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CHANGELOG.md

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Changelog

All notable changes to the project will be documented in this file.

===================================================================================

Development Version

Changes and Fixes

  • added example with embedding matplotlib figures in a scene
  • add Line.eval2d() useful for plotting
  • improvements to the addons.BaseCutter as per #1263 by @natabma
  • add applications.MorphByLandmarkPlotter class
  • add applications.MorphBySplinesPlotter class
  • fix memory leaks in Text2D and Allebly classes #1269 by @shBLOCK
  • add volume.extract_components()
  • add applications.ImageEditor Plotter-derived class
  • add pointcloud.project_point_on_variety() function

Soft-breaking Changes

  • small changes to the API of the addons.BaseCutter class

Hard-breaking Changes

  • None

New/Revised Examples

examples/pyplot/embed_matplotlib2.py
examples/basic/cut_interactive.py
examples/volumetric/slice_plane3.py
examples/volumetric/image_editor.py
examples/advanced/measure_curvature2.py

To Do

  • fix trasform in image.tomesh() is not transmitted to mesh

(Internal) Broken Examples

Examples that are not fully functional and need some fixing:

advanced/warp4b.py (problem with picker?)
sliders3d.py crashes when moving the scene
interpolate_scalar4.py misplaced scalarbar
markpoint.py (misplaced leader indicator)
cut_and_cap.py (incomplete capping)
tests/issues/discussion_800.py (incomplete capping of tube)

(Internal) Known issues

umap_viewer3d should be revised trackviewer (some problems with removing a track, and z spacing) pyplot.plot cannot plot constant line or single point numpy2volume0.py (volume alphas look bad)

(Internal) Broken exports to .npz:

Fails to export correctly to npz format

boolean.py
cartoony.py
mesh_lut.py
mesh_map2cell.py
texturecubes.py
meshquality.py
streamlines1.py

===================================================================================

Version 2024.5.4

Changes and Fixes

  • general code cleanup with pylint.
  • add utils.compute_hessian()
  • fix issue #1224 for cells coloring in jupyter notebook for k3d
  • add support for STEP files format (needs opencascade lib) #1222
  • fix nan case in scalarbar3d()
  • add .rename() method to set any object name.
  • fix bug #1230 in line.find_index_at_position() by @natabma
  • Add lazy initialization for normals (#1231) by @CorpsSansOrganes
  • add chemistry module to represent molecules and proteins
  • fix to Box class by @dbotwinick

Soft-breaking Changes

Changes that may break existing code whose fixing is trivial:

Hard-breaking Changes

Changes that will break existing code and need active thinking and some work to adapt

  • None

New/Revised Examples

examples/pyplot/plot_fxy0.py
examples/volumetric/image_editor.py
examples/other/pysr_regression.py
examples/other/chemistry1.py
tests/issues/issue_1230.py

===================================================================================

Version 2024.5.3

Changes and Fixes

  • add settings.force_single_precision_points = False in #1137 by @JeffreyWardman and @sean-d-zydex
  • fix Volume masking in #1146 by @ivishalanand
  • fix LegendBox in #1153 by @GerritFischer
  • add mesh.laplacian_diffusion()
  • fix DistanceTool in #1158
  • fix shapes.Plane.normal in #1159 by @smoothumut
  • add Arrow.top_point() and Arrow.base_point() to extract current arrow position #1163 @smoothumut
  • fix Arrow.top_index to produce the correct index value
  • add assembly.Group.objects by @smoothumut
  • add addons.DrawingWidget class for tracing on planar props
  • add Video(..., scale=1) keyword in #1168 by @YongcaiHuang
  • modify legosurface(boundary=True) default in #1166
  • make load functions compatible with pathlib #1176 by @Louis-Pujol
  • fixed broken link to example #1175 by @jo-mueller
  • add documentation to Mesh.boolean() #1173 by @jkunimune
  • raise an error when calling cell_normals before compute_normals() #1172 by @jkunimune
  • add documentation warning as computing normals can affect appearence of the mesh #1174 by @jkunimune
  • add documentation about Cube and Box having duplicated vertices to allow defining normals #1171
  • add documentation do address the behaviour of mesh.volume() and mesh.is_closed() wrt duplicated vertices.
  • add plotter.reset_clipping_range() to reset the camera clipping range based on the bounds of the visible actors #1170
  • fix issue with find_cell() in #1095
  • improvements to volume.isosurface_discrete() in #1180 by @snownontrace
  • fix bug on video frame by resetting camera clipping range in #1180 by @snownontrace
  • changes in the scalarbar2d object.
  • fix purging of nan in pyplot.plot()
  • fix line trace to skip first point
  • adjust volume transfer function for transparency @Poisoned
  • fixing axes type 10 by @Poisoned
  • improvements to input/output functionality for Assembly @ttsesm
  • added mesh.remove_all_lines() method
  • added keyword Plane(edge_direction=...) by @smoothumut
  • added isolines(..., n=list()) option to pass specific values.
  • in file_io.screenshot() add fourth channel representing trasparency @miek0tube
  • remove obsolete class CellCenters which is now function object.cell_centers()

