This processor will remove specified bad lines from CCD/DDD images, generally due to faulty lines/rows in the detector. More...

#include <processor.h>

Inheritance diagram for EMAN::BadLineXYProcessor:

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Collaboration diagram for EMAN::BadLineXYProcessor:

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

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

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

virtual 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 = "math.xybadlines"

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 remove specified bad lines from CCD/DDD images, generally due to faulty lines/rows in the detector.

Parameters

cols	x locations of bad vertical lines
rows	y locations of bad horizontal lines

Definition at line 7396 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::BadLineXYProcessor::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 7411 of file processor.h.

                {
                        return "This processor will correct defective pixel columns/rows by averaging adjacent pixel values";
                }

◆ get_name()

virtual string EMAN::BadLineXYProcessor::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 7401 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::BadLineXYProcessor::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 7416 of file processor.h.

                {
                        TypeDict d;
                        d.put("cols", EMObject::INTARRAY, "X coordinates of bad vertical lines");
                        d.put("rows", EMObject::INTARRAY, "Y coordinates of bad horizontal lines.");
                        d.put("neighbornorm", EMObject::INT, "Interpolate neighboring pixels, then divides by this factor. Default = 1.0.");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7406 of file processor.h.

                {
                        return new BadLineXYProcessor();
                }

◆ process_inplace()

void BadLineXYProcessor::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 7820 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
 
        if (image->get_zsize()>1) throw ImageDimensionException("Error: math.xybadlines works only on 2D images");
        
        int nx=image->get_xsize();
        int ny=image->get_ysize();
 
        vector <int> cols = params.set_default("cols",vector <int> ());
        vector <int> rows = params.set_default("rows",vector <int> ());
        float nnorm = params.set_default("neighbornorm",1.0f);//sqrt(2.0f));
 
        int mincol = *min_element(cols.begin(),cols.end());
        int maxcol = *max_element(cols.begin(),cols.end());
 
        int minrow = *min_element(rows.begin(),rows.end());
        int maxrow = *max_element(rows.begin(),rows.end());
 
        int start;
        int ogl;
        int ngl;
        bool inflag;
        int pos;
 
        ogl = 0;
        for (int x=mincol-1; x<=maxcol+1; x++) {
                inflag = false;
                for (int i=0; i<=cols.size(); i++) if (x==cols[i]) inflag = true;
                if (inflag == true) continue;
                else {
                        inflag = false;
                        for (int i=0; i<=cols.size(); i++) if ((x-1)==cols[i]) inflag = true;
                        if (inflag == true){
                                ngl = x;
                                start = ogl+1;
                                for (int c=start; c<ngl; c++) {
                                        //printf("Fixing column %d\n",c);
                                        pos = c-ogl;
                                        for (int y=0; y<ny; y++) {
                                                float val = ((image->get_value_at(ogl,y)*(ngl-ogl-pos)+image->get_value_at(ngl,y)*pos)) / (nnorm*(ngl-ogl));
                                                image->set_value_at(c,y,val);
                                        }
                                }
                                ogl = x;
                        }
                        else ogl = x;
                }
        }
 
        ogl = 0;
        for (int y=minrow-1; y<=maxrow+1; y++) {
                inflag = false;
                for (int i=0; i<=rows.size(); i++) if (y==rows[i]) inflag = true;
                if (inflag == true) continue;
                else {
                        inflag = false;
                        for (int i=0; i<=rows.size(); i++) if ((y-1)==rows[i]) inflag = true;
                        if (inflag == true){
                                ngl = y;
                                for (int r=ogl+1; r<ngl; r++) {
                                        //printf("Fixing row %d\n",r);
                                        pos = r-ogl;
                                        for (int x=0; x<nx; x++) {
                                                float val = ((image->get_value_at(x,ogl)*(ngl-ogl-pos)+image->get_value_at(x,ngl)*pos)) / (nnorm*(ngl-ogl));
                                                image->set_value_at(x,r,val);
                                        }
                                }
                                ogl = y;
                        }
                        else ogl = y;
                }
        }
}

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

Member Data Documentation

◆ NAME

const string BadLineXYProcessor::NAME = "math.xybadlines"

static

Definition at line 7425 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