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Commit 31499b97 by Maarten L. Hekkelman
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Fix the 3d alignment code

parent 45f33e4b
Showing with 375 additions and 422 deletions
include/cif++/Matrix.hpp deleted 100644 → 0
/*-
* SPDX-License-Identifier: BSD-2-Clause
*
* Copyright Maarten L. Hekkelman, Radboud University 2008-2011.
* Copyright (c) 2021 NKI/AVL, Netherlands Cancer Institute
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
// --------------------------------------------------------------------
// uBlas compatible matrix types
#pragma once
#include <iostream>
#include <vector>
// matrix is m x n, addressing i,j is 0 <= i < m and 0 <= j < n
// element m i,j is mapped to [i * n + j] and thus storage is row major
template <typename T>
class MatrixBase
{
public:
using value_type = T;
virtual ~MatrixBase() {}
virtual uint32_t dim_m() const = 0;
virtual uint32_t dim_n() const = 0;
virtual value_type &operator()(uint32_t i, uint32_t j) { throw std::runtime_error("unimplemented method"); }
virtual value_type operator()(uint32_t i, uint32_t j) const = 0;
MatrixBase &operator*=(const value_type &rhs);
MatrixBase &operator-=(const value_type &rhs);
};
template <typename T>
MatrixBase<T> &MatrixBase<T>::operator*=(const T &rhs)
{
for (uint32_t i = 0; i < dim_m(); ++i)
{
for (uint32_t j = 0; j < dim_n(); ++j)
{
operator()(i, j) *= rhs;
}
}
return *this;
}
template <typename T>
MatrixBase<T> &MatrixBase<T>::operator-=(const T &rhs)
{
for (uint32_t i = 0; i < dim_m(); ++i)
{
for (uint32_t j = 0; j < dim_n(); ++j)
{
operator()(i, j) -= rhs;
}
}
return *this;
}
template <typename T>
std::ostream &operator<<(std::ostream &lhs, const MatrixBase<T> &rhs)
{
lhs << '[' << rhs.dim_m() << ',' << rhs.dim_n() << ']' << '(';
for (uint32_t i = 0; i < rhs.dim_m(); ++i)
{
lhs << '(';
for (uint32_t j = 0; j < rhs.dim_n(); ++j)
{
if (j > 0)
lhs << ',';
lhs << rhs(i, j);
}
lhs << ')';
}
lhs << ')';
return lhs;
}
template <typename T>
class Matrix : public MatrixBase<T>
{
public:
using value_type = T;
template <typename T2>
Matrix(const MatrixBase<T2> &m)
: m_m(m.dim_m())
, m_n(m.dim_n())
{
m_data = new value_type[m_m * m_n];
for (uint32_t i = 0; i < m_m; ++i)
{
for (uint32_t j = 0; j < m_n; ++j)
operator()(i, j) = m(i, j);
}
}
Matrix()
: m_data(nullptr)
, m_m(0)
, m_n(0)
{
}
Matrix(const Matrix &m)
: m_m(m.m_m)
, m_n(m.m_n)
{
m_data = new value_type[m_m * m_n];
std::copy(m.m_data, m.m_data + (m_m * m_n), m_data);
}
Matrix &operator=(const Matrix &m)
{
value_type *t = new value_type[m.m_m * m.m_n];
std::copy(m.m_data, m.m_data + (m.m_m * m.m_n), t);
delete[] m_data;
m_data = t;
m_m = m.m_m;
m_n = m.m_n;
return *this;
}
Matrix(uint32_t m, uint32_t n, T v = T())
: m_m(m)
, m_n(n)
{
m_data = new value_type[m_m * m_n];
std::fill(m_data, m_data + (m_m * m_n), v);
}
virtual ~Matrix()
{
delete[] m_data;
}
virtual uint32_t dim_m() const { return m_m; }
virtual uint32_t dim_n() const { return m_n; }
virtual value_type operator()(uint32_t i, uint32_t j) const
{
assert(i < m_m);
assert(j < m_n);
return m_data[i * m_n + j];
}
virtual value_type &operator()(uint32_t i, uint32_t j)
{
assert(i < m_m);
assert(j < m_n);
return m_data[i * m_n + j];
}
template <typename Func>
void each(Func f)
{
for (uint32_t i = 0; i < m_m * m_n; ++i)
f(m_data[i]);
}
template <typename U>
Matrix &operator/=(U v)
{
for (uint32_t i = 0; i < m_m * m_n; ++i)
m_data[i] /= v;
return *this;
}
private:
value_type *m_data;
uint32_t m_m, m_n;
};
// --------------------------------------------------------------------
template <typename T>
class SymmetricMatrix : public MatrixBase<T>
{
public:
typedef typename MatrixBase<T>::value_type value_type;
SymmetricMatrix(uint32_t n, T v = T())
: m_owner(true)
, m_n(n)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
m_data = new value_type[N];
std::fill(m_data, m_data + N, v);
}
SymmetricMatrix(const T *data, uint32_t n)
: m_owner(false)
, m_data(const_cast<T *>(data))
, m_n(n)
{
}
virtual ~SymmetricMatrix()
{
if (m_owner)
delete[] m_data;
}
virtual uint32_t dim_m() const { return m_n; }
virtual uint32_t dim_n() const { return m_n; }
T operator()(uint32_t i, uint32_t j) const;
virtual T &operator()(uint32_t i, uint32_t j);
// erase two rows, add one at the end (for neighbour joining)
void erase_2(uint32_t i, uint32_t j);
template <typename Func>
void each(Func f)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
for (uint32_t i = 0; i < N; ++i)
f(m_data[i]);
}
template <typename U>
SymmetricMatrix &operator/=(U v)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
for (uint32_t i = 0; i < N; ++i)
m_data[i] /= v;
return *this;
}
private:
bool m_owner;
value_type *m_data;
uint32_t m_n;
};
template <typename T>
inline T SymmetricMatrix<T>::operator()(uint32_t i, uint32_t j) const
{
return i < j
? m_data[(j * (j + 1)) / 2 + i]
: m_data[(i * (i + 1)) / 2 + j];
}
template <typename T>
inline T &SymmetricMatrix<T>::operator()(uint32_t i, uint32_t j)
{
if (i > j)
std::swap(i, j);
assert(j < m_n);
return m_data[(j * (j + 1)) / 2 + i];
}
template <typename T>
void SymmetricMatrix<T>::erase_2(uint32_t di, uint32_t dj)
{
uint32_t s = 0, d = 0;
for (uint32_t i = 0; i < m_n; ++i)
{
for (uint32_t j = 0; j < i; ++j)
{
if (i != di and j != dj and i != dj and j != di)
{
if (s != d)
m_data[d] = m_data[s];
++d;
}
++s;
}
}
--m_n;
}
template <typename T>
class IdentityMatrix : public MatrixBase<T>
{
public:
typedef typename MatrixBase<T>::value_type value_type;
IdentityMatrix(uint32_t n)
: m_n(n)
{
}
virtual uint32_t dim_m() const { return m_n; }
virtual uint32_t dim_n() const { return m_n; }
virtual value_type operator()(uint32_t i, uint32_t j) const
{
value_type result = 0;
if (i == j)
result = 1;
return result;
}
private:
uint32_t m_n;
};
// --------------------------------------------------------------------
// matrix functions
template <typename T>
Matrix<T> operator*(const MatrixBase<T> &lhs, const MatrixBase<T> &rhs)
{
Matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
for (uint32_t i = 0; i < result.dim_m(); ++i)
{
for (uint32_t j = 0; j < result.dim_n(); ++j)
{
for (uint32_t li = 0, rj = 0; li < lhs.dim_m() and rj < rhs.dim_n(); ++li, ++rj)
result(i, j) += lhs(li, j) * rhs(i, rj);
}
}
return result;
}
template <typename T>
Matrix<T> operator*(const MatrixBase<T> &lhs, T rhs)
{
Matrix<T> result(lhs);
result *= rhs;
return result;
}
template <typename T>
Matrix<T> operator-(const MatrixBase<T> &lhs, const MatrixBase<T> &rhs)
{
Matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
for (uint32_t i = 0; i < result.dim_m(); ++i)
{
for (uint32_t j = 0; j < result.dim_n(); ++j)
{
result(i, j) = lhs(i, j) - rhs(i, j);
}
}
return result;
}
template <typename T>
Matrix<T> operator-(const MatrixBase<T> &lhs, T rhs)
{
Matrix<T> result(lhs.dim_m(), lhs.dim_n());
result -= rhs;
return result;
}
// template <typename T>
// symmetric_matrix<T> hammingDistance(const MatrixBase<T> &lhs, T rhs);
// template <typename T>
// std::vector<T> sum(const MatrixBase<T> &m);
src/Point.cpp
...@@ -28,12 +28,378 @@ ...@@ -28,12 +28,378 @@
#include <valarray> #include <valarray>
#include "cif++/Point.hpp" #include "cif++/Point.hpp"
#include "cif++/Matrix.hpp"
namespace mmcif namespace mmcif
{ {
// -------------------------------------------------------------------- // --------------------------------------------------------------------
// uBlas compatible matrix types
// matrix is m x n, addressing i,j is 0 <= i < m and 0 <= j < n
// element m i,j is mapped to [i * n + j] and thus storage is row major
template <typename T>
class MatrixBase
{
public:
using value_type = T;
virtual ~MatrixBase() {}
virtual uint32_t dim_m() const = 0;
virtual uint32_t dim_n() const = 0;
virtual value_type &operator()(uint32_t i, uint32_t j) { throw std::runtime_error("unimplemented method"); }
virtual value_type operator()(uint32_t i, uint32_t j) const = 0;
MatrixBase &operator*=(const value_type &rhs);
MatrixBase &operator-=(const value_type &rhs);
};
template <typename T>
MatrixBase<T> &MatrixBase<T>::operator*=(const T &rhs)
{
for (uint32_t i = 0; i < dim_m(); ++i)
{
for (uint32_t j = 0; j < dim_n(); ++j)
{
operator()(i, j) *= rhs;
}
}
return *this;
}
template <typename T>
MatrixBase<T> &MatrixBase<T>::operator-=(const T &rhs)
{
for (uint32_t i = 0; i < dim_m(); ++i)
{
for (uint32_t j = 0; j < dim_n(); ++j)
{
operator()(i, j) -= rhs;
}
}
return *this;
}
template <typename T>
class Matrix : public MatrixBase<T>
{
public:
using value_type = T;
template <typename T2>
Matrix(const MatrixBase<T2> &m)
: m_m(m.dim_m())
, m_n(m.dim_n())
{
m_data = new value_type[m_m * m_n];
for (uint32_t i = 0; i < m_m; ++i)
{
for (uint32_t j = 0; j < m_n; ++j)
operator()(i, j) = m(i, j);
}
}
Matrix()
: m_data(nullptr)
, m_m(0)
, m_n(0)
{
}
Matrix(const Matrix &m)
: m_m(m.m_m)
, m_n(m.m_n)
{
m_data = new value_type[m_m * m_n];
std::copy(m.m_data, m.m_data + (m_m * m_n), m_data);
}
Matrix &operator=(const Matrix &m)
{
value_type *t = new value_type[m.m_m * m.m_n];
std::copy(m.m_data, m.m_data + (m.m_m * m.m_n), t);
delete[] m_data;
m_data = t;
m_m = m.m_m;
m_n = m.m_n;
return *this;
}
Matrix(uint32_t m, uint32_t n, T v = T())
: m_m(m)
, m_n(n)
{
m_data = new value_type[m_m * m_n];
std::fill(m_data, m_data + (m_m * m_n), v);
}
virtual ~Matrix()
{
delete[] m_data;
}
virtual uint32_t dim_m() const { return m_m; }
virtual uint32_t dim_n() const { return m_n; }
virtual value_type operator()(uint32_t i, uint32_t j) const
{
assert(i < m_m);
assert(j < m_n);
return m_data[i * m_n + j];
}
virtual value_type &operator()(uint32_t i, uint32_t j)
{
assert(i < m_m);
assert(j < m_n);
return m_data[i * m_n + j];
}
template <typename Func>
void each(Func f)
{
for (uint32_t i = 0; i < m_m * m_n; ++i)
f(m_data[i]);
}
template <typename U>
Matrix &operator/=(U v)
{
for (uint32_t i = 0; i < m_m * m_n; ++i)
