aligner.cpp File Reference

#include "emfft.h"
#include "cmp.h"
#include "aligner.h"
#include "emdata.h"
#include "processor.h"
#include "util.h"
#include "symmetry.h"
#include <gsl/gsl_multimin.h>
#include "plugins/aligner_template.h"

Include dependency graph for aligner.cpp:

Go to the source code of this file.

Defines

#define EMAN2_ALIGNER_DEBUG   0
 
Id
aligner.cpp,v 1.225 2011/03/07 18:12:17 john Exp


Functions

static double refalifn (const gsl_vector *v, void *params)
static double refalifnfast (const gsl_vector *v, void *params)
static Transform refalin3d_perturbquat (const Transform *const t, const float &spincoeff, const float &n0, const float &n1, const float &n2, const float &x, const float &y, const float &z)
static double refalifn3dquat (const gsl_vector *v, void *params)
float frm_2d_Align (EMData *this_img, EMData *to, float *frm2dhhat, EMData *selfpcsfft, int p_max_input, int rsize, float &com_this_x, float &com_this_y, float &com_with_x, float &com_with_y, const string &cmp_name, const Dict &cmp_params)
void EMAN::dump_aligners ()
map< string, vector< string > > EMAN::dump_aligners_list ()


Define Documentation

#define EMAN2_ALIGNER_DEBUG   0

Id
aligner.cpp,v 1.225 2011/03/07 18:12:17 john Exp

Definition at line 54 of file aligner.cpp.


Function Documentation

float @0::frm_2d_Align ( EMData this_img,
EMData to,
float *  frm2dhhat,
EMData selfpcsfft,
int  p_max_input,
int  rsize,
float &  com_this_x,
float &  com_this_y,
float &  com_with_x,
float &  com_with_y,
const string &  cmp_name,
const Dict cmp_params 
) [static]

Definition at line 2178 of file aligner.cpp.

References EMAN::EMData::cmp(), EMAN::EMData::copy(), EMAN::EMData::do_ift(), EMAN::EMData::get_data(), EMAN::EMData::get_ysize(), in, EMAN::EMData::rotate(), EMAN::EMData::set_attr(), EMAN::Transform::set_trans(), and EMAN::EMData::translate().

Referenced by EMAN::FRM2DAligner::align().

02179 {
02180         int size=rsize;
02181         float dx,dy;
02182         int bw=size/2;
02183         int MAXR=this_img->get_ysize()/2;
02184         //int MAXR=size;
02185         unsigned long tsize=2*size;
02186         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02187         unsigned long index0=0;
02188         int i=0, j=0, m=0, n=0, r=0;
02189         int loop_rho=0, rho_best=0;
02190 
02191         float* gnr2   = new float[size*2];
02192         float* maxcor = new float[size+1];                  // MAXR need change
02193 
02194         int p_max=p_max_input;
02195         float* result = new float[5*(p_max+1)];
02196         float* cr=new float[size*(bw+1)];
02197         float* ci=new float[size*(bw+1)];
02198         EMData *data_in=new EMData;
02199         data_in->set_complex(true);
02200         data_in->set_fftodd(false);
02201         data_in->set_ri(true);
02202         data_in->set_size(size+2,size,1);
02203         float *in=data_in->get_data();
02204 
02205         float *self_sampl_fft = selfpcsfft->get_data(); // ming f(r)
02206 
02207         float maxcor_sofar=0.0f;
02208         int p=0;
02209 
02210         for(p=0; p<=p_max; ++p){
02211                 ind1=p*size*bw;
02212                 for (i=0;i<size;++i)
02213                         for (j=0;j<bw+1;++j){
02214                                 cr[i*(bw+1)+j]=0.0;
02215                                 ci[i*(bw+1)+j]=0.0;
02216                         }
02217         for(n=0;n<bw;++n){                                // loop for n
02218                 ind2=(ind1+n);
02219                 index0=n*(bw+1);
02220                         for(r=0;r<=MAXR;++r) {
02221                         ind3=(ind2+r*bw)*size;
02222                         for(m=0;m<size;m++){              // take back hat{h(n,r,p)}(m)
02223                                 ind4=(ind3+m)*2;
02224                                     ind41=ind4+1;
02225                                     gnr2[2*m]=frm2dhhat[ind4];
02226                                     gnr2[2*m+1]=frm2dhhat[ind41];
02227                                 }
02228                         for(m=0;m<bw;++m){
02229                                         float tempr=self_sampl_fft[2*m+r*(size+2)]*r;
02230                                 float tempi=self_sampl_fft[2*m+1+r*(size+2)]*r;
02231                                 float gnr2_r=gnr2[2*m];
02232                                 float gnr2_i=gnr2[2*m+1];
02233                                 cr[n*(bw+1)+m]+=gnr2_r*tempr+gnr2_i*tempi;
02234                                         ci[n*(bw+1)+m]+=gnr2_i*tempr-gnr2_r*tempi;
02235                                         if(n!=0){                                       // m,-n
02236                                         if(m!= 0){
02237                                                 int ssize=tsize-2*m;    // ssize = 2*size-2m
02238                                                 int ssize1=ssize+1;
02239                                                 float gnr2_r=gnr2[ssize];
02240                                                 float gnr2_i=gnr2[ssize1];
02241                                                         cr[(size-n)*(bw+1)+m]+=gnr2_r*tempr-gnr2_i*tempi;
02242                                                 ci[(size-n)*(bw+1)+m]-=gnr2_i*tempr+gnr2_r*tempi;
02243                                         }
02244                                                 else{
02245                                                         cr[(size-n)*(bw+1)+m]+=*(gnr2)*tempr-*(gnr2+1)*tempi;
02246                                                         ci[(size-n)*(bw+1)+m]-=*(gnr2+1)*tempr+*(gnr2)*tempi;
02247                                                 }
02248                                 }
02249                                 }
02250                         }
02251         }
02252         for (int cii=0; cii<size*(bw+1);++cii){
02253                         in[2*cii]=cr[cii];
02254                         in[2*cii+1]=ci[cii];
02255                         //printf("cii=%d,in[2i+1]=%f\n",cii, cr[cii]);
02256         }
02257 
02258         EMData *data_out;
02259                 data_out=data_in->do_ift();
02260                 float *c=data_out->get_data();
02261                 float tempr=0.0f, corre_fcs=999.0f;
02262 
02263             int n_best=0, m_best=0;
02264         float temp=-100.0f;
02265                 for(n=0;n<size;++n){// move Tri_2D to Tri = c(phi,phi';rho)
02266                         for(m=0;m<size;++m){
02267                                 temp=c[n*size+m];
02268                                 if(temp>tempr) {
02269                                         tempr=temp;
02270                                         n_best=n;
02271                                         m_best=m;
02272                                 }
02273                         }
02274                 }
02275                 delete data_out;
02276 
02277                 float corre,Phi2,Phi,Tx,Ty,Vx, Vy;
02278 
02279                 //for (n_best=0;n_best<bw;n_best++)
02280                   //  for (m_best=0;m_best<2*bw;m_best++){
02281                 //n_best=0;
02282                 //m_best=70;
02283                 Phi2=n_best*M_PI/bw;  // ming this is reference image rotation angle
02284                 Phi=m_best*M_PI/bw;   // ming this is particle image rotation angle
02285                 Vx=p*cos(Phi);//should use the angle of the centered one
02286                 Vy=-p*sin(Phi);
02287                 Tx=Vx+(floor(com_this_x+0.5f)-floor(com_with_x+0.5f));
02288                 Ty=Vy+(floor(com_this_y+0.5f)-floor(com_with_y+0.5f));
02289 
02290                 dx=-Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image,
02291                 dy=-Ty; // need to convert to raw image
02292 
02293                 EMData *this_tmp=this_img->copy();//ming change to to
02294                 this_tmp->rotate(-(Phi2-Phi)*180.0f,0.0f,0.0f);
02295                 this_tmp->translate(dx,dy,0.0);
02296 
02297                 corre=this_tmp->cmp(cmp_name,to,cmp_params);
02298                 //printf("corre=%f\n",corre);
02299                 delete this_tmp;
02300                 if(corre<=corre_fcs) { //ming, cmp use smaller value stands for more similarity
02301                         corre_fcs=corre;
02302                         result[0+5*p] = float(p);       // rho
02303                         result[1+5*p] = corre;          // correlation_fcs
02304                         result[2+5*p] = (Phi2-Phi)*180.0f;      // rotation angle
02305                         result[3+5*p] = Tx;             // Translation_x
02306                         result[4+5*p] = Ty;             // Translation_y
02307                 }
02308                 maxcor[p]=corre_fcs;                            //  maximum correlation for current rho
02309                 if(corre_fcs<maxcor_sofar) {
02310                         maxcor_sofar=corre_fcs;                 // max correlation up to current rho
02311                     rho_best=p;                         // the rho value with maxinum correlation value
02312                 }
02313                 if(p>=4){
02314                         if(maxcor[p] < maxcor[p-1] && maxcor[p-1] < maxcor[p-2]&& maxcor[p-2] < maxcor[p-3] && maxcor[p-3] < maxcor[p-4]){
02315                                 loop_rho=1;
02316                                 break; //exit p loop
02317                         }
02318                 }
02319         } // end for p
02320         //}//test my method
02321         if(loop_rho == 1)
02322                 p=p+1;
02323         int rb5=5*rho_best;
02324         float fsc      = result[1+rb5];
02325         float ang_keep = result[2+rb5];
02326         float Tx       = result[3+rb5];
02327         float Ty       = result[4+rb5];
02328         delete[] gnr2;
02329         delete[] maxcor;
02330         delete[] result;
02331         delete cr;
02332         cr=0;
02333         delete ci;
02334         ci=0;
02335         delete data_in; // ming add
02336         dx = -Tx;               // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image,
02337         dy = -Ty;               // need to convert to raw image
02338         this_img->rotate(-ang_keep,0,0); // ming change this to this_img??
02339         this_img->translate(dx,dy,0.0); // ming change this to this_img
02340 
02341 
02342         Transform  tsoln(Dict("type","2d","alpha",ang_keep));
02343         tsoln.set_trans(dx,dy);
02344         this_img->set_attr("xform.align2d",&tsoln);
02345 #ifdef DEBUG
02346         float fsc_best=this_img->cmp(cmp_name,to,cmp_params);
02347         printf("rho_best=%d fsc=%f fsc_best=%f dx=%f dy=%f ang_keep=%f com_withx=%f com_selfx=%f com_selfy=%f\n",rho_best,fsc,fsc_best,dx,dy,ang_keep,com_with_x,com_this_x,com_this_y);
02348 #endif
02349         return fsc;     // return the fsc coefficients
02350 } // FRM2D aligner sub_class

