EMAN::SymSearchProcessor Class Reference

Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel. More...

#include <processor.h>

Inheritance diagram for EMAN::SymSearchProcessor:

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Collaboration diagram for EMAN::SymSearchProcessor:

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List of all members.

Public Member Functions

virtual void process_inplace (EMData *image)
 To process an image in-place.
virtual string get_name () const
 Get the processor's name.
virtual string get_desc () const
 Get the descrition of this specific processor.
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 = "misc.symsearch"

Detailed Description

Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel.

Author:
Wen Jiang <wjiang@bcm.tmc.edu>
Date:
2005-1-9
Parameters:
sym[in] the list of symmetries to search
thresh[in] the minimal level of symmetry to be accepted (0-1)
output_symlabel[in] if output the symmetry label map in which the pixel value is the index of symmetry in the symmetry list
symlabel_map[out] the optional return map when output_symlabel=1

Definition at line 5192 of file processor.h.


Member Function Documentation

virtual string EMAN::SymSearchProcessor::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 5202 of file processor.h.

05203                 {
05204                         return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel.";
05205                 }

virtual string EMAN::SymSearchProcessor::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 5197 of file processor.h.

References NAME.

05198                 {
05199                         return NAME;
05200                 }

virtual TypeDict EMAN::SymSearchProcessor::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 5212 of file processor.h.

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

05213                 {
05214                         TypeDict d;
05215                         d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search");
05216                         d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)");
05217                         d.put("output_symlabel", EMObject::INT, "if output the symmetry label map in which the pixel value is the index of symmetry in the symmetry list");
05218                         d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1");
05219                         return d;
05220                 }

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

Definition at line 5207 of file processor.h.

05208                 {
05209                         return new SymSearchProcessor();
05210                 }

void SymSearchProcessor::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 5848 of file processor.cpp.

References EMAN::EMData::copy(), EMAN::Util::fast_floor(), EMAN::EMData::get_data(), EMAN::Symmetry3D::get_symmetries(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), LOGWARN, EMAN::Processor::params, EMAN::Dict::put(), EMAN::Dict::size(), t, EMAN::EMData::to_zero(), EMAN::Util::trilinear_interpolate(), v, and x.

05849 {
05850         if (!image) {
05851                 LOGWARN("NULL Image");
05852                 return;
05853         }
05854         float thresh = params["thresh"];
05855         int output_symlabel = params["output_symlabel"];
05856 
05857         // set up all the symmetry transforms for all the searched symmetries
05858         const vector<string> sym_list = params["sym"];
05859         int sym_num = sym_list.size();
05860         vector< vector< Transform > > transforms(sym_num);
05861         vector< float* > symvals(sym_num);
05862         for (int i =0; i < sym_num; i++) {
05863                 vector<Transform> sym_transform =  Symmetry3D::get_symmetries(sym_list[i]);
05864                 transforms[i] = sym_transform;
05865                 symvals[i] = new float[sym_transform.size()]; // new float(nsym);
05866         }
05867 
05868         EMData *orig = image->copy();
05869 
05870         image->to_zero();
05871 
05872         int nx= image->get_xsize();
05873         int ny= image->get_ysize();
05874         int nz= image->get_zsize();
05875         int xy = nx * ny;
05876         float * data = image->get_data();
05877         float * sdata = orig->get_data();
05878 
05879         EMData *symlabel = 0;
05880         float * ldata = symlabel->get_data();
05881         if (output_symlabel) {
05882                 symlabel = image->copy();
05883                 symlabel->to_zero();
05884                 ldata = symlabel->get_data();
05885         }
05886 
05887         for (int k = 0; k < nz; k++) {
05888                 for (int j = 0; j < ny; j++) {
05889                         for(int i = 0; i < nx; i++) {
05890                                 size_t index = (size_t)k * nx * ny + j * nx + i;
05891                                 float val = sdata[ index ];
05892                                 float bestmean = val, bestsymlevel = FLT_MAX;
05893                                 int bestsym = 0;
05894                                 for( int sym = 0; sym< sym_num; sym++) {
05895                                         int cur_sym_num = transforms[sym].size();
05896                                         float *symval = symvals[sym];
05897                                         // first find out all the symmetry related location values
05898                                         for( int s = 0; s < cur_sym_num; s++){
05899                                                 Transform r = transforms[sym][s];
05900                                                 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2);
05901                                                 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2);
05902                                                 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2);
05903 
05904                                                 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1)
05905                                                         && z2 < (nz - 1)) {
05906                                                         float x = (float)Util::fast_floor(x2);
05907                                                         float y = (float)Util::fast_floor(y2);
05908                                                         float z = (float)Util::fast_floor(z2);
05909 
05910                                                         float t = x2 - x;
05911                                                         float u = y2 - y;
05912                                                         float v = z2 - z;
05913 
05914                                                         size_t ii = x + y * nx + z * (size_t)xy;
05915 
05916                                                         symval[s]=
05917                                                                 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],
05918                                                                                                                         sdata[ii + nx + 1], sdata[ii + nx * ny],
05919                                                                                                                         sdata[ii + xy + 1], sdata[ii + xy + nx],
05920                                                                                                                         sdata[ii + xy + nx + 1], t, u, v);
05921                                                 }
05922                                                 else {
05923                                                         symval[s] = 0.0 ;
05924                                                 }
05925                                         }
05926                                         float tmean=0, tsigma=0;
05927                                         for( int s = 0; s < cur_sym_num; s++) {
05928                                                 tmean += symval[s];
05929                                                 tsigma += symval[s] * symval[s];
05930                                         }
05931                                         tmean /= cur_sym_num;
05932                                         tsigma = tsigma/cur_sym_num - tmean*tmean;
05933                                         if (tsigma < bestsymlevel ) {
05934                                                 bestsymlevel = tsigma;
05935                                                 bestmean = tmean;
05936                                                 bestsym = sym;
05937                                         }
05938                                 }
05939                                 if ( bestsymlevel > thresh) {
05940                                         if (output_symlabel) ldata[index] = (float)bestsym;
05941                                         data[index] = bestmean;
05942                                 }
05943                                 else {
05944                                         if (output_symlabel) ldata[index] = -1;
05945                                         data[index] = val;
05946                                 }
05947                         }
05948                 }
05949         }
05950         if( orig )
05951         {
05952                 delete orig;
05953                 orig = 0;
05954         }
05955         for (int i =0; i < sym_num; i++) {
05956                 if( symvals[i] )
05957                 {
05958                         delete symvals[i];
05959                         symvals[i] = 0;
05960                 }
05961         }
05962         if (symlabel) params.put("symlabel_map", EMObject(symlabel));
05963 }


Member Data Documentation

const string SymSearchProcessor::NAME = "misc.symsearch" [static]

Definition at line 5222 of file processor.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
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