EMAN::FRCCmp Class Reference

FRCCmp returns a quality factor based on FRC between images. More...

#include <cmp.h>

Inheritance diagram for EMAN::FRCCmp:

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Collaboration diagram for EMAN::FRCCmp:

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List of all members.

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

static CmpNEW ()

Static Public Attributes

static const string NAME = "frc"

Detailed Description

FRCCmp returns a quality factor based on FRC between images.

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.


Member Function Documentation

float FRCCmp::cmp ( EMData image,
EMData with 
) const [virtual]

To compare 'image' with another image passed in through its parameters.

An optional transformation may be used to transform the 2 images.

Parameters:
image The first image to be compared.
with The second image to be comppared.
Returns:
The comparison result. Smaller better by default

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::Ctf::CTF_SNR, EMAN::EMData::do_fft(), EMAN::EMData::do_fft_inplace(), ENTERFUNC, EXITFUNC, 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::Cmp::params, 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 }

string EMAN::FRCCmp::get_desc (  )  const [inline, virtual]

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                 }

string EMAN::FRCCmp::get_name (  )  const [inline, virtual]

Get the Cmp's name.

Each Cmp is identified by a unique name.

Returns:
The Cmp's name.

Implements EMAN::Cmp.

Definition at line 513 of file cmp.h.

References NAME.

00514                 {
00515                         return NAME;
00516                 }

TypeDict EMAN::FRCCmp::get_param_types (  )  const [inline, virtual]

Get Cmp parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns:
A dictionary containing the parameter info.

Implements EMAN::Cmp.

Definition at line 528 of file cmp.h.

References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and 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                 }

static Cmp* EMAN::FRCCmp::NEW (  )  [inline, static]

Definition at line 523 of file cmp.h.

00524                 {
00525                         return new FRCCmp();
00526                 }


Member Data Documentation

const string FRCCmp::NAME = "frc" [static]

Definition at line 541 of file cmp.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:48:10 2011 for EMAN2 by  doxygen 1.4.7