IMP  2.1.1
The Integrative Modeling Platform
align2D.h
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1 /*!
2  * \file align2D.h
3  * \brief Alignment of images in 2D
4  * Copyright 2007-2013 IMP Inventors. All rights reserved.
5 */
6 
7 #ifndef IMPEM2D_ALIGN_2D_H
8 #define IMPEM2D_ALIGN_2D_H
9 
10 #include "IMP/em2d/em2d_config.h"
12 #include "IMP/algebra/utility.h"
14 #include "IMP/algebra/Vector2D.h"
15 #include <algorithm>
16 #include <vector>
17 
18 IMPEM2D_BEGIN_NAMESPACE
19 
20 //! Definition of the result of an alignment. Contains the transformation
21 //! to apply to the matrix to align and the cross correlation of the solution
22 typedef std::pair<algebra::Transformation2D,double> ResultAlign2D;
23 
24 //! Aligns completely two matrices (rotationally and translationally).
25 //! Uses the autocorrelation function to speed up the rotational alignment
26 /*!
27  \param[in] input Reference matrix
28  \param[in] m_to_align Matrix to align to the reference
29  \param[in] apply if true, apply the transformation
30  to m_to_align after alignment
31  \return The result. Check the definition of ResultAlign2D
32 */
33 IMPEM2DEXPORT ResultAlign2D get_complete_alignment(const cv::Mat &input,
34  cv::Mat &m_to_align,bool apply=false);
35 
36 //! Aligns two matrices rotationally. Based on the autocorrelation function
37 //! of the matrices.
38 /*!
39  \param[in] input Reference matrix
40  \param[in] m_to_align Matrix to align to the reference
41  \param[in] apply if true, apply the transformation
42  to m_to_align after alignment
43  \return The result. Check the definition of ResultAlign2D
44 */
45 IMPEM2DEXPORT em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input,
46  cv::Mat &m_to_align,bool apply=false);
47 
48 
49 //! Aligns two matrices translationally
50 /*!
51  \param[in] input Reference matrix
52  \param[in] m_to_align Matrix to align to the reference
53  \param[in] apply if true, apply the transformation
54  to m_to_align after alignment
55  \return The result. Check the definition of ResultAlign2D
56 */
57 IMPEM2DEXPORT ResultAlign2D get_translational_alignment(const cv::Mat &input,
58  cv::Mat &m_to_align,bool apply=false);
59 
60 
61 //! Aligns two matrices rotationally and translationally without
62 //! performing preprocessing. Preprocessed data must be provided.
63 /*!
64  \param[in] input first matrix
65  \param[in] INPUT fft of the first matrix
66  \param[in] POLAR1 fft of the autocorrelation (in polars) of the input.
67  \param[in] m_to_align the matrix to align with the input
68  \param[in] POLAR2 fft of the autocorrelation (in polars) of m_to_align
69  \param[in] apply true if m_to_align is transformed at the end
70  \return The result. Check the definition of ResultAlign2D
71 */
73  const cv::Mat &input,
74  const cv::Mat &INPUT,const cv::Mat &POLAR1,
75  cv::Mat &m_to_align,const cv::Mat &POLAR2,bool apply=false);
76 
77 //! Computes the rotational alignment for two autocorrelation matrices
78 //! It is assumed that the arguments are FFTs
79 /*!
80  \param[in] POLAR1 fft of the first autocorrelation (in polars)
81  \param[in] POLAR2 fft of the second autocorrelation (in polars)
82  \return The result. Check the definition of ResultAlign2D
83 */
85  const cv::Mat &POLAR1,
86  const cv::Mat &POLAR2);
87 
88 //! Aligns two matrices translationally without preprocessing. The preprocessed
89 //! data must be provided.
90 /*!
91  \param[in] M1 the dft the first matrix (input)
92  \param[in] M2 the dft of the matrix to align with the input
93  \return The result. Check the definition of ResultAlign2D
94 */
96  const cv::Mat &M1,
97  const cv::Mat &M2);
98 
99 
100 
101 
102 
103 //! Aligns two matrices (rotation and translation) using centers and
104 //! no preprocessing. Preprocessed data must be provided.
105 /*!
106  \param[in] center1 weighted centroid of the reference matrix
107  \param[in] center2 weighted centroid of the matrix to align
108  \param[in] AUTOC_POLAR1 fft of the autocorrelation (in polars) of the input.
109  \param[in] AUTOC_POLAR2 fft of the autocorrelation (in polars) of m_to_align
110  \return The result. Check the definition of ResultAlign2D
111 */
112 IMPEM2DEXPORT ResultAlign2D
114  const algebra::Vector2D &center1,
115  const algebra::Vector2D &center2,
116  const cv::Mat &AUTOC_POLAR1,
117  const cv::Mat &AUTOC_POLAR2);
118 
119 
120 IMPEM2D_END_NAMESPACE
121 
122 #endif /* IMPEM2D_ALIGN_2D_H */
std::pair< algebra::Transformation2D, double > ResultAlign2D
Definition: align2D.h:22
ResultAlign2D get_complete_alignment_with_centers_no_preprocessing(const algebra::Vector2D &center1, const algebra::Vector2D &center2, const cv::Mat &AUTOC_POLAR1, const cv::Mat &AUTOC_POLAR2)
ResultAlign2D get_translational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Aligns two matrices translationally.
ResultAlign2D get_complete_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Simple 2D vector class.
2D transformations. Copyright 2007-2013 IMP Inventors. All rights reserved.
ResultAlign2D get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
Functions to deal with very common math operations.
Funtions related with rotations in em2d Copyright 2007-2013 IMP Inventors. All rights reserved...
ResultAlign2D get_translational_alignment_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2)
em2d::ResultAlign2D get_complete_alignment_no_preprocessing(const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)