#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 | |
static Processor * | NEW () |
Static Public Attributes | |
static 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 3447 of file processor.h.
void MeanShrinkProcessor::accrue_mean | ( | EMData * | to, | |
const EMData *const | from, | |||
const int | shrinkfactor | |||
) | [private] |
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.
to | the smaller image that will store the mean values | |
from | the larger image that will be used to calculate the mean values | |
shrinkfactor | the shrink amount |
Definition at line 2279 of file processor.cpp.
References EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), rdata, and EMAN::EMData::scale_pixel().
Referenced by process(), and process_inplace().
02280 { 02281 const float * const data = from->get_const_data(); 02282 float* rdata = to->get_data(); 02283 02284 size_t nx = from->get_xsize(); 02285 size_t ny = from->get_ysize(); 02286 size_t nz = from->get_zsize(); 02287 size_t nxy = nx*ny; 02288 02289 02290 size_t shrunken_nx = nx / shrink_factor; 02291 size_t shrunken_ny = ny / shrink_factor; 02292 size_t shrunken_nz = 1; 02293 size_t shrunken_nxy = shrunken_nx * shrunken_ny; 02294 02295 int normalize_shrink_factor = shrink_factor * shrink_factor; 02296 int z_shrink_factor = 1; 02297 02298 if (nz > 1) { 02299 shrunken_nz = nz / shrink_factor; 02300 normalize_shrink_factor *= shrink_factor; 02301 z_shrink_factor = shrink_factor; 02302 } 02303 02304 float invnormfactor = 1.0f/(float)normalize_shrink_factor; 02305 02306 for (size_t k = 0; k < shrunken_nz; k++) { 02307 size_t k_min = k * shrink_factor; 02308 size_t k_max = k * shrink_factor + z_shrink_factor; 02309 size_t cur_k = k * shrunken_nxy; 02310 02311 for (size_t j = 0; j < shrunken_ny; j++) { 02312 size_t j_min = j * shrink_factor; 02313 size_t j_max = j * shrink_factor + shrink_factor; 02314 size_t cur_j = j * shrunken_nx + cur_k; 02315 02316 for (size_t i = 0; i < shrunken_nx; i++) { 02317 size_t i_min = i * shrink_factor; 02318 size_t i_max = i * shrink_factor + shrink_factor; 02319 02320 float sum = 0; 02321 for (size_t kk = k_min; kk < k_max; kk++) { 02322 size_t cur_kk = kk * nxy; 02323 02324 for (size_t jj = j_min; jj < j_max; jj++) { 02325 size_t cur_jj = jj * nx + cur_kk; 02326 for (size_t ii = i_min; ii < i_max; ii++) { 02327 sum += data[ii + cur_jj]; 02328 } 02329 } 02330 } 02331 rdata[i + cur_j] = sum * invnormfactor; 02332 } 02333 } 02334 } 02335 to->scale_pixel((float)shrink_factor); 02336 }
void MeanShrinkProcessor::accrue_mean_one_p_five | ( | EMData * | to, | |
const EMData *const | from | |||
) | [private] |
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.
to | the smaller image that will store the mean values | |
from | the larger image that will be used to calculate the mean values |
Definition at line 2339 of file processor.cpp.
References EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::scale_pixel(), and EMAN::EMData::update().
Referenced by process(), and process_inplace().
02340 { 02341 int nx0 = from->get_xsize(), ny0 = from->get_ysize(); // the original size 02342 02343 int nx = to->get_xsize(), ny = to->get_ysize(); 02344 02345 float *data = to->get_data(); 02346 const float * const data0 = from->get_const_data(); 02347 02348 for (int j = 0; j < ny; j++) { 02349 int jj = int(j * 1.5); 02350 float jw0 = 1.0F, jw1 = 0.5F; // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels 02351 if ( j%2 ) { 02352 jw0 = 0.5F; 02353 jw1 = 1.0F; 02354 } 02355 for (int i = 0; i < nx; i++) { 02356 int ii = int(i * 1.5); 02357 float iw0 = 1.0F, iw1 = 0.5F; 02358 float w = 0.0F; 02359 02360 if ( i%2 ) { 02361 iw0 = 0.5F; 02362 iw1 = 1.0F; 02363 } 02364 if ( jj < ny0 ) { 02365 if ( ii < nx0 ) { 02366 data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ; 02367 w += jw0 * iw0 ; 02368 if ( ii+1 < nx0 ) { 02369 data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1; 02370 w += jw0 * iw1; 02371 } 02372 } 02373 if ( jj +1 < ny0 ) { 02374 if ( ii < nx0 ) { 02375 data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0; 02376 w += jw1 * iw0; 02377 if ( ii+1 < nx0 ) { 02378 data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1; 02379 w += jw1 * iw1; 02380 } 02381 } 02382 } 02383 } 02384 if ( w>0 ) data[j * nx + i] /= w; 02385 } 02386 } 02387 02388 to->update(); 02389 to->scale_pixel((float)1.5); 02390 }
string EMAN::MeanShrinkProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 3470 of file processor.h.
