remove from settings

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"show_plots": False, # show plots during construction

"show_gmsh": False, # show gmsh GUI

"write_mesh": False, # write mesh to file

"phases": 2, # 1: only external contour, 2: external and internal contour

"trab_refinement": False, # True: refine trabecular mesh at the center

"center_square_length_factor": 0.6, # size ratio of the refinement square: 0 < l_f < 1

"n_elms_longitudinal": 3, # number of elements in the longitudinal direction

"n_elms_transverse_trab": 3, # number of elements in the transverse direction for the trabecular compartment

"n_elms_transverse_cort": 3, # number of elements in the transverse direction for the cortical compartment

"n_elms_radial": 5, # number of elements in the radial direction ! Should be 10 if trab_refinement is True !

"mesh_analysis": False, # True: perform mesh analysis (plot JAC det in GMSH GUI)

https://github.com/artorg-unibe-ch/spline-mesher/blob/2df8e0e7404e65f1478cef3e83fac9c2747d04b5/standalone.py#L30

    "outputpath": f"{os.getcwd()}/04_OUTPUT",
}
meshing_settings = {
    "aspect": 100,  # aspect ratio of the plots
    "slice": 1,  # slice of the image to be plotted
    "undersampling": 1,  # undersampling factor of the image
    "slicing_coefficient": 10,  # 5, 10, 20 working on 2234
    "inside_val": int(0),  # threshold value for the inside of the mask
    "outside_val": int(1),  # threshold value for the outside of the mask
    "lower_thresh": float(0),  # lower threshold for the mask
    "upper_thresh": float(0.9),  # upper threshold for the mask
    "s": 5,  # smoothing factor of the spline
    "k": 3,  # degree of the spline
    "interp_points": 200,  # number of points to interpolate the spline
    "debug_orientation": 0,  # 0: no debug, 1: debug orientation after Mahalanobis sorting # TODO: remove from settings
    "show_plots": False,  # show plots during construction
    "show_gmsh": False,  # show gmsh GUI
    "write_mesh": False,  # write mesh to file
    "location": "cort_ext",
    "thickness_tol": 180e-3,  # minimum cortical thickness tolerance: 3 * XCTII voxel size
    "phases": 2,  # 1: only external contour, 2: external and internal contour
    "trab_refinement": False,  # True: refine trabecular mesh at the center
    "center_square_length_factor": 0.6,  # size ratio of the refinement square: 0 < l_f < 1
    "n_elms_longitudinal": 3,  # number of elements in the longitudinal direction
    "n_elms_transverse_trab": 3,  # number of elements in the transverse direction for the trabecular compartment
    "n_elms_transverse_cort": 3,  # number of elements in the transverse direction for the cortical compartment
    "n_elms_radial": 5,  # number of elements in the radial direction ! Should be 10 if trab_refinement is True !
    "mesh_analysis": False,  # True: perform mesh analysis (plot JAC det in GMSH GUI)
}

# sitk_image = transformer.hfe_input(

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Closed in 904767c0720da28a90ad24f41832d28e7cba561d