Medit: fast and light mesh inspection and vizualization

1. Installation
2. Prerequisite
3. Mesh inspection with Medit
4. Solution vizualization
5. Animation
6. Modification of default view and preferences
7. Mesh edition:
8. To go further: read the documentation or the code

This file is available online at:
https://sed-bso.gitlabpages.inria.fr/formations/MdB-Medit/MdB-Medit.html

Medit is a software dedicated to fast and light mesh inspection and vizualization (based on shortcuts).

1. Installation

Official repository: https://github.com/ISCDtoolbox/Medit.
My fork (adds support of retina screen + multiple solution fields):https://github.com/Algiane/Medit.

Get sources

wget https://github.com/Algiane/Medit/archive/refs/heads/master.zip -O medit.zip
unzip medit.zip

Install dependencies
- on Ubuntu
  - development tools:
```
apt install -y cmake g++
```
  - graphic tools:
```
apt install -y freeglut3-dev
```
- on Mac OSX Here I suppose that Xcode development tools and homebrew are already installed
  - development tools:
```
brew install -y cmake
```
  - graphic tools:
```
brew install freeglut
```

Build and install Medit (and add it to your PATH)

cd Medit-master && cmake -S. -Bbuild
make install -Cbuild
export PATH=$HOME/bin:$PATH

2. Prerequisite

A mouse;
A terminal;

A mesh at medit .mesh file format (GMF file format v5, readable using the libMeshb library);

cat > 1tri.mesh <<EOF
MeshVersionFormatted 2

Dimension 2

Vertices 3
0. 0. 0
1. 0. 0
0. 1. 1

Triangles 1
1 2 3 0

Edges
2
1 2 0
1 3 1

End
EOF

Optionnally: a solution file at medit .sol file format:

cat > 1tri.sol <<EOF
MeshVersionFormatted 2

Dimension 2

SolAtVertices 3
1
1
5.
4.
3.
End
EOF

Figure 1: Mesh example

Download the meshes needed for this MdB:

wget https://static.bordeaux.inria.fr/mmg/MdB-meshes.zip
unzip MdB-meshes.zip

3. Mesh inspection with Medit

File opening:
- In your terminal:
```
medit MdB-meshes/medit-visu.mesh
```
- /!\ bug on hdpi screen: run medit with src r option rif mesh appears on lower half quarter of the graphic window (see [[2]])
```
medit -r MdB-meshes/medit-visu.mesh
```

Figure 2: Hdpi bug

Number of entities in the mesh and bounding box size are printed in terminal;

Medit can be launched with other options (tested later):
- -a: to load a series of files and create 'a'nimations;
- -s: to forbid the construction 's'urfaces in a mesh containing only volume elements.

Mouse commands:
- left click + movement: mesh rotation;
- middle click + movement: mesh translation;
- right click: menu with shortcuts reminder;
- Maj + left click on mesh element: highlight element and prints element index, connectivity, reference and point coordinates in terminal;
- Maj + middle click on mesh point: highlight point (and solution if exists) and prints point index, coordinates and reference (and solution value if exists).

Main shortcuts (has to be runned with the medit window selected):
- h: online 'h'elp;
- z: 'z'oom in, Z: 'Z'oom view;
- +~/-~: scale object;
- b: 'b'ackground color;
- g: show/hide 'g'eometric features (ridge edges, corners and required points provided in the mesh);
- c: show/hide 'c'olors (from element type?), e: show/hide 'e'ntity colors from materials (ref fields of the mesh)
- l: show/hide mesh 'l'ines;
- f: show/hide mesh 'f'aces;
- P: show/hide 'P'points numbering;
- F: show/hide 'F'aces numbering;
- # in Medit window + <n> in the terminal: shows element, face and point of index <n>;
- V: center 'V'iew on selected entity.
- s: 's'uppress selected element; (/!\ no possible undo);
  Useful to check for element duplication or recovering. Try to suppress triangle num 29… there is a duplicated triangle below (you dan suppress it too, to check that it is the only one)!
- r: 'r'emove selected material, R: undo previous 'R' removal;
- N: show/hide 'N'ormals and tangent (if present in the mesh file);
- O: 'O'pposite normals;
- n: show/hide smooth shading computed from 'n'ormals;

Deal with cutting planes in 3D:
- F1: Clip/ unclip plane;
- F2: Enable/disable plane displacement (same movements as for mesh displacement);
- F3: Enable/disable mesh displacement with freezed plane;
- F4: Show/hide volume elements;
- C: cut/uncut elements that intersect cutting plane;
- right click -> clipping -> Toogle plane: show/hide representation of the cutting plane;
- right click -> clipping -> Inverse orient: invert cutting plane;

