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name Punditsdkoslkdosdkoskdo

Numpy modify array in place?

I have the following code which is attempting to normalize the values of an m x n array (It will be used as input to a neural network, where m is the number of training examples and n is the number of features).

However, when I inspect the array in the interpreter after the script runs, I see that the values are not normalized; that is, they still have the original values. I guess this is because the assignment to the array variable inside the function is only seen within the function.

How can I do this normalization in place? Or do I have to return a new array from the normalize function?

import numpy

def normalize(array, imin = -1, imax = 1):
    """I = Imin + (Imax-Imin)*(D-Dmin)/(Dmax-Dmin)"""

    dmin = array.min()
    dmax = array.max()

    array = imin + (imax - imin)*(array - dmin)/(dmax - dmin)
    print array[0]


def main():

    array = numpy.loadtxt('test.csv', delimiter=',', skiprows=1)
    for column in array.T:
        normalize(column)

    return array

if __name__ == "__main__":
    a = main()

If you want to apply mathematical operations to a numpy array in-place, you can simply use the standard in-place operators +=, -=, /=, etc. So for example:

>>> def foo(a):
...     a += 10
... 
>>> a = numpy.arange(10)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> foo(a)
>>> a
array([10, 11, 12, 13, 14, 15, 16, 17, 18, 19])

The in-place version of these operations is a tad faster to boot, especially for larger arrays:

>>> def normalize_inplace(array, imin=-1, imax=1):
...         dmin = array.min()
...         dmax = array.max()
...         array -= dmin
...         array *= imax - imin
...         array /= dmax - dmin
...         array += imin
...     
>>> def normalize_copy(array, imin=-1, imax=1):
...         dmin = array.min()
...         dmax = array.max()
...         return imin + (imax - imin) * (array - dmin) / (dmax - dmin)
... 
>>> a = numpy.arange(10000, dtype='f')
>>> %timeit normalize_inplace(a)
10000 loops, best of 3: 144 us per loop
>>> %timeit normalize_copy(a)
10000 loops, best of 3: 146 us per loop
>>> a = numpy.arange(1000000, dtype='f')
>>> %timeit normalize_inplace(a)
100 loops, best of 3: 12.8 ms per loop
>>> %timeit normalize_copy(a)
100 loops, best of 3: 16.4 ms per loop
  • 25
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This is a trick that it is slightly more general than the other useful answers here:

def normalize(array, imin = -1, imax = 1):
    """I = Imin + (Imax-Imin)*(D-Dmin)/(Dmax-Dmin)"""

    dmin = array.min()
    dmax = array.max()

    array[...] = imin + (imax - imin)*(array - dmin)/(dmax - dmin)

Here we are assigning values to the view array[...] rather than assigning these values to some new local variable within the scope of the function.

x = np.arange(5, dtype='float')
print x
normalize(x)
print x

>>> [0. 1. 2. 3. 4.]
>>> [-1.  -0.5  0.   0.5  1. ]

EDIT:

It's slower; it allocates a new array. But it may be valuable if you are doing something more complicated where builtin in-place operations are cumbersome or don't suffice.

def normalize2(array, imin=-1, imax=1):
    dmin = array.min()
    dmax = array.max()

    array -= dmin;
    array *= (imax - imin)
    array /= (dmax-dmin)
    array += imin

A = np.random.randn(200**3).reshape([200] * 3)
%timeit -n5 -r5 normalize(A)
%timeit -n5 -r5 normalize2(A)

>> 47.6 ms ± 678 µs per loop (mean ± std. dev. of 5 runs, 5 loops each)
>> 26.1 ms ± 866 µs per loop (mean ± std. dev. of 5 runs, 5 loops each)
  • 7
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def normalize(array, imin = -1, imax = 1):
    """I = Imin + (Imax-Imin)*(D-Dmin)/(Dmax-Dmin)"""

    dmin = array.min()
    dmax = array.max()


    array -= dmin;
    array *= (imax - imin)
    array /= (dmax-dmin)
    array += imin

    print array[0]
  • 4
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      • 1
    • I mean, for that you'd have to benchmark. It depends on the size of the array. For small-ish problems, I would certainly just create the new array.

There is a nice way to do in-place normalization when using numpy. np.vectorize is is very usefull when combined with a lambda function when applied to an array. See the example below:

import numpy as np

def normalizeMe(value,vmin,vmax):

    vnorm = float(value-vmin)/float(vmax-vmin)

    return vnorm

imin = 0
imax = 10
feature = np.random.randint(10, size=10)

# Vectorize your function (only need to do it once)
temp = np.vectorize(lambda val: normalizeMe(val,imin,imax)) 
normfeature = temp(np.asarray(feature))

print feature
print normfeature

One can compare the performance with a generator expression, however there are likely many other ways to do this.

%%timeit
temp = np.vectorize(lambda val: normalizeMe(val,imin,imax)) 
normfeature1 = temp(np.asarray(feature))
10000 loops, best of 3: 25.1 µs per loop


%%timeit
normfeature2 = [i for i in (normalizeMe(val,imin,imax) for val in feature)]
100000 loops, best of 3: 9.69 µs per loop

%%timeit
normalize(np.asarray(feature))
100000 loops, best of 3: 12.7 µs per loop

So vectorize is definitely not the fastest, but can be conveient in cases where performance is not as important.

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