Main Page | Modules | Namespace List | Class Hierarchy | Alphabetical List | Class List | Directories | File List | Namespace Members | Class Members | File Members

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

rotational alignment using angular correlation More...

#include <aligner.h>

Inheritance diagram for EMAN::RotationalAligner:

Inheritance graph
[legend]
Collaboration diagram for EMAN::RotationalAligner:

Collaboration graph
[legend]
List of all members.

Public Member Functions

virtual EMDataalign (EMData *this_img, EMData *to_img, const string &cmp_name="dot", 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

AlignerNEW ()
EMDataalign_180_ambiguous (EMData *this_img, EMData *to_img, int rfp_mode=2, int zscore=0)

Static Public Attributes

const string NAME = "rotational"

Detailed Description

rotational alignment using angular correlation

Parameters:
rfp_mode Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding

Definition at line 285 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 291 of file aligner.h.

References align().

00292                 {
00293                         return align(this_img, to_img, "dot", Dict());
00294                 }

EMData * RotationalAligner::align EMData this_img,
EMData to_img,
const string &  cmp_name = "dot",
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 440 of file aligner.cpp.

References align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), InvalidParameterException, EMAN::EMData::process(), EMAN::EMData::set_attr(), and EMAN::Dict::set_default().

00442 {
00443         if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL");
00444         
00445 #ifdef EMAN2_USING_CUDA
00446         if(EMData::usecuda == 1) {
00447                 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
00448                 //if(!to->getcudarwdata()) to->copy_to_cuda();
00449         }
00450 #endif
00451 
00452         // Perform 180 ambiguous alignment
00453         int rfp_mode = params.set_default("rfp_mode",2);
00454         int zscore = params.set_default("zscore",0);
00455         int ambig180 = params.set_default("ambig180",0);
00456         
00457         EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode,zscore);
00458         Transform * tmp = rot_aligned->get_attr("xform.align2d");
00459         Dict rot = tmp->get_rotation("2d");
00460         float rotate_angle_solution = rot["alpha"];
00461         delete tmp;
00462 
00463         // Don't resolve the 180 degree ambiguity here
00464         if (ambig180) {
00465                 return rot_aligned;
00466         }
00467         
00468         EMData *rot_align_180 = rot_aligned->process("math.rotate.180");
00469 
00470         // Generate the comparison metrics for both rotational candidates
00471         float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params);
00472         float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params);
00473 
00474         // Decide on the result
00475         float score = 0.0;
00476         EMData* result = NULL;
00477         if (rot_cmp < rot_180_cmp){
00478                 result = rot_aligned;
00479                 score = rot_cmp;
00480                 delete rot_align_180; rot_align_180 = 0;
00481         } else {
00482                 result = rot_align_180;
00483                 score = rot_180_cmp;
00484                 delete rot_aligned; rot_aligned = 0;
00485                 rotate_angle_solution = rotate_angle_solution-180.0f;
00486         }
00487 
00488 //      Transform* t = get_align_attr("xform.align2d",result);
00489 //      t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00490         Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution));
00491         result->set_attr("xform.align2d",&tmp2);
00492         return result;
00493 }

EMData * RotationalAligner::align_180_ambiguous EMData this_img,
EMData to_img,
int  rfp_mode = 2,
int  zscore = 0
[static]
 

Definition at line 386 of file aligner.cpp.

References EMAN::EMData::calc_ccfx(), data, EMAN::Util::find_max(), EMAN::EMData::get_data(), EMAN::EMData::get_xsize(), EMAN::EMData::get_ysize(), InvalidParameterException, EMAN::EMData::make_rotational_footprint(), EMAN::EMData::make_rotational_footprint_cmc(), EMAN::EMData::make_rotational_footprint_e1(), EMAN::EMData::process(), and EMAN::EMData::set_attr().

Referenced by EMAN::RotateTranslateAligner::align(), and align().

00386                                                                                                        {
00387 
00388         // Make translationally invariant rotational footprints
00389         EMData* this_img_rfp, * to_rfp;
00390         if (rfp_mode == 0) {
00391                 this_img_rfp = this_img->make_rotational_footprint_e1();
00392                 to_rfp = to->make_rotational_footprint_e1();
00393         } else if (rfp_mode == 1) {
00394                 this_img_rfp = this_img->make_rotational_footprint();
00395                 to_rfp = to->make_rotational_footprint();
00396         } else if (rfp_mode == 2) {
00397                 this_img_rfp = this_img->make_rotational_footprint_cmc();
00398                 to_rfp = to->make_rotational_footprint_cmc();
00399         } else {
00400                 throw InvalidParameterException("rfp_mode must be 0,1 or 2");
00401         }
00402         int this_img_rfp_nx = this_img_rfp->get_xsize();
00403 
00404         // Do row-wise correlation, returning a sum.
00405         EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize(),false,false,zscore);
00406 // cf->process_inplace("normalize");
00407 // cf->write_image("ralisum.hdf",-1);
00408 //      
00409 // EMData *cf2 = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize(),true);
00410 // cf2->write_image("ralistack.hdf",-1);
00411 // delete cf2;
00412 
00413         // Delete them, they're no longer needed
00414         delete this_img_rfp; this_img_rfp = 0;
00415         delete to_rfp; to_rfp = 0;
00416 
00417         // Now solve the rotational alignment by finding the max in the column sum
00418         float *data = cf->get_data();
00419         
00420         float peak = 0;
00421         int peak_index = 0;
00422         Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
00423 
00424         if( cf ) {
00425                 delete cf;
00426                 cf = 0;
00427         }
00428         float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
00429 
00430         // Return the result
00431         Transform tmp(Dict("type","2d","alpha",rot_angle));
00432         cf=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00433 //      Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
00434 //      Dict d("type","2d","alpha",rot_angle);
00435 //      t->set_rotation(d);
00436         cf->set_attr("xform.align2d",&tmp);
00437         return cf;
00438 }

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

Implements EMAN::Aligner.

Definition at line 301 of file aligner.h.

00302                 {
00303                         return "Performs rotational alignment, even on poorly centered images, but leaves a 180 degree ambiguity which requires a translational alignment to resolve. Usually called internally by rotate_translate aligner.";
00304                 }

virtual string EMAN::RotationalAligner::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 296 of file aligner.h.

00297                 {
00298                         return NAME;
00299                 }

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

Implements EMAN::Aligner.

Definition at line 313 of file aligner.h.

References EMAN::TypeDict::put().

00314                 {
00315                         TypeDict d;
00316                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding.");
00317                         d.put("zscore", EMObject::INT,"Either 0 or 1. If set, will convert per-radius CCF curves into Z-score significnace curves before averaging. In theory this should produce better results by focusing on radii with more alignment information. (default=false)");
00318                         d.put("ambig180", EMObject::INT,"Either 0 or 1. If set, will not try and resolve the 180 degree ambiguity. If not set, it will assume the particle is well centered and resolve the ambiguity that way. default=false");
00319                         return d;
00320                 }

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

Definition at line 306 of file aligner.h.

00307                 {
00308                         return new RotationalAligner();
00309                 }


Member Data Documentation

const string RotationalAligner::NAME = "rotational" [static]
 

Definition at line 60 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:41:46 2013 for EMAN2 by  doxygen 1.3.9.1