Try to eliminate beamstop in electron diffraction patterns. More...

#include <processor.h>

Inheritance diagram for EMAN::BeamstopProcessor:

Collaboration diagram for EMAN::BeamstopProcessor:

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Public Member Functions
void	process_inplace (EMData *image)
	To process an image in-place. More...

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

string	get_desc () const
	Get the descrition of this specific processor. More...

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

Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

virtual void	process_list_inplace (vector< EMData * > &images)
	To process multiple images using the same algorithm. More...

virtual Dict	get_params () const
	Get the processor parameters in a key/value dictionary. More...

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

Static Public Member Functions
static Processor *	NEW ()

Static Public Member Functions inherited from EMAN::Processor
static string	get_group_desc ()
	Get the description of this group of processors. More...

static void	EMFourierFilterInPlace (EMData *fimage, Dict params)
	Compute a Fourier-filter processed image in place. More...

static EMData *	EMFourierFilter (EMData *fimage, Dict params)
	Compute a Fourier-processor processed image without altering the original image. More...

Static Public Attributes
static const string	NAME = "mask.beamstop"

Additional Inherited Members
Public Types inherited from EMAN::Processor
enum	fourier_filter_types { TOP_HAT_LOW_PASS , TOP_HAT_HIGH_PASS , TOP_HAT_BAND_PASS , TOP_HOMOMORPHIC , GAUSS_LOW_PASS , GAUSS_HIGH_PASS , GAUSS_BAND_PASS , GAUSS_INVERSE , GAUSS_HOMOMORPHIC , BUTTERWORTH_LOW_PASS , BUTTERWORTH_HIGH_PASS , BUTTERWORTH_HOMOMORPHIC , KAISER_I0 , KAISER_SINH , KAISER_I0_INVERSE , KAISER_SINH_INVERSE , SHIFT , TANH_LOW_PASS , TANH_HIGH_PASS , TANH_HOMOMORPHIC , TANH_BAND_PASS , RADIAL_TABLE , CTF_ }
	Fourier filter Processor type enum. More...

Protected Attributes inherited from EMAN::Processor
Dict	params

Detailed Description

Try to eliminate beamstop in electron diffraction patterns.

If value1<0 also does radial subtract.

Parameters

value1	sig multiplier
value2	x of center
value3	y of center

Definition at line 5589 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::BeamstopProcessor::get_desc ( ) const

inlinevirtual

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns: The description of this processor.

Implements EMAN::Processor.

Definition at line 5604 of file processor.h.

                {
                        return "Try to eliminate beamstop in electron diffraction patterns. value1=sig multiplier; value2,value3 are x,y of center, if value1<0 also does radial subtract.";
                }

◆ get_name()

string EMAN::BeamstopProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Implements EMAN::Processor.

Definition at line 5594 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::BeamstopProcessor::get_param_types ( ) const

inlinevirtual

Get processor 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::Processor.

Definition at line 5609 of file processor.h.

                {
                        TypeDict d;
                        d.put("value1", EMObject::FLOAT, "sig multiplier");
                        d.put("value2", EMObject::FLOAT, "x of center");
                        d.put("value3", EMObject::FLOAT, "y of center");
                        return d;
                }

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

◆ NEW()

static Processor * EMAN::BeamstopProcessor::NEW ( )

inlinestatic

Definition at line 5599 of file processor.h.

                {
                        return new BeamstopProcessor();
                }

◆ process_inplace()

void BeamstopProcessor::process_inplace ( EMData * image )

virtual

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters

image The image to be processed.

Implements EMAN::Processor.

Definition at line 4227 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
        if (image->get_zsize() > 1) {
                LOGERR("BeamstopProcessor doesn't support 3D model");
                throw ImageDimensionException("3D model not supported");
        }
 
        float value1 = params["value1"];
        float value2 = params["value2"];
        float value3 = params["value3"];
 
        float thr = fabs(value1);
        float *data = image->get_data();
        int cenx = (int) value2;
        int ceny = (int) value3;
 
        int nx = image->get_xsize();
        int ny = image->get_ysize();
 
        if (cenx <= 0) {
                cenx = nx / 2;
        }
 
        if (ceny <= 0) {
                ceny = ny / 2;
        }
 
        int mxr = (int) floor(sqrt(2.0f) * nx / 2);
 
        float *mean_values = new float[mxr];
        float *sigma_values = new float[mxr];
        double sum = 0;
        int count = 0;
        double square_sum = 0;
 
        for (int i = 0; i < mxr; i++) {
                sum = 0;
                count = 0;
                square_sum = 0;
                int nitems = 6 * i + 2;
 
                for (int j = 0; j < nitems; j++) {
                        float ang = j * 2 * M_PI / nitems;
                        int x0 = (int) floor(cos(ang) * i + cenx);
                        int y0 = (int) floor(sin(ang) * i + ceny);
 
                        if (x0 < 0 || y0 < 0 || x0 >= nx || y0 >= ny) {
                                continue;
                        }
 
                        float f = data[x0 + y0 * nx];
                        sum += f;
                        square_sum += f * f;
                        count++;
                }
 
                mean_values[i] = (float)sum / count;
                sigma_values[i] = (float) sqrt(square_sum / count - mean_values[i] * mean_values[i]);
        }
 
 
        for (int k = 0; k < 5; k++) {
                for (int i = 0; i < mxr; i++) {
                        sum = 0;
                        count = 0;
                        square_sum = 0;
                        int nitems = 6 * i + 2;
                        double thr1 = mean_values[i] - sigma_values[i] * thr;
                        double thr2 = mean_values[i] + sigma_values[i];
 
                        for (int j = 0; j < nitems; j++) {
                                float ang = j * 2 * M_PI / nitems;
                                int x0 = (int) floor(cos(ang) * i + cenx);
                                int y0 = (int) floor(sin(ang) * i + ceny);
 
                                if (x0 < 0 || y0 < 0 || x0 >= nx || y0 >= ny ||
                                        data[x0 + y0 * nx] < thr1 || data[x0 + y0 * nx] > thr2) {
                                        continue;
                                }
 
                                sum += data[x0 + y0 * nx];
                                square_sum += data[x0 + y0 * nx] * data[x0 + y0 * nx];
                                count++;
                        }
 
                        mean_values[i] = (float) sum / count;
                        sigma_values[i] = (float) sqrt(square_sum / count - mean_values[i] * mean_values[i]);
                }
        }
 
        for (int i = 0; i < nx; i++) {
                for (int j = 0; j < ny; j++) {
 
                        int r = Util::round(hypot((float) i - cenx, (float) j - ceny));
 
                        if (value1 < 0) {
                                if (data[i + j * nx] < (mean_values[r] - sigma_values[r] * thr)) {
                                        data[i + j * nx] = 0;
                                }
                                else {
                                        data[i + j * nx] -= mean_values[r];
                                }
                                continue;
                        }
                        if (data[i + j * nx] > (mean_values[r] - sigma_values[r] * thr)) {
                                continue;
                        }
                        data[i + j * nx] = mean_values[r];
                }
        }
 
        if( mean_values )
        {
                delete[]mean_values;
                mean_values = 0;
        }
 
        if( sigma_values )
        {
                delete[]sigma_values;
                sigma_values = 0;
        }
 
        image->update();
}

References ImageDimensionException, LOGERR, LOGWARN, EMAN::Processor::params, EMAN::Util::round(), and sqrt().

Member Data Documentation

◆ NAME

const string BeamstopProcessor::NAME = "mask.beamstop"

static

Definition at line 5618 of file processor.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

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ NAME