#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 1246 of file aligner.h.
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.
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 2486 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().
02488 { 02489 if (!this_img) { 02490 return 0; 02491 } 02492 if (to && !EMUtil::is_same_size(this_img, to)) 02493 throw ImageDimensionException("Images must be the same size to perform translational alignment"); 02494 02495 int nx=this_img->get_xsize(); 02496 int ny=this_img->get_ysize(); 02497 int size =(int)floor(M_PI*ny/4.0); 02498 size =Util::calc_best_fft_size(size);//ming bestfftsize(size); 02499 int MAXR=ny/2; 02500 //int MAXR=size; 02501 EMData *this_temp=this_img->copy(); // ming change avg to to 02502 FloatPoint com_test,com_test1; 02503 com_test=this_temp->calc_center_of_mass();//ming add 02504 float com_this_x=com_test[0]; 02505 float com_this_y=com_test[1]; 02506 delete this_temp; 02507 02508 02509 EMData *that_temp=to->copy(); 02510 com_test1=that_temp->calc_center_of_mass(); 02511 float com_with_x=com_test1[0]; 02512 float com_with_y=com_test1[1]; 02513 delete that_temp; 02514 02515 EMData *avg_frm=to->copy(); 02516 float dx,dy; 02517 //float dx=-(com_with_x-nx/2); //ming 02518 //float dy=-(com_with_y-ny/2); //ming 02519 //avg_frm->translate(dx,dy,0.0); 02520 EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine 02521 //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1); 02522 EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR)); 02523 02524 float *sampl_fft=withpcsfft->get_data(); // 02525 delete avg_frm; 02526 delete withpcs; 02527 02528 int bw=size/2; 02529 unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0; 02530 float pi2=2.0*M_PI, r2; 02531 02532 EMData *data_in=new EMData; 02533 data_in->set_complex(true); 02534 data_in->set_ri(1); 02535 data_in->set_size(2*size,1,1); 02536 float * comp_in=data_in->get_data(); 02537 02538 int p_max=3; 02539 float *frm2dhhat=0; 02540 02541 if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){ 02542 cout <<"Error in allocating memory 13. \n"; 02543 exit(1); 02544 } 02545 //printf("p_max=%d\n",p_max); 02546 float *sb=0, *cb=0; // sin(beta) and cos(beta) for get h_hat, 300>size 02547 if((sb=new float[size])==NULL||(cb=new float[size])==NULL) { 02548 cout <<"can't allocate more memory, terminating. \n"; 02549 exit(1); 02550 } 02551 for(int i=0;i<size;++i) { // beta sampling, to calculate beta' and r' 02552 float beta=i*M_PI/bw; 02553 sb[i]=sin(beta); 02554 cb[i]=cos(beta); 02555 } 02556 02557 for(int p=0; p<=p_max; ++p){ 02558 ind1=p*size*bw; 02559 float pp2=(float)(p*p); 02560 for(int n=0;n<bw;++n){ /* loop for n */ 02561 ind2=ind1+n; 02562 for(int r=0;r<=MAXR;++r) { 02563 ind3=(ind2+r*bw)*size; 02564 float rr2=(float)(r*r); 02565 float rp2=(float)(r*p); 02566 for(int i=0;i<size;++i){ // beta sampling, to get beta' and r' 02567 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i])); // r2->r' 02568 int r1=(int)floor(r2+0.5f); // for computing gn(r') 02569 if(r1>MAXR){ 02570 comp_in[2*i]=0.0f; 02571 comp_in[2*i+1]=0.0f; 02572 } 02573 else{ 02574 float gn_r=sampl_fft[2*n+r1*(size+2)]; // real part of gn(r') 02575 float gn_i=sampl_fft[2*n+1+r1*(size+2)]; // imaginary part of gn(r') 02576 float sb2, cb2, cn, sn; 02577 if(n!=0){ 02578 if(r2 != 0.0){ 02579 sb2=r*sb[i]/r2; 02580 cb2=(r*cb[i]-p)/r2; 02581 } 02582 else{ 02583 sb2=0.0; 02584 cb2=1.0; 02585 } 02586 if(sb2>1.0) sb2= 1.0f; 02587 if(sb2<-1.0)sb2=-1.0f; 02588 if(cb2>1.0) cb2= 1.0f; 02589 if(cb2<-1.0)cb2=-1.0f; 02590 float beta2=atan2(sb2,cb2); 02591 if(beta2<0.0) beta2+=pi2; 02592 float nb2=n*beta2; 02593 cn=cos(nb2); 02594 sn=sin(nb2); 02595 } 02596 else{ 02597 cn=1.0f; sn=0.0f; 02598 } 02599 comp_in[2*i]=cn*gn_r-sn*gn_i; 02600 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r); 02601 } 02602 } 02603 EMData *data_out; 02604 data_out=data_in->do_fft(); 02605 float * comp_out=data_out->get_data(); 02606 for(int m=0;m<size;m++){ // store hat{h(n,r,p)}(m) 02607 ind4=(ind3+m)*2; 02608 ind41=ind4+1; 02609 frm2dhhat[ind4]=comp_out[2*m]; 02610 frm2dhhat[ind41]=comp_out[2*m+1]; 02611 } 02612 delete data_out; 02613 } 02614 } 02615 } 02616 02617 delete[] sb; 02618 delete[] cb; 02619 delete data_in; 02620 delete withpcsfft; 02621 02622 float dot_frm0=0.0f, dot_frm1=0.0f; 02623 EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0; 02624 //dr_frm=this_img->copy(); 02625 for (int iFlip=0;iFlip<=1;++iFlip){ 02626 if (iFlip==0){dr_frm=this_img->copy(); da_nFlip=this_img->copy();} 02627 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();} 02628 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming // image mirror about Y axis, so y keeps the same 02629 02630 dx=-(com_this_x-nx/2); //ming 02631 dy=-(com_this_y-ny/2); //ming 02632 dr_frm->translate(dx,dy,0.0); // this 02633 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR); 02634 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1); 02635 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR); 02636 delete selfpcs; 02637 delete dr_frm; 02638 if(iFlip==0) 02639 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); 02640 else 02641 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); 02642 delete selfpcsfft; 02643 } 02644 02645 delete[] frm2dhhat; 02646 if(dot_frm0 <=dot_frm1) { 02647 #ifdef DEBUG 02648 printf("best_corre=%f, no flip\n",dot_frm0); 02649 #endif 02650 delete da_yFlip; 02651 return da_nFlip; 02652 } 02653 else { 02654 #ifdef DEBUG 02655 printf("best_corre=%f, flipped\n",dot_frm1); 02656 #endif 02657 delete da_nFlip; 02658 return da_yFlip; 02659 } 02660 }
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] |
virtual TypeDict EMAN::FRM2DAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1271 of file aligner.h.
References EMAN::EMObject::INT, and 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 }
static Aligner* EMAN::FRM2DAligner::NEW | ( | ) | [inline, static] |
const string FRM2DAligner::NAME = "frm2d" [static] |