#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" |
This is for use as a course aligner. For refineing alignments, use the refine_3d_grid aligner. In general this aligner is not used much and is mostly depreciated.
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 1051 of file aligner.h.
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 1060 of file aligner.h. References align(). 01061 { 01062 return align(this_img, to_img, "ccc.tomo", Dict()); 01063 }
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 1864 of file aligner.cpp. References EMAN::EMData::process(), EMAN::EMData::set_attr(), t, and xform_align_nbest(). 01865 { 01866 01867 vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params); 01868 01869 Dict t; 01870 Transform* tr = (Transform*) alis[0]["xform.align3d"]; 01871 t["transform"] = tr; 01872 EMData* soln = this_img->process("xform",t); 01873 soln->set_attr("xform.align3d",tr); 01874 delete tr; tr = 0; 01875 01876 return soln; 01877 01878 }
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Implements EMAN::Aligner. Definition at line 1075 of file aligner.h. 01076 { 01077 return "3D rotational and translational alignment using specified ranges and maximum shifts"; 01078 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 1070 of file aligner.h. 01071 {
01072 return NAME;
01073 }
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Implements EMAN::Aligner. Definition at line 1085 of file aligner.h. References EMAN::TypeDict::put(). 01086 { 01087 TypeDict d; 01088 d.put("daz", EMObject::FLOAT,"The angle increment in the azimuth direction. Default is 10"); 01089 d.put("az0", EMObject::FLOAT,"Lower bound for the azimuth direction. Default it 0"); 01090 d.put("az1", EMObject::FLOAT,"Upper bound for the azimuth direction. Default it 180.0"); 01091 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10"); 01092 d.put("phi0", EMObject::FLOAT,"Lower bound for the phi direction. Default it 0"); 01093 d.put("phi1", EMObject::FLOAT,"Upper bound for the phi direction. Default it 360.0"); 01094 d.put("dalt", EMObject::FLOAT,"The angle increment in the altitude direction. Default is 10"); 01095 d.put("alt0", EMObject::FLOAT,"Lower bound for the altitude direction. Default it 0"); 01096 d.put("alt1", EMObject::FLOAT,"Upper bound for the altitude direction. Default it 360.0"); 01097 d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)"); 01098 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."); 01099 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."); 01100 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."); 01101 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"); 01102 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out."); 01103 return d; 01104 }
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Definition at line 1080 of file aligner.h. 01081 { 01082 return new RT3DGridAligner(); 01083 }
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See Aligner comments for more details.
Reimplemented from EMAN::Aligner. Definition at line 1880 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(). 01880 { 01881 01882 if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) { 01883 throw ImageDimensionException("This aligner only works for 3D images"); 01884 } 01885 01886 int searchx = 0; 01887 int searchy = 0; 01888 int searchz = 0; 01889 01890 bool dotrans = params.set_default("dotrans",1); 01891 if (params.has_key("search")) { 01892 vector<string> check; 01893 check.push_back("searchx"); 01894 check.push_back("searchy"); 01895 check.push_back("searchz"); 01896 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) { 01897 if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters"); 01898 } 01899 int search = params["search"]; 01900 searchx = search; 01901 searchy = search; 01902 searchz = search; 01903 } else { 01904 searchx = params.set_default("searchx",3); 01905 searchy = params.set_default("searchy",3); 01906 searchz = params.set_default("searchz",3); 01907 } 01908 01909 float lalt = params.set_default("alt0",0.0f); 01910 float laz = params.set_default("az0",0.0f); 01911 float lphi = params.set_default("phi0",0.0f); 01912 float ualt = params.set_default("alt1",180.0f); // I am using 179.9 rather than 180 to avoid resampling 01913 