def skeletonize_river_mask(I, es, npad=20):
"""
Skeletonize a binary river mask. Crops mask to river extents, reflects the
mask at the appropriate borders, skeletonizes, then un-crops the mask.
INPUTS:
I - binary river mask to skeletonize
es - NSEW "exit sides" corresponding to the upstream and downstream
sides of the image that intersect the river. e.g. 'NS', 'EN', 'WS'
npad - (Optional) number of pixels to reflect I before skeletonization
to remove edge effects of skeletonization
"""
Ic, crop_pads = iu.crop_binary_im(I)
# Number of pixels to mirror - maximum of 2% of each dimension or npad pixels
n_vert = max(int(I.shape[0] * 0.02 / 2), npad)
n_horiz = max(int(I.shape[1] * 0.02 / 2), npad)
pads = [[0, 0], [0, 0]]
if 'N' in es:
pads[0][0] = n_vert
if 'E' in es:
pads[1][1] = n_horiz
if 'S' in es:
pads[0][1] = n_vert
if 'W' in es:
pads[1][0] = n_horiz
pads = tuple([tuple(pads[0]), tuple(pads[1])])
# Generate padded image
Ip = np.pad(Ic, pads, mode='reflect')
# Skeletonize padded image
Iskel = morphology.skeletonize(Ip)
# Remove padding
Iskel = Iskel[pads[0][0]:Iskel.shape[0] - pads[0][1],
pads[1][0]:Iskel.shape[1] - pads[1][1]]
# Add back what was cropped so skeleton image is original size
crop_pads_add = ((crop_pads[1], crop_pads[3]), (crop_pads[0],
crop_pads[2]))
Iskel = np.pad(Iskel,
crop_pads_add,
mode='constant',
constant_values=(0, 0))
# Ensure skeleton is prepared for analysis by RivGraph
# Simplify the skeleton (i.e. remove pixels that don't alter connectivity)
Iskel = skel_simplify(Iskel)
# Fill small skeleton holes, re-skeletonize, and re-simplify
Iskel = iu.fill_holes(Iskel, maxholesize=4)
Iskel = morphology.skeletonize(Iskel)
Iskel = skel_simplify(Iskel)
# Fill single pixel holes
Iskel = iu.fill_holes(Iskel, maxholesize=1)
return Iskel
def test_crop_binary_im():
"""Test crop_binary_im()."""
I = np.zeros((5, 5))
I[0, 0] = 1
I[1, 2:5] = 1
Icrop, pads = im_utils.crop_binary_im(I)
# assertions
assert np.shape(Icrop) == (2, 5)
assert np.all(pads == [0, 0, 0, 3])
def skeletonize_river_mask(I, es, padscale=2):
"""
Skeletonizes a binary mask of a river channel network. Differs from
skeletonize mask above by using knowledge of the exit sides of the river
with respect to the mask (I) to avoid edge effects of skeletonization by
mirroring the mask at its ends, then trimming it after processing. As with
skeletonize_mask, skeleton simplification is performed.
Parameters
----------
I : np.array
Binary river mask to skeletonize.
es : str
A two-character string (from N, E, S, or W) that denotes which sides
of the image the river intersects (upstream first) -- e.g. 'NS', 'EW',
'NW', etc.
padscale : int, optional
Pad multiplier that sets the size of the padding. Multplies the blob
size along the axis of the image that the blob intersect to determine
the padding distance. The default is 2.
Returns
-------
Iskel : np.array
The skeletonization of I.
"""
# Crop image
Ic, crop_pads = imu.crop_binary_im(I)
# Pad image (reflects channels at image edges)
Ip, pads = pad_river_im(Ic, es, pm=padscale)
# Skeletonize padded image
Iskel = morphology.skeletonize(Ip)
# Remove padding
Iskel = Iskel[pads[0]:Iskel.shape[0] - pads[1],
pads[3]:Iskel.shape[1] - pads[2]]
# Add back what was cropped so skeleton image is original size
crop_pads_add = ((crop_pads[1], crop_pads[3]), (crop_pads[0],
crop_pads[2]))
Iskel = np.pad(Iskel,
crop_pads_add,
mode='constant',
constant_values=(0, 0))
# Ensure skeleton is prepared for analysis by RivGraph
# Simplify the skeleton (i.e. remove pixels that don't alter connectivity)
Iskel = simplify_skel(Iskel)
# Fill small skeleton holes, re-skeletonize, and re-simplify
Iskel = imu.fill_holes(Iskel, maxholesize=4)
Iskel = morphology.skeletonize(Iskel)
Iskel = simplify_skel(Iskel)
# Fill single pixel holes
Iskel = imu.fill_holes(Iskel, maxholesize=1)
# The handling of edges can leave pieces of the skeleton stranded (i.e.
# disconnected from the main skeleton). Remove those here by keeping the
# largest blob.
Iskel = imu.largest_blobs(Iskel, nlargest=1, action='keep')
return Iskel