                 cudarwdata(cudadata), cudarodata(0), num_bytes(x*y*z*sizeof(float)), nextlistitem(0), prevlistitem(0), roneedsupdate(0), cudadirtybit(1),
00293                 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),
00294                 yoff(0), zoff(0), all_translation(), path(""), pathnum(0), rot_fp(0)
00295 {
00296         ENTERFUNC;
00297 
00298         // used to replace cube 'pixel'
00299         attr_dict["apix_x"] = 1.0f;
00300         attr_dict["apix_y"] = 1.0f;
00301         attr_dict["apix_z"] = 1.0f;
00302 
00303         EMData::totalalloc++;
00304 #ifdef MEMDEBUG2
00305         printf("EMDATA+  %4d    %p\n",EMData::totalalloc,this);
00306 #endif
00307 
00308         update();
00309         EXITFUNC;
00310 }
00311 
00312 #endif //EMAN2_USING_CUDA
00313 
00314 //debug
00315 using std::cout;
00316 using std::endl;
00317 EMData::~EMData()
00318 {
00319         ENTERFUNC;
00320         free_memory();
00321 
00322 #ifdef EMAN2_USING_CUDA
00323         if(cudarwdata){rw_free();}
00324         if(cudarodata){ro_free();}
00325 #endif // EMAN2_USING_CUDA
00326         EMData::totalalloc--;
00327 #ifdef MEMDEBUG2
00328         printf("EMDATA-  %4d    %p\n",EMData::totalalloc,this);
00329 #endif
00330         EXITFUNC;
00331 }
00332 
00333 void EMData::clip_inplace(const Region & area,const float& fill_value)
00334 {
00335         // Added by d.woolford
00336         ENTERFUNC;
00337 
00338 //      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);
00339         // Store the current dimension values
00340         int prev_nx = nx, prev_ny = ny, prev_nz = nz;
00341         size_t prev_size = (size_t)nx*ny*nz;
00342 
00343         // Get the zsize, ysize and xsize of the final area, these are the new dimension sizes of the pixel data
00344         int new_nz = ( area.size[2]==0 ? 1 : (int)area.size[2]);
00345         int new_ny = ( area.size[1]==0 ? 1 : (int)area.size[1]);
00346         int new_nx = (int)area.size[0];
00347 
00348         if ( new_nz < 0 || new_ny < 0 || new_nx < 0 )
00349         {
00350                 // Negative image dimensions were never tested nor considered when creating this implementation
00351                 throw ImageDimensionException("New image dimensions are negative - this is not supported in the clip_inplace operation");
00352         }
00353 
00354         size_t new_size = (size_t)new_nz*new_ny*new_nx;
00355 
00356         // Get the translation values, they are used to construct the ClipInplaceVariables object
00357         int x0 = (int) area.origin[0];
00358         int y0 = (int) area.origin[1];
00359         int z0 = (int) area.origin[2];
00360 
00361         // Get a object that calculates all the interesting variables associated with the clip inplace operation
00362         ClipInplaceVariables civ(prev_nx, prev_ny, prev_nz, new_nx, new_ny, new_nz, x0, y0, z0);
00363 
00364         get_data(); // Do this here to make sure rdata is up to date, applicable if GPU stuff is occuring
00365         // Double check to see if any memory shifting even has to occur
00366         if ( x0 > prev_nx || y0 > prev_ny || z0 > prev_nz || civ.x_iter == 0 || civ.y_iter == 0 || civ.z_iter == 0)
00367         {
00368                 // In this case the volume has been shifted beyond the location of the pixel rdata and
00369                 // the client should expect to see a volume with nothing in it.
00370 
00371                 // Set size calls realloc,
00372                 set_size(new_nx, new_ny, new_nz);
00373 
00374                 // Set pixel memory to zero - the client should expect to see nothing
00375                 EMUtil::em_memset(rdata, 0, (size_t)new_nx*new_ny*new_nz);
00376 
00377                 return;
00378         }
00379 
00380         // Resize the volume before memory shifting occurs if the new volume is larger than the previous volume
00381         // All of the pixel rdata is guaranteed to be at the start of the new volume because realloc (called in set size)
00382         // guarantees this.
00383         if ( new_size > prev_size )
00384                 set_size(new_nx, new_ny, new_nz);
00385 
00386         // Store the clipped row size.
00387         size_t clipped_row_size = (civ.x_iter) * sizeof(float);
00388 
00389         // Get the new sector sizes to save multiplication later.
00390         size_t new_sec_size = new_nx * new_ny;
00391         size_t prev_sec_size = prev_nx * prev_ny;
00392 
00393         // Determine the memory locations of the source and destination pixels - at the point nearest
00394         // to the beginning of the volume (rdata)
00395         size_t src_it_begin = civ.prv_z_bottom*prev_sec_size + civ.prv_y_front*prev_nx + civ.prv_x_left;
00396         size_t dst_it_begin = civ.new_z_bottom*new_sec_size + civ.new_y_front*new_nx + civ.new_x_left;
00397 
00398         // This loop is in the forward direction (starting at points nearest to the beginning of the volume)
00399         // it copies memory only when the destination pointer is less the source pointer - therefore
00400         // ensuring that no memory "copied to" is yet to be "copied from"
00401         for (int i = 0; i < civ.z_iter; ++i) {
00402                 for (int j = 0; j < civ.y_iter; ++j) {
00403 
00404                         // Determine the memory increments as dependent on i and j
00405                         // This could be optimized so that not so many multiplications are occurring...
00406                         size_t dst_inc = dst_it_begin + j*new_nx + i*new_sec_size;
00407                         size_t src_inc = src_it_begin + j*prev_nx + i*prev_sec_size;
00408                         float* local_dst = rdata + dst_inc;
00409                         float* local_src = rdata + src_inc;
00410 
00411                         if ( dst_inc >= src_inc )
00412                         {
00413                                 // this is fine, it will happen now and then and it will be necessary to continue.
00414                                 // the tempatation is to break, but you can't do that (because the point where memory intersects
00415                                 // could be in this slice - and yes, this aspect could be optimized).
00416                                 continue;
00417                         }
00418 
00419                         // Asserts are compiled only in debug mode
00420                         // This situation not encountered in testing thus far
00421                         Assert( dst_inc < new_size && src_inc < prev_size && dst_inc >= 0 && src_inc >= 0 );
00422 
00423                         // Finally copy the memory
00424                         EMUtil::em_memcpy(local_dst, local_src, clipped_row_size);
00425                 }
00426         }
00427 
00428         // Determine the memory locations of the source and destination pixels - at the point nearest
00429         // to the end of the volume (rdata+new_size)
00430         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;
00431         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;
00432 
00433         // This loop is in the reverse direction (starting at points nearest to the end of the volume).
00434         // It copies memory only when the destination pointer is greater than  the source pointer therefore
00435         // ensuring that no memory "copied to" is yet to be "copied from"
00436         for (int i = 0; i < civ.z_iter; ++i) {
00437                 for (int j = 0; j < civ.y_iter; ++j) {
00438 
00439                         // Determine the memory increments as dependent on i and j
00440                         size_t dst_inc = dst_it_end - j*new_nx - i*new_sec_size;
00441                         size_t src_inc = src_it_end - j*prev_nx - i*prev_sec_size;
00442                         float* local_dst = rdata + dst_inc;
00443                         float* local_src = rdata + src_inc;
00444 
00445                         if (dst_inc <= (src_inc + civ.x_iter ))
00446                         {
00447                                 // Overlap
00448                                 if ( dst_inc > src_inc )
00449                                 {
00450                                         // Because the memcpy operation is the forward direction, and this "reverse
00451                                         // direction" loop is proceeding in a backwards direction, it is possible
00452                                         // that memory copied to is yet to be copied from (because memcpy goes forward).
00453                                         // In this scenario pixel memory "copied to" is yet to be "copied from"
00454                                         // i.e. there is overlap
00455 
00456                                         // memmove handles overlapping cases.
00457                                         // memmove could use a temporary buffer, or could go just go backwards
00458                                         // the specification doesn't say how the function behaves...
00459                                         // If memmove creates a temporary buffer is clip_inplace no longer inplace?
00460                                         memmove(local_dst, local_src, clipped_row_size);
00461                                 }
00462                                 continue;
00463                         }
00464 
00465                         // This situation not encountered in testing thus far
00466                         Assert( dst_inc < new_size && src_inc < prev_size && dst_inc >= 0 && src_inc >= 0 );
00467 
00468                         // Perform the memory copy
00469                         EMUtil::em_memcpy(local_dst, local_src, clipped_row_size);
00470                 }
00471         }
00472 
00473         // Resize the volume after memory shifting occurs if the new volume is smaller than the previous volume
00474         // set_size calls realloc, guaranteeing that the pixel rdata is in the right location.
00475         if ( new_size < prev_size )
00476                 set_size(new_nx, new_ny, new_nz);
00477 
00478         // Now set all the edges to zero
00479 
00480         // Set the extra bottom z slices to the fill_value
00481         if (  z0 < 0 )
00482         {
00483                 //EMUtil::em_memset(rdata, 0, (-z0)*new_sec_size*sizeof(float));
00484                 size_t inc = (-z0)*new_sec_size;
00485                 std::fill(rdata,rdata+inc,fill_value);
00486         }
00487 
00488         // Set the extra top z slices to the fill_value
00489         if (  civ.new_z_top > 0 )
00490         {
00491                 float* begin_pointer = rdata + (new_nz-civ.new_z_top)*new_sec_size;
00492                 //EMUtil::em_memset(begin_pointer, 0, (civ.new_z_top)*new_sec_size*sizeof(float));
00493                 float* end_pointer = begin_pointer+(civ.new_z_top)*new_sec_size;
00494                 std::fill(begin_pointer,end_pointer,fill_value);
00495         }
00496 
00497         // Next deal with x and y edges by iterating through each slice
00498         for ( int i = civ.new_z_bottom; i < civ.new_z_bottom + civ.z_iter; ++i )
00499         {
00500                 // Set the extra front y components to the fill_value
00501                 if ( y0 < 0 )
00502                 {
00503                         float* begin_pointer = rdata + i*new_sec_size;
00504                         //EMUtil::em_memset(begin_pointer, 0, (-y0)*new_nx*sizeof(float));
00505                         float* end_pointer = begin_pointer+(-y0)*new_nx;
00506                         std::fill(begin_pointer,end_pointer,fill_value);
00507                 }
00508 
00509                 // Set the extra back y components to the fill_value
00510                 if ( civ.new_y_back > 0 )
00511                 {
00512                         float* begin_pointer = rdata + i*new_sec_size + (new_ny-civ.new_y_back)*new_nx;
00513                         //EMUtil::em_memset(begin_pointer, 0, (civ.new_y_back)*new_nx*sizeof(float));
00514                         float* end_pointer = begin_pointer+(civ.new_y_back)*new_nx;
00515                         std::fill(begin_pointer,end_pointer,fill_value);
00516                 }
00517 
00518                 // Iterate through the y to set each correct x component to the fill_value
00519                 for (int j = civ.new_y_front; j <civ.new_y_front + civ.y_iter; ++j)
00520                 {
00521                         // Set the extra left x components to the fill_value
00522                         if ( x0 < 0 )
00523                         {
00524                                 float* begin_pointer = rdata + i*new_sec_size + j*new_nx;
00525                                 //EMUtil::em_memset(begin_pointer, 0, (-x0)*sizeof(float));
00526                                 float* end_pointer = begin_pointer+(-x0);
00527                                 std::fill(begin_pointer,end_pointer,fill_value);
00528                         }
00529 
00530                         // Set the extra right x components to the fill_value
00531                         if ( civ.new_x_right > 0 )
00532                         {
00533                                 float* begin_pointer = rdata + i*new_sec_size + j*new_nx + (new_nx - civ.new_x_right);
00534                                 //EMUtil::em_memset(begin_pointer, 0, (civ.new_x_right)*sizeof(float));
00535                                 float* end_pointer = begin_pointer+(civ.new_x_right);
00536                                 std::fill(begin_pointer,end_pointer,fill_value);
00537                         }
00538 
00539                 }
00540         }
00541 
00542 // These couts may be useful
00543 //      cout << "start starts " << civ.prv_x_left << " " << civ.prv_y_front << " " << civ.prv_z_bottom << endl;
00544 //      cout << "start ends " << civ.prv_x_right << " " << civ.prv_y_back << " " << civ.prv_z_top << endl;
00545 //      cout << "dst starts " << civ.new_x_left << " " << civ.new_y_front << " " << civ.new_z_bottom << endl;
00546 //      cout << "dst ends " << civ.new_x_right << " " << civ.new_y_back << " " << civ.new_z_top << endl;
00547 //      cout << "total iter z - " << civ.z_iter << " y - " << civ.y_iter << " x - " << civ.x_iter << endl;
00548 //      cout << "=====" << endl;
00549 //      cout << "dst_end is " << dst_it_end << " src end is " << src_it_end << endl;
00550 //      cout << "dst_begin is " << dst_it_begin << " src begin is " << src_it_begin << endl;
00551 
00552         // Update appropriate attributes (Copied and pasted from get_clip)
00553         if( attr_dict.has_key("origin_x") && attr_dict.has_key("origin_y") &&
00554         attr_dict.has_key("origin_z") )
00555         {
00556                 float xorigin = attr_dict["origin_x"];
00557                 float yorigin = attr_dict["origin_y"];
00558                 float zorigin = attr_dict["origin_z"];
00559 
00560                 float apix_x = attr_dict["apix_x"];
00561                 float apix_y = attr_dict["apix_y"];
00562                 float apix_z = attr_dict["apix_z"];
00563 
00564                 set_xyz_origin(xorigin + apix_x * area.origin[0],
00565                         yorigin + apix_y * area.origin[1],
00566                         zorigin + apix_z * area.origin[2]);
00567         }
00568 
00569         // Set the update flag because the size of the image has changed and stats should probably be recalculated if requested.
00570         update();
00571 
00572         EXITFUNC;
00573 }
00574 
00575 EMData *EMData::get_clip(const Region & area, const float fill) const
00576 {
00577         ENTERFUNC;
00578         if (get_ndim() != area.get_ndim()) {
00579                 LOGERR("cannot get %dD clip out of %dD image", area.get_ndim(),get_ndim());
00580                 return 0;
00581         }
00582 
00583         EMData *result = new EMData();
00584 
00585         // Ensure that all of the metadata of this is stored in the new object
00586         // Originally added to ensure that euler angles were retained when preprocessing (zero padding) images
00587         // prior to insertion into the 3D for volume in the reconstruction phase (see reconstructor.cpp/h).
00588         result->attr_dict = this->attr_dict;
00589         int zsize = (int)area.size[2];
00590         if (zsize == 0 && nz <= 1) {
00591                 zsize = 1;
00592         }
00593         int ysize = (ny<=1 && (int)area.size[1]==0 ? 1 : (int)area.size[1]);
00594 
00595         if ( (int)area.size[0] < 0 || ysize < 0 || zsize < 0 )
00596         {
00597                 // Negative image dimensions not supported - added retrospectively by d.woolford (who didn't write get_clip but wrote clip_inplace)
00598                 throw ImageDimensionException("New image dimensions are negative - this is not supported in the the get_clip operation");
00599         }
00600 
00601 //#ifdef EMAN2_USING_CUDA
00602         // Strategy is always to prefer using the GPU if possible
00603 //      bool use_gpu = false;
00604 //      if ( gpu_operation_preferred() ) {
00605 //              result->set_size_cuda((int)area.size[0], ysize, zsize);
00606                 //CudaDataLock lock(this); // Just so we never have to recopy this data to and from the GPU
00607 //              result->get_cuda_data(); // Force the allocation - set_size_cuda is lazy
00608                 // Setting the value is necessary seeing as cuda data is not automatically zeroed
00609 //              result->to_value(fill); // This will automatically use the GPU.
