#include "emfft.h"
#include "cmp.h"
#include "aligner.h"
#include "emdata.h"
#include "processor.h"
#include "util.h"
#include "symmetry.h"
#include <gsl/gsl_multimin.h>
#include "plugins/aligner_template.h"
Include dependency graph for aligner.cpp:
Go to the source code of this file.
Defines | |
#define | EMAN2_ALIGNER_DEBUG 0 |
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Functions | |
double | refalifn (const gsl_vector *v, void *params) |
double | refalifnfast (const gsl_vector *v, void *params) |
Transform | refalin3d_perturbquat (const Transform *const t, const float &spincoeff, const float &n0, const float &n1, const float &n2, const float &x, const float &y, const float &z) |
double | refalifn3dquat (const gsl_vector *v, void *params) |
float | frm_2d_Align (EMData *this_img, EMData *to, float *frm2dhhat, EMData *selfpcsfft, int p_max_input, int rsize, float &com_this_x, float &com_this_y, float &com_with_x, float &com_with_y, const string &cmp_name, const Dict &cmp_params) |
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Definition at line 54 of file aligner.cpp. |
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Definition at line 2310 of file aligner.cpp. References EMAN::EMData::cmp(), EMAN::EMData::copy(), EMAN::EMData::do_ift(), EMAN::EMData::get_data(), EMAN::EMData::get_ysize(), in, EMAN::EMData::rotate(), EMAN::EMData::set_attr(), EMAN::EMData::set_complex(), EMAN::EMData::set_fftodd(), EMAN::EMData::set_ri(), EMAN::EMData::set_size(), EMAN::Transform::set_trans(), and EMAN::EMData::translate(). Referenced by EMAN::FRM2DAligner::align(). 02311 { 02312 int size=rsize; 02313 float dx,dy; 02314 int bw=size/2; 02315 int MAXR=this_img->get_ysize()/2; 02316 //int MAXR=size; 02317 unsigned long tsize=2*size; 02318 unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0; 02319 unsigned long index0=0; 02320 int i=0, j=0, m=0, n=0, r=0; 02321 int loop_rho=0, rho_best=0; 02322 02323 float* gnr2 = new float[size*2]; 02324 float* maxcor = new float[size+1]; // MAXR need change 02325 02326 int p_max=p_max_input; 02327 float* result = new float[5*(p_max+1)]; 02328 float* cr=new float[size*(bw+1)]; 02329 float* ci=new float[size*(bw+1)]; 02330 EMData *data_in=new EMData; 02331 data_in->set_complex(true); 02332 data_in->set_fftodd(false); 02333 data_in->set_ri(true); 02334 data_in->set_size(size+2,size,1); 02335 float *in=data_in->get_data(); 02336 02337 float *self_sampl_fft = selfpcsfft->get_data(); // ming f(r) 02338 02339 float maxcor_sofar=0.0f; 02340 int p=0; 02341 02342 for(p=0; p<=p_max; ++p){ 02343 ind1=p*size*bw; 02344 for (i=0;i<size;++i) 02345 for (j=0;j<bw+1;++j){ 02346 cr[i*(bw+1)+j]=0.0; 02347 ci[i*(bw+1)+j]=0.0; 02348 } 02349 for(n=0;n<bw;++n){ // loop for n 02350 ind2=(ind1+n); 02351 index0=n*(bw+1); 02352 for(r=0;r<=MAXR;++r) { 02353 ind3=(ind2+r*bw)*size; 02354 for(m=0;m<size;m++){ // take back hat{h(n,r,p)}(m) 02355 ind4=(ind3+m)*2; 02356 ind41=ind4+1; 02357 gnr2[2*m]=frm2dhhat[ind4]; 02358 gnr2[2*m+1]=frm2dhhat[ind41]; 02359 } 02360 for(m=0;m<bw;++m){ 02361 float tempr=self_sampl_fft[2*m+r*(size+2)]*r; 02362 float tempi=self_sampl_fft[2*m+1+r*(size+2)]*r; 02363 float gnr2_r=gnr2[2*m]; 02364 float gnr2_i=gnr2[2*m+1]; 02365 cr[n*(bw+1)+m]+=gnr2_r*tempr+gnr2_i*tempi; 02366 ci[n*(bw+1)+m]+=gnr2_i*tempr-gnr2_r*tempi; 02367 if(n!