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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 987 of file aligner.h.

References align().

00988                                         {
00989                                                 return align(this_img, to_img, "frc", Dict());
00990                                         }

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 2052 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().

02054 {
02055         if (!this_img) {
02056                 return 0;
02057         }
02058         if (to && !EMUtil::is_same_size(this_img, to))
02059                 throw ImageDimensionException("Images must be the same size to perform translational alignment");
02060 
02061         int nx=this_img->get_xsize();
02062         int ny=this_img->get_ysize();
02063         int size =(int)floor(M_PI*ny/4.0);
02064         size =Util::calc_best_fft_size(size);//ming   bestfftsize(size);
02065         int MAXR=ny/2;
02066         //int MAXR=size;
02067         EMData *this_temp=this_img->copy(); // ming change avg to to
02068         FloatPoint com_test,com_test1;
02069         com_test=this_temp->calc_center_of_mass();//ming add
02070         float com_this_x=com_test[0];
02071         float com_this_y=com_test[1];
02072         delete this_temp;
02073 
02074 
02075         EMData *that_temp=to->copy();
02076         com_test1=that_temp->calc_center_of_mass();
02077         float com_with_x=com_test1[0];
02078         float com_with_y=com_test1[1];
02079         delete that_temp;
02080 
02081         EMData *avg_frm=to->copy();
02082         float dx,dy;
02083         //float dx=-(com_with_x-nx/2); //ming
02084         //float dy=-(com_with_y-ny/2); //ming
02085         //avg_frm->translate(dx,dy,0.0);
02086         EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine
02087         //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1);
02088         EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR));
02089 
02090         float *sampl_fft=withpcsfft->get_data(); //
02091         delete avg_frm;
02092         delete withpcs;
02093 
02094         int bw=size/2;
02095         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02096         float pi2=2.0*M_PI, r2;
02097 
02098         EMData *data_in=new EMData;
02099         data_in->set_complex(true);
02100         data_in->set_ri(1);
02101         data_in->set_size(2*size,1,1);
02102         float * comp_in=data_in->get_data();
02103 
02104         int p_max=3;
02105         float *frm2dhhat=0;
02106 
02107         if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){
02108                 cout <<"Error in allocating memory 13. \n";
02109                 exit(1);
02110         }
02111         //printf("p_max=%d\n",p_max);
02112         float *sb=0, *cb=0;             // sin(beta) and cos(beta) for get h_hat, 300>size
02113         if((sb=new float[size])==NULL||(cb=new float[size])==NULL) {
02114                 cout <<"can't allocate more memory, terminating. \n";
02115                 exit(1);
02116         }
02117         for(int i=0;i<size;++i) {        // beta sampling, to calculate beta' and r'
02118                 float beta=i*M_PI/bw;
02119                 sb[i]=sin(beta);
02120                 cb[i]=cos(beta);
02121         }
02122 
02123         for(int p=0; p<=p_max; ++p){
02124                 ind1=p*size*bw;
02125         float pp2=(float)(p*p);
02126                 for(int n=0;n<bw;++n){         /* loop for n */
02127                 ind2=ind1+n;
02128                 for(int r=0;r<=MAXR;++r) {
02129                                 ind3=(ind2+r*bw)*size;
02130                         float rr2=(float)(r*r);
02131                                 float rp2=(float)(r*p);
02132                         for(int i=0;i<size;++i){                            // beta sampling, to get beta' and r'
02133                                 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i]));   // r2->r'
02134                                 int r1=(int)floor(r2+0.5f);                        // for computing gn(r')
02135                                 if(r1>MAXR){
02136                                         comp_in[2*i]=0.0f;
02137                                         comp_in[2*i+1]=0.0f;
02138                                 }
02139                                 else{
02140                                         float gn_r=sampl_fft[2*n+r1*(size+2)];           // real part of gn(r')
02141                                         float gn_i=sampl_fft[2*n+1+r1*(size+2)];           // imaginary part of gn(r')
02142                                                 float sb2, cb2, cn, sn;
02143                                                 if(n!=0){
02144                                                         if(r2 != 0.0){
02145                                                                 sb2=r*sb[i]/r2;
02146                                                                 cb2=(r*cb[i]-p)/r2;
02147                                                         }
02148                                                 else{
02149                                                                 sb2=0.0;
02150                                                                 cb2=1.0;
02151                                                         }
02152                                                 if(sb2>1.0) sb2= 1.0f;
