001/*****************************************************************************
002 * Copyright by The HDF Group.                                               *
003 * Copyright by the Board of Trustees of the University of Illinois.         *
004 * All rights reserved.                                                      *
005 *                                                                           *
006 * This file is part of the HDF Java Products distribution.                  *
007 * The full copyright notice, including terms governing use, modification,   *
008 * and redistribution, is contained in the files COPYING and Copyright.html. *
009 * COPYING can be found at the root of the source code distribution tree.    *
010 * Or, see https://support.hdfgroup.org/products/licenses.html               *
011 * If you do not have access to either file, you may request a copy from     *
012 * help@hdfgroup.org.                                                        *
013 ****************************************************************************/
014
015package hdf.object.h5;
016
017import hdf.hdf5lib.H5;
018import hdf.hdf5lib.HDF5Constants;
019import hdf.hdf5lib.exceptions.HDF5Exception;
020
021public final class H5Utils {
022
023    private static final org.slf4j.Logger log = org.slf4j.LoggerFactory.getLogger(H5Utils.class);
024
025    /**
026     * Set up a hyperslab selection within a dataset.
027     *
028     * @param did
029     *            IN dataset ID
030     * @param dsetDims
031     *            IN dimensions
032     * @param startDims
033     *            IN start dimensions
034     * @param selectedStride
035     *            IN selected stride values
036     * @param selectedDims
037     *            IN selected dimensions
038     * @param spaceIDs
039     *            IN/OUT memory and file space IDs -- spaceIDs[0]=mspace, spaceIDs[1]=fspace
040     *
041     * @return total number of data points selected
042     *
043     * @throws HDF5Exception
044     *             If there is an error at the HDF5 library level.
045     */
046    public static final long selectHyperslab(long did, long[] dsetDims, long[] startDims, long[] selectedStride,
047            long[] selectedDims, long[] spaceIDs) throws HDF5Exception {
048        if (dsetDims == null) {
049            log.debug("selectHyperslab(): dsetDims is null");
050            return -1;
051        }
052
053        int rank = dsetDims.length;
054        if ((startDims != null) && (startDims.length != rank)) {
055            log.debug("selectHyperslab(): startDims rank didn't match dsetDims rank");
056            return -1;
057        }
058        if ((selectedStride != null) && (selectedStride.length != rank)) {
059            log.debug("selectHyperslab(): selectedStride rank didn't match startDims rank");
060            return -1;
061        }
062        if ((selectedDims != null) && (selectedDims.length != rank)) {
063            log.debug("selectHyperslab(): selectedDims rank didn't match startDims rank");
064            return -1;
065        }
066
067        long lsize = 1;
068
069        boolean isAllSelected = true;
070        for (int i = 0; i < rank; i++) {
071            if (selectedDims != null) {
072                lsize *= selectedDims[i];
073                if (selectedDims[i] < dsetDims[i]) {
074                    isAllSelected = false;
075                }
076            }
077        }
078
079        log.trace("selectHyperslab(): isAllSelected={}", isAllSelected);
080
081        if (isAllSelected) {
082            spaceIDs[0] = HDF5Constants.H5S_ALL;
083            spaceIDs[1] = HDF5Constants.H5S_ALL;
084        }
085        else {
086            spaceIDs[1] = H5.H5Dget_space(did);
087
088            // When a 1D dataspace is used for a chunked dataset, reading is very slow.
089            //
090            // It is a known problem within the HDF5 library.
091            // mspace = H5.H5Screate_simple(1, lsize, null);
092            spaceIDs[0] = H5.H5Screate_simple(rank, selectedDims, null);
093            H5.H5Sselect_hyperslab(spaceIDs[1], HDF5Constants.H5S_SELECT_SET, startDims, selectedStride, selectedDims, null);
094        }
095
096        return lsize;
097    }
098
099    public static final long getTotalSelectedSpacePoints(long did, long[] dsetDims, long[] startDims,
100            long[] selectedStride, long[] selectedDims, long[] spaceIDs) throws HDF5Exception {
101        long totalSelectedSpacePoints = selectHyperslab(did, dsetDims, startDims, selectedStride, selectedDims, spaceIDs);
102
103        log.trace("getTotalSelectedSpacePoints(): selected {} points in dataset's dataspace", totalSelectedSpacePoints);
104
105        if (totalSelectedSpacePoints == 0) {
106            log.debug("getTotalSelectedSpacePoints(): No data to read. Dataset or selected subset is empty.");
107            throw new HDF5Exception("No data to read.\nEither the dataset or the selected subset is empty.");
108        }
109
110        if (totalSelectedSpacePoints < Integer.MIN_VALUE || totalSelectedSpacePoints > Integer.MAX_VALUE) {
111            log.debug("getTotalSelectedSpacePoints(): totalSelectedSpacePoints outside valid Java int range; unsafe cast");
112            throw new HDF5Exception("Invalid int size");
113        }
114
115        if (log.isDebugEnabled()) {
116            // check is storage space is allocated
117            try {
118                long ssize = H5.H5Dget_storage_size(did);
119                log.trace("getTotalSelectedSpacePoints(): Storage space allocated = {} bytes", ssize);
120            }
121            catch (Exception ex) {
122                log.debug("getTotalSelectedSpacePoints(): check if storage space is allocated:", ex);
123            }
124        }
125
126        return totalSelectedSpacePoints;
127    }
128
129}