#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 83 of file averager.cpp. 00084 : sigma_image(0), nimg_n0(0), ignore0(0), nimg(0) 00085 { 00086 00087 }
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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 89 of file averager.cpp. References 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. 00090 { 00091 if (!image) { 00092 return; 00093 } 00094 00095 if (nimg >= 1 && !EMUtil::is_same_size(image, result)) { 00096 LOGERR("%sAverager can only process same-size Image", 00097 get_name().c_str()); 00098 return; 00099 } 00100 00101 nimg++; 00102 00103 int nx = image->get_xsize(); 00104 int ny = image->get_ysize(); 00105 int nz = image->get_zsize(); 00106 size_t image_size = nx * ny * nz; 00107 00108 if (nimg == 1) { 00109 result = new EMData(); 00110 result->set_size(nx, ny, nz); 00111 sigma_image = params.set_default("sigma", (EMData*)0); 00112 ignore0 = params["ignore0"]; 00113 00114 nimg_n0 = new int[image_size]; 00115 for (size_t i = 0; i < image_size; i++) { 00116 nimg_n0[i] = 0; 00117 } 00118 } 00119 00120 float *result_data = result->get_data(); 00121 float *sigma_image_data = 0; 00122 if (sigma_image) { 00123 sigma_image->set_size(nx, ny, nz); 00124 sigma_image_data = sigma_image->get_data(); 00125 } 00126 00127 float * image_data = image->get_data(); 00128 00129 if (!ignore0) { 00130 for (size_t j = 0; j < image_size; j++) { 00131 float f = image_data[j]; 00132 result_data[j] += f; 00133 if (sigma_image_data) { 00134 sigma_image_data[j] += f * f; 00135 } 00136 } 00137 } 00138 else { 00139 for (size_t j = 0; j < image_size; j++) { 00140 float f = image_data[j]; 00141 if (f) { 00142 result_data[j] += f; 00143 if (sigma_image_data) { 00144 sigma_image_data[j] += f * f; 00145 } 00146 nimg_n0[j]++; 00147 } 00148 } 00149 } 00150 }
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Finish up the averaging and return the result.
Implements EMAN::Averager. Definition at line 152 of file averager.cpp. References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), nimg, nimg_n0, sigma_image, sqrt(), and EMAN::EMData::update(). 00153 { 00154 if (result && nimg > 1) { 00155 size_t image_size = result->get_xsize() * result->get_ysize() * result->get_zsize(); 00156 float * result_data = result->get_data(); 00157 00158 if (!ignore0) { 00159 for (size_t j = 0; j < image_size; j++) { 00160 result_data[j] /= nimg; 00161 } 00162 00163 if (sigma_image) { 00164 float * sigma_image_data = sigma_image->get_data(); 00165 00166 for (size_t j = 0; j < image_size; j++) { 00167 float f1 = sigma_image_data[j] / nimg; 00168 float f2 = result_data[j]; 00169 sigma_image_data[j] = sqrt(f1 - f2 * f2); 00170 } 00171 00172 sigma_image->update(); 00173 } 00174 } 00175 else { 00176 for (size_t j = 0; j < image_size; j++) { 00177 result_data[j] /= nimg_n0[j]; 00178 } 00179 if (sigma_image) { 00180 float * sigma_image_data = sigma_image->get_data(); 00181 00182 for (size_t j = 0; j < image_size; j++) { 00183 float f1 = sigma_image_data[j] / nimg_n0[j]; 00184 float f2 = result_data[j]; 00185 sigma_image_data[j] = sqrt(f1 - f2 * f2); 00186 } 00187 00188 sigma_image->update(); 00189 } 00190 } 00191 00192 result->update(); 00193 } 00194 00195 if( nimg_n0 ) 00196 { 00197 delete [] nimg_n0; 00198 nimg_n0 = 0; 00199 } 00200 00201 return result; 00202 }
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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(). |