00610 //              use_gpu = true;
00611 //      } else { // cpu == True
00612 //              result->set_size((int)area.size[0], ysize, zsize);
00613 //              if (fill != 0.0) { result->to_value(fill); };
00614 //      }
00615 //#else
00616         result->set_size((int)area.size[0], ysize, zsize);
00617         if (fill != 0.0) { result->to_value(fill); };
00618 //#endif //EMAN2_USING_CUDA
00619 
00620         int x0 = (int) area.origin[0];
00621         x0 = x0 < 0 ? 0 : x0;
00622 
00623         int y0 = (int) area.origin[1];
00624         y0 = y0 < 0 ? 0 : y0;
00625 
00626         int z0 = (int) area.origin[2];
00627         z0 = z0 < 0 ? 0 : z0;
00628 
00629         int x1 = (int) (area.origin[0] + area.size[0]);
00630         x1 = x1 > nx ? nx : x1;
00631 
00632         int y1 = (int) (area.origin[1] + area.size[1]);
00633         y1 = y1 > ny ? ny : y1;
00634 
00635         int z1 = (int) (area.origin[2] + area.size[2]);
00636         z1 = z1 > nz ? nz : z1;
00637         if (z1 <= 0) {
00638                 z1 = 1;
00639         }
00640 
00641         result->insert_clip(this,-((IntPoint)area.origin));
00642 
00643         if( attr_dict.has_key("apix_x") && attr_dict.has_key("apix_y") &&
00644                 attr_dict.has_key("apix_z") )
00645         {
00646                 if( attr_dict.has_key("origin_x") && attr_dict.has_key("origin_y") &&
00647                     attr_dict.has_key("origin_z") )
00648                 {
00649                         float xorigin = attr_dict["origin_x"];
00650                         float yorigin = attr_dict["origin_y"];
00651                         float zorigin = attr_dict["origin_z"];
00652 
00653                         float apix_x = attr_dict["apix_x"];
00654                         float apix_y = attr_dict["apix_y"];
00655                         float apix_z = attr_dict["apix_z"];
00656 
00657                         result->set_xyz_origin(xorigin + apix_x * area.origin[0],
00658                                                                    yorigin + apix_y * area.origin[1],
00659                                                                zorigin + apix_z * area.origin[2]);
00660                 }
00661         }
00662 
00663 //#ifdef EMAN2_USING_CUDA
00664 //      if (use_gpu) result->gpu_update();
00665 //      else result->update();
00666 //#else
00667         result->update();
00668 //#endif // EMAN2_USING_CUDA
00669 
00670 
00671         result->set_path(path);
00672         result->set_pathnum(pathnum);
00673 
00674         EXITFUNC;
00675         return result;
00676 }
00677 
00678 
00679 EMData *EMData::get_top_half() const
00680 {
00681         ENTERFUNC;
00682 
00683         if (get_ndim() != 3) {
00684                 throw ImageDimensionException("3D only");
00685         }
00686 
00687         EMData *half = new EMData();
00688         half->attr_dict = attr_dict;
00689         half->set_size(nx, ny, nz / 2);
00690 
00691         float *half_data = half->get_data();
00692         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);
00693 
00694         float apix_z = attr_dict["apix_z"];
00695         float origin_z = attr_dict["origin_z"];
00696         origin_z += apix_z * nz / 2;
00697         half->attr_dict["origin_z"] = origin_z;
00698         half->update();
00699 
00700         EXITFUNC;
00701         return half;
00702 }
00703 
00704 
00705 EMData *EMData::get_rotated_clip(const Transform &xform,
00706                                                                  const IntSize &size, float)
00707 {
00708         EMData *result = new EMData();
00709         result->set_size(size[0],size[1],size[2]);
00710 
00711         if (nz==1) {
00712                 for (int y=-size[1]/2; y<(size[1]+1)/2; y++) {
00713                         for (int x=-size[0]/2; x<(size[0]+1)/2; x++) {
00714                                 Vec3f xv=xform.transform(Vec3f((float)x,(float)y,0.0f));
00715                                 float v = 0;
00716 
00717                                 if (xv[0]<0||xv[1]<0||xv[0]>nx-2||xv[1]>ny-2) v=0.;
00718                                 else v=sget_value_at_interp(xv[0],xv[1]);
00719                                 result->set_value_at(x+size[0]/2,y+size[1]/2,v);
00720                         }
00721                 }
00722         }
00723         else {
00724                 for (int z=-size[2]/2; z<(size[2]+1)/2; z++) {
00725                         for (int y=-size[1]/2; y<(size[1]+1)/2; y++) {
00726                                 for (int x=-size[0]/2; x<(size[0]+1)/2; x++) {
00727                                         Vec3f xv=xform.transform(Vec3f((float)x,(float)y,0.0f));
00728                                         float v = 0;
00729 
00730                                         if (xv[0]<0||xv[1]<0||xv[2]<0||xv[0]>nx-2||xv[1]>ny-2||xv[2]>nz-2) v=0.;
00731                                         else v=sget_value_at_interp(xv[0],xv[1],xv[2]);
00732                                         result->set_value_at(x+size[0]/2,y+size[1]/2,z+size[2]/2,v);
00733                                 }
00734                         }
00735                 }
00736         }
00737         result->update();
00738 
00739         return result;
00740 }
00741 
00742 
00743 EMData* EMData::window_center(int l) {
00744         ENTERFUNC;
00745         // sanity checks
00746         int n = nx;
00747         if (is_complex()) {
00748                 LOGERR("Need real-space data for window_center()");
00749                 throw ImageFormatException(
00750                         "Complex input image; real-space expected.");
00751         }
00752         if (is_fftpadded()) {
00753                 // image has been fft-padded, compute the real-space size
00754                 n -= (2 - int(is_fftodd()));
00755         }
00756         int corner = n/2 - l/2;
00757         int ndim = get_ndim();
00758         EMData* ret;
00759         switch (ndim) {
00760                 case 3:
00761                         if ((n != ny) || (n != nz)) {
00762                                 LOGERR("Need the real-space image to be cubic.");
00763                                 throw ImageFormatException(
00764                                                 "Need cubic real-space image.");
00765                         }
00766                         ret = get_clip(Region(corner, corner, corner, l, l, l));
00767                         break;
00768                 case 2:
00769                         if (n != ny) {
00770                                 LOGERR("Need the real-space image to be square.");
00771                                 throw ImageFormatException(
00772                                                 "Need square real-space image.");
00773                         }
00774                         //cout << "Using corner " << corner << endl;
00775                         ret = get_clip(Region(corner, corner, l, l));
00776                         break;
00777                 case 1:
00778                         ret = get_clip(Region(corner, l));
00779                         break;
00780                 default:
00781                         throw ImageDimensionException(
00782                                         "window_center only supports 1-d, 2-d, and 3-d images");
00783         }
00784         return ret;
00785         EXITFUNC;
00786 }
00787 
00788 
00789 float *EMData::setup4slice(bool redo)
00790 {
00791         ENTERFUNC;
00792 
00793         if (!is_complex()) {
00794                 throw ImageFormatException("complex image only");
00795         }
00796 
00797         if (get_ndim() != 3) {
00798                 throw ImageDimensionException("3D only");
00799         }
00800 
00801         if (supp) {
00802                 if (redo) {
00803                         EMUtil::em_free(supp);
00804                         supp = 0;
00805                 }
00806                 else {
00807                         EXITFUNC;
00808                         return supp;
00809                 }
00810         }
00811 
00812         const int SUPP_ROW_SIZE = 8;
00813         const int SUPP_ROW_OFFSET = 4;
00814         const int supp_size = SUPP_ROW_SIZE + SUPP_ROW_OFFSET;
00815 
00816         supp = (float *) EMUtil::em_calloc(supp_size * ny * nz, sizeof(float));
00817         int nxy = nx * ny;
00818         int supp_xy = supp_size * ny;
00819         float * data = get_data();
00820 
00821         for (int z = 0; z < nz; z++) {
00822                 size_t cur_z1 = z * nxy;
00823                 size_t cur_z2 = z * supp_xy;
00824 
00825                 for (int y = 0; y < ny; y++) {
00826                         size_t cur_y1 = y * nx;
00827                         size_t cur_y2 = y * supp_size;
00828 
00829                         for (int x = 0; x < SUPP_ROW_SIZE; x++) {
00830                                 size_t k = (x + SUPP_ROW_OFFSET) + cur_y2 + cur_z2;
00831                                 supp[k] = data[x + cur_y1 + cur_z1];
00832                         }
00833                 }
00834         }
00835 
00836         for (int z = 1, zz = nz - 1; z < nz; z++, zz--) {
00837                 size_t cur_z1 = zz * nxy;
00838                 size_t cur_z2 = z * supp_xy;
00839 
00840                 for (int y = 1, yy = ny - 1; y < ny; y++, yy--) {
00841                         supp[y * 12 + cur_z2] = data[4 + yy * nx + cur_z1];
00842                         supp[1 + y * 12 + cur_z2] = -data[5 + yy * nx + cur_z1];
00843                         supp[2 + y * 12 + cur_z2] = data[2 + yy * nx + cur_z1];
00844                         supp[3 + y * 12 + cur_z2] = -data[3 + yy * nx + cur_z1];
00845                 }
00846         }
00847 
00848         EXITFUNC;
00849         return supp;
00850 }
00851 
00852 
00853 void EMData::scale(float s)
00854 {
00855         ENTERFUNC;
00856         Transform t;
00857         t.set_scale(s);
00858         transform(t);
00859         EXITFUNC;
00860 }
00861 
00862 
00863 void EMData::translate(int dx, int dy, int dz)
00864 {
00865         ENTERFUNC;
00866         translate(Vec3i(dx, dy, dz));
00867         EXITFUNC;
00868 }
00869 
00870 
00871 void EMData::translate(float dx, float dy, float dz)
00872 {
00873         ENTERFUNC;
00874         int dx_ = Util::round(dx);
00875         int dy_ = Util::round(dy);
00876         int dz_ = Util::round(dz);
00877         if( ( (dx-dx_) == 0 ) && ( (dy-dy_) == 0 ) && ( (dz-dz_) == 0 )) {
00878                 translate(dx_, dy_, dz_);
00879         }
00880         else {
00881                 translate(Vec3f(dx, dy, dz));
00882         }
00883         EXITFUNC;
00884 }
00885 
00886 
00887 void EMData::translate(const Vec3i &translation)
00888 {
00889         ENTERFUNC;
00890 
00891         //if traslation is 0, do nothing
00892         if( translation[0] == 0 && translation[1] == 0 && translation[2] == 0) {
00893                 EXITFUNC;
00894                 return;
00895         }
00896 
00897         Dict params("trans",static_cast< vector<int> >(translation));
00898         process_inplace("xform.translate.int",params);
00899 
00900         // update() - clip_inplace does the update
00901         all_translation += translation;
00902 
00903         EXITFUNC;
00904 }
00905 
00906 
00907 void EMData::translate(const Vec3f &translation)
00908 {
00909         ENTERFUNC;
00910 
00911         if( translation[0] == 0.0f && translation[1] == 0.0f && translation[2] == 0.0f ) {
00912                 EXITFUNC;
00913                 return;
00914         }
00915 
00916         Transform* t = new Transform();
00917         t->set_trans(translation);
00918         process_inplace("xform",Dict("transform",t));
00919         delete t;
00920 
00921         all_translation += translation;
00922         EXITFUNC;
00923 }
00924 
00925 
00926 void EMData::rotate(float az, float alt, float phi)
00927 {
00928         Dict d("type","eman");
00929         d["az"] = az;
00930         d["alt"] = alt;
00931         d["phi"] = phi;
00932         Transform t(d);
00933         transform(t);
00934 }
00935 
00936 
00937 
00938 void EMData::rotate(const Transform & t)
00939 {
00940         cout << "Deprecation warning in EMData::rotate. Please consider using EMData::transform() instead " << endl;
00941         transform(t);
00942 }
00943 
00944 float EMData::max_3D_pixel_error(const Transform &t1, const Transform & t2, float r) {
00945         
00946         Transform t;
00947         int r0 = (int)r;
00948         float ddmax = 0.0f;
00949 
00950         t = t2*t1.inverse();
00951         for (int i=0; i<int(2*M_PI*r0+0.5); i++) {
00952                 float ang = (float)i/r;
00953                 Vec3f v = Vec3f(r0*cos(ang), r0*sin(ang), 0.0f);
00954                 Vec3f d = t*v-v;
00955 #ifdef _WIN32
00956                 ddmax = _cpp_max(ddmax,d[0]*d[0]+d[1]*d[1]+d[2]*d[2]);
00957 #else
00958                 ddmax = std::max(ddmax,d[0]*d[0]+d[1]*d[1]+d[2]*d[2]);
00959 #endif  //_WIN32
00960         }
00961         return std::sqrt(ddmax);
00962 }
00963 
00964 void EMData::rotate_translate(float az, float alt, float phi, float dx, float dy, float dz)
00965 {
00966         cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00967 //      Transform3D t( az, alt, phi,Vec3f(dx, dy, dz));
00968         Transform t;
00969         t.set_rotation(Dict("type", "eman", "az", az, "alt", alt, "phi", phi));
00970         t.set_trans(dx, dy, dz);
00971         rotate_translate(t);
00972 }
00973 
00974 
00975 void EMData::rotate_translate(float az, float alt, float phi, float dx, float dy,
00976                                                           float dz, float pdx, float pdy, float pdz)
00977 {
00978         cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00979 //      Transform3D t(Vec3f(dx, dy, dz), az, alt, phi, Vec3f(pdx,pdy,pdz));
00980 //      rotate_translate(t);
00981 
00982         Transform t;
00983         t.set_pre_trans(Vec3f(dx, dy, dz));
00984         t.set_rotation(Dict("type", "eman", "az", az, "alt", alt, "phi", phi));
00985         t.set_trans(pdx, pdy, pdz);
00986         rotate_translate(t);
00987 }
00988 
00989 //void EMData::rotate_translate(const Transform3D & RA)
00990 //{
00991 //      cout << "Deprecation warning in EMData::rotate_translate. Please consider using EMData::transform() instead " << endl;
00992 //      ENTERFUNC;
00993 //
00994 //#if EMDATA_EMAN2_DEBUG
00995 //      std::cout << "start rotate_translate..." << std::endl;
00996 //#endif
00997 //
00998 //      float scale       = RA.get_scale();
00999 //      Vec3f dcenter     = RA.get_center();
01000 //      Vec3f translation = RA.get_posttrans();
01001 //      Dict rotation      = RA.get_rotation(Transform3D::EMAN);
01003 //      Transform3D RAInv = RA.inverse(); // We're rotating the coordinate system, not the data
01005 //#if EMDATA_EMAN2_DEBUG
01006 //      vector<string> keys = rotation.keys();
01007 //      vector<string>::const_iterator it;
01008 //      for(it=keys.begin(); it!=keys.end(); ++it) {
01010 //              std::cout << *it << " : " << (float)rotation.get(*it) << std::endl;
01011 //      }
01012 //#endif
01013 //      float inv_scale = 1.0f;
01014 //
01015 //      if (scale != 0) {
01016 //              inv_scale = 1.0f / scale;
01017 //      }
01018 //
01019 //      float *src_data = 0;
01020 //      float *des_data = 0;
01021 //
01022 //      src_data = get_data();
01023 //      des_data = (float *) EMUtil::em_malloc(nx * ny * nz * sizeof(float));
01024 //
01025 //      if (nz == 1) {
01026 //              float x2c =  nx / 2 - dcenter[0] + RAInv[0][3];
01027 //              float y2c =  ny / 2 - dcenter[1] + RAInv[1][3];
01028 //              float y   = -ny / 2 + dcenter[1]; // changed 0 to 1 in dcenter and below
01029 //              for (int j = 0; j < ny; j++, y += 1.0f) {
01030 //                      float x = -nx / 2 + dcenter[0];
01031 //                      for (int i = 0; i < nx; i++, x += 1.0f) {
01032 //                              float x2 = RAInv[0][0]*x + RAInv[0][1]*y + x2c;
01033 //                              float y2 = RAInv[1][0]*x + RAInv[1][1]*y + y2c;
01034 //
01035 //                              if (x2 < 0 || x2 >= nx || y2 < 0 || y2 >= ny ) {
01036 //                                      des_data[i + j * nx] = 0; // It may be tempting to set this value to the
01037 //                                      // mean but in fact this is not a good thing to do. Talk to S.Ludtke about it.
01038 //                              }
01039 //                              else {
01040 //                                      int ii = Util::fast_floor(x2);
01041 //                                      int jj = Util::fast_floor(y2);
01042 //                                      int k0 = ii + jj * nx;
01043 //                                      int k1 = k0 + 1;
01044 //                                      int k2 = k0 + nx;
01045 //                                      int k3 = k0 + nx + 1;
01046 //
01047 //                                      if (ii == nx - 1) {
01048 //                                              k1--;
01049 //                                              k3--;
01050 //                                      }
01051 //                                      if (jj == ny - 1) {
01052 //                                              k2 -= nx;
01053 //                                              k3 -= nx;
01054 //                                      }
01055 //
01056 //                                      float t = x2 - ii;
01057 //                                      float u = y2 - jj;
01058 //
01059 //                                      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
01060 //                              }
01061 //                      }
01062 //              }
01063 //      }
01064 //      else {
01065 //#if EMDATA_EMAN2_DEBUG
01066 //              std::cout << "This is the 3D case." << std::endl    ;
01067 //#endif
01068 //
01069 //              Transform3D mx = RA;
01070 //              mx.set_scale(inv_scale);
01071 //
01072 //#if EMDATA_EMAN2_DEBUG
01075 //#endif
01076 //
01077 //              int nxy = nx * ny;
01078 //              int l = 0;
01079 //
01080 //              float x2c =  nx / 2 - dcenter[0] + RAInv[0][3];;
01081 //              float y2c =  ny / 2 - dcenter[1] + RAInv[1][3];;
01082 //              float z2c =  nz / 2 - dcenter[2] + RAInv[2][3];;
01083 //
01084 //              float z   = -nz / 2 + dcenter[2]; //
01085 //
01086 //              size_t ii, k0, k1, k2, k3, k4, k5, k6, k7;
01087 //              for (int k = 0; k < nz; k++, z += 1.0f) {
01088 //                      float y   = -ny / 2 + dcenter[1]; //
01089 //                      for (int j = 0; j < ny; j++,   y += 1.0f) {
01090 //                              float x = -nx / 2 + dcenter[0];
01091 //                              for (int i = 0; i < nx; i++, l++ ,  x += 1.0f) {
01092 //                                      float x2 = RAInv[0][0] * x + RAInv[0][1] * y + RAInv[0][2] * z + x2c;
01093 //                                      float y2 = RAInv[1][0] * x + RAInv[1][1] * y + RAInv[1][2] * z + y2c;
01094 //                                      float z2 = RAInv[2][0] * x + RAInv[2][1] * y + RAInv[2][2] * z + z2c;
01095 //
01096 //
01097 //                                      if (x2 < 0 || y2 < 0 || z2 < 0 ||
01098 //                                              x2 >= nx  || y2 >= ny  || z2>= nz ) {
01099 //                                              des_data[l] = 0;
01100 //                                      }
01101 //                                      else {
01102 //                                              int ix = Util::fast_floor(x2);
01103 //                                              int iy = Util::fast_floor(y2);
01104 //                                              int iz = Util::fast_floor(z2);
01105 //                                              float tuvx = x2-ix;
01106 //                                              float tuvy = y2-iy;
01107 //                                              float tuvz = z2-iz;
01108 //                                              ii = ix + iy * nx + iz * nxy;
01109 //
01110 //                                              k0 = ii;
01111 //                                              k1 = k0 + 1;
01112 //                                              k2 = k0 + nx;
01113 //                                              k3 = k0 + nx+1;
01114 //                                              k4 = k0 + nxy;
01115 //                                              k5 = k1 + nxy;
01116 //                                              k6 = k2 + nxy;
01117 //                                              k7 = k3 + nxy;
01118 //
01119 //                                              if (ix == nx - 1) {
01120 //                                                      k1--;
01121 //                                                      k3--;
01122 //                                                      k5--;
01123 //                                                      k7--;
01124 //                                              }
01125 //                                              if (iy == ny - 1) {
01126 //                                                      k2 -= nx;
01127 //                                                      k3 -= nx;
01128 //                                                      k6 -= nx;
01129 //                                                      k7 -= nx;
01130 //                                              }
01131 //                                              if (iz == nz - 1) {
01132 //                                                      k4 -= nxy;
01133 //                                                      k5 -= nxy;
01134 //                                                      k6 -= nxy;
01135 //                                                      k7 -= nxy;
01136 //                                              }
01137 //
01138 //                                              des_data[l] = Util::trilinear_interpolate(src_data[k0],
01139 //                                                        src_data[k1],
01140 //                                                        src_data[k2],
01141 //                                                        src_data[k3],
01142 //                                                        src_data[k4],
01143 //                                                        src_data[k5],
01144 //                                                        src_data[k6],
01145 //                                                        src_data[k7],
01146 //                                                        tuvx, tuvy, tuvz);
01147 //#if EMDATA_EMAN2_DEBUG
01148 //                                              printf(" ix=%d \t iy=%d \t iz=%d \t value=%f \n", ix ,iy, iz, des_data[l] );
01149 //                                              std::cout << src_data[ii] << std::endl;
01150 //#endif
01151 //                                      }
01152 //                              }
01153 //                      }
01154 //              }
01155 //      }
01156 //
01157 //      if( rdata )
01158 //      {
01159 //              EMUtil::em_free(rdata);
01160 //              rdata = 0;
01161 //      }
01162 //      rdata = des_data;
01163 //
01164 //      scale_pixel(inv_scale);
01165 //
01166 //      attr_dict["origin_x"] = (float) attr_dict["origin_x"] * inv_scale;
01167 //      attr_dict["origin_y"] = (float) attr_dict["origin_y"] * inv_scale;
01168 //      attr_dict["origin_z"] = (float) attr_dict["origin_z"] * inv_scale;
01169 //
01170 //      update();
01171 //      all_translation += translation;
01172 //      EXITFUNC;
01173 //}
01174 
01175 
01176 
01177 
01178 void EMData::rotate_x(int dx)
01179 {
01180         ENTERFUNC;
01181 
01182         if (get_ndim() > 2) {
01183                 throw ImageDimensionException("no 3D image");
01184         }
01185 
01186 
01187         size_t row_size = nx * sizeof(float);
01188         float *tmp = (float*)EMUtil::em_malloc(row_size);
01189         float * data = get_data();
01190 
01191         for (int y = 0; y < ny; y++) {
01192                 int y_nx = y * nx;
01193                 for (int x = 0; x < nx; x++) {
01194                         tmp[x] = data[y_nx + (x + dx) % nx];
01195                 }
01196                 EMUtil::em_memcpy(&data[y_nx], tmp, row_size);
01197         }
01198 
01199         update();
01200         if( tmp )
01201         {
01202                 delete[]tmp;
