#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 3368 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 2244 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(). 02245 { 02246 const float * const data = from->get_const_data(); 02247 float* rdata = to->get_data(); 02248 02249 size_t nx = from->get_xsize(); 02250 size_t ny = from->get_ysize(); 02251 size_t nz = from->get_zsize(); 02252 size_t nxy = nx*ny; 02253 02254 02255 size_t shrunken_nx = nx / shrink_factor; 02256 size_t shrunken_ny = ny / shrink_factor; 02257 size_t shrunken_nz = 1; 02258 size_t shrunken_nxy = shrunken_nx * shrunken_ny; 02259 02260 int normalize_shrink_factor = shrink_factor * shrink_factor; 02261 int z_shrink_factor = 1; 02262 02263 if (nz > 1) { 02264 shrunken_nz = nz / shrink_factor; 02265 normalize_shrink_factor *= shrink_factor; 02266 z_shrink_factor = shrink_factor; 02267 } 02268 02269 float invnormfactor = 1.0f/(float)normalize_shrink_factor; 02270 02271 for (size_t k = 0; k < shrunken_nz; k++) { 02272 size_t k_min = k * shrink_factor; 02273 size_t k_max = k * shrink_factor + z_shrink_factor; 02274 size_t cur_k = k * shrunken_nxy; 02275 02276 for (size_t j = 0; j < shrunken_ny; j++) { 02277 size_t j_min = j * shrink_factor; 02278 size_t j_max = j * shrink_factor + shrink_factor; 02279 size_t cur_j = j * shrunken_nx + cur_k; 02280 02281 for (size_t i = 0; i < shrunken_nx; i++) { 02282 size_t i_min = i * shrink_factor; 02283 size_t i_max = i * shrink_factor + shrink_factor; 02284 02285 float sum = 0; 02286 for (size_t kk = k_min; kk < k_max; kk++) { 02287 size_t cur_kk = kk * nxy; 02288 02289 for (size_t jj = j_min; jj < j_max; jj++) { 02290 size_t cur_jj = jj * nx + cur_kk; 02291 for (size_t ii = i_min; ii < i_max; ii++) { 02292 sum += data[ii + cur_jj]; 02293 } 02294 } 02295 } 02296 rdata[i + cur_j] = sum * invnormfactor; 02297 } 02298 } 02299 } 02300 to->scale_pixel((float)shrink_factor); 02301 }
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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 2304 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(). 02305 { 02306 int nx0 = from->get_xsize(), ny0 = from->get_ysize(); // the original size 02307 02308 int nx = to->get_xsize(), ny = to->get_ysize(); 02309 02310 float *data = to->get_data(); 02311 const float * const data0 = from->get_const_data(); 02312 02313 for (int j = 0; j < ny; j++) { 02314 int jj = int(j * 1.5); 02315 float jw0 = 1.0F, jw1 = 0.5F; // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels 02316 if ( j%2 ) { 02317 jw0 = 0.5F; 02318 jw1 = 1.0F; 02319 } 02320 for (int i = 0; i < nx; i++) { 02321 int ii = int(i * 1.5); 02322 float iw0 = 1.0F, iw1 = 0.5F; 02323 float w = 0.0F; 02324 02325 if ( i%2 ) { 02326 iw0 = 0.5F; 02327 iw1 = 1.0F; 02328 } 02329 if ( jj < ny0 ) { 02330 if ( ii < nx0 ) { 02331 data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ; 02332 w += jw0 * iw0 ; 02333 if ( ii+1 < nx0 ) { 02334 data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1; 02335 w += jw0 * iw1; 02336 } 02337 } 02338 if ( jj +1 < ny0 ) { 02339 if ( ii < nx0 ) { 02340 data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0; 02341 w += jw1 * iw0; 02342 if ( ii+1 < nx0 ) { 02343 data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1; 02344 w += jw1 * iw1; 02345 } 02346 } 02347 } 02348 } 02349 if ( w>0 ) data[j * nx + i] /= w; 02350 } 02351 } 02352 02353 to->update(); 02354 to->scale_pixel((float)1.5); 02355 }
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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 3391 of file processor.h. 03392 { 03393 return "Shrink an image by a given amount , using the mean value found in the pixel neighborhood."; 03394 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3396 of file processor.h. 03397 {
03398 return NAME;
03399 }
