C# Wrapper for HDF.PInvoke Library
Get Started
$ dotnet add package HDF5-CSharpReadme
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
V1.17.0 (25.03.2023):
- Update Breaking Change inside Dependecy PureHDF (previously HDF5.NET)
V1.16.3 (25.01.2023):
- Update Dependecy PureHDF (previously HDF5.NET)
V1.16.2 (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
V1.16.1 (12.11.2022):
- Hdf5.WriteCompounds is missing the write attributes fix #248
V1.16.0 (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):
- https://github.com/LiorBanai/HDF5-CSharp/issues/224: Memory increased #224
V1.15.2 (14.07.2022):
- https://github.com/LiorBanai/HDF5-CSharp/issues/213: [NET5+] Add support for newly added primitive types #213
- https://github.com/LiorBanai/HDF5-CSharp/issues/216: Nullable support for "ReadObject" #216 (additional changes)
V1.15.1:
- https://github.com/LiorBanai/HDF5-CSharp/issues/219: Add Support for Reference Nullable Types #219
V1.15.0:
- https://github.com/LiorBanai/HDF5-CSharp/issues/216: Nullable support for "ReadObject" #216
V1.14.3:
- https://github.com/LiorBanai/HDF5-CSharp/issues/215: [BUG] Compound struct - missing memory release #215
V1.14.2:
- https://github.com/LiorBanai/HDF5-CSharp/issues/214: [BUG] OpenAttributeIfExists Tries to open dataset instead of attribute #214
- https://github.com/LiorBanai/HDF5-CSharp/issues/212: [IMPROVEMENT] Add Throw if not exists boolean flag or Mandatory Attribute? #212
V1.14.1:
- https://github.com/LiorBanai/HDF5-CSharp/issues/211: [IMPROVEMENT] don't try to open group if it does not exist #211