Eigen - 将稀疏矩阵存储为二进制

计算科学 稀疏矩阵 本征 数据存储
2021-11-26 20:14:46

我需要在 Eigen 中存储大型稀疏矩阵。除了Eigen/Unsupported中的以下函数外，我在库中找不到任何东西。saveMarket 的问题在于，它以文本格式保存。由于矩阵的大小，我需要将稀疏矩阵存储为二进制文件。有没有一种简单的方法来调整下面的函数以存储为二进制文件。以及重新加载矩阵的简单方法？

template<typename SparseMatrixType>
bool saveMarket(const SparseMatrixType& mat, const std::string& filename, int sym = 0)
{
  typedef typename SparseMatrixType::Scalar Scalar;
  std::ofstream out(filename.c_str(),std::ios::out);
  if(!out)
    return false;

  out.flags(std::ios_base::scientific);
  out.precision(64);
  std::string header; 
  internal::putMarketHeader<Scalar>(header, sym); 
  out << header << std::endl; 
  out << mat.rows() << " " << mat.cols() << " " << mat.nonZeros() << "\n";
  int count = 0;
  for(int j=0; j<mat.outerSize(); ++j)
    for(typename SparseMatrixType::InnerIterator it(mat,j); it; ++it)
    {
    ++ count;
    internal::PutMatrixElt(it.value(), it.row()+1, it.col()+1, out);
    // out << it.row()+1 << " " << it.col()+1 << " " << it.value() << "\n";
}
  out.close();
  return true;
}
1个回答

我已经推出了自己的。这是一个MCVE：

#include <Eigen/Core>
#include <Eigen/Sparse>
#include <iostream>
#include <fstream>
#include <vector>

using namespace Eigen;

typedef Triplet<int> Trip;

template <typename T, int whatever, typename IND>
void Serialize(SparseMatrix<T, whatever, IND>& m) {
    std::vector<Trip> res;
    int sz = m.nonZeros();
    m.makeCompressed();

    fstream writeFile;
    writeFile.open("matrix", ios::binary | ios::out);

    if(writeFile.is_open())
    {
        IND rows, cols, nnzs, outS, innS;
        rows = m.rows()     ;
        cols = m.cols()     ;
        nnzs = m.nonZeros() ;
        outS = m.outerSize();
        innS = m.innerSize();

        writeFile.write((const char *)&(rows), sizeof(IND));
        writeFile.write((const char *)&(cols), sizeof(IND));
        writeFile.write((const char *)&(nnzs), sizeof(IND));
        writeFile.write((const char *)&(innS), sizeof(IND));
        writeFile.write((const char *)&(outS), sizeof(IND));

        writeFile.write((const char *)(m.valuePtr()),       sizeof(T  ) * m.nonZeros());
        writeFile.write((const char *)(m.outerIndexPtr()),  sizeof(IND) * m.outerSize());
        writeFile.write((const char *)(m.innerIndexPtr()),  sizeof(IND) * m.nonZeros());

        writeFile.close();
    }
}

template <typename T, int whatever, typename IND>
void Deserialize(SparseMatrix<T, whatever, IND>& m) {
    fstream readFile;
    readFile.open("matrix", ios::binary | ios::in);
    if(readFile.is_open())
    {
        IND rows, cols, nnz, inSz, outSz;
        readFile.read((char*)&rows , sizeof(IND));
        readFile.read((char*)&cols , sizeof(IND));
        readFile.read((char*)&nnz  , sizeof(IND));
        readFile.read((char*)&inSz , sizeof(IND));
        readFile.read((char*)&outSz, sizeof(IND));

        m.resize(rows, cols);
        m.makeCompressed();
        m.resizeNonZeros(nnz);

        readFile.read((char*)(m.valuePtr())     , sizeof(T  ) * nnz  );
        readFile.read((char*)(m.outerIndexPtr()), sizeof(IND) * outSz);
        readFile.read((char*)(m.innerIndexPtr()), sizeof(IND) * nnz );

        m.finalize();
        readFile.close();

    } // file is open
}


int main(int argc, char *argv[]){
    int rows, cols;
    rows = cols = 6;
    SparseMatrix<double> A(rows,cols), B;

    std::vector<Trip> trp, tmp;

    trp.push_back(Trip(0, 0, rand()));
    trp.push_back(Trip(1, 1, rand()));
    trp.push_back(Trip(2, 2, rand()));
    trp.push_back(Trip(3, 3, rand()));
    trp.push_back(Trip(4, 4, rand()));
    trp.push_back(Trip(5, 5, rand()));
    trp.push_back(Trip(2, 4, rand()));
    trp.push_back(Trip(3, 1, rand()));

    A.setFromTriplets(trp.begin(), trp.end());
    cout << A.nonZeros() << endl;   // Prints 8
    cout << A.size() << endl;       // Prints 36
    cout << A << endl;              // Prints the matrix along with the sparse matrix stuff

    Serialize(A);

    Deserialize(B);

    cout << B.nonZeros() << endl;   // Prints 8
    cout << B.size() << endl;       // Prints 36
    cout << B << endl;              // Prints the reconstructed matrix along with the sparse matrix stuff

    return 0;
}
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