#include "emfft.h"
#include "cmp.h"
#include "aligner.h"
#include "averager.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) |
void | refalidf (const gsl_vector *v, void *params, gsl_vector *df) |
void | refalifdf (const gsl_vector *v, void *params, double *f, gsl_vector *df) |
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 | symquat (const gsl_vector *v, void *params) |
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 55 of file aligner.cpp. |
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Definition at line 2887 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(). 02888 { 02889 int size=rsize; 02890 float dx,dy; 02891 int bw=size/2; 02892 int MAXR=this_img->get_ysize()/2; 02893 //int MAXR=size; 02894 unsigned long tsize=2*size; 02895 unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0; 02896 unsigned long index0=0; 02897 int i=0, j=0, m=0, n=0, r=0; 02898 int loop_rho=0, rho_best=0; 02899 02900 float* gnr2 = new float[size*2]; 02901 float* maxcor = new float[size+1]; // MAXR need change 02902 02903 int p_max=p_max_input; 02904 float* result = new float[5*(p_max+1)]; 02905 float* cr=new float[size*(bw+1)]; 02906 float* ci=new float[size*(bw+1)]; 02907 EMData *data_in=new EMData; 02908 data_in->set_complex(true); 02909 data_in->set_fftodd(false); 02910 data_in->set_ri(true); 02911 data_in->set_size(size+2,size,1); 02912 float *in=data_in->get_data(); 02913 02914 float *self_sampl_fft = selfpcsfft->get_data(); // ming f(r) 02915 02916 float maxcor_sofar=0.0f; 02917 int p=0; 02918 02919 for(p=0; p<=p_max; ++p){ 02920 ind1=p*size*bw; 02921 for (i=0;i<size;++i) 02922 for (j=0;j<bw+1;++j){ 02923 cr[i*(bw+1)+j]=0.0; 02924 ci[i*(bw+1)+j]=0.0; 02925 } 02926 for(n=0;n<bw;++n){ // loop for n 02927 ind2=(ind1+n); 02928 index0=n*(bw+1); 02929 for(r=0;r<=MAXR;++r) { 02930 ind3=(ind2+r*bw)*size; 02931 for(m=0;m<size;m++){ // take back hat{h(n,r,p)}(m) 02932 ind4=(ind3+m)*2; 02933 ind41=ind4+1; 02934 gnr2[2*m]=frm2dhhat[ind4]; 02935 gnr2[2*m+1]=frm2dhhat[ind41]; 02936 } 02937 for(m=0;m<bw;++m){ 02938 float tempr=self_sampl_fft[2*m+r*(size+2)]*r; 02939 float tempi=self_sampl_fft[2*m+1+r*(size+2)]*r; 02940 float gnr2_r=gnr2[2*m]; 02941 float gnr2_i=gnr2[2*m+1]; 02942 cr[n*(bw+1)+m]+=gnr2_r*tempr+gnr2_i*tempi; 02943 ci[n*(bw+1)+m]+=gnr2_i*tempr-gnr2_r*tempi; 02944 if(n!=0){ // m,-n 02945 if(m!= 0){ 02946 int ssize=tsize-2*m; // ssize = 2*size-2m 02947 int ssize1=ssize+1; 02948 float gnr2_r=gnr2[ssize]; 02949 float gnr2_i=gnr2[ssize1]; 02950 cr[(size-n)*(bw+1)+m]+=gnr2_r*tempr-gnr2_i*tempi; 02951 ci[(size-n)*(bw+1)+m]-=gnr2_i*tempr+gnr2_r*tempi; 02952 } 02953 else{ 02954 cr[(size-n)*(bw+1)+m]+=*(gnr2)*tempr-*(gnr2+1)*tempi; 02955 ci[(size-n)*(bw+1)+m]-=*(gnr2+1)*tempr+*(gnr2)*tempi; 02956 } 02957 } 02958 } 02959 } 02960 } 02961 for (int cii=0; cii<size*(bw+1);++cii){ 02962 in[2*cii]=cr[cii]; 02963 in[2*cii+1]=ci[cii]; 02964 //printf("cii=%d,in[2i+1]=%f\n",cii, cr[cii]); 02965 } 02966 02967 EMData *data_out; 02968 data_out=data_in->do_ift(); 02969 float *c=data_out->get_data(); 02970 float tempr=0.0f, corre_fcs=999.0f; 02971 02972 int n_best=0, m_best=0; 02973 float temp=-100.0f; 02974 for(n=0;n<size;++n){// move Tri_2D to Tri = c(phi,phi';rho) 02975 for(m=0;m<size;++m){ 