mcell/libs/pybind11/tests/test_eigen.cpp

/*
    tests/eigen.cpp -- automatic conversion of Eigen types

    Copyright (c) 2016 Wenzel Jakob <[email protected]>

    All rights reserved. Use of this source code is governed by a
    BSD-style license that can be found in the LICENSE file.
*/

#include "pybind11_tests.h"
#include "constructor_stats.h"
#include <pybind11/eigen.h>
#include <pybind11/stl.h>

#if defined(_MSC_VER)
#  pragma warning(disable: 4996) // C4996: std::unary_negation is deprecated
#endif

#include <Eigen/Cholesky>

using MatrixXdR = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;



// Sets/resets a testing reference matrix to have values of 10*r + c, where r and c are the
// (1-based) row/column number.
template <typename M> void reset_ref(M &x) {
    for (int i = 0; i < x.rows(); i++) for (int j = 0; j < x.cols(); j++)
        x(i, j) = 11 + 10*i + j;
}

// Returns a static, column-major matrix
Eigen::MatrixXd &get_cm() {
    static Eigen::MatrixXd *x;
    if (!x) {
        x = new Eigen::MatrixXd(3, 3);
        reset_ref(*x);
    }
    return *x;
}
// Likewise, but row-major
MatrixXdR &get_rm() {
    static MatrixXdR *x;
    if (!x) {
        x = new MatrixXdR(3, 3);
        reset_ref(*x);
    }
    return *x;
}
// Resets the values of the static matrices returned by get_cm()/get_rm()
void reset_refs() {
    reset_ref(get_cm());
    reset_ref(get_rm());
}

// Returns element 2,1 from a matrix (used to test copy/nocopy)
double get_elem(Eigen::Ref<const Eigen::MatrixXd> m) { return m(2, 1); };


// Returns a matrix with 10*r + 100*c added to each matrix element (to help test that the matrix
// reference is referencing rows/columns correctly).
template <typename MatrixArgType> Eigen::MatrixXd adjust_matrix(MatrixArgType m) {
    Eigen::MatrixXd ret(m);
    for (int c = 0; c < m.cols(); c++) for (int r = 0; r < m.rows(); r++)
        ret(r, c) += 10*r + 100*c;
    return ret;
}

struct CustomOperatorNew {
    CustomOperatorNew() = default;

    Eigen::Matrix4d a = Eigen::Matrix4d::Zero();
    Eigen::Matrix4d b = Eigen::Matrix4d::Identity();

    EIGEN_MAKE_ALIGNED_OPERATOR_NEW;
};

TEST_SUBMODULE(eigen, m) {
    using FixedMatrixR = Eigen::Matrix<float, 5, 6, Eigen::RowMajor>;
    using FixedMatrixC = Eigen::Matrix<float, 5, 6>;
    using DenseMatrixR = Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor>;
    using DenseMatrixC = Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic>;
    using FourRowMatrixC = Eigen::Matrix<float, 4, Eigen::Dynamic>;
    using FourColMatrixC = Eigen::Matrix<float, Eigen::Dynamic, 4>;
    using FourRowMatrixR = Eigen::Matrix<float, 4, Eigen::Dynamic>;
    using FourColMatrixR = Eigen::Matrix<float, Eigen::Dynamic, 4>;
    using SparseMatrixR = Eigen::SparseMatrix<float, Eigen::RowMajor>;
    using SparseMatrixC = Eigen::SparseMatrix<float>;

    m.attr("have_eigen") = true;

    // various tests
    m.def("double_col", [](const Eigen::VectorXf &x) -> Eigen::VectorXf { return 2.0f * x; });
    m.def("double_row", [](const Eigen::RowVectorXf &x) -> Eigen::RowVectorXf { return 2.0f * x; });
    m.def("double_complex", [](const Eigen::VectorXcf &x) -> Eigen::VectorXcf { return 2.0f * x; });
    m.def("double_threec", [](py::EigenDRef<Eigen::Vector3f> x) { x *= 2; });
    m.def("double_threer", [](py::EigenDRef<Eigen::RowVector3f> x) { x *= 2; });
    m.def("double_mat_cm", [](Eigen::MatrixXf x) -> Eigen::MatrixXf { return 2.0f * x; });
    m.def("double_mat_rm", [](DenseMatrixR x) -> DenseMatrixR { return 2.0f * x; });

