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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

AlignerNEW ()

Static Public Attributes

const string NAME = "frm2d"

Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 1252 of file aligner.h.

References align().

01253                                         {
01254                                                 return align(this_img, to_img, "frc", Dict());
01255                                         }

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 2446 of file aligner.cpp.

References EMAN::EMData::calc_center_of_mass(), EMAN::EMData::copy(), EMAN::EMData::do_fft(), frm_2d_Align(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), ImageDimensionException, nx, ny, EMAN::EMData::oneDfftPolar(), EMAN::EMData::set_complex(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), sqrt(), EMAN::EMData::translate(), and EMAN::EMData::unwrap_largerR().

02448 {
02449         if (!this_img) {
02450                 return 0;
02451         }
02452         if (to && !EMUtil::is_same_size(this_img, to))
02453                 throw ImageDimensionException("Images must be the same size to perform translational alignment");
02454 
02455         int nx=this_img->get_xsize();
02456         int ny=this_img->get_ysize();
02457         int size =(int)floor(M_PI*ny/4.0);
02458         size =Util::calc_best_fft_size(size);//ming   bestfftsize(size);
02459         int MAXR=ny/2;
02460         //int MAXR=size;
02461         EMData *this_temp=this_img->copy(); // ming change avg to to
02462         FloatPoint com_test,com_test1;
02463         com_test=this_temp->calc_center_of_mass();//ming add
02464         float com_this_x=com_test[0];
02465         float com_this_y=com_test[1];
02466         delete this_temp;
02467 
02468 
02469         EMData *that_temp=to->copy();
02470         com_test1=that_temp->calc_center_of_mass();
02471         float com_with_x=com_test1[0];
02472         float com_with_y=com_test1[1];
02473         delete that_temp;
02474 
02475         EMData *avg_frm=to->copy();
02476         float dx,dy;
02477         //float dx=-(com_with_x-nx/2); //ming
02478         //float dy=-(com_with_y-ny/2); //ming
02479         //avg_frm->translate(dx,dy,0.0);
02480         EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine
02481         //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1);
02482         EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR));
02483 
02484         float *sampl_fft=withpcsfft->get_data(); //
02485         delete avg_frm;
02486         delete withpcs;
02487 
02488         int bw=size/2;
02489         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02490         float pi2=2.0*M_PI, r2;
02491 
02492         EMData *data_in=new EMData;
02493         data_in->set_complex(true);
02494         data_in->set_ri(1);
02495         data_in->set_size(2*size,1,1);
02496         float * comp_in=data_in->get_data();
02497 
02498         int p_max=3;
02499         float *frm2dhhat=0;
02500 
02501         if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){
02502                 cout <<"Error in allocating memory 13. \n";
02503                 exit(1);
02504         }
02505         //printf("p_max=%d\n",p_max);
02506         float *sb=0, *cb=0;             // sin(beta) and cos(beta) for get h_hat, 300>size
02507         if((sb=new float[size])==NULL||(cb=new float[size])==NULL) {
02508                 cout <<"can't allocate more memory, terminating. \n";
02509                 exit(1);
02510         }
02511         for(int i=0;i<size;++i) {        // beta sampling, to calculate beta' and r'
02512                 float beta=i*M_PI/bw;
02513                 sb[i]=sin(beta);
02514                 cb[i]=cos(beta);
02515         }
02516 
02517         for(int p=0; p<=p_max; ++p){
02518                 ind1=p*size*bw;
02519         float pp2=(float)(p*p);
02520                 for(int n=0;n<bw;++n){         /* loop for n */
02521                 ind2=ind1+n;
02522                 for(int r=0;r<=MAXR;++r) {
02523                                 ind3=(ind2+r*bw)*size;
02524                         float rr2=(float)(r*r);
02525                                 float rp2=(float)(r*p);
02526                         for(int i=0;i<size;++i){                            // beta sampling, to get beta' and r'
02527                                 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i]));   // r2->r'
02528                                 int r1=(int)floor(r2+0.5f);                        // for computing gn(r')
02529                                 if(r1>MAXR){
02530                                         comp_in[2*i]=0.0f;
02531                                         comp_in[2*i+1]=0.0f;
02532                                 }
02533                                 else{
02534                                         float gn_r=sampl_fft[2*n+r1*(size+2)];           // real part of gn(r')
02535                                         float gn_i=sampl_fft[2*n+1+r1*(size+2)];           // imaginary part of gn(r')
02536                                                 float sb2, cb2, cn, sn;
02537                                                 if(n!=0){
02538                                                         if(r2 != 0.0){
02539                                                                 sb2=r*sb[i]/r2;
02540                                                                 cb2=(r*cb[i]-p)/r2;
02541                                                         }
02542                                                 else{
02543                                                                 sb2=0.0;
