#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 987 of file aligner.h. References align(). 00988 { 00989 return align(this_img, to_img, "frc", Dict()); 00990 }
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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 2052 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(). 02054 { 02055 if (!this_img) { 02056 return 0; 02057 } 02058 if (to && !EMUtil::is_same_size(this_img, to)) 02059 throw ImageDimensionException("Images must be the same size to perform translational alignment"); 02060 02061 int nx=this_img->get_xsize(); 02062 int ny=this_img->get_ysize(); 02063 int size =(int)floor(M_PI*ny/4.0); 02064 size =Util::calc_best_fft_size(size);//ming bestfftsize(size); 02065 int MAXR=ny/2; 02066 //int MAXR=size; 02067 EMData *this_temp=this_img->copy(); // ming change avg to to 02068 FloatPoint com_test,com_test1; 02069 com_test=this_temp->calc_center_of_mass();//ming add 02070 float com_this_x=com_test[0]; 02071 float com_this_y=com_test[1]; 02072 delete this_temp; 02073 02074 02075 EMData *that_temp=to->copy(); 02076 com_test1=that_temp->calc_center_of_mass(); 02077 float com_with_x=com_test1[0]; 02078 float com_with_y=com_test1[1]; 02079 delete that_temp; 02080 02081 EMData *avg_frm=to->copy(); 02082 float dx,dy; 02083 //float dx=-(com_with_x-nx/2); //ming 02084 //float dy=-(com_with_y-ny/2); //ming 02085 //avg_frm->translate(dx,dy,0.0); 02086 EMData *withpcs=avg_frm->unwrap_largerR(0,MAXR,size,float(MAXR)); // ming, something wrong inside this subroutine 02087 //EMData *withpcs=avg_frm->unwrap(-1,-1,-1,0,0,1); 02088 EMData *withpcsfft=withpcs->oneDfftPolar(size, float(MAXR), float(MAXR)); 02089 02090 float *sampl_fft=withpcsfft->get_data(); // 02091 delete avg_frm; 02092 delete withpcs; 02093 02094 int bw=size/2; 02095 unsigned long ind1=0, ind2=0, ind3=0, ind4=0, ind41=0; 02096 float pi2=2.0*M_PI, r2; 02097 02098 EMData *data_in=new EMData; 02099 data_in->set_complex(true); 02100 data_in->set_ri(1); 02101 data_in->set_size(2*size,1,1); 02102 float * comp_in=data_in->get_data(); 02103 02104 int p_max=3; 02105 float *frm2dhhat=0; 02106 02107 if( (frm2dhhat=(float *)malloc((p_max+1)*(size+2)*bw*size*2* sizeof(float)))==NULL){ 02108 cout <<"Error in allocating memory 13. \n"; 02109 exit(1); 02110 } 02111 //printf("p_max=%d\n",p_max); 02112 float *sb=0, *cb=0; // sin(beta) and cos(beta) for get h_hat, 300>size 02113 if((sb=new float[size])==NULL||(cb=new float[size])==NULL) { 02114 cout <<"can't allocate more memory, terminating. \n"; 02115 exit(1); 02116 } 02117 for(int i=0;i<size;++i) { // beta sampling, to calculate beta' and r' 02118 float beta=i*M_PI/bw; 02119 sb[i]=sin(beta); 02120 cb[i]=cos(beta); 02121 } 02122 02123 for(int p=0; p<=p_max; ++p){ 02124 ind1=p*size*bw; 02125 float pp2=(float)(p*p); 02126 for(int n=0;n<bw;++n){ /* loop for n */ 02127 ind2=ind1+n; 02128 for(int r=0;r<=MAXR;++r) { 02129 ind3=(ind2+r*bw)*size; 02130 float rr2=(float)(r*r); 02131 float rp2=(float)(r*p); 02132 for(int i=0;i<size;++i){ // beta sampling, to get beta' and r' 02133 r2=std::sqrt((float)(rr2+pp2-2.0*rp2*cb[i])); // r2->r' 02134 int r1=(int)floor(r2+0.5f); // for computing gn(r') 02135 if(r1>MAXR){ 02136 comp_in[2*i]=0.0f; 02137 comp_in[2*i+1]=0.0f; 02138 } 02139 else{ 02140 float gn_r=sampl_fft[2*n+r1*(size+2)]; // real part of gn(r') 02141 float gn_i=sampl_fft[2*n+1+r1*(size+2)]; // imaginary part of gn(r') 02142 float sb2, cb2, cn, sn; 02143 if(n!