Disabled external gits

cs440-acg/ext/eigen/doc/examples/.krazy

@@ -0,0 +1,2 @@
+EXCLUDE copyright
+EXCLUDE license

cs440-acg/ext/eigen/doc/examples/CMakeLists.txt

@@ -0,0 +1,21 @@
+file(GLOB examples_SRCS "*.cpp")
+
+foreach(example_src ${examples_SRCS})
+  get_filename_component(example ${example_src} NAME_WE)
+  add_executable(${example} ${example_src})
+  if(EIGEN_STANDARD_LIBRARIES_TO_LINK_TO)
+    target_link_libraries(${example} ${EIGEN_STANDARD_LIBRARIES_TO_LINK_TO})
+  endif()
+  add_custom_command(
+    TARGET ${example}
+    POST_BUILD
+    COMMAND ${example}
+    ARGS >${CMAKE_CURRENT_BINARY_DIR}/${example}.out
+  )
+  add_dependencies(all_examples ${example})
+endforeach(example_src)
+
+check_cxx_compiler_flag("-std=c++11" EIGEN_COMPILER_SUPPORT_CPP11)
+if(EIGEN_COMPILER_SUPPORT_CPP11)
+ei_add_target_property(nullary_indexing COMPILE_FLAGS "-std=c++11")
+endif()

cs440-acg/ext/eigen/doc/examples/CustomizingEigen_Inheritance.cpp

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+#include <Eigen/Core>
+#include <iostream>
+
+class MyVectorType : public Eigen::VectorXd
+{
+public:
+    MyVectorType(void):Eigen::VectorXd() {}
+
+    // This constructor allows you to construct MyVectorType from Eigen expressions
+    template<typename OtherDerived>
+    MyVectorType(const Eigen::MatrixBase<OtherDerived>& other)
+        : Eigen::VectorXd(other)
+    { }
+
+    // This method allows you to assign Eigen expressions to MyVectorType
+    template<typename OtherDerived>
+    MyVectorType& operator=(const Eigen::MatrixBase <OtherDerived>& other)
+    {
+        this->Eigen::VectorXd::operator=(other);
+        return *this;
+    }
+};
+
+int main()
+{
+  MyVectorType v = MyVectorType::Ones(4);
+  v(2) += 10;
+  v = 2 * v;
+  std::cout << v.transpose() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Cwise_erf.cpp

@@ -0,0 +1,9 @@
+#include <Eigen/Core>
+#include <unsupported/Eigen/SpecialFunctions>
+#include <iostream>
+using namespace Eigen;
+int main()
+{
+  Array4d v(-0.5,2,0,-7);
+  std::cout << v.erf() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Cwise_erfc.cpp

@@ -0,0 +1,9 @@
+#include <Eigen/Core>
+#include <unsupported/Eigen/SpecialFunctions>
+#include <iostream>
+using namespace Eigen;
+int main()
+{
+  Array4d v(-0.5,2,0,-7);
+  std::cout << v.erfc() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Cwise_lgamma.cpp

@@ -0,0 +1,9 @@
+#include <Eigen/Core>
+#include <unsupported/Eigen/SpecialFunctions>
+#include <iostream>
+using namespace Eigen;
+int main()
+{
+  Array4d v(0.5,10,0,-1);
+  std::cout << v.lgamma() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/DenseBase_middleCols_int.cpp

@@ -0,0 +1,15 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main(void)
+{
+    int const N = 5;
+    MatrixXi A(N,N);
+    A.setRandom();
+    cout << "A =\n" << A << '\n' << endl;
+    cout << "A(1..3,:) =\n" << A.middleCols(1,3) << endl;
+    return 0;
+}

cs440-acg/ext/eigen/doc/examples/DenseBase_middleRows_int.cpp

@@ -0,0 +1,15 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main(void)
+{
+    int const N = 5;
+    MatrixXi A(N,N);
+    A.setRandom();
+    cout << "A =\n" << A << '\n' << endl;
+    cout << "A(2..3,:) =\n" << A.middleRows(2,2) << endl;
+    return 0;
+}

cs440-acg/ext/eigen/doc/examples/DenseBase_template_int_middleCols.cpp

@@ -0,0 +1,15 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main(void)
+{
+    int const N = 5;
+    MatrixXi A(N,N);
+    A.setRandom();
+    cout << "A =\n" << A << '\n' << endl;
+    cout << "A(:,1..3) =\n" << A.middleCols<3>(1) << endl;
+    return 0;
+}

cs440-acg/ext/eigen/doc/examples/DenseBase_template_int_middleRows.cpp

@@ -0,0 +1,15 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main(void)
+{
+    int const N = 5;
+    MatrixXi A(N,N);
+    A.setRandom();
+    cout << "A =\n" << A << '\n' << endl;
+    cout << "A(1..3,:) =\n" << A.middleRows<3>(1) << endl;
+    return 0;
+}

cs440-acg/ext/eigen/doc/examples/QuickStart_example.cpp

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+#include <iostream>
+#include <Eigen/Dense>
+
+using Eigen::MatrixXd;
+
+int main()
+{
+  MatrixXd m(2,2);
+  m(0,0) = 3;
+  m(1,0) = 2.5;
+  m(0,1) = -1;
+  m(1,1) = m(1,0) + m(0,1);
+  std::cout << m << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/QuickStart_example2_dynamic.cpp

@@ -0,0 +1,15 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  MatrixXd m = MatrixXd::Random(3,3);
+  m = (m + MatrixXd::Constant(3,3,1.2)) * 50;
+  cout << "m =" << endl << m << endl;
+  VectorXd v(3);
+  v << 1, 2, 3;
+  cout << "m * v =" << endl << m * v << endl;
+}

cs440-acg/ext/eigen/doc/examples/QuickStart_example2_fixed.cpp

@@ -0,0 +1,15 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  Matrix3d m = Matrix3d::Random();
+  m = (m + Matrix3d::Constant(1.2)) * 50;
+  cout << "m =" << endl << m << endl;
+  Vector3d v(1,2,3);
+  
+  cout << "m * v =" << endl << m * v << endl;
+}

cs440-acg/ext/eigen/doc/examples/TemplateKeyword_flexible.cpp

@@ -0,0 +1,22 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+
+template <typename Derived1, typename Derived2>
+void copyUpperTriangularPart(MatrixBase<Derived1>& dst, const MatrixBase<Derived2>& src)
+{
+  /* Note the 'template' keywords in the following line! */
+  dst.template triangularView<Upper>() = src.template triangularView<Upper>();
+}
+
+int main()
+{
+  MatrixXi m1 = MatrixXi::Ones(5,5);
+  MatrixXi m2 = MatrixXi::Random(4,4);
+  std::cout << "m2 before copy:" << std::endl;
+  std::cout << m2 << std::endl << std::endl;
+  copyUpperTriangularPart(m2, m1.topLeftCorner(4,4));
+  std::cout << "m2 after copy:" << std::endl;
+  std::cout << m2 << std::endl << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/TemplateKeyword_simple.cpp

