libflann-dev 1.8.4-4.1 / usr / include / flann / io / hdf5.h

/***********************************************************************
 * Software License Agreement (BSD License)
 *
 * Copyright 2008-2009  Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
 * Copyright 2008-2009  David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
 *
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 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright
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 *    notice, this list of conditions and the following disclaimer in the
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#ifndef FLANN_HDF5_H_
#define FLANN_HDF5_H_

#include <hdf5.h>

#include "flann/util/matrix.h"


namespace flann
{

namespace
{

template<typename T>
hid_t get_hdf5_type()
{
    throw FLANNException("Unsupported type for IO operations");
}

template<>
hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
template<>
hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
template<>
hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
template<>
hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
template<>
hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
template<>
hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
template<>
hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
template<>
hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
template<>
hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
template<>
hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
template<>
hid_t get_hdf5_type<long double>() { return H5T_NATIVE_LDOUBLE; }
}


#define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));

template<typename T>
void save_to_file(const flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
{

#if H5Eset_auto_vers == 2
    H5Eset_auto( H5E_DEFAULT, NULL, NULL );
#else
    H5Eset_auto( NULL, NULL );
#endif

    herr_t status;
    hid_t file_id;
    file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
    if (file_id < 0) {
        file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
    }
    CHECK_ERROR(file_id,"Error creating hdf5 file.");

    hsize_t     dimsf[2];              // dataset dimensions
    dimsf[0] = dataset.rows;
    dimsf[1] = dataset.cols;

    hid_t space_id = H5Screate_simple(2, dimsf, NULL);
    hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);

    hid_t dataset_id;
#if H5Dcreate_vers == 2
    dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
#else
    dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
#endif

    if (dataset_id<0) {
#if H5Dopen_vers == 2
        dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
#else
        dataset_id = H5Dopen(file_id, name.c_str());
#endif
    }
    CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");

    status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.ptr() );
    CHECK_ERROR(status, "Error writing to dataset");

    H5Sclose(memspace_id);
    H5Sclose(space_id);
    H5Dclose(dataset_id);
    H5Fclose(file_id);

}


template<typename T>
void load_from_file(flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
{
    herr_t status;
    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
    CHECK_ERROR(file_id,"Error opening hdf5 file.");

    hid_t dataset_id;
#if H5Dopen_vers == 2
    dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
#else
    dataset_id = H5Dopen(file_id, name.c_str());
#endif
    CHECK_ERROR(dataset_id,"Error opening dataset in file.");

    hid_t space_id = H5Dget_space(dataset_id);

    hsize_t dims_out[2];
    H5Sget_simple_extent_dims(space_id, dims_out, NULL);

    dataset = flann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);

    status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
    CHECK_ERROR(status, "Error reading dataset");

    H5Sclose(space_id);
    H5Dclose(dataset_id);
    H5Fclose(file_id);
}


#ifdef HAVE_MPI

namespace mpi
{
/**
 * Loads a the hyperslice corresponding to this processor from a hdf5 file.
 * @param flann_dataset Dataset where the data is loaded
 * @param filename HDF5 file name
 * @param name Name of dataset inside file
 */
template<typename T>
void load_from_file(flann::Matrix<T>& dataset, const std::string& filename, const std::string& name)
{
    MPI_Comm comm  = MPI_COMM_WORLD;
    MPI_Info info  = MPI_INFO_NULL;

    int mpi_size, mpi_rank;
    MPI_Comm_size(comm, &mpi_size);
    MPI_Comm_rank(comm, &mpi_rank);

    herr_t status;

    hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
    H5Pset_fapl_mpio(plist_id, comm, info);
    hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
    CHECK_ERROR(file_id,"Error opening hdf5 file.");
    H5Pclose(plist_id);
    hid_t dataset_id;
#if H5Dopen_vers == 2
    dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
#else
    dataset_id = H5Dopen(file_id, name.c_str());
#endif
    CHECK_ERROR(dataset_id,"Error opening dataset in file.");

    hid_t space_id = H5Dget_space(dataset_id);
    hsize_t dims[2];
    H5Sget_simple_extent_dims(space_id, dims, NULL);

    hsize_t count[2];
    hsize_t offset[2];

    hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
    hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));

    count[0] = cnt;
    count[1] = dims[1];
    offset[0] = mpi_rank*item_cnt;
    offset[1] = 0;

    hid_t memspace_id = H5Screate_simple(2,count,NULL);

    H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);

    dataset = flann::Matrix<T>(new T[count[0]*count[1]], count[0], count[1]);

    plist_id = H5Pcreate(H5P_DATASET_XFER);
//    H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
    status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset[0]);
    CHECK_ERROR(status, "Error reading dataset");

    H5Pclose(plist_id);
    H5Sclose(space_id);
    H5Sclose(memspace_id);
    H5Dclose(dataset_id);
    H5Fclose(file_id);
}
}
#endif // HAVE_MPI
} // namespace flann::mpi

#endif /* FLANN_HDF5_H_ */