TomoAverager averages a list of volumes in Fourier space. More...

#include <averager.h>

Inheritance diagram for EMAN::TomoAverager:

Collaboration diagram for EMAN::TomoAverager:

[legend]

Public Member Functions
	TomoAverager ()

virtual	~TomoAverager ()

void	add_image (EMData *image)
	To add an image to the Averager. More...

EMData *	finish ()
	Finish up the averaging and return the result. More...

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

string	get_desc () const

TypeDict	get_param_types () const
	Get Averager parameter information in a dictionary. More...

virtual void	mult (const float &)
	Multiply the result image by some floating point constant This is useful when weighting the input images prior to calling add_image - a situation where it is likely you want to divide by the sum of the weights. More...

Public Member Functions inherited from EMAN::Averager
	Averager ()

virtual	~Averager ()

virtual void	add_image_list (const vector< EMData * > &images)
	To add multiple images to the Averager. More...

virtual void	set_params (const Dict &new_params)
	Set the Averager parameters using a key/value dictionary. More...

Static Public Member Functions
static Averager *	NEW ()

Static Public Attributes
static const string	NAME = "mean.tomo"

Private Attributes
EMData *	norm_image

float	thresh_sigma

float	overlap

int	nimg

Additional Inherited Members
Protected Attributes inherited from EMAN::Averager
Dict	params

EMData *	result

Detailed Description

TomoAverager averages a list of volumes in Fourier space.

It excludes values near zero from the average, assuming they are part of the missing-cone/wedge. A threshold

Parameters

thresh_sigma a number, multiplied by the standard deviation of the image, below-which values are considered zero

Definition at line 345 of file averager.h.

Constructor & Destructor Documentation

◆ TomoAverager()

TomoAverager::TomoAverager ( )

Definition at line 93 of file averager.cpp.

        : norm_image(0),nimg(0),overlap(0)
{
 
}

Referenced by NEW().

◆ ~TomoAverager()

virtual EMAN::TomoAverager::~TomoAverager ( )

inlinevirtual

Definition at line 349 of file averager.h.

                {
                        if (norm_image!=0) delete norm_image;
                        if (result!=0) delete result;
                }

References norm_image, and EMAN::Averager::result.

Member Function Documentation

◆ add_image()

void TomoAverager::add_image ( EMData * image )

virtual

To add an image to the Averager.

This image will be averaged in this function.

Parameters

image The image to be averaged.

Reimplemented from EMAN::Averager.

Definition at line 99 of file averager.cpp.

{
        if (!image) {
                return;
        }
 
        if (!image->is_complex()) {
                image=image->do_fft();
                image->set_attr("free_me",(int)1);
        }
                
        if (result!=0 && !EMUtil::is_same_size(image, result)) {
                LOGERR("%s Averager can only process same-size Images",
                           get_name().c_str());
                return;
        }
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
        int nz = image->get_zsize();
//      size_t image_size = (size_t)nx * ny * nz;
 
        if (norm_image == 0) {
//              printf("init average %d %d %d",nx,ny,nz);
                result = image->copy_head();
                result->to_zero();
                
                norm_image = image->copy_head();
                norm_image->to_zero();
                
                thresh_sigma = (float)params.set_default("thresh_sigma", 0.5);
                overlap=0.0f;
                nimg=0;
        }
 
        float *result_data = result->get_data();
        float *norm_data = norm_image->get_data();
        float *data = image->get_data();
        
        vector<float> threshv;
        threshv=image->calc_radial_dist(nx/2,0,1,4);
        for (int i=0; i<nx/2; i++) threshv[i]*=threshv[i]*thresh_sigma;  // The value here is amplitude, we square to make comparison less expensive
        
        size_t j=0;
        // Add any values above threshold to the result image, and add 1 to the corresponding pixels in the norm image
        int k=0;
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nx; x+=2, j+=2) {
                                float rf=Util::hypot3(x/2,y<ny/2?y:ny-y,z<nz/2?z:nz-z); // origin at 0,0; periodic
                                int r=int(rf);
                                if (r>ny/2) continue;
                                float f=data[j];        // real
                                float g=data[j+1];      // imag
                                float inten=f*f+g*g;
                                
                                if (inten<threshv[r]) continue;
                                
                                k+=1;
                                result_data[j]  +=f;
                                result_data[j+1]+=g;
                                
                                norm_data[j]  +=1.0;
                                norm_data[j+1]+=1.0;
                        }
                }
        }
//      printf("%d %d\n",k,nx*ny*nz);
        overlap+=(float)k/(nx*ny*nz);
        nimg++;
        
        if (image->has_attr("free_me")) delete image;
}

References EMAN::EMData::calc_radial_dist(), get_name(), EMAN::Util::hypot3(), EMAN::EMUtil::is_same_size(), LOGERR, nimg, norm_image, overlap, EMAN::Averager::params, EMAN::Averager::result, EMAN::Dict::set_default(), thresh_sigma, x, and y.

