EMAN::ImageAverager Class Reference

ImageAverager averages a list of images. More...

#include <averager.h>

Inheritance diagram for EMAN::ImageAverager:

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Collaboration diagram for EMAN::ImageAverager:

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List of all members.

Public Member Functions

 ImageAverager ()
void add_image (EMData *image)
 To add an image to the Averager.
EMDatafinish ()
 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

static AveragerNEW ()

Static Public Attributes

static const string NAME = "mean"

Private Attributes

EMDatasigma_image
int * nimg_n0
int ignore0
int nimg

Detailed Description

ImageAverager averages a list of images.

It optionally makes a sigma image.

Parameters:
sigma sigma value
ignore0 if set, ignore zero value pixels

Definition at line 170 of file averager.h.


Constructor & Destructor Documentation

ImageAverager::ImageAverager (  ) 

Definition at line 85 of file averager.cpp.

Referenced by NEW().

00086         : sigma_image(0), nimg_n0(0), ignore0(0), nimg(0)
00087 {
00088 
00089 }


Member Function Documentation

void ImageAverager::add_image ( EMData image  )  [virtual]

To add an image to the Averager.

This image will be averaged in this function.

Parameters:
image The image to be averaged.

Implements EMAN::Averager.

Definition at line 91 of file averager.cpp.

References EMAN::EMData::get_data(), get_name(), ignore0, EMAN::EMUtil::is_same_size(), LOGERR, nimg, nimg_n0, nx, ny, EMAN::Averager::params, EMAN::Averager::result, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and sigma_image.

00092 {
00093         if (!image) {
00094                 return;
00095         }
00096 
00097         if (nimg >= 1 && !EMUtil::is_same_size(image, result)) {
00098                 LOGERR("%sAverager can only process same-size Image",
00099                            get_name().c_str());
00100                 return;
00101         }
00102 
00103         nimg++;
00104 
00105         int nx = image->get_xsize();
00106         int ny = image->get_ysize();
00107         int nz = image->get_zsize();
00108         size_t image_size = nx * ny * nz;
00109 
00110         if (nimg == 1) {
00111                 result = new EMData();
00112                 result->set_size(nx, ny, nz);
00113                 sigma_image = params.set_default("sigma", (EMData*)0);
00114                 ignore0 = params["ignore0"];
00115 
00116                 nimg_n0 = new int[image_size];
00117                 for (size_t i = 0; i < image_size; i++) {
00118                         nimg_n0[i] = 0;
00119                 }
00120         }
00121 
00122         float *result_data = result->get_data();
00123         float *sigma_image_data = 0;
00124         if (sigma_image) {
00125                 sigma_image->set_size(nx, ny, nz);
00126                 sigma_image_data = sigma_image->get_data();
00127         }
00128 
00129         float * image_data = image->get_data();
00130 
00131         if (!ignore0) {
00132                 for (size_t j = 0; j < image_size; j++) {
00133                         float f = image_data[j];
00134                         result_data[j] += f;
00135                         if (sigma_image_data) {
00136                                 sigma_image_data[j] += f * f;
00137                         }
00138                 }
00139         }
00140         else {
00141                 for (size_t j = 0; j < image_size; j++) {
00142                         float f = image_data[j];
00143                         if (f) {
00144                                 result_data[j] += f;
00145                                 if (sigma_image_data) {
00146                                         sigma_image_data[j] += f * f;
00147                                 }
00148                                 nimg_n0[j]++;
00149                         }
00150                 }
00151         }
00152 }

EMData * ImageAverager::finish (  )  [virtual]

Finish up the averaging and return the result.

Returns:
The averaged image.

Implements EMAN::Averager.

Definition at line 154 of file averager.cpp.

References EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ignore0, nimg, nimg_n0, EMAN::Averager::result, sigma_image, sqrt(), and EMAN::EMData::update().

