EMAN::DistanceSegmentProcessor Class Reference

Segment a volume about:homeinto subvolumes based on a center separation value. More...

#include <processor.h>

Inheritance diagram for EMAN::DistanceSegmentProcessor:

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Collaboration diagram for EMAN::DistanceSegmentProcessor:

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List of all members.

Public Member Functions

string get_name () const
 Get the processor's name.
virtual EMDataprocess (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 ProcessorNEW ()

Static Public Attributes

static const string NAME = "segment.distance"

Detailed Description

Segment a volume about:homeinto subvolumes based on a center separation value.

For linear densities such as skeletons this should fill linear regions with uniformly separated points

Author:
Steve Ludtke
Date:
2010/07/14

Definition at line 704 of file processor.h.


Member Function Documentation

string EMAN::DistanceSegmentProcessor::get_desc (  )  const [inline, virtual]

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 730 of file processor.h.

00731                 {
00732                         return "Segments a volume into pieces separated by distances in the specified range.";
00733                 }

string EMAN::DistanceSegmentProcessor::get_name (  )  const [inline, virtual]

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 707 of file processor.h.

References NAME.

00708                 {
00709                         return NAME;
00710                 }

TypeDict EMAN::DistanceSegmentProcessor::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.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Processor.

Definition at line 715 of file processor.h.

References EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and EMAN::TypeDict::put().

00716                 {
00717                         TypeDict d ;
00718                         d.put("thr",EMObject::FLOAT,"Optional : Isosurface threshold value. Pixels below this will not be segment centers (default = 0.9)");
00719                         d.put("minsegsep",EMObject::FLOAT,"Required: Minimum segment separation in pixels. Segments too close will trigger a reseed");
00720                         d.put("maxsegsep",EMObject::FLOAT,"Required: Maximum segment separation in pixels. Segments too close will trigger a reseed");
00721                         d.put("verbose",EMObject::INT,"Be verbose while running");
00722                         return d;
00723                 }

static Processor* EMAN::DistanceSegmentProcessor::NEW (  )  [inline, static]

Definition at line 725 of file processor.h.

00726                 {
00727                         return new DistanceSegmentProcessor();
00728                 }

EMData * DistanceSegmentProcessor::process ( const EMData *const   image  )  [virtual]

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.

Parameters:
image The image will be copied, actual process happen on copy of image.
Returns:
the image processing result, may or may not be the same size of the input image

Reimplemented from EMAN::Processor.

Definition at line 788 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::Processor::params, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::EMData::set_value_at(), x, and y.

00789 {
00790         EMData * result = image->copy();
00791 
00792         float thr = params.set_default("thr",0.9f);
00793         float minsegsep = params.set_default("minsegsep",5.0f);
00794         float maxsegsep = params.set_default("maxsegsep",5.1f);
00795         int verbose = params.set_default("verbose",0);
00796 
00797         vector<Pixel> pixels=image->calc_highest_locations(thr);
00798 
00799         vector<float> centers(3);       // only 1 to start
00800         int nx=image->get_xsize();
00801         int ny=image->get_ysize();
00802         int nz=image->get_zsize();
00803 //      int nxy=nx*ny;
00804 
00805         // seed the process with the highest valued point
00806         centers[0]=(float)pixels[0].x;
00807         centers[1]=(float)pixels[0].y;
00808         centers[2]=(float)pixels[0].z;
00809         pixels.erase(pixels.begin());
00810 
00811         // outer loop. We add one center per iteration
00812         // This is NOT a very efficient algorithm, it assumes points are fairly sparse
00813         while (pixels.size()>0) {
00814                 // iterate over pixels until we find a new center (then stop), delete any 'bad' pixels
00815                 // no iterators because we remove elements
00816 
00817                 for (unsigned int i=0; i<pixels.size(); i++) {
00818 
00819                         Pixel p=pixels[i];
00820                         // iterate over existing centers to see if this pixel should be removed ... technically we only should need to check the last center
00821                         for (unsigned int j=0; j<centers.size(); j+=3) {
00822                                 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
00823                                 if (d<minsegsep) {              // conflicts with existing center, erase
00824                                         pixels.erase(pixels.begin()+i);
00825                                         i--;
00826                                         break;
00827                                 }
00828                         }
00829                 }
00830 
00831                 int found=0;
00832                 for (unsigned int i=0; i<pixels.size() && found==0; i++) {
00833                         Pixel p=pixels[i];
00834 
00835                         // iterate again to see if this may be a new valid center. Start at the end so we tend to build chains
00836                         for (unsigned int j=centers.size()-3; j>0; j-=3) {
00837                                 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
00838                                 if (d<maxsegsep) {              // we passed minsegsep question already, so we know we're in the 'good' range
00839                                         centers.push_back((float)p.x);
00840                                         centers.push_back((float)p.y);
00841                                         centers.push_back((float)p.z);
00842                                         pixels.erase(pixels.begin()+i); // in the centers list now, don't need it any more
00843                                         found=1;
00844                                         break;
00845                                 }
00846                         }
00847                 }
00848 
00849                 // If we went through the whole list and didn't find one, we need to reseed again
00850                 if (!found && pixels.size()) {
00851                         if (verbose) printf("New chain\n");
00852                         centers.push_back((float)pixels[0].x);
00853                         centers.push_back((float)pixels[0].y);
00854                         centers.push_back((float)pixels[0].z);
00855                         pixels.erase(pixels.begin());
00856                 }
00857 
00858                 if (verbose) printf("%d points found\n",(int)(centers.size()/3));
00859         }
00860 
00861         // after we have our list of centers classify pixels
00862         for (int z=0; z<nz; z++) {
00863                 for (int y=0; y<ny; y++) {
00864                         for (int x=0; x<nz; x++) {
00865                                 if (image->get_value_at(x,y,z)<thr) {
00866                                         result->set_value_at(x,y,z,-1.0);               //below threshold -> -1 (unclassified)
00867                                         continue;
00868                                 }
00869                                 int bcls=-1;                    // best matching class
00870                                 float bdist=(float)(nx+ny+nz);  // distance for best class
00871                                 for (unsigned int c=0; c<centers.size()/3; c++) {
00872                                         float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]);
00873                                         if (d<bdist) { bdist=d; bcls=c; }
00874                                 }
00875                                 result->set_value_at(x,y,z,(float)bcls);                // set the pixel to the class number
00876                         }
00877                 }
00878         }
00879 
00880         result->set_attr("segment_centers",centers);
00881 
00882         return result;
00883 }

void DistanceSegmentProcessor::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.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 781 of file processor.cpp.

00782 {
00783         printf("Process inplace not implemented. Please use process.\n");
00784         return;
00785 }


Member Data Documentation

const string DistanceSegmentProcessor::NAME = "segment.distance" [static]

Definition at line 735 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:09:37 2012 for EMAN2 by  doxygen 1.4.7