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EMAN::GradientPlaneRemoverProcessor Class Reference

Gradient removed by least square plane fit. More...

#include <processor.h>

Inheritance diagram for EMAN::GradientPlaneRemoverProcessor:

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Collaboration diagram for EMAN::GradientPlaneRemoverProcessor:
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List of all members.

Public Member Functions

void process_inplace (EMData *image)
 To process an image in-place.
string get_name () const
 Get the processor's name.
string get_desc () const
 Get the descrition of this specific processor.
TypeDict get_param_types () const
 Get processor parameter information in a dictionary.

Static Public Member Functions

ProcessorNEW ()

Static Public Attributes

const string NAME = "filter.gradientPlaneRemover"

Detailed Description

Gradient removed by least square plane fit.

Parameters:
mask[in] optional EMData object to mask the pixels used to fit the plane
changeZero[in] optional bool to specify if the zero value pixels are modified
planeParam[out] optional return parameters [nx, ny, nz, cx, cy, cz] for the fitted plane defined as (x-cx)*nx+(y-cy)*ny+(z-cz)*nz=0
Author:
Wen Jiang
Date:
2006/7/18

Definition at line 3614 of file processor.h.


Member Function Documentation

string EMAN::GradientPlaneRemoverProcessor::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 3628 of file processor.h.

03629                 {
03630                         return "Remove gradient by least square plane fit";
03631                 }

string EMAN::GradientPlaneRemoverProcessor::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 3619 of file processor.h.

Referenced by process_inplace().

03620                 {
03621                         return NAME;
03622                 }

TypeDict EMAN::GradientPlaneRemoverProcessor::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 3633 of file processor.h.

References EMAN::TypeDict::put().

03634                 {
03635                         TypeDict d;
03636                         d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0");
03637                         d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0");
03638                         d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output");
03639                         return d;
03640                 }

Processor* EMAN::GradientPlaneRemoverProcessor::NEW  )  [inline, static]
 

Definition at line 3623 of file processor.h.

03624                 {
03625                         return new GradientPlaneRemoverProcessor();
03626                 }

void GradientPlaneRemoverProcessor::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 2693 of file processor.cpp.

References dm, EMAN::EMData::get_data(), get_name(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), ImageDimensionException, LOGERR, LOGWARN, nx, ny, EMAN::EMData::update(), and V.

