ALPSCore reference
archive_read.cpp
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1 /*
2  * Copyright (C) 1998-2018 ALPS Collaboration. See COPYRIGHT.TXT
3  * All rights reserved. Use is subject to license terms. See LICENSE.TXT
4  * For use in publications, see ACKNOWLEDGE.TXT
5  */
6 
7 #include <iostream>
8 #include <vector>
9 
10 #include <hdf5.h>
11 
12 #include <alps/hdf5/archive.hpp>
13 #include <alps/utilities/cast.hpp>
14 
15 #include "common.hpp"
16 #include "archivecontext.hpp"
17 
18 namespace alps {
19  namespace hdf5 {
20  namespace detail {
21  // helpers
22 
23  template<typename T>
24  bool hdf5_read_scalar_data_helper(T & value, data_type const &data_id, type_type const &native_id);
25  template<typename T>
26  bool hdf5_read_scalar_attribute_helper(T & value, attribute_type const &attribute_id, type_type const &native_id);
27  template<typename T>
28  bool hdf5_read_vector_data_helper(T * value, data_type const &data_id, type_type const &native_id,
29  std::vector<std::size_t> const &chunk,
30  std::vector<std::size_t> const &offset,
31  std::vector<std::size_t> const &data_size);
32  template<typename T>
33  bool hdf5_read_vector_attribute_helper(std::string const &path, T * value, attribute_type const &attribute_id, type_type const &native_id,
34  std::vector<std::size_t> const &chunk,
35  std::vector<std::size_t> const &data_size);
36  }
37 
38  template<typename T>
39  auto archive::read(std::string path, T & value) const -> ONLY_NATIVE(T, void) {
40  ALPS_HDF5_FAKE_THREADSAFETY
41  if (context_ == NULL)
42  throw archive_closed("the archive is closed" + ALPS_STACKTRACE);
43  if ((path = complete_path(path)).find_last_of('@') == std::string::npos) {
44  if (!is_data(path))
45  throw path_not_found("the path does not exist: " + path + ALPS_STACKTRACE);
46  else if (!is_scalar(path))
47  throw wrong_type("scalar - vector conflict in path: " + path + ALPS_STACKTRACE);
48  detail::data_type data_id(H5Dopen2(context_->file_id_, path.c_str(), H5P_DEFAULT));
49  detail::type_type type_id(H5Dget_type(data_id));
50  detail::type_type native_id(H5Tget_native_type(type_id, H5T_DIR_ASCEND));
51  if (H5Tget_class(native_id) == H5T_STRING && !detail::check_error(H5Tis_variable_str(type_id))) {
52  std::string raw(H5Tget_size(type_id) + 1, '\0');
53  detail::check_error(H5Dread(data_id, native_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, &raw[0]));
54  value = cast< T >(raw);
55  } else if (H5Tget_class(native_id) == H5T_STRING) {
56  char * raw;
57  detail::check_error(H5Dread(data_id, native_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, &raw));
58  value = cast< T >(std::string(raw));
59  detail::check_error(H5Dvlen_reclaim(type_id, detail::space_type(H5Dget_space(data_id)), H5P_DEFAULT, &raw));
60  } else if(detail::hdf5_read_scalar_data_helper(value, data_id, native_id)) {
61  } else
62  throw wrong_type("invalid type" + ALPS_STACKTRACE);
63  } else {
64  if (!is_attribute(path))
65  throw path_not_found("the path does not exist: " + path + ALPS_STACKTRACE);
66  else if (!is_scalar(path))
67  throw wrong_type("scalar - vector conflict in path: " + path + ALPS_STACKTRACE);
68  detail::attribute_type attribute_id(H5Aopen_by_name(
69  context_->file_id_
70  , path.substr(0, path.find_last_of('@')).c_str()
71  , path.substr(path.find_last_of('@') + 1).c_str()
72  , H5P_DEFAULT, H5P_DEFAULT
73  ));
74  detail::type_type type_id(H5Aget_type(attribute_id));
75  detail::type_type native_id(H5Tget_native_type(type_id, H5T_DIR_ASCEND));
76  if (H5Tget_class(native_id) == H5T_STRING && !detail::check_error(H5Tis_variable_str(type_id))) {
77  std::string raw(H5Tget_size(type_id) + 1, '\0');
78  detail::check_error(H5Aread(attribute_id, native_id, &raw[0]));
79  value = cast< T >(raw);
