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 1650 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 1656 of file aligner.h.

References align().

01657                                         {
01658                                                 return align(this_img, to_img, "frc", Dict());
01659                                         }

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 2888 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().

02890 {
02891         if (!this_img) {
02892                 return 0;
02893         }
02894         if (to && !EMUtil::is_same_size(this_img, to))
02895                 throw ImageDimensionException("Images must be the same size to perform translational alignment");
02896 
02897         int nx=this_img->get_xsize();
02898         int ny=this_img->get_ysize();
02899         int size =(int)floor(M_PI*ny/4.0);
02900         size =Util::calc_best_fft_size(size);//ming   bestfftsize(size);
02901         int MAXR=ny/2;
02902         //int MAXR=size;
02903         EMData *this_temp=this_img->copy(); // ming change avg to to
02904         FloatPoint com_test,com_test1;
02905         com_test=this_temp->calc_center_of_mass();//ming add
02906         float com_this_x=com_test[0];
02907         float com_this_y=com_test[1];
02908         delete this_temp;
02909 
02910 
02911         EMData *that_temp=to->copy();
02912         com_test1=that_temp->calc_center_of_mass();
02913         float com_with_x=com_test1[0];
02914         float com_with_y=com_test1[1];
02915         delete that_temp;
02916 
02917         EMData *avg_frm=to->copy();
02918         float dx,dy;
02919         //float dx=-(com_with_x-nx/2); //ming
02920         //float dy=-(com_with_y-ny/2); //ming
02921         //avg_frm->translate(dx,dy,0.0);
02922         EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine
02923         //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1);
02924         EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR));
02925 
02926         float *sampl_fft=withpcsfft->get_data(); //
02927         delete avg_frm;
02928         delete withpcs;
02929 
02930         int bw=size/2;
02931         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
02932         float pi2=2.0*M_PI, r2;
02933 
02934         EMData *data_in=new EMData;
02935         data_in->set_complex(true);
02936         data_in->set_ri(1);
02937         data_in->set_size(2*size,1,1);
02938         float * comp_in=data_in->get_data();
02939 
02940         int p_max=3;
02941         float *frm2dhhat=0;
02942 
02943         if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){
02944                 cout <<"Error in allocating memory 13. \n";
02945                 exit(1);
02946         }
02947         //printf("p_max=%d\n",p_max);
02948         float *sb=0, *cb=0;             // sin(beta) and cos(beta) for get h_hat, 300>size
02949         if((sb=new float[size])==NULL||(cb=new float[size])==NULL) {
02950                 cout <<"can't allocate more memory, terminating. \n";
02951                 exit(1);
02952         }
02953         for(int i=0;i<size;++i) {        // beta sampling, to calculate beta' and r'
02954                 float beta=i*M_PI/bw;
02955                 sb[i]=sin(beta);
02956                 cb[i]=cos(beta);
02957         }
02958 
02959         for(int p=0; p<=p_max; ++p){
02960                 ind1=p*size*bw;
02961         float pp2=(float)(p*p);
02962                 for(int n=0;n<bw;++n){         /* loop for n */
02963                 ind2=ind1+n;
02964                 for(int r=0;r<=MAXR;++r) {
02965                                 ind3=(ind2+r*bw)*size;
02966                         float rr2=(float)(r*r);
02967                                 float rp2=(float)(r*p);
02968                         for(int i=0;i<size;++i){                            // beta sampling, to get beta' and r'
02969                                 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i]));   // r2->r'
02970                                 int r1=(int)floor(r2+0.5f);                        // for computing gn(r')
02971                                 if(r1>MAXR){
02972                                         comp_in[2*i]=0.0f;
02973                                         comp_in[2*i+1]=0.0f;
02974                                 }
02975                                 else{
02976                                         float gn_r=sampl_fft[2*n+r1*(size+2)];           // real part of gn(r')
02977                                         float gn_i=sampl_fft[2*n+1+r1*(size+2)];           // imaginary part of gn(r')
02978                                                 float sb2, cb2, cn, sn;
02979                                                 if(n!=0){
02980                                                         if(r2 != 0.0){
02981                                                                 sb2=r*sb[i]/r2;
02982                                                                 cb2=(r*cb[i]-p)/r2;
02983                                                         }
02984                                                 else{
02985                                                                 sb2=0.0;
02986                                                                 cb2=1.0;
02987                                                         }
02988                                                 if(sb2>1.0) sb2= 1.0f;
