jackieee / airway-geometry

Scripts for processing human airway geometries for CFD simulation

airway-geometry

Scripts for processing human airway geometries for CFD simulation

• extract_topo.tcl : ICEM script for extracting useful topology (face curves, tracheal curve, etc.) from a input STL geometry.
• create_trachea.tcl : ICEM script for attaching tracheal flow extension to mesh. To use, rename the curve around the tracheal opening to crv.inlet and its corresponding surface to srf.inlet; then run the script.
• create_trach_cyl.tcl : ICEM script for attaching tracheal flow extension with circular cross-section to mesh. To use, rename the curve around the tracheal opening to crv.inlet and its corresponding surface to srf.inlet; then run the script.
• create_trach_smth.tcl : ICEM script for attaching a tracheal flow extension. Use after using extract_topo.tcl. The major difference with the above script is that the attached flow extension has a smoother transition.
• surf_from_pts.tcl : ICEM script for creating an extended box around the face. To use, rename the curves around the face crv.face.1, ... , crv.face.2 (in counter-clockwise order from the perspective of the face) and the points pnt.1, ... , pnt.4 in top->bottom, right->left order.
• triangle-io.jl : Julia functions for loading and saving in Jonathan Shewchuk's Triangle format.
• remove-dup.xml : MeshLab filter script for removing duplicate vertices (useful on output of mesh-plane-cut.jl)
• cut-mean-mesh.sh : Script for cutting a box around the mean mesh and also cutting the tracheal plane (requires MeshLab and Julia).
• cut-mesh-plane.jl : Julia script to cut a mesh along a plane. Identical to MeshMixer's 'plane cut' function easier to automate. Requires installation of Triangle.
• bend-mesh.jl : One step in processing meshes is to take angled cross-sections across different parts of the mesh. This script takes a mesh generated with such cross-sections and transforms it back to a straightened mesh.
• OFF.jl : Julia functions for loading/saving OFF files.
• signed_distance.ijm : ImageJ/Fiji script to compute the signed distance of a stack of images and save it as 32-bit TIFF. Requires input stack to be named 'avg'.
• smooth_mask.ijm : Used by signed_distance.ijm, this is an ImageJ script that reads smooth_maska.png and smooth_maskb.png and constructs a smoothing mask with more gradual transition between non-smoothed and smoothed regions.