Steffen Neumann authored on 23/09/2021 12:34:25 | 1 | 1 |
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+// |
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+// $Id$ |
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+// |
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+// |
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+// Original author: Austin Keller <atkeller .@. uw.edu> |
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+// |
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+// Licensed under the Apache License, Version 2.0 (the "License"); |
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+// you may not use this file except in compliance with the License. |
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+// You may obtain a copy of the License at |
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+// |
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+// http://www.apache.org/licenses/LICENSE-2.0 |
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+// |
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+// Unless required by applicable law or agreed to in writing, software |
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+// distributed under the License is distributed on an "AS IS" BASIS, |
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+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. |
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+// See the License for the specific language governing permissions and |
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+// limitations under the License. |
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+// |
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+ |
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+#include "MatrixIO.hpp" |
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+ |
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+namespace pwiz |
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+{
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+namespace analysis |
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+{
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+ using namespace std; |
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+ using namespace DemuxTypes; |
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+ using namespace Eigen; |
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+ |
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+ void MatrixIO::GetWriteStream(ofstream& out, const string& filename) |
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+ {
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+ out.open(filename, ios::out | ios::binary | ios::trunc); |
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+ } |
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+ |
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+ void MatrixIO::WriteBinary(ofstream& out, boost::shared_ptr<MatrixType> matrix) |
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+ {
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+ MatrixType::Index rows = matrix->rows(), cols = matrix->cols(); |
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+ out.write(reinterpret_cast<char*>(&rows), sizeof(MatrixType::Index)); |
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+ out.write(reinterpret_cast<char*>(&cols), sizeof(MatrixType::Index)); |
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+ // Store as row-major |
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+ if (matrix->IsRowMajor) |
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+ out.write(reinterpret_cast<char*>(matrix->data()), rows * cols * sizeof(MatrixType::Scalar)); |
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+ else |
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+ {
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+ for (int row = 0; row < rows; ++row) |
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+ {
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+ for (int col = 0; col < cols; ++col) |
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+ {
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+ out.write(reinterpret_cast<char*>(&(*matrix)(row, col)), sizeof(MatrixType::Scalar)); |
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+ } |
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+ } |
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+ } |
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+ } |
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+ |
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+ void MatrixIO::WriteBinary(const string& filename, boost::shared_ptr<MatrixType> matrix) |
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+ {
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+ ofstream out; |
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+ GetWriteStream(out, filename); |
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+ if (!out.is_open()) |
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+ {
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+ throw runtime_error("Could not open file");
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+ } |
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+ WriteBinary(out, matrix); |
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+ out.flush(); |
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+ out.close(); |
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+ } |
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+ |
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+ void MatrixIO::GetReadStream(ifstream& in, const string& filename) |
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+ {
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+ in.open(filename, ios::in | ios::binary); |
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+ } |
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+ |
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+ void MatrixIO::ReadBinary(ifstream& in, boost::shared_ptr<MatrixType> matrix) |
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+ {
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+ MatrixType::Index rows = 0, cols = 0; |
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+ in.read(reinterpret_cast<char*>(&rows), sizeof(MatrixType::Index)); |
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+ in.read(reinterpret_cast<char*>(&cols), sizeof(MatrixType::Index)); |
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+ matrix->resize(rows, cols); |
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+ // File should be stored as row major |
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+ if (matrix->IsRowMajor) |
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+ in.read(reinterpret_cast<char *>(matrix->data()), rows * cols * sizeof(MatrixType::Scalar)); |
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+ else |
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+ {
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+ vector<double> flattened(rows * cols); |
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+ in.read(reinterpret_cast<char *>(&flattened[0]), rows * cols * sizeof(MatrixType::Scalar)); |
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+ Map<Matrix<MatrixType::Scalar, Dynamic, Dynamic, RowMajor>> readMatrix(&flattened[0], rows, cols); |
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+ *matrix = readMatrix; |
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+ } |
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+ } |
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+ |
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+ void MatrixIO::ReadBinary(const string& filename, boost::shared_ptr<MatrixType> matrix) |
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+ {
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+ ifstream in; |
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+ GetReadStream(in, filename); |
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+ if (!in.is_open()) |
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+ {
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+ throw runtime_error("Could not open file");
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+ } |
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+ ReadBinary(in, matrix); |
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+ in.close(); |
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+ } |
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+} // namespace analysis |
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+} // namespace pwiz |
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\ No newline at end of file |