#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 5226 of file processor.h.
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Get the descrition of this specific processor. This function must be overwritten by a subclass.
Implements EMAN::Processor. Definition at line 5236 of file processor.h. 05237 { 05238 return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel."; 05239 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5231 of file processor.h. References NAME. 05232 { 05233 return NAME; 05234 }
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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 5246 of file processor.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRINGARRAY. 05247 { 05248 TypeDict d; 05249 d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search"); 05250 d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)"); 05251 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"); 05252 d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1"); 05253 return d; 05254 }
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Definition at line 5241 of file processor.h. 05242 { 05243 return new SymSearchProcessor(); 05244 }
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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.
Implements EMAN::Processor. Definition at line 5813 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. 05814 { 05815 if (!image) { 05816 LOGWARN("NULL Image"); 05817 return; 05818 } 05819 float thresh = params["thresh"]; 05820 int output_symlabel = params["output_symlabel"]; 05821 05822 // set up all the symmetry transforms for all the searched symmetries 05823 const vector<string> sym_list = params["sym"]; 05824 int sym_num = sym_list.size(); 05825 vector< vector< Transform > > transforms(sym_num); 05826 vector< float* > symvals(sym_num); 05827 for (int i =0; i < sym_num; i++) { 05828 vector<Transform> sym_transform = Symmetry3D::get_symmetries(sym_list[i]); 05829 transforms[i] = sym_transform; 05830 symvals[i] = new float[sym_transform.size()]; // new float(nsym); 05831 } 05832 05833 EMData *orig = image->copy(); 05834 05835 image->to_zero(); 05836 05837 int nx= image->get_xsize(); 05838 int ny= image->get_ysize(); 05839 int nz= image->get_zsize(); 05840 int xy = nx * ny; 05841 float * data = image->get_data(); 05842 float * sdata = orig->get_data(); 05843 05844 EMData *symlabel = 0; 05845 float * ldata = symlabel->get_data(); 05846 if (output_symlabel) { 05847 symlabel = image->copy(); 05848 symlabel->to_zero(); 05849 ldata = symlabel->get_data(); 05850 } 05851 05852 for (int k = 0; k < nz; k++) { 05853 for (int j = 0; j < ny; j++) { 05854 for(int i = 0; i < nx; i++) { 05855 size_t index = k * nx * ny + j * nx + i; 05856 float val = sdata[ index ]; 05857 float bestmean = val, bestsymlevel = FLT_MAX; 05858 int bestsym = 0; 05859 for( int sym = 0; sym< sym_num; sym++) { 05860 int cur_sym_num = transforms[sym].size(); 05861 float *symval = symvals[sym]; 05862 // first find out all the symmetry related location values 05863 for( int s = 0; s < cur_sym_num; s++){ 05864 Transform r = transforms[sym][s]; 05865 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2); 05866 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2); 05867 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2); 05868 05869 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1) 05870 && z2 < (nz - 1)) { 05871 float x = (float)Util::fast_floor(x2); 05872 float y = (float)Util::fast_floor(y2); 05873 float z = (float)Util::fast_floor(z2); 05874 05875 float t = x2 - x; 05876 float u = y2 - y; 05877 float v = z2 - z; 05878 05879 int ii = (int) (x + y * nx + z * xy); 05880 05881 symval[s]= 05882 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], 05883 sdata[ii + nx + 1], sdata[ii + nx * ny], 05884 sdata[ii + xy + 1], sdata[ii + xy + nx], 05885 sdata[ii + xy + nx + 1], t, u, v); 05886 } 05887 else { 05888 symval[s] = 0.0 ; 05889 } 05890 } 05891 float tmean=0, tsigma=0; 05892 for( int s = 0; s < cur_sym_num; s++) { 05893 tmean += symval[s]; 05894 tsigma += symval[s] * symval[s]; 05895 } 05896 tmean /= cur_sym_num; 05897 tsigma = tsigma/cur_sym_num - tmean*tmean; 05898 if (tsigma < bestsymlevel ) { 05899 bestsymlevel = tsigma; 05900 bestmean = tmean; 05901 bestsym = sym; 05902 } 05903 } 05904 if ( bestsymlevel > thresh) { 05905 if (output_symlabel) ldata[index] = (float)bestsym; 05906 data[index] = bestmean; 05907 } 05908 else { 05909 if (output_symlabel) ldata[index] = -1; 05910 data[index] = val; 05911 } 05912 } 05913 } 05914 } 05915 if( orig ) 05916 { 05917 delete orig; 05918 orig = 0; 05919 } 05920 for (int i =0; i < sym_num; i++) { 05921 if( symvals[i] ) 05922 { 05923 delete symvals[i]; 05924 symvals[i] = 0; 05925 } 05926 } 05927 if (symlabel) params.put("symlabel_map", EMObject(symlabel)); 05928 }
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Definition at line 5256 of file processor.h. Referenced by get_name(). |