EMAN::KmeansSegmentProcessor Class Reference

#include <processor.h>

Inheritance diagram for EMAN::KmeansSegmentProcessor:

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Collaboration diagram for EMAN::KmeansSegmentProcessor:

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List of all members.

Public Member Functions

string get_name () const
 Get the processor's name.
virtual EMDataprocess (const EMData *const image)
 To proccess an image out-of-place.
void process_inplace (EMData *image)
 To process an image in-place.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "segment.kmeans"

Detailed Description

Parameters:
ctf[in] A Ctf object to use
Author:
Steve Ludtke
Date:
2008/11/03

Definition at line 679 of file processor.h.


Member Function Documentation

string EMAN::KmeansSegmentProcessor::get_desc (  )  const [inline, virtual]

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 709 of file processor.h.

00710                 {
00711                         return "Performs K-means segmentation on a volume. Note that this method uses random seeds, and thus will return different results each time it is run. Returned map contains number of segment for each voxel (or 0 for unsegmented voxels). Segmentation centers are stored in 'segmentcenters' attribute, consisting of a list of 3n floats in x,y,z triples.";
00712                 }

string EMAN::KmeansSegmentProcessor::get_name (  )  const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 682 of file processor.h.

References NAME.

00683                 {
00684                         return NAME;
00685                 }

TypeDict EMAN::KmeansSegmentProcessor::get_param_types (  )  const [inline, virtual]

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 690 of file processor.h.

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

00691                 {
00692                         TypeDict d ;
00693                         d.put("nseg", EMObject::INT, "Number of segments to divide the image into. default=12" );
00694                         d.put("thr",EMObject::FLOAT,"Isosurface threshold value. Pixels below this will not be segmented");
00695                         d.put("ampweight",EMObject::INT,"If set, will weight centers by voxel amplitude. default = 1");
00696                         d.put("maxsegsize",EMObject::FLOAT,"Maximum radial distance from segment center to member voxel. Default=10000");
00697                         d.put("minsegsep",EMObject::FLOAT,"Minimum segment separation. Segments too close will trigger a reseed");
00698                         d.put("maxiter",EMObject::FLOAT,"Maximum number of iterations to run before stopping. Default=100");
00699                         d.put("maxvoxmove",EMObject::FLOAT,"Maximum number of voxels that can move before quitting. Default=25");
00700                         d.put("verbose",EMObject::INT,"Be verbose while running");
00701                         return d;
00702                 }

static Processor* EMAN::KmeansSegmentProcessor::NEW (  )  [inline, static]

Definition at line 704 of file processor.h.

00705                 {
00706                         return new KmeansSegmentProcessor();
00707                 }

EMData * KmeansSegmentProcessor::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 819 of file processor.cpp.

References EMAN::EMData::copy(), EMAN::Util::get_frand(), EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Util::hypot3(), nx, ny, EMAN::Processor::params, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::set_value_at(), x, and y.

