#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 5313 of file processor.h.
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Definition at line 1332 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(). 01333 { 01334 static vector<Vec3i> two_six_connected; 01335 if (two_six_connected.size() == 0) { 01336 for(int i = -1; i <= 1; ++i) { 01337 for(int j = -1; j <= 1; ++j) { 01338 for(int k = -1; k <= 1; ++k) { 01339 if ( j != 0 || i != 0 || k != 0) { 01340 two_six_connected.push_back(Vec3i(i,j,k)); 01341 } 01342 } 01343 } 01344 } 01345 } 01346 01347 vector<Vec3i> ret; 01348 for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) { 01349 for(vector<Vec3i>::const_iterator it2 = coords.begin(); it2 != coords.end(); ++it2 ) { 01350 if (mask->get_value_at((*it2)[0],(*it2)[1],(*it2)[2]) != mask_value) throw; 01351 Vec3i c = (*it)+(*it2); 01352 01353 if ( c[0] < 0 || c[0] >= mask->get_xsize()) continue; 01354 if ( c[1] < 0 || c[1] >= mask->get_ysize()) continue; 01355 if ( c[2] < 0 || c[2] >= mask->get_zsize()) continue; 01356 01357 if( mask->get_value_at(c[0],c[1],c[2]) == mask_value ) { 01358 if (find(ret.begin(),ret.end(),c) == ret.end()) { 01359 if (find(region.begin(),region.end(),c) == region.end()) { 01360 region.push_back(c); 01361 ret.push_back(c); 01362 } 01363 } 01364 } 01365 } 01366 } 01367 return ret; 01368 }
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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 5328 of file processor.h. 05329 { 05330 return "Does a watershed"; 05331 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5318 of file processor.h. 05319 {
05320 return NAME;
05321 }
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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 5333 of file processor.h. References EMAN::TypeDict::put(). 05334 { 05335 TypeDict d; 05336 d.put("xpoints", EMObject::FLOATARRAY,"x coordinates"); 05337 d.put("ypoints", EMObject::FLOATARRAY,"y coordinates"); 05338 d.put("zpoints", EMObject::FLOATARRAY,"z coordinates"); 05339 d.put("minval", EMObject::FLOAT,"min value"); 05340 return d; 05341 }
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Definition at line 5323 of file processor.h. 05324 { 05325 return new WatershedProcessor(); 05326 }
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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 1257 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. 01257 { 01258 vector<float> xpoints = params["xpoints"]; 01259 vector<float> ypoints = params["ypoints"]; 01260 vector<float> zpoints = params["zpoints"]; 01261 01262 vector<int> x(xpoints.begin(),xpoints.end()); 01263 vector<int> y(ypoints.begin(),ypoints.end()); 01264 vector<int> z(zpoints.begin(),zpoints.end()); 01265 01266 01267 // throw if vector lengths are unequal 01268 01269 // float maxval = -99999; 01270 /* 01271 for(unsigned int i = 0; i < xpoints.size(); ++i) { 01272 float val = image->get_value_at(x[i],y[i],z[i]); 01273 if (val > maxval) { 01274 maxval = val; 01275 } 01276 }*/ 01277 01278 float minval = params["minval"]; 01279 01280 EMData* mask = new EMData(*image); 01281 mask->to_zero(); 01282 01283 // Set the original mask values 01284 for(unsigned int i = 0; i < xpoints.size(); ++i) { 01285 try { 01286 mask->set_value_at(x[i],y[i],z[i], (float)(i+1)); 01287 } catch (...) { 01288 continue; 01289 } 01290 } 01291 mask->write_image("seeds2.mrc"); 01292 // int dis = 500; 01293 // float dx = (maxval-minval)/((float) dis - 1); 01294 01295 01296 // for(int i = 0; i < dis; ++i) { 01297 // float val = maxval-i*dx; 01298 01299 while( true ) { 01300 bool cont= false; 01301 for(unsigned int j = 0; j < xpoints.size(); ++j) 01302 { 01303 01304 Vec3i coord(x[j],y[j],z[j]); 01305 vector<Vec3i> region; 01306 region.push_back(coord); 01307 vector<Vec3i> find_region_input = region; 01308 while (true) { 01309 vector<Vec3i> v = find_region(mask,find_region_input, j+1, region); 01310 if (v.size() == 0 ) break; 01311 else find_region_input = v; 01312 } 01313 01314 vector<Vec3i> tmp(region.begin(),region.end()); 01315 region.clear(); 01316 for(vector<Vec3i>::const_iterator it = tmp.begin(); it != tmp.end(); ++it ) { 01317 vector<Vec3i> tmp2 = watershed(mask, image, minval, *it, j+1); 01318 copy(tmp2.begin(),tmp2.end(),back_inserter(region)); 01319 } 01320 if (region.size() != 0) cont = true; 01321 } 01322 01323 if (!cont) break; 01324 } 01325 // } 01326 01327 memcpy(image->get_data(),mask->get_data(),sizeof(float)*image->get_size()); 01328 image->update(); 01329 }
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Definition at line 1370 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(). 01371 { 01372 static vector<Vec3i> two_six_connected; 01373 if (two_six_connected.size() == 0) { 01374 for(int i = -1; i <= 1; ++i) { 01375 for(int j = -1; j <= 1; ++j) { 01376 for(int k = -1; k <= 1; ++k) { 01377 if ( j != 0 || i != 0 || k != 0) { 01378 two_six_connected.push_back(Vec3i(i,j,k)); 01379 } 01380 } 01381 } 01382 } 01383 } 01384 01385 if (mask->get_value_at(coordinate[0],coordinate[1],coordinate[2]) != mask_value) throw; 01386 01387 vector<Vec3i> ret; 01388 for(vector<Vec3i>::const_iterator it = two_six_connected.begin(); it != two_six_connected.end(); ++it ) { 01389 Vec3i c = (*it)+coordinate; 01390 01391 if ( c[0] < 0 || c[0] >= image->get_xsize()) continue; 01392 if ( c[1] < 0 || c[1] >= image->get_ysize()) continue; 01393 if ( c[2] < 0 || c[2] >= image->get_zsize()) continue; 01394 01395 // cout << image->get_value_at(c[0],c[1],c[2] ) << " " << threshold << endl; 01396 if( image->get_value_at(c[0],c[1],c[2]) != 0 && (mask->get_value_at(c[0],c[1],c[2]) == 0 )) { 01397 //cout << "Added something " << mask_value << endl; 01398 mask->set_value_at(c[0],c[1],c[2], (float)mask_value); 01399 ret.push_back(c); 01400 } 01401 } 01402 return ret; 01403 }
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Definition at line 176 of file processor.cpp. |