#include <processor.h>
Inheritance diagram for EMAN::WatershedProcessor:
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "segment.watershed" |
Private Member Functions | |
vector< Vec3i > | watershed (EMData *mask, EMData *image, const float &threshold, const Vec3i &cordinate, const int mask_value) |
vector< Vec3i > | find_region (EMData *mask, const vector< Vec3i > &coords, const int mask_value, vector< Vec3i > ®ion) |
xpoints | x coordinates | |
ypoints | y coordinates | |
zpoints | z coordinates | |
minval | min value |
Definition at line 5568 of file processor.h.
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.
Implements EMAN::Processor.
Definition at line 5583 of file processor.h.
virtual string EMAN::WatershedProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique 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.
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] |
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.
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 }
const string WatershedProcessor::NAME = "segment.watershed" [static] |