#include <cmp.h>
Inheritance diagram for EMAN::FRCCmp:
Public Member Functions | |
float | cmp (EMData *image, EMData *with) const |
To compare 'image' with another image passed in through its parameters. | |
string | get_name () const |
Get the Cmp's name. | |
string | get_desc () const |
TypeDict | get_param_types () const |
Get Cmp parameter information in a dictionary. | |
Static Public Member Functions | |
Cmp * | NEW () |
Static Public Attributes | |
const string | NAME = "frc" |
Fourier ring correlation (FRC) is a measure of statistical dependency between two averages, computed by comparison of rings in Fourier space. 1 means prefect agreement. 0 means no correlation.
Definition at line 508 of file cmp.h.
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To compare 'image' with another image passed in through its parameters. An optional transformation may be used to transform the 2 images.
Implements EMAN::Cmp. Definition at line 1126 of file cmp.cpp. References EMAN::Ctf::apix, EMAN::EMData::calc_fourier_shell_correlation(), EMAN::EMData::calc_radial_dist(), EMAN::Ctf::compute_1d(), EMAN::EMData::copy(), EMAN::EMData::do_fft(), EMAN::EMData::do_fft_inplace(), EMAN::EMObject::f, EMAN::EMData::get_attr(), EMAN::EMData::get_attr_default(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Util::goodf(), EMAN::EMData::has_attr(), InvalidCallException, EMAN::EMData::is_complex(), norm(), ny, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::update(), EMAN::Cmp::validate_input_args(), and weight. 01127 { 01128 ENTERFUNC; 01129 validate_input_args(image, with); 01130 01131 int snrweight = params.set_default("snrweight", 0); 01132 int ampweight = params.set_default("ampweight", 0); 01133 int sweight = params.set_default("sweight", 1); 01134 int nweight = params.set_default("nweight", 0); 01135 int zeromask = params.set_default("zeromask",0); 01136 float minres = params.set_default("minres",500.0f); 01137 float maxres = params.set_default("maxres",2.0f); 01138 01139 vector < float >fsc; 01140 bool use_cpu = true; 01141 //#ifdef EMAN2_USING_CUDA 01142 //if(image->getcudarwdata() && with->getcudarwdata()) { 01143 //throw UnexpectedBehaviorException("CUDA FRC cmp under construction...."); 01144 /* 01145 if (zeromask) throw UnexpectedBehaviorException("ZeroMask is not yet supported in CUDA"); 01146 01147 if (!image->is_complex()) { 01148 image=image->do_fft_cuda(); 01149 image->set_attr("free_me",1); 01150 } 01151 if (!with->is_complex()) { 01152 with=with->do_fft_cuda(); 01153 with->set_attr("free_me",1); 01154 } 01155 image->copy_rw_to_ro(); 01156 image->bindcudaarrayA(true); 01157 with->copy_rw_to_ro(); 01158 with->bindcudaarrayB(true); 01159 01160 float* fscarr = calc_fourier_shell_correlation_cuda(image->get_xsize(), image->get_ysize(), image->get_zsize(), 1); 01161 01162 use_cpu = false; 01163 */ 01164 //} 01165 01166 //#endif 01167 if (use_cpu) { 01168 if (zeromask) { 01169 image=image->copy(); 01170 with=with->copy(); 01171 01172 int sz=image->get_xsize()*image->get_ysize()*image->get_zsize(); 01173 float *d1=image->get_data(); 01174 float *d2=with->get_data(); 01175 01176 for (int i=0; i<sz; i++) { 01177 if (d1[i]==0.0 || d2[i]==0.0) { d1[i]=0.0; d2[i]=0.0; } 01178 } 01179 01180 image->update(); 01181 with->update(); 01182 image->do_fft_inplace(); 01183 with->do_fft_inplace(); 01184 image->set_attr("free_me",1); 01185 with->set_attr("free_me",1); 01186 } 01187 01188 01189 if (!image->is_complex()) { 01190 image=image->do_fft(); 01191 image->set_attr("free_me",1); 01192 } 01193 if (!with->is_complex()) { 01194 with=with->do_fft(); 01195 with->set_attr("free_me",1); 01196 } 01197 01198 fsc = image->calc_fourier_shell_correlation(with,1); 01199 } 01200 01201 int ny = image->get_ysize(); 01202 int ny2=ny/2+1; 01203 01204 // The fast hypot here was supposed to speed things up. Little effect 01205 // if (image->get_zsize()>1) fsc = image->calc_fourier_shell_correlation(with,1); 01206 // else { 01207 // double *sxy = (double *)malloc(ny2*sizeof(double)*4); 01208 // double *sxx = sxy+ny2; 01209 // double *syy = sxy+2*ny2; 01210 // double *norm= sxy+3*ny2; 01211 // 01212 // float *df1=image->get_data(); 01213 // float *df2=with->get_data(); 01214 // int nx2=image->get_xsize(); 01215 // 01216 // for (int y=-ny/2; y<ny/2; y++) { 01217 // for (int x=0; x<nx2/2; x++) { 01218 // if (x==0 && y<0) continue; // skip Friedel pair 01219 // short r=Util::hypot_fast_int(x,y); 01220 // if (r>ny2-1) continue; 01221 // int l=x*2+(y<0?ny+y:y)*nx2; 