#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 3654 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 3668 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 3659 of file processor.h.
References NAME.
Referenced by process_inplace().
03660 { 03661 return NAME; 03662 }
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 3673 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOATARRAY, EMAN::EMObject::INT, and EMAN::TypeDict::put().
03674 { 03675 TypeDict d; 03676 d.put("mask", EMObject::EMDATA, "mask object: nonzero pixel positions will be used to fit plane. default = 0"); 03677 d.put("changeZero", EMObject::INT, "if zero pixels are modified when removing gradient. default = 0"); 03678 d.put("planeParam", EMObject::FLOATARRAY, "fitted plane parameters output"); 03679 return d; 03680 }
static Processor* EMAN::GradientPlaneRemoverProcessor::NEW | ( | ) | [inline, static] |
Definition at line 3663 of file processor.h.
03664 { 03665 return new GradientPlaneRemoverProcessor(); 03666 }
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 2800 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.
02801 { 02802 if (!image) { 02803 LOGWARN("NULL Image"); 02804 return; 02805 } 02806 02807 int nz = image->get_zsize(); 02808 if (nz > 1) { 02809 LOGERR("%s Processor doesn't support 3D model", get_name().c_str()); 02810 throw ImageDimensionException("3D map not supported"); 02811 } 02812 02813 int nx = image->get_xsize(); 02814 int ny = image->get_ysize(); 02815 float *d = image->get_data(); 02816 EMData *mask = 0; 02817 float *dm = 0; 02818 if (params.has_key("mask")) { 02819 mask = params["mask"]; 02820 if (nx!=mask->get_xsize() || ny!=mask->get_ysize()) { 02821 LOGERR("%s Processor requires same size mask image", get_name().c_str()); 02822 throw ImageDimensionException("wrong size mask image"); 02823 } 02824 dm = mask->get_data(); 02825 } 02826 int count = 0; 02827 if (dm) { 02828 for(int i=0; i<nx*ny; i++) { 02829 if(dm[i]) count++; 02830 } 02831 } 02832 else { 02833 count = nx * ny; 02834 } 02835 if(count<3) { 02836 LOGERR("%s Processor requires at least 3 pixels to fit a plane", get_name().c_str()); 02837 throw ImageDimensionException("too few usable pixels to fit a plane"); 02838 } 02839 // Allocate the working space 02840 gsl_vector *S=gsl_vector_calloc(3); 02841 gsl_matrix *A=gsl_matrix_calloc(count,3); 02842 gsl_matrix *V=gsl_matrix_calloc(3,3); 02843 02844 double m[3] = {0, 0, 0}; 02845 int index=0; 02846 if (dm) { 02847 for(int j=0; j<ny; j++){ 02848 for(int i=0; i<nx; i++){ 02849 int ij=j*nx+i; 02850 if(dm[ij]) { 02851 m[0]+=i; // x 02852 m[1]+=j; // y 02853 m[2]+=d[ij]; // z 02854 /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \ 02855 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/ 02856 index++; 02857 } 02858 } 02859 } 02860 } 02861 else { 02862 for(int j=0; j<ny; j++){ 02863 for(int i=0; i<nx; i++){ 02864 int ij=j*nx+i; 02865 m[0]+=i; // x 02866 m[1]+=j; // y 02867 m[2]+=d[ij]; // z 02868 /*printf("index=%d/%d\ti,j=%d,%d\tval=%g\txm,ym,zm=%g,%g,%g\n", \ 02869 index,count,i,j,d[ij],m[0]/(index+1),m[1]/(index+1),m[2]/(index+1));*/ 02870 index++; 02871 } 02872 } 02873 } 02874 02875 for(int i=0; i<3; i++) m[i]/=count; // compute center of the plane 02876 02877 index=0; 02878 if (dm) { 02879 for(int j=0; j<ny; j++){ 02880 for(int i=0; i<nx; i++){ 02881 int ij=j*nx+i; 02882 if(dm[ij]) { 02883 //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]); 02884 gsl_matrix_set(A,index,0,i-m[0]); 02885 gsl_matrix_set(A,index,1,j-m[1]); 02886 gsl_matrix_set(A,index,2,d[ij]-m[2]); 02887 index++; 02888 } 02889 } 02890 } 02891 mask->update(); 02892 } 02893 else { 02894 for(int j=0; j<ny; j++){ 02895 for(int i=0; i<nx; i++){ 02896 int ij=j*nx+i; 02897 //printf("index=%d/%d\ti,j=%d,%d\tval=%g\n",index,count,i,j,d[index]); 02898 gsl_matrix_set(A,index,0,i-m[0]); 02899 gsl_matrix_set(A,index,1,j-m[1]); 02900 gsl_matrix_set(A,index,2,d[ij]-m[2]); 02901 index++; 02902 } 02903 } 02904 } 02905 02906 // SVD decomposition and use the V vector associated with smallest singular value as the plan normal 02907 gsl_linalg_SV_decomp_jacobi(A, V, S); 02908 02909 double n[3]; 02910 for(int i=0; i<3; i++) n[i] = gsl_matrix_get(V, i, 2); 02911 02912 #ifdef DEBUG 02913 printf("S=%g,%g,%g\n",gsl_vector_get(S,0), gsl_vector_get(S,1), gsl_vector_get(S,2)); 02914 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)); 02915 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)); 02916 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)); 02917 printf("Fitted plane: p0=%g,%g,%g\tn=%g,%g,%g\n",m[0],m[1],m[2],n[0],n[1],n[2]); 02918 #endif 02919 02920 int changeZero = 0; 02921 if (params.has_key("changeZero")) changeZero = params["changeZero"]; 02922 if (changeZero) { 02923 for(int j=0; j<nx; j++){ 02924 for(int i=0; i<ny; i++){ 02925 int ij = j*nx+i; 02926 d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]); 02927 } 02928 } 02929 } 02930 else { 02931 for(int j=0; j<nx; j++){ 02932 for(int i=0; i<ny; i++){ 02933 int ij = j*nx+i; 02934 if(d[ij]) d[ij]-=static_cast<float>(-((i-m[0])*n[0]+(j-m[1])*n[1])/n[2]+m[2]); 02935 } 02936 } 02937 } 02938 image->update(); 02939 // set return plane parameters 02940 vector< float > planeParam; 02941 planeParam.resize(6); 02942 for(int i=0; i<3; i++) planeParam[i] = static_cast<float>(n[i]); 02943 for(int i=0; i<3; i++) planeParam[i+3] = static_cast<float>(m[i]); 02944 params["planeParam"]=EMObject(planeParam); 02945 }
const string GradientPlaneRemoverProcessor::NAME = "filter.gradientPlaneRemover" [static] |