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haesleinhuepf / napari-process-points-and-surfaces

Process and analyze surfaces using vedo in napari.
BSD 3-Clause "New" or "Revised" License
22 stars 4 forks source link

Open3d vedo conversion #23

Closed haesleinhuepf closed 1 year ago

haesleinhuepf commented 2 years ago

closes #14 closes #22 closes #34 closes #38 closes #39 closes #45 closes #48 closes #49

haesleinhuepf commented 2 years ago

I'm stuck here because the mesh smoothing in vedo delivers weird results:

This is how it looks at the moment (example notebook):

image

Compared to the open3d-version:

image

haesleinhuepf commented 1 year ago

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 ===========================================
haesleinhuepf commented 1 year ago

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

jo-mueller commented 1 year ago

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.

haesleinhuepf commented 1 year ago

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

jo-mueller commented 1 year ago

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.

codecov-commenter commented 1 year ago

Codecov Report

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Coverage data is based on head (72d9c95) compared to base (b1eee05). Patch coverage: 76.61% of modified lines in pull request are covered.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #23 +/- ## =========================================== + Coverage 53.55% 68.89% +15.34% =========================================== Files 3 8 +5 Lines 338 929 +591 =========================================== + Hits 181 640 +459 - Misses 157 289 +132 ``` | [Impacted Files](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase) | Coverage Δ | | |---|---|---| | [...\_points\_and\_surfaces/\_surface\_annotation\_widget.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fc3VyZmFjZV9hbm5vdGF0aW9uX3dpZGdldC5weQ==) | `14.54% <0.00%> (-2.88%)` | :arrow_down: | | [...ari\_process\_points\_and\_surfaces/\_quantification.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fcXVhbnRpZmljYXRpb24ucHk=) | `70.00% <65.47%> (-7.35%)` | :arrow_down: | | [napari\_process\_points\_and\_surfaces/\_vedo.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fdmVkby5weQ==) | `68.75% <68.75%> (ø)` | | | [napari\_process\_points\_and\_surfaces/\_\_init\_\_.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fX2luaXRfXy5weQ==) | `82.05% <79.65%> (ø)` | | | [...rocess\_points\_and\_surfaces/\_tests/test\_function.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fdGVzdHMvdGVzdF9mdW5jdGlvbi5weQ==) | `100.00% <100.00%> (ø)` | | | [...\_process\_points\_and\_surfaces/\_tests/test\_open3d.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fdGVzdHMvdGVzdF9vcGVuM2QucHk=) | `100.00% <100.00%> (ø)` | | | [...\_points\_and\_surfaces/\_tests/test\_vedo\_functions.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fdGVzdHMvdGVzdF92ZWRvX2Z1bmN0aW9ucy5weQ==) | `100.00% <100.00%> (ø)` | | | [napari\_process\_points\_and\_surfaces/\_utils.py](https://codecov.io/gh/haesleinhuepf/napari-process-points-and-surfaces/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase#diff-bmFwYXJpX3Byb2Nlc3NfcG9pbnRzX2FuZF9zdXJmYWNlcy9fdXRpbHMucHk=) | `100.00% <100.00%> (ø)` | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Robert+Haase)

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jo-mueller commented 1 year ago

Awesome!