01203                 tmp = 0;
01204         }
01205         EXITFUNC;
01206 }
01207 
01208 double EMData::dot_rotate_translate(EMData * with, float dx, float dy, float da, const bool mirror)
01209 {
01210         ENTERFUNC;
01211 
01212         if (!EMUtil::is_same_size(this, with)) {
01213                 LOGERR("images not same size");
01214                 throw ImageFormatException("images not same size");
01215         }
01216 
01217         if (get_ndim() == 3) {
01218                 LOGERR("1D/2D Images only");
01219                 throw ImageDimensionException("1D/2D only");
01220         }
01221 
01222         float *this_data = 0;
01223 
01224         this_data = get_data();
01225 
01226         float da_rad = da*(float)M_PI/180.0f;
01227 
01228         float *with_data = with->get_data();
01229         float mx0 = cos(da_rad);
01230         float mx1 = sin(da_rad);
01231         float y = -ny / 2.0f;
01232         float my0 = mx0 * (-nx / 2.0f - 1.0f) + nx / 2.0f - dx;
01233         float my1 = -mx1 * (-nx / 2.0f - 1.0f) + ny / 2.0f - dy;
01234         double result = 0;
01235 
01236         for (int j = 0; j < ny; j++) {
01237                 float x2 = my0 + mx1 * y;
01238                 float y2 = my1 + mx0 * y;
01239 
01240                 int ii = Util::fast_floor(x2);
01241                 int jj = Util::fast_floor(y2);
01242                 float t = x2 - ii;
01243                 float u = y2 - jj;
01244 
01245                 for (int i = 0; i < nx; i++) {
01246                         t += mx0;
01247                         u -= mx1;
01248 
01249                         if (t >= 1.0f) {
01250                                 ii++;
01251                                 t -= 1.0f;
01252                         }
01253 
01254                         if (u >= 1.0f) {
01255                                 jj++;
01256                                 u -= 1.0f;
01257                         }
01258 
01259                         if (t < 0) {
01260                                 ii--;
01261                                 t += 1.0f;
01262                         }
01263 
01264                         if (u < 0) {
01265                                 jj--;
01266                                 u += 1.0f;
01267                         }
01268 
01269                         if (ii >= 0 && ii <= nx - 2 && jj >= 0 && jj <= ny - 2) {
01270                                 int k0 = ii + jj * nx;
01271                                 int k1 = k0 + 1;
01272                                 int k2 = k0 + nx + 1;
01273                                 int k3 = k0 + nx;
01274 
01275                                 float tt = 1 - t;
01276                                 float uu = 1 - u;
01277                                 int idx = i + j * nx;
01278                                 if (mirror) idx = nx-1-i+j*nx; // mirroring of Transforms is always about the y axis
01279                                 result += (this_data[k0] * tt * uu + this_data[k1] * t * uu +
01280                                                    this_data[k2] * t * u + this_data[k3] * tt * u) * with_data[idx];
01281                         }
01282                 }
01283                 y += 1.0f;
01284         }
01285 
01286         EXITFUNC;
01287         return result;
01288 }
01289 
01290 
01291 EMData *EMData::little_big_dot(EMData * with, bool do_sigma)
01292 {
01293         ENTERFUNC;
01294 
01295         if (get_ndim() > 2) {
01296                 throw ImageDimensionException("1D/2D only");
01297         }
01298 
01299         EMData *ret = copy_head();
01300         ret->set_size(nx,ny,nz);
01301         ret->to_zero();
01302 
01303         int nx2 = with->get_xsize();
01304         int ny2 = with->get_ysize();
01305         float em = with->get_edge_mean();
01306 
01307         float *data = get_data();
01308         float *with_data = with->get_data();
01309         float *ret_data = ret->get_data();
01310 
01311         float sum2 = (Util::square((float)with->get_attr("sigma")) +
01312                                   Util::square((float)with->get_attr("mean")));
01313         if (do_sigma) {
01314                 for (int j = ny2 / 2; j < ny - ny2 / 2; j++) {
01315                         for (int i = nx2 / 2; i < nx - nx2 / 2; i++) {
01316                                 float sum = 0;
01317                                 float sum1 = 0;
01318                                 float summ = 0;
01319                                 int k = 0;
01320 
01321                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01322                                         for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01323                                                 int l = ii + jj * nx;
01324                                                 sum1 += Util::square(data[l]);
01325                                                 summ += data[l];
01326                                                 sum += data[l] * with_data[k];
01327                                                 k++;
01328                                         }
01329                                 }
01330                                 float tmp_f1 = (sum1 / 2.0f - sum) / (nx2 * ny2);
01331                                 float tmp_f2 = Util::square((float)with->get_attr("mean") -
01332                                                                                         summ / (nx2 * ny2));
01333                                 ret_data[i + j * nx] = sum2 + tmp_f1 - tmp_f2;
01334                         }
01335                 }
01336         }
01337         else {
01338                 for (int j = ny2 / 2; j < ny - ny2 / 2; j++) {
01339                         for (int i = nx2 / 2; i < nx - nx2 / 2; i++) {
01340                                 float eml = 0;
01341                                 float dot = 0;
01342                                 float dot2 = 0;
01343 
01344                                 for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01345                                         eml += data[ii + (j - ny2 / 2) * nx] + data[ii + (j + ny2 / 2 - 1) * nx];
01346                                 }
01347 
01348                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01349                                         eml += data[i - nx2 / 2 + jj * nx] + data[i + nx2 / 2 - 1 + jj * nx];
01350                                 }
01351 
01352                                 eml /= (nx2 + ny2) * 2.0f;
01353                                 int k = 0;
01354 
01355                                 for (int jj = j - ny2 / 2; jj < j + ny2 / 2; jj++) {
01356                                         for (int ii = i - nx2 / 2; ii < i + nx2 / 2; ii++) {
01357                                                 dot += (data[ii + jj * nx] - eml) * (with_data[k] - em);
01358                                                 dot2 += Util::square(data[ii + jj * nx] - eml);
01359                                                 k++;
01360                                         }
01361                                 }
01362 
01363                                 dot2 = std::sqrt(dot2);
01364 
01365                                 if (dot2 == 0) {
01366                                         ret_data[i + j * nx] = 0;
01367                                 }
01368                                 else {
01369                                         ret_data[i + j * nx] = dot / (nx2 * ny2 * dot2 * (float)with->get_attr("sigma"));
01370                                 }
01371                         }
01372                 }
01373         }
01374 
01375         ret->update();
01376 
01377         EXITFUNC;
01378         return ret;
01379 }
01380 
01381 
01382 EMData *EMData::do_radon()
01383 {
01384         ENTERFUNC;
01385 
01386         if (get_ndim() != 2) {
01387                 throw ImageDimensionException("2D only");
01388         }
01389 
01390         if (nx != ny) {
01391                 throw ImageFormatException("square image only");
01392         }
01393 
01394         EMData *result = new EMData();
01395         result->set_size(nx, ny, 1);
01396         result->to_zero();
01397         float *result_data = result->get_data();
01398 
01399         EMData *this_copy = this;
01400         this_copy = copy();
01401 
01402         for (int i = 0; i < nx; i++) {
01403                 Transform t(Dict("type","2d","alpha",(float) M_PI * 2.0f * i / nx));
01404                 this_copy->transform(t);
01405 
01406                 float *copy_data = this_copy->get_data();
01407 
01408                 for (int y = 0; y < nx; y++) {
01409                         for (int x = 0; x < nx; x++) {
01410                                 if (Util::square(x - nx / 2) + Util::square(y - nx / 2) <= nx * nx / 4) {
01411                                         result_data[i + y * nx] += copy_data[x + y * nx];
01412                                 }
01413                         }
01414                 }
01415 
01416                 this_copy->update();
01417         }
01418 
01419         result->update();
01420 
01421         if( this_copy )
01422         {
01423                 delete this_copy;
01424                 this_copy = 0;
01425         }
01426 
01427         EXITFUNC;
01428         return result;
01429 }
01430 
01431 void EMData::zero_corner_circulant(const int radius)
01432 {
01433         if ( nz > 1 && nz < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - nz is too small");
01434         if ( ny > 1 && ny < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - ny is too small");
01435         if ( nx > 1 && nx < (2*radius+1) ) throw ImageDimensionException("Error: cannot zero corner - nx is too small");
01436 
01437         int it_z = radius;
01438         int it_y = radius;
01439         int it_x = radius;
01440 
01441         if ( nz == 1 ) it_z = 0;
01442         if ( ny == 1 ) it_y = 0;
01443         if ( nx == 1 ) it_z = 0;
01444 
01445         if ( nz == 1 && ny == 1 )
01446         {
01447                 for ( int x = -it_x; x <= it_x; ++x )
01448                         get_value_at_wrap(x) = 0;
01449 
01450         }
01451         else if ( nz == 1 )
01452         {
01453                 for ( int y = -it_y; y <= it_y; ++y)
01454                         for ( int x = -it_x; x <= it_x; ++x )
01455                                 get_value_at_wrap(x,y) = 0;
01456         }
01457         else
01458         {
01459                 for( int z = -it_z; z <= it_z; ++z )
01460                         for ( int y = -it_y; y <= it_y; ++y)
01461                                 for ( int x = -it_x; x < it_x; ++x )
01462                                         get_value_at_wrap(x,y,z) = 0;
01463 
01464         }
01465 
01466 }
01467 
01468 EMData *EMData::calc_ccf(EMData * with, fp_flag fpflag,bool center)
01469 {
01470         ENTERFUNC;
01471 
01472         if( with == 0 ) {
01473 #ifdef EMAN2_USING_CUDA //CUDA 
01474         if(EMData::usecuda == 1 && cudarwdata) {
01475                 //cout << "calc ccf" << endl;
01476                 EMData* ifft = 0;
01477                 bool delifft = false;
01478                 int offset = 0;
01479                 
01480                 //do fft if not alreay done
01481                 if(!is_complex()){
01482                         ifft = do_fft_cuda();
01483                         delifft = true;
01484                         offset = 2 - nx%2;
01485                 }else{
01486                         ifft = this;
01487                 }
01488                 calc_conv_cuda(ifft->cudarwdata,ifft->cudarwdata,nx + offset, ny, nz); //this is the business end, results go in afft
01489                 
01490                 EMData * conv = ifft->do_ift_cuda();
01491                 if(delifft) delete ifft;
01492                 conv->update();
01493                         
01494                 return conv;
01495         }
01496 #endif
01497                 EXITFUNC;
01498                 return convolution(this,this,fpflag, center);
01499         }
01500         else if ( with == this ){ // this if statement is not necessary, the correlation function tests to see if with == this
01501                 EXITFUNC;
01502                 return correlation(this, this, fpflag,center);
01503         }
01504         else {
01505 
01506 #ifdef EMAN2_USING_CUDA //CUDA 
01507                 // assume always get rw data (makes life a lot easier!!! 
01508                 // also assume that both images are the same size. When using CUDA we are only interested in speed, not flexibility!!
01509                 // P.S. (I feel like I am pounding square pegs into a round holes with CUDA)
01510                 if(EMData::usecuda == 1 && cudarwdata && with->cudarwdata) {
01511                         //cout << "using CUDA for ccf" << endl;
01512                         EMData* afft = 0;
01513                         EMData* bfft = 0;
01514                         bool delafft = false, delbfft = false;
01515                         int offset = 0;
01516                         
01517                         //do ffts if not alreay done
01518                         if(!is_complex()){
01519                                 afft = do_fft_cuda();
01520                                 delafft = true;
01521                                 offset = 2 - nx%2;
01522                                 //cout << "Do cuda FFT A" << endl;
01523                         }else{
01524                                 afft = this;
01525                         }
01526                         if(!with->is_complex()){
01527                                 bfft = with->do_fft_cuda();
01528                                 //cout << "Do cuda FFT B" << endl;
01529                                 delbfft = true;
01530                         }else{
01531                                 bfft = with;
01532                         }
01533 
01534                         calc_ccf_cuda(afft->cudarwdata,bfft->cudarwdata,nx + offset, ny, nz); //this is the business end, results go in afft
01535                         
01536                         if(delbfft) delete bfft;
01537                         
01538                         EMData * corr = afft->do_ift_cuda();
01539                         if(delafft) delete afft;
01540                         //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.
01541                         corr->update();
01542                         
01543                         return corr;
01544                 }
01545 #endif
01546                 
01547                 // If the argument EMData pointer is not the same size we automatically resize it
01548                 bool undoresize = false;
01549                 int wnx = with->get_xsize(); int wny = with->get_ysize(); int wnz = with->get_zsize();
01550                 if (!(is_complex()^with->is_complex()) && (wnx != nx || wny != ny || wnz != nz) ) {
01551                         Region r((wnx-nx)/2, (wny-ny)/2, (wnz-nz)/2,nx,ny,nz);
01552                         with->clip_inplace(r);
01553                         undoresize = true;
01554                 }
01555 
01556                 EMData* cor = correlation(this, with, fpflag, center);
01557 
01558                 // If the argument EMData pointer was resized, it is returned to its original dimensions
01559                 if ( undoresize ) {
01560                         Region r((nx-wnx)/2, (ny-wny)/2,(nz-wnz)/2,wnx,wny,wnz);
01561                         with->clip_inplace(r);
01562                 }
01563 
01564                 EXITFUNC;
01565                 return cor;
01566         }
01567 }
01568 
01569 EMData *EMData::calc_ccfx( EMData * const with, int y0, int y1, bool no_sum, bool flip)
01570 {
01571         ENTERFUNC;
01572 
01573         if (!with) {
01574                 LOGERR("NULL 'with' image. ");
01575                 throw NullPointerException("NULL input image");
01576         }
01577 
01578         if (!EMUtil::is_same_size(this, with)) {
01579                 LOGERR("images not same size: (%d,%d,%d) != (%d,%d,%d)",
01580                            nx, ny, nz,
01581                            with->get_xsize(), with->get_ysize(), with->get_zsize());
01582                 throw ImageFormatException("images not same size");
01583         }
01584         if (get_ndim() > 2) {
01585                 LOGERR("2D images only");
01586                 throw ImageDimensionException("2D images only");
01587         }
01588 
01589         if (y1 <= y0) {
01590                 y1 = ny;
01591         }
01592 
01593         if (y0 >= y1) {
01594                 y0 = 0;
01595         }
01596 
01597         if (y0 < 0) {
01598                 y0 = 0;
01599         }
01600 
01601         if (y1 > ny) {
01602                 y1 = ny;
01603         }
01604         if (is_complex_x() || with->is_complex_x() ) throw; // Woops don't support this anymore!
01605 
01606         static int nx_fft = 0;
01607         static int ny_fft = 0;
01608         static EMData f1;
01609         static EMData f2;
01610         static EMData rslt;
01611 
01612         int height = y1-y0;
01613         int width = (nx+2-(nx%2));
01614         if (width != nx_fft || height != ny_fft ) {
01615                 f1.set_size(width,height);
01616                 f2.set_size(width,height);
01617                 rslt.set_size(nx,height);
01618                 nx_fft = width;
01619                 ny_fft = height;
01620         }
01621 
01622 #ifdef EMAN2_USING_CUDA
01623         if (EMData::usecuda == 1 && cudarwdata && with->cudarwdata) {
01624                 //cout << "calc_ccfx CUDA" << endl;
01625                 if(!f1.cudarwdata) f1.rw_alloc();
01626                 if(!f2.cudarwdata) f2.rw_alloc();
01627                 if(!rslt.cudarwdata) rslt.rw_alloc();
01628                 cuda_dd_fft_real_to_complex_nd(cudarwdata, f1.cudarwdata, nx, 1, 1, height);
01629                 cuda_dd_fft_real_to_complex_nd(with->cudarwdata, f2.cudarwdata, nx, 1, 1, height);
01630                 calc_ccf_cuda(f1.cudarwdata, f2.cudarwdata, nx, ny, nz);
01631                 cuda_dd_fft_complex_to_real_nd(f1.cudarwdata, rslt.cudarwdata, nx, 1, 1, height);
01632                 if(no_sum){
01633                         EMData* result = new EMData(rslt);
01634                         return result;
01635                 }
01636                 EMData* cf = new EMData(0,0,nx,1,1); //cuda constructor
01637                 cf->runcuda(emdata_column_sum(rslt.cudarwdata, nx, ny));
01638                 cf->update();
01639                 
01640                 EXITFUNC;
01641                 return cf;
01642         }
01643 #endif
01644 
01645         float *d1 = get_data();
01646         float *d2 = with->get_data();
01647         float *f1d = f1.get_data();
01648         float *f2d = f2.get_data();
01649         for (int j = 0; j < height; j++) {
01650                 EMfft::real_to_complex_1d(d1 + j * nx, f1d+j*width, nx);
01651                 EMfft::real_to_complex_1d(d2 + j * nx, f2d+j*width, nx);
01652         }
01653 
01654         if(flip == false) {
01655                 for (int j = 0; j < height; j++) {
01656                         float *f1a = f1d + j * width;
01657                         float *f2a = f2d + j * width;
01658 
01659                         for (int i = 0; i < width / 2; i++) {
01660                                 float re1 = f1a[2*i];
01661                                 float re2 = f2a[2*i];
01662                                 float im1 = f1a[2*i+1];
01663                                 float im2 = f2a[2*i+1];
01664 
01665                                 f1d[j*width+i*2] = re1 * re2 + im1 * im2;
01666                                 f1d[j*width+i*2+1] = im1 * re2 - re1 * im2;
01667                         }
01668                 }
01669         } else {
01670                 for (int j = 0; j < height; j++) {
01671                         float *f1a = f1d + j * width;
01672                         float *f2a = f2d + j * width;
01673 
01674                         for (int i = 0; i < width / 2; i++) {
01675                                 float re1 = f1a[2*i];
01676                                 float re2 = f2a[2*i];
01677                                 float im1 = f1a[2*i+1];
01678                                 float im2 = f2a[2*i+1];
01679 
01680                                 f1d[j*width+i*2] = re1 * re2 - im1 * im2;
01681                                 f1d[j*width+i*2+1] = im1 * re2 + re1 * im2;
01682                         }
01683                 }
01684         }
01685 
01686         float* rd = rslt.get_data();
01687         for (int j = y0; j < y1; j++) {
01688                 EMfft::complex_to_real_1d(f1d+j*width, rd+j*nx, nx);
01689         }
01690 
01691         if (no_sum) {
01692                 rslt.update(); // This is important in terms of the copy - the returned object won't have the correct flags unless we do this
01693                 EXITFUNC;
01694                 return new EMData(rslt);
01695         } else {
01696                 EMData *cf = new EMData(nx,1,1);
01697                 cf->to_zero();
01698                 float *c = cf->get_data();
01699                 for (int j = 0; j < height; j++) {
01700                         for(int i = 0; i < nx; ++i) {
01701                                 c[i] += rd[i+j*nx];
01702                         }
01703                 }
01704                 cf->update();
01705                 EXITFUNC;
01706                 return cf;
01707         }
01708 }
01709 
01710 EMData *EMData::make_rotational_footprint_cmc( bool unwrap) {
01711         ENTERFUNC;
01712         update_stat();
01713         // Note that rotational_footprint caching saves a large amount of time
01714         // but this is at the expense of memory. Note that a policy is hardcoded here,
01715         // that is that caching is only employed when premasked is false and unwrap
01716         // is true - this is probably going to be what is used in most scenarios
01717         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01718         // generated by e2speedtest.
01719         if ( rot_fp != 0 && unwrap == true) {
01720                 return new EMData(*rot_fp);
01721         }
01722 
01723         static EMData obj_filt;
01724         EMData* filt = &obj_filt;
01725         filt->set_complex(true);
01726 
01727 
01728         // The filter object is nothing more than a cached high pass filter
01729         // Ultimately it is used an argument to the EMData::mult(EMData,prevent_complex_multiplication (bool))
01730         // function in calc_mutual_correlation. Note that in the function the prevent_complex_multiplication
01731         // set to true, which is used for speed reasons.
01732         if (filt->get_xsize() != nx+2-(nx%2) || filt->get_ysize() != ny ||
01733                    filt->get_zsize() != nz ) {
01734                 filt->set_size(nx+2-(nx%2), ny, nz);
01735                 filt->to_one();
01736 
01737                 filt->process_inplace("filter.highpass.gauss", Dict("cutoff_abs", 1.5f/nx));
01738         }
01739 
01740         EMData *ccf = this->calc_mutual_correlation(this, true,filt);
01741         ccf->sub(ccf->get_edge_mean());
01742         EMData *result = ccf->unwrap();
01743         delete ccf; ccf = 0;
01744 
01745         EXITFUNC;
01746         if ( unwrap == true)
01747         {
01748         // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01749 
01750 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01751 // to throw any exception
01752 // if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01753 
01754 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01755 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01756                 rot_fp = result;
01757                 return new EMData(*rot_fp);
01758         }
01759         else return result;
01760 }
01761 
01762 EMData *EMData::make_rotational_footprint( bool unwrap) {
01763         ENTERFUNC;
01764         update_stat();
01765         // Note that rotational_footprint caching saves a large amount of time
01766         // but this is at the expense of memory. Note that a policy is hardcoded here,
01767         // that is that caching is only employed when premasked is false and unwrap
01768         // is true - this is probably going to be what is used in most scenarios
01769         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01770         // generated by e2speedtest.
01771         if ( rot_fp != 0 && unwrap == true) {
01772                 return new EMData(*rot_fp);
01773         }
01774 
01775         EMData* ccf = this->calc_ccf(this,CIRCULANT,true);
01776         ccf->sub(ccf->get_edge_mean());
01777         //ccf->process_inplace("xform.phaseorigin.tocenter"); ccf did the centering
01778         EMData *result = ccf->unwrap();
01779         delete ccf; ccf = 0;
01780 
01781         EXITFUNC;
01782         if ( unwrap == true)
01783         { // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01784 
01785 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01786 // to throw any exception
01787 // if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01788 
01789 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01790 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01791                 rot_fp = result;
01792                 return new EMData(*rot_fp);
01793         }
01794         else return result;
01795 }
01796 
01797 EMData *EMData::make_rotational_footprint_e1( bool unwrap)
01798 {
01799         ENTERFUNC;
01800 
01801         update_stat();
01802         // Note that rotational_footprint caching saves a large amount of time
01803         // but this is at the expense of memory. Note that a policy is hardcoded here,
01804         // that is that caching is only employed when premasked is false and unwrap
01805         // is true - this is probably going to be what is used in most scenarios
01806         // as advised by Steve Ludtke - In terms of performance this caching doubles the metric
01807         // generated by e2speedtest.
01808         if ( rot_fp != 0 && unwrap == true) {
01809                 return new EMData(*rot_fp);
01810         }
01811 
01812         static EMData obj_filt;
01813         EMData* filt = &obj_filt;
01814         filt->set_complex(true);
01815 //      Region filt_region;
01816 
01817 //      if (nx & 1) {
01818 //              LOGERR("even image xsize only");                throw ImageFormatException("even image xsize only");
01819 //      }
01820 
01821         int cs = (((nx * 7 / 4) & 0xfffff8) - nx) / 2; // this pads the image to 1 3/4 * size with result divis. by 8
01822 
01823         static EMData big_clip;
01824         int big_x = nx+2*cs;
01825         int big_y = ny+2*cs;
01826         int big_z = 1;
01827         if ( nz != 1 ) {
01828                 big_z = nz+2*cs;
01829         }
01830 
01831 
01832         if ( big_clip.get_xsize() != big_x || big_clip.get_ysize() != big_y || big_clip.get_zsize() != big_z ) {
01833                 big_clip.set_size(big_x,big_y,big_z);
01834         }
01835         // It is important to set all newly established pixels around the boundaries to the mean
01836         // If this is not done then the associated rotational alignment routine breaks, in fact
01837         // everythin just goes foo.
01838 
01839         big_clip.to_value(get_edge_mean());
01840 
01841         if (nz != 1) {
01842                 big_clip.insert_clip(this,IntPoint(cs,cs,cs));
01843         } else  {
01844                 big_clip.insert_clip(this,IntPoint(cs,cs,0));
01845         }
01846         
01847         // The filter object is nothing more than a cached high pass filter
01848         // Ultimately it is used an argument to the EMData::mult(EMData,prevent_complex_multiplication (bool))
01849         // function in calc_mutual_correlation. Note that in the function the prevent_complex_multiplication
01850         // set to true, which is used for speed reasons.
01851         if (filt->get_xsize() != big_clip.get_xsize() +2-(big_clip.get_xsize()%2) || filt->get_ysize() != big_clip.get_ysize() ||
01852                    filt->get_zsize() != big_clip.get_zsize()) {
01853                 filt->set_size(big_clip.get_xsize() + 2-(big_clip.get_xsize()%2), big_clip.get_ysize(), big_clip.get_zsize());
01854                 filt->to_one();
01855                 filt->process_inplace("filter.highpass.gauss", Dict("cutoff_abs", 1.5f/nx));
01856 #ifdef EMAN2_USING_CUDA
01857                 /*
01858                 if(EMData::usecuda == 1 && big_clip.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                 */
01863 #endif
01864         }
01865 #ifdef EMAN2_USING_CUDA
01866         /*
01867         if(EMData::usecuda == 1 && big_clip.cudarwdata && !filt->cudarwdata)
01868         {
01869                 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
01870         }
01871         */
01872 #endif
01873         
01874         EMData *mc = big_clip.calc_mutual_correlation(&big_clip, true,filt);
01875         mc->sub(mc->get_edge_mean());
01876 
01877         static EMData sml_clip;
01878         int sml_x = nx * 3 / 2;
01879         int sml_y = ny * 3 / 2;
01880         int sml_z = 1;
01881         if ( nz != 1 ) {
01882                 sml_z = nz * 3 / 2;
01883         }
01884 
01885         if ( sml_clip.get_xsize() != sml_x || sml_clip.get_ysize() != sml_y || sml_clip.get_zsize() != sml_z ) {
01886                 sml_clip.set_size(sml_x,sml_y,sml_z);   }
01887         if (nz != 1) {
01888                 sml_clip.insert_clip(mc,IntPoint(-cs+nx/4,-cs+ny/4,-cs+nz/4));
01889         } else {
01890                 sml_clip.insert_clip(mc,IntPoint(-cs+nx/4,-cs+ny/4,0));
01891         }
01892                 
01893         delete mc; mc = 0;
01894         EMData * result = NULL;
01895         
01896         if (nz == 1) {
01897                 if (!unwrap) {
01898 #ifdef EMAN2_USING_CUDA
01899                         //if(EMData::usecuda == 1 && sml_clip.cudarwdata) throw UnexpectedBehaviorException("shap masking is not yet supported by CUDA");
01900 #endif
01901                         result = sml_clip.process("mask.sharp", Dict("outer_radius", -1, "value", 0));
01902 
01903                 }
01904                 else {
01905                         result = sml_clip.unwrap();
01906                 }
01907         }
01908         else {
01909                 // I am not sure why there is any consideration of non 2D images, but it was here
01910                 // in the first port so I kept when I cleaned this function up (d.woolford)
01911 //              result = clipped_mc;
01912                 result = new EMData(sml_clip);
01913         }
01914         
01915 #ifdef EMAN2_USING_CUDA
01916         //if (EMData::usecuda == 1) 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
01917 #endif
01918         EXITFUNC;
01919         if ( unwrap == true)
01920         { // this if statement reflects a strict policy of caching in only one scenario see comments at beginning of function block
01921 
01922                 // Note that the if statement at the beginning of this function ensures that rot_fp is not zero, so there is no need
01923                 // to throw any exception
01924                 if ( rot_fp != 0 ) throw UnexpectedBehaviorException("The rotational foot print is only expected to be cached if it is not NULL");
01925 
01926                 // Here is where the caching occurs - the rot_fp takes ownsherhip of the pointer, and a deep copied EMData object is returned.
01927                 // The deep copy invokes a cost in terms of CPU cycles and memory, but prevents the need for complicated memory management (reference counting)
01928                 rot_fp = result;
01929                 return new EMData(*rot_fp);
01930         }
01931         else return result;
01932 }
01933 
01934 EMData *EMData::make_footprint(int type)
01935 {
01936 //      printf("Make fp %d\n",type);
01937         if (type==0) {
01938                 EMData *un=make_rotational_footprint_e1(); // Use EMAN1's footprint strategy
01939                 if (un->get_ysize() <= 6) {
01940                         throw UnexpectedBehaviorException("In EMData::make_footprint. The rotational footprint is too small");
01941                 }
01942                 EMData *tmp=un->get_clip(Region(0,4,un->get_xsize(),un->get_ysize()-6));        // 4 and 6 are empirical
01943                 EMData *cx=tmp->calc_ccfx(tmp,0,-1,1);
01944                 EMData *fp=cx->get_clip(Region(0,0,cx->get_xsize()/2,cx->get_ysize()));
01945                 delete un;
01946                 delete tmp;
01947                 delete cx;
01948                 return fp;
01949         }
01950         else if (type==1 || type==2 ||type==5 || type==6) {
01951                 int i,j,kx,ky,lx,ly;
01952 
01953                 EMData *fft=do_fft();
01954 
01955                 // map for x,y -> radius for speed
01956                 int rmax=(get_xsize()+1)/2;
01957                 float *rmap=(float *)malloc(rmax*rmax*sizeof(float));
01958                 for (i=0; i<rmax; i++) {
01959                         for (j=0; j<rmax; j++) {
01960 #ifdef _WIN32
01961                                 rmap[i+j*rmax]=_hypotf((float)i,(float)j);
01962 #else
01963                                 rmap[i+j*rmax]=hypot((float)i,(float)j);
01964 #endif  //_WIN32
01965 //                              printf("%d\t%d\t%f\n",i,j,rmap[i+j*rmax]);
01966                         }
01967                 }
01968 
01969                 EMData *fp=new EMData(rmax*2+2,rmax*2,1);
01970                 fp->set_complex(1);
01971                 fp->to_zero();
01972 
01973                 // Two vectors in to complex space (kx,ky) and (lx,ly)
01974                 // We are computing the bispectrum, f(k).f(l).f*(k+l)
01975                 // but integrating out two dimensions, leaving |k|,|l|
01976                 for (kx=-rmax+1; kx<rmax; kx++) {
01977                         for (ky=-rmax+1; ky<rmax; ky++) {
01978                                 for (lx=-rmax+1; lx<rmax; lx++) {
01979                                         for (ly=-rmax+1; ly<rmax; ly++) {
01980                                                 int ax=kx+lx;
01981                                                 int ay=ky+ly;
01982                                                 if (abs(ax)>=rmax || abs(ay)>=rmax) continue;
01983                                                 int r1=(int)floor(.5+rmap[abs(kx)+rmax*abs(ky)]);
01984                                                 int r2=(int)floor(.5+rmap[abs(lx)+rmax*abs(ly)]);
01985 //                                              if (r1>500 ||r2>500) printf("%d\t%d\t%d\t%d\t%d\t%d\n",kx,ky,lx,ly,r1,r2);
01986 //                                              float r3=rmap[ax+rmax*ay];
01987                                                 if (r1+r2>=rmax) continue;
01988 
01989                                                 std::complex<float> p=fft->get_complex_at(kx,ky)*fft->get_complex_at(lx,ly)*conj(fft->get_complex_at(ax,ay));
01990                                                 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
01991 //                                              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
01992 //                                              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
01993                                                 fp->set_value_at(r1*2+1,r2,fp->get_value_at(r1*2+1,r2)+1);                      // a normalization counter
01994                                         }
01995                                 }
01996                         }
01997                 }
01998 
01999                 // Normalizes the pixels based on the accumulated counts then sets the imaginary components back to zero
02000                 if (type==5 || type==6) {
02001                         for (i=0; i<rmax*2; i+=2) {
02002                                 for (j=0; j<rmax; j++) {
02003                                         float norm=fp->get_value_at(i+1,j);
02004 #ifdef _WIN32
02005                                         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));
02006                                         fp->set_value_at(i,j,pow(fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm), 1.0f/3.0f));
02007 #else
02008                                         fp->set_value_at(i,rmax*2-j-1,cbrt(fp->get_value_at(i,j)/(norm==0?1.0:norm)));
02009                                         fp->set_value_at(i,j,cbrt(fp->get_value_at(i,j)/(norm==0?1.0:norm)));
02010 #endif  //_WIN32
02011                                         fp->set_value_at(i+1,j,0.0);
02012                                 }
02013                         }
02014                 }
02015                 else {
02016                         for (i=0; i<rmax*2; i+=2) {
02017                                 for (j=0; j<rmax; j++) {
02018                                         float norm=fp->get_value_at(i+1,j);
02019                                         fp->set_value_at(i,rmax*2-j-1,fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm));
02020                                         fp->set_value_at(i,j,fp->get_value_at(i,j)/(norm==0.0f?1.0f:norm));
02021                                         fp->set_value_at(i+1,j,0.0);
02022                                 }
02023                         }
02024                 }
02025 
02026                 free(rmap);
02027                 if (type==2||type==6) {
02028                         EMData *f2=fp->do_ift();
02029                         if (f2->get_value_at(0,0)<0) f2->mult(-1.0f);
02030                         f2->process_inplace("xform.phaseorigin.tocorner");
02031                         delete fp;
02032                         return f2;
02033                 }
02034                 return fp;
02035         }
02036         else if (type==3 || type==4) {
02037                 int h,i,j,kx,ky,lx,ly;
02038 
02039                 EMData *fft=do_fft();
02040 
02041                 // map for x,y -> radius for speed
02042                 int rmax=(get_xsize()+1)/2;
02043                 float *rmap=(float *)malloc(rmax*rmax*sizeof(float));
02044                 for (i=0; i<rmax; i++) {
02045                         for (j=0; j<rmax; j++) {
02046 #ifdef _WIN32
02047                                 rmap[i+j*rmax]=_hypotf((float)i,(float)j);
02048 #else
02049                                 rmap[i+j*rmax]=hypot((float)i,(float)j);
02050 #endif  //_WIN32
02051 //                              printf("%d\t%d\t%f\n",i,j,rmap[i+j*rmax]);
02052                         }
02053                 }
02054 
02055                 EMData *fp=new EMData(rmax*2+2,rmax*2,16);
02056 
02057                 fp->set_complex(1);
02058                 fp->to_zero();
02059 
02060                 // Two vectors in to complex space (kx,ky) and (lx,ly)
02061                 // We are computing the bispectrum, f(k).f(l).f*(k+l)
02062                 // but integrating out two dimensions, leaving |k|,|l|
02063                 for (kx=-rmax+1; kx<rmax; kx++) {
02064                         for (ky=-rmax+1; ky<rmax; ky++) {
02065                                 for (lx=-rmax+1; lx<rmax; lx++) {
02066                                         for (ly=-rmax+1; ly<rmax; ly++) {
02067                                                 int ax=kx+lx;
02068                                                 int ay=ky+ly;
02069                                                 if (abs(ax)>=rmax || abs(ay)>=rmax) continue;
02070                                                 float rr1=rmap[abs(kx)+rmax*abs(ky)];
02071                                                 float rr2=rmap[abs(lx)+rmax*abs(ly)];
02072                                                 int r1=(int)floor(.5+rr1);
02073                                                 int r2=(int)floor(.5+rr2);
02074 //                                              if (r1>500 ||r2>500) printf("%d\t%d\t%d\t%d\t%d\t%d\n",kx,ky,lx,ly,r1,r2);
02075 //                                              float r3=rmap[ax+rmax*ay];
02076                                                 if (r1+r2>=rmax || rr1==0 ||rr2==0) continue;
02077 
02078                                                 std::complex<float> p=fft->get_complex_at(kx,ky)*fft->get_complex_at(lx,ly)*conj(fft->get_complex_at(ax,ay));
02079                                                 int dot=(int)floor((kx*lx+ky*ly)/(rr1*rr2)*7.5);                                        // projection of k on l 0-31
02080                                                 if (dot<0) dot=16+dot;
02081 //                                              int dot=(int)floor((kx*lx+ky*ly)/(rr1*rr2)*7.5+8.0);                                    // projection of k on l 0-15
02082                                                 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
02083 //                                              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
02084 //                                              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
02085                                                 fp->set_value_at(r1*2+1,r2,dot,fp->get_value_at(r1*2+1,r2,dot)+1);                      // a normalization counter
02086                                         }
02087                                 }
02088                         }
02089                 }
02090 
02091                 // Normalizes the pixels based on the accumulated counts then sets the imaginary components back to zero
02092                 for (i=0; i<rmax*2; i+=2) {
02093                         for (j=0; j<rmax; j++) {
02094                                 for (h=0; h<16; h++) {
02095                                         float norm=fp->get_value_at(i+1,j,h);
02096 //                                      fp->set_value_at(i,rmax*2-j-1,h,cbrt(fp->get_value_at(i,j,h)/(norm==0?1.0:norm)));
02097 //                                      fp->set_value_at(i,j,h,cbrt(fp->get_value_at(i,j,h)/(norm==0?1.0:norm)));
02098                                         fp->set_value_at(i,rmax*2-j-1,h,(fp->get_value_at(i,j,h)/(norm==0.0f?1.0f:norm)));
02099                                         fp->set_value_at(i,j,h,(fp->get_value_at(i,j,h)/(norm==0.0f?1.0f:norm)));
02100         //                              fp->set_value_at(i,rmax*2-j-1,fp->get_value_at(i,j)/(norm==0?1.0:norm));
02101         //                              fp->set_value_at(i,j,fp->get_value_at(i,j)/(norm==0?1.0:norm));
02102                                         fp->set_value_at(i+1,j,h,0.0);
02103                                 }
02104                         }
02105                 }
02106 
02107                 free(rmap);
02108                 if (type==4) {
02109                         EMData *f2=fp->do_ift();
02110                         if (f2->get_value_at(0,0,0)<0) f2->mult(-1.0f);
02111                         f2->process_inplace("xform.phaseorigin.tocorner");
02112                         delete fp;
02113                         return f2;
02114                 }
02115                 return fp;
02116         }
02117         throw UnexpectedBehaviorException("There is not implementation for the parameters you specified");
02118 }
02119 
02120 
02121 EMData *EMData::calc_mutual_correlation(EMData * with, bool tocenter, EMData * filter)
02122 {
02123         ENTERFUNC;
02124 
02125         if (with && !EMUtil::is_same_size(this, with)) {
02126                 LOGERR("images not same size");
02127                 throw ImageFormatException( "images not same size");
02128         }
02129 
02130 #ifdef EMAN2_USING_CUDA
02131         if(EMData::usecuda == 1 && cudarwdata && with->cudarwdata)
02132         {       
02133 
02134                 EMData* this_fft = do_fft_cuda();
02135 
02136                 EMData *cf = 0;
02137                 if (with && with != this) {
02138                         cf = with->do_fft_cuda();
02139                 }else{
02140                         cf = this_fft->copy();
02141                 }
02142                 
02143                 if (filter) {
02144                         if (!EMUtil::is_same_size(filter, cf)) {
02145                                 LOGERR("improperly sized filter");
02146                                 throw ImageFormatException("improperly sized filter");
02147                         }
02148                         mult_complex_efficient_cuda(cf->cudarwdata, filter->cudarwdata, cf->get_xsize(), cf->get_ysize(), cf->get_zsize(), 1);
02149                         mult_complex_efficient_cuda(this_fft->cudarwdata, filter->cudarwdata, this_fft->get_xsize(), this_fft->get_ysize(), this_fft->get_zsize(), 1);
02150                 }
02151                 
02152                 mcf_cuda(this_fft->cudarwdata, cf->cudarwdata, this_fft->get_xsize(), this_fft->get_ysize(), this_fft->get_zsize());
02153                 
02154                 EMData *f2 = cf->do_ift_cuda();
02155 
02156                 if (tocenter) {
02157                         f2->process_inplace("xform.phaseorigin.tocenter");
02158                 }
02159 
02160                 if( cf )
02161                 {
02162                         delete cf;
02163                         cf = 0;
02164                 }
02165 
02166                 if( this_fft )
02167                 {
02168                         delete this_fft;
02169                         this_fft = 0;
02170                 }
02171 
02172                 f2->set_attr("label", "MCF");
02173                 f2->set_path("/tmp/eman.mcf");
02174                 f2->update();
02175 
02176                 EXITFUNC;
02177                 return f2;
02178         }
02179 #endif
02180 
02181         EMData *this_fft = 0;
02182         this_fft = do_fft();
02183 
02184         if (!this_fft) {
02185 
02186                 LOGERR("FFT returns NULL image");
02187                 throw NullPointerException("FFT returns NULL image");
02188         }
02189 
02190         this_fft->ap2ri(); //this is not needed!
