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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 = "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 5313 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 1332 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().

01333 {
01334         static vector<Vec3i> two_six_connected;
01335         if (two_six_connected.size() == 0) {
01336                 for(int i = -1; i <= 1; ++i) {
01337                         for(int j = -1; j <= 1; ++j) {
01338                                 for(int  k = -1; k <= 1; ++k) {
01339                                         if ( j != 0 || i != 0 || k != 0) {
01340                                                 two_six_connected.push_back(Vec3i(i,j,k));
01341                                         }
01342                                 }
01343                         }
01344                 }
01345         }
01346 
01347         vector<Vec3i> ret;
01348         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01349                 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) {
01350                         if  (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw;
01351                         Vec3i c = (*it)+(*it2);
01352 
01353                         if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue;
01354                         if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue;
01355                         if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue;
01356 
01357                         if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) {
01358                                 if (find(ret.begin(),ret.end(),c) == ret.end()) {
01359                                         if (find(region.begin(),region.end(),c) == region.end()) {
01360                                                 region.push_back(c);
01361                                                 ret.push_back(c);
01362                                         }
01363                                 }
01364                         }
01365                 }
01366         }
01367         return ret;
01368 }

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 5328 of file processor.h.

05329                 {
05330                         return "Does a watershed";
05331                 }

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 5318 of file processor.h.

05319                 {
05320                         return NAME;
05321                 }

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 5333 of file processor.h.

References EMAN::TypeDict::put().

05334                 {
05335                         TypeDict d;
05336                         d.put("xpoints", EMObject::FLOATARRAY,"x coordinates");
05337                         d.put("ypoints", EMObject::FLOATARRAY,"y coordinates");
05338                         d.put("zpoints", EMObject::FLOATARRAY,"z coordinates");
05339                         d.put("minval", EMObject::FLOAT,"min value");
05340                         return d;
05341                 }

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

Definition at line 5323 of file processor.h.

05324                 {
05325                         return new WatershedProcessor();
05326                 }

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 1257 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.

01257                                                        {
01258         vector<float> xpoints = params["xpoints"];
01259         vector<float> ypoints = params["ypoints"];
01260         vector<float> zpoints = params["zpoints"];
01261 
01262         vector<int> x(xpoints.begin(),xpoints.end());
01263         vector<int> y(ypoints.begin(),ypoints.end());
01264         vector<int> z(zpoints.begin(),zpoints.end());
01265 
01266 
01267         // throw if vector lengths are unequal
01268 
01269 //      float maxval = -99999;
01270         /*
01271         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01272                 float val = image->get_value_at(x[i],y[i],z[i]);
01273                 if (val > maxval) {
01274                         maxval = val;
01275                 }
01276         }*/
01277 
01278         float minval = params["minval"];
01279 
01280         EMData* mask = new EMData(*image);
01281         mask->to_zero();
01282 
01283         // Set the original mask values
01284         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01285                 try {
01286                         mask->set_value_at(x[i],y[i],z[i], (float)(i+1));
01287                 } catch (...) {
01288                         continue;
01289                 }
01290         }
01291         mask->write_image("seeds2.mrc");
01292 //      int dis = 500;
01293 //      float dx = (maxval-minval)/((float) dis - 1);
01294 
01295 
01296 //      for(int i = 0; i < dis; ++i) {
01297 //              float val = maxval-i*dx;
01298 
01299                 while( true ) {
01300                         bool cont= false;
01301                         for(unsigned int j = 0; j < xpoints.size(); ++j)
01302                         {
01303 
01304                                 Vec3i coord(x[j],y[j],z[j]);
01305                                 vector<Vec3i> region;
01306                                 region.push_back(coord);
01307                                 vector<Vec3i> find_region_input = region;
01308                                 while (true) {
01309                                         vector<Vec3i> v = find_region(mask,find_region_input, j+1, region);
01310                                         if (v.size() == 0 ) break;
01311                                         else find_region_input = v;
01312                                 }
01313 
01314                                 vector<Vec3i> tmp(region.begin(),region.end());
01315                                 region.clear();
01316                                 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) {
01317                                         vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1);
01318                                         copy(tmp2.begin(),tmp2.end(),back_inserter(region));
01319                                 }
01320                                 if (region.size() != 0) cont = true;
01321                         }
01322 
01323                         if (!cont) break;
01324                 }
01325 //      }
01326 
01327         memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size());
01328         image->update();
01329 }

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

Definition at line 1370 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().

01371 {
01372         static vector<Vec3i> two_six_connected;
01373         if (two_six_connected.size() == 0) {
01374                 for(int i = -1; i <= 1; ++i) {
01375                         for(int j = -1; j <= 1; ++j) {
01376                                 for(int  k = -1; k <= 1; ++k) {
01377                                         if ( j != 0 || i != 0 || k != 0) {
01378                                                 two_six_connected.push_back(Vec3i(i,j,k));
01379                                         }
01380                                 }
01381                         }
01382                 }
01383         }
01384 
01385         if  (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw;
01386 
01387         vector<Vec3i> ret;
01388         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01389                 Vec3i c = (*it)+coordinate;
01390 
01391                 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue;
01392                 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue;
01393                 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue;
01394 
01395         //      cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl;
01396                 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) {
01397                         //cout << "Added something " << mask_value << endl;
01398                         mask->set_value_at(c[0],c[1],c[2], (float)mask_value);
01399                         ret.push_back(c);
01400                 }
01401         }
01402         return ret;
01403 }


Member Data Documentation

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

Definition at line 176 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:16 2010 for EMAN2 by  doxygen 1.3.9.1