#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 | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "segment.kmeans" |
ctf[in] | A Ctf object to use |
Definition at line 720 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 750 of file processor.h. 00751 { 00752 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."; 00753 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 723 of file processor.h. 00724 {
00725 return NAME;
00726 }
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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 731 of file processor.h. References EMAN::TypeDict::put(). 00732 { 00733 TypeDict d ; 00734 d.put("nseg", EMObject::INT, "Number of segments to divide the image into. default=12" ); 00735 d.put("thr",EMObject::FLOAT,"Isosurface threshold value. Pixels below this will not be segmented"); 00736 d.put("ampweight",EMObject::INT,"If set, will weight centers by voxel amplitude. default = 1"); 00737 d.put("maxsegsize",EMObject::FLOAT,"Maximum radial distance from segment center to member voxel. Default=10000"); 00738 d.put("minsegsep",EMObject::FLOAT,"Minimum segment separation. Segments too close will trigger a reseed"); 00739 d.put("maxiter",EMObject::FLOAT,"Maximum number of iterations to run before stopping. Default=100"); 00740 d.put("maxvoxmove",EMObject::FLOAT,"Maximum number of voxels that can move before quitting. Default=25"); 00741 d.put("verbose",EMObject::INT,"Be verbose while running"); 00742 return d; 00743 }
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Definition at line 745 of file processor.h. 00746 { 00747 return new KmeansSegmentProcessor(); 00748 }
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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.
Reimplemented from EMAN::Processor. Definition at line 870 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::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::set_value_at(), x, and y. 00871 { 00872 EMData * result = image->copy(); 00873 00874 int nseg = params.set_default("nseg",12); 00875 float thr = params.set_default("thr",-1.0e30f); 00876 int ampweight = params.set_default("ampweight",1); 00877 float maxsegsize = params.set_default("maxsegsize",10000.0f); 00878 float minsegsep = params.set_default("minsegsep",0.0f); 00879 int maxiter = params.set_default("maxiter",100); 00880 int maxvoxmove = params.set_default("maxvoxmove",25); 00881 int verbose = params.set_default("verbose",0); 00882 00883 vector<float> centers(nseg*3); 00884 vector<float> count(nseg); 00885 int nx=image->get_xsize(); 00886 int ny=image->get_ysize(); 00887 int nz=image->get_zsize(); 00888 // int nxy=nx*ny; 00889 00890 // seed 00891 for (int i=0; i<nseg*3; i+=3) { 00892 centers[i]= Util::get_frand(0.0f,(float)nx); 00893 centers[i+1]=Util::get_frand(0.0f,(float)ny); 00894 centers[i+2]=Util::get_frand(0.0f,(float)nz); 00895 } 00896 00897 for (int iter=0; iter<maxiter; iter++) { 00898 // **** classify 00899 size_t pixmov=0; // count of moved pixels 00900 for (int z=0; z<nz; z++) { 00901 for (int y=0; y<ny; y++) { 00902 for (int x=0; x<nz; x++) { 00903 if (image->get_value_at(x,y,z)<thr) { 00904 result->set_value_at(x,y,z,-1.0); //below threshold -> -1 (unclassified) 00905 continue; 00906 } 00907 int bcls=-1; // best matching class 00908 float bdist=(float)(nx+ny+nz); // distance for best class 00909 for (int c=0; c<nseg; c++) { 00910 float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]); 00911 if (d<bdist) { bdist=d; bcls=c; } 00912 } 00913 if ((int)result->get_value_at(x,y,z)!=bcls) pixmov++; 00914 if (bdist>maxsegsize) result->set_value_at(x,y,z,-1); // pixel is too far from any center 00915 else result->set_value_at(x,y,z,(float)bcls); // set the pixel to the class number 00916 } 00917 } 00918 } 00919 00920 // **** adjust centers 00921 for (int i=0; i<nseg*3; i++) centers[i]=0; 00922 for (int i=0; i<nseg; i++) count[i]=0; 00923 00924 // weighted sums 00925 for (int z=0; z<nz; z++) { 00926 for (int y=0; y<ny; y++) { 00927 for (int x=0; x<nz; x++) { 00928 int cls = (int)result->get_value_at(x,y,z); 00929 if (cls==-1) continue; 00930 float w=1.0; 00931 if (ampweight) w=image->get_value_at(x,y,z); 00932 00933 centers[cls*3]+=x*w; 00934 centers[cls*3+1]+=y*w; 00935 centers[cls*3+2]+=z*w; 00936 count[cls]+=w; 00937 } 00938 } 00939 } 00940 00941 // now each becomes center of mass, or gets randomly reseeded 00942 int nreseed=0; 00943 for (int c=0; c<nseg; c++) { 00944 // reseed 00945 if (count[c]==0) { 00946 nreseed++; 00947 do { 00948 centers[c*3]= Util::get_frand(0.0f,(float)nx); 00949 centers[c*3+1]=Util::get_frand(0.0f,(float)ny); 00950 centers[c*3+2]=Util::get_frand(0.0f,(float)nz); 00951 } 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 00952 } 00953 // center of mass 00954 else { 00955 centers[c*3]/=count[c]; 00956 centers[c*3+1]/=count[c]; 00957 centers[c*3+2]/=count[c]; 00958 } 00959 } 00960 00961 // with minsegsep, check separation 00962 if (minsegsep>0) { 00963 for (int c1=0; c1<nseg-1; c1++) { 00964 for (int c2=c1+1; c2<nseg; c2++) { 00965 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) { 00966 nreseed++; 00967 do { 00968 centers[c1*3]= Util::get_frand(0.0f,(float)nx); 00969 centers[c1*3+1]=Util::get_frand(0.0f,(float)ny); 00970 centers[c1*3+2]=Util::get_frand(0.0f,(float)nz); 00971 } while (image->get_value_at((int)centers[c1*3],(int)centers[c1*3+1],(int)centers[c1*3+2])<thr); 00972 } 00973 } 00974 } 00975 } 00976 00977 00978 if (verbose) printf("Iteration %3d: %6ld voxels moved, %3d classes reseeded\n",iter,pixmov,nreseed); 00979 if (nreseed==0 && pixmov<(size_t)maxvoxmove) break; // termination conditions met 00980 } 00981 00982 result->set_attr("segment_centers",centers); 00983 00984 return result; 00985 }
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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.
Implements EMAN::Processor. Definition at line 987 of file processor.cpp. 00988 { 00989 printf("Process inplace not implemented. Please use process.\n"); 00990 return; 00991 }
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Definition at line 74 of file processor.cpp. |