@ladybugmem/icebug 0.1.0

package/vendor/include/networkit/algebraic/CSRMatrix.hpp

@@ -0,0 +1,11 @@
+#ifndef NETWORKIT_ALGEBRAIC_CSR_MATRIX_HPP_
+#define NETWORKIT_ALGEBRAIC_CSR_MATRIX_HPP_
+
+#include <networkit/algebraic/CSRGeneralMatrix.hpp>
+
+// For compatibility with the previous CSRMatrix implementation.
+namespace NetworKit {
+using CSRMatrix = CSRGeneralMatrix<double>;
+} // namespace NetworKit
+
+#endif // NETWORKIT_ALGEBRAIC_CSR_MATRIX_HPP_

package/vendor/include/networkit/algebraic/DenseMatrix.hpp

@@ -0,0 +1,537 @@
+/*
+ * DenseMatrix.hpp
+ *
+ *  Created on: Nov 25, 2015
+ *      Author: Michael Wegner (michael.wegner@student.kit.edu)
+ */
+
+#ifndef NETWORKIT_ALGEBRAIC_DENSE_MATRIX_HPP_
+#define NETWORKIT_ALGEBRAIC_DENSE_MATRIX_HPP_
+
+#include <cassert>
+#include <iostream>
+#include <vector>
+
+#include <networkit/Globals.hpp>
+#include <networkit/algebraic/AlgebraicGlobals.hpp>
+#include <networkit/algebraic/Vector.hpp>
+#include <networkit/graph/Graph.hpp>
+
+namespace NetworKit {
+
+/**
+ * @ingroup algebraic
+ * Represents a dense matrix. Use this matrix to run LU decompositions and LU solves.
+ * Note that most matrices are rather sparse s.t. CSRMatrix might be a better representation.
+ */
+class DenseMatrix final {
+private:
+    count nRows;
+    count nCols;
+    std::vector<double> entries;
+    double zero;
+
+public:
+    /** Default constructor */
+    DenseMatrix();
+
+    /**
+     * Constructs the DenseMatrix with size @a dimension x @a dimension.
+     * @param dimension Defines how many rows and columns this matrix has.
+     * @param zero The zero element (default is 0.0).
+     */
+    DenseMatrix(count dimension, double zero = 0.0);
+
+    /**
+     * Constructs the DenseMatrix with size @a nRows x @a nCols.
+     * @param nRows Number of rows.
+     * @param nCols Number of columns.
+     * @param zero The zero element (default is 0.0).
+     */
+    DenseMatrix(count nRows, count nCols, double zero = 0.0);
+
+    /**
+     * Constructs the @a dimension x @a dimension DenseMatrix from the elements at position @a
+     * positions with values @values.
+     * @param dimension Defines how many rows and columns this matrix has.
+     * @param triplets The nonzero elements.
+     * @param zero The zero element (default is 0.0).
+     */
+    DenseMatrix(count dimension, const std::vector<Triplet> &triplets, double zero = 0.0);
+
+    /**
+     * Constructs the @a nRows x @a nCols DenseMatrix from the elements at position @a positions
+     * with values @values.
+     * @param nRows Defines how many rows this matrix has.
+     * @param nCols Defines how many columns this matrix has.
+     * @param triplets The nonzero elements.
+     * @param zero The zero element (default is 0.0).
+     */
+    DenseMatrix(count nRows, count nCols, const std::vector<Triplet> &triplets, double zero = 0.0);
+
+    /**
+     * Constructs an instance of DenseMatrix given the number of rows (@a nRows) and the number of
+     * columns (@a nCols) and its values (@a entries).
+     * @param nRows Number of rows.
+     * @param nCols Number of columns.
+     * @param entries Entries of the matrix.
+     * @param zero The zero element (default is 0.0).
+     * @note The size of the @a entries vector should be equal to @a nRows * @a nCols.
