#include <averager.h>
Inheritance diagram for EMAN::ImageAverager:
Public Member Functions | |
ImageAverager () | |
void | add_image (EMData *image) |
To add an image to the Averager. | |
EMData * | finish () |
Finish up the averaging and return the result. | |
string | get_name () const |
Get the Averager's name. | |
string | get_desc () const |
TypeDict | get_param_types () const |
Get Averager parameter information in a dictionary. | |
virtual void | mult (const float &) |
Multiply the result image by some floating point constant This is useful when weighting the input images prior to calling add_image - a situation where it is likely you want to divide by the sum of the weights. | |
Static Public Member Functions | |
Averager * | NEW () |
Static Public Attributes | |
const string | NAME = "mean" |
Private Attributes | |
EMData * | sigma_image |
int * | nimg_n0 |
int | ignore0 |
int | nimg |
It optionally makes a sigma image.
sigma | sigma value | |
ignore0 | if set, ignore zero value pixels |
Definition at line 170 of file averager.h.
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Definition at line 188 of file averager.cpp. 00189 : sigma_image(0), nimg_n0(0), ignore0(0), nimg(0) 00190 { 00191 00192 }
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To add an image to the Averager. This image will be averaged in this function.
Implements EMAN::Averager. Definition at line 194 of file averager.cpp. References EMAN::EMData::copy_head(), EMAN::EMData::get_data(), get_name(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ignore0, EMAN::EMUtil::is_same_size(), LOGERR, nimg, nimg_n0, nx, ny, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and sigma_image. 00195 { 00196 if (!image) { 00197 return; 00198 } 00199 00200 if (nimg >= 1 && !EMUtil::is_same_size(image, result)) { 00201 LOGERR("%sAverager can only process same-size Image", 00202 get_name().c_str()); 00203 return; 00204 } 00205 00206 nimg++; 00207 00208 int nx = image->get_xsize(); 00209 int ny = image->get_ysize(); 00210 int nz = image->get_zsize(); 00211 size_t image_size = (size_t)nx * ny * nz; 00212 00213 if (nimg == 1) { 00214 result = image->copy_head(); 00215 result->set_size(nx, ny, nz); 00216 sigma_image = params.set_default("sigma", (EMData*)0); 00217 ignore0 = params["ignore0"]; 00218 00219 nimg_n0 = new int[image_size]; 00220 for (size_t i = 0; i < image_size; ++i) { 00221 nimg_n0[i] = 0; 00222 } 00223 } 00224 00225 float *result_data = result->get_data(); 00226 float *sigma_image_data = 0; 00227 if (sigma_image) { 00228 sigma_image->set_size(nx, ny, nz); 00229 sigma_image_data = sigma_image->get_data(); 00230 } 00231 00232 float * image_data = image->get_data(); 00233 00234 if (!ignore0) { 00235 for (size_t j = 0; j < image_size; ++j) { 00236 float f = image_data[j]; 00237 result_data[j] += f; 00238 if (sigma_image_data) { 00239 sigma_image_data[j] += f * f; 00240 } 00241 } 00242 } 00243 else { 00244 for (size_t j = 0; j < image_size; ++j) { 00245 float f = image_data[j]; 00246 if (f) { 00247 result_data[j] += f; 00248 if (sigma_image_data) { 00249 sigma_image_data[j] += f * f; 00250 } 00251 nimg_n0[j]++; 00252 } 00253 } 00254 } 00255 }
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Finish up the averaging and return the result.
Implements EMAN::Averager. Definition at line 257 of file averager.cpp. References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), nimg, nimg_n0, EMAN::EMData::set_attr(), sigma_image, sqrt(), and EMAN::EMData::update(). 00258 { 00259 if (result && nimg > 1) { 00260 size_t image_size = (size_t)result->get_xsize() * result->get_ysize() * result->get_zsize(); 00261 float * result_data = result->get_data(); 00262 00263 if (!ignore0) { 00264 for (size_t j = 0; j < image_size; ++j) { 00265 result_data[j] /= nimg; 00266 } 00267 00268 if (sigma_image) { 00269 float * sigma_image_data = sigma_image->get_data(); 00270 00271 for (size_t j = 0; j < image_size; ++j) { 00272 float f1 = sigma_image_data[j] / nimg; 00273 float f2 = result_data[j]; 00274 sigma_image_data[j] = sqrt(f1 - f2 * f2); 00275 } 00276 00277 sigma_image->update(); 00278 } 00279 } 00280 else { 00281 for (size_t j = 0; j < image_size; ++j) { 00282 if (nimg_n0[j]>0) result_data[j] /= nimg_n0[j]; 00283 } 00284 if (sigma_image) { 00285 float * sigma_image_data = sigma_image->get_data(); 00286 00287 for (size_t j = 0; j < image_size; ++j) { 00288 float f1 = sigma_image_data[j] / nimg_n0[j]; 00289 float f2 = result_data[j]; 00290 sigma_image_data[j] = sqrt(f1 - f2 * f2); 00291 } 00292 00293 sigma_image->update(); 00294 } 00295 } 00296 00297 result->update(); 00298 00299 } 00300 result->set_attr("ptcl_repr",nimg); 00301 00302 if( nimg_n0 ) 00303 { 00304 delete [] nimg_n0; 00305 nimg_n0 = 0; 00306 } 00307 00308 return result; 00309 }
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Implements EMAN::Averager. Definition at line 183 of file averager.h. 00184 { 00185 return "Simple mean average of images"; 00186 }
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Get the Averager's name. Each Averager is identified by a unique name.
Implements EMAN::Averager. Definition at line 178 of file averager.h. Referenced by add_image(). 00179 {
00180 return NAME;
00181 }
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Get Averager 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::Averager. Definition at line 193 of file averager.h. References EMAN::TypeDict::put(). 00194 { 00195 TypeDict d; 00196 d.put("sigma", EMObject::EMDATA, "sigma value"); 00197 d.put("ignore0", EMObject::INT, "if set, ignore zero value pixels"); 00198 return d; 00199 }
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Multiply the result image by some floating point constant This is useful when weighting the input images prior to calling add_image - a situation where it is likely you want to divide by the sum of the weights. Hence call mult after all of the weighted images have been added.
Reimplemented from EMAN::Averager. Definition at line 201 of file averager.h. 00201 { }
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Definition at line 188 of file averager.h. 00189 { 00190 return new ImageAverager(); 00191 }
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Definition at line 208 of file averager.h. Referenced by add_image(). |
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Definition at line 45 of file averager.cpp. |
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Definition at line 209 of file averager.h. Referenced by add_image(), and finish(). |
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Definition at line 207 of file averager.h. Referenced by add_image(), and finish(). |
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Definition at line 206 of file averager.h. Referenced by add_image(), and finish(). |