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flann: drop untested hdf5.h
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Alexander Alekhin
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commit
043e7e3516
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/***********************************************************************
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* Software License Agreement (BSD License)
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*
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* Copyright 2008-2009 Marius Muja (mariusm@cs.ubc.ca). All rights reserved.
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* Copyright 2008-2009 David G. Lowe (lowe@cs.ubc.ca). All rights reserved.
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*
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions
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* are met:
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*
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* 1. Redistributions of source code must retain the above copyright
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* notice, this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright
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* notice, this list of conditions and the following disclaimer in the
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* documentation and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
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* IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
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* OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
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* IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
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* INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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* NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
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* THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*************************************************************************/
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#ifndef OPENCV_FLANN_HDF5_H_
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#define OPENCV_FLANN_HDF5_H_
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#include <hdf5.h>
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#include "matrix.h"
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namespace cvflann
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{
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namespace
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{
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template<typename T>
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hid_t get_hdf5_type()
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{
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throw FLANNException("Unsupported type for IO operations");
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}
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template<>
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hid_t get_hdf5_type<char>() { return H5T_NATIVE_CHAR; }
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template<>
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hid_t get_hdf5_type<unsigned char>() { return H5T_NATIVE_UCHAR; }
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template<>
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hid_t get_hdf5_type<short int>() { return H5T_NATIVE_SHORT; }
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template<>
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hid_t get_hdf5_type<unsigned short int>() { return H5T_NATIVE_USHORT; }
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template<>
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hid_t get_hdf5_type<int>() { return H5T_NATIVE_INT; }
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template<>
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hid_t get_hdf5_type<unsigned int>() { return H5T_NATIVE_UINT; }
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template<>
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hid_t get_hdf5_type<long>() { return H5T_NATIVE_LONG; }
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template<>
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hid_t get_hdf5_type<unsigned long>() { return H5T_NATIVE_ULONG; }
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template<>
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hid_t get_hdf5_type<float>() { return H5T_NATIVE_FLOAT; }
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template<>
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hid_t get_hdf5_type<double>() { return H5T_NATIVE_DOUBLE; }
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}
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#define CHECK_ERROR(x,y) if ((x)<0) throw FLANNException((y));
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template<typename T>
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void save_to_file(const cvflann::Matrix<T>& dataset, const String& filename, const String& name)
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{
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#if H5Eset_auto_vers == 2
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H5Eset_auto( H5E_DEFAULT, NULL, NULL );
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#else
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H5Eset_auto( NULL, NULL );
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#endif
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herr_t status;
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hid_t file_id;
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file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
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if (file_id < 0) {
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file_id = H5Fcreate(filename.c_str(), H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT);
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}
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CHECK_ERROR(file_id,"Error creating hdf5 file.");
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hsize_t dimsf[2]; // dataset dimensions
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dimsf[0] = dataset.rows;
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dimsf[1] = dataset.cols;
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hid_t space_id = H5Screate_simple(2, dimsf, NULL);
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hid_t memspace_id = H5Screate_simple(2, dimsf, NULL);
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hid_t dataset_id;
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#if H5Dcreate_vers == 2
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dataset_id = H5Dcreate2(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
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#else
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dataset_id = H5Dcreate(file_id, name.c_str(), get_hdf5_type<T>(), space_id, H5P_DEFAULT);
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#endif
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if (dataset_id<0) {
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#if H5Dopen_vers == 2
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dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
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#else
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dataset_id = H5Dopen(file_id, name.c_str());
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#endif
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}
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CHECK_ERROR(dataset_id,"Error creating or opening dataset in file.");
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status = H5Dwrite(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, H5P_DEFAULT, dataset.data );
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CHECK_ERROR(status, "Error writing to dataset");
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H5Sclose(memspace_id);
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H5Sclose(space_id);
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H5Dclose(dataset_id);
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H5Fclose(file_id);
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}
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template<typename T>
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void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
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{
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herr_t status;
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hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
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CHECK_ERROR(file_id,"Error opening hdf5 file.");
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hid_t dataset_id;
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#if H5Dopen_vers == 2
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dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
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#else
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dataset_id = H5Dopen(file_id, name.c_str());
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#endif
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CHECK_ERROR(dataset_id,"Error opening dataset in file.");
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hid_t space_id = H5Dget_space(dataset_id);
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hsize_t dims_out[2];
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H5Sget_simple_extent_dims(space_id, dims_out, NULL);
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dataset = cvflann::Matrix<T>(new T[dims_out[0]*dims_out[1]], dims_out[0], dims_out[1]);
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status = H5Dread(dataset_id, get_hdf5_type<T>(), H5S_ALL, H5S_ALL, H5P_DEFAULT, dataset[0]);
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CHECK_ERROR(status, "Error reading dataset");
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H5Sclose(space_id);
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H5Dclose(dataset_id);
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H5Fclose(file_id);
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}
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#ifdef HAVE_MPI
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namespace mpi
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{
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/**
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* Loads a the hyperslice corresponding to this processor from a hdf5 file.
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* @param flann_dataset Dataset where the data is loaded
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* @param filename HDF5 file name
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* @param name Name of dataset inside file
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*/
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template<typename T>
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void load_from_file(cvflann::Matrix<T>& dataset, const String& filename, const String& name)
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{
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Info info = MPI_INFO_NULL;
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int mpi_size, mpi_rank;
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MPI_Comm_size(comm, &mpi_size);
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MPI_Comm_rank(comm, &mpi_rank);
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herr_t status;
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hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
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H5Pset_fapl_mpio(plist_id, comm, info);
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hid_t file_id = H5Fopen(filename.c_str(), H5F_ACC_RDWR, plist_id);
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CHECK_ERROR(file_id,"Error opening hdf5 file.");
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H5Pclose(plist_id);
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hid_t dataset_id;
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#if H5Dopen_vers == 2
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dataset_id = H5Dopen2(file_id, name.c_str(), H5P_DEFAULT);
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#else
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dataset_id = H5Dopen(file_id, name.c_str());
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#endif
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CHECK_ERROR(dataset_id,"Error opening dataset in file.");
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hid_t space_id = H5Dget_space(dataset_id);
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hsize_t dims[2];
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H5Sget_simple_extent_dims(space_id, dims, NULL);
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hsize_t count[2];
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hsize_t offset[2];
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hsize_t item_cnt = dims[0]/mpi_size+(dims[0]%mpi_size==0 ? 0 : 1);
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hsize_t cnt = (mpi_rank<mpi_size-1 ? item_cnt : dims[0]-item_cnt*(mpi_size-1));
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count[0] = cnt;
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count[1] = dims[1];
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offset[0] = mpi_rank*item_cnt;
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offset[1] = 0;
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hid_t memspace_id = H5Screate_simple(2,count,NULL);
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H5Sselect_hyperslab(space_id, H5S_SELECT_SET, offset, NULL, count, NULL);
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dataset.rows = count[0];
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dataset.cols = count[1];
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dataset.data = new T[dataset.rows*dataset.cols];
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plist_id = H5Pcreate(H5P_DATASET_XFER);
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H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
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status = H5Dread(dataset_id, get_hdf5_type<T>(), memspace_id, space_id, plist_id, dataset.data);
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CHECK_ERROR(status, "Error reading dataset");
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H5Pclose(plist_id);
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H5Sclose(space_id);
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H5Sclose(memspace_id);
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H5Dclose(dataset_id);
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H5Fclose(file_id);
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}
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}
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#endif // HAVE_MPI
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} // namespace cvflann::mpi
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#endif /* OPENCV_FLANN_HDF5_H_ */
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