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 5523 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 1388 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().

01389 {
01390         static vector<Vec3i> two_six_connected;
01391         if (two_six_connected.size() == 0) {
01392                 for(int i = -1; i <= 1; ++i) {
01393                         for(int j = -1; j <= 1; ++j) {
01394                                 for(int  k = -1; k <= 1; ++k) {
01395                                         if ( j != 0 || i != 0 || k != 0) {
01396                                                 two_six_connected.push_back(Vec3i(i,j,k));
01397                                         }
01398                                 }
01399                         }
01400                 }
01401         }
01402 
01403         vector<Vec3i> ret;
01404         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01405                 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) {
01406                         if  (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw;
01407                         Vec3i c = (*it)+(*it2);
01408 
01409                         if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue;
01410                         if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue;
01411                         if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue;
01412 
01413                         if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) {
01414                                 if (find(ret.begin(),ret.end(),c) == ret.end()) {
01415                                         if (find(region.begin(),region.end(),c) == region.end()) {
01416                                                 region.push_back(c);
01417                                                 ret.push_back(c);
01418                                         }
01419                                 }
01420                         }
01421                 }
01422         }
01423         return ret;
01424 }

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 5538 of file processor.h.

05539                 {
05540                         return "Does a watershed";
05541                 }

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 5528 of file processor.h.

References NAME.

05529                 {
05530                         return NAME;
05531                 }

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 5543 of file processor.h.

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

05544                 {
05545                         TypeDict d;
05546                         d.put("xpoints", EMObject::FLOATARRAY,"x coordinates");
05547                         d.put("ypoints", EMObject::FLOATARRAY,"y coordinates");
05548                         d.put("zpoints", EMObject::FLOATARRAY,"z coordinates");
05549                         d.put("minval", EMObject::FLOAT,"min value");
05550                         return d;
05551                 }

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

Definition at line 5533 of file processor.h.

05534                 {
05535                         return new WatershedProcessor();
05536                 }

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 1313 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.

01313                                                        {
01314         vector<float> xpoints = params["xpoints"];
01315         vector<float> ypoints = params["ypoints"];
01316         vector<float> zpoints = params["zpoints"];
01317 
01318         vector<int> x(xpoints.begin(),xpoints.end());
01319         vector<int> y(ypoints.begin(),ypoints.end());
01320         vector<int> z(zpoints.begin(),zpoints.end());
01321 
01322 
01323         // throw if vector lengths are unequal
01324 
01325 //      float maxval = -99999;
01326         /*
01327         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01328                 float val = image->get_value_at(x[i],y[i],z[i]);
01329                 if (val > maxval) {
01330                         maxval = val;
01331                 }
01332         }*/
01333 
01334         float minval = params["minval"];
01335 
01336         EMData* mask = new EMData(*image);
01337         mask->to_zero();
01338 
01339         // Set the original mask values
01340         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01341                 try {
01342                         mask->set_value_at(x[i],y[i],z[i], (float)(i+1));
01343                 } catch (...) {
01344                         continue;
01345                 }
01346         }
01347         mask->write_image("seeds2.mrc");
01348 //      int dis = 500;
01349 //      float dx = (maxval-minval)/((float) dis - 1);
01350 
01351 
01352 //      for(int i = 0; i < dis; ++i) {
01353 //              float val = maxval-i*dx;
01354 
01355                 while( true ) {
01356                         bool cont= false;
01357                         for(unsigned int j = 0; j < xpoints.size(); ++j)
01358                         {
01359 
01360                                 Vec3i coord(x[j],y[j],z[j]);
01361                                 vector<Vec3i> region;
01362                                 region.push_back(coord);
01363                                 vector<Vec3i> find_region_input = region;
01364                                 while (true) {
01365                                         vector<Vec3i> v = find_region(mask,find_region_input, j+1, region);
01366                                         if (v.size() == 0 ) break;
01367                                         else find_region_input = v;
01368                                 }
01369 
01370                                 vector<Vec3i> tmp(region.begin(),region.end());
01371                                 region.clear();
01372                                 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) {
01373                                         vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1);
01374                                         copy(tmp2.begin(),tmp2.end(),back_inserter(region));
01375                                 }
01376                                 if (region.size() != 0) cont = true;
01377                         }
01378 
01379                         if (!cont) break;
01380                 }
01381 //      }
01382 
01383         memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size());
01384         image->update();
01385 }

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

Definition at line 1426 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().

01427 {
01428         static vector<Vec3i> two_six_connected;
01429         if (two_six_connected.size() == 0) {
01430                 for(int i = -1; i <= 1; ++i) {
01431                         for(int j = -1; j <= 1; ++j) {
01432                                 for(int  k = -1; k <= 1; ++k) {
01433                                         if ( j != 0 || i != 0 || k != 0) {
01434                                                 two_six_connected.push_back(Vec3i(i,j,k));
01435                                         }
01436                                 }
01437                         }
01438                 }
01439         }
01440 
01441         if  (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw;
01442 
01443         vector<Vec3i> ret;
01444         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01445                 Vec3i c = (*it)+coordinate;
01446 
01447                 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue;
01448                 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue;
01449                 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue;
01450 
01451         //      cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl;
01452                 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) {
01453                         //cout << "Added something " << mask_value << endl;
01454                         mask->set_value_at(c[0],c[1],c[2], (float)mask_value);
01455                         ret.push_back(c);
01456                 }
01457         }
01458         return ret;
01459 }


Member Data Documentation

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

Definition at line 5553 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Nov 17 12:46:49 2011 for EMAN2 by  doxygen 1.4.7