=0){ // m,-n 02368 if(m!= 0){ 02369 int ssize=tsize-2*m; // ssize = 2*size-2m 02370 int ssize1=ssize+1; 02371 float gnr2_r=gnr2[ssize]; 02372 float gnr2_i=gnr2[ssize1]; 02373 cr[(size-n)*(bw+1)+m]+=gnr2_r*tempr-gnr2_i*tempi; 02374 ci[(size-n)*(bw+1)+m]-=gnr2_i*tempr+gnr2_r*tempi; 02375 } 02376 else{ 02377 cr[(size-n)*(bw+1)+m]+=*(gnr2)*tempr-*(gnr2+1)*tempi; 02378 ci[(size-n)*(bw+1)+m]-=*(gnr2+1)*tempr+*(gnr2)*tempi; 02379 } 02380 } 02381 } 02382 } 02383 } 02384 for (int cii=0; cii<size*(bw+1);++cii){ 02385 in[2*cii]=cr[cii]; 02386 in[2*cii+1]=ci[cii]; 02387 //printf("cii=%d,in[2i+1]=%f\n",cii, cr[cii]); 02388 } 02389 02390 EMData *data_out; 02391 data_out=data_in->do_ift(); 02392 float *c=data_out->get_data(); 02393 float tempr=0.0f, corre_fcs=999.0f; 02394 02395 int n_best=0, m_best=0; 02396 float temp=-100.0f; 02397 for(n=0;n<size;++n){// move Tri_2D to Tri = c(phi,phi';rho) 02398 for(m=0;m<size;++m){ 02399 temp=c[n*size+m]; 02400 if(temp>tempr) { 02401 tempr=temp; 02402 n_best=n; 02403 m_best=m; 02404 } 02405 } 02406 } 02407 delete data_out; 02408 02409 float corre,Phi2,Phi,Tx,Ty,Vx, Vy; 02410 02411 //for (n_best=0;n_best<bw;n_best++) 02412 // for (m_best=0;m_best<2*bw;m_best++){ 02413 //n_best=0; 02414 //m_best=70; 02415 Phi2=n_best*M_PI/bw; // ming this is reference image rotation angle 02416 Phi=m_best*M_PI/bw; // ming this is particle image rotation angle 02417 Vx=p*cos(Phi);//should use the angle of the centered one 02418 Vy=-p*sin(Phi); 02419 Tx=Vx+(floor(com_this_x+0.5f)-floor(com_with_x+0.5f)); 02420 Ty=Vy+(floor(com_this_y+0.5f)-floor(com_with_y+0.5f)); 02421 02422 dx=-Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image, 02423 dy=-Ty; // need to convert to raw image 02424 02425 EMData *this_tmp=this_img->copy();//ming change to to 02426 this_tmp->rotate(-(Phi2-Phi)*180.0f,0.0f,0.0f); 02427 this_tmp->translate(dx,dy,0.0); 02428 02429 corre=this_tmp->cmp(cmp_name,to,cmp_params); 02430 //printf("corre=%f\n",corre); 02431 delete this_tmp; 02432 if(corre<=corre_fcs) { //ming, cmp use smaller value stands for more similarity 02433 corre_fcs=corre; 02434 result[0+5*p] = float(p); // rho 02435 result[1+5*p] = corre; // correlation_fcs 02436 result[2+5*p] = (Phi2-Phi)*180.0f; // rotation angle 02437 result[3+5*p] = Tx; // Translation_x 02438 result[4+5*p] = Ty; // Translation_y 02439 } 02440 maxcor[p]=corre_fcs; // maximum correlation for current rho 02441 if(corre_fcs<maxcor_sofar) { 02442 maxcor_sofar=corre_fcs; // max correlation up to current rho 02443 rho_best=p; // the rho value with maxinum correlation value 02444 } 02445 if(p>=4){ 02446 if(maxcor[p] < maxcor[p-1] && maxcor[p-1] < maxcor[p-2]&& maxcor[p-2] < maxcor[p-3] && maxcor[p-3] < maxcor[p-4]){ 02447 loop_rho=1; 02448 break; //exit p loop 02449 } 02450 } 02451 } // end for p 02452 //}//test my method 02453 if(loop_rho == 1) 02454 p=p+1; 02455 int rb5=5*rho_best; 02456 float fsc = result[1+rb5]; 