#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 1146 of file aligner.h.
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 1155 of file aligner.h. References align(). 01156 { 01157 return align(this_img, to_img, "ccc.tomo", Dict()); 01158 }
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See Aligner comments for more details.
Implements EMAN::Aligner. Definition at line 2088 of file aligner.cpp. References EMAN::EMData::process(), EMAN::EMData::set_attr(), t, and xform_align_nbest(). 02089 { 02090 02091 vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params); 02092 02093 Dict t; 02094 Transform* tr = (Transform*) alis[0]["xform.align3d"]; 02095 t["transform"] = tr; 02096 EMData* soln = this_img->process("xform",t); 02097 soln->set_attr("xform.align3d",tr); 02098 delete tr; tr = 0; 02099 02100 return soln; 02101 02102 }
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Implements EMAN::Aligner. Definition at line 1170 of file aligner.h. 01171 { 01172 return "3D rotational and translational alignment using specified ranges and maximum shifts"; 01173 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 1165 of file aligner.h. 01166 {
01167 return NAME;
01168 }
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Implements EMAN::Aligner. Definition at line 1180 of file aligner.h. References EMAN::TypeDict::put(). 01181 { 01182 TypeDict d; 01183 d.put("daz", EMObject::FLOAT,"The angle increment in the azimuth direction. Default is 10"); 01184 d.put("az0", EMObject::FLOAT,"Lower bound for the azimuth direction. Default it 0"); 01185 d.put("az1", EMObject::FLOAT,"Upper bound for the azimuth direction. Default it 180.0"); 01186 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10"); 01187 d.put("phi0", EMObject::FLOAT,"Lower bound for the phi direction. Default it 0"); 01188 d.put("phi1", EMObject::FLOAT,"Upper bound for the phi direction. Default it 360.0"); 01189 d.put("dalt", EMObject::FLOAT,"The angle increment in the altitude direction. Default is 10"); 01190 d.put("alt0", EMObject::FLOAT,"Lower bound for the altitude direction. Default it 0"); 01191 d.put("alt1", EMObject::FLOAT,"Upper bound for the altitude direction. Default it 360.0"); 01192 d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)"); 01193 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."); 01194 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."); 01195 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."); 01196 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"); 01197 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out."); 01198 return d; 01199 }
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Definition at line 1175 of file aligner.h. 01176 { 01177 return new RT3DGridAligner(); 01178 }
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See Aligner comments for more details.
Reimplemented from EMAN::Aligner. Definition at line 2104 of file aligner.cpp. References EMAN::EMData::calc_ccf(), EMAN::EMData::calc_max_location_wrap(), calc_max_location_wrap_cuda(), EMAN::Cmp::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(). 02104 { 02105 02106 if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) { 02107 throw ImageDimensionException("This aligner only works for 3D images"); 02108 } 02109 02110 int searchx = 0; 02111 int searchy = 0; 02112 int searchz = 0; 02113 02114 bool dotrans = params.set_default("dotrans",1); 02115 if (params.has_key("search")) { 02116 vector<string> check; 02117 check.push_back("searchx"); 02118 check.push_back("searchy"); 02119 check.push_back("searchz"); 02120 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) { 02121 if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters"); 02122 } 02123 int search = params["search"]; 02124 searchx = search; 02125 searchy = search; 02126 searchz = search; 02127 } else { 02128 searchx = params.set_default("searchx",3); 02129 searchy = params.set_default("searchy",3); 02130 searchz = params.set_default("searchz",3); 02131 } 02132 02133 float lalt = params.set_default("alt0",0.0f); 02134 float laz = params.set_default("az0",0.0f); 02135 float lphi = params.set_default("phi0",0.0f); 02136 float ualt = params.set_default("alt1",180.0f); // I am using 179.9 rather than 180 to avoid resampling 02137 float uphi = params.set_default("phi1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 02138 float uaz = params.set_default("az1",360.0f); // I am using 359.9 rather than 180 to avoid resampling 0 = 360 (for