This function clamps the min and max vals in the image at minval and maxval at mean-n*sigma and mean+n*sigma, respectively. More...

#include <processor.h>

Inheritance diagram for EMAN::NSigmaClampingProcessor:

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Collaboration diagram for EMAN::NSigmaClampingProcessor:

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Public Member Functions
	NSigmaClampingProcessor ()

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

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

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

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

Public Member Functions inherited from EMAN::ClampingProcessor
	ClampingProcessor ()

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::ClampingProcessor
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.clampminmax.nsigma"

Static Public Attributes inherited from EMAN::ClampingProcessor
static const string	NAME = "threshold.clampminmax"

Protected Attributes
float	default_sigma

Protected Attributes inherited from EMAN::ClampingProcessor
float	default_max

float	default_min

Protected Attributes inherited from EMAN::Processor
Dict	params

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...

Detailed Description

This function clamps the min and max vals in the image at minval and maxval at mean-n*sigma and mean+n*sigma, respectively.

The parameter specified by the user is n, the default value of n is 2.

Parameters

nsigma	The number (n) of sigmas to clamp min and max vals at, so that the clamped boundaries are mean-nsigma and mean+nsigma
tomean	Replace outlying pixels values with the mean pixel value instead

Definition at line 3074 of file processor.h.

Constructor & Destructor Documentation

◆ NSigmaClampingProcessor()

EMAN::NSigmaClampingProcessor::NSigmaClampingProcessor ( )

inline

Definition at line 3077 of file processor.h.

3077: default_sigma(2.0) {}

EMAN::NSigmaClampingProcessor::default_sigma

float default_sigma

Definition: processor.h:3108

Referenced by NEW().

Member Function Documentation

◆ get_desc()

string EMAN::NSigmaClampingProcessor::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.

Reimplemented from EMAN::ClampingProcessor.

Definition at line 3100 of file processor.h.

                        {
                                return "This function clamps the min and max vals in the image at minval and maxval at mean-n*sigma and mean+n*sigma, respectively. The parameter specified by the user is n, the default value of n is 2.";
                        }

◆ get_name()

string EMAN::NSigmaClampingProcessor::get_name ( ) const

inlinevirtual

Get the processor's name.

Each processor is identified by a unique name.

Returns: The processor's name.

Reimplemented from EMAN::ClampingProcessor.

Definition at line 3079 of file processor.h.

                        {
                                return NAME;
                        }

References NAME.

◆ get_param_types()

TypeDict EMAN::NSigmaClampingProcessor::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::ClampingProcessor.

Definition at line 3089 of file processor.h.

                        {
                                TypeDict d;
                                d.put("nsigma", EMObject::FLOAT, "The number (n) of sigmas to clamp min and max vals at, so that the clamped boundaries are mean-n*sigma and mean+n*sigma" );
                                d.put("tomean", EMObject::BOOL, "Replace outlying pixels values with the mean pixel value instead" );
                                d.put("tozero", EMObject::BOOL, "Replace outlying pixels values with zero" );
                                return d;
                        }

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

◆ NEW()

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

inlinestatic

Definition at line 3084 of file processor.h.

                        {
                                return new NSigmaClampingProcessor();
                        }

References NSigmaClampingProcessor().

◆ process_inplace()

void NSigmaClampingProcessor::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.

Reimplemented from EMAN::ClampingProcessor.

Definition at line 12624 of file processor.cpp.

{
        float nsigma = params.set_default("nsigma",default_sigma);
        float sigma = image->get_attr("sigma");
        float mean = image->get_attr("mean");
        params.put("minval",mean - nsigma*sigma);
        params.put("maxval",mean + nsigma*sigma);
 
        ClampingProcessor::process_inplace(image);
}

References default_sigma, EMAN::Processor::params, EMAN::ClampingProcessor::process_inplace(), EMAN::Dict::put(), and EMAN::Dict::set_default().

Member Data Documentation

◆ default_sigma

float EMAN::NSigmaClampingProcessor::default_sigma

protected

Definition at line 3108 of file processor.h.

Referenced by process_inplace().

◆ NAME

const string NSigmaClampingProcessor::NAME = "threshold.clampminmax.nsigma"

static

Definition at line 3105 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

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NSigmaClampingProcessor()

Member Function Documentation

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ NEW()

◆ process_inplace()

Member Data Documentation

◆ default_sigma

◆ NAME