EMAN::MedianShrinkProcessor Class Reference

MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood. More...

#include <processor.h>

Inheritance diagram for EMAN::MedianShrinkProcessor:

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

Collaboration graph
[legend]
List of all members.

Public Member Functions

virtual EMDataprocess (const EMData *const image)
 The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function.
virtual void process_inplace (EMData *image)
 Median shrink the image.
string get_desc () const
 Get the descrition of this specific processor.
virtual string get_name () const
 Get the processor's name.
virtual TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

static ProcessorNEW ()

Static Public Attributes

static const string NAME = "math.medianshrink"

Private Member Functions

void accrue_median (EMData *to, const EMData *const from, const int shrink_factor)
 Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace.

Detailed Description

MeanShrinkProcessor shrinks an image by in an integer amount taking the median of the pixel neighbourhood.

Author:
David Woolford (But is basically a copy of the old EMData::median_shrink, probably written by Steven Ludtke )
Date:
May 2008
Parameters:
n The shrink factor

Definition at line 3515 of file processor.h.


Member Function Documentation

void MedianShrinkProcessor::accrue_median ( EMData to,
const EMData *const   from,
const int  shrink_factor 
) [private]

Accrue the local median in the image 'from' to the image 'to' using the given shrinkfactor An internal function that encapsulates a routine common to both process and process inplace.

Parameters:
to the smaller image that will store the calculated median values
from the larger image that will be used to calculate the median values
shrink_factor the shrink amount

Definition at line 2036 of file processor.cpp.

References EMAN::EMData::get_const_data(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), rdata, and EMAN::EMData::scale_pixel().

Referenced by process(), and process_inplace().

02037 {
02038 
02039         int nx_old = from->get_xsize();
02040         int ny_old = from->get_ysize();
02041 
02042         int threed_shrink_factor = shrink_factor * shrink_factor;
02043         int z_shrink_factor = 1;
02044         if (from->get_zsize() > 1) {
02045                 threed_shrink_factor *= shrink_factor;
02046                 z_shrink_factor = shrink_factor;
02047         }
02048 
02049         float *mbuf = new float[threed_shrink_factor];
02050 
02051 
02052         int nxy_old = nx_old * ny_old;
02053 
02054         int nx = to->get_xsize();
02055         int ny = to->get_ysize();
02056         int nz = to->get_zsize();
02057         int nxy_new = nx * ny;
02058 
02059         float * rdata = to->get_data();
02060         const float *const data_copy = from->get_const_data();
02061 
02062         for (int l = 0; l < nz; l++) {
02063                 int l_min = l * shrink_factor;
02064                 int l_max = l * shrink_factor + z_shrink_factor;
02065                 int cur_l = l * nxy_new;
02066 
02067                 for (int j = 0; j < ny; j++) {
02068                         int j_min = j * shrink_factor;
02069                         int j_max = (j + 1) * shrink_factor;
02070                         int cur_j = j * nx + cur_l;
02071 
02072                         for (int i = 0; i < nx; i++) {
02073                                 int i_min = i * shrink_factor;
02074                                 int i_max = (i + 1) * shrink_factor;
02075 
02076                                 int k = 0;
02077                                 for (int l2 = l_min; l2 < l_max; l2++) {
02078                                         int cur_l2 = l2 * nxy_old;
02079 
02080                                         for (int j2 = j_min; j2 < j_max; j2++) {
02081                                                 int cur_j2 = j2 * nx_old + cur_l2;
02082 
02083                                                 for (int i2 = i_min; i2 < i_max; i2++) {
02084                                                         mbuf[k] = data_copy[i2 + cur_j2];
02085                                                         ++k;
02086                                                 }
02087                                         }
02088                                 }
02089 
02090                                 for (k = 0; k < threed_shrink_factor / 2 + 1; k++) {
02091                                         for (int i2 = k + 1; i2 < threed_shrink_factor; i2++) {
02092                                                 if (mbuf[i2] < mbuf[k]) {
02093                                                         float f = mbuf[i2];
02094                                                         mbuf[i2] = mbuf[k];
02095                                                         mbuf[k] = f;
02096                                                 }
02097                                         }
02098                                 }
02099 
02100                                 rdata[i + cur_j] = mbuf[threed_shrink_factor / 2];
02101                         }
02102                 }
02103         }
02104 
02105         if( mbuf )
02106         {
02107                 delete[]mbuf;
02108                 mbuf = 0;
02109         }
02110 
02111         to->scale_pixel((float)shrink_factor);
02112 }

string EMAN::MedianShrinkProcessor::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 3538 of file processor.h.

