This processor will try and remove outliers (and optionally exactly zero values), replacing any identified values with the local mean value. More...

#include <processor.h>

Inheritance diagram for EMAN::OutlierProcessor:

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Collaboration diagram for EMAN::OutlierProcessor:

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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...

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

string	get_desc () const
	Get the descrition of this specific processor. 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 ="threshold.outlier.localmean"

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

This processor will try and remove outliers (and optionally exactly zero values), replacing any identified values with the local mean value.

Parameters

sigma	outliers are defined as mean+-x*sigma where x is the specified value
fix_zero	if set, any values that are exactly zero will be treated as outliers)

Definition at line 5553 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::OutlierProcessor::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 5576 of file processor.h.

                {
                        return "Identifies any pixels that are outliers and adjusts them to be the average of any nearby non-outlier pixels. Operates iteratively when required, so large 'outlier' areas can be corrected.";
                }

◆ get_name()

string EMAN::OutlierProcessor::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 5558 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::OutlierProcessor::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 5568 of file processor.h.

                {
                        TypeDict d;
                        d.put("fix_zero", EMObject::BOOL, "If set, any pixels that are exactly zero are considered to be outliers, default=false");
                        d.put("sigma", EMObject::FLOAT, "outliers are defined as mean+-x*sigma where x is the specified value, default=3.0");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 5563 of file processor.h.

                {
                        return new OutlierProcessor();
                }

◆ process_inplace()

void OutlierProcessor::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 4166 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        bool fix_zero=(bool)params.set_default("fix_zero",0);
        float sigmamult=(float)params.set_default("sigma",3.0);
 
        if (sigmamult<=0.0) throw InvalidValueException(sigmamult,"threshold.outlier.localmean: sigma must be >0");
 
        float hithr=(float)image->get_attr("mean")+(float)(image->get_attr("sigma"))*sigmamult;
        float lothr=(float)image->get_attr("mean")-(float)(image->get_attr("sigma"))*sigmamult;
 
        int nx=image->get_xsize();
        int ny=image->get_ysize();
        int nz=image->get_zsize();
 
        // This isn't optimally efficient
        EMData *im[2];
        im[0]=image;
        im[1]=image->copy_head();
 
        if (nz==1) {
                int repeat=1;
                while (repeat) {
                        memcpy(im[1]->get_data(),im[0]->get_data(),image->get_xsize()*image->get_ysize()*image->get_zsize()*sizeof(float));
                        repeat=0;
                        for (int y=0; y<ny; y++) {
                                for (int x=0; x<nx; x++) {
                                        // if the pixel is an outlier
                                        float pix=im[1]->get_value_at(x,y);
                                        if (pix>hithr || pix<lothr || (pix==0 && fix_zero)) {
                                                int y0=0>y-1?0:y-1;
                                                int y1=y>=ny-1?ny-1:y+1;
                                                int x0=0>x-1?0:x-1;
                                                int x1=x>=nx-1?nx-1:x+1;
                                                float c=0.0f,nc=0.0f;
                                                for (int yy=y0; yy<=y1; yy++) {
                                                        for (int xx=x0; xx<=x1; xx++) {
                                                                float lpix=im[1]->get_value_at(xx,yy);
                                                                if (lpix>hithr || lpix<lothr || (lpix==0 && fix_zero)) continue;
                                                                c+=lpix;
                                                                nc++;
                                                        }
                                                }
                                                if (nc!=0) im[0]->set_value_at(x,y,c/nc);
                                                else repeat=1;
                                        }
                                }
                        }
                }
        }
        else {
                throw ImageDimensionException("threshold.outlier.localmean: 3D not yet implemented");
        }
        delete im[1];
}

References get_data(), ImageDimensionException, InvalidValueException, LOGWARN, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

Member Data Documentation

◆ NAME

const string OutlierProcessor::NAME ="threshold.outlier.localmean"

static

Definition at line 5581 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