02976 temp=c[n*size+m]; 02977 if(temp>tempr) { 02978 tempr=temp; 02979 n_best=n; 02980 m_best=m; 02981 } 02982 } 02983 } 02984 delete data_out; 02985 02986 float corre,Phi2,Phi,Tx,Ty,Vx, Vy; 02987 02988 //for (n_best=0;n_best<bw;n_best++) 02989 // for (m_best=0;m_best<2*bw;m_best++){ 02990 //n_best=0; 02991 //m_best=70; 02992 Phi2=n_best*M_PI/bw; // ming this is reference image rotation angle 02993 Phi=m_best*M_PI/bw; // ming this is particle image rotation angle 02994 Vx=p*cos(Phi);//should use the angle of the centered one 02995 Vy=-p*sin(Phi); 02996 Tx=Vx+(floor(com_this_x+0.5f)-floor(com_with_x+0.5f)); 02997 Ty=Vy+(floor(com_this_y+0.5f)-floor(com_with_y+0.5f)); 02998 02999 dx=-Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image, 03000 dy=-Ty; // need to convert to raw image 03001 03002 EMData *this_tmp=this_img->copy();//ming change to to 03003 this_tmp->rotate(-(Phi2-Phi)*180.0f,0.0f,0.0f); 03004 this_tmp->translate(dx,dy,0.0); 03005 03006 corre=this_tmp->cmp(cmp_name,to,cmp_params); 03007 //printf("corre=%f\n",corre); 03008 delete this_tmp; 03009 if(corre<=corre_fcs) { //ming, cmp use smaller value stands for more similarity 03010 corre_fcs=corre; 03011 result[0+5*p] = float(p); // rho 03012 result[1+5*p] = corre; // correlation_fcs 03013 result[2+5*p] = (Phi2-Phi)*180.0f; // rotation angle 03014 result[3+5*p] = Tx; // Translation_x 03015 result[4+5*p] = Ty; // Translation_y 03016 } 03017 maxcor[p]=corre_fcs; // maximum correlation for current rho 03018 if(corre_fcs<maxcor_sofar) { 03019 maxcor_sofar=corre_fcs; // max correlation up to current rho 03020 rho_best=p; // the rho value with maxinum correlation value 03021 } 03022 if(p>=4){ 03023 if(maxcor[p] < maxcor[p-1] && maxcor[p-1] < maxcor[p-2]&& maxcor[p-2] < maxcor[p-3] && maxcor[p-3] < maxcor[p-4]){ 03024 loop_rho=1; 03025 break; //exit p loop 03026 } 03027 } 03028 } // end for p 03029 //}//test my method 03030 if(loop_rho == 1) 03031 p=p+1; 03032 int rb5=5*rho_best; 03033 float fsc = result[1+rb5]; 03034 float ang_keep = result[2+rb5]; 03035 float Tx = result[3+rb5]; 03036 float Ty = result[4+rb5]; 03037 delete[] gnr2; 03038 delete[] maxcor; 03039 delete[] result; 03040 delete cr; 03041 cr=0; 03042 delete ci; 03043 ci=0; 03044 delete data_in; // ming add 03045 dx = -Tx; // the Rota & Trans value (Tx,Ty, ang_keep) are for the projection image, 03046 dy = -Ty; // need to convert to raw image 03047 this_img->rotate(-ang_keep,0,0); // ming change this to this_img?? 03048 this_img->translate(dx,dy,0.0); // ming change this to this_img 03049 03050 03051 Transform tsoln(Dict("type","2d","alpha",ang_keep)); 03052 tsoln.set_trans(dx,dy); 03053 this_img->set_attr("xform.align2d",&tsoln); 03054 #ifdef DEBUG 03055 float fsc_best=this_img->cmp(cmp_name,to,cmp_params); 03056 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); 03057 #endif 03058 return fsc; // return the fsc coefficients 03059 } // FRM2D aligner sub_class