    // test_eigen_ref_to_python
    // Different ways of passing via Eigen::Ref; the first and second are the Eigen-recommended
    m.def("cholesky1", [](Eigen::Ref<MatrixXdR> x) -> Eigen::MatrixXd { return x.llt().matrixL(); });
    m.def("cholesky2", [](const Eigen::Ref<const MatrixXdR> &x) -> Eigen::MatrixXd { return x.llt().matrixL(); });
    m.def("cholesky3", [](const Eigen::Ref<MatrixXdR> &x) -> Eigen::MatrixXd { return x.llt().matrixL(); });
    m.def("cholesky4", [](Eigen::Ref<const MatrixXdR> x) -> Eigen::MatrixXd { return x.llt().matrixL(); });

    // test_eigen_ref_mutators
    // Mutators: these add some value to the given element using Eigen, but Eigen should be mapping into
    // the numpy array data and so the result should show up there.  There are three versions: one that
    // works on a contiguous-row matrix (numpy's default), one for a contiguous-column matrix, and one
    // for any matrix.
    auto add_rm = [](Eigen::Ref<MatrixXdR> x, int r, int c, double v) { x(r,c) += v; };
    auto add_cm = [](Eigen::Ref<Eigen::MatrixXd> x, int r, int c, double v) { x(r,c) += v; };

    // Mutators (Eigen maps into numpy variables):
    m.def("add_rm", add_rm); // Only takes row-contiguous
    m.def("add_cm", add_cm); // Only takes column-contiguous
    // Overloaded versions that will accept either row or column contiguous:
    m.def("add1", add_rm);
    m.def("add1", add_cm);
    m.def("add2", add_cm);
    m.def("add2", add_rm);
    // This one accepts a matrix of any stride:
    m.def("add_any", [](py::EigenDRef<Eigen::MatrixXd> x, int r, int c, double v) { x(r,c) += v; });

    // Return mutable references (numpy maps into eigen varibles)
    m.def("get_cm_ref", []() { return Eigen::Ref<Eigen::MatrixXd>(get_cm()); });
    m.def("get_rm_ref", []() { return Eigen::Ref<MatrixXdR>(get_rm()); });
    // The same references, but non-mutable (numpy maps into eigen variables, but is !writeable)
    m.def("get_cm_const_ref", []() { return Eigen::Ref<const Eigen::MatrixXd>(get_cm()); });
    m.def("get_rm_const_ref", []() { return Eigen::Ref<const MatrixXdR>(get_rm()); });

    m.def("reset_refs", reset_refs); // Restores get_{cm,rm}_ref to original values

    // Increments and returns ref to (same) matrix
    m.def("incr_matrix", [](Eigen::Ref<Eigen::MatrixXd> m, double v) {
        m += Eigen::MatrixXd::Constant(m.rows(), m.cols(), v);
        return m;
    }, py::return_value_policy::reference);

    // Same, but accepts a matrix of any strides
    m.def("incr_matrix_any", [](py::EigenDRef<Eigen::MatrixXd> m, double v) {
        m += Eigen::MatrixXd::Constant(m.rows(), m.cols(), v);
        return m;
    }, py::return_value_policy::reference);

    // Returns an eigen slice of even rows
    m.def("even_rows", [](py::EigenDRef<Eigen::MatrixXd> m) {
        return py::EigenDMap<Eigen::MatrixXd>(
                m.data(), (m.rows() + 1) / 2, m.cols(),
                py::EigenDStride(m.outerStride(), 2 * m.innerStride()));
    }, py::return_value_policy::reference);

