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

rotational, translational alignment More...

#include <aligner.h>

Inheritance diagram for EMAN::RotateTranslateAligner:

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Collaboration diagram for EMAN::RotateTranslateAligner:

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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

AlignerNEW ()

Static Public Attributes

const string NAME = "rotate_translate"

Detailed Description

rotational, translational alignment

Parameters:
maxshift Maximum translation in pixels
nozero Zero translation not permitted (useful for CCD images)
rfp_mode Either 0,1 or 2. A temporary flag for testing the rotational foot print

Definition at line 412 of file aligner.h.


Member Function Documentation

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

Implements EMAN::Aligner.

Definition at line 418 of file aligner.h.

References align().

00419                 {
00420                         return align(this_img, to_img, "sqeuclidean", Dict());
00421                 }

EMData * RotateTranslateAligner::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 706 of file aligner.cpp.

References EMAN::EMData::align(), EMAN::RotationalAligner::align_180_ambiguous(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::Transform::get_rotation(), EMAN::EMData::process(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_rotation(), and t.

00708 {
00709 
00710 #ifdef EMAN2_USING_CUDA
00711         if(EMData::usecuda == 1) {
00712                 //if(!this_img->getcudarwdata()) this_img->copy_to_cuda();
00713                 //if(!to->getcudarwdata()) to->copy_to_cuda();
00714         }
00715 #endif
00716 
00717         // Get the 180 degree ambiguously rotationally aligned and its 180 degree rotation counterpart
00718         int zscore = params.set_default("zscore",0);
00719         int rfp_mode = params.set_default("rfp_mode",2);
00720         EMData *rot_align  =  RotationalAligner::align_180_ambiguous(this_img,to,rfp_mode,zscore);
00721         Transform * tmp = rot_align->get_attr("xform.align2d");
00722         Dict rot = tmp->get_rotation("2d");
00723         float rotate_angle_solution = rot["alpha"];
00724         delete tmp;
00725 
00726         EMData *rot_align_180 = rot_align->process("math.rotate.180");
00727 
00728         Dict trans_params;
00729         trans_params["intonly"]  = 0;
00730         trans_params["maxshift"] = params.set_default("maxshift", -1);
00731         trans_params["useflcf"]=params.set_default("useflcf",0);
00732 
00733         // Do the first case translational alignment
00734         trans_params["nozero"]   = params.set_default("nozero",false);
00735         EMData* rot_trans = rot_align->align("translational", to, trans_params, cmp_name, cmp_params);
00736         if( rot_align ) { // Clean up
00737                 delete rot_align;
00738                 rot_align = 0;
00739         }
00740 
00741         // Do the second case translational alignment
00742         EMData*  rot_180_trans = rot_align_180->align("translational", to, trans_params, cmp_name, cmp_params);
00743         if( rot_align_180 )     { // Clean up
00744                 delete rot_align_180;
00745                 rot_align_180 = 0;
00746         }
00747 
00748         // Finally decide on the result
00749         float cmp1 = rot_trans->cmp(cmp_name, to, cmp_params);
00750         float cmp2 = rot_180_trans->cmp(cmp_name, to, cmp_params);
00751 
00752         EMData *result = 0;
00753         if (cmp1 < cmp2) { // All comparators are defined so default return is "smaller is better"
00754                 if( rot_180_trans )     {
00755                         delete rot_180_trans;
00756                         rot_180_trans = 0;
00757                 }
00758                 result = rot_trans;
00759         }
00760         else {
00761                 if( rot_trans ) {
00762                         delete rot_trans;
00763                         rot_trans = 0;
00764                 }
00765                 result = rot_180_trans;
00766                 rotate_angle_solution -= 180.f;
00767         }
00768 
00769         Transform* t = result->get_attr("xform.align2d");
00770         t->set_rotation(Dict("type","2d","alpha",rotate_angle_solution));
00771         result->set_attr("xform.align2d",t);
00772         delete t;
00773 
00774         return result;
00775 }

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

Implements EMAN::Aligner.

Definition at line 428 of file aligner.h.

00429                 {
00430                         return "Performs rotational alignment and follows this with translational alignment.";
00431                 }

virtual string EMAN::RotateTranslateAligner::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 423 of file aligner.h.

00424                 {
00425                         return NAME;
00426                 }

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

Implements EMAN::Aligner.

Definition at line 438 of file aligner.h.

References EMAN::TypeDict::put().

00439                 {
00440                         TypeDict d;
00441                         //d.put("usedot", EMObject::INT);
00442                         d.put("maxshift", EMObject::INT, "Maximum translation in pixels");
00443                         d.put("nozero", EMObject::INT,"Zero translation not permitted (useful for CCD images)");
00444                         d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print");
00445                         d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment");
00446                         d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)");
00447                         return d;
00448                 }

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

Definition at line 433 of file aligner.h.

00434                 {
00435                         return new RotateTranslateAligner();
00436                 }


Member Data Documentation

const string RotateTranslateAligner::NAME = "rotate_translate" [static]
 

Definition at line 63 of file aligner.cpp.


The documentation for this class was generated from the following files:
Generated on Tue Jun 11 13:47:42 2013 for EMAN2 by  doxygen 1.3.9.1