EMAN::StripeXYProcessor Class Reference

This processor will remove localized 'striping' along the x/y axes, caused by issues with CCD/CMOS readout. More...

#include <processor.h>

Inheritance diagram for EMAN::StripeXYProcessor:

Collaboration diagram for EMAN::StripeXYProcessor:

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.xystripefix"

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 localized 'striping' along the x/y axes, caused by issues with CCD/CMOS readout.

In theory this should be done by dark/gain correction, but in many cases, there are residual effects that this will help eliminate.

Parameters

threshold	an isosurface threshold at which all desired features are visible
radius	a normalization size similar to an lp= value
apix	Angstrom per pixel ratio

Definition at line 7433 of file processor.h.

Member Function Documentation

get_desc()

virtual string EMAN::StripeXYProcessor::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 7448 of file processor.h.

                {
                        return "This processor will remove localized 'striping' along the x/y axes, caused by issues with CCD/CMOS readout. In theory this should be done by dark/gain correction, but in many cases, there are residual effects that this will help eliminate. This can produce high-pass filter-like effects, so generally large length values are suggested. Integration covers +-xlen/ylen. Y and X axes are corrected sequentially, not simultaneously, Y first";
                }

get_name()

virtual string EMAN::StripeXYProcessor::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 7438 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::StripeXYProcessor::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 7453 of file processor.h.

                {
                        TypeDict d;
                        d.put("xlen", EMObject::INT, "Integration 1/2 length on x axis in pixels. Default=10");
                        d.put("ylen", EMObject::INT, "Integration 1/2 length on y axis in pixels. Default=10");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 7443 of file processor.h.

                {
                        return new StripeXYProcessor();
                }

process_inplace()

void StripeXYProcessor::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 7899 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
        int xlen = params.set_default("xlen",10);
        int ylen = params.set_default("ylen",10);
 
        int nx=image->get_attr("nx");
        int ny=image->get_attr("ny");
        EMData *tmp=new EMData(nx,ny,1);
 
        // we do this in real-space, since the integration size is small, and we don't want Fourier edge effects
        // we use a 'moving window' to avoid summing the same points multiple times
        // start with y
        if (ylen>0) {
                for (int x=0; x<nx; x++) {
                        float sum=0.0;
                        float sumn=0.0;
                        for (int y=0; y<(ylen<ny?ylen:ny); y++) { sum+=image->get_value_at(x,y); sumn+=1.0; } // we seed the process with a 1/2 stripe
                        // now loop over each final pixel
                        for (int y=0; y<ny; y++) {
                                if (y+ylen<ny) { sum+=image->get_value_at(x,y+ylen); sumn+=1.0; }
                                if (y-ylen-1>=0) { sum-=image->get_value_at(x,y-ylen-1); sumn-=1.0; }
                                tmp->set_value_at_fast(x,y,sum/sumn);
                        }
                }
                tmp->write_image("tmp.hdf",0);
                image->sub(*tmp);
        }
 
        // now x
        if (xlen>0) {
                for (int y=0; y<ny; y++) {
                        float sum=0.0;
                        float sumn=0.0;
                        for (int x=0; x<(xlen<nx?xlen:nx); x++) { sum+=image->get_value_at(x,y); sumn+=1.0; } // we seed the process with a 1/2 stripe
                        // now loop over each final pixel
                        for (int x=0; x<nx; x++) {
                                if (x+xlen<nx) { sum+=image->get_value_at(x+xlen,y); sumn+=1.0; }
                                if (x-xlen-1>=0) { sum-=image->get_value_at(x-xlen-1,y); sumn-=1.0; }
                                tmp->set_value_at_fast(x,y,sum/sumn);
                        }
                }
                tmp->write_image("tmp.hdf",1);
                image->sub(*tmp);
        }
 
        delete tmp;
}

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

Member Data Documentation

NAME

const string StripeXYProcessor::NAME = "math.xystripefix"

static

Definition at line 7461 of file processor.h.

Referenced by get_name().

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

• processor.h
• processor.cpp