01222 // sxy[r]+=df1[l]*df2[l]+df1[l+1]*df2[l+1]; 01223 // sxx[r]+=df1[l]*df1[l]; 01224 // syy[r]+=df2[l]*df2[l]; 01225 // norm[r]+=1.0; 01226 // } 01227 // } 01228 // fsc.resize(ny2*3); 01229 // for (int r=0; r<ny2; r++) { 01230 // fsc[r]=r*0.5/ny2; 01231 // fsc[ny2+r]=sxy[r]/(sqrt(sxx[r])*sqrt(syy[r])); 01232 // fsc[ny2*2+r]=norm[r]; 01233 // } 01234 // free(sxy); 01235 // } 01236 01237 vector<float> snr; 01238 if (snrweight) { 01239 Ctf *ctf = NULL; 01240 if (!image->has_attr("ctf")) { 01241 if (!with->has_attr("ctf")) throw InvalidCallException("SNR weight with no CTF parameters"); 01242 ctf=with->get_attr("ctf"); 01243 } 01244 else ctf=image->get_attr("ctf"); 01245 01246 float ds=1.0f/(ctf->apix*ny); 01247 snr=ctf->compute_1d(ny,ds,Ctf::CTF_SNR); 01248 if(ctf) {delete ctf; ctf=0;} 01249 } 01250 01251 vector<float> amp; 01252 if (ampweight) amp=image->calc_radial_dist(ny/2,0,1,0); 01253 01254 // Min/max modifications to weighting 01255 float pmin,pmax; 01256 if (minres>0) pmin=((float)image->get_attr("apix_x")*image->get_ysize())/minres; //cutoff in pixels, assume square 01257 else pmin=0; 01258 if (maxres>0) pmax=((float)image->get_attr("apix_x")*image->get_ysize())/maxres; 01259 else pmax=0; 01260 01261 double sum=0.0, norm=0.0; 01262 01263 for (int i=0; i<ny/2; i++) { 01264 double weight=1.0; 01265 if (sweight) weight*=fsc[(ny2)*2+i]; 01266 if (ampweight) weight*=amp[i]; 01267 if (snrweight) weight*=snr[i]; 01268 // if (snrweight) { 01269 // if (snr[i]>0) weight*=sqrt(snr[i]); 01270 // else weight=0; 01271 // } 01272 //if(snr[i]<0) printf("snr[%d] = %1.5g\n",i,snr[i]); 01273 if (pmin>0) weight*=(tanh(5.0*(i-pmin)/pmin)+1.0)/2.0; 01274 if (pmax>0) weight*=(1.0-tanh(i-pmax))/2.0; 01275 01276 sum+=weight*fsc[ny2+i]; 01277 norm+=weight; 01278 // printf("%d\t%f\t%f\n",i,weight,fsc[ny/2+1+i]); 01279 } 01280 01281 // This performs a weighting that tries to normalize FRC by correcting from the number of particles represented by the average 01282 sum/=norm; 01283 if (nweight && with->get_attr_default("ptcl_repr",0) && sum>=0 && sum<1.0) { 01284 sum=sum/(1.0-sum); // convert to SNR 01285 sum/=(float)with->get_attr_default("ptcl_repr",0); // divide by ptcl represented 01286 sum=sum/(1.0+sum); // convert back to correlation 01287 } 01288 01289 if (image->has_attr("free_me")) delete image; 01290 if (with->has_attr("free_me")) delete with; 01291 01292 EXITFUNC; 01293 01294 01295 if (!Util::goodf(&sum)) sum=-3.0e38; 01296 //.Note the negative! This is because EMAN2 follows the convention that 01297 // smaller return values from comparitors indicate higher similarity - 01298 // this enables comparitors to be used in a generic fashion. 01299 return (float)-sum; 01300 }
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Implements EMAN::Cmp. Definition at line 518 of file cmp.h. 00519 { 00520 return "Computes the mean Fourier Ring Correlation between the image and reference (with optional weighting factors)."; 00521 }
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Get the Cmp's name. Each Cmp is identified by a unique name.
Implements EMAN::Cmp. Definition at line 513 of file cmp.h. 00514 {
00515 return NAME;
00516 }
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Get Cmp parameter information in a dictionary. Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.
Implements EMAN::Cmp. Definition at line 528 of file cmp.h. References EMAN::TypeDict::put(). 00529 { 00530 TypeDict d; 00531 d.put("snrweight", EMObject::INT, "If set, the SNR of 'this' will be used to weight the result. If 'this' lacks CTF info, it will check 'with'. (default=0)"); 00532 d.put("ampweight", EMObject::INT, "If set, the amplitude of 'this' will be used to weight the result (default=0)"); 00533 d.put("sweight", EMObject::INT, "If set, weight the (1-D) average by the number of pixels in each ring (default=1)"); 00534 d.put("nweight", EMObject::INT, "Downweight similarity based on number of particles in reference (default=0)"); 00535 d.put("zeromask", EMObject::INT, "Treat regions in either image that are zero as a mask"); 00536 d.put("minres", EMObject::FLOAT, "Lowest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=500"); 00537 d.put("maxres", EMObject::FLOAT, "Highest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=10"); 00538 return d; 00539 }
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Definition at line 523 of file cmp.h. 00524 { 00525 return new FRCCmp(); 00526 }
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