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EMAN::BoxStatProcessor Class Reference

BoxStatProcessor files are a kind of neighborhood processors. More...

#include <processor.h>

Inheritance diagram for EMAN::BoxStatProcessor:

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Collaboration diagram for EMAN::BoxStatProcessor:

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List of all members.

Public Member Functions

void process_inplace (EMData *image)
 To process an image in-place.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

string get_group_desc ()
 Get the description of this group of processors.

Protected Member Functions

virtual void process_pixel (float *pixel, const float *array, int n) const =0

Detailed Description

BoxStatProcessor files are a kind of neighborhood processors.

These processors compute every output pixel using information from a reduced region on the neighborhood of the input pixel. The classical form are the 3x3 processors. BoxStatProcessors could perform diverse tasks ranging from noise reduction, to differential , to mathematical morphology. BoxStatProcessor class is the base class. Specific BoxStatProcessor needs to define process_pixel(float *pixel, const float *array, int n).

Parameters:
radius The radius of the search box, default is 1 which results in a 3x3 box (3 = 2xradius + 1)

Definition at line 2943 of file processor.h.


Member Function Documentation

string EMAN::BoxStatProcessor::get_group_desc  )  [inline, static]
 

Get the description of this group of processors.

This function is defined in a parent class. It gives a introduction to a group of processors.

Returns:
The description of this group of processors.

Reimplemented from EMAN::Processor.

Definition at line 2948 of file processor.h.

02949                 {
02950                         return "BoxStatProcessor files are a kind of neighborhood processors. These processors compute every output pixel using information from a reduced region on the neighborhood of the input pixel. The classical form are the 3x3 processors. BoxStatProcessors could perform diverse tasks ranging from noise reduction, to differential , to mathematical morphology. BoxStatProcessor class is the base class. Specific BoxStatProcessor needs to define process_pixel(float *pixel, const float *array, int n).";
02951                 }

TypeDict EMAN::BoxStatProcessor::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.

Reimplemented in EMAN::PeakOnlyProcessor.

Definition at line 2953 of file processor.h.

References EMAN::TypeDict::put().

02954                 {
02955                         TypeDict d;
02956                         d.put("radius", EMObject::INT, "The radius of the search box, default is 1 which results in a 3x3 box (3 = 2xradius + 1)");
02957                         return d;
02958                 }

void BoxStatProcessor::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 1729 of file processor.cpp.

References data, EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), LOGWARN, nx, ny, process_pixel(), EMAN::Dict::set_default(), and EMAN::EMData::update().

01730 {
01731         if (!image) {
01732                 LOGWARN("NULL Image");
01733                 return;
01734         }
01735 
01736         int nx = image->get_xsize();
01737         int ny = image->get_ysize();
01738         int nz = image->get_zsize();
01739 
01740         int n = params.set_default("radius",1);
01741         int areasize = 2 * n + 1;
01742 
01743         int matrix_size = areasize * areasize;
01744         if (nz > 1) {
01745                 matrix_size *= areasize;
01746         }
01747 
01748         float *array = new float[matrix_size];
01749 //      image->process_inplace("normalize");
01750 
01751         float *data = image->get_data();
01752         size_t total_size = (size_t)nx * (size_t)ny * (size_t)nz;
01753         float *data2 = new float[total_size];
01754         memcpy(data2, data, total_size * sizeof(float));
01755 
01756         int z_begin = 0;
01757         int z_end = 1;
01758         int nzz=0;
01759         if (nz > 1) {
01760                 z_begin = n;
01761                 z_end = nz - n;
01762                 nzz=n;
01763         }
01764 
01765         int nxy = nx * ny;
01766 
01767         for (int k = z_begin; k < z_end; k++) {
01768                 size_t knxy = (size_t)k * nxy;
01769 
01770                 for (int j = n; j < ny - n; j++) {
01771                         int jnx = j * nx;
01772 
01773                         for (int i = n; i < nx - n; i++) {
01774                                 size_t s = 0;
01775 
01776                                 for (int i2 = i - n; i2 <= i + n; i2++) {
01777                                         for (int j2 = j - n; j2 <= j + n; j2++) {
01778                                                 for (int k2 = k - nzz; k2 <= k + nzz; k2++) {
01779                                                         array[s] = data2[i2 + j2 * nx + (size_t)k2 * nxy];
01780                                                         ++s;
01781                                                 }
01782                                         }
01783                                 }
01784 
01785                                 process_pixel(&data[i + jnx + knxy], array, matrix_size);
01786                         }
01787                 }
01788         }
01789 
01790         image->update();
01791 
01792         if( data2 )
01793         {
01794                 delete[]data2;
01795                 data2 = 0;
01796         }
01797 }

virtual void EMAN::BoxStatProcessor::process_pixel float *  pixel,
const float *  array,
int  n
const [protected, pure virtual]
 

Implemented in EMAN::BoxMedianProcessor, EMAN::BoxSigmaProcessor, EMAN::BoxMaxProcessor, EMAN::MinusPeakProcessor, and EMAN::PeakOnlyProcessor.

Referenced by process_inplace().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:52:06 2011 for EMAN2 by  doxygen 1.3.9.1