Configuration

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

HFE

### Mesher

• meshing: Type of meshing. Options are ‘spline’ or ‘full-block’. Default is ‘spline’.

• element_size: Size of the elements. Default is 1.2747.

• air_elements: Whether to keep air elements for a full-block mesh in x-y direction. Default is False.

### Image Processing

• origaim_separate: For Hosseini Dataset, whether image parameters are read from original aim. Default is False.

• mask_separate: Whether to use two separate mask files (CORTMASK and TRABMASK). Default is True.

• imtype: Type of image. Options are ‘NATIVE’ or ‘BMD’. Default is ‘NATIVE’.

• bvtv_scaling: Scaling of BVTV. Options are 0 (no scaling) or 1 (scaling of BVTV 61um to BVTV 11.4um). Default is 1.

• bvtv_slope: BVTV slope. Default is 0.963.

• bvtv_intercept: BVTV intercept. Default is 0.03814.

• BVTVd_comparison: Whether to run the comparison in imutils.compute_bvtv_d_seg(). Default is False.

• BVTVd_as_BVTV: Whether to use BVTVd as BVTV. Default is False.

• SEG_correction: Whether to apply a seg correction if BVTVd_as_BVTV is False. Default is True.

• BMC_conservation: Whether to conserve BMC. Default is False.

### Homogenization

• fabric_type: Type of fabric. Options are ‘local’ or ‘global’. Default is ‘local’.

• roi_bvtv_size: Size of ROI BVTV. Default is 5.

• STL_tolerance: Tolerance for STL. Default is 0.2.

• ROI_kernel_size_cort: Kernel size for cortical ROI. Default is 5.

• ROI_kernel_size_trab: Kernel size for trabecular ROI. Default is 5.

• ROI_BVTV_size_cort: Diameter of sphere with same volume as FE element. Default is 1.3453.

• ROI_BVTV_size_trab: Diameter of Arias Moreno et al. 2019. Default is 4.0.

• isotropic_cortex: Whether cortex fabric is isotropic. Default is False.

• orthotropic_cortex: Whether cortex fabric is orthotropic. Default is True.

### Loadcase

• full_nonlinear_loadcases: Whether to compute non-linear loadcases. Default is False.

• BC_mode: Boundary condition mode. Default is 0.

• control: Loading boundary conditions. Options are ‘force’ or ‘displacement’. Default is ‘displacement’.

• start_step_size: Starting step size. Default is 0.2.

• time_for_displacement: Time for displacement. Default is 1.

• min_step_size: Minimum step size. Default is 0.0000000001.

• max_step_size: Maximum step size. Default is 0.3.

• load_displacement: Load displacement in mm. Default is -1.0.

### Abaqus

• nlgeom: Affects NLGEOM parameter in Abaqus simulation. Options are ‘on’ or ‘off’. Default is ‘on’.

• abaqus_nprocs: Number of processors for Abaqus. Default is 8.

• abaqus_memory: Memory for Abaqus in MB. Default is 6000.

• delete_odb: Whether to delete odb after retrieving data. Default is False.

• max_increments: Maximum number of increments. Default is 1000.

• umat: Path to UMAT file. Default is 02_CODE/abq/UMAT_BIPHASIC.f.

### Strain Localisation

• strain_analysis: Whether to use strain localisation for the analysis. Default is True.

### Registration

• registration: Whether to use registered data for longitudinal studies. Default is False.

### Optimization

• fz_max_factor: Maximum factor for Fz. Default is 0.5.

• fx_fy_max_factor: Maximum factor for Fx and Fy. Default is 1.3.

• mx_my_max_factor: Maximum factor for Mx and My. Default is 1.

• mz_max_factor: Maximum factor for Mz. Default is 0.8.

### Old Config

• nphases: Number of phases. Default is 1.

• ftype: File type. Default is iso.

• verification_file: Verification file. Default is 1.