◆ finish()

EMData * TomoAverager::finish ( )

virtual

Finish up the averaging and return the result.

Returns: The averaged image.

Implements EMAN::Averager.

Definition at line 173 of file averager.cpp.

{
        if (norm_image==0 || result==0 || nimg==0) return NULL;
        
        int nx = result->get_xsize();
        int ny = result->get_ysize();
        int nz = result->get_zsize();
        size_t image_size = (size_t)nx * ny * nz;
        
        float *result_data = result->get_data();
        float *norm_data = norm_image->get_data();
        
//      printf("finish average %d %d %d",nx,ny,nz);
        // normalize the average
        for (size_t j = 0; j < image_size; j++) {
                if (norm_data[j]==0.0) result_data[j]=0.0;
                else result_data[j]/=norm_data[j];
        }
        
        norm_image->update();
        result->update();
        
        EMData *ret;
        if ((int)params.set_default("doift", 1))
                ret = result->do_ift();
        else
                ret = result->copy();
        
        ret->set_attr("ptcl_repr",norm_image->get_attr("maximum"));
        ret->set_attr("mean_coverage",(float)(overlap/nimg));
        if ((int)params.set_default("save_norm", 0)) 
                norm_image->write_image("norm.hdf");
        
        if (params.has_key("normout")) {
                EMData *normout=(EMData*) params["normout"];
                normout->set_data(norm_image->copy()->get_data());
                normout->update();
        }
        
        delete result;
        delete norm_image;
        result=0;
        norm_image=0;
        
        return ret;
}

References EMAN::Dict::has_key(), nimg, norm_image, overlap, EMAN::Averager::params, EMAN::Averager::result, and EMAN::Dict::set_default().

◆ get_desc()

string EMAN::TomoAverager::get_desc ( ) const

inlinevirtual

Implements EMAN::Averager.

Definition at line 363 of file averager.h.

                {
                        return "Average of volumes in Fourier space, excluding any pixels with near 0 intensity.";
                }

◆ get_name()

string EMAN::TomoAverager::get_name ( ) const

inlinevirtual

Get the Averager's name.

Each Averager is identified by a unique name.

Returns: The Averager's name.

Implements EMAN::Averager.

Definition at line 358 of file averager.h.

                {
                        return NAME;
                }

References NAME.

Referenced by add_image().

◆ get_param_types()

TypeDict EMAN::TomoAverager::get_param_types ( ) const

inlinevirtual

Get Averager 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.

Reimplemented from EMAN::Averager.

Definition at line 373 of file averager.h.

                {
                        TypeDict d;
                        d.put("thresh_sigma", EMObject::FLOAT, "multiplied by the standard deviation of the image, below-which values are considered zero. Default = .01");
                        d.put("save_norm", EMObject::INT, "If set, will save the normalization volume as norm.hdf. Mainly for debugging purposes.");
                        d.put("normout", EMObject::EMDATA, "If set, will save the normalization volume in the given EMData object.");
                        d.put("doift", EMObject::INT, "IFT the resulting volume. Default is 1.");
 
                        return d;
                }

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

◆ mult()

virtual void EMAN::TomoAverager::mult ( const float & s )

inlinevirtual

Multiply the result image by some floating point constant This is useful when weighting the input images prior to calling add_image - a situation where it is likely you want to divide by the sum of the weights.

Hence call mult after all of the weighted images have been added.

Parameters

s	the scaling factor.

Exceptions

NullPointerException if the EMData pointer (result) is NULL

Reimplemented from EMAN::Averager.

Definition at line 384 of file averager.h.

384{ }

◆ NEW()

static Averager * EMAN::TomoAverager::NEW ( )

inlinestatic

Definition at line 368 of file averager.h.

                {
                        return new TomoAverager();
                }

References TomoAverager().

Member Data Documentation

◆ NAME

const string TomoAverager::NAME = "mean.tomo"

static

Definition at line 386 of file averager.h.

Referenced by get_name().

◆ nimg

int EMAN::TomoAverager::nimg

private

Definition at line 392 of file averager.h.

Referenced by add_image(), and finish().

◆ norm_image

EMData* EMAN::TomoAverager::norm_image

private

Definition at line 389 of file averager.h.

Referenced by add_image(), finish(), and ~TomoAverager().

◆ overlap

float EMAN::TomoAverager::overlap

private

Definition at line 391 of file averager.h.

Referenced by add_image(), and finish().

◆ thresh_sigma

float EMAN::TomoAverager::thresh_sigma

private

Definition at line 390 of file averager.h.

Referenced by add_image().

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

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TomoAverager()

◆ ~TomoAverager()

Member Function Documentation

◆ add_image()

◆ finish()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ mult()

◆ NEW()

Member Data Documentation

◆ NAME

◆ nimg

◆ norm_image

◆ overlap

◆ thresh_sigma