03471 { 03472 return "Shrink an image by a given amount , using the mean value found in the pixel neighborhood."; 03473 }
virtual string EMAN::MeanShrinkProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 3475 of file processor.h.
References NAME.
03476 { 03477 return NAME; 03478 }
virtual TypeDict EMAN::MeanShrinkProcessor::get_param_types | ( | ) | const [inline, virtual] |
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 3484 of file processor.h.
References EMAN::EMObject::FLOAT, and EMAN::TypeDict::put().
03485 { 03486 TypeDict d; 03487 d.put("n", EMObject::FLOAT, "The shrink factor"); 03488 return d; 03489 }
static Processor* EMAN::MeanShrinkProcessor::NEW | ( | ) | [inline, static] |
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
image | the image that will be used to generate a 'mean shrunken' image |
ImageFormatException | if the image is complex | |
ImageDimensionException | if the image is 1D | |
InvalidValueException | if the shrink amount is a nonzero integer, unless it is 1.5, which is an exceptional circumstance |
Reimplemented from EMAN::Processor.
Definition at line 2174 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(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update().
02175 { 02176 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02177 02178 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02179 02180 float shrink_factor0 = params.set_default("n",0.0f); 02181 int shrink_factor = int(shrink_factor0); 02182 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02183 throw InvalidValueException(shrink_factor0, 02184 "mean shrink: shrink factor must be >1 integer or 1.5"); 02185 } 02186 02187 int nx = image->get_xsize(); 02188 int ny = image->get_ysize(); 02189 int nz = image->get_zsize(); 02190 02191 02192 // here handle the special averaging by 1.5 for 2D case 02193 if (shrink_factor0==1.5 ) { 02194 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02195 02196 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02197 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02198 EMData* result = new EMData(shrunken_nx,shrunken_ny,1); 02199 02200 accrue_mean_one_p_five(result,image); 02201 result->update(); 02202 02203 return result; 02204 } 02205 02206 int shrunken_nx = nx / shrink_factor; 02207 int shrunken_ny = ny / shrink_factor; 02208 int shrunken_nz = 1; 02209 02210 if (nz > 1) { 02211 shrunken_nz = nz / shrink_factor; 02212 } 02213 02214 // EMData* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz); 02215 EMData* result = image->copy_head(); 02216 result->set_size(shrunken_nx,shrunken_ny,shrunken_nz); 02217 accrue_mean(result,image,shrink_factor); 02218 02219 result->update(); 02220 02221 return result; 02222 }
void MeanShrinkProcessor::process_inplace | ( | EMData * | image | ) | [virtual] |
Mean shrink inplace.
image | the image that will be 'mean shrunken' inplace |
ImageFormatException | if the image is complex | |
ImageDimensionException | if the image is 1D | |
InvalidValueException | if the shrink amount is a nonzero integer, unless it is 1.5, which is an exceptional circumstance |
Implements EMAN::Processor.
Definition at line 2224 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(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::to_zero(), and EMAN::EMData::update().
02225 { 02226 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02227 02228 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02229 02230 float shrink_factor0 = params.set_default("n",0.0f); 02231 int shrink_factor = int(shrink_factor0); 02232 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02233 throw InvalidValueException(shrink_factor0, 02234 "mean shrink: shrink factor must be >1 integer or 1.5"); 02235 } 02236 02237 /* if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || 02238 (nz > 1 && (nz % shrink_factor != 0))) { 02239 throw InvalidValueException(shrink_factor, 02240 "Image size not divisible by shrink factor"); 02241 }*/ 02242 02243 int nx = image->get_xsize(); 02244 int ny = image->get_ysize(); 02245 int nz = image->get_zsize(); 02246 // here handle the special averaging by 1.5 for 2D case 02247 if (shrink_factor0==1.5 ) { 02248 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02249 02250 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02251 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02252 02253 EMData* orig = image->copy(); 02254 image->set_size(shrunken_nx, shrunken_ny, 1); // now nx = shrunken_nx, ny = shrunken_ny 02255 image->to_zero(); 02256 02257 accrue_mean_one_p_five(image,orig); 02258 02259 if( orig ) { 02260 delete orig; 02261 orig = 0; 02262 } 02263 image->update(); 02264 02265 return; 02266 } 02267 02268 accrue_mean(image,image,shrink_factor); 02269 02270 int shrunken_nx = nx / shrink_factor; 02271 int shrunken_ny = ny / shrink_factor; 02272 int shrunken_nz = 1; 02273 if (nz > 1) shrunken_nz = nz / shrink_factor; 02274 02275 image->update(); 02276 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02277 }
const string MeanShrinkProcessor::NAME = "math.meanshrink" [static] |