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Python

Automatic phase correction of NMR spectra

Martin Fitzpatrick

• 2 min read

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.

import nmrglue as ng

dic, data = ng.bruker.read("/Users/mxf793/Data/THPNH/Extract/1d/103/")
data = ng.bruker.remove_digital_filter(dic, data)

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)





[<matplotlib.lines.Line2D at 0x10cc7d090>]
png
data_fft = ng.proc_base.fft(data)
plt.figure(figsize=(10,4))
plt.plot(data_fft)

[<matplotlib.lines.Line2D at 0x10d0588d0>]
png
data_pc_pm = ng.proc_base.autops(data_fft,'peak_minima')

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

plt.figure(figsize=(10,4))
plt.plot(data_pc_pm)

[<matplotlib.lines.Line2D at 0x10d2e6710>]
png
data_pc_acme = ng.proc_base.autops(data_fft,'acme')

Warning: Maximum number of function evaluations has been exceeded.

plt.figure(figsize=(10,4))
plt.plot(data_pc_acme)

[<matplotlib.lines.Line2D at 0x10d4db850>]
png