02153                                                 if(sb2<-1.0)sb2=-1.0f;
02154                                                 if(cb2>1.0) cb2= 1.0f;
02155                                                 if(cb2<-1.0)cb2=-1.0f;
02156                                                 float beta2=atan2(sb2,cb2);
02157                                                 if(beta2<0.0) beta2+=pi2;
02158                                                 float nb2=n*beta2;
02159                                                 cn=cos(nb2);
02160                                                         sn=sin(nb2);
02161                                                 }
02162                                         else{
02163                                                         cn=1.0f; sn=0.0f;
02164                                                 }
02165                                                 comp_in[2*i]=cn*gn_r-sn*gn_i;
02166                                                 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r);
02167                                 }
02168                         }
02169                         EMData *data_out;
02170                         data_out=data_in->do_fft();
02171                         float * comp_out=data_out->get_data();
02172                         for(int m=0;m<size;m++){                                     // store hat{h(n,r,p)}(m)
02173                                         ind4=(ind3+m)*2;
02174                                         ind41=ind4+1;
02175                                         frm2dhhat[ind4]=comp_out[2*m];
02176                                         frm2dhhat[ind41]=comp_out[2*m+1];
02177                                 }
02178                         delete data_out;
02179                         }
02180                 }
02181         }
02182 
02183         delete[] sb;
02184         delete[] cb;
02185         delete data_in;
02186         delete withpcsfft;
02187 
02188         float dot_frm0=0.0f, dot_frm1=0.0f;
02189         EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0;
02190         //dr_frm=this_img->copy();
02191         for (int iFlip=0;iFlip<=1;++iFlip){
02192                 if (iFlip==0){dr_frm=this_img->copy();  da_nFlip=this_img->copy();}
02193                 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();}
02194                 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming   // image mirror about Y axis, so y keeps the same
02195 
02196                 dx=-(com_this_x-nx/2); //ming
02197                 dy=-(com_this_y-ny/2); //ming
02198                 dr_frm->translate(dx,dy,0.0); // this
02199                 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR);
02200                 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1);
02201                 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR);
02202                 delete selfpcs;
02203                 delete dr_frm;
02204                 if(iFlip==0)
02205                         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);
02206                 else
02207                         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);
02208                 delete selfpcsfft;
02209         }
02210 
02211         delete[] frm2dhhat;
02212         if(dot_frm0 <=dot_frm1) {
02213 #ifdef DEBUG
02214                 printf("best_corre=%f, no flip\n",dot_frm0);
02215 #endif
02216                 delete da_yFlip;
02217                 return da_nFlip;
02218         }
02219         else {
02220 #ifdef DEBUG
02221                 printf("best_corre=%f, flipped\n",dot_frm1);
02222 #endif
02223                 delete da_nFlip;
02224                 return da_yFlip;
02225         }
02226 }

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

Implements EMAN::Aligner.

Definition at line 997 of file aligner.h.

00998                                         {
00999                                                 return "FRM2D uses two rotational parameters and one translational parameter";
01000                                         }

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 992 of file aligner.h.

00993                                         {
00994                                                 return NAME;
00995                                         }

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

Implements EMAN::Aligner.

Definition at line 1006 of file aligner.h.

References EMAN::TypeDict::put().

01007                                         {
01008                                                         TypeDict d;
01009                                                         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.");
01010 
01011                                                         //d.put("p_max", EMObject::FLOAT,"p_max is");
01012                                                         return d;
01013                                         }

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

Definition at line 1002 of file aligner.h.

01003                                         {
01004                                                 return new FRM2DAligner();
01005                                         }


Member Data Documentation

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

Definition at line 70 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:47:11 2010 for EMAN2 by  doxygen 1.3.9.1