02457 float ang_keep = result[2+rb5]; 02458 float Tx = result[3+rb5]; 02459 float Ty = result[4+rb5]; 02460 delete[] gnr2; 02461 delete[] maxcor; 02462 delete[] result; 02463 delete cr; 02464 cr=0; 02465 delete ci; 02466 ci=0; 02467 delete data_in; // ming add 02468 dx = -Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image, 02469 dy = -Ty; // need to convert to raw image 02470 this_img->rotate(-ang_keep,0,0); // ming change this to this_img?? 02471 this_img->translate(dx,dy,0.0); // ming change this to this_img 02472 02473 02474 Transform tsoln(Dict("type","2d","alpha",ang_keep)); 02475 tsoln.set_trans(dx,dy); 02476 this_img->set_attr("xform.align2d",&tsoln); 02477 #ifdef DEBUG 02478 float fsc_best=this_img->cmp(cmp_name,to,cmp_params); 02479 printf("rho_best=%d fsc=%f fsc_best=%f dx=%f dy=%f ang_keep=%f com_withx=%f com_selfx=%f com_selfy=%f\n",rho_best,fsc,fsc_best,dx,dy,ang_keep,com_with_x,com_this_x,com_this_y); 02480 #endif 02481 return fsc; // return the fsc coefficients 02482 } // FRM2D aligner sub_class
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Definition at line 1323 of file aligner.cpp. References EMAN::Cmp::cmp(), EMAN::EMData::process(), EMAN::Transform::set_mirror(), EMAN::Transform::set_scale(), EMAN::Transform::set_trans(), t, v, x, and y. 01324 { 01325 Dict *dict = (Dict *) params; 01326 01327 double x = gsl_vector_get(v, 0); 01328 double y = gsl_vector_get(v, 1); 01329 double a = gsl_vector_get(v, 2); 01330 01331 EMData *this_img = (*dict)["this"]; 01332 EMData *with = (*dict)["with"]; 01333 bool mirror = (*dict)["mirror"]; 01334 01335 // float mean = (float)this_img->get_attr("mean"); 01336 // if ( Util::goodf(&mean) ) { 01337 // //cout << "tmps mean is nan even before rotation" << endl; 01338 // } 01339 01340 Transform t(Dict("type","2d","alpha",static_cast<float>(a))); 01341 // Transform3D t3d(Transform3D::EMAN, (float)a, 0.0f, 0.0f); 01342 // t3d.set_posttrans( (float) x, (float) y); 01343 // tmp->rotate_translate(t3d); 01344 t.set_trans((float)x,(float)y); 01345 t.set_mirror(mirror); 01346 if (v->size>3) { 01347 float sca=(float)gsl_vector_get(v, 3); 01348 if (sca<.7 || sca>1.3) return 1.0e20; 01349 t.set_scale((float)gsl_vector_get(v, 3)); 01350 } 01351 EMData *tmp = this_img->process("xform",Dict("transform",&t)); 01352 01353 // printf("GSL %f %f %f %d %f\n",x,y,a,mirror,(float)gsl_vector_get(v, 3)); 01354 Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]); 01355 double result = c->cmp(tmp,with); 01356 01357 // DELETE AT SOME STAGE, USEFUL FOR PRERELEASE STUFF 01358 // float test_result = (float)result; 01359 // if ( Util::goodf(&test_result) ) { 01360 // cout << "result " << result << " " << x << " " << y << " " << a << endl; 01361 // cout << (float)this_img->get_attr("mean") << " " << (float)tmp->get_attr("mean") << " " << (float)with->get_attr("mean") << endl; 01362 // tmp->write_image("tmp.hdf"); 01363 // with->write_image("with.hdf"); 01364 // this_img->write_image("this_img.hdf"); 01365 // EMData* t = this_img->copy(); 01366 // cout << (float)t->get_attr("mean") << endl; 01367 // t->rotate_translate( t3d ); 01368 // cout << (float)t->get_attr("mean") << endl; 01369 // cout << "exit" << endl; 01371 // cout << (float)t->get_attr("mean") << endl; 01372 // cout << "now exit" << endl; 01373 // delete t; 01374 // } 01375 01376 01377 if ( tmp != 0 ) delete tmp; 01378 01379 return result; 01380 }