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Definition at line 1617 of file aligner.cpp. References refalifn(), v, and vp. 01617 { 01618 // we do this using a simple local difference estimate due to the expense of the calculation. 01619 // The step has to be large enough for the similarity metric 01620 // To provide an accurate change in value. 01621 static double lstep[4] = { 0.05, 0.05, 0.1, 0.01 }; 01622 01623 gsl_vector *vc = gsl_vector_alloc(v->size); 01624 gsl_vector_memcpy(vc,v); 01625 01626 double f = refalifn(v,params); 01627 for (unsigned int i=0; i<v->size; i++) { 01628 double *vp = gsl_vector_ptr(vc,i); 01629 *vp+=lstep[i]; 01630 double f2 = refalifn(vc,params); 01631 *vp-=lstep[i]; 01632 01633 gsl_vector_set(df,i,(f2-f)/lstep[i]); 01634 } 01635 01636 gsl_vector_free(vc); 01637 return; 01638 }
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Definition at line 1640 of file aligner.cpp. References refalifn(), v, and vp. 01640 { 01641 // we do this using a simple local difference estimate due to the expense of the calculation. 01642 // The step has to be large enough for the similarity metric 01643 // To provide an accurate change in value. 01644 static double lstep[4] = { 0.05, 0.05, 0.1, 0.01 }; 01645 01646 gsl_vector *vc = gsl_vector_alloc(v->size); 01647 gsl_vector_memcpy(vc,v); 01648 01649 *f = refalifn(v,params); 01650 for (unsigned int i=0; i<v->size; i++) { 01651 double *vp = gsl_vector_ptr(vc,i); 01652 *vp+=lstep[i]; 01653 double f2 = refalifn(vc,params); 01654 *vp-=lstep[i]; 01655 01656 gsl_vector_set(df,i,(f2-*f)/lstep[i]); 01657 } 01658 01659 gsl_vector_free(vc); 01660 return; 01661 01662 }
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Definition at line 1585 of file aligner.cpp. References EMAN::Cmp::cmp(), EMAN::Dict::has_key(), EMAN::EMData::mult(), EMAN::EMData::process(), EMAN::Transform::set_mirror(), EMAN::Transform::set_scale(), EMAN::Transform::set_trans(), t, v, x, and y. Referenced by refalidf(), and refalifdf(). 01586 { 01587 Dict *dict = (Dict *) params; 01588 01589 double x = gsl_vector_get(v, 0); 01590 double y = gsl_vector_get(v, 1); 01591 double a = gsl_vector_get(v, 2); 01592 01593 EMData *this_img = (*dict)["this"]; 01594 EMData *with = (*dict)["with"]; 01595 bool mirror = (*dict)["mirror"]; 01596 01597 Transform t(Dict("type","2d","alpha",static_cast<float>(a))); 01598 t.set_trans((float)x,(float)y); 01599 t.set_mirror(mirror); 01600 if (v->size>3) { 01601 float sca=(float)gsl_vector_get(v, 3); 01602 if (sca<.7 || sca>1.3) return 1.0e20; 01603 t.set_scale((float)gsl_vector_get(v, 3)); 01604 } 01605 EMData *tmp = this_img->process("xform",Dict("transform",&t)); 01606 if (dict->has_key("mask")) tmp->mult(*(EMData *)((*dict)["mask"])); 01607 01608 // printf("GSL %f %f %f %d %f\n",x,y,a,mirror,(float)gsl_vector_get(v, 3)); 01609 Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]); 01610 double result = c->cmp(tmp,with); 01611 01612 if (tmp != 0) delete tmp; 01613 01614 return result; 01615 }
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Definition at line 1996 of file aligner.cpp. References EMAN::Cmp::cmp(), EMAN::EMData::process(), refalin3d_perturbquat(), t, v, x, and y. 01997 { 01998 Dict *dict = (Dict *) params; 01999 02000 double n0 = gsl_vector_get(v, 0); 02001 double n1 = gsl_vector_get(v, 1); 02002 double n2 = gsl_vector_get(v, 2); 02003 double x = gsl_vector_get(v, 3); 02004 double y = gsl_vector_get(v, 4); 02005 double z = gsl_vector_get(v, 5); 02006 02007 EMData *this_img = (*dict)["this"]; 02008 EMData *with = (*dict)["with"]; 02009 02010 Transform* t = (*dict)["transform"]; 02011 float spincoeff = (*dict)["spincoeff"]; 02012 02013 Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z); 02014 02015 EMData *tmp = this_img->process("xform",Dict("transform",&soln)); 02016 Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]); 02017 double result = c->cmp(tmp,with); 02018 if ( tmp != 0 ) delete tmp; 02019 02020 //cout << result << endl; 02021 return result; 02022 }