+     */
+    DenseMatrix(count nRows, count nCols, const std::vector<double> &entries, double zero = 0.0);
+
+    /** Default destructor */
+    ~DenseMatrix() = default;
+
+    /** Default copy constructor */
+    DenseMatrix(const DenseMatrix &other) = default;
+
+    /** Default move constructor */
+    DenseMatrix(DenseMatrix &&other) = default;
+
+    /** Default copy assignment operator */
+    DenseMatrix &operator=(DenseMatrix &&other) = default;
+
+    /** Default move assignment operator */
+    DenseMatrix &operator=(const DenseMatrix &other) = default;
+
+    /**
+     * Compares this matrix to @a other and returns true if the shapes and entries are the same,
+     * otherwise returns false.
+     * @param other
+     */
+    bool operator==(const DenseMatrix &other) const {
+        bool equal =
+            nRows == other.nRows && nCols == other.nCols && entries.size() == other.entries.size();
+        if (equal) {
+            forElementsInRowOrder([&](index i, index j, double value) {
+                if (other(i, j) != value) {
+                    equal = false;
+                    return;
+                }
+            });
+        }
+        return equal;
+    }
+
+    /**
+     * Compares this matrix to @a other and returns true if the shape and zero
+     * element are the same as well as
+     * all entries are the same (within the absolute error range of @a eps), otherwise returns
+     * false.
+     * @param other
+     * @param eps
+     */
+    bool isApprox(const DenseMatrix &other, const double eps = 0.01) const {
+        bool equal =
+            nRows == other.nRows && nCols == other.nCols && entries.size() == other.entries.size();
+        if (equal) {
+            forElementsInRowOrder([&](index i, index j, double value) {
+                if (std::abs(other(i, j) - value) > eps) {
+                    equal = false;
+                    return;
+                }
+            });
+        }
+        return equal;
+    }
+
+    /**
+     * @return Number of rows.
+     */
+    inline count numberOfRows() const { return nRows; }
+
+    /**
+     * @return Number of columns.
+     */
+    inline count numberOfColumns() const { return nCols; }
+
+    /**
+     * Returns the zero element of the matrix.
+     */
+    inline double getZero() const { return zero; }
+
+    /**
+     * @param i The row index.
+     * @return Number of non-zeros in row @a i.
+     * @note This function is linear in the number of columns of the matrix.
+     */
+    count nnzInRow(index i) const;
+
+    /**
+     * @return Number of non-zeros in this matrix.
+     * @note This function takes nRows * nCols operations.
+     */
+    count nnz() const;
+
+    /**
+     * @return Value at matrix position (i,j).
+     */
+    double operator()(index i, index j) const;
+
+    /**
+     * Set the matrix at position (@a i, @a j) to @a value.
+     */
+    double &operator()(index i, index j);
+
+    /**
+     * Set the matrix at position (@a i, @a j) to @a value.
+     */
+    void setValue(index i, index j, double value);
+
+    /**
+     * @return Row @a i of this matrix as vector.
+     */
+    Vector row(index i) const;
+
+    /**
+     * @return Column @a j of this matrix as vector.
+     */
+    Vector column(index j) const;
+
+    /**
+     * @return The main diagonal of this matrix.
+     */
+    Vector diagonal() const;
+
+    /**
+     * Adds this matrix to @a other and returns the result.
+     * @return The sum of this matrix and @a other.
+     */
+    DenseMatrix operator+(const DenseMatrix &other) const;
+
+    /**
+     * Adds @a other to this matrix.
+     * @return Reference to this matrix.
+     */
+    DenseMatrix &operator+=(const DenseMatrix &other);
+
+    /**
+     * Subtracts @a other from this matrix and returns the result.
+     * @return The difference of this matrix and @a other.
+     *
+     */
+    DenseMatrix operator-(const DenseMatrix &other) const;
+
+    /**
+     * Subtracts @a other from this matrix.
+     * @return Reference to this matrix.
