OXIESEC PANEL

Name	Size	Modified	Perms
📁 ..	-	10/28/2024 06:50:42 AM	rwxr-xr-x
📄 all_indices.h	5.82 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 allocator.h	5.92 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 any.h	8.06 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 autotuned_index.h	20.36 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 composite_index.h	5.85 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 config.h	1.75 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 defines.h	4.61 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 dist.h	26.9 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 dummy.h	251 bytes	05/12/2017 03:45:27 AM	rw-r--r--
📄 dynamic_bitset.h	4.45 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 flann.hpp	2.31 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 flann_base.hpp	8.65 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 general.h	1.99 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 ground_truth.h	3.23 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 hdf5.h	7.13 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 heap.h	4.01 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 hierarchical_clustering_index.h	25.42 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 index_testing.h	10.56 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 kdtree_index.h	19.22 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 kdtree_single_index.h	19.7 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 kmeans_index.h	36.05 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 linear_index.h	3.61 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 logger.h	3.63 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 lsh_index.h	15.19 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 lsh_table.h	17.51 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 matrix.h	3.21 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 miniflann.hpp	5.75 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 nn_index.h	5.91 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 object_factory.h	2.83 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 params.h	3.2 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 random.h	3.61 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 result_set.h	14.64 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 sampling.h	2.78 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 saving.h	5.64 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 simplex_downhill.h	5.61 KB	05/12/2017 03:45:27 AM	rw-r--r--
📄 timer.h	2.47 KB	05/12/2017 03:45:27 AM	rw-r--r--

Editing: 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.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions
 * are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
 * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
 * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
 * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
 * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
 * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *************************************************************************/

#ifndef OPENCV_FLANN_HDF5_H_
#define OPENCV_FLANN_HDF5_H_

#include <hdf5.h>

#include "matrix.h"

namespace cvflann
{

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; }
}

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

template<typename T>
void save_to_file(const cvflann::Matrix<T>& dataset, const String& filename, const 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.data );
    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(cvflann::Matrix<T>& dataset, const String& filename, const 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 = cvflann::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(cvflann::Matrix<T>& dataset, const String& filename, const 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.rows = count[0];
    dataset.cols = count[1];
    dataset.data = new T[dataset.rows*dataset.cols];

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.data);
    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 cvflann::mpi

#endif /* OPENCV_FLANN_HDF5_H_ */