#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 2446 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(). 02448 { 02449 if (!this_img) { 02450 return 0; 02451 } 02452 if (to && !EMUtil::is_same_size(this_img, to)) 02453 throw ImageDimensionException("Images must be the same size to perform translational alignment"); 02454 02455 int nx=this_img->get_xsize(); 02456 int ny=this_img->get_ysize(); 02457 int size =(int)floor(M_PI*ny/4.0); 02458 size =Util::calc_best_fft_size(size);//ming bestfftsize(size); 02459 int MAXR=ny/2; 02460 //int MAXR=size; 02461 EMData *this_temp=this_img->copy(); // ming change avg to to 02462 FloatPoint com_test,com_test1; 02463 com_test=this_temp->calc_center_of_mass();//ming add 02464 float com_this_x=com_test[0]; 02465 float com_this_y=com_test[1]; 02466 delete this_temp; 02467 02468 02469 EMData *that_temp=to->copy(); 02470 com_test1=that_temp->calc_center_of_mass(); 02471 float com_with_x=com_test1[0]; 02472 float com_with_y=com_test1[1]; 02473 delete that_temp; 02474 02475 EMData *avg_frm=to->copy(); 02476 float dx,dy; 02477 //float dx=-(com_with_x-nx/2); //ming 02478 //float dy=-(com_with_y-ny/2); //ming 02479 //avg_frm->translate(dx,dy,0.0); 02480 EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine 02481 //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1); 02482 EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR)); 02483 02484 float *sampl_fft=withpcsfft->get_data(); // 02485 delete avg_frm; 02486 delete withpcs; 02487 02488 int bw=size/2; 02489 unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0; 02490 float pi2=2.0*M_PI, r2; 02491 02492 EMData *data_in=new EMData; 02493 data_in->set_complex(true); 02494 data_in->set_ri(1); 02495 data_in->set_size(2*size,1,1); 02496 float * comp_in=data_in->get_data(); 02497 02498 int p_max=3; 02499 float *frm2dhhat=0; 02500 02501 if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){ 02502 cout <<"Error in allocating memory 13. \n"; 02503 exit(1); 02504 } 02505 //printf("p_max=%d\n",p_max); 02506 float *sb=0, *cb=0; // sin(beta) and cos(beta) for get h_hat, 300>size 02507 if((sb=new float[size])==NULL||(cb=new float[size])==NULL) { 02508 cout <<"can't allocate more memory, terminating. \n"; 02509 exit(1); 02510 } 02511 for(int i=0;i<size;++i) { // beta sampling, to calculate beta' and r' 02512 float beta=i*M_PI/bw; 02513 sb[i]=sin(beta); 02514 cb[i]=cos(beta); 02515 } 02516 02517 for(int p=0; p<=p_max; ++p){ 02518 ind1=p*size*bw; 02519 float pp2=(float)(p*p); 02520 for(int n=0;n<bw;++n){ /* loop for n */ 02521 ind2=ind1+n; 02522 for(int r=0;r<=MAXR;++r) { 02523 ind3=(ind2+r*bw)*size; 02524 float rr2=(float)(r*r); 02525 float rp2=(float)(r*p); 02526 for(int i=0;i<size;++i){ // beta sampling, to get beta' and r' 02527 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i])); // r2->r' 02528 int r1=(int)floor(r2+0.5f); // for computing gn(r') 02529 if(r1>MAXR){ 02530 comp_in[2*i]=0.0f; 02531 comp_in[2*i+1]=0.0f; 02532 } 02533 else{ 02534 float gn_r=sampl_fft[2*n+r1*(size+2)]; // real part of gn(r') 02535 float gn_i=sampl_fft[2*n+1+r1*(size+2)]; // imaginary part of gn(r') 02536 float sb2, cb2, cn, sn; 02537 if(n!=0){ 02538 if(r2 != 0.0){ 02539 sb2=r*sb[i]/r2; 02540 cb2=(r*cb[i]-p)/r2; 02541 } 02542 else{ 02543 sb2=0.0; 02544 cb2=1.0; 02545 } 02546 if(sb2>1.0) sb2= 1.0f; 02547 if(sb2<-1.0)sb2=-1.0f; 02548 if(cb2>1.0) cb2= 1.0f; 02549 if(cb2<-1.0)cb2=-1.0f; 02550 float beta2=atan2(sb2,cb2); 02551 if(beta2<0.0) beta2+=pi2; 02552 float nb2=n*beta2; 02553 cn=cos(nb2); 02554 sn=sin(nb2); 02555 } 02556 else{ 02557 cn=1.0f; sn=0.0f; 02558 } 02559 comp_in[2*i]=cn*gn_r-sn*gn_i; 02560 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r); 02561 } 02562 } 02563 EMData *data_out; 02564 data_out=data_in->do_fft(); 02565 float * comp_out=data_out->get_data(); 02566 for(int m=0;m<size;m++){ // store hat{h(n,r,p)}(m) 02567 ind4=(ind3+m)*2; 02568 ind41=ind4+1; 02569 frm2dhhat[ind4]=comp_out[2*m]; 02570 frm2dhhat[ind41]=comp_out[2*m+1]; 02571 } 02572 delete data_out; 02573 } 02574 } 02575 } 02576 02577 delete[] sb; 02578 delete[] cb; 02579 delete data_in; 02580 delete withpcsfft; 02581 02582 float dot_frm0=0.0f, dot_frm1=0.0f; 02583 EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0; 02584 //dr_frm=this_img->copy(); 02585 for (int iFlip=0;iFlip<=1;++iFlip){ 02586 if (iFlip==0){dr_frm=this_img->copy(); da_nFlip=this_img->copy();} 02587 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();} 02588 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming // image mirror about Y axis, so y keeps the same 02589 02590 dx=-(com_this_x-nx/2); //ming 02591 dy=-(com_this_y-ny/2); //ming 02592 dr_frm->translate(dx,dy,0.0); // this 02593 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR); 02594 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1); 02595 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR); 02596 delete selfpcs; 02597 delete dr_frm; 02598 if(iFlip==0) 02599 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); 02600 else 02601 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); 02602 delete selfpcsfft; 02603 } 02604 02605 delete[] frm2dhhat; 02606 if(dot_frm0 <=dot_frm1) { 02607 #ifdef DEBUG 02608 printf("best_corre=%f, no flip\n",dot_frm0); 02609 #endif 02610 delete da_yFlip; 02611 return da_nFlip; 02612 } 02613 else { 02614 #ifdef DEBUG 02615 printf("best_corre=%f, flipped\n",dot_frm1); 02616 #endif 02617 delete da_nFlip; 02618 return da_yFlip; 02619 } 02620 }
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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. |