Adding coordinates to an array in Python 3

Question

So I have image data which I am iterating through in order to find the pixel which have useful data in them, I then need to find these coordinates subject to a conditional statement and then put these into an array or DataFrame. The code I have so far is:

pix_coor = np.empty((0,2))

for (x,y), value in np.ndenumerate(data_int):
  if value >= sigma3:
    pix_coor.append([x,y])

where data is just an image array (129,129). All the pixels that have a value larger than sigma3 are useful and the other ones I dont need.

Creating an empty array works fine but when I append this it doesn't seem to work, I need to end up with an array which has two columns of x and y values for the useful pixels. Any ideas?

Divakar · Accepted Answer · 2016-12-21 11:06:43Z

2

You could simply use np.argwhere for a vectorized solution -

pix_coor = np.argwhere(data_int >= sigma3)

answered Dec 21, 2016 at 11:06

Divakar

222k19 gold badges273 silver badges374 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

Shain · Accepted Answer · 2016-12-21 11:08:24Z

In numpy, array.append is not an inplace operation, instead it copies the entire array into newly allocated memory (big enough to hold it along with the new values), and returns the new array. Therefore it should be used as such:

  new_arr = arr.append(values)

Obviously, this is not an efficient way to add elements one by one.

You should use probably a regular python list for this.

Alternatively, pre allocate the numpy array with all values and then resize it:

 pix_coor = np.empty((data_int.size, 2), int)
 c = 0
 for (x, y), value in np.ndenumerate(data_int):
     if value >= sigma3:
         pix_coor[c] = (x, y)
         c += 1
 numpy.resize(pix_coor, (c, 2))

Note that I used np.empty((data_int.size, 2), int), since your coordinates are integral, while numpy defaults to floats.

Collectives™ on Stack Overflow

Adding coordinates to an array in Python 3

2 Answers 2

Comments

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

Comments

Your Answer

Sign up or log in

Post as a guest

Related