#include <processor.h>
Inheritance diagram for EMAN::SymSearchProcessor:
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 Processor * | NEW () |
Static Public Attributes | |
static const string | NAME = "misc.symsearch" |
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 5230 of file processor.h.
virtual string EMAN::SymSearchProcessor::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 5240 of file processor.h.
05241 { 05242 return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel."; 05243 }
virtual string EMAN::SymSearchProcessor::get_name | ( | ) | const [inline, virtual] |
Get the processor's name.
Each processor is identified by a unique name.
Implements EMAN::Processor.
Definition at line 5235 of file processor.h.
References NAME.
05236 { 05237 return NAME; 05238 }
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.
Reimplemented from EMAN::Processor.
Definition at line 5250 of file processor.h.
References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRINGARRAY.
05251 { 05252 TypeDict d; 05253 d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search"); 05254 d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)"); 05255 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"); 05256 d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1"); 05257 return d; 05258 }
static Processor* EMAN::SymSearchProcessor::NEW | ( | ) | [inline, static] |
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.
image | The image to be processed. |
Implements EMAN::Processor.
Definition at line 5876 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.
05877 { 05878 if (!image) { 05879 LOGWARN("NULL Image"); 05880 return; 05881 } 05882 float thresh = params["thresh"]; 05883 int output_symlabel = params["output_symlabel"]; 05884 05885 // set up all the symmetry transforms for all the searched symmetries 05886 const vector<string> sym_list = params["sym"]; 05887 int sym_num = sym_list.size(); 05888 vector< vector< Transform > > transforms(sym_num); 05889 vector< float* > symvals(sym_num); 05890 for (int i =0; i < sym_num; i++) { 05891 vector<Transform> sym_transform = Symmetry3D::get_symmetries(sym_list[i]); 05892 transforms[i] = sym_transform; 05893 symvals[i] = new float[sym_transform.size()]; // new float(nsym); 05894 } 05895 05896 EMData *orig = image->copy(); 05897 05898 image->to_zero(); 05899 05900 int nx= image->get_xsize(); 05901 int ny= image->get_ysize(); 05902 int nz= image->get_zsize(); 05903 int xy = nx * ny; 05904 float * data = image->get_data(); 05905 float * sdata = orig->get_data(); 05906 05907 EMData *symlabel = 0; 05908 float * ldata = symlabel->get_data(); 05909 if (output_symlabel) { 05910 symlabel = image->copy(); 05911 symlabel->to_zero(); 05912 ldata = symlabel->get_data(); 05913 } 05914 05915 for (int k = 0; k < nz; k++) { 05916 for (int j = 0; j < ny; j++) { 05917 for(int i = 0; i < nx; i++) { 05918 size_t index = (size_t)k * nx * ny + j * nx + i; 05919 float val = sdata[ index ]; 05920 float bestmean = val, bestsymlevel = FLT_MAX; 05921 int bestsym = 0; 05922 for( int sym = 0; sym< sym_num; sym++) { 05923 int cur_sym_num = transforms[sym].size(); 05924 float *symval = symvals[sym]; 05925 // first find out all the symmetry related location values 05926 for( int s = 0; s < cur_sym_num; s++){ 05927 Transform r = transforms[sym][s]; 05928 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2); 05929 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2); 05930 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2); 05931 05932 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1) 05933 && z2 < (nz - 1)) { 05934 float x = (float)Util::fast_floor(x2); 05935 float y = (float)Util::fast_floor(y2); 05936 float z = (float)Util::fast_floor(z2); 05937 05938 float t = x2 - x; 05939 float u = y2 - y; 05940 float v = z2 - z; 05941 05942 size_t ii = x + y * nx + z * (size_t)xy; 05943 05944 symval[s]= 05945 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], 05946 sdata[ii + nx + 1], sdata[ii + nx * ny], 05947 sdata[ii + xy + 1], sdata[ii + xy + nx], 05948 sdata[ii + xy + nx + 1], t, u, v); 05949 } 05950 else { 05951 symval[s] = 0.0 ; 05952 } 05953 } 05954 float tmean=0, tsigma=0; 05955 for( int s = 0; s < cur_sym_num; s++) { 05956 tmean += symval[s]; 05957 tsigma += symval[s] * symval[s]; 05958 } 05959 tmean /= cur_sym_num; 05960 tsigma = tsigma/cur_sym_num - tmean*tmean; 05961 if (tsigma < bestsymlevel ) { 05962 bestsymlevel = tsigma; 05963 bestmean = tmean; 05964 bestsym = sym; 05965 } 05966 } 05967 if ( bestsymlevel > thresh) { 05968 if (output_symlabel) ldata[index] = (float)bestsym; 05969 data[index] = bestmean; 05970 } 05971 else { 05972 if (output_symlabel) ldata[index] = -1; 05973 data[index] = val; 05974 } 05975 } 05976 } 05977 } 05978 if( orig ) 05979 { 05980 delete orig; 05981 orig = 0; 05982 } 05983 for (int i =0; i < sym_num; i++) { 05984 if( symvals[i] ) 05985 { 05986 delete symvals[i]; 05987 symvals[i] = 0; 05988 } 05989 } 05990 if (symlabel) params.put("symlabel_map", EMObject(symlabel)); 05991 }
const string SymSearchProcessor::NAME = "misc.symsearch" [static] |