[SOLVED] How to make moving window faster?

Issue

I use a moving window to buffer raster data (numpy array). It is very slow and I am wondering if it is possible to improve the code to make it faster:
My actual arrays have the shape (1349, 1368) and consist of zeros and ones.

import numpy as np

clouds = np.array([[[0, 0, 0, 0, 0], 
                    [0, 0, 0, 1, 0],
                    [0, 0, 1, 1, 1],
                    [0, 0, 0, 0, 1],
                    [0, 0, 0, 0, 1],
                    ]])  

cloudShadow = np.array([[[1, 0, 0, 1, 1], 
                         [0, 1, 1, 0, 0],
                         [0, 1, 0, 0, 0],
                         [0, 0, 0, 0, 0],
                         [0, 0, 0, 0, 1],
                         ]])

row_up_cloudShadow = 1      
row_low_cloudShadow = 0     
col_left_cloudShadow = 1  
col_right_cloudShadow = 0 


row = []
for i in range(len(np.where(clouds == 1)[0])):
    row_xy = list(range((np.where(clouds == 1)[0][i] - row_up_cloudShadow), (np.where(clouds == 1)[0][i] + row_low_cloudShadow) +1))
    row.append(row_xy)


col = []
for i in range(len(np.where(clouds == 1)[1])):
    col_xy = list(range((np.where(clouds == 1)[1][i] - col_left_cloudShadow), (np.where(clouds == 1)[1][i] + col_right_cloudShadow) +1))
    col.append(col_xy)

buffer = []
for i in range(0, np.count_nonzero(clouds == 1)):
    
    for j in range(len(row[0])):
        z = row[i][j]
        
        for u in range(len(col[0])):
            s = col[i][u]
            
            buffer.append(np.array([z,s]))

buffer = np.asarray(buffer)
buffer = np.where(buffer < 0, 0, buffer)

data_buff_cloudShadow = np.zeros(clouds.shape)
for i in range(len(buffer)):
    data_buff_cloudShadow[buffer[i][0]][buffer[i][1]] = 1

cloudShadow_buff = np.where(data_buff_cloudShadow == 1, cloudShadow, 0)

Solution

Here are some specific guidelines to make your code faster:

  1. Avoid repeating the same calculation: In your first two loops you do the same calculation (np.where(clouds == 1)) many times, so that you could refactor to:
row_idxs, col_idxs = np.where(clouds == 1)

for ridx in row_idxs:
    row_xy = list(
        range(ridx - row_up_cloudShadow, ridx + row_low_cloudShadow +1)
    )
    row.append(row_xy)

for cidx in col_idxs:
    col_xy = list(
        range(cidx - col_left_cloudShadow, cidx + col_right_cloudShadow +1)
    )
    col.append(col_xy)
  1. Remove loops wherever possible: Anything you can do with only Numpy functionality will be faster. Here, the last for-loop can be avoided using Numpy indexing:
data_buff_cloudShadow = np.zeros(clouds.shape)
data_buff_cloudShadow[buffer[:, 0], buffer[:, 1]] = 1
  1. Avoid conversions between Pythons list datatype and Numpy’s ndarray whenever possible. This specifically applies to intermediate results. Try to re-imagine your problem in terms of full arrays, as quite a number of problems can be represented that way. Here, you might be able to use np.meshgrid to represent coordinates easier.

For moving windows, you might benefit from looking into numpy.lib.stride_tricks.sliding_window_view for a moving window directly built into Numpy.

For further very helpful information, see https://numpy.org/learn/.

Answered By – FabianGD

Answer Checked By – Katrina (BugsFixing Volunteer)

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