# integration example: integrate_1dΒΆ

This example shows how to use nmrglue to integrate a 1D NMRPipe spectra. The script reads in ppm peak limits from limits.in and takes a simple summation integral of each peak using the spectra contained in 1d_data.ft. The integration values are writting to area.out and a plot is make showing the integration limits and values overlayed on the spectra to plot.png.

#! /usr/bin/env python
# Example scipt to show integration of a 1D spectrum

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

# read in the data from a NMRPipe file
length = data.shape[0]

# read in the integration limits
peak_list = np.recfromtxt("limits.in")

# determind the ppm scale
uc = ng.pipe.make_uc(dic, data)
ppm_scale = uc.ppm_scale()

# plot the spectrum
fig = plt.figure()
ax.plot(ppm_scale, data, 'k-')

# prepare the output file
f = open("area.out", 'w')
f.write("#Name\tStart\tStop\tArea\n")

# loop over the integration limits
for name, start, end in peak_list:
min = uc(start, "ppm")
max = uc(end, "ppm")
if min > max:
min, max = max, min

# extract the peak
peak = data[min:max + 1]
peak_scale = ppm_scale[min:max + 1]

# plot the integration lines, limits and name of peaks
ax.plot(peak_scale, peak.cumsum() / 100. + peak.max(), 'g-')
ax.plot(peak_scale, [0] * len(peak_scale), 'r-')
ax.text(peak_scale[0], 0.5 * peak.sum() / 100. + peak.max(), name,
fontsize=8)

# write out the integration info
tup = (name, peak_scale[0], peak_scale[-1], peak.sum())
f.write("%s\t%.3f\t%.3f\t%E\n" % tup)

# close the output file and save the plot
f.close()
ax.set_xlim(ppm_scale[0], ppm_scale[-1])
fig.savefig("plot.png")

#Peak   Start   Stop
CO1     183.40  178.97
CO2     178.97  175.33
# Now some more
Ca      65.77   49.46
Cb1     49.46   43.75
Cb2     43.75   39.00
Cg1     37.73   33.86
Cg2     33.86   32.00
Cd1     32.00   29.62
Cd2     29.62   26.98
Ce      26.98   12.10


Results:

#Name	Start	Stop	Area
CO1	183.395	178.976	2.884854E+08
CO2	178.976	175.333	1.205766E+08
Ca	65.774	49.457	4.906673E+08
Cb1	49.457	43.750	3.062952E+08
Cb2	43.750	38.991	2.336557E+08
Cg1	37.729	33.868	3.073099E+08
Cg2	33.868	31.998	1.470495E+08
Cd1	31.998	29.618	4.963560E+08
Cd2	29.618	26.972	3.168956E+08
Ce	26.972	12.111	2.024605E+08