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A python class for scientific visualization of 3D objects with VTK
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README.md

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A pure python module for scientific visualization, analysis and animation of 3D objects and point clouds based on VTK and numpy.

Download and Install:

Use pip to install:

pip install vtkplotter

Windows-10 users can place this file vtkplotter.bat on the desktop to drag&drop files to visualize. (Need to edit the path of the local Anaconda installation).

Documentation

Automatically generated documentation can be found here.

Features

Intuitive and straightforward API which can be combined with VTK seamlessly in a program, whilst mantaining access to the full range of VTK native classes.

It includes a large set of working examples for all the following functionalities:

  • Import meshes from VTK format, STL, Wavefront OBJ, 3DS, XML, Neutral, GMSH, OFF, PCD (PointCloud), volumetric TIFF stacks, DICOM, SLC, MHD, 2D images PNG, JPEG.
  • Export meshes as ASCII or binary to VTK, STL, OBJ, PLY formats.
  • Mesh analysis through the built-in methods of VTK package. Additional analysis tools like Moving Least Squares, mesh morphing.
  • Tools to visualize and edit meshes (cutting a mesh with another mesh, slicing, normalizing, moving vertex positions, etc..). Interactive cutter widget.
  • Split mesh based on surface connectivity. Extract the largest connected area.
  • Calculate mass properties, like area, volume, center of mass, average size 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 a mesh.
  • Create primitive objects like: spheres, arrows, cubes, torus, ellipsoids...
  • Generate glyphs (associating a mesh to each vertex of a source mesh).
  • Create animations easily by just defining the position of the displayed objects in the 3D scene. Add trailing lines and shadows to moving objects is also supported.
  • Straightforward support for multiple sync-ed or independent renderers in the same window.
  • Registration (alignment) of meshes with different techniques.
  • Mesh smoothing with Laplacian and WindowedSinc algorithms.
  • Delaunay triangulation in 2D and 3D.
  • Generate meshes by joining nearby lines in space.
  • Find the closest path from one point to another, travelling along the edges of a mesh.
  • Find the intersection of a mesh with a line (or with another mesh).
  • Analysis of Point Clouds:
    • Moving Least Squares smoothing of 2D, 3D and 4D clouds
    • Fit lines, planes and spheres and ellipses in space
    • Identify outliers in a distribution of points
    • Decimate a cloud to a uniform distribution.
  • Basic histogramming and function plotting in 1D and 2D.
  • Interpolate scalar and vectorial fields with Radial Basis Functions and Thin Plate Splines.
  • Analysis of volumetric datasets:
    • Isosurfacing of volumes
    • Direct maximum projection 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
  • Add sliders and buttons to interact with the scene and the individual objects.
  • Fully customizable axis style.
  • Draw latex-formatted formulas on the rending window.
  • Examples using SHTools package for spherical harmonics expansion of a mesh shape.
  • Integration with the Qt5 framework.
  • Support for FEniCS/Dolfin platform for visualization of finite-element calculations.
  • Visualization of tensors.
  • Export a 3D scene and embed it into a web page.
  • Embed the 3D rendering in a jupyter notebook with K3D (can export an interactive 3D-snapshot page here).
  • Interoperability with the trimesh library.

Command Line Interface

Visualize a mesh from a terminal window with:

vtkplotter 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]

Voxel-data (mhd, vti, slc, tiff, dicom etc..) files can be visualized with options -g. E.g.:
vtkplotter -g examples/data/embryo.slc

isohead

To visualize multiple files or files time-sequences try -n or -s options. Use -h for the complete list of options.

Use a slider to control isosurfacing of a volume: Load and browse a sequence of meshes: Slice a 3D volume with a plane: Visualize colorized voxels:
vtkplotter head.vti vtkplotter -s *.vtk vtkplotter
--slicer embr.slc
vtkplotter --lego embryo.slc
isohead viz_raycast viz_slicer lego

GUI

A Graphic User Interface is available (mainly useful to Windows 10 users): gui

Examples Gallery

A get-started tutorial script is available for download:

git clone https://github.com/marcomusy/vtkplotter.git
cd vtkplotter/examples
python tutorial.py

More than 260 working examples can be found in directories (scroll down to see the screenshots):
examples/basic
examples/advanced
examples/volumetric
examples/simulations
examples/other
examples/other/dolfin
examples/other/trimesh
examples/notebooks.

Apply a Moving Least Squares algorithm to obtain a smooth surface from a to a large cloud of scattered points in space (script)
rabbit
airplanes
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).
gyro
qsine2
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)
Visualizing a Turing system of reaction-diffusion between two molecules1 (script)
turing
dolf
Support for the FEniCS/Dolfin platform for visualization of PDE and finite element solutions (see here)

References

  • M. Musy, G. Dalmasso, J. Sharpe and N. Sime, "vtkplotter: 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 using vtkplotter so far:

  1. X. Diego et al.: "Key features of Turing systems are determined purely by network topology", Physical Review X, 20 June 2018.
  2. 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.
  3. G. Dalmasso et al., "Evolution in space and time of 3D volumetric images", in preparation.

Have you found this software useful for your research? Please cite it as:
M. Musy et al. "vtkplotter, 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.

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