Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

EMAN::NormalizeToLeastSquareProcessor Class Reference

use least square method to normalize More...

#include <processor.h>

Inheritance diagram for EMAN::NormalizeToLeastSquareProcessor:

Inheritance graph
[legend]
Collaboration diagram for EMAN::NormalizeToLeastSquareProcessor:

Collaboration graph
[legend]
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

ProcessorNEW ()

Static Public Attributes

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 4192 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 4217 of file processor.h.

04218                 {
04219                         return "use least square method to normalize";
04220                 }

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 4197 of file processor.h.

04198                 {
04199                         return NAME;
04200                 }

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 4207 of file processor.h.

References EMAN::TypeDict::put().

04208                 {
04209                         TypeDict d;
04210                         d.put("to", EMObject::EMDATA, "reference image normalize to");
04211                         d.put("ignore_zero", EMObject::BOOL, "If set, ignores any pixels which are exactly zero in either image. Defaut = True.");
04212                         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)");
04213                         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)");
04214                         return d;
04215                 }

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

Definition at line 4202 of file processor.h.

04203                 {
04204                         return new NormalizeToLeastSquareProcessor();
04205                 }

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 3651 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, nx, ny, EMAN::EMData::set_attr(), EMAN::Dict::set_default(), t, and EMAN::EMData::update().

03652 {
03653         if (!image) {
03654                 LOGWARN("NULL Image");
03655                 return;
03656         }
03657 
03658         EMData *to = params["to"];
03659 
03660         bool ignore_zero = params.set_default("ignore_zero",true);
03661 
03662         float low_threshold = FLT_MIN;
03663         string low_thr_name = "low_threshold";
03664         if (params.has_key(low_thr_name)) {
03665                 low_threshold = params[low_thr_name];
03666         }
03667 
03668         float high_threshold = FLT_MAX;
03669         string high_thr_name = "high_threshold";
03670         if (params.has_key(high_thr_name)) {
03671                 high_threshold = params[high_thr_name];
03672         }
03673 
03674         float *rawp = image->get_data();
03675         float *refp = to->get_data();
03676 
03677         int nx = image->get_xsize();
03678         int ny = image->get_ysize();
03679         int nz = image->get_zsize();
03680         size_t size = nx * ny * nz;
03681 
03682         float sum_x = 0;
03683         float sum_y = 0;
03684         int count = 0;
03685 
03686         float sum_x_mean = 0;
03687         float sum_tt = 0;
03688         float b = 0;
03689 
03690         // This is really inefficient, who coded it ?   --steve
03691         if (ignore_zero) {
03692                 for (size_t i = 0; i < size; i++) {
03693                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0 && rawp[i] != 0.0) {
03694                                 count++;
03695                                 sum_x += refp[i];
03696                                 sum_y += rawp[i];
03697                         }
03698                 }
03699 
03700                 sum_x_mean = sum_x / count;
03701                 sum_tt = 0;
03702                 b = 0;
03703 
03704                 float t;
03705                 for (size_t i = 0; i < size; i++) {
03706                         if (refp[i] >= low_threshold && refp[i] <= high_threshold && refp[i] != 0.0 && rawp[i] != 0.0) {
03707                                 t = refp[i] - sum_x_mean;
03708                                 sum_tt += t * t;
03709                                 b += t * rawp[i];
03710                         }
03711                 }
03712         }
03713         else {
03714                         for (size_t i = 0; i < size; i++) {
03715                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03716                                 count++;
03717                                 sum_x += refp[i];
03718                                 sum_y += rawp[i];
03719                         }
03720                 }
03721 
03722                 sum_x_mean = sum_x / count;
03723                 sum_tt = 0;
03724                 b = 0;
03725 
03726                 float t;
03727                 for (size_t i = 0; i < size; i++) {
03728                         if (refp[i] >= low_threshold && refp[i] <= high_threshold) {
03729                                 t = refp[i] - sum_x_mean;
03730                                 sum_tt += t * t;
03731                                 b += t * rawp[i];
03732                         }
03733                 }
03734         }
03735 
03736         b /= sum_tt;
03737 
03738         float a = (sum_y - sum_x * b) / count;
03739         float scale = 1 / b;
03740         float shift = -a / b;
03741 
03742         for (size_t i = 0; i < size; i++) {
03743                 rawp[i] = (rawp[i] - a) / b;
03744         }
03745 
03746         image->update();
03747 
03748         params["scale"] = scale;
03749         params["shift"] = shift;
03750 
03751         image->set_attr("norm_mult",scale);
03752         image->set_attr("norm_add",shift);
03753 
03754 }


Member Data Documentation

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

Definition at line 148 of file processor.cpp.


The documentation for this class was generated from the following files:
Generated on Thu Dec 9 13:48:07 2010 for EMAN2 by  doxygen 1.3.9.1