Automatic phase correction of NMR spectra

My book Create Simple GUI Applications with Python & Qt5 has been updated! New chapters on the Model View architecture and custom widgets.

This notebook demonstrates automatic phase correction algorithms implemented for nmrglue. Two standard algorithms are implemented:

• ACME algorithm by Chen Li et al. Journal of Magnetic Resonance 158 (2002) 164-168

• Naive peak minima minimisation

The outputs for the two algorithms are shown below. Automatic phase correction can be used through the addition of an autops function to the proc_base set alongside the algorithm name to employ for scoring of phase. Custom algorithms can be provided via the same parameter.

In [1]:
import nmrglue as ng

data = ng.bruker.remove_digital_filter(dic, data)

In [2]:
%matplotlib inline

In [3]:
import matplotlib.pyplot as plt
plt.figure(figsize=(10,4))
plt.plot(data)

/usr/local/lib/python2.7/site-packages/numpy/core/numeric.py:462: ComplexWarning: Casting complex values to real discards the imaginary part
return array(a, dtype, copy=False, order=order)

Out[3]:
[]
In [4]:
data_fft = ng.proc_base.fft(data)
plt.figure(figsize=(10,4))
plt.plot(data_fft)

Out[4]:
[]
In [5]:
data_pc_pm = ng.proc_base.autops(data_fft,'peak_minima')

Optimization terminated successfully.
Current function value: 0.000037
Iterations: 90
Function evaluations: 165

In [6]:
plt.figure(figsize=(10,4))
plt.plot(data_pc_pm)

Out[6]:
[]
In [7]:
data_pc_acme = ng.proc_base.autops(data_fft,'acme')

Warning: Maximum number of function evaluations has been exceeded.

In [8]:
plt.figure(figsize=(10,4))
plt.plot(data_pc_acme)

Out[8]:
[]