Vedo

A python module for scientific analysis of 3D objects based on VTK and numpy

Project README

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vedo is a lightweight and powerful python module for scientific analysis and visualization of 3d objects.

✨ Philosophy

Inspired by the vpython manifesto "3D programming for ordinary mortals", vedo makes it easy to work with 3D pointclouds, meshes and volumes, in just a few lines of code, even for less experienced programmers.

vedo is based on VTK and numpy, with no other dependencies.

💾 Installation

pip install vedo
additional installation details (click to expand)
  • As some of the features work better and faster on the older VTK version 8 you can install it via:
    pip install vtk==8.1.2

  • To install the latest dev version of vedo:
    pip install -U git+https://github.com/marcomusy/vedo.git

  • To install from the conda-forge channel:
    conda install -c conda-forge vedo

  • For windows users, we suggest to install anaconda (or miniconda). Command line in windows-10 will then look something like e.g.:
    python c:\path_to\anaconda3\Scripts\vedo panther.stl


📌 Done? Run any of the built-in examples. In a terminal, type e.g.:

vedo -r covid19

Visualize a file from web URL (or your dropbox!), type:

vedo https://vedo.embl.es/examples/data/panther.stl.gz

📙 Documentation

The webpage of the library with documentation is available here.

📌 Need help? Have any question, or wish to ask for a missing feature? Do not hesitate to open a issue (or send an email).

🎨 Features

The vedo library includes a large set of working examples for a wide range of functionalities:

working with polygonal meshes and point clouds (click to expand)
  • Import meshes from VTK format, STL, Wavefront OBJ, 3DS, Dolfin-XML, Neutral, GMSH, OFF, PCD (PointCloud),
  • Export meshes as ASCII or binary to VTK, STL, OBJ, PLY ... formats.
  • Analysis tools like Moving Least Squares, mesh morphing and more..
  • Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..).
  • Split mesh based on surface connectivity. Extract the largest connected area.
  • Calculate areas, volumes, center of mass, average sizes etc.
  • Calculate vertex and face normals, curvatures, feature edges. Fill mesh holes.
  • Subdivide faces of a mesh, increasing the number of vertex points. Mesh simplification.
  • Coloring and thresholding of meshes based on associated scalar or vectorial data.
  • Point-surface operations: find nearest points, determine if a point lies inside or outside of a mesh.
  • Create primitive shapes: spheres, arrows, cubes, torus, ellipsoids...
  • Generate glyphs (associate a mesh to every vertex of a source mesh).
  • Create animations easily by just setting the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is supported.
  • Straightforward support for multiple sync-ed or independent renderers in the same window.
  • Registration (alignment) of meshes with different techniques.
  • Mesh smoothing.
  • Delaunay triangulation in 2D and 3D.
  • Generate meshes by joining nearby lines in space.
  • Find the closest path from one point to another, traveling along the edges of a mesh.
  • Find the intersection of a mesh with lines, planes or other meshes.
  • Interpolate scalar and vectorial fields with Radial Basis Functions and Thin Plate Splines.
  • Add sliders and buttons to interact with the scene and the individual objects.
  • Visualization of tensors.
  • Analysis of Point Clouds:
  • Moving Least Squares smoothing of 2D, 3D and 4D clouds
  • Fit lines, planes, spheres and ellipsoids in space
  • Identify outliers in a distribution of points
  • Decimate a cloud to a uniform distribution.
working with volumetric data and tetrahedral meshes
  • Import data from VTK format volumetric TIFF stacks, DICOM, SLC, MHD and more
  • Import 2D images as PNG, JPEG, BMP
  • Isosurfacing of volumes
  • Composite and maximum projection volumetric rendering
  • Generate volumetric signed-distance data from an input surface mesh
  • Probe volumes with lines and planes
  • Generate stream-lines and stream-tubes from vectorial fields
  • Slice and crop volumes
  • Support for other volumetric structures (structured and grid data)
plotting and histogramming in 2D and 3D
  • Polygonal 3D text rendering with Latex-like syntax and unicode characters, with 14 different fonts.
  • Fully customizable axis styles
  • donut plots and pie charts
  • Scatter plots in 2D and 3D
  • Surface function plotting
  • 1D customizable histograms
  • 2D hexagonal histograms
  • Polar plots, spherical plots and histogramming
  • Draw latex-formatted formulas in the rendering window.
  • Quiver, violin, whisker and stream-line plots
  • Graphical markers analogous to matplotlib
integration with other libraries
  • Integration with the Qt5 framework.
  • Support for FEniCS/Dolfin platform for visualization of PDE/FEM solutions.
  • Interoperability with the trimesh, pyvista and pymeshlab libraries.
  • Export 3D scenes and embed them into a web page.
  • Embed 3D scenes in jupyter notebooks with K3D (can export an interactive 3D-snapshot page here).

⌨ Command Line Interface

Visualize a polygonal mesh from a terminal window simply with e.g.:

vedo my_mesh.obj

Volumetric files (mhd, vti, slc, tiff, DICOM etc..) can be visualized in different modes:

Volume 3D slicing
vedo --slicer embryo.slc
Ray-casting
vedo -g
2D slicing
vedo --slicer2d
Colorize voxels
vedo --lego
slicer isohead viz_slicer lego

Type vedo -h for the complete list of options.

🐾 Examples

vedo currently includes 300+ working examples and notebooks.

cubecut greyscott quatumsine
Easily work with volumes, tetrahedral and polygonal meshes. Turing system of reaction-diffusion between two molecules. Quantum-tunnelling of a particle in a box hitting a sinusoidal potential.
trimesh dolf whisker
Interoperability with external libraries like trimesh, pyvista, and pymeshlab. Support for the FEniCS/Dolfin library for PDE and finite element solutions. Advanced 2D/3D histogramming and plotting capablities.

Galleries

Check out the example galleries organized by subject here:


📜 References

Scientific publications leveraging vedo (formerly known as vtkplotter):

  • X. Diego et al.: "Key features of Turing systems are determined purely by network topology", Physical Review X, 20 June 2018.
  • M. Musy, K. Flaherty et al.: "A Quantitative Method for Staging Mouse Limb Embryos based on Limb Morphometry", Development, 5 April 2018, doi: 10.1242/dev.154856.
  • G. Dalmasso et al., "Evolution in space and time of 3D volumetric images", in preparation.
  • F. Claudi, A. L. Tyson, T. Branco, "Brainrender. A python based software for visualisation of neuroanatomical and morphological data.", DOI.
  • J. S. Bennett, D. Sijacki, "Resolving shocks and filaments in galaxy formation simulations: effects on gas properties and star formation in the circumgalactic medium", Monthly Notices of the Royal Astronomical Society, Vol. 499, Issue 1, Nov. 2020, DOI.
  • J.D.P. Deshapriya et al., "Spectral analysis of craters on (101955) Bennu". (DOI: 10.1016/j.icarus.2020.114252)

Have you found this software useful for your research? Star ✨ the project and cite it as:

M. Musy et al., "vedo, a python module for scientific analysis and visualization of 3D objects and point clouds", Zenodo, 2021, doi: 10.5281/zenodo.4609336.

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Open Source Agenda is not affiliated with "Vedo" Project. README Source: marcomusy/vedo
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