This is a FSC comparitor for tomography. More...

#include <cmp.h>

Inheritance diagram for EMAN::TomoFscCmp:

Collaboration diagram for EMAN::TomoFscCmp:

[legend]

Public Member Functions
virtual float	cmp (EMData image, EMData with) const
	To compare 'image' with another image passed in through its parameters. More...

virtual string	get_name () const
	Get the Cmp's name. More...

virtual 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 = "fsc.tomo"

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

This is a FSC comparitor for tomography.

I only counts voxels above a threshold, which is obtained from subtomogram metadata

Author: John Flanagan

Date: 2012-2-02

Parameters

sigmas	The number of times the standard deviation of Fourier amplitudes to accept
minres	The minimum resolution to accept
maxes	The maximum resolution to accept
apix	The angstroms per pixel to use

Definition at line 447 of file cmp.h.

Member Function Documentation

◆ cmp()

float TomoFscCmp::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 856 of file cmp.cpp.

{
        ENTERFUNC;
        bool usecpu = 1;
        bool del_imagefft = 0;
        bool del_withfft = 0;
        float score = 1.0f;
        
        //get parameters
        if (!image->has_attr("spt_wedge_mean") || !image->has_attr("spt_wedge_sigma"))  throw InvalidCallException("Rubbish!!! Image Subtomogram does not have mena and/or sigma amps metadata");
        // BAD DESIGN!!!! The fact that I have to load attrs into a variable before I can do operations on them is silly
        
        //get threshold information
        float image_meanwedgeamp = image->get_attr("spt_wedge_mean");
        float image_sigmawedgeamp = image->get_attr("spt_wedge_sigma");
        
        // Use with amp stats if avaliable otherwise effectivly ignore
        float with_meanwedgeamp = image_meanwedgeamp;
        float with_sigmawedgeamp = image_sigmawedgeamp;
        if (with->has_attr("spt_wedge_mean") && with->has_attr("spt_wedge_sigma"))
        {
                with_meanwedgeamp = with->get_attr("spt_wedge_mean");
                with_sigmawedgeamp = with->get_attr("spt_wedge_sigma");
        }
 
        float apix = params.set_default("apix",image->get_attr_default("apix_x", 1.0f));
        //get min and max res
        float minres = params.set_default("minres",std::numeric_limits<float>::max());
        float maxres = params.set_default("maxres", 0.0f);
 
        // Find threshold
        float sigmas = params.set_default("sigmas",5.0f);
        float img_amp_thres = pow(image_meanwedgeamp + sigmas*image_sigmawedgeamp, 2.0f);
        float with_amp_thres = pow(with_meanwedgeamp + sigmas*with_sigmawedgeamp, 2.0f);
        
        // take negative of score
        float negative = (float)params.set_default("negative", 1.0f);
        if (negative) negative=-1.0; else negative=1.0;
        //get apix, use param apix, if not specified use apix_x, if this is not specified then apix=1.0
        
        //Check to ensure that images are complex
        EMData* image_fft = image;
        EMData* with_fft = with;
        
#ifdef EMAN2_USING_CUDA 
        //do CUDA FFT, does not allow minres, maxres yet
        if(EMData::usecuda == 1 && image->getcudarwdata() && with->getcudarwdata()) {
                if(!image->is_complex()){
                        del_imagefft = 1;
                        image_fft = image->do_fft_cuda();
                }
                if(!with->is_complex()){
                        del_withfft = 1;
                        with_fft = with->do_fft_cuda();
                }
                score = fsc_tomo_cmp_cuda(image_fft->getcudarwdata(), with_fft->getcudarwdata(), img_amp_thres, with_amp_thres, 0.0, 0.0, image_fft->get_xsize(), image_fft->get_ysize(), image_fft->get_zsize());
                usecpu = 0;
        }
#endif  
        if(usecpu){
                if(!image->is_complex()){
                        del_imagefft = 1;
                        image_fft = image->do_fft();
                }
                if(!with->is_complex()){
                        del_withfft = 1;
                        with_fft = with->do_fft();
                }
                