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+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+
+void copyUpperTriangularPart(MatrixXf& dst, const MatrixXf& src)
+{
+  dst.triangularView<Upper>() = src.triangularView<Upper>();
+}
+
+int main()
+{
+  MatrixXf m1 = MatrixXf::Ones(4,4);
+  MatrixXf m2 = MatrixXf::Random(4,4);
+  std::cout << "m2 before copy:" << std::endl;
+  std::cout << m2 << std::endl << std::endl;
+  copyUpperTriangularPart(m2, m1);
+  std::cout << "m2 after copy:" << std::endl;
+  std::cout << m2 << std::endl << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialInplaceLU.cpp

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+#include <iostream>
+struct init {
+  init() { std::cout << "[" << "init" << "]" << std::endl; }
+};
+init init_obj;
+// [init]
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  MatrixXd A(2,2);
+  A << 2, -1, 1, 3;
+  cout << "Here is the input matrix A before decomposition:\n" << A << endl;
+cout << "[init]" << endl;
+
+cout << "[declaration]" << endl;
+  PartialPivLU<Ref<MatrixXd> > lu(A);
+  cout << "Here is the input matrix A after decomposition:\n" << A << endl;
+cout << "[declaration]" << endl;
+
+cout << "[matrixLU]" << endl;
+  cout << "Here is the matrix storing the L and U factors:\n" << lu.matrixLU() << endl;
+cout << "[matrixLU]" << endl;
+
+cout << "[solve]" << endl;
+  MatrixXd A0(2,2); A0 << 2, -1, 1, 3;
+  VectorXd b(2);    b << 1, 2;
+  VectorXd x = lu.solve(b);
+  cout << "Residual: " << (A0 * x - b).norm() << endl;
+cout << "[solve]" << endl;
+
+cout << "[modifyA]" << endl;
+  A << 3, 4, -2, 1;
+  x = lu.solve(b);
+  cout << "Residual: " << (A0 * x - b).norm() << endl;
+cout << "[modifyA]" << endl;
+
+cout << "[recompute]" << endl;
+  A0 = A; // save A
+  lu.compute(A);
+  x = lu.solve(b);
+  cout << "Residual: " << (A0 * x - b).norm() << endl;
+cout << "[recompute]" << endl;
+
+cout << "[recompute_bis0]" << endl;
+  MatrixXd A1(2,2);
+  A1 << 5,-2,3,4;
+  lu.compute(A1);
+  cout << "Here is the input matrix A1 after decomposition:\n" << A1 << endl;
+cout << "[recompute_bis0]" << endl;
+
+cout << "[recompute_bis1]" << endl;
+  x = lu.solve(b);
+  cout << "Residual: " << (A1 * x - b).norm() << endl;
+cout << "[recompute_bis1]" << endl;
+
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgComputeTwice.cpp

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+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix2f A, b;
+   LLT<Matrix2f> llt;
+   A << 2, -1, -1, 3;
+   b << 1, 2, 3, 1;
+   cout << "Here is the matrix A:\n" << A << endl;
+   cout << "Here is the right hand side b:\n" << b << endl;
+   cout << "Computing LLT decomposition..." << endl;
+   llt.compute(A);
+   cout << "The solution is:\n" << llt.solve(b) << endl;
+   A(1,1)++;
+   cout << "The matrix A is now:\n" << A << endl;
+   cout << "Computing LLT decomposition..." << endl;
+   llt.compute(A);
+   cout << "The solution is now:\n" << llt.solve(b) << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgExComputeSolveError.cpp

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+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   MatrixXd A = MatrixXd::Random(100,100);
+   MatrixXd b = MatrixXd::Random(100,50);
+   MatrixXd x = A.fullPivLu().solve(b);
+   double relative_error = (A*x - b).norm() / b.norm(); // norm() is L2 norm
+   cout << "The relative error is:\n" << relative_error << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgExSolveColPivHouseholderQR.cpp

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+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix3f A;
+   Vector3f b;
+   A << 1,2,3,  4,5,6,  7,8,10;
+   b << 3, 3, 4;
+   cout << "Here is the matrix A:\n" << A << endl;
+   cout << "Here is the vector b:\n" << b << endl;
+   Vector3f x = A.colPivHouseholderQr().solve(b);
+   cout << "The solution is:\n" << x << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgExSolveLDLT.cpp

@@ -0,0 +1,16 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix2f A, b;
+   A << 2, -1, -1, 3;
+   b << 1, 2, 3, 1;
+   cout << "Here is the matrix A:\n" << A << endl;
+   cout << "Here is the right hand side b:\n" << b << endl;
+   Matrix2f x = A.ldlt().solve(b);
+   cout << "The solution is:\n" << x << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgInverseDeterminant.cpp

@@ -0,0 +1,16 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix3f A;
+   A << 1, 2, 1,
+        2, 1, 0,
+        -1, 1, 2;
+   cout << "Here is the matrix A:\n" << A << endl;
+   cout << "The determinant of A is " << A.determinant() << endl;
+   cout << "The inverse of A is:\n" << A.inverse() << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgRankRevealing.cpp

@@ -0,0 +1,20 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix3f A;
+   A << 1, 2, 5,
+        2, 1, 4,
+        3, 0, 3;
+   cout << "Here is the matrix A:\n" << A << endl;
+   FullPivLU<Matrix3f> lu_decomp(A);
+   cout << "The rank of A is " << lu_decomp.rank() << endl;
+   cout << "Here is a matrix whose columns form a basis of the null-space of A:\n"
+        << lu_decomp.kernel() << endl;
+   cout << "Here is a matrix whose columns form a basis of the column-space of A:\n"
+        << lu_decomp.image(A) << endl; // yes, have to pass the original A
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgSVDSolve.cpp

@@ -0,0 +1,15 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   MatrixXf A = MatrixXf::Random(3, 2);
+   cout << "Here is the matrix A:\n" << A << endl;
+   VectorXf b = VectorXf::Random(3);
+   cout << "Here is the right hand side b:\n" << b << endl;
+   cout << "The least-squares solution is:\n"
+        << A.bdcSvd(ComputeThinU | ComputeThinV).solve(b) << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgSelfAdjointEigenSolver.cpp

@@ -0,0 +1,18 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix2f A;
+   A << 1, 2, 2, 3;
+   cout << "Here is the matrix A:\n" << A << endl;
+   SelfAdjointEigenSolver<Matrix2f> eigensolver(A);
+   if (eigensolver.info() != Success) abort();
+   cout << "The eigenvalues of A are:\n" << eigensolver.eigenvalues() << endl;
+   cout << "Here's a matrix whose columns are eigenvectors of A \n"
+        << "corresponding to these eigenvalues:\n"
+        << eigensolver.eigenvectors() << endl;
+}

cs440-acg/ext/eigen/doc/examples/TutorialLinAlgSetThreshold.cpp

@@ -0,0 +1,16 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix2d A;
+   A << 2, 1,
+        2, 0.9999999999;
+   FullPivLU<Matrix2d> lu(A);
+   cout << "By default, the rank of A is found to be " << lu.rank() << endl;
+   lu.setThreshold(1e-5);
+   cout << "With threshold 1e-5, the rank of A is found to be " << lu.rank() << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_accessors.cpp

@@ -0,0 +1,24 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  ArrayXXf  m(2,2);
+  
+  // assign some values coefficient by coefficient
+  m(0,0) = 1.0; m(0,1) = 2.0;
+  m(1,0) = 3.0; m(1,1) = m(0,1) + m(1,0);
+  
+  // print values to standard output
+  cout << m << endl << endl;
+ 
+  // using the comma-initializer is also allowed
+  m << 1.0,2.0,
+       3.0,4.0;
+     
+  // print values to standard output
+  cout << m << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_addition.cpp

@@ -0,0 +1,23 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  ArrayXXf a(3,3);
+  ArrayXXf b(3,3);
+  a << 1,2,3,
+       4,5,6,
+       7,8,9;
+  b << 1,2,3,
+       1,2,3,
+       1,2,3;
+       
+  // Adding two arrays
+  cout << "a + b = " << endl << a + b << endl << endl;
+
+  // Subtracting a scalar from an array
+  cout << "a - 2 = " << endl << a - 2 << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_cwise_other.cpp

@@ -0,0 +1,19 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  ArrayXf a = ArrayXf::Random(5);
+  a *= 2;
+  cout << "a =" << endl 
+       << a << endl;
+  cout << "a.abs() =" << endl 
+       << a.abs() << endl;
+  cout << "a.abs().sqrt() =" << endl 
+       << a.abs().sqrt() << endl;
+  cout << "a.min(a.abs().sqrt()) =" << endl 
+       << a.min(a.abs().sqrt()) << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_interop.cpp

@@ -0,0 +1,22 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  MatrixXf m(2,2);
+  MatrixXf n(2,2);
+  MatrixXf result(2,2);
+
+  m << 1,2,
+       3,4;
+  n << 5,6,
+       7,8;
+  
+  result = (m.array() + 4).matrix() * m;
+  cout << "-- Combination 1: --" << endl << result << endl << endl;
+  result = (m.array() * n.array()).matrix() * m;
+  cout << "-- Combination 2: --" << endl << result << endl << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_interop_matrix.cpp

@@ -0,0 +1,26 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  MatrixXf m(2,2);
+  MatrixXf n(2,2);
+  MatrixXf result(2,2);
+
+  m << 1,2,
+       3,4;
+  n << 5,6,
+       7,8;
+
+  result = m * n;
+  cout << "-- Matrix m*n: --" << endl << result << endl << endl;
+  result = m.array() * n.array();
+  cout << "-- Array m*n: --" << endl << result << endl << endl;
+  result = m.cwiseProduct(n);
+  cout << "-- With cwiseProduct: --" << endl << result << endl << endl;
+  result = m.array() + 4;
+  cout << "-- Array m + 4: --" << endl << result << endl << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ArrayClass_mult.cpp

@@ -0,0 +1,16 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  ArrayXXf a(2,2);
+  ArrayXXf b(2,2);
+  a << 1,2,
+       3,4;
+  b << 5,6,
+       7,8;
+  cout << "a * b = " << endl << a * b << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_BlockOperations_block_assignment.cpp

@@ -0,0 +1,18 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  Array22f m;
+  m << 1,2,
+       3,4;
+  Array44f a = Array44f::Constant(0.6);
+  cout << "Here is the array a:" << endl << a << endl << endl;
+  a.block<2,2>(1,1) = m;
+  cout << "Here is now a with m copied into its central 2x2 block:" << endl << a << endl << endl;
+  a.block(0,0,2,3) = a.block(2,1,2,3);
+  cout << "Here is now a with bottom-right 2x3 block copied into top-left 2x3 block:" << endl << a << endl << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_BlockOperations_colrow.cpp

@@ -0,0 +1,17 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+
+int main()
+{
+  Eigen::MatrixXf m(3,3);
+  m << 1,2,3,
+       4,5,6,
+       7,8,9;
+  cout << "Here is the matrix m:" << endl << m << endl;
+  cout << "2nd Row: " << m.row(1) << endl;
+  m.col(2) += 3 * m.col(0);
+  cout << "After adding 3 times the first column into the third column, the matrix m is:\n";
+  cout << m << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_BlockOperations_corner.cpp

@@ -0,0 +1,17 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+
+int main()
+{
+  Eigen::Matrix4f m;
+  m << 1, 2, 3, 4,
+       5, 6, 7, 8,
+       9, 10,11,12,
+       13,14,15,16;
+  cout << "m.leftCols(2) =" << endl << m.leftCols(2) << endl << endl;
+  cout << "m.bottomRows<2>() =" << endl << m.bottomRows<2>() << endl << endl;
+  m.topLeftCorner(1,3) = m.bottomRightCorner(3,1).transpose();
+  cout << "After assignment, m = " << endl << m << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_BlockOperations_print_block.cpp

@@ -0,0 +1,20 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+
+int main()
+{
+  Eigen::MatrixXf m(4,4);
+  m <<  1, 2, 3, 4,
+        5, 6, 7, 8,
+        9,10,11,12,
+       13,14,15,16;
+  cout << "Block in the middle" << endl;
+  cout << m.block<2,2>(1,1) << endl << endl;
+  for (int i = 1; i <= 3; ++i)
+  {
+    cout << "Block of size " << i << "x" << i << endl;
+    cout << m.block(0,0,i,i) << endl << endl;
+  }
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_BlockOperations_vector.cpp

@@ -0,0 +1,14 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+
+int main()
+{
+  Eigen::ArrayXf v(6);
+  v << 1, 2, 3, 4, 5, 6;
+  cout << "v.head(3) =" << endl << v.head(3) << endl << endl;
+  cout << "v.tail<3>() = " << endl << v.tail<3>() << endl << endl;
+  v.segment(1,4) *= 2;
+  cout << "after 'v.segment(1,4) *= 2', v =" << endl << v << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_PartialLU_solve.cpp

