H5Ex_T_Commit.java

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/************************************************************
  This example shows how to commit a named datatype to a
  file, and read back that datatype.  The program first
  defines a compound datatype, commits it to a file, then
  closes the file.  Next, it reopens the file, opens the
  datatype, and outputs the names of its fields to the
  screen.
 ************************************************************/

import java.util.EnumSet;
import java.util.HashMap;
import java.util.Map;

import hdf.hdf5lib.H5;
import hdf.hdf5lib.HDF5Constants;

public class H5Ex_T_Commit {
    private static String FILENAME           = "H5Ex_T_Commit.h5";
    private static String DATATYPENAME       = "Sensor_Type";
    protected static final int INTEGERSIZE   = 4;
    protected static final int DOUBLESIZE    = 8;
    protected final static int MAXSTRINGSIZE = 80;

    // Values for the various classes of datatypes
    enum H5T_class {
        H5T_NO_CLASS(HDF5Constants.H5T_NO_CLASS),   // error
        H5T_INTEGER(HDF5Constants.H5T_INTEGER),     // integer types
        H5T_FLOAT(HDF5Constants.H5T_FLOAT),         // floating-point types
        H5T_TIME(HDF5Constants.H5T_TIME),           // date and time types
        H5T_STRING(HDF5Constants.H5T_STRING),       // character string types
        H5T_BITFIELD(HDF5Constants.H5T_BITFIELD),   // bit field types
        H5T_OPAQUE(HDF5Constants.H5T_OPAQUE),       // opaque types
        H5T_COMPOUND(HDF5Constants.H5T_COMPOUND),   // compound types
        H5T_REFERENCE(HDF5Constants.H5T_REFERENCE), // reference types
        H5T_ENUM(HDF5Constants.H5T_ENUM),           // enumeration types
        H5T_VLEN(HDF5Constants.H5T_VLEN),           // Variable-Length types
        H5T_ARRAY(HDF5Constants.H5T_ARRAY),         // Array types
        H5T_COMPLEX(HDF5Constants.H5T_COMPLEX),     // Complex number types
        H5T_NCLASSES(12);                           // this must be last

        private static final Map<Long, H5T_class> lookup = new HashMap<Long, H5T_class>();

        static
        {
            for (H5T_class s : EnumSet.allOf(H5T_class.class))
                lookup.put(s.getCode(), s);
        }

        private long code;

        H5T_class(long layout_type) { this.code = layout_type; }

        public long getCode() { return this.code; }

        public static H5T_class get(long typeclass_id) { return lookup.get(typeclass_id); }
    }

    // The supporting Sensor_Datatype class.
    private static class Sensor_Datatype {
        static int numberMembers = 4;
        static int[] memberDims  = {1, 1, 1, 1};

        String[] memberNames       = {"Serial number", "Location", "Temperature (F)", "Pressure (inHg)"};
        long[] memberFileTypes     = {HDF5Constants.H5T_STD_I32BE, HDF5Constants.H5T_C_S1,
                                      HDF5Constants.H5T_IEEE_F64BE, HDF5Constants.H5T_IEEE_F64BE};
        static int[] memberStorage = {INTEGERSIZE, MAXSTRINGSIZE, DOUBLESIZE, DOUBLESIZE};

        // Data size is the storage size for the members not the object.
        static long getDataSize()
        {
            long data_size = 0;
            for (int indx = 0; indx < numberMembers; indx++)
                data_size += memberStorage[indx] * memberDims[indx];
            return data_size;
        }

        static int getOffset(int memberItem)
        {
            int data_offset = 0;
            for (int indx = 0; indx < memberItem; indx++)
                data_offset += memberStorage[indx];
            return data_offset;
        }
    }

    private static void CreateDataType()
    {
        long file_id              = HDF5Constants.H5I_INVALID_HID;
        long strtype_id           = HDF5Constants.H5I_INVALID_HID;
        long filetype_id          = HDF5Constants.H5I_INVALID_HID;
        Sensor_Datatype datatypes = new Sensor_Datatype();
        // Create a new file using default properties.
        try {
            file_id = H5.H5Fcreate(FILENAME, HDF5Constants.H5F_ACC_TRUNC, HDF5Constants.H5P_DEFAULT,
                                   HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create string datatype.
        try {
            strtype_id = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
            if (strtype_id >= 0)
                H5.H5Tset_size(strtype_id, MAXSTRINGSIZE);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Create the compound datatype for the file. Because the standard
        // types we are using for the file may have different sizes than
        // the corresponding native types, we must manually calculate the
        // offset of each member.
        try {
            filetype_id = H5.H5Tcreate(HDF5Constants.H5T_COMPOUND, Sensor_Datatype.getDataSize());
            if (filetype_id >= 0) {
                for (int indx = 0; indx < Sensor_Datatype.numberMembers; indx++) {
                    long type_id = datatypes.memberFileTypes[indx];
                    if (type_id == HDF5Constants.H5T_C_S1)
                        type_id = strtype_id;
                    H5.H5Tinsert(filetype_id, datatypes.memberNames[indx], Sensor_Datatype.getOffset(indx),
                                 type_id);
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Commit the compound datatype to the file, creating a named datatype.
        try {
            if ((file_id >= 0) && (filetype_id >= 0))
                H5.H5Tcommit(file_id, DATATYPENAME, filetype_id, HDF5Constants.H5P_DEFAULT,
                             HDF5Constants.H5P_DEFAULT, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the file type.
        try {
            if (filetype_id >= 0)
                H5.H5Tclose(filetype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the str type.
        try {
            if (strtype_id >= 0)
                H5.H5Tclose(strtype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            if (file_id >= 0)
                H5.H5Fclose(file_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    private static void ReadDataType()
    {
        long file_id      = HDF5Constants.H5I_INVALID_HID;
        long typeclass_id = HDF5Constants.H5I_INVALID_HID;
        long filetype_id  = HDF5Constants.H5I_INVALID_HID;

        // Open an existing file.
        try {
            file_id = H5.H5Fopen(FILENAME, HDF5Constants.H5F_ACC_RDONLY, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Open named datatype.
        try {
            if (file_id >= 0)
                filetype_id = H5.H5Topen(file_id, DATATYPENAME, HDF5Constants.H5P_DEFAULT);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Output the data to the screen.
        System.out.println("Named datatype:  " + DATATYPENAME + ":");

        // Get datatype class. If it isn't compound, we won't print anything.
        try {
            if (filetype_id >= 0)
                typeclass_id = H5.H5Tget_class(filetype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
        // Read data.
        try {
            if (H5T_class.get(typeclass_id) == H5T_class.H5T_COMPOUND) {
                System.out.println("   Class: H5T_COMPOUND");
                int nmembs = H5.H5Tget_nmembers(filetype_id);
                // Iterate over compound datatype members.
                for (int indx = 0; indx < nmembs; indx++) {
                    String member_name = H5.H5Tget_member_name(filetype_id, indx);
                    System.out.println("    " + member_name);
                }
            }
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Terminate access to the mem type.
        try {
            if (filetype_id >= 0)
                H5.H5Tclose(filetype_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }

        // Close the file.
        try {
            if (file_id >= 0)
                H5.H5Fclose(file_id);
        }
        catch (Exception e) {
            e.printStackTrace();
        }
    }

    public static void main(String[] args)
    {
        H5Ex_T_Commit.CreateDataType();
        // Now we begin the read section of this example. Here we assume
        // the dataset and array have the same name and rank, but can have
        // any size. Therefore we must allocate a new array to read in
        // data using malloc().
        H5Ex_T_Commit.ReadDataType();
    }
}