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https://github.com/LiorBanai/HDF5-CSharp
C# wrapper for windows/Linux systems for reading and writing H5 files
https://github.com/LiorBanai/HDF5-CSharp
csharp hdf5
Last synced: 3 months ago
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C# wrapper for windows/Linux systems for reading and writing H5 files
- Host: GitHub
- URL: https://github.com/LiorBanai/HDF5-CSharp
- Owner: LiorBanai
- License: mit
- Fork: true (reyntjesr/Hdf5DotnetTools)
- Created: 2019-12-03T11:43:26.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-01-15T08:22:30.000Z (5 months ago)
- Last Synced: 2024-01-15T11:12:57.183Z (5 months ago)
- Topics: csharp, hdf5
- Language: C#
- Homepage:
- Size: 53.3 MB
- Stars: 51
- Watchers: 4
- Forks: 26
- Open Issues: 19
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: license.md
Lists
- awesome-dotnet-datascience - HDF5-CSharp - Set of tools that help in reading and writing hdf5 files for .net environments. (Data loading)
README
HDF5-CSharp: C# Wrapper for HDF5 library 
 
[](https://www.nuget.org/packages/HDF5-CSharp/)
[](https://www.nuget.org/packages/HDF5-CSharp/) [](https://www.paypal.com/donate/?business=MCP57TBRAAVXA&no_recurring=0&item_name=Support+Open+source+Projects+%28Analogy+Log+Viewer%2C+HDF5-CSHARP%2C+etc%29¤cy_code=USD) [](https://ko-fi.com/F1F77IVQT)
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.
```csharp
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
```csharp
///
/// create a matrix and fill it with numbers
///
///
/// the matrix
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 {
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("/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(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:
```csharp
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:
```csharp
[AttributeUsage(AttributeTargets.All, AllowMultiple = true)]
public sealed class Hdf5EntryNameAttribute : Attribute
{
public string Name { get; }
public Hdf5EntryNameAttribute(string name)
{
Name = name;
}
}
```
example:
```csharp
private class TestClass : IEquatable
{
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:
```csharp
public class Settings
{
public DateTimeType DateTimeType { get; set; }
public bool LowerCaseNaming { get; set; }
}
public enum DateTimeType
{
Ticks,
UnixTimeSeconds,
UnixTimeMilliseconds
}
```
usage:
```csharp
[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
```csharp
public static class Hdf5Utils
{
public static Action LogDebug;
public static Action LogInfo;
public static Action LogWarning;
public static Action LogError;
}
```
in order to log errors use this code snippet:
```csharp
Hdf5.Hdf5Settings.EnableErrorReporting(true);
Hdf5Utils.LogDebug = (string s) => {...}
Hdf5Utils.LogInfo = (string s) => {...}
Hdf5Utils.LogWarning = (string s) => {...}
Hdf5Utils.LogError = (string s) => {...}
```
## Other resources:
- [PureHDF](https://github.com/Apollo3zehn/PureHDF) : A pure .NET library that makes reading of HDF5 files (groups, datasets, attributes, links, ...) very easy.