#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 | |
Processor * | NEW () |
Static Public Attributes | |
const string | NAME = "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 5454 of file processor.h.
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Definition at line 1425 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(). 01426 { 01427 static vector<Vec3i> two_six_connected; 01428 if (two_six_connected.size() == 0) { 01429 for(int i = -1; i <= 1; ++i) { 01430 for(int j = -1; j <= 1; ++j) { 01431 for(int k = -1; k <= 1; ++k) { 01432 if ( j != 0 || i != 0 || k != 0) { 01433 two_six_connected.push_back(Vec3i(i,j,k)); 01434 } 01435 } 01436 } 01437 } 01438 } 01439 01440 vector<Vec3i> ret; 01441 for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) { 01442 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) { 01443 if (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw; 01444 Vec3i c = (*it)+(*it2); 01445 01446 if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue; 01447 if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue; 01448 if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue; 01449 01450 if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) { 01451 if (find(ret.begin(),ret.end(),c) == ret.end()) { 01452 if (find(region.begin(),region.end(),c) == region.end()) { 01453 region.push_back(c); 01454 ret.push_back(c); 01455 } 01456 } 01457 } 01458 } 01459 } 01460 return ret; 01461 }
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 5469 of file processor.h. 05470 { 05471 return "Does a watershed"; 05472 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5459 of file processor.h. 05460 {
05461 return NAME;
05462 }
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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 5474 of file processor.h. References EMAN::TypeDict::put(). 05475 { 05476 TypeDict d; 05477 d.put("xpoints", EMObject::FLOATARRAY,"x coordinates"); 05478 d.put("ypoints", EMObject::FLOATARRAY,"y coordinates"); 05479 d.put("zpoints", EMObject::FLOATARRAY,"z coordinates"); 05480 d.put("minval", EMObject::FLOAT,"min value"); 05481 return d; 05482 }
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Definition at line 5464 of file processor.h. 05465 { 05466 return new WatershedProcessor(); 05467 }
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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.
Implements EMAN::Processor. Definition at line 1350 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. 01350 { 01351 vector<float> xpoints = params["xpoints"]; 01352 vector<float> ypoints = params["ypoints"]; 01353 vector<float> zpoints = params["zpoints"]; 01354 01355 vector<int> x(xpoints.begin(),xpoints.end()); 01356 vector<int> y(ypoints.begin(),ypoints.end()); 01357 vector<int> z(zpoints.begin(),zpoints.end()); 01358 01359 01360 // throw if vector lengths are unequal 01361 01362 // float maxval = -99999; 01363 /* 01364 for(unsigned int i = 0; i < xpoints.size(); ++i) { 01365 float val = image->get_value_at(x[i],y[i],z[i]); 01366 if (val > maxval) { 01367 maxval = val; 01368 } 01369 }*/ 01370 01371 float minval = params["minval"]; 01372 01373 EMData* mask = new EMData(*image); 01374 mask->to_zero(); 01375 01376 // Set the original mask values 01377 for(unsigned int i = 0; i < xpoints.size(); ++i) { 01378 try { 01379 mask->set_value_at(x[i],y[i],z[i], (float)(i+1)); 01380 } catch (...) { 01381 continue; 01382 } 01383 } 01384 mask->write_image("seeds2.mrc"); 01385 // int dis = 500; 01386 // float dx = (maxval-minval)/((float) dis - 1); 01387 01388 01389 // for(int i = 0; i < dis; ++i) { 01390 // float val = maxval-i*dx; 01391 01392 while( true ) { 01393 bool cont= false; 01394 for(unsigned int j = 0; j < xpoints.size(); ++j) 01395 { 01396 01397 Vec3i coord(x[j],y[j],z[j]); 01398 vector<Vec3i> region; 01399 region.push_back(coord); 01400 vector<Vec3i> find_region_input = region; 01401 while (true) { 01402 vector<Vec3i> v = find_region(mask,find_region_input, j+1, region); 01403 if (v.size() == 0 ) break; 01404 else find_region_input = v; 01405 } 01406 01407 vector<Vec3i> tmp(region.begin(),region.end()); 01408 region.clear(); 01409 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) { 01410 vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1); 01411 copy(tmp2.begin(),tmp2.end(),back_inserter(region)); 01412 } 01413 if (region.size() != 0) cont = true; 01414 } 01415 01416 if (!cont) break; 01417 } 01418 // } 01419 01420 memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size()); 01421 image->update(); 01422 }
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Definition at line 1463 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(). 01464 { 01465 static vector<Vec3i> two_six_connected; 01466 if (two_six_connected.size() == 0) { 01467 for(int i = -1; i <= 1; ++i) { 01468 for(int j = -1; j <= 1; ++j) { 01469 for(int k = -1; k <= 1; ++k) { 01470 if ( j != 0 || i != 0 || k != 0) { 01471 two_six_connected.push_back(Vec3i(i,j,k)); 01472 } 01473 } 01474 } 01475 } 01476 } 01477 01478 if (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw; 01479 01480 vector<Vec3i> ret; 01481 for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) { 01482 Vec3i c = (*it)+coordinate; 01483 01484 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue; 01485 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue; 01486 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue; 01487 01488 // cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl; 01489 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) { 01490 //cout << "Added something " << mask_value << endl; 01491 mask->set_value_at(c[0],c[1],c[2], (float)mask_value); 01492 ret.push_back(c); 01493 } 01494 } 01495 return ret; 01496 }
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Definition at line 181 of file processor.cpp. |