@@ -0,0 +1,18 @@
+#include <Eigen/Core>
+#include <Eigen/LU>
+#include <iostream>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+   Matrix3f A;
+   Vector3f b;
+   A << 1,2,3,  4,5,6,  7,8,10;
+   b << 3, 3, 4;
+   cout << "Here is the matrix A:" << endl << A << endl;
+   cout << "Here is the vector b:" << endl << b << endl;
+   Vector3f x = A.lu().solve(b);
+   cout << "The solution is:" << endl << x << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_broadcast_1nn.cpp

@@ -0,0 +1,24 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  Eigen::MatrixXf m(2,4);
+  Eigen::VectorXf v(2);
+  
+  m << 1, 23, 6, 9,
+       3, 11, 7, 2;
+       
+  v << 2,
+       3;
+
+  MatrixXf::Index index;
+  // find nearest neighbour
+  (m.colwise() - v).colwise().squaredNorm().minCoeff(&index);
+
+  cout << "Nearest neighbour is column " << index << ":" << endl;
+  cout << m.col(index) << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_broadcast_simple.cpp

@@ -0,0 +1,21 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+int main()
+{
+  Eigen::MatrixXf mat(2,4);
+  Eigen::VectorXf v(2);
+  
+  mat << 1, 2, 6, 9,
+         3, 1, 7, 2;
+         
+  v << 0,
+       1;
+       
+  //add v to each column of m
+  mat.colwise() += v;
+  
+  std::cout << "Broadcasting result: " << std::endl;
+  std::cout << mat << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_broadcast_simple_rowwise.cpp

@@ -0,0 +1,20 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+int main()
+{
+  Eigen::MatrixXf mat(2,4);
+  Eigen::VectorXf v(4);
+  
+  mat << 1, 2, 6, 9,
+         3, 1, 7, 2;
+         
+  v << 0,1,2,3;
+       
+  //add v to each row of m
+  mat.rowwise() += v.transpose();
+  
+  std::cout << "Broadcasting result: " << std::endl;
+  std::cout << mat << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_colwise.cpp

@@ -0,0 +1,13 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+int main()
+{
+  Eigen::MatrixXf mat(2,4);
+  mat << 1, 2, 6, 9,
+         3, 1, 7, 2;
+  
+  std::cout << "Column's maximum: " << std::endl
+   << mat.colwise().maxCoeff() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_maxnorm.cpp

@@ -0,0 +1,20 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+int main()
+{
+  MatrixXf mat(2,4);
+  mat << 1, 2, 6, 9,
+         3, 1, 7, 2;
+  
+  MatrixXf::Index   maxIndex;
+  float maxNorm = mat.colwise().sum().maxCoeff(&maxIndex);
+  
+  std::cout << "Maximum sum at position " << maxIndex << std::endl;
+
+  std::cout << "The corresponding vector is: " << std::endl;
+  std::cout << mat.col( maxIndex ) << std::endl;
+  std::cout << "And its sum is is: " << maxNorm << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_reductions_bool.cpp

@@ -0,0 +1,21 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  ArrayXXf a(2,2);
+  
+  a << 1,2,
+       3,4;
+
+  cout << "(a > 0).all()   = " << (a > 0).all() << endl;
+  cout << "(a > 0).any()   = " << (a > 0).any() << endl;
+  cout << "(a > 0).count() = " << (a > 0).count() << endl;
+  cout << endl;
+  cout << "(a > 2).all()   = " << (a > 2).all() << endl;
+  cout << "(a > 2).any()   = " << (a > 2).any() << endl;
+  cout << "(a > 2).count() = " << (a > 2).count() << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_reductions_norm.cpp

@@ -0,0 +1,28 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  VectorXf v(2);
+  MatrixXf m(2,2), n(2,2);
+  
+  v << -1,
+       2;
+  
+  m << 1,-2,
+       -3,4;
+
+  cout << "v.squaredNorm() = " << v.squaredNorm() << endl;
+  cout << "v.norm() = " << v.norm() << endl;
+  cout << "v.lpNorm<1>() = " << v.lpNorm<1>() << endl;
+  cout << "v.lpNorm<Infinity>() = " << v.lpNorm<Infinity>() << endl;
+
+  cout << endl;
+  cout << "m.squaredNorm() = " << m.squaredNorm() << endl;
+  cout << "m.norm() = " << m.norm() << endl;
+  cout << "m.lpNorm<1>() = " << m.lpNorm<1>() << endl;
+  cout << "m.lpNorm<Infinity>() = " << m.lpNorm<Infinity>() << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_reductions_operatornorm.cpp

@@ -0,0 +1,18 @@
+#include <Eigen/Dense>
+#include <iostream>
+
+using namespace Eigen;
+using namespace std;
+
+int main()
+{
+  MatrixXf m(2,2);
+  m << 1,-2,
+       -3,4;
+
+  cout << "1-norm(m)     = " << m.cwiseAbs().colwise().sum().maxCoeff()
+       << " == "             << m.colwise().lpNorm<1>().maxCoeff() << endl;
+
+  cout << "infty-norm(m) = " << m.cwiseAbs().rowwise().sum().maxCoeff()
+       << " == "             << m.rowwise().lpNorm<1>().maxCoeff() << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_rowwise.cpp

@@ -0,0 +1,13 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+int main()
+{
+  Eigen::MatrixXf mat(2,4);
+  mat << 1, 2, 6, 9,
+         3, 1, 7, 2;
+  
+  std::cout << "Row's maximum: " << std::endl
+   << mat.rowwise().maxCoeff() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_ReductionsVisitorsBroadcasting_visitors.cpp

@@ -0,0 +1,26 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+using namespace Eigen;
+
+int main()
+{
+  Eigen::MatrixXf m(2,2);
+  
+  m << 1, 2,
+       3, 4;
+
+  //get location of maximum
+  MatrixXf::Index maxRow, maxCol;
+  float max = m.maxCoeff(&maxRow, &maxCol);
+
+  //get location of minimum
+  MatrixXf::Index minRow, minCol;
+  float min = m.minCoeff(&minRow, &minCol);
+
+  cout << "Max: " << max <<  ", at: " <<
+     maxRow << "," << maxCol << endl;
+  cout << "Min: " << min << ", at: " <<
+     minRow << "," << minCol << endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_simple_example_dynamic_size.cpp

@@ -0,0 +1,22 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+
+int main()
+{
+  for (int size=1; size<=4; ++size)
+  {
+    MatrixXi m(size,size+1);         // a (size)x(size+1)-matrix of int's
+    for (int j=0; j<m.cols(); ++j)   // loop over columns
+      for (int i=0; i<m.rows(); ++i) // loop over rows
+        m(i,j) = i+j*size;           // to access matrix coefficients,
+                                     // use operator()(int,int)
+    std::cout << m << "\n\n";
+  }
+
+  VectorXf v(4); // a vector of 4 float's
+  // to access vector coefficients, use either operator () or operator []
+  v[0] = 1; v[1] = 2; v(2) = 3; v(3) = 4;
+  std::cout << "\nv:\n" << v << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/Tutorial_simple_example_fixed_size.cpp

