#include <aligner.h>
Inheritance diagram for EMAN::FRM2DAligner:
Public Member Functions | |
virtual EMData * | align (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 EMData * | align (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 Aligner * | NEW () |
Static Public Attributes | |
static const string | NAME = "frm2d" |
Definition at line 1341 of file aligner.h.
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.
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. |
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] |
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] |
const string FRM2DAligner::NAME = "frm2d" [static] |