#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 745 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 775 of file processor.h. 00776 { 00777 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."; 00778 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 748 of file processor.h. 00749 {
00750 return NAME;
00751 }
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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 756 of file processor.h. References EMAN::TypeDict::put(). 00757 { 00758 TypeDict d ; 00759 d.put("nseg", EMObject::INT, "Number of segments to divide the image into. default=12" ); 00760 d.put("thr",EMObject::FLOAT,"Isosurface threshold value. Pixels below this will not be segmented"); 00761 d.put("ampweight",EMObject::INT,"If set, will weight centers by voxel amplitude. default = 1"); 00762 d.put("maxsegsize",EMObject::FLOAT,"Maximum radial distance from segment center to member voxel. Default=10000"); 00763 d.put("minsegsep",EMObject::FLOAT,"Minimum segment separation. Segments too close will trigger a reseed"); 00764 d.put("maxiter",EMObject::FLOAT,"Maximum number of iterations to run before stopping. Default=100"); 00765 d.put("maxvoxmove",EMObject::FLOAT,"Maximum number of voxels that can move before quitting. Default=25"); 00766 d.put("verbose",EMObject::INT,"Be verbose while running"); 00767 return d; 00768 }
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Definition at line 770 of file processor.h. 00771 { 00772 return new KmeansSegmentProcessor(); 00773 }
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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 907 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. 00908 { 00909 EMData * result = image->copy(); 00910 00911 int nseg = params.set_default("nseg",12); 00912 float thr = params.set_default("thr",-1.0e30f); 00913 int ampweight = params.set_default("ampweight",1); 00914 float maxsegsize = params.set_default("maxsegsize",10000.0f); 00915 float minsegsep = params.set_default("minsegsep",0.0f); 00916 int maxiter = params.set_default("maxiter",100); 00917 int maxvoxmove = params.set_default("maxvoxmove",25); 00918 int verbose = params.set_default("verbose",0); 00919 00920 vector<float> centers(nseg*3); 00921 vector<float> count(nseg); 00922 int nx=image->get_xsize(); 00923 int ny=image->get_ysize(); 00924 int nz=image->get_zsize(); 00925 // int nxy=nx*ny; 00926 00927 // seed 00928 for (int i=0; i<nseg*3; i+=3) { 00929 centers[i]= Util::get_frand(0.0f,(float)nx); 00930 centers[i+1]=Util::get_frand(0.0f,(float)ny); 00931 centers[i+2]=Util::get_frand(0.0f,(float)nz); 00932 } 00933 00934 for (int iter=0; iter<maxiter; iter++) { 00935 // **** classify 00936 size_t pixmov=0; // count of moved pixels 00937 for (int z=0; z<nz; z++) { 00938 for (int y=0; y<ny; y++) { 00939 for (int x=0; x<nz; x++) { 00940 if (image->get_value_at(x,y,z)<thr) { 00941 result->set_value_at(x,y,z,-1.0); //below threshold -> -1 (unclassified) 00942 continue; 00943 } 00944 int bcls=-1; // best matching class 00945 float bdist=(float)(nx+ny+nz); // distance for best class 00946 for (int c=0; c<nseg; c++) { 00947 float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]); 00948 if (d<bdist) { bdist=d; bcls=c; } 00949 } 00950 if ((int)result->get_value_at(x,y,z)!=bcls) pixmov++; 00951 if (bdist>maxsegsize) result->set_value_at(x,y,z,-1); // pixel is too far from any center 00952 else result->set_value_at(x,y,z,(float)bcls); // set the pixel to the class number 00953 } 00954 } 00955 } 00956 00957 // **** adjust centers 00958 for (int i=0; i<nseg*3; i++) centers[i]=0; 00959 for (int i=0; i<nseg; i++) count[i]=0; 00960 00961 // weighted sums 00962 for (int z=0; z<nz; z++) { 00963 for (int y=0; y<ny; y++) { 00964 for (int x=0; x<nz; x++) { 00965 int cls = (int)result->get_value_at(x,y,z); 00966 if (cls==-1) continue; 00967 float w=1.0; 00968 if (ampweight) w=image->get_value_at(x,y,z); 00969 00970 centers[cls*3]+=x*w; 00971 centers[cls*3+1]+=y*w; 00972 centers[cls*3+2]+=z*w; 00973 count[cls]+=w; 00974 } 00975 } 00976 } 00977 00978 // now each becomes center of mass, or gets randomly reseeded 00979 int nreseed=0; 00980 for (int c=0; c<nseg; c++) { 00981 // reseed 00982 if (count[c]==0) { 00983 nreseed++; 00984 do { 00985 centers[c*3]= Util::get_frand(0.0f,(float)nx); 00986 centers[c*3+1]=Util::get_frand(0.0f,(float)ny); 00987 centers[c*3+2]=Util::get_frand(0.0f,(float)nz); 00988 } 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 00989 } 00990 // center of mass 00991 else { 00992 centers[c*3]/=count[c]; 00993 centers[c*3+1]/=count[c]; 00994 centers[c*3+2]/=count[c]; 00995 } 00996 } 00997 00998 // with minsegsep, check separation 00999 if (minsegsep>0) { 01000 for (int c1=0; c1<nseg-1; c1++) { 01001 for (int c2=c1+1; c2<nseg; c2++) { 01002 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) { 01003 nreseed++; 01004 do { 01005 centers[c1*3]= Util::get_frand(0.0f,(float)nx); 01006 centers[c1*3+1]=Util::get_frand(0.0f,(float)ny); 01007 centers[c1*3+2]=Util::get_frand(0.0f,(float)nz); 01008 } while (image->get_value_at((int)centers[c1*3],(int)centers[c1*3+1],(int)centers[c1*3+2])<thr); 01009 } 01010 } 01011 } 01012 } 01013 01014 01015 if (verbose) printf("Iteration %3d: %6ld voxels moved, %3d classes reseeded\n",iter,pixmov,nreseed); 01016 if (nreseed==0 && pixmov<(size_t)maxvoxmove) break; // termination conditions met 01017 } 01018 01019 result->set_attr("segment_centers",centers); 01020 01021 return result; 01022 }
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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 1024 of file processor.cpp. 01025 { 01026 printf("Process inplace not implemented. Please use process.\n"); 01027 return; 01028 }
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Definition at line 77 of file processor.cpp. |