#include <aligner.h>
Inheritance diagram for EMAN::RotateTranslateFlipAligner:
Public Member Functions | |
virtual EMData * | align (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 EMData * | align (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 | |
Aligner * | NEW () |
TypeDict | static_get_param_types () |
Static Public Attributes | |
const string | NAME = "rotate_translate_flip" |
flip | ||
usedot | ||
maxshift | Maximum translation in pixels | |
rfp_mode | Either 0,1 or 2. A temporary flag for testing the rotational foot print |
Definition at line 807 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 812 of file aligner.h. References align(). 00813 { 00814 return align(this_img, to_img, "sqeuclidean", Dict()); 00815 }
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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.
Implements EMAN::Aligner. Definition at line 778 of file aligner.cpp. References EMAN::EMData::align(), EMAN::EMData::cmp(), EMAN::EMData::get_attr(), EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::EMData::set_attr(), EMAN::Dict::set_default(), EMAN::Transform::set_mirror(), and t. 00780 { 00781 // Get the non flipped rotational, tranlsationally aligned image 00782 Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",2),"useflcf",params.set_default("useflcf",0)); 00783 EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params); 00784 00785 // Do the same alignment, but using the flipped version of the image 00786 EMData *flipped = params.set_default("flip", (EMData *) 0); 00787 bool delete_flag = false; 00788 if (flipped == 0) { 00789 flipped = to->process("xform.flip", Dict("axis", "x")); 00790 delete_flag = true; 00791 } 00792 00793 EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params); 00794 Transform * t = rot_trans_align_flip->get_attr("xform.align2d"); 00795 t->set_mirror(true); 00796 rot_trans_align_flip->set_attr("xform.align2d",t); 00797 delete t; 00798 00799 // Now finally decide on what is the best answer 00800 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00801 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00802 00803 if (delete_flag){ 00804 if(flipped) { 00805 delete flipped; 00806 flipped = 0; 00807 } 00808 } 00809 00810 EMData *result = 0; 00811 if (cmp1 < cmp2 ) { 00812 00813 if( rot_trans_align_flip ) { 00814 delete rot_trans_align_flip; 00815 rot_trans_align_flip = 0; 00816 } 00817 result = rot_trans_align; 00818 } 00819 else { 00820 if( rot_trans_align ) { 00821 delete rot_trans_align; 00822 rot_trans_align = 0; 00823 } 00824 result = rot_trans_align_flip; 00825 result->process_inplace("xform.flip",Dict("axis","x")); 00826 } 00827 00828 return result; 00829 }
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Implements EMAN::Aligner. Definition at line 822 of file aligner.h. 00823 { 00824 return " Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution"; 00825 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 817 of file aligner.h. 00818 {
00819 return NAME;
00820 }
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Implements EMAN::Aligner. Definition at line 832 of file aligner.h. 00833 { 00834 return static_get_param_types(); 00835 }
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Definition at line 827 of file aligner.h. 00828 { 00829 return new RotateTranslateFlipAligner(); 00830 }
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Definition at line 837 of file aligner.h. References EMAN::TypeDict::put(). 00837 { 00838 TypeDict d; 00839 00840 d.put("flip", EMObject::EMDATA); 00841 d.put("usedot", EMObject::INT); 00842 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00843 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print"); 00844 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00845 return d; 00846 }
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Definition at line 71 of file aligner.cpp. |