#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 | |
static Aligner * | NEW () |
Static Public Attributes | |
static 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.
EMData * RT3DGridAligner::align | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const string & | cmp_name = "ccc.tomo" , |
|||
const Dict & | cmp_params = Dict() | |||
) | const [virtual] |
See Aligner comments for more details.
Implements EMAN::Aligner.
Definition at line 1890 of file aligner.cpp.
References EMAN::EMData::process(), EMAN::EMData::set_attr(), t, and xform_align_nbest().
Referenced by align().
01891 { 01892 01893 vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params); 01894 01895 Dict t; 01896 Transform* tr = (Transform*) alis[0]["xform.align3d"]; 01897 t["transform"] = tr; 01898 EMData* soln = this_img->process("xform",t); 01899 soln->set_attr("xform.align3d",tr); 01900 delete tr; tr = 0; 01901 01902 return soln; 01903 01904 }
virtual string EMAN::RT3DGridAligner::get_desc | ( | ) | const [inline, virtual] |
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 }
virtual string EMAN::RT3DGridAligner::get_name | ( | ) | const [inline, virtual] |
virtual TypeDict EMAN::RT3DGridAligner::get_param_types | ( | ) | const [inline, virtual] |
Implements EMAN::Aligner.
Definition at line 1085 of file aligner.h.
References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, and 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 }
static Aligner* EMAN::RT3DGridAligner::NEW | ( | ) | [inline, static] |
vector< Dict > RT3DGridAligner::xform_align_nbest | ( | EMData * | this_img, | |
EMData * | to_img, | |||
const unsigned int | nsoln, | |||
const string & | cmp_name, | |||
const Dict & | cmp_params | |||
) | const [virtual] |
See Aligner comments for more details.
Reimplemented from EMAN::Aligner.
Definition at line 1906 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::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, EMAN::Aligner::params, phi, EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::Dict::set_default(), EMAN::Transform::set_trans(), sqrt(), and t.
Referenced by align().
01906 { 01907 01908 if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) { 01909 throw ImageDimensionException("This aligner only works for 3D images"); 01910 } 01911 01912 int searchx = 0; 01913 int searchy = 0; 01914 int searchz = 0; 01915 01916 bool dotrans = params.set_default("dotrans",1); 01917 if (params.has_key("search")) { 01918 vector<string> check; 01919 check.push_back("searchx"); 01920 check.push_back("searchy"); 01921 check.push_back("searchz"); 01922 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) { 01923 if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters"); 01924 } 01925 int search = params["search"]; 01926 searchx = search; 01927 searchy = search; 01928 searchz = search; 01929 } else { 01930 searchx = params.set_default("searchx",3); 01931 searchy = params.set_default("searchy",3); 01932 searchz = params.set_default("searchz",3); 01933 } 01934 01935 float lalt = params.set_default("alt0",0.0f); 01936 float laz = params.set_default("az0",0.0f); 01937 float lphi = params.set_default("phi0",0.0f); 01938 float ualt = params.set_default("alt1",180.0f); // I am using 179.9 rather than 180 to avoid resampling 01939 float uphi = params.set_default("phi1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01940 float uaz = params.set_default("az1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 01941 float dalt = params.set_default("dalt",10.f); 01942 float daz = params.set_default("daz",10.f); 01943 float dphi = params.set_default("dphi",10.f); 01944 bool verbose = params.set_default("verbose",false); 01945 01946 //in case we arre aligning tomos 01947 Dict altered_cmp_params(cmp_params); 01948 if (cmp_name == "ccc.tomo") { 01949 altered_cmp_params.set_default("searchx", searchx); 01950 altered_cmp_params.set_default("searchy", searchy); 01951 altered_cmp_params.set_default("searchz", searchz); 01952 altered_cmp_params.set_default("norm", true); 01953 } 01954 01955 vector<Dict> solns; 01956 if (nsoln == 0) return solns; // What was the user thinking? 