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EMAN::RT3DGridAligner Class Reference

rotational and translational alignment using a square qrid of Altitude and Azimuth values (the phi range is specifiable) This aligner is ported from the original tomohunter.py - it is less efficient than searching on the sphere (RT3DSphereAligner), but very useful if you want to search in a specific, small, local area. More...

#include <aligner.h>

Inheritance diagram for EMAN::RT3DGridAligner:

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Collaboration diagram for EMAN::RT3DGridAligner:
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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.grid"

Detailed Description

rotational and translational alignment using a square qrid of Altitude and Azimuth values (the phi range is specifiable) This aligner is ported from the original tomohunter.py - it is less efficient than searching on the sphere (RT3DSphereAligner), but very useful if you want to search in a specific, small, local area.

Author:
David Woolford (ported from Mike Schmid's e2tomohunter code - Mike Schmid is the intellectual author)
Date:
June 23 2009

Definition at line 665 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::RT3DGridAligner::align EMData this_img,
EMData to_img
const [inline, virtual]
 

See Aligner comments for more details.

Implements EMAN::Aligner.

Definition at line 674 of file aligner.h.

References align().

00675                         {
00676                                 return align(this_img, to_img, "dot.tomo", Dict());
00677                         }

EMData * RT3DGridAligner::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 1379 of file aligner.cpp.

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

01380 {
01381 
01382         vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params);
01383 
01384         Dict t;
01385         Transform* tr = (Transform*) alis[0]["xform.align3d"];
01386         t["transform"] = tr;
01387         EMData* soln = this_img->process("xform",t);
01388         soln->set_attr("xform.align3d",tr);
01389         delete tr; tr = 0;
01390 
01391         return soln;
01392 
01393 }

virtual string EMAN::RT3DGridAligner::get_desc  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 689 of file aligner.h.

00690                         {
00691                                 return "3D rotational and translational alignment using specified ranges and maximum shifts";
00692                         }

virtual string EMAN::RT3DGridAligner::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 684 of file aligner.h.

00685                         {
00686                                 return NAME;
00687                         }

virtual TypeDict EMAN::RT3DGridAligner::get_param_types  )  const [inline, virtual]
 

Implements EMAN::Aligner.

Definition at line 699 of file aligner.h.

References EMAN::TypeDict::put().

00700                         {
00701                                 TypeDict d;
00702                                 d.put("daz", EMObject::FLOAT,"The angle increment in the azimuth direction. Default is 10");
00703                                 d.put("raz", EMObject::FLOAT,"The range of angles to sample in the azimuth direction. Default is 360.");
00704                                 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10.");
00705                                 d.put("rphi", EMObject::FLOAT,"The range of angles to sample in the phi direction. Default is 180.");
00706                                 d.put("dalt", EMObject::FLOAT,"The angle increment in the altitude direction. Default is 10.");
00707                                 d.put("ralt", EMObject::FLOAT,"The range of angles to sample in the altitude direction. Default is 180.");
00708                                 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.");
00709                                 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.");
00710                                 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.");
00711                                 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");
00712                                 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
00713                                 return d;
00714                         }

Aligner* EMAN::RT3DGridAligner::NEW  )  [inline, static]
 

Definition at line 694 of file aligner.h.

00695                         {
00696                                 return new RT3DGridAligner();
00697                         }

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 1395 of file aligner.cpp.

References EMAN::EMData::calc_ccf(), EMAN::EMData::calc_max_location_wrap(), EMAN::EMData::cmp(), copy(), EMAN::EMData::get_ndim(), EMAN::Dict::has_key(), ImageDimensionException, InvalidParameterException, phi, EMAN::EMData::process(), EMAN::Dict::set_default(), and t.

Referenced by align().

