#include <aligner.h>
Inheritance diagram for EMAN::RT3DGridAligner:
Public Member Functions | |
virtual EMData * | align (EMData *this_img, EMData *to_img, const string &cmp_name="ccc.tomo", const Dict &cmp_params=Dict()) const |
See Aligner comments for more details. | |
virtual EMData * | align (EMData *this_img, EMData *to_img) const |
See Aligner comments for more details. | |
virtual vector< Dict > | xform_align_nbest (EMData *this_img, EMData *to_img, const unsigned int nsoln, const string &cmp_name, const Dict &cmp_params) const |
See Aligner comments for more details. | |
virtual string | get_name () const |
Get the Aligner's name. | |
virtual string | get_desc () const |
virtual TypeDict | get_param_types () const |
Static Public Member Functions | |
Aligner * | NEW () |
Static Public Attributes | |
const string | NAME = "rotate_translate_3d_grid" |
daz | The angle increment in the azimuth direction | |
laz | Lower bound for the azimuth direction | |
uaz | Upper bound for the azimuth direction | |
dphi | The angle increment in the phi direction | |
lphi | Lower bound for the phi direction | |
uphi | Upper bound for the phi direction | |
dalt | The angle increment in the altitude direction | |
lalt | Lower bound for the altitude direction | |
ualt | Upper bound for the altitude direction | |
dotrans | Do a translational search | |
search | The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive | |
searchx | The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters | |
searchy | The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters | |
searchz | The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters | |
verbose | Turn this on to have useful information printed to standard out |
Definition at line 1036 of file aligner.h.
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 1045 of file aligner.h. References align(). 01046 { 01047 return align(this_img, to_img, "ccc.tomo", Dict()); 01048 }
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 1846 of file aligner.cpp. References EMAN::EMData::process(), EMAN::EMData::set_attr(), t, and xform_align_nbest(). 01847 { 01848 01849 vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params); 01850 01851 Dict t; 01852 Transform* tr = (Transform*) alis[0]["xform.align3d"]; 01853 t["transform"] = tr; 01854 EMData* soln = this_img->process("xform",t); 01855 soln->set_attr("xform.align3d",tr); 01856 delete tr; tr = 0; 01857 01858 return soln; 01859 01860 }
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Implements EMAN::Aligner. Definition at line 1060 of file aligner.h. 01061 { 01062 return "3D rotational and translational alignment using specified ranges and maximum shifts"; 01063 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 1055 of file aligner.h. 01056 {
01057 return NAME;
01058 }
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Implements EMAN::Aligner. Definition at line 1070 of file aligner.h. References EMAN::TypeDict::put(). 01071 { 01072 TypeDict d; 01073 d.put("daz", EMObject::FLOAT,"The angle increment in the azimuth direction. Default is 10"); 01074 d.put("az0", EMObject::FLOAT,"Lower bound for the azimuth direction. Default it 0"); 01075 d.put("az1", EMObject::FLOAT,"Upper bound for the azimuth direction. Default it 180.0"); 01076 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10"); 01077 d.put("phi0", EMObject::FLOAT,"Lower bound for the phi direction. Default it 0"); 01078 d.put("phi1", EMObject::FLOAT,"Upper bound for the phi direction. Default it 360.0"); 01079 d.put("dalt", EMObject::FLOAT,"The angle increment in the altitude direction. Default is 10"); 01080 d.put("alt0", EMObject::FLOAT,"Lower bound for the altitude direction. Default it 0"); 01081 d.put("alt1", EMObject::FLOAT,"Upper bound for the altitude direction. Default it 360.0"); 01082 d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)"); 01083 d.put("search", EMObject::INT,"The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive."); 01084 d.put("searchx", EMObject::INT,"The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3."); 01085 d.put("searchy", EMObject::INT,"The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3."); 01086 d.put("searchz", EMObject::INT,"The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3"); 01087 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out."); 01088 return d; 01089 }
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Definition at line 1065 of file aligner.h. 01066 { 01067 return new RT3DGridAligner(); 01068 }
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See Aligner comments for more details.