01957 for (unsigned int i = 0; i < nsoln; ++i ) { 01958 Dict d; 01959 d["score"] = 1.e24; 01960 Transform t; // identity by default 01961 d["xform.align3d"] = &t; // deep copy is going on here 01962 solns.push_back(d); 01963 } 01964 01965 bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0; 01966 EMData * tofft = 0; 01967 if(dotrans || tomography){ 01968 tofft = to->do_fft(); 01969 } 01970 01971 #ifdef EMAN2_USING_CUDA 01972 if(EMData::usecuda == 1) { 01973 if(!this_img->getcudarodata()) this_img->copy_to_cudaro(); // safer call 01974 if(!to->getcudarwdata()) to->copy_to_cuda(); 01975 if(to->getcudarwdata()){if(tofft) tofft->copy_to_cuda();} 01976 } 01977 #endif 01978 01979 Dict d; 01980 d["type"] = "eman"; // d is used in the loop below 01981 Transform trans = Transform(); 01982 bool use_cpu = true; 01983 for ( float alt = lalt; alt <= ualt; alt += dalt) { 01984 // An optimization for the range of az is made at the top of the sphere 01985 // If you think about it, this is just a coarse way of making this approach slightly more efficient 01986 for ( float az = laz; az < uaz; az += daz ){ 01987 if (verbose) { 01988 cout << "Trying angle alt " << alt << " az " << az << endl; 01989 } 01990 for( float phi = lphi; phi < uphi; phi += dphi ) { 01991 d["alt"] = alt; 01992 d["phi"] = phi; 01993 d["az"] = az; 01994 Transform t(d); 01995 EMData* transformed = this_img->process("xform",Dict("transform",&t)); 01996 01997 //need to do things a bit diffrent if we want to compare two tomos 01998 float best_score = 0.0f; 01999 if(dotrans || tomography){ 02000 EMData* ccf = transformed->calc_ccf(tofft); 02001 #ifdef EMAN2_USING_CUDA 02002 if(to->getcudarwdata()){ 02003 use_cpu = false;; 02004 CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz); 02005 trans.set_trans((float)-data->px, (float)-data->py, (float)-data->pz); 02006 t = trans*t; //composite transfrom to reflect the fact that we have done a rotation first and THEN a transformation 02007 if (tomography) { 02008 float2 stats = get_stats_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize()); 02009 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 02010 } else { 02011 best_score = -data->peak; 02012 } 02013 delete data; 02014 } 02015 #endif 02016 if(use_cpu){ 02017 if(tomography) ccf->process_inplace("normalize"); 02018 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz); 02019 trans.set_trans((float)-point[0], (float)-point[1], (float)-point[2]); 02020 t = trans*t; //composite transfrom to reflect the fact that we have done a rotation first and THEN a transformation 02021 best_score = -ccf->get_value_at_wrap(point[0], point[1], point[2]); 02022 } 02023 delete ccf; ccf =0; 02024 delete transformed; transformed = 0; 02025 } 02026 02027 if(!tomography){ 02028 if(!transformed) transformed = this_img->process("xform",Dict("transform",&t)); 02029 best_score = transformed->cmp(cmp_name,to,cmp_params); //this is not very efficient as it creates a new cmp object for each iteration 02030 delete transformed; transformed = 0; 02031 } 02032 02033 unsigned int j = 0; 02034 for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) { 02035 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy 02036 vector<Dict>::reverse_iterator rit = solns.rbegin(); 02037 copy(rit+1,solns.rend()-j,rit); 02038 Dict& d = (*it); 02039 d["score"] = best_score; 02040 d["xform.align3d"] = &t; 02041 break; 02042 } 02043 } 02044 } 02045 } 02046 } 02047 02048 //Free up resources (for an expensive opperation like this move data to and from device is a small % of time) 02049 #ifdef EMAN2_USING_CUDA 02050 to->copy_from_device(); 02051 this_img->ro_free(); 02052 #endif 02053 02054 if(tofft) {delete tofft; tofft = 0;} 02055 return solns; 02056 02057 }
const string RT3DGridAligner::NAME = "rotate_translate_3d_grid" [static] |