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Definition at line 1664 of file aligner.cpp. References EMAN::EMData::dot_rotate_translate(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), v, x, and y. 01665 { 01666 Dict *dict = (Dict *) params; 01667 EMData *this_img = (*dict)["this"]; 01668 EMData *img_to = (*dict)["with"]; 01669 bool mirror = (*dict)["mirror"]; 01670 01671 double x = gsl_vector_get(v, 0); 01672 double y = gsl_vector_get(v, 1); 01673 double a = gsl_vector_get(v, 2); 01674 01675 double r = this_img->dot_rotate_translate(img_to, (float)x, (float)y, (float)a, mirror); 01676 int nsec = this_img->get_xsize() * this_img->get_ysize(); 01677 double result = 1.0 - r / nsec; 01678 01679 // cout << result << " x " << x << " y " << y << " az " << a << endl; 01680 return result; 01681 }
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Definition at line 1946 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(), EMAN::SymAlignProcessorQuat::align(), refalifn3dquat(), and symquat(). 01947 { 01948 Vec3f normal(n0,n1,n2); 01949 normal.normalize(); 01950 01951 float omega = spincoeff*sqrt(n0*n0 + n1*n1 + n2*n2); // Here we compute the spin by the rotation axis vector length 01952 Dict d; 01953 d["type"] = "spin"; 01954 d["omega"] = omega; 01955 d["n1"] = normal[0]; 01956 d["n2"] = normal[1]; 01957 d["n3"] = normal[2]; 01958 //cout << omega << " " << normal[0] << " " << normal[1] << " " << normal[2] << " " << n0 << " " << n1 << " " << n2 << endl; 01959 01960 Transform q(d); 01961 q.set_trans((float)x,(float)y,(float)z); 01962 01963 q = q*(*t); //compose transforms 01964 01965 return q; 01966 }
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Definition at line 1968 of file aligner.cpp. References EMAN::Cmp::cmp(), EMAN::EMData::process(), refalin3d_perturbquat(), t, v, x, and y. 01969 { 01970 Dict *dict = (Dict *) params; 01971 01972 double n0 = gsl_vector_get(v, 0); 01973 double n1 = gsl_vector_get(v, 1); 01974 double n2 = gsl_vector_get(v, 2); 01975 double x = gsl_vector_get(v, 3); 01976 double y = gsl_vector_get(v, 4); 01977 double z = gsl_vector_get(v, 5); 01978 01979 EMData* volume = (*dict)["volume"]; 01980 float spincoeff = (*dict)["spincoeff"]; 01981 Transform* t = (*dict)["transform"]; 01982 01983 Transform soln = refalin3d_perturbquat(t,spincoeff,(float)n0,(float)n1,(float)n2,(float)x,(float)y,(float)z); 01984 01985 EMData *tmp = volume->process("xform",Dict("transform",&soln)); 01986 EMData *symtmp = tmp->process("xform.applysym",Dict("sym",(*dict)["sym"])); 01987 Cmp* c = (Cmp*) ((void*)(*dict)["cmp"]); 01988 double result = c->cmp(symtmp,tmp); 01989 delete tmp; 01990 delete symtmp; 01991 01992 //cout << result << endl; 01993 return result; 01994 }
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