80  } else if (H5Tget_class(native_id) == H5T_STRING) {
81  char * raw;
82  detail::check_error(H5Aread(attribute_id, native_id, &raw));
83  value = cast< T >(std::string(raw));
84  } else if(detail::hdf5_read_scalar_attribute_helper(value, attribute_id, native_id)) {
85  } else throw wrong_type("invalid type" + ALPS_STACKTRACE);
86  }
87  }
88  #define ALPS_HDF5_READ_SCALAR(T) template void archive::read<T>(std::string, T &) const;
89  ALPS_FOREACH_NATIVE_HDF5_TYPE(ALPS_HDF5_READ_SCALAR);
90 
91  template<typename T>
92  auto archive::read(std::string path, T * value, std::vector<std::size_t> chunk, std::vector<std::size_t> offset) const -> ONLY_NATIVE(T, void) {
93  ALPS_HDF5_FAKE_THREADSAFETY
94  if (context_ == NULL)
95  throw archive_closed("the archive is closed" + ALPS_STACKTRACE);
96  std::vector<std::size_t> data_size = extent(path);
97  if (offset.size() == 0)
98  offset = std::vector<std::size_t>(dimensions(path), 0);
99  if (data_size.size() != chunk.size() || data_size.size() != offset.size())
100  throw archive_error("wrong size or offset passed for path: " + path + ALPS_STACKTRACE);
101  for (std::size_t i = 0; i < data_size.size(); ++i)
102  if (data_size[i] < chunk[i] + offset[i])
103  throw archive_error("passed size of offset exeed data size for path: " + path + ALPS_STACKTRACE);
104  if (is_null(path))
105  value = NULL;
106  else {
107  for (std::size_t i = 0; i < data_size.size(); ++i)
108  if (chunk[i] == 0)
109  throw archive_error("size is zero in one dimension in path: " + path + ALPS_STACKTRACE);
110  if ((path = complete_path(path)).find_last_of('@') == std::string::npos) {
111  if (!is_data(path))
112  throw path_not_found("the path does not exist: " + path + ALPS_STACKTRACE);
113  if (is_scalar(path))
114  throw archive_error("scalar - vector conflict in path: " + path + ALPS_STACKTRACE);
115  detail::data_type data_id(H5Dopen2(context_->file_id_, path.c_str(), H5P_DEFAULT));
116  detail::type_type type_id(H5Dget_type(data_id));
117  detail::type_type native_id(H5Tget_native_type(type_id, H5T_DIR_ASCEND));
118  if (H5Tget_class(native_id) == H5T_STRING && !detail::check_error(H5Tis_variable_str(type_id)))
119  throw std::logic_error("multidimensional dataset of fixed string datas is not implemented (" + path + ")" + ALPS_STACKTRACE);
120  else if (H5Tget_class(native_id) == H5T_STRING) {
121  std::size_t len = std::accumulate(chunk.begin(), chunk.end(), std::size_t(1), std::multiplies<std::size_t>());
122  std::unique_ptr<char * []> raw(
123  new char * [len]
124  );
125  if (std::equal(chunk.begin(), chunk.end(), data_size.begin())) {
126  detail::check_error(H5Dread(data_id, native_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, raw.get()));
127  cast(raw.get(), raw.get() + len, value);
128  detail::check_error(H5Dvlen_reclaim(type_id, detail::space_type(H5Dget_space(data_id)), H5P_DEFAULT, raw.get()));
129  } else {
130  std::vector<hsize_t> offset_hid(offset.begin(), offset.end()),
131  chunk_hid(chunk.begin(), chunk.end());
132  detail::space_type space_id(H5Dget_space(data_id));
133  detail::check_error(H5Sselect_hyperslab(space_id, H5S_SELECT_SET, &offset_hid.front(), NULL, &chunk_hid.front(), NULL));
134  detail::space_type mem_id(H5Screate_simple(static_cast<int>(chunk_hid.size()), &chunk_hid.front(), NULL));
135  detail::check_error(H5Dread(data_id, native_id, mem_id, space_id, H5P_DEFAULT, raw.get()));
136  cast(raw.get(), raw.get() + len, value);
137  detail::check_error(H5Dvlen_reclaim(type_id, mem_id, H5P_DEFAULT, raw.get()));
138  }
139  } else if(detail::hdf5_read_vector_data_helper(value, data_id, native_id, chunk, offset, data_size)) {
140  } else throw wrong_type("invalid type" + ALPS_STACKTRACE);
141  } else {
142  if (!is_attribute(path))
143  throw path_not_found("the path does not exist: " + path + ALPS_STACKTRACE);