00155 {
00156         if (result && nimg > 1) {
00157                 size_t image_size = result->get_xsize() * result->get_ysize() * result->get_zsize();
00158                 float * result_data = result->get_data();
00159 
00160                 if (!ignore0) {
00161                         for (size_t j = 0; j < image_size; j++) {
00162                                 result_data[j] /= nimg;
00163                         }
00164 
00165                         if (sigma_image) {
00166                                 float * sigma_image_data = sigma_image->get_data();
00167 
00168                                 for (size_t j = 0; j < image_size; j++) {
00169                                         float f1 = sigma_image_data[j] / nimg;
00170                                         float f2 = result_data[j];
00171                                         sigma_image_data[j] = sqrt(f1 - f2 * f2);
00172                                 }
00173 
00174                                 sigma_image->update();
00175                         }
00176                 }
00177                 else {
00178                         for (size_t j = 0; j < image_size; j++) {
00179                                 result_data[j] /= nimg_n0[j];
00180                         }
00181                         if (sigma_image) {
00182                                 float * sigma_image_data = sigma_image->get_data();
00183 
00184                                 for (size_t j = 0; j < image_size; j++) {
00185                                         float f1 = sigma_image_data[j] / nimg_n0[j];
00186                                         float f2 = result_data[j];
00187                                         sigma_image_data[j] = sqrt(f1 - f2 * f2);
00188                                 }
00189 
00190                                 sigma_image->update();
00191                         }
00192                 }
00193 
00194                 result->update();
00195         }
00196 
00197         if( nimg_n0 )
00198         {
00199                 delete [] nimg_n0;
00200                 nimg_n0 = 0;
00201         }
00202 
00203         return result;
00204 }

string EMAN::ImageAverager::get_desc (  )  const [inline, virtual]

Implements EMAN::Averager.

Definition at line 183 of file averager.h.

00184                 {
00185                         return "Simple mean average of images";
00186                 }

string EMAN::ImageAverager::get_name (  )  const [inline, virtual]

Get the Averager's name.

Each Averager is identified by a unique name.

Returns:
The Averager's name.

Implements EMAN::Averager.

Definition at line 178 of file averager.h.

References NAME.

Referenced by add_image().

00179                 {
00180                         return NAME;
00181                 }

TypeDict EMAN::ImageAverager::get_param_types (  )  const [inline, virtual]

Get Averager parameter information in a dictionary.

Each parameter has one record in the dictionary. Each record contains its name, data-type, and description.

Returns:
A dictionary containing the parameter info.

Reimplemented from EMAN::Averager.

Definition at line 193 of file averager.h.

References EMAN::EMObject::EMDATA, EMAN::EMObject::INT, and 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                 }

virtual void EMAN::ImageAverager::mult ( const float &   )  [inline, virtual]

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.

Parameters:
s the scaling factor.
Exceptions:
NullPointerException if the EMData pointer (result) is NULL

Reimplemented from EMAN::Averager.

Definition at line 201 of file averager.h.

00201 { }

static Averager* EMAN::ImageAverager::NEW (  )  [inline, static]

Definition at line 188 of file averager.h.

References ImageAverager().

00189                 {
00190                         return new ImageAverager();
00191                 }


Member Data Documentation

int EMAN::ImageAverager::ignore0 [private]

Definition at line 208 of file averager.h.

Referenced by add_image(), and finish().

const string ImageAverager::NAME = "mean" [static]

Definition at line 203 of file averager.h.

Referenced by get_name().

int EMAN::ImageAverager::nimg [private]

Definition at line 209 of file averager.h.

Referenced by add_image(), and finish().

int* EMAN::ImageAverager::nimg_n0 [private]

Definition at line 207 of file averager.h.

Referenced by add_image(), and finish().

EMData* EMAN::ImageAverager::sigma_image [private]

Definition at line 206 of file averager.h.

Referenced by add_image(), and finish().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:42:20 2010 for EMAN2 by  doxygen 1.4.7