aligner.cpp File Reference

#include "emfft.h"
#include "cmp.h"
#include "aligner.h"
#include "averager.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 1.266 2012/04/26 16:08:24 gtang 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 symquat (const gsl_vector *v, void *params)
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 1.266 2012/04/26 16:08:24 gtang Exp

Definition at line 55 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 2712 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().

02713 {
02714         int size=rsize;
02715         float dx,dy;
02716         int bw=size/2;
02717         int MAXR=this_img->get_ysize()/2;
02718         //int MAXR=size;
02719         unsigned long tsize=2*size;
02720         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02721         unsigned long index0=0;
02722         int i=0, j=0, m=0, n=0, r=0;
02723         int loop_rho=0, rho_best=0;
02724 
02725         float* gnr2   = new float[size*2];
02726         float* maxcor = new float[size+1];                  // MAXR need change
02727 
02728         int p_max=p_max_input;
02729         float* result = new float[5*(p_max+1)];
02730         float* cr=new float[size*(bw+1)];
02731         float* ci=new float[size*(bw+1)];
02732         EMData *data_in=new EMData;
02733         data_in->set_complex(true);
02734         data_in->set_fftodd(false);
02735         data_in->set_ri(true);
02736         data_in->set_size(size+2,size,1);
02737         float *in=data_in->get_data();
02738 
02739         float *self_sampl_fft = selfpcsfft->get_data(); // ming f(r)
02740 
02741         float maxcor_sofar=0.0f;
02742         int p=0;
02743 
02744         for(p=0; p<=p_max; ++p){
02745                 ind1=p*size*bw;
02746                 for (i=0;i<size;++i)
02747                         for (j=0;j<bw+1;++j){
02748                                 cr[i*(bw+1)+j]=0.0;
02749                                 ci[i*(bw+1)+j]=0.0;
02750                         }
02751         for(n=0;n<bw;++n){                                // loop for n
02752                 ind2=(ind1+n);
02753                 index0=n*(bw+1);
02754                         for(r=0;r<=MAXR;++r) {
02755                         ind3=(ind2+r*bw)*size;
02756                         for(m=0;m<size;m++){              // take back hat{h(n,r,p)}(m)
02757                                 ind4=(ind3+m)*2;
02758                                     ind41=ind4+1;
02759                                     gnr2[2*m]=frm2dhhat[ind4];
02760                                     gnr2[2*m+1]=frm2dhhat[ind41];
02761                                 }
02762                         for(m=0;m<bw;++m){
02763                                         float tempr=self_sampl_fft[2*m+r*(size+2)]*r;
02764                                 float tempi=self_sampl_fft[2*m+1+r*(size+2)]*r;
02765                                 float gnr2_r=gnr2[2*m];
02766                                 float gnr2_i=gnr2[2*m+1];
02767                                 cr[n*(bw+1)+m]+=gnr2_r*tempr+gnr2_i*tempi;
02768                                         ci[n*(bw+1)+m]+=gnr2_i*tempr-gnr2_r*tempi;
02769                                         if(n!=0){                                       // m,-n
02770                                         if(m!= 0){
02771                                                 int ssize=tsize-2*m;    // ssize = 2*size-2m
02772                                                 int ssize1=ssize+1;
02773                                                 float gnr2_r=gnr2[ssize];
02774                                                 float gnr2_i=gnr2[ssize1];
02775                                                         cr[(size-n)*(bw+1)+m]+=gnr2_r*tempr-gnr2_i*tempi;
02776                                                 ci[(size-n)*(bw+1)+m]-=gnr2_i*tempr+gnr2_r*tempi;
02777                                         }
02778                                                 else{
02779                                                         cr[(size-n)*(bw+1)+m]+=*(gnr2)*tempr-*(gnr2+1)*tempi;
02780                                                         ci[(size-n)*(bw+1)+m]-=*(gnr2+1)*tempr+*(gnr2)*tempi;
02781                                                 }
02782                                 }
02783                                 }
02784                         }
02785         }
02786         for (int cii=0; cii<size*(bw+1);++cii){
02787                         in[2*cii]=cr[cii];
02788                         in[2*cii+1]=ci[cii];
02789                         //printf("cii=%d,in[2i+1]=%f\n",cii, cr[cii]);
02790         }
02791 
02792         EMData *data_out;
02793                 data_out=data_in->do_ift();
02794                 float *c=data_out->get_data();
02795                 float tempr=0.0f, corre_fcs=999.0f;
02796 
02797             int n_best=0, m_best=0;
02798         float temp=-100.0f;
02799                 for(n=0;n<size;++n){// move Tri_2D to Tri = c(phi,phi';rho)
02800                         for(m=0;m<size;++m){
02801                                 temp=c[n*size+m];
02802                                 if(temp>tempr) {
02803                                         tempr=temp;
02804                                         n_best=n;
02805                                         m_best=m;
02806                                 }
02807                         }
02808                 }
02809                 delete data_out;
02810 
02811                 float corre,Phi2,Phi,Tx,Ty,Vx, Vy;
02812 
02813                 //for (n_best=0;n_best<bw;n_best++)
02814                   //  for (m_best=0;m_best<2*bw;m_best++){
02815                 //n_best=0;
02816                 //m_best=70;
02817                 Phi2=n_best*M_PI/bw;  // ming this is reference image rotation angle
02818                 Phi=m_best*M_PI/bw;   // ming this is particle image rotation angle
02819                 Vx=p*cos(Phi);//should use the angle of the centered one
02820                 Vy=-p*sin(Phi);
02821                 Tx=Vx+(floor(com_this_x+0.5f)-floor(com_with_x+0.5f));
02822                 Ty=Vy+(floor(com_this_y+0.5f)-floor(com_with_y+0.5f));
02823 
02824                 dx=-Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image,
02825                 dy=-Ty; // need to convert to raw image
02826 
02827                 EMData *this_tmp=this_img->copy();//ming change to to
02828                 this_tmp->rotate(-(Phi2-Phi)*180.0f,0.0f,0.0f);
02829                 this_tmp->translate(dx,dy,0.0);
02830 
02831                 corre=this_tmp->cmp(cmp_name,to,cmp_params);
02832                 //printf("corre=%f\n",corre);
02833                 delete this_tmp;
02834                 if(corre<=corre_fcs) { //ming, cmp use smaller value stands for more similarity
02835                         corre_fcs=corre;
02836                         result[0+5*p] = float(p);       // rho
02837                         result[1+5*p] = corre;          // correlation_fcs
02838                         result[2+5*p] = (Phi2-Phi)*180.0f;      // rotation angle
02839                         result[3+5*p] = Tx;             // Translation_x
02840                         result[4+5*p] = Ty;             // Translation_y
02841                 }
02842                 maxcor[p]=corre_fcs;                            //  maximum correlation for current rho
02843                 if(corre_fcs<maxcor_sofar) {
02844                         maxcor_sofar=corre_fcs;                 // max correlation up to current rho
02845                     rho_best=p;                         // the rho value with maxinum correlation value
02846                 }
02847                 if(p>=4){
02848                         if(maxcor[p] < maxcor[p-1] && maxcor[p-1] < maxcor[p-2]&& maxcor[p-2] < maxcor[p-3] && maxcor[p-3] < maxcor[p-4]){
02849                                 loop_rho=1;
02850                                 break; //exit p loop
02851                         }
02852                 }
02853         } // end for p
02854         //}//test my method
02855         if(loop_rho == 1)
02856                 p=p+1;
02857         int rb5=5*rho_best;
02858         float fsc      = result[1+rb5];
02859         float ang_keep = result[2+rb5];
02860         float Tx       = result[3+rb5];
02861         float Ty       = result[4+rb5];
02862         delete[] gnr2;
02863         delete[] maxcor;
02864         delete[] result;
02865         delete cr;
02866         cr=0;
02867         delete ci;
02868         ci=0;
02869         delete data_in; // ming add
02870         dx = -Tx;               // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image,
02871         dy = -Ty;               // need to convert to raw image
02872         this_img->rotate(-ang_keep,0,0); // ming change this to this_img??
02873         this_img->translate(dx,dy,0.0); // ming change this to this_img
02874 
02875 
02876         Transform  tsoln(Dict("type","2d","alpha",ang_keep));
02877         tsoln.set_trans(dx,dy);
02878         this_img->set_attr("xform.align2d",&tsoln);
02879 #ifdef DEBUG
02880         float fsc_best=this_img->cmp(cmp_name,to,cmp_params);
02881         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);
02882 #endif
02883         return fsc;     // return the fsc coefficients
02884 } // FRM2D aligner sub_class