01395                                                                                                                                                                {
01396 
01397         if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) {
01398                 throw ImageDimensionException("This aligner only works for 3D images");
01399         }
01400 
01401         int searchx = 0;
01402         int searchy = 0;
01403         int searchz = 0;
01404 
01405         if (params.has_key("search")) {
01406                 vector<string> check;
01407                 check.push_back("searchx");
01408                 check.push_back("searchy");
01409                 check.push_back("searchz");
01410                 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) {
01411                         if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters");
01412                 }
01413                 int search  = params["search"];
01414                 searchx = search;
01415                 searchy = search;
01416                 searchz = search;
01417         } else {
01418                 searchx = params.set_default("searchx",3);
01419                 searchy = params.set_default("searchy",3);
01420                 searchz = params.set_default("searchz",3);
01421         }
01422 
01423         float ralt = params.set_default("ralt",180.f);
01424         float rphi = params.set_default("rphi",180.f);
01425         float raz = params.set_default("raz",180.f);
01426         float dalt = params.set_default("dalt",10.f);
01427         float daz = params.set_default("daz",10.f);
01428         float dphi = params.set_default("dphi",10.f);
01429         float threshold = params.set_default("threshold",0.f);
01430         if (threshold < 0.0f) throw InvalidParameterException("The threshold parameter must be greater than or equal to zero");
01431         bool verbose = params.set_default("verbose",false);
01432 
01433         vector<Dict> solns;
01434         if (nsoln == 0) return solns; // What was the user thinking?
01435         for (unsigned int i = 0; i < nsoln; ++i ) {
01436                 Dict d;
01437                 d["score"] = 1.e24;
01438                 Transform t; // identity by default
01439                 d["xform.align3d"] = &t; // deep copy is going on here
01440                 solns.push_back(d);
01441         }
01442         Dict d;
01443         d["type"] = "eman"; // d is used in the loop below
01444         for ( float alt = 0.0f; alt <= ralt; alt += dalt) {
01445                 // An optimization for the range of az is made at the top of the sphere
01446                 // If you think about it, this is just a coarse way of making this approach slightly more efficient
01447                 if (verbose) {
01448                         cout << "Trying angle " << alt << endl;
01449                 }
01450 
01451                 float begin_az = -raz;
01452                 float end_az = raz;
01453                 if (alt == 0.0f) {
01454                         begin_az = 0.0f;
01455                         end_az = 0.0f;
01456                 }
01457 
01458                 for ( float az = begin_az; az <= end_az; az += daz ){
01459                         for( float phi = -rphi-az; phi <= rphi-az; phi += dphi ) {
01460                                 d["alt"] = alt;
01461                                 d["phi"] = phi;
01462                                 d["az"] = az;
01463                                 Transform t(d);
01464                                 EMData* transformed = this_img->process("xform",Dict("transform",&t));
01465                                 EMData* ccf = transformed->calc_ccf(to);
01466 
01467                                 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz);
01468                                 Dict altered_cmp_params(cmp_params);
01469                                 if (cmp_name == "dot.tomo") {
01470                                         altered_cmp_params["ccf"] = ccf;
01471                                         altered_cmp_params["tx"] = point[0];
01472                                         altered_cmp_params["ty"] = point[1];
01473                                         altered_cmp_params["tz"] = point[2];
01474                                 }
01475 
01476                                 float best_score = transformed->cmp(cmp_name,to,altered_cmp_params);
01477                                 delete transformed; transformed =0;
01478                                 delete ccf; ccf = 0;
01479 
01480                                 unsigned int j = 0;
01481                                 for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) {
01482                                         if ( (float)(*it)["score"] > best_score ) {  // Note greater than - EMAN2 preferes minimums as a matter of policy
01483                                                 vector<Dict>::reverse_iterator rit = solns.rbegin();
01484                                                 copy(rit+1,solns.rend()-j,rit);
01485                                                 Dict& d = (*it);
01486                                                 d["score"] = best_score;
01487                                                 d["xform.align3d"] = &t;
01488                                                 break;
01489                                         }
01490                                 }
01491                         }
01492                 }
01493         }
01494 
01495         return solns;
01496 
01497 }


Member Data Documentation

const string RT3DGridAligner::NAME = "rt.3d.grid" [static]
 

Definition at line 64 of file aligner.cpp.


The documentation for this class was generated from the following files:
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