perodic functions) 02139 float dalt = params.set_default("dalt",10.f); 02140 float daz = params.set_default("daz",10.f); 02141 float dphi = params.set_default("dphi",10.f); 02142 bool verbose = params.set_default("verbose",false); 02143 02144 //in case we arre aligning tomos 02145 Dict altered_cmp_params(cmp_params); 02146 if (cmp_name == "ccc.tomo") { 02147 altered_cmp_params.set_default("searchx", searchx); 02148 altered_cmp_params.set_default("searchy", searchy); 02149 altered_cmp_params.set_default("searchz", searchz); 02150 altered_cmp_params.set_default("norm", true); 02151 } 02152 02153 vector<Dict> solns; 02154 if (nsoln == 0) return solns; // What was the user thinking? 02155 for (unsigned int i = 0; i < nsoln; ++i ) { 02156 Dict d; 02157 d["score"] = 1.e24; 02158 Transform t; // identity by default 02159 d["xform.align3d"] = &t; // deep copy is going on here 02160 solns.push_back(d); 02161 } 02162 02163 bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0; 02164 EMData * tofft = 0; 02165 if(dotrans || tomography){ 02166 tofft = to->do_fft(); 02167 } 02168 02169 #ifdef EMAN2_USING_CUDA 02170 if(EMData::usecuda == 1) { 02171 if(!this_img->getcudarodata()) this_img->copy_to_cudaro(); // safer call 02172 if(!to->getcudarwdata()) to->copy_to_cuda(); 02173 if(to->getcudarwdata()){if(tofft) tofft->copy_to_cuda();} 02174 } 02175 #endif 02176 02177 Dict d; 02178 d["type"] = "eman"; // d is used in the loop below 02179 Transform trans = Transform(); 02180 Cmp* c = Factory <Cmp>::get(cmp_name, cmp_params); 02181 bool use_cpu = true; 02182 for ( float alt = lalt; alt <= ualt; alt += dalt) { 02183 // An optimization for the range of az is made at the top of the sphere 02184 // If you think about it, this is just a coarse way of making this approach slightly more efficient 02185 for ( float az = laz; az < uaz; az += daz ){ 02186 if (verbose) { 02187 cout << "Trying angle alt " << alt << " az " << az << endl; 02188 } 02189 for( float phi = lphi; phi < uphi; phi += dphi ) { 02190 d["alt"] = alt; 02191 d["phi"] = phi; 02192 d["az"] = az; 02193 Transform t(d); 02194 EMData* transformed = this_img->process("xform",Dict("transform",&t)); 02195 02196 //need to do things a bit diffrent if we want to compare two tomos 02197 float best_score = 0.0f; 02198 if(dotrans || tomography){ 02199 EMData* ccf = transformed->calc_ccf(tofft); 02200 #ifdef EMAN2_USING_CUDA 02201 if(to->getcudarwdata()){ 02202 use_cpu = false;; 02203 CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz); 02204 trans.set_trans((float)-data->px, (float)-data->py, (float)-data->pz); 02205 t = trans*t; //composite transfrom to reflect the fact that we have done a rotation first and THEN a transformation 02206 if (tomography) { 02207 float2 stats = get_stats_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize()); 02208 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 02209 } else { 02210 best_score = -data->peak; 02211 } 02212 delete data; 02213 } 02214 #endif 02215 if(use_cpu){ 02216 if(tomography) ccf->process_inplace("normalize"); 02217 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz); 02218 trans.set_trans((float)-point[0], (float)-point[1], (float)-point[2]); 02219 t = trans*t; //composite transfrom to reflect the fact that we have done a rotation first and THEN a transformation 02220 best_score = -ccf->get_value_at_wrap(point[0], point[1], point[2]); 02221 } 02222 delete ccf; ccf =0; 02223 delete transformed; transformed = 0; 02224 } 02225 02226 if(!tomography){ 02227 if(!transformed) transformed = this_img->process("xform",Dict("transform",&t)); 02228 best_score = c->cmp(to,transformed); 02229 delete transformed; transformed = 0; 02230 } 02231 02232 unsigned int j = 0; 02233 for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) { 02234 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy 02235 vector<Dict>::reverse_iterator rit = solns.rbegin(); 02236 copy(rit+1,solns.rend()-j,rit); 02237 Dict& d = (*it); 02238 d["score"] = best_score; 02239 d["xform.align3d"] = &t; 02240 break; 02241 } 02242 } 02243 } 02244 } 02245 } 02246 02247 //Free up resources (for an expensive opperation like this move data to and from device is a small % of time) 02248 #ifdef EMAN2_USING_CUDA 02249 to->copy_from_device(); 02250 this_img->ro_free(); 02251 #endif 02252 02253 if(tofft) {delete tofft; tofft = 0;} 02254 return solns; 02255 02256 }
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Definition at line 79 of file aligner.cpp. |