# Using HDF5.jl and reading h5 data to Julia?

**URL:** <https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232>\
**Category:** General Usage\
**Tags:** question, package\
**Created:** [January 19, 2023, 8:31pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232 "2023-01-19T20:31:38Z")\
**Posts on this page:** 10\
**Page:** 1

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**Author:** ![marianoarnaiz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/marianoarnaiz/32/19377_2.png) [@marianoarnaiz](https://discourse.julialang.org/u/marianoarnaiz)\
**Post date:** [January 19, 2023, 8:31pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/1 "2023-01-19T20:31:38Z")

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Hi all!  
I am new to .h5 data, so maybe I can get some help.  
I got some data from my research group. They work in Python and apparently somthin like this works for them:

> import h5py  
> data, time, delta, name = read\_hdf5(fname)

But I can’t read the file, if i run:

> using HDF5  
> data = h5read(“STROMBOLI.h5”)

I get

> HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 1:  
> #000: H5O.c line 128 in H5Oopen(): unable to open object  
> major: Object header  
> minor: Can’t open object  
> #001: H5VLcallback.c line 5386 in H5VL\_object\_open(): object open failed  
> major: Virtual Object Layer  
> minor: Can’t open object  
> #002: H5VLcallback.c line 5353 in H5VL\_\_object\_open(): object open failed  
> major: Virtual Object Layer  
> minor: Can’t open object  
> #003: H5VLnative\_object.c line 58 in H5VL\_\_native\_object\_open(): unable to open object by name  
> major: Object header  
> minor: Can’t open object  
> #004: H5Oint.c line 625 in H5O\_open\_name(): object not found  
> major: Object header  
> minor: Object not found  
> #005: H5Gloc.c line 442 in H5G\_loc\_find(): can’t find object  
> major: Symbol table  
> minor: Object not found  
> #006: H5Gtraverse.c line 837 in H5G\_traverse(): internal path traversal failed  
> major: Symbol table  
> minor: Object not found  
> #007: H5Gtraverse.c line 613 in H5G\_\_traverse\_real(): traversal operator failed  
> major: Symbol table  
> minor: Callback failed  
> #008: H5Gloc.c line 399 in H5G\_\_loc\_find\_cb(): object ‘data’ doesn’t exist  
> major: Symbol table  
> minor: Object not found  
> ERROR: Error opening object //data  
> Stacktrace:  
> [1] error(::String, ::String, ::String, ::String)  
> @ Base ./error.jl:42  
> [2] h5o\_open  
> @ ~/.julia/packages/HDF5/T1b9x/src/HDF5.jl:2334 [inlined]  
> [3] h5o\_open  
> @ ~/.julia/packages/HDF5/T1b9x/src/HDF5.jl:2114 [inlined]  
> [4] o\_open(parent::HDF5File, path::String)  
> @ HDF5 ~/.julia/packages/HDF5/T1b9x/src/HDF5.jl:876  
> [5] getindex  
> @ ~/.julia/packages/HDF5/T1b9x/src/HDF5.jl:887 [inlined]  
> [6] h5read(::String, ::String)  
> @ HDF5 ~/.julia/packages/HDF5/T1b9x/src/HDF5.jl:729  
> [7] top-level scope  
> @ none:1

Help, please!

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<div class="post-metadata">

**Author:** ![tomaklutfu](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/tomaklutfu/32/2411_2.png) [@tomaklutfu](https://discourse.julialang.org/u/tomaklutfu)\
**Post date:** [January 20, 2023, 5:28am UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/2 "2023-01-20T05:28:12Z")

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Can you check the current working folder with `pwd()` and make sure `STROMBOLI.h5` is in that folder?

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**Author:** ![marianoarnaiz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/marianoarnaiz/32/19377_2.png) [@marianoarnaiz](https://discourse.julialang.org/u/marianoarnaiz)\
**Post date:** [January 20, 2023, 5:44am UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/3 "2023-01-20T05:44:12Z")

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Yeap I am in the right place with the right file.

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**Author:** ![mkitti](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkitti/32/12459_2.png) [@mkitti](https://discourse.julialang.org/u/mkitti)\
**Post date:** [January 20, 2023, 6:42am UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/4 "2023-01-20T06:42:55Z")

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What dataset are you trying to read within the HDF5 file? This is supposed to be specified by the second argument to h5read.

Otherwise use `h5open`.

See the documentation for further details:  
[https://juliaio.github.io/HDF5.jl/stable/](https://juliaio.github.io/HDF5.jl/stable/)

I do not see a `read_hdf5` function in the h5py documentation. This must be a custom function.

