sallyhjkim / vedo Goto Github PK

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

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 less experienced programmers.

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

pip install vedo

# To get the latest dev version use instead:
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

Automatically generated 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).

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

Visualize a polygonal mesh from a terminal window simply with:

vedo my_mesh.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:

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

Type vedo -h for the complete list of options.

vedo currently includes 300+ working examples and notebooks.

Create a simple 3D animation in exactly 10 lines of code.	Turing system of reaction-diffusion between two molecules.	Quantum-tunnelling of a particle in a box hitting a sinusoidal potential.
Interoperability with the trimesh library.	Support for the FEniCS/Dolfin library for PDE and finite element solutions.	Advanced 2D histogramming and plotting capablities.

Run any of the built-in examples from command line by typing:

vedo --run covid19

covid19	caption	font	fonts
wave_equation	doubleslit	tunnelling1	morphing_2d
least_squares2d	mesh_lut	particle_simulator	gyroscope1
customaxes	intersect2d	goniometer	tet_threshold
plot_density3d	meshquality	isolines	tet_cutmesh1
geological	multirender	cartoony	streamlines4
graph_network	graph_lineage	silhouette1	silhouette2
gyroscope2	thinplate_grid	trail	quadratic_morphing
shrink	mesh_custom	spring	lorentz
sliders1	fitspheres1	fxy	histo_1D
plot2_errband	histo_2D	histo_hex	plot5_spheric
boolean	brownian2D	gas	self_org_maps2d
geodesic	convexHull	flatarrow	latex
legosurface	streamlines2	office.py	value-iteration
shadow	multiple_pend	interpolateVolume	histo_polar
plot7_stream	histo_violin	plot3_pip	histo_spheric
read_vts	donut	extrude	plot1_errbars
elastodynamics	heatconv	stokes	stokes_lshape

Presentations at interantional conferences:

• M. Musy, G. Dalmasso, J. Sharpe and N. Sime, "vedo: plotting in FEniCS with python", (link). Poster at the FEniCS'2019 Conference, Carnegie Institution for Science Department of Terrestrial Magnetism, Washington DC, June 2019.
• G. Dalmasso, "Evolution in space and time of 3D volumetric images". Talk at the Conference for Image-based Modeling and Simulation of Morphogenesis. Max Planck Institute for the Physics of Complex Systems, Dresden, Germany, March 2019.

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." bioRxiv 2020.02.23.961748; doi: https://doi.org/10.1101/2020.02.23.961748

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 visualization and analysis of 3D objects and point clouds based on VTK (Visualization Toolkit)", Zenodo, 10 February 2019, doi: 10.5281/zenodo.2561402.