#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.
|
||||||||||||||||
|
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 }
|
|
||||||||||||
|
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 }
|
|
|
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 }
|
|
|
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 }
|
|
|
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 }
|
|
|
Definition at line 3400 of file processor.h. 03401 {
03402 return new MeanShrinkProcessor();
03403 }
|
|
|
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 }
|
|
|
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 }
|
|
|
Definition at line 125 of file processor.cpp. |
1.3.9.1