Enumerate 2D array and append to new array

Question

I'm trying to enumerate a 2D NumPy array of shape (512, 512) with pixel values, to output [y_index, x_index, pixel_value]. Output array should have shape (262144, 3): 262144 pixels from 512x512 matrix and 3 for columns pixel value, y coordinate and x coordinate.

I used ndenumerate but how to store values in an array? My attempt at last line is incorrect:

img = as_np_array[:, :, 0]
img = img.reshape(512, 512)
coordinates = np.empty([262,144, 3])
for index, x in np.ndenumerate(img):
    coordinates = np.append(coordinates, [[x], index[0], index[1]])

Intel Core i7 2.7GHz (4 cores) takes 7-10 minutes. Is there a more efficient way?

Can't you use three variables for pixel value, x coordinate and y coordinate. In that case, you can use the existing array, and ycoord, xcoord = numpy.mgrid[0:img.shape[0],0:img.shape[1]]. — 9769953
– 9769953, Commented Sep 5, 2019 at 5:29
Thank you for your response. Sorry, but I didn't understand your particular format of answer. Basically I need an array output with 3 columns: pixel value, and its x & y coordinates. Reason I need that format specifically is because I need to then save it as a CSV file to have that specific data format/structure. You have ycoord, xcoord but I need everything in one array output. — Hazzaldo
– Hazzaldo, Commented Sep 5, 2019 at 12:57
Not necessarily: you could also create a double loop over the x- and y-coordinates, and then output a line of x, y, pixel_value to the CSV file. In which case, you neither need that large a 2D array, nor my solution, but just something like for x in range(512): for y in range(512): csv.write(x, y, img[y,x]). — 9769953
– 9769953, Commented Sep 5, 2019 at 13:01
Many thanks for this suggestion. I'm just trying out this code right now. I tried this code as a test run with a small array example: array2 = np.array([[1,1,1], [2,2,2], [3,3,3]]) with open('csv_test.csv', 'w', newline='') as f: thewriter = csv.writer(f) thewriter.writerow(['x_coord', 'y_coord', 'pixel_value']) for y in np.nditer(array2): for x in np.nditer(y): thewriter.writerow([x, y, array2[y,x]]), but I got the error: index 3 is out of bounds for axis 0 with size 3. Not sure why is that? Is np.nditer the issue or is it something else? — Hazzaldo
– Hazzaldo, Commented Sep 5, 2019 at 13:59
Because np.nditer steps through the flattened array, which is larger than one dimension. Also, your code doesn't not reflect what I wrote. I step through the dimensions (shape) of the array; you step through the array itself, and use the values inside the to index the array: for y in np.nditer(array2): ... array2[y,x]. That's not going to work (except in some very special cases). — 9769953
– 9769953, Commented Sep 5, 2019 at 14:07

CypherX · Accepted Answer · 2019-09-10 02:19:30Z

1

You could use numpy.indices to do this. What you want ultimately is image_data with y, x indices and the corresponding pixels (px). There are three columns in image_data.

row, col = np.indices(img.shape)
y, x, px = row.flatten(), col.flatten(), img.flatten()
image_data = np.array([y, x, px]).T

Detailed Example:

img = np.arange(20).reshape(5, 4)

def process_image_data(img):
    row, col = np.indices(img.shape)
    return (row.flatten(), col.flatten(), img.flatten())

y, x, px = process_image_data(img)

answered Sep 10, 2019 at 2:19

CypherX

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Hazzaldo · Accepted Answer · 2019-09-10 00:18:48Z

0

The solution that worked for me is this:

with open('img_pixel_coor1.csv', 'w', newline='') as f:
    headernames = ['y_coord', 'x_coord', 'pixel_value']
    thewriter = csv.DictWriter(f, fieldnames=headernames)
    thewriter.writeheader()     
    for index, pix in np.ndenumerate(img):
        thewriter.writerow({'y_coord' : index[0], 'x_coord' : index[1], 'pixel_value' : pix})

answered Sep 10, 2019 at 0:18

Hazzaldo

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