144  if (is_scalar(path))
145  throw wrong_type("scalar - vector conflict in path: " + path + ALPS_STACKTRACE);
146  hid_t parent_id;
147  if (is_group(path.substr(0, path.find_last_of('@'))))
148  parent_id = detail::check_error(H5Gopen2(context_->file_id_, path.substr(0, path.find_last_of('@')).c_str(), H5P_DEFAULT));
149  else if (is_data(path.substr(0, path.find_last_of('@') - 1)))
150  parent_id = detail::check_error(H5Dopen2(context_->file_id_, path.substr(0, path.find_last_of('@')).c_str(), H5P_DEFAULT));
151  else
152  throw path_not_found("unknown path: " + path.substr(0, path.find_last_of('@')) + ALPS_STACKTRACE);
153  detail::attribute_type attribute_id(H5Aopen(parent_id, path.substr(path.find_last_of('@') + 1).c_str(), H5P_DEFAULT));
154  detail::type_type type_id(H5Aget_type(attribute_id));
155  detail::type_type native_id(H5Tget_native_type(type_id, H5T_DIR_ASCEND));
156  if (H5Tget_class(native_id) == H5T_STRING && !detail::check_error(H5Tis_variable_str(type_id)))
157  throw std::logic_error("multidimensional dataset of fixed string datas is not implemented (" + path + ")" + ALPS_STACKTRACE);
158  else if (H5Tget_class(native_id) == H5T_STRING) {
159  std::size_t len = std::accumulate(chunk.begin(), chunk.end(), std::size_t(1), std::multiplies<std::size_t>());
160  std::unique_ptr<char *[]> raw(
161  new char * [len]
162  );
163  if (std::equal(chunk.begin(), chunk.end(), data_size.begin())) {
164  detail::check_error(H5Aread(attribute_id, native_id, raw.get()));
165  cast(raw.get(), raw.get() + len, value);
166  } else
167  throw std::logic_error("non continous multidimensional dataset as attributes are not implemented (" + path + ")" + ALPS_STACKTRACE);
168  detail::check_error(H5Dvlen_reclaim(type_id, detail::space_type(H5Aget_space(attribute_id)), H5P_DEFAULT, raw.get()));
169  } else if (H5Tget_class(native_id) == H5T_STRING) {
170  char ** raw = NULL;
171  detail::check_error(H5Aread(attribute_id, native_id, raw));
172  throw std::logic_error("multidimensional dataset of variable len string datas is not implemented (" + path + ")" + ALPS_STACKTRACE);
173  } else if(detail::hdf5_read_vector_attribute_helper(path, value, attribute_id, native_id, chunk, data_size)) {
174  } else throw wrong_type("invalid type" + ALPS_STACKTRACE);
175  if (is_group(path.substr(0, path.find_last_of('@'))))
176  detail::check_group(parent_id);
177  else
178  detail::check_data(parent_id);
179  }
180  }
181  }
182  #define ALPS_HDF5_READ_VECTOR(T) template void archive::read<T>(std::string, T *, std::vector<std::size_t>, std::vector<std::size_t>) const;
183  ALPS_FOREACH_NATIVE_HDF5_TYPE(ALPS_HDF5_READ_VECTOR)
184  }
185 }
alps::hdf5::path_not_found
Definition: errors.hpp:34
ALPS_HDF5_READ_SCALAR
#define ALPS_HDF5_READ_SCALAR(T)
Definition: archive_read.cpp:88
alps::hdf5::wrong_type
Definition: errors.hpp:35
alps::hdf5::archive_closed
Definition: errors.hpp:31
alps::hdf5::ALPS_FOREACH_NATIVE_HDF5_TYPE
ALPS_FOREACH_NATIVE_HDF5_TYPE(ALPS_HDF5_READ_SCALAR)
ONLY_NATIVE
#define ONLY_NATIVE(T, R)
Definition: archive.hpp:56
ALPS_HDF5_FAKE_THREADSAFETY
#define ALPS_HDF5_FAKE_THREADSAFETY
Definition: common.hpp:25
alps::hdf5::archive::read
auto read(std::string path, T *, std::vector< std::size_t >, std::vector< std::size_t >=std::vector< std::size_t >()) const -> typename std::enable_if<!is_native_type< T >::value, void >::type
Definition: archive.hpp:163
alps::cast
U cast(T const &)
Definition: cast.hpp:151
ALPS_STACKTRACE
#define ALPS_STACKTRACE
Definition: stacktrace.hpp:37
alps::is_scalar
Metafunction-predicate: returns true_type if type T is scalar.
Definition: is_scalar.hpp:24
ALPS_HDF5_READ_VECTOR
#define ALPS_HDF5_READ_VECTOR(T)
Definition: archive_read.cpp:182
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