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:

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Collaboration diagram for EMAN::MedianShrinkProcessor:

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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 3521 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 2017 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().

02018 {
02019 
02020         int nx_old = from->get_xsize();
02021         int ny_old = from->get_ysize();
02022 
02023         int threed_shrink_factor = shrink_factor * shrink_factor;
02024         int z_shrink_factor = 1;
02025         if (from->get_zsize() > 1) {
02026                 threed_shrink_factor *= shrink_factor;
02027                 z_shrink_factor = shrink_factor;
02028         }
02029 
02030         float *mbuf = new float[threed_shrink_factor];
02031 
02032 
02033         int nxy_old = nx_old * ny_old;
02034 
02035         int nx = to->get_xsize();
02036         int ny = to->get_ysize();
02037         int nz = to->get_zsize();
02038         int nxy_new = nx * ny;
02039 
02040         float * rdata = to->get_data();
02041         const float *const data_copy = from->get_const_data();
02042 
02043         for (int l = 0; l < nz; l++) {
02044                 int l_min = l * shrink_factor;
02045                 int l_max = l * shrink_factor + z_shrink_factor;
02046                 size_t cur_l = (size_t)l * nxy_new;
02047 
02048                 for (int j = 0; j < ny; j++) {
02049                         int j_min = j * shrink_factor;
02050                         int j_max = (j + 1) * shrink_factor;
02051                         size_t cur_j = j * nx + cur_l;
02052 
02053                         for (int i = 0; i < nx; i++) {
02054                                 int i_min = i * shrink_factor;
02055                                 int i_max = (i + 1) * shrink_factor;
02056 
02057                                 size_t k = 0;
02058                                 for (int l2 = l_min; l2 < l_max; l2++) {
02059                                         size_t cur_l2 = l2 * nxy_old;
02060 
02061                                         for (int j2 = j_min; j2 < j_max; j2++) {
02062                                                 size_t cur_j2 = j2 * nx_old + cur_l2;
02063 
02064                                                 for (int i2 = i_min; i2 < i_max; i2++) {
02065                                                         mbuf[k] = data_copy[i2 + cur_j2];
02066                                                         ++k;
02067                                                 }
02068                                         }
02069                                 }
02070 
02071                                 for (k = 0; k < size_t(threed_shrink_factor / 2 + 1); k++) {
02072                                         for (int i2 = k + 1; i2 < threed_shrink_factor; i2++) {
02073                                                 if (mbuf[i2] < mbuf[k]) {
02074                                                         float f = mbuf[i2];
02075                                                         mbuf[i2] = mbuf[k];
02076                                                         mbuf[k] = f;
02077                                                 }
02078                                         }
02079                                 }
02080 
02081                                 rdata[i + cur_j] = mbuf[threed_shrink_factor / 2];
02082                         }
02083                 }
02084         }
02085 
02086         if( mbuf )
02087         {
02088                 delete[]mbuf;
02089                 mbuf = 0;
02090         }
02091 
02092         to->scale_pixel((float)shrink_factor);
02093 }

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 3544 of file processor.h.

03545                 {
03546                         return "Shrink an image by a given amount , using the median value found in the pixel neighborhood.";
03547                 }

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 3549 of file processor.h.

References NAME.

03550                 {
03551                         return NAME;
03552                 }

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 3558 of file processor.h.

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

03559                 {
03560                         TypeDict d;
03561                         d.put("n", EMObject::INT, "The shrink factor");
03562                         return d;
03563                 }

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

Definition at line 3553 of file processor.h.

03554                 {
03555                         return new MedianShrinkProcessor();
03556                 }

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 1984 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().

01985 {
01986         if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
01987 
01988         int shrink_factor =  params.set_default("n",0);
01989         if (shrink_factor <= 1) {
01990                 throw InvalidValueException(shrink_factor,
01991                                                                         "median shrink: shrink factor must > 1");
01992         }
01993         int nx = image->get_xsize();
01994         int ny = image->get_ysize();
01995         int nz = image->get_zsize();
01996 
01997 
01998 //      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
01999 //              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
02000 //      }
02001 
02002 
02003         int shrunken_nx = nx / shrink_factor;
02004         int shrunken_ny = ny / shrink_factor;
02005         int shrunken_nz = 1;
02006         if (nz > 1) shrunken_nz = nz / shrink_factor;
02007 
02008 //      EMData* ret = new EMData(shrunken_nx, shrunken_ny, shrunken_nz);
02009         EMData *ret = image->copy_head();
02010         ret->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
02011 
02012         accrue_median(ret,image,shrink_factor);
02013         ret->update();
02014         return ret;
02015 }

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 1948 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().

01949 {
01950         if (image->is_complex()) throw ImageFormatException("Error, the median shrink processor does not work on complex images");
01951 
01952         int shrink_factor =  params.set_default("n",0);
01953         if (shrink_factor <= 1) {
01954                 throw InvalidValueException(shrink_factor,
01955                                                                         "median shrink: shrink factor must > 1");
01956         }
01957 
01958         int nx = image->get_xsize();
01959         int ny = image->get_ysize();
01960         int nz = image->get_zsize();
01961 
01962 //      if ((nx % shrink_factor != 0) || (ny % shrink_factor != 0) || (nz > 1 && (nz % shrink_factor != 0))) {
01963 //              throw InvalidValueException(shrink_factor, "Image size not divisible by shrink factor");
01964 //      }
01965 
01966 
01967         int shrunken_nx = nx / shrink_factor;
01968         int shrunken_ny = ny / shrink_factor;
01969         int shrunken_nz = 1;
01970         if (nz > 1) shrunken_nz = nz / shrink_factor;
01971 
01972         EMData* copy = image->copy();
01973         image->set_size(shrunken_nx, shrunken_ny, shrunken_nz);
01974         accrue_median(image,copy,shrink_factor);
01975         image->update();
01976         if( copy )
01977         {
01978                 delete copy;
01979                 copy = 0;
01980         }
01981 }


Member Data Documentation

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

Definition at line 3565 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 12:44:03 2013 for EMAN2 by  doxygen 1.4.7