https://github.com/juliaio/hdf5.jl

Save and load data in the HDF5 file format from Julia
https://github.com/juliaio/hdf5.jl

data-storage hacktoberfest hdf5 hdf5-binaries hdf5-files hdf5-library jld julia julia-language mat

Last synced: about 1 month ago
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Save and load data in the HDF5 file format from Julia

• Host: GitHub
• URL: https://github.com/juliaio/hdf5.jl
• Owner: JuliaIO
• License: mit
• Created: 2012-10-01T01:08:41.000Z (about 12 years ago)
• Default Branch: master
• Last Pushed: 2024-06-03T10:12:30.000Z (6 months ago)
• Last Synced: 2024-06-11T17:31:50.374Z (5 months ago)
• Topics: data-storage, hacktoberfest, hdf5, hdf5-binaries, hdf5-files, hdf5-library, jld, julia, julia-language, mat
• Language: Julia
• Homepage: https://juliaio.github.io/HDF5.jl
• Size: 9.73 MB
• Stars: 379
• Watchers: 18
• Forks: 137
• Open Issues: 98
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE.txt

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README

        


  

  



_HDF5 interface for the Julia language_

-

[HDF5](https://www.hdfgroup.org/solutions/hdf5/) is a file format and library for storing and

accessing data, commonly used for scientific data. HDF5 files can be created and read by numerous

[programming languages](https://en.wikipedia.org/wiki/Hierarchical_Data_Format#Interfaces). This

package provides an interface to the HDF5 library for the Julia language.

[![Stable](https://img.shields.io/badge/documentation-blue.svg)](https://JuliaIO.github.io/HDF5.jl/stable)

[![Build Status](https://github.com/JuliaIO/HDF5.jl/workflows/CI/badge.svg?branch=master)](https://github.com/JuliaIO/HDF5.jl/actions)

[![Coverage](https://codecov.io/gh/JuliaIO/HDF5.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/JuliaIO/HDF5.jl)

### Changelog

Please see [HISTORY.md](HISTORY.md) and the [release notes](https://github.com/JuliaIO/HDF5.jl/releases). Most changes have deprecation warnings and may not be listed in the [HISTORY.md](HISTORY.md) file.

### Installation

```julia

julia>]

pkg> add HDF5

```

For custom build instructions please refer to the [documentation](https://juliaio.github.io/HDF5.jl/stable/#Using-custom-or-system-provided-HDF5-binaries).

### Quickstart

```julia

using HDF5

```

To read and write a variable to a file, one approach is to use the filename:

```julia

A = collect(reshape(1:120, 15, 8))

h5write("/tmp/test2.h5", "mygroup2/A", A)

data = h5read("/tmp/test2.h5", "mygroup2/A", (2:3:15, 3:5))

```

where the last line reads back just `A[2:3:15, 3:5]` from the dataset.

More fine-grained control can be obtained using functional syntax:

```julia

h5open("mydata.h5", "w") do file

    write(file, "A", A)  # alternatively, say "@write file A"

end

c = h5open("mydata.h5", "r") do file

    read(file, "A")

end

```

This allows you to add variables as they are generated to an open HDF5 file.

You don't have to use the `do` syntax (`file = h5open("mydata.h5", "w")` works

just fine), but an advantage is that it will automatically close the file (`close(file)`)

for you, even in cases of error.

Julia's high-level wrapper, providing a dictionary-like interface, may

also be of interest:

```julia

using HDF5

h5open("test.h5", "w") do file

    g = create_group(file, "mygroup") # create a group

    g["dset1"] = 3.2                  # create a scalar dataset inside the group

    attributes(g)["Description"] = "This group contains only a single dataset" # an attribute

end

```

Convenience functions for attributes attached to datasets are also provided:

```julia

A = Vector{Int}(1:10)

h5write("bar.h5", "foo", A)

h5writeattr("bar.h5", "foo", Dict("c"=>"value for metadata parameter c","d"=>"metadata d"))

h5readattr("bar.h5", "foo")

```