• all_mask: Whether all elements containing part of a mask are converted to FE mesh. Default is True.

• adjust_element_size: Whether to adjust element size to fit into common region. Default is True.

Mesh

### Image Settings

• img_basepath: Base path for the images. Default is 01_DATA.

• meshpath: Path where the mesh files are stored. Default is 03_MESH.

• outputpath: Path where the output files are stored. Default is 03_OUTPUT/MESHES/.

### Meshing Settings

• 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.

• 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 200.

• dp_simplification_outer: Ramer-Douglas-Peucker simplification factor for the periosteal contour. Default is 3.

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

• thickness_tol: Minimum cortical thickness tolerance. Default is 0.5.

• phases: Number of phases. Default is 2.

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

• mesh_order: Order of the mesh. Options are 1 (linear) or 2 (quadratic). Default is 1.

• sweep_factor: Factor for the sweep used in hydra for the sensitivity analysis. Default is 1.

• n_elms_longitudinal: Number of elements longitudinally. Default is 3.

• n_elms_transverse_trab: Number of transverse elements in trabecular bone. Default is 15.

• n_elms_transverse_cort: Number of transverse elements in cortical bone. Default is 3.

• n_elms_radial: Number of radial elements. Default is 20.

• ellipsoid_fitting: Whether to use ellipsoid fitting. Default is True.

• show_plots: Whether to show plots during construction. Default is False.

• show_gmsh: Whether to show GMSH GUI. Default is False.

• write_mesh: Whether to write mesh to file. Default is True.

• trab_refinement: Whether to refine trabecular mesh at the center. Default is False.

• mesh_analysis: Whether to perform mesh analysis. Default is True.

Paths

### Paths

• origaimdir: Directory for original aim files. Default is 00_ORIGAIM/TIBIA.

• aimdir: Directory for aim files. Default is 01_DATA/TIBIA/.

• feadir: Directory for FEA simulations. Default is 04_SIMULATIONS/TIBIA.

• sumdir: Directory for summaries. Default is 05_SUMMARIES/TIBIA.

• commondir: Directory for common region images. Default is 01_DATA/BATCH/FEA_noReg/IMAGES/.

• folder_bc_psl_loadcases: Directory for BC PSL loadcases. Default is 02_CODE/abq/BC_PSL/.

• boundary_conditions: Path to boundary conditions file. Default is 02_CODE/abq/BC_PSL/boundary_conditions.inp.

• odb_OF_python_script: Path to ODB OF Python script. Default is 02_CODE/src/hfe_abq/readODB_acc.py.

• odb_python_script: Path to ODB Python script. Default is 02_CODE/src/hfe_abq/readODB_acc.py.

### Filenames

• filename_postfix_cort_mask: Postfix for cortical mask filename. Default is _CORT_MASK_UNCOMP.AIM.

• filename_postfix_trab_mask: Postfix for trabecular mask filename. Default is _TRAB_MASK_UNCOMP.AIM.

• filename_postfix_mask: Postfix for mask filename if mask separate is False. Default is _MASK.AIM.

• filename_postfix_bmd: Postfix for BMD filename. Default is _UNCOMP.AIM.

• filename_postfix_seg: Postfix for segmentation filename. Default is _UNCOMP_SEG.AIM.

• filename_postfix_common: Postfix for common region mask filename if registration is True. Default is _common_region_MASK.mhd.

• filename_postfix_transform: Postfix for transformation filename if registration is True. Default is _transformation.tfm.

### Version

• verification_files: Number of verification files. Default is 1.

• current_version: Current version of the configuration. Default is 04_strain.

• site_bone: Site bone. Options are ‘Radius’ or ‘Tibia’. Default is ‘Tibia’.

Simulations

### Simulations

• grayscale_filenames: List of grayscale filenames. Example: C0001234.

• folder_id: Mapping of folder IDs. Example: C0001234: pat_001.