Question

Does anybody know a simple library to read data from HDF files in .NET framework?

Answer 1

When I was working on this problem a while ago, I couldn’t find anything for HDF4 for .NET. (Which I suppose makes sense since the HDF4 isn’t really supported any more and HDF4 was first created around 1995.)

What I ended up doing was rolling my own library to do very specific commands to communicate the HDF files. Much of it isn’t worth sharing, but the following might help with the P/Invoke signatures (not all of them may have been tested, etc.).

public class HDF4
{
    #region DLL Imports
    private const string HDF4DLL = "hm421m.dll";

    #region file / dataset access

    [DllImport(HDF4DLL)]
    public static extern int SDcreate(int sd_id, string name, DataTypeDefinitions data_type, int rank, int[] dimsizes);

    [DllImport(HDF4DLL)]
    public static extern int SDstart(string filename, AccessCodes access_mode);

    [DllImport(HDF4DLL)]
    public static extern short SDendaccess(int sds_id);

    [DllImport(HDF4DLL)]
    public static extern short SDend(int sd_id);

    #endregion

    #region data access

    [DllImport(HDF4DLL)]
    public static extern int SDselect(int sd_id, int sds_index);

    [DllImport(HDF4DLL)]
    public static extern int SDreaddata(int sds_id, int[] start, int[] stride, int[] edge, IntPtr buffer);

    [DllImport(HDF4DLL)]
    public static extern int SDwritedata(int sds_id, int[] start, int[] stride, int[] edge, IntPtr buffer);

    [DllImport(HDF4DLL)]
    public static extern short SDgetdatastrs(int sds_id, StringBuilder label, StringBuilder unit, StringBuilder format, int length);

    [DllImport(HDF4DLL)]
    public static extern short SDsetdatastrs(int sds_id, string label, string unit, string format, string coordsys);

    #endregion

    #region dim

    [DllImport(HDF4DLL)]
    public static extern int SDgetdimid(int sds_id, int dim_index);

    [DllImport(HDF4DLL)]
    public static extern short SDdiminfo(int dim_id, StringBuilder name, out int size, out DataTypeDefinitions datay_type, out int num_attrs);

    [DllImport(HDF4DLL)]
    public static extern short SDgetdimstrs(int dim_id, StringBuilder label, StringBuilder unit, StringBuilder format, int length);

    [DllImport(HDF4DLL)]
    public static extern short SDgetdimscale(int dim_id, IntPtr data);

    [DllImport(HDF4DLL)]
    public static extern short SDsetdimname(int dim_id, string dim_name);

    [DllImport(HDF4DLL)]
    public static extern short SDsetdimscale(int dim_id, int count, DataTypeDefinitions data_type, IntPtr data);

    [DllImport(HDF4DLL)]
    public static extern short SDsetdimstrs(int dim_id, string label, string unit, string format);

    #endregion

    #region lookups / checks

    [DllImport(HDF4DLL)]
    public static extern int SDcheckempty(int sds_id, out bool emptySDS);

    [DllImport(HDF4DLL)]
    public static extern int SDnametoindex(int sd_id, string sds_name);

    [DllImport(HDF4DLL)]
    public static extern int SDfileinfo(int sd_id, out int num_datasets, out int num_global_attrs);

    [DllImport(HDF4DLL)]
    public static extern short SDgetinfo(int sds_id, StringBuilder sds_name, out int rank, [In, Out] int[] dimsizes, out DataTypeDefinitions data_type,
        out int num_attrs);

    [DllImport(HDF4DLL)]
    public static extern bool SDiscoordvar(int sds_id);


    #endregion

    #region attr

    [DllImport(HDF4DLL)]
    public static extern int SDfindattr(int obj_id, string attr_name);

    [DllImport(HDF4DLL)]
    public static extern short SDattrinfo(int obj_id, int attr_index, StringBuilder attr_name, out DataTypeDefinitions data_type, out int count);

    [DllImport(HDF4DLL)]
    public static extern short SDreadattr(int obj_id, int attr_index, StringBuilder attr_buff);

    [DllImport(HDF4DLL)]
    public static extern short SDsetattr(int obj_id, string attr_name, DataTypeDefinitions data_type, int count, StringBuilder values);

    #endregion

    #endregion

    #region Enums / Consts

    public const uint DFNT_NATIVE = 4096;
    public const int MAX_VAR_DIMS = 32;