02191         EMData *cf = 0;
02192 
02193         if (with && with != this) {
02194                 cf = with->do_fft();
02195                 if (!cf) {
02196                         LOGERR("FFT returns NULL image");
02197                         throw NullPointerException("FFT returns NULL image");
02198                 }
02199                 cf->ap2ri(); //nor is this!
02200         }
02201         else {
02202                 cf = this_fft->copy();
02203         }
02204         
02205         if (filter) {
02206                 if (!EMUtil::is_same_size(filter, cf)) {
02207                         LOGERR("improperly sized filter");
02208                         throw ImageFormatException("improperly sized filter");
02209                 }
02210                 
02211                 cf->mult_complex_efficient(*filter,true); //insanely this is required....
02212                 this_fft->mult(*filter,true);
02213                 //cf->mult_complex_efficient(*filter,7); // takes advantage of the fact that the filter is 1 everywhere but near the origin
02214                 //this_fft->mult_complex_efficient(*filter,7);
02215                 /*cf->mult_complex_efficient(*filter,5);
02216                 this_fft->mult_complex_efficient(*filter,5);*/
02217         }
02218 
02219         float *rdata1 = this_fft->get_data();
02220         float *rdata2 = cf->get_data();
02221         size_t this_fft_size = (size_t)this_fft->get_xsize() * this_fft->get_ysize() * this_fft->get_zsize();
02222 
02223         if (with == this) {
02224                 for (size_t i = 0; i < this_fft_size; i += 2) {
02225                         rdata2[i] = std::sqrt(rdata1[i] * rdata2[i] + rdata1[i + 1] * rdata2[i + 1]);
02226                         rdata2[i + 1] = 0;
02227                 }
02228 
02229                 this_fft->update();
02230                 cf->update();
02231         }
02232         else {
02233                 for (size_t i = 0; i < this_fft_size; i += 2) {
02234                         rdata2[i] = (rdata1[i] * rdata2[i] + rdata1[i + 1] * rdata2[i + 1]);
02235                         rdata2[i + 1] = (rdata1[i + 1] * rdata2[i] - rdata1[i] * rdata2[i + 1]);
02236                 }
02237                 
02238                 //This seems like a bug, but it probably is never used....
02239                 for (size_t i = 0; i < this_fft_size; i += 2) {
02240                         float t = Util::square(rdata2[i]) + Util::square(rdata2[i + 1]);
02241                         if (t != 0) {
02242                                 t = pow(t, 0.25f);
02243                                 rdata2[i] /= t;
02244                                 rdata2[i + 1] /= t;
02245                         }
02246                 }
02247                 this_fft->update();
02248                 cf->update();
02249         }
02250 
02251         EMData *f2 = cf->do_ift();
02252 
02253         if (tocenter) {
02254                 f2->process_inplace("xform.phaseorigin.tocenter");
02255         }
02256 
02257         if( cf )
02258         {
02259                 delete cf;
02260                 cf = 0;
02261         }
02262 
02263         if( this_fft )
02264         {
02265                 delete this_fft;
02266                 this_fft = 0;
02267         }
02268 
02269         f2->set_attr("label", "MCF");
02270         f2->set_path("/tmp/eman.mcf");
02271 
02272         EXITFUNC;
02273         return f2;
02274 }
02275 
02276 
02277 vector < float > EMData::calc_hist(int hist_size, float histmin, float histmax,const float& brt, const float& cont)
02278 {
02279         ENTERFUNC;
02280 
02281         static size_t prime[] = { 1, 3, 7, 11, 17, 23, 37, 59, 127, 253, 511 };
02282 
02283         if (histmin == histmax) {
02284                 histmin = get_attr("minimum");
02285                 histmax = get_attr("maximum");
02286         }
02287 
02288         vector <float> hist(hist_size, 0.0);
02289 
02290         int p0 = 0;
02291         int p1 = 0;
02292         size_t size = (size_t)nx * ny * nz;
02293         if (size < 300000) {
02294                 p0 = 0;
02295                 p1 = 0;
02296         }
02297         else if (size < 2000000) {
02298                 p0 = 2;
02299                 p1 = 3;
02300         }
02301         else if (size < 8000000) {
02302                 p0 = 4;
02303                 p1 = 6;
02304         }
02305         else {
02306                 p0 = 7;
02307                 p1 = 9;
02308         }
02309 
02310         if (is_complex() && p0 > 0) {
02311                 p0++;
02312                 p1++;
02313         }
02314 
02315         size_t di = 0;
02316 //      float norm = 0;
02317         size_t n = hist.size();
02318 
02319         float * data = get_data();
02320         for (int k = p0; k <= p1; ++k) {
02321                 if (is_complex()) {
02322                         di = prime[k] * 2;
02323                 }
02324                 else {
02325                         di = prime[k];
02326                 }
02327 
02328 //              norm += (float)size / (float) di;
02329                 float w = (float)n / (histmax - histmin);
02330 
02331                 for(size_t i=0; i<=size-di; i += di) {
02332                         float val;
02333                         if (cont != 1.0f || brt != 0)val = cont*(data[i]+brt);
02334                         else val = data[i];
02335                         int j = Util::round((val - histmin) * w);
02336                         if (j >= 0 && j < (int) n) {
02337                                 hist[j] += 1;
02338                         }
02339                 }
02340         }
02341 /*
02342         for (size_t i = 0; i < hist.size(); ++i) {
02343                 if (norm != 0) {
02344                         hist[i] = hist[i] / norm;
02345                 }
02346         }
02347 */
02348         return hist;
02349 
02350         EXITFUNC;
02351 }
02352 
02353 
02354 
02355 
02356 
02357 vector<float> EMData::calc_az_dist(int n, float a0, float da, float rmin, float rmax)
02358 {
02359         ENTERFUNC;
02360 
02361         a0=a0*M_PI/180.0f;
02362         da=da*M_PI/180.0f;
02363 
02364         if (get_ndim() > 2) {
02365                 throw ImageDimensionException("no 3D image");
02366         }
02367 
02368         float *yc = new float[n];
02369 
02370         vector<float>   vd(n);
02371         for (int i = 0; i < n; i++) {
02372                 yc[i] = 0.00001f;
02373         }
02374 
02375         float * data = get_data();
02376         if (is_complex()) {
02377                 int c = 0;
02378                 for (int y = 0; y < ny; y++) {
02379                         for (int x = 0; x < nx; x += 2, c += 2) {
02380                                 int x1 = x / 2;
02381                                 int y1 = y<ny/2?y:y-ny;
02382                                 float r = (float)Util::hypot_fast(x1,y1);
02383 
02384                                 if (r >= rmin && r <= rmax) {
02385                                         float a = 0;
02386 
02387                                         if (y != ny / 2 || x != 0) {
02388                                                 a = (atan2((float)y1, (float)x1) - a0) / da;
02389                                         }
02390 
02391                                         int i = (int)(floor(a));
02392                                         a -= i;
02393 
02394                                         if (i == 0) {
02395                                                 vd[0] += data[c] * (1.0f - a);
02396                                                 yc[0] += (1.0f - a);
02397                                         }
02398                                         else if (i == n - 1) {
02399                                                 vd[n - 1] += data[c] * a;
02400                                                 yc[n - 1] += a;
02401                                         }
02402                                         else if (i > 0 && i < (n - 1)) {
02403                                                 float h = 0;
02404                                                 if (is_ri()) {
02405 #ifdef  _WIN32
02406                                                         h = (float)_hypot(data[c], data[c + 1]);
02407 #else
02408                                                         h = (float)hypot(data[c], data[c + 1]);
02409 #endif  //_WIN32
02410                                                 }
02411                                                 else {
02412                                                         h = data[c];
02413                                                 }
02414 
02415                                                 vd[i] += h * (1.0f - a);
02416                                                 yc[i] += (1.0f - a);
02417                                                 vd[i + 1] += h * a;
02418                                                 yc[i + 1] += a;
02419                                         }
02420                                 }
02421                         }
02422                 }
02423         }
02424         else {
02425                 int c = 0;
02426                 float half_nx = (nx - 1) / 2.0f;
02427                 float half_ny = (ny - 1) / 2.0f;
02428 
02429                 for (int y = 0; y < ny; y++) {
02430                         for (int x = 0; x < nx; x++, c++) {
02431                                 float y1 = y - half_ny;
02432                                 float x1 = x - half_nx;
02433 #ifdef  _WIN32
02434                                 float r = (float)_hypot(x1, y1);
02435 #else
02436                                 float r = (float)hypot(x1, y1);
02437 #endif
02438 
02439                                 if (r >= rmin && r <= rmax) {
02440                                         float a = 0;
02441                                         if (x1 != 0 || y1 != 0) {
02442                                                 a = atan2(y1, x1);
02443                                                 if (a < 0) {
02444                                                         a += M_PI * 2;
02445                                                 }
02446                                         }
02447 
02448                                         a = (a - a0) / da;
02449                                         int i = static_cast < int >(floor(a));
02450                                         a -= i;
02451 
02452                                         if (i == 0) {
02453                                                 vd[0] += data[c] * (1.0f - a);
02454                                                 yc[0] += (1.0f - a);
02455                                         }
02456                                         else if (i == n - 1) {
02457                                                 vd[n - 1] += data[c] * a;
02458                                                 yc[n - 1] += (a);
02459                                         }
02460                                         else if (i > 0 && i < (n - 1)) {
02461                                                 vd[i] += data[c] * (1.0f - a);
02462                                                 yc[i] += (1.0f - a);
02463                                                 vd[i + 1] += data[c] * a;
02464                                                 yc[i + 1] += a;
02465                                         }
02466                                 }
02467                         }
02468                 }
02469         }
02470 
02471 
02472         for (int i = 0; i < n; i++) {
02473                 vd[i] /= yc[i];
02474         }
02475 
02476         if( yc )
02477         {
02478                 delete[]yc;
02479                 yc = 0;
02480         }
02481 
02482         return vd;
02483 
02484         EXITFUNC;
02485 }
02486 
02487 
02488 EMData *EMData::unwrap(int r1, int r2, int xs, int dx, int dy, bool do360, bool weight_radial) const
02489 {
02490         ENTERFUNC;
02491 
02492         if (get_ndim() != 2) {
02493                 throw ImageDimensionException("2D image only");
02494         }
02495 
02496         int p = 1;
02497         if (do360) {
02498                 p = 2;
02499         }
02500 
02501         if (xs < 1) {
02502                 xs = (int) Util::fast_floor(p * M_PI * ny / 4);
02503                 xs -= xs % 8;
02504                 if (xs<=8) xs=16;
02505         }
02506 
02507         if (r1 < 0) {
02508                 r1 = 4;
02509         }
02510 
02511 #ifdef  _WIN32
02512         int rr = ny / 2 - 2 - (int) Util::fast_floor(static_cast<float>(_hypot(dx, dy)));
02513 #else
02514         int rr = ny / 2 - 2 - (int) Util::fast_floor(static_cast<float>(hypot(dx, dy)));
02515 #endif  //_WIN32
02516         rr-=rr%2;
02517         if (r2 <= r1 || r2 > rr) {
02518                 r2 = rr;
02519         }
02520 
02521         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");
02522 
02523 #ifdef EMAN2_USING_CUDA
02524         if (EMData::usecuda == 1 && isrodataongpu()){
02525                 //cout << " CUDA unwrap" << endl;
02526                 EMData* result = new EMData(0,0,xs,(r2-r1),1);
02527                 if(!result->rw_alloc()) throw UnexpectedBehaviorException("Bad alloc");
02528                 bindcudaarrayA(true);
02529                 emdata_unwrap(result->cudarwdata, r1, r2, xs, p, dx, dy, weight_radial, nx, ny);
02530                 unbindcudaarryA();
02531                 result->update();
02532                 return result;
02533         }
02534 #endif
02535 
02536         EMData *ret = new EMData();
02537         ret->set_size(xs, r2 - r1, 1);
02538         const float *const d = get_const_data();
02539         float *dd = ret->get_data();
02540         float pfac = (float)p/(float)xs;
02541 
02542         int nxon2 = nx/2;
02543         int nyon2 = ny/2;
02544         for (int x = 0; x < xs; x++) {
02545                 float ang = x * M_PI * pfac;
02546                 float si = sin(ang);
02547                 float co = cos(ang);
02548 
02549                 for (int y = 0; y < r2 - r1; y++) {
02550                         float ypr1 = (float)y + r1;
02551                         float xx = ypr1 * co + nxon2 + dx;
02552                         float yy = ypr1 * si + nyon2 + dy;
02553 //                      float t = xx - Util::fast_floor(xx);
02554 //                      float u = yy - Util::fast_floor(yy);
02555                         float t = xx - (int)xx;
02556                         float u = yy - (int)yy;
02557 //                      int k = (int) Util::fast_floor(xx) + (int) (Util::fast_floor(yy)) * nx;
02558                         int k = (int) xx + ((int) yy) * nx;
02559                         float val = Util::bilinear_interpolate(d[k], d[k + 1], d[k + nx], d[k + nx+1], t,u);
02560                         if (weight_radial) val *=  ypr1;
02561                         dd[x + y * xs] = val;
02562                 }
02563 
02564         }
02565         ret->update();
02566 
02567         EXITFUNC;
02568         return ret;
02569 }
02570 
02571 // NOTE : x axis is from 0 to 0.5  (Nyquist), and thus properly handles non-square images
02572 // complex only
02573 void EMData::apply_radial_func(float x0, float step, vector < float >array, bool interp)
02574 {
02575         ENTERFUNC;
02576 
02577         if (!is_complex()) throw ImageFormatException("apply_radial_func requires a complex image");
02578 
02579         int n = static_cast < int >(array.size());
02580 
02581         if (n*step>2.0) printf("Warning, apply_radial_func takes x0 and step with respect to Nyquist (0.5)\n");
02582 
02583 //      printf("%f %f %f\n",array[0],array[25],array[50]);
02584 
02585         ap2ri();
02586 
02587         size_t ndims = get_ndim();
02588         float * data = get_data();
02589         if (ndims == 2) {
02590                 int k = 0;
02591                 for (int j = 0; j < ny; j++) {
02592                         for (int i = 0; i < nx; i += 2, k += 2) {
02593                                 float r;
02594 #ifdef  _WIN32
02595                                 if (j<ny/2) r = (float)_hypot(i/(float)(nx*2), j/(float)ny);
02596                                 else r = (float)_hypot(i/(float)(nx*2), (ny-j)/(float)ny);
02597 #else
02598                                 if (j<ny/2) r = (float)hypot(i/(float)(nx*2), j/(float)ny);
02599                                 else r = (float)hypot(i/(float)(nx*2), (ny-j)/(float)ny);
02600 #endif  //_WIN32
02601                                 r = (r - x0) / step;
02602 
02603                                 int l = 0;
02604                                 if (interp) {
02605                                         l = (int) floor(r);
02606                                 }
02607                                 else {
02608                                         l = (int) floor(r + 1);
02609                                 }
02610 
02611 
02612                                 float f = 0;
02613                                 if (l >= n - 2) {
02614                                         f = array[n - 1];
02615                                 }
02616                                 else {
02617                                         if (interp) {
02618                                                 r -= l;
02619                                                 f = (array[l] * (1.0f - r) + array[l + 1] * r);
02620                                         }
02621                                         else {
02622                                                 f = array[l];
02623                                         }
02624                                 }
02625 
02626                                 data[k] *= f;
02627                                 data[k + 1] *= f;
02628                         }
02629                 }
02630         }
02631         else if (ndims == 3) {
02632                 int k = 0;
02633                 for (int m = 0; m < nz; m++) {
02634                         float mnz;
02635                         if (m<nz/2) mnz=m*m/(float)(nz*nz);
02636                         else { mnz=(nz-m)/(float)nz; mnz*=mnz; }
02637 
02638                         for (int j = 0; j < ny; j++) {
02639                                 float jny;
02640                                 if (j<ny/2) jny= j*j/(float)(ny*ny);
02641                                 else { jny=(ny-j)/(float)ny; jny*=jny; }
02642 
02643                                 for (int i = 0; i < nx; i += 2, k += 2) {
02644                                         float r = std::sqrt((i * i / (nx*nx*4.0f)) + jny + mnz);
02645                                         r = (r - x0) / step;
02646 
02647                                         int l = 0;
02648                                         if (interp) {
02649                                                 l = (int) floor(r);
02650                                         }
02651                                         else {
02652                                                 l = (int) floor(r + 1);
02653                                         }
02654 
02655 
02656                                         float f = 0;
02657                                         if (l >= n - 2) {
02658                                                 f = array[n - 1];
02659                                         }
02660                                         else {
02661                                                 if (interp) {
02662                                                         r -= l;
02663                                                         f = (array[l] * (1.0f - r) + array[l + 1] * r);
02664                                                 }
02665                                                 else {
02666                                                         f = array[l];
02667                                                 }
02668                                         }
02669 
02670                                         data[k] *= f;
02671                                         data[k + 1] *= f;
02672                                 }
02673                         }
02674                 }
02675 
02676         }
02677 
02678         update();
02679         EXITFUNC;
02680 }
02681 
02682 vector<float> EMData::calc_radial_dist(int n, float x0, float dx, bool inten)
02683 {
02684         ENTERFUNC;
02685 
02686         vector<float>ret(n);
02687         vector<float>norm(n);
02688 
02689         int x,y,z,i;
02690         int step=is_complex()?2:1;
02691         int isinten=get_attr_default("is_intensity",0);
02692 
02693         if (isinten&&!inten) { throw InvalidParameterException("Must set inten for calc_radial_dist with intensity image"); }
02694 
02695         for (i=0; i<n; i++) ret[i]=norm[i]=0.0;
02696         float * data = get_data();
02697 
02698         // We do 2D separately to avoid the hypot3 call
02699         if (nz==1) {
02700                 for (y=i=0; y<ny; y++) {
02701                         for (x=0; x<nx; x+=step,i+=step) {
02702                                 float r,v;
02703                                 if (step==2) {          //complex
02704                                         if (x==0 && y>ny/2) continue;
02705                                         r=(float)(Util::hypot_fast(x/2,y<ny/2?y:ny-y));         // origin at 0,0; periodic
02706                                         if (!inten) {
02707 #ifdef  _WIN32
02708                                                 if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02709 #else
02710                                                 if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02711 #endif
02712                                                 else v=data[i];                                                 // amp/phase, just get amp
02713                                         } else {
02714                                                 if (isinten) v=data[i];
02715                                                 else if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02716                                                 else v=data[i]*data[i];
02717                                         }
02718                                 }
02719                                 else {
02720                                         r=(float)(Util::hypot_fast(x-nx/2,y-ny/2));
02721                                         if (inten) v=data[i]*data[i];
02722                                         else v=data[i];
02723                                 }
02724                                 r=(r-x0)/dx;
02725                                 int f=int(r);   // safe truncation, so floor isn't needed
02726                                 r-=float(f);    // r is now the fractional spacing between bins
02727 //                              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);
02728                                 if (f>=0 && f<n) {
02729                                         ret[f]+=v*(1.0f-r);