+     */
+    DenseMatrix &operator-=(const DenseMatrix &other);
+
+    /**
+     * Multiplies this matrix with a scalar specified in @a scalar and returns the result.
+     * @return The result of multiplying this matrix with @a scalar.
+     */
+    DenseMatrix operator*(double scalar) const;
+
+    /**
+     * Multiplies this matrix with a scalar specified in @a scalar.
+     * @return Reference to this matrix.
+     */
+    DenseMatrix &operator*=(double scalar);
+
+    /**
+     * Multiplies this matrix with @a vector and returns the result.
+     * @return The result of multiplying this matrix with @a vector.
+     */
+    Vector operator*(const Vector &vector) const;
+
+    /**
+     * Multiplies this matrix with @a other and returns the result in a new matrix.
+     * @return The result of multiplying this matrix with @a other.
+     */
+    DenseMatrix operator*(const DenseMatrix &other) const;
+
+    /**
+     * Divides this matrix by a divisor specified in @a divisor and returns the result in a new
+     * matrix.
+     * @return The result of dividing this matrix by @a divisor.
+     */
+    DenseMatrix operator/(double divisor) const;
+
+    /**
+     * Divides this matrix by a divisor specified in @a divisor.
+     * @return Reference to this matrix.
+     */
+    DenseMatrix &operator/=(double divisor);
+
+    /**
+     * Transposes this matrix and returns it.
+     */
+    DenseMatrix transpose() const;
+
+    /**
+     * Extracts a matrix with rows and columns specified by @a rowIndices and @a columnIndices from
+     * this matrix. The order of rows and columns is equal to the order in @a rowIndices and @a
+     * columnIndices. It is also possible to specify a row or column more than once to get
+     * duplicates.
+     * @param rowIndices
+     * @param columnIndices
+     */
+    DenseMatrix extract(const std::vector<index> &rowIndices,
+                        const std::vector<index> &columnIndices) const;
+
+    /**
+     * Assign the contents of the matrix @a source to this matrix at rows and columns specified by
+     * @a rowIndices and
+     * @a columnIndices. That is, entry (i,j) of @a source is assigned to entry (rowIndices[i],
+     * columnIndices[j]) of this matrix. Note that the dimensions of @rowIndices and @a
+     * columnIndices must coincide with the number of rows and columns of @a source.
+     * @param rowIndices
+     * @param columnIndices
+     * @param source
+     */
+    void assign(const std::vector<index> &rowIndices, const std::vector<index> &columnIndices,
+                const DenseMatrix &source);
+
+    /**
+     * Applies the unary function @a unaryElementFunction to each value in the matrix. Note that it
+     * must hold that the function applied to the zero element of this matrix returns the zero
+     * element.
+     * @param unaryElementFunction
+     */
+    template <typename F>
+    void apply(F unaryElementFunction);
+
+    /**
+     * Returns the (weighted) adjacency matrix of the (weighted) Graph @a graph.
+     * @param graph
+     */
+    static DenseMatrix adjacencyMatrix(const Graph &graph, double zero = 0.0);
+
+    /**
+     * Creates a diagonal matrix with dimension equal to the dimension of the Vector @a
+     * diagonalElements. The values on the diagonal are the ones stored in @a diagonalElements (i.e.
+     * D(i,i) = diagonalElements[i]).
+     * @param diagonalElements
+     */
+    static DenseMatrix diagonalMatrix(const Vector &diagonalElements, double zero = 0.0);
+
+    /**
+     * Returns the (weighted) incidence matrix of the (weighted) Graph @a graph.
+     * @param graph
+     */
+    static DenseMatrix incidenceMatrix(const Graph &graph, double zero = 0.0);
+
+    /**
+     * Returns the (weighted) Laplacian matrix of the (weighteD) Graph @a graph.
+     * @param graph
+     */
+    static DenseMatrix laplacianMatrix(const Graph &graph, double zero = 0.0);
+
+    /**
+     * Decomposes the given @a matrix into lower L and upper U matrix (in-place).
