demo13 of Im2mesh package
demo13 - How to use Gmsh as mesh generator in Im2mesh package
Cite as: Ma, J., & Li, Y. (2025). Im2mesh: A MATLAB/Octave package for generating finite element mesh based on 2D multi-phase image (2.1.5). Zenodo. https://doi.org/10.5281/zenodo.14847059
Table of Contents
Note
I suggest familiarizing yourself with Im2mesh_GUI before learning Im2mesh package. With graphical user interface, Im2mesh_GUI will help you better understand the workflow and parameters of Im2mesh package.
Im2mesh_GUI: https://www.mathworks.com/matlabcentral/fileexchange/179684-im2mesh_gui-2d-image-to-finite-element-mesh
If you are using Im2mesh package in MATLAB, you need to install MATLAB Image Processing Toolbox and Mapping Toolbox because Im2mesh package use a few functions in these toolboxes.
Setup
Before we start, please set folder "Im2mesh_Matlab" as your current folder of MATLAB.
clearvars
Set default image size.
x = 250; y = 250; width = 250; height = 250;
set(groot, 'DefaultFigurePosition', [x,y,width,height])
% To reset:
% set(groot, 'DefaultFigurePosition', 'factory')
We add the folder 'mesh2d-master' to the path of MATLAB.
addpath(genpath('mesh2d-master'))
We need to know the location of gmesh.exe
% for example
path_to_gmsh = 'C:\Users\Jason\Downloads\gmsh-4.13.1-Windows64\gmsh.exe';
Get boundries from image
We have demostrate how to do this in example3 of demo01.mlx
im = imread('Shape.tif');
if size(im,3) == 3; im = rgb2gray( im ); end
opt = []; % reset opt
opt.tolerance = 0.3;
opt.tf_mesh = false;
bounds = im2mesh( im, opt );
% bounds is the simplified polygonal boundaries
plotBounds( bounds );
Phase selection before meshing
Suppose we don't need the background.
select_phase = [2 3 4];
bounds = bounds( select_phase );
plotBounds( bounds );
Unstructured triangular mesh
Write geo file for Gmsh
geo file is a text file that contains Gmsh’s own scripting language. It’s used to define geometry and mesh generation instructions for Gmsh.
We use function bounds2geo to generate geo file.
% setup parameters
opt = []; % reset
opt.sizeMin = 0.1;
opt.sizeMax = 6;
opt.algthm = 6;
opt.recombAll = 0;
opt.recombAlgthm = 3;
opt.eleOrder = 1;
opt.num_split = 0;
opt.grad_mode = 0;
path_to_geo = 'gmshTemp.geo';
bounds2geo( bounds, path_to_geo, opt );
We will see a geo file 'gmshTemp.geo' generated in the current working folder of MATLAB.
There are many parameters for function bounds2geo. You can open bounds2geo.m to take a look at their meanings
Here is the general guideline for choosing the value of these parameters:
1. To generate triangular mesh, you can set opt.algthm to 1-7 and set opt.recombAll to 0.
2. To generate unstructured quadrilateral mesh, you can set opt.algthm to 8 and set opt.recombAll to 1. You can try different opt.recombAlgthm.
3. To generate quasi-structured quadrilateral mesh, you can set opt.algthm to 11 and set opt.recombAll to 0.
4. When opt.grad_mode is 0, you can adjust the value of opt.sizeMax to achieve better mesh quality. Typical value of opt.sizeMax is 4 to 20.
5. When opt.grad_mode is 1, you can adjust opt.sizeAtBound, opt.sizeSlope, and opt.sizeMax to achieve better mesh quality.
6. When opt.grad_mode is 2, you can set opt.sizeAtBound to a larger value (e.g., 10-500) and adjust opt.sizeSlope.
Generate mesh via Gmsh
After we got the geo file, we use the following command to send the geo file to Gmsh. Gmsh will generate a m file 'gmshTemp.m'.
path_to_m = 'gmshTemp.m';
verbosity = 3;
str=sprintf('"%s" "%s" -o "%s" -v %i -save', ...
path_to_gmsh, path_to_geo, path_to_m, verbosity );
system(str);
When we run the m file, we will see a struct variable 'msh' in the workspace of MATLAB.
% run m file
run(path_to_m)
msh
Then, we can use function extractMsh to extract nodes and elements from the struct variable 'msh'. Function extractMsh also works for quadratic elements.
[vert,ele,tnum] = extractMsh( msh );
Plot mesh
plotMeshes(vert,ele,tnum)
We can use function tricost to check the mesh quality. Function tricost is written by by Darren Engwirda.
tricost( vert, ele, tnum );
Export mesh via Gmsh
After we got the mesh, we can use Gmsh or the functions in demo03 to export it. Suppose we want to export as stl file 'gmshExport.stl'.
path_to_file = 'gmshExport.stl';
verbosity = 3;
str=sprintf('"%s" "%s" -o "%s" -v %i -save', ...
path_to_gmsh, path_to_geo, path_to_file, verbosity );
system(str);
We should be able to see a file 'gmshExport.stl' in current working folder of Matlab.
Unstructured quadrilateral mesh
Write geo file and generate mesh via Gmsh
We can use Gmsh to generate unstructured quadrilateral mesh by setting opt.algthm to 8 and set opt.recombAll to 1.
% setup parameters
opt = []; % reset
opt.sizeMin = 0.1;
opt.sizeMax = 6;
opt.algthm = 8;
opt.recombAll = 1;
opt.recombAlgthm = 3;
opt.eleOrder = 1;
opt.num_split = 0;
opt.grad_mode = 0;
path_to_geo = 'gmshTemp.geo';
bounds2geo( bounds, path_to_geo, opt );
path_to_m = 'gmshTemp.m';
verbosity = 3;
str=sprintf('"%s" "%s" -o "%s" -v %i -save', ...
path_to_gmsh, path_to_geo, path_to_m, verbosity );
system(str);
Gmsh will generate a m file. When we run the m file, we will see a struct variable 'msh' in the workspace of MATLAB.
% run m file
run(path_to_m)
msh
Then, we can use function extractMsh to extract nodes and elements from the struct variable 'msh'. Function extractMsh also works for quadratic elements.
[vert,ele,tnum] = extractMsh( msh );
Plot mesh
plotMeshes(vert,ele,tnum)
Awesome!
Mesh quality
We can use function MeshQualityQuads (written by Allan Peter Engsig-Karup) to evaluate mesh quality.
[Q,theta] = MeshQualityQuads( ele(:,1:4), vert(:,1), vert(:,2) );
Mean value of Q
mean_Q = mean(Q)
mean_Q = 0.6407
Standard deviation of theta (in degree)
std_theta = std( rad2deg(theta(:)) )
std_theta = 15.1891
Plot histogram of Q
histogram( Q, 'BinWidth', 0.02, 'BinLimits', [0,1], ...
'EdgeColor', 'none');
xlabel('Q','FontSize',10,'FontWeight','bold');
pbaspect([2 0.6 1]);
After we got the mesh, we can use Gmsh or the functions in demo03 to export it.
% reset image size
set(groot, 'DefaultFigurePosition', 'factory')
% end of demo