hdf5.h

00001 /***********************************************************************
00002  * Software License Agreement (BSD License)
00003  *
00004  * Copyright 2008-2009  Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
00005  * Copyright 2008-2009  David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
00006  *
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00008  * modification, are permitted provided that the following conditions
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00010  *
00011  * 1. Redistributions of source code must retain the above copyright
00012  *    notice, this list of conditions and the following disclaimer.
00013  * 2. Redistributions in binary form must reproduce the above copyright
00014  *    notice, this list of conditions and the following disclaimer in the
00015  *    documentation and/or other materials provided with the distribution.
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00017  * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
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00028 
00029 
00030 #ifndef OPENCV_FLANN_HDF5_H_
00031 #define OPENCV_FLANN_HDF5_H_
00032 
00033 #include <hdf5.h>
00034 
00035 #include "matrix.h"
00036 
00037 
00038 namespace cvflann
00039 {
00040 
00041 namespace
00042 {
00043 
00044 template<typename T>
00045 hid_t get_hdf5_type()
00046 {
00047     throw FLANNException("Unsupported type for IO operations");
00048 }
00049 
00050 template<>
00051 hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
00052 template<>
00053 hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
00054 template<>
00055 hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
00056 template<>
00057 hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
00058 template<>
00059 hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
00060 template<>
00061 hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
00062 template<>
00063 hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
00064 template<>
00065 hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
00066 template<>
00067 hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
00068 template<>
00069 hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
00070 }
00071 
00072 
00073 #define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
00074 
00075 template<typename T>
00076 void save_to_file(const cvflann::Matrix<T>& dataset, const String& filename, const String& name)
00077 {
00078 
00079 #if H5Eset_auto_vers == 2
00080     H5Eset_auto( H5E_DEFAULT, NULL, NULL );
00081 #else
00082     H5Eset_auto( NULL, NULL );
00083 #endif
00084 
00085     herr_t status;
00086     hid_t file_id;
00087     file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
00088     if (file_id < 0) {
00089         file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
00090     }
00091     CHECK_ERROR(file_id,"Error creating hdf5 file.");
00092 
00093     hsize_t     dimsf[2];              // dataset dimensions
00094     dimsf[0] = dataset.rows;
00095     dimsf[1] = dataset.cols;
00096 
00097     hid_t space_id = H5Screate_simple(2, dimsf, NULL);
00098     hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);
00099 
00100     hid_t dataset_id;
00101 #if H5Dcreate_vers == 2
00102     dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
00103 #else
00104     dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
00105 #endif
00106 
00107     if (dataset_id<0) {
00108 #if H5Dopen_vers == 2
00109         dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
00110 #else
00111         dataset_id = H5Dopen(file_id, name.c_str());
00112 #endif
00113     }
00114     CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");
00115 
00116     status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.data );
00117     CHECK_ERROR(status, "Error writing to dataset");
00118 
00119     H5Sclose(memspace_id);
00120     H5Sclose(space_id);
00121     H5Dclose(dataset_id);
00122     H5Fclose(file_id);
00123 
00124 }
00125 
00126 
00127 template<typename T>
00128 void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
00129 {
00130     herr_t status;
00131     hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
00132     CHECK_ERROR(file_id,"Error opening hdf5 file.");
00133 
00134     hid_t dataset_id;
00135 #if H5Dopen_vers == 2
00136     dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
00137 #else
00138     dataset_id = H5Dopen(file_id, name.c_str());
00139 #endif
00140     CHECK_ERROR(dataset_id,"Error opening dataset in file.");
00141 
00142     hid_t space_id = H5Dget_space(dataset_id);
00143 
00144     hsize_t dims_out[2];
00145     H5Sget_simple_extent_dims(space_id, dims_out, NULL);
00146 
00147     dataset = cvflann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);
00148 
00149     status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
00150     CHECK_ERROR(status, "Error reading dataset");
00151 
00152     H5Sclose(space_id);
00153     H5Dclose(dataset_id);
00154     H5Fclose(file_id);
00155 }
00156 
00157 
00158 #ifdef HAVE_MPI
00159 
00160 namespace mpi
00161 {
00162 /**
00163  * Loads a the hyperslice corresponding to this processor from a hdf5 file.
00164  * @param flann_dataset Dataset where the data is loaded
00165  * @param filename HDF5 file name
00166  * @param name Name of dataset inside file
00167  */
00168 template<typename T>
00169 void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
00170 {
00171     MPI_Comm comm  = MPI_COMM_WORLD;
00172     MPI_Info info  = MPI_INFO_NULL;
00173 
00174     int mpi_size, mpi_rank;
00175     MPI_Comm_size(comm, &mpi_size);
00176     MPI_Comm_rank(comm, &mpi_rank);
00177 
00178     herr_t status;
00179 
00180     hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
00181     H5Pset_fapl_mpio(plist_id, comm, info);
00182     hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
00183     CHECK_ERROR(file_id,"Error opening hdf5 file.");
00184     H5Pclose(plist_id);
00185     hid_t dataset_id;
00186 #if H5Dopen_vers == 2
00187     dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
00188 #else
00189     dataset_id = H5Dopen(file_id, name.c_str());
00190 #endif
00191     CHECK_ERROR(dataset_id,"Error opening dataset in file.");
00192 
00193     hid_t space_id = H5Dget_space(dataset_id);
00194     hsize_t dims[2];
00195     H5Sget_simple_extent_dims(space_id, dims, NULL);
00196 
00197     hsize_t count[2];
00198     hsize_t offset[2];
00199 
00200     hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
00201     hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));
00202 
00203     count[0] = cnt;
00204     count[1] = dims[1];
00205     offset[0] = mpi_rank*item_cnt;
00206     offset[1] = 0;
00207 
00208     hid_t memspace_id = H5Screate_simple(2,count,NULL);
00209 
00210     H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
00211 
00212     dataset.rows = count[0];
00213     dataset.cols = count[1];
00214     dataset.data = new T[dataset.rows*dataset.cols];
00215 
00216     plist_id = H5Pcreate(H5P_DATASET_XFER);
00217     H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
00218     status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset.data);
00219     CHECK_ERROR(status, "Error reading dataset");
00220 
00221     H5Pclose(plist_id);
00222     H5Sclose(space_id);
00223     H5Sclose(memspace_id);
00224     H5Dclose(dataset_id);
00225     H5Fclose(file_id);
00226 }
00227 }
00228 #endif // HAVE_MPI
00229 } // namespace cvflann::mpi
00230 
00231 #endif /* OPENCV_FLANN_HDF5_H_ */
00232