EMAN::NormalizeToLeastSquareProcessor Class Reference

use least square method to normalize More...

#include <processor.h>

Inheritance diagram for EMAN::NormalizeToLeastSquareProcessor:

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Collaboration diagram for EMAN::NormalizeToLeastSquareProcessor:

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List of all members.

Public Member Functions

void process_inplace (EMData *image)
 To process an image in-place.
string get_name () const
 Get the processor's name.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.
string get_desc () const
 Get the descrition of this specific processor.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "normalize.toimage"

Detailed Description

use least square method to normalize

Parameters:
to reference image normalize to
low_threshold only take into account the reference image's pixel value between high and low threshold (zero is ignored)
high_threshold only take into account the reference image's pixel value between high and low threshold (zero is ignored)

Definition at line 4447 of file processor.h.


Member Function Documentation

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

Get the descrition of this specific processor.

This function must be overwritten by a subclass.

Returns:
The description of this processor.

Implements EMAN::Processor.

Definition at line 4472 of file processor.h.

04473                 {
04474                         return "use least square method to normalize";
04475                 }

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

Get the processor's name.

Each processor is identified by a unique name.

Returns:
The processor's name.

Implements EMAN::Processor.

Definition at line 4452 of file processor.h.

References NAME.

04453                 {
04454                         return NAME;
04455                 }

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

Get processor 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::Processor.

Definition at line 4462 of file processor.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, and EMAN::TypeDict::put().

04463                 {
04464                         TypeDict d;
04465                         d.put("to", EMObject::EMDATA, "reference image normalize to");
04466                         d.put("ignore_zero", EMObject::BOOL, "If set, ignores any pixels which are exactly zero in either image. Defaut = True.");
04467                         d.put("low_threshold", EMObject::FLOAT, "only take into account the reference image's pixel value between high and low threshold (zero is always ignored)");
04468                         d.put("high_threshold", EMObject::FLOAT, "only take into account the reference image's pixel value between high and low threshold (zero is always ignored)");
04469                         return d;
04470                 }

static Processor* EMAN::NormalizeToLeastSquareProcessor::NEW (  )  [inline, static]

Definition at line 4457 of file processor.h.

04458                 {
04459                         return new NormalizeToLeastSquareProcessor();
04460                 }

void NormalizeToLeastSquareProcessor::process_inplace ( EMData image  )  [virtual]

To process an image in-place.

For those processors which can only be processed out-of-place, override this function to just print out some error message to remind user call the out-of-place version.

Parameters:
image The image to be processed.

Implements EMAN::Processor.

Definition at line 3857 of file processor.cpp.

References b, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), LOGWARN, EMAN::Processor::params, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and EMAN::EMData::update().

03858 {
03859         if (!image) {
03860                 LOGWARN("NULL Image");
03861                 return;
03862         }
03863 
03864         EMData *to = params["to"];
03865 
03866         bool ignore_zero = params.set_default("ignore_zero",true);
03867 
03868         float low_threshold = FLT_MIN;
03869         string low_thr_name = "low_threshold";
03870         if (params.has_key(low_thr_name)) {
03871                 low_threshold = params[low_thr_name];
03872         }
03873 
03874         float high_threshold = FLT_MAX;
03875         string high_thr_name = "high_threshold";
03876         if (params.has_key(high_thr_name)) {
03877                 high_threshold = params[high_thr_name];
03878         }
03879 
03880         float *rawp = image->get_data();
03881         float *refp = to->get_data();
03882 
03883         int nx = image->get_xsize();
03884         int ny = image->get_ysize();
03885         int nz = image->get_zsize();
03886         size_t size = (size_t)nx * ny * nz;
03887 
03888         float sum_x = 0;
03889         float sum_y = 0;
03890         size_t count = 0;
03891 
03892         float sum_x_mean = 0;
03893         float sum_tt = 0;
03894         float b = 0;
03895 
03896         // This is really inefficient, who coded it ?   --steve
03897         if (ignore_zero) {
03898                 for (size_t i = 0; i < size; ++i) {
03899                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0f && rawp[i] != 0.0f) {
03900                                 count++;
03901                                 sum_x += refp[i];
03902                                 sum_y += rawp[i];
03903                         }
03904                 }
03905 
03906                 sum_x_mean = sum_x / count;
03907                 sum_tt = 0;
03908                 b = 0;
03909 
03910                 float t;
03911                 for (size_t i = 0; i < size; ++i) {
03912                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0f && rawp[i] != 0.0f) {
03913                                 t = refp[i] - sum_x_mean;
03914                                 sum_tt += t * t;
03915                                 b += t * rawp[i];
03916                         }
03917                 }
03918         }
03919         else {
03920                         for (size_t i = 0; i < size; ++i) {
03921                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03922                                 count++;
03923                                 sum_x += refp[i];
03924                                 sum_y += rawp[i];
03925                         }
03926                 }
03927 
03928                 sum_x_mean = sum_x / count;
03929                 sum_tt = 0;
03930                 b = 0;
03931 
03932                 float t;
03933                 for (size_t i = 0; i < size; ++i) {
03934                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03935                                 t = refp[i] - sum_x_mean;
03936                                 sum_tt += t * t;
03937                                 b += t * rawp[i];
03938                         }
03939                 }
03940         }
03941 
03942         b /= sum_tt;
03943 
03944         float a = (sum_y - sum_x * b) / count;
03945         float scale = 1 / b;
03946         float shift = -a / b;
03947 
03948         for (size_t i = 0; i < size; ++i) {
03949                 rawp[i] = (rawp[i] - a) / b;
03950         }
03951 
03952         image->update();
03953 
03954         params["scale"] = scale;
03955         params["shift"] = shift;
03956 
03957         image->set_attr("norm_mult",scale);
03958         image->set_attr("norm_add",shift);
03959 
03960 }


Member Data Documentation

const string NormalizeToLeastSquareProcessor::NAME = "normalize.toimage" [static]

Definition at line 4477 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu May 3 10:10:28 2012 for EMAN2 by  doxygen 1.4.7