watershed issue

[Tony Yu]

On Fri, Dec 30, 2011 at 5:39 AM, jip <jeanpatrick.pommier at gmail.com> wrote:

> Dear Emmanuelle,
>
> Sorry for the delay.
> I have rewritten a clearer script
> <https://docs.google.com/open?id=0B-YDFMbEy1grODU1Y2U0OTgtMzk1MS00MzkxLTliOWItYmMyOTNlOGI3ODRj>I
> hope.
> First, it takes a 12bits image<https://docs.google.com/open?id=0B-YDFMbEy1grNWJlYTkwYzYtMjk0ZS00NGVlLWFjMzktMmU3OWU1ODgwMDhm>(cy3 in the archive), isolates a region andremoves the background<https://docs.google.com/open?id=0B-YDFMbEy1grNDZjOWZjZjAtMGVmMS00ZTM2LTgwYzctMjZkM2JiMjFmYjBh>
> .
> Regional maxima are found to get markers for watershed.
> Three kind of maps are also prepared.
> Each map, with the markers image, is submitted to the watershed
> algorithm.Segmentation is performed with watershed as indicated here<http://scikits-image.org/docs/dev/auto_examples/plot_watershed.html#example-plot-watershed-py>,
> as follow:
> segmentation=watershed(map,markers,mask)
> map:grayscale image
> markers:label image
> mask:binary image
>
>
There's a small typo here: watershed should be called as:

     watershed(map, makers, mask=mask)

More specifically, in your code, you have:

    sk.morphology.watershed(bassin_hi,markers,top>30)

but it should be called as:

    sk.morphology.watershed(bassin_hi,markers,mask=top>30)

Without specifying `mask=`, you're setting the connectivity parameter in
watershed. Even with this correction, something seems to be off since
watershed seems to return blank images. Without the masks, it gives what I
would expect. I'm not sure what's going on the masked output.

-Tony
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