#include <processor.h>
Inheritance diagram for EMAN::MeanShrinkProcessor:
Public Member Functions | |
virtual EMData * | process (const EMData *const image) |
The meanshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function. | |
virtual void | process_inplace (EMData *image) |
Mean shrink inplace. | |
string | get_desc () const |
Get the descrition of this specific processor. | |
virtual string | get_name () const |
Get the processor's name. | |
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 = "math.meanshrink" |
Private Member Functions | |
void | accrue_mean (EMData *to, const EMData *const from, const int shrinkfactor) |
Accrue the local mean in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace. | |
void | accrue_mean_one_p_five (EMData *to, const EMData *const from) |
Accrue the local mean in the image 'from' to the image 'to' using the the special case shrink factor of 1.5 This is an internal function that encapsulates a routine common to both process and process inplace. |
n | The shrink factor |
Definition at line 3406 of file processor.h.
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Accrue the local mean in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace.
Definition at line 2272 of file processor.cpp. References data, EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), nx, ny, rdata, and EMAN::EMData::scale_pixel(). Referenced by process(), and process_inplace(). 02273 { 02274 const float * const data = from->get_const_data(); 02275 float* rdata = to->get_data(); 02276 02277 size_t nx = from->get_xsize(); 02278 size_t ny = from->get_ysize(); 02279 size_t nz = from->get_zsize(); 02280 size_t nxy = nx*ny; 02281 02282 02283 size_t shrunken_nx = nx / shrink_factor; 02284 size_t shrunken_ny = ny / shrink_factor; 02285 size_t shrunken_nz = 1; 02286 size_t shrunken_nxy = shrunken_nx * shrunken_ny; 02287 02288 int normalize_shrink_factor = shrink_factor * shrink_factor; 02289 int z_shrink_factor = 1; 02290 02291 if (nz > 1) { 02292 shrunken_nz = nz / shrink_factor; 02293 normalize_shrink_factor *= shrink_factor; 02294 z_shrink_factor = shrink_factor; 02295 } 02296 02297 float invnormfactor = 1.0f/(float)normalize_shrink_factor; 02298 02299 for (size_t k = 0; k < shrunken_nz; k++) { 02300 size_t k_min = k * shrink_factor; 02301 size_t k_max = k * shrink_factor + z_shrink_factor; 02302 size_t cur_k = k * shrunken_nxy; 02303 02304 for (size_t j = 0; j < shrunken_ny; j++) { 02305 size_t j_min = j * shrink_factor; 02306 size_t j_max = j * shrink_factor + shrink_factor; 02307 size_t cur_j = j * shrunken_nx + cur_k; 02308 02309 for (size_t i = 0; i < shrunken_nx; i++) { 02310 size_t i_min = i * shrink_factor; 02311 size_t i_max = i * shrink_factor + shrink_factor; 02312 02313 float sum = 0; 02314 for (size_t kk = k_min; kk < k_max; kk++) { 02315 size_t cur_kk = kk * nxy; 02316 02317 for (size_t jj = j_min; jj < j_max; jj++) { 02318 size_t cur_jj = jj * nx + cur_kk; 02319 for (size_t ii = i_min; ii < i_max; ii++) { 02320 sum += data[ii + cur_jj]; 02321 } 02322 } 02323 } 02324 rdata[i + cur_j] = sum * invnormfactor; 02325 } 02326 } 02327 } 02328 to->scale_pixel((float)shrink_factor); 02329 }
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Accrue the local mean in the image 'from' to the image 'to' using the the special case shrink factor of 1.5 This is an internal function that encapsulates a routine common to both process and process inplace.
