#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 5266 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 5276 of file processor.h. 05277 { 05278 return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel."; 05279 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5271 of file processor.h. References NAME. 05272 { 05273 return NAME; 05274 }
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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 5286 of file processor.h. References EMAN::EMObject::EMDATA, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::STRINGARRAY. 05287 { 05288 TypeDict d; 05289 d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search"); 05290 d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)"); 05291 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"); 05292 d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1"); 05293 return d; 05294 }
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Definition at line 5281 of file processor.h. 05282 { 05283 return new SymSearchProcessor(); 05284 }
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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 5920 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. 05921 { 05922 if (!image) { 05923 LOGWARN("NULL Image"); 05924 return; 05925 } 05926 float thresh = params["thresh"]; 05927 int output_symlabel = params["output_symlabel"]; 05928 05929 // set up all the symmetry transforms for all the searched symmetries 05930 const vector<string> sym_list = params["sym"]; 05931 int sym_num = sym_list.size(); 05932 vector< vector< Transform > > transforms(sym_num); 05933 vector< float* > symvals(sym_num); 05934 for (int i =0; i < sym_num; i++) { 05935 vector<Transform> sym_transform = Symmetry3D::get_symmetries(sym_list[i]); 05936 transforms[i] = sym_transform; 05937 symvals[i] = new float[sym_transform.size()]; // new float(nsym); 05938 } 05939 05940 EMData *orig = image->copy(); 05941 05942 image->to_zero(); 05943 05944 int nx= image->get_xsize(); 05945 int ny= image->get_ysize(); 05946 int nz= image->get_zsize(); 05947 int xy = nx * ny; 05948 float * data = image->get_data(); 05949 float * sdata = orig->get_data(); 05950 05951 EMData *symlabel = 0; 05952 float * ldata = symlabel->get_data(); 05953 if (output_symlabel) { 05954 symlabel = image->copy(); 05955 symlabel->to_zero(); 05956 ldata = symlabel->get_data(); 05957 } 05958 05959 for (int k = 0; k < nz; k++) { 05960 for (int j = 0; j < ny; j++) { 05961 for(int i = 0; i < nx; i++) { 05962 size_t index = k * nx * ny + j * nx + i; 05963 float val = sdata[ index ]; 05964 float bestmean = val, bestsymlevel = FLT_MAX; 05965 int bestsym = 0; 05966 for( int sym = 0; sym< sym_num; sym++) { 05967 int cur_sym_num = transforms[sym].size(); 05968 float *symval = symvals[sym]; 05969 // first find out all the symmetry related location values 05970 for( int s = 0; s < cur_sym_num; s++){ 05971 Transform r = transforms[sym][s]; 05972 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2); 05973 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2); 05974 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2); 05975 05976 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1) 05977 && z2 < (nz - 1)) { 05978 float x = (float)Util::fast_floor(x2); 05979 float y = (float)Util::fast_floor(y2); 05980 float z = (float)Util::fast_floor(z2); 05981 05982 float t = x2 - x; 05983 float u = y2 - y; 05984 float v = z2 - z; 05985 05986 int ii = (int) (x + y * nx + z * xy); 05987 05988 symval[s]= 05989 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], 05990 sdata[ii + nx + 1], sdata[ii + nx * ny], 05991 sdata[ii + xy + 1], sdata[ii + xy + nx], 05992 sdata[ii + xy + nx + 1], t, u, v); 05993 } 05994 else { 05995 symval[s] = 0.0 ; 05996 } 05997 } 05998 float tmean=0, tsigma=0; 05999 for( int s = 0; s < cur_sym_num; s++) { 06000 tmean += symval[s]; 06001 tsigma += symval[s] * symval[s]; 06002 } 06003 tmean /= cur_sym_num; 06004 tsigma = tsigma/cur_sym_num - tmean*tmean; 06005 if (tsigma < bestsymlevel ) { 06006 bestsymlevel = tsigma; 06007 bestmean = tmean; 06008 bestsym = sym; 06009 } 06010 } 06011 if ( bestsymlevel > thresh) { 06012 if (output_symlabel) ldata[index] = (float)bestsym; 06013 data[index] = bestmean; 06014 } 06015 else { 06016 if (output_symlabel) ldata[index] = -1; 06017 data[index] = val; 06018 } 06019 } 06020 } 06021 } 06022 if( orig ) 06023 { 06024 delete orig; 06025 orig = 0; 06026 } 06027 for (int i =0; i < sym_num; i++) { 06028 if( symvals[i] ) 06029 { 06030 delete symvals[i]; 06031 symvals[i] = 0; 06032 } 06033 } 06034 if (symlabel) params.put("symlabel_map", EMObject(symlabel)); 06035 }
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Definition at line 5296 of file processor.h. Referenced by get_name(). |