                //loop over all voxels
                int count = 0;
                double sum_imgamp_sq = 0.0;
                double sum_withamp_sq = 0.0;
                double cong = 0.0;
                float* img_data = image_fft->get_data();
                float* with_data = with_fft->get_data();
        
                int nx  = image_fft->get_xsize();
                int ny  = image_fft->get_ysize();
                int nz  = image_fft->get_zsize();
                int ny2 = ny/2;
                int nz2 = nz/2;
        
                //compute FSC
                int ii, kz, ky;
                for (int iz = 0; iz < nz; iz++) {
                        if(iz > nz2) kz = nz-iz; else kz=iz;
                        for (int iy = 0; iy < ny; iy++) {
                                if(iy > ny2) ky = ny-iy; else ky=iy;
                                for (int ix = 0; ix < nx; ix+=2) {
                                        //compute spatial frequency and convert to resolution stat
                                        float freq = std::sqrt(kz*kz + ky*ky + ix*ix/4.0f)/float(nz);
                                        float reso = apix/freq;
                                        
                                        //only look within a resolution domain
                                        if(reso < minres && reso > maxres){
                                                ii = ix + (iy  + iz * ny)* nx;
                                                float img_r = img_data[ii];
                                                float img_i = img_data[ii+1];
                                                float with_r = with_data[ii];
                                                float with_i = with_data[ii+1];
                                                double img_amp_sq = img_r*img_r + img_i*img_i;
                                                double with_amp_sq = with_r*with_r + with_i*with_i;
 
                                                if((img_amp_sq >  img_amp_thres) && (with_amp_sq >  with_amp_thres)){
                                                        count ++;
                                                        sum_imgamp_sq += img_amp_sq;
                                                        sum_withamp_sq += with_amp_sq;
                                                        cong += img_r*with_r + img_i*with_i;
                                                }
                                        }
                                }
                        }
                }
                
                if(count > 0){ 
                        score = (float)(cong/sqrt(sum_imgamp_sq*sum_withamp_sq));
                }else{
                        score = 1.0f;
                }
        }
        
        //avoid mem leaks
        if(del_imagefft) delete image_fft;
        if(del_withfft) delete with_fft;
        
        return negative*score;
        EXITFUNC;
}

References ENTERFUNC, EXITFUNC, fsc_tomo_cmp_cuda(), InvalidCallException, EMAN::Cmp::params, EMAN::Dict::set_default(), and sqrt().

◆ get_desc()

virtual string EMAN::TomoFscCmp::get_desc ( ) const

inlinevirtual

Implements EMAN::Cmp.

Definition at line 457 of file cmp.h.

                {
                        return "EXPERIMENTAL - Fsc with consideration given for the missing wedge. Not ready for routine use.";
                }

◆ get_name()

virtual string EMAN::TomoFscCmp::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 452 of file cmp.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::TomoFscCmp::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 467 of file cmp.h.

                {
                        TypeDict d;
                        d.put("normalize", EMObject::EMDATA,"Return the negative value (which is EMAN2 convention), Defalut is true(1)");
                        d.put("sigmas", EMObject::FLOAT, "The number of times the standard deviation of Fourier amplitudes to accept");
                        d.put("minres", EMObject::FLOAT, "The minimum resolution to accept (1/A) Default is inf");
                        d.put("maxres", EMObject::FLOAT, "The maximum resolution to accept (1/A) Default=0.0");
                        d.put("apix", EMObject::FLOAT, "The angstroms per pixel to use. Default = apix_x(1.0 if not present)");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 462 of file cmp.h.

                {
                        return new TomoFscCmp();
                }

Member Data Documentation

◆ NAME

const string TomoFscCmp::NAME = "fsc.tomo"

static

Definition at line 478 of file cmp.h.

Referenced by get_name().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ cmp()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

Member Data Documentation

◆ NAME