This processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. More...

#include <processor.h>

Inheritance diagram for EMAN::LocalNormProcessor:

[legend]

Collaboration diagram for EMAN::LocalNormProcessor:

[legend]

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 = "normalize.local"

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 attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display.

threshold is an isosurface threshold at which all desired features are visible, radius is a normalization size similar to an lp= value.

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 7470 of file processor.h.

Member Function Documentation

◆ get_desc()

virtual string EMAN::LocalNormProcessor::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 7485 of file processor.h.

                {
                        return "This processor attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. threshold is an isosurface threshold at which all desired features are visible, radius is a feature size over which to equalize.";
                }

◆ get_name()

virtual string EMAN::LocalNormProcessor::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 7475 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

virtual TypeDict EMAN::LocalNormProcessor::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 7490 of file processor.h.

                {
                        TypeDict d;
                        d.put("threshold", EMObject::FLOAT, "Only values above the threshold will be used to compute the normalization. Generally a good isosurface value.");
                        d.put("radius", EMObject::FLOAT, "Fourier filter radius expressed in pixels in Fourier space. cutoff_pixels in filter.lowpass.gauss");
                        d.put("apix", EMObject::FLOAT, "Angstroms per pixel");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 7480 of file processor.h.

                {
                        return new LocalNormProcessor();
                }

◆ process_inplace()

void LocalNormProcessor::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 7952 of file processor.cpp.

{
        if (!image) {
                LOGWARN("NULL Image");
                return;
        }
        float apix = params["apix"];
        float threshold = params["threshold"];
        float radius = params["radius"];
 
        if (apix > 0) {
                int ny = image->get_ysize();
                radius = ny * apix / radius;
                //printf("Norm filter radius=%1.1f\n", radius);
        }
 
        EMData *blur = image->copy();
        EMData *maskblur = image->copy();
 
        maskblur->process_inplace("threshold.binary", Dict("value", threshold));
        maskblur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
//      maskblur->process_inplace("filter.highpass.tanh", Dict("highpass", -10.0f));
        maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
//      maskblur->process_inplace("threshold.belowtozero", Dict("minval", 0.001f));
 
 
        blur->process_inplace("threshold.belowtozero", Dict("minval", threshold));
        blur->process_inplace("filter.lowpass.gauss", Dict("cutoff_pixels", radius));
//      blur->process_inplace("filter.highpass.tanh", Dict("cutoff_abs", -10.0f));
 
        maskblur->div(*blur);
        image->mult(*maskblur);
//      maskblur->write_image("norm.mrc", 0, EMUtil::IMAGE_MRC);
 
        if( maskblur )
        {
                delete maskblur;
                maskblur = 0;
        }
 
        if( blur )
        {
                delete blur;
                blur = 0;
        }
}

References LOGWARN, and EMAN::Processor::params.

Member Data Documentation

◆ NAME

const string LocalNormProcessor::NAME = "normalize.local"

static

Definition at line 7499 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