Plotting and output

Plotting

The plotting functions require a Makie backend: CairoMakie for images, GLMakie for interactive windows, or WGLMakie for the browser.

• plot_mesh: the compartments of a mesh, with colors and transparency per compartment;

• plot_field: a field on the mesh, such as the magnetization (magnitude, real or imaginary part, or phase);

• plot_hardi: values (signals, ADCs) in many directions, as a glyph;

• plot_surfaces: the surfaces of a geometry, before meshing.

The functions with a ! (plot_mesh!, plot_field!, plot_hardi!) plot into a given axis, for figures with several panels:

using CairoMakie
fig = Figure()
plot_mesh!(Axis3(fig[1, 1]; aspect = :data), mesh)
plot_field!(Axis3(fig[1, 2]; aspect = :data), mesh, u)
fig

In 3D, the surfaces of the compartments are shown: samples of periodic tissue show the cross-sections of the cells on the faces of the box.

Following the time stepping

The Plotter callback plots the gradient, the signal attenuation and the magnetization during the time stepping (live with GLMakie). Printer prints information, and VTKWriter saves the magnetization at the time steps for ParaView.

Files

• save_field saves a field on the mesh in the VTK format;

• save_geometry and load_geometry store a geometry in a JLD2 file (using JLD2);

• SpinDoctor.read_gmsh reads volume meshes in the Gmsh format.