EMAN::ImageAverager Class Reference

ImageAverager averages a list of images. More...

#include <averager.h>

Inheritance diagram for EMAN::ImageAverager:

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Collaboration diagram for EMAN::ImageAverager:

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List of all members.

Public Member Functions
	ImageAverager ()
void	add_image (EMData *image)
	To add an image to the Averager.
EMData *	finish ()
	Finish up the averaging and return the result.
string	get_name () const
	Get the Averager's name.
string	get_desc () const
TypeDict	get_param_types () const
	Get Averager parameter information in a dictionary.
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.
Static Public Member Functions
static Averager *	NEW ()
Private Attributes
EMData *	sigma_image
int *	nimg_n0
int	ignore0
int	nimg

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Detailed Description

ImageAverager 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 170 of file averager.h.

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Constructor & Destructor Documentation

ImageAverager::ImageAverager

(

)

Definition at line 73 of file averager.cpp.

Referenced by NEW().

        : sigma_image(0), nimg_n0(0), ignore0(0), nimg(0)
{

}

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Member Function Documentation

void ImageAverager::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.

Implements EMAN::Averager.

Definition at line 79 of file averager.cpp.

References EMAN::EMData::get_data(), get_name(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ignore0, EMAN::EMUtil::is_same_size(), LOGERR, nimg, nimg_n0, nx, ny, EMAN::Averager::params, EMAN::Averager::result, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and sigma_image.

{
        if (!image) {
                return;
        }

        if (nimg >= 1 && !EMUtil::is_same_size(image, result)) {
                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 = nx * ny * nz;

        if (nimg == 1) {
                result = new EMData();
                result->set_size(nx, ny, nz);
                sigma_image = params.set_default("sigma", (EMData*)0);
                ignore0 = params["ignore0"];

                nimg_n0 = new int[image_size];
                for (size_t i = 0; i < image_size; i++) {
                        nimg_n0[i] = 0;
                }
        }

        float *result_data = result->get_data();
        float *sigma_image_data = 0;
        if (sigma_image) {
                sigma_image->set_size(nx, ny, nz);
                sigma_image_data = sigma_image->get_data();
        }

        float * image_data = image->get_data();

        if (!ignore0) {
                for (size_t j = 0; j < image_size; j++) {
                        float f = image_data[j];
                        result_data[j] += f;
                        if (sigma_image_data) {
                                sigma_image_data[j] += f * f;
                        }
                }
        }
        else {
                for (size_t j = 0; j < image_size; j++) {
                        float f = image_data[j];
                        if (f) {
                                result_data[j] += f;
                                if (sigma_image_data) {
                                        sigma_image_data[j] += f * f;
                                }
                                nimg_n0[j]++;
                        }
                }
        }
}

EMData * ImageAverager::finish

(

)

[virtual]

Finish up the averaging and return the result.

Returns:

The averaged image.

Implements EMAN::Averager.

Definition at line 142 of file averager.cpp.

References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ignore0, nimg, nimg_n0, EMAN::Averager::result, sigma_image, sqrt(), and EMAN::EMData::update().

{
        if (result && nimg > 1) {
                size_t image_size = result->get_xsize() * result->get_ysize() * result->get_zsize();
                float * result_data = result->get_data();

                if (!ignore0) {
                        for (size_t j = 0; j < image_size; j++) {
                                result_data[j] /= nimg;
                        }

                        if (sigma_image) {
                                float * sigma_image_data = sigma_image->get_data();

                                for (size_t j = 0; j < image_size; j++) {
                                        float f1 = sigma_image_data[j] / nimg;
                                        float f2 = result_data[j];
                                        sigma_image_data[j] = sqrt(f1 - f2 * f2);
                                }

                                sigma_image->update();
                        }
                }
                else {
                        for (size_t j = 0; j < image_size; j++) {
                                result_data[j] /= nimg_n0[j];
                        }
                        if (sigma_image) {
                                float * sigma_image_data = sigma_image->get_data();

                                for (size_t j = 0; j < image_size; j++) {
                                        float f1 = sigma_image_data[j] / nimg_n0[j];
                                        float f2 = result_data[j];
                                        sigma_image_data[j] = sqrt(f1 - f2 * f2);
                                }

                                sigma_image->update();
                        }
                }

                result->update();
        }

        if( nimg_n0 )
        {
                delete [] nimg_n0;
                nimg_n0 = 0;
        }

        return result;
}

string EMAN::ImageAverager::get_name

(

)

const [inline, virtual]

Get the Averager's name.

Each Averager is identified by a unique name.

Returns:

The Averager's name.

Implements EMAN::Averager.

Definition at line 178 of file averager.h.

Referenced by add_image().

                {
                        return "mean";
                }

string EMAN::ImageAverager::get_desc

(

)

const [inline, virtual]

Implements EMAN::Averager.

Definition at line 183 of file averager.h.

                {
                        return "Simple mean average of images";
                }

static Averager* EMAN::ImageAverager::NEW

(

)

[inline, static]

Definition at line 188 of file averager.h.

References ImageAverager().

                {
                        return new ImageAverager();
                }

TypeDict EMAN::ImageAverager::get_param_types

(

)

const [inline, virtual]

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 193 of file averager.h.

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

                {
                        TypeDict d;
                        d.put("sigma", EMObject::EMDATA, "sigma value");
                        d.put("ignore0", EMObject::INT, "if set, ignore zero value pixels");
                        return d;
                }

virtual void EMAN::ImageAverager::mult

(

const float &

s

)

[inline, virtual]

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 201 of file averager.h.

{ }

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Member Data Documentation

EMData* EMAN::ImageAverager::sigma_image [private]

Definition at line 204 of file averager.h.

Referenced by add_image(), and finish().

int* EMAN::ImageAverager::nimg_n0 [private]

Definition at line 205 of file averager.h.

Referenced by add_image(), and finish().

int EMAN::ImageAverager::ignore0 [private]

Definition at line 206 of file averager.h.

Referenced by add_image(), and finish().

int EMAN::ImageAverager::nimg [private]

Definition at line 207 of file averager.h.

Referenced by add_image(), and finish().

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

• averager.h
• averager.cpp