#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 = "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 5523 of file processor.h.
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Definition at line 1388 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(). 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 }
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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 5538 of file processor.h. 05539 { 05540 return "Does a watershed"; 05541 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5528 of file processor.h. 05529 {
05530 return NAME;
05531 }
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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 5543 of file processor.h. References 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 }
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Definition at line 5533 of file processor.h. 05534 { 05535 return new WatershedProcessor(); 05536 }
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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 1313 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. 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 }
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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(), EMAN::EMData::set_value_at(), and EMAN::Vec3i. 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 }
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Definition at line 79 of file processor.cpp. |