#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 | |
| Aligner * | NEW () |
Static Public Attributes | |
| const string | NAME = "frm2d" |
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Implements EMAN::Aligner. Definition at line 1252 of file aligner.h. References align(). 01253 {
01254 return align(this_img, to_img, "frc", Dict());
01255 }
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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.
Implements EMAN::Aligner. Definition at line 2486 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(). 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 }
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Implements EMAN::Aligner. Definition at line 1262 of file aligner.h. 01263 {
01264 return "FRM2D uses two rotational parameters and one translational parameter";
01265 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 1257 of file aligner.h. 01258 {
01259 return NAME;
01260 }
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Implements EMAN::Aligner. Definition at line 1271 of file aligner.h. References 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 }
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Definition at line 1267 of file aligner.h. 01268 {
01269 return new FRM2DAligner();
01270 }
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Definition at line 79 of file aligner.cpp. |
1.3.9.1