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Some implementations of nppas.subdivide_* produce empty meshes when processing gastruloid #57

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haesleinhuepf opened this issue Feb 18, 2023 · 4 comments · May be fixed by #59
Open

Some implementations of nppas.subdivide_* produce empty meshes when processing gastruloid #57

haesleinhuepf opened this issue Feb 18, 2023 · 4 comments · May be fixed by #59
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@jo-mueller
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@haesleinhuepf
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haesleinhuepf commented Feb 18, 2023 •
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... not sure why.

To reproduce:

import napari_process_points_and_surfaces as nppas
gastruloid = nppas.gastruloid()

subdivided_gastruloid = nppas.subdivide_loop_vedo(gastruloid, number_of_iterations=1)
subdivided_gastruloid

image

Workaround 1: Use nppas.subdivide_adaptive()

Workarounnd 2: install open3d and use this:

import napari_process_points_and_surfaces as nppas
gastruloid = nppas.gastruloid()

subdivided_gastruloid = nppas.subdivide_loop(gastruloid, number_of_iterations=1)
nppas.SurfaceTuple(subdivided_gastruloid)

image
@haesleinhuepf haesleinhuepf added the bug Something isn't working label Feb 18, 2023
@haesleinhuepf
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nppas.subdivide_linear and subdivide_butterfly appear to have the same issue.

nppas.subdivide_adaptive appears to work though.

@haesleinhuepf haesleinhuepf changed the title subdivide_loop_vedo produces empty mesh Some implementations of nppas.subdivide_* produce empty meshes when processing gastruloid Feb 18, 2023
haesleinhuepf added a commit that referenced this issue Feb 19, 2023
@haesleinhuepf
disabled dysfunctional functions / menus
538e4df 
see #57
This was referenced Feb 19, 2023
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@haesleinhuepf
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haesleinhuepf commented Feb 20, 2023 •
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Hey Johannes @jo-mueller ,

would you mind taking care of this issue? Also see the related PR-draft. Feel free to use its branch to test things.

Thanks!

@jo-mueller
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Hi @haesleinhuepf ,

I can have a look. Judging from what @marcomusy suggested here, would it be an option to implement the vedo isosurface method in nppas as an option to marching cubes (as opposed to augmenting marching cubes with multiple failsafes)?

Nonetheless, these failsafes should ultimately be available, too.

@haesleinhuepf
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implement the vedo isosurface method in nppas as an option to marching cubes

Yes, let's do this step by step. If nppas has a isosurface function, we can play with it. If I understand it right, it is an alternative to marching cubes, no? If it does its job well, we could use it, recommend it in the documentation and then deprecate the partially broken marching cubes.

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WIP: Fix subdivide functions haesleinhuepf/napari-process-points-and-surfaces
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