Dev #281
Dev #281
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Surface mesh create wasn't create all faces. Now it is fixed.
Also : -add two methods to Mesh to list faces and vertices.
-generalised coordinates
-add `write_polygon_mesh` to export mesh into .ply to visualised with blinder
Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed
Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link
Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing
Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet...
For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place.
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Hello @sophietheis do you have a bit of time to review this and test your code from this branch? Thank you :) G |
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Hello, |
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To use the dev branch: git fetch
git switch dev
pip install .[dev] # editable install is broken don't use -e
make testsAnd then your code Thanks again! |
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Do you want to keep "lineage" stuff ? I added a lineage attribute to Epithelium, which is a networkx digraph, to keep track of lineage. There is no notion of time. It only takes cell division into account, I don't keep track of cell disappearance.
I got this error at the first install :
I initiated submodule pybind11 and it fixed the problem.
We probably need to find a better way to manage the repulsion grid as it raises pandas error when pandas is updated... I don't know what a better method would be.
It seems that the last version of jupyter notebook (7.0.6) doesn't work with ipyvolume (do not work with other widget either), nothing is display. I haven't found a solution, so I switched back to version 6.5.4, and it works well.
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I can't push because of this error: If you have an idea how to fix it. Otherwise, I will clone the repo in the hope that would fix the problem 🤞 |
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strange .. pybind11 should not be necessary any more. The other submodule is notebooks. There is this METADATA error I need to track down, scikit-build has problems. I'll look into it |
Fix pandas issue
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Well I don't really understand, I remove everything about pybind11, now install work; but I still can"t push. I think there is something weird/broken in my git config for this repo because I have no issue with my other repository. |
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great thanks! |
> Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded.
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Hi @sophietheis can you approve the PR by doing a review (in the "Files Changes" tab)? Thanks, I'll merge following that |
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never mind, I'll force the merge |
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