Working with multiple columns from a data file

Question

I have a file in which I need to use the first column. The remaining columns need to be integrated with respect to the first. Lets say my file looks like this:

100 1.0 1.1 1.2 1.3 0.9
110 1.8 1.9 2.0 2.1 2.2
120 1.8 1.9 2.0 2.1 2.2
130 2.0 2.1 2.3 2.4 2.5

Could I write a piece of code that takes the second column and integrates with the first then the third and integrates with respect to the first and so on? For my code I have:

import scipy as sp
first_col=dat[:,0] #first column from data file
cols=dat[:,1:] #other columns from data file

col2 = cols[:,0]  # gets the first column from variable cols
I = sp.integrate.cumtrapz(col2, first_col, initial = 0) #integration step

This works only for the first row from the variable col, however, I don't want to write this out for all the other columns, it would look discussing (the thought of it makes me shiver). I have seen similar questions but haven't been able to relate the answers to mine and the ones that are more or less the same have vague answers. Any ideas?

you can use `genfromtxt` and then perform all the integration yourself as an alternative — Matthew, May 05 '15 at 12:49
What parameters would allow me to cycle through the columns? — skitt1z1, May 05 '15 at 13:04
if ive understood what you want right, you want to apply the same integration over several columns, so `data = sp.genfromtxt("file.txt") ; for col in data[0]: ; integrate(data[:,0], data[:,col])` where `integrate` is a def function. (though the answer seems to do what you want without having to write it yourself!) — Matthew, May 05 '15 at 13:19

score 1 · Accepted Answer · answered May 05 '15 at 13:07

The function cumtrapz accepts an axis argument. For example, suppose you put your first column in x and the remaining columns in y, and they have these values:

In [61]: x
Out[61]: array([100, 110, 120, 130])

In [62]: y
Out[62]: 
array([[ 1.1,  2.1,  2. ,  1.1,  1.1],
       [ 2. ,  2.1,  1. ,  1.2,  2.1],
       [ 1.2,  1. ,  1.1,  1. ,  1.2],
       [ 2. ,  1.1,  1.2,  2. ,  1.2]])

You can integrate each column of y with respect to x as follows:

In [63]: cumtrapz(y, x=x, axis=0, initial=0)
Out[63]: 
array([[  0. ,   0. ,   0. ,   0. ,   0. ],
       [ 15.5,  21. ,  15. ,  11.5,  16. ],
       [ 31.5,  36.5,  25.5,  22.5,  32.5],
       [ 47.5,  47. ,  37. ,  37.5,  44.5]])

This worked fantastically! I should have seen this after using cumtrapz myself... — skitt1z1, May 05 '15 at 13:21

Working with multiple columns from a data file

1 Answers1