#include <processor.h>
Inheritance diagram for EMAN::DistanceSegmentProcessor:
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.distance" |
For linear densities such as skeletons this should fill linear regions with uniformly separated points
Definition at line 679 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 705 of file processor.h. 00706 { 00707 return "Segments a volume into pieces separated by distances in the specified range."; 00708 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 682 of file processor.h. 00683 {
00684 return NAME;
00685 }
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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 690 of file processor.h. References EMAN::TypeDict::put(). 00691 { 00692 TypeDict d ; 00693 d.put("thr",EMObject::FLOAT,"Optional : Isosurface threshold value. Pixels below this will not be segment centers (default = 0.9)"); 00694 d.put("minsegsep",EMObject::FLOAT,"Required: Minimum segment separation in pixels. Segments too close will trigger a reseed"); 00695 d.put("maxsegsep",EMObject::FLOAT,"Required: Maximum segment separation in pixels. Segments too close will trigger a reseed"); 00696 d.put("verbose",EMObject::INT,"Be verbose while running"); 00697 return d; 00698 }
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Definition at line 700 of file processor.h. 00701 { 00702 return new DistanceSegmentProcessor(); 00703 }
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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 784 of file processor.cpp. References EMAN::EMData::calc_highest_locations(), EMAN::EMData::copy(), 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, EMAN::Pixel::x, y, EMAN::Pixel::y, and EMAN::Pixel::z. 00785 { 00786 EMData * result = image->copy(); 00787 00788 float thr = params.set_default("thr",0.9f); 00789 float minsegsep = params.set_default("minsegsep",5.0f); 00790 float maxsegsep = params.set_default("maxsegsep",5.1f); 00791 int verbose = params.set_default("verbose",0); 00792 00793 vector<Pixel> pixels=image->calc_highest_locations(thr); 00794 00795 vector<float> centers(3); // only 1 to start 00796 int nx=image->get_xsize(); 00797 int ny=image->get_ysize(); 00798 int nz=image->get_zsize(); 00799 // int nxy=nx*ny; 00800 00801 // seed the process with the highest valued point 00802 centers[0]=(float)pixels[0].x; 00803 centers[1]=(float)pixels[0].y; 00804 centers[2]=(float)pixels[0].z; 00805 pixels.erase(pixels.begin()); 00806 00807 // outer loop. We add one center per iteration 00808 // This is NOT a very efficient algorithm, it assumes points are fairly sparse 00809 while (pixels.size()>0) { 00810 // iterate over pixels until we find a new center (then stop), delete any 'bad' pixels 00811 // no iterators because we remove elements 00812 00813 for (unsigned int i=0; i<pixels.size(); i++) { 00814 00815 Pixel p=pixels[i]; 00816 // iterate over existing centers to see if this pixel should be removed ... technically we only should need to check the last center 00817 for (unsigned int j=0; j<centers.size(); j+=3) { 00818 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z); 00819 if (d<minsegsep) { // conflicts with existing center, erase 00820 pixels.erase(pixels.begin()+i); 00821 i--; 00822 break; 00823 } 00824 } 00825 } 00826 00827 int found=0; 00828 for (unsigned int i=0; i<pixels.size() && found==0; i++) { 00829 Pixel p=pixels[i]; 00830 00831 // iterate again to see if this may be a new valid center. Start at the end so we tend to build chains 00832 for (unsigned int j=centers.size()-3; j>0; j-=3) { 00833 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z); 00834 if (d<maxsegsep) { // we passed minsegsep question already, so we know we're in the 'good' range 00835 centers.push_back((float)p.x); 00836 centers.push_back((float)p.y); 00837 centers.push_back((float)p.z); 00838 pixels.erase(pixels.begin()+i); // in the centers list now, don't need it any more 00839 found=1; 00840 break; 00841 } 00842 } 00843 } 00844 00845 // If we went through the whole list and didn't find one, we need to reseed again 00846 if (!found && pixels.size()) { 00847 if (verbose) printf("New chain\n"); 00848 centers.push_back((float)pixels[0].x); 00849 centers.push_back((float)pixels[0].y); 00850 centers.push_back((float)pixels[0].z); 00851 pixels.erase(pixels.begin()); 00852 } 00853 00854 if (verbose) printf("%d points found\n",(int)(centers.size()/3)); 00855 } 00856 00857 // after we have our list of centers classify pixels 00858 for (int z=0; z<nz; z++) { 00859 for (int y=0; y<ny; y++) { 00860 for (int x=0; x<nz; x++) { 00861 if (image->get_value_at(x,y,z)<thr) { 00862 result->set_value_at(x,y,z,-1.0); //below threshold -> -1 (unclassified) 00863 continue; 00864 } 00865 int bcls=-1; // best matching class 00866 float bdist=(float)(nx+ny+nz); // distance for best class 00867 for (unsigned int c=0; c<centers.size()/3; c++) { 00868 float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]); 00869 if (d<bdist) { bdist=d; bcls=c; } 00870 } 00871 result->set_value_at(x,y,z,(float)bcls); // set the pixel to the class number 00872 } 00873 } 00874 } 00875 00876 result->set_attr("segment_centers",centers); 00877 00878 return result; 00879 }
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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 777 of file processor.cpp. 00778 { 00779 printf("Process inplace not implemented. Please use process.\n"); 00780 return; 00781 }
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Definition at line 78 of file processor.cpp. |