open .srs OMNIC #715
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Hello everyone, "WARNING | (UserWarning) Only implemented for rapidscan" Is this implementation already being scheduled? |
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Replies: 5 comments 3 replies
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Hello,
Thanks you for your message.
There is indeed several types of series files (.srs) and for now only the rapid scan type is implemented, or at least for all types of rapid scan files I am aware of....
I can try to extend the reader for your type of file in few weeks, without warranty of success: these binary file formats are proprietary and reading them requires some reverse engineering.
If you are interested can you post a sample .srs file (preferably a few of them) and let us know the type if experiment to which it corresponds ? I will look at it by mid August/end august.
Best regards
Arnaud
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Objet: [spectrochempy/spectrochempy] open .srs OMNIC (Discussion #715)
Hello everyone,
I'm new to this package, but I'm having some issue in opening series ThermoFisher data files (.srs)
It seems that is not implemented yet, since the following warning appears on my console when I try to open one of my file.
"WARNING | (UserWarning) Only implemented for rapidscan"
Is this implementation already being scheduled?
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Hello, I am following up on this thread because I face the same issue (I am new to Spectrochempy and Python in general).
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Both files from the "spectrochempy_data/testdata/irdata/omnic_series" repository from Github. If relevant, here are some information about my system: Thank you for your time and attention. |
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Hello @Micsyl Thank you for your message. There are several .srs format (TGA, kinetics, rapid-scans, .. and probably sub-formats with these categories). So the safest way to update the omnic reader is to use would be to use one of your sample file and comparing the output of spectrochempy with that of OMNIC. Best regards |
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Hello @atravert , Thank you for your answer. Obviously, I have no clue of the precise format of my file. The FTIR machine that I am using does not give much info about it and there is no Omnic reader that I can access; the machine only returns the chemical composition corresponding to the spectra. Here is a link to get a sample file: https://we.tl/t-WqAHwrLAHS Best regards, have a nice day |
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Thank you. Here is the omnic display from your file:
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Hello @Micsyl, I have updated the reader, which is now able to read the set of spectra of your file (and the background if needed). Before pushing this update I'd like to add a test so as to ensure that the reader works fine at each update of spectrochempy or of external libraries used by spectrochempy. Thanks, |
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Hello @atravert, That is very good news, thank you for your efforts. Have a nice day |
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Hello @Micsyl, The update has been pushed to the development branch few days ago (see here for the installation). You can use the following to read your sample file which has been added to the spectrochempy_data repository. # to read the spectra of a high speed series
a = scp.read_srs("irdata/omnic_series/high_speed.srs")
# to read the background:
a = scp.read_srs("irdata/omnic_series/high_speed.srs", return_bg=True)Best regards |
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Hello @Micsyl,
The update has been pushed to the development branch few days ago (see here for the installation). You can use the following to read your sample file which has been added to the spectrochempy_data repository.
Best regards
Arnaud.