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

static ProcessorNEW ()

Static Public Attributes

static 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 3579 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 3593 of file processor.h.

03594                 {
03595                         return "Remove gradient by least square plane fit";
03596                 }

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 3584 of file processor.h.

References NAME.

Referenced by process_inplace().

03585                 {
03586                         return NAME;
03587                 }

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 3598 of file processor.h.

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

03599                 {
03600                         TypeDict d;
03601                         d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0");
03602                         d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0");
03603                         d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output");
03604                         return d;
03605                 }

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

Definition at line 3588 of file processor.h.

03589                 {
03590                         return new GradientPlaneRemoverProcessor();
03591                 }

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 2740 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, EMAN::Processor::params, EMAN::EMData::update(), and V.

02741 {
02742         if (!image) {
02743                 LOGWARN("NULL Image");
02744                 return;
02745         }
02746 
02747         int nz = image->get_zsize();
02748         if (nz > 1) {
02749                 LOGERR("%s Processor doesn't support 3D model", get_name().c_str());
02750                 throw ImageDimensionException("3D map not supported");
02751         }
02752 
02753         int nx = image->get_xsize();
02754         int ny = image->get_ysize();
02755         float *d = image->get_data();
02756         EMData *mask = 0;
02757         float *dm = 0;
02758         if (params.has_key("mask")) {
02759                 mask = params["mask"];
02760                 if (nx!=mask->get_xsize() || ny!=mask->get_ysize()) {
02761                         LOGERR("%s Processor requires same size mask image", get_name().c_str());
02762                         throw ImageDimensionException("wrong size mask image");
02763                 }
02764                 dm = mask->get_data();
02765         }
02766         int count = 0;
02767         if (dm) {
02768                 for(int i=0; i<nx*ny; i++) {
02769                         if(dm[i]) count++;
02770                 }
02771         }
02772         else {
02773                 count = nx * ny;
02774         }
02775         if(count<3) {
02776                 LOGERR("%s Processor requires at least 3 pixels to fit a plane", get_name().c_str());
02777                 throw ImageDimensionException("too few usable pixels to fit a plane");
02778         }
02779         // Allocate the working space
02780         gsl_vector *S=gsl_vector_calloc(3);
02781         gsl_matrix *A=gsl_matrix_calloc(count,3);
02782         gsl_matrix *V=gsl_matrix_calloc(3,3);
02783 
02784         double m[3] = {0, 0, 0};
02785         int index=0;
02786         if (dm) {
02787                 for(int j=0; j<ny; j++){
02788                         for(int i=0; i<nx; i++){
02789                                 int ij=j*nx+i;
02790                                 if(dm[ij]) {
02791                                         m[0]+=i;        // x
02792                                         m[1]+=j;        // y
02793                                         m[2]+=d[ij];    // z
02794                                         /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
02795                                                 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
02796                                         index++;
02797                                 }
02798                         }
02799                 }
02800         }
02801         else {
02802                 for(int j=0; j<ny; j++){
02803                         for(int i=0; i<nx; i++){
02804                                 int ij=j*nx+i;
02805                                         m[0]+=i;        // x
02806                                         m[1]+=j;        // y
02807                                         m[2]+=d[ij];    // z
02808                                         /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \
02809                                                 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/
02810                                         index++;
02811                         }
02812                 }
02813         }
02814 
02815         for(int i=0; i<3; i++) m[i]/=count;     // compute center of the plane
02816 
02817         index=0;
02818         if (dm) {
02819                 for(int j=0; j<ny; j++){
02820                         for(int i=0; i<nx; i++){
02821                                 int ij=j*nx+i;
02822                                 if(dm[ij]) {
02823                                         //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
02824                                         gsl_matrix_set(A,index,0,i-m[0]);
02825                                         gsl_matrix_set(A,index,1,j-m[1]);
02826                                         gsl_matrix_set(A,index,2,d[ij]-m[2]);
02827                                         index++;
02828                                 }
02829                         }
02830                 }
02831                 mask->update();
02832         }
02833         else {
02834                 for(int j=0; j<ny; j++){
02835                         for(int i=0; i<nx; i++){
02836                                 int ij=j*nx+i;
02837                                         //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]);
02838                                         gsl_matrix_set(A,index,0,i-m[0]);
02839                                         gsl_matrix_set(A,index,1,j-m[1]);
02840                                         gsl_matrix_set(A,index,2,d[ij]-m[2]);
02841                                         index++;
02842                         }
02843                 }
02844         }
02845 
02846         // SVD decomposition and use the V vector associated with smallest singular value as the plan normal
02847         gsl_linalg_SV_decomp_jacobi(A, V, S);
02848 
02849         double n[3];
02850         for(int i=0; i<3; i++) n[i] = gsl_matrix_get(V, i, 2);
02851 
02852         #ifdef DEBUG
02853         printf("S=%g,%g,%g\n",gsl_vector_get(S,0), gsl_vector_get(S,1), gsl_vector_get(S,2));
02854         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));
02855         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));
02856         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));
02857         printf("Fitted plane: p0=%g,%g,%g\tn=%g,%g,%g\n",m[0],m[1],m[2],n[0],n[1],n[2]);
02858         #endif
02859 
02860         int changeZero = 0;
02861         if (params.has_key("changeZero")) changeZero = params["changeZero"];
02862         if (changeZero) {
02863                 for(int j=0; j<nx; j++){
02864                         for(int i=0; i<ny; i++){
02865                                 int ij = j*nx+i;
02866                                 d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
02867                         }
02868                 }
02869         }
02870         else {
02871                 for(int j=0; j<nx; j++){
02872                         for(int i=0; i<ny; i++){
02873                                 int ij = j*nx+i;
02874                                 if(d[ij]) d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]);
02875                         }
02876                 }
02877         }
02878         image->update();
02879         // set return plane parameters
02880         vector< float > planeParam;
02881         planeParam.resize(6);
02882         for(int i=0; i<3; i++) planeParam[i] = static_cast<float>(n[i]);
02883         for(int i=0; i<3; i++) planeParam[i+3] = static_cast<float>(m[i]);
02884         params["planeParam"]=EMObject(planeParam);
02885 }


Member Data Documentation

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

Definition at line 3607 of file processor.h.

Referenced by get_name().


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