Replace all elements of Python NumPy Array that are greater than some value
Question:
I have a 2D NumPy array and would like to replace all values in it greater than or equal to a threshold T with 255.0. To my knowledge, the most fundamental way would be:
shape = arr.shape
result = np.zeros(shape)
for x in range(0, shape[0]):
for y in range(0, shape[1]):
if arr[x, y] >= T:
result[x, y] = 255

What is the most concise and pythonic way to do this?

Is there a faster (possibly less concise and/or less pythonic) way to do this?
This will be part of a window/level adjustment subroutine for MRI scans of the human head. The 2D numpy array is the image pixel data.
Answers:
I think both the fastest and most concise way to do this is to use NumPy’s builtin Fancy indexing. If you have an ndarray
named arr
, you can replace all elements >255
with a value x
as follows:
arr[arr > 255] = x
I ran this on my machine with a 500 x 500 random matrix, replacing all values >0.5 with 5, and it took an average of 7.59ms.
In [1]: import numpy as np
In [2]: A = np.random.rand(500, 500)
In [3]: timeit A[A > 0.5] = 5
100 loops, best of 3: 7.59 ms per loop
Since you actually want a different array which is arr
where arr < 255
, and 255
otherwise, this can be done simply:
result = np.minimum(arr, 255)
More generally, for a lower and/or upper bound:
result = np.clip(arr, 0, 255)
If you just want to access the values over 255, or something more complicated, @mtitan8’s answer is more general, but np.clip
and np.minimum
(or np.maximum
) are nicer and much faster for your case:
In [292]: timeit np.minimum(a, 255)
100000 loops, best of 3: 19.6 µs per loop
In [293]: %%timeit
.....: c = np.copy(a)
.....: c[a>255] = 255
.....:
10000 loops, best of 3: 86.6 µs per loop
If you want to do it inplace (i.e., modify arr
instead of creating result
) you can use the out
parameter of np.minimum
:
np.minimum(arr, 255, out=arr)
or
np.clip(arr, 0, 255, arr)
(the out=
name is optional since the arguments in the same order as the function’s definition.)
For inplace modification, the boolean indexing speeds up a lot (without having to make and then modify the copy separately), but is still not as fast as minimum
:
In [328]: %%timeit
.....: a = np.random.randint(0, 300, (100,100))
.....: np.minimum(a, 255, a)
.....:
100000 loops, best of 3: 303 µs per loop
In [329]: %%timeit
.....: a = np.random.randint(0, 300, (100,100))
.....: a[a>255] = 255
.....:
100000 loops, best of 3: 356 µs per loop
For comparison, if you wanted to restrict your values with a minimum as well as a maximum, without clip
you would have to do this twice, with something like
np.minimum(a, 255, a)
np.maximum(a, 0, a)
or,
a[a>255] = 255
a[a<0] = 0
You can consider using numpy.putmask:
np.putmask(arr, arr>=T, 255.0)
Here is a performance comparison with the Numpy’s builtin indexing:
In [1]: import numpy as np
In [2]: A = np.random.rand(500, 500)
In [3]: timeit np.putmask(A, A>0.5, 5)
1000 loops, best of 3: 1.34 ms per loop
In [4]: timeit A[A > 0.5] = 5
1000 loops, best of 3: 1.82 ms per loop
I think you can achieve this the quickest by using the where
function:
For example looking for items greater than 0.2 in a numpy array and replacing those with 0:
import numpy as np
nums = np.random.rand(4,3)
print np.where(nums > 0.2, 0, nums)
Another way is to use np.place
which does inplace replacement and works with multidimentional arrays:
import numpy as np
# create 2x3 array with numbers 0..5
arr = np.arange(6).reshape(2, 3)
# replace 0 with 10
np.place(arr, arr == 0, 10)
You can also use &
, 
(and/or) for more flexibility:
values between 5 and 10: A[(A>5)&(A<10)]
values greater than 10 or smaller than 5: A[(A<5)(A>10)]
Lets us assume you have a numpy
array that has contains the value from 0 all the way up to 20 and you want to replace numbers greater than 10 with 0
import numpy as np
my_arr = np.arange(0,21) # creates an array
my_arr[my_arr > 10] = 0 # modifies the value
Note this will however modify the original array to avoid overwriting the original array try using
arr.copy()
to create a new detached copy of the original array and modify that instead.
import numpy as np
my_arr = np.arange(0,21)
my_arr_copy = my_arr.copy() # creates copy of the orignal array
my_arr_copy[my_arr_copy > 10] = 0
np.where() works great!
np.where(arr > 255, 255, arr)
example:
FF = np.array([[0, 0],
[1, 0],
[0, 1],
[1, 1]])
np.where(FF == 1, '+', '')
Out[]:
array([['', ''],
['+', ''],
['', '+'],
['+', '+']], dtype='<U1')