EMAN::Refine3DAlignerGrid Class Reference
[a function or class that is CUDA enabled]

Refine alignment. More...

#include <aligner.h>

Inheritance diagram for EMAN::Refine3DAlignerGrid:

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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
 To align 'this_img' with another image passed in through its parameters.
virtual EMDataalign (EMData *this_img, EMData *to_img) const
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 AlignerNEW ()

Static Public Attributes

static const string NAME = "refine_3d_grid"

Detailed Description

Refine alignment.

Refines a preliminary 3D alignment using a sampling grid. This is a port from tomohunter, but the az sampling scheme is altered cuch that the points on the sphere are equidistant (Improves speed several hundered times). The distance between the points on the sphere is 'delta' and the range(distance from the pole, 0,0,0 position) is given as 'range'. IN general this refinement scheme is a bit slower than the Quaternion Simplex aligner, but perfroms better in the presence of noise(according to current dogma).

Parameters:
xform.align3d The Transform from the previous course alignment. If unspecified the identity matrix is used
delta The angluar distance bewteen points on the spehere used in the grid
range The size of the grid. Measured in angluar distance from the north pole
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
Date:
Mar 2011

Definition at line 916 of file aligner.h.


Member Function Documentation

virtual EMData* EMAN::Refine3DAlignerGrid::align ( EMData this_img,
EMData to_img 
) const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 922 of file aligner.h.

References align().

00923                         {
00924                                 return align(this_img, to_img, "sqeuclidean", Dict());
00925                         }

EMData * Refine3DAlignerGrid::align ( EMData this_img,
EMData to_img,
const string &  cmp_name = "sqeuclidean",
const Dict cmp_params = Dict() 
) const [virtual]

To align 'this_img' with another image passed in through its parameters.

The alignment uses a user-given comparison method to compare the two images. If none is given, a default one is used.

Parameters:
this_img The image to be compared.
to_img 'this_img" is aligned with 'to_img'.
cmp_name The comparison method to compare the two images.
cmp_params The parameter dictionary for comparison method.
Returns:
The aligned image.

Implements EMAN::Aligner.

Definition at line 1715 of file aligner.cpp.

References EMAN::EMData::calc_ccf(), EMAN::EMData::calc_max_location_wrap(), calc_max_location_wrap_cuda(), EMAN::EMData::cmp(), data, EMAN::EMData::do_fft(), EMAN::EMData::get_attr(), EMAN::EMData::get_ndim(), get_stats_cuda(), EMAN::Transform::get_trans(), 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::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_trans(), sqrt(), and t.

Referenced by align().

01717 {
01718         if ( this_img->get_ndim() != 3 || to->get_ndim() != 3 ) {
01719                 throw ImageDimensionException("This aligner only works for 3D images");
01720         }
01721 
01722         Transform* t;
01723         if (params.has_key("xform.align3d") ) {
01724                 // Unlike the 2d refine aligner, this class doesn't require the starting transform's
01725                 // parameters to form the starting guess. Instead the Transform itself
01726                 // is perturbed carefully (using quaternion rotation) to overcome problems that arise
01727                 // when you use orthogonally-based Euler angles
01728                 t = params["xform.align3d"];
01729         }else {
01730                 t = new Transform(); // is the identity
01731         }
01732         
01733         int searchx = 0;
01734         int searchy = 0;
01735         int searchz = 0;
01736         
01737         bool dotrans = params.set_default("dotrans",1);
01738         if (params.has_key("search")) {
01739                 vector<string> check;
01740                 check.push_back("searchx");
01741                 check.push_back("searchy");
01742                 check.push_back("searchz");
01743                 for(vector<string>::const_iterator cit = check.begin(); cit != check.end(); ++cit) {
01744                         if (params.has_key(*cit)) throw InvalidParameterException("The search parameter is mutually exclusive of the searchx, searchy, and searchz parameters");
01745                 }
01746                 int search  = params["search"];
01747                 searchx = search;
01748                 searchy = search;
01749                 searchz = search;
01750         } else {
01751                 searchx = params.set_default("searchx",3);
01752                 searchy = params.set_default("searchy",3);
01753                 searchz = params.set_default("searchz",3);
01754         }       
01755         
01756         float delta = params.set_default("delta",1.0f);
01757         float range = params.set_default("range",10.0f);
01758         bool verbose = params.set_default("verbose",false);
01759         
01760         bool tomography = (cmp_name == "ccc.tomo") ? 1 : 0;
01761         EMData * tofft = 0;
01762         if(dotrans || tomography){
01763                 tofft = to->do_fft();
01764         }
01765         
01766 #ifdef EMAN2_USING_CUDA 
01767         if(EMData::usecuda == 1) {
01768                 if(!this_img->isrodataongpu()) this_img->copy_to_cudaro();
01769                 if(!to->cudarwdata) to->copy_to_cuda();
01770                 if(to->cudarwdata){if(tofft) tofft->copy_to_cuda();}
01771         }
01772 #endif
01773 
01774         Dict d;
01775         d["type"] = "eman"; // d is used in the loop below
01776         Dict best;
01777         best["score"] = 0.0f;
01778         bool use_cpu = true;
01779         Transform tran = Transform();
01780         for ( float alt = 0; alt < range; alt += delta) {
01781                 // now compute a sane az step size 
01782                 float saz = 360;
01783                 if(alt != 0) saz = delta/sin(alt*M_PI/180.0f); // This gives consistent az step sizes(arc lengths)
01784                 for ( float az = 0; az < 360; az += saz ){
01785                         if (verbose) {
01786                                 cout << "Trying angle alt " << alt << " az " << az << endl;
01787                         }
01788                         // account for any changes in az
01789                         for( float phi = -range-az; phi < range-az; phi += delta ) {
01790                                 d["alt"] = alt;
01791                                 d["phi"] = phi; 
01792                                 d["az"] = az;
01793                                 Transform tr(d);
01794                                 tr = tr*(*t);   // compose transforms, this moves to the pole (aprox)
01795                                 
01796                                 EMData* transformed = this_img->process("xform",Dict("transform",&tr));
01797                                 
01798                                 //need to do things a bit diffrent if we want to compare two tomos
01799                                 float score = 0.0f;
01800                                 if(dotrans || tomography){
01801                                         EMData* ccf = transformed->calc_ccf(tofft);
01802 #ifdef EMAN2_USING_CUDA 
01803                                         if(to->cudarwdata){
01804                                                 use_cpu = false;
01805                                                 CudaPeakInfo* data = calc_max_location_wrap_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz);
01806                                                 tran.set_trans((float)-data->px, (float)-data->py, (float)-data->pz);
01807                                                 //CudaPeakInfoFloat* data = calc_max_location_wrap_intp_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize(), searchx, searchy, searchz);
01808                                                 //tran.set_trans(-data->xintp, -data->yintp, -data->zintp);
01809                                                 tr = tran*tr;
01810                                                 if (tomography) {
01811                                                         float2 stats = get_stats_cuda(ccf->cudarwdata, ccf->get_xsize(), ccf->get_ysize(), ccf->get_zsize());
01812                                                         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
01813                                                 } else {
01814                                                         score = -data->peak;
01815                                                 }
01816                                                 delete data;
01817                                         }
01818 #endif
01819                                         if(use_cpu){
01820                                                 if(tomography) ccf->process_inplace("normalize");
01821                                                 //vector<float> fpoint = ccf->calc_max_location_wrap_intp(searchx,searchy,searchz);
01822                                                 //tran.set_trans(-fpoint[0], -fpoint[1], -fpoint[2]);
01823                                                 //score = -fpoint[3];
01824                                                 IntPoint point = ccf->calc_max_location_wrap(searchx,searchy,searchz);
01825                                                 tran.set_trans((float)-point[0], (float)-point[1], (float)-point[2]);
01826                                                 score = -ccf->get_value_at_wrap(point[0], point[1], point[2]);
01827                                                 tr = tran*tr;
01828                                                 
01829                                         }
01830                                         delete ccf; ccf =0;
01831                                         delete transformed; transformed = 0;// this is to stop a mem leak
01832                                 }
01833 
01834                                 if(!tomography){
01835                                         if(!transformed) transformed = this_img->process("xform",Dict("transform",&tr)); // we are returning a map
01836                                         score = transformed->cmp(cmp_name,to,cmp_params); //this is not very efficient as it creates a new cmp object for each iteration
01837                                         delete transformed; transformed = 0;// this is to stop a mem leak
01838                                 }
01839                                 
01840                                 if(score < float(best["score"])) {
01841                                         best["score"] = score;
01842                                         best["xform.align3d"] = &tr; // I wonder if this will cause a mem leak?
01843                                 }       
01844                         }
01845                 }
01846         }
01847 
01848         if(tofft) {delete tofft; tofft = 0;}
01849         
01850         //make aligned map;
01851         EMData* best_match = this_img->process("xform",Dict("transform", best["xform.align3d"])); // we are returning a map
01852         best_match->set_attr("xform.align3d", best["xform.align3d"]);
01853         best_match->set_attr("score", float(best["score"]));
01854         
01855         //debug....
01856         Transform* zz = best_match->get_attr("xform.align3d");
01857         Vec3f zzz = zz->get_trans();
01858         cout << "x " << float(zzz[0]) << " y " << float(zzz[1]) << " z " << float(zzz[2]) << endl;
01859         
01860         return best_match;
01861         
01862 }

virtual string EMAN::Refine3DAlignerGrid::get_desc (  )  const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 932 of file aligner.h.

00933                         {
00934                                 return "Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.";
00935                         }

virtual string EMAN::Refine3DAlignerGrid::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 927 of file aligner.h.

References NAME.

00928                         {
00929                                 return NAME;
00930                         }

virtual TypeDict EMAN::Refine3DAlignerGrid::get_param_types (  )  const [inline, virtual]

Implements EMAN::Aligner.

Definition at line 942 of file aligner.h.

References EMAN::EMObject::BOOL, EMAN::EMObject::FLOAT, EMAN::EMObject::INT, EMAN::TypeDict::put(), and EMAN::EMObject::TRANSFORM.

00943                         {
00944                                 TypeDict d;
00945                                 d.put("xform.align3d", EMObject::TRANSFORM,"The Transform storing the starting guess. If unspecified the identity matrix is used");
00946                                 d.put("delta", EMObject::FLOAT, "The angular step size. Default is 1." );
00947                                 d.put("range", EMObject::FLOAT, "The angular range size. Default is 10." );
00948                                 d.put("dotrans", EMObject::BOOL,"Do a translational search. Default is True(1)");
00949                                 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.");
00950                                 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.");
00951                                 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.");
00952                                 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");
00953                                 d.put("maxshift", EMObject::INT,"Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.");
00954                                 d.put("verbose", EMObject::BOOL,"Turn this on to have useful information printed to standard out.");
00955                                 return d;
00956                         }

static Aligner* EMAN::Refine3DAlignerGrid::NEW (  )  [inline, static]

Definition at line 937 of file aligner.h.

00938                         {
00939                                 return new Refine3DAlignerGrid();
00940                         }


Member Data Documentation

const string Refine3DAlignerGrid::NAME = "refine_3d_grid" [static]

Definition at line 958 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Thu Mar 10 22:59:05 2011 for EMAN2 by  doxygen 1.4.7