Definition at line 2332 of file processor.cpp. References data, EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), nx, ny, EMAN::EMData::scale_pixel(), and EMAN::EMData::update(). Referenced by process(), and process_inplace(). 02333 { 02334 int nx0 = from->get_xsize(), ny0 = from->get_ysize(); // the original size 02335 02336 int nx = to->get_xsize(), ny = to->get_ysize(); 02337 02338 float *data = to->get_data(); 02339 const float * const data0 = from->get_const_data(); 02340 02341 for (int j = 0; j < ny; j++) { 02342 int jj = int(j * 1.5); 02343 float jw0 = 1.0F, jw1 = 0.5F; // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels 02344 if ( j%2 ) { 02345 jw0 = 0.5F; 02346 jw1 = 1.0F; 02347 } 02348 for (int i = 0; i < nx; i++) { 02349 int ii = int(i * 1.5); 02350 float iw0 = 1.0F, iw1 = 0.5F; 02351 float w = 0.0F; 02352 02353 if ( i%2 ) { 02354 iw0 = 0.5F; 02355 iw1 = 1.0F; 02356 } 02357 if ( jj < ny0 ) { 02358 if ( ii < nx0 ) { 02359 data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ; 02360 w += jw0 * iw0 ; 02361 if ( ii+1 < nx0 ) { 02362 data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1; 02363 w += jw0 * iw1; 02364 } 02365 } 02366 if ( jj +1 < ny0 ) { 02367 if ( ii < nx0 ) { 02368 data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0; 02369 w += jw1 * iw0; 02370 if ( ii+1 < nx0 ) { 02371 data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1; 02372 w += jw1 * iw1; 02373 } 02374 } 02375 } 02376 } 02377 if ( w>0 ) data[j * nx + i] /= w; 02378 } 02379 } 02380 02381 to->update(); 02382 to->scale_pixel((float)1.5); 02383 }
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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 3429 of file processor.h. 03430 { 03431 return "Shrink an image by a given amount , using the mean value found in the pixel neighborhood."; 03432 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3434 of file processor.h. 03435 {
03436 return NAME;
03437 }
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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 3443 of file processor.h. References EMAN::TypeDict::put(). 03444 { 03445 TypeDict d; 03446 d.put("n", EMObject::FLOAT, "The shrink factor"); 03447 return d; 03448 }
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Definition at line 3438 of file processor.h. 03439 { 03440 return new MeanShrinkProcessor(); 03441 }
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The meanshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function. This latter approach mallocs and copies more memory than necessary
Reimplemented from EMAN::Processor. Definition at line 2167 of file processor.cpp. References accrue_mean(), accrue_mean_one_p_five(), EMAN::EMData::copy_head(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), nx, ny, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update(). 02168 { 02169 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02170 02171 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02172 02173 float shrink_factor0 = params.set_default("n",0.0f); 02174 int shrink_factor = int(shrink_factor0); 02175 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02176 throw InvalidValueException(shrink_factor0, 02177 "mean shrink: shrink factor must be >1 integer or 1.5"); 02178 } 02179 02180 int nx = image->get_xsize(); 02181 int ny = image->get_ysize(); 02182 int nz = image->get_zsize(); 02183 02184 02185 // here handle the special averaging by 1.5 for 2D case 02186 if (shrink_factor0==1.5 ) { 02187 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02188 02189 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02190 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02191 EMData* result = new EMData(shrunken_nx,shrunken_ny,1); 02192 02193 accrue_mean_one_p_five(result,image); 02194 result->update(); 02195 02196 return result; 02197 } 02198 02199 int shrunken_nx = nx / shrink_factor; 02200 int shrunken_ny = ny / shrink_factor; 02201 int shrunken_nz = 1; 02202 02203 if (nz > 1) { 02204 shrunken_nz = nz / shrink_factor; 02205 } 02206 02207 // EMData* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz); 02208 EMData* result = image->copy_head(); 02209 result->set_size(shrunken_nx,shrunken_ny,shrunken_nz); 02210 accrue_mean(result,image,shrink_factor); 02211 02212 result->update(); 02213 02214 return result; 02215 }
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Mean shrink inplace.
Implements EMAN::Processor. Definition at line 2217 of file processor.cpp. References accrue_mean(), accrue_mean_one_p_five(), EMAN::EMData::copy(), EMAN::EMData::get_ndim(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageDimensionException, ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), nx, ny, EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::to_zero(), and EMAN::EMData::update(). 02218 { 02219 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02220 02221 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02222 02223 float shrink_factor0 = params.set_default("n",0.0f); 02224 int shrink_factor = int(shrink_factor0); 02225 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02226 throw InvalidValueException(shrink_factor0, 02227 "mean shrink: shrink factor must be >1 integer or 1.5"); 02228 } 02229 02230 /* if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || 02231 (nz > 1 && (nz % shrink_factor != 0))) { 02232 throw InvalidValueException(shrink_factor, 02233 "Image size not divisible by shrink factor"); 02234 }*/ 02235 02236 int nx = image->get_xsize(); 02237 int ny = image->get_ysize(); 02238 int nz = image->get_zsize(); 02239 // here handle the special averaging by 1.5 for 2D case 02240 if (shrink_factor0==1.5 ) { 02241 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02242 02243 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02244 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02245 02246 EMData* orig = image->copy(); 02247 image->set_size(shrunken_nx, shrunken_ny, 1); // now nx = shrunken_nx, ny = shrunken_ny 02248 image->to_zero(); 02249 02250 accrue_mean_one_p_five(image,orig); 02251 02252 if( orig ) { 02253 delete orig; 02254 orig = 0; 02255 } 02256 image->update(); 02257 02258 return; 02259 } 02260 02261 accrue_mean(image,image,shrink_factor); 02262 02263 int shrunken_nx = nx / shrink_factor; 02264 int shrunken_ny = ny / shrink_factor; 02265 int shrunken_nz = 1; 02266 if (nz > 1) shrunken_nz = nz / shrink_factor; 02267 02268 image->update(); 02269 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02270 }
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Definition at line 131 of file processor.cpp. |