@@ -0,0 +1,15 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+
+int main()
+{
+  Matrix3f m3;
+  m3 << 1, 2, 3, 4, 5, 6, 7, 8, 9;
+  Matrix4f m4 = Matrix4f::Identity();
+  Vector4i v4(1, 2, 3, 4);
+
+  std::cout << "m3\n" << m3 << "\nm4:\n"
+    << m4 << "\nv4:\n" << v4 << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/class_Block.cpp

@@ -0,0 +1,27 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+template<typename Derived>
+Eigen::Block<Derived>
+topLeftCorner(MatrixBase<Derived>& m, int rows, int cols)
+{
+  return Eigen::Block<Derived>(m.derived(), 0, 0, rows, cols);
+}
+
+template<typename Derived>
+const Eigen::Block<const Derived>
+topLeftCorner(const MatrixBase<Derived>& m, int rows, int cols)
+{
+  return Eigen::Block<const Derived>(m.derived(), 0, 0, rows, cols);
+}
+
+int main(int, char**)
+{
+  Matrix4d m = Matrix4d::Identity();
+  cout << topLeftCorner(4*m, 2, 3) << endl; // calls the const version
+  topLeftCorner(m, 2, 3) *= 5;              // calls the non-const version
+  cout << "Now the matrix m is:" << endl << m << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_CwiseBinaryOp.cpp

@@ -0,0 +1,18 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+// define a custom template binary functor
+template<typename Scalar> struct MakeComplexOp {
+  EIGEN_EMPTY_STRUCT_CTOR(MakeComplexOp)
+  typedef complex<Scalar> result_type;
+  complex<Scalar> operator()(const Scalar& a, const Scalar& b) const { return complex<Scalar>(a,b); }
+};
+
+int main(int, char**)
+{
+  Matrix4d m1 = Matrix4d::Random(), m2 = Matrix4d::Random();
+  cout << m1.binaryExpr(m2, MakeComplexOp<double>()) << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_CwiseUnaryOp.cpp

@@ -0,0 +1,19 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+// define a custom template unary functor
+template<typename Scalar>
+struct CwiseClampOp {
+  CwiseClampOp(const Scalar& inf, const Scalar& sup) : m_inf(inf), m_sup(sup) {}
+  const Scalar operator()(const Scalar& x) const { return x<m_inf ? m_inf : (x>m_sup ? m_sup : x); }
+  Scalar m_inf, m_sup;
+};
+
+int main(int, char**)
+{
+  Matrix4d m1 = Matrix4d::Random();
+  cout << m1 << endl << "becomes: " << endl << m1.unaryExpr(CwiseClampOp<double>(-0.5,0.5)) << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_CwiseUnaryOp_ptrfun.cpp

@@ -0,0 +1,20 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+// define function to be applied coefficient-wise
+double ramp(double x)
+{
+  if (x > 0)
+    return x;
+  else 
+    return 0;
+}
+
+int main(int, char**)
+{
+  Matrix4d m1 = Matrix4d::Random();
+  cout << m1 << endl << "becomes: " << endl << m1.unaryExpr(ptr_fun(ramp)) << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_FixedBlock.cpp

@@ -0,0 +1,27 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+template<typename Derived>
+Eigen::Block<Derived, 2, 2>
+topLeft2x2Corner(MatrixBase<Derived>& m)
+{
+  return Eigen::Block<Derived, 2, 2>(m.derived(), 0, 0);
+}
+
+template<typename Derived>
+const Eigen::Block<const Derived, 2, 2>
+topLeft2x2Corner(const MatrixBase<Derived>& m)
+{
+  return Eigen::Block<const Derived, 2, 2>(m.derived(), 0, 0);
+}
+
+int main(int, char**)
+{
+  Matrix3d m = Matrix3d::Identity();
+  cout << topLeft2x2Corner(4*m) << endl; // calls the const version
+  topLeft2x2Corner(m) *= 2;              // calls the non-const version
+  cout << "Now the matrix m is:" << endl << m << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_FixedVectorBlock.cpp

@@ -0,0 +1,27 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+template<typename Derived>
+Eigen::VectorBlock<Derived, 2>
+firstTwo(MatrixBase<Derived>& v)
+{
+  return Eigen::VectorBlock<Derived, 2>(v.derived(), 0);
+}
+
+template<typename Derived>
+const Eigen::VectorBlock<const Derived, 2>
+firstTwo(const MatrixBase<Derived>& v)
+{
+  return Eigen::VectorBlock<const Derived, 2>(v.derived(), 0);
+}
+
+int main(int, char**)
+{
+  Matrix<int,1,6> v; v << 1,2,3,4,5,6;
+  cout << firstTwo(4*v) << endl; // calls the const version
+  firstTwo(v) *= 2;              // calls the non-const version
+  cout << "Now the vector v is:" << endl << v << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/class_VectorBlock.cpp

@@ -0,0 +1,27 @@
+#include <Eigen/Core>
+#include <iostream>
+using namespace Eigen;
+using namespace std;
+
+template<typename Derived>
+Eigen::VectorBlock<Derived>
+segmentFromRange(MatrixBase<Derived>& v, int start, int end)
+{
+  return Eigen::VectorBlock<Derived>(v.derived(), start, end-start);
+}
+
+template<typename Derived>
+const Eigen::VectorBlock<const Derived>
+segmentFromRange(const MatrixBase<Derived>& v, int start, int end)
+{
+  return Eigen::VectorBlock<const Derived>(v.derived(), start, end-start);
+}
+
+int main(int, char**)
+{
+  Matrix<int,1,6> v; v << 1,2,3,4,5,6;
+  cout << segmentFromRange(2*v, 2, 4) << endl; // calls the const version
+  segmentFromRange(v, 1, 3) *= 5;              // calls the non-const version
+  cout << "Now the vector v is:" << endl << v << endl;
+  return 0;
+}

cs440-acg/ext/eigen/doc/examples/function_taking_eigenbase.cpp

@@ -0,0 +1,18 @@
+#include <iostream>
+#include <Eigen/Core>
+using namespace Eigen;
+
+template <typename Derived>
+void print_size(const EigenBase<Derived>& b)
+{
+  std::cout << "size (rows, cols): " << b.size() << " (" << b.rows()
+            << ", " << b.cols() << ")" << std::endl;
+}
+
+int main()
+{
+    Vector3f v;
+    print_size(v);
+    // v.asDiagonal() returns a 3x3 diagonal matrix pseudo-expression
+    print_size(v.asDiagonal());
+}

cs440-acg/ext/eigen/doc/examples/function_taking_ref.cpp

@@ -0,0 +1,19 @@
+#include <iostream>
+#include <Eigen/SVD>
+using namespace Eigen;
+using namespace std;
+
+float inv_cond(const Ref<const MatrixXf>& a)
+{
+  const VectorXf sing_vals = a.jacobiSvd().singularValues();
+  return sing_vals(sing_vals.size()-1) / sing_vals(0);
+}
+
+int main()
+{
+  Matrix4f m = Matrix4f::Random();
+  cout << "matrix m:" << endl << m << endl << endl;
+  cout << "inv_cond(m):          " << inv_cond(m)                      << endl;
+  cout << "inv_cond(m(1:3,1:3)): " << inv_cond(m.topLeftCorner(3,3))   << endl;
+  cout << "inv_cond(m+I):        " << inv_cond(m+Matrix4f::Identity()) << endl;
+}

