PureHDF.VOL.Hsds 1.0.0-beta.10

This is a prerelease version of PureHDF.VOL.Hsds.
There is a newer version of this package available.
See the version list below for details.
dotnet add package PureHDF.VOL.Hsds --version 1.0.0-beta.10                
NuGet\Install-Package PureHDF.VOL.Hsds -Version 1.0.0-beta.10                
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="PureHDF.VOL.Hsds" Version="1.0.0-beta.10" />                
For projects that support PackageReference, copy this XML node into the project file to reference the package.
paket add PureHDF.VOL.Hsds --version 1.0.0-beta.10                
#r "nuget: PureHDF.VOL.Hsds, 1.0.0-beta.10"                
#r directive can be used in F# Interactive and Polyglot Notebooks. Copy this into the interactive tool or source code of the script to reference the package.
// Install PureHDF.VOL.Hsds as a Cake Addin
#addin nuget:?package=PureHDF.VOL.Hsds&version=1.0.0-beta.10&prerelease

// Install PureHDF.VOL.Hsds as a Cake Tool
#tool nuget:?package=PureHDF.VOL.Hsds&version=1.0.0-beta.10&prerelease                

PureHDF

GitHub Actions NuGet

A pure C# library without native dependencies that makes reading and writing of HDF5 files (groups, datasets, attributes, ...) very easy.

The minimum supported target framework is .NET Standard 2.0 which includes

  • .NET Framework 4.6.1+
  • .NET Core (all versions)
  • .NET 5+

This library runs on all platforms (ARM, x86, x64) and operating systems (Linux, Windows, MacOS, Raspbian, etc) that are supported by the .NET ecosystem without special configuration.

The implemention follows the HDF5 File Format Specification (HDF5 1.10).

Please read the docs for samples and API documentation.

Installation

dotnet add package PureHDF --prerelease

Quick Start

Reading

// root group
var file = H5File.OpenRead("path/to/file.h5");

// sub group
var group = file.Group("path/to/group");

// attribute
var attribute = group.Attribute("my-attribute");
var attributeData = attribute.Read<int>();

// dataset
var dataset = group.Dataset("my-dataset");
var datasetData = dataset.Read<double>();

See the docs to learn more about data types, multidimensional arrays, chunks, compression, slicing and more.

Writing

The first step is to create a new H5File instance:

var file = new H5File();

A H5File derives from the H5Group type because it represents the root group. H5Group implements the IDictionary interface, where the keys represent the links in an HDF5 file and the value determines the type of the link: either it is another H5Group or a H5Dataset.

You can create an empty group like this:

var group = new H5Group();

If the group should have some datasets, just add them using the dictionary collection initializer - just like with a normal dictionary:

var group = new H5Group()
{
    ["numerical-dataset"] = new double[] { 2.0, 3.1, 4.2 },
    ["string-dataset"] = new string[] { "One", "Two", "Three" }
}

Datasets and attributes can both be created either by instantiating their specific class (H5Dataset, H5Attribute) or by just providing some kind of data. This data can be nearly anything: arrays, scalars, numerical values, strings, anonymous types, enums, complex objects, structs, bool values, etc. However, whenever you want to provide more details like the dimensionality of the attribute or dataset, the chunk layout or the filters to be applied to a dataset, you need to instantiate the appropriate class.

But first, let's see how to add attributes. Attributes cannot be added directly using the dictionary collection initializer because that is only for datasets. However, every H5Group has an Attribute property which accepts our attributes:

var group = new H5Group()
{
    Attributes = new()
    {
        ["numerical-attribute"] = new double[] { 2.0, 3.1, 4.2 },
        ["string-attribute"] = new string[] { "One", "Two", "Three" }
    }
}

The full example with the root group, a subgroup, two datasets and two attributes looks like this:

var file = new H5File()
{
    ["my-group"] = new H5Group()
    {
        ["numerical-dataset"] = new double[] { 2.0, 3.1, 4.2 },
        ["string-dataset"] = new string[] { "One", "Two", "Three" },
        Attributes = new()
        {
            ["numerical-attribute"] = new double[] { 2.0, 3.1, 4.2 },
            ["string-attribute"] = new string[] { "One", "Two", "Three" }
        }
    }
};

The last step is to write the defined file to the drive:

file.Write("path/to/file.h5");

See the docs to learn more about data types, multidimensional arrays, chunks, compression, slicing and more.

Development

The tests of PureHDF are executed against .NET 6 and .NET 7 so these two runtimes are required. Please note that due to an currently unknown reason the writing tests cannot be run in parallel to other tests because some unrelated temp files are in use although they should not be and thus cannot be accessed by the unit tests.

If you are using Visual Studio Code as your IDE, you can simply execute one of the predefined test tasks by selecting Run Tasks from the global menu (Ctrl+Shift+P). The following test tasks are predefined:

  • tests: common
  • tests: writing
  • tests: filters
  • tests: HSDS

The HSDS tests require a python installation to be present on the system with the venv package available.

