EMAN::WatershedProcessor Class Reference

'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged More...

#include <processor.h>

Inheritance diagram for EMAN::WatershedProcessor:

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Collaboration diagram for EMAN::WatershedProcessor:

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List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual string get_desc () const
 Get the descrition of this specific processor.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "segment.watershed"

Private Member Functions

vector< Vec3iwatershed (EMData *mask, EMData *image, const float &threshold, const Vec3i &cordinate, const int mask_value)
vector< Vec3ifind_region (EMData *mask, const vector< Vec3i > &coords, const int mask_value, vector< Vec3i > &region)

Detailed Description

'paints' a circle into the image at x,y,z with values inside r1 set to v1, values between r1 and r2 will be set to a value between v1 and v2, and values outside r2 will be unchanged

Parameters:
xpoints x coordinates
ypoints y coordinates
zpoints z coordinates
minval min value

Definition at line 5492 of file processor.h.


Member Function Documentation

vector< Vec3i > WatershedProcessor::find_region ( EMData mask,
const vector< Vec3i > &  coords,
const int  mask_value,
vector< Vec3i > &  region 
) [private]

Definition at line 1453 of file processor.cpp.

References EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), and EMAN::EMData::get_zsize().

Referenced by process_inplace().

01454 {
01455         static vector<Vec3i> two_six_connected;
01456         if (two_six_connected.size() == 0) {
01457                 for(int i = -1; i <= 1; ++i) {
01458                         for(int j = -1; j <= 1; ++j) {
01459                                 for(int  k = -1; k <= 1; ++k) {
01460                                         if ( j != 0 || i != 0 || k != 0) {
01461                                                 two_six_connected.push_back(Vec3i(i,j,k));
01462                                         }
01463                                 }
01464                         }
01465                 }
01466         }
01467 
01468         vector<Vec3i> ret;
01469         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01470                 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) {
01471                         if  (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw;
01472                         Vec3i c = (*it)+(*it2);
01473 
01474                         if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue;
01475                         if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue;
01476                         if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue;
01477 
01478                         if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) {
01479                                 if (find(ret.begin(),ret.end(),c) == ret.end()) {
01480                                         if (find(region.begin(),region.end(),c) == region.end()) {
01481                                                 region.push_back(c);
01482                                                 ret.push_back(c);
01483                                         }
01484                                 }
01485                         }
01486                 }
01487         }
01488         return ret;
01489 }

virtual string EMAN::WatershedProcessor::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 5507 of file processor.h.

05508                 {
05509                         return "Does a watershed";
05510                 }

virtual string EMAN::WatershedProcessor::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 5497 of file processor.h.

References NAME.

05498                 {
05499                         return NAME;
05500                 }

virtual TypeDict EMAN::WatershedProcessor::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 5512 of file processor.h.

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

05513                 {
05514                         TypeDict d;
05515                         d.put("xpoints", EMObject::FLOATARRAY,"x coordinates");
05516                         d.put("ypoints", EMObject::FLOATARRAY,"y coordinates");
05517                         d.put("zpoints", EMObject::FLOATARRAY,"z coordinates");
05518                         d.put("minval", EMObject::FLOAT,"min value");
05519                         return d;
05520                 }

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

Definition at line 5502 of file processor.h.

05503                 {
05504                         return new WatershedProcessor();
05505                 }

void WatershedProcessor::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 1378 of file processor.cpp.

References copy(), find_region(), EMAN::EMData::get_data(), EMAN::EMData::get_size(), EMAN::Processor::params, EMAN::EMData::set_value_at(), EMAN::EMData::to_zero(), EMAN::EMData::update(), v, watershed(), EMAN::EMData::write_image(), x, and y.

01378                                                        {
01379         vector<float> xpoints = params["xpoints"];
01380         vector<float> ypoints = params["ypoints"];
01381         vector<float> zpoints = params["zpoints"];
01382 
01383         vector<int> x(xpoints.begin(),xpoints.end());
01384         vector<int> y(ypoints.begin(),ypoints.end());
01385         vector<int> z(zpoints.begin(),zpoints.end());
01386 
01387 
01388         // throw if vector lengths are unequal
01389 
01390 //      float maxval = -99999;
01391         /*
01392         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01393                 float val = image->get_value_at(x[i],y[i],z[i]);
01394                 if (val > maxval) {
01395                         maxval = val;
01396                 }
01397         }*/
01398 
01399         float minval = params["minval"];
01400 
01401         EMData* mask = new EMData(*image);
01402         mask->to_zero();
01403 
01404         // Set the original mask values
01405         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01406                 try {
01407                         mask->set_value_at(x[i],y[i],z[i], (float)(i+1));
01408                 } catch (...) {
01409                         continue;
01410                 }
01411         }
01412         mask->write_image("seeds2.mrc");
01413 //      int dis = 500;
01414 //      float dx = (maxval-minval)/((float) dis - 1);
01415 
01416 
01417 //      for(int i = 0; i < dis; ++i) {
01418 //              float val = maxval-i*dx;
01419 
01420                 while( true ) {
01421                         bool cont= false;
01422                         for(unsigned int j = 0; j < xpoints.size(); ++j)
01423                         {
01424 
01425                                 Vec3i coord(x[j],y[j],z[j]);
01426                                 vector<Vec3i> region;
01427                                 region.push_back(coord);
01428                                 vector<Vec3i> find_region_input = region;
01429                                 while (true) {
01430                                         vector<Vec3i> v = find_region(mask,find_region_input, j+1, region);
01431                                         if (v.size() == 0 ) break;
01432                                         else find_region_input = v;
01433                                 }
01434 
01435                                 vector<Vec3i> tmp(region.begin(),region.end());
01436                                 region.clear();
01437                                 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) {
01438                                         vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1);
01439                                         copy(tmp2.begin(),tmp2.end(),back_inserter(region));
01440                                 }
01441                                 if (region.size() != 0) cont = true;
01442                         }
01443 
01444                         if (!cont) break;
01445                 }
01446 //      }
01447 
01448         memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size());
01449         image->update();
01450 }

vector< Vec3i > WatershedProcessor::watershed ( EMData mask,
EMData image,
const float &  threshold,
const Vec3i cordinate,
const int  mask_value 
) [private]

Definition at line 1491 of file processor.cpp.

References EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), and EMAN::EMData::set_value_at().

Referenced by process_inplace().

01492 {
01493         static vector<Vec3i> two_six_connected;
01494         if (two_six_connected.size() == 0) {
01495                 for(int i = -1; i <= 1; ++i) {
01496                         for(int j = -1; j <= 1; ++j) {
01497                                 for(int  k = -1; k <= 1; ++k) {
01498                                         if ( j != 0 || i != 0 || k != 0) {
01499                                                 two_six_connected.push_back(Vec3i(i,j,k));
01500                                         }
01501                                 }
01502                         }
01503                 }
01504         }
01505 
01506         if  (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw;
01507 
01508         vector<Vec3i> ret;
01509         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01510                 Vec3i c = (*it)+coordinate;
01511 
01512                 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue;
01513                 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue;
01514                 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue;
01515 
01516         //      cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl;
01517                 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) {
01518                         //cout << "Added something " << mask_value << endl;
01519                         mask->set_value_at(c[0],c[1],c[2], (float)mask_value);
01520                         ret.push_back(c);
01521                 }
01522         }
01523         return ret;
01524 }


Member Data Documentation

const string WatershedProcessor::NAME = "segment.watershed" [static]

Definition at line 5522 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:49:31 2011 for EMAN2 by  doxygen 1.4.7