Failed to load Bruker Data

[NightflyerX]

Hi, I tried reading a Bruker NMR file, but somehow I only get a weird spectra:

#%matplotlib inline
import matplotlib.pyplot as plt
import nmrglue as ng
import numpy as np
import scipy as sp
import os
import glob

plt.style.use('ggplot')
print("                                            ")
class process_nmr:

    def getpath(self):
        self.filepath = os.path.dirname(os.path.realpath(__file__))

nmr = process_nmr()
nmr.getpath()
d = nmr.filepath

print(d)

path = "./" #Current dir
dirlist = os.listdir(d) #get dirlist
dirlist = list(filter(lambda x : ( x.find(".") == -1 ), dirlist)) #filter files in dirlist

print(dirlist)

root_folder = nmr.filepath 
zero_fill_size = 32768
data = [] # <1>
for folder in dirlist:
    print(folder)
    dic, data = ng.fileio.bruker.read(os.path.join(root_folder,folder))
    # remove the digital filter
    data = ng.bruker.remove_digital_filter(dic, data)

    # process the spectrum
    data = ng.proc_base.zf_size(data, 32768)    # zero fill to 32768 points
    data = ng.proc_base.fft(data)               # Fourier transform
    data = ng.proc_base.ps(data, p0=-50.0)      # phase correction
    data = ng.proc_base.di(data)                # discard the imaginaries
    data = ng.proc_base.rev(data)               # reverse the data


fig = plt.figure(figsize=(12,4))
ax = fig.add_subplot(1,1,1)
#ax.plot(np.arange(0, data.shape[0]), data) # <1>
ax.plot(data) # <1>

plt.show()

RawData from Bruker

[kaustubhmote]

Apart from the correct phasing, and optionally using a different way remove the digital filter, I find that I can read and process the spectrum correctly using nearly the same script as you.

dic, data = ng.bruker.read("./")
datap = ng.proc_base.em(data, lb=1/dic["acqus"]["SW_h"])
datap = ng.proc_base.fft(data)
datap = ng.bruker.remove_digital_filter(dic, datap, post_proc=True)
datap = ng.proc_autophase.autops(datap, fn='acme', disp=False)
datap = ng.proc_base.rev(datap)
udic = ng.bruker.guess_udic(dic, datap, strip_fake=True)
uc = {i: ng.fileiobase.uc_from_udic(udic, dim=i) for i in range(udic["ndim"])}

fig, ax = plt.subplots(figsize=(8, 2))
ax.plot(uc[0].ppm_scale(), datap.real, linewidth=0.5)
ax.set_ylim(-1e7, 1e8)
ax.set_xlim(4.1, 1.0)
ax.set_title("zoomed in to better see the small peaks", fontsize=12)
plt.show()

[NightflyerX]

Wow, thank you so much :) It works like a charm. Adding the integrals like in the examples was still a pain though - but works now.