Ah, your issue with the thickening was that label by default does not consider diagonally-adjancent pixels as adjacent. You need to pass connectivity=2 for this to be the case. But actually labelling the holes rather than the edges is a rather better option. =) The final image looks very pretty and could make a nice company logo. =P

On 9 Jan 2018, 1:03 PM +1100, Randy Heiland <randy.heiland@gmail.com>, wrote:

Argh. Nevermind... need to flip black/white on canny edges:  1-(edges*1)

On Mon, Jan 8, 2018 at 8:55 PM, Randy Heiland <randy.heiland@gmail.com> wrote:

Thanks Juan. I understand better what the  ndi.measurements.label can do for me now. I've tweaked my previous script and attached the resulting output. Does it make sense that I need to "thicken" the contours in order to get the desired features/regions, or is there something I'm still missing?

------------

from skimage.morphology import disk

from skimage.feature import canny

from skimage.filters import rank

from scipy import ndimage as ndi

import matplotlib.pyplot as plt

import numpy as np

image = disk(100)

for ix in range(200):

  for iy in range(200):

    xdel=ix-100

    ydel=iy-100

    if (xdel*xdel/50 + ydel*ydel/10) < 110:

      image[iy,ix]=0

    elif (xdel*xdel/10 + ydel*ydel/50) < 110:

      image[iy,ix]=0

edges = canny(image*255.)  # canny expect grayscale, i.e. 0-255 ??!

thicken = rank.gradient(edges, disk(1)) < 5

bdy = thicken.astype(np.uint8)*255

labeled_array, num_features = ndi.measurements.label(edges*1)

print("num_features (edges*1)=",num_features)

labeled_array2, num_features2 = ndi.measurements.label(bdy)

print("num_features (thick)=",num_features2)

fill = ndi.binary_fill_holes(edges)

fig, axes = plt.subplots(ncols=2, nrows=2, figsize=(6, 7))

ax = axes.ravel()

ax[0].imshow(edges*1, cmap=plt.cm.gray, interpolation='nearest')

ax[0].set_title('Canny edges')

ax[1].imshow(labeled_array, cmap=plt.cm.spectral, interpolation='nearest')

ax[1].set_title('labeled_array')

ax[2].imshow(bdy, cmap=plt.cm.gray, interpolation='nearest')

ax[2].set_title('bdy')

ax[3].imshow(labeled_array2, cmap=plt.cm.spectral, interpolation='nearest')

ax[3].set_title('labeled_array2')

plt.axis('off')

plt.show()

-->

num_features (edges*1)= 216
num_features (thick)= 6

-Randy

On Sun, Jan 7, 2018 at 11:36 PM, Juan Nunez-Iglesias <jni.soma@gmail.com> wrote:

Oh, I see what's happening. So, in your case, both void spaces are actually holes from the perspective of the binary_fill_holes algorithm, so they both get filled. I suggest you

a) label both contours using ndi.label

b) use binary_fill_holes on each label separately

c) subtract the filled inner hole from the filled outer hole (you can optionally add back in the inner contour if you care about that single-pixel precision)

This requires being able to robustly identify the inner and outer contours, but I don't think that should be too hard? If you only have two, you can certainly find them by finding the "larger" of the two bounding boxes. You can use skimage.measure.regionprops for this.

I hope that helps!

Juan.

On 8 Jan 2018, 12:21 PM +1100, Randy Heiland <randy.heiland@gmail.com>, wrote:

Sure - thanks.

from skimage.morphology import disk

from skimage.feature import canny

from scipy import ndimage as ndi

import matplotlib.pyplot as plt

image = disk(100)

for ix in range(200):

  for iy in range(200):

    xdel=ix-100

    ydel=iy-100

    if (xdel*xdel/50 + ydel*ydel/10) < 110:

      image[iy,ix]=0

    elif (xdel*xdel/10 + ydel*ydel/50) < 110:

      image[iy,ix]=0

edges = canny(image*255.)  # canny expect grayscale, i.e. 0-255 ??!

fill = ndi.binary_fill_holes(edges)   # I don't understand the params; can I seed a region to fill?

fig, axes = plt.subplots(ncols=3, figsize=(9, 3))

ax = axes.ravel()

ax[0].imshow(image, cmap=plt.cm.gray, interpolation='nearest')

#ax[0].imshow(invert_img, cmap=plt.cm.gray)

#ax[0].set_title('Inverted image')

ax[0].set_title('Original image')

ax[1].imshow(edges*1, cmap=plt.cm.gray, interpolation='nearest')

ax[1].set_title('Canny edges')

ax[2].imshow(fill, cmap=plt.cm.spectral, interpolation='nearest')

ax[2].set_title('Fill')

plt.show()

On Sun, Jan 7, 2018 at 6:57 PM, Juan Nunez-Iglesias <jni.soma@gmail.com> wrote:

Hi Randy, I was going to suggest binary fill holes. Do you mind posting your image and the code you’ve tried so we can troubleshoot?

Thanks,

Juan.

On 8 Jan 2018, 9:48 AM +1100, Randy Heiland <randy.heiland@gmail.com>, wrote:

If I have a binary image with, say, just a contour boundary (simple example: a white background with a black circle, i.e. an "o"), how can I fill the inside of the contour? I've played with both the watershed segmentation and the scipy.ndimage.binary_fill_holes, without success.

thanks, Randy

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