These are chat archives for fiji/fiji

Nov 2017
Alison Walter
Nov 29 2017 22:08 UTC

Hello @kapoorlab! I cloned both of your repos, and neither one built for me. I was able to get your imglib2-algorithm fork to build by adding dependencies to the pom for mpicbg and apache commons-math3. However, imglib2-algorithm cannot depend on mpicbg since it is GPL licensed. Additionally, it would cause imglib2-algorithm to depend on ImageJ 1.x.

For the Bubbleator, the enforcer is failing and it can’t find imports for preProcessing.Otsu, preProcessing.PrePipeline, and preProcessing.Utils. It looks like these are only being used for Otsu and Dothinning. Imagej-ops has an Otsu command you could use, and if Dothinning is an erosion operation imagej-ops has that as well.

In terms of using some of the implementations on my shape-rois branch, I definitely think there are places where this would be nice! I think your Ellipsoid and HyperEllipsoid classes could possibly extend ClosedEllipsoid or at least implement the Ellipsoid interface. You might also be able to use my DefaultLine implementation for your tangent lines. However, in order to display the ROIs on my shape-rois branch you’d need to convert them to ImageJ 1.x ROIs still. Though I am working on converters to do this in imagej-legacy (see roi-converters branch).

On a separate note, do Ellipsoid and GeneralEllipsoid need to be separate classes? Could you just add an additional constructor to Ellipsoid and a getCoefficients() method? It just seems to me like it would be simpler if they were one class rather than constantly dealing with a Pair<Ellipsoid, GeneralEllipsoid>, but I haven’t fully thought through the repercussions.

Additionally, in your RansacEllipsoid#GetEllipsePoints(...) method it looks like you’re converting to an ImageJ 1.x EllipseRoi just to get the coordinates of the boundary pixels. Unfortunately I don’t know if we currently have an implementation that can do this, but it would be nice to have. If anyone else knows a way, please let me know!

Those are my thoughts/comments, sorry its so long! Feel free to let me know if you have any questions!

Varun Kapoor
Nov 29 2017 23:25 UTC
Thanks @awalter17 The dependency on mpicbg is due to the polynomial Ransac fits which uses mpicbg models, if I have to remove that dependency I would have to make this one a Ellipsoid only Ransac fit. The preProcessing is another repo, Here I want to keep all the preprocessing and segmentation pipelines so that if more than one plugin needs similar methods they can all depend on this one repo and use the methods here.
I think I can make an additional constructor for Ellipsoid to combine these two representations into one. I will clone your repo tomorrow and work on extending the ClosedEllipsoid and using the DefaultLine for drawing the tangent lines. Thanks for your comments, I will modify the code accordingly.