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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

ProcessorNEW ()

Static Public Attributes

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 5609 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 1462 of file processor.cpp.

References EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), and EMAN::Vec3i.

Referenced by process_inplace().

01463 {
01464         static vector<Vec3i> two_six_connected;
01465         if (two_six_connected.size() == 0) {
01466                 for(int i = -1; i <= 1; ++i) {
01467                         for(int j = -1; j <= 1; ++j) {
01468                                 for(int  k = -1; k <= 1; ++k) {
01469                                         if ( j != 0 || i != 0 || k != 0) {
01470                                                 two_six_connected.push_back(Vec3i(i,j,k));
01471                                         }
01472                                 }
01473                         }
01474                 }
01475         }
01476 
01477         vector<Vec3i> ret;
01478         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01479                 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) {
01480                         if  (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw;
01481                         Vec3i c = (*it)+(*it2);
01482 
01483                         if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue;
01484                         if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue;
01485                         if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue;
01486 
01487                         if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) {
01488                                 if (find(ret.begin(),ret.end(),c) == ret.end()) {
01489                                         if (find(region.begin(),region.end(),c) == region.end()) {
01490                                                 region.push_back(c);
01491                                                 ret.push_back(c);
01492                                         }
01493                                 }
01494                         }
01495                 }
01496         }
01497         return ret;
01498 }

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 5624 of file processor.h.

05625                 {
05626                         return "Does a watershed";
05627                 }

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 5614 of file processor.h.

05615                 {
05616                         return NAME;
05617                 }

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 5629 of file processor.h.

References EMAN::TypeDict::put().

05630                 {
05631                         TypeDict d;
05632                         d.put("xpoints", EMObject::FLOATARRAY,"x coordinates");
05633                         d.put("ypoints", EMObject::FLOATARRAY,"y coordinates");
05634                         d.put("zpoints", EMObject::FLOATARRAY,"z coordinates");
05635                         d.put("minval", EMObject::FLOAT,"min value");
05636                         return d;
05637                 }

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

Definition at line 5619 of file processor.h.

05620                 {
05621                         return new WatershedProcessor();
05622                 }

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 1387 of file processor.cpp.

References copy(), find_region(), EMAN::EMData::get_data(), EMAN::EMData::get_size(), EMAN::EMData::set_value_at(), EMAN::EMData::to_zero(), EMAN::EMData::update(), v, EMAN::Vec3i, watershed(), EMAN::EMData::write_image(), x, and y.

01387                                                        {
01388         vector<float> xpoints = params["xpoints"];
01389         vector<float> ypoints = params["ypoints"];
01390         vector<float> zpoints = params["zpoints"];
01391 
01392         vector<int> x(xpoints.begin(),xpoints.end());
01393         vector<int> y(ypoints.begin(),ypoints.end());
01394         vector<int> z(zpoints.begin(),zpoints.end());
01395 
01396 
01397         // throw if vector lengths are unequal
01398 
01399 //      float maxval = -99999;
01400         /*
01401         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01402                 float val = image->get_value_at(x[i],y[i],z[i]);
01403                 if (val > maxval) {
01404                         maxval = val;
01405                 }
01406         }*/
01407 
01408         float minval = params["minval"];
01409 
01410         EMData* mask = new EMData(*image);
01411         mask->to_zero();
01412 
01413         // Set the original mask values
01414         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01415                 try {
01416                         mask->set_value_at(x[i],y[i],z[i], (float)(i+1));
01417                 } catch (...) {
01418                         continue;
01419                 }
01420         }
01421         mask->write_image("seeds2.mrc");
01422 //      int dis = 500;
01423 //      float dx = (maxval-minval)/((float) dis - 1);
01424 
01425 
01426 //      for(int i = 0; i < dis; ++i) {
01427 //              float val = maxval-i*dx;
01428 
01429                 while( true ) {
01430                         bool cont= false;
01431                         for(unsigned int j = 0; j < xpoints.size(); ++j)
01432                         {
01433 
01434                                 Vec3i coord(x[j],y[j],z[j]);
01435                                 vector<Vec3i> region;
01436                                 region.push_back(coord);
01437                                 vector<Vec3i> find_region_input = region;
01438                                 while (true) {
01439                                         vector<Vec3i> v = find_region(mask,find_region_input, j+1, region);
01440                                         if (v.size() == 0 ) break;
01441                                         else find_region_input = v;
01442                                 }
01443 
01444                                 vector<Vec3i> tmp(region.begin(),region.end());
01445                                 region.clear();
01446                                 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) {
01447                                         vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1);
01448                                         copy(tmp2.begin(),tmp2.end(),back_inserter(region));
01449                                 }
01450                                 if (region.size() != 0) cont = true;
01451                         }
01452 
01453                         if (!cont) break;
01454                 }
01455 //      }
01456 
01457         memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size());
01458         image->update();
01459 }

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

Definition at line 1500 of file processor.cpp.

References EMAN::EMData::get_value_at(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::EMData::set_value_at(), and EMAN::Vec3i.

Referenced by process_inplace().

01501 {
01502         static vector<Vec3i> two_six_connected;
01503         if (two_six_connected.size() == 0) {
01504                 for(int i = -1; i <= 1; ++i) {
01505                         for(int j = -1; j <= 1; ++j) {
01506                                 for(int  k = -1; k <= 1; ++k) {
01507                                         if ( j != 0 || i != 0 || k != 0) {
01508                                                 two_six_connected.push_back(Vec3i(i,j,k));
01509                                         }
01510                                 }
01511                         }
01512                 }
01513         }
01514 
01515         if  (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw;
01516 
01517         vector<Vec3i> ret;
01518         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01519                 Vec3i c = (*it)+coordinate;
01520 
01521                 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue;
01522                 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue;
01523                 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue;
01524 
01525         //      cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl;
01526                 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) {
01527                         //cout << "Added something " << mask_value << endl;
01528                         mask->set_value_at(c[0],c[1],c[2], (float)mask_value);
01529                         ret.push_back(c);
01530                 }
01531         }
01532         return ret;
01533 }


Member Data Documentation

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

Definition at line 79 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:42:42 2013 for EMAN2 by  doxygen 1.3.9.1