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EMAN::RT3DSphereAligner Class Reference

3D rotational and translational alignment using spherical sampling, can reduce the search space based on symmetry. More...

#include <aligner.h>

Inheritance diagram for EMAN::RT3DSphereAligner:

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Collaboration diagram for EMAN::RT3DSphereAligner:
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List of all members.

Public Member Functions

virtual EMDataalign (EMData *this_img, EMData *to_img, const string &cmp_name, const Dict &cmp_params) const
 See Aligner comments for more details.
virtual EMDataalign (EMData *this_img, EMData *to_img) const
 See Aligner comments for more details.
virtual vector< Dictxform_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

AlignerNEW ()

Static Public Attributes

const string NAME = "rt.3d.sphere"

Detailed Description

3D rotational and translational alignment using spherical sampling, can reduce the search space based on symmetry.

can also make use of different OrientationGenerators (random, for example) 160-180% more efficient than the RT3DGridAligner

Author:
David Woolford
Date:
June 23 2009

Definition at line 725 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RT3DSphereAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

See Aligner comments for more details.

Implements EMAN::Aligner.

Definition at line 734 of file aligner.h.

References align().

00735                         {
00736                                 return align(this_img, to_img, "sqeuclidean", Dict());
00737                         }

EMData * RT3DSphereAligner::align EMData this_img,
EMData to_img,
const string &  cmp_name,
const Dict cmp_params
const [virtual]
 

See Aligner comments for more details.

Implements EMAN::Aligner.

Definition at line 1499 of file aligner.cpp.

References EMAN::EMData::process(), EMAN::EMData::set_attr(), t, and xform_align_nbest().

01500 {
01501 
01502         vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params);
01503 
01504         Dict t;
01505         Transform* tr = (Transform*) alis[0]["xform.align3d"];
01506         t["transform"] = tr;
01507         EMData* soln = this_img->process("xform",t);
01508         soln->set_attr("xform.align3d",tr);
01509         delete tr; tr = 0;
01510 
01511         return soln;
01512 
01513 }

virtual string EMAN::RT3DSphereAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 749 of file aligner.h.

00750                         {
00751                                 return "3D rotational and translational alignment using spherical sampling. Can reduce the search space if symmetry is supplied";
00752                         }

virtual string EMAN::RT3DSphereAligner::get_name  )  const [inline, virtual]
 

Get the Aligner's name.

Each Aligner is identified by a unique name.

Returns:
The Aligner's name.

Implements EMAN::Aligner.

Definition at line 744 of file aligner.h.

00745                         {
00746                                 return NAME;
00747                         }

virtual TypeDict EMAN::RT3DSphereAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 759 of file aligner.h.

References EMAN::TypeDict::put().

00760                         {
00761                                 TypeDict d;
00762                                 d.put("sym", EMObject::STRING,"The symmtery to use as the basis of the spherical sampling. Default is c1 (asymmetry).");
00763                                 d.put("orientgen", EMObject::STRING,"Advanced. The orientation generation strategy. Default is eman");
00764                                 d.put("delta", EMObject::FLOAT,"Angle the separates points on the sphere. This is exclusive of the \'n\' paramater. Default is 10");
00765                                 d.put("n", EMObject::INT,"An alternative to the delta argument, this is the number of points you want generated on the sphere. Default is OFF");
00766                                 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10.");
00767                                 d.put("rphi", EMObject::FLOAT,"The range of angles to sample in the phi direction. Default is 180.");
00768                                 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.");
00769                                 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.");
00770                                 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.");
00771                                 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");
00772                                 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
00773                                 return d;
00774                         }

Aligner* EMAN::RT3DSphereAligner::NEW  )  [inline, static]
 

Definition at line 754 of file aligner.h.

00755                         {
00756                                 return new RT3DSphereAligner();
00757                         }

vector< Dict > RT3DSphereAligner::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 1515 of file aligner.cpp.

References EMAN::EMData::calc_ccf(), EMAN::EMData::calc_max_location_wrap(), EMAN::EMData::cmp(), copy(), EMAN::Symmetry3D::gen_orientations(), EMAN::Factory< T >::get(), EMAN::EMData::get_ndim(), EMAN::Dict::has_key(), ImageDimensionException, InvalidParameterException, phi, EMAN::EMData::process(), EMAN::Dict::set_default(), and t.

Referenced by align().

