EMAN::FFTWedgeProcessor Class Reference

Mask out (or in) peaks in Fourier space based on the average amplitude at each spatial frequency. More...

#include <processor.h>

Inheritance diagram for EMAN::FFTWedgeProcessor:

Collaboration diagram for EMAN::FFTWedgeProcessor:

Public Member Functions
void	process_inplace (EMData *image)
	To process an image in-place. More...
string	get_name () const
	Get the processor's name. More...
string	get_desc () const
	Get the descrition of this specific processor. More...
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 = "mask.fft.wedge"

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

Mask out (or in) peaks in Fourier space based on the average amplitude at each spatial frequency.

Definition at line 5452 of file processor.h.

Member Function Documentation

get_desc()

string EMAN::FFTWedgeProcessor::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 5466 of file processor.h.

                {
                        return "Sets a wedge to zero in Fourier space around the +-Z axis along X as a tilt axis to (somewhat) emulate the missing wedge in a tomography experiment. For example, anglemin=-30, anglemax=30 to roughly emulate at -60 to +60 tilt series";
                }

get_name()

string EMAN::FFTWedgeProcessor::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 5457 of file processor.h.

                {
                        return NAME;
                }

References NAME.

get_param_types()

TypeDict EMAN::FFTWedgeProcessor::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 5471 of file processor.h.

                {
                        TypeDict d;
                        d.put("anglemin", EMObject::FLOAT, "Minimum angle (degrees) in Y-Z plane to zero (default -30)");
                        d.put("anglemax", EMObject::FLOAT, "Maximum angle (degrees) in Y-Z plane to zero (default 30)");
                        d.put("rmin", EMObject::FLOAT, "Radius in Fourier pixels at which to start zeroing. This permits some very low resolution to be preserved. (default 1)");
                        return d;
                }

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

NEW()

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

inlinestatic

Definition at line 5461 of file processor.h.

                {
                        return new FFTWedgeProcessor();
                }

process_inplace()

void FFTWedgeProcessor::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 1036 of file processor.cpp.

{
        EMData *fft;
 
        if (!image) throw InvalidParameterException("FFTWedgeProcessor: no image provided");
        if (!image->is_complex()) fft = image->do_fft();
        else fft = image;
 
 
        int nx=fft->get_xsize();
        int ny=fft->get_ysize();
        int nz=fft->get_zsize();
        if (nz==1) throw ImageDimensionException("FFTWedgeProcessor only works on 3-D images");
        
        float anglemin = (float)params.set_default("anglemin",-30.0f);
        float anglemax = (float)params.set_default("anglemax",30.0f);
        float rmin = (float)params.set_default("rmin",1.0f);
        
        for (int z=-nz/2; z<nz/2; z++) {
                for (int y=-ny/2; y<ny/2; y++) {
                        for (int x=0; x<nx/2; x++) {
                                float ang=90.0f;
                                if (z!=0) ang=atan((float(y)/ny)/fabs(float(z)/nz))*180.0/M_PI;
                                if (ang<anglemin||ang>anglemax || Util::hypot3(x,y,z)<rmin) continue;
                                fft->set_complex_at(x,y,z,0.0f);
                        }
                }
        }       
        
        if (fft!=image) {
                EMData *ift=fft->do_ift();
                memcpy(image->get_data(),ift->get_data(),(nx-2)*ny*nz*sizeof(float));
                delete fft;
                delete ift;
        }
        image->update();
 
//      image->update();
}

References EMAN::Util::hypot3(), ImageDimensionException, InvalidParameterException, EMAN::Processor::params, EMAN::Dict::set_default(), x, and y.

Member Data Documentation

NAME

const string FFTWedgeProcessor::NAME = "mask.fft.wedge"

static

Definition at line 5480 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