#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 3312 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 2213 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(). 02214 { 02215 const float * const data = from->get_const_data(); 02216 float* rdata = to->get_data(); 02217 02218 size_t nx = from->get_xsize(); 02219 size_t ny = from->get_ysize(); 02220 size_t nz = from->get_zsize(); 02221 size_t nxy = nx*ny; 02222 02223 02224 size_t shrunken_nx = nx / shrink_factor; 02225 size_t shrunken_ny = ny / shrink_factor; 02226 size_t shrunken_nz = 1; 02227 size_t shrunken_nxy = shrunken_nx * shrunken_ny; 02228 02229 int normalize_shrink_factor = shrink_factor * shrink_factor; 02230 int z_shrink_factor = 1; 02231 02232 if (nz > 1) { 02233 shrunken_nz = nz / shrink_factor; 02234 normalize_shrink_factor *= shrink_factor; 02235 z_shrink_factor = shrink_factor; 02236 } 02237 02238 float invnormfactor = 1.0f/(float)normalize_shrink_factor; 02239 02240 for (size_t k = 0; k < shrunken_nz; k++) { 02241 size_t k_min = k * shrink_factor; 02242 size_t k_max = k * shrink_factor + z_shrink_factor; 02243 size_t cur_k = k * shrunken_nxy; 02244 02245 for (size_t j = 0; j < shrunken_ny; j++) { 02246 size_t j_min = j * shrink_factor; 02247 size_t j_max = j * shrink_factor + shrink_factor; 02248 size_t cur_j = j * shrunken_nx + cur_k; 02249 02250 for (size_t i = 0; i < shrunken_nx; i++) { 02251 size_t i_min = i * shrink_factor; 02252 size_t i_max = i * shrink_factor + shrink_factor; 02253 02254 float sum = 0; 02255 for (size_t kk = k_min; kk < k_max; kk++) { 02256 size_t cur_kk = kk * nxy; 02257 02258 for (size_t jj = j_min; jj < j_max; jj++) { 02259 size_t cur_jj = jj * nx + cur_kk; 02260 for (size_t ii = i_min; ii < i_max; ii++) { 02261 sum += data[ii + cur_jj]; 02262 } 02263 } 02264 } 02265 rdata[i + cur_j] = sum * invnormfactor; 02266 } 02267 } 02268 } 02269 to->scale_pixel((float)shrink_factor); 02270 }
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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 2273 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(). 02274 { 02275 int nx0 = from->get_xsize(), ny0 = from->get_ysize(); // the original size 02276 02277 int nx = to->get_xsize(), ny = to->get_ysize(); 02278 02279 float *data = to->get_data(); 02280 const float * const data0 = from->get_const_data(); 02281 02282 for (int j = 0; j < ny; j++) { 02283 int jj = int(j * 1.5); 02284 float jw0 = 1.0F, jw1 = 0.5F; // 3x3 -> 2x2, so each new pixel should have 2.25 of the old pixels 02285 if ( j%2 ) { 02286 jw0 = 0.5F; 02287 jw1 = 1.0F; 02288 } 02289 for (int i = 0; i < nx; i++) { 02290 int ii = int(i * 1.5); 02291 float iw0 = 1.0F, iw1 = 0.5F; 02292 float w = 0.0F; 02293 02294 if ( i%2 ) { 02295 iw0 = 0.5F; 02296 iw1 = 1.0F; 02297 } 02298 if ( jj < ny0 ) { 02299 if ( ii < nx0 ) { 02300 data[j * nx + i] = data0[ jj * nx0 + ii ] * jw0 * iw0 ; 02301 w += jw0 * iw0 ; 02302 if ( ii+1 < nx0 ) { 02303 data[j * nx + i] += data0[ jj * nx0 + ii + 1] * jw0 * iw1; 02304 w += jw0 * iw1; 02305 } 02306 } 02307 if ( jj +1 < ny0 ) { 02308 if ( ii < nx0 ) { 02309 data[j * nx + i] += data0[ (jj+1) * nx0 + ii ] * jw1 * iw0; 02310 w += jw1 * iw0; 02311 if ( ii+1 < nx0 ) { 02312 data[j * nx + i] += data0[ (jj+1) * nx0 + ii + 1] * jw1 * iw1; 02313 w += jw1 * iw1; 02314 } 02315 } 02316 } 02317 } 02318 if ( w>0 ) data[j * nx + i] /= w; 02319 } 02320 } 02321 02322 to->update(); 02323 to->scale_pixel((float)1.5); 02324 }
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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 3335 of file processor.h. 03336 { 03337 return "Shrink an image by a given amount , using the mean value found in the pixel neighborhood."; 03338 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 3340 of file processor.h. 03341 {
03342 return NAME;
03343 }
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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 3349 of file processor.h. References EMAN::TypeDict::put(). 03350 { 03351 TypeDict d; 03352 d.put("n", EMObject::FLOAT, "The shrink factor"); 03353 return d; 03354 }