=0){ 02144 if(r2 != 0.0){ 02145 sb2=r*sb[i]/r2; 02146 cb2=(r*cb[i]-p)/r2; 02147 } 02148 else{ 02149 sb2=0.0; 02150 cb2=1.0; 02151 } 02152 if(sb2>1.0) sb2= 1.0f; 02153 if(sb2<-1.0)sb2=-1.0f; 02154 if(cb2>1.0) cb2= 1.0f; 02155 if(cb2<-1.0)cb2=-1.0f; 02156 float beta2=atan2(sb2,cb2); 02157 if(beta2<0.0) beta2+=pi2; 02158 float nb2=n*beta2; 02159 cn=cos(nb2); 02160 sn=sin(nb2); 02161 } 02162 else{ 02163 cn=1.0f; sn=0.0f; 02164 } 02165 comp_in[2*i]=cn*gn_r-sn*gn_i; 02166 comp_in[2*i+1]=-(cn*gn_i+sn*gn_r); 02167 } 02168 } 02169 EMData *data_out; 02170 data_out=data_in->do_fft(); 02171 float * comp_out=data_out->get_data(); 02172 for(int m=0;m<size;m++){ // store hat{h(n,r,p)}(m) 02173 ind4=(ind3+m)*2; 02174 ind41=ind4+1; 02175 frm2dhhat[ind4]=comp_out[2*m]; 02176 frm2dhhat[ind41]=comp_out[2*m+1]; 02177 } 02178 delete data_out; 02179 } 02180 } 02181 } 02182 02183 delete[] sb; 02184 delete[] cb; 02185 delete data_in; 02186 delete withpcsfft; 02187 02188 float dot_frm0=0.0f, dot_frm1=0.0f; 02189 EMData *da_nFlip=0, *da_yFlip=0, *dr_frm=0; 02190 //dr_frm=this_img->copy(); 02191 for (int iFlip=0;iFlip<=1;++iFlip){ 02192 if (iFlip==0){dr_frm=this_img->copy(); da_nFlip=this_img->copy();} 02193 else {dr_frm=this_img->copy(); da_yFlip=this_img->copy();} 02194 if(iFlip==1) {com_this_x=nx-com_this_x; } //ming // image mirror about Y axis, so y keeps the same 02195 02196 dx=-(com_this_x-nx/2); //ming 02197 dy=-(com_this_y-ny/2); //ming 02198 dr_frm->translate(dx,dy,0.0); // this 02199 EMData *selfpcs = dr_frm->unwrap_largerR(0,MAXR,size, (float)MAXR); 02200 //EMData *selfpcs=dr_frm->unwrap(-1,-1,-1,0,0,1); 02201 EMData *selfpcsfft = selfpcs->oneDfftPolar(size, (float)MAXR, (float)MAXR); 02202 delete selfpcs; 02203 delete dr_frm; 02204 if(iFlip==0) 02205 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); 02206 else 02207 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); 02208 delete selfpcsfft; 02209 } 02210 02211 delete[] frm2dhhat; 02212 if(dot_frm0 <=dot_frm1) { 02213 #ifdef DEBUG 02214 printf("best_corre=%f, no flip\n",dot_frm0); 02215 #endif 02216 delete da_yFlip; 02217 return da_nFlip; 02218 } 02219 else { 02220 #ifdef DEBUG 02221 printf("best_corre=%f, flipped\n",dot_frm1); 02222 #endif 02223 delete da_nFlip; 02224 return da_yFlip; 02225 } 02226 }
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Implements EMAN::Aligner. Definition at line 997 of file aligner.h. 00998 { 00999 return "FRM2D uses two rotational parameters and one translational parameter"; 01000 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 992 of file aligner.h. 00993 {
00994 return NAME;
00995 }
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Implements EMAN::Aligner. Definition at line 1006 of file aligner.h. References EMAN::TypeDict::put(). 01007 { 01008 TypeDict d; 01009 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."); 01010 01011 //d.put("p_max", EMObject::FLOAT,"p_max is"); 01012 return d; 01013 }
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Definition at line 1002 of file aligner.h. 01003 { 01004 return new FRM2DAligner(); 01005 }
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Definition at line 70 of file aligner.cpp. |