EMAN::FRM2DAligner Class Reference

#include <aligner.h>

Inheritance diagram for EMAN::FRM2DAligner:

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Collaboration diagram for EMAN::FRM2DAligner:

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List of all members.

Public Member Functions

virtual EMDataalign (EMData *this_img, EMData *to_img, const string &cmp_name, const Dict &cmp_params=Dict()) const
 To align 'this_img' with another image passed in through its parameters.
virtual EMDataalign (EMData *this_img, EMData *to_img) const
string get_name () const
 Get the Aligner's name.
string get_desc () const
virtual TypeDict get_param_types () const

Static Public Member Functions

static AlignerNEW ()

Static Public Attributes

static const string NAME = "frm2d"

Detailed Description

Definition at line 1341 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::FRM2DAligner::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 1347 of file aligner.h.

References align().

01348                                         {
01349                                                 return align(this_img, to_img, "frc", Dict());
01350                                         }

EMData * FRM2DAligner::align ( EMData this_img,
EMData to_img,
const string &  cmp_name,
const Dict cmp_params = Dict() 
) const [virtual]

To align 'this_img' with another image passed in through its parameters.

The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.

Parameters:
this_img The image to be compared.
to_img 'this_img" is aligned with 'to_img'.
cmp_name The comparison method to compare the two images.
cmp_params The parameter dictionary for comparison method.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 2703 of file aligner.cpp.

References EMAN::Util::calc_best_fft_size(), EMAN::EMData::calc_center_of_mass(), EMAN::EMData::copy(), EMAN::EMData::do_fft(), frm_2d_Align(), EMAN::EMData::get_data(), ImageDimensionException, EMAN::EMUtil::is_same_size(), nx, EMAN::EMData::oneDfftPolar(), EMAN::EMData::set_complex(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), sqrt(), EMAN::EMData::translate(), and EMAN::EMData::unwrap_largerR().

Referenced by align().