Reimplemented from EMAN::Aligner. Definition at line 1862 of file aligner.cpp. References EMAN::EMData::calc_ccf(), EMAN::EMData::calc_max_location_wrap(), calc_max_location_wrap_cuda(), EMAN::EMData::cmp(), copy(), data, EMAN::EMData::do_fft(), EMAN::Dict::end(), EMAN::EMData::get_ndim(), get_stats_cuda(), EMAN::EMData::get_value_at_wrap(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), EMAN::EMData::get_zsize(), EMAN::Dict::has_key(), ImageDimensionException, InvalidParameterException, CudaPeakInfo::peak, phi, EMAN::EMData::process(), EMAN::EMData::process_inplace(), CudaPeakInfo::px, CudaPeakInfo::py, CudaPeakInfo::pz, EMAN::Dict::set_default(), EMAN::Transform::set_trans(), sqrt(), and t. Referenced by align(). 01862 { 01863 01864 if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) { 01865 throw ImageDimensionException("This aligner only works for 3D images"); 01866 } 01867 01868 int searchx = 0; 01869 int searchy = 0; 01870 int searchz = 0; 01871 01872 bool dotrans = params.set_default("dotrans",1); 01873 if (params.has_key("search")) { 01874 vector<string> check; 01875 check.push_back("searchx"); 01876 check.push_back("searchy"); 01877 check.push_back("searchz"); 01878 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) { 01879 if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters"); 01880 } 01881 int search = params["search"]; 01882 searchx = search; 01883 searchy = search; 01884 searchz = search; 01885 } else { 01886 searchx = params.set_default("searchx",3); 01887 searchy = params.set_default("searchy",3); 01888 searchz = params.set_default("searchz",3); 01889 } 01890 01891 float lalt = params.set_default("alt0",0.0f); 01892 float laz = params.set_default("az0",0.0f); 01893 float lphi = params.set_default("phi0",0.0f); 01894 float ualt = params.set_default("alt1",180.0f); // I am using 179.9 rather than 180 to avoid resampling 01895 float uphi = params.set_default("phi1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01896 float uaz = params.set_default("az1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01897 float dalt = params.set_default("dalt",10.f); 01898 float daz = params.set_default("daz",10.f); 01899 float dphi = params.set_default("dphi",10.f); 01900 bool verbose = params.set_default("verbose",false); 01901 01902 //in case we arre aligning tomos 01903 Dict altered_cmp_params(cmp_params); 01904 if (cmp_name == "ccc.tomo") { 01905 altered_cmp_params.set_default("searchx", searchx); 01906 altered_cmp_params.set_default("searchy", searchy); 01907 altered_cmp_params.set_default("searchz", searchz); 01908 altered_cmp_params.set_default("norm", true); 01909 } 01910 01911 vector<Dict> solns; 01912 if (nsoln == 0) return solns; // What was the user thinking? 01913 for (unsigned int i = 0; i < nsoln; ++i ) { 01914 Dict d; 01915 d["score"] = 1.e24; 01916 Transform t; // identity by default 01917 d["xform.align3d"] = &t; // deep copy is going on here 01918 solns.push_back(d); 01919 } 01920 01921 bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0; 01922 EMData * tofft = 0; 01923 if(dotrans || tomography){ 01924 tofft = to->do_fft(); 01925 } 01926 01927 #ifdef EMAN2_USING_CUDA 01928 if(EMData::usecuda == 1) { 01929 if(!this_img->isrodataongpu()) this_img->copy_to_cudaro(); 01930 if(!to->cudarwdata) to->copy_to_cuda(); 01931 if(to->cudarwdata){if(tofft) tofft->copy_to_cuda();} 01932 } 01933 #endif 01934 01935 Dict d; 01936 d["type"] = "eman"; // d is used in the loop below 01937 bool use_cpu = true; 01938 for ( float alt = lalt; alt <= ualt; alt += dalt) { 01939 // An optimization for the range of az is made at the top of the sphere 01940 // If you think about it, this is just a coarse way of making this approach slightly more efficient 01941 for ( float az = laz; az < uaz; az += daz ){ 01942 if (verbose) { 01943 cout << "Trying angle alt " << alt << " az " << az << endl; 01944 } 01945 for( float phi = lphi; phi < uphi; phi += dphi ) { 01946 d["alt"] = alt; 01947 d["phi"] = phi; 01948 d["az"] = az; 01949 Transform t(d); 01950 EMData* transformed = this_img->process("xform",Dict("transform",&t)); 01951 01952 //need to do things a bit diffrent if we want to compare two tomos 01953 float best_score; 01954 if(dotrans || tomography){ 01955 EMData* ccf = transformed->calc_ccf(tofft); 01956 #ifdef EMAN2_USING_CUDA 01957 if(to->cudarwdata){ 01958 use_cpu = false; 01959 float2 stats = get_stats_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize()); 01960 CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz); 01961 t.set_trans((float)-data->px, (float)-data->py, (float)-data->pz); 01962 best_score = -(data->peak - stats.x)/sqrt(stats.y); // Normalize, this is better than calling the norm processor since we only need to normalize one point 01963 } 01964 #endif 01965 if(use_cpu){ 01966 if(tomography) ccf->process_inplace("normalize"); 01967 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz); 01968 t.set_trans((float)-point[0], (float)-point[1], (float)-point[2]); 01969 best_score = -ccf->get_value_at_wrap(point[0], point[1], point[2]); 01970 delete transformed; // this is to stop a mem leak 01971 transformed = this_img->process("xform",Dict("transform",&t)); 01972 } 01973 delete ccf; ccf =0; 01974 } 01975 01976 if(!tomography){ 01977 best_score = transformed->cmp(cmp_name,to,cmp_params); //this is not very efficient as it creates a new cmp object for each iteration 01978 01979 } 01980 delete transformed; transformed = 0; 01981 01982 unsigned int j = 0; 01983 for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) { 01984 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy 01985 vector<Dict>::reverse_iterator rit = solns.rbegin(); 01986 copy(rit+1,solns.rend()-j,rit); 01987 Dict& d = (*it); 01988 d["score"] = best_score; 01989 d["xform.align3d"] = &t; 01990 break; 01991 } 01992 } 01993 } 01994 } 01995 } 01996 01997 if(tofft) {delete tofft; tofft = 0;} 01998 return solns; 01999 02000 }
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Definition at line 76 of file aligner.cpp. |