Support contours in future.manual_segmentation

[aaronsnoswell]

Description

This PR updates the functions future.manual_segmentation.manual_polygon_segmentation and future.manual_segmentation.manual_lasso_segmentation. The changes add a second return parameter that is the actual list of contour points. This is sometimes more useful to an end user than the mask only.

NB: This will break previous APIs that depended on these functions. Old code might have looked like this (from the docstrings);

camera = data.camera()
mask = manual_segmentation.manual_lasso_segmentation(camera)
io.imshow(mask)  
io.show()

Now, users will have to add a temporary variable to catch the contour, even if they are not interested in it; viz.

mask, _ = manual_segmentation.manual_lasso_segmentation(camera)

Docstrings are updated and the changes were fairly minimal - I haven't read all of PEP8, but I believe it should still be compatible (unless multiple return statements are a no-no).

Checklist

[It's fine to submit PRs which are a work in progress! But before they are merged, all PRs should provide:]

• Clean style in the spirit of PEP8
• Docstrings for all functions
• Gallery example in ./doc/examples (new features only)
• Unit tests

Release notes message:

 ``future.manual_segmentation.manual_polygon_segmentation`` and
  ``future.manual_segmentation.manual_lasso_segmentation`` were updated to also
  return the contour points picked, not just a mask image.

[pep8speaks]

Hello @aaronsnoswell! Thanks for updating the PR.

Cheers ! There are no PEP8 issues in this Pull Request. 🍻

Comment last updated on February 16, 2018 at 06:49 Hours UTC

[soupault]

Quite useful enhancement! Couple of remarks from me, otherwise ok

[soupault]

The shape of contours is clearly not correct here. Has to be a list of lists or something similar.

[soupault]

Keep it a one-liner. If more detailed description is required, put it 2 lines below.
Also, fix a double whitespace.

[soupault]

Same for the shape here.

[soupault]

Update return_all parameter description for both functions to include also info on contours.

[soupault]

@aaronsnoswell hi! Did you have time to make the requested changes?

[soupault]

While returning polygon vertices (PVs) / contour points (CPs) would be a nice addition to the manual segmentation functions, it comes here with a challenge. With return_all set to False, the polygons/masks are post-processed in a way that the polygons/masks drawn later zero out the areas of the ones drawn earlier when they overlap. In such cases, the returned PVs/CPs are not correct, since they are recorded from the regions before post-processing. The correct implementation would first post-process the polygons/masks and then recompute the PVs/CPs. For polygon vertices, this becomes quite complicated already, and I am not sure whether we want to go further in the direction of implementing advanced parts of image editing tools in skimage.

I would advocate for keeping the manual segmentaiton tools as simple as possible (or, perhaps, even removing them at some point) and encouraging users to learn and utilize the professional tools for image annotation (such as Napari, ITK-SNAP, Slicer3D, etc).

Since there has been no activity on this PR for a while and the implementation is somewhat early-stage, I propose to close the PR until further notice.