02705 {
02706         if (!this_img) {
02707                 return 0;
02708         }
02709         if (to && !EMUtil::is_same_size(this_img, to))
02710                 throw ImageDimensionException("Images must be the same size to perform translational alignment");
02711 
02712         int nx=this_img->get_xsize();
02713         int ny=this_img->get_ysize();
02714         int size =(int)floor(M_PI*ny/4.0);
02715         size =Util::calc_best_fft_size(size);//ming   bestfftsize(size);
02716         int MAXR=ny/2;
02717         //int MAXR=size;
02718         EMData *this_temp=this_img->copy(); // ming change avg to to
02719         FloatPoint com_test,com_test1;
02720         com_test=this_temp->calc_center_of_mass();//ming add
02721         float com_this_x=com_test[0];
02722         float com_this_y=com_test[1];
02723         delete this_temp;
02724 
02725 
02726         EMData *that_temp=to->copy();
02727         com_test1=that_temp->calc_center_of_mass();
02728         float com_with_x=com_test1[0];
02729         float com_with_y=com_test1[1];
02730         delete that_temp;
02731 
02732         EMData *avg_frm=to->copy();
02733         float dx,dy;
02734         //float dx=-(com_with_x-nx/2); //ming
02735         //float dy=-(com_with_y-ny/2); //ming
02736         //avg_frm->translate(dx,dy,0.0);
02737         EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine
02738         //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1);
02739         EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR));
02740 
02741         float *sampl_fft=withpcsfft->get_data(); //
02742         delete avg_frm;
02743         delete withpcs;
02744 
02745         int bw=size/2;
02746         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02747         float pi2=2.0*M_PI, r2;
02748 
02749         EMData *data_in=new EMData;
02750         data_in->set_complex(true);
02751         data_in->set_ri(1);
02752         data_in->set_size(2*size,1,1);
02753         float * comp_in=data_in->get_data();
02754 
02755         int p_max=3;
02756         float *frm2dhhat=0;
02757 
02758         if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){
02759                 cout <<"Error in allocating memory 13. \n";
02760                 exit(1);
02761         }
02762         //printf("p_max=%d\n",p_max);
02763         float *sb=0, *cb=0;             // sin(beta) and cos(beta) for get h_hat, 300>size
02764         if((sb=new float[size])==NULL||(cb=new float[size])==NULL) {
02765                 cout <<"can't allocate more memory, terminating. \n";
02766                 exit(1);
02767         }
02768         for(int i=0;i<size;++i) {        // beta sampling, to calculate beta' and r'
02769                 float beta=i*M_PI/bw;
02770                 sb[i]=sin(beta);
02771                 cb[i]=cos(beta);
02772         }
02773 
02774         for(int p=0; p<=p_max; ++p){
02775                 ind1=p*size*bw;
02776         float pp2=(float)(p*p);
02777                 for(int n=0;n<bw;++n){         /* loop for n */
02778                 ind2=ind1+n;
02779                 for(int r=0;r<=MAXR;++r) {
02780                                 ind3=(ind2+r*bw)*size;
02781                         float rr2=(float)(r*r);
02782                                 float rp2=(float)(r*p);
02783                         for(int i=0;i<size;++i){                            // beta sampling, to get beta' and r'
02784                                 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i]));   // r2->r'
02785                                 int r1=(int)floor(r2+0.5f);                        // for computing gn(r')
02786                                 if(r1>MAXR){
02787                                         comp_in[2*i]=0.0f;
02788                                         comp_in[2*i+1]=0.0f;
02789                                 }
02790                                 else{
02791                                         float gn_r=sampl_fft[2*n+r1*(size+2)];           // real part of gn(r')
02792                                         float gn_i=sampl_fft[2*n+1+r1*(size+2)];           // imaginary part of gn(r')
02793                                                 float sb2, cb2, cn, sn;
02794                                                 if(n!=0){
02795                                                         if(r2 != 0.0){
02796                                                                 sb2=r*sb[i]/r2;
02797                                                                 cb2=(r*cb[i]-p)/r2;
02798                                                         }
02799                                                 else{
02800                                                                 sb2=0.0;
02801                                                                 cb2=1.0;
02802                                                         }
02803                                                 if(sb2>1.0) sb2= 1.0f;
02804                                                 if(sb2<-1.0)sb2=-1.0f;
02805                                                 if(cb2>1.0) cb2= 1.0f;
02806                                                 if(cb2<-1.0)cb2=-1.0f;
02807                                                 float beta2=atan2(sb2,cb2);
02808                                                 if(beta2<0.0) beta2+=pi2;
02809                                                 float nb2=n*beta2;
02810                                                 cn=cos(nb2);
02811                                                         sn=sin(nb2);
02812                                                 }
02813                                         else{
02814                                                         cn=1.0f; sn=0.0f;
02815                                                 }
02816                                                 comp_in[2*i]=cn*gn_r-sn*gn_i;
02817                                                 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r);
02818                                 }
02819                         }
02820                         EMData *data_out;
02821                         data_out=data_in->do_fft();
02822                         float * comp_out=data_out->get_data();
02823                         for(int m=0;m<size;m++){                                     // store hat{h(n,r,p)}(m)
02824                                         ind4=(ind3+m)*2;
02825                                         ind41=ind4+1;
02826                                         frm2dhhat[ind4]=comp_out[2*m];
02827                                         frm2dhhat[ind41]=comp_out[2*m+1];
02828                                 }
02829                         delete data_out;
02830                         }
02831                 }
02832         }
02833 
02834         delete[] sb;
02835         delete[] cb;
02836         delete data_in;
02837         delete withpcsfft;
02838 
02839         float dot_frm0=0.0f, dot_frm1=0.0f;
02840         EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0;
02841         //dr_frm=this_img->copy();
02842         for (int iFlip=0;iFlip<=1;++iFlip){
02843                 if (iFlip==0){dr_frm=this_img->copy();  da_nFlip=this_img->copy();}
02844                 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();}
02845                 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming   // image mirror about Y axis, so y keeps the same
02846 
02847                 dx=-(com_this_x-nx/2); //ming
02848                 dy=-(com_this_y-ny/2); //ming
02849                 dr_frm->translate(dx,dy,0.0); // this
02850                 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR);
02851                 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1);
02852                 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR);
02853                 delete selfpcs;
02854                 delete dr_frm;
02855                 if(iFlip==0)
02856                         dot_frm0=frm_2d_Align(da_nFlip,to, frm2dhhat, selfpcsfft, p_max, size, com_this_x, com_this_y, com_with_x, com_with_y,cmp_name,cmp_params);
02857                 else
02858                         dot_frm1=frm_2d_Align(da_yFlip,to, frm2dhhat, selfpcsfft, p_max, size, com_this_x, com_this_y, com_with_x, com_with_y,cmp_name,cmp_params);
02859                 delete selfpcsfft;
02860         }
02861 
02862         delete[] frm2dhhat;
02863         if(dot_frm0 <=dot_frm1) {
02864 #ifdef DEBUG
02865                 printf("best_corre=%f, no flip\n",dot_frm0);
02866 #endif
02867                 delete da_yFlip;
02868                 return da_nFlip;
02869         }
02870         else {
02871 #ifdef DEBUG
02872                 printf("best_corre=%f, flipped\n",dot_frm1);
02873 #endif
02874                 delete da_nFlip;
02875                 return da_yFlip;
02876         }
02877 }

string EMAN::FRM2DAligner::get_desc (  )  const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 1357 of file aligner.h.

01358                                         {
01359                                                 return "FRM2D uses two rotational parameters and one translational parameter";
01360                                         }

string EMAN::FRM2DAligner::get_name (  )  const [inline, virtual]

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 1352 of file aligner.h.

References NAME.

01353                                         {
01354                                                 return NAME;
01355                                         }

virtual TypeDict EMAN::FRM2DAligner::get_param_types (  )  const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 1366 of file aligner.h.

References EMAN::EMObject::INT, and EMAN::TypeDict::put().

01367                                         {
01368                                                         TypeDict d;
01369                                                         d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.");
01370 
01371                                                         //d.put("p_max", EMObject::FLOAT,"p_max is");
01372                                                         return d;
01373                                         }

static Aligner* EMAN::FRM2DAligner::NEW (  )  [inline, static]

Definition at line 1362 of file aligner.h.

01363                                         {
01364                                                 return new FRM2DAligner();
01365                                         }


Member Data Documentation

const string FRM2DAligner::NAME = "frm2d" [static]

Definition at line 1375 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:45:13 2011 for EMAN2 by  doxygen 1.4.7