00820 {
00821         EMData * result = image->copy();
00822 
00823         int nseg = params.set_default("nseg",12);
00824         float thr = params.set_default("thr",-1.0e30f);
00825         int ampweight = params.set_default("ampweight",1);
00826         float maxsegsize = params.set_default("maxsegsize",10000.0f);
00827         float minsegsep = params.set_default("minsegsep",0.0f);
00828         int maxiter = params.set_default("maxiter",100);
00829         int maxvoxmove = params.set_default("maxvoxmove",25);
00830         int verbose = params.set_default("verbose",0);
00831 
00832         vector<float> centers(nseg*3);
00833         vector<float> count(nseg);
00834         int nx=image->get_xsize();
00835         int ny=image->get_ysize();
00836         int nz=image->get_zsize();
00837 //      int nxy=nx*ny;
00838 
00839         // seed
00840         for (int i=0; i<nseg*3; i+=3) {
00841                 centers[i]=  Util::get_frand(0.0f,(float)nx);
00842                 centers[i+1]=Util::get_frand(0.0f,(float)ny);
00843                 centers[i+2]=Util::get_frand(0.0f,(float)nz);
00844         }
00845 
00846         for (int iter=0; iter<maxiter; iter++) {
00847                 // **** classify
00848                 size_t pixmov=0;                // count of moved pixels
00849                 for (int z=0; z<nz; z++) {
00850                         for (int y=0; y<ny; y++) {
00851                                 for (int x=0; x<nz; x++) {
00852                                         if (image->get_value_at(x,y,z)<thr) {
00853                                                 result->set_value_at(x,y,z,-1.0);               //below threshold -> -1 (unclassified)
00854                                                 continue;
00855                                         }
00856                                         int bcls=-1;                    // best matching class
00857                                         float bdist=(float)(nx+ny+nz);  // distance for best class
00858                                         for (int c=0; c<nseg; c++) {
00859                                                 float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]);
00860                                                 if (d<bdist) { bdist=d; bcls=c; }
00861                                         }
00862                                         if ((int)result->get_value_at(x,y,z)!=bcls) pixmov++;
00863                                         if (bdist>maxsegsize) result->set_value_at(x,y,z,-1);           // pixel is too far from any center
00864                                         else result->set_value_at(x,y,z,(float)bcls);           // set the pixel to the class number
00865                                 }
00866                         }
00867                 }
00868 
00869                 // **** adjust centers
00870                 for (int i=0; i<nseg*3; i++) centers[i]=0;
00871                 for (int i=0; i<nseg; i++) count[i]=0;
00872 
00873                 // weighted sums
00874                 for (int z=0; z<nz; z++) {
00875                         for (int y=0; y<ny; y++) {
00876                                 for (int x=0; x<nz; x++) {
00877                                         int cls = (int)result->get_value_at(x,y,z);
00878                                         if (cls==-1) continue;
00879                                         float w=1.0;
00880                                         if (ampweight) w=image->get_value_at(x,y,z);
00881 
00882                                         centers[cls*3]+=x*w;
00883                                         centers[cls*3+1]+=y*w;
00884                                         centers[cls*3+2]+=z*w;
00885                                         count[cls]+=w;
00886                                 }
00887                         }
00888                 }
00889 
00890                 // now each becomes center of mass, or gets randomly reseeded
00891                 int nreseed=0;
00892                 for (int c=0; c<nseg; c++) {
00893                         // reseed
00894                         if (count[c]==0) {
00895                                 nreseed++;
00896                                 do {
00897                                         centers[c*3]=  Util::get_frand(0.0f,(float)nx);
00898                                         centers[c*3+1]=Util::get_frand(0.0f,(float)ny);
00899                                         centers[c*3+2]=Util::get_frand(0.0f,(float)nz);
00900                                 } while (image->get_value_at((int)centers[c*3],(int)centers[c*3+1],(int)centers[c*3+2])<thr);           // This makes sure the new point is inside density
00901                         }
00902                         // center of mass
00903                         else {
00904                                 centers[c*3]/=count[c];
00905                                 centers[c*3+1]/=count[c];
00906                                 centers[c*3+2]/=count[c];
00907                         }
00908                 }
00909 
00910                 // with minsegsep, check separation
00911                 if (minsegsep>0) {
00912                         for (int c1=0; c1<nseg-1; c1++) {
00913                                 for (int c2=c1+1; c2<nseg; c2++) {
00914                                         if (Util::hypot3(centers[c1*3]-centers[c2*3],centers[c1*3+1]-centers[c2*3+1],centers[c1*3+2]-centers[c2*3+2])<=minsegsep) {
00915                                                 nreseed++;
00916                                                 do {
00917                                                         centers[c1*3]=  Util::get_frand(0.0f,(float)nx);
00918                                                         centers[c1*3+1]=Util::get_frand(0.0f,(float)ny);
00919                                                         centers[c1*3+2]=Util::get_frand(0.0f,(float)nz);
00920                                                 } while (image->get_value_at((int)centers[c1*3],(int)centers[c1*3+1],(int)centers[c1*3+2])<thr);
00921                                         }
00922                                 }
00923                         }
00924                 }
00925 
00926 
00927                 if (verbose) printf("Iteration %3d: %6ld voxels moved, %3d classes reseeded\n",iter,pixmov,nreseed);
00928                 if (nreseed==0 && pixmov<(size_t)maxvoxmove) break;             // termination conditions met
00929         }
00930 
00931         result->set_attr("segment_centers",centers);
00932 
00933         return result;
00934 }

void KmeansSegmentProcessor::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 936 of file processor.cpp.

00937 {
00938         printf("Process inplace not implemented. Please use process.\n");
00939         return;
00940 }


Member Data Documentation

const string KmeansSegmentProcessor::NAME = "segment.kmeans" [static]

Definition at line 714 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue May 25 17:16:23 2010 for EMAN2 by  doxygen 1.4.7