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mesh

  • Create meshed system of objects. Use it to run FBEM.
  • Examples of use available in FBEM/example

Features:

  • Create: define simple objects, set density of grid points.
  • Transform: rotate, translate in space
  • Combine: combine objects in a nested dictionary; on each level a transform can be applied.
  • Triangulate: create a triangular mesh (defined by coordinates of nodes, and indices of nodes in each triangle).
  • Visualize: mesh.plot

Create mesh

  • Look at examples
  • Unmeshed objects are kept in a form of nested dictionaries (e.g. (1) object1 -> rotate; (2) object2 -> translate; (3): combine (1)+(2))
  • Meshed objected are stored as Triangulation class with attributes coordinates, triangulation (triangles), velocities;
    • Note: there is some inconsistency with triangulation read from FBEM input files; they are read as two arrays: coordinates, triangles.

mesh.plot

There are different ways to visualize 3D objects in Python: matplotlib, mayavi, trimesh, vedo.

  • Therefore there are several python files for each of these methods. None are perfect. The latest I have been using is vedo.
  • matplotlib is good when you do not want or cannot install other packages for 3D visualization.
  • examples in mesh.plot.example

vedo a.k.a. vtkplotter

  • https://github.com/marcomusy/vedo
  • vedo is built on top of trimesh(?), therefore they work in a similar way.
  • vedo has more features; can plot frame axes, arrows, etc

Installation

Requirements:

vtk=8 # vedo works slower with vtk=9
vedo=2020.4.2

Install via conda-forge channel.

Axes options:

Lights

  • plane.lighting('off') can help with the plane being too light/too dark.
  • But cilia shapes become unrealistic with this option

camera

  • when adding something to the screen should keep resetcam=False
  • plotter.add() resets camera if not render=False
  • in show() set resetcam=False even if camera option is used.

trimesh

Feature-rich library to work with triangular meshes.

  • Visualization of meshes is only one application.
  • Can possibly use it to work with the meshes, e.g.,
    • combine meshes
    • check orientaiton of triangles
    • subdivide meshes

Installation

https://github.com/mikedh/trimesh/

conda install trimesh      # 3.8.4
conda install networkx     # 2.5 # for visualization
# for a pop-up window when run from a script (don't need if run from jupyter lab)
conda install pyglet	   # 1.5.7 
vtk=8 # ?

Usage

  • Hotkeys when called from a python script:
    • w: toggle wireframe view
    • a: toggle axes

mayavi

  • Class MeshViewer to visualize triangulated mesh and velocities, forces
  • mayavi is a very good tool, but I had problems with Windows installation on my machine.

Installation

From conda-forge

mayavi>=4.6
vtk=8

matplotlib

  • Works rather slow.
  • Right now no arrows implemented and can't set aspect ratio.