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`.