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@ -10,9 +10,11 @@ |
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#include "src/exceptions/invalid_argument.h" |
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#include "src/exceptions/out_of_range.h" |
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#include "src/exceptions/file_IO_exception.h" |
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#include "src/storage/BitVector.h" |
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#include "src/misc/const_templates.h" |
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#include "Eigen/Sparse" |
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#include "gmm/gmm_matrix.h" |
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#include "log4cplus/logger.h" |
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#include "log4cplus/loggingmacros.h" |
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@ -471,7 +473,7 @@ public: |
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LOG4CPLUS_ERROR(logger, "Trying to convert a matrix that is not in a readable state to an Eigen matrix."); |
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throw mrmc::exceptions::invalid_state("Trying to convert a matrix that is not in a readable state to an Eigen matrix."); |
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} else { |
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// Create a |
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// Create the resulting matrix. |
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int_fast32_t eigenRows = static_cast<int_fast32_t>(rowCount); |
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Eigen::SparseMatrix<T, Eigen::RowMajor, int_fast32_t>* mat = new Eigen::SparseMatrix<T, Eigen::RowMajor, int_fast32_t>(eigenRows, eigenRows); |
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@ -488,6 +490,7 @@ public: |
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// than an average row, the other solution might be faster. |
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// The desired conversion method may be set by an appropriate define. |
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#define MRMC_USE_TRIPLETCONVERT |
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# ifdef MRMC_USE_TRIPLETCONVERT |
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// FIXME: Wouldn't it be more efficient to add the elements in |
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@ -503,10 +506,12 @@ public: |
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// and add the corresponding triplet. |
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uint_fast64_t rowStart; |
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uint_fast64_t rowEnd; |
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uint_fast64_t zeroCount = 0; |
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for (uint_fast64_t row = 0; row <= rowCount; ++row) { |
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rowStart = rowIndications[row]; |
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rowEnd = rowIndications[row + 1]; |
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while (rowStart < rowEnd) { |
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if (valueStorage[rowStart] == 0) zeroCount++; |
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tripletList.push_back(IntTriplet(row, columnIndications[rowStart], valueStorage[rowStart])); |
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++rowStart; |
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} |
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@ -514,7 +519,8 @@ public: |
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// Then add the elements on the diagonal. |
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for (uint_fast64_t i = 0; i <= rowCount; ++i) { |
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tripletList.push_back(IntTriplet(i, i, diagonalStorage[i])); |
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if (diagonalStorage[i] == 0) zeroCount++; |
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// tripletList.push_back(IntTriplet(i, i, diagonalStorage[i])); |
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} |
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// Let Eigen create a matrix from the given list of triplets. |
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@ -530,16 +536,19 @@ public: |
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// them to the matrix individually. |
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uint_fast64_t rowStart; |
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uint_fast64_t rowEnd; |
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uint_fast64_t count = 0; |
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for (uint_fast64_t row = 0; row < rowCount; ++row) { |
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rowStart = rowIndications[row]; |
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rowEnd = rowIndications[row + 1]; |
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// Insert the element on the diagonal. |
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mat->insert(row, row) = diagonalStorage[row]; |
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count++; |
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// Insert the elements that are not on the diagonal |
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while (rowStart < rowEnd) { |
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mat->insert(row, columnIndications[rowStart]) = valueStorage[rowStart]; |
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count++; |
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++rowStart; |
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} |
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} |
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@ -556,6 +565,57 @@ public: |
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return nullptr; |
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} |
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/*! |
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* Converts the matrix into a sparse matrix in the GMMXX format. |
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* @return A pointer to a column-major sparse matrix in GMMXX format. |
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*/ |
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gmm::csr_matrix<T>* toGMMXXSparseMatrix() { |
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// Prepare the resulting matrix. |
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gmm::csr_matrix<T>* result = new gmm::csr_matrix<T>(rowCount, rowCount); |
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LOG4CPLUS_INFO(logger, "Starting copy1."); |
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// Copy over the row indications as GMMXX uses the very same internal format. |
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result->jc.reserve(rowCount + 1); |
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std::copy(rowIndications, rowIndications + (rowCount + 1), result->jc.begin()); |
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LOG4CPLUS_INFO(logger, "Done copy1."); |
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// For the column indications and the actual values, we have to gather |
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// the values in a temporary array first, as we have to integrate |
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// the values from the diagonal. |
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uint_fast64_t realNonZeros = getNonZeroEntryCount() + getDiagonalNonZeroEntryCount(); |
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uint_fast64_t* tmpColumnIndicationsArray = new uint_fast64_t[realNonZeros]; |
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uint_fast64_t* tmpValueArray = new uint_fast64_t[realNonZeros]; |
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T zero(0); |
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uint_fast64_t currentPosition = 0; |
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for (uint_fast64_t i = 0; i < rowCount; ++i) { |
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bool includedDiagonal = false; |
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for (uint_fast64_t j = rowIndications[i]; j < rowIndications[i + 1]; ++j) { |
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if (diagonalStorage[i] != zero && !includedDiagonal && columnIndications[j] > i) { |
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includedDiagonal = true; |
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tmpColumnIndicationsArray[currentPosition] = i; |
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tmpValueArray[currentPosition] = diagonalStorage[i]; |
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++currentPosition; |
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} |
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tmpColumnIndicationsArray[currentPosition] = columnIndications[j]; |
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tmpValueArray[currentPosition] = valueStorage[j]; |
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} |
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} |
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LOG4CPLUS_INFO(logger, "Starting copy2."); |
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// Now, we can copy the temporary array to the GMMXX format. |
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result->ir.reserve(realNonZeros); |
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std::copy(tmpColumnIndicationsArray, tmpColumnIndicationsArray + realNonZeros, result->ir.begin()); |
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delete[] tmpColumnIndicationsArray; |
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// And do the same thing with the actual values. |
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result->pr.resize(realNonZeros); |
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std::copy(tmpValueArray, tmpValueArray + realNonZeros, result->pr.begin()); |
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delete[] tmpValueArray; |
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LOG4CPLUS_INFO(logger, "Done copy2."); |
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return result; |