    // Returns an eigen slice of even columns
    m.def("even_cols", [](py::EigenDRef<Eigen::MatrixXd> m) {
        return py::EigenDMap<Eigen::MatrixXd>(
                m.data(), m.rows(), (m.cols() + 1) / 2,
                py::EigenDStride(2 * m.outerStride(), m.innerStride()));
    }, py::return_value_policy::reference);

    // Returns diagonals: a vector-like object with an inner stride != 1
    m.def("diagonal", [](const Eigen::Ref<const Eigen::MatrixXd> &x) { return x.diagonal(); });
    m.def("diagonal_1", [](const Eigen::Ref<const Eigen::MatrixXd> &x) { return x.diagonal<1>(); });
    m.def("diagonal_n", [](const Eigen::Ref<const Eigen::MatrixXd> &x, int index) { return x.diagonal(index); });

    // Return a block of a matrix (gives non-standard strides)
    m.def("block", [](const Eigen::Ref<const Eigen::MatrixXd> &x, int start_row, int start_col, int block_rows, int block_cols) {
        return x.block(start_row, start_col, block_rows, block_cols);
    });

    // test_eigen_return_references, test_eigen_keepalive
    // return value referencing/copying tests:
    class ReturnTester {
        Eigen::MatrixXd mat = create();
    public:
        ReturnTester() { print_created(this); }
        ~ReturnTester() { print_destroyed(this); }
        static Eigen::MatrixXd create() { return Eigen::MatrixXd::Ones(10, 10); }
        static const Eigen::MatrixXd createConst() { return Eigen::MatrixXd::Ones(10, 10); }
        Eigen::MatrixXd &get() { return mat; }
        Eigen::MatrixXd *getPtr() { return &mat; }
        const Eigen::MatrixXd &view() { return mat; }
        const Eigen::MatrixXd *viewPtr() { return &mat; }
        Eigen::Ref<Eigen::MatrixXd> ref() { return mat; }
        Eigen::Ref<const Eigen::MatrixXd> refConst() { return mat; }
        Eigen::Block<Eigen::MatrixXd> block(int r, int c, int nrow, int ncol) { return mat.block(r, c, nrow, ncol); }
        Eigen::Block<const Eigen::MatrixXd> blockConst(int r, int c, int nrow, int ncol) const { return mat.block(r, c, nrow, ncol); }
        py::EigenDMap<Eigen::Matrix2d> corners() { return py::EigenDMap<Eigen::Matrix2d>(mat.data(),
                    py::EigenDStride(mat.outerStride() * (mat.outerSize()-1), mat.innerStride() * (mat.innerSize()-1))); }
        py::EigenDMap<const Eigen::Matrix2d> cornersConst() const { return py::EigenDMap<const Eigen::Matrix2d>(mat.data(),
                    py::EigenDStride(mat.outerStride() * (mat.outerSize()-1), mat.innerStride() * (mat.innerSize()-1))); }
    };
    using rvp = py::return_value_policy;
    py::class_<ReturnTester>(m, "ReturnTester")
        .def(py::init<>())
        .def_static("create", &ReturnTester::create)
        .def_static("create_const", &ReturnTester::createConst)
        .def("get", &ReturnTester::get, rvp::reference_internal)
        .def("get_ptr", &ReturnTester::getPtr, rvp::reference_internal)
        .def("view", &ReturnTester::view, rvp::reference_internal)
        .def("view_ptr", &ReturnTester::view, rvp::reference_internal)
        .def("copy_get", &ReturnTester::get)   // Default rvp: copy
        .def("copy_view", &ReturnTester::view) //         "
        .def("ref", &ReturnTester::ref) // Default for Ref is to reference
        .def("ref_const", &ReturnTester::refConst) // Likewise, but const
        .def("ref_safe", &ReturnTester::ref, rvp::reference_internal)
        .def("ref_const_safe", &ReturnTester::refConst, rvp::reference_internal)
        .def("copy_ref", &ReturnTester::ref, rvp::copy)
        .def("copy_ref_const", &ReturnTester::refConst, rvp::copy)
        .def("block", &ReturnTester::block)
        .def("block_safe", &ReturnTester::block, rvp::reference_internal)
        .def("block_const", &ReturnTester::blockConst, rvp::reference_internal)
        .def("copy_block", &ReturnTester::block, rvp::copy)
        .def("corners", &ReturnTester::corners, rvp::reference_internal)
        .def("corners_const", &ReturnTester::cornersConst, rvp::reference_internal)
        ;

    // test_special_matrix_objects
    // Returns a DiagonalMatrix with diagonal (1,2,3,...)
    m.def("incr_diag", [](int k) {
        Eigen::DiagonalMatrix<int, Eigen::Dynamic> m(k);
        for (int i = 0; i < k; i++) m.diagonal()[i] = i+1;
        return m;
    });

    // Returns a SelfAdjointView referencing the lower triangle of m
    m.def("symmetric_lower", [](const Eigen::MatrixXi &m) {
            return m.selfadjointView<Eigen::Lower>();
    });
    // Returns a SelfAdjointView referencing the lower triangle of m
    m.def("symmetric_upper", [](const Eigen::MatrixXi &m) {
            return m.selfadjointView<Eigen::Upper>();
    });

    // Test matrix for various functions below.
    Eigen::MatrixXf mat(5, 6);
    mat << 0,  3,  0,  0,  0, 11,
           22, 0,  0,  0, 17, 11,
           7,  5,  0,  1,  0, 11,
           0,  0,  0,  0,  0, 11,
           0,  0, 14,  0,  8, 11;

    // test_fixed, and various other tests
    m.def("fixed_r", [mat]() -> FixedMatrixR { return FixedMatrixR(mat); });
    m.def("fixed_r_const", [mat]() -> const FixedMatrixR { return FixedMatrixR(mat); });
    m.def("fixed_c", [mat]() -> FixedMatrixC { return FixedMatrixC(mat); });
    m.def("fixed_copy_r", [](const FixedMatrixR &m) -> FixedMatrixR { return m; });
    m.def("fixed_copy_c", [](const FixedMatrixC &m) -> FixedMatrixC { return m; });
    // test_mutator_descriptors
    m.def("fixed_mutator_r", [](Eigen::Ref<FixedMatrixR>) {});
    m.def("fixed_mutator_c", [](Eigen::Ref<FixedMatrixC>) {});
    m.def("fixed_mutator_a", [](py::EigenDRef<FixedMatrixC>) {});
    // test_dense
    m.def("dense_r", [mat]() -> DenseMatrixR { return DenseMatrixR(mat); });
    m.def("dense_c", [mat]() -> DenseMatrixC { return DenseMatrixC(mat); });
    m.def("dense_copy_r", [](const DenseMatrixR &m) -> DenseMatrixR { return m; });
    m.def("dense_copy_c", [](const DenseMatrixC &m) -> DenseMatrixC { return m; });
    // test_sparse, test_sparse_signature
    m.def("sparse_r", [mat]() -> SparseMatrixR { return Eigen::SparseView<Eigen::MatrixXf>(mat); });
    m.def("sparse_c", [mat]() -> SparseMatrixC { return Eigen::SparseView<Eigen::MatrixXf>(mat); });
    m.def("sparse_copy_r", [](const SparseMatrixR &m) -> SparseMatrixR { return m; });
    m.def("sparse_copy_c", [](const SparseMatrixC &m) -> SparseMatrixC { return m; });
    // test_partially_fixed
    m.def("partial_copy_four_rm_r", [](const FourRowMatrixR &m) -> FourRowMatrixR { return m; });
    m.def("partial_copy_four_rm_c", [](const FourColMatrixR &m) -> FourColMatrixR { return m; });
    m.def("partial_copy_four_cm_r", [](const FourRowMatrixC &m) -> FourRowMatrixC { return m; });
    m.def("partial_copy_four_cm_c", [](const FourColMatrixC &m) -> FourColMatrixC { return m; });

    // test_cpp_casting
    // Test that we can cast a numpy object to a Eigen::MatrixXd explicitly
    m.def("cpp_copy", [](py::handle m) { return m.cast<Eigen::MatrixXd>()(1, 0); });
    m.def("cpp_ref_c", [](py::handle m) { return m.cast<Eigen::Ref<Eigen::MatrixXd>>()(1, 0); });
    m.def("cpp_ref_r", [](py::handle m) { return m.cast<Eigen::Ref<MatrixXdR>>()(1, 0); });
    m.def("cpp_ref_any", [](py::handle m) { return m.cast<py::EigenDRef<Eigen::MatrixXd>>()(1, 0); });


    // test_nocopy_wrapper
    // Test that we can prevent copying into an argument that would normally copy: First a version
    // that would allow copying (if types or strides don't match) for comparison:
    m.def("get_elem", &get_elem);
    // Now this alternative that calls the tells pybind to fail rather than copy:
    m.def("get_elem_nocopy", [](Eigen::Ref<const Eigen::MatrixXd> m) -> double { return get_elem(m); },
            py::arg().noconvert());
    // Also test a row-major-only no-copy const ref:
    m.def("get_elem_rm_nocopy", [](Eigen::Ref<const Eigen::Matrix<long, -1, -1, Eigen::RowMajor>> &m) -> long { return m(2, 1); },
            py::arg().noconvert());

    // test_issue738
    // Issue #738: 1xN or Nx1 2D matrices were neither accepted nor properly copied with an
    // incompatible stride value on the length-1 dimension--but that should be allowed (without
    // requiring a copy!) because the stride value can be safely ignored on a size-1 dimension.
    m.def("iss738_f1", &adjust_matrix<const Eigen::Ref<const Eigen::MatrixXd> &>, py::arg().noconvert());
    m.def("iss738_f2", &adjust_matrix<const Eigen::Ref<const Eigen::Matrix<double, -1, -1, Eigen::RowMajor>> &>, py::arg().noconvert());

    // test_issue1105
    // Issue #1105: when converting from a numpy two-dimensional (Nx1) or (1xN) value into a dense
    // eigen Vector or RowVector, the argument would fail to load because the numpy copy would fail:
    // numpy won't broadcast a Nx1 into a 1-dimensional vector.
    m.def("iss1105_col", [](Eigen::VectorXd) { return true; });
    m.def("iss1105_row", [](Eigen::RowVectorXd) { return true; });

    // test_named_arguments
    // Make sure named arguments are working properly:
    m.def("matrix_multiply", [](const py::EigenDRef<const Eigen::MatrixXd> A, const py::EigenDRef<const Eigen::MatrixXd> B)
            -> Eigen::MatrixXd {
        if (A.cols() != B.rows()) throw std::domain_error("Nonconformable matrices!");
        return A * B;
    }, py::arg("A"), py::arg("B"));

    // test_custom_operator_new
    py::class_<CustomOperatorNew>(m, "CustomOperatorNew")
        .def(py::init<>())
        .def_readonly("a", &CustomOperatorNew::a)
        .def_readonly("b", &CustomOperatorNew::b);

    // test_eigen_ref_life_support
    // In case of a failure (the caster's temp array does not live long enough), creating
    // a new array (np.ones(10)) increases the chances that the temp array will be garbage
    // collected and/or that its memory will be overridden with different values.
    m.def("get_elem_direct", [](Eigen::Ref<const Eigen::VectorXd> v) {
        py::module::import("numpy").attr("ones")(10);
        return v(5);
    });
    m.def("get_elem_indirect", [](std::vector<Eigen::Ref<const Eigen::VectorXd>> v) {
        py::module::import("numpy").attr("ones")(10);
        return v[0](5);
    });
}