01515                                                                                                                                                                  {
01516 
01517         if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) {
01518                 throw ImageDimensionException("This aligner only works for 3D images");
01519         }
01520 
01521         int searchx = 0;
01522         int searchy = 0;
01523         int searchz = 0;
01524 
01525         if (params.has_key("search")) {
01526                 vector<string> check;
01527                 check.push_back("searchx");
01528                 check.push_back("searchy");
01529                 check.push_back("searchz");
01530                 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) {
01531                         if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters");
01532                 }
01533                 int search  = params["search"];
01534                 searchx = search;
01535                 searchy = search;
01536                 searchz = search;
01537         } else {
01538                 searchx = params.set_default("searchx",3);
01539                 searchy = params.set_default("searchy",3);
01540                 searchz = params.set_default("searchz",3);
01541         }
01542 
01543         float rphi = params.set_default("rphi",180.f);
01544         float dphi = params.set_default("dphi",10.f);
01545         float threshold = params.set_default("threshold",0.f);
01546         if (threshold < 0.0f) throw InvalidParameterException("The threshold parameter must be greater than or equal to zero");
01547         bool verbose = params.set_default("verbose",false);
01548 
01549         vector<Dict> solns;
01550         if (nsoln == 0) return solns; // What was the user thinking?
01551         for (unsigned int i = 0; i < nsoln; ++i ) {
01552                 Dict d;
01553                 d["score"] = 1.e24;
01554                 Transform t; // identity by default
01555                 d["xform.align3d"] = &t; // deep copy is going on here
01556                 solns.push_back(d);
01557         }
01558 
01559         Dict d;
01560         d["inc_mirror"] = true; // This should probably always be true for 3D case. If it ever changes we might have to make inc_mirror a parameter
01561         if ( params.has_key("delta") && params.has_key("n") ) {
01562                 throw InvalidParameterException("The delta and n parameters are mutually exclusive in the RT3DSphereAligner aligner");
01563         } else if ( params.has_key("n") ) {
01564                 d["n"] = params["n"];
01565         } else {
01566                 // If they didn't specify either then grab the default delta - if they did supply delta we're still safe doing this
01567                 d["delta"] = params.set_default("delta",10.f);
01568         }
01569 
01570         Symmetry3D* sym = Factory<Symmetry3D>::get((string)params.set_default("sym","c1"));
01571         vector<Transform> transforms = sym->gen_orientations((string)params.set_default("orientgen","eman"),d);
01572 
01573         float verbose_alt = -1.0f;;
01574         for(vector<Transform>::const_iterator trans_it = transforms.begin(); trans_it != transforms.end(); trans_it++) {
01575                 Dict params = trans_it->get_params("eman");
01576                 float az = params["az"];
01577                 if (verbose) {
01578                         float alt = params["alt"];
01579                         if ( alt != verbose_alt ) {
01580                                 verbose_alt = alt;
01581                                 cout << "Trying angle " << alt << endl;
01582                         }
01583                 }
01584                 for( float phi = -rphi-az; phi <= rphi-az; phi += dphi ) {
01585                         params["phi"] = phi;
01586                         Transform t(params);
01587                         EMData* transformed = this_img->process("xform",Dict("transform",&t));
01588                         EMData* ccf = transformed->calc_ccf(to);
01589                         IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz);
01590                         Dict altered_cmp_params(cmp_params);
01591                         if (cmp_name == "dot.tomo") {
01592                                 altered_cmp_params["ccf"] = ccf;
01593                                 altered_cmp_params["tx"] = point[0];
01594                                 altered_cmp_params["ty"] = point[1];
01595                                 altered_cmp_params["tz"] = point[2];
01596                         }
01597 
01598                         float best_score = transformed->cmp(cmp_name,to,altered_cmp_params);
01599                         delete transformed; transformed =0;
01600                         delete ccf; ccf =0;
01601 
01602                         unsigned int j = 0;
01603                         for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) {
01604                                 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy
01605                                         vector<Dict>::reverse_iterator rit = solns.rbegin();
01606                                         copy(rit+1,solns.rend()-j,rit);
01607                                         Dict& d = (*it);
01608                                         d["score"] = best_score;
01609                                         d["xform.align3d"] = &t; // deep copy is going on here
01610                                         break;
01611                                 }
01612                         }
01613 
01614                 }
01615         }
01616         delete sym; sym = 0;
01617         return solns;
01618 
01619 }


Member Data Documentation

const string RT3DSphereAligner::NAME = "rt.3d.sphere" [static]
 

Definition at line 65 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Fri Apr 30 15:39:12 2010 for EMAN2 by  doxygen 1.3.9.1