HDF5-CSharp 1.16.2

.NET 6.0 .NET Standard 2.0
dotnet add package HDF5-CSharp --version 1.16.2
NuGet\Install-Package HDF5-CSharp -Version 1.16.2
This command is intended to be used within the Package Manager Console in Visual Studio, as it uses the NuGet module's version of Install-Package.
<PackageReference Include="HDF5-CSharp" Version="1.16.2" />
For projects that support PackageReference, copy this XML node into the project file to reference the package.
paket add HDF5-CSharp --version 1.16.2
#r "nuget: HDF5-CSharp, 1.16.2"
#r directive can be used in F# Interactive, C# scripting and .NET Interactive. Copy this into the interactive tool or source code of the script to reference the package.
// Install HDF5-CSharp as a Cake Addin
#addin nuget:?package=HDF5-CSharp&version=1.16.2

// Install HDF5-CSharp as a Cake Tool
#tool nuget:?package=HDF5-CSharp&version=1.16.2

HDF5-CSharp helps 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" }
        };
    int 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");
    int 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);

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.Hdf5Settings.LowerCaseNaming = true;
           Hdf5.Hdf5Settings.DateTimeType = DateTimeType.UnixTimeMilliseconds;
       }
           
  • Logging: use can set logging callback via: Hdf5Utils.LogError, Hdf5Utils.LogInfo, etc
public static class Hdf5Utils
   {
       public static Action<string> LogError;
       public static Action<string> LogInfo;
       public static Action<string> LogDebug;
       public static Action<string> LogCritical;
   }

in order to log errors use this code snippet:

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

History

V1.15.6.2 (18.11.2022):

  • File close problem #249
  • Hdf5.WriteCompounds is missing the write attributes fix (move write to created compound name and not group id) #248

V1.15.6.1 (12.11.2022):

  • Hdf5.WriteCompounds is missing the write attributes fix #248

V1.16.0.0 (11.09.2022):

  • Add net 7 target framework.

V1.15.4.1 (03.08.2022):

  • Replace net.6.0-windows target with net6.0.

V1.15.3 (23.07.2022):

V1.15.2 (14.07.2022):

V1.15.1:

V1.15.0:

V1.14.3:

V1.14.2:

V1.14.1:

Product Versions
.NET net5.0 net5.0-windows net6.0 net6.0-android net6.0-ios net6.0-maccatalyst net6.0-macos net6.0-tvos net6.0-windows net7.0
.NET Core netcoreapp2.0 netcoreapp2.1 netcoreapp2.2 netcoreapp3.0 netcoreapp3.1
.NET Standard netstandard2.0 netstandard2.1
.NET Framework net461 net462 net463 net47 net471 net472 net48
MonoAndroid monoandroid
MonoMac monomac
MonoTouch monotouch
Tizen tizen40 tizen60
Xamarin.iOS xamarinios
Xamarin.Mac xamarinmac
Xamarin.TVOS xamarintvos
Xamarin.WatchOS xamarinwatchos
Compatible target framework(s)
Additional computed target framework(s)
Learn more about Target Frameworks and .NET Standard.

NuGet packages (1)

Showing the top 1 NuGet packages that depend on HDF5-CSharp:

Package Downloads
TensorFlow.Keras

Keras for .NET Keras is an API designed for human beings, not machines. Keras follows best practices for reducing cognitive load: it offers consistent & simple APIs, it minimizes the number of user actions required for common use cases, and it provides clear & actionable error messages.

GitHub repositories (1)

Showing the top 1 popular GitHub repositories that depend on HDF5-CSharp:

Repository Stars
SciSharp/TensorFlow.NET
.NET Standard bindings for Google's TensorFlow for developing, training and deploying Machine Learning models in C# and F#.
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