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 4408 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 4433 of file processor.h.

04434                 {
04435                         return "use least square method to normalize";
04436                 }

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 4413 of file processor.h.

References NAME.

04414                 {
04415                         return NAME;
04416                 }

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 4423 of file processor.h.

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

04424                 {
04425                         TypeDict d;
04426                         d.put("to", EMObject::EMDATA, "reference image normalize to");
04427                         d.put("ignore_zero", EMObject::BOOL, "If set, ignores any pixels which are exactly zero in either image. Defaut = True.");
04428                         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)");
04429                         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)");
04430                         return d;
04431                 }

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

Definition at line 4418 of file processor.h.

04419                 {
04420                         return new NormalizeToLeastSquareProcessor();
04421                 }

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 3803 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().

03804 {
03805         if (!image) {
03806                 LOGWARN("NULL Image");
03807                 return;
03808         }
03809 
03810         EMData *to = params["to"];
03811 
03812         bool ignore_zero = params.set_default("ignore_zero",true);
03813         
03814         float low_threshold = FLT_MIN;
03815         string low_thr_name = "low_threshold";
03816         if (params.has_key(low_thr_name)) {
03817                 low_threshold = params[low_thr_name];
03818         }
03819 
03820         float high_threshold = FLT_MAX;
03821         string high_thr_name = "high_threshold";
03822         if (params.has_key(high_thr_name)) {
03823                 high_threshold = params[high_thr_name];
03824         }
03825 
03826         float *rawp = image->get_data();
03827         float *refp = to->get_data();
03828 
03829         int nx = image->get_xsize();
03830         int ny = image->get_ysize();
03831         int nz = image->get_zsize();
03832         size_t size = nx * ny * nz;
03833 
03834         float sum_x = 0;
03835         float sum_y = 0;
03836         int count = 0;
03837 
03838         float sum_x_mean = 0;
03839         float sum_tt = 0;
03840         float b = 0;
03841         
03842         // This is really inefficient, who coded it ?   --steve
03843         if (ignore_zero) {
03844                 for (size_t i = 0; i < size; i++) {
03845                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0 && rawp[i] != 0.0) {
03846                                 count++;
03847                                 sum_x += refp[i];
03848                                 sum_y += rawp[i];
03849                         }
03850                 }
03851 
03852                 sum_x_mean = sum_x / count;
03853                 sum_tt = 0;
03854                 b = 0;
03855 
03856                 float t;
03857                 for (size_t i = 0; i < size; i++) {
03858                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0 && rawp[i] != 0.0) {
03859                                 t = refp[i] - sum_x_mean;
03860                                 sum_tt += t * t;
03861                                 b += t * rawp[i];
03862                         }
03863                 }
03864         }
03865         else {
03866                         for (size_t i = 0; i < size; i++) {
03867                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03868                                 count++;
03869                                 sum_x += refp[i];
03870                                 sum_y += rawp[i];
03871                         }
03872                 }
03873 
03874                 sum_x_mean = sum_x / count;
03875                 sum_tt = 0;
03876                 b = 0;
03877 
03878                 float t;
03879                 for (size_t i = 0; i < size; i++) {
03880                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03881                                 t = refp[i] - sum_x_mean;
03882                                 sum_tt += t * t;
03883                                 b += t * rawp[i];
03884                         }
03885                 }       
03886         }
03887 
03888         b /= sum_tt;
03889 
03890         float a = (sum_y - sum_x * b) / count;
03891         float scale = 1 / b;
03892         float shift = -a / b;
03893 
03894         for (size_t i = 0; i < size; i++) {
03895                 rawp[i] = (rawp[i] - a) / b;
03896         }
03897 
03898         image->update();
03899 
03900         params["scale"] = scale;
03901         params["shift"] = shift;
03902 
03903         image->set_attr("norm_mult",scale);
03904         image->set_attr("norm_add",shift);
03905 
03906 }


Member Data Documentation

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

Definition at line 4438 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:43:45 2010 for EMAN2 by  doxygen 1.4.7