EMAN::SetSFProcessor Class Reference

Sets the structure factor based on a 1D s/intensity curve as an XYData object. More...

#include <processor.h>

Inheritance diagram for EMAN::SetSFProcessor:

Collaboration diagram for EMAN::SetSFProcessor:

Public Member Functions
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::FourierAnlProcessor
void	process_inplace (EMData *image)
	To process an image in-place. 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::FourierAnlProcessor
static string	get_group_desc ()
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 = "filter.setstrucfac"

Protected Member Functions
void	create_radial_func (vector< float > &radial_mask, EMData *image) const
Protected Member Functions inherited from EMAN::FourierAnlProcessor
virtual void	preprocess (EMData *)

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

Sets the structure factor based on a 1D s/intensity curve as an XYData object.

Parameters

strucfac	XYData object with the curve to be imposed as intensity as a function of s
apix	A/pix value. Overrides and replaces apix_x/y/z in image

Definition at line 7911 of file processor.h.

Member Function Documentation

create_radial_func()

void SetSFProcessor::create_radial_func ( vector< float > &  radial_mask, EMData *  image  ) const

protectedvirtual

Implements EMAN::FourierAnlProcessor.

Definition at line 8376 of file processor.cpp.

                                                                                        {
        // The radial mask comes in with the existing radial image profile
        // The radial mask runs from 0 to the corner in Fourier space
 
        XYData *sf = 0;
        if (params.has_key("filename")) {
                sf=new XYData;
                sf->read_file((const char *)params["filename"]);
        }
        else sf = params["strucfac"];
        if(params.has_key("apix")) {
                image->set_attr("apix_x", (float)params["apix"]);
                image->set_attr("apix_y", (float)params["apix"]);
                image->set_attr("apix_z", (float)params["apix"]);
                if (image->has_attr("ctf")) {
                        Ctf *ctf=image->get_attr("ctf");
                        ctf->apix=(float)params["apix"];
                        image->set_attr("ctf",ctf);
                        delete(ctf);
                }
        }
        float scale=params.set_default("scale",1.0f);
 
        float apix=image->get_attr("apix_x");
        int ny=image->get_ysize();
        int n = radial_mask.size();
        int nmax=(int)floor(sf->get_x(sf->get_size()-1)*apix*ny);               // This is the radius at which we have our last valid value from the curve
        if (nmax>n) nmax=n;
 
        if ((nmax)<3) throw InvalidParameterException("Insufficient structure factor data for SetSFProcessor to be meaningful");
 
        int i;
        radial_mask[0]=1;
        for (i=1; i<nmax; i++) {
//              if (radial_mask[i]>0)
//              {
//                      radial_mask[i]= sqrt(n*sf->get_yatx(i/(apix*2.0f*n),false)/radial_mask[i]);
//              }
                if (radial_mask[i]>0) {
                        radial_mask[i]= sqrt((ny*ny*ny)*scale*sf->get_yatx(i/(apix*ny))/radial_mask[i]);
                }
                else if (i>0) radial_mask[i]=radial_mask[i-1];  // For points where the existing power spectrum was 0
        
        }
 
        // Continue to use a fixed factor after we run out of 'sf' values
 
        while (i<n) {
                radial_mask[i]=radial_mask[nmax-1];
                i++;
        }
 
        if (params.has_key("filename")) delete sf;
}

References EMAN::Ctf::apix, EMAN::XYData::get_size(), EMAN::XYData::get_x(), EMAN::XYData::get_yatx(), EMAN::Dict::has_key(), InvalidParameterException, EMAN::Processor::params, EMAN::XYData::read_file(), EMAN::Dict::set_default(), and sqrt().

get_desc()

virtual string EMAN::SetSFProcessor::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 7920 of file processor.h.

                {
                        return "Filters the image so its 1-D power spectrum matches a supplied S,Y curve. If the S axis does not extend to Nyquist, only a uniform scaling will be applied beyond the end of the supplied curve. ";
                }

get_name()

virtual string EMAN::SetSFProcessor::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 7915 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

virtual TypeDict EMAN::SetSFProcessor::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::FourierAnlProcessor.

Definition at line 7930 of file processor.h.

                {
                        TypeDict d;
                        d.put("strucfac", EMObject::XYDATA, "An XYData object contaning the intensity (not amplitude) to be imposed as a function of S");
                        d.put("filename", EMObject::STRING, "Filename of a text file containing s,y data as an alternative to passing an XYData object.");
                        d.put("scale", EMObject::XYDATA, "A constant to multiply strucfac by to rescale the output. Setting to 1/ny^3 provides an alternative normalization. default = 1.0");
                        d.put("apix", EMObject::FLOAT, " Override A/pix in the image header (changes x,y and z)");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 7925 of file processor.h.

                {
                        return new SetSFProcessor();
                }

Member Data Documentation

NAME

const string SetSFProcessor::NAME = "filter.setstrucfac"

static

Definition at line 7940 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