03539                 {
03540                         return "Shrink an image by a given amount , using the median value found in the pixel neighborhood.";
03541                 }

virtual string EMAN::MedianShrinkProcessor::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 3543 of file processor.h.

References NAME.

03544                 {
03545                         return NAME;
03546                 }

virtual TypeDict EMAN::MedianShrinkProcessor::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 3552 of file processor.h.

References EMAN::EMObject::INT, and EMAN::TypeDict::put().

03553                 {
03554                         TypeDict d;
03555                         d.put("n", EMObject::INT, "The shrink factor");
03556                         return d;
03557                 }

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

Definition at line 3547 of file processor.h.

03548                 {
03549                         return new MedianShrinkProcessor();
03550                 }

EMData * MedianShrinkProcessor::process ( const EMData *const   image  )  [virtual]

The medianshrink processor has its own process function to minise memory usage - if this function was not over written the base Processor class would create copy of the input image and hand it to the process_inplace function.

This latter approach mallocs and copies more memory than necessary

Parameters:
image the image that will be used to generate a 'median shrunken' image
Exceptions:
ImageFormatException if the image is complex
InvalidValueException if the shrink amount is not a non zero, positive integer
InvalidValueException if any of the image dimensions are not divisible by the the shrink amount

Reimplemented from EMAN::Processor.

Definition at line 2003 of file processor.cpp.

References accrue_median(), EMAN::EMData::copy_head(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update().

02004 {
02005         if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
02006 
02007         int shrink_factor =  params.set_default("n",0);
02008         if (shrink_factor <= 1) {
02009                 throw InvalidValueException(shrink_factor,
02010                                                                         "median shrink: shrink factor must > 1");
02011         }
02012         int nx = image->get_xsize();
02013         int ny = image->get_ysize();
02014         int nz = image->get_zsize();
02015 
02016 
02017 //      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
02018 //              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
02019 //      }
02020 
02021 
02022         int shrunken_nx = nx / shrink_factor;
02023         int shrunken_ny = ny / shrink_factor;
02024         int shrunken_nz = 1;
02025         if (nz > 1) shrunken_nz = nz / shrink_factor;
02026 
02027 //      EMData* ret = new EMData(shrunken_nx, shrunken_ny, shrunken_nz);
02028         EMData *ret = image->copy_head();
02029         ret->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
02030 
02031         accrue_median(ret,image,shrink_factor);
02032         ret->update();
02033         return ret;
02034 }

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

Median shrink the image.

Parameters:
image the image the image that will be 'median shrunken' inplace
Exceptions:
ImageFormatException if the image is complex
InvalidValueException if the shrink amount is not a non zero, positive integer
InvalidValueException if any of the image dimensions are not divisible by the the shrink amount

Implements EMAN::Processor.

Definition at line 1967 of file processor.cpp.

References accrue_median(), EMAN::EMData::copy(), copy(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), ImageFormatException, InvalidValueException, EMAN::EMData::is_complex(), EMAN::Processor::params, EMAN::Dict::set_default(), EMAN::EMData::set_size(), and EMAN::EMData::update().

01968 {
01969         if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
01970 
01971         int shrink_factor =  params.set_default("n",0);
01972         if (shrink_factor <= 1) {
01973                 throw InvalidValueException(shrink_factor,
01974                                                                         "median shrink: shrink factor must > 1");
01975         }
01976 
01977         int nx = image->get_xsize();
01978         int ny = image->get_ysize();
01979         int nz = image->get_zsize();
01980 
01981 //      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
01982 //              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
01983 //      }
01984 
01985 
01986         int shrunken_nx = nx / shrink_factor;
01987         int shrunken_ny = ny / shrink_factor;
01988         int shrunken_nz = 1;
01989         if (nz > 1) shrunken_nz = nz / shrink_factor;
01990 
01991         EMData* copy = image->copy();
01992         image->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
01993         accrue_median(image,copy,shrink_factor);
01994         image->update();
01995         if( copy )
01996         {
01997                 delete copy;
01998                 copy = 0;
01999         }
02000 }


Member Data Documentation

const string MedianShrinkProcessor::NAME = "math.medianshrink" [static]

Definition at line 3559 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Mon Jul 19 12:43:32 2010 for EMAN2 by  doxygen 1.4.7