Napari-process-points-and-surfaces

Latest version: v0.5.0

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0.5.0

What's Changed
* Fix lightning after calling the first nppas function from the napari-menu by haesleinhuepf based on code in napari-threedee in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/77

Before:
![image](https://user-images.githubusercontent.com/12660498/230784206-6fbb4f97-b006-41d6-bfb6-ef1727d1f042.png)

After:
![image](https://user-images.githubusercontent.com/12660498/230784279-24fda8d4-60cf-4530-912b-1bfebc869c9d.png)

Backwards compatibility breaking changes
* Compared to 0.4.2, the faces of marching cubes results are inverted. To undo this, call `nppas.invert_faces(surface)`.

**Full Changelog**: https://github.com/haesleinhuepf/napari-process-points-and-surfaces/compare/0.4.2...0.5.0

0.4.2

What's Changed
* Add reconstruct surface from point clouds by jo-mueller in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/68
* Add connected components by jo-mueller in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/72

![](https://user-images.githubusercontent.com/12660498/227264245-149e7ccb-9fff-44af-aa26-ff091d85706a.png)

**Full Changelog**: https://github.com/haesleinhuepf/napari-process-points-and-surfaces/compare/0.4.1...0.4.2

0.4.1

What's Changed
* add DOI badge to readme by kevinyamauchi in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/63
* Add moving least squares functions for pointclouds and surfaces by jo-mueller in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/65
* Code quality by haesleinhuepf in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/66


**Full Changelog**: https://github.com/haesleinhuepf/napari-process-points-and-surfaces/compare/0.4.0...0.4.1

0.4.0

New features
* `set_vertex_values()` allows setting values on a surface from code
* `create_convex_hull_from_surface` (Menu: `Tools > Surfaces > Convex hull (vedo, nppas)`)
* `remove_duplicate_vertices` (Menu: `Tools > Surfaces > Remove duplicate vertices (vedo, nppas)`) (thanks to jo-mueller )
* `smooth_surface` (Menu: `Tools > Surfaces > Smooth (vedo, nppas)`)
* `subdivide_adaptive` (Menu: `Tools > Surfaces > Subdivide adaptive (vedo, nppas)`) (thanks to jo-mueller )
* `subdivide_centroid` (Menu: `Tools > Surfaces > Subdivide centroid (vedo, nppas)`)
* `decimate_quadric` (Menu: `Tools > Surfaces > Decimate surface (quadric, vedo, nppas)`)
* `decimate_pro` (Menu: `Tools > Surfaces > Decimate surface (pro, vedo, nppas)`)
* `sample_points_from_surface` (Menu: `Tools > Points > Create points from surface (vedo, nppas)`)
* `subsample_points` (Menu: `Tools > Points > Subsample points (vedo, nppas)`)
* `create_convex_hull_from_points` (Menu: `Tools > Surfaces > Convex hull of points (vedo, nppas)`)
* `fill_holes_in_surface` (Menu: `Tools > Surfaces > Fill holes (vedo, nppas)`) (thanks to jo-mueller )
* `gastruloid` (Menu: `File > Open Samples > nppas > Gastruloid`) is derived from AV Luque and JV Veenvliet (2023) which is licensed [CC-BY](https://creativecommons.org/licenses/by/4.0/legalcode) and can be downloaded from here: https://zenodo.org/record/7603081 (thanks for the support to Cryaaa)
* `marching_cubes()` is an alias for `all_labels_to_surface()`
* `surface_quality_table()`, `add_quality()` and `Quality` now support measuring curvature
* `SurfaceTuple` objects can now be rendered in Jupyter notebooks
* For `surface_to_binary_volume()` the `as_large_as_image` parameter is now optional

Bug fixes
* fix error when mesh not clicked by kevinyamauchi in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/26

Backwards compatiblity breaking changes
nppas does not have open3d as dependency anymore. However, functions using open3d still exist (and are deprecated). To make use of them, you need to install open3d manually as described [here](http://www.open3d.org/docs/release/getting_started.html).

Deprecated functions
* `add_spherefitted_curvature()` is deprecated, use `add_quality(..., Quality.SPHERE_FITTED_CURVATURE_..._VOXEL)`.
* `add_curvature()` is deprecated. Use `add_curvature_scalars()` instead,
* `spherefitted_curvature` is deprecated. Use `add_quality(..., Quality.SPHERE_FITTED_CURVATURE_..._VOXEL)` instead,
* `_knot_mesh()` and `example_data_knot()` are deprecated,
* `_standford_bunny()` is deprecated. Use `_vedo_stanford_bunny()` instead,
* `to_vector_d()` is deprecated,
* `to_vector_i()` is deprecated,
* `to_vector_double()` is deprecated,
* `to_numpy()` is deprecated. Use `numpy.asarray()` instead.
* `to_mesh()` is deprecated. Use `to_vedo_mesh()` instead,
* `to_point_cloud()` is deprecated. Use `to_napari_points_data()` instead.
* `to_surface()` is deprecated. Use `to_napari_surface_data()` instead,
* `convex_hull()` is deprecated. Use `convex_hull_from_surface()` instead,
* `filter_smooth_simple()` is deprecated. Use `smooth_surface()` instead.
* `filter_smooth_laplacian()` is deprecated. Use `smooth_surface()` instead.
* `filter_smooth_taubin()` is deprecated. Use `smooth_surface()` instead.
* `simplify_vertex_clustering()` is deprecated. Use `decimate_quadric()` or `decimate_pro()` instead.
* `simplify_quadric_decimation()` is deprecated. Use `decimate_quadric()` instead.
* `subdivide_loop()` is deprecated. Use `subdivide_adaptive()` or `subdivide_centroid()` instead.
* `sample_points_uniformly()` is deprecated. Use `sample_points_from_surface()` instead,
* `sample_points_poisson_disk()` is deprecated. Use `sample_points_from_surface()` instead,
* `voxel_down_sample()` is deprecated. Use `subsample_points()` instead,
* `points_to_convex_hull_surface()` is deprecated. Use `create_convex_hull_from_points()` instead
* `surface_from_point_cloud_alpha_shape()` is deprecated. Use `create_convex_hull_from_points()` instead.
* `surface_from_point_cloud_ball_pivoting()` is deprecated. Use `create_convex_hull_from_points()` instead.
* `fill_holes()` is deprecated. Use `fill_holes_in_surface()` instead.

Miscellaneous
* The menus `Tools > Measurement > Surface quality`, `Surface quality table` and `Surface curvature` were moved to `Tools > Measurement maps`
* Measuring sphere-fitted curvature leading to `NaN` results do no longer lead to an error but to a warning instead.
* Menus in `Tools > Surfaces > Example data` have been moved to `File > Open Samples`
* Menu `Tools > Measurement > Surface quality/annotation to table (nppas)` has been moved to `Tools > Measurement tables`

New Contributors
* kevinyamauchi made their first contribution in https://github.com/haesleinhuepf/napari-process-points-and-surfaces/pull/26

**Full Changelog**: https://github.com/haesleinhuepf/napari-process-points-and-surfaces/compare/0.3.3...0.4.0

0.3.3

New features
* Surface measurements in tabular form
* Manual annotation widget (thanks to jo-mueller martinschatz-cz kevinyamauchi and alisterburt)

![img.png](https://github.com/haesleinhuepf/napari-process-points-and-surfaces/raw/main/docs/surface_annotation.png)

0.3.2

New functions
* Surface to binary (thanks to jo-mueller for the code-snippet)

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