Continuum removal algorithm in python

Question

I'm using python 2.7 (on jupyter notebook, win10 64 bit) to perform my analysis. I need to perform continuum removal (CR) on a reflectance spectrum data. I need it to be as described [here][1].

EDITED:

I used the following code to perform CR on a reflectance spectrum:

from scipy.spatial import ConvexHull
import numpy as np
import matplotlib.pyplot as plt

i = Xdata.iloc[15,:] #get the data from a pandas df
ii = i.tolist()
mat = np.column_stack((wavelenght_list,ii))
hull = ConvexHull(mat)
plt.plot(mat[:,0], mat[:,1], 'o')
for simplex in hull.simplices:
    plt.plot(mat[simplex, 0], mat[simplex, 1], 'k-')

The result I get is:

[![enter image description here][2]][2]

I have 3 questions about it:

1. Why it did not capture the local maxima at 550?

2. How can I remove the baseline of the convelHull (the black curve)?

3. How can I divide my spectrum by the "upper" conveHull in order to get CR spectrum? [1]: http://www.harrisgeospatial.com/docs/ContinuumRemoval.html [2]: https://i.stack.imgur.com/C5qah.jpg

UPDATE: Thanks you all for your help- I found a more suitable module for my needs to perform the continuum removal algorithm: spectro in pysptools

Answer 1

You will need to fit a convex hull to the data (e.g., reflectance as a function of the wavelength). The SciPy packages has the tool you need, see https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.ConvexHull.html.

After that you will need to subtract the convex hull value from the actual value after interpolation along the convex hull, see https://docs.scipy.org/doc/scipy/reference/interpolate.html.