02730                                         norm[f]+=(1.0f-r);
02731                                         if (f<n-1) {
02732                                                 ret[f+1]+=v*r;
02733                                                 norm[f+1]+=r;
02734                                         }
02735                                 }
02736                         }
02737                 }
02738         }
02739         else {
02740                 size_t i;       //3D file may have >2G size
02741                 for (z=i=0; z<nz; ++z) {
02742                         for (y=0; y<ny; ++y) {
02743                                 for (x=0; x<nx; x+=step,i+=step) {
02744                                         float r,v;
02745                                         if (step==2) {  //complex
02746                                                 if (x==0 && z<nz/2) continue;
02747                                                 if (x==0 && z==nz/2 && y<ny/2) continue;
02748                                                 r=Util::hypot3(x/2,y<ny/2?y:ny-y,z<nz/2?z:nz-z);        // origin at 0,0; periodic
02749                                                 if (!inten) {
02750 #ifdef  _WIN32
02751                                                         if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02752 #else
02753                                                         if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02754 #endif  //_WIN32
02755                                                         else v=data[i];                                                 // amp/phase, just get amp
02756                                                 } else {
02757                                                         if (isinten) v=data[i];
02758                                                         else if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02759                                                         else v=data[i]*data[i];
02760                                                 }
02761                                         }
02762                                         else {
02763                                                 r=Util::hypot3(x-nx/2,y-ny/2,z-nz/2);
02764                                                 if (inten) v=data[i]*data[i];
02765                                                 else v=data[i];
02766                                         }
02767                                         r=(r-x0)/dx;
02768                                         int f=int(r);   // safe truncation, so floor isn't needed
02769                                         r-=float(f);    // r is now the fractional spacing between bins
02770                                         if (f>=0 && f<n) {
02771                                                 ret[f]+=v*(1.0f-r);
02772                                                 norm[f]+=(1.0f-r);
02773                                                 if (f<n-1) {
02774                                                         ret[f+1]+=v*r;
02775                                                         norm[f+1]+=r;
02776                                                 }
02777                                         }
02778                                 }
02779                         }
02780                 }
02781         }
02782 
02783         for (i=0; i<n; i++) ret[i]/=norm[i]?norm[i]:1.0f;       // Normalize
02784 
02785         EXITFUNC;
02786 
02787         return ret;
02788 }
02789 
02790 vector<float> EMData::calc_radial_dist(int n, float x0, float dx, int nwedge, float offset, bool inten)
02791 {
02792         ENTERFUNC;
02793 
02794         if (nz > 1) {
02795                 LOGERR("2D images only.");
02796                 throw ImageDimensionException("2D images only");
02797         }
02798         int isinten=get_attr_default("is_intensity",0);
02799 
02800         if (isinten&&!inten) { throw InvalidParameterException("Must set inten for calc_radial_dist with intensity image"); }
02801 
02802 
02803         vector<float>ret(n*nwedge);
02804         vector<float>norm(n*nwedge);
02805 
02806         int x,y,i;
02807         int step=is_complex()?2:1;
02808         float astep=static_cast<float>(M_PI*2.0/nwedge);
02809         if (is_complex()) astep/=2;                                                     // Since we only have the right 1/2 of Fourier space
02810         float* data = get_data();
02811         for (i=0; i<n*nwedge; i++) ret[i]=norm[i]=0.0;
02812 
02813         // We do 2D separately to avoid the hypot3 call
02814         for (y=i=0; y<ny; y++) {
02815                 for (x=0; x<nx; x+=step,i+=step) {
02816                         float r,v,a;
02817                         int bin;
02818                         if (is_complex()) {
02819 #ifdef  _WIN32
02820                                 r=static_cast<float>(_hypot(x/2.0,y<ny/2?y:ny-y));              // origin at 0,0; periodic
02821 #else
02822                                 r=static_cast<float>(hypot(x/2.0,y<ny/2?y:ny-y));               // origin at 0,0; periodic
02823 #endif
02824                                 a=atan2(float(y<ny/2?y:y-ny),x/2.0f);
02825                                 if (!inten) {
02826 #ifdef  _WIN32
02827                                         if (is_ri()) v=static_cast<float>(_hypot(data[i],data[i+1]));   // real/imag, compute amplitude
02828 #else
02829                                         if (is_ri()) v=static_cast<float>(hypot(data[i],data[i+1]));    // real/imag, compute amplitude
02830 #endif  //_WIN32
02831                                         else v=data[i];                                                 // amp/phase, just get amp
02832                                 } else {
02833                                         if (isinten) v=data[i];
02834                                         else if (is_ri()) v=data[i]*data[i]+data[i+1]*data[i+1];
02835                                         else v=data[i]*data[i];
02836                                 }
02837                                 bin=n*int(floor((a+M_PI/2.0f+offset)/astep));
02838                         }
02839                         else {
02840 #ifdef  _WIN32
02841                                 r=static_cast<float>(_hypot(x-nx/2,y-ny/2));
02842 #else
02843                                 r=static_cast<float>(hypot(x-nx/2,y-ny/2));
02844 #endif  //_WIN32
02845                                 a=atan2(float(y-ny/2),float(x-nx/2));
02846                                 if (inten) v=data[i]*data[i];
02847                                 else v=data[i];
02848                                 bin=n*int(floor((a+M_PI+offset)/astep));
02849                         }
02850                         if (bin>=nwedge*n) bin-=nwedge*n;
02851                         if (bin<0) bin+=nwedge*n;
02852                         r=(r-x0)/dx;
02853                         int f=int(r);   // safe truncation, so floor isn't needed
02854                         r-=float(f);    // r is now the fractional spacing between bins
02855 //                      printf("%d %d %d %d %1.3f %1.3f\n",x,y,bin,f,r,a);
02856                         if (f>=0 && f<n) {
02857                                 ret[f+bin]+=v*(1.0f-r);
02858                                 norm[f+bin]+=(1.0f-r);
02859                                 if (f<n-1) {
02860                                         ret[f+1+bin]+=v*r;
02861                                         norm[f+1+bin]+=r;
02862                                 }
02863                         }
02864                 }
02865         }
02866 
02867         for (i=0; i<n*nwedge; i++) ret[i]/=norm[i]?norm[i]:1.0f;        // Normalize
02868         EXITFUNC;
02869 
02870         return ret;
02871 }
02872 
02873 void EMData::cconj() {
02874         ENTERFUNC;
02875         if (!is_complex() || !is_ri())
02876                 throw ImageFormatException("EMData::conj requires a complex, ri image");
02877         int nxreal = nx -2 + int(is_fftodd());
02878         int nxhalf = nxreal/2;
02879         for (int iz = 0; iz < nz; iz++)
02880                 for (int iy = 0; iy < ny; iy++)
02881                         for (int ix = 0; ix <= nxhalf; ix++)
02882                                 cmplx(ix,iy,iz) = conj(cmplx(ix,iy,iz));
02883         EXITFUNC;
02884 }
02885 
02886 void EMData::update_stat() const
02887 {
02888         ENTERFUNC;
02889 //      printf("update stat %f %d\n",(float)attr_dict["mean"],flags);
02890         if (!(flags & EMDATA_NEEDUPD))
02891         {
02892                 EXITFUNC;
02893                 return;
02894         }
02895         if (rdata==0) return;
02896 
02897         float* data = get_data();
02898         float max = -FLT_MAX;
02899         float min = -max;
02900 
02901         double sum = 0;
02902         double square_sum = 0;
02903 
02904         int step = 1;
02905         if (is_complex() && !is_ri()) {
02906                 step = 2;
02907         }
02908 
02909         int n_nonzero = 0;
02910 
02911         size_t size = (size_t)nx*ny*nz;
02912         for (size_t i = 0; i < size; i += step) {
02913                 float v = data[i];
02914         #ifdef _WIN32
02915                 max = _cpp_max(max,v);
02916                 min = _cpp_min(min,v);
02917         #else
02918                 max=std::max<float>(max,v);
02919                 min=std::min<float>(min,v);
02920         #endif  //_WIN32
02921                 sum += v;
02922                 square_sum += v * (double)(v);
02923                 if (v != 0) n_nonzero++;
02924         }
02925 
02926         size_t n = size / step;
02927         double mean = sum / n;
02928 
02929 #ifdef _WIN32
02930         float sigma = (float)std::sqrt( _cpp_max(0.0,(square_sum - sum*sum / n)/(n-1)));
02931         n_nonzero = _cpp_max(1,n_nonzero);
02932         double sigma_nonzero = std::sqrt( _cpp_max(0,(square_sum  - sum*sum/n_nonzero)/(n_nonzero-1)));
02933 #else
02934         float sigma = (float)std::sqrt(std::max<double>(0.0,(square_sum - sum*sum / n)/(n-1)));
02935         n_nonzero = std::max<int>(1,n_nonzero);
02936         double sigma_nonzero = std::sqrt(std::max<double>(0,(square_sum  - sum*sum/n_nonzero)/(n_nonzero-1)));
02937 #endif  //_WIN32
02938         double mean_nonzero = sum / n_nonzero; // previous version overcounted! G2
02939 
02940         attr_dict["minimum"] = min;
02941         attr_dict["maximum"] = max;
02942         attr_dict["mean"] = (float)(mean);
02943         attr_dict["sigma"] = (float)(sigma);
02944         attr_dict["square_sum"] = (float)(square_sum);
02945         attr_dict["mean_nonzero"] = (float)(mean_nonzero);
02946         attr_dict["sigma_nonzero"] = (float)(sigma_nonzero);
02947         attr_dict["is_complex"] = (int) is_complex();
02948         attr_dict["is_complex_ri"] = (int) is_ri();
02949 
02950         flags &= ~EMDATA_NEEDUPD;
02951 
02952         if (rot_fp != 0)
02953         {
02954                 delete rot_fp; rot_fp = 0;
02955         }
02956 
02957         EXITFUNC;
02958 //      printf("done stat %f %f %f\n",(float)mean,(float)max,(float)sigma);
02959 }
02960 
02965 bool EMData::operator==(const EMData& that) const {
02966         if(this != &that) {
02967                 return false;
02968         }
02969         else {
02970                 return true;
02971         }
02972 }
02973 
02974 bool EMData::equal(const EMData& that) const {
02975         if (that.get_xsize() != nx || that.get_ysize() != ny || that.get_zsize() != nz ) return false;
02976 
02977         const float*  d1 = that.get_const_data();
02978         float* d2 = get_data();
02979 
02980         for(size_t i =0; i < get_size(); ++i,++d1,++d2) {
02981                 if ((*d1) != (*d2)) return false;
02982         }
02983 
02984 //      if(attr_dict != that.attr_dict) {
02985 //              return false;
02986 //      }
02987 
02988         return true;
02989 }
02990 
02991 EMData * EMAN::operator+(const EMData & em, float n)
02992 {
02993         EMData * r = em.copy();
02994         r->add(n);
02995         return r;
02996 }
02997 
02998 EMData * EMAN::operator-(const EMData & em, float n)
02999 {
03000         EMData* r = em.copy();
03001         r->sub(n);
03002         return r;
03003 }
03004 
03005 EMData * EMAN::operator*(const EMData & em, float n)
03006 {
03007         EMData* r = em.copy();
03008         r ->mult(n);
03009         return r;
03010 }
03011 
03012 EMData * EMAN::operator/(const EMData & em, float n)
03013 {
03014         EMData * r = em.copy();
03015         r->div(n);
03016         return r;
03017 }
03018 
03019 
03020 EMData * EMAN::operator+(float n, const EMData & em)
03021 {
03022         EMData * r = em.copy();
03023         r->add(n);
03024         return r;
03025 }
03026 
03027 EMData * EMAN::operator-(float n, const EMData & em)
03028 {
03029         EMData * r = em.copy();
03030         r->mult(-1.0f);
03031         r->add(n);
03032         return r;
03033 }
03034 
03035 EMData * EMAN::operator*(float n, const EMData & em)
03036 {
03037         EMData * r = em.copy();
03038         r->mult(n);
03039         return r;
03040 }
03041 
03042 EMData * EMAN::operator/(float n, const EMData & em)
03043 {
03044         EMData * r = em.copy();
03045         r->to_one();
03046         r->mult(n);
03047         r->div(em);
03048 
03049         return r;
03050 }
03051 
03052 EMData * EMAN::rsub(const EMData & em, float n)
03053 {
03054         return EMAN::operator-(n, em);
03055 }
03056 
03057 EMData * EMAN::rdiv(const EMData & em, float n)
03058 {
03059         return EMAN::operator/(n, em);
03060 }
03061 
03062 EMData * EMAN::operator+(const EMData & a, const EMData & b)
03063 {
03064         EMData * r = a.copy();
03065         r->add(b);
03066         return r;
03067 }
03068 
03069 EMData * EMAN::operator-(const EMData & a, const EMData & b)
03070 {
03071         EMData * r = a.copy();
03072         r->sub(b);
03073         return r;
03074 }
03075 
03076 EMData * EMAN::operator*(const EMData & a, const EMData & b)
03077 {
03078         EMData * r = a.copy();
03079         r->mult(b);
03080         return r;
03081 }
03082 
03083 EMData * EMAN::operator/(const EMData & a, const EMData & b)
03084 {
03085         EMData * r = a.copy();
03086         r->div(b);
03087         return r;
03088 }
03089 
03090 void EMData::set_xyz_origin(float origin_x, float origin_y, float origin_z)
03091 {
03092         attr_dict["origin_x"] = origin_x;
03093         attr_dict["origin_y"] = origin_y;
03094         attr_dict["origin_z"] = origin_z;
03095 }
03096 
03097 #if 0
03098 void EMData::calc_rcf(EMData * with, vector < float >&sum_array)
03099 {
03100         ENTERFUNC;
03101 
03102         int array_size = sum_array.size();
03103         float da = 2 * M_PI / array_size;
03104         float *dat = new float[array_size + 2];
03105         float *dat2 = new float[array_size + 2];
03106         int nx2 = nx * 9 / 20;
03107 
03108         float lim = 0;
03109         if (fabs(translation[0]) < fabs(translation[1])) {
03110                 lim = fabs(translation[1]);
03111         }
03112         else {
03113                 lim = fabs(translation[0]);
03114         }
03115 
03116         nx2 -= static_cast < int >(floor(lim));
03117 
03118         for (int i = 0; i < array_size; i++) {
03119                 sum_array[i] = 0;
03120         }
03121 
03122         float sigma = attr_dict["sigma"];
03123         float with_sigma = with->get_attr_dict().get("sigma");
03124 
03125         vector<float> vdata, vdata2;
03126         for (int i = 8; i < nx2; i += 6) {
03127                 vdata = calc_az_dist(array_size, 0, da, i, i + 6);
03128                 vdata2 = with->calc_az_dist(array_size, 0, da, i, i + 6);
03129                 Assert(vdata.size() <= array_size + 2);
03130                 Assert(cdata2.size() <= array_size + 2);
03131                 std::copy(vdata.begin(), vdata.end(), dat);
03132                 std::copy(vdata2.begin(), vdata2.end(), dat2);
03133 
03134                 EMfft::real_to_complex_1d(dat, dat, array_size);
03135                 EMfft::real_to_complex_1d(dat2, dat2, array_size);
03136 
03137                 for (int j = 0; j < array_size + 2; j += 2) {
03138                         float max = dat[j] * dat2[j] + dat[j + 1] * dat2[j + 1];
03139                         float max2 = dat[j + 1] * dat2[j] - dat2[j + 1] * dat[j];
03140                         dat[j] = max;
03141                         dat[j + 1] = max2;
03142                 }
03143 
03144                 EMfft::complex_to_real_1d(dat, dat, array_size);
03145                 float norm = array_size * array_size * (4.0f * sigma) * (4.0f * with_sigma);
03146 
03147                 for (int j = 0; j < array_size; j++) {
03148                         sum_array[j] += dat[j] * (float) i / norm;
03149                 }
03150         }
03151 
03152         if( dat )
03153         {
03154                 delete[]dat;
03155                 dat = 0;
03156         }
03157 
03158         if( dat2 )
03159         {
03160                 delete[]dat2;
03161                 dat2 = 0;
03162         }
03163         EXITFUNC;
03164 }
03165 
03166 #endif
03167 
03168 void EMData::add_incoherent(EMData * obj)
03169 {
03170         ENTERFUNC;
03171 
03172         if (!obj) {
03173                 LOGERR("NULL image");
03174                 throw NullPointerException("NULL image");
03175         }
03176 
03177         if (!obj->is_complex() || !is_complex()) {
03178                 throw ImageFormatException("complex images only");
03179         }
03180 
03181         if (!EMUtil::is_same_size(this, obj)) {
03182                 throw ImageFormatException("images not same size");
03183         }
03184 
03185         ri2ap();
03186         obj->ri2ap();
03187 
03188         float *dest = get_data();
03189         float *src = obj->get_data();
03190         size_t size = (size_t)nx * ny * nz;
03191         for (size_t j = 0; j < size; j += 2) {
03192 #ifdef  _WIN32
03193                 dest[j] = (float) _hypot(src[j], dest[j]);
03194 #else
03195                 dest[j] = (float) hypot(src[j], dest[j]);
03196 #endif  //_WIN32
03197                 dest[j + 1] = 0;
03198         }
03199 
03200         obj->update();
03201         update();
03202         EXITFUNC;
03203 }
03204 
03205 
03206 float EMData::calc_dist(EMData * second_img, int y_index) const
03207 {
03208         ENTERFUNC;
03209 
03210         if (get_ndim() != 1) {
03211                 throw ImageDimensionException("'this' image is 1D only");
03212         }
03213 
03214         if (second_img->get_xsize() != nx || ny != 1) {
03215                 throw ImageFormatException("image xsize not same");
03216         }
03217 
03218         if (y_index > second_img->get_ysize() || y_index < 0) {
03219                 return -1;
03220         }
03221 
03222         float ret = 0;
03223         float *d1 = get_data();
03224         float *d2 = second_img->get_data() + second_img->get_xsize() * y_index;
03225 
03226         for (int i = 0; i < nx; i++) {
03227                 ret += Util::square(d1[i] - d2[i]);
03228         }
03229         EXITFUNC;
03230         return std::sqrt(ret);
03231 }
03232 
03233 
03234 EMData * EMData::calc_fast_sigma_image( EMData* mask)
03235 {
03236         ENTERFUNC;
03237 
03238         bool maskflag = false;
03239         if (mask == 0) {
03240                 mask = new EMData(nx,ny,nz);
03241                 mask->process_inplace("testimage.circlesphere");
03242                 maskflag = true;
03243         }
03244 
03245         if (get_ndim() != mask->get_ndim() ) throw ImageDimensionException("The dimensions do not match");
03246 
03247         int mnx = mask->get_xsize(); int mny = mask->get_ysize(); int mnz = mask->get_zsize();
03248 
03249         if ( mnx > nx || mny > ny || mnz > nz)
03250                 throw ImageDimensionException("Can not calculate variance map using an image that is larger than this image");
03251 
03252         size_t P = 0;
03253         for(size_t i = 0; i < mask->get_size(); ++i){
03254                 if (mask->get_value_at(i) != 0){
03255                         ++P;
03256                 }
03257         }
03258         float normfac = 1.0f/(float)P;
03259 
03260 //      bool undoclip = false;
03261 
03262         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
03263 //      if ( mnx < nx || mny < ny || mnz < nz) {
03264         Region r;
03265         if (ny == 1) r = Region((mnx-nxc)/2,nxc);
03266         else if (nz == 1) r = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
03267         else r = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03268         mask->clip_inplace(r,0.0);
03269         //Region r((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03270         //mask->clip_inplace(r);
03271         //undoclip = true;
03272         //}
03273 
03274         // Here we generate the local average of the squares
03275         Region r2;
03276         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
03277         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
03278         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
03279         EMData* squared = get_clip(r2,get_edge_mean());
03280 
03281         EMData* tmp = squared->copy();
03282         Dict pow;
03283         pow["pow"] = 2.0f;
03284         squared->process_inplace("math.pow",pow);
03285         EMData* s = mask->convolute(squared);//ming, mask squared exchange
03286         squared->mult(normfac);
03287 
03288         EMData* m = mask->convolute(tmp);//ming, tmp mask exchange
03289         m->mult(normfac);
03290         m->process_inplace("math.pow",pow);
03291         delete tmp; tmp = 0;
03292         s->sub(*m);
03293         // Here we finally generate the standard deviation image
03294         s->process_inplace("math.sqrt");
03295 
03296 //      if ( undoclip ) {
03297 //              Region r((nx-mnx)/2, (ny-mny)/2, (nz-mnz)/2,mnx,mny,mnz);
03298 //              mask->clip_inplace(r);
03299 //      }
03300 
03301         if (maskflag) {
03302                 delete mask;
03303                 mask = 0;
03304         } else {
03305                 Region r;
03306                 if (ny == 1) r = Region((nxc-mnx)/2,mnx);
03307                 else if (nz == 1) r = Region((nxc-mnx)/2, (nyc-mny)/2,mnx,mny);
03308                 else r = Region((nxc-mnx)/2, (nyc-mny)/2,(nzc-mnz)/2,mnx,mny,mnz);
03309                 mask->clip_inplace(r);
03310         }
03311 
03312         delete squared;
03313         delete m;
03314 
03315         s->process_inplace("xform.phaseorigin.tocenter");
03316         Region r3;
03317         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
03318         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
03319         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
03320         s->clip_inplace(r3);
03321         EXITFUNC;
03322         return s;
03323 }
03324 
03325 //  The following code looks strange - does anybody know it?  Please let me know, pawel.a.penczek@uth.tmc.edu  04/09/06.
03326 // 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).
03327 EMData *EMData::calc_flcf(EMData * with)
03328 {
03329         ENTERFUNC;
03330         EMData *this_copy=this;
03331         this_copy=copy();
03332 
03333         int mnx = with->get_xsize(); int mny = with->get_ysize(); int mnz = with->get_zsize();
03334         int nxc = nx+mnx; int nyc = ny+mny; int nzc = nz+mnz;
03335 
03336         // Ones is a circular/spherical mask, consisting of 1s.
03337         EMData* ones = new EMData(mnx,mny,mnz);
03338         ones->process_inplace("testimage.circlesphere");
03339 
03340         // Get a copy of with, we will eventually resize it
03341         EMData* with_resized = with->copy();
03342         with_resized->process_inplace("normalize");
03343         with_resized->mult(*ones);
03344 
03345         EMData* s = calc_fast_sigma_image(ones);// Get the local sigma image
03346 
03347         Region r1;
03348         if (ny == 1) r1 = Region((mnx-nxc)/2,nxc);
03349         else if (nz == 1) r1 = Region((mnx-nxc)/2, (mny-nyc)/2,nxc,nyc);
03350         else r1 = Region((mnx-nxc)/2, (mny-nyc)/2,(mnz-nzc)/2,nxc,nyc,nzc);
03351         with_resized->clip_inplace(r1,0.0);
03352 
03353         Region r2;
03354         if (ny == 1) r2 = Region((nx-nxc)/2,nxc);
03355         else if (nz == 1) r2 = Region((nx-nxc)/2, (ny-nyc)/2,nxc,nyc);
03356         else r2 = Region((nx-nxc)/2, (ny-nyc)/2,(nz-nzc)/2,nxc,nyc,nzc);
03357         this_copy->clip_inplace(r2,0.0);
03358 
03359         EMData* corr = this_copy->calc_ccf(with_resized); // the ccf results should have same size as sigma
03360 
03361         corr->process_inplace("xform.phaseorigin.tocenter");
03362         Region r3;
03363         if (ny == 1) r3 = Region((nxc-nx)/2,nx);
03364         else if (nz == 1) r3 = Region((nxc-nx)/2, (nyc-ny)/2,nx,ny);
03365         else r3 = Region((nxc-nx)/2, (nyc-ny)/2,(nzc-nz)/2,nx,ny,nz);
03366         corr->clip_inplace(r3);
03367 
03368         corr->div(*s);
03369 
03370         delete with_resized; delete ones; delete this_copy; delete s;
03371         EXITFUNC;
03372         return corr;
03373 }
03374 
03375 EMData *EMData::convolute(EMData * with)
03376 {
03377         ENTERFUNC;
03378 
03379         EMData *f1 = do_fft();
03380         if (!f1) {
03381                 LOGERR("FFT returns NULL image");
03382                 throw NullPointerException("FFT returns NULL image");
03383         }
03384 
03385         f1->ap2ri();
03386 
03387         EMData *cf = 0;
03388         if (with) {
03389                 cf = with->do_fft();
03390                 if (!cf) {
03391                         LOGERR("FFT returns NULL image");
03392                         throw NullPointerException("FFT returns NULL image");
03393                 }
03394                 cf->ap2ri();
03395         }
03396         else {
03397                 cf = f1->copy();
03398         }
03399         //printf("cf_x=%d, f1y=%d, thisx=%d, withx=%d\n",cf->get_xsize(),f1->get_ysize(),this->get_xsize(),with->get_xsize());
03400         if (with && !EMUtil::is_same_size(f1, cf)) {
03401                 LOGERR("images not same size");
03402                 throw ImageFormatException("images not same size");
03403         }
03404 
03405         float *rdata1 = f1->get_data();
03406         float *rdata2 = cf->get_data();
03407         size_t cf_size = (size_t)cf->get_xsize() * cf->get_ysize() * cf->get_zsize();
03408 
03409         float re,im;
03410 
03411         for (size_t i = 0; i < cf_size; i += 2) {
03412                 re = rdata1[i] * rdata2[i] - rdata1[i + 1] * rdata2[i + 1];
03413                 im = rdata1[i + 1] * rdata2[i] + rdata1[i] * rdata2[i + 1];
03414                 rdata2[i]=re;
03415                 rdata2[i+1]=im;
03416         }
03417         cf->update();
03418         EMData *f2 = cf->do_ift();//ming change cf to cf_temp
03419         //printf("cf_x=%d, f2x=%d, thisx=%d, withx=%d\n",cf->get_xsize(),f2->get_xsize(),this->get_xsize(),with->get_xsize());
03420         if( cf )
03421         {
03422                 delete cf;
03423                 cf = 0;
03424         }
03425 
03426         if( f1 )
03427         {
03428                 delete f1;
03429                 f1=0;
03430         }
03431 
03432         EXITFUNC;
03433         return f2;
03434 }
03435 
03436 
03437 void EMData::common_lines(EMData * image1, EMData * image2,
03438                                                   int mode, int steps, bool horizontal)
03439 {
03440         ENTERFUNC;
03441 
03442         if (!image1 || !image2) {
03443                 throw NullPointerException("NULL image");
03444         }
03445 
03446         if (mode < 0 || mode > 2) {
03447                 throw OutofRangeException(0, 2, mode, "invalid mode");
03448         }
03449 
03450         if (!image1->is_complex()) {
03451                 image1 = image1->do_fft();
03452         }
03453         if (!image2->is_complex()) {
03454                 image2 = image2->do_fft();
03455         }
03456 
03457         image1->ap2ri();
03458         image2->ap2ri();
03459 
03460         if (!EMUtil::is_same_size(image1, image2)) {
03461                 throw ImageFormatException("images not same sizes");
03462         }
03463 
03464         int image2_nx = image2->get_xsize();
03465         int image2_ny = image2->get_ysize();
03466 
03467         int rmax = image2_ny / 4 - 1;
03468         int array_size = steps * rmax * 2;
03469         float *im1 = new float[array_size];
03470         float *im2 = new float[array_size];
03471         for (int i = 0; i < array_size; i++) {
03472                 im1[i] = 0;
03473                 im2[i] = 0;
03474         }
03475 
03476         set_size(steps * 2, steps * 2, 1);
03477 
03478         float *image1_data = image1->get_data();
03479         float *image2_data = image2->get_data();
03480 
03481         float da = M_PI / steps;
03482         float a = -M_PI / 2.0f + da / 2.0f;
03483         int jmax = 0;
03484 
03485         for (int i = 0; i < steps * 2; i += 2, a += da) {
03486                 float s1 = 0;
03487                 float s2 = 0;
03488                 int i2 = i * rmax;
03489                 int j = 0;
03490 
03491                 for (float r = 3.0f; r < rmax - 3.0f; j += 2, r += 1.0f) {
03492                         float x = r * cos(a);
03493                         float y = r * sin(a);
03494 
03495                         if (x < 0) {
03496                                 x = -x;
03497                                 y = -y;
03498                                 LOGERR("CCL ERROR %d, %f !\n", i, -x);
03499                         }
03500 
03501                         int k = (int) (floor(x) * 2 + floor(y + image2_ny / 2) * image2_nx);
03502                         int l = i2 + j;
03503                         float x2 = x - floor(x);
03504                         float y2 = y - floor(y);
03505 
03506                         im1[l] = Util::bilinear_interpolate(image1_data[k],
03507                                                                                                 image1_data[k + 2],
03508                                                                                                 image1_data[k + image2_nx],
03509                                                                                                 image1_data[k + 2 + image2_nx], x2, y2);
03510 
03511                         im2[l] = Util::bilinear_interpolate(image2_data[k],
03512                                                                                                 image2_data[k + 2],
03513                                                                                                 image2_data[k + image2_nx],
03514                                                                                                 image2_data[k + 2 + image2_nx], x2, y2);
03515 
03516                         k++;
03517 
03518                         im1[l + 1] = Util::bilinear_interpolate(image1_data[k],
03519                                                                                                         image1_data[k + 2],
03520                                                                                                         image1_data[k + image2_nx],
03521                                                                                                         image1_data[k + 2 + image2_nx], x2, y2);
03522 
03523                         im2[l + 1] = Util::bilinear_interpolate(image2_data[k],
03524                                                                                                         image2_data[k + 2],
03525                                                                                                         image2_data[k + image2_nx],
03526                                                                                                         image2_data[k + 2 + image2_nx], x2, y2);
03527 
03528                         s1 += Util::square_sum(im1[l], im1[l + 1]);
03529                         s2 += Util::square_sum(im2[l], im2[l + 1]);
03530                 }
03531 
03532                 jmax = j - 1;
03533                 float sqrt_s1 = std::sqrt(s1);
03534                 float sqrt_s2 = std::sqrt(s2);
03535 
03536                 int l = 0;
03537                 for (float r = 1; r < rmax; r += 1.0f) {
03538                         int i3 = i2 + l;
03539                         im1[i3] /= sqrt_s1;
03540                         im1[i3 + 1] /= sqrt_s1;
03541                         im2[i3] /= sqrt_s2;
03542                         im2[i3 + 1] /= sqrt_s2;
03543                         l += 2;
03544                 }
03545         }
03546         float * data = get_data();
03547 
03548         switch (mode) {
03549         case 0:
03550                 for (int m1 = 0; m1 < 2; m1++) {
03551                         for (int m2 = 0; m2 < 2; m2++) {
03552 
03553                                 if (m1 == 0 && m2 == 0) {
03554                                         for (int i = 0; i < steps; i++) {
03555                                                 int i2 = i * rmax * 2;
03556                                                 for (int j = 0; j < steps; j++) {
03557                                                         int l = i + j * steps * 2;
03558                                                         int j2 = j * rmax * 2;
03559                                                         data[l] = 0;
03560                                                         for (int k = 0; k < jmax; k++) {
03561                                                                 data[l] += im1[i2 + k] * im2[j2 + k];
03562                                                         }
03563                                                 }
03564                                         }
03565                                 }
03566                                 else {
03567                                         int steps2 = steps * m2 + steps * steps * 2 * m1;
03568 
03569                                         for (int i = 0; i < steps; i++) {
03570                                                 int i2 = i * rmax * 2;
03571                                                 for (int j = 0; j < steps; j++) {
03572                                                         int j2 = j * rmax * 2;
03573                                                         int l = i + j * steps * 2 + steps2;
03574                                                         data[l] = 0;
03575 
03576                                                         for (int k = 0; k < jmax; k += 2) {
03577                                                                 i2 += k;
03578                                                                 j2 += k;
03579                                                                 data[l] += im1[i2] * im2[j2];
03580                                                                 data[l] += -im1[i2 + 1] * im2[j2 + 1];
03581                                                         }
03582                                                 }
03583                                         }
03584                                 }
03585                         }
03586                 }
03587 
03588                 break;
03589         case 1:
03590                 for (int m1 = 0; m1 < 2; m1++) {
03591                         for (int m2 = 0; m2 < 2; m2++) {
03592                                 int steps2 = steps * m2 + steps * steps * 2 * m1;
03593                                 int p1_sign = 1;
03594                                 if (m1 != m2) {
03595                                         p1_sign = -1;
03596                                 }
03597 
03598                                 for (int i = 0; i < steps; i++) {
03599                                         int i2 = i * rmax * 2;
03600 
03601                                         for (int j = 0; j < steps; j++) {
03602                                                 int j2 = j * rmax * 2;
03603 
03604                                                 int l = i + j * steps * 2 + steps2;
03605                                                 data[l] = 0;
03606                                                 float a = 0;
03607 
03608                                                 for (int k = 0; k < jmax; k += 2) {
03609                                                         i2 += k;
03610                                                         j2 += k;
03611 
03612 #ifdef  _WIN32
03613                                                         float a1 = (float) _hypot(im1[i2], im1[i2 + 1]);
03614 #else
03615                                                         float a1 = (float) hypot(im1[i2], im1[i2 + 1]);
03616 #endif  //_WIN32
03617                                                         float p1 = atan2(im1[i2 + 1], im1[i2]);
03618                                                         float p2 = atan2(im2[j2 + 1], im2[j2]);
03619 
03620                                                         data[l] += Util::angle_sub_2pi(p1_sign * p1, p2) * a1;
03621                                                         a += a1;
03622                                                 }
03623 
03624                                                 data[l] /= (float)(a * M_PI / 180.0f);
03625                                         }
03626                                 }
03627                         }
03628                 }
03629 
03630                 break;
03631         case 2:
03632                 for (int m1 = 0; m1 < 2; m1++) {
03633                         for (int m2 = 0; m2 < 2; m2++) {
03634                                 int steps2 = steps * m2 + steps * steps * 2 * m1;
03635 
03636                                 for (int i = 0; i < steps; i++) {
03637                                         int i2 = i * rmax * 2;
03638 
03639                                         for (int j = 0; j < steps; j++) {
03640                                                 int j2 = j * rmax * 2;
03641                                                 int l = i + j * steps * 2 + steps2;
03642                                                 data[l] = 0;
03643 
03644                                                 for (int k = 0; k < jmax; k += 2) {
03645                                                         i2 += k;
03646                                                         j2 += k;
03647 #ifdef  _WIN32
03648                                                         data[l] += (float) (_hypot(im1[i2], im1[i2 + 1]) * _hypot(im2[j2], im2[j2 + 1]));
03649 #else
03650                                                         data[l] += (float) (hypot(im1[i2], im1[i2 + 1]) * hypot(im2[j2], im2[j2 + 1]));
03651 #endif  //_WIN32
03652                                                 }
03653                                         }
03654                                 }
03655                         }
03656                 }
03657 
03658                 break;
03659         default:
03660                 break;
03661         }
03662 
03663         if (horizontal) {
03664                 float *tmp_array = new float[ny];
03665                 for (int i = 1; i < nx; i++) {
03666                         for (int j = 0; j < ny; j++) {
03667                                 tmp_array[j] = get_value_at(i, j);
03668                         }
03669                         for (int j = 0; j < ny; j++) {
03670                                 set_value_at(i, j, 0, tmp_array[(j + i) % ny]);
03671                         }
03672                 }
03673                 if( tmp_array )
03674                 {
03675                         delete[]tmp_array;
03676                         tmp_array = 0;
03677                 }
03678         }
03679 
03680         if( im1 )
03681         {
03682                 delete[]im1;
03683                 im1 = 0;
03684         }
03685 
03686         if( im2 )
03687         {
03688                 delete im2;
03689                 im2 = 0;
03690         }
03691 
03692 
03693         image1->update();
03694         image2->update();
03695         if( image1 )
03696         {
03697                 delete image1;
03698                 image1 = 0;
03699         }
03700         if( image2 )
03701         {
03702                 delete image2;
03703                 image2 = 0;
03704         }
03705         update();
03706         EXITFUNC;
03707 }
03708 
03709 
03710 
03711 void EMData::common_lines_real(EMData * image1, EMData * image2,
03712                                                            int steps, bool horiz)
03713 {
03714         ENTERFUNC;
03715 
03716         if (!image1 || !image2) {
03717                 throw NullPointerException("NULL image");
03718         }
03719 
03720         if (!EMUtil::is_same_size(image1, image2)) {
03721                 throw ImageFormatException("images not same size");
03722         }
03723 
03724         int steps2 = steps * 2;
03725         int image_ny = image1->get_ysize();
03726         EMData *image1_copy = image1->copy();
03727         EMData *image2_copy = image2->copy();
03728 
03729         float *im1 = new float[steps2 * image_ny];
03730         float *im2 = new float[steps2 * image_ny];
03731 
03732         EMData *images[] = { image1_copy, image2_copy };
03733         float *ims[] = { im1, im2 };
03734 
03735         for (int m = 0; m < 2; m++) {
03736                 float *im = ims[m];
03737                 float a = M_PI / steps2;
03738                 Transform t(Dict("type","2d","alpha",-a));
03739                 for (int i = 0; i < steps2; i++) {
03740                         images[i]->transform(t);
03741                         float *data = images[i]->get_data();
03742 
03743                         for (int j = 0; j < image_ny; j++) {
03744                                 float sum = 0;
03745                                 for (int k = 0; k < image_ny; k++) {
03746                                         sum += data[j * image_ny + k];
03747                                 }
03748                                 im[i * image_ny + j] = sum;
03749                         }
03750 
03751                         float sum1 = 0;
03752                         float sum2 = 0;
03753                         for (int j = 0; j < image_ny; j++) {
03754                                 int l = i * image_ny + j;
03755                                 sum1 += im[l];
03756                                 sum2 += im[l] * im[l];
03757                         }
03758 
03759                         float mean = sum1 / image_ny;
03760                         float sigma = std::sqrt(sum2 / image_ny - sum1 * sum1);
03761 
03762                         for (int j = 0; j < image_ny; j++) {
03763                                 int l = i * image_ny + j;
03764                                 im[l] = (im[l] - mean) / sigma;
03765                         }
03766 
03767                         images[i]->update();
03768                         a += M_PI / steps;
03769                 }
03770         }
03771 
03772         set_size(steps2, steps2, 1);
03773         float *data1 = get_data();
03774 
03775         if (horiz) {
03776                 for (int i = 0; i < steps2; i++) {
03777                         for (int j = 0, l = i; j < steps2; j++, l++) {
03778                                 if (l == steps2) {
03779                                         l = 0;
03780                                 }
03781 
03782                                 float sum = 0;
03783                                 for (int k = 0; k < image_ny; k++) {
03784                                         sum += im1[i * image_ny + k] * im2[l * image_ny + k];
03785                                 }
03786                                 data1[i + j * steps2] = sum;
03787                         }
03788                 }
03789         }
03790         else {
03791                 for (int i = 0; i < steps2; i++) {
03792                         for (int j = 0; j < steps2; j++) {
03793                                 float sum = 0;
03794                                 for (int k = 0; k < image_ny; k++) {
03795                                         sum += im1[i * image_ny + k] * im2[j * image_ny + k];
03796                                 }
03797                                 data1[i + j * steps2] = sum;