02544                                                                 cb2=1.0;
02545                                                         }
02546                                                 if(sb2>1.0) sb2= 1.0f;
02547                                                 if(sb2<-1.0)sb2=-1.0f;
02548                                                 if(cb2>1.0) cb2= 1.0f;
02549                                                 if(cb2<-1.0)cb2=-1.0f;
02550                                                 float beta2=atan2(sb2,cb2);
02551                                                 if(beta2<0.0) beta2+=pi2;
02552                                                 float nb2=n*beta2;
02553                                                 cn=cos(nb2);
02554                                                         sn=sin(nb2);
02555                                                 }
02556                                         else{
02557                                                         cn=1.0f; sn=0.0f;
02558                                                 }
02559                                                 comp_in[2*i]=cn*gn_r-sn*gn_i;
02560                                                 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r);
02561                                 }
02562                         }
02563                         EMData *data_out;
02564                         data_out=data_in->do_fft();
02565                         float * comp_out=data_out->get_data();
02566                         for(int m=0;m<size;m++){                                     // store hat{h(n,r,p)}(m)
02567                                         ind4=(ind3+m)*2;
02568                                         ind41=ind4+1;
02569                                         frm2dhhat[ind4]=comp_out[2*m];
02570                                         frm2dhhat[ind41]=comp_out[2*m+1];
02571                                 }
02572                         delete data_out;
02573                         }
02574                 }
02575         }
02576 
02577         delete[] sb;
02578         delete[] cb;
02579         delete data_in;
02580         delete withpcsfft;
02581 
02582         float dot_frm0=0.0f, dot_frm1=0.0f;
02583         EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0;
02584         //dr_frm=this_img->copy();
02585         for (int iFlip=0;iFlip<=1;++iFlip){
02586                 if (iFlip==0){dr_frm=this_img->copy();  da_nFlip=this_img->copy();}
02587                 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();}
02588                 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming   // image mirror about Y axis, so y keeps the same
02589 
02590                 dx=-(com_this_x-nx/2); //ming
02591                 dy=-(com_this_y-ny/2); //ming
02592                 dr_frm->translate(dx,dy,0.0); // this
02593                 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR);
02594                 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1);
02595                 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR);
02596                 delete selfpcs;
02597                 delete dr_frm;
02598                 if(iFlip==0)
02599                         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);
02600                 else
02601                         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);
02602                 delete selfpcsfft;
02603         }
02604 
02605         delete[] frm2dhhat;
02606         if(dot_frm0 <=dot_frm1) {
02607 #ifdef DEBUG
02608                 printf("best_corre=%f, no flip\n",dot_frm0);
02609 #endif
02610                 delete da_yFlip;
02611                 return da_nFlip;
02612         }
02613         else {
02614 #ifdef DEBUG
02615                 printf("best_corre=%f, flipped\n",dot_frm1);
02616 #endif
02617                 delete da_nFlip;
02618                 return da_yFlip;
02619         }
02620 }

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

Implements EMAN::Aligner.

Definition at line 1262 of file aligner.h.

01263                                         {
01264                                                 return "FRM2D uses two rotational parameters and one translational parameter";
01265                                         }

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 1257 of file aligner.h.

01258                                         {
01259                                                 return NAME;
01260                                         }

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

Implements EMAN::Aligner.

Definition at line 1271 of file aligner.h.

References EMAN::TypeDict::put().

01272                                         {
01273                                                         TypeDict d;
01274                                                         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.");
01275 
01276                                                         //d.put("p_max", EMObject::FLOAT,"p_max is");
01277                                                         return d;
01278                                         }

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

Definition at line 1267 of file aligner.h.

01268                                         {
01269                                                 return new FRM2DAligner();
01270                                         }


Member Data Documentation

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

Definition at line 79 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Mar 10 22:59:51 2011 for EMAN2 by  doxygen 1.3.9.1