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:

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Collaboration diagram for EMAN::RotationalAligner:

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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

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

Static Public Attributes

static 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 218 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 224 of file aligner.h.

References align().

00225                 {
00226                         return align(this_img, to_img, "dot", Dict());
00227                 }

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 304 of file aligner.cpp.

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

Referenced by align().

00306 {
00307         if (!to) throw InvalidParameterException("Can not rotational align - the image to align to is NULL");
00308         
00309 #ifdef EMAN2_USING_CUDA
00310         if(EMData::usecuda == 1) {
00311                 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
00312                 //if(!to->getcudarwdata()) to->copy_to_cuda();
00313         }
00314 #endif
00315 
00316         // Perform 180 ambiguous alignment
00317         int rfp_mode = params.set_default("rfp_mode",0);
00318         EMData* rot_aligned = RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode);
00319         Transform * tmp = rot_aligned->get_attr("xform.align2d");
00320         Dict rot = tmp->get_rotation("2d");
00321         float rotate_angle_solution = rot["alpha"];
00322         delete tmp;
00323 
00324         EMData *rot_align_180 = rot_aligned->process("math.rotate.180");
00325 
00326         // Generate the comparison metrics for both rotational candidates
00327         float rot_cmp = rot_aligned->cmp(cmp_name, to, cmp_params);
00328         float rot_180_cmp = rot_align_180->cmp(cmp_name, to, cmp_params);
00329 
00330         // Decide on the result
00331         float score = 0.0;
00332         EMData* result = NULL;
00333         if (rot_cmp < rot_180_cmp){
00334                 result = rot_aligned;
00335                 score = rot_cmp;
00336                 delete rot_align_180; rot_align_180 = 0;
00337         } else {
00338                 result = rot_align_180;
00339                 score = rot_180_cmp;
00340                 delete rot_aligned; rot_aligned = 0;
00341                 rotate_angle_solution = rotate_angle_solution-180.0f;
00342         }
00343 
00344 //      Transform* t = get_align_attr("xform.align2d",result);
00345 //      t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00346         Transform tmp2(Dict("type","2d","alpha",rotate_angle_solution));
00347         result->set_attr("xform.align2d",&tmp2);
00348         return result;
00349 }

EMData * RotationalAligner::align_180_ambiguous ( EMData this_img,
EMData to_img,
int  rfp_mode = 0 
) [static]

Definition at line 256 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().

00256                                                                                             {
00257 
00258         // Make translationally invariant rotational footprints
00259         EMData* this_img_rfp, * to_rfp;
00260         if (rfp_mode == 0) {
00261                 this_img_rfp = this_img->make_rotational_footprint_e1();
00262                 to_rfp = to->make_rotational_footprint_e1();
00263         } else if (rfp_mode == 1) {
00264                 this_img_rfp = this_img->make_rotational_footprint();
00265                 to_rfp = to->make_rotational_footprint();
00266         } else if (rfp_mode == 2) {
00267                 this_img_rfp = this_img->make_rotational_footprint_cmc();
00268                 to_rfp = to->make_rotational_footprint_cmc();
00269         } else {
00270                 throw InvalidParameterException("rfp_mode must be 0,1 or 2");
00271         }
00272         int this_img_rfp_nx = this_img_rfp->get_xsize();
00273 
00274         // Do row-wise correlation, returning a sum.
00275         EMData *cf = this_img_rfp->calc_ccfx(to_rfp, 0, this_img->get_ysize());
00276         
00277         // Delete them, they're no longer needed
00278         delete this_img_rfp; this_img_rfp = 0;
00279         delete to_rfp; to_rfp = 0;
00280 
00281         // Now solve the rotational alignment by finding the max in the column sum
00282         float *data = cf->get_data();
00283         
00284         float peak = 0;
00285         int peak_index = 0;
00286         Util::find_max(data, this_img_rfp_nx, &peak, &peak_index);
00287 
00288         if( cf ) {
00289                 delete cf;
00290                 cf = 0;
00291         }
00292         float rot_angle = (float) (peak_index * 180.0f / this_img_rfp_nx);
00293 
00294         // Return the result
00295         Transform tmp(Dict("type","2d","alpha",rot_angle));
00296         cf=this_img->process("xform",Dict("transform",(Transform*)&tmp));
00297 //      Transform* t = get_set_align_attr("xform.align2d",cf,this_img);
00298 //      Dict d("type","2d","alpha",rot_angle);
00299 //      t->set_rotation(d);
00300         cf->set_attr("xform.align2d",&tmp);
00301         return cf;
00302 }

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

Implements EMAN::Aligner.

Definition at line 234 of file aligner.h.

00235                 {
00236                         return "Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment";
00237                 }

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 229 of file aligner.h.

References NAME.

00230                 {
00231                         return NAME;
00232                 }

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

Implements EMAN::Aligner.

Definition at line 246 of file aligner.h.

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

00247                 {
00248                         TypeDict d;
00249                         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.");
00250                         return d;
00251                 }

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

Definition at line 239 of file aligner.h.

00240                 {
00241                         return new RotationalAligner();
00242                 }


Member Data Documentation

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

Definition at line 253 of file aligner.h.

Referenced by get_name().


The documentation for this class was generated from the following files:
Generated on Tue Jul 12 13:47:50 2011 for EMAN2 by  doxygen 1.4.7