Calculating the area under multiple Peaks using Python-CodePudding

My problem is calculating the area under the peaks in my FT-IR analysis. I usually work with Origin but I would like to see if I get a better result working with Python. The data I'm using is linked here and the code is below. The problem I'm facing is, I don't know how to find the start and the end of the peak to calculate the area and how to set a Baseline.

I found this answered question about how to calculate the area under multiple peaks but I don't know how to implement it in my code:

CodePudding user response：

Okay, I have quickly added the code from the other post to your beginning and checked that it works. Unfortunately, the file that you linked did not work with your code, so I had to change some stuff in the beginning to make it work (in a very unelegant way, because I do not really know how to work with dataframes). If your local file is different and processing the file in this way does not work, then just exchange my beginning by yours.

import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import peakutils

df = pd.read_csv(r'CuCO3.csv', skiprows=5)

data = np.asarray([[float(y) for y in x[0].split(",")] for x in df.to_numpy()])
Wavenumber = np.arange(700, 916)
Absorbance = data[700:916,1]

indices = peakutils.indexes(Absorbance, thres=0.35, min_dist=0.1)
peak_values = [Absorbance[i] for i in indices]
peak_Wavenumbers = [Wavenumber[i] for i in indices]

plt.figure()
plt.scatter(peak_Wavenumbers, peak_values)
plt.plot(Wavenumber, Absorbance)
plt.show()

ixpeak = Wavenumber.searchsorted(peak_Wavenumbers)
ixmin = np.array([np.argmin(i) for i in np.split(Absorbance, ixpeak)])
ixmin[1:]  = ixpeak
mins = Wavenumber[ixmin]

# split up the x and y values based on those minima
xsplit = np.split(Wavenumber, ixmin[1:-1])
ysplit = np.split(Absorbance, ixmin[1:-1])

# find the areas under each peak
areas = [np.trapz(ys, xs) for xs, ys in zip(xsplit, ysplit)]

# plotting stuff
plt.figure(figsize=(5, 7))
plt.subplots_adjust(hspace=.33)
plt.subplot(211)
plt.plot(Wavenumber, Absorbance, label='trace 0')
plt.plot(peak_Wavenumbers, Absorbance[ixpeak], ' ', c='red', ms=10, label='peaks')
plt.plot(mins, Absorbance[ixmin], 'x', c='green', ms=10, label='mins')
plt.xlabel('dep')
plt.ylabel('indep')
plt.title('Example data')
plt.ylim(-.1, 1.6)
plt.legend()

plt.subplot(212)
plt.bar(np.arange(len(areas)), areas)
plt.xlabel('Peak number')
plt.ylabel('Area under peak')
plt.title('Area under the peaks of trace 0')
plt.show()