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EMAN::RT3DSphereAligner Class Reference
[a function or class that is CUDA enabled]

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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List of all members.

Public Member Functions

virtual EMDataalign (EMData *this_img, EMData *to_img, const string &cmp_name="sqeuclidean", const Dict &cmp_params=Dict()) 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 = "rotate_translate_3d"

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) 2X more efficient than the RT3DGridAligner The aligner actually aligns the reference to the 'moving' and then takes the inverse of the resulting transform. This is necessary because, in the case of symmetry (i.e. not c1), the reference symmetry axis must be aligned to the EMAN2 symmetry axis, restricting the search space to the asymmetrical points on a sphere. We note that if the reference symmetry axis is not aligned to the EMAN2 symmetry axis, the best thing is to do a full search (i.e. specify sym='c1') unless you really know what you are doing!

Parameters:
sym The symmtery to use as the basis of the spherical sampling
orietgen Advanced. The orientation generation strategy
delta Angle the separates points on the sphere. This is exclusive of the 'n' paramater
n An alternative to the delta argument, this is the number of points you want generated on the sphere
dphi The angle increment in the phi direction
lphi Lower bound for the phi direction
uphi Upper bound for the phi 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
Author:
John Flanagan and David Woolford
Date:
Feb 2011

Definition at line 1602 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 1611 of file aligner.h.

References align().

01612                         {
01613                                 return align(this_img, to_img, "sqeuclidean", Dict());
01614                         }

EMData * RT3DSphereAligner::align EMData this_img,
EMData to_img,
const string &  cmp_name = "sqeuclidean",
const Dict cmp_params = Dict()
const [virtual]
 

See Aligner comments for more details.

Implements EMAN::Aligner.

Definition at line 2591 of file aligner.cpp.

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

02592 {
02593 
02594         vector<Dict> alis = xform_align_nbest(this_img,to,1,cmp_name,cmp_params);
02595 
02596         Dict t;
02597         Transform* tr = (Transform*) alis[0]["xform.align3d"];
02598         t["transform"] = tr;
02599         EMData* soln = this_img->process("xform",t);
02600         soln->set_attr("xform.align3d",tr);
02601         delete tr; tr = 0;
02602 
02603         return soln;
02604 
02605 }

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

Implements EMAN::Aligner.

Definition at line 1626 of file aligner.h.

01627                         {
01628                                 return "3D rotational and translational alignment using spherical sampling. Can reduce the search space if symmetry is supplied";
01629                         }

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 1621 of file aligner.h.

01622                         {
01623                                 return NAME;
01624                         }

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

Implements EMAN::Aligner.

Definition at line 1636 of file aligner.h.

References EMAN::TypeDict::put().

01637                         {
01638                                 TypeDict d;
01639                                 d.put("sym", EMObject::STRING,"The symmtery to use as the basis of the spherical sampling. Default is c1 (asymmetry).");
01640                                 d.put("orientgen", EMObject::STRING,"Advanced. The orientation generation strategy. Default is eman");
01641                                 d.put("delta", EMObject::FLOAT,"Angle the separates points on the sphere. This is exclusive of the \'n\' paramater. Default is 10");
01642                                 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");
01643                                 d.put("dphi", EMObject::FLOAT,"The angle increment in the phi direction. Default is 10");
01644                                 d.put("phi0", EMObject::FLOAT,"Lower bound for phi. Default it 0");
01645                                 d.put("phi1", EMObject::FLOAT,"Upper bound for phi. Default it 360");
01646                                 d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)");
01647                                 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.");
01648                                 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.");
01649                                 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.");
01650                                 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");
01651                                 d.put("initxform", EMObject::TRANSFORM,"The Transform storing the starting position. If unspecified the identity matrix is used");
01652                                 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
01653                                 return d;
01654                         }

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

Definition at line 1631 of file aligner.h.

01632                         {
01633                                 return new RT3DSphereAligner();
01634                         }

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 2607 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::Symmetry3D::gen_orientations(), EMAN::Factory< T >::get(), 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::Transform::invert(), 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().