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp

@@ -0,0 +1,11 @@
+/*
+This program is presented in several fragments in the doc page.
+Every fragment is in its own file; this file simply combines them.
+*/
+
+#include "make_circulant.cpp.preamble"
+#include "make_circulant.cpp.traits"
+#include "make_circulant.cpp.expression"
+#include "make_circulant.cpp.evaluator"
+#include "make_circulant.cpp.entry"
+#include "make_circulant.cpp.main"

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.entry

@@ -0,0 +1,5 @@
+template <class ArgType>
+Circulant<ArgType> makeCirculant(const Eigen::MatrixBase<ArgType>& arg)
+{
+  return Circulant<ArgType>(arg.derived());
+}

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.evaluator

@@ -0,0 +1,32 @@
+namespace Eigen {
+  namespace internal {
+    template<typename ArgType>
+    struct evaluator<Circulant<ArgType> >
+      : evaluator_base<Circulant<ArgType> >
+    {
+      typedef Circulant<ArgType> XprType;
+      typedef typename nested_eval<ArgType, XprType::ColsAtCompileTime>::type ArgTypeNested;
+      typedef typename remove_all<ArgTypeNested>::type ArgTypeNestedCleaned;
+      typedef typename XprType::CoeffReturnType CoeffReturnType;
+
+      enum { 
+        CoeffReadCost = evaluator<ArgTypeNestedCleaned>::CoeffReadCost,
+        Flags = Eigen::ColMajor 
+      };
+      
+      evaluator(const XprType& xpr)
+        : m_argImpl(xpr.m_arg), m_rows(xpr.rows())
+      { }
+
+      CoeffReturnType coeff(Index row, Index col) const
+      {
+        Index index = row - col;
+        if (index < 0) index += m_rows;
+        return m_argImpl.coeff(index);
+      }
+
+      evaluator<ArgTypeNestedCleaned> m_argImpl;
+      const Index m_rows;
+    };
+  }
+}

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.expression

@@ -0,0 +1,20 @@
+template <class ArgType>
+class Circulant : public Eigen::MatrixBase<Circulant<ArgType> >
+{
+public:
+  Circulant(const ArgType& arg)
+    : m_arg(arg)
+  { 
+    EIGEN_STATIC_ASSERT(ArgType::ColsAtCompileTime == 1,
+                        YOU_TRIED_CALLING_A_VECTOR_METHOD_ON_A_MATRIX);
+  }
+
+  typedef typename Eigen::internal::ref_selector<Circulant>::type Nested; 
+
+  typedef Eigen::Index Index;
+  Index rows() const { return m_arg.rows(); }
+  Index cols() const { return m_arg.rows(); }
+
+  typedef typename Eigen::internal::ref_selector<ArgType>::type ArgTypeNested;
+  ArgTypeNested m_arg;
+};

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.main

@@ -0,0 +1,8 @@
+int main()
+{
+  Eigen::VectorXd vec(4);
+  vec << 1, 2, 4, 8;
+  Eigen::MatrixXd mat;
+  mat = makeCirculant(vec);
+  std::cout << mat << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.preamble

@@ -0,0 +1,4 @@
+#include <Eigen/Core>
+#include <iostream>
+
+template <class ArgType> class Circulant;

cs440-acg/ext/eigen/doc/examples/make_circulant.cpp.traits

@@ -0,0 +1,19 @@
+namespace Eigen {
+  namespace internal {
+    template <class ArgType>
+    struct traits<Circulant<ArgType> >
+    {
+      typedef Eigen::Dense StorageKind;
+      typedef Eigen::MatrixXpr XprKind;
+      typedef typename ArgType::StorageIndex StorageIndex;
+      typedef typename ArgType::Scalar Scalar;
+      enum { 
+        Flags = Eigen::ColMajor,
+        RowsAtCompileTime = ArgType::RowsAtCompileTime,
+        ColsAtCompileTime = ArgType::RowsAtCompileTime,
+        MaxRowsAtCompileTime = ArgType::MaxRowsAtCompileTime,
+        MaxColsAtCompileTime = ArgType::MaxRowsAtCompileTime
+      };
+    };
+  }
+}

cs440-acg/ext/eigen/doc/examples/make_circulant2.cpp

@@ -0,0 +1,52 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+
+// [circulant_func]
+template<class ArgType>
+class circulant_functor {
+  const ArgType &m_vec;
+public:
+  circulant_functor(const ArgType& arg) : m_vec(arg) {}
+
+  const typename ArgType::Scalar& operator() (Index row, Index col) const {
+    Index index = row - col;
+    if (index < 0) index += m_vec.size();
+    return m_vec(index);
+  }
+};
+// [circulant_func]
+
+// [square]
+template<class ArgType>
+struct circulant_helper {
+  typedef Matrix<typename ArgType::Scalar,
+                 ArgType::SizeAtCompileTime,
+                 ArgType::SizeAtCompileTime,
+                 ColMajor,
+                 ArgType::MaxSizeAtCompileTime,
+                 ArgType::MaxSizeAtCompileTime> MatrixType;
+};
+// [square]
+
+// [makeCirculant]
+template <class ArgType>
+CwiseNullaryOp<circulant_functor<ArgType>, typename circulant_helper<ArgType>::MatrixType>
+makeCirculant(const Eigen::MatrixBase<ArgType>& arg)
+{
+  typedef typename circulant_helper<ArgType>::MatrixType MatrixType;
+  return MatrixType::NullaryExpr(arg.size(), arg.size(), circulant_functor<ArgType>(arg.derived()));
+}
+// [makeCirculant]
+
+// [main]
+int main()
+{
+  Eigen::VectorXd vec(4);
+  vec << 1, 2, 4, 8;
+  Eigen::MatrixXd mat;
+  mat = makeCirculant(vec);
+  std::cout << mat << std::endl;
+}
+// [main]

