Read SIMPSON files with SimPYson

from simpyson.io import SimpReader
import matplotlib.pyplot as plt

In the examples folder, you can find the files ethanol.in, ethanol.fid, and ethanol.spe.

• ethanol.in is a standard input file for a SIMPSON simulation of the ethanol molecule.
• ethanol.fid represents the simulated free induction decay (FID) of the ethanol molecule.
• ethanol.spe represents the NMR spectra of the ethanol molecule.

SimPYson provides the SimpReader class, which reads a SIMPSON fid, spe and xreim files. When a fid file is read SimpReader creates a Python object with the following data:

• real - The real part of the FID.
• imag - The imaginary part of the FID.
• np - The number of points.
• sw - The spectral width.
• time - The time in milliseconds.

fid = SimpReader('../../examples/ethanol.fid', format='fid')

for key, values in fid.data.items():
    print(key, values)

real [95.9999136 63.5468932 20.9678205 ...  0.         0.         0.       ]
imag [ 0.        52.0761046 48.2650021 ...  0.         0.         0.       ]
np 4096.0
sw 10000.0
time [0.00000000e+00 1.00024420e+00 2.00048840e+00 ... 4.09399951e+03
 4.09499976e+03 4.09600000e+03]

The data can be easily plotted using matplotlib

plt.plot(fid.data['time'], fid.data['real'])
plt.xlabel('Time (ms)')

Text(0.5, 0, 'Time (ms)')

When reading spe files the following data is extracted:

• real - The real part of the spectrum.
• imag - The imaginary part of the spectrum.
• np - The number of points.
• sw - The spectral width.
• hz - The frequency in Hz.

spe = SimpReader('../../examples/ethanol.spe', format='spe')

for key, value in spe.data.items():
    print(key, value)

real [0.18006085 0.19032725 0.1798519  ... 0.19060431 0.18027098 0.19046516]
imag [-20.1918974 -20.1791859 -20.0945303 ... -20.3742075 -20.2894344
 -20.2766117]
np 4096.0
sw 10000.0
hz [-5000.         -4997.55799756 -4995.11599512 ...  4995.11599512
  4997.55799756  5000.        ]

The ¹H NMR spectra of ethanol show 3 ¹H NMR peaks: - Triplet from the CH₃ group - Quartet from the CH₂ group - Single from the OH group

You can edit jcoupling in the file examples/ethanol.in to see the effect of J-coupling on the spliting of the ¹H peaks

plt.plot(spe.data['hz'], spe.data['real'])
plt.xlabel('Frequency (Hz)')
plt.xlim(3000, 0)

(3000.0, 0.0)

The data can be converted from frequency (Hz) to ppm by providing the external magnetic field (B₀) in either Tesla or MHz, and specify the nucleus being observed

spe_ppm = SimpReader('../../examples/ethanol.spe', format='spe', b0='400MHz', nucleus='1H')
plt.plot(spe_ppm.data['ppm'], spe_ppm.data['real'])
plt.xlabel('$^1$H (ppm)')
plt.xlim(8, 0)

(8.0, 0.0)

Lastly, you can convert any fid file into a spe easily by using .to_spe()

conv_spe = fid.to_spe()

plt.plot(conv_spe.data['hz'], conv_spe.data['real'], label = 'Converted')
plt.plot(spe.data['hz'], spe.data['real'], label = 'Original')
plt.xlim(3000, 0)
plt.xlabel('Frequency (Hz)')
plt.legend()

<matplotlib.legend.Legend at 0x1ab91469490>

The data can be easily exported to a .csv file

import pandas as pd

df = pd.DataFrame(fid.data)
df.to_csv('fid.csv', index=False)