02607                                                                                                                                                                  {
02608 
02609         if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) {
02610                 throw ImageDimensionException("This aligner only works for 3D images");
02611         }
02612 
02613         int searchx = 0;
02614         int searchy = 0;
02615         int searchz = 0;
02616          
02617         bool dotrans = params.set_default("dotrans",1);
02618         if (params.has_key("search")) {
02619                 vector<string> check;
02620                 check.push_back("searchx");
02621                 check.push_back("searchy");
02622                 check.push_back("searchz");
02623                 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) {
02624                         if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters");
02625                 }
02626                 int search  = params["search"];
02627                 searchx = search;
02628                 searchy = search;
02629                 searchz = search;
02630         } else {
02631                 searchx = params.set_default("searchx",3);
02632                 searchy = params.set_default("searchy",3);
02633                 searchz = params.set_default("searchz",3);
02634         }
02635 
02636         Transform* initxform;
02637         if (params.has_key("initxform") ) {
02638                 // Unlike the 2d refine aligner, this class doesn't require the starting transform's
02639                 // parameters to form the starting guess. Instead the Transform itself
02640                 // is perturbed carefully (using quaternion rotation) to overcome problems that arise
02641                 // when you use orthogonally-based Euler angles
02642                 initxform = params["initxform"];
02643         }else {
02644                 initxform = new Transform(); // is the identity
02645         }
02646         
02647         float lphi = params.set_default("phi0",0.0f);
02648         float uphi = params.set_default("phi1",360.0f);
02649         float dphi = params.set_default("dphi",10.f);
02650         float threshold = params.set_default("threshold",0.f);
02651         if (threshold < 0.0f) throw InvalidParameterException("The threshold parameter must be greater than or equal to zero");
02652         bool verbose = params.set_default("verbose",false);
02653         
02654         //in case we arre aligning tomos
02655         Dict altered_cmp_params(cmp_params);
02656         if (cmp_name == "ccc.tomo") {
02657                 altered_cmp_params.set_default("searchx", searchx);
02658                 altered_cmp_params.set_default("searchy", searchy);
02659                 altered_cmp_params.set_default("searchz", searchz);
02660                 altered_cmp_params.set_default("norm", true);
02661         }
02662 
02663         vector<Dict> solns;
02664         if (nsoln == 0) return solns; // What was the user thinking?
02665         for (unsigned int i = 0; i < nsoln; ++i ) {
02666                 Dict d;
02667                 d["score"] = 1.e24;
02668                 Transform t; // identity by default
02669                 d["xform.align3d"] = &t; // deep copy is going on here
02670                 solns.push_back(d);
02671         }
02672 
02673         Dict d;
02674         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
02675         if ( params.has_key("delta") && params.has_key("n") ) {
02676                 throw InvalidParameterException("The delta and n parameters are mutually exclusive in the RT3DSphereAligner aligner");
02677         } else if ( params.has_key("n") ) {
02678                 d["n"] = params["n"];
02679         } else {
02680                 // If they didn't specify either then grab the default delta - if they did supply delta we're still safe doing this
02681                 d["delta"] = params.set_default("delta",10.f);
02682         }
02683 
02684         if ((string)params.set_default("orientgen","eman")=="eman") d["perturb"]=0;
02685         Symmetry3D* sym = Factory<Symmetry3D>::get((string)params.set_default("sym","c1"));
02686         vector<Transform> transforms = sym->gen_orientations((string)params.set_default("orientgen","eman"),d);
02687 
02688         bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0;
02689         
02690         //precompute fixed FT, saves a LOT of time!!!
02691         EMData * this_imgfft = 0;
02692         if(dotrans || tomography){
02693                 this_imgfft = this_img->do_fft();
02694         }
02695         
02696 #ifdef EMAN2_USING_CUDA 
02697         if(EMData::usecuda == 1) {
02698                 cout << "Using CUDA for 3D alignment" << endl;
02699                 if(!to->getcudarodata()) to->copy_to_cudaro(); // Safer call
02700                 if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
02701                 if(this_imgfft) this_imgfft->copy_to_cuda();
02702         }
02703 #endif
02704 
02705         Transform trans = Transform();
02706         Cmp* c = Factory <Cmp>::get(cmp_name, cmp_params);
02707         
02708         bool use_cpu = true;
02709         for(vector<Transform>::const_iterator trans_it = transforms.begin(); trans_it != transforms.end(); trans_it++) {
02710                 Dict params = trans_it->get_params("eman");
02711                 
02712                 if (verbose) {
