Make a curve or surface non-convex (planar or concave), iteratively. More...

#include <processor.h>

Inheritance diagram for EMAN::NonConvexProcessor:

Collaboration diagram for EMAN::NonConvexProcessor:

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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 = "math.nonconvex"

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

Make a curve or surface non-convex (planar or concave), iteratively.

Author: Steve Ludtke

Date: 2011/08/11

Definition at line 5239 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::NonConvexProcessor::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 5253 of file processor.h.

                {
                        return "Makes a curve or plane monotonically decreasing and non-convex. Useful in generating background curves from power spectra. Anchored at edges and (in 2d) at the center. If local value > mean(surrounding values) => mean(surrounding values).";
                }

◆ get_name()

string EMAN::NonConvexProcessor::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 5244 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::NonConvexProcessor::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 5258 of file processor.h.

                {
                        TypeDict d;
/*                      d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0");
                        d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0");
                        d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output");*/
                        return d;
                }

◆ NEW()

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

inlinestatic

Definition at line 5248 of file processor.h.

                {
                        return new NonConvexProcessor();
                }

◆ process_inplace()

void NonConvexProcessor::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 3724 of file processor.cpp.

                                                       {
        if (!image) { LOGWARN("NULL IMAGE"); return; }
        //int isinten=image->get_attr_default("is_intensity",0);
 
        // 1-D
        if (image->get_ysize()==1) {
 
        }
        // 2-D
        else if (image->get_zsize()==1) {
//              if (!isinten) throw ImageDimensionException("Only complex intensity images currently supported by NonConvexProcessor");
                int nx2=image->get_xsize()/2;
                int ny2=image->get_ysize()/2;
                vector<float> rdist = image->calc_radial_dist(nx2*1.5,0,1,false);               // radial distribution to make sure nonconvex values decrease radially
                // Make sure rdist is decreasing (or flat)
                for (int i=1; i<nx2; i++) {
                        if (rdist[i]>rdist[i-1]) rdist[i]=rdist[i-1];
                }
 
                image->process_inplace("xform.fourierorigin.tocenter");
                EMData* binary=image->copy();
 
                // First we eliminate convex points from the input image (set to zero)
                for (int x=0; x<image->get_xsize(); x+=2) {
                        for (int y=1; y<image->get_ysize()-1; y++) {
                                int r=(int)hypot((float)(x/2),(float)(y-ny2));
                                float cen=(*binary)(x,y);
                                if (x==0 || x==nx2*2-2 || (cen>(*binary)(x+2,y) || cen>(*binary)(x-2,y) || cen>(*binary)(x,y+1) || cen >(*binary)(x,y-1) || (*binary)(x,y)>rdist[r])) {         // point is considered nonconvex if lower than surrounding values and lower than mean
                                        image->set_value_at_fast(x/2+nx2,y,0.0);        // we are turning image into a full real-space intensity image for now
                                        image->set_value_at_fast(nx2-x/2,ny2*2-y-1,0.0);
                                }
                                else {
                                        image->set_value_at_fast(x/2+nx2,y,cen);        // we are turning image into a full real-space intensity image for now
                                        image->set_value_at_fast(nx2-x/2,ny2*2-y-1,cen);        // It will contain non-zero values only for nonconvex points
                                }
                        }
                }
                image->set_value_at_fast(nx2+1,ny2,(*binary)(2,ny2));   // We keep the points near the Fourier origin as a central anchor even though it's convex
                image->set_value_at_fast(nx2-1,ny2,(*binary)(2,ny2));   // We keep the points near the Fourier origin as a central anchor even though it's convex
                image->set_value_at_fast(nx2,ny2+1,(*binary)(0,ny2+1)); // We keep the points near the Fourier origin as a central anchor even though it's convex
                image->set_value_at_fast(nx2,ny2-1,(*binary)(0,ny2-1)); // We keep the points near the Fourier origin as a central anchor even though it's convex
                for (int y=0; y<ny2*2; y++) image->set_value_at_fast(0,y,0.0f);
 
                // Now make a binary version of the convex points
                float *idat=image->get_data();
                float *bdat=binary->get_data();
                int nxy=(nx2*ny2*4);
                for (int i=0; i<nxy; i++) {
                        bdat[i]=idat[i]==0?0:1.0f;              // binary version of the convex points in image
                }
                binary->update();
 
                // We now use a Gaussian filter on both images, to use Gaussian interpolation to fill in zero values
                image->set_complex(false);              // so we can use a Gaussian filter on it
                binary->set_complex(false);
 
/*              image->write_image("con.hdf",0);*/
                image->set_fftpad(false);
                binary->set_fftpad(false);
 
                // Gaussian blur of both images
                image->process_inplace("filter.lowpass.gauss",Dict("cutoff_abs",0.04f));
                binary->process_inplace("filter.lowpass.gauss",Dict("cutoff_abs",0.04f));
 
/*              image->write_image("con.hdf",1);
                binary->write_image("con.hdf",2);*/
 
                for (int x=0; x<image->get_xsize(); x+=2) {
                        for (int y=0; y<image->get_ysize(); y++) {
                                float bv=binary->get_value_at(x/2+nx2,y);
                                image->set_value_at_fast(x,y,image->get_value_at(x/2+nx2,y)/(bv<=0?1.0f:bv));
                                image->set_value_at_fast(x+1,y,0.0);
                        }
                }
                image->set_complex(true);
                image->set_fftpad(true);
                image->process_inplace("xform.fourierorigin.tocorner");
                delete binary;
        }
        else throw ImageDimensionException("3D maps not yet supported by NonConvexProcessor");
 
}

References EMAN::EMData::calc_radial_dist(), ImageDimensionException, LOGWARN, x, and y.

Member Data Documentation

◆ NAME

const string NonConvexProcessor::NAME = "math.nonconvex"

static

Definition at line 5267 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