Soft-breaking Changes

Changes that may break existing code whose fixing is trivial:

  • change object.points() to object.points everywhere.
  • change object.cell_centers to object.cell_centers().points everywhere.
  • change Picture() to Image() everywhere.

Hard-breaking Changes

Changes that will break existing code and need active thinking and some work to adapt

  • None

New/Revised Examples

examples/advanced/spline_draw2.py
examples/volumetric/isosurfaces2.py
examples/pyplot/fit_curve2.py

tests/issues/issue_1146.py
tests/issues/discussion_1190.py
tests/issues/test_sph_harm2.py
tests/issues/issue_1218.py

tests/snippets/test_interactive_plotxy1.py
tests/snippets/test_interactive_plotxy2.py
tests/snippets/test_elastic_pendulum.py

===================================================================================

Version 2024.5.2

Changes and Fixes

Soft-breaking Changes

Changes that will break existing code whose fixing is trivial:

  • remove concatenate=True keyword from apply_transform() discussed in #1111

Hard-breaking Changes

Changes that will break existing code and need active thinking and work to adapt

  • None

New/Revised Examples

examples/basic/interaction_modes3.py
examples/basic/interaction_modes4.py
examples/basic/buttons3.py
examples/advanced/warp4b.py
examples/other/magic-class1.py
examples/other/iminuit2.py
examples/other/meshlib1.py
tests/issues/issue_1077.py

===================================================================================

Version 2024.5.1

Changes and Fixes

  • fixes to extrude() method thanks to @JeffreyWardman
  • add utils.madcad2vedo conversion as per #976 by @JeffreyWardman
  • add utils.camera_to_dict()
  • add Axes(title_backface_color=...) keyword
  • fix labels() and labels2d()
  • add shapes.plot_scalar() plot a scalar along a line.
  • add support for tetgenpy
  • add transformations.compute_main_axes()
  • add transformations.__call__() to apply a transformation
  • fix small bug in pointcloud.distance_to()
  • add applications.MorphPlotter() to morph a polygonal mesh to a target mesh
  • add smooth_data() to smooth/diffuse data attributes
  • add shapes.Tubes()
  • add utils.Minimizer() class
  • add CellCenters(Points) class
  • add core.apply_transform_from_actor()
  • add add volume.slab()
  • add mesh.generate_random_points() to generate random points onto a surface
  • add tetmesh.generate_random_points() to generate random points in a tet mesh
  • rename integrate_arrays_over_domain() to integrate_data
  • extend volume.operation() to support logic operations as per #1002
  • add pointcloud.relax_point_positions() method
  • add pointcloud.auto_distance() method calculates the distance to the closest point in the same cloud of points.
  • fixed mesh.collapse_edges() after #992
  • add mesh.cut_closed_surface()
  • fix image.clone() in #1011
  • add transformations.TransformInterpolator class
  • add Line.find_index_at_position() finds the index of the line vertex that is closest to a point
  • add visual.LightKit class which provides "natural" lighting from 4 sources.
  • add fast-simplification example by @Louis-Pujol in #992
  • add metadata "shape" to volume.slice_plane() in #1018
  • fix core.mark_boundaries() method
  • add callbacks for cutters in #1020 and examples/volumetric/slice_plane3.py
  • add utils.andrews_curves() function.
  • add transformations.LinearTransform.transpose() method.
  • add pointcloud.generate_segments() to generate a continous line from un-ordered points in 3d
  • fix assembly.__add__() by @j042 in #1036
  • small fix to Ruler3D class.
  • add plotter.render_hidden_lines() method
  • add slot for triangle strips in constructor Mesh([verts, faces, lines, strips]) in #1019
  • internally use "import vedo.vtkclasses as vtki" instead of "vtk" to avoid confusion
  • add join_with_strips() in #1043
  • improvements to shapes.Ellipsoid() and bug fixes in #978 by @daniel-a-diaz
  • improvements to pointcloud.pca_ellipsoid() and bug fixes
  • improvements to pointcloud.pca_ellipse() and bug fixes
  • fix Plotter a toggle keypress
  • fix viz on jupyter notebook as per #994
  • fix mesh.imprint()
  • small fix to applications.Slicer2DPlotter
  • automatically apply the actor transform to an object actor that was moved manually (via eg "InteractorStyleTrackballActor") in #1045 and #1046 by @sergei9838
  • add support to RectilinearGrid and StructuredGrid data (experimental).
  • improvements to RayCastPlotter
  • add visual.scalar_range() to control mesh coloring.
  • fix shapes.Text3D.text() by @gioda
  • add volume.isosurface_discrete() method