static double refalifn ( const gsl_vector *  v,
void *  params 
) [static]

Definition at line 1310 of file aligner.cpp.

References EMAN::Cmp::cmp(), EMAN::EMData::process(), t, x, and y.

Referenced by EMAN::RefineAligner::align().

01311 {
01312         Dict *dict = (Dict *) params;
01313 
01314         double x = gsl_vector_get(v, 0);
01315         double y = gsl_vector_get(v, 1);
01316         double a = gsl_vector_get(v, 2);
01317 
01318         EMData *this_img = (*dict)["this"];
01319         EMData *with = (*dict)["with"];
01320         bool mirror = (*dict)["mirror"];
01321 
01322 //      float mean = (float)this_img->get_attr("mean");
01323 //      if ( Util::goodf(&mean) ) {
01324 //              //cout << "tmps mean is nan even before rotation" << endl;
01325 //      }
01326 
01327         Transform t(Dict("type","2d","alpha",static_cast<float>(a)));
01328 //      Transform3D t3d(Transform3D::EMAN, (float)a, 0.0f, 0.0f);
01329 //      t3d.set_posttrans( (float) x, (float) y);
01330 //      tmp->rotate_translate(t3d);
01331         t.set_trans((float)x,(float)y);
01332         t.set_mirror(mirror);
01333         if (v->size>3) {
01334                 float sca=(float)gsl_vector_get(v, 3);
01335                 if (sca<.7 || sca>1.3) return 1.0e20;
01336                 t.set_scale((float)gsl_vector_get(v, 3));
01337         }
01338         EMData *tmp = this_img->process("xform",Dict("transform",&t));
01339 
01340 //      printf("GSL %f %f %f %d %f\n",x,y,a,mirror,(float)gsl_vector_get(v, 3));
01341         Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]);
01342         double result = c->cmp(tmp,with);
01343 
01344         // DELETE AT SOME STAGE, USEFUL FOR PRERELEASE STUFF
01345         //      float test_result = (float)result;
01346 //      if ( Util::goodf(&test_result) ) {
01347 //              cout << "result " << result << " " << x << " " << y << " " << a << endl;
01348 //              cout << (float)this_img->get_attr("mean") << " " << (float)tmp->get_attr("mean") << " " << (float)with->get_attr("mean") << endl;
01349 //              tmp->write_image("tmp.hdf");
01350 //              with->write_image("with.hdf");
01351 //              this_img->write_image("this_img.hdf");
01352 //              EMData* t = this_img->copy();
01353 //              cout << (float)t->get_attr("mean") << endl;
01354 //              t->rotate_translate( t3d );
01355 //              cout << (float)t->get_attr("mean") << endl;
01356 //              cout << "exit" << endl;
01358 //              cout << (float)t->get_attr("mean") << endl;
01359 //              cout << "now exit" << endl;
01360 //              delete t;
01361 //      }
01362 
01363 
01364         if ( tmp != 0 ) delete tmp;
01365 
01366         return result;
01367 }

static double refalifn3dquat ( const gsl_vector *  v,
void *  params 
) [static]

Definition at line 1545 of file aligner.cpp.

References EMAN::Cmp::cmp(), EMAN::EMData::process(), refalin3d_perturbquat(), t, x, and y.

Referenced by EMAN::Refine3DAlignerQuaternion::align().

01546 {
01547         Dict *dict = (Dict *) params;
01548 
01549         double n0 = gsl_vector_get(v, 0);
01550         double n1 = gsl_vector_get(v, 1);
01551         double n2 = gsl_vector_get(v, 2);
01552         double x = gsl_vector_get(v, 3);
01553         double y = gsl_vector_get(v, 4);
01554         double z = gsl_vector_get(v, 5);
01555 
01556         EMData *this_img = (*dict)["this"];
01557         EMData *with = (*dict)["with"];
01558 //      bool mirror = (*dict)["mirror"];
01559 
01560         Transform* t = (*dict)["transform"];
01561         float spincoeff = (*dict)["spincoeff"];
01562 
01563         Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z);
01564 
01565         EMData *tmp = this_img->process("xform",Dict("transform",&soln));
01566         Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]);
01567         double result = c->cmp(tmp,with);
01568         if ( tmp != 0 ) delete tmp;
01569         delete t; t = 0;
01570         //cout << result << endl;
01571         return result;
01572 }

static double refalifnfast ( const gsl_vector *  v,
void *  params 
) [static]

Definition at line 1369 of file aligner.cpp.

References EMAN::EMData::dot_rotate_translate(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), x, and y.

Referenced by EMAN::RefineAligner::align().

01370 {
01371         Dict *dict = (Dict *) params;
01372         EMData *this_img = (*dict)["this"];
01373         EMData *img_to = (*dict)["with"];
01374         bool mirror = (*dict)["mirror"];
01375 
01376         double x = gsl_vector_get(v, 0);
01377         double y = gsl_vector_get(v, 1);
01378         double a = gsl_vector_get(v, 2);
01379 
01380         double r = this_img->dot_rotate_translate(img_to, (float)x, (float)y, (float)a, mirror);
01381         int nsec = this_img->get_xsize() * this_img->get_ysize();
01382         double result = 1.0 - r / nsec;
01383 
01384 //      cout << result << " x " << x << " y " << y << " az " << a <<  endl;
01385         return result;
01386 }

static Transform refalin3d_perturbquat ( const Transform *const   t,
const float &  spincoeff,
const float &  n0,
const float &  n1,
const float &  n2,
const float &  x,
const float &  y,
const float &  z 
) [static]

Definition at line 1523 of file aligner.cpp.

References EMAN::Vec3< Type >::normalize(), q, and sqrt().

Referenced by EMAN::Refine3DAlignerQuaternion::align(), and refalifn3dquat().

01524 {
01525         Vec3f normal(n0,n1,n2);
01526         normal.normalize();
01527         
01528         float omega = spincoeff*sqrt(n0*n0 + n1*n1 + n2*n2); // Here we compute the spin by the rotation axis vector length
01529         Dict d;
01530         d["type"] = "spin";
01531         d["Omega"] = omega;
01532         d["n1"] = normal[0];
01533         d["n2"] = normal[1];
01534         d["n3"] = normal[2];
01535         //cout << omega << " " << normal[0] << " " << normal[1] << " " << normal[2] << " " << n0 << " " << n1 << " " << n2 << endl;
01536         
01537         Transform q(d);
01538         q.set_trans((float)x,(float)y,(float)z);
01539         
01540         q = q*(*t); //compose transforms        
01541         
01542         return q;
01543 }


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