TOPSPIN 4 Incompatible to read processed files

[witheve17]

Bruker has recently updated there processed file format so when you try to use nmr glue to read a processed file it reds incorrectly the 2rr, and 1r files. I am not sure what changes in the new topspin.

[jjhelmus]

Can you provide an example file which has the new format?

[witheve17]

I have attached the zipped experimental folder 189.zip

[jjhelmus]

I do not have access to TOPSPIN so I do not know how this data is expected to look. Plotting the data using the current development version of nmrglue gives a plot that is similar to the thumb.png file:

Do you have any 1D data and a plot that I could compare with?

[witheve17]

Hi Jonathan,

Thank you for replying. This is how the data is supposed to look. However when I import the data using nmrglue this is what I get for plotting.

This is the code that I use to import the data.

dic, data = ng.bruker.read_pdata('/opt/topspin35pl7/data/Velencia_ABBrushOp/155/pdata/1') udic = ng.bruker.guess_udic(dic, data) uc=ng.fileiobase.uc_from_udic(udic) ppm = uc.ppm_scale() cl = data.std() 2 1.2 ** np.arange(10) fig = plt.figure() ax = fig.add_subplot(111) ax.contour(data, cl, colors='blue') plt.show()

This is the resulting graphic.

[/var/folders/yr/7qr6dznx18vgw9w70hvn_dzh001tkf/T/com.microsoft.Outlook/Content.MSO/96ACEECE.tmp]

How ever in topspin there is just one major peak.

Before this I erase nmrglue from my conda nmr processing environment and reinstalled into the environment using conda. When I evaluate the comman conda list:

nmrglue 0.5 py35_0 jjhelmus is the version that I have,

I am operating Mac Osx HighSierra I use jupyter notebook as my python interface.

Thank you for your attention to this matter.

Best,

Velencia Witherspoon NRC-NIST Postdoctoral Fellow Functional Polymers Group Material Science and Engineering Division National Institute of Standards and Technology Email: vjw@nist.govmailto:vjw@nist.gov Phone: 301-975-4736

From: "Jonathan J. Helmus" notifications@github.com Reply-To: jjhelmus/nmrglue reply@reply.github.com Date: Tuesday, October 16, 2018 at 10:11 PM To: jjhelmus/nmrglue nmrglue@noreply.github.com Cc: "Witherspoon, Velencia J. (Fed)" velencia.witherspoon@nist.gov, Author author@noreply.github.com Subject: Re: [jjhelmus/nmrglue] TOPSPIN 4 Incompatible to read processed files (#86)

I do not have access to TOPSPIN so I do not know how this data is expected to look. Plotting the data using the current development version of nmrglue gives a plot that is similar to the on in the thumb.png file:

[figure_1]https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F1050278%2F47057819-ef470800-d187-11e8-8818-6b84d9b9cc5e.png&data=02%7C01%7Cvelencia.witherspoon%40nist.gov%7Ccc8cb273b96e43b7d23508d633d5d877%7C2ab5d82fd8fa4797a93e054655c61dec%7C1%7C0%7C636753390902384825&sdata=4Y%2Bh8h8NtU0c5tvUM6H2d6xC5vcFL5lLgNzuFG1GsaQ%3D&reserved=0

Do you have any 1D data and a plot that I could compare with?

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[kaustubhmote]

~This seems to be related to #81. The change in Topspin 4.0 is the switch to storing the raw and processed data as floats rather than integers~. I can reproduce the issue with nmrglue v0.5 ~and v0.6~, but it seems to work fine with v0.7-dev.

@witheve17, you will have to download the current development version from github and install it manually to be able to read the data in correctly.

Edit: This works fine with v0.6 so a pip install nmrglue should also suffice here.

The correct reason why this fails with nmrglue 0.5 is a bug in reordering the submatrix, which was fixed by commit 3ee5d7ea. Additionally, to get the the exact data you seen in Topspin, you need to scale the raw data, which is also done in v0.6 by #43.

[jjhelmus]

I agree with @kaustubhmote, upgrading to nmrglue version 0.6 should fix the issue. If you want to install the development version you can do this using pip install git+https://github.com/jjhelmus/nmrglue.git.

[witheve17]

Hi Thank I have completely uninstalled and re-installed nmrglue and the issue has been fixed.

-- Velencia Witherspoon NRC-NIST Postdoctoral Fellow Functional Polymers Group Material Science and Engineering Division National Institute of Standards and Technology Email: vjw@nist.govmailto:vjw@nist.gov Phone: 301-975-4736

From: "Jonathan J. Helmus" notifications@github.com Reply-To: jjhelmus/nmrglue reply@reply.github.com Date: Tuesday, October 23, 2018 at 10:34 AM To: jjhelmus/nmrglue nmrglue@noreply.github.com Cc: "Witherspoon, Velencia J. (Fed)" velencia.witherspoon@nist.gov, Mention mention@noreply.github.com Subject: Re: [jjhelmus/nmrglue] TOPSPIN 4 Incompatible to read processed files (#86)

I agree with @kaustubhmotehttps://github.com/kaustubhmote, upgrading to nmrglue version 0.6 should fix the issue. If you want to install the development version you can do this using pip install git+https://github.com/jjhelmus/nmrglue.git.

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[jjhelmus]

Great to hear!