#include <processor.h>
Inheritance diagram for EMAN::GradientPlaneRemoverProcessor:
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "filter.gradientPlaneRemover" |
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 |
Definition at line 3658 of file processor.h.
string EMAN::GradientPlaneRemoverProcessor::get_desc | ( | ) | const [inline, virtual] |
Get the descrition of this specific processor.
This function must be overwritten by a subclass.
Implements EMAN::Processor.
Definition at line 3672 of file processor.h.
string EMAN::GradientPlaneRemoverProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 3663 of file processor.h.
References NAME.
Referenced by process_inplace().
03664 { 03665 return NAME; 03666 }
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.
Reimplemented from EMAN::Processor.
Definition at line 3677 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOATARRAY, EMAN::EMObject::INT, and EMAN::TypeDict::put().
03678 { 03679 TypeDict d; 03680 d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0"); 03681 d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0"); 03682 d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output"); 03683 return d; 03684 }
static Processor* EMAN::GradientPlaneRemoverProcessor::NEW | ( | ) | [inline, static] |
Definition at line 3667 of file processor.h.
03668 { 03669 return new GradientPlaneRemoverProcessor(); 03670 }
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 2859 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.
02860 { 02861 if (!image) { 02862 LOGWARN("NULL Image"); 02863 return; 02864 } 02865 02866 int nz = image->get_zsize(); 02867 if (nz > 1) { 02868 LOGERR("%s Processor doesn't support 3D model", get_name().c_str()); 02869 throw ImageDimensionException("3D map not supported"); 02870 } 02871 02872 int nx = image->get_xsize(); 02873 int ny = image->get_ysize(); 02874 float *d = image->get_data(); 02875 EMData *mask = 0; 02876 float *dm = 0; 02877 if (params.has_key("mask")) { 02878 mask = params["mask"]; 02879 if (nx!=mask->get_xsize() || ny!=mask->get_ysize()) { 02880 LOGERR("%s Processor requires same size mask image", get_name().c_str()); 02881 throw ImageDimensionException("wrong size mask image"); 02882 } 02883 dm = mask->get_data(); 02884 } 02885 int count = 0; 02886 if (dm) { 02887 for(int i=0; i<nx*ny; i++) { 02888 if(dm[i]) count++; 02889 } 02890 } 02891 else { 02892 count = nx * ny; 02893 } 02894 if(count<3) { 02895 LOGERR("%s Processor requires at least 3 pixels to fit a plane", get_name().c_str()); 02896 throw ImageDimensionException("too few usable pixels to fit a plane"); 02897 } 02898 // Allocate the working space 02899 gsl_vector *S=gsl_vector_calloc(3); 02900 gsl_matrix *A=gsl_matrix_calloc(count,3); 02901 gsl_matrix *V=gsl_matrix_calloc(3,3); 02902 02903 double m[3] = {0, 0, 0}; 02904 int index=0; 02905 if (dm) { 02906 for(int j=0; j<ny; j++){ 02907 for(int i=0; i<nx; i++){ 02908 int ij=j*nx+i; 02909 if(dm[ij]) { 02910 m[0]+=i; // x 02911 m[1]+=j; // y 02912 m[2]+=d[ij]; // z 02913 /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \ 02914 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/ 02915 index++; 02916 } 02917 } 02918 } 02919 } 02920 else { 02921 for(int j=0; j<ny; j++){ 02922 for(int i=0; i<nx; i++){ 02923 int ij=j*nx+i; 02924 m[0]+=i; // x 02925 m[1]+=j; // y 02926 m[2]+=d[ij]; // z 02927 /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \ 02928 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/ 02929 index++; 02930 } 02931 } 02932 } 02933 02934 for(int i=0; i<3; i++) m[i]/=count; // compute center of the plane 02935 02936 index=0; 02937 if (dm) { 02938 for(int j=0; j<ny; j++){ 02939 for(int i=0; i<nx; i++){ 02940 int ij=j*nx+i; 02941 if(dm[ij]) { 02942 //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]); 02943 gsl_matrix_set(A,index,0,i-m[0]); 02944 gsl_matrix_set(A,index,1,j-m[1]); 02945 gsl_matrix_set(A,index,2,d[ij]-m[2]); 02946 index++; 02947 } 02948 } 02949 } 02950 mask->update(); 02951 } 02952 else { 02953 for(int j=0; j<ny; j++){ 02954 for(int i=0; i<nx; i++){ 02955 int ij=j*nx+i; 02956 //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]); 02957 gsl_matrix_set(A,index,0,i-m[0]); 02958 gsl_matrix_set(A,index,1,j-m[1]); 02959 gsl_matrix_set(A,index,2,d[ij]-m[2]); 02960 index++; 02961 } 02962 } 02963 } 02964 02965 // SVD decomposition and use the V vector associated with smallest singular value as the plan normal 02966 gsl_linalg_SV_decomp_jacobi(A, V, S); 02967 02968 double n[3]; 02969 for(int i=0; i<3; i++) n[i] = gsl_matrix_get(V, i, 2); 02970 02971 #ifdef DEBUG 02972 printf("S=%g,%g,%g\n",gsl_vector_get(S,0), gsl_vector_get(S,1), gsl_vector_get(S,2)); 02973 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)); 02974 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)); 02975 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)); 02976 printf("Fitted plane: p0=%g,%g,%g\tn=%g,%g,%g\n",m[0],m[1],m[2],n[0],n[1],n[2]); 02977 #endif 02978 02979 int changeZero = 0; 02980 if (params.has_key("changeZero")) changeZero = params["changeZero"]; 02981 if (changeZero) { 02982 for(int j=0; j<nx; j++){ 02983 for(int i=0; i<ny; i++){ 02984 int ij = j*nx+i; 02985 d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]); 02986 } 02987 } 02988 } 02989 else { 02990 for(int j=0; j<nx; j++){ 02991 for(int i=0; i<ny; i++){ 02992 int ij = j*nx+i; 02993 if(d[ij]) d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]); 02994 } 02995 } 02996 } 02997 image->update(); 02998 // set return plane parameters 02999 vector< float > planeParam; 03000 planeParam.resize(6); 03001 for(int i=0; i<3; i++) planeParam[i] = static_cast<float>(n[i]); 03002 for(int i=0; i<3; i++) planeParam[i+3] = static_cast<float>(m[i]); 03003 params["planeParam"]=EMObject(planeParam); 03004 }
const string GradientPlaneRemoverProcessor::NAME = "filter.gradientPlaneRemover" [static] |