Segment a volume about:homeinto subvolumes based on a center separation value. More...

#include <processor.h>

Inheritance diagram for EMAN::DistanceSegmentProcessor:

Collaboration diagram for EMAN::DistanceSegmentProcessor:

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

virtual EMData *	process (const EMData *const image)
	To proccess an image out-of-place. More...

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

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

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

Public Member Functions inherited from EMAN::Processor
virtual	~Processor ()

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 = "segment.distance"

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

Segment a volume about:homeinto subvolumes based on a center separation value.

For linear densities such as skeletons this should fill linear regions with uniformly separated points

Author: Steve Ludtke

Date: 2010/07/14

Definition at line 1703 of file processor.h.

Member Function Documentation

◆ get_desc()

string EMAN::DistanceSegmentProcessor::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 1729 of file processor.h.

                {
                        return "Segments a volume into pieces separated by distances in the specified range.";
                }

◆ get_name()

string EMAN::DistanceSegmentProcessor::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 1706 of file processor.h.

                {
                        return NAME;
                }

References NAME.

◆ get_param_types()

TypeDict EMAN::DistanceSegmentProcessor::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 1714 of file processor.h.

                {
                        TypeDict d ;
                        d.put("thr",EMObject::FLOAT,"Optional : Isosurface threshold value. Pixels below this will not be segment centers (default = 0.9)");
                        d.put("minsegsep",EMObject::FLOAT,"Required: Minimum segment separation in pixels. Segments too close will trigger a reseed");
                        d.put("maxsegsep",EMObject::FLOAT,"Required: Maximum segment separation in pixels. Segments too close will trigger a reseed");
                        d.put("verbose",EMObject::INT,"Be verbose while running");
                        return d;
                }

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

◆ NEW()

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

inlinestatic

Definition at line 1724 of file processor.h.

                {
                        return new DistanceSegmentProcessor();
                }

◆ process()

EMData * DistanceSegmentProcessor::process ( const EMData *const image )

virtual

To proccess an image out-of-place.

For those processors which can only be processed out-of-place, override this function to give the right behavior.

Parameters

image The image will be copied, actual process happen on copy of image.

Returns: the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 1595 of file processor.cpp.

{
        EMData * result = image->copy();
 
        float thr = params.set_default("thr",0.9f);
        float minsegsep = params.set_default("minsegsep",5.0f);
        float maxsegsep = params.set_default("maxsegsep",5.1f);
        int verbose = params.set_default("verbose",0);
 
        vector<Pixel> pixels=image->calc_highest_locations(thr);
 
        vector<float> centers(3);       // only 1 to start
        int nx=image->get_xsize();
        int ny=image->get_ysize();
        int nz=image->get_zsize();
//      int nxy=nx*ny;
 
        // seed the process with the highest valued point
        centers[0]=(float)pixels[0].x;
        centers[1]=(float)pixels[0].y;
        centers[2]=(float)pixels[0].z;
        pixels.erase(pixels.begin());
 
        // outer loop. We add one center per iteration
        // This is NOT a very efficient algorithm, it assumes points are fairly sparse
        while (pixels.size()>0) {
                // iterate over pixels until we find a new center (then stop), delete any 'bad' pixels
                // no iterators because we remove elements
 
                for (unsigned int i=0; i<pixels.size(); i++) {
 
                        Pixel p=pixels[i];
                        // iterate over existing centers to see if this pixel should be removed ... technically we only should need to check the last center
                        for (unsigned int j=0; j<centers.size(); j+=3) {
                                float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
                                if (d<minsegsep) {              // conflicts with existing center, erase
                                        pixels.erase(pixels.begin()+i);
                                        i--;
                                        break;
                                }
                        }
                }
 
                int found=0;
                for (unsigned int i=0; i<pixels.size() && found==0; i++) {
                        Pixel p=pixels[i];
 
                        // iterate again to see if this may be a new valid center. Start at the end so we tend to build chains
                        for (unsigned int j=centers.size()-3; j>0; j-=3) {
                                float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
                                if (d<maxsegsep) {              // we passed minsegsep question already, so we know we're in the 'good' range
                                        centers.push_back((float)p.x);
                                        centers.push_back((float)p.y);
                                        centers.push_back((float)p.z);
                                        pixels.erase(pixels.begin()+i); // in the centers list now, don't need it any more
                                        found=1;
                                        break;
                                }
                        }
                }
 
                // If we went through the whole list and didn't find one, we need to reseed again
                if (!found && pixels.size()) {
                        if (verbose) printf("New chain\n");
                        centers.push_back((float)pixels[0].x);
                        centers.push_back((float)pixels[0].y);
                        centers.push_back((float)pixels[0].z);
                        pixels.erase(pixels.begin());
                }
 
                if (verbose) printf("%d points found\n",(int)(centers.size()/3));
        }
 
        // after we have our list of centers classify pixels
        for (int z=0; z<nz; z++) {
                for (int y=0; y<ny; y++) {
                        for (int x=0; x<nz; x++) {
                                if (image->get_value_at(x,y,z)<thr) {
                                        result->set_value_at(x,y,z,-1.0);               //below threshold -> -1 (unclassified)
                                        continue;
                                }
                                int bcls=-1;                    // best matching class
                                float bdist=(float)(nx+ny+nz);  // distance for best class
                                for (unsigned int c=0; c<centers.size()/3; c++) {
                                        float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]);
                                        if (d<bdist) { bdist=d; bcls=c; }
                                }
                                result->set_value_at(x,y,z,(float)bcls);                // set the pixel to the class number
                        }
                }
        }
 
        result->set_attr("segment_centers",centers);
 
        return result;
}

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

◆ process_inplace()

void DistanceSegmentProcessor::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 1588 of file processor.cpp.

{
        printf("Process inplace not implemented. Please use process.\n");
        return;
}

Member Data Documentation

◆ NAME

const string DistanceSegmentProcessor::NAME = "segment.distance"

static

Definition at line 1734 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()

◆ process_inplace()

Member Data Documentation

◆ NAME