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

Definition at line 1564 of file aligner.cpp.

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

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

01565 {
01566         Dict *dict = (Dict *) params;
01567 
01568         double x = gsl_vector_get(v, 0);
01569         double y = gsl_vector_get(v, 1);
01570         double a = gsl_vector_get(v, 2);
01571 
01572         EMData *this_img = (*dict)["this"];
01573         EMData *with = (*dict)["with"];
01574         bool mirror = (*dict)["mirror"];
01575 
01576 //      float mean = (float)this_img->get_attr("mean");
01577 //      if ( Util::goodf(&mean) ) {
01578 //              //cout << "tmps mean is nan even before rotation" << endl;
01579 //      }
01580 
01581         Transform t(Dict("type","2d","alpha",static_cast<float>(a)));
01582 //      Transform3D t3d(Transform3D::EMAN, (float)a, 0.0f, 0.0f);
01583 //      t3d.set_posttrans( (float) x, (float) y);
01584 //      tmp->rotate_translate(t3d);
01585         t.set_trans((float)x,(float)y);
01586         t.set_mirror(mirror);
01587         if (v->size>3) {
01588                 float sca=(float)gsl_vector_get(v, 3);
01589                 if (sca<.7 || sca>1.3) return 1.0e20;
01590                 t.set_scale((float)gsl_vector_get(v, 3));
01591         }
01592         EMData *tmp = this_img->process("xform",Dict("transform",&t));
01593 
01594 //      printf("GSL %f %f %f %d %f\n",x,y,a,mirror,(float)gsl_vector_get(v, 3));
01595         Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]);
01596         double result = c->cmp(tmp,with);
01597 
01598         // DELETE AT SOME STAGE, USEFUL FOR PRERELEASE STUFF
01599         //      float test_result = (float)result;
01600 //      if ( Util::goodf(&test_result) ) {
01601 //              cout << "result " << result << " " << x << " " << y << " " << a << endl;
01602 //              cout << (float)this_img->get_attr("mean") << " " << (float)tmp->get_attr("mean") << " " << (float)with->get_attr("mean") << endl;
01603 //              tmp->write_image("tmp.hdf");
01604 //              with->write_image("with.hdf");
01605 //              this_img->write_image("this_img.hdf");
01606 //              EMData* t = this_img->copy();
01607 //              cout << (float)t->get_attr("mean") << endl;
01608 //              t->rotate_translate( t3d );
01609 //              cout << (float)t->get_attr("mean") << endl;
01610 //              cout << "exit" << endl;
01612 //              cout << (float)t->get_attr("mean") << endl;
01613 //              cout << "now exit" << endl;
01614 //              delete t;
01615 //      }
01616 
01617 
01618         if (tmp != 0) delete tmp;
01619         
01620         return result;
01621 }

