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SCIInstitute / Cleaver

A MultiMaterial Tetrahedral Meshing Library and Application
https://cleaver.readthedocs.io
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Consistency in geometry information when using sizing field #96

Closed A-ep93 closed 3 years ago

A-ep93 commented 3 years ago

Hello, I am using cleaver through segment mesher in slicer and we faced a problem which is also discussed here We want to use sizing field to manually determine the regions where we want coarse or fine mesh however we were not able to do this. One reason can be this: Cleaver makes changes to the volume size (adds padding) and discards spacing, origin, and axis direction information when importing/exporting sizing fields, so it is hard to know what image geometry cleaver expects. We think this should be fixed so that cleaver uses image geometry information (origin, spacing, axis directions) consistently in all inputs and outputs.

jessdtate commented 3 years ago

Thanks @A-ep93. As far as I know, the current Cleaver module in Slice uses Cleaver 1.0. Could you clarify whether you have tested this in Slicer or with the newest version of Cleaver2? We have made some effort to address this concern (#81).

A-ep93 commented 3 years ago

Thanks for your response @jessdtate. Actually, we did this with the Segmentmesher module of slicer that uses cleaver 2.

jessdtate commented 3 years ago

Thanks for the clarification. The fork that Segmentmesher is using for Cleaver is 3 years old (https://github.com/lassoan/Cleaver2). I'm not sure what the best way forward with this. You could try building the module against this fork, or perhaps @lassoan can update their fork? We can look into merging some of the build changes in that fork, but it may be inconsistent with future plans for Cleaver.

lassoan commented 3 years ago

I haven't updated Cleaver version in Slicer because I only saw cosmetic changes, but maybe I missed important fixes. It is not a problem to update the Cleaver2 git hash in SlicerSegmentMesher at all. I'll also remove the old Cleaver1 extension to reduce confusion.

A-ep93 commented 3 years ago

Thank you very much @lassoan. That is great. Can you kindly please let me know when you will be able to update the cleaver2 for segmentmesher?

fluviolobo commented 3 years ago

This would also be of great interest to my team @lassoan. Will an update be posted on the weekly summary emails?

lassoan commented 3 years ago

3D Slicer's SegmentMesher extension now uses latest version of Cleaver2.