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.heil...@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.s...@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.heil...@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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>
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