Module: Skeletonise Surfaces

Description:

In a 2D skeleton, i.e. skeleton containing surfaces, this module sort of pierces these surfaces and reapplies a skeletonisation so as to obtain a curvilinear skeleton.

Left: Initial object, a set of connected balls, two of which (shown in transparent) contain a cavity. Centre: resulting 26-connected ultimate skeleton, containing a surface aroung each cavity. Right: result of this module on the centre skeleton.

Connections:

Image

[required]
The input image, of type HxUniformScalarField3 comes in through this port.

Ports:

Threshold

Used to define, along with the comparison operator, which pixels are in the object.

Comparison

Used to define how the threshold value is used for defining the object.

Connectivity

Specifies the connectivity, either 6- or 18- or 26-connectivity.

Illustration of the different connectivities in 3D. (a): 6-, (b): 18-, and (c): 26-connectivity (in case you didn't figure it out, n-connectivity means n pixels in the neighbourhood).

Density

In the case of border surfaces, this sort of indicates the number of pixels to anchor to the border.

Closed

Indicates whether there are closed surfaces to process, as those must first be "pierced", as in the illustration above. If not sure, keep this option on.

Boundary_condition

How border pixels are handled, or what is outside the image. If periodic is chosen, supposes the left side of the image is touching the right (idem for up and down, front and back). The default background is what you'd intuitively expect, and with a typical processing sequence, i.e. when you're skeletonising an REV (Representative Elementary Volume) you might get detached connected components near the border, resulting in non-closed surfaces in the skeleton of the dual structure surrounding that component. Anyway, that's considered an open surface since the part touching the image border is the open part, outside being considered the background.

Action button

Push the button to start the computation.

Commands:

Additional options can be accessed when typing in the console Skeletonise_Surfaces COMMAND_NAME. Typing the command again usually reverts back to original settings.

`verbose`

Displays timing information after the computation. Retype to hide info.

`create`

Runs the computation. Returns the name of the output, so it can be used in a script, such as set RESULT [Skeletonise_Surfaces create].