Soft Breaking Changes

Changes that can break existing code whose fixing is trivial:

  • change clone2d(scale=...) to clone2d(size=...)
  • remove shapes.StreamLines(object) becomes object.compute_streamlines()
  • split mesh.decimate() into mesh.decimate(), mesh.decimate_pro() and mesh.decimate_binned() as per #992
  • modified core.clean() after #992
  • remove import_window() for obj files and create load_obj() by @zhouzq-thu in #891
  • add smooth_mls_12d(..., n=0) to fix the number of neighbors in the smoothing
  • modified API for mesh.binarize()
  • plotter.add_hover_legend() now returns the id of the callback.
  • removed settings.render_lines_as_tubes and settings.hidden_line_removal, add plotter.render_hidden_lines() method
  • fix close(), close_window() is now obsolete and removed.

Hard Breaking Changes

Changes that will break existing code and need active thinking and work to adapt

  • None

New/Revised Examples

examples/basic/sliders_hsv.py
examples/basic/buttons1.py
examples/basic/buttons2.py
examples/basic/input_box.py

examples/advanced/warp4b.py
examples/advanced/diffuse_data.py
examples/advanced/moving_least_squares1D.py

examples/volumetric/slab_vol.py
examples/volumetric/streamlines1.py
examples/volumetric/streamlines2.py
examples/volumetric/streamlines3.py
examples/volumetric/streamlines4.py
examples/volumetric/office.py
examples/volumetric/slice_plane1.py
examples/volumetric/slice_plane3.py
examples/volumetric/mesh2volume.py
examples/volumetric/read_volume3.py
examples/volumetric/rectl_grid1.py
examples/volumetric/struc_grid1.py
examples/volumetric/app_raycaster.py
examples/volumetric/isosurfaces1.py
examples/volumetric/isosurfaces2.py

examples/simulations/mag_field1.py
examples/pyplot/andrews_cluster.py

examples/other/madcad1.py
examples/other/tetgen1.py
examples/other/nelder-mead.py
examples/other/fast_simpl.py

tests/issues/issue_968.py
tests/issues/issue_1025.py
tests/issues/test_force_anim.py
tests/snippets/test_discourse_1956.py
tests/snippets/test_ellipsoid_main_axes.py
tests/snippets/test_compare_fit1.py

===================================================================================

Version 2023.5.0

Main changes

Major internal refactoring.

Breaking changes

  • rename internal list plt.actors which now become plt.objects
  • rename .points() to property .vertices. Hence: mesh.points() -> mesh.vertices mesh.points(newpoints) -> mesh.vertices = newpoints
  • rename .cell_centers() to property .cell_centers
  • rename .faces() to property .cells
  • rename .lines() to property .lines
  • rename .edges() to property .edges
  • rename .normals() and split it into property .vertex_normals and property .cell_normals
  • rename picture.Picture2D(...) which becomes Image(...).clone2d() (see examples/pyplot/embed_matplotlib.py).
  • rename Volume.probe_points() which becomes points.probe(volume)
  • rename Volume.probe_line() which becomes line.probe(volume)
  • rename Volume.probe_plane() which becomes plane.probe(volume)
  • rename file_io.load_transform(). LinearTransform("file.mat") substitutes it.
  • rename transform_with_landmarks() to align_with_landmarks()
  • rename find_cells_in() to find_cells_in_bounds()
  • rename mesh.is_inside(pt) moved to mesh.contains(pt)
  • rename Slicer2DPlotter moved to application module.Slicer2DPlotter
  • rename and moved method voronoi() to points.generate_voronoi()
  • rename class Ruler to Ruler3D

