Speeding up a numpy loop

0 votes
I have the following code using numpy arrays but it works very slow :

# Intersection of an octree and a trajectory
def intersection(octree, trajectory):
    # Initialize numpy arrays
    ox = octree.get("x")
    oy = octree.get("y")
    oz = octree.get("z")
    oe = octree.get("extent")/2
    tx = trajectory.get("x")
    ty = trajectory.get("y")
    tz = trajectory.get("z")
    result = np.zeros(np.size(ox))
    # Loop over elements
    for i in range(0, np.size(tx)):
        for j in range(0, np.size(ox)):
            if (tx[i] > ox[j]-oe[j] and
                tx[i] < ox[j]+oe[j] and
                ty[i] > oy[j]-oe[j] and
                ty[i] < oy[j]+oe[j] and
                tz[i] > oz[j]-oe[j] and
                tz[i] < oz[j]+oe[j]):
                result[j] += 1
    # Finalize
    return result
 

How can I rewrite the function to speed up the calculation?
Mar 15 in Python by ana1504.k
• 5,990 points
44 views

1 answer to this question.

Your answer

Your name to display (optional):
Privacy: Your email address will only be used for sending these notifications.
0 votes
You are allocating 10000 lists of size 100000. The first thing to do would be to stop using range for the nested j loop and use the generator version xrange instead. This will save you time and space allocating all those lists.

The next one would be to use vectorized operations:

for i in xrange(0, np.size(tx)):
    index = (ox-oe < tx[i]) & (ox+oe > tx[i]) & (oy-oe < ty[i]) & (oy+oe > ty[i]) & (oz-oe < tz[i]) & (oz+oe > tz[i])
    result[index] += 1
answered Mar 15 by SDeb
• 9,540 points

Related Questions In Python

0 votes
1 answer

Need help writing a dataframe into a csv with the help of a loop

Using the following logic you can arrive ...READ MORE

answered Apr 17, 2018 in Python by anonymous
596 views
0 votes
1 answer

Pandas DataFrames in a loop, df.to_csv()

can you try something like this? not ...READ MORE

answered Sep 25, 2018 in Python by Priyaj
• 56,120 points
385 views
0 votes
1 answer

How to round a floating point number up to certain decimal place in Python?

This is normal (and has nothing to do ...READ MORE

answered Oct 8, 2018 in Python by charlie_brown
• 7,710 points
20 views
+1 vote
2 answers

View onto a numpy array?

 just index it as you normally would. ...READ MORE

answered Oct 18, 2018 in Python by roberto
34 views
0 votes
1 answer
0 votes
1 answer

Printing a large numpy array

numpy.set_printoptions(threshold='nan') READ MORE

answered Jul 20, 2018 in Python by Nietzsche's daemon
• 4,260 points
61 views
0 votes
1 answer

Return a list inside a for loop while iterating over the elements of another list

The print() is getting called multiple times ...READ MORE

answered Sep 21, 2018 in Python by SDeb
• 9,540 points
22 views
0 votes
1 answer

Shorter way to write a Python for loop

You can use the enumerate iterator: for i, ...READ MORE

answered Jan 17 in Python by SDeb
• 9,540 points
17 views

© 2018 Brain4ce Education Solutions Pvt. Ltd. All rights Reserved.
"PMP®","PMI®", "PMI-ACP®" and "PMBOK®" are registered marks of the Project Management Institute, Inc. MongoDB®, Mongo and the leaf logo are the registered trademarks of MongoDB, Inc.