Field3D
SparseDataReader.h
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1 //----------------------------------------------------------------------------//
2 
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35 
36 //----------------------------------------------------------------------------//
37 
42 //----------------------------------------------------------------------------//
43 
44 #ifndef _INCLUDED_Field3D_SparseDataReader_H_
45 #define _INCLUDED_Field3D_SparseDataReader_H_
46 
47 //----------------------------------------------------------------------------//
48 
49 #include <hdf5.h>
50 #include <string.h> // for memcpy
51 #include "Hdf5Util.h"
52 
53 //----------------------------------------------------------------------------//
54 
55 #include "ns.h"
56 
58 
59 //----------------------------------------------------------------------------//
60 // SparseDataReader
61 //----------------------------------------------------------------------------//
62 
67 template <class Data_T>
69 {
70 public:
71 
72  // Constructors --------------------------------------------------------------
73 
76  SparseDataReader(hid_t location, int valuesPerBlock, int occupiedBlocks);
77 
78  // Main methods --------------------------------------------------------------
79 
82  void readBlock(int idx, Data_T &result);
83 
86  void readBlockList(int idx, const std::vector<Data_T*>& memoryList);
87 
88 private:
89 
90  // Data members --------------------------------------------------------------
91 
96 
98 
99  const std::string k_dataStr;
100 };
101 
102 //----------------------------------------------------------------------------//
103 // SparseDataReader implementations
104 //----------------------------------------------------------------------------//
105 
106 template <class Data_T>
107 SparseDataReader<Data_T>::SparseDataReader(hid_t location, int valuesPerBlock,
108  int occupiedBlocks)
109  : m_valuesPerBlock(valuesPerBlock),
110  k_dataStr("data")
111 {
112  using namespace Hdf5Util;
113  using namespace Exc;
114 
115  hsize_t dims[2];
116  hsize_t memDims[1];
117 
118  // Open the data set
119  m_dataSet.open(location, k_dataStr, H5P_DEFAULT);
120  if (m_dataSet.id() < 0)
121  throw OpenDataSetException("Couldn't open data set: " + k_dataStr);
122 
123  // Get the space and type
126  if (m_fileDataSpace.id() < 0)
127  throw GetDataSpaceException("Couldn't get data space");
128  if (m_dataType.id() < 0)
129  throw GetDataTypeException("Couldn't get data type");
130 
131  // Make the memory data space
132  memDims[0] = m_valuesPerBlock;
133  m_memDataSpace.create(H5S_SIMPLE);
134  H5Sset_extent_simple(m_memDataSpace.id(), 1, memDims, NULL);
135 
136  // Get the dimensions and check they match
137  H5Sget_simple_extent_dims(m_fileDataSpace.id(), dims, NULL);
138  if (dims[1] != static_cast<hsize_t>(m_valuesPerBlock)) {
139  throw FileIntegrityException("Block length mismatch in "
140  "SparseDataReader");
141  }
142  if (dims[0] != static_cast<hsize_t>(occupiedBlocks))
143  throw FileIntegrityException("Block count mismatch in "
144  "SparseDataReader");
145 }
146 
147 //----------------------------------------------------------------------------//
148 
149 template <class Data_T>
150 void SparseDataReader<Data_T>::readBlock(int idx, Data_T &result)
151 {
152  using namespace Hdf5Util;
153  using namespace Exc;
154 
155  hsize_t offset[2];
156  hsize_t count[2];
157  herr_t status;
158 
159  offset[0] = idx; // Index of block
160  offset[1] = 0; // Index of first data in block. Always 0
161  count[0] = 1; // Number of columns to read. Always 1
162  count[1] = m_valuesPerBlock; // Number of values in one column
163 
164  status = H5Sselect_hyperslab(m_fileDataSpace.id(), H5S_SELECT_SET,
165  offset, NULL, count, NULL);
166  if (status < 0) {
167  throw ReadHyperSlabException("Couldn't select slab " +
168  boost::lexical_cast<std::string>(idx));
169  }
170 
171  status = H5Dread(m_dataSet.id(), DataTypeTraits<Data_T>::h5type(),
173  H5P_DEFAULT, &result);
174 }
175 
176 //----------------------------------------------------------------------------//
177 
178 template <class Data_T>
180 (int idxLo, const std::vector<Data_T*>& memoryList)
181 {
182  using namespace Hdf5Util;
183  using namespace Exc;
184 
185  hsize_t offset[2];
186  hsize_t count[2];
187  herr_t status;
188 
189  offset[0] = idxLo; // Index of block
190  offset[1] = 0; // Index of first data in block. Always 0
191  count[0] = memoryList.size(); // Number of columns to read.
