Newbie - peakpicking varian nmr -broken? tried github update. varian to pipe flips spectra?

[Harry Robson]

Hi all,

I am a complete newbie to nmrglue (and not an expert on nmr instruments, or python), but figured I would give it a go in the spirit of increasing reproducibility etc.

I am having an issue. Basically I could not get the peakpicking to work as  it was giving an error. But I did notice there was a recently corrected piece of the code which seems along these lines (https://github.com/jjhelmus/nmrglue/pull/196). I have tried updating my version with 

pip install git+https://github.com/jjhelmus/nmrglue

and

pip install git+https://github.com/jjhelmus/nmrglue@global

(I think these are both correct, and repetition is redundant, but I am new to GitHub too)

I now get a new error "slice indices must be integers or None or have an __index__ method". This is from using the following code:

#import modules

import numpy
import scipy
import matplotlib
import IPython
import nmrglue as ng
import numpy as np
import matplotlib.pyplot as plt

#read in, fourier transform, phase, set threshold and peakpick

dic,data = ng.varian.read("foldername_of_FID")

datamod = ng.proc_base.fft(data) 

datamod = ng.proc_autophase.autops(datamod, 'acme')

threshold = 1e6
peaks = ng.peakpick.pick(datamod, pthres=threshold)

So is this just a newbie being dumb? Possibly I didn't update it correctly? 

Kind regards,

Harry.

[Kaustubh Mote]

Hi Harry

Your code is correct, and I can reproduce this error now.

The most likely cause is that `ndimage.find_objects` in scipy now returns slices instead of lists, and we are trying to convert them back to slices, which is no longer correct. The fix is rather simple and I have tested that this does indeed solve the issue. If you open a github issue at this link, I can quickly fix this.

Thanks for pointing this out. I think there may be several other places where such changes may be required due to the changes in numpy/scipy.

Kaustubh.

[Kaustubh Mote]

Hi Harry,

Seems like I introduced this bug with a previous commit (#196). So I fixed it already. You should try to reinstall from github and see that the function works now.

[Harry Robson]

Thanks so much! And thanks for the advice on opening github issues. I'll take note for future

Harry.