Napari fails to create ellipse when specifying center and radius in 3 dimensions

🐛 Bug

The documentation for creating ellipses states that either the 4 corner vertices must be specified, or a center position and radius must be specified. I find that when attempting to create ellipses the second way, napari throws an error because it expects that the 4 corner method will be used instead. I suspect the issue originates in napari/layers/shapes/_shapes_models/ellipse.py on line 71 where it uses an if statement instead of else if.

To Reproduce

Steps to reproduce the behavior:

1. Attempt to add an ellipse to a layer in 3 dimensions by specifying a center and radius

Error message:

~/anaconda3/lib/python3.7/site-packages/napari/layers/shapes/_shapes_models/ellipse.py in data(self, data)
     74                     "Data shape does not match a ellipse. Ellipse expects four corner vertices, {number} provided.",
     75                     deferred=True,
---> 76                     number=len(data),
     77                 )
     78             )

ValueError: Data shape does not match a ellipse. Ellipse expects four corner vertices, 2 provided.

Offending code in ellipse.py

@data.setter
    def data(self, data):
        data = np.array(data).astype(float)

        if len(self.dims_order) != data.shape[1]:
            self._dims_order = list(range(data.shape[1]))

        if len(data) == 2 and data.shape[1] == 2:
            data = center_radii_to_corners(data[0], data[1])

        if len(data) != 4:
            raise ValueError(
                trans._(
                    "Data shape does not match a ellipse. Ellipse expects four corner vertices, {number} provided.",
                    deferred=True,
                    number=len(data),
                )
            )

        self._data = data

[Carreau]

I can give it a shot.

On Fri, Mar 25, 2022 at 4:12 PM Nicholas Sofroniew @.***> wrote:

@Carreau https://github.com/Carreau do you want to give implementing something based on #4258 (comment) https://github.com/napari/napari/issues/4258#issuecomment-1073413637 a go?

— Reply to this email directly, view it on GitHub https://github.com/napari/napari/issues/4258#issuecomment-1079125812, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACR5T4WUV5TYTCX4SGCSKTVBXJVXANCNFSM5QW2IEOA . You are receiving this because you were mentioned.Message ID: @.***>

[Carreau]

We could let the ellipse accept a 2xD array for center/ radii in more than two D. It should actually work almost out of the box as most of the functions I think would work in D dimensions, we just need to update a bunch of doc strings. The ellipse API will then accept either 2xD for center radius or 4xD for corner representation (though now I think about it that should maybe be 2**D x D for the number of corners if all corners are specified …

@Carreau do you want to give implementing something based on #4258 (comment) a go?

For info, most of the 3D rendering of ellipses is completely borked, and render non planar aligned ellipses in wrong orientation and stretching. #4330 should start fixing the rendering.

So I’ve been banging my head as why other representation don’t visually work.

2**D x D for the number of corners if all corners are specified

That should still be (4,D) for ellipses, (2**D, D) would be for D-ellipsoids but I don’t think that should be in the shape layer, should it ? Do we want D-ellipsoids ? or D-shapes in General ?

https://miegakure.com/ and in particular https://www.youtube.com/watch?v=vZp0ETdD37E show some complexities with ND-shapes, and I’m unsure we want to tackle it in napari.

On top of that it would also be unclear to me how to manipulate a 2**D ellipsoid, in particular if the multiple axes are not axis aligned.