Gebert Doctoral Project Workflow and Programs

My doctoral project results in a biomechanical workflow maintained in this GