#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 772 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. 00773 { 00774 EMData * result = image->copy(); 00775 00776 float thr = params.set_default("thr",0.9f); 00777 float minsegsep = params.set_default("minsegsep",5.0f); 00778 float maxsegsep = params.set_default("maxsegsep",5.1f); 00779 int verbose = params.set_default("verbose",0); 00780 00781 vector<Pixel> pixels=image->calc_highest_locations(thr); 00782 00783 vector<float> centers(3); // only 1 to start 00784 int nx=image->get_xsize(); 00785 int ny=image->get_ysize(); 00786 int nz=image->get_zsize(); 00787 // int nxy=nx*ny; 00788 00789 // seed the process with the highest valued point 00790 centers[0]=(float)pixels[0].x; 00791 centers[1]=(float)pixels[0].y; 00792 centers[2]=(float)pixels[0].z; 00793 pixels.erase(pixels.begin()); 00794 00795 // outer loop. We add one center per iteration 00796 // This is NOT a very efficient algorithm, it assumes points are fairly sparse 00797 while (pixels.size()>0) { 00798 // iterate over pixels until we find a new center (then stop), delete any 'bad' pixels 00799 // no iterators because we remove elements 00800 00801 for (unsigned int i=0; i<pixels.size(); i++) { 00802 00803 Pixel p=pixels[i]; 00804 // iterate over existing centers to see if this pixel should be removed ... technically we only should need to check the last center 00805 for (unsigned int j=0; j<centers.size(); j+=3) { 00806 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z); 00807 if (d<minsegsep) { // conflicts with existing center, erase 00808 pixels.erase(pixels.begin()+i); 00809 i--; 00810 break; 00811 } 00812 } 00813 } 00814 00815 int found=0; 00816 for (unsigned int i=0; i<pixels.size() && found==0; i++) { 00817 Pixel p=pixels[i]; 00818 00819 // iterate again to see if this may be a new valid center. Start at the end so we tend to build chains 00820 for (unsigned int j=centers.size()-3; j>0; j-=3) { 00821 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z); 00822 if (d<maxsegsep) { // we passed minsegsep question already, so we know we're in the 'good' range 00823 centers.push_back((float)p.x); 00824 centers.push_back((float)p.y); 00825 centers.push_back((float)p.z); 00826 pixels.erase(pixels.begin()+i); // in the centers list now, don't need it any more 00827 found=1; 00828 break; 00829 } 00830 } 00831 } 00832 00833 // If we went through the whole list and didn't find one, we need to reseed again 00834 if (!found && pixels.size()) { 00835 if (verbose) printf("New chain\n"); 00836 centers.push_back((float)pixels[0].x); 00837 centers.push_back((float)pixels[0].y); 00838 centers.push_back((float)pixels[0].z); 00839 pixels.erase(pixels.begin()); 00840 } 00841 00842 if (verbose) printf("%d points found\n",(int)(centers.size()/3)); 00843 } 00844 00845 // after we have our list of centers classify pixels 00846 for (int z=0; z<nz; z++) { 00847 for (int y=0; y<ny; y++) { 00848 for (int x=0; x<nz; x++) { 00849 if (image->get_value_at(x,y,z)<thr) { 00850 result->set_value_at(x,y,z,-1.0); //below threshold -> -1 (unclassified) 00851 continue; 00852 } 00853 int bcls=-1; // best matching class 00854 float bdist=(float)(nx+ny+nz); // distance for best class 00855 for (unsigned int c=0; c<centers.size()/3; c++) { 00856 float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]); 00857 if (d<bdist) { bdist=d; bcls=c; } 00858 } 00859 result->set_value_at(x,y,z,(float)bcls); // set the pixel to the class number 00860 } 00861 } 00862 } 00863 00864 result->set_attr("segment_centers",centers); 00865 00866 return result; 00867 }
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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 765 of file processor.cpp. 00766 { 00767 printf("Process inplace not implemented. Please use process.\n"); 00768 return; 00769 }
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Definition at line 75 of file processor.cpp. |