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 5568 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 1460 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().

01461 {
01462         static vector<Vec3i> two_six_connected;
01463         if (two_six_connected.size() == 0) {
01464                 for(int i = -1; i <= 1; ++i) {
01465                         for(int j = -1; j <= 1; ++j) {
01466                                 for(int  k = -1; k <= 1; ++k) {
01467                                         if ( j != 0 || i != 0 || k != 0) {
01468                                                 two_six_connected.push_back(Vec3i(i,j,k));
01469                                         }
01470                                 }
01471                         }
01472                 }
01473         }
01474 
01475         vector<Vec3i> ret;
01476         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01477                 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) {
01478                         if  (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw;
01479                         Vec3i c = (*it)+(*it2);
01480 
01481                         if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue;
01482                         if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue;
01483                         if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue;
01484 
01485                         if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) {
01486                                 if (find(ret.begin(),ret.end(),c) == ret.end()) {
01487                                         if (find(region.begin(),region.end(),c) == region.end()) {
01488                                                 region.push_back(c);
01489                                                 ret.push_back(c);
01490                                         }
01491                                 }
01492                         }
01493                 }
01494         }
01495         return ret;
01496 }

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 5583 of file processor.h.

05584                 {
05585                         return "Does a watershed";
05586                 }

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 5573 of file processor.h.

References NAME.

05574                 {
05575                         return NAME;
05576                 }

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 5588 of file processor.h.

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

05589                 {
05590                         TypeDict d;
05591                         d.put("xpoints", EMObject::FLOATARRAY,"x coordinates");
05592                         d.put("ypoints", EMObject::FLOATARRAY,"y coordinates");
05593                         d.put("zpoints", EMObject::FLOATARRAY,"z coordinates");
05594                         d.put("minval", EMObject::FLOAT,"min value");
05595                         return d;
05596                 }

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

Definition at line 5578 of file processor.h.

05579                 {
05580                         return new WatershedProcessor();
05581                 }

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 1385 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.

01385                                                        {
01386         vector<float> xpoints = params["xpoints"];
01387         vector<float> ypoints = params["ypoints"];
01388         vector<float> zpoints = params["zpoints"];
01389 
01390         vector<int> x(xpoints.begin(),xpoints.end());
01391         vector<int> y(ypoints.begin(),ypoints.end());
01392         vector<int> z(zpoints.begin(),zpoints.end());
01393 
01394 
01395         // throw if vector lengths are unequal
01396 
01397 //      float maxval = -99999;
01398         /*
01399         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01400                 float val = image->get_value_at(x[i],y[i],z[i]);
01401                 if (val > maxval) {
01402                         maxval = val;
01403                 }
01404         }*/
01405 
01406         float minval = params["minval"];
01407 
01408         EMData* mask = new EMData(*image);
01409         mask->to_zero();
01410 
01411         // Set the original mask values
01412         for(unsigned int i = 0; i < xpoints.size(); ++i) {
01413                 try {
01414                         mask->set_value_at(x[i],y[i],z[i], (float)(i+1));
01415                 } catch (...) {
01416                         continue;
01417                 }
01418         }
01419         mask->write_image("seeds2.mrc");
01420 //      int dis = 500;
01421 //      float dx = (maxval-minval)/((float) dis - 1);
01422 
01423 
01424 //      for(int i = 0; i < dis; ++i) {
01425 //              float val = maxval-i*dx;
01426 
01427                 while( true ) {
01428                         bool cont= false;
01429                         for(unsigned int j = 0; j < xpoints.size(); ++j)
01430                         {
01431 
01432                                 Vec3i coord(x[j],y[j],z[j]);
01433                                 vector<Vec3i> region;
01434                                 region.push_back(coord);
01435                                 vector<Vec3i> find_region_input = region;
01436                                 while (true) {
01437                                         vector<Vec3i> v = find_region(mask,find_region_input, j+1, region);
01438                                         if (v.size() == 0 ) break;
01439                                         else find_region_input = v;
01440                                 }
01441 
01442                                 vector<Vec3i> tmp(region.begin(),region.end());
01443                                 region.clear();
01444                                 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) {
01445                                         vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1);
01446                                         copy(tmp2.begin(),tmp2.end(),back_inserter(region));
01447                                 }
01448                                 if (region.size() != 0) cont = true;
01449                         }
01450 
01451                         if (!cont) break;
01452                 }
01453 //      }
01454 
01455         memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size());
01456         image->update();
01457 }

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

Definition at line 1498 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().

01499 {
01500         static vector<Vec3i> two_six_connected;
01501         if (two_six_connected.size() == 0) {
01502                 for(int i = -1; i <= 1; ++i) {
01503                         for(int j = -1; j <= 1; ++j) {
01504                                 for(int  k = -1; k <= 1; ++k) {
01505                                         if ( j != 0 || i != 0 || k != 0) {
01506                                                 two_six_connected.push_back(Vec3i(i,j,k));
01507                                         }
01508                                 }
01509                         }
01510                 }
01511         }
01512 
01513         if  (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw;
01514 
01515         vector<Vec3i> ret;
01516         for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) {
01517                 Vec3i c = (*it)+coordinate;
01518 
01519                 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue;
01520                 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue;
01521                 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue;
01522 
01523         //      cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl;
01524                 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) {
01525                         //cout << "Added something " << mask_value << endl;
01526                         mask->set_value_at(c[0],c[1],c[2], (float)mask_value);
01527                         ret.push_back(c);
01528                 }
01529         }
01530         return ret;
01531 }


Member Data Documentation

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

Definition at line 5598 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:10:42 2012 for EMAN2 by  doxygen 1.4.7