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 4449 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 4474 of file processor.h.

04475                 {
04476                         return "use least square method to normalize";
04477                 }

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 4454 of file processor.h.

References NAME.

04455                 {
04456                         return NAME;
04457                 }

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 4464 of file processor.h.

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

04465                 {
04466                         TypeDict d;
04467                         d.put("to", EMObject::EMDATA, "reference image normalize to");
04468                         d.put("ignore_zero", EMObject::BOOL, "If set, ignores any pixels which are exactly zero in either image. Defaut = True.");
04469                         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)");
04470                         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)");
04471                         return d;
04472                 }

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

Definition at line 4459 of file processor.h.

04460                 {
04461                         return new NormalizeToLeastSquareProcessor();
04462                 }

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 3863 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().

03864 {
03865         if (!image) {
03866                 LOGWARN("NULL Image");
03867                 return;
03868         }
03869 
03870         EMData *to = params["to"];
03871 
03872         bool ignore_zero = params.set_default("ignore_zero",true);
03873 
03874         float low_threshold = FLT_MIN;
03875         string low_thr_name = "low_threshold";
03876         if (params.has_key(low_thr_name)) {
03877                 low_threshold = params[low_thr_name];
03878         }
03879 
03880         float high_threshold = FLT_MAX;
03881         string high_thr_name = "high_threshold";
03882         if (params.has_key(high_thr_name)) {
03883                 high_threshold = params[high_thr_name];
03884         }
03885 
03886         float *rawp = image->get_data();
03887         float *refp = to->get_data();
03888 
03889         int nx = image->get_xsize();
03890         int ny = image->get_ysize();
03891         int nz = image->get_zsize();
03892         size_t size = (size_t)nx * ny * nz;
03893 
03894         float sum_x = 0;
03895         float sum_y = 0;
03896         size_t count = 0;
03897 
03898         float sum_x_mean = 0;
03899         float sum_tt = 0;
03900         float b = 0;
03901 
03902         // This is really inefficient, who coded it ?   --steve
03903         if (ignore_zero) {
03904                 for (size_t i = 0; i < size; ++i) {
03905                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0f && rawp[i] != 0.0f) {
03906                                 count++;
03907                                 sum_x += refp[i];
03908                                 sum_y += rawp[i];
03909                         }
03910                 }
03911 
03912                 sum_x_mean = sum_x / count;
03913                 sum_tt = 0;
03914                 b = 0;
03915 
03916                 float t;
03917                 for (size_t i = 0; i < size; ++i) {
03918                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0f && rawp[i] != 0.0f) {
03919                                 t = refp[i] - sum_x_mean;
03920                                 sum_tt += t * t;
03921                                 b += t * rawp[i];
03922                         }
03923                 }
03924         }
03925         else {
03926                         for (size_t i = 0; i < size; ++i) {
03927                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03928                                 count++;
03929                                 sum_x += refp[i];
03930                                 sum_y += rawp[i];
03931                         }
03932                 }
03933 
03934                 sum_x_mean = sum_x / count;
03935                 sum_tt = 0;
03936                 b = 0;
03937 
03938                 float t;
03939                 for (size_t i = 0; i < size; ++i) {
03940                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03941                                 t = refp[i] - sum_x_mean;
03942                                 sum_tt += t * t;
03943                                 b += t * rawp[i];
03944                         }
03945                 }
03946         }
03947 
03948         b /= sum_tt;
03949 
03950         float a = (sum_y - sum_x * b) / count;
03951         float scale = 1 / b;
03952         float shift = -a / b;
03953 
03954         for (size_t i = 0; i < size; ++i) {
03955                 rawp[i] = (rawp[i] - a) / b;
03956         }
03957 
03958         image->update();
03959 
03960         params["scale"] = scale;
03961         params["shift"] = shift;
03962 
03963         image->set_attr("norm_mult",scale);
03964         image->set_attr("norm_add",shift);
03965 
03966 }


Member Data Documentation

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

Definition at line 4479 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:44:17 2013 for EMAN2 by  doxygen 1.4.7