+     * @param matrix The matrix to decompose into LU.
+     */
+    static void LUDecomposition(DenseMatrix &matrix);
+
+    /**
+     * Computes the solution vector x to the system @a LU * x = @a b where @a LU is a matrix
+     * decomposed into L and U.
+     * @param LU Matrix decomposed into lower L and upper U matrix.
+     * @param b Right-hand side.
+     * @return Solution vector x to the linear equation system LU * x = b.
+     */
+    static Vector LUSolve(const DenseMatrix &LU, const Vector &b);
+
+    /**
+     * Computes @a A @a binaryOp @a B on the elements of matrix @a A and matrix @a B.
+     * @param A
+     * @param B
+     * @param binaryOp Function handling (double, double) -> double
+     * @return @a A @a binaryOp @a B.
+     * @note @a A and @a B must have the same dimensions.
+     */
+    template <typename L>
+    static DenseMatrix binaryOperator(const DenseMatrix &A, const DenseMatrix &B, L binaryOp);
+
+    /**
+     * Iterate over all elements of row @a row in the matrix and call handler(index column,
+     * double value)
+     */
+    template <typename L>
+    void forElementsInRow(index row, L handle) const;
+
+    /**
+     * Iterate in parallel over all elements of row @a row in the matrix and call
+     * handler(index column, double value)
+     */
+    template <typename L>
+    void parallelForElementsInRow(index row, L handle) const;
+
+    /**
+     * Iterate over all elements of the matrix in row order and call handler (lambda
+     * closure).
+     */
+    template <typename L>
+    void forElementsInRowOrder(L handle) const;
+
+    /**
+     * Iterate in parallel over all rows and call handler (lambda closure) on elements of
+     * the matrix.
+     */
+    template <typename L>
+    void parallelForElementsInRowOrder(L handle) const;
+
+    /**
+     * Iterate over all non-zero elements of row @a row in the matrix and call handler(index column,
+     * double value).
+     * @note This is a DenseMatrix! Therefore this operation needs O(numberOfRows()) time regardless
+     * of the number of non-zeros actually present.
+     */
+    template <typename L>
+    void forNonZeroElementsInRow(index row, L handle) const;
+
+    /**
+     * Iterate in parallel over all non-zero elements of row @a row in the matrix and call
+     * handler(index column, double value)
+     * @note This is a DenseMatrix! Therefore this operation needs O(numberOfRows()) sequential time
+     * regardless of the number of non-zeros actually present.
+     */
+    template <typename L>
+    void parallelForNonZeroElementsInRow(index row, L handle) const;
+
+    /**
+     * Iterate over all non-zero elements of the matrix in row order and call handler (lambda
+     * closure).
+     * @note This is a DenseMatrix! Therefore this operation needs O(numberOfRows() *
+     * numberOfColumns()) time regardless of the number of non-zeros actually present.
+     */
+    template <typename L>
+    void forNonZeroElementsInRowOrder(L handle) const;
+
+    /**
+     * Iterate in parallel over all rows and call handler (lambda closure) on non-zero elements of
+     * the matrix.
+     * @note This is a DenseMatrix! Therefore this operation needs O(numberOfRows() *
+     * numberOfColumns()) sequential time regardless of the number of non-zeros actually present.
