#ifndef STORM_STORAGE_SPARSEMATRIX_H_
#define STORM_STORAGE_SPARSEMATRIX_H_
// To detect whether the usage of TBB is possible, this include is neccessary
#include "storm-config.h"
#ifdef STORM_HAVE_INTELTBB
# include "utility/OsDetection.h" // This fixes a potential dependency ordering problem between GMM and TBB
# include <new>
# include "tbb/tbb.h"
# include <iterator>
#endif
#include <algorithm>
#include <iostream>
#include <cstdint>
#include <iterator>
#include "src/storage/BitVector.h"
#include "src/utility/constants.h"
#include "src/exceptions/InvalidArgumentException.h"
#include "src/exceptions/OutOfRangeException.h"
// Forward declaration for adapter classes.
namespace storm {
namespace adapters {
class GmmxxAdapter;
class EigenAdapter;
class StormAdapter;
}
}
namespace storm {
namespace storage {
#ifdef STORM_HAVE_INTELTBB
// Forward declaration of the TBB Helper class.
template <typename M, typename V, typename T>
class tbbHelper_MatrixRowVectorScalarProduct;
#endif
/*!
* A class that holds a possibly non-square matrix in the compressed row storage format. That is, it is supposed
* to store non-zero entries only, but zeros may be explicitly stored if necessary for certain operations.
* Likewise, the matrix is intended to store one value per column only. However, the functions provided by the
* matrix are implemented in a way that makes it safe to store several entries per column.
*
* The creation of a matrix can be done in several ways. If the number of rows, columns and entries is known
* prior to creating the matrix, the matrix can be constructed using this knowledge, which saves reallocations.
* On the other hand, if either one of these values is not known a priori, the matrix can be constructed as an
* empty matrix that needs to perform reallocations as more and more entries are inserted in the matrix.
*
* It should be observed that due to the nature of the sparse matrix format, entries can only be inserted in
* order, i.e. row by row and column by column.
*/
template<typename T>
class SparseMatrix {
public:
// Declare adapter classes as friends to use internal data.
friend class storm::adapters::GmmxxAdapter;
friend class storm::adapters::EigenAdapter;
friend class storm::adapters::StormAdapter;
#ifdef STORM_HAVE_INTELTBB
// Declare the helper class for TBB as friend.
template <typename M, typename V, typename TPrime>
friend class tbbHelper_MatrixRowVectorScalarProduct;
#endif
typedef typename std::vector<std::pair<uint_fast64_t, T>>::iterator iterator;
typedef typename std::vector<std::pair<uint_fast64_t, T>>::const_iterator const_iterator;
/*!
* This class represents a number of consecutive rows of the matrix.
*/
class rows {
public:
/*!
* Constructs an object that represents the rows defined by the value of the first entry, the column
* of the first entry and the number of entries in this row set.
*
* @param columnAndValuePtr A pointer to the columnd and value of the first entry of the rows.
* @param entryCount The number of entrys in the rows.
*/
rows(std::pair<uint_fast64_t, T>* columnAndValuePtr, uint_fast64_t entryCount);
/*!
* Retrieves an iterator that points to the beginning of the rows.
*
* @return An iterator that points to the beginning of the rows.
*/
iterator begin();
/*!
* Retrieves an iterator that points past the last entry of the rows.
*
* @return An iterator that points past the last entry of the rows.
*/
iterator end();
private:
// The pointer to the columnd and value of the first entry.
std::pair<uint_fast64_t, T>* columnAndValuePtr;
// The number of non-zero entries in the rows.
uint_fast64_t entryCount;
};
/*!
* This class represents a number of consecutive rows of the matrix.
*/
class const_rows {
public:
/*!
* Constructs an object that represents the rows defined by the value of the first entry, the column
* of the first entry and the number of entries in this row set.
*
* @param columnAndValuePtr A pointer to the columnd and value of the first entry of the rows.
