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

New Contributors

• @daizhirui made their first contribution in #983
• @JeffreyWardman made their first contribution in #988
• @PeterMitrano made their first contribution in #1000
• @Louis-Pujol made their first contribution in #1016

Full Changelog: v2023.5.0...v2024.5.1

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

2023.4.6

This release only fixes a bunch of small but annoying bugs in the previous.

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

2023.4.4

Main changes

• New API docs
• added cli functionality with vedo --search-code to inspect the code for keywords
• method tomesh() changed to generate_mesh()
• fix for mark_boundaries()
• use vtkStaticCellLocator instead of vtkCellLocator
• improved pointcloud.density() function
• add utils.progressbar()
• add trame examples
• add utils.is_ragged() to check if an array is homogeneuos (not ragged)
• fix shapes.Lines() class
• add shapes.ThickTube() as per #800
• add settings.backend_autoclose (default is True) to automatically close Plotter after show() in jupyter notebooks, #802
• fix k3d backend - remove pinning to 2.7.4 #808
• in Text2D and Text3D shortcut to symbols are now formatted as :gamma and no more as \gamma
• fix mesh.stretch() thanks to @mikaeltulldahl in #807
• fixes to cmap()
• added mesh.is_manifold() method #813
• added utils.open3d2vedo() and utils.vedo2open3d converters as per #663
• added mesh.non_manifold_faces() to detect and (try to) remove non-manifold faces of a triangular mesh #813 #663 and SlicerIGT/SlicerBoneReconstructionPlanner#35
• added pointcloud.compute_acoplanarity() method
• add pipeline visualization with syntax any_vedo_obj.pipeline.show() or interactively by clicking an object and pressing y.
• fixes to Button class
• in map_points_to_cells() added keyword move in #819 @19kdc3
• fix flagpost() by creating a new class addons.Flagpost() in #821 @ZiguoAtGitHub
• add vedo.io.Video(backend='imageio') support for video generation
• add vedo.io.Video.split_frames() of an already existing video file.
• add Picture2D class
• add mesh.slice()
• added __repr_html__ for all types (thanks to @haesleinhuepf input)
• added treelib for pipeline representation
• fixes to dolfin support MeshActor

---

New/Revised Examples

examples/basic/mousehover0.py
examples/advanced/timer_callback0.py
examples/simulations/lorenz.py
examples/pyplot/embed_matplotlib.py
examples/other/trame_ex1.py
examples/other/trame_ex2.py
examples/other/trame_ex3.py
examples/other/make_video.py
examples/other/dolfin/ex06_elasticity4.py
examples/notebooks/test_types.ipynb
examples/notebooks/slider2d.ipynb

2023.4.3

Main changes

• Important fixes for numpy 1.24 @jo-mueller (also relevant to brainglobe/brainrender#226 (comment) by @FedeClaudi @johnmbarrett )
• fixed interface to pymeshlab==2022.2.post2
• fixed #774 intersect_with_line()
• fixed exporting to x3d for assemblies
• added support to calarbars into assemblies, thanks to @j042 in #779
• fix typos #780
• settings.allow_interaction is now (temporarily) disabled.
• added example basic/shadow3.py (thanks to @paul0noah in #767)
• fix on OSX window focusing
• various fixes for windows OS

• add VTK_HEXAHEDRON to vedo.vtkclasses by @j042 in #762
• minor typo fix by @j042 in #780
• Keep scalarbar(s) in Assembly by @j042 in #779

New Contributors

• @j042 made their first contribution in #762

New/Revised examples

examples/basic/shadow3.py
examples/other/pymeshlab1.py
examples/other/pymeshlab2.py

Full Changelog: v2022.4.2...v2023.4.3

2022.4.2

Main changes

---

base.py

• added basegrid.extract_cells_on_plane()
• added basegrid.extract_cells_on_sphere()
• added basegrid.extract_cells_on_cylinder()
• added count_vertices() method
• added copy_data_from() method to transfer all cell and point data from an object to another.
• fixed metadata association

---

pointcloud.py

• added cut_with_planes() to cut at once with multiple planes
• added generate_random_data() for testing purposes
• renamed vignette() to flagpole()
• added new flagpost() similar to the above
• added new property pointcloud.cellcolorsand pointcolors
  to access and modify colors by RGBA assignment.
• added compute_camera_distance() to calculate the distance from points to the camera.
  A pointdata array is created with name 'DistanceToCamera'.
• added cut_with_scalars() to cut polygonal data with some input scalar data.

---

mesh.py

• improved binarize() method thanks to @vfmatzkin
• added collide_with() to fix crashing of intersect_with() in special cases
• added check_validity()
• added method=4 for subdivide()
• added intersect_with_plane()
• added boolean(..., method=1)
• added intersect_with_multiplanes() to generate a set of lines from cutting a mesh in n intervals
  between a minimum and maximum distance from a plane of given origin and normal.

