--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancStone/Sources/Toolbox/LinearAlgebra.h	Tue Jul 07 16:21:02 2020 +0200
@@ -0,0 +1,299 @@
+/**
+ * Stone of Orthanc
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2020 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation, either version 3 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Affero General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#pragma once
+
+// Patch for ublas in Boost 1.64.0
+// https://github.com/dealii/dealii/issues/4302
+#include <boost/version.hpp>
+#if BOOST_VERSION >= 106300  // or 64, need to check
+#  include <boost/serialization/array_wrapper.hpp>
+#endif
+
+#include <DicomFormat/DicomMap.h>
+
+#include <boost/numeric/ublas/matrix.hpp>
+#include <boost/numeric/ublas/vector.hpp>
+
+namespace OrthancStone
+{
+  typedef boost::numeric::ublas::matrix<double>   Matrix;
+  typedef boost::numeric::ublas::vector<double>   Vector;
+
+  // logs, debugging...
+  std::ostream& operator<<(std::ostream& s, const Vector& vec);
+  std::ostream& operator<<(std::ostream& s, const Matrix& m);
+
+  namespace LinearAlgebra
+  {
+    void Print(const Vector& v);
+
+    void Print(const Matrix& m);
+
+    bool ParseVector(Vector& target,
+                     const std::string& s);
+
+    bool ParseVector(Vector& target,
+                     const Orthanc::DicomMap& dataset,
+                     const Orthanc::DicomTag& tag);
+
+    inline void AssignVector(Vector& v,
+                             double v1,
+                             double v2)
+    {
+      v.resize(2);
+      v[0] = v1;
+      v[1] = v2;
+    }
+
+
+    inline void AssignVector(Vector& v,
+                             double v1)
+    {
+      v.resize(1);
+      v[0] = v1;
+    }
+
+
+    inline void AssignVector(Vector& v,
+                             double v1,
+                             double v2,
+                             double v3)
+    {
+      v.resize(3);
+      v[0] = v1;
+      v[1] = v2;
+      v[2] = v3;
+    }
+
+
+    inline void AssignVector(Vector& v,
+                             double v1,
+                             double v2,
+                             double v3,
+                             double v4)
+    {
+      v.resize(4);
+      v[0] = v1;
+      v[1] = v2;
+      v[2] = v3;
+      v[3] = v4;
+    }
+
+
+    inline Vector CreateVector(double v1)
+    {
+      Vector v;
+      AssignVector(v, v1);
+      return v;
+    }
+
+    
+    inline Vector CreateVector(double v1,
+                               double v2)
+    {
+      Vector v;
+      AssignVector(v, v1, v2);
+      return v;
+    }
+
+    
+    inline Vector CreateVector(double v1,
+                               double v2,
+                               double v3)
+    {
+      Vector v;
+      AssignVector(v, v1, v2, v3);
+      return v;
+    }
+
+    
+    inline Vector CreateVector(double v1,
+                               double v2,
+                               double v3,
+                               double v4)
+    {
+      Vector v;
+      AssignVector(v, v1, v2, v3, v4);
+      return v;
+    }
+
+
+    inline bool IsNear(double x,
+                       double y,
+                       double threshold)
+    {
+      return fabs(x - y) <= threshold;
+    }
+
+    inline bool IsNear(double x,
+                       double y)
+    {
+      // As most input is read as single-precision numbers, we take the
+      // epsilon machine for float32 into consideration to compare numbers
+      return IsNear(x, y, 10.0 * std::numeric_limits<float>::epsilon());
+    }
+
+    inline bool IsCloseToZero(double x)
+    {
+      return IsNear(x, 0.0);
+    }
+
+    void NormalizeVector(Vector& u);
+
+    void CrossProduct(Vector& result,
+                      const Vector& u,
+                      const Vector& v);
+
+    double DotProduct(const Vector& u, const Vector& v);
+
+    void FillMatrix(Matrix& target,
+                    size_t rows,
+                    size_t columns,
+                    const double values[]);
+
+    void FillVector(Vector& target,
+                    size_t size,
+                    const double values[]);
+
+    void Convert(Matrix& target,
+                 const Vector& source);
+
+    inline Matrix Transpose(const Matrix& a)
+    {
+      return boost::numeric::ublas::trans(a);
+    }
+
+
+    inline Matrix IdentityMatrix(size_t size)
+    {
+      return boost::numeric::ublas::identity_matrix<double>(size);
+    }
+
+
+    inline Matrix ZeroMatrix(size_t size1,
+                             size_t size2)
+    {
+      return boost::numeric::ublas::zero_matrix<double>(size1, size2);
+    }
+
+
+    inline Matrix Product(const Matrix& a,
+                          const Matrix& b)
+    {
+      return boost::numeric::ublas::prod(a, b);
+    }
+
+
+    inline Vector Product(const Matrix& a,
+                          const Vector& b)
+    {
+      return boost::numeric::ublas::prod(a, b);
+    }
+
+
+    inline Matrix Product(const Matrix& a,
+                          const Matrix& b,
+                          const Matrix& c)
+    {
+      return Product(a, Product(b, c));
+    }
+
+
+    inline Matrix Product(const Matrix& a,
+                          const Matrix& b,
+                          const Matrix& c,
+                          const Matrix& d)
+    {
+      return Product(a, Product(b, c, d));
+    }
+
+
+    inline Matrix Product(const Matrix& a,
+                          const Matrix& b,
+                          const Matrix& c,
+                          const Matrix& d,
+                          const Matrix& e)
+    {
+      return Product(a, Product(b, c, d, e));
+    }
+
+
+    inline Vector Product(const Matrix& a,
+                          const Matrix& b,
+                          const Vector& c)
+    {
+      return Product(Product(a, b), c);
+    }
+
+
+    inline Vector Product(const Matrix& a,
+                          const Matrix& b,
+                          const Matrix& c,
+                          const Vector& d)
+    {
+      return Product(Product(a, b, c), d);
+    }
+
+
+    double ComputeDeterminant(const Matrix& a);
+
+    bool IsOrthogonalMatrix(const Matrix& q,
+                            double threshold);
+
+    bool IsOrthogonalMatrix(const Matrix& q);
+
+    bool IsRotationMatrix(const Matrix& r,
+                          double threshold);
+
+    bool IsRotationMatrix(const Matrix& r);
+
+    void InvertUpperTriangularMatrix(Matrix& output,
+                                     const Matrix& k); 
+
+    /**
+     * This function computes the RQ decomposition of a 3x3 matrix,
+     * using Givens rotations. Reference: Algorithm A4.1 (page 579) of
+     * "Multiple View Geometry in Computer Vision" (2nd edition).  The
+     * output matrix "Q" is a rotation matrix, and "R" is upper
+     * triangular.
+     **/
+    void RQDecomposition3x3(Matrix& r,
+                            Matrix& q,
+                            const Matrix& a);
+
+    void InvertMatrix(Matrix& target,
+                      const Matrix& source);
+
+    // This is the same as "InvertMatrix()", but without exception
+    bool InvertMatrixUnsafe(Matrix& target,
+                            const Matrix& source);
+
+    void CreateSkewSymmetric(Matrix& s,
+                             const Vector& v);
+  
+    Matrix InvertScalingTranslationMatrix(const Matrix& t);
+
+    bool IsShearMatrix(const Matrix& shear);  
+
+    Matrix InvertShearMatrix(const Matrix& shear);
+  };
+}