dimension input error with Get Polygon Points from 2D Binary Mask node

[Fritze]

Hi Jan,

I finally had time to integrate your great Get Polygon Points from 2D Binary Mask node into my KNIME workflows. It works great!

However, when using the node on bitmasks of labelings that were produced by the trackmate tracker node, I came across the following error :

WARN  Get Polygon Points from 2D Binary Mask 0:671      Error while executing row: 020.png_020.png#track_0! Cause: No matching 'net.imagej.ops.Ops$Geometric$Contour' op

Request:
-    net.imagej.ops.Ops$Geometric$Contour(
        ArrayImg,
        Boolean)

Candidates:
1.     (Polygon2D out) =
    net.imagej.ops.geom.geom2d.DefaultContour(
        RandomAccessibleInterval in,
        boolean useJacobs)
    Inputs do not conform to op rules
        in = ArrayImg [156x119x132]
        useJacobs = true

I suspect the problem might be that my input is "three-dimensional" since the bitmasks also contain the time dimension (132 in this case) after tracking. Maybe this is what is causing the error? Would there we a way of ignoring the 3rd dimension (if it is time) maybe? Best and thanks a lot, Friedrich

[imagejan]

Hi @Fritze, and sorry for the delayed reply!

Indeed, the contour implementation in imagej-ops only supports 2D polygons. We should probably emit a more informative warning in this case.

What do you mean by "ignoring" the 3rd dimension, would you like the node to only process the first slice in this case? If you have one polygon per frame, I'd suggest using the Splitter node (maybe followed by Unpivoting) and then get the polygon points for every row.

I'm also open for other suggestions how this node should be improved.

[Fritze]

Hi @imagejan,

Thanks for the reply. You are right, I was a bit confused by the error message but it makes sense that the node takes only 2D bitmasks without the time dimension. A specific warning would probably help.

I now use the Feature Calculator node after the Trackmate Tracker to get a bitmask for each frame. Then I can use Get Polygon points from 2D Binary Mask and everything works like a charm. Sorry for the confusion and thanks a lot again for developing this !