DataSetD.h

Go to the documentation of this file.

/**
 *  \file RMF/HDF5/DataSetD.h
 *  \brief Handle read/write of Model data from/to files.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */

#ifndef RMF_HDF5_DATA_SET_D_H
#define RMF_HDF5_DATA_SET_D_H

#include "RMF/config.h"
#include "types.h"
#include "Object.h"
#include "MutableAttributes.h"
#include "ConstDataSetD.h"
#include "infrastructure_macros.h"
#include <algorithm>

RMF_ENABLE_WARNINGS
namespace RMF {
namespace HDF5 {

/** Wrap an HDF5 data set. Typedefs and python types are provided for
    data sets in 1,2, and 3 dimensions with all the supported types. They are
   named as
    RMF::HDF5::IndexDataSet2D (or RMF.HDF5.IndexDataSet2).
   See
   \external{https://support.hdfgroup.org/HDF5/doc/RM/RM_H5D.html,
   the HDF5 manual} for more information.
 */
template <class TypeTraits, unsigned int D>
class DataSetD : public MutableAttributes<ConstDataSetD<TypeTraits, D> > {
  typedef MutableAttributes<ConstDataSetD<TypeTraits, D> > P;
  friend class Group;

 protected:
  typedef DataSetCreationPropertiesD<TypeTraits, D> CreationProperties;
  typedef DataSetAccessPropertiesD<TypeTraits, D> AccessProperties;

  DataSetD(std::shared_ptr<SharedHandle> parent, std::string name,
           CreationProperties props)
      : P(parent, name, props) {}
  DataSetD(std::shared_ptr<SharedHandle> parent, std::string name,
           AccessProperties props)
      : P(parent, name, props) {}

 public:
#if !defined(SWIG) && !defined(RMF_DOXYGEN)
  DataSetD(hid_t file, std::string name, AccessProperties props)
      : P(file, name, props) {}
#endif
  typedef DataSetIndexD<D> Index;
  DataSetD() {}

  void set_value(const DataSetIndexD<D>& ijk, typename TypeTraits::Type value) {
    RMF_IF_CHECK { P::check_index(ijk); }
    // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
    RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
                                      ijk.get(), P::get_ones(), P::get_ones(),
                                      nullptr));
    TypeTraits::write_value_dataset(Object::get_handle(),
                                    P::get_input_data_space().get_hid(),
                                    P::get_data_space(), value);
  }
  RMF_SHOWABLE(DataSetD, "DataSet" << D << "D " << P::get_name());
#ifndef SWIG
  typedef DataSetIndexD<D - 1> RowIndex;
  void set_row(const RowIndex& ijkr, const typename TypeTraits::Types& value) {
    DataSetIndexD<D> ijk;
    std::copy(ijkr.begin(), ijkr.end(), ijk.begin());
    ijk[D - 1] = 0;
    RMF_IF_CHECK { P::check_index(ijk); }
    hsize_t size[D];
    std::fill(size, size + D - 1, 1);
    size[D - 1] = P::get_size()[D - 1];  // set last to size of row
    // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
    RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
                                      ijk.get(), P::get_ones(), &size[0],
                                      nullptr));
    TypeTraits::write_values_dataset(Object::get_handle(),
                                     P::get_row_data_space().get_hid(),
                                     P::get_data_space(), value);
  }
#endif
  //! Write a rectangular block starting at ln of size size
  void set_block(const Index& lb, const Index& size,
                 const typename TypeTraits::Types& value) {
    RMF_IF_CHECK {
      P::check_index(lb);
      Index last = lb;
      // offset size by one and check...
      unsigned int total = 1;
      for (unsigned int i = 0; i < D; ++i) {
        total *= size[i];
        last[i] += size[i] - 1;
      }
      RMF_USAGE_CHECK(total == value.size(),
                      RMF::internal::get_error_message(
                          "Block has size ", total, " but found ", value.size(),
                          " values"));
      P::check_index(last);
    }
    // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
    RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
                                      lb.get(), P::get_ones(), size.get(),
                                      nullptr));
    hsize_t sz = value.size();
    RMF_HDF5_HANDLE(input, H5Screate_simple(1, &sz, nullptr), &H5Sclose);
    TypeTraits::write_values_dataset(Object::get_handle(), input,
                                     P::get_data_space(), value);
  }
  void set_size(const DataSetIndexD<D>& ijk) {
    hsize_t nd[D];
    std::copy(ijk.begin(), ijk.end(), nd);
    ;
    RMF_HDF5_CALL(H5Dset_extent(Object::get_handle(), &nd[0]));
    P::initialize_handles();
  }
};

#ifndef RMF_DOXYGEN

#define RMF_HDF5_DECLARE_DATA_SET(lcname, Ucname, PassValue, ReturnValue,   \
                                  PassValues, ReturnValues)                 \
  typedef DataSetD<Ucname##Traits, 1> Ucname##DataSet1D;                    \
  typedef std::vector<Ucname##DataSet1D> Ucname##DataSet1Ds;                \
  typedef DataSetD<Ucname##Traits, 2> Ucname##DataSet2D;                    \
  typedef std::vector<Ucname##DataSet2D> Ucname##DataSet2Ds;                \
  typedef DataSetD<Ucname##Traits, 3> Ucname##DataSet3D;                    \
  typedef std::vector<Ucname##DataSet3D> Ucname##DataSet3Ds;                \
  typedef MutableAttributes<Ucname##DataSet1D> Ucname##DataSet1DAttributes; \
  typedef MutableAttributes<Ucname##DataSet2D> Ucname##DataSet2DAttributes; \
  typedef MutableAttributes<Ucname##DataSet3D> Ucname##DataSet3DAttributes; \
  typedef std::vector<Ucname##DataSet1DAttributes>                          \
      Ucname##DataSet1DAttributesList;                                      \
  typedef std::vector<Ucname##DataSet2DAttributes>                          \
      Ucname##DataSet2DAttributesList;                                      \
  typedef std::vector<Ucname##DataSet3DAttributes>                          \
      Ucname##DataSet3DAttributesList

/** \name Basic data set types
     \ingroup hdf5
     @{
 */
RMF_HDF5_FOREACH_TYPE(RMF_HDF5_DECLARE_DATA_SET);
/** @} */
#endif

} /* namespace HDF5 */
} /* namespace RMF */

RMF_DISABLE_WARNINGS

#endif /* RMF_HDF5_DATA_SET_D_H */