#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 3449 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 2285 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(). 02286 { 02287 const float * const data = from->get_const_data(); 02288 float* rdata = to->get_data(); 02289 02290 size_t nx = from->get_xsize(); 02291 size_t ny = from->get_ysize(); 02292 size_t nz = from->get_zsize(); 02293 size_t nxy = nx*ny; 02294 02295 02296 size_t shrunken_nx = nx / shrink_factor; 02297 size_t shrunken_ny = ny / shrink_factor; 02298 size_t shrunken_nz = 1; 02299 size_t shrunken_nxy = shrunken_nx * shrunken_ny; 02300 02301 int normalize_shrink_factor = shrink_factor * shrink_factor; 02302 int z_shrink_factor = 1; 02303 02304 if (nz > 1) { 02305 shrunken_nz = nz / shrink_factor; 02306 normalize_shrink_factor *= shrink_factor; 02307 z_shrink_factor = shrink_factor; 02308 } 02309 02310 float invnormfactor = 1.0f/(float)normalize_shrink_factor; 02311 02312 for (size_t k = 0; k < shrunken_nz; k++) { 02313 size_t k_min = k * shrink_factor; 02314 size_t k_max = k * shrink_factor + z_shrink_factor; 02315 size_t cur_k = k * shrunken_nxy; 02316 02317 for (size_t j = 0; j < shrunken_ny; j++) { 02318 size_t j_min = j * shrink_factor; 02319 size_t j_max = j * shrink_factor + shrink_factor; 02320 size_t cur_j = j * shrunken_nx + cur_k; 02321 02322 for (size_t i = 0; i < shrunken_nx; i++) { 02323 size_t i_min = i * shrink_factor; 02324 size_t i_max = i * shrink_factor + shrink_factor; 02325 02326 float sum = 0; 02327 for (size_t kk = k_min; kk < k_max; kk++) { 02328 size_t cur_kk = kk * nxy; 02329 02330 for (size_t jj = j_min; jj < j_max; jj++) { 02331 size_t cur_jj = jj * nx + cur_kk; 02332 for (size_t ii = i_min; ii < i_max; ii++) { 02333 sum += data[ii + cur_jj]; 02334 } 02335 } 02336 } 02337 rdata[i + cur_j] = sum * invnormfactor; 02338 } 02339 } 02340 } 02341 to->scale_pixel((float)shrink_factor); 02342 }
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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 2345 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(). 02346 { 02347 int nx0 = from->get_xsize(), ny0 = from->get_ysize(); // the original size 02348 02349 int nx = to->get_xsize(), ny = to->get_ysize(); 02350 02351 float *data = to->get_data(); 02352 const float * const data0 = from->get_const_data(); 02353 02354 for (int j = 0; j < ny; j++) { 02355 int jj = int(j * 1.5); 02356 float jw0 = 1.0F, jw1 = 0.5F; // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels 02357 if ( j%2 ) { 02358 jw0 = 0.5F; 02359 jw1 = 1.0F; 02360 } 02361 for (int i = 0; i < nx; i++) { 02362 int ii = int(i * 1.5); 02363 float iw0 = 1.0F, iw1 = 0.5F; 02364 float w = 0.0F; 02365 02366 if ( i%2 ) { 02367 iw0 = 0.5F; 02368 iw1 = 1.0F; 02369 } 02370 if ( jj < ny0 ) { 02371 if ( ii < nx0 ) { 02372 data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ; 02373 w += jw0 * iw0 ; 02374 if ( ii+1 < nx0 ) { 02375 data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1; 02376 w += jw0 * iw1; 02377 } 02378 } 02379 if ( jj +1 < ny0 ) { 02380 if ( ii < nx0 ) { 02381 data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0; 02382 w += jw1 * iw0; 02383 if ( ii+1 < nx0 ) { 02384 data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1; 02385 w += jw1 * iw1; 02386 } 02387 } 02388 } 02389 } 02390 if ( w>0 ) data[j * nx + i] /= w; 02391 } 02392 } 02393 02394 to->update(); 02395 to->scale_pixel((float)1.5); 02396 }
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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 3472 of file processor.h. 03473 { 03474 return "Shrink an image by a given amount , using the mean value found in the pixel neighborhood."; 03475 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3477 of file processor.h. 03478 {
03479 return NAME;
03480 }
