#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 5192 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 5202 of file processor.h. 05203 {
05204 return "Identifiy the best symmetry in the given symmetry list for each pixel and then apply the best symmetry to each pixel.";
05205 }
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Get the processor's name. Each processor is identified by a unique name.
Implements EMAN::Processor. Definition at line 5197 of file processor.h. 05198 {
05199 return NAME;
05200 }
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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 5212 of file processor.h. References EMAN::TypeDict::put(). 05213 {
05214 TypeDict d;
05215 d.put("sym", EMObject::STRINGARRAY, "the list of symmetries to search");
05216 d.put("thresh", EMObject::FLOAT, "the minimal level of symmetry to be accepted (0-1)");
05217 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");
05218 d.put("symlabel_map", EMObject::EMDATA, "the optional return map when output_symlabel=1");
05219 return d;
05220 }
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Definition at line 5207 of file processor.h. 05208 {
05209 return new SymSearchProcessor();
05210 }
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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 5848 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. 05849 {
05850 if (!image) {
05851 LOGWARN("NULL Image");
05852 return;
05853 }
05854 float thresh = params["thresh"];
05855 int output_symlabel = params["output_symlabel"];
05856
05857 // set up all the symmetry transforms for all the searched symmetries
05858 const vector<string> sym_list = params["sym"];
05859 int sym_num = sym_list.size();
05860 vector< vector< Transform > > transforms(sym_num);
05861 vector< float* > symvals(sym_num);
05862 for (int i =0; i < sym_num; i++) {
05863 vector<Transform> sym_transform = Symmetry3D::get_symmetries(sym_list[i]);
05864 transforms[i] = sym_transform;
05865 symvals[i] = new float[sym_transform.size()]; // new float(nsym);
05866 }
05867
05868 EMData *orig = image->copy();
05869
05870 image->to_zero();
05871
05872 int nx= image->get_xsize();
05873 int ny= image->get_ysize();
05874 int nz= image->get_zsize();
05875 int xy = nx * ny;
05876 float * data = image->get_data();
05877 float * sdata = orig->get_data();
05878
05879 EMData *symlabel = 0;
05880 float * ldata = symlabel->get_data();
05881 if (output_symlabel) {
05882 symlabel = image->copy();
05883 symlabel->to_zero();
05884 ldata = symlabel->get_data();
05885 }
05886
05887 for (int k = 0; k < nz; k++) {
05888 for (int j = 0; j < ny; j++) {
05889 for(int i = 0; i < nx; i++) {
05890 size_t index = (size_t)k * nx * ny + j * nx + i;
05891 float val = sdata[ index ];
05892 float bestmean = val, bestsymlevel = FLT_MAX;
05893 int bestsym = 0;
05894 for( int sym = 0; sym< sym_num; sym++) {
05895 int cur_sym_num = transforms[sym].size();
05896 float *symval = symvals[sym];
05897 // first find out all the symmetry related location values
05898 for( int s = 0; s < cur_sym_num; s++){
05899 Transform r = transforms[sym][s];
05900 float x2 = (float)(r[0][0] * (i-nx/2) + r[0][1] * (j-ny/2) + r[0][2] * (k-nz/2) + nx / 2);
05901 float y2 = (float)(r[1][0] * (i-nx/2) + r[1][1] * (j-ny/2) + r[1][2] * (k-nz/2) + ny / 2);
05902 float z2 = (float)(r[2][0] * (i-nx/2) + r[2][1] * (j-ny/2) + r[2][2] * (k-nz/2) + nz / 2);
05903
05904 if (x2 >= 0 && y2 >= 0 && z2 >= 0 && x2 < (nx - 1) && y2 < (ny - 1)
05905 && z2 < (nz - 1)) {
05906 float x = (float)Util::fast_floor(x2);
05907 float y = (float)Util::fast_floor(y2);
05908 float z = (float)Util::fast_floor(z2);
05909
05910 float t = x2 - x;
05911 float u = y2 - y;
05912 float v = z2 - z;
05913
05914 size_t ii = x + y * nx + z * (size_t)xy;
05915
05916 symval[s]=
05917 Util::trilinear_interpolate(sdata[ii], sdata[ii + 1], sdata[ii + nx],
05918 sdata[ii + nx + 1], sdata[ii + nx * ny],
05919 sdata[ii + xy + 1], sdata[ii + xy + nx],
05920 sdata[ii + xy + nx + 1], t, u, v);
05921 }
05922 else {
05923 symval[s] = 0.0 ;
05924 }
05925 }
05926 float tmean=0, tsigma=0;
05927 for( int s = 0; s < cur_sym_num; s++) {
05928 tmean += symval[s];
05929 tsigma += symval[s] * symval[s];
05930 }
05931 tmean /= cur_sym_num;
05932 tsigma = tsigma/cur_sym_num - tmean*tmean;
05933 if (tsigma < bestsymlevel ) {
05934 bestsymlevel = tsigma;
05935 bestmean = tmean;
05936 bestsym = sym;
05937 }
05938 }
05939 if ( bestsymlevel > thresh) {
05940 if (output_symlabel) ldata[index] = (float)bestsym;
05941 data[index] = bestmean;
05942 }
05943 else {
05944 if (output_symlabel) ldata[index] = -1;
05945 data[index] = val;
05946 }
05947 }
05948 }
05949 }
05950 if( orig )
05951 {
05952 delete orig;
05953 orig = 0;
05954 }
05955 for (int i =0; i < sym_num; i++) {
05956 if( symvals[i] )
05957 {
05958 delete symvals[i];
05959 symvals[i] = 0;
05960 }
05961 }
05962 if (symlabel) params.put("symlabel_map", EMObject(symlabel));
05963 }
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Definition at line 175 of file processor.cpp. |
1.3.9.1