vedo: A Python repository from icemtel

vedo is a fast and lightweight 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 three-dimensional meshes and volumes, creating displays and animations in just a few lines of code, even for those with less programming experience.

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

🎯 Table of Contents

💾 Installation

Use pip to install. Type:

pip install vedo

# To get the latest dev version use:
pip install -U git+https://github.com/marcomusy/vedo.git

or from the conda-forge channel:

conda install -c conda-forge vedo

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

vedo -r covid19

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

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

Visualize a whole scene, type:

vedo https://vedo.embl.es/examples/geo_scene.npy

Windows-10 users can place vedo.bat on the desktop to drag&drop files to visualize (need to edit the path of your local python installation).

📙 Documentation

Automatically generated documentation can be found here.

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

🎨 Features

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

working with polygonal meshes and point clouds (click triangle 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 ellipses 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 a volume 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

- 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 plots

- Stream line plots

- Point markers analogous to matplotlib

Moreover:

Polygonal 3D text rendering with Latex-like syntax and unicode characters, with 14 different fonts.
Integration with the Qt5 framework.
Support for FEniCS/Dolfin platform for visualization of finite-element calculations.
Interoperability with the trimesh library.
Export 3D scenes and embed 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:

vedo mymesh.obj
# valid formats: [vtk,vtu,vts,vtp,vtm,ply,obj,stl,3ds,dolfin-xml,neutral,gmsh,
#                 pcd,xyz,txt,byu,tif,off,slc,vti,mhd,dcm,dem,nrrd,nii,bmp,png,jpg]

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

Slice a volume in the 3 planes: `vedo --slicer embryo.slc`	Ray-casting rendering: `-g embryo.slc`	2D slice: `--slicer2d`	Colorize voxels: `--lego`

To visualize multiple files or files time-sequences try -n or -s options. Use -h for the complete list of options.
A GUI is also available (mainly useful to Windows 10 users) which can be invoked with command vedo.

🐾 Examples

300+ working examples can be found in directories:
examples/basic
examples/advanced
examples/volumetric
examples/tetmesh
examples/simulations
examples/pyplot
examples/other
examples/other/dolfin
examples/other/trimesh
notebooks


Apply a Moving Least Squares algorithm to obtain a smooth surface from a to a large cloud of scattered points in space (script)	Create a simple 3D animation in exactly 10 lines of code (script). Trails and shadows can be added to moving objects easily

Simulation of a gyroscope hanging from a spring (script)	Quantum-tunnelling effect integrating the Schroedinger equation with 4th order Runge-Kutta method. The animation shows the evolution of a particle in a box hitting a sinusoidal potential barrier. (script)

Turing system of reaction-diffusion between two molecules (script)	Interoperability with the trimesh library (see here)

Support for the FEniCS/Dolfin platform for visualization of PDE and finite element solutions (see here)

Random Gallery of Examples

Run any of the following built-in examples from command line. Type: