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ezh5-eigen: C++ interface for HDF5 with Eigen3 support

Theoretically simple and straightforward to use C++11 to HDF5 library.
Based off of mileschen360/ezh5

Features

  • Reading/writing of basic data types (int,double,std::complex<T>,std::string)
  • Reading/writing of Eigen vectors and matrices (e.g. Eigen::VectorXd, Eigen::Matrix Xcd)
  • Appending of basic data types into vectors
  • Appending of Eigen vectors into a "matrix"

Interface

using namespace ezh5;
{
  File f ("universe.h5", H5F_ACC_TRUNC);  // create a file object called f
  //------------------------------------------------------------------------------
  // Set basic+Eigen datatypes 
  //------------------------------------------------------------------------------
  f["step"]=1;

  //vector support
  std::vector<double> v(4) = {1.5,2.5,3.5,4.5};
  f["myVector"]=v;

  //Eigen support
  Eigen::VectorXcd evc(10);
  evc.setRandom();
  f["evc"]=evc;

  Eigen::MatrixXd ev(2,5);
  ev<<1,2,3,4,5,6,7,8,9,10;
  f["ev"]=ev;
  //------------------------------------------------------------------------------
  // Append basic+Eigen datatypes
  //------------------------------------------------------------------------------
  
  //append by keeping the node around
  auto toKeep=f["vecOfInts"];
  toKeep.append(1);
  toKeep.append(2);
  toKeep.append(3);
  //alternative interface
  toKeep << 4;
  toKeep << 5 << 6;

  //append eigen vectors
  Eigen::VectorXd eigv(4);
  eigv << 1,2,3,4;
  auto eNode = f["evAppend"];
  eNode.append(eigv).append(eigv);
  eNode << eigv;
  eNode << eigv;

  //destructor closes file
}
{
  File g ("universe.h5", H5F_ACC_RDONLY);
  //------------------------------------------------------------------------------
  // Straightforward reading interface
  //------------------------------------------------------------------------------
  int step;
  g["step"] >> step;
  std::vector<double> v;
  g["v"] >> v;
  Eigen::MatrixXd ev;
  g["ev"] >> ev;
  Eigen::VectorXcd evc;
  g["evc"] >> evc;

  std::vector<int> test;
  g["vecOfInts"] >> test; //automatic vector
  
  //append vectors become matrices
  Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic,Eigen::RowMajor> evMatrix;
  g["evAppend"] >> evMatrix;
}

Installation Usage

Simply compile ezh5.cc along with your codebase and include ezh5.h in your files and you're good to go!

Requires both HDF5 and Eigen to be installed

Installing HDF5

Mac

I suggest using homebrew (preferred)

brew install hdf5

or MacPorts

port install hdf5

Linux

  • Ubuntu: apt-get install libhdf5-serial-dev hdf5-tools
  • Fedora: dnf install hdf5-devel

Contributors

  • Ryan Levy - major modifications and appending support
  • Xiongjie Yu - Original port and initial Eigen support
  • M. Chen - Original open source base code and style of ezh5

TODO

  • Append Eigen Matrices (requires a bit of work when extracting the resulting matrix)
  • Better documentation +/- Doxygen