RMF
DataSetD.h
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1 /**
2  * \file RMF/HDF5/DataSetD.h
3  * \brief Handle read/write of Model data from/to files.
4  *
5  * Copyright 2007-2022 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef RMF_HDF5_DATA_SET_D_H
10 #define RMF_HDF5_DATA_SET_D_H
11 
12 #include "RMF/config.h"
13 #include "types.h"
14 #include "Object.h"
15 #include "MutableAttributes.h"
16 #include "ConstDataSetD.h"
17 #include "infrastructure_macros.h"
18 #include <algorithm>
19 
20 RMF_ENABLE_WARNINGS
21 namespace RMF {
22 namespace HDF5 {
23 
24 /** Wrap an HDF5 data set. Typedefs and python types are provided for
25  data sets in 1,2, and 3 dimensions with all the supported types. They are
26  named as
27  RMF::HDF5::IndexDataSet2D (or RMF.HDF5.IndexDataSet2).
28  See
29  \external{https://docs.hdfgroup.org/releases/hdf5/v1_14/v1_14_4/documentation/doxygen/group___h5_d.html,
30  the HDF5 manual} for more information.
31  */
32 template <class TypeTraits, unsigned int D>
33 class DataSetD : public MutableAttributes<ConstDataSetD<TypeTraits, D> > {
34  typedef MutableAttributes<ConstDataSetD<TypeTraits, D> > P;
35  friend class Group;
36 
37  protected:
38  typedef DataSetCreationPropertiesD<TypeTraits, D> CreationProperties;
39  typedef DataSetAccessPropertiesD<TypeTraits, D> AccessProperties;
40 
41  DataSetD(std::shared_ptr<SharedHandle> parent, std::string name,
42  CreationProperties props)
43  : P(parent, name, props) {}
44  DataSetD(std::shared_ptr<SharedHandle> parent, std::string name,
45  AccessProperties props)
46  : P(parent, name, props) {}
47 
48  public:
49 #if !defined(SWIG) && !defined(RMF_DOXYGEN)
50  DataSetD(hid_t file, std::string name, AccessProperties props)
51  : P(file, name, props) {}
52 #endif
53  typedef DataSetIndexD<D> Index;
54  DataSetD() {}
55 
56  void set_value(const DataSetIndexD<D>& ijk, typename TypeTraits::Type value) {
57  RMF_IF_CHECK { P::check_index(ijk); }
58  // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
59  RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
60  ijk.get(), P::get_ones(), P::get_ones(),
61  nullptr));
62  TypeTraits::write_value_dataset(Object::get_handle(),
63  P::get_input_data_space().get_hid(),
64  P::get_data_space(), value);
65  }
66  RMF_SHOWABLE(DataSetD, "DataSet" << D << "D " << P::get_name());
67 #ifndef SWIG
68  typedef DataSetIndexD<D - 1> RowIndex;
69  void set_row(const RowIndex& ijkr, const typename TypeTraits::Types& value) {
70  DataSetIndexD<D> ijk;
71  std::copy(ijkr.begin(), ijkr.end(), ijk.begin());
72  ijk[D - 1] = 0;
73  RMF_IF_CHECK { P::check_index(ijk); }
74  hsize_t size[D];
75  std::fill(size, size + D - 1, 1);
76  size[D - 1] = P::get_size()[D - 1]; // set last to size of row
77  // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
78  RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
79  ijk.get(), P::get_ones(), &size[0],
80  nullptr));
81  TypeTraits::write_values_dataset(Object::get_handle(),
82  P::get_row_data_space().get_hid(),
83  P::get_data_space(), value);
84  }
85 #endif
86  //! Write a rectangular block starting at ln of size size
87  void set_block(const Index& lb, const Index& size,
88  const typename TypeTraits::Types& value) {
89  RMF_IF_CHECK {
90  P::check_index(lb);
91  Index last = lb;
92  // offset size by one and check...
93  unsigned int total = 1;
94  for (unsigned int i = 0; i < D; ++i) {
95  total *= size[i];
96  last[i] += size[i] - 1;
97  }
98  RMF_USAGE_CHECK(total == value.size(),
99  RMF::internal::get_error_message(
100  "Block has size ", total, " but found ", value.size(),
101  " values"));
102  P::check_index(last);
103  }
104  // RMF_HDF5_HANDLE(sel, H5Dget_space(h_->get_hid()), &H5Sclose);
105  RMF_HDF5_CALL(H5Sselect_hyperslab(P::get_data_space(), H5S_SELECT_SET,
106  lb.get(), P::get_ones(), size.get(),
107  nullptr));
108  hsize_t sz = value.size();
109  RMF_HDF5_HANDLE(input, H5Screate_simple(1, &sz, nullptr), &H5Sclose);
110  TypeTraits::write_values_dataset(Object::get_handle(), input,
111  P::get_data_space(), value);
112  }
113  void set_size(const DataSetIndexD<D>& ijk) {
114  hsize_t nd[D];
115  std::copy(ijk.begin(), ijk.end(), nd);
116  ;
117  RMF_HDF5_CALL(H5Dset_extent(Object::get_handle(), &nd[0]));
118  P::initialize_handles();
119  }
120 };
121 
122 #ifndef RMF_DOXYGEN
123 
124 #define RMF_HDF5_DECLARE_DATA_SET(lcname, Ucname, PassValue, ReturnValue, \
125  PassValues, ReturnValues) \
126  typedef DataSetD<Ucname##Traits, 1> Ucname##DataSet1D; \
127  typedef std::vector<Ucname##DataSet1D> Ucname##DataSet1Ds; \
128  typedef DataSetD<Ucname##Traits, 2> Ucname##DataSet2D; \
129  typedef std::vector<Ucname##DataSet2D> Ucname##DataSet2Ds; \
130  typedef DataSetD<Ucname##Traits, 3> Ucname##DataSet3D; \
131  typedef std::vector<Ucname##DataSet3D> Ucname##DataSet3Ds; \
132  typedef MutableAttributes<Ucname##DataSet1D> Ucname##DataSet1DAttributes; \
133  typedef MutableAttributes<Ucname##DataSet2D> Ucname##DataSet2DAttributes; \
134  typedef MutableAttributes<Ucname##DataSet3D> Ucname##DataSet3DAttributes; \
135  typedef std::vector<Ucname##DataSet1DAttributes> \
136  Ucname##DataSet1DAttributesList; \
137  typedef std::vector<Ucname##DataSet2DAttributes> \
138  Ucname##DataSet2DAttributesList; \
139  typedef std::vector<Ucname##DataSet3DAttributes> \
140  Ucname##DataSet3DAttributesList
141 
142 /** \name Basic data set types
143  \ingroup hdf5
144  @{
145  */
146 RMF_HDF5_FOREACH_TYPE(RMF_HDF5_DECLARE_DATA_SET);
147 /** @} */
148 #endif
149 
150 } /* namespace HDF5 */
151 } /* namespace RMF */
152 
153 RMF_DISABLE_WARNINGS
154 
155 #endif /* RMF_HDF5_DATA_SET_D_H */
MutableAttributes.h
Handle read/write of Model data from/to files.
infrastructure_macros.h
Various general useful macros for IMP.
RMF::HDF5::Index
int Index
Definition: HDF5/types.h:38
ConstDataSetD.h
Handle read/write of Model data from/to files.
RMF::HDF5::DataSetD::set_block
void set_block(const Index &lb, const Index &size, const typename TypeTraits::Types &value)
Write a rectangular block starting at ln of size size.
Definition: DataSetD.h:87
RMF_HDF5_CALL
#define RMF_HDF5_CALL(v)
Definition: HDF5/infrastructure_macros.h:28
Object.h
Handle read/write of Model data from/to files.
types.h
Handle read/write of Model data from/to files.