HDF5-CSharp: C# Wrapper for HDF5 library

Hdf5 Wrapper: Set of tools that help in reading and writing hdf5 files for .net environments

Usage

write an object to an HDF5 file

In the example below an object is created with some arrays and other variables The object is written to a file and than read back in a new object.

     private class TestClassWithArray
        {
            public double[] TestDoubles { get; set; }
            public string[] TestStrings { get; set; }
            public int TestInteger { get; set; }
            public double TestDouble { get; set; }
            public bool TestBoolean { get; set; }
            public string TestString { get; set; }
        }
     var testClass = new TestClassWithArray() {
                    TestInteger = 2,
                    TestDouble = 1.1,
                    TestBoolean = true,
                    TestString = "test string",
                    TestDoubles = new double[] { 1.1, 1.2, -1.1, -1.2 },
                    TestStrings = new string[] { "one", "two", "three", "four" }
        };
    long fileId = Hdf5.CreateFile("testFile.H5");

    Hdf5.WriteObject(fileId, testClass, "testObject");

    TestClassWithArray readObject = new TestClassWithArray();

    readObject = Hdf5.ReadObject(fileId, readObject, "testObject");

    Hdf5.CloseFile(fileId);

Write a dataset and append new data to it

    /// <summary>
    /// create a matrix and fill it with numbers
    /// </summary>
    /// <param name="offset"></param>
    /// <returns>the matrix </returns>
    private static double[,]createDataset(int offset = 0)
    {
      var dset = new double[10, 5];
      for (var i = 0; i < 10; i++)
        for (var j = 0; j < 5; j++)
        {
          double x = i + j * 5 + offset;
          dset[i, j] = (j == 0) ? x : x / 10;
        }
      return dset;
    }

    // create a list of matrices
    dsets = new List<double[,]> {
                createDataset(),
                createDataset(10),
                createDataset(20) };

    string filename = Path.Combine(folder, "testChunks.H5");
    long fileId = Hdf5.CreateFile(filename);    

    // create a dataset and append two more datasets to it
    using (var chunkedDset = new ChunkedDataset<double>("/test", fileId, dsets.First()))
    {
      foreach (var ds in dsets.Skip(1))
        chunkedDset.AppendDataset(ds);
    }

    // read rows 9 to 22 of the dataset
    ulong begIndex = 8;
    ulong endIndex = 21;
    var dset = Hdf5.ReadDataset<double>(fileId, "/test", begIndex, endIndex);
    Hdf5.CloseFile(fileId);

for more example see unit test project

Reading H5 File:

you can use the following two method to read the structure of an existing file:

string fileName = @"FileStructure.h5";
var tree = Hdf5.ReadTreeFileStructure(fileName);
var flat = Hdf5.ReadFlatFileStructure(fileName);

in tree-like format you can drill inside the hierarchy of the file while the flat option shows all the name is the groups and datasets.

Additional settings

• Hdf5EntryNameAttribute: control the name of the field/property in the h5 file:

    [AttributeUsage(AttributeTargets.All, AllowMultiple = true)]
   public sealed class Hdf5EntryNameAttribute : Attribute
   {
       public string Name { get; }
       public Hdf5EntryNameAttribute(string name)
       {
           Name = name;
       }
   }

example:

private class TestClass : IEquatable<TestClass>
        {
            public int TestInteger { get; set; }
            public double TestDouble { get; set; }
            public bool TestBoolean { get; set; }
            public string TestString { get; set; }
            [Hdf5EntryNameAttribute("Test_time")]
            public DateTime TestTime { get; set; }
        }

• Time and fields names in H5 file:

    public class Settings
   {
       public DateTimeType DateTimeType { get; set; }
       public bool LowerCaseNaming { get; set; }
   }

   public enum DateTimeType
   {
       Ticks,
       UnixTimeSeconds,
       UnixTimeMilliseconds
   }
   

usage:

       [ClassInitialize()]
       public static void ClassInitialize(TestContext context)
       {
           Hdf5.Settings.LowerCaseNaming = true;
           Hdf5.Settings.DateTimeType = DateTimeType.UnixTimeMilliseconds;
       }
           

• Logging: use can set logging callback via: Hdf5Utils.LogError, Hdf5Utils.LogInfo, etc

public static class Hdf5Utils
   {
       public static Action<string> LogDebug;
       public static Action<string> LogInfo;
       public static Action<string> LogWarning;
       public static Action<string> LogError;
   }

in order to log errors use this code snippet:

            Hdf5.Hdf5Settings.EnableErrorReporting(true);
            Hdf5Utils.LogDebug = (string s) => {...}
            Hdf5Utils.LogInfo = (string s) => {...}
            Hdf5Utils.LogWarning = (string s) => {...}
            Hdf5Utils.LogError = (string s) => {...}

Other resources:

• PureHDF : A pure .NET library that makes reading of HDF5 files (groups, datasets, attributes, links, ...) very easy.