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Definition at line 3344 of file processor.h. 03345 { 03346 return new MeanShrinkProcessor(); 03347 }
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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 2108 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(). 02109 { 02110 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02111 02112 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02113 02114 float shrink_factor0 = params.set_default("n",0.0f); 02115 int shrink_factor = int(shrink_factor0); 02116 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02117 throw InvalidValueException(shrink_factor0, 02118 "mean shrink: shrink factor must be >1 integer or 1.5"); 02119 } 02120 02121 int nx = image->get_xsize(); 02122 int ny = image->get_ysize(); 02123 int nz = image->get_zsize(); 02124 02125 02126 // here handle the special averaging by 1.5 for 2D case 02127 if (shrink_factor0==1.5 ) { 02128 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02129 02130 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02131 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02132 EMData* result = new EMData(shrunken_nx,shrunken_ny,1); 02133 02134 accrue_mean_one_p_five(result,image); 02135 result->update(); 02136 02137 return result; 02138 } 02139 02140 int shrunken_nx = nx / shrink_factor; 02141 int shrunken_ny = ny / shrink_factor; 02142 int shrunken_nz = 1; 02143 02144 if (nz > 1) { 02145 shrunken_nz = nz / shrink_factor; 02146 } 02147 02148 // EMData* result = new EMData(shrunken_nx,shrunken_ny,shrunken_nz); 02149 EMData* result = image->copy_head(); 02150 result->set_size(shrunken_nx,shrunken_ny,shrunken_nz); 02151 accrue_mean(result,image,shrink_factor); 02152 02153 result->update(); 02154 02155 return result; 02156 }
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Mean shrink inplace.
Implements EMAN::Processor. Definition at line 2158 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(). 02159 { 02160 if (image->is_complex()) throw ImageFormatException("Error, the mean shrink processor does not work on complex images"); 02161 02162 if (image->get_ndim() == 1) { throw ImageDimensionException("Error, mean shrink works only for 2D & 3D images"); } 02163 02164 float shrink_factor0 = params.set_default("n",0.0f); 02165 int shrink_factor = int(shrink_factor0); 02166 if (shrink_factor0 <= 1.0F || ((shrink_factor0 != shrink_factor) && (shrink_factor0 != 1.5F) ) ) { 02167 throw InvalidValueException(shrink_factor0, 02168 "mean shrink: shrink factor must be >1 integer or 1.5"); 02169 } 02170 02171 /* if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || 02172 (nz > 1 && (nz % shrink_factor != 0))) { 02173 throw InvalidValueException(shrink_factor, 02174 "Image size not divisible by shrink factor"); 02175 }*/ 02176 02177 int nx = image->get_xsize(); 02178 int ny = image->get_ysize(); 02179 int nz = image->get_zsize(); 02180 // here handle the special averaging by 1.5 for 2D case 02181 if (shrink_factor0==1.5 ) { 02182 if (nz > 1 ) throw InvalidValueException(shrink_factor0, "mean shrink: only support 2D images for shrink factor = 1.5"); 02183 02184 int shrunken_nx = (int(nx / 1.5)+1)/2*2; // make sure the output size is even 02185 int shrunken_ny = (int(ny / 1.5)+1)/2*2; 02186 02187 EMData* orig = image->copy(); 02188 image->set_size(shrunken_nx, shrunken_ny, 1); // now nx = shrunken_nx, ny = shrunken_ny 02189 image->to_zero(); 02190 02191 accrue_mean_one_p_five(image,orig); 02192 02193 if( orig ) { 02194 delete orig; 02195 orig = 0; 02196 } 02197 image->update(); 02198 02199 return; 02200 } 02201 02202 accrue_mean(image,image,shrink_factor); 02203 02204 int shrunken_nx = nx / shrink_factor; 02205 int shrunken_ny = ny / shrink_factor; 02206 int shrunken_nz = 1; 02207 if (nz > 1) shrunken_nz = nz / shrink_factor; 02208 02209 image->update(); 02210 image->set_size(shrunken_nx, shrunken_ny, shrunken_nz); 02211 }
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Definition at line 123 of file processor.cpp. |