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 5310 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 5320 of file processor.h.

05321                 {
05322                         return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel.";
05323                 }

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 5315 of file processor.h.

References NAME.

05316                 {
05317                         return NAME;
05318                 }

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 5330 of file processor.h.

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

05331                 {
05332                         TypeDict d;
05333                         d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search");
05334                         d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)");
05335                         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");
05336                         d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1");
05337                         return d;
05338                 }

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

Definition at line 5325 of file processor.h.

05326                 {
05327                         return new SymSearchProcessor();
05328                 }

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 6103 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.

06104 {
06105         if (!image) {
06106                 LOGWARN("NULL Image");
06107                 return;
06108         }
06109         float thresh = params["thresh"];
06110         int output_symlabel = params["output_symlabel"];
06111 
06112         // set up all the symmetry transforms for all the searched symmetries
06113         const vector<string> sym_list = params["sym"];
06114         int sym_num = sym_list.size();
06115         vector< vector< Transform > > transforms(sym_num);
06116         vector< float* > symvals(sym_num);
06117         for (int i =0; i < sym_num; i++) {
06118                 vector<Transform> sym_transform =  Symmetry3D::get_symmetries(sym_list[i]);
06119                 transforms[i] = sym_transform;
06120                 symvals[i] = new float[sym_transform.size()]; // new float(nsym);
06121         }
06122 
06123         EMData *orig = image->copy();
06124 
06125         image->to_zero();
06126 
06127         int nx= image->get_xsize();
06128         int ny= image->get_ysize();
06129         int nz= image->get_zsize();
06130         int xy = nx * ny;
06131         float * data = image->get_data();
06132         float * sdata = orig->get_data();
06133 
06134         EMData *symlabel = 0;
06135         float * ldata = symlabel->get_data();
06136         if (output_symlabel) {
06137                 symlabel = image->copy();
06138                 symlabel->to_zero();
06139                 ldata = symlabel->get_data();
06140         }
06141 
06142         for (int k = 0; k < nz; k++) {
06143                 for (int j = 0; j < ny; j++) {
06144                         for(int i = 0; i < nx; i++) {
06145                                 size_t index = (size_t)k * nx * ny + j * nx + i;
06146                                 float val = sdata[ index ];
06147                                 float bestmean = val, bestsymlevel = FLT_MAX;
06148                                 int bestsym = 0;
06149                                 for( int sym = 0; sym< sym_num; sym++) {
06150                                         int cur_sym_num = transforms[sym].size();
06151                                         float *symval = symvals[sym];
06152                                         // first find out all the symmetry related location values
06153                                         for( int s = 0; s < cur_sym_num; s++){
06154                                                 Transform r = transforms[sym][s];
06155                                                 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2);
06156                                                 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2);
06157                                                 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2);
06158 
06159                                                 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1)
06160                                                         && z2 < (nz - 1)) {
06161                                                         float x = (float)Util::fast_floor(x2);
06162                                                         float y = (float)Util::fast_floor(y2);
06163                                                         float z = (float)Util::fast_floor(z2);
06164 
06165                                                         float t = x2 - x;
06166                                                         float u = y2 - y;
06167                                                         float v = z2 - z;
06168 
06169                                                         size_t ii = x + y * nx + z * (size_t)xy;
06170 
06171                                                         symval[s]=
06172                                                                 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],
06173                                                                                                                         sdata[ii + nx + 1], sdata[ii + nx * ny],
06174                                                                                                                         sdata[ii + xy + 1], sdata[ii + xy + nx],
06175                                                                                                                         sdata[ii + xy + nx + 1], t, u, v);
06176                                                 }
06177                                                 else {
06178                                                         symval[s] = 0.0 ;
06179                                                 }
06180                                         }
06181                                         float tmean=0, tsigma=0;
06182                                         for( int s = 0; s < cur_sym_num; s++) {
06183                                                 tmean += symval[s];
06184                                                 tsigma += symval[s] * symval[s];
06185                                         }
06186                                         tmean /= cur_sym_num;
06187                                         tsigma = tsigma/cur_sym_num - tmean*tmean;
06188                                         if (tsigma < bestsymlevel ) {
06189                                                 bestsymlevel = tsigma;
06190                                                 bestmean = tmean;
06191                                                 bestsym = sym;
06192                                         }
06193                                 }
06194                                 if ( bestsymlevel > thresh) {
06195                                         if (output_symlabel) ldata[index] = (float)bestsym;
06196                                         data[index] = bestmean;
06197                                 }
06198                                 else {
06199                                         if (output_symlabel) ldata[index] = -1;
06200                                         data[index] = val;
06201                                 }
06202                         }
06203                 }
06204         }
06205         if( orig )
06206         {
06207                 delete orig;
06208                 orig = 0;
06209         }
06210         for (int i =0; i < sym_num; i++) {
06211                 if( symvals[i] )
06212                 {
06213                         delete symvals[i];
06214                         symvals[i] = 0;
06215                 }
06216         }
06217         if (symlabel) params.put("symlabel_map", EMObject(symlabel));
06218 }


Member Data Documentation

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

Definition at line 5340 of file processor.h.

Referenced by get_name().


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