    [Flags]
    public enum DataTypeDefinitions : uint
    {
        DFNT_CHAR8      = 4,
        DFNT_CHAR       = 4,
        DFNT_UCHAR8     = 3,
        DFNT_UCHAR      = 3,
        DFNT_INT8       = 20,
        DFNT_UINT8      = 21,
        DFNT_INT16      = 22,
        DFNT_UINT16     = 23,
        DFNT_INT32      = 24,
        DFNT_UINT32     = 25,
        DFNT_FLOAT32    = 5,
        DFNT_FLOAT64    = 6,
        DFNT_NINT8      = DFNT_NATIVE | DFNT_INT8,
        DFNT_NUINT8     = DFNT_NATIVE | DFNT_UINT8,
        DFNT_NINT16     = DFNT_NATIVE | DFNT_INT16,
        DFNT_NUINT16    = DFNT_NATIVE | DFNT_UINT16,
        DFNT_NINT32     = DFNT_NATIVE | DFNT_INT32,
        DFNT_NUINT32    = DFNT_NATIVE | DFNT_UINT32,
        DFNT_NFLOAT32   = DFNT_NATIVE | DFNT_FLOAT32,
        DFNT_NFLOAT64   = DFNT_NATIVE | DFNT_FLOAT64
    }

    public enum AccessCodes
    {
        DFACC_READ      = 1,
        DFACC_WRITE     = 2,
        DFACC_CREATE    = 4,
        DFACC_ALL       = 7,
        DFACC_RDONLY    = 1,
        DFACC_RDWR      = 3
    }

    #endregion

    #region Helper Functions

    public static double[] SDgetdimscaledouble(int dim_id, int size)
    {
        double d = 0;
        IntPtr p = Marshal.AllocHGlobal(Marshal.SizeOf(d) * size);
        SDgetdimscale(dim_id, p);
        double[] dest = new double[size];
        Marshal.Copy(p, dest, 0, size);
        Marshal.FreeHGlobal(p);
        return dest;
    }

    public static void SDsetdimscaledouble(int dim_id, double[] d)
    {
        IntPtr p = Marshal.AllocHGlobal(Marshal.SizeOf(d[0])*d.Length);
        Marshal.Copy(d, 0, p, d.Length);
        int res = SDsetdimscale(dim_id, d.Length, DataTypeDefinitions.DFNT_FLOAT64, p);
        Marshal.FreeHGlobal(p);
    }

    public static double SDreaddouble(int sds_id, int[] start, int[] edge)
    {
        double d = 0;
        IntPtr p = Marshal.AllocHGlobal(Marshal.SizeOf(d));
        SDreaddata(sds_id, start, null, edge, p);
        double[] dest = new double[1];
        Marshal.Copy(p, dest, 0, 1);
        d = dest[0];
        Marshal.FreeHGlobal(p);
        return d;
    }

    public static void SDwritedouble(int sds_id, int[] start, int[] edge, double d)
    {
        IntPtr p = Marshal.AllocHGlobal(Marshal.SizeOf(d));
        double[] a = new double[1];
        a[0] = d;
        Marshal.Copy(a, 0, p, 1);
        int res = SDwritedata(sds_id, start, null, edge, p);
        Marshal.FreeHGlobal(p);
    }

    #endregion
}

So from this, you could create objects for the File, DataSets, Dimensions, Attributes, etc. For the file, here’s a snippet:

public class HDFFile : IDisposable
{
    // snip

    public static HDFFile New(string fullfilename)
    {
        HDFFile hdf = new HDFFile(fullfilename);

        hdf._sdId = HDF4.SDstart(fullfilename, HDF4.AccessCodes.DFACC_CREATE);

        return hdf;
    }

    public static HDFFile Open(string fullfilename)
    {
        HDFFile hdf = new HDFFile(fullfilename);

        hdf._sdId = HDF4.SDstart(fullfilename, HDF4.AccessCodes.DFACC_RDWR);

        if (hdf._sdId == -1)
            throw new Exception("Could not open " + fullfilename);

        hdf.Load();

        return hdf;
    }

    private void Load()
    {
        int num_ds = 0;
        int num_global = 0;
        HDF4.SDfileinfo(_sdId, out num_ds, out num_global);

        for (int i = 0; i < num_ds; i++)
        {
            HDFDataSet hds = HDFDataSet.Load(_sdId, i);
            if (!string.IsNullOrEmpty(hds.Name))
                _dataSets.Add(hds);
        }

        _attributes = HDFAttribute.Load(_sdId, num_global);
    }

    // snip
}