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
EMDatanormimage
int ignore0
int nimg
int freenorm

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 183 of file averager.cpp.

Referenced by NEW().

00184         : sigma_image(0), ignore0(0), normimage(0), freenorm(0), nimg(0)
00185 {
00186 
00187 }


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 189 of file averager.cpp.

References EMAN::EMData::copy_head(), freenorm, EMAN::EMData::get_data(), get_name(), EMAN::EMData::get_value_at(), ignore0, EMAN::EMUtil::is_same_size(), LOGERR, nimg, normimage, nx, ny, EMAN::Averager::params, EMAN::Averager::result, EMAN::Dict::set_default(), EMAN::EMData::set_size(), EMAN::EMData::set_value_at_fast(), sigma_image, and EMAN::EMData::to_zero().

00190 {
00191         if (!image) {
00192                 return;
00193         }
00194 
00195         if (nimg >= 1 && !EMUtil::is_same_size(image, result)) {
00196                 LOGERR("%sAverager can only process same-size Image",
00197                            get_name().c_str());
00198                 return;
00199         }
00200 
00201         nimg++;
00202 
00203         int nx = image->get_xsize();
00204         int ny = image->get_ysize();
00205         int nz = image->get_zsize();
00206         size_t image_size = (size_t)nx * ny * nz;
00207 
00208         if (nimg == 1) {
00209                 result = image->copy_head();
00210                 result->set_size(nx, ny, nz);
00211                 sigma_image = params.set_default("sigma", (EMData*)0);
00212                 ignore0 = params["ignore0"];
00213 
00214                 normimage = params.set_default("normimage", (EMData*)0);
00215                 if (ignore0 && normimage==0) { normimage=new EMData(nx,ny,nz); freenorm=1; }
00216                 if (normimage) normimage->to_zero();
00217         }
00218 
00219         float *result_data = result->get_data();
00220         float *sigma_image_data = 0;
00221         if (sigma_image) {
00222                 sigma_image->set_size(nx, ny, nz);
00223                 sigma_image_data = sigma_image->get_data();
00224         }
00225 
00226         float * image_data = image->get_data();
00227 
00228         if (!ignore0) {
00229                 for (size_t j = 0; j < image_size; ++j) {
00230                         float f = image_data[j];
00231                         result_data[j] += f;
00232                         if (sigma_image_data) {
00233                                 sigma_image_data[j] += f * f;
00234                         }
00235                 }
00236         }
00237         else {
00238                 for (size_t j = 0; j < image_size; ++j) {
00239                         float f = image_data[j];
00240                         if (f) {
00241                                 result_data[j] += f;
00242                                 if (sigma_image_data) {
00243                                         sigma_image_data[j] += f * f;
00244                                 }
00245                                 normimage->set_value_at_fast(j,normimage->get_value_at(j)+1.0);
00246                         }
00247                 }
00248         }
00249 }

EMData * ImageAverager::finish (  )  [virtual]

Finish up the averaging and return the result.

Returns:
The averaged image.

Implements EMAN::Averager.

Definition at line 251 of file averager.cpp.

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

00252 {
00253         if (result && nimg > 1) {
00254                 size_t image_size = (size_t)result->get_xsize() * result->get_ysize() * result->get_zsize();
00255                 float * result_data = result->get_data();
00256 
00257                 if (!ignore0) {
00258                         for (size_t j = 0; j < image_size; ++j) {
00259                                 result_data[j] /= nimg;
00260                         }
00261 
00262                         if (sigma_image) {
00263                                 float * sigma_image_data = sigma_image->get_data();
00264 
00265                                 for (size_t j = 0; j < image_size; ++j) {
00266                                         float f1 = sigma_image_data[j] / nimg;
00267                                         float f2 = result_data[j];
00268                                         sigma_image_data[j] = sqrt(f1 - f2 * f2);
00269                                 }
00270 
00271                                 sigma_image->update();
00272                         }
00273                 }
00274                 else {
00275                         for (size_t j = 0; j < image_size; ++j) {
00276                                 if (normimage->get_value_at(j)>0) result_data[j] /= normimage->get_value_at(j);
00277                         }
00278                         if (sigma_image) {
00279                                 float * sigma_image_data = sigma_image->get_data();
00280 
00281                                 for (size_t j = 0; j < image_size; ++j) {
00282                                         float f1 = 0;
00283                                         if (normimage->get_value_at(j)>0) f1=sigma_image_data[j] / normimage->get_value_at(j);
00284                                         float f2 = result_data[j];
00285                                         sigma_image_data[j] = sqrt(f1 - f2 * f2);
00286                                 }
00287 
00288                                 sigma_image->update();
00289                         }
00290                 }
00291 
00292                 result->update();
00293 
00294         }               
00295         result->set_attr("ptcl_repr",nimg);
00296 
00297         if (freenorm) { delete normimage; normimage=(EMData*)0; }
00298 
00299         return result;
00300 }

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("normimage", EMObject::EMDATA, "In conjunction with ignore0, the number of non zero values for each pixel will be stored in this image.");
00198                         d.put("ignore0", EMObject::INT, "if set, ignore zero value pixels");
00199                         return d;
00200                 }

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 202 of file averager.h.

00202 { }

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::freenorm [private]

Definition at line 210 of file averager.h.

Referenced by add_image(), and finish().

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 204 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().

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

Definition at line 207 of file averager.h.

Referenced by add_image(), and finish().

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

Definition at line 207 of file averager.h.

Referenced by add_image(), and finish().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:42:51 2013 for EMAN2 by  doxygen 1.4.7