cs440-acg/ext/eigen/doc/examples/matrixfree_cg.cpp

@@ -0,0 +1,129 @@
+#include <iostream>
+#include <Eigen/Core>
+#include <Eigen/Dense>
+#include <Eigen/IterativeLinearSolvers>
+#include <unsupported/Eigen/IterativeSolvers>
+
+class MatrixReplacement;
+using Eigen::SparseMatrix;
+
+namespace Eigen {
+namespace internal {
+  // MatrixReplacement looks-like a SparseMatrix, so let's inherits its traits:
+  template<>
+  struct traits<MatrixReplacement> :  public Eigen::internal::traits<Eigen::SparseMatrix<double> >
+  {};
+}
+}
+
+// Example of a matrix-free wrapper from a user type to Eigen's compatible type
+// For the sake of simplicity, this example simply wrap a Eigen::SparseMatrix.
+class MatrixReplacement : public Eigen::EigenBase<MatrixReplacement> {
+public:
+  // Required typedefs, constants, and method:
+  typedef double Scalar;
+  typedef double RealScalar;
+  typedef int StorageIndex;
+  enum {
+    ColsAtCompileTime = Eigen::Dynamic,
+    MaxColsAtCompileTime = Eigen::Dynamic,
+    IsRowMajor = false
+  };
+
+  Index rows() const { return mp_mat->rows(); }
+  Index cols() const { return mp_mat->cols(); }
+
+  template<typename Rhs>
+  Eigen::Product<MatrixReplacement,Rhs,Eigen::AliasFreeProduct> operator*(const Eigen::MatrixBase<Rhs>& x) const {
+    return Eigen::Product<MatrixReplacement,Rhs,Eigen::AliasFreeProduct>(*this, x.derived());
+  }
+
+  // Custom API:
+  MatrixReplacement() : mp_mat(0) {}
+
+  void attachMyMatrix(const SparseMatrix<double> &mat) {
+    mp_mat = &mat;
+  }
+  const SparseMatrix<double> my_matrix() const { return *mp_mat; }
+
+private:
+  const SparseMatrix<double> *mp_mat;
+};
+
+
+// Implementation of MatrixReplacement * Eigen::DenseVector though a specialization of internal::generic_product_impl:
+namespace Eigen {
+namespace internal {
+
+  template<typename Rhs>
+  struct generic_product_impl<MatrixReplacement, Rhs, SparseShape, DenseShape, GemvProduct> // GEMV stands for matrix-vector
+  : generic_product_impl_base<MatrixReplacement,Rhs,generic_product_impl<MatrixReplacement,Rhs> >
+  {
+    typedef typename Product<MatrixReplacement,Rhs>::Scalar Scalar;
+
+    template<typename Dest>
+    static void scaleAndAddTo(Dest& dst, const MatrixReplacement& lhs, const Rhs& rhs, const Scalar& alpha)
+    {
+      // This method should implement "dst += alpha * lhs * rhs" inplace,
+      // however, for iterative solvers, alpha is always equal to 1, so let's not bother about it.
+      assert(alpha==Scalar(1) && "scaling is not implemented");
+      EIGEN_ONLY_USED_FOR_DEBUG(alpha);
+
+      // Here we could simply call dst.noalias() += lhs.my_matrix() * rhs,
+      // but let's do something fancier (and less efficient):
+      for(Index i=0; i<lhs.cols(); ++i)
+        dst += rhs(i) * lhs.my_matrix().col(i);
+    }
+  };
+
+}
+}
+
+int main()
+{
+  int n = 10;
+  Eigen::SparseMatrix<double> S = Eigen::MatrixXd::Random(n,n).sparseView(0.5,1);
+  S = S.transpose()*S;
+
+  MatrixReplacement A;
+  A.attachMyMatrix(S);
+
+  Eigen::VectorXd b(n), x;
+  b.setRandom();
+
+  // Solve Ax = b using various iterative solver with matrix-free version:
+  {
+    Eigen::ConjugateGradient<MatrixReplacement, Eigen::Lower|Eigen::Upper, Eigen::IdentityPreconditioner> cg;
+    cg.compute(A);
+    x = cg.solve(b);
+    std::cout << "CG:       #iterations: " << cg.iterations() << ", estimated error: " << cg.error() << std::endl;
+  }
+
+  {
+    Eigen::BiCGSTAB<MatrixReplacement, Eigen::IdentityPreconditioner> bicg;
+    bicg.compute(A);
+    x = bicg.solve(b);
+    std::cout << "BiCGSTAB: #iterations: " << bicg.iterations() << ", estimated error: " << bicg.error() << std::endl;
+  }
+
+  {
+    Eigen::GMRES<MatrixReplacement, Eigen::IdentityPreconditioner> gmres;
+    gmres.compute(A);
+    x = gmres.solve(b);
+    std::cout << "GMRES:    #iterations: " << gmres.iterations() << ", estimated error: " << gmres.error() << std::endl;
+  }
+
+  {
+    Eigen::DGMRES<MatrixReplacement, Eigen::IdentityPreconditioner> gmres;
+    gmres.compute(A);
+    x = gmres.solve(b);
+    std::cout << "DGMRES:   #iterations: " << gmres.iterations() << ", estimated error: " << gmres.error() << std::endl;
+  }
+
+  {
+    Eigen::MINRES<MatrixReplacement, Eigen::Lower|Eigen::Upper, Eigen::IdentityPreconditioner> minres;
+    minres.compute(A);
+    x = minres.solve(b);
+    std::cout << "MINRES:   #iterations: " << minres.iterations() << ", estimated error: " << minres.error() << std::endl;
+  }
+}