Other changes

  • improvements in how vtk classes are imported (allow lazy import)
  • improvements to method mesh.clone2d()
  • improvements in Slicer3DPlotter thanks to @daniel-a-diaz in #925
  • improvements in applications.Browser
  • add new vedo.transformations.py module.
  • add plotter.pick_area() thanks to @ZiguoAtGitHub and @RubendeBruin feedback.
  • add texture to npz files thanks to @zhouzq-thu in #918
  • add background radial gradients
  • add utils.line_line_distance() function
  • add utils.segment_segment_distance() function
  • add plotter.initialize_interactor() method
  • add object hinting by hovering mouse (see flag_labels1.py)
  • add colors.lut_color_at(value) the color of the lookup table at value.
  • add .show(..., screenshot="myfile.png") keyword
  • add object.coordinates same as object.vertices
  • add move() to move single points or objects
  • add copy() as alias to clone()
  • add "Roll" to camera dictionary (thanks @baba-yaga )
  • add applications.Slicer3DTwinPlotter thanks to @daniel-a-diaz
  • add radii feature to smooth_mls_2d() by @jo-mueller (now store results in arrays mesh.pointdata['MLSVariance'] and mesh.pointdata['MLSValidPoint'])
  • passing a vtkCamera to show(camera=...) triggers a copy of the input which is therefore not muted by any subsequent interaction (thanks @baba-yaga )

Bug Fixes

  • bug fix in closest_point() thanks to @goncalo-pt
  • bug fix in tformat thanks to @JohnsWor in #913
  • bug fix in windows OS in timers callbacks thanks to @jonaslindemann
  • bug fix to non linear tranforms mode. Now it can be instantiated with a dictionary
  • bug fix in meshlab interface thanks to @JeffreyWardman in #924
  • bug fix changed mp = matplotlib.colormaps[name] in colors.py

New/Revised Examples

examples/basic/buttons.py
examples/basic/input_box.py
examples/basic/sliders2.py
examples/basic/spline_tool.py
examples/basic/interaction_modes2.py
examples/advanced/timer_callback1.py
examples/advanced/timer_callback2.py
examples/advanced/warp4a.py
examples/advanced/warp4b.py
examples/pyplot/embed_matplotlib.py
examples/pyplot/plot_fxy2.py
examples/simulations/springs_fem.py
examples/simulations/lorenz.py
examples/volumetric/numpy2volume0.py
examples/volumetric/slicer1.py
examples/volumetric/tet_astyle.py
examples/volumetric/tet_cut1.py
examples/volumetric/tet_cut2.py
examples/other/flag_labels1.py

===================================================================================

Version 2023.4.5

Main changes

  • Rename module io.py to file_io.py to avoid overriding stlib io.
  • Complete revision of cutter widgets functionality
  • Integration in napari thanks to @jo-mueller

Breaking changes

  • method plotter.add() no more accepts keyword render=True/False. Please use plotter.add().render() explicitly. Same thing for plotter.remove().

Other fixes and improvements

  • added gpu acceleration for CLI volumetric visualization in #832 by @zhang-qiang-github
  • fixes for k3d jupyter backend
  • added plotter.fov(value) (field of view, the so called "fish-eye" effect)
  • fix ploter.get_meshes()
  • fix for plotter.remove(unpack_assemblies=False) method
  • fix for io.import_window() method
  • added cut_with_cookiecutter() to cut 2D contours.
  • fix shapes.NormalLines() class
  • added vedo.interactor_modes module
  • added vedo.interactor_modes.BlenderStyle class
  • added base.pointdata.clear() to remove all associated data
  • added volume.hide_voxels() for visualization
  • added Event.timerid attribute
  • fix to Volume.operation by @DanKrsi
  • fix links in pyplot examples by @androbaza
  • fix screenshot_scale and remove it from settings.
  • allow initializing ScalarBar with a tuple range (min, max)
  • Update API Documentation for Changing Backend by @bhacha
  • Add application.Browser().play() to autoplay a slider
  • Add pad() to padding a Volume with zeros voxels (useful to dilate())
  • Add ProgressBarWidget() to show a progress bar in the rendering window
  • Fix Scalarbar3D logscale and change separator symbol by @XushanLu
  • Fix vedo/interactor_modes.mouse_left_move() by @MiticoDan
  • Added applications.AnimationPlayer class by @mikaeltulldahl
  • fix convex hull in 2D by @ManuGraiph

New/Revised Examples

examples/basic/sliders_range.py
examples/basic/interaction_modes.py
examples/advanced/timer_callback3.py
examples/advanced/warp6.py
examples/pyplot/histo_1d_e.py
examples/other/tensor_grid2.py
examples/simulations/airplane1.py
examples/simulations/lorenz.py
examples/simulations/gas.py
examples/simulations/aspring2_player.py