SigmaAverager averages a list of images. More...

#include <averager.h>

Inheritance diagram for EMAN::SigmaAverager:

Collaboration diagram for EMAN::SigmaAverager:

[legend]

Public Member Functions
	SigmaAverager ()

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 = "sigma"

Private Attributes
EMData *	mean_image

EMData *	normimage

int	ignore0

int	nimg

int	freenorm

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

EMData *	result

Detailed Description

SigmaAverager averages a list of images.

It optionally makes a sigma image.

Parameters

sigma	sigma value
ignore0	if set, ignore zero value pixels

Definition at line 646 of file averager.h.

Constructor & Destructor Documentation

◆ SigmaAverager()

SigmaAverager::SigmaAverager ( )

Definition at line 346 of file averager.cpp.

        : mean_image(0), ignore0(0), normimage(0), freenorm(0), nimg(0)
{
 
}

Referenced by NEW().

Member Function Documentation

◆ add_image()

void SigmaAverager::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 352 of file averager.cpp.

{
        if (!image) {
                return;
        }
 
        if (nimg >= 1 && !EMUtil::is_same_size(image, mean_image)) {
                LOGERR("%sAverager can only process same-size Image",
                           get_name().c_str());
                return;
        }
 
        nimg++;
 
        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 (nimg == 1) {
                mean_image = image->copy_head();
                mean_image->set_size(nx, ny, nz);
 
                result = image->copy_head();
                result->set_size(nx, ny, nz);
 
                ignore0 = params["ignore0"];
                normimage = params.set_default("normimage", (EMData*)0);
                if (ignore0 && normimage==0) { normimage=new EMData(nx,ny,nz); freenorm=1; }
                if (normimage) normimage->to_zero();
        }
 
        float *mean_image_data = mean_image->get_data();
        float *result_data = result->get_data();
        float * image_data = image->get_data();
 
        if (!ignore0) {
                for (size_t j = 0; j < image_size; ++j) {
                        float f = image_data[j];
                        mean_image_data[j] += f;
                        if (result_data) {
                                result_data[j] += f * f;
                        }
                }
        }
        else {
                for (size_t j = 0; j < image_size; ++j) {
                        float f = image_data[j];
                        if (f) {
                                mean_image_data[j] += f;
                                if (result_data) {
                                        result_data[j] += f * f;
                                }
                                normimage->set_value_at_fast(j,normimage->get_value_at(j)+1.0);
                        }
                }
        }
}

References freenorm, get_name(), ignore0, EMAN::EMUtil::is_same_size(), LOGERR, mean_image, nimg, normimage, EMAN::Averager::params, EMAN::Averager::result, and EMAN::Dict::set_default().

◆ finish()

EMData * SigmaAverager::finish ( )

virtual

Finish up the averaging and return the result.

Returns: The averaged image.

Implements EMAN::Averager.

Definition at line 411 of file averager.cpp.

{
        if (mean_image && nimg > 1) {
                size_t image_size = (size_t)mean_image->get_xsize() * mean_image->get_ysize() * mean_image->get_zsize();
                float * mean_image_data = mean_image->get_data();
                if (!ignore0) {
                        for (size_t j = 0; j < image_size; ++j) {
                                mean_image_data[j] /= nimg;
                        }
 
                        float * result_data = result->get_data();
                        
                        for (size_t j = 0; j < image_size; ++j) {
                                float f1 = result_data[j] / nimg;
                                float f2 = mean_image_data[j];
                                result_data[j] = sqrt(f1 - f2 * f2);
                        }
 
                        result->update();
                }
                else {
                        for (size_t j = 0; j < image_size; ++j) {
                                if (normimage->get_value_at(j)>0) mean_image_data[j] /= normimage->get_value_at(j);
                        }
 
                        float * result_data = result->get_data();
 
                        for (size_t j = 0; j < image_size; ++j) {
                                float f1 = 0;
                                if (normimage->get_value_at(j)>0) f1=result_data[j] / normimage->get_value_at(j);
                                float f2 = mean_image_data[j];
                                result_data[j] = sqrt(f1 - f2 * f2);
                        
                                result->update();
                        }
                }
 
                mean_image->update();
                mean_image->set_attr("ptcl_repr",nimg);
 
                result->set_attr("ptcl_repr",nimg);
 
                if (freenorm) { delete normimage; normimage=(EMData*)0; }
 
                return result;
        }
        else {
                LOGERR("%sAverager requires >=2 images", get_name().c_str());
        }
}

References freenorm, get_name(), ignore0, LOGERR, mean_image, nimg, normimage, EMAN::Averager::result, and sqrt().

◆ get_desc()

string EMAN::SigmaAverager::get_desc ( ) const

inlinevirtual

Implements EMAN::Averager.

Definition at line 659 of file averager.h.

                {
                        return "Computes the standard deviation of images";
                }

◆ get_name()

string EMAN::SigmaAverager::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 654 of file averager.h.

                {
                        return NAME;
                }

References NAME.

Referenced by add_image(), and finish().

◆ get_param_types()

TypeDict EMAN::SigmaAverager::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 669 of file averager.h.

                {
                        TypeDict d;
                        //d.put("sigma", EMObject::EMDATA, "sigma value");
                        d.put("normimage", EMObject::EMDATA, "In conjunction with ignore0, the number of non zero values for each pixel will be stored in this image.");
                        d.put("ignore0", EMObject::INT, "if set, ignore zero value pixels");
                        return d;
                }

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

◆ mult()

virtual void EMAN::SigmaAverager::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 678 of file averager.h.

678{ }

◆ NEW()

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

inlinestatic

Definition at line 664 of file averager.h.

                {
                        return new SigmaAverager();
                }

References SigmaAverager().

Member Data Documentation

◆ freenorm

int EMAN::SigmaAverager::freenorm

private

Definition at line 686 of file averager.h.

Referenced by add_image(), and finish().

◆ ignore0

int EMAN::SigmaAverager::ignore0

private

Definition at line 684 of file averager.h.

Referenced by add_image(), and finish().

◆ mean_image

EMData* EMAN::SigmaAverager::mean_image

private

Definition at line 683 of file averager.h.

Referenced by add_image(), and finish().

◆ NAME

const string SigmaAverager::NAME = "sigma"

static

Definition at line 680 of file averager.h.

Referenced by get_name().

◆ nimg

int EMAN::SigmaAverager::nimg

private

Definition at line 685 of file averager.h.

Referenced by add_image(), and finish().

◆ normimage

EMData * EMAN::SigmaAverager::normimage

private

Definition at line 683 of file averager.h.

Referenced by add_image(), and finish().

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

◆ SigmaAverager()

Member Function Documentation

◆ add_image()

◆ finish()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ mult()

◆ NEW()

Member Data Documentation

◆ freenorm

◆ ignore0

◆ mean_image

◆ NAME

◆ nimg

◆ normimage