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 #77

Before:

After:

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: 0.4.2...0.5.0

0.4.2

What's Changed

• Add reconstruct surface from point clouds by @jo-mueller in #68
• Add connected components by @jo-mueller in #72

Full Changelog: 0.4.1...0.4.2

0.4.1

What's Changed

• add DOI badge to readme by @kevinyamauchi in #63
• Add moving least squares functions for pointclouds and surfaces by @jo-mueller in #65
• Code quality by @haesleinhuepf in #66

Full Changelog: 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 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 #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.

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 #26

Full Changelog: 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)

0.3.2

New functions

• Surface to binary (thanks to @jo-mueller for the code-snippet)

0.3.1

Bugfix:

• Points to Labels (nppas) menu entry crashed napari (thanks to @PanosOik for reporting!)

0.3.0

Changes

• Example data (knot, Stanford Bunny, elipsoid) were scaled so that one can work with them conveniently in napari

0.2.1

Bug fixes

• Example data (bunny and knot) wasn't shipped via pypi and not available

Renamed menu entries

• "Create X from Y" instead "Y to X"

0.1.5

Changes

• Upstream changes enable SurfaceData in workflows and for on-the-fly processing of timelape data (thanks to @jo-mueller for pushing this forward)