#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 | |
Processor * | NEW () |
Static Public Attributes | |
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 5261 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 5271 of file processor.h. 05272 { 05273 return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel."; 05274 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5266 of file processor.h. 05267 {
05268 return NAME;
05269 }
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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 5281 of file processor.h. References EMAN::TypeDict::put(). 05282 { 05283 TypeDict d; 05284 d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search"); 05285 d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)"); 05286 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"); 05287 d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1"); 05288 return d; 05289 }
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Definition at line 5276 of file processor.h. 05277 { 05278 return new SymSearchProcessor(); 05279 }
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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 5962 of file processor.cpp. References EMAN::EMData::copy(), data, 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, nx, ny, EMAN::Dict::put(), EMAN::Dict::size(), t, EMAN::EMData::to_zero(), EMAN::Util::trilinear_interpolate(), v, x, and y. 05963 { 05964 if (!image) { 05965 LOGWARN("NULL Image"); 05966 return; 05967 } 05968 float thresh = params["thresh"]; 05969 int output_symlabel = params["output_symlabel"]; 05970 05971 // set up all the symmetry transforms for all the searched symmetries 05972 const vector<string> sym_list = params["sym"]; 05973 int sym_num = sym_list.size(); 05974 vector< vector< Transform > > transforms(sym_num); 05975 vector< float* > symvals(sym_num); 05976 for (int i =0; i < sym_num; i++) { 05977 vector<Transform> sym_transform = Symmetry3D::get_symmetries(sym_list[i]); 05978 transforms[i] = sym_transform; 05979 symvals[i] = new float[sym_transform.size()]; // new float(nsym); 05980 } 05981 05982 EMData *orig = image->copy(); 05983 05984 image->to_zero(); 05985 05986 int nx= image->get_xsize(); 05987 int ny= image->get_ysize(); 05988 int nz= image->get_zsize(); 05989 int xy = nx * ny; 05990 float * data = image->get_data(); 05991 float * sdata = orig->get_data(); 05992 05993 EMData *symlabel = 0; 05994 float * ldata = symlabel->get_data(); 05995 if (output_symlabel) { 05996 symlabel = image->copy(); 05997 symlabel->to_zero(); 05998 ldata = symlabel->get_data(); 05999 } 06000 06001 for (int k = 0; k < nz; k++) { 06002 for (int j = 0; j < ny; j++) { 06003 for(int i = 0; i < nx; i++) { 06004 size_t index = (size_t)k * nx * ny + j * nx + i; 06005 float val = sdata[ index ]; 06006 float bestmean = val, bestsymlevel = FLT_MAX; 06007 int bestsym = 0; 06008 for( int sym = 0; sym< sym_num; sym++) { 06009 int cur_sym_num = transforms[sym].size(); 06010 float *symval = symvals[sym]; 06011 // first find out all the symmetry related location values 06012 for( int s = 0; s < cur_sym_num; s++){ 06013 Transform r = transforms[sym][s]; 06014 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2); 06015 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2); 06016 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2); 06017 06018 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1) 06019 && z2 < (nz - 1)) { 06020 float x = (float)Util::fast_floor(x2); 06021 float y = (float)Util::fast_floor(y2); 06022 float z = (float)Util::fast_floor(z2); 06023 06024 float t = x2 - x; 06025 float u = y2 - y; 06026 float v = z2 - z; 06027 06028 size_t ii = x + y * nx + z * (size_t)xy; 06029 06030 symval[s]= 06031 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx], 06032 sdata[ii + nx + 1], sdata[ii + nx * ny], 06033 sdata[ii + xy + 1], sdata[ii + xy + nx], 06034 sdata[ii + xy + nx + 1], t, u, v); 06035 } 06036 else { 06037 symval[s] = 0.0 ; 06038 } 06039 } 06040 float tmean=0, tsigma=0; 06041 for( int s = 0; s < cur_sym_num; s++) { 06042 tmean += symval[s]; 06043 tsigma += symval[s] * symval[s]; 06044 } 06045 tmean /= cur_sym_num; 06046 tsigma = tsigma/cur_sym_num - tmean*tmean; 06047 if (tsigma < bestsymlevel ) { 06048 bestsymlevel = tsigma; 06049 bestmean = tmean; 06050 bestsym = sym; 06051 } 06052 } 06053 if ( bestsymlevel > thresh) { 06054 if (output_symlabel) ldata[index] = (float)bestsym; 06055 data[index] = bestmean; 06056 } 06057 else { 06058 if (output_symlabel) ldata[index] = -1; 06059 data[index] = val; 06060 } 06061 } 06062 } 06063 } 06064 if( orig ) 06065 { 06066 delete orig; 06067 orig = 0; 06068 } 06069 for (int i =0; i < sym_num; i++) { 06070 if( symvals[i] ) 06071 { 06072 delete symvals[i]; 06073 symvals[i] = 0; 06074 } 06075 } 06076 if (symlabel) params.put("symlabel_map", EMObject(symlabel)); 06077 }
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Definition at line 176 of file processor.cpp. |