Diff: include/opencv2/flann/hdf5.h

Revision:

0:0e0631af0305

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/include/opencv2/flann/hdf5.h	Fri Jan 29 04:53:38 2021 +0000
@@ -0,0 +1,231 @@
+/***********************************************************************
+ * 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_ */