+     */
+    template <typename L>
+    void parallelForNonZeroElementsInRowOrder(L handle) const;
+};
+
+template <typename F>
+void DenseMatrix::apply(F unaryElementFunction) {
+#pragma omp parallel for
+    for (omp_index k = 0; k < static_cast<omp_index>(entries.size()); ++k) {
+        entries[k] = unaryElementFunction(entries[k]);
+    }
+}
+
+template <typename L>
+inline DenseMatrix DenseMatrix::binaryOperator(const DenseMatrix &A, const DenseMatrix &B,
+                                               L binaryOp) {
+    assert(A.nRows == B.nRows && A.nCols == B.nCols);
+
+    std::vector<double> resultEntries(A.numberOfRows() * A.numberOfColumns(), 0.0);
+
+#pragma omp parallel for
+    for (omp_index i = 0; i < static_cast<omp_index>(A.numberOfRows()); ++i) {
+        index offset = i * A.numberOfColumns();
+        for (index j = offset; j < offset + A.numberOfColumns(); ++j) {
+            resultEntries[j] = binaryOp(A.entries[j], B.entries[j]);
+        }
+    }
+
+    return DenseMatrix(A.numberOfRows(), A.numberOfColumns(), resultEntries);
+}
+
+template <typename L>
+inline void DenseMatrix::forElementsInRow(index i, L handle) const {
+    index offset = i * numberOfColumns();
+    for (index k = offset, j = 0; k < offset + numberOfColumns(); ++k, ++j) {
+        handle(j, entries[k]);
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::parallelForElementsInRow(index i, L handle) const {
+    index offset = i * numberOfColumns();
+#pragma omp parallel for
+    for (omp_index j = 0; j < static_cast<omp_index>(numberOfColumns()); ++j) {
+        handle(j, entries[offset + j]);
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::forElementsInRowOrder(L handle) const {
+    for (index i = 0; i < nRows; ++i) {
+        index offset = i * numberOfColumns();
+        for (index k = offset, j = 0; k < offset + numberOfColumns(); ++k, ++j) {
+            handle(i, j, entries[k]);
+        }
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::parallelForElementsInRowOrder(L handle) const {
+#pragma omp parallel for
+    for (omp_index i = 0; i < static_cast<omp_index>(nRows); ++i) {
+        index offset = i * numberOfColumns();
+        for (index k = offset, j = 0; k < offset + numberOfColumns(); ++k, ++j) {
+            handle(i, j, entries[k]);
+        }
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::forNonZeroElementsInRow(index row, L handle) const {
+    for (index j = 0, k = row * numberOfColumns(); j < numberOfColumns(); ++j, ++k) {
+        if (entries[k] != getZero()) {
+            handle(j, entries[k]);
+        }
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::parallelForNonZeroElementsInRow(index row, L handle) const {
+#pragma omp parallel for
+    for (omp_index j = 0; j < static_cast<omp_index>(numberOfColumns()); ++j) {
+        index k = row * numberOfColumns() + j;
+        if (entries[k] != getZero()) {
+            handle(j, entries[k]);
+        }
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::forNonZeroElementsInRowOrder(L handle) const {
+    for (index i = 0; i < numberOfRows(); ++i) {
+        for (index j = 0, k = i * numberOfColumns(); j < numberOfColumns(); ++j, ++k) {
+            if (entries[k] != getZero()) {
+                handle(i, j, entries[k]);
+            }
+        }
+    }
+}
+
+template <typename L>
+inline void DenseMatrix::parallelForNonZeroElementsInRowOrder(L handle) const {
+#pragma omp parallel for
+    for (omp_index i = 0; i < static_cast<omp_index>(numberOfRows()); ++i) {
+        for (index j = 0, k = i * numberOfColumns(); j < numberOfColumns(); ++j, ++k) {
+            if (entries[k] != getZero()) {
+                handle(i, j, entries[k]);
+            }
+        }
+    }
+}
+
+// print functions for test debugging / output
+inline std::ostream &operator<<(std::ostream &os, const DenseMatrix &M) {
+    for (index row = 0; row < M.numberOfRows(); ++row) {
+        if (row != 0)
+            os << std::endl;
+        for (index col = 0; col < M.numberOfColumns(); ++col) {
+            if (col != 0)
+                os << ", ";
+            os << M(row, col);
+        }
+    }
+    return os;
+}
+
+} /* namespace NetworKit */
+
+#endif // NETWORKIT_ALGEBRAIC_DENSE_MATRIX_HPP_