ProMeshScripts

Biofilm grid generation requires four 2d point coordinates specifying the bounding box of the biofilm as a rectangle. Additionally so called towers, 2d polygons, are specified by 2d point coordinates to define sub-populations or domains of bacteria.

• polygonal_mesh_from_txt - creates 2d polygonal meshes from plain text files.

Build instructions

This will vary depending from where the script should be run from.

• In the case the script is used within the ProMesh's GUI, i.e. in the live script editor, just copy and paste the script polygonal_mesh_from_txt.lua to this editor and adjust parameters as you need.
• In the case ugshell is used, one needs to enable an additional plugin, ProMesh, during the build process of ug4. To install the plugin use ughub installPackage ProMesh and activate it during the build process via cmake -DProMesh=ON in your BUILD folder, then execute make.

More details on usage are provided below.

Parameters

• Documented inline
• Invoke ugshell -helpMe to print parameters

Usage (GUI)

1. Make sure you create a new mesh in ProMesh GUI (upper left corner)
2. Copy and paste into ProMesh live script editor
3. Adjust parameters (OPTIONAL)
4. Execute

Usage (ugshell)

Run the following command string: ugshell -ex polygonal_mesh_from_txt.lua -helpMe to show usage:

 (number) -doubleThreshold   = 0.0001 : Double removal threshold (default = 0.0001)
 
 [option] -helpMe            = true :  (default = false)
 
 (string) -inputFolder       = nil : Input folder containing towers (default = nil)
 
 [option] -joinCornersNot    = false : Join corners (default = false)
 
 (number) -minAngleTower     = 25 : Dihedral for towers (default = 25)
 
 (number) -minAngleVol       = 25 : Dihedral for volumes (default = 25)
 
 (number) -numBoundaries     = 4 : Number of boundaries (default = 4)
 
 (number) -numPreRefinements = 2 : Number of tower refinements (default = 2)
 
 (number) -numRefinements    = 2 : Number of volume refinements (default = 2)
 
 (number) -outproc           = 0 : Sets the output-proc to id. (default = 0)
 
 (string) -outputFileName    = nil : File name to output UGX (default = nil)
 
 (number) -smoothingAlpha    = 0.1 : Alpha for smoothing (default = 0.1)
 
 (number) -v1x               = 0 : Top left x (default = 0)
 
 (number) -v1y               = -118.57 : Top left y (default = -118.57)
 
 (number) -v2x               = 122.9 : Top right x (default = 122.9)
 
 (number) -v2y               = -118.57 : Top right y (default = -118.57)
 
 (number) -v3x               = 0 : Bottom left x (default = 0)
 
 (number) -v3y               = 0 : Bottom left y (default = 0)
 
 (number) -v4x               = 122.9 : Bottom right x (default = 122.9)
 
 (number) -v4y               = 0 : Bottom right y (default = 0)
 
 (number) -zCoordinate       = 0 : Fixed z coordinate (default = 0)
 
 (number) numSmoothingSteps  = 1 : Number of smoothing steps (default = 1)

Example (Will assume all tower files are in a certain folder and grid will be saved in test.ugx):

ugshell -ex polygonal_mesh_from_txt.lua -inputFolder path/to/tower/files.txt -outputFileName test.ugx

Note that the vertices of the rectangle can be specifeid via -v1x,-v1y,-v2x,-v2y,-v3x,-v3y,-v4x,-v4y.

The file should be stored in a .ugx file on your disk with specified output name. Parameters can be made available to the command line user by using the scripts ug_util.lua provided in ugbase/scripts.

Version

Scripts have been tested with ProMesh 4.3.17 and ugshell (commit f46bab4).