ACloudViewer  3.9.4
A Modern Library for 3D Data Processing
hdf5.h
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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>
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>
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>
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 {
170 template<typename T>
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_ */
filename
std::string filename
Definition: PointCloudIO.cpp:47
name
std::string name
Definition: FileIOFactory.cpp:129
count
int count
Definition: FileIOFactory.cpp:132
offset
int offset
Definition: FileIOFactory.cpp:135
NULL
#define NULL
Definition: UVUnwrapping.cpp:40
flann::Matrix_::cols
size_t cols
Definition: matrix.h:73
flann::Matrix_::rows
size_t rows
Definition: matrix.h:72
flann::Matrix::ptr
T * ptr() const
Definition: matrix.h:127
CHECK_ERROR
#define CHECK_ERROR(x, y)
Definition: hdf5.h:75
flann::save_to_file
void save_to_file(const flann::Matrix< T > &dataset, const std::string &filename, const std::string &name)
Definition: hdf5.h:78
flann::load_from_file
void load_from_file(flann::Matrix< T > &dataset, const std::string &filename, const std::string &name)
Definition: hdf5.h:130