m_data[i] /= v;
return *this;
}
private:
value_type *m_data;
uint32_t m_m, m_n;
};
// --------------------------------------------------------------------
template <typename T>
class SymmetricMatrix : public MatrixBase<T>
{
public:
typedef typename MatrixBase<T>::value_type value_type;
SymmetricMatrix(uint32_t n, T v = T())
: m_owner(true)
, m_n(n)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
m_data = new value_type[N];
std::fill(m_data, m_data + N, v);
}
SymmetricMatrix(const T *data, uint32_t n)
: m_owner(false)
, m_data(const_cast<T *>(data))
, m_n(n)
{
}
virtual ~SymmetricMatrix()
{
if (m_owner)
delete[] m_data;
}
virtual uint32_t dim_m() const { return m_n; }
virtual uint32_t dim_n() const { return m_n; }
T operator()(uint32_t i, uint32_t j) const;
virtual T &operator()(uint32_t i, uint32_t j);
// erase two rows, add one at the end (for neighbour joining)
void erase_2(uint32_t i, uint32_t j);
template <typename Func>
void each(Func f)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
for (uint32_t i = 0; i < N; ++i)
f(m_data[i]);
}
template <typename U>
SymmetricMatrix &operator/=(U v)
{
uint32_t N = (m_n * (m_n + 1)) / 2;
for (uint32_t i = 0; i < N; ++i)
m_data[i] /= v;
return *this;
}
private:
bool m_owner;
value_type *m_data;
uint32_t m_n;
};
template <typename T>
inline T SymmetricMatrix<T>::operator()(uint32_t i, uint32_t j) const
{
return i < j
? m_data[(j * (j + 1)) / 2 + i]
: m_data[(i * (i + 1)) / 2 + j];
}
template <typename T>
inline T &SymmetricMatrix<T>::operator()(uint32_t i, uint32_t j)
{
if (i > j)
std::swap(i, j);
assert(j < m_n);
return m_data[(j * (j + 1)) / 2 + i];
}
template <typename T>
void SymmetricMatrix<T>::erase_2(uint32_t di, uint32_t dj)
{
uint32_t s = 0, d = 0;
for (uint32_t i = 0; i < m_n; ++i)
{
for (uint32_t j = 0; j < i; ++j)
{
if (i != di and j != dj and i != dj and j != di)
{
if (s != d)
m_data[d] = m_data[s];
++d;
}
++s;
}
}
--m_n;
}
template <typename T>
class IdentityMatrix : public MatrixBase<T>
{
public:
typedef typename MatrixBase<T>::value_type value_type;
IdentityMatrix(uint32_t n)
: m_n(n)
{
}
virtual uint32_t dim_m() const { return m_n; }
virtual uint32_t dim_n() const { return m_n; }
virtual value_type operator()(uint32_t i, uint32_t j) const
{
value_type result = 0;
if (i == j)
result = 1;
return result;
}
private:
uint32_t m_n;
};
// --------------------------------------------------------------------
// matrix functions
template <typename T>
Matrix<T> operator*(const MatrixBase<T> &lhs, const MatrixBase<T> &rhs)
{
Matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
for (uint32_t i = 0; i < result.dim_m(); ++i)
{
for (uint32_t j = 0; j < result.dim_n(); ++j)
{
for (uint32_t li = 0, rj = 0; li < lhs.dim_m() and rj < rhs.dim_n(); ++li, ++rj)
result(i, j) += lhs(li, j) * rhs(i, rj);
}
}
return result;
}
template <typename T>
Matrix<T> operator*(const MatrixBase<T> &lhs, T rhs)
{
Matrix<T> result(lhs);
result *= rhs;
return result;
}
template <typename T>
Matrix<T> operator-(const MatrixBase<T> &lhs, const MatrixBase<T> &rhs)
{
Matrix<T> result(std::min(lhs.dim_m(), rhs.dim_m()), std::min(lhs.dim_n(), rhs.dim_n()));
for (uint32_t i = 0; i < result.dim_m(); ++i)
{
for (uint32_t j = 0; j < result.dim_n(); ++j)
{
result(i, j) = lhs(i, j) - rhs(i, j);
}
}