cs440-acg/ext/eigen/doc/examples/nullary_indexing.cpp

@@ -0,0 +1,66 @@
+#include <Eigen/Core>
+#include <iostream>
+
+using namespace Eigen;
+
+// [functor]
+template<class ArgType, class RowIndexType, class ColIndexType>
+class indexing_functor {
+  const ArgType &m_arg;
+  const RowIndexType &m_rowIndices;
+  const ColIndexType &m_colIndices;
+public:
+  typedef Matrix<typename ArgType::Scalar,
+                 RowIndexType::SizeAtCompileTime,
+                 ColIndexType::SizeAtCompileTime,
+                 ArgType::Flags&RowMajorBit?RowMajor:ColMajor,
+                 RowIndexType::MaxSizeAtCompileTime,
+                 ColIndexType::MaxSizeAtCompileTime> MatrixType;
+
+  indexing_functor(const ArgType& arg, const RowIndexType& row_indices, const ColIndexType& col_indices)
+    : m_arg(arg), m_rowIndices(row_indices), m_colIndices(col_indices)
+  {}
+
+  const typename ArgType::Scalar& operator() (Index row, Index col) const {
+    return m_arg(m_rowIndices[row], m_colIndices[col]);
+  }
+};
+// [functor]
+
+// [function]
+template <class ArgType, class RowIndexType, class ColIndexType>
+CwiseNullaryOp<indexing_functor<ArgType,RowIndexType,ColIndexType>, typename indexing_functor<ArgType,RowIndexType,ColIndexType>::MatrixType>
+indexing(const Eigen::MatrixBase<ArgType>& arg, const RowIndexType& row_indices, const ColIndexType& col_indices)
+{
+  typedef indexing_functor<ArgType,RowIndexType,ColIndexType> Func;
+  typedef typename Func::MatrixType MatrixType;
+  return MatrixType::NullaryExpr(row_indices.size(), col_indices.size(), Func(arg.derived(), row_indices, col_indices));
+}
+// [function]
+
+
+int main()
+{
+  std::cout << "[main1]\n";
+  Eigen::MatrixXi A = Eigen::MatrixXi::Random(4,4);
+  Array3i ri(1,2,1);
+  ArrayXi ci(6); ci << 3,2,1,0,0,2;
+  Eigen::MatrixXi B = indexing(A, ri, ci);
+  std::cout << "A =" << std::endl;
+  std::cout << A << std::endl << std::endl;
+  std::cout << "A([" << ri.transpose() << "], [" << ci.transpose() << "]) =" << std::endl;
+  std::cout << B << std::endl;
+  std::cout << "[main1]\n";
+
+  std::cout << "[main2]\n";
+  B =  indexing(A, ri+1, ci);
+  std::cout << "A(ri+1,ci) =" << std::endl;
+  std::cout << B << std::endl << std::endl;
+#if __cplusplus >= 201103L
+  B =  indexing(A, ArrayXi::LinSpaced(13,0,12).unaryExpr([](int x){return x%4;}), ArrayXi::LinSpaced(4,0,3));
+  std::cout << "A(ArrayXi::LinSpaced(13,0,12).unaryExpr([](int x){return x%4;}), ArrayXi::LinSpaced(4,0,3)) =" << std::endl;
+  std::cout << B << std::endl << std::endl;
+#endif
+  std::cout << "[main2]\n";
+}
+

cs440-acg/ext/eigen/doc/examples/tut_arithmetic_add_sub.cpp

@@ -0,0 +1,22 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+
+int main()
+{
+  Matrix2d a;
+  a << 1, 2,
+       3, 4;
+  MatrixXd b(2,2);
+  b << 2, 3,
+       1, 4;
+  std::cout << "a + b =\n" << a + b << std::endl;
+  std::cout << "a - b =\n" << a - b << std::endl;
+  std::cout << "Doing a += b;" << std::endl;
+  a += b;
+  std::cout << "Now a =\n" << a << std::endl;
+  Vector3d v(1,2,3);
+  Vector3d w(1,0,0);
+  std::cout << "-v + w - v =\n" << -v + w - v << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_arithmetic_dot_cross.cpp

@@ -0,0 +1,15 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+using namespace std;
+int main()
+{
+  Vector3d v(1,2,3);
+  Vector3d w(0,1,2);
+
+  cout << "Dot product: " << v.dot(w) << endl;
+  double dp = v.adjoint()*w; // automatic conversion of the inner product to a scalar
+  cout << "Dot product via a matrix product: " << dp << endl;
+  cout << "Cross product:\n" << v.cross(w) << endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_arithmetic_matrix_mul.cpp

@@ -0,0 +1,19 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+int main()
+{
+  Matrix2d mat;
+  mat << 1, 2,
+         3, 4;
+  Vector2d u(-1,1), v(2,0);
+  std::cout << "Here is mat*mat:\n" << mat*mat << std::endl;
+  std::cout << "Here is mat*u:\n" << mat*u << std::endl;
+  std::cout << "Here is u^T*mat:\n" << u.transpose()*mat << std::endl;
+  std::cout << "Here is u^T*v:\n" << u.transpose()*v << std::endl;
+  std::cout << "Here is u*v^T:\n" << u*v.transpose() << std::endl;
+  std::cout << "Let's multiply mat by itself" << std::endl;
+  mat = mat*mat;
+  std::cout << "Now mat is mat:\n" << mat << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_arithmetic_redux_basic.cpp

@@ -0,0 +1,16 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace std;
+int main()
+{
+  Eigen::Matrix2d mat;
+  mat << 1, 2,
+         3, 4;
+  cout << "Here is mat.sum():       " << mat.sum()       << endl;
+  cout << "Here is mat.prod():      " << mat.prod()      << endl;
+  cout << "Here is mat.mean():      " << mat.mean()      << endl;
+  cout << "Here is mat.minCoeff():  " << mat.minCoeff()  << endl;
+  cout << "Here is mat.maxCoeff():  " << mat.maxCoeff()  << endl;
+  cout << "Here is mat.trace():     " << mat.trace()     << endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_arithmetic_scalar_mul_div.cpp

@@ -0,0 +1,17 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+
+int main()
+{
+  Matrix2d a;
+  a << 1, 2,
+       3, 4;
+  Vector3d v(1,2,3);
+  std::cout << "a * 2.5 =\n" << a * 2.5 << std::endl;
+  std::cout << "0.1 * v =\n" << 0.1 * v << std::endl;
+  std::cout << "Doing v *= 2;" << std::endl;
+  v *= 2;
+  std::cout << "Now v =\n" << v << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_matrix_coefficient_accessors.cpp

@@ -0,0 +1,18 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+
+int main()
+{
+  MatrixXd m(2,2);
+  m(0,0) = 3;
+  m(1,0) = 2.5;
+  m(0,1) = -1;
+  m(1,1) = m(1,0) + m(0,1);
+  std::cout << "Here is the matrix m:\n" << m << std::endl;
+  VectorXd v(2);
+  v(0) = 4;
+  v(1) = v(0) - 1;
+  std::cout << "Here is the vector v:\n" << v << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_matrix_resize.cpp

@@ -0,0 +1,18 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+
+int main()
+{
+  MatrixXd m(2,5);
+  m.resize(4,3);
+  std::cout << "The matrix m is of size "
+            << m.rows() << "x" << m.cols() << std::endl;
+  std::cout << "It has " << m.size() << " coefficients" << std::endl;
+  VectorXd v(2);
+  v.resize(5);
+  std::cout << "The vector v is of size " << v.size() << std::endl;
+  std::cout << "As a matrix, v is of size "
+            << v.rows() << "x" << v.cols() << std::endl;
+}

cs440-acg/ext/eigen/doc/examples/tut_matrix_resize_fixed_size.cpp

@@ -0,0 +1,12 @@
+#include <iostream>
+#include <Eigen/Dense>
+
+using namespace Eigen;
+
+int main()
+{
+  Matrix4d m;
+  m.resize(4,4); // no operation
+  std::cout << "The matrix m is of size "
+            << m.rows() << "x" << m.cols() << std::endl;
+}