236 lines
7.2 KiB
C++
236 lines
7.2 KiB
C++
/***********************************************************************
|
|
* 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_
|
|
|
|
//! @cond IGNORED
|
|
|
|
#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
|
|
|
|
//! @endcond
|
|
|
|
#endif /* OPENCV_FLANN_HDF5_H_ */
|