The Dude - 5 months ago 26

Python Question

The situation is as follows:

I have a 2D numpy array. Its shape is (1002, 1004). Each element contains a value between 0 and Inf. What I now want to do is determine the first 1000 maximum values and store the corresponding indices in to a list named x and a list named y. This is because I want to plot the maximum values and the indices actually correspond to real time x and y position of the value.

What I have so far is:

`x = numpy.zeros(500)`

y = numpy.zeros(500)

for idx in range(500):

x[idx] = numpy.unravel_index(full.argmax(), full.shape)[0]

y[idx] = numpy.unravel_index(full.argmax(), full.shape)[1]

full[full == full.max()] = 0.

print os.times()

Here full is my 2D numpy array. As can be seen from the for loop, I only determine the first 500 maximum values at the moment. This however already takes about 5 s. For the first 1000 maximum values, the user time should actually be around 0.5 s. I've noticed that a very time consuming part is setting the previous maximum value to 0 each time. How can I speed things up?

Thank you so much!

Answer

If you have numpy 1.8, you can use the `argpartition`

function or method.
Here's a script that calculates `x`

and `y`

:

```
import numpy as np
# Create an array to work with.
np.random.seed(123)
full = np.random.randint(1, 99, size=(8, 8))
# Get the indices for the largest `num_largest` values.
num_largest = 8
indices = (-full).argpartition(num_largest, axis=None)[:num_largest]
# OR, if you want to avoid the temporary array created by `-full`:
# indices = full.argpartition(full.size - num_largest, axis=None)[-num_largest:]
x, y = np.unravel_index(indices, full.shape)
print "full:"
print full
print "x =", x
print "y =", y
print "Largest values:", full[x, y]
print "Compare to: ", np.sort(full, axis=None)[-num_largest:]
```

Output:

```
full:
[[67 93 18 84 58 87 98 97]
[48 74 33 47 97 26 84 79]
[37 97 81 69 50 56 68 3]
[85 40 67 85 48 62 49 8]
[93 53 98 86 95 28 35 98]
[77 41 4 70 65 76 35 59]
[11 23 78 19 16 28 31 53]
[71 27 81 7 15 76 55 72]]
x = [0 2 4 4 0 1 4 0]
y = [6 1 7 2 7 4 4 1]
Largest values: [98 97 98 98 97 97 95 93]
Compare to: [93 95 97 97 97 98 98 98]
```