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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 1728 of file aligner.h.

References align().

01729                                         {
01730                                                 return align(this_img, to_img, "frc", Dict());
01731                                         }

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 3063 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().

03065 {
03066         if (!this_img) {
03067                 return 0;
03068         }
03069         if (to && !EMUtil::is_same_size(this_img, to))
03070                 throw ImageDimensionException("Images must be the same size to perform translational alignment");
03071 
03072         int nx=this_img->get_xsize();
03073         int ny=this_img->get_ysize();
03074         int size =(int)floor(M_PI*ny/4.0);
03075         size =Util::calc_best_fft_size(size);//ming   bestfftsize(size);
03076         int MAXR=ny/2;
03077         //int MAXR=size;
03078         EMData *this_temp=this_img->copy(); // ming change avg to to
03079         FloatPoint com_test,com_test1;
03080         com_test=this_temp->calc_center_of_mass();//ming add
03081         float com_this_x=com_test[0];
03082         float com_this_y=com_test[1];
03083         delete this_temp;
03084 
03085 
03086         EMData *that_temp=to->copy();
03087         com_test1=that_temp->calc_center_of_mass();
03088         float com_with_x=com_test1[0];
03089         float com_with_y=com_test1[1];
03090         delete that_temp;
03091 
03092         EMData *avg_frm=to->copy();
03093         float dx,dy;
03094         //float dx=-(com_with_x-nx/2); //ming
03095         //float dy=-(com_with_y-ny/2); //ming
03096         //avg_frm->translate(dx,dy,0.0);
03097         EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine
03098         //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1);
03099         EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR));
03100 
03101         float *sampl_fft=withpcsfft->get_data(); //
03102         delete avg_frm;
03103         delete withpcs;
03104 
03105         int bw=size/2;
03106         unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0;
03107         float pi2=2.0*M_PI, r2;
03108 
03109         EMData *data_in=new EMData;
03110         data_in->set_complex(true);
03111         data_in->set_ri(1);
03112         data_in->set_size(2*size,1,1);
03113         float * comp_in=data_in->get_data();
03114 
03115         int p_max=3;
03116         float *frm2dhhat=0;
03117 
03118         if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){
03119                 cout <<"Error in allocating memory 13. \n";
03120                 exit(1);
03121         }
03122         //printf("p_max=%d\n",p_max);
03123         float *sb=0, *cb=0;             // sin(beta) and cos(beta) for get h_hat, 300>size
03124         if((sb=new float[size])==NULL||(cb=new float[size])==NULL) {
03125                 cout <<"can't allocate more memory, terminating. \n";
03126                 exit(1);
03127         }
03128         for(int i=0;i<size;++i) {        // beta sampling, to calculate beta' and r'
03129                 float beta=i*M_PI/bw;
03130                 sb[i]=sin(beta);
03131                 cb[i]=cos(beta);
03132         }
03133 
03134         for(int p=0; p<=p_max; ++p){
03135                 ind1=p*size*bw;
03136         float pp2=(float)(p*p);
03137                 for(int n=0;n<bw;++n){         /* loop for n */
03138                 ind2=ind1+n;
03139                 for(int r=0;r<=MAXR;++r) {
03140                                 ind3=(ind2+r*bw)*size;
03141                         float rr2=(float)(r*r);
03142                                 float rp2=(float)(r*p);
03143                         for(int i=0;i<size;++i){                            // beta sampling, to get beta' and r'
03144                                 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i]));   // r2->r'
03145                                 int r1=(int)floor(r2+0.5f);                        // for computing gn(r')
03146                                 if(r1>MAXR){
03147                                         comp_in[2*i]=0.0f;
03148                                         comp_in[2*i+1]=0.0f;
03149                                 }
03150                                 else{
03151                                         float gn_r=sampl_fft[2*n+r1*(size+2)];           // real part of gn(r')
03152                                         float gn_i=sampl_fft[2*n+1+r1*(size+2)];           // imaginary part of gn(r')
03153                                                 float sb2, cb2, cn, sn;
03154                                                 if(n!=0){
03155                                                         if(r2 != 0.0){
03156                                                                 sb2=r*sb[i]/r2;
03157                                                                 cb2=(r*cb[i]-p)/r2;
03158                                                         }
03159                                                 else{
03160                                                                 sb2=0.0;
03161                                                                 cb2=1.0;
03162                                                         }
03163                                                 if(sb2>1.0) sb2= 1.0f;
03164                                                 if(sb2<-1.0)sb2=-1.0f;
03165                                                 if(cb2>1.0) cb2= 1.0f;
03166                                                 if(cb2<-1.0)cb2=-1.0f;
03167                                                 float beta2=atan2(sb2,cb2);
03168                                                 if(beta2<0.0) beta2+=pi2;
03169                                                 float nb2=n*beta2;
03170                                                 cn=cos(nb2);
03171                                                         sn=sin(nb2);
03172                                                 }
03173                                         else{
03174                                                         cn=1.0f; sn=0.0f;
03175                                                 }
03176                                                 comp_in[2*i]=cn*gn_r-sn*gn_i;
03177                                                 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r);
03178                                 }
03179                         }
03180                         EMData *data_out;
03181                         data_out=data_in->do_fft();
03182                         float * comp_out=data_out->get_data();
03183                         for(int m=0;m<size;m++){                                     // store hat{h(n,r,p)}(m)
03184                                         ind4=(ind3+m)*2;
03185                                         ind41=ind4+1;
03186                                         frm2dhhat[ind4]=comp_out[2*m];
03187                                         frm2dhhat[ind41]=comp_out[2*m+1];
03188                                 }
03189                         delete data_out;
03190                         }
03191                 }
03192         }
03193 
03194         delete[] sb;
03195         delete[] cb;
03196         delete data_in;
03197         delete withpcsfft;
03198 
03199         float dot_frm0=0.0f, dot_frm1=0.0f;
03200         EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0;
03201         //dr_frm=this_img->copy();
03202         for (int iFlip=0;iFlip<=1;++iFlip){
03203                 if (iFlip==0){dr_frm=this_img->copy();  da_nFlip=this_img->copy();}
03204                 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();}
03205                 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming   // image mirror about Y axis, so y keeps the same
03206 
03207                 dx=-(com_this_x-nx/2); //ming
03208                 dy=-(com_this_y-ny/2); //ming
03209                 dr_frm->translate(dx,dy,0.0); // this
03210                 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR);
03211                 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1);
03212                 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR);
03213                 delete selfpcs;
03214                 delete dr_frm;
03215                 if(iFlip==0)
03216                         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);
03217                 else
03218                         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);
03219                 delete selfpcsfft;
03220         }
03221 
03222         delete[] frm2dhhat;
03223         if(dot_frm0 <=dot_frm1) {
03224 #ifdef DEBUG
03225                 printf("best_corre=%f, no flip\n",dot_frm0);
03226 #endif
03227                 delete da_yFlip;
03228                 return da_nFlip;
03229         }
03230         else {
03231 #ifdef DEBUG
03232                 printf("best_corre=%f, flipped\n",dot_frm1);
03233 #endif
03234                 delete da_nFlip;
03235                 return da_yFlip;
03236         }
03237 }

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

Implements EMAN::Aligner.

Definition at line 1738 of file aligner.h.

01739                                         {
01740                                                 return "FRM2D uses two rotational parameters and one translational parameter";
01741                                         }

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 1733 of file aligner.h.

01734                                         {
01735                                                 return NAME;
01736                                         }

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

Implements EMAN::Aligner.

Definition at line 1747 of file aligner.h.

References EMAN::TypeDict::put().

01748                                         {
01749                                                         TypeDict d;
01750                                                         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.");
01751 
01752                                                         //d.put("p_max", EMObject::FLOAT,"p_max is");
01753                                                         return d;
01754                                         }

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

Definition at line 1743 of file aligner.h.

01744                                         {
01745                                                 return new FRM2DAligner();
01746                                         }


Member Data Documentation

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

Definition at line 87 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:47:50 2013 for EMAN2 by  doxygen 1.3.9.1