Read EDF (European Data Format) files in Julia

[Charles Novaes de Santana]

Dear all,

Does any of you know if there is a library or a function to read EDF files with Julia?

http://www.edfplus.info/specs/edf.html

EDF is a format for exchange and storage of multichannel biological and physical signals. In our case, we have polysomnographic data stored in this format.

We use to read this kind of data using functions written in R or Matlab, or to use a free open-source software (edfbrowser) to convert the data to ASCII. But as we always use Julia to do the analysis of the converted data I was wondering if there is something written in Julia to read them in their original format.

Thanks in advance for any help.

Best,

Charles

--

Um axé! :)

--
Charles Novaes de Santana, PhD
http://www.imedea.uib-csic.es/~charles

[Tobias Knopp]

I have recently created functions for reading and writing a similar format (Analyze/Nifti). Its not very complicated.

Something like the following to give you a start:

function load_edf(filename::String)

  header = Dict{ASCIIString,Any}()

  open(filename,"r") do fd
    version =  bytestring( read(fd, Uint8, 8) )
    header["version"] = version

    localPatientId =  bytestring( read(fd, Uint8, 80) )
    header["version"] = localPatientId

    ...

    # here the data would be read
  end
  return data, header
end

[Charles Novaes de Santana]

Hi Tobias,

Thank you for this good start! ;) I was just wondering if there was any built function to do this before starting to do my own function. Tomorrow is Monday, if I don't find any built function I will move towards the direction you indicated ;) The R and Matlab functions I use can also help.

Have a nice Sunday!

Best,

Charles

[Samuele Carcagno]

Hi Charles,

if you start creating your own function it may be useful to look at the
BDF.jl package https://github.com/sam81/BDF.jl which deals with Biosemi
BDF files closely related to EDF files
http://www.biosemi.com/faq/file_format.htm

there is a fork of BDF.jl here https://github.com/codles/BDF.jl that
appears to have started to add support for EDF files, but I haven't
tested it.

Cheers,

Sam

> http://www.edfplus.info/specs/__edf.html

> <http://www.edfplus.info/specs/edf.html>
>
> EDF is a format for exchange and storage of multichannel
> biological and physical signals. In our case, we have
> polysomnographic data stored in this format.
>
> We use to read this kind of data using functions written in R or
> Matlab, or to use a free open-source software (edfbrowser) to
> convert the data to ASCII. But as we always use Julia to do the
> analysis of the converted data I was wondering if there is
> something written in Julia to read them in their original format.
>
> Thanks in advance for any help.
>
> Best,
>
> Charles
> --
> Um axé! :)
>
> --
> Charles Novaes de Santana, PhD

> http://www.imedea.uib-csic.es/__~charles

[Charles Novaes de Santana]

Great news! Thanks for the information, Sam! I will try this before starting something from scratch!

Best,

Charles