Inserting values into array without indices

Question

I am trying to parse some .out files to get a value E contained within each file, and then plot these value against theta and r as a 3d surface plot. The values of theta and r are contained in the .out file title names: H2O.r{}theta{}.out. I.e. r is given in the first {} and theta is then given in the next {}. r is given to 2 d.p and theta is given to 1 d.p. in the file names, e.g. r = 0.90, theta = 190.0.

I am having a hard time iterating through the files, and extracting this information into an array E . I have come across an error:

IndexError: only integers, slices (:), ellipsis (...), numpy.newaxis (None) and integer or boolean arrays are valid indices.

However, if I change my r array to int to get rid of this error, then all of the values in r will become 0. Addtionally, my code to extract E from the file will no longer work as I will inputting 'H2O.r0.00theta70.out', a file which doesn't exist. Does anybody have any suggestions ?

from numpy import *
import matplotlib.pyplot as plt
import os
os.chdir('C:/Users/myName/ex2/all')

theta = arange(70.0, 161.0, 1, dtype = float)
r = arange(0.70, 1.95, 0.05, dtype = float)
r_2dp = [ '%.2f' % elem for elem in r_O ] # string array, with rounding to match the file names
E = zeros((theta.shape[0],r.shape[0]))

def extract(filename):    #extract value from file
        filename = open(filename,"r")
        for line in filename:
            if 'SCF Done' in line:
                l = line.split()
                p = float(l[4])
        return p

for i in r_2dp:    #create E array that will allow me to plot E vs r vs theta
    for j in theta:
        for filename in os.listdir('C:/Users/myName/ex2/all'):
            if filename.startswith('H2O'):
                filename = 'H2O.r{}theta{}.out'.format(i,j)                
                E[i,j] = extract(filename)

If I see this correctly, r_2dp is a string array; when you later loop through it and set E[i, j], i is a string which probably is the cause of the error you get. — Cleb
– Cleb, Commented Dec 16, 2017 at 0:11
Hi, I understand why the error comes up, I just don't know how I can avoid it. I need r_2dp to be a string array so that the filename = ... works. I don't know how to do this otherwise — loolipop
– loolipop, Commented Dec 16, 2017 at 0:13

Cleb · Accepted Answer · 2017-12-16 12:41:08Z

1

One solution would be to associate an index with the filename which you can accomplish using enumerate; I think you can just change your loop to

for i, fn in enumerate(r_2dp):
    for j, ti in enumerate(theta):
        for filename in os.listdir('C:/Users/myName/ex2/all'):
            if filename.startswith('H2O'):
                filename = 'H2O.r{}theta{}.out'.format(fn,ti)                
                E[j,i] = extract(filename)

Please note that I changed E[i,j] to E[j,i] to get the dimensions correctly; you could also change the order of the two for-loops or initialize E the other way round...

Untested, as we cannot access your file, but the general idea should work...

edited Dec 16, 2017 at 12:41

answered Dec 16, 2017 at 0:26

Cleb

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3 Comments

loolipop Over a year ago

Hi, this works if I enumerate for theta too, as this was a list of floats. But now I think there is a problem with the array size I am trying to fit these data values in to: IndexError: index 25 is out of bounds for axis 1 with size 25 . If I print E, some of the elements are populated with the right-looking values, but most are still 0

Cleb Over a year ago

@loolipop: True, you also need enumerate for theta. To get rid of this error, either use E[j, i] or change the order of your loops for r_2dp and theta or initialze E the other way round. Again, untested.

loolipop Over a year ago

Yep thankyou ! I also needed to remove the for filename in os.listdir... line as I was already in this directory, and this with the .format(fn,ti) meant that an infinite number of filename kept on being generated

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