Shape characterization Computes a set of values characteristic of the shape of a volume. More...

#include <analyzer.h>

Inheritance diagram for EMAN::ShapeAnalyzer:

Collaboration diagram for EMAN::ShapeAnalyzer:

[legend]

Public Member Functions
	ShapeAnalyzer ()

virtual int	insert_image (EMData *image)
	insert a image to the list of input images More...

virtual vector< EMData * >	analyze ()
	main function for Analyzer, analyze input images and create output images More...

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

string	get_desc () const
	Get the Analyzer's description. More...

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

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

virtual	~Analyzer ()

virtual int	insert_images_list (vector< EMData * > image_list)
	insert a list of images to the list of input images More...

virtual void	set_params (const Dict &new_params)
	Set the Analyzer parameters using a key/value dictionary. More...

virtual Dict	get_params () const
	Get the Reconstructor's parameters in a key/value dictionary. More...

Static Public Member Functions
static Analyzer *	NEW ()

Static Public Attributes
static const string	NAME = "shape"

Protected Attributes
int	verbose

vector< EMData * >	ret

Protected Attributes inherited from EMAN::Analyzer
Dict	params

vector< EMData * >	images

Detailed Description

Shape characterization Computes a set of values characteristic of the shape of a volume.

The first 3 values are distributions along X, Y and Z axes respectively, and are not orientation independent.

Author: Steve Ludtke

Date: 12/29/2013

Parameters

verbose Display progress if set, more detail with larger numbers

Definition at line 177 of file analyzer.h.

Constructor & Destructor Documentation

◆ ShapeAnalyzer()

EMAN::ShapeAnalyzer::ShapeAnalyzer ( )

inline

Definition at line 180 of file analyzer.h.

180: verbose(0) {}

EMAN::ShapeAnalyzer::verbose

int verbose

Definition: analyzer.h:215

Referenced by NEW().

Member Function Documentation

◆ analyze()

vector< EMData * > ShapeAnalyzer::analyze ( )

virtual

main function for Analyzer, analyze input images and create output images

Returns: vector<EMData *> result os images analysis

Implements EMAN::Analyzer.

Definition at line 122 of file analyzer.cpp.

                                        {
        int verbose = params.set_default("verbose",0);
        EMData *mx = new EMData(4,2,1); // result is 4 values
        mx->to_zero();
        ret.push_back(mx);
 
        if (images.size()!=1) throw ImageDimensionException("Shape computation accepts only a single volume as input");
        int nx=images[0]->get_xsize();
        int ny=images[0]->get_ysize();
        int nz=images[0]->get_zsize();
        if (nz==1 || ny==1 || nz==1) throw ImageDimensionException("Map must be 3-D");
 
        if (verbose>0) printf("Shape size: %d %d %d\n",nx,ny,nz);
 
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nx; x++) {
                                int xx=x-nx/2;
                                int yy=y-ny/2;
                                int zz=z-nz/2;
                                float v=images[0]->get_value_at(x,y,z);
                                mx->set_value_at(0,0,mx->get_value_at(0,0)+v*(xx*xx));
                                mx->set_value_at(1,0,mx->get_value_at(1,0)+v*(yy*yy));
                                mx->set_value_at(2,0,mx->get_value_at(2,0)+v*(zz*zz));
                                mx->set_value_at(3,0,mx->get_value_at(3,0)+v*(xx*xx+yy*yy+zz*zz));
                                // sum(m*r^2), in which r is the distance to the center. Used for minicircle classification
                                mx->set_value_at(0,1,mx->get_value_at(0,0)+v*abs(xx));
                                mx->set_value_at(1,1,mx->get_value_at(1,0)+v*abs(yy));
                                mx->set_value_at(2,1,mx->get_value_at(2,0)+v*abs(zz));
                                mx->set_value_at(3,1,mx->get_value_at(3,0)+v*(float)sqrt((float)(xx*xx+yy*yy+zz*zz)));
                        }
                }
        }
        mx->mult(1.0f/(nx*ny*nz));
 
        return ret;
}

References ImageDimensionException, EMAN::Analyzer::images, EMAN::Analyzer::params, ret, EMAN::Dict::set_default(), sqrt(), verbose, x, and y.

◆ get_desc()

string EMAN::ShapeAnalyzer::get_desc ( ) const

inlinevirtual

Get the Analyzer's description.

Returns: The Analyzer's description.

Implements EMAN::Analyzer.

Definition at line 195 of file analyzer.h.

                {
                        return "Experimental. Computes a set of values characterizing a 3-D volume. Returns a 3x2x1 image containing X, Y and Z axial distributions using axis squared and axis linear weighting.";
                }

◆ get_name()

string EMAN::ShapeAnalyzer::get_name ( ) const

inlinevirtual

Get the Analyzer's name.

Each Analyzer is identified by a unique name.

Returns: The Analyzer's name.

Implements EMAN::Analyzer.

Definition at line 190 of file analyzer.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::ShapeAnalyzer::get_param_types ( ) const

inlinevirtual

Get Analyzer 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.

Implements EMAN::Analyzer.

Definition at line 205 of file analyzer.h.

                {
                        TypeDict d;
                        d.put("verbose", EMObject::INT, "Display progress if set, more detail with larger numbers");
                        return d;
                }

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

◆ insert_image()

virtual int EMAN::ShapeAnalyzer::insert_image ( EMData * image )

inlinevirtual

insert a image to the list of input images

Parameters

image

Returns: int 0 for success, <0 for fail

Implements EMAN::Analyzer.

Definition at line 182 of file analyzer.h.

                                                        {
                        images.push_back(image);
                        if (images.size()>1) { printf("ShapeAnalyzer takes only a single image\n"); return 1; }
                        return 0;
                }

References EMAN::Analyzer::images.

◆ NEW()

static Analyzer * EMAN::ShapeAnalyzer::NEW ( )

inlinestatic

Definition at line 200 of file analyzer.h.

                {
                        return new ShapeAnalyzer();
                }

References ShapeAnalyzer().

Member Data Documentation

◆ NAME

const string EMAN::ShapeAnalyzer::NAME = "shape"

static

Definition at line 212 of file analyzer.h.

Referenced by get_name().

◆ ret

vector<EMData *> EMAN::ShapeAnalyzer::ret

protected

Definition at line 216 of file analyzer.h.

Referenced by analyze().

◆ verbose

int EMAN::ShapeAnalyzer::verbose

protected

Definition at line 215 of file analyzer.h.

Referenced by analyze().

The documentation for this class was generated from the following files:

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ShapeAnalyzer()

Member Function Documentation

◆ analyze()

◆ get_desc()

◆ get_name()

◆ get_param_types()

◆ insert_image()

◆ NEW()

Member Data Documentation

◆ NAME

◆ ret

◆ verbose