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**Author:** ![marianoarnaiz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/marianoarnaiz/32/19377_2.png) [@marianoarnaiz](https://discourse.julialang.org/u/marianoarnaiz)\
**Post date:** [January 20, 2023, 12:22pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/5 "2023-01-20T12:22:50Z")

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There is one called data and one called time. How can I access those?

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**Author:** ![PetrKryslUCSD](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/petrkryslucsd/32/215825_2.png) [@PetrKryslUCSD](https://discourse.julialang.org/u/PetrKryslUCSD)\
**Post date:** [January 20, 2023, 3:05pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/6 "2023-01-20T15:05:11Z")

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I use h5open and read. See DataDrop.jl.

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**Author:** ![stephancb](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/stephancb/32/14243_2.png) [@stephancb](https://discourse.julialang.org/u/stephancb)\
**Post date:** [January 20, 2023, 4:07pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/7 "2023-01-20T16:07:21Z")

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I don’t have the `STROMBOLI.h5` file, but an example for exploration of another file might be:

Find out what is in the file:

```julia
julia> h5open("data/eiscat/MAD6400_2022-12-12_manda_60@uhf.hdf5", "r")
🗂️ HDF5.File: (read-only) data/eiscat/MAD6400_2022-12-12_manda_60@uhf.hdf5
├─ 📂 Data
│ └─ 🔢 Table Layout
└─ 📂 Metadata
   ├─ 🔢 Data Parameters
   ├─ 🔢 Experiment Notes
   ├─ 🔢 Experiment Parameters
   ... more metadata

```

Get all datasets without loading them (in case they are big):

```julia
datasets=HDF5.get_datasets(h5file)
6-element Vector{HDF5.Dataset}:
 🔢 HDF5.Dataset: /Data/Table Layout (file: data/eiscat/MAD6400_2022-12-12_manda_60@uhf.hdf5 xfer_mode: 0)
 🔢 HDF5.Dataset: /Metadata/Data Parameters ...
... more metadata sets

```

The actual data is the 1st set, the others are metadata (which are probably important as well).

```julia
julia> h5data=datasets[1]

```

```julia
julia> size(h5data)
(94776,)

```

So I get a vector of named tuples:

```julia
julia> keys(h5data[1])
(:year, :month, :day, :hour, :min, :sec, :recno, :kindat, ....

```

Print parameters `gdalt` and `ne`, the first three vector elements:

```julia
julia> foreach(x -> println("height = $(x[:gdalt]), ne = $(x[:ne])"), h5data[1:3])
height = 20.169572265625, ne = 2.282413824e9
height = 20.5092578125, ne = 1.0e6
height = 20.86676953125, ne = 2.51701408e8

```

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<div class="post-metadata">

**Author:** ![marianoarnaiz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/marianoarnaiz/32/19377_2.png) [@marianoarnaiz](https://discourse.julialang.org/u/marianoarnaiz)\
**Post date:** [January 23, 2023, 7:03pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/8 "2023-01-23T19:03:49Z")

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Hey thanks @stephancb  
This really help :).

Could you tell me how to access the none databases? This is a picture of the structure of my file and I need the info saved in the yellow tags too:

 ![Screenshot 2023-01-23 at 8.01.17 PM](https://global.discourse-cdn.com/julialang/original/3X/8/7/8750ab2834472128ba84dd505554d24720afe3b8.png)

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<div class="post-metadata">

**Author:** ![mkitti](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/mkitti/32/12459_2.png) [@mkitti](https://discourse.julialang.org/u/mkitti)\
**Post date:** [January 23, 2023, 10:08pm UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/9 "2023-01-23T22:08:36Z")

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The things in the yellow tags are attributes.

There are currently two interfaces to get to this information via the `attrs` or `attributes` methods. `attrs` is meant to more closely emulate the h5py interface. See below for more information.

[https://juliaio.github.io/HDF5.jl/stable/interface/attributes/](https://juliaio.github.io/HDF5.jl/stable/interface/attributes/)

What do you mean by the “none databases”?

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<div class="post-metadata">

**Author:** ![marianoarnaiz](https://sea2.discourse-cdn.com/julialang/user_avatar/discourse.julialang.org/marianoarnaiz/32/19377_2.png) [@marianoarnaiz](https://discourse.julialang.org/u/marianoarnaiz)\
**Post date:** [January 24, 2023, 6:28am UTC](https://discourse.julialang.org/t/using-hdf5-jl-and-reading-h5-data-to-julia/93232/10 "2023-01-24T06:28:23Z")

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Oh! They are attributes. I did not know that. There is info stored there and I did not know how to access it. thanks!