Link multiple meshes for comparative views: Open multiple files (or multiple times the same file) at the same time
```
medit MdB-meshes/medit-visu.mesh MdB-meshes/medit-visu.mesh MdB-meshes/medit-visu.o.mesh
```
- you can link mesh serially using Alt-c on origin window (for 'c'opy), Alt-l on window to link (for 'l'ink);
- try to link window B with window A, then window C with B. Now, modifications of the view done in A are reported in B and C too.
Exploded view:
- F5: switch between Eploded / normal view;
- F6: increase explosion factor;
- F7: decrease explosion factor;
Look between triangles 2389 and 2720: there is quasi degenerated triangle! By default, only the surface of mesh is represented, exploded view of tetra can be preinted using cutting plane.

View without surface reconstruction:
- You can set the number of a given entity to 0 in the .mesh file to ignore it (check the diff between medit-visu.mesh and medit-visu-nosurf.mesh). By default, Medit reconstruct surface triangles from tetra.
```
diff  MdB-meshes/medit-visu.mesh  MdB-meshes/medit-visu-nosurf.mesh
medit MdB-meshes/medit-visu-nosurf.mesh
```
  Shadows in colors are due to the orientation of created triangles. Removing shading with n solve the visu issue.
- To forbid this reconstruction and visualize only volume elements:
```
medit -s MdB-meshes/medit-visu-nosurf.mesh
```
  Try to find vertex 2816, to center the mesh and to explode the view: there is a degenerated tetra too. To have a better view, we can remove some of the neighbouring tets.

4. Solution vizualization

If a .sol file is attached to your mesh, it is automatically opened. Open naca-multiSols.mesh fild:

medit MdB-meshes/naca-multiSols

Main shortcuts to visualize sol fields are:

m: to show/hide the color 'm'ap of the solution;
p: to show/hide the palette of colors (palette range can be modified using Medit preferences);
o: to show isolines (In 3D isosurfaces can be shown using menu).
k: to view scalar field as an elevation coeff (to combine with mesh lines l and isolines o)
> and <: to view next or previous solution field;
w: show/hide vectors of vectorial field;
v: add streamline passing to a selected vertex (for a vectorial field).

You can test the last 2 options on the second field of the mesh. When a vertex is clicked, the index of the field and the field value at point is printed in the terminal.
Go to the field number 9:

a SDP tensorial field is seen as an ellipsoïd that represent the unit ball prescribed by the SDP tensor (surface of the ellipsoid is at distance 1 of the vertex in the metric space prescribed by the tensor). It is very useful when computing anisotropic size map for mesh adaptation

Note that the Data menu appears only if there is a solution attached to the mesh and changes depending on the solution type (with multiple solutions it doesn't change and shows only a part of the possibilities).

5. Animation

You can open and visualize a temporal solution by:

saving a series of meshes under the form <basename>.<i>.mesh, where i is an integer that provides the time step (i values have to be contiguous);
running medit with -a option followed by the indices of the first and last time step that you want to visualize:

medit -a 1 400 MdB-meshes/anim/lag-mot2D

right-click -> animation -> play sequence: runs the animation;
animation can be saved at ppm format (series of images) using right-click -> animation -> Toogle imgSave and playing the animation;
then, ppm files can be converted into animated gif using convert (ImageMagick: https://imagemagick.org/index.php):

infile="lag-mot2D"
lastit=100

# rename files to have all indices in same format (order of images is wrong otherwise)
for i in {1..$lastit}
do
 printf -v ic "%03d" $i
 mv $infile.$i.ppm $infile.$ic.ppm
done
convert *.ppm -coalesce -delay 1 video.gif

6. Modification of default view and preferences

Open mesh medit-visu.mesh:

medit MdB-meshes/medit-visu.mesh

E: allows to 'E'dit colors and transparancy of a given material (an element has to be selected).
- Diffuse values allow to change colors (first 3 values) transparancy (last value) of material.
W: 'W'rites configuration file
- if file is named DEFAULT.medit, it applies to all meshes, otherwise, preferences applies only to mesh with same basename that the .medit file.
- file can be manually edited to choose a given color palette, background colors, windows size, etc..
- entire list of readed keywords is available in the parsop function of parsop.c file. For example, you can change: linecolor, linewidth, edgewidth, isowidth, pointsize, sunposition…

7. Mesh edition: