#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 811 of file aligner.h.
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Implements EMAN::Aligner. Definition at line 816 of file aligner.h. References align(). 00817 { 00818 return align(this_img, to_img, "sqeuclidean", Dict()); 00819 }
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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 793 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. 00795 { 00796 // Get the non flipped rotational, tranlsationally aligned image 00797 Dict rt_params("maxshift", params["maxshift"], "rfp_mode", params.set_default("rfp_mode",2),"useflcf",params.set_default("useflcf",0),"zscore",params.set_default("zscore",0)); 00798 EMData *rot_trans_align = this_img->align("rotate_translate",to,rt_params,cmp_name, cmp_params); 00799 00800 // Do the same alignment, but using the flipped version of the image 00801 EMData *flipped = params.set_default("flip", (EMData *) 0); 00802 bool delete_flag = false; 00803 if (flipped == 0) { 00804 flipped = to->process("xform.flip", Dict("axis", "x")); 00805 delete_flag = true; 00806 } 00807 00808 EMData * rot_trans_align_flip = this_img->align("rotate_translate", flipped, rt_params, cmp_name, cmp_params); 00809 Transform * t = rot_trans_align_flip->get_attr("xform.align2d"); 00810 t->set_mirror(true); 00811 rot_trans_align_flip->set_attr("xform.align2d",t); 00812 delete t; 00813 00814 // Now finally decide on what is the best answer 00815 float cmp1 = rot_trans_align->cmp(cmp_name, to, cmp_params); 00816 float cmp2 = rot_trans_align_flip->cmp(cmp_name, flipped, cmp_params); 00817 00818 if (delete_flag){ 00819 if(flipped) { 00820 delete flipped; 00821 flipped = 0; 00822 } 00823 } 00824 00825 EMData *result = 0; 00826 if (cmp1 < cmp2 ) { 00827 00828 if( rot_trans_align_flip ) { 00829 delete rot_trans_align_flip; 00830 rot_trans_align_flip = 0; 00831 } 00832 result = rot_trans_align; 00833 } 00834 else { 00835 if( rot_trans_align ) { 00836 delete rot_trans_align; 00837 rot_trans_align = 0; 00838 } 00839 result = rot_trans_align_flip; 00840 result->process_inplace("xform.flip",Dict("axis","x")); 00841 } 00842 00843 return result; 00844 }
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Implements EMAN::Aligner. Definition at line 826 of file aligner.h. 00827 { 00828 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"; 00829 }
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Get the Aligner's name. Each Aligner is identified by a unique name.
Implements EMAN::Aligner. Definition at line 821 of file aligner.h. 00822 {
00823 return NAME;
00824 }
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Implements EMAN::Aligner. Definition at line 836 of file aligner.h. 00837 { 00838 return static_get_param_types(); 00839 }
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Definition at line 831 of file aligner.h. 00832 { 00833 return new RotateTranslateFlipAligner(); 00834 }
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Definition at line 841 of file aligner.h. References EMAN::TypeDict::put(). 00841 { 00842 TypeDict d; 00843 00844 d.put("flip", EMObject::EMDATA); 00845 d.put("usedot", EMObject::INT); 00846 d.put("maxshift", EMObject::INT, "Maximum translation in pixels"); 00847 d.put("rfp_mode", EMObject::INT,"Either 0,1 or 2. A temporary flag for testing the rotational foot print"); 00848 d.put("useflcf", EMObject::INT,"Use Fast Local Correlation Function rather than CCF for translational alignment"); 00849 d.put("zscore", EMObject::INT,"Either 0 or 1. This option is passed directly to the rotational aligner (default=false)"); 00850 return d; 00851 }
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Definition at line 71 of file aligner.cpp. |