02694 {
02695         if (!image) {
02696                 LOGWARN("NULL Image");
02697                 return;
02698         }
02699 
02700         int nz = image->get_zsize();
02701         if (nz > 1) {
02702                 LOGERR("%s Processor doesn't support 3D model", get_name().c_str());
02703                 throw ImageDimensionException("3D map not supported");
02704         }
02705 
02706         int nx = image->get_xsize();
02707         int ny = image->get_ysize();
02708         float *d = image->get_data();
02709         EMData *mask = 0;
02710         float *dm = 0;
02711         if (params.has_key("mask")) {
02712                 mask = params["mask"];
02713                 if (nx!=mask->get_xsize() || ny!=mask->get_ysize()) {
02714                         LOGERR("%s Processor requires same size mask image", get_name().c_str());
02715                         throw ImageDimensionException("wrong size mask image");
02716                 }
02717                 dm = mask->get_data();
02718         }
02719         int count = 0;
02720         if (dm) {
02721                 for(int i=0; i<nx*ny; i++) {
02722                         if(dm[i]) count++;
02723                 }
02724         }
02725         else {
02726                 count = nx * ny;
02727         }
02728         if(count<3) {
02729                 LOGERR("%s Processor requires at least 3 pixels to fit a plane", get_name().c_str());
02730                 throw ImageDimensionException("too few usable pixels to fit a plane");
02731         }
02732         // Allocate the working space
02733         gsl_vector *S=gsl_vector_calloc(3);
02734         gsl_matrix *A=gsl_matrix_calloc(count,3);
02735         gsl_matrix *V=gsl_matrix_calloc(3,3);
02736 
02737         double m[3] = {0, 0, 0};
02738         int index=0;
02739         if (dm) {
02740                 for(int j=0; j<ny; j++){
02741                         for(int i=0; i<nx; i++){
02742                                 int ij=j*nx+i;
02743                                 if(dm[ij]) {
02744                                         m[0]+=i;        // x
02745                                         m[1]+=j;        // y
02746                                         m[2]+=d[ij];    // z
02747                                         /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
02748                                                 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
02749                                         index++;
02750                                 }
02751                         }
02752                 }
02753         }
02754         else {
02755                 for(int j=0; j<ny; j++){
02756                         for(int i=0; i<nx; i++){
02757                                 int ij=j*nx+i;
02758                                         m[0]+=i;        // x
02759                                         m[1]+=j;        // y
02760                                         m[2]+=d[ij];    // z
02761                                         /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
02762                                                 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
02763                                         index++;
02764                         }
02765                 }
02766         }
02767 
02768         for(int i=0; i<3; i++) m[i]/=count;     // compute center of the plane
02769 
02770         index=0;
02771         if (dm) {
02772                 for(int j=0; j<ny; j++){
02773                         for(int i=0; i<nx; i++){
02774                                 int ij=j*nx+i;
02775                                 if(dm[ij]) {
02776                                         //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
02777                                         gsl_matrix_set(A,index,0,i-m[0]);
02778                                         gsl_matrix_set(A,index,1,j-m[1]);
02779                                         gsl_matrix_set(A,index,2,d[ij]-m[2]);
02780                                         index++;
02781                                 }
02782                         }
02783                 }
02784                 mask->update();
02785         }
02786         else {
02787                 for(int j=0; j<ny; j++){
02788                         for(int i=0; i<nx; i++){
02789                                 int ij=j*nx+i;
02790                                         //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
02791                                         gsl_matrix_set(A,index,0,i-m[0]);
02792                                         gsl_matrix_set(A,index,1,j-m[1]);
02793                                         gsl_matrix_set(A,index,2,d[ij]-m[2]);
02794                                         index++;
02795                         }
02796                 }
02797         }
02798 
02799         // SVD decomposition and use the V vector associated with smallest singular value as the plan normal
02800         gsl_linalg_SV_decomp_jacobi(A, V, S);
02801 
02802         double n[3];
02803         for(int i=0; i<3; i++) n[i] = gsl_matrix_get(V, i, 2);
02804 
02805         #ifdef DEBUG
02806         printf("S=%g,%g,%g\n",gsl_vector_get(S,0), gsl_vector_get(S,1), gsl_vector_get(S,2));
02807         printf("V[0,:]=%g,%g,%g\n",gsl_matrix_get(V,0,0), gsl_matrix_get(V,0,1),gsl_matrix_get(V,0,2));
02808         printf("V[1,:]=%g,%g,%g\n",gsl_matrix_get(V,1,0), gsl_matrix_get(V,1,1),gsl_matrix_get(V,1,2));
02809         printf("V[2,:]=%g,%g,%g\n",gsl_matrix_get(V,2,0), gsl_matrix_get(V,2,1),gsl_matrix_get(V,2,2));
02810         printf("Fitted plane: p0=%g,%g,%g\tn=%g,%g,%g\n",m[0],m[1],m[2],n[0],n[1],n[2]);
02811         #endif
02812 
02813         int changeZero = 0;
02814         if (params.has_key("changeZero")) changeZero = params["changeZero"];
02815         if (changeZero) {
02816                 for(int j=0; j<nx; j++){
02817                         for(int i=0; i<ny; i++){
02818                                 int ij = j*nx+i;
02819                                 d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
02820                         }
02821                 }
02822         }
02823         else {
02824                 for(int j=0; j<nx; j++){
02825                         for(int i=0; i<ny; i++){
02826                                 int ij = j*nx+i;
02827                                 if(d[ij]) d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
02828                         }
02829                 }
02830         }
02831         image->update();
02832         // set return plane parameters
02833         vector< float > planeParam;
02834         planeParam.resize(6);
02835         for(int i=0; i<3; i++) planeParam[i] = static_cast<float>(n[i]);
02836         for(int i=0; i<3; i++) planeParam[i+3] = static_cast<float>(m[i]);
02837         params["planeParam"]=EMObject(planeParam);
02838 }


Member Data Documentation

const string GradientPlaneRemoverProcessor::NAME = "filter.gradientPlaneRemover" [static]
 

Definition at line 129 of file processor.cpp.


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