02713                         float alt = params["alt"];
02714                         float az = params["az"];
02715                         cout << "Trying angle alt: " << alt << " az: " << az << endl;
02716                 }
02717 
02718                 for( float phi = lphi; phi < uphi; phi += dphi ) { 
02719                         params["phi"] = phi;
02720                         Transform t(params);
02721                         t = t*(*initxform);
02722                         
02723                         EMData* transformed;
02724                         transformed = to->process("xform",Dict("transform",&t));
02725                                 
02726                         //need to do things a bit diffrent if we want to compare two tomos
02727                         float best_score = 0.0f;
02728                         // Dotrans is effectievly ignored for tomography
02729                         if(dotrans || tomography){
02730                                 EMData* ccf = transformed->calc_ccf(this_imgfft);
02731 #ifdef EMAN2_USING_CUDA 
02732                                 if(EMData::usecuda == 1){
02733                                         // I use the following code rather than ccc.tomo to avoid doing two CCCs
02734                                         use_cpu = false;
02735                                         CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz);
02736                                         trans.set_trans((float)-data->px, (float)-data->py, (float)-data->pz);
02737                                         t = trans*t;    //composite transform to reflect the fact that we have done a rotation first and THEN a transformation
02738                                         if (tomography) {
02739                                                 float2 stats = get_stats_cuda(ccf->getcudarwdata(), ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize());
02740                                                 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
02741                                         } else {
02742                                                 best_score = -data->peak;
02743                                         }
02744                                         delete data;
02745                                 }
02746 #endif
02747                                 if(use_cpu){
02748                                         // I use the following code rather than ccc.tomo to avoid doing two CCCs
02749                                         if(tomography) ccf->process_inplace("normalize");
02750                                         IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz);
02751                                         trans.set_trans((float)-point[0], (float)-point[1], (float)-point[2]);
02752                                         t = trans*t;    //composite transform to reflect the fact that we have done a rotation first and THEN a transformation
02753                                         best_score = -ccf->get_value_at_wrap(point[0], point[1], point[2]);
02754                                 }
02755                                 delete ccf; ccf =0;
02756                                 delete transformed; transformed = 0;// this is to stop a mem leak
02757                         }
02758 
02759                         if(!tomography){
02760                                 if(!transformed) transformed = to->process("xform",Dict("transform",&t));
02761                                 best_score = c->cmp(this_img,transformed);
02762                                 delete transformed; transformed = 0;
02763                         }
02764 
02765                         unsigned int j = 0;
02766                         //cout << "alt " <<float(t.get_rotation("eman").get("alt")) << " az " << float(t.get_rotation("eman").get("az")) << " phi " << float(t.get_rotation("eman").get("phi")) << endl;
02767                         for ( vector<Dict>::iterator it = solns.begin(); it != solns.end(); ++it, ++j ) {
02768                                 if ( (float)(*it)["score"] > best_score ) { // Note greater than - EMAN2 preferes minimums as a matter of policy
02769                                         vector<Dict>::reverse_iterator rit = solns.rbegin();
02770                                         copy(rit+1,solns.rend()-j,rit);
02771                                         Dict& d = (*it);
02772                                         d["score"] = best_score;
02773                                         t.invert(); //We actually moved the ref onto the moving, so we need to invert to do the opposite(this is done b/c the ref is aligned to the sym axis, whereas the mvoing is not)
02774                                         d["xform.align3d"] = &t; // deep copy is going on here
02775                                         break;
02776                                 }
02777                         }
02778 
02779                 }
02780         }
02781         
02782         if(this_imgfft) {delete this_imgfft; this_imgfft = 0;}
02783         if(sym!=0) delete sym;
02784         if (c != 0) delete c;
02785         
02786         return solns;
02787 
02788 }


Member Data Documentation

const string RT3DSphereAligner::NAME = "rotate_translate_3d" [static]
 

Definition at line 85 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Mon Aug 13 13:41:32 2012 for EMAN2 by  doxygen 1.3.9.1