02989                                                 if(sb2<-1.0)sb2=-1.0f;
02990                                                 if(cb2>1.0) cb2= 1.0f;
02991                                                 if(cb2<-1.0)cb2=-1.0f;
02992                                                 float beta2=atan2(sb2,cb2);
02993                                                 if(beta2<0.0) beta2+=pi2;
02994                                                 float nb2=n*beta2;
02995                                                 cn=cos(nb2);
02996                                                         sn=sin(nb2);
02997                                                 }
02998                                         else{
02999                                                         cn=1.0f; sn=0.0f;
03000                                                 }
03001                                                 comp_in[2*i]=cn*gn_r-sn*gn_i;
03002                                                 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r);
03003                                 }
03004                         }
03005                         EMData *data_out;
03006                         data_out=data_in->do_fft();
03007                         float * comp_out=data_out->get_data();
03008                         for(int m=0;m<size;m++){                                     // store hat{h(n,r,p)}(m)
03009                                         ind4=(ind3+m)*2;
03010                                         ind41=ind4+1;
03011                                         frm2dhhat[ind4]=comp_out[2*m];
03012                                         frm2dhhat[ind41]=comp_out[2*m+1];
03013                                 }
03014                         delete data_out;
03015                         }
03016                 }
03017         }
03018 
03019         delete[] sb;
03020         delete[] cb;
03021         delete data_in;
03022         delete withpcsfft;
03023 
03024         float dot_frm0=0.0f, dot_frm1=0.0f;
03025         EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0;
03026         //dr_frm=this_img->copy();
03027         for (int iFlip=0;iFlip<=1;++iFlip){
03028                 if (iFlip==0){dr_frm=this_img->copy();  da_nFlip=this_img->copy();}
03029                 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();}
03030                 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming   // image mirror about Y axis, so y keeps the same
03031 
03032                 dx=-(com_this_x-nx/2); //ming
03033                 dy=-(com_this_y-ny/2); //ming
03034                 dr_frm->translate(dx,dy,0.0); // this
03035                 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR);
03036                 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1);
03037                 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR);
03038                 delete selfpcs;
03039                 delete dr_frm;
03040                 if(iFlip==0)
03041                         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);
03042                 else
03043                         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);
03044                 delete selfpcsfft;
03045         }
03046 
03047         delete[] frm2dhhat;
03048         if(dot_frm0 <=dot_frm1) {
03049 #ifdef DEBUG
03050                 printf("best_corre=%f, no flip\n",dot_frm0);
03051 #endif
03052                 delete da_yFlip;
03053                 return da_nFlip;
03054         }
03055         else {
03056 #ifdef DEBUG
03057                 printf("best_corre=%f, flipped\n",dot_frm1);
03058 #endif
03059                 delete da_nFlip;
03060                 return da_yFlip;
03061         }
03062 }

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

Implements EMAN::Aligner.

Definition at line 1666 of file aligner.h.

01667                                         {
01668                                                 return "FRM2D uses two rotational parameters and one translational parameter";
01669                                         }

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 1661 of file aligner.h.

References NAME.

01662                                         {
01663                                                 return NAME;
01664                                         }

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

Implements EMAN::Aligner.

Definition at line 1675 of file aligner.h.

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

01676                                         {
01677                                                         TypeDict d;
01678                                                         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.");
01679 
01680                                                         //d.put("p_max", EMObject::FLOAT,"p_max is");
01681                                                         return d;
01682                                         }

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

Definition at line 1671 of file aligner.h.

01672                                         {
01673                                                 return new FRM2DAligner();
01674                                         }


Member Data Documentation

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

Definition at line 1684 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:08:52 2012 for EMAN2 by  doxygen 1.4.7