Automating jMRUI

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This topic contains 11 replies, has 4 voices, and was last updated by  Lukasz Priba 2 months ago.

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  • #1455

    Amber Howell
    Participant

    Is there a way to use a bash or matlab script to automate processing in jMRUI? I want to do some simple processing (zero-fill, hard-phase, apodize, and then save) numerous spectra, which can get seriously time consuming in the GUI. Is this possible and, if so, do you have any suggestions for getting started?

    Thanks!

    #1456

    Michal Jablonski
    Moderator

    Hi,

    Do it once, save batch file (bottom right side of the screen).
    Later run batch processing. (In Wizard bottom left ). Choose files to process, output directory and your batch file. Run it.

    We are working on an improved version of batch processing, should be available quite soon.

    Best regards

    Michal Jablonski
    jMRUI development team

    #1457

    Amber Howell
    Participant

    Hello! Thank you, that was very helpful. Doing batch processing the wizard completes, but I’m getting some where errors.
    My process is : select .rda file, batch file, and output directory.
    My batch file is:
    example.batch
    ZEROFILLING 2048
    HARDPHASESIGNAL 4.1 0.0
    APODIZE Gaussian 4.0

    The script says zerofilling and hard phasing failed, but apodized worked.

    I saved the batch file directly from the GUI, so I’m not sure why it isn’t processing correctly. Any help would be appreciated!

    #1459

    Michal Jablonski
    Moderator

    Dear Amber,

    There was a small bug there. Already fixed.

    Please find two jar files with plugins that were causing troubles. Replace the jar files directly in your jMRUI installation.

    Download

    Michal Jablonski
    jMRUI development team

    #1464

    Amber Howell
    Participant

    Apodize and Zerofilling worked! However, hardphase is still failing. Could this be the same problem with the jar file?

    Thanks!

    #1466

    Michal Jablonski
    Moderator

    Which version of jMRUI are you using?

    Please try this Download. It seems that nothing was changed recently in hardphase. If the problem persists please inform me.

    MJ

    Michal Jablonski
    jMRUI development team

    #1467

    Amber Howell
    Participant

    I’m using version 5.2. Hardphase is working now, thanks!
    The batch automatically outputs a file into the output directly as a .mrui file. I’ve been saving my files as .txt files so I can copy certain parts of the spectra into another template. Is there a way to save the output as a .txt file or convert the .mrui files to .txt files?

    Thank you so much!

    #1468

    Amber Howell
    Participant

    Just to clarify, the text file contains points on the spectra. I’m extracting one of the peaks from the spectra (just copy/pasting ~600 rows from column C in the .txt file that is generated). So, accessing these values from the .mrui file would also work. Any help would be appreciated!

    #1585

    Candace Fleischer
    Participant

    Hello,
    I am having the same problem with HardPhaseAll and Zerofilling failing when running a batch script. I replaced the two plugins provided above and I am still having this problem. I am running jmrui v5.2 in Linux. I included the error message below. Additionally, the batch script doesn’t end properly so after each iteration, I need to manually quit the batch jmrui processing for the script to continue.

    Thanks!

    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory > HARDPHASEALL -77.9 2.386…
    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory Failed!

    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory > APODIZE Lorentzian 2.0…
    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory Done!

    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory > ZEROFILLING 1024…
    08-Apr-2016 12:04:21 WARNING mrui.MruiLogger warning Plugin cannot be initialised for this command
    java.lang.NullPointerException
    at mrui.preprocessing.zerofilling.ZeroFillingPrepro.beginPreprocessing(Unknown Source)
    at mrui.plugin.preprocessing.PreprocessingPlugin.defaultBatch(Unknown Source)
    at mrui.preprocessing.zerofilling.ZeroFillingPrepro.batchPerform(Unknown Source)
    at mrui.plugin.PluginManager.executeBatch(Unknown Source)
    at mrui.history.Batch.executeLine(Unknown Source)
    at mrui.history.Batch.runABatch(Unknown Source)
    at mrui.history.Batch.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
    08-Apr-2016 12:04:21 INFO mrui.history.BatchDialog appendTextToHistory Failed!

    #1586

    Amber Howell
    Participant

    You’re using slightly different options for apodize and hardphase than I was. The plugins worked for me, but I selected Gaussian for apodize and I selected hardphase > signal individually. I would say that the new plug-ins may not work for those options. Otherwise, I would suggest deleting the two old plugs and pasting in the new ones again.

    Also, are you using this in windows or in linux? I believe the new plugins didn’t work for me in linux, so I’ve been using JMRUI on my windows terminal where they do work.

    For when the batch doesn’t stop, the way I planned on getting around this is to write in a wait command directly into the terminal, find the process id, and then kill that process after wait it done. This has been the only way I could figure out how to get around the batch freezing at the end.

    #1587

    Candace Fleischer
    Participant

    Thanks for your reply, Amber. I am using Linux for the batch analysis. I had to make a new .sh file to run the jmruicl command, which does work, but it doesn’t do the preprocessing correctly.

    Are there plugins that will enable batch pre/processing in Linux?

    #2093

    Lukasz Priba
    Participant

    Hi,

    Has there been any further developments with on closing the cmd after the quantitation is it still done by introducing a pause with a wait and killing the process once it’s done?

    Lukasz

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