Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

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:

Inheritance graph
[legend]
Collaboration diagram for EMAN::DistanceSegmentProcessor:

Collaboration graph
[legend]
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

ProcessorNEW ()

Static Public Attributes

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 679 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 705 of file processor.h.

00706                 {
00707                         return "Segments a volume into pieces separated by distances in the specified range.";
00708                 }

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 682 of file processor.h.

00683                 {
00684                         return NAME;
00685                 }

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 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                 }

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

Definition at line 700 of file processor.h.

00701                 {
00702                         return new DistanceSegmentProcessor();
00703                 }

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 783 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.

00784 {
00785         EMData * result = image->copy();
00786 
00787         float thr = params.set_default("thr",0.9f);
00788         float minsegsep = params.set_default("minsegsep",5.0f);
00789         float maxsegsep = params.set_default("maxsegsep",5.1f);
00790         int verbose = params.set_default("verbose",0);
00791 
00792         vector<Pixel> pixels=image->calc_highest_locations(thr);
00793 
00794         vector<float> centers(3);       // only 1 to start
00795         int nx=image->get_xsize();
00796         int ny=image->get_ysize();
00797         int nz=image->get_zsize();
00798 //      int nxy=nx*ny;
00799 
00800         // seed the process with the highest valued point
00801         centers[0]=(float)pixels[0].x;
00802         centers[1]=(float)pixels[0].y;
00803         centers[2]=(float)pixels[0].z;
00804         pixels.erase(pixels.begin());
00805 
00806         // outer loop. We add one center per iteration
00807         // This is NOT a very efficient algorithm, it assumes points are fairly sparse
00808         while (pixels.size()>0) {
00809                 // iterate over pixels until we find a new center (then stop), delete any 'bad' pixels
00810                 // no iterators because we remove elements
00811 
00812                 for (unsigned int i=0; i<pixels.size(); i++) {
00813 
00814                         Pixel p=pixels[i];
00815                         // iterate over existing centers to see if this pixel should be removed ... technically we only should need to check the last center
00816                         for (unsigned int j=0; j<centers.size(); j+=3) {
00817                                 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
00818                                 if (d<minsegsep) {              // conflicts with existing center, erase
00819                                         pixels.erase(pixels.begin()+i);
00820                                         i--;
00821                                         break;
00822                                 }
00823                         }
00824                 }
00825 
00826                 int found=0;
00827                 for (unsigned int i=0; i<pixels.size() && found==0; i++) {
00828                         Pixel p=pixels[i];
00829 
00830                         // iterate again to see if this may be a new valid center. Start at the end so we tend to build chains
00831                         for (unsigned int j=centers.size()-3; j>0; j-=3) {
00832                                 float d=Util::hypot3(centers[j]-p.x,centers[j+1]-p.y,centers[j+2]-p.z);
00833                                 if (d<maxsegsep) {              // we passed minsegsep question already, so we know we're in the 'good' range
00834                                         centers.push_back((float)p.x);
00835                                         centers.push_back((float)p.y);
00836                                         centers.push_back((float)p.z);
00837                                         pixels.erase(pixels.begin()+i); // in the centers list now, don't need it any more
00838                                         found=1;
00839                                         break;
00840                                 }
00841                         }
00842                 }
00843 
00844                 // If we went through the whole list and didn't find one, we need to reseed again
00845                 if (!found && pixels.size()) {
00846                         if (verbose) printf("New chain\n");
00847                         centers.push_back((float)pixels[0].x);
00848                         centers.push_back((float)pixels[0].y);
00849                         centers.push_back((float)pixels[0].z);
00850                         pixels.erase(pixels.begin());
00851                 }
00852 
00853                 if (verbose) printf("%d points found\n",(int)(centers.size()/3));
00854         }
00855 
00856         // after we have our list of centers classify pixels
00857         for (int z=0; z<nz; z++) {
00858                 for (int y=0; y<ny; y++) {
00859                         for (int x=0; x<nz; x++) {
00860                                 if (image->get_value_at(x,y,z)<thr) {
00861                                         result->set_value_at(x,y,z,-1.0);               //below threshold -> -1 (unclassified)
00862                                         continue;
00863                                 }
00864                                 int bcls=-1;                    // best matching class
00865                                 float bdist=(float)(nx+ny+nz);  // distance for best class
00866                                 for (unsigned int c=0; c<centers.size()/3; c++) {
00867                                         float d=Util::hypot3(x-centers[c*3],y-centers[c*3+1],z-centers[c*3+2]);
00868                                         if (d<bdist) { bdist=d; bcls=c; }
00869                                 }
00870                                 result->set_value_at(x,y,z,(float)bcls);                // set the pixel to the class number
00871                         }
00872                 }
00873         }
00874 
00875         result->set_attr("segment_centers",centers);
00876 
00877         return result;
00878 }

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 776 of file processor.cpp.

00777 {
00778         printf("Process inplace not implemented. Please use process.\n");
00779         return;
00780 }


Member Data Documentation

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

Definition at line 79 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Mon May 2 13:29:55 2011 for EMAN2 by  doxygen 1.3.9.1