Configuration

This section provides the configuration settings for the spline-mesher project.

Image Settings

The following settings are used to configure the image paths and filenames:

  • img_basefilename: Base filename for the images. For example “C0001234”.

  • img_basepath: Base path for the images. Default is the current working directory concatenated with “/01_AIM”.

  • meshpath: Path where the mesh files are stored. Default is the current working directory concatenated with “/03_MESH”.

  • outputpath: Path where the output files are stored. Default is the current working directory concatenated with “/04_OUTPUT”.

Meshing Settings

The following settings are used to configure the meshing process:

  • aspect: Aspect ratio of the plots. Default is 100.

  • _slice: Slice of the image to be plotted. Default is 1.

  • undersampling: Undersampling factor of the image. Default is 1.

  • slicing_coefficient: Using every nth slice of the image for the spline reconstruction. Default is 20.

  • inside_val: Threshold value for the inside of the mask. Default is 0.

  • outside_val: Threshold value for the outside of the mask. Default is 1.

  • lower_thresh: Lower threshold for the mask. Default is 0.0.

  • upper_thresh: Upper threshold for the mask. Default is 0.9.

  • s: Smoothing factor of the spline. Default is 500.

  • k: Degree of the spline. Default is 3.

  • interp_points: Number of points to interpolate the spline. Default is 1000.

  • dp_simplification_outer: Ramer-Douglas-Peucker simplification factor for the periosteal contour. Default is 5.

  • dp_simplification_inner: Ramer-Douglas-Peucker simplification factor for the endosteal contour. Default is 5.

  • thickness_tol: Minimum cortical thickness tolerance. Default is 1.

  • phases: Number of phases for contouring. Default is 2 (1: only external contour, 2: external and internal contour).

  • center_square_length_factor: Size ratio of the refinement square. Default is 0.4.

  • mesh_order: Element order for the mesh. Default is 1 (1: linear, 2: quadratic, >2: higher order, not tested).

  • n_elms_longitudinal: Number of elements in the longitudinal direction. Default is 3.

  • n_elms_transverse_trab: Number of elements in the transverse direction for the trabecular compartment. Default is 15.

  • n_elms_transverse_cort: Number of elements in the transverse direction for the cortical compartment. Default is 3.

  • n_elms_radial: Number of elements in the radial direction. Default is 20. - Note: Should be 10 if trab_refinement is True.

  • ellipsoid_fitting: Perform ellipsoid fitting in the inner trabecular compartment. Default is True.

  • show_plots: Show plots during construction. Default is False.

  • show_gmsh: Show GMSH GUI. Default is False.

  • write_mesh: Write mesh to file. Default is True.

  • trab_refinement: Refine trabecular mesh at the center. Default is False. - Note: Should be set to False if ellipsoid_fitting is True.

  • mesh_analysis: Perform mesh analysis (plot JAC det in GMSH GUI). Default is True.