Comparison Table

Overwhelmed by the number of different HDF 5 libraries? Here is a comparison table:

Note: The following table considers only projects listed on Nuget.org

Name Arch Platform Kind Mode Version License Maintainer Comment
v1.10
PureHDF all all managed rw 1.10.* MIT Apollo3zehn
HDF5-CSharp x86,x64 Win,Lin,Mac HL rw 1.10.6 MIT LiorBanai
SciSharp.Keras.HDF5 x86,x64 Win,Lin,Mac HL rw 1.10.5 MIT SciSharp fork of HDF-CSharp
ILNumerics.IO.HDF5 x64 Win,Lin HL rw ? proprietary IL_Numerics_GmbH probably 1.10
LiteHDF x86,x64 Win,Lin,Mac HL ro 1.10.5 MIT silkfire
hdflib x86,x64 Windows HL wo 1.10.6 MIT bdebree
Mbc.Hdf5Utils x86,x64 Win,Lin,Mac HL rw 1.10.6 Apache-2.0 bqstony
HDF.PInvoke x86,x64 Windows bindings rw 1.8,1.10.6 HDF5 hdf,gheber
HDF.PInvoke.1.10 x86,x64 Win,Lin,Mac bindings rw 1.10.6 HDF5 hdf,Apollo3zehn
HDF.PInvoke.NETStandard x86,x64 Win,Lin,Mac bindings rw 1.10.5 HDF5 surban
v1.8
HDF5DotNet.x64 x64 Windows HL rw 1.8 HDF5 thieum
HDF5DotNet.x86 x86 Windows HL rw 1.8 HDF5 thieum
sharpHDF x64 Windows HL rw 1.8 MIT bengecko
HDF.PInvoke x86,x64 Windows bindings rw 1.8,1.10.6 HDF5 hdf,gheber
hdf5-v120-complete x86,x64 Windows native rw 1.8 HDF5 daniel.gracia
hdf5-v120 x86,x64 Windows native rw 1.8 HDF5 keen

Abbreviations:

Term .NET API Native dependencies
managed high-level none
HL high-level C-library
bindings low-level C-library
native none C-library
Product Compatible and additional computed target framework versions.
.NET net6.0 is compatible.  net6.0-android was computed.  net6.0-ios was computed.  net6.0-maccatalyst was computed.  net6.0-macos was computed.  net6.0-tvos was computed.  net6.0-windows was computed.  net7.0 was computed.  net7.0-android was computed.  net7.0-ios was computed.  net7.0-maccatalyst was computed.  net7.0-macos was computed.  net7.0-tvos was computed.  net7.0-windows was computed.  net8.0 was computed.  net8.0-android was computed.  net8.0-browser was computed.  net8.0-ios was computed.  net8.0-maccatalyst was computed.  net8.0-macos was computed.  net8.0-tvos was computed.  net8.0-windows was computed. 
Compatible target framework(s)
Included target framework(s) (in package)
Learn more about Target Frameworks and .NET Standard.

NuGet packages

This package is not used by any NuGet packages.

GitHub repositories

This package is not used by any popular GitHub repositories.

Version Downloads Last updated
2.1.0 46 6/28/2024
2.0.1 41 6/26/2024
2.0.0 41 6/24/2024
1.0.0 46 6/24/2024
1.0.0-beta.27 45 6/21/2024
1.0.0-beta.26 43 6/18/2024
1.0.0-beta.25 38 6/14/2024
1.0.0-beta.24 38 6/13/2024
1.0.0-beta.23 43 5/30/2024
1.0.0-beta.22 45 5/29/2024
1.0.0-beta.21 45 5/28/2024
1.0.0-beta.20 40 5/28/2024
1.0.0-beta.19 52 5/27/2024
1.0.0-beta.18 52 5/20/2024
1.0.0-beta.17 40 5/16/2024
1.0.0-beta.16 21 5/3/2024
1.0.0-beta.15 30 5/1/2024
1.0.0-beta.14 50 4/25/2024
1.0.0-beta.13 43 4/25/2024
1.0.0-beta.12 55 4/12/2024
1.0.0-beta.11 45 4/10/2024
1.0.0-beta.10 55 3/27/2024
1.0.0-beta.9 61 3/25/2024
1.0.0-beta.8 53 3/20/2024
1.0.0-beta.7 49 3/11/2024
1.0.0-beta.6 49 3/11/2024
1.0.0-beta.5 62 2/2/2024
1.0.0-beta.4 52 1/26/2024
1.0.0-beta.3 51 1/19/2024
1.0.0-beta.2 80 9/15/2023
1.0.0-beta.1 71 9/9/2023
1.0.0-alpha.25 104 3/23/2023