#include <processor.h>
Inheritance diagram for EMAN::KmeansSegmentProcessor:
Public Member Functions | |
string | get_name () const |
Get the processor's name. | |
virtual EMData * | process (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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "segment.kmeans" |
ctf[in] | A Ctf object to use |
Definition at line 679 of file processor.h.
string EMAN::KmeansSegmentProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
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.
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.
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 }
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.
image | The image will be copied, actual process happen on copy of 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.
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 }
const string KmeansSegmentProcessor::NAME = "segment.kmeans" [static] |