speed improvements (particularly for small masks in large images)

maskslic/slic_superpixels.py

@@ -46,6 +46,11 @@ def place_seed_points(image, img, mask, n_segments, spacing, q=99.99):
  segments_x = np.zeros(n_segments, dtype=np.int64)
 
  m_inv = np.copy(mask)
+ nz = np.nonzero(m_inv)
+ p = [np.min(nz[0]), np.min(nz[1]), np.min(nz[2])]
+ pend = [np.max(nz[0]), np.max(nz[1]), np.max(nz[2])]
+ # cropping to bounding box around ROI
+ m_inv = m_inv[p[0]:pend[0]+1, p[1]:pend[1]+1, p[2]:pend[2]+1]
 
  # SEED STEP 1: n seeds are placed as far as possible from every other seed and the edge.
 
@@ -73,7 +78,8 @@ def place_seed_points(image, img, mask, n_segments, spacing, q=99.99):
  # plt.imshow(pdtrans[0, :, :])
  # plt.show()
 
- if ii < 2:
+ # TODO temporarily just sticking to the original method until new method has been validated.
+ if ii < 1E6:
  sizes = ndi.sum(mask_dtrans, pdtrans, range(nb_labels + 1))
  # Use the maximum locations for the first two points
  coords1 = np.nonzero(pdtrans == np.argmax(sizes))
@@ -137,6 +143,10 @@ def place_seed_points(image, img, mask, n_segments, spacing, q=99.99):
  # plt.axis('off')
  # plt.show()
 
+ segments_z = segments_z + p[0]
+ segments_x = segments_x + p[1]
+ segments_y = segments_y + p[2]
+
  segments_color = np.zeros((segments_z.shape[0], image.shape[3]))
  segments = np.concatenate([segments_z[..., np.newaxis],
  segments_x[..., np.newaxis],