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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 3405 of file processor.h. References EMAN::TypeDict::put(). 03406 { 03407 TypeDict d; 03408 d.put("n", EMObject::FLOAT, "The shrink factor"); 03409 return d; 03410 }
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Definition at line 3400 of file processor.h. 03401 { 03402 return new MeanShrinkProcessor(); 03403 }
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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 2139 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(). 02140 { 02141 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02142 02143 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02144 02145 float shrink_factor0 = params.set_default("n",0.0f); 02146 int shrink_factor = int(shrink_factor0); 02147 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02148 throw InvalidValueException(shrink_factor0, 02149 "mean shrink: shrink factor must be >1 integer or 1.5"); 02150 } 02151 02152 int nx = image->get_xsize(); 02153 int ny = image->get_ysize(); 02154 int nz = image->get_zsize(); 02155 02156 02157 // here handle the special averaging by 1.5 for 2D case 02158 if (shrink_factor0==1.5 ) { 02159 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02160 02161 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02162 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02163 EMData* result = new EMData(shrunken_nx,shrunken_ny,1); 02164 02165 accrue_mean_one_p_five(result,image); 02166 result->update(); 02167 02168 return result; 02169 } 02170 02171 int shrunken_nx = nx / shrink_factor; 02172 int shrunken_ny = ny / shrink_factor; 02173 int shrunken_nz = 1; 02174 02175 if (nz > 1) { 02176 shrunken_nz = nz / shrink_factor; 02177 } 02178 02179 // EMData* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz); 02180 EMData* result = image->copy_head(); 02181 result->set_size(shrunken_nx,shrunken_ny,shrunken_nz); 02182 accrue_mean(result,image,shrink_factor); 02183 02184 result->update(); 02185 02186 return result; 02187 }
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Mean shrink inplace.
Implements EMAN::Processor. Definition at line 2189 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(). 02190 { 02191 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02192 02193 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02194 02195 float shrink_factor0 = params.set_default("n",0.0f); 02196 int shrink_factor = int(shrink_factor0); 02197 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02198 throw InvalidValueException(shrink_factor0, 02199 "mean shrink: shrink factor must be >1 integer or 1.5"); 02200 } 02201 02202 /* if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || 02203 (nz > 1 && (nz % shrink_factor != 0))) { 02204 throw InvalidValueException(shrink_factor, 02205 "Image size not divisible by shrink factor"); 02206 }*/ 02207 02208 int nx = image->get_xsize(); 02209 int ny = image->get_ysize(); 02210 int nz = image->get_zsize(); 02211 // here handle the special averaging by 1.5 for 2D case 02212 if (shrink_factor0==1.5 ) { 02213 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02214 02215 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02216 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02217 02218 EMData* orig = image->copy(); 02219 image->set_size(shrunken_nx, shrunken_ny, 1); // now nx = shrunken_nx, ny = shrunken_ny 02220 image->to_zero(); 02221 02222 accrue_mean_one_p_five(image,orig); 02223 02224 if( orig ) { 02225 delete orig; 02226 orig = 0; 02227 } 02228 image->update(); 02229 02230 return; 02231 } 02232 02233 accrue_mean(image,image,shrink_factor); 02234 02235 int shrunken_nx = nx / shrink_factor; 02236 int shrunken_ny = ny / shrink_factor; 02237 int shrunken_nz = 1; 02238 if (nz > 1) shrunken_nz = nz / shrink_factor; 02239 02240 image->update(); 02241 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02242 }
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Definition at line 125 of file processor.cpp. |