---

plotter.py

• fixed key bindings for uppercase hits.
• added method add_hint() to generate a pop-up message on hovering an object
• fix output of template camera when pressing "C"
• improved move_camera()
• added key-press R to reset camera viewup to closest orthogonal viewup
  added corresponding method plotter.reset_viewup()
• added press . to fly to last clicked point and zoom in

---

picture.py

• generate false colors for an image with Picture().cmap()

---

pyplot.py

• clicking on a histogram shows the bin value
• add as2d() method to freeze a plot in 2d canvas, without mouse interaction (experimental)

---

shapes.py

• Added support for chinese and japanese chars
• Added font "ComicMono"
• added possibility to create a disc sector in Disc(angle_range=...)

---

tetmesh.py

• added compute_tets_volume()
• added check_validity()

---

volume.py

• added vtkFlyingEdges3D instead of contouring, which is faster.

---

Examples

New/Revised

examples/basic/color_mesh_cells1.py
examples/basic/color_mesh_cells2.py
examples/pyplot/fit_curve.py
examples/pyplot/histo_2d_a.py
examples/pyplot/histo_2d_b.py
examples/other/flag_labels2.py
examples/volumetric/image_false_colors.py

2022.4.1

This version includes various fixes, but the most important thing is that it implements the snake_case naming scheme (instead of camelCase) for all class methods and functions, so e.g. code like this
(in vedo==2022.3.1):

mesh = Mesh("bunny.obj")
mesh.cutWithPlane()

now becomes (in vedo==2022.4.1):

mesh = Mesh("bunny.obj")
mesh.cut_with_plane()     ##### <----

Check out the docs in case of doubts.

See discussion #705
@jkissi @zhang-qiang-github @XushanLu @Gjacquenot @FedeClaudi @ManuGraiph @infinity77 @lukablagoje @LogWell @Amin-Fakia @nantille

---

addons.py

• improved slider callback interface

---

mesh.py

• fixed issue #593

---

volume.py

• can warp scalars in a volumetric dataset with warp()

New/Revised Examples

examples/pyplot/fill_gap.py
examples/basic/sliders_hsv.py
examples/volumetric/slicer2.py
examples/volumetric/warp_scalars.py
examples/other/qt_window3.py

2022.3.0

Main changes

• pep8 parsing with pylint and general cleanup of the code.
• Volume(np_array) does not need array to be transposed anymore. Warning: this may cause flipping of the x-z axes!

---

applications.py

• added SplinePlotter object

---

pointcloud.py

• bug fix in clone()
• added labels2D()
• added logscale for colormapping in method cmap(..., logscale=True)
• added explicit label formatting for scalarbars, @XushanLu

---

plotter.py

• added breakInteraction() to break window interaction and return to the python execution flow

---

picture.py

• added class MatplotlibPicture to embed matplotlib figures as 2d objects in the scene.

---

shapes.py

• Added text() method to update 3d text on the fly, by @mkerrin
• Added pcaEllipse() analogous to pcaEllipsoid() for 2D problems.

---

utils.py

• added getUV() method to get the texture coordinates of a 3D point

---

volume.py

• Volume(np_array) does not need array to be transposed anymore. Warning: this may cause flipping of the x-z axes!
• added slicePlane(autocrop=False)

---

Examples

New/Revised

examples/basic/input_box.py
examples/basic/pca_ellipse.py
examples/advanced/capping_mesh.py
examples/volumetric/numpy2volume2.py
examples/volumetric/numpy2volume1.py
examples/pyplot/fourier_epicycles.py
examples/pyplot/histo_pca.py
examples/pyplot/histo_1d_b.py
examples/other/flag_labels.py
examples/other/remesh_tetgen.py
examples/other/pymeshlab2.py

2022.2.3

This release includes various improvements and bug fixes

---

base.py

• alignToBoundingBox() change the default behavior to match exactly the target (affine transform) @jsaintauret
• added getRGBA() to obtain the actual colors from an object as rendered

---

pointcloud.py

• addTrail() simplified.

---

mesh.py

• isInside(..., returnIds=True) fixed bug

---

plotter.py

• added lookAt(plane='xy') to move the camera to face one of the cartesian planes
• removed plotter.load() as not really necessary and potentially confusing

---

pyplot.py

• add legends to Figures thanks to new method addLegend()

---

shapes.py

• moved volume.streamLines to shapes.StreamLines

---

volume.py

• added mask(vol) to mask the visualization of a volume

---

Examples

New/Revised

examples/basic/shadow2.py
examples/basic/deleteMeshPoints.py
examples/basic/ssao.py
examples/basic/align6.py
examples/basic/pca_ellipsoid.py
examples/advanced/gyroid.py
examples/volumetric/volumeOperations.py
examples/volumetric/streamlines1.py

examples/simulations/orbitals.py
examples/simulations/mag_field1.py
examples/simulations/mag_field2.py
examples/simulations/pendulum_3d.py

examples/pyplot/histo_1d_b.py
examples/pyplot/fitPolynomial1.py
examples/pyplot/plot_extra_yaxis.py

examples/other/pygeodesic1.py
examples/other/qt_cutter.py

Deleted

examples/other/animation1.py
examples/other/animation2.py
examples/simulations/alien_life.py
examples/simulations/cell_colony.py