c# - HDF5 Example code

Question

Using HDF5DotNet, can anyone point me at example code, which will open an hdf5 file, extract the contents of a dataset, and print the contents to standard output?

So far I have the following:

        H5.Open();
        var h5 = H5F.open("example.h5", H5F.OpenMode.ACC_RDONLY);
        var dataset = H5D.open(h5, "/Timings/aaPCBTimes");
        var space = H5D.getSpace(dataset);
        var size = H5S.getSimpleExtentDims(space);

Then it gets a bit confusing.

I actually want to do some processing on the contents of the dataset but I think once I have dump to standard output I can work it out from there.

UPDATE: I've hacked around this sufficient to solve my own problem. I failed to realise a dataset was a multi-array - I thought it was more like a db table. In the unlikely event anyone is interested,

double[,] dataArray = new double[size[0], 6];
var wrapArray = new H5Array<double>(dataArray);
var dataType = H5D.getType(d);
H5D.read(dataset, dataType, wrapArray);
Console.WriteLine(dataArray[0, 0]);

Answer 1

Try this:

using System;
using HDF5DotNet;

namespace CSharpExample1
{
    class Program
    {
    // Function used with 
    static int myFunction(H5GroupId id, string objectName, Object param)
    {
        Console.WriteLine("The object name is {0}", objectName);
        Console.WriteLine("The object parameter is {0}", param);
        return 0;
    }

    static void Main(string[] args)
    {
        try
        {
            // We will write and read an int array of this length.
            const int DATA_ARRAY_LENGTH = 12;

            // Rank is the number of dimensions of the data array.
            const int RANK = 1;

            // Create an HDF5 file.
            // The enumeration type H5F.CreateMode provides only the legal 
            // creation modes.  Missing H5Fcreate parameters are provided
            // with default values.
            H5FileId fileId = H5F.create("myCSharp.h5", 
                                         H5F.CreateMode.ACC_TRUNC);

            // Create a HDF5 group.  
            H5GroupId groupId = H5G.create(fileId, "/cSharpGroup", 0);
            H5GroupId subGroup = H5G.create(groupId, "mySubGroup", 0);   

            // Demonstrate getObjectInfo
            ObjectInfo info = H5G.getObjectInfo(fileId, "/cSharpGroup", true);
            Console.WriteLine("cSharpGroup header size is {0}", info.headerSize);
            Console.WriteLine("cSharpGroup nlinks is {0}", info.nHardLinks);
            Console.WriteLine("cSharpGroup fileno is {0} {1}", 
                 info.fileNumber[0], info.fileNumber[1]);
            Console.WriteLine("cSharpGroup objno is {0} {1}", 
                 info.objectNumber[0], info.objectNumber[1]);
            Console.WriteLine("cSharpGroup type is {0}", info.objectType);


            H5G.close(subGroup);

            // Prepare to create a data space for writing a 1-dimensional 
            // signed integer array.
            ulong[] dims = new ulong[RANK];
            dims[0] = DATA_ARRAY_LENGTH;

            // Put descending ramp data in an array so that we can
            // write it to the file.
            int[] dset_data = new int[DATA_ARRAY_LENGTH];
            for (int i = 0; i < DATA_ARRAY_LENGTH; i++)
                dset_data[i] = DATA_ARRAY_LENGTH - i;

            // Create a data space to accommodate our 1-dimensional array.
            // The resulting H5DataSpaceId will be used to create the 
            // data set.
            H5DataSpaceId spaceId = H5S.create_simple(RANK, dims);

            // Create a copy of a standard data type.  We will use the 
            // resulting H5DataTypeId to create the data set.  We could
            // have  used the HST.H5Type data directly in the call to 
            // H5D.create, but this demonstrates the use of H5T.copy 
            // and the use of a H5DataTypeId in H5D.create.
            H5DataTypeId typeId = H5T.copy(H5T.H5Type.NATIVE_INT);

            // Find the size of the type
            uint typeSize = H5T.getSize(typeId);
            Console.WriteLine("typeSize is {0}", typeSize);

            // Set the order to big endian
            H5T.setOrder(typeId, H5T.Order.BE);

            // Set the order to little endian
            H5T.setOrder(typeId, H5T.Order.LE);

            // Create the data set.
            H5DataSetId dataSetId = H5D.create(fileId, "/csharpExample", 
                                               typeId, spaceId);

            // Write the integer data to the data set.

            H5D.write(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
                              new H5Array<int>(dset_data));

            // If we were writing a single value it might look like this.
            //  int singleValue = 100;
            //  H5D.writeScalar(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT),
            //     ref singleValue);

            // Create an integer array to receive the read data.
            int[] readDataBack = new int[DATA_ARRAY_LENGTH];

            // Read the integer data back from the data set
            H5D.read(dataSetId, new H5DataTypeId(H5T.H5Type.NATIVE_INT), 
                new H5Array<int>(readDataBack));

            // Echo the data
            for(int i=0;i<DATA_ARRAY_LENGTH;i++)
            {
               Console.WriteLine(readDataBack[i]);
            }  

            // Close all the open resources.
            H5D.close(dataSetId);

            // Reopen and close the data sets to show that we can.
            dataSetId = H5D.open(fileId, "/csharpExample");
            H5D.close(dataSetId);
            dataSetId = H5D.open(groupId, "/csharpExample");
            H5D.close(dataSetId);

            H5S.close(spaceId);
            H5T.close(typeId);
            H5G.close(groupId);

            //int x = 10;
            //H5T.enumInsert<int>(typeId, "myString", ref x);
            //H5G.close(groupId);
            H5GIterateDelegate myDelegate;
            myDelegate = myFunction;
            int x = 9;
            int index = H5G.iterate(fileId, "/cSharpGroup",
                myDelegate, x, 0);

            // Reopen the group id to show that we can.
            groupId = H5G.open(fileId, "/cSharpGroup");
            H5G.close(groupId);

            H5F.close(fileId);

            // Reopen and reclose the file.
            H5FileId openId = H5F.open("myCSharp.h5", 
                                       H5F.OpenMode.ACC_RDONLY);
            H5F.close(openId);
        }
        // This catches all the HDF exception classes.  Because each call
        // generates unique exception, different exception can be handled
        // separately.  For example, to catch open errors we could have used
        // catch (H5FopenException openException).
        catch (HDFException e)
        {
            Console.WriteLine(e.Message);
        }

        Console.WriteLine("Processing complete!");
        Console.ReadLine();
    }
}
}