EMAN::OptSubCmp Class Reference

Uses math.sub.optimal to remove the density of the reference from the image as much as possible. More...

#include <cmp.h>

Inheritance diagram for EMAN::OptSubCmp:

Collaboration diagram for EMAN::OptSubCmp:

Public Member Functions
	OptSubCmp ()
float	cmp (EMData *image, EMData *with) const
	To compare 'image' with another image passed in through its parameters. More...
string	get_name () const
	Get the Cmp's name. More...
string	get_desc () const
TypeDict	get_param_types () const
	Get Cmp parameter information in a dictionary. More...
Public Member Functions inherited from EMAN::Cmp
virtual	~Cmp ()
virtual Dict	get_params () const
	Get the Cmp parameters in a key/value dictionary. More...
virtual void	set_params (const Dict &new_params)
	Set the Cmp parameters using a key/value dictionary. More...

Static Public Member Functions
static Cmp *	NEW ()

Static Public Attributes
static const string	NAME = "optsub"

Additional Inherited Members
Protected Member Functions inherited from EMAN::Cmp
void	validate_input_args (const EMData *image, const EMData *with) const
Protected Attributes inherited from EMAN::Cmp
Dict	params

Detailed Description

Uses math.sub.optimal to remove the density of the reference from the image as much as possible.

What is left should be pure noise if there is a good match. If the match is not as good there should be additional residual power. This comparator returns the average residual power after subtraction weighted in various ways

Definition at line 524 of file cmp.h.

Constructor & Destructor Documentation

OptSubCmp()

EMAN::OptSubCmp::OptSubCmp ( )

inline

Definition at line 527 of file cmp.h.

{}

Referenced by NEW().

Member Function Documentation

cmp()

float OptSubCmp::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 1575 of file cmp.cpp.

{
        ENTERFUNC;
        validate_input_args(image, with);
 
//      int snrweight = params.set_default("snrweight", 0);
//      int ampweight = params.set_default("ampweight", 0);
//      int sweight = params.set_default("sweight", 1);
//      int nweight = params.set_default("nweight", 0);
        int ctfweight = params.set_default("ctfweight",0);
        int zeromask = params.set_default("zeromask",0);
//      int swap = params.set_default("swap",0);
        float minres = params.set_default("minres",200.0f);
        float maxres = params.set_default("maxres",10.0f);
        EMData *mask = params.set_default("mask",(EMData *)NULL);
        
//      float ds=1.0f/((float)image->get_attr("apix_x")*(int)image->get_ysize());
        float apix=(float)image->get_attr("apix_x");
 
        // Sometimes we will get the "raw" image with CTF as image and sometimes as with, we always want to subtract the less noisy
        // reference, so if one has CTF parameters (even if ctfweight isn't used) we always pass it in as the primary
        EMData *diff;
        if (image->has_attr("ctf")) diff=image->process("math.sub.optimal",Dict("ref",with,"return_presigma",1,"low_cutoff_frequency",apix/minres ,"high_cutoff_frequency",apix/maxres,"ctfweight",ctfweight));
        else diff=with->process("math.sub.optimal",Dict("ref",image,"return_presigma",1,"low_cutoff_frequency",apix/minres ,"high_cutoff_frequency",apix/maxres,"ctfweight",ctfweight));
 
        if (mask!=NULL) diff->mult(*mask);
        if (zeromask) {
                EMData *tmp=with->process("threshold.notzero");
                diff->mult(*tmp);
                delete tmp;
        }
        
//      diff->process_inplace("filter.highpass.tophat",Dict("cutoff_freq",(float)1.0/minres));
//      diff->process_inplace("filter.lowpass.tophat",Dict("cutoff_freq",(float)1.0/maxres));
        
        float ret=(float)diff->get_attr("sigma")/(float)diff->get_attr("sigma_presub");
        delete diff;
        return ret;
        
        
//      EMData *diff=image->process("math.sub.optimal",Dict("ref",with,"return_fft",1));
//      
//      // Very expensive to use a mask, since it requires another ift/fft pair
//      if (mask!=NULL) {
//              EMData *tmp = diff->do_ift();
//              tmp->mult(*mask);
//              delete diff;
//              diff=tmp->do_fft();
//              delete tmp;
//      }
//      
//      // This gives us basically the 1-D power spectrum of what's left after subtraction (and masking)
//      vector<float> dist=diff->calc_radial_dist(diff->get_ysize()/2,0.0f,1.0f,1);
//      int s0=int(floor(1.0/(minres*ds)));
//      int s1=int(ceil(1.0/(maxres*ds)));
//      if (s0<2) s0=2;
//      
//      if (s1<=s0) throw InvalidCallException("OptSubCmp error. minres must be greater than maxres.");
// //   printf("%d %d\n",s0,s1);
//      
//      double sum=0.0f,sum2=0.0f;
//      for (int i=s0; i<s1; i++) sum+=dist[i]*i;
//      sum/=image->get_size()*s1;
//      
//      delete diff;
//      return sum;
}

References ENTERFUNC, EMAN::Cmp::params, EMAN::Dict::set_default(), and EMAN::Cmp::validate_input_args().

get_desc()

string EMAN::OptSubCmp::get_desc ( ) const

inlinevirtual

Implements EMAN::Cmp.

Definition at line 536 of file cmp.h.

                {
                        return "Residual power left in the image after optimally subtracting the reference with math.sub.optimal. Smaller values indicate a closer match.";
                }

get_name()

string EMAN::OptSubCmp::get_name ( ) const

inlinevirtual

Get the Cmp's name.

Each Cmp is identified by a unique name.

Returns

The Cmp's name.

Implements EMAN::Cmp.

Definition at line 531 of file cmp.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

TypeDict EMAN::OptSubCmp::get_param_types ( ) const

inlinevirtual

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 546 of file cmp.h.

                {
                        TypeDict d;
                        d.put("minres", EMObject::FLOAT, "Lowest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=200");
                        d.put("maxres", EMObject::FLOAT, "Highest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables.  Default=10");
                        d.put("zeromask", EMObject::BOOL, "Treat zero regions in 'with' as a mask");
                        d.put("ctfweight", EMObject::BOOL, "Weight frequencies using CTF");
//                      d.put("swap", EMObject::BOOL, "Swaps the identity of this and with, since A->B comparisons are not equivalent to B->A");
                        d.put("mask", EMObject::EMDATA, "Real space mask. Only computes the residual power under the mask. Significant speed penalty if specified. Default=None.");
                        return d;
                }

References EMAN::EMObject::BOOL, EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, and EMAN::TypeDict::put().

NEW()

static Cmp * EMAN::OptSubCmp::NEW ( )

inlinestatic

Definition at line 541 of file cmp.h.

                {
                        return new OptSubCmp();
                }

References OptSubCmp().

Member Data Documentation

NAME

const string OptSubCmp::NAME = "optsub"

static

Definition at line 558 of file cmp.h.

Referenced by get_name().

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The documentation for this class was generated from the following files:

• cmp.h
• cmp.cpp