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Definition at line 1558 of file aligner.cpp. References EMAN::Cmp::cmp(), EMAN::EMData::process(), refalin3d_perturbquat(), t, v, x, and y. 01559 { 01560 Dict *dict = (Dict *) params; 01561 01562 double n0 = gsl_vector_get(v, 0); 01563 double n1 = gsl_vector_get(v, 1); 01564 double n2 = gsl_vector_get(v, 2); 01565 double x = gsl_vector_get(v, 3); 01566 double y = gsl_vector_get(v, 4); 01567 double z = gsl_vector_get(v, 5); 01568 01569 EMData *this_img = (*dict)["this"]; 01570 EMData *with = (*dict)["with"]; 01571 // bool mirror = (*dict)["mirror"]; 01572 01573 Transform* t = (*dict)["transform"]; 01574 float spincoeff = (*dict)["spincoeff"]; 01575 01576 Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z); 01577 01578 EMData *tmp = this_img->process("xform",Dict("transform",&soln)); 01579 Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]); 01580 double result = c->cmp(tmp,with); 01581 if ( tmp != 0 ) delete tmp; 01582 delete t; t = 0; 01583 //cout << result << endl; 01584 return result; 01585 }
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Definition at line 1382 of file aligner.cpp. References EMAN::EMData::dot_rotate_translate(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), v, x, and y. 01383 { 01384 Dict *dict = (Dict *) params; 01385 EMData *this_img = (*dict)["this"]; 01386 EMData *img_to = (*dict)["with"]; 01387 bool mirror = (*dict)["mirror"]; 01388 01389 double x = gsl_vector_get(v, 0); 01390 double y = gsl_vector_get(v, 1); 01391 double a = gsl_vector_get(v, 2); 01392 01393 double r = this_img->dot_rotate_translate(img_to, (float)x, (float)y, (float)a, mirror); 01394 int nsec = this_img->get_xsize() * this_img->get_ysize(); 01395 double result = 1.0 - r / nsec; 01396 01397 // cout << result << " x " << x << " y " << y << " az " << a << endl; 01398 return result; 01399 }
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Definition at line 1536 of file aligner.cpp. References EMAN::Vec3< Type >::normalize(), q, EMAN::Transform::set_trans(), sqrt(), EMAN::Vec3f, x, and y. Referenced by EMAN::Refine3DAlignerQuaternion::align(), and refalifn3dquat(). 01537 { 01538 Vec3f normal(n0,n1,n2); 01539 normal.normalize(); 01540 01541 float omega = spincoeff*sqrt(n0*n0 + n1*n1 + n2*n2); // Here we compute the spin by the rotation axis vector length 01542 Dict d; 01543 d["type"] = "spin"; 01544 d["Omega"] = omega; 01545 d["n1"] = normal[0]; 01546 d["n2"] = normal[1]; 01547 d["n3"] = normal[2]; 01548 //cout << omega << " " << normal[0] << " " << normal[1] << " " << normal[2] << " " << n0 << " " << n1 << " " << n2 << endl; 01549 01550 Transform q(d); 01551 q.set_trans((float)x,(float)y,(float)z); 01552 01553 q = q*(*t); //compose transforms 01554 01555 return q; 01556 }
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