1 /***********************************************************************
2 * Software License Agreement (BSD License)
3 *
4 * Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
5 * Copyright 2008-2009 David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
6 *
7 * Redistribution and use in source and binary forms, with or without
8 * modification, are permitted provided that the following conditions
9 * are met:
10 *
11 * 1. Redistributions of source code must retain the above copyright
12 * notice, this list of conditions and the following disclaimer.
13 * 2. Redistributions in binary form must reproduce the above copyright
14 * notice, this list of conditions and the following disclaimer in the
15 * documentation and/or other materials provided with the distribution.
16 *
17 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
18 * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
19 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
20 * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
21 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
22 * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
23 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
24 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
25 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
26 * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
27 *************************************************************************/
28
29
30 #ifndef FLANN_HDF5_H_
31 #define FLANN_HDF5_H_
32
33 #include <hdf5.h>
34
35 #include "flann/util/matrix.h"
36
37
38 namespace flann
39 {
40
41 namespace
42 {
43
44 template<typename T>
get_hdf5_type()45 hid_t get_hdf5_type()
46 {
47 throw FLANNException("Unsupported type for IO operations");
48 }
49
50 template<>
51 hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
52 template<>
53 hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
54 template<>
55 hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
56 template<>
57 hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
58 template<>
59 hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
60 template<>
61 hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
62 template<>
63 hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
64 template<>
65 hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
66 template<>
67 hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
68 template<>
69 hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
70 template<>
71 hid_t get_hdf5_type<long double>() { return H5T_NATIVE_LDOUBLE; }
72 }
73
74
75 #define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
76
77 template<typename T>
save_to_file(const flann::Matrix<T> & dataset,const std::string & filename,const std::string & name)78 void save_to_file(const flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
79 {
80
81 #if H5Eset_auto_vers == 2
82 H5Eset_auto( H5E_DEFAULT, NULL, NULL );
83 #else
84 H5Eset_auto( NULL, NULL );
85 #endif
86
87 herr_t status;
88 hid_t file_id;
89 file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
90 if (file_id < 0) {
91 file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
92 }
93 CHECK_ERROR(file_id,"Error creating hdf5 file.");
94
95 hsize_t dimsf[2]; // dataset dimensions
96 dimsf[0] = dataset.rows;
97 dimsf[1] = dataset.cols;
98
99 hid_t space_id = H5Screate_simple(2, dimsf, NULL);
100 hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);
101
102 hid_t dataset_id;
103 #if H5Dcreate_vers == 2
104 dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
105 #else
106 dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
107 #endif
108
109 if (dataset_id<0) {
110 #if H5Dopen_vers == 2
111 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
112 #else
113 dataset_id = H5Dopen(file_id, name.c_str());
114 #endif
115 }
116 CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");
117
118 status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.ptr() );
119 CHECK_ERROR(status, "Error writing to dataset");
120
121 H5Sclose(memspace_id);
122 H5Sclose(space_id);
123 H5Dclose(dataset_id);
124 H5Fclose(file_id);
125
126 }
127
128
129 template<typename T>
load_from_file(flann::Matrix<T> & dataset,const std::string & filename,const std::string & name)130 void load_from_file(flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
131 {
132 herr_t status;
133 hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
134 CHECK_ERROR(file_id,"Error opening hdf5 file.");
135
136 hid_t dataset_id;
137 #if H5Dopen_vers == 2
138 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
139 #else
140 dataset_id = H5Dopen(file_id, name.c_str());
141 #endif
142 CHECK_ERROR(dataset_id,"Error opening dataset in file.");
143
144 hid_t space_id = H5Dget_space(dataset_id);
145
146 hsize_t dims_out[2];
147 H5Sget_simple_extent_dims(space_id, dims_out, NULL);
148
149 dataset = flann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);
150
151 status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
152 CHECK_ERROR(status, "Error reading dataset");
153
154 H5Sclose(space_id);
155 H5Dclose(dataset_id);
156 H5Fclose(file_id);
157 }
158
159
160 #ifdef HAVE_MPI
161
162 namespace mpi
163 {
164 /**
165 * Loads a the hyperslice corresponding to this processor from a hdf5 file.
166 * @param flann_dataset Dataset where the data is loaded
167 * @param filename HDF5 file name
168 * @param name Name of dataset inside file
169 */
170 template<typename T>
load_from_file(flann::Matrix<T> & dataset,const std::string & filename,const std::string & name)171 void load_from_file(flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
172 {
173 MPI_Comm comm = MPI_COMM_WORLD;
174 MPI_Info info = MPI_INFO_NULL;
175
176 int mpi_size, mpi_rank;
177 MPI_Comm_size(comm, &mpi_size);
178 MPI_Comm_rank(comm, &mpi_rank);
179
180 herr_t status;
181
182 hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
183 H5Pset_fapl_mpio(plist_id, comm, info);
184 hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
185 CHECK_ERROR(file_id,"Error opening hdf5 file.");
186 H5Pclose(plist_id);
187 hid_t dataset_id;
188 #if H5Dopen_vers == 2
189 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
190 #else
191 dataset_id = H5Dopen(file_id, name.c_str());
192 #endif
193 CHECK_ERROR(dataset_id,"Error opening dataset in file.");
194
195 hid_t space_id = H5Dget_space(dataset_id);
196 hsize_t dims[2];
197 H5Sget_simple_extent_dims(space_id, dims, NULL);
198
199 hsize_t count[2];
200 hsize_t offset[2];
201
202 hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
203 hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));
204
205 count[0] = cnt;
206 count[1] = dims[1];
207 offset[0] = mpi_rank*item_cnt;
208 offset[1] = 0;
209
210 hid_t memspace_id = H5Screate_simple(2,count,NULL);
211
212 H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
213
214 dataset = flann::Matrix<T>(new T[count[0]*count[1]], count[0], count[1]);
215
216 plist_id = H5Pcreate(H5P_DATASET_XFER);
217 // H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
218 status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset[0]);
219 CHECK_ERROR(status, "Error reading dataset");
220
221 H5Pclose(plist_id);
222 H5Sclose(space_id);
223 H5Sclose(memspace_id);
224 H5Dclose(dataset_id);
225 H5Fclose(file_id);
226 }
227 }
228 #endif // HAVE_MPI
229 } // namespace flann::mpi
230
231 #endif /* FLANN_HDF5_H_ */
232