todo.md

ciclope 2 DO:

General

• Support for quadratic 10-node tetrahedra elements (TETRA10)
• Support and document use of ParOSol solver
• Boundary tolerance parameter to mesh2tetrafe function
• plot field mid-planes with Paraview
• BCs as in Cox et. al 2022. “Heterogeneous Tissue Modulus Improved Prediction of Mechanical Behavior in Osteoporotic Vertebral Cancellous Bone.”
• voxel uFE with heterogeneous material mapping
• fix voxel and tetraFE models flippedlr
• packaging
  • allow usage of ciclope as a script and as module:
• voxelFE: vol2ugrid (in meshio format!)
• voxelFE: mesh2voxelFE

JOSS paper review

• rerun jupyter notebooks
• upload LHDL reproduction dataset to Zenodo or github
• ethics LHDL dataset
• single trabecula test dataset upload Tests:
• preprocess.remove_unconnected
• voxelFE.vol2ugrid
• voxelFE.mesh2voxelfe
• tetraFE.shell_mesh
• tetraFE.cgal_mesh
• tetraFE.mesh2tetrafe
• everything with unittest

Documentation

• comment FULL notebooks
• Read The Docs page
  • sphinx-build -nW --keep-going -b html docs/ docs/_build/html
  • import documentation
  • clean API reference
  • clean notebooks Examples
  • usage
    • FE model generation - analysis definition
      • BCs
    • FE model generation - material mapping
      • add refs to material heterogeneity
      • add E=f(GV) explanation and plotting
    • shell_mesh
    • as a module - ciclope.methods
      • voxelFE: material mapping
      • tetraFE: material mapping
      • post-processing of results
        • ccx2paraview
        • PARAVIEW plot midplanes
      • cgal_mesh
      • vol2ugrid and mesh2voxelfe
      • mesh2tetrafe
    • as a script
    • prefect flow
• add package to ORMIR packages
• add picture of CT 2 FE ciclope.main() pipeline
• Ex01 and Ex02 from JCW_2022 notebook pipelines (voxel and tetra)
• add installation notes 2 readme
• link to CalculiX examples

Pre-processing

• add caps
• write midplanes images (.PNG)
• 3D dataset embedding
• analysis template write with parameter substitution (driving node coordinates)
• merge pybonemorph to ciclope.utils.preprocess
• Center Of Mass
• periosteum mask
• purge_mesh
• endosteum contour
• cortical bone mask

Post-processing

• Field mid-planes plotting with PARAVIEW
• CalculiX postprocessing
  • process CalculiX output with dat2txt.py
  • produce Force displacement plot with pandas
  • Paraview midplane plots

    export PYTHONPATH="/home/gianthk/Applications/ParaView-5.9.0-RC1-MPI-Linux-Python3.8-64bit/lib:/home/gianthk/Applications/ParaView-5.9.0-RC1-MPI-Linux-Python3.8-64bit/lib/python3.8/site-packages"```

  • convergence plots with monitor.py

Examples

• ex01: material property mapping with voxel-uFE
  • GV -> BMD -> E
• ex03: material property mapping with tetra-FE
  • plot displacement field midplanes with paraview
  • rescale U3 to reach 2 kN
  • comment NB
  • multi-material tetrahedra-FE (tooth+embedding)
• Example prefect pipeline
  • launch pipeline from master CSV table
  • ciclope voxelFE pipeline
  • execute calculix
  • multiple load configurations
    • (comp, tens, shear, torsion, bending)
    • read input_template params from table (e.g. different displ amplitude)
• Example postprocessing of results
  • midplanes Smises plots with Paraview
  • generate HTML report with plotly
  • write results to master
  • CalculiX postprocessing
• steel caps
• embedding

Validation

• check bone mass after material mapping vs ashing data