Closed haesleinhuepf closed 1 year ago
I'm stuck here because the mesh smoothing in vedo delivers weird results:
This is how it looks at the moment (example notebook):
Compared to the open3d-version:
Tests pass locally:
(bio39) C:\structure\code\napari-process-points-and-surfaces>pytest
================================================= test session starts =================================================
platform win32 -- Python 3.9.15, pytest-7.2.0, pluggy-1.0.0
PyQt5 5.15.7 -- Qt runtime 5.15.6 -- Qt compiled 5.15.6
rootdir: C:\structure\code\napari-process-points-and-surfaces
plugins: anyio-3.6.2, dash-2.7.1, napari-0.4.17, napari-plugin-engine-0.2.0, npe2-0.6.1, qt-4.2.0
collected 5 items
napari_process_points_and_surfaces\_tests\test_function.py ..... [100%]
================================================== warnings summary ===================================================
..\..\..\Users\haase\mambaforge\envs\bio39\lib\site-packages\vispy\app\backends\_qt.py:93
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\vispy\app\backends\_qt.py:93: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
if LooseVersion(QT_VERSION_STR) >= '5.4.0':
..\..\..\Users\haase\AppData\Roaming\Python\Python39\site-packages\setuptools\_distutils\version.py:346
C:\Users\haase\AppData\Roaming\Python\Python39\site-packages\setuptools\_distutils\version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
other = LooseVersion(other)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:341: DeprecationWarning: nppas.convex_hull() is deprecated. Use nppas.convex_hull_from_surface() instead.
warnings.warn("nppas.convex_hull() is deprecated. Use nppas.convex_hull_from_surface() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:312: DeprecationWarning: nppas.to_mesh() is deprecated. Use nppas.to_vedo_mesh() instead.
warnings.warn("nppas.to_mesh() is deprecated. Use nppas.to_vedo_mesh() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py: 13 warnings
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:289: DeprecationWarning: nppas.to_vector_d() is deprecated.
warnings.warn("nppas.to_vector_d() is deprecated.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:295: DeprecationWarning: nppas.to_vector_i() is deprecated.
warnings.warn("nppas.to_vector_i() is deprecated.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py: 10 warnings
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:329: DeprecationWarning: nppas.to_surface() is deprecated. Use nppas.to_napari_surface_data() instead.
warnings.warn("nppas.to_surface() is deprecated. Use nppas.to_napari_surface_data() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py: 23 warnings
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:307: DeprecationWarning: nppas.to_numpy() is deprecated. Use np.asarray() instead.
warnings.warn("nppas.to_numpy() is deprecated. Use np.asarray() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:361: DeprecationWarning: nppas.filter_smooth_simple() is deprecated. Use nppas.smooth_surface() instead.
warnings.warn("nppas.filter_smooth_simple() is deprecated. Use nppas.smooth_surface() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:402: DeprecationWarning: nppas.filter_smooth_taubin() is deprecated. Use nppas.smooth_surface() instead.
warnings.warn("nppas.filter_smooth_taubin() is deprecated. Use nppas.smooth_surface() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:381: DeprecationWarning: nppas.filter_smooth_laplacian() is deprecated. Use nppas.smooth_surface() instead.
warnings.warn("nppas.filter_smooth_laplacian() is deprecated. Use nppas.smooth_surface() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:446: DeprecationWarning: nppas.simplify_quadric_decimation() is deprecated. Open an issue if you are using this function and/or if you know a good replacement https://github.com/haesleinhuepf/napari-process-points-and-surfaces/issues.
warnings.warn("nppas.simplify_quadric_decimation() is deprecated. Open an issue if you are using this function and/or if you know a good replacement https://github.com/haesleinhuepf/napari-process-points-and-surfaces/issues.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:422: DeprecationWarning: nppas.simplify_vertex_clustering() is deprecated. Open an issue if you are using this function and/or if you know a good replacement https://github.com/haesleinhuepf/napari-process-points-and-surfaces/issues.