* @param entryCount The number of entrys in the rows.
*/
const_rows(std::pair<uint_fast64_t, T> const* columnAndValuePtr, uint_fast64_t entryCount);
/*!
* Retrieves an iterator that points to the beginning of the rows.
*
* @return An iterator that points to the beginning of the rows.
*/
const_iterator begin() const;
/*!
* Retrieves an iterator that points past the last entry of the rows.
*
* @return An iterator that points past the last entry of the rows.
*/
const_iterator end() const;
private:
// The pointer to the columnd and value of the first entry.
std::pair<uint_fast64_t, T> const* columnAndValuePtr;
// The number of non-zero entries in the rows.
uint_fast64_t entryCount;
};
/*!
* An enum representing the internal state of the matrix. After creation, the matrix is UNINITIALIZED.
* Only after a call to finalize(), the status of the matrix is set to INITIALIZED and the matrix can be
* used.
*/
enum MatrixStatus { UNINITIALIZED, INITIALIZED };
/*!
* Constructs a sparse matrix object with the given number of rows, columns and number of entries.
*
* @param rows The number of rows of the matrix.
* @param columns The number of columns of the matrix.
* @param entries The number of entries of the matrix.
*/
SparseMatrix(uint_fast64_t rows = 0, uint_fast64_t columns = 0, uint_fast64_t entries = 0);
/*!
* Constructs a sparse matrix by performing a deep-copy of the given matrix.
*
* @param other The matrix from which to copy the content.
*/
SparseMatrix(SparseMatrix<T> const& other);
/*!
* Constructs a sparse matrix by moving the contents of the given matrix to the newly created one.
*
* @param other The matrix from which to move the content.
*/
SparseMatrix(SparseMatrix<T>&& other);
/*!
* Constructs a sparse matrix by copying the given contents.
*
* @param columnCount The number of columns of the matrix.
* @param rowIndications The row indications vector of the matrix to be constructed.
* @param columnsAndValues The vector containing the columns and values of the entries in the matrix.
*/
SparseMatrix(uint_fast64_t columnCount, std::vector<uint_fast64_t> const& rowIndications, std::vector<std::pair<uint_fast64_t, T>> const& columnsAndValues);
/*!
* Constructs a sparse matrix by copying the given contents.
*
* @param columnCount The number of columns of the matrix.
* @param rowIndications The row indications vector of the matrix to be constructed.
* @param columnIndications The column indications vector of the matrix to be constructed.
* @param values The vector containing the values of the entries in the matrix.
*/
SparseMatrix(uint_fast64_t columnCount, std::vector<uint_fast64_t> const& rowIndications, std::vector<uint_fast64_t> const& columnIndications, std::vector<T> const& values);
/*!
* Constructs a sparse matrix by moving the given contents.
*
* @param columnCount The number of columns of the matrix.
* @param rowIndications The row indications vector of the matrix to be constructed.
* @param columnIndications The column indications vector of the matrix to be constructed.
* @param values The vector containing the values of the entries in the matrix.
*/
SparseMatrix(uint_fast64_t columnCount, std::vector<uint_fast64_t>&& rowIndications, std::vector<uint_fast64_t>&& columnIndications, std::vector<T>&& values);
/*!
* Constructs a sparse matrix by moving the given contents.
*
* @param columnCount The number of columns of the matrix.
* @param rowIndications The row indications vector of the matrix to be constructed.
* @param columnsAndValues The vector containing the columns and values of the entries in the matrix.
*/
SparseMatrix(uint_fast64_t columnCount, std::vector<uint_fast64_t>&& rowIndications, std::vector<std::pair<uint_fast64_t, T>>&& columnsAndValues);
/*!
* Assigns the contents of the given matrix to the current one by deep-copying its contents.
*
* @param other The matrix from which to copy-assign.
*/
SparseMatrix<T>& operator=(SparseMatrix<T> const& other);
/*!
* Assigns the contents of the given matrix to the current one by moving its contents.
*
* @param other The matrix from which to move to contents.
*/
SparseMatrix<T>& operator=(SparseMatrix<T>&& other);
/*!
* Determines whether the current and the given matrix are semantically equal.
*
* @param other The matrix with which to compare the current matrix.
* @return True iff the given matrix is semantically equal to the current one.
*/
bool operator==(SparseMatrix<T> const& other) const;
/*!
* Sets the matrix entry at the given row and column to the given value. After all entries have been added,
* a call to finalize(false) is mandatory.
*
* Note: this is a linear setter. That is, it must be called consecutively for each entry, row by row and
* column by column. As multiple entries per column are admitted, consecutive calls to this method are
* admitted to mention the same row-column-pair. If rows are skipped entirely, the corresponding rows are
* treated as empty. If these constraints are not met, an exception is thrown.
*
* @param row The row in which the matrix entry is to be set.
* @param column The column in which the matrix entry is to be set.
* @param value The value that is to be set at the specified row and column.
*/
void addNextValue(uint_fast64_t row, uint_fast64_t column,T const& value);
/*
* Finalizes the sparse matrix to indicate that initialization process has been completed and the matrix
* may now be used. This must be called after all entries have been added to the matrix via addNextValue.
*
* @param overriddenRowCount If this is set to a value that is greater than the current number of rows,
* this will cause the finalize method to add empty rows at the end of the matrix until the given row count
* has been matched. Note that this will *not* override the row count that has been given upon construction
* (if any), but will only take effect if the matrix has been created without the number of rows given.
* @param overriddenColumnCount If this is set to a value that is greater than the current number of columns,
* this will cause the finalize method to set the number of columns to the given value. Note that this will
* *not* override the column count that has been given upon construction (if any), but will only take effect
* if the matrix has been created without the number of columns given. By construction, the matrix will have
* no entries in the columns that have been added this way.
*/
void finalize(uint_fast64_t overriddenRowCount = 0, uint_fast64_t overriddenColumnCount = 0);
/*!
* Returns the number of rows of the matrix.
*
* @return The number of rows of the matrix.
*/
uint_fast64_t getRowCount() const;
/*!
* Returns the number of columns of the matrix.
*
* @return The number of columns of the matrix.
*/
uint_fast64_t getColumnCount() const;
/*!
* Returns the number of entries in the matrix.
*
* @return The number of entries in the matrix.
*/
uint_fast64_t getEntryCount() const;
/*!
* Checks whether the matrix was initialized properly and is ready for further use.
*
* @return True iff the matrix was initialized properly and is ready for further use.
*/
bool isInitialized() const;
/*!
* This function makes the given rows absorbing.
*
* @param rows A bit vector indicating which rows are to be made absorbing.
*/
void makeRowsAbsorbing(storm::storage::BitVector const& rows);
/*!
* This function makes the groups of rows given by the bit vector absorbing.
*
* @param rowGroupConstraint A bit vector indicating which row groups to make absorbing.
* @param rowGroupIndices A vector indicating which rows belong to a given row group.
*/
void makeRowsAbsorbing(storm::storage::BitVector const& rowGroupConstraint, std::vector<uint_fast64_t> const& rowGroupIndices);
/*!
* This function makes the given row absorbing. This means that all entries will be set to 0 except the one
* at the specified column, which is set to 1 instead.
*
* @param row The row to be made absorbing.
* @param column The index of the column whose value is to be set to 1.
*/
void makeRowAbsorbing(const uint_fast64_t row, const uint_fast64_t column);
/*
* Sums the entries in the given row and columns.
*
* @param row The row whose entries to add.
* @param columns A bit vector that indicates which columns to add.
* @return The sum of the entries in the given row and columns.
*/
T getConstrainedRowSum(uint_fast64_t row, storm::storage::BitVector const& columns) const;
/*!
* Computes a vector whose i-th entry is the sum of the entries in the i-th selected row where only those
* entries are added that are in selected columns.
*
* @param rowConstraint A bit vector that indicates for which rows to compute the constrained sum.
* @param columnConstraint A bit vector that indicates which columns to add in the selected rows.
*
* @return A vector whose elements are the sums of the selected columns in each row.
*/
std::vector<T> getConstrainedRowSumVector(storm::storage::BitVector const& rowConstraint, storm::storage::BitVector const& columnConstraint) const;
/*!
* Computes a vector whose entries represent the sums of selected columns for all rows in selected row
* groups.
*
* @param rowGroupConstraint A bit vector that indicates which row groups are to be considered.
* @param rowGroupIndices A vector indicating which rows belong to a given row group.
* @param columnConstraint A bit vector that indicates which columns to sum.
* @return A vector whose entries represent the sums of selected columns for all rows in selected row
* groups.
*/
std::vector<T> getConstrainedRowSumVector(storm::storage::BitVector const& rowGroupConstraint, std::vector<uint_fast64_t> const& rowGroupIndices, storm::storage::BitVector const& columnConstraint) const;
/*!
* Creates a submatrix of the current matrix by dropping all rows and columns whose bits are not
* set to one in the given bit vector.
*
* @param constraint A bit vector indicating which rows and columns to keep.
* @return A matrix corresponding to a submatrix of the current matrix in which only rows and columns given
* by the constraint are kept and all others are dropped.
*/
SparseMatrix getSubmatrix(storm::storage::BitVector const& constraint) const;
/*!
* Creates a submatrix of the current matrix by keeping only certain row groups and columns.
*
* @param rowGroupConstraint A bit vector indicating which row groups and columns to keep.
* @param rowGroupIndices A vector indicating which rows belong to a given row group.
* @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for
* each row in row group i. This can then be used for inserting other values later.
* @return A matrix corresponding to a submatrix of the current matrix in which only row groups and columns
* given by the row group constraint are kept and all others are dropped.
*/
SparseMatrix getSubmatrix(storm::storage::BitVector const& rowGroupConstraint, std::vector<uint_fast64_t> const& rowGroupIndices, bool insertDiagonalEntries = false) const;
/*!
* Creates a submatrix of the current matrix by keeping only row groups and columns in the given row group
* and column constraint, respectively.
*
* @param rowGroupConstraint A bit vector indicating which row groups to keep.
* @param columnConstraint A bit vector indicating which columns to keep.
* @param rowGroupIndices A vector indicating which rows belong to a given row group.
* @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for
* each row in row group i. This can then be used for inserting other values later.
* @return A matrix corresponding to a submatrix of the current matrix in which only row groups and columns
* given by the row group constraint are kept and all others are dropped.
*/
SparseMatrix getSubmatrix(storm::storage::BitVector const& rowGroupConstraint, storm::storage::BitVector const& columnConstraint, std::vector<uint_fast64_t> const& rowGroupIndices, bool insertDiagonalEntries = false) const;
/*!
* Creates a submatrix of the current matrix by selecting one row out of each row group.
*
* @param rowGroupdToRowIndexMapping A mapping from each row group index to a selected row in this group.
* @param rowGroupIndices A vector indicating which rows belong to a given row group.
* @param insertDiagonalEntries If set to true, the resulting matrix will have zero entries in column i for
* each row in row group i. This can then be used for inserting other values later.
* @return A submatrix of the current matrix by selecting one row out of each row group.
*/
SparseMatrix getSubmatrix(std::vector<uint_fast64_t> const& rowGroupToRowIndexMapping, std::vector<uint_fast64_t> const& rowGroupIndices, bool insertDiagonalEntries = true) const;
/*!
* Transposes the matrix.
*
* @return A sparse matrix that represents the transpose of this matrix.
*/
storm::storage::SparseMatrix<T> transpose() const;
/*!
* Transforms the matrix into an equation system. That is, it transforms the matrix A into a matrix (1-A).
*/
void convertToEquationSystem();
/*!
* Inverts all entries on the diagonal, i.e. sets the diagonal values to one minus their previous value.
* Requires the matrix to contain each diagonal entry and to be square.
*/
void invertDiagonal();
/*!
* Negates (w.r.t. addition) all entries that are not on the diagonal.
*/
void negateAllNonDiagonalEntries();
/*!
* Sets all diagonal elements to zero.
*/
void deleteDiagonalEntries();
/*!
* Calculates the Jacobi decomposition of this sparse matrix. For this operation, the matrix must be square.
*
* @return A pair (L+U, D^-1) containing the matrix L+U and the inverted diagonal matrix D^-1.
*/
std::pair<storm::storage::SparseMatrix<T>, storm::storage::SparseMatrix<T>> getJacobiDecomposition() const;
/*!
* Performs a pointwise matrix multiplication of the matrix with the given matrix and returns a vector
* containing the sum of the entries in each row of the resulting matrix.
*
* @param otherMatrix A reference to the matrix with which to perform the pointwise multiplication. This
* matrix must be a submatrix of the current matrix in the sense that it may not have entries at indices
* where there is no entry in the current matrix.
* @return A vector containing the sum of the entries in each row of the matrix resulting from pointwise
* multiplication of the current matrix with the given matrix.
*/
std::vector<T> getPointwiseProductRowSumVector(storm::storage::SparseMatrix<T> const& otherMatrix) const;
/*!
* Multiplies the matrix with the given vector and writes the result to given result vector.
*
* @param vector The vector with which to multiply the matrix.
* @param result The vector that is supposed to hold the result of the multiplication after the operation.
* @return The product of the matrix and the given vector as the content of the given result vector.
*/
void multiplyWithVector(std::vector<T> const& vector, std::vector<T>& result) const;
/*!
* Returns an object representing the consecutive rows given by the parameters.
*
* @param startRow The starting row.
* @param endRow The ending row (which is included in the result).
* @return An object representing the consecutive rows given by the parameters.
*/
const_rows getRows(uint_fast64_t startRow, uint_fast64_t endRow) const;
/*!
* Returns an object representing the consecutive rows given by the parameters.
*
* @param startRow The starting row.
* @param endRow The ending row (which is included in the result).
* @return An object representing the consecutive rows given by the parameters.
*/
rows getRows(uint_fast64_t startRow, uint_fast64_t endRow);
/*!
* Returns an object representing the given row.
*
* @param row The row to get.
* @return An object representing the given row.
*/
const_rows getRow(uint_fast64_t row) const;
/*!
* Returns an object representing the given row.
*
* @param row The row to get.
* @return An object representing the given row.
*/
rows getRow(uint_fast64_t row);
/*!
* Retrieves an iterator that points to the beginning of the given row.
*
* @param row The row to the beginning of which the iterator has to point.
* @return An iterator that points to the beginning of the given row.
*/
const_iterator begin(uint_fast64_t row = 0) const;
/*!
* Retrieves an iterator that points to the beginning of the given row.
*
* @param row The row to the beginning of which the iterator has to point.
* @return An iterator that points to the beginning of the given row.
*/
iterator begin(uint_fast64_t row = 0);
/*!
* Retrieves an iterator that points past the end of the given row.
*
* @param row The row past the end of which the iterator has to point.
* @return An iterator that points past the end of the given row.
*/
const_iterator end(uint_fast64_t row = 0) const;
/*!
* Retrieves an iterator that points past the end of the given row.
*
* @param row The row past the end of which the iterator has to point.
* @return An iterator that points past the end of the given row.
*/
iterator end(uint_fast64_t row = 0);
/*!
* Retrieves an iterator that points past the end of the last row of the matrix.
*
* @return An iterator that points past the end of the last row of the matrix.
*/
const_iterator end() const;
/*!
* Retrieves an iterator that points past the end of the last row of the matrix.
*
* @return An iterator that points past the end of the last row of the matrix.
*/
iterator end();
/*!
* Computes the sum of the entries in a given row.
*
* @param row The row that is to be summed.
* @return The sum of the selected row.
*/
T getRowSum(uint_fast64_t row) const;
/*!
* Checks if the current matrix is a submatrix of the given matrix, where a matrix A is called a submatrix
* of B if B has no entries in position where A has none. Additionally, the matrices must be of equal size.
*
* @param matrix The matrix that possibly is a supermatrix of the current matrix.
* @return True iff the current matrix is a submatrix of the given matrix.
*/
bool isSubmatrixOf(SparseMatrix<T> const& matrix) const;
template<typename TPrime>
friend std::ostream& operator<<(std::ostream& out, SparseMatrix<TPrime> const& matrix);
/*!
* Returns the size of the matrix in memory measured in bytes.
*
* @return The size of the matrix in memory measured in bytes.
*/
uint_fast64_t getSizeInMemory() const;
/*!
* Calculates a hash value over all values contained in the matrix.
*
* @return size_t A hash value for this matrix.
*/
std::size_t hash() const;
private:
/*!
* Prepares the internal storage of the matrix. This relies on the number of entries and the number of rows
* being set correctly. They may, however, be zero, in which case the insertion of elements in the matrix
* will cause occasional reallocations.
*/
void prepareInternalStorage();
/*!
* Checks whether the matrix is properly initialized and throws an exception otherwise.
*/
void checkReady(std::string const& methodName) const;
// A flag indicating whether the number of rows was set upon construction.
bool rowCountSet;
// The number of rows of the matrix.
uint_fast64_t rowCount;
// A flag indicating whether the number of columns was set upon construction.
bool columnCountSet;
// The number of columns of the matrix.
uint_fast64_t columnCount;
// The number of entries in the matrix.
uint_fast64_t entryCount;
// Stores whether the storage of the matrix was preallocated or not.
bool storagePreallocated;
// The storage for the columns and values of all entries in the matrix.
std::vector<std::pair<uint_fast64_t, T>> columnsAndValues;
// A vector containing the indices at which each given row begins. This index is to be interpreted as an
// index in the valueStorage and the columnIndications vectors. Put differently, the values of the entries
// in row i are valueStorage[rowIndications[i]] to valueStorage[rowIndications[i + 1]] where the last
// entry is not included anymore.
std::vector<uint_fast64_t> rowIndications;
// The internal status of the matrix.
MatrixStatus internalStatus;
// Stores the current number of entries in the matrix. This is used for inserting an entry into a matrix
// with preallocated storage.
uint_fast64_t currentEntryCount;
// Stores the row of the last entry in the matrix. This is used for correctly inserting an entry into a
// matrix.
uint_fast64_t lastRow;
// Stores the column of the currently last entry in the matrix. This is used for correctly inserting an
// entry into a matrix.
uint_fast64_t lastColumn;
};
#ifdef STORM_HAVE_INTELTBB
/*!
* This function is a helper for the parallel execution of the multipliyWithVector method.
* It uses Intel's TBB parallel_for paradigm to split up the row/vector multiplication and summation.
*/
template <typename M, typename V, typename T>
class tbbHelper_MatrixRowVectorScalarProduct {
public:
tbbHelper_MatrixRowVectorScalarProduct(M const* matrixA, V const* vectorX, V * resultVector);
void operator() (const tbb::blocked_range<uint_fast64_t>& r) const;
private:
V * resultVector;
V const* vectorX;
M const* matrixA;
};
#endif
} // namespace storage
} // namespace storm
#endif // STORM_STORAGE_SPARSEMATRIX_H_