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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 3486 of file processor.h. References EMAN::TypeDict::put(). 03487 { 03488 TypeDict d; 03489 d.put("n", EMObject::FLOAT, "The shrink factor"); 03490 return d; 03491 }
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Definition at line 3481 of file processor.h. 03482 { 03483 return new MeanShrinkProcessor(); 03484 }
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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 2180 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(). 02181 { 02182 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02183 02184 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02185 02186 float shrink_factor0 = params.set_default("n",0.0f); 02187 int shrink_factor = int(shrink_factor0); 02188 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02189 throw InvalidValueException(shrink_factor0, 02190 "mean shrink: shrink factor must be >1 integer or 1.5"); 02191 } 02192 02193 int nx = image->get_xsize(); 02194 int ny = image->get_ysize(); 02195 int nz = image->get_zsize(); 02196 02197 02198 // here handle the special averaging by 1.5 for 2D case 02199 if (shrink_factor0==1.5 ) { 02200 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02201 02202 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02203 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02204 EMData* result = new EMData(shrunken_nx,shrunken_ny,1); 02205 02206 accrue_mean_one_p_five(result,image); 02207 result->update(); 02208 02209 return result; 02210 } 02211 02212 int shrunken_nx = nx / shrink_factor; 02213 int shrunken_ny = ny / shrink_factor; 02214 int shrunken_nz = 1; 02215 02216 if (nz > 1) { 02217 shrunken_nz = nz / shrink_factor; 02218 } 02219 02220 // EMData* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz); 02221 EMData* result = image->copy_head(); 02222 result->set_size(shrunken_nx,shrunken_ny,shrunken_nz); 02223 accrue_mean(result,image,shrink_factor); 02224 02225 result->update(); 02226 02227 return result; 02228 }
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Mean shrink inplace.
Implements EMAN::Processor. Definition at line 2230 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(). 02231 { 02232 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02233 02234 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02235 02236 float shrink_factor0 = params.set_default("n",0.0f); 02237 int shrink_factor = int(shrink_factor0); 02238 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02239 throw InvalidValueException(shrink_factor0, 02240 "mean shrink: shrink factor must be >1 integer or 1.5"); 02241 } 02242 02243 /* if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || 02244 (nz > 1 && (nz % shrink_factor != 0))) { 02245 throw InvalidValueException(shrink_factor, 02246 "Image size not divisible by shrink factor"); 02247 }*/ 02248 02249 int nx = image->get_xsize(); 02250 int ny = image->get_ysize(); 02251 int nz = image->get_zsize(); 02252 // here handle the special averaging by 1.5 for 2D case 02253 if (shrink_factor0==1.5 ) { 02254 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02255 02256 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02257 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02258 02259 EMData* orig = image->copy(); 02260 image->set_size(shrunken_nx, shrunken_ny, 1); // now nx = shrunken_nx, ny = shrunken_ny 02261 image->to_zero(); 02262 02263 accrue_mean_one_p_five(image,orig); 02264 02265 if( orig ) { 02266 delete orig; 02267 orig = 0; 02268 } 02269 image->update(); 02270 02271 return; 02272 } 02273 02274 accrue_mean(image,image,shrink_factor); 02275 02276 int shrunken_nx = nx / shrink_factor; 02277 int shrunken_ny = ny / shrink_factor; 02278 int shrunken_nz = 1; 02279 if (nz > 1) shrunken_nz = nz / shrink_factor; 02280 02281 image->update(); 02282 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02283 }
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Definition at line 126 of file processor.cpp. |