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

Definition at line 1826 of file aligner.cpp.

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

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

01827 {
01828         Dict *dict = (Dict *) params;
01829 
01830         double n0 = gsl_vector_get(v, 0);
01831         double n1 = gsl_vector_get(v, 1);
01832         double n2 = gsl_vector_get(v, 2);
01833         double x = gsl_vector_get(v, 3);
01834         double y = gsl_vector_get(v, 4);
01835         double z = gsl_vector_get(v, 5);
01836 
01837         EMData *this_img = (*dict)["this"];
01838         EMData *with = (*dict)["with"];
01839 
01840         Transform* t = (*dict)["transform"];
01841         float spincoeff = (*dict)["spincoeff"];
01842 
01843         Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z);
01844 
01845         EMData *tmp = this_img->process("xform",Dict("transform",&soln));
01846         Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]);
01847         double result = c->cmp(tmp,with);
01848         if ( tmp != 0 ) delete tmp;
01849 
01850         //cout << result << endl;
01851         return result;
01852 }

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

Definition at line 1623 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().

01624 {
01625         Dict *dict = (Dict *) params;
01626         EMData *this_img = (*dict)["this"];
01627         EMData *img_to = (*dict)["with"];
01628         bool mirror = (*dict)["mirror"];
01629 
01630         double x = gsl_vector_get(v, 0);
01631         double y = gsl_vector_get(v, 1);
01632         double a = gsl_vector_get(v, 2);
01633 
01634         double r = this_img->dot_rotate_translate(img_to, (float)x, (float)y, (float)a, mirror);
01635         int nsec = this_img->get_xsize() * this_img->get_ysize();
01636         double result = 1.0 - r / nsec;
01637 
01638 //      cout << result << " x " << x << " y " << y << " az " << a <<  endl;
01639         return result;
01640 }

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 1776 of file aligner.cpp.

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

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

01777 {
01778         Vec3f normal(n0,n1,n2);
01779         normal.normalize();
01780         
01781         float omega = spincoeff*sqrt(n0*n0 + n1*n1 + n2*n2); // Here we compute the spin by the rotation axis vector length
01782         Dict d;
01783         d["type"] = "spin";
01784         d["Omega"] = omega;
01785         d["n1"] = normal[0];
01786         d["n2"] = normal[1];
01787         d["n3"] = normal[2];
01788         //cout << omega << " " << normal[0] << " " << normal[1] << " " << normal[2] << " " << n0 << " " << n1 << " " << n2 << endl;
01789         
01790         Transform q(d);
01791         q.set_trans((float)x,(float)y,(float)z);
01792         
01793         q = q*(*t); //compose transforms        
01794         
01795         return q;
01796 }

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

Definition at line 1798 of file aligner.cpp.

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

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

01799 {
01800         Dict *dict = (Dict *) params;
01801 
01802         double n0 = gsl_vector_get(v, 0);
01803         double n1 = gsl_vector_get(v, 1);
01804         double n2 = gsl_vector_get(v, 2);
01805         double x = gsl_vector_get(v, 3);
01806         double y = gsl_vector_get(v, 4);
01807         double z = gsl_vector_get(v, 5);
01808 
01809         EMData* volume = (*dict)["volume"];
01810         float spincoeff = (*dict)["spincoeff"];
01811         Transform* t = (*dict)["transform"];
01812 
01813         Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z);
01814 
01815         EMData *tmp = volume->process("xform",Dict("transform",&soln));
01816         EMData *symtmp = tmp->process("xform.applysym",Dict("sym",(*dict)["sym"]));
01817         Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]);
01818         double result = c->cmp(symtmp,tmp);
01819         delete tmp;
01820         delete symtmp;
01821 
01822         //cout << result << endl;
01823         return result;
01824 }


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