EstervQrCode 2.0.0
Library for qr code manipulation
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hdf5.h
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,
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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 OPENCV_FLANN_HDF5_H_
31#define OPENCV_FLANN_HDF5_H_
32
34
35#include <hdf5.h>
36
37#include "matrix.h"
38
39
40namespace cvflann
41{
42
43namespace
44{
45
46template<typename T>
47hid_t get_hdf5_type()
48{
49 throw FLANNException("Unsupported type for IO operations");
50}
51
52template<>
53hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
54template<>
55hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
56template<>
57hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
58template<>
59hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
60template<>
61hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
62template<>
63hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
64template<>
65hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
66template<>
67hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
68template<>
69hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
70template<>
71hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
72}
73
74
75#define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
76
77template<typename T>
78void save_to_file(const cvflann::Matrix<T>& dataset, const String& filename, const 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.data );
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
129template<typename T>
130void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const 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 = cvflann::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
162namespace mpi
163{
170template<typename T>
171void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const 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.rows = count[0];
215 dataset.cols = count[1];
216 dataset.data = new T[dataset.rows*dataset.cols];
217
218 plist_id = H5Pcreate(H5P_DATASET_XFER);
219 H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
220 status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset.data);
221 CHECK_ERROR(status, "Error reading dataset");
222
223 H5Pclose(plist_id);
224 H5Sclose(space_id);
225 H5Sclose(memspace_id);
226 H5Dclose(dataset_id);
227 H5Fclose(file_id);
228}
229}
230#endif // HAVE_MPI
231} // namespace cvflann::mpi
232
234
235#endif /* OPENCV_FLANN_HDF5_H_ */
cv::T
InputArrayOfArrays InputArrayOfArrays InputOutputArray InputOutputArray InputOutputArray InputOutputArray Size InputOutputArray InputOutputArray T
Definition calib3d.hpp:1867
count
int count
Definition core_c.h:1413
filename
const char const char ** filename
Definition core_c.h:2630
dims
int dims
Definition core_c.h:464
offset
CvArr CvPoint offset
Definition imgproc_c.h:88
cvflann
Definition flann.hpp:60