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
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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
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19 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
20 * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
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26 * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
27 *************************************************************************/
28
29
30 #ifndef OPENCV_FLANN_HDF5_H_
31 #define OPENCV_FLANN_HDF5_H_
32
33 #include <hdf5.h>
34
35 #include "matrix.h"
36
37
38 namespace cvflann
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 }
71
72
73 #define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
74
75 template<typename T>
save_to_file(const cvflann::Matrix<T> & dataset,const String & filename,const String & name)76 void save_to_file(const cvflann::Matrix<T>& dataset, const String& filename, const String& name)
77 {
78
79 #if H5Eset_auto_vers == 2
80 H5Eset_auto( H5E_DEFAULT, NULL, NULL );
81 #else
82 H5Eset_auto( NULL, NULL );
83 #endif
84
85 herr_t status;
86 hid_t file_id;
87 file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
88 if (file_id < 0) {
89 file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
90 }
91 CHECK_ERROR(file_id,"Error creating hdf5 file.");
92
93 hsize_t dimsf[2]; // dataset dimensions
94 dimsf[0] = dataset.rows;
95 dimsf[1] = dataset.cols;
96
97 hid_t space_id = H5Screate_simple(2, dimsf, NULL);
98 hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);
99
100 hid_t dataset_id;
101 #if H5Dcreate_vers == 2
102 dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
103 #else
104 dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
105 #endif
106
107 if (dataset_id<0) {
108 #if H5Dopen_vers == 2
109 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
110 #else
111 dataset_id = H5Dopen(file_id, name.c_str());
112 #endif
113 }
114 CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");
115
116 status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.data );
117 CHECK_ERROR(status, "Error writing to dataset");
118
119 H5Sclose(memspace_id);
120 H5Sclose(space_id);
121 H5Dclose(dataset_id);
122 H5Fclose(file_id);
123
124 }
125
126
127 template<typename T>
load_from_file(cvflann::Matrix<T> & dataset,const String & filename,const String & name)128 void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
129 {
130 herr_t status;
131 hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
132 CHECK_ERROR(file_id,"Error opening hdf5 file.");
133
134 hid_t dataset_id;
135 #if H5Dopen_vers == 2
136 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
137 #else
138 dataset_id = H5Dopen(file_id, name.c_str());
139 #endif
140 CHECK_ERROR(dataset_id,"Error opening dataset in file.");
141
142 hid_t space_id = H5Dget_space(dataset_id);
143
144 hsize_t dims_out[2];
145 H5Sget_simple_extent_dims(space_id, dims_out, NULL);
146
147 dataset = cvflann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);
148
149 status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
150 CHECK_ERROR(status, "Error reading dataset");
151
152 H5Sclose(space_id);
153 H5Dclose(dataset_id);
154 H5Fclose(file_id);
155 }
156
157
158 #ifdef HAVE_MPI
159
160 namespace mpi
161 {
162 /**
163 * Loads a the hyperslice corresponding to this processor from a hdf5 file.
164 * @param flann_dataset Dataset where the data is loaded
165 * @param filename HDF5 file name
166 * @param name Name of dataset inside file
167 */
168 template<typename T>
load_from_file(cvflann::Matrix<T> & dataset,const String & filename,const String & name)169 void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
170 {
171 MPI_Comm comm = MPI_COMM_WORLD;
172 MPI_Info info = MPI_INFO_NULL;
173
174 int mpi_size, mpi_rank;
175 MPI_Comm_size(comm, &mpi_size);
176 MPI_Comm_rank(comm, &mpi_rank);
177
178 herr_t status;
179
180 hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
181 H5Pset_fapl_mpio(plist_id, comm, info);
182 hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
183 CHECK_ERROR(file_id,"Error opening hdf5 file.");
184 H5Pclose(plist_id);
185 hid_t dataset_id;
186 #if H5Dopen_vers == 2
187 dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
188 #else
189 dataset_id = H5Dopen(file_id, name.c_str());
190 #endif
191 CHECK_ERROR(dataset_id,"Error opening dataset in file.");
192
193 hid_t space_id = H5Dget_space(dataset_id);
194 hsize_t dims[2];
195 H5Sget_simple_extent_dims(space_id, dims, NULL);
196
197 hsize_t count[2];
198 hsize_t offset[2];
199
200 hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
201 hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));
202
203 count[0] = cnt;
204 count[1] = dims[1];
205 offset[0] = mpi_rank*item_cnt;
206 offset[1] = 0;
207
208 hid_t memspace_id = H5Screate_simple(2,count,NULL);
209
210 H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
211
212 dataset.rows = count[0];
213 dataset.cols = count[1];
214 dataset.data = new T[dataset.rows*dataset.cols];
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.data);
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 cvflann::mpi
230
231 #endif /* OPENCV_FLANN_HDF5_H_ */
232