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} |
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/*! |
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* Returns the number of non-zero entries that are not on the diagonal. |
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* @returns The number of non-zero entries that are not on the diagonal. |
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@ -564,6 +624,19 @@ public: |
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return nonZeroEntryCount; |
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} |
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/*! |
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* Returns the number of non-zero entries on the diagonal. |
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* @return The number of non-zero entries on the diagonal. |
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*/ |
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uint_fast64_t getDiagonalNonZeroEntryCount() const { |
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uint_fast64_t result = 0; |
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T zero(0); |
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for (uint_fast64_t i = 0; i < rowCount; ++i) { |
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if (diagonalStorage[i] != zero) ++result; |
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} |
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return result; |
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} |
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/*! |
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* This function makes the given row absorbing. This means that all |
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* entries in will be set to 0 and the value 1 will be written |
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@ -594,6 +667,104 @@ public: |
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return true; |
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} |
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/* |
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* Computes the sum of the elements in the given row whose column bits |
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* are set to one on the given constraint. |
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* @param row The row whose elements to add. |
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* @param constraint A bit vector that indicates which columns to add. |
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* @return The sum of the elements in the given row whose column bits |
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* are set to one on the given constraint. |
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*/ |
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T getConstrainedRowSum(const uint_fast64_t row, const mrmc::storage::BitVector& constraint) { |
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T result(0); |
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for (uint_fast64_t i = rowIndications[row]; i < rowIndications[row + 1]; ++i) { |
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if (constraint.get(columnIndications[i])) { |
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result += valueStorage[i]; |
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} |
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} |
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return result; |
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} |
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/*! |
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* Computes a vector in which each element is the sum of those elements in the |
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* corresponding row whose column bits are set to one in the given constraint. |
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* @param constraint A bit vector that indicates which columns to add. |
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* @param resultVector A pointer to the resulting vector that has at least |
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* as many elements as there are bits set to true in the constraint. |
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*/ |
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void getConstrainedRowCountVector(const mrmc::storage::BitVector& constraint, T* resultVector) { |
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for (uint_fast64_t row = 0; row < rowCount; ++row) { |
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resultVector[row] = getConstrainedRowSum(row, constraint); |
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} |
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} |
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/*! |
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* Creates a sub-matrix of the current matrix by dropping all rows and |
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* columns whose bits are not set to one in the given bit vector. |
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* @param constraint A bit vector indicating which rows and columns to drop. |
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* @return A pointer to a sparse matrix that is a sub-matrix of the current one. |
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*/ |
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SquareSparseMatrix* getSubmatrix(mrmc::storage::BitVector& constraint) { |
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LOG4CPLUS_DEBUG(logger, "Creating a sub-matrix with " << constraint.getNumberOfSetBits() << " rows."); |
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// Check for valid constraint. |
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if (constraint.getNumberOfSetBits() == 0) { |
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LOG4CPLUS_ERROR(logger, "Trying to create a sub-matrix of size 0."); |
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throw mrmc::exceptions::invalid_argument("Trying to create a sub-matrix of size 0."); |
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} |
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// First, we need to determine the number of non-zero entries of the |
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// sub-matrix. |
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uint_fast64_t subNonZeroEntries = 0; |
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for (auto rowIndex : constraint) { |
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for (uint_fast64_t i = rowIndications[rowIndex]; i < rowIndications[rowIndex + 1]; ++i) { |
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if (constraint.get(columnIndications[i])) { |
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++subNonZeroEntries; |
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} |
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} |
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} |
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LOG4CPLUS_DEBUG(logger, "Done counting non-zeros."); |
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// Create and initialize resulting matrix. |
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SquareSparseMatrix* result = new SquareSparseMatrix(constraint.getNumberOfSetBits()); |
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result->initialize(subNonZeroEntries); |
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// Create a temporary array that stores for each index whose bit is set |
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// to true the number of bits that were set before that particular index. |
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uint_fast64_t* bitsSetBeforeIndex = new uint_fast64_t[rowCount]; |
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uint_fast64_t lastIndex = 0; |
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uint_fast64_t currentNumberOfSetBits = 0; |
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for (auto index : constraint) { |
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while (lastIndex <= index) { |
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bitsSetBeforeIndex[lastIndex++] = currentNumberOfSetBits; |
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} |
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++currentNumberOfSetBits; |
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} |
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// Copy over selected entries. |
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uint_fast64_t rowCount = 0; |
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for (auto rowIndex : constraint) { |
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result->addNextValue(rowCount, rowCount, diagonalStorage[rowIndex]); |
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for (uint_fast64_t i = rowIndications[rowIndex]; i < rowIndications[rowIndex + 1]; ++i) { |
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if (constraint.get(columnIndications[i])) { |
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result->addNextValue(rowCount, bitsSetBeforeIndex[columnIndications[i]], valueStorage[i]); |
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} |
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} |
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++rowCount; |
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} |
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// Dispose of the temporary array. |
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delete[] bitsSetBeforeIndex; |
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// Finalize sub-matrix and return result. |
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result->finalize(); |
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LOG4CPLUS_DEBUG(logger, "Done creating sub-matrix."); |
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return result; |
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} |
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/*! |
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* Returns the size of the matrix in memory measured in bytes. |
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* @return The size of the matrix in memory measured in bytes. |
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dehnert
12 years ago