cosmotool/src/hdf5_array.hpp

/*+
This is CosmoTool (./src/hdf5_array.hpp) -- Copyright (C) Guilhem Lavaux (2007-2014)

guilhem.lavaux@gmail.com

This software is a computer program whose purpose is to provide a toolbox for cosmological
data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)

This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or 
data to be ensured and,  more generally, to use and operate it in the 
same conditions as regards security. 

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
+*/
#ifndef __COSMO_HDF5_ARRAY_HPP
#define __COSMO_HDF5_ARRAY_HPP


#include <string>
#include <stdint.h>
#include <boost/static_assert.hpp>
#include <boost/utility.hpp>
#include <boost/mpl/assert.hpp>
#include <boost/multi_array.hpp>
#include <boost/type_traits/is_same.hpp> 
#include <boost/type_traits/is_floating_point.hpp> 
#include <boost/preprocessor/cat.hpp>
#include <boost/preprocessor/stringize.hpp>
#include <boost/preprocessor/seq/for_each.hpp>
#include <vector>
#include <H5Cpp.h>

namespace CosmoTool {

  //!_______________________________________________________________________________________
  //!     
  //!     map types to HDF5 types
  //!         
  //!     
  //!     Leo Goodstadt (04 March 2013), improved with enable_if by Guilhem Lavaux (May 2014)
  //!_______________________________________________________________________________________ 

  template<typename T, class Enable = void> struct get_hdf5_data_type
  {
    static H5::DataType type()  
      {   
          BOOST_MPL_ASSERT_MSG(0, Unknown_HDF5_data_type, ()); 
          return H5::PredType::NATIVE_DOUBLE; 
      }
  };
  
  #define HDF5_TYPE(tl, thdf5) \
  template<typename T> struct get_hdf5_data_type<T, typename boost::enable_if<boost::is_same<T, tl> >::type>  \
    { static H5::DataType type() { return H5::PredType::thdf5; }; }
  
  HDF5_TYPE(char              , NATIVE_CHAR);
  HDF5_TYPE(long long         , NATIVE_LLONG);
  HDF5_TYPE(unsigned long long, NATIVE_ULLONG);
  HDF5_TYPE(int8_t            , NATIVE_INT8);
  HDF5_TYPE(uint8_t           , NATIVE_UINT8);
  HDF5_TYPE(int16_t           , NATIVE_INT16);
  HDF5_TYPE(uint16_t          , NATIVE_UINT16);
  HDF5_TYPE(int32_t           , NATIVE_INT32);
  HDF5_TYPE(uint32_t          , NATIVE_UINT32);
  HDF5_TYPE(int64_t           , NATIVE_INT64);
  HDF5_TYPE(uint64_t          , NATIVE_UINT64);
  HDF5_TYPE(float             , NATIVE_FLOAT);
  HDF5_TYPE(double            , NATIVE_DOUBLE);
  HDF5_TYPE(long double       , NATIVE_LDOUBLE);
  
  #undef HDF5_TYPE

//!_______________________________________________________________________________________
//!     
//!     write_hdf5 multi_array
//!         
//!     \author leo Goodstadt (04 March 2013)
//!     
//!_______________________________________________________________________________________
  template<typename ArrayType,  typename hdf5_data_type>
  void hdf5_write_array(H5::CommonFG& fg, const std::string& data_set_name, 
                        const ArrayType& data, 
                        const hdf5_data_type& datatype)
  {
      std::vector<hsize_t> dimensions(data.shape(), data.shape() + data.num_dimensions());
      H5::DataSpace dataspace(data.num_dimensions(), dimensions.data());

      H5::DataSet dataset = fg.createDataSet(data_set_name, datatype, dataspace);

      dataset.write(data.data(), datatype);
  }
  
  /* HDF5 complex type */
  template<typename T>
  class hdf5_ComplexType
  {
  public:
    H5::CompType type;
    
    hdf5_ComplexType()
      : type(sizeof(std::complex<T>))
    {
      get_hdf5_data_type<T> hdf_data_type;
      type.insertMember("r", 0, hdf_data_type.type());
      type.insertMember("i", sizeof(T), hdf_data_type.type());
      type.pack();
    }
    
    static const hdf5_ComplexType<T> *ctype()
    {
      static hdf5_ComplexType<T> singleton;
      
      return &singleton;
    }
  };

  template<> struct get_hdf5_data_type<std::complex<float> > { 
    static H5::DataType type() { 
      return hdf5_ComplexType<float>::ctype()->type; 
    }
  };

  template<> struct get_hdf5_data_type<std::complex<double> > { 
    static H5::DataType type() { 
      return hdf5_ComplexType<double>::ctype()->type; 
    }
  };


  template<typename ArrayType>
  void hdf5_write_array(H5::CommonFG& fg, const std::string& data_set_name, const ArrayType& data )
  {
      typedef typename ArrayType::element T;
      get_hdf5_data_type<T> hdf_data_type;
      
      hdf5_write_array(fg, data_set_name, data, hdf_data_type.type());
  }
  
  // HDF5 array reader
  //
  // Author Guilhem Lavaux (May 2014)
  
  class InvalidDimensions: virtual std::exception {
  };
  
  template<std::size_t r>
  struct hdf5_extent_gen {
    typedef typename boost::detail::multi_array::extent_gen<r> type;
    
    static inline type build(hsize_t *d)
    {
      return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
    }
  };

  template<>
  struct hdf5_extent_gen<0> {    
    static inline boost::multi_array_types::extent_gen build(hsize_t *d)
    {
      return boost::extents;
    }
  };

  template<typename ArrayType, typename hdf5_data_type>
  void hdf5_read_array(H5::CommonFG& fg, const std::string& data_set_name, 
                       ArrayType& data, 
                       const hdf5_data_type& datatype)
  {
      H5::DataSet dataset = fg.openDataSet(data_set_name);
      H5::DataSpace dataspace = dataset.getSpace();
      std::vector<hsize_t> dimensions(data.num_dimensions());
      
      if (dataspace.getSimpleExtentNdims() != data.num_dimensions())
        {
          throw InvalidDimensions();
        }
            
      dataspace.getSimpleExtentDims(dimensions.data());
      data.resize(hdf5_extent_gen<ArrayType::dimensionality>::build(dimensions.data()));
      dataset.read(data.data(), datatype);
  }

  template<typename ArrayType>
  void hdf5_read_array(H5::CommonFG& fg, const std::string& data_set_name, ArrayType& data )
  {
      typedef typename ArrayType::element T;
      
      get_hdf5_data_type<T> hdf_data_type;
      hdf5_read_array(fg, data_set_name, data, hdf_data_type.type());
  }


#define CTOOL_HDF5_NAME(STRUCT) BOOST_PP_CAT(hdf5_,STRUCT)
#define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \
     { \
       ::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \
       position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \
       const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \
       type.insertMember(field_name,  position, t.type()); \
     } 
  
#define CTOOL_STRUCT_TYPE(STRUCT, TNAME, ATTRIBUTES) \
namespace CosmoTool { \
    class TNAME {  \
    public:  \
      H5::CompType type;  \
  \
      TNAME() : type(sizeof(STRUCT)) \
      {  \
        long position; \
        BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \
      }  \
      \
      static const TNAME *ctype() \
      { \
        static TNAME singleton; \
        return &singleton; \
      } \
    }; \
    template<> struct get_hdf5_data_type<STRUCT> { \
        static H5::DataType type() { return TNAME::ctype()->type; }; \
    }; \
};

};

#endif