Can't use Rainbows to access Chemstation directory and HPLC datafiles.

[ddalland]

Thank you for providing this Python code, which I am hoping to use for a chemistry project. Unfortunately, it is not working for me so far. When I run the following cell in Jupyter notebook to read the Chemstation data in folder 55.D: "import rainbow as rb datadir = rb.read('/Users/ (...) /VTNA-4/55.D')" Datadir only contains a name '55.D' and the metadata: {'vendor': 'Agilent', 'vialpos': '55'}. When I then try to read one of my .ch files (datadir.get_file('dad1C.ch')), I get an error message saying that "Data file dad1C.ch not found in 55.D.". I have also tried to apply the method rb.agilent.chemstation.parse_ch('dad1C.ch'), but this returns None, suggesting that the file cannot be read. Do you know my rainbows is not working in my case? I can access the data using a program called UniChrom, but this is less useful than using Python. A colleague of mine has used rainbows successfully in the way I have attempted, but he has used data from a newer version of the chemstation software, maybe that makes the difference?

PS: the files in my directory 55.D are as follows: ['.ipynb_checkpoints', 'ACQRES.REG', 'dad1.uv', 'dad1A.ch', 'dad1B.ch', 'dad1C.ch', 'dad1D.ch', 'dad1E.ch', 'LCDIAG.REG', 'Report.TXT', 'Report00.CSV', 'REPORT01.CSV', 'REPORT02.CSV', 'REPORT03.CSV', 'REPORT04.CSV', 'REPORT05.CSV', 'RUN.LOG', 'SAMPLE.MAC', 'Untitled.ipynb']

[ekwan]

Would you be able to share the .D file as a zip so we can look at it?

[ddalland]

Yes, sure. Here it is along with another one in case that's useful. Thank you! 55.D.zip 37.D.zip

[ekwan]

My colleague James is looking into this and we will get back to you!

[ekwan]

We looked at this and it seems to be a different format. What version of ChemStation are you using? Are you able to provide a decoded version from UniChrom?

[ddalland]

Thank you for looking into it. The HPLC and chemstation software is of the old type (new at the time of Windows vista I think), but I don't know which format exactly, I can ask my colleagues and get back to you. I have sent pdf's, a csv and some screenshots showing what I got when I opened the .ch and .uv files in 55.D using UniChrom. opened data.zip

[ekwan]

Hi! Thanks very much! Please give us a week or so to look at this. We'll get back to you!

[ddalland]

Hi! Did you get time to have a look at it? I might need to find another solution if you didn't find a way around it. Thanks

[ekwan]

Sorry not yet. We can have a look this week.

On Sun, Nov 26, 2023 at 5:34 AM ddalland @.***> wrote:

Hi! Did you get time to have a look at it? I might need to find another solution if you didn't find a way around it. Thanks

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[ekwan]

(It was Thanksgiving last week, so everyone was with their family.)

On Sun, Nov 26, 2023 at 6:06 AM Eugene Kwan @.***> wrote:

Sorry not yet. We can have a look this week.

On Sun, Nov 26, 2023 at 5:34 AM ddalland @.***> wrote:

Hi! Did you get time to have a look at it? I might need to find another solution if you didn't find a way around it. Thanks

— Reply to this email directly, view it on GitHub https://github.com/evanyeyeye/rainbow/issues/5#issuecomment-1826746884, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABOBNITAAXCODM2CZ7NQSGLYGMLL7AVCNFSM6AAAAAA6X5ZWO6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRWG42DMOBYGQ . You are receiving this because you commented.Message ID: @.***>

[ekwan]

Looks like we fixed the problem. James will post here soon. Have you got some more files we can test on?

[ddalland]

No worries! I hope thanksgiving was great. Thank you for working on it! Here are 4 HPLC sample files where I have opened 2 of the .ch files for each folder and saved the corresponding .csv files and report pdf files. [Uploading HPLC data.zip…]()

[ekwan]

Thanks! Something is wrong with that link...

[ddalland]

Woops, I hope this works: HPLC data.zip

[JMarvi3]

@ddalland Could you take a look at Pull Request #7 to ensure that it resolves your issue?

Also, could we have your permission to use one of your data directories, redacted (identifying information removed), as part of a unit test for Rainbow?

[ddalland]

I have checked, and it does fix it. Thank you! I would not mind if you use any of the data directories for any purpose.

[ekwan]

Closed by PR #7.