float uphi = params.set_default("phi1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01914 float uaz = params.set_default("az1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01915 float dalt = params.set_default("dalt",10.f); 01916 float daz = params.set_default("daz",10.f); 01917 float dphi = params.set_default("dphi",10.f); 01918 bool verbose = params.set_default("verbose",false); 01919 01920 //in case we arre aligning tomos 01921 Dict altered_cmp_params(cmp_params); 01922 if (cmp_name == "ccc.tomo") { 01923 altered_cmp_params.set_default("searchx", searchx); 01924 altered_cmp_params.set_default("searchy", searchy); 01925 altered_cmp_params.set_default("searchz", searchz); 01926 altered_cmp_params.set_default("norm", true); 01927 } 01928 01929 vector<Dict> solns; 01930 if (nsoln == 0) return solns; // What was the user thinking? 01931 for (unsigned int i = 0; i < nsoln; ++i ) { 01932 Dict d; 01933 d["score"] = 1.e24; 01934 Transform t; // identity by default 01935 d["xform.align3d"] = &t; // deep copy is going on here 01936 solns.push_back(d); 01937 } 01938 01939 bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0; 01940 EMData * tofft = 0; 01941 if(dotrans || tomography){ 01942 tofft = to->do_fft(); 01943 } 01944 01945 #ifdef EMAN2_USING_CUDA 01946 if(EMData::usecuda == 1) { 01947 if(!this_img->isrodataongpu()) this_img->copy_to_cudaro(); 01948 if(!to->cudarwdata) to->copy_to_cuda(); 01949 if(to->cudarwdata){if(tofft) tofft->copy_to_cuda();} 01950 } 01951 #endif 01952 01953 Dict d; 01954 d["type"] = "eman"; // d is used in the loop below 01955 Transform trans = Transform(); 01956 bool use_cpu = true; 01957 for ( float alt = lalt; alt <= ualt; alt += dalt) { 01958 // An optimization for the range of az is made at the top of the sphere 01959 // If you think about it, this is just a coarse way of making this approach slightly more efficient 01960 for ( float az = laz; az < uaz; az += daz ){ 01961 if (verbose) { 01962 cout << "Trying angle alt " << alt << " az " << az << endl; 01963 } 01964 for( float phi = lphi; phi < uphi; phi += dphi ) { 01965 d["alt"] = alt; 01966 d["phi"] = phi; 01967 d["az"] = az; 01968 Transform t(d); 01969 EMData* transformed = this_img->process("xform",Dict("transform",&t)); 01970 01971 //need to do things a bit diffrent if we want to compare two tomos 01972 float best_score = 0.0f; 01973 if(dotrans || tomography){ 01974 EMData* ccf = transformed->calc_ccf(tofft); 01975 #ifdef EMAN2_USING_CUDA 01976 if(to->cudarwdata){ 01977 use_cpu = false;; 01978 CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz); 01979 trans.set_trans((float)-data->px, (float)-data->py, (float)-data->pz); 01980 t = trans*t; //composite transfrom 01981 if (tomography) { 01982 float2 stats = get_stats_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize()); 01983 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 01984 } else { 01985 best_score = -data->peak; 01986 } 01987 delete data; 01988 } 01989 #endif 01990 if(use_cpu){ 01991 if(tomography) ccf->process_inplace("normalize"); 01992 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz); 01993 trans.set_trans((float)-point[0], (float)-point[1], (float)-point[2]); 01994 t = trans*t; //composite transfrom 01995 best_score = -ccf->get_value_at_wrap(point[0], point[1], point[2]); 01996 } 01997 delete ccf; ccf =0; 01998 delete transformed; transformed = 0; 01999 } 02000 02001 if(!tomography){ 02002 if(!transformed) transformed = this_img->process("xform",Dict("transform",&t)); 02003 best_score = transformed->cmp(cmp_name,to,cmp_params); //this is not very efficient as it creates a new cmp object for each iteration 02004 delete transformed; transformed = 0; 02005 } 02006 02007 unsigned int j = 0; 02008 for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) { 02009 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy 02010 vector<Dict>::reverse_iterator rit = solns.rbegin(); 02011 copy(rit+1,solns.rend()-j,rit); 02012 Dict& d = (*it); 02013 d["score"] = best_score; 02014 d["xform.align3d"] = &t; 02015 break; 02016 } 02017 } 02018 } 02019 } 02020 } 02021 02022 if(tofft) {delete tofft; tofft = 0;} 02023 return solns; 02024 02025 }
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Definition at line 76 of file aligner.cpp. |