HDF5Utils.h

/*
 * This file is part of the statismo library.
 *
 * Author: Marcel Luethi (marcel.luethi@unibas.ch)
 *
 * Copyright (c) 2011 University of Basel
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * Redistributions of source code must retain the above copyright notice,
 * this list of conditions and the following disclaimer.
 *
 * Redistributions in binary form must reproduce the above copyright
 * notice, this list of conditions and the following disclaimer in the
 * documentation and/or other materials provided with the distribution.
 *
 * Neither the name of the project's author nor the names of its
 * contributors may be used to endorse or promote products derived from
 * this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
 * FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
 * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 */


#ifndef HDF5UTILS_H_
#define HDF5UTILS_H_

#include "CommonTypes.h"


namespace H5 {
class CommonFG;
class Group;
class H5File;
class H5Object;
class DataSet;
}

namespace statismo {

class HDF5Utils {
  public:



    static H5::H5File openOrCreateFile(const std::string filename);


    static H5::Group openPath(H5::H5File& fg, const std::string& path, bool createPath=false);

    static void readMatrix(const H5::CommonFG& fg, const char* name, MatrixType& matrix);

    static void readMatrix(const H5::CommonFG& fg, const char* name, unsigned nCols, MatrixType& matrix);

    template <class T>
    static void readMatrixOfType(const H5::CommonFG& fg, const char* name, typename GenericEigenType<T>::MatrixType& matrix);

    static H5::DataSet writeMatrix(const H5::CommonFG& fg, const char* name, const MatrixType& matrix);

    template <class T>
    static H5::DataSet writeMatrixOfType(const H5::CommonFG& fg, const char* name, const typename GenericEigenType<T>::MatrixType& matrix);


    static void readVector(const H5::CommonFG& fg, const char* name, unsigned nElements, VectorType& vector);

    static void readVector(const H5::CommonFG& fg, const char* name, VectorType& vector);

    template <class T>
    static void readVectorOfType(const H5::CommonFG& fg, const char* name, typename GenericEigenType<T>::VectorType& vector);

    static H5::DataSet writeVector(const H5::CommonFG& fg, const char* name, const VectorType& vector);

    template <class T>
    static H5::DataSet writeVectorOfType(const H5::CommonFG& fg, const char* name, const typename GenericEigenType<T>::VectorType& vector);


    static void dumpFileToHDF5( const char* filename, const H5::CommonFG& fg, const char* name);

    static void getFileFromHDF5(const H5::CommonFG& fg, const char* name, const char* filename);

    static H5::DataSet writeString(const H5::CommonFG& fg, const char* name, const std::string& s);

    static std::string readString(const H5::CommonFG& fg, const char* name);

    static void writeStringAttribute(const H5::H5Object& group, const char* name, const std::string& s);

    static void writeIntAttribute(const H5::H5Object& fg, const char* name, int value);



    static std::string readStringAttribute(const H5::H5Object& group, const char* name);

    static int readIntAttribute(const H5::H5Object& group, const char* name);


    static int readInt(const H5::CommonFG& fg, const char* name);

    static H5::DataSet writeInt(const H5::CommonFG& fg, const char* name, int value);

    static float readFloat(const H5::CommonFG& fg, const char* name);

    static H5::DataSet writeFloat(const H5::CommonFG& fg, const char* name, float value);

    template<typename T>
    static void readArray(const H5::CommonFG& fg, const char* name, std::vector<T> & array);

    template<typename T>
    static H5::DataSet writeArray(const H5::CommonFG& fg, const char* name, std::vector<T> const& array );


    static bool existsObjectWithName(const H5::CommonFG& fg, const std::string& name);

};

} // namespace statismo

#include "HDF5Utils.hxx"

#endif /* HDF5UTILS_H_ */