Bridge Rotational Coordinate Calculation Issues

[jab0707]

In the computeRotationalBridges method, the solveTrajectDist function is called to solve the trajectory distance equation in calculating the rotational coordinates. This uses the ichol_autocomp function to compute a precondition matrix based on the Incomplete Cholesky factorization of the gradient operator matrix of the valve bridge. This factorization seems to fail in some cases (unclear why) and if removed the resulting solution is either unaffected or in some cases improved.

[axel-loewe]

Looping in @lisapankewitz as this is code added by CobivecoX.

[lisapankewitz]

Dear Jake,

Thanks for the feedback!
The factorization seems to be more successful if the mesh is finer.

One could for now probably for that case introduce a warning and add a try catch statement to continue without factorization. Let me think about this issue a bit further and get back to you!

Have a great day!

[jab0707]

I also found that in the apicobasal calculations for the bridges there were sometimes a few outlier values that ruin the calculation. I added some checks for this to fix those outliers as well as some path fixing (some of the code expects/demands that the working directory be the examples directory) and some of the python/conda calls.
As I have been going I have been collecting the fixes and changes I needed to get it to work on this fork of the repo: https://github.com/jab0707/Cobiveco/tree/jake_bergquist_bugfixes

[lisapankewitz]

Thanks so much, @jab0707, your feedback and interaction are so much appreciated!
Let me have a look at them.

[axel-loewe]

I don't know what you are trying to use the coordinates for @jab0707 but if you don't need the bridge region in particular, CobiVeCo 1.0 might be a good fallback solution for you before these issues get fixed: https://github.com/KIT-IBT/Cobiveco/releases/tag/v1.0

[jab0707]

I like the inclusion of all of the 4 valves into the model. I have gotten CobivecoX working on two of our models so far, with another 15 in the pipeline to be processed, so I do not mind working through issues as I go. The resulting models without the cut AV plane are much nicer in my opinion so it is worth the additional effort.

[lisapankewitz]

Hi @jab0707,
I just head a look at your branch and thought your edits were very useful.
Would you mind creating a PR?

If not, I could also create one but most likely not before the weekend, as I have a few other tasks in my plate. If that is fine with you, that would also work.
Really appreciate your feedback and set of eyes :)
Have a lovely day!

[jab0707]

#13