Convert a string with brackets to numpy array

Question

Description of the problem:

I have an array-like structure in a dataframe column as a string (I read the dataframe from a csv file).

One string element of this column looks like this:

In  [1]: df.iloc[0]['points']    
Out [2]: '[(-0.0426, -0.7231, -0.4207), (0.2116, -0.1733, -0.1013), (...)]'

so it's really an array-like structure, which looks 'ready for numpy' to me.

numpy.fromstring() doesn't help as it doesn't like brackets:
convert string representation of array to numpy array in python

A simple numpy.array() on the string itself, if I copy and paste it in the array() function is returning me a numpy array.
But if I fill the array() function with the variable containing the string like that: np.array(df.iloc[0]['points']) it does not work, giving me a ValueError: could not convert string to float

Convert string to numpy array

The question:

Is there any function to do that in a simple way (without replacing or regex-ing the brackets)?

The first question is: where did this data come from? Is it something you’re generating? Or something generated by some program or library? If you can fix things so that the data get created in a form that’s actually meant to be parsed, or at least find an explanation of exactly what the format is and how you’re supposed to use it, that will be a lot better than reverse engineering by guessing so you can write a hacky parser. — abarnert
– abarnert, Commented Aug 17, 2018 at 15:53
Anyway, this looks like someone wrote the repr of a list of tuples to a file. That’s a really bad idea, but if you can’t change that, you may be able to reverse it by calling ast.literal_eval on each string. That will work with the example you posted, but no guarantee that it will work with all of your data, or that you won’t get float rounding problems that wouldn’t be there with properly serialized data. It’s a hack, not a solution. — abarnert
– abarnert, Commented Aug 17, 2018 at 15:55
The string (print) representation of a structured array is a list of tuples. The repr string will include dtype information. But since this is a cell in a DataFrame, there may be other possibilites. Did you load this df from a csv file? Are there quote strings like this in that file? — hpaulj
– hpaulj, Commented Aug 17, 2018 at 21:03

jpp · Accepted Answer · 2018-08-17 15:17:58Z

11

You can use ast.literal_eval before passing to numpy.array:

from ast import literal_eval
import numpy as np

x = '[(-0.0426, -0.7231, -0.4207), (0.2116, -0.1733, -0.1013)]'

res = np.array(literal_eval(x))

print(res)

array([[-0.0426, -0.7231, -0.4207],
       [ 0.2116, -0.1733, -0.1013]])

You can do the equivalent with strings in a Pandas series, but it's not clear if you need to aggregate across rows. If this is the case, you can combine a list of NumPy arrays derived using the above logic.

The docs explain types acceptable to literal_eval:

Safely evaluate an expression node or a string containing a Python literal or container display. The string or node provided may only consist of the following Python literal structures: strings, bytes, numbers, tuples, lists, dicts, sets, booleans, and None.

So we are effectively converting a string to a list of tuples, which np.array can then convert to a NumPy array.

edited Aug 17, 2018 at 15:17

answered Aug 17, 2018 at 15:03

jpp

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2 Comments

swiss_knight Over a year ago

Wonderful! I didn't know this module!

hpaulj Over a year ago

literal_eval is parsing the string that looks like a list of tuples. It handles basic Python structures. JSON does something similar, but for a more restricted syntax.

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