03798                         }
03799                 }
03800         }
03801 
03802         update();
03803 
03804         if( image1_copy )
03805         {
03806                 delete image1_copy;
03807                 image1_copy = 0;
03808         }
03809 
03810         if( image2_copy )
03811         {
03812                 delete image2_copy;
03813                 image2_copy = 0;
03814         }
03815 
03816         if( im1 )
03817         {
03818                 delete[]im1;
03819                 im1 = 0;
03820         }
03821 
03822         if( im2 )
03823         {
03824                 delete[]im2;
03825                 im2 = 0;
03826         }
03827         EXITFUNC;
03828 }
03829 
03830 
03831 void EMData::cut_slice(const EMData *const map, const Transform& transform, bool interpolate)
03832 {
03833         ENTERFUNC;
03834 
03835         if (!map) throw NullPointerException("NULL image");
03836         // These restrictions should be ultimately restricted so that all that matters is get_ndim() = (map->get_ndim() -1)
03837         if ( get_ndim() != 2 ) throw ImageDimensionException("Can not call cut slice on an image that is not 2D");
03838         if ( map->get_ndim() != 3 ) throw ImageDimensionException("Can not cut slice from an image that is not 3D");
03839         // Now check for complex images - this is really just being thorough
03840         if ( is_complex() ) throw ImageFormatException("Can not call cut slice on an image that is complex");
03841         if ( map->is_complex() ) throw ImageFormatException("Can not cut slice from a complex image");
03842 
03843 
03844         float *sdata = map->get_data();
03845         float *ddata = get_data();
03846 
03847         int map_nx = map->get_xsize();
03848         int map_ny = map->get_ysize();
03849         int map_nz = map->get_zsize();
03850         int map_nxy = map_nx * map_ny;
03851 
03852         int ymax = ny/2;
03853         if ( ny % 2 == 1 ) ymax += 1;
03854         int xmax = nx/2;
03855         if ( nx % 2 == 1 ) xmax += 1;
03856         for (int y = -ny/2; y < ymax; y++) {
03857                 for (int x = -nx/2; x < xmax; x++) {
03858                         Vec3f coord(x,y,0);
03859                         Vec3f soln = transform*coord;
03860 
03861 //                      float xx = (x+pretrans[0]) * (*ort)[0][0] +  (y+pretrans[1]) * (*ort)[0][1] + pretrans[2] * (*ort)[0][2] + posttrans[0];
03862 //                      float yy = (x+pretrans[0]) * (*ort)[1][0] +  (y+pretrans[1]) * (*ort)[1][1] + pretrans[2] * (*ort)[1][2] + posttrans[1];
03863 //                      float zz = (x+pretrans[0]) * (*ort)[2][0] +  (y+pretrans[1]) * (*ort)[2][1] + pretrans[2] * (*ort)[2][2] + posttrans[2];
03864 
03865 
03866 //                      xx += map_nx/2;
03867 //                      yy += map_ny/2;
03868 //                      zz += map_nz/2;
03869 
03870                         float xx = soln[0]+map_nx/2;
03871                         float yy = soln[1]+map_ny/2;
03872                         float zz = soln[2]+map_nz/2;
03873 
03874                         int l = (x+nx/2) + (y+ny/2) * nx;
03875 
03876                         float t = xx - floor(xx);
03877                         float u = yy - floor(yy);
03878                         float v = zz - floor(zz);
03879 
03880                         if (xx < 0 || yy < 0 || zz < 0 ) {
03881                                 ddata[l] = 0;
03882                                 continue;
03883                         }
03884                         if (interpolate) {
03885                                 if ( xx > map_nx - 1 || yy > map_ny - 1 || zz > map_nz - 1) {
03886                                         ddata[l] = 0;
03887                                         continue;
03888                                 }
03889                                 int k = (int) (Util::fast_floor(xx) + Util::fast_floor(yy) * map_nx + Util::fast_floor(zz) * map_nxy);
03890 
03891 
03892                                 if (xx < (map_nx - 1) && yy < (map_ny - 1) && zz < (map_nz - 1)) {
03893                                         ddata[l] = Util::trilinear_interpolate(sdata[k],
03894                                                                 sdata[k + 1], sdata[k + map_nx],sdata[k + map_nx + 1],
03895                                                                 sdata[k + map_nxy], sdata[k + map_nxy + 1], sdata[k + map_nx + map_nxy],
03896                                                                 sdata[k + map_nx + map_nxy + 1],t, u, v);
03897                                 }
03898                                 else if ( xx == (map_nx - 1) && yy == (map_ny - 1) && zz == (map_nz - 1) ) {
03899                                         ddata[l] += sdata[k];
03900                                 }
03901                                 else if ( xx == (map_nx - 1) && yy == (map_ny - 1) ) {
03902                                         ddata[l] +=     Util::linear_interpolate(sdata[k], sdata[k + map_nxy],v);
03903                                 }
03904                                 else if ( xx == (map_nx - 1) && zz == (map_nz - 1) ) {
03905                                         ddata[l] += Util::linear_interpolate(sdata[k], sdata[k + map_nx],u);
03906                                 }
03907                                 else if ( yy == (map_ny - 1) && zz == (map_nz - 1) ) {
03908                                         ddata[l] += Util::linear_interpolate(sdata[k], sdata[k + 1],t);
03909                                 }
03910                                 else if ( xx == (map_nx - 1) ) {
03911                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + map_nx], sdata[k + map_nxy], sdata[k + map_nxy + map_nx],u,v);
03912                                 }
03913                                 else if ( yy == (map_ny - 1) ) {
03914                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + 1], sdata[k + map_nxy], sdata[k + map_nxy + 1],t,v);
03915                                 }
03916                                 else if ( zz == (map_nz - 1) ) {
03917                                         ddata[l] += Util::bilinear_interpolate(sdata[k], sdata[k + 1], sdata[k + map_nx], sdata[k + map_nx + 1],t,u);
03918                                 }
03919 
03920 //                              if (k >= map->get_size()) {
03921 //                                      cout << xx << " " << yy << " " <<  zz << " " << endl;
03922 //                                      cout << k << " " << get_size() << endl;
03923 //                                      cout << get_xsize() << " " << get_ysize() << " " << get_zsize() << endl;
03924 //                                      throw;
03925 //                                      }
03926 //
03927 //                              ddata[l] = Util::trilinear_interpolate(sdata[k],
03928 //                                              sdata[k + 1], sdata[k + map_nx],sdata[k + map_nx + 1],
03929 //                                              sdata[k + map_nxy], sdata[k + map_nxy + 1], sdata[k + map_nx + map_nxy],
03930 //                                              sdata[k + map_nx + map_nxy + 1],t, u, v);
03931                         }
03932                         else {
03933                                 if ( xx > map_nx - 1 || yy > map_ny - 1 || zz > map_nz - 1) {
03934                                         ddata[l] = 0;
03935                                         continue;
03936                                 }
03937                                 size_t k = Util::round(xx) + Util::round(yy) * map_nx + Util::round(zz) * (size_t)map_nxy;
03938                                 ddata[l] = sdata[k];
03939                         }
03940 
03941                 }
03942         }
03943 
03944         update();
03945 
03946         EXITFUNC;
03947 }
03948 
03949 EMData *EMData::unwrap_largerR(int r1,int r2,int xs, float rmax_f) {
03950         float *d,*dd;
03951         int do360=2;
03952         int rmax = (int)(rmax_f+0.5f);
03953         unsigned long i;
03954         unsigned int nvox=get_xsize()*get_ysize();//ming
03955         float maxmap=0.0f, minmap=0.0f;
03956         float temp=0.0f, diff_den=0.0f, norm=0.0f;
03957         float cut_off_va =0.0f;
03958 
03959         d=get_data();
03960         maxmap=-1000000.0f;
03961         minmap=1000000.0f;
03962         for (i=0;i<nvox;i++){
03963                 if(d[i]>maxmap) maxmap=d[i];
03964                 if(d[i]<minmap) minmap=d[i];
03965         }
03966         diff_den = maxmap-minmap;
03967         for(i=0;i<nvox;i++) {
03968                 temp = (d[i]-minmap)/diff_den;
03969                 if(cut_off_va != 0.0) {               // cut off the lowerset ?% noisy information
03970                         if(temp < cut_off_va)
03971                                 d[i] = 0.0f;                   // set the empty part density=0.0
03972                         else
03973                                 d[i] = temp-cut_off_va;
03974                 }
03975                 else    d[i] = temp;
03976         }
03977 
03978         for(i=0;i<nvox;i++) {
03979                 temp=d[i];
03980                 norm += temp*temp;
03981         }
03982         for(i=0;i<nvox;i++)             d[i] /= norm;                      //  y' = y/norm(y)
03983 
03984         if (xs<1) {
03985                 xs = (int) floor(do360*M_PI*get_ysize()/4); // ming
03986                 xs=Util::calc_best_fft_size(xs); // ming
03987         }
03988         if (r1<0) r1=0;
03989         float maxext=ceil(0.6f*std::sqrt((float)(get_xsize()*get_xsize()+get_ysize()*get_ysize())));// ming add std::
03990 
03991         if (r2<r1) r2=(int)maxext;
03992         EMData *ret = new EMData;
03993 
03994         ret->set_size(xs,r2+1,1);
03995 
03996         dd=ret->get_data();
03997 
03998         for (int i=0; i<xs; i++) {
03999                 float si=sin(i*M_PI*2/xs);
04000                 float co=cos(i*M_PI*2/xs);
04001                 for (int r=0; r<=maxext; r++) {
04002                         float x=(r+r1)*co+get_xsize()/2; // ming
04003                         float y=(r+r1)*si+get_ysize()/2; // ming
04004                         if(x<0.0 || x>=get_xsize()-1.0 || y<0.0 || y>=get_ysize()-1.0 || r>rmax){    //Ming , ~~~~ rmax need pass here
04005                                 for(;r<=r2;r++)                                   // here r2=MAXR
04006                                         dd[i+r*xs]=0.0;
04007                         break;
04008                     }
04009                         int x1=(int)floor(x);
04010                         int y1=(int)floor(y);
04011                         float t=x-x1;
04012                         float u=y-y1;
04013                         float f11= d[x1+y1*get_xsize()]; // ming
04014                         float f21= d[(x1+1)+y1*get_xsize()]; // ming
04015                         float f12= d[x1+(y1+1)*get_xsize()]; // ming
04016                         float f22= d[(x1+1)+(y1+1)*get_xsize()]; // ming
04017                         dd[i+r*xs] = (1-t)*(1-u)*f11+t*(1-u)*f21+t*u*f22+(1-t)*u*f12;
04018                 }
04019         }
04020         update();
04021         ret->update();
04022         return ret;
04023 }
04024 
04025 
04026 EMData *EMData::oneDfftPolar(int size, float rmax, float MAXR){         // sent MAXR value here later!!
04027         float *pcs=get_data();
04028         EMData *imagepcsfft = new EMData;
04029         imagepcsfft->set_size((size+2), (int)MAXR+1, 1);
04030         float *d=imagepcsfft->get_data();
04031 
04032         EMData *data_in=new EMData;
04033         data_in->set_size(size,1,1);
04034         float *in=data_in->get_data();
04035 
04036         for(int row=0; row<=(int)MAXR; ++row){
04037                 if(row<=(int)rmax) {
04038                         for(int i=0; i<size;++i)        in[i] = pcs[i+row*size]; // ming
04039                         data_in->set_complex(false);
04040                         data_in->do_fft_inplace();
04041                         for(int j=0;j<size+2;j++)  d[j+row*(size+2)]=in[j];
04042                 }
04043                 else for(int j=0;j<size+2;j++) d[j+row*(size+2)]=0.0;
04044         }
04045         imagepcsfft->update();
04046         delete data_in;
04047         return imagepcsfft;
04048 }
04049 
04050 void EMData::uncut_slice(EMData * const map, const Transform& transform) const
04051 {
04052         ENTERFUNC;
04053 
04054         if (!map) throw NullPointerException("NULL image");
04055         // These restrictions should be ultimately restricted so that all that matters is get_ndim() = (map->get_ndim() -1)
04056         if ( get_ndim() != 2 ) throw ImageDimensionException("Can not call cut slice on an image that is not 2D");
04057         if ( map->get_ndim() != 3 ) throw ImageDimensionException("Can not cut slice from an image that is not 3D");
04058         // Now check for complex images - this is really just being thorough
04059         if ( is_complex() ) throw ImageFormatException("Can not call cut slice on an image that is complex");
04060         if ( map->is_complex() ) throw ImageFormatException("Can not cut slice from a complex image");
04061 
04062 //      Transform3D r( 0, 0, 0); // EMAN by default
04063 //      if (!ort) {
04064 //              ort = &r;
04065 //      }
04066 
04067         float *ddata = map->get_data();
04068         float *sdata = get_data();
04069 
04070         int map_nx = map->get_xsize();
04071         int map_ny = map->get_ysize();
04072         int map_nz = map->get_zsize();
04073         int map_nxy = map_nx * map_ny;
04074         float map_nz_round_limit = (float) map_nz-0.5f;
04075         float map_ny_round_limit = (float) map_ny-0.5f;
04076         float map_nx_round_limit = (float) map_nx-0.5f;
04077 /*
04078         Vec3f posttrans = ort->get_posttrans();
04079         Vec3f pretrans = ort->get_pretrans();*/
04080 
04081         int ymax = ny/2;
04082         if ( ny % 2 == 1 ) ymax += 1;
04083         int xmax = nx/2;
04084         if ( nx % 2 == 1 ) xmax += 1;
04085         for (int y = -ny/2; y < ymax; y++) {
04086                 for (int x = -nx/2; x < xmax; x++) {
04087                         Vec3f coord(x,y,0);
04088                         Vec3f soln = transform*coord;
04089 //                      float xx = (x+pretrans[0]) * (*ort)[0][0] +  (y+pretrans[1]) * (*ort)[0][1] + pretrans[2] * (*ort)[0][2] + posttrans[0];
04090 //                      float yy = (x+pretrans[0]) * (*ort)[1][0] +  (y+pretrans[1]) * (*ort)[1][1] + pretrans[2] * (*ort)[1][2] + posttrans[1];
04091 //                      float zz = (x+pretrans[0]) * (*ort)[2][0] +  (y+pretrans[1]) * (*ort)[2][1] + pretrans[2] * (*ort)[2][2] + posttrans[2];
04092 //
04093 //                      xx += map_nx/2;
04094 //                      yy += map_ny/2;
04095 //                      zz += map_nz/2;
04096 //
04097                         float xx = soln[0]+map_nx/2;
04098                         float yy = soln[1]+map_ny/2;
04099                         float zz = soln[2]+map_nz/2;
04100 
04101                         // These 0.5 offsets are here because the round function rounds to the nearest whole number.
04102                         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;
04103 
04104                         size_t k = Util::round(xx) + Util::round(yy) * map_nx + Util::round(zz) * (size_t)map_nxy;
04105                         int l = (x+nx/2) + (y+ny/2) * nx;
04106                         ddata[k] = sdata[l];
04107                 }
04108         }
04109 
04110         map->update();
04111         EXITFUNC;
04112 }
04113 
04114 EMData *EMData::extract_box(const Transform& cs, const Region& r)
04115 {
04116         vector<float> cs_matrix = cs.get_matrix();
04117         
04118         EMData* box = new EMData();
04119         box->set_size((r.get_width()-r.x_origin()), (r.get_height()-r.y_origin()), (r.get_depth()-r.z_origin()));
04120         int box_nx = box->get_xsize();
04121         int box_ny = box->get_ysize();
04122         int box_nxy = box_nx*box_ny;
04123         float* bdata = box->get_data();
04124         float* ddata = get_data();
04125         
04126         for (int x = r.x_origin(); x < r.get_width(); x++) {
04127                 for (int y = r.y_origin(); y < r.get_height(); y++) {
04128                         for (int z = r.z_origin(); z < r.get_depth(); z++) {
04129                                 //float xb = cs_matrix[0]*x + cs_matrix[1]*y + cs_matrix[2]*z + cs_matrix[3];
04130                                 //float yb = cs_matrix[4]*x + cs_matrix[5]*y + cs_matrix[6]*z + cs_matrix[7];
04131                                 //float zb = cs_matrix[8]*x + cs_matrix[9]*y + cs_matrix[10]*z + cs_matrix[11];
04132                                 float xb = cs_matrix[0]*x + y*cs_matrix[4] + z*cs_matrix[8] + cs_matrix[3];
04133                                 float yb = cs_matrix[1]*x + y*cs_matrix[5] + z*cs_matrix[9] + cs_matrix[7];
04134                                 float zb = cs_matrix[2]*x + y*cs_matrix[6] + z*cs_matrix[10] + cs_matrix[11];
04135                                 float t = xb - Util::fast_floor(xb);
04136                                 float u = yb - Util::fast_floor(yb);
04137                                 float v = zb - Util::fast_floor(zb);
04138                                 
04139                                 //cout << x << " " << y << " " << z << " Box " << xb << " " << yb << " " << zb << endl;
04140                                 int l = (x - r.x_origin()) + (y - r.y_origin())*box_nx + (z - r.z_origin())*box_nxy;
04141                                 int k = (int) (Util::fast_floor(xb) + Util::fast_floor(yb) * nx + Util::fast_floor(zb) * nxy);
04142                                 //cout << k << " " << l << endl;
04143                                 if ( xb > nx - 1 || yb > ny - 1 || zb > nz - 1) {
04144                                         bdata[l] = 0;
04145                                         continue;
04146                                 }
04147                                 if (xb < 0 || yb < 0 || zb < 0){
04148                                         bdata[l] = 0;
04149                                         continue;
04150                                 }
04151 
04152                                 if (xb < (nx - 1) && yb < (ny - 1) && zb < (nz - 1)) {
04153                                         bdata[l] = Util::trilinear_interpolate(ddata[k], ddata[k + 1], ddata[k + nx],ddata[k + nx + 1], ddata[k + nxy], ddata[k + nxy + 1], ddata[k + nx + nxy], ddata[k + nx + nxy + 1],t, u, v);
04154                                 }
04155                         }
04156                 }
04157         }
04158         
04159         return box;
04160 }
04161 
04162 void EMData::save_byteorder_to_dict(ImageIO * imageio)
04163 {
04164         string image_endian = "ImageEndian";
04165         string host_endian = "HostEndian";
04166 
04167         if (imageio->is_image_big_endian()) {
04168                 attr_dict[image_endian] = "big";
04169         }
04170         else {
04171                 attr_dict[image_endian] = "little";
04172         }
04173 
04174         if (ByteOrder::is_host_big_endian()) {
04175                 attr_dict[host_endian] = "big";
04176         }
04177         else {
04178                 attr_dict[host_endian] = "little";
04179         }
04180 }
04181 
04182 EMData* EMData::compute_missingwedge(float wedgeangle, float start, float stop)
04183 {               
04184         EMData* test = new EMData();
04185         test->set_size(nx,ny,nz);
04186         
04187         float ratio = tan((90.0f-wedgeangle)*M_PI/180.0f);
04188         
04189         int offset_i = 2*int(start*nz/2);
04190         int offset_f = int(stop*nz/2);
04191         
04192         int step = 0;
04193         float sum = 0.0;
04194         double square_sum = 0.0;
04195         for (int j = 0; j < offset_f; j++){
04196                 for (int k = offset_i; k < offset_f; k++) {
04197                         for (int i = 0; i < nx; i+=2) {
04198                                 if (i < int(k*ratio)) {
04199                                         test->set_value_at(i, j, k, 1.0);
04200                                         float v = std::sqrt(pow(get_value_at_wrap(i, j, k),2) + pow(get_value_at_wrap(i+1, j, k),2));
04201                                         sum += v;
04202                                         square_sum += v * (double)(v);
04203                                         step++;
04204                                 }
04205                         }
04206                 }
04207         }
04208         
04209         float mean = sum / step;
04210         
04211         #ifdef _WIN32
04212         float sigma = (float)std::sqrt( _cpp_max(0.0,(square_sum - sum*mean)/(step-1)));
04213         #else
04214         float sigma = (float)std::sqrt(std::max<double>(0.0,(square_sum - sum*mean)/(step-1)));
04215         #endif  //_WIN32
04216         
04217         cout << "Mean sqr wedge amp " << mean << " Sigma Squ wedge Amp " << sigma << endl;
04218         set_attr("spt_wedge_mean", mean);
04219         set_attr("spt_wedge_sigma", sigma);
04220         
04221         return test;
04222 }
04223 
04224 
04225 
04226 
04227         
04228         

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