192  count[1] = m_valuesPerBlock; // Number of values in one column
193 
194  status = H5Sselect_hyperslab(m_fileDataSpace.id(), H5S_SELECT_SET,
195  offset, NULL, count, NULL);
196  if (status < 0) {
197  throw ReadHyperSlabException("Couldn't select slab " +
198  boost::lexical_cast<std::string>(idxLo));
199  }
200 
201  // Make the memory data space ---
202 
203  Hdf5Util::H5ScopedScreate localMemDataSpace;
204  hsize_t memDims[2];
205  memDims[0] = memoryList.size();
206  memDims[1] = m_valuesPerBlock;
207  localMemDataSpace.create(H5S_SIMPLE);
208  H5Sset_extent_simple(localMemDataSpace.id(), 2, memDims, NULL);
209 
210  // Setup the temporary memory region ---
211 
212  int bytesPerValue = 0;
213  {
214  hid_t t = DataTypeTraits<Data_T>::h5type();
215  if (t == H5T_NATIVE_CHAR)
216  bytesPerValue = 1;
217  else if (t == H5T_NATIVE_SHORT)
218  bytesPerValue = 2;
219  else if (t == H5T_NATIVE_FLOAT)
220  bytesPerValue = 4;
221  else if (t == H5T_NATIVE_DOUBLE)
222  bytesPerValue = 8;
223  }
224 
225  int dim = sizeof(Data_T) / bytesPerValue;
226  std::vector<Data_T> bigblock(memoryList.size() * m_valuesPerBlock/dim);
227 
228  status = H5Dread(m_dataSet.id(),
230  localMemDataSpace.id(),
231  m_fileDataSpace.id(),
232  H5P_DEFAULT, &bigblock[0]);
233 
234  if (status < 0) {
235  throw Hdf5DataReadException("Couldn't read slab " +
236  boost::lexical_cast<std::string>(idxLo));
237  }
238 
239  // Distribute block data into memory slots ---
240  for (size_t i = 0; i < memoryList.size(); ++i) {
241  memcpy(memoryList[i],
242  &bigblock[i * m_valuesPerBlock / dim],
243  bytesPerValue * m_valuesPerBlock);
244  }
245 }
246 
247 //----------------------------------------------------------------------------//
248 
250 
251 //----------------------------------------------------------------------------//
252 
253 #endif
void open(hid_t dataset_id)
Definition: Hdf5Util.h:365
#define FIELD3D_NAMESPACE_HEADER_CLOSE
Definition: ns.h:58
Hdf5Util::H5ScopedScreate m_memDataSpace
Scoped object - opens a dataset on creation and closes it on destruction.
Definition: Hdf5Util.h:381
void readBlockList(int idx, const std::vector< Data_T * > &memoryList)
Reads a series of blocks, storing each block of data in memoryList, which is assumed to contain enoug...
SparseDataReader(hid_t location, int valuesPerBlock, int occupiedBlocks)
Constructor. Requires knowledge of the Hdf5 location where data is stored.
Scoped object - opens a dataset on creation and closes it on destruction.
Definition: Hdf5Util.h:325
Contains various utility functions for Hdf5.
Hdf5Util::H5ScopedDget_space m_fileDataSpace
void open(hid_t dataset_id)
Definition: Hdf5Util.h:393
void readBlock(int idx, Data_T &result)
Reads a block, storing the data in result, which is assumed to contain enough room for m_valuesPerBlo...
const std::string k_dataStr
This class gets used by SparseFieldIO and SparseFileManager to read the block data. On creation it will open the data set and not close it until the object is destroyed.
void open(hid_t parentLocation, const std::string &name, hid_t dapl_id)
Definition: Hdf5Util.h:337
static hid_t h5type()
Hdf5Util::H5ScopedDget_type m_dataType
Scoped object - creates a dataspace on creation and closes it on destruction.
Definition: Hdf5Util.h:213
Hdf5Util::H5ScopedDopen m_dataSet
void create(H5S_class_t type)
Definition: Hdf5Util.h:225
Scoped object - opens a dataset on creation and closes it on destruction.
Definition: Hdf5Util.h:353
hid_t id() const
Query the hid_t value.
Definition: Hdf5Util.h:90
#define FIELD3D_NAMESPACE_OPEN
Definition: ns.h:56