return result;
}
template <typename T>
Matrix<T> operator-(const MatrixBase<T> &lhs, T rhs)
{
Matrix<T> result(lhs.dim_m(), lhs.dim_n());
result -= rhs;
return result;
}
template<class M1, typename T>
void cofactors(const M1& m, SymmetricMatrix<T>& cf)
{
const size_t ixs[4][3] =
{
{ 1, 2, 3 },
{ 0, 2, 3 },
{ 0, 1, 3 },
{ 0, 1, 2 }
};
for (size_t x = 0; x < 4; ++x)
{
const size_t* ix = ixs[x];
for (size_t y = x; y < 4; ++y)
{
const size_t* iy = ixs[y];
cf(x, y) =
m(ix[0], iy[0]) * m(ix[1], iy[1]) * m(ix[2], iy[2]) +
m(ix[0], iy[1]) * m(ix[1], iy[2]) * m(ix[2], iy[0]) +
m(ix[0], iy[2]) * m(ix[1], iy[0]) * m(ix[2], iy[1]) -
m(ix[0], iy[2]) * m(ix[1], iy[1]) * m(ix[2], iy[0]) -
m(ix[0], iy[1]) * m(ix[1], iy[0]) * m(ix[2], iy[2]) -
m(ix[0], iy[0]) * m(ix[1], iy[2]) * m(ix[2], iy[1]);
if ((x + y) % 2 == 1)
cf(x, y) *= -1;
}
}
}
// --------------------------------------------------------------------
Quaternion Normalize(Quaternion q) Quaternion Normalize(Quaternion q)
{ {
...@@ -225,6 +591,7 @@ Quaternion AlignPoints(const std::vector<Point>& pa, const std::vector<Point>& p ...@@ -225,6 +591,7 @@ Quaternion AlignPoints(const std::vector<Point>& pa, const std::vector<Point>& p
M(1, 2) * M(2, 0) * M(0, 1) + M(1, 2) * M(2, 0) * M(0, 1) +
M(2, 1) * M(1, 0) * M(0, 2)); M(2, 1) * M(1, 0) * M(0, 2));
// E is the determinant of N:
double E = double E =
(N(0,0) * N(1,1) - N(0,1) * N(0,1)) * (N(2,2) * N(3,3) - N(2,3) * N(2,3)) + (N(0,0) * N(1,1) - N(0,1) * N(0,1)) * (N(2,2) * N(3,3) - N(2,3) * N(2,3)) +
(N(0,1) * N(0,2) - N(0,0) * N(2,1)) * (N(2,1) * N(3,3) - N(2,3) * N(1,3)) + (N(0,1) * N(0,2) - N(0,0) * N(2,1)) * (N(2,1) * N(3,3) - N(2,3) * N(1,3)) +
...@@ -240,41 +607,18 @@ Quaternion AlignPoints(const std::vector<Point>& pa, const std::vector<Point>& p ...@@ -240,41 +607,18 @@ Quaternion AlignPoints(const std::vector<Point>& pa, const std::vector<Point>& p
Matrix<double> li = IdentityMatrix<double>(4) * lm; Matrix<double> li = IdentityMatrix<double>(4) * lm;
Matrix<double> t = N - li; Matrix<double> t = N - li;
// calculate a Matrix of cofactors for t // calculate a Matrix of cofactors for t, since N is symmetric, t must be symmetric as well and so will be cf
Matrix<double> cf(4, 4); SymmetricMatrix<double> cf(4);
cofactors(t, cf);
const uint32_t ixs[4][3] = int maxR = 0;
{ for (int r = 1; r < 4; ++r)
{ 1, 2, 3 },
{ 0, 2, 3 },
{ 0, 1, 3 },
{ 0, 1, 2 }
};
uint32_t maxR = 0;
for (uint32_t r = 0; r < 4; ++r)
{ {
const uint32_t* ir = ixs[r]; if (cf(r, 0) > cf(maxR, 0))
for (uint32_t c = 0; c < 4; ++c)
{
const uint32_t* ic = ixs[c];
cf(r, c) =
t(ir[0], ic[0]) * t(ir[1], ic[1]) * t(ir[2], ic[2]) +
t(ir[0], ic[1]) * t(ir[1], ic[2]) * t(ir[2], ic[0]) +
t(ir[0], ic[2]) * t(ir[1], ic[0]) * t(ir[2], ic[1]) -
t(ir[0], ic[2]) * t(ir[1], ic[1]) * t(ir[2], ic[0]) -
t(ir[0], ic[1]) * t(ir[1], ic[0]) * t(ir[2], ic[2]) -
t(ir[0], ic[0]) * t(ir[1], ic[2]) * t(ir[2], ic[1]);
}
if (r > maxR and cf(r, 0) > cf(maxR, 0))
maxR = r; maxR = r;
} }
// NOTE the negation of the y here, why? Maybe I swapped r/c above? Quaternion q(cf(maxR, 0), cf(maxR, 1), cf(maxR, 2), cf(maxR, 3));
Quaternion q(cf(maxR, 0), cf(maxR, 1), -cf(maxR, 2), cf(maxR, 3));
q = Normalize(q); q = Normalize(q);
return q; return q;
......
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