#include <reconstructor.h>
Inheritance diagram for EMAN::BackProjectionReconstructor:
Public Member Functions | |
BackProjectionReconstructor () | |
virtual | ~BackProjectionReconstructor () |
virtual void | setup () |
Initialize the reconstructor. | |
virtual int | insert_slice (const EMData *const slice, const Transform &euler, const float weight=1.0) |
Insert an image slice to the reconstructor. | |
virtual EMData * | finish (bool doift=true) |
Finish reconstruction and return the complete model. | |
virtual string | get_name () const |
Get the unique name of this class (especially for factory based instantiation access). | |
virtual string | get_desc () const |
Get a clear, concise description of this class. | |
virtual TypeDict | get_param_types () const |
Static Public Member Functions | |
Reconstructor * | NEW () |
Static Public Attributes | |
const string | NAME = "back_projection" |
Private Member Functions | |
BackProjectionReconstructor (const BackProjectionReconstructor &that) | |
BackProjectionReconstructor & | operator= (const BackProjectionReconstructor &) |
void | load_default_settings () |
EMData * | preprocess_slice (const EMData *const slice, const Transform &t) |
While you can just insert unprocessed slices, if you call preprocess_slice yourself, and insert the returned slice instead, repeatedly, it can save a fair bit of computation. |
Back-projection is a method of 3D reconstruction from 2D projections. It is based on superposing 3D functions ("back-projection bodies") obtained by translating the 2D projections along the directions of projection.
Definition at line 659 of file reconstructor.h.
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Definition at line 662 of file reconstructor.h. 00662 { load_default_settings(); }
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Definition at line 664 of file reconstructor.h. 00664 {}
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Finish reconstruction and return the complete model.
Reimplemented from EMAN::Reconstructor. Definition at line 1920 of file reconstructor.cpp. References EMAN::EMData::add(), EMAN::Factory< T >::get(), EMAN::Symmetry3D::get_nsym(), EMAN::Symmetry3D::get_syms(), EMAN::EMData::mult(), and EMAN::EMData::transform(). 01921 { 01922 01923 Symmetry3D* sym = Factory<Symmetry3D>::get((string)params["sym"]); 01924 vector<Transform> syms = sym->get_syms(); 01925 01926 for ( vector<Transform>::const_iterator it = syms.begin(); it != syms.end(); ++it ) { 01927 01928 EMData tmpcopy(*image); 01929 tmpcopy.transform(*it); 01930 image->add(tmpcopy); 01931 } 01932 01933 image->mult(1.0f/(float)sym->get_nsym()); 01934 delete sym; 01935 01936 EMData *ret = image; 01937 image = 0 ; 01938 return ret; 01939 }
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Get a clear, concise description of this class.
Implements EMAN::FactoryBase. Definition at line 685 of file reconstructor.h. 00686 { 00687 return "Simple (unfiltered) back-projection reconstruction. Weighting by contributing particles in the class average is optional and default behaviour"; 00688 }
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Get the unique name of this class (especially for factory based instantiation access).
Implements EMAN::FactoryBase. Definition at line 680 of file reconstructor.h. 00681 {
00682 return NAME;
00683 }
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Implements EMAN::FactoryBase. Definition at line 695 of file reconstructor.h. References EMAN::TypeDict::put(). 00696 { 00697 TypeDict d; 00698 d.put("size", EMObject::INT, "Necessary. The x and y dimensions of the input images."); 00699 d.put("weight", EMObject::FLOAT, "Optional. A temporary value set prior to slice insertion, indicative of the inserted slice's weight. Default sis 1."); 00700 d.put("sym", EMObject::STRING, "Optional. The symmetry to impose on the final reconstruction. Default is c1"); 00701 d.put("zsample", EMObject::INT, "Optional. The z dimensions of the reconstructed volume."); 00702 return d; 00703 }
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Insert an image slice to the reconstructor. To insert multiple image slices, call this function multiple times.
Reimplemented from EMAN::Reconstructor. |
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Definition at line 713 of file reconstructor.h. 00714 { 00715 params["weight"] = 1.0; 00716 params["use_weights"] = true; 00717 params["size"] = 0; 00718 params["sym"] = "c1"; 00719 params["zsample"] = 0; 00720 }
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Definition at line 690 of file reconstructor.h. 00691 { 00692 return new BackProjectionReconstructor(); 00693 }
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While you can just insert unprocessed slices, if you call preprocess_slice yourself, and insert the returned slice instead, repeatedly, it can save a fair bit of computation. The default operation just returns a copy of the image, as the preprocessing is reconstructor-specific.
Reimplemented from EMAN::Reconstructor. Definition at line 1850 of file reconstructor.cpp. References EMAN::Transform::get_mirror(), EMAN::Transform::get_scale(), EMAN::Transform::get_trans_2d(), EMAN::EMData::process(), EMAN::EMData::process_inplace(), EMAN::Transform::set_rotation(), t, EMAN::EMData::transform(), and EMAN::Vec2f. 01851 { 01852 01853 EMData* return_slice = slice->process("normalize.edgemean"); 01854 return_slice->process_inplace("filter.linearfourier"); 01855 01856 Transform tmp(t); 01857 tmp.set_rotation(Dict("type","eman")); // resets the rotation to 0 implicitly 01858 Vec2f trans = tmp.get_trans_2d(); 01859 float scale = tmp.get_scale(); 01860 bool mirror = tmp.get_mirror(); 01861 if (trans[0] != 0 || trans[1] != 0 || scale != 1.0 ) { 01862 return_slice->transform(tmp); 01863 } else if ( mirror == true ) { 01864 return_slice = slice->process("xform.flip",Dict("axis","x")); 01865 } 01866 01867 return return_slice; 01868 }
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Initialize the reconstructor.
Implements EMAN::Reconstructor. Definition at line 1839 of file reconstructor.cpp. References EMAN::EMData::set_size(). 01840 { 01841 int size = params["size"]; 01842 image = new EMData(); 01843 nx = size; 01844 ny = size; 01845 if ( (int) params["zsample"] != 0 ) nz = params["zsample"]; 01846 else nz = size; 01847 image->set_size(nx, ny, nz); 01848 }
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Definition at line 80 of file reconstructor.cpp. |