warnings.warn("nppas.simplify_vertex_clustering() is deprecated. Open an issue if you are using this function and/or if you know a good replacement https://github.com/haesleinhuepf/napari-process-points-and-surfaces/issues.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:467: DeprecationWarning: nppas.subdivide_loop() is deprecated. Use nppas.subdivide_loop_vedo() instead.
warnings.warn("nppas.subdivide_loop() is deprecated. Use nppas.subdivide_loop_vedo() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:487: DeprecationWarning: nppas.sample_points_uniformly() is deprecated. Use nppas.sample_points_from_surface() instead.
warnings.warn("nppas.sample_points_uniformly() is deprecated. Use nppas.sample_points_from_surface() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:510: DeprecationWarning: nppas.sample_points_poisson_disk() is deprecated. Use nppas.sample_points_from_surface() instead.
warnings.warn("nppas.sample_points_poisson_disk() is deprecated. Use nppas.sample_points_from_surface() instead.",
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:527: DeprecationWarning: nppas.voxel_down_sample() is deprecated. Use nppas.subsample_points() instead.
warnings.warn(
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:321: DeprecationWarning: nppas.to_point_cloud() is deprecated. Use nppas.to_napari_points_data() instead.
warnings.warn("nppas.to_point_cloud() is deprecated. Use nppas.to_napari_points_data() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:550: DeprecationWarning: nppas.points_to_convex_hull_surface() is deprecated. Use nppas.create_convex_hull_from_points() instead.
warnings.warn("nppas.points_to_convex_hull_surface() is deprecated. Use nppas.create_convex_hull_from_points() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:628: DeprecationWarning: nppas.fill_holes() is deprecated. Use nppas.fill_holes_in_surface() instead.
warnings.warn(
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:597: DeprecationWarning: nppas.surface_from_point_cloud_ball_pivoting() is deprecated. Use nppas.create_convex_hull_from_points() instead.
warnings.warn("nppas.surface_from_point_cloud_ball_pivoting() is deprecated. Use nppas.create_convex_hull_from_points() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:301: DeprecationWarning: nppas.to_vector_double() is deprecated.
warnings.warn("nppas.to_vector_double() is deprecated.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_something
C:\structure\code\napari-process-points-and-surfaces\napari_process_points_and_surfaces\__init__.py:571: DeprecationWarning: nppas.surface_from_point_cloud_alpha_shape() is deprecated. Use nppas.create_convex_hull_from_points() instead.
warnings.warn("nppas.surface_from_point_cloud_alpha_shape() is deprecated. Use nppas.create_convex_hull_from_points() instead.", DeprecationWarning)
napari_process_points_and_surfaces/_tests/test_function.py::test_curvature
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\vedo\pointcloud.py:463: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.
C, residue, rank, _ = np.linalg.lstsq(A, f) # solve AC=f
napari_process_points_and_surfaces/_tests/test_function.py: 64 warnings
C:\Users\haase\mambaforge\envs\bio39\lib\site-packages\vedo\colors.py:779: PendingDeprecationWarning: The get_cmap function will be deprecated in a future version. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.
mp = _cm_mpl.get_cmap(name=name)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
========================================== 5 passed, 150 warnings in 17.35s ===========================================
Hi @jo-mueller ,
can you do me a favor and try out this branch? Especially in the context of napari-stress it might be important to check if common workflows still work. All menus with open3d
in the name were removed and thus, I presume we need to update documentation in napari-stress if those used open3d-nppas-menus.
Thanks!
Best, Robert
can you do me a favor and try out this branch?
Can do. I'll probably do a napari-stress release next week and make sure that it's not broken by this.
I'll probably do a napari-stress release next week
Please let me know in advance @jo-mueller . I can release nppas then as well and you could link the right version here: https://github.com/campaslab/napari-stress/blob/97f0e1c3153b5d1ec0997b69d4ec936735783512/setup.cfg#L52
Hi @haesleinhuepf Looks alright to me. I found a small bug in the remove_duplicate_vertices
function (it was missing the return type annotation, PR coming). Once that is merged it should be fine on the napari-stress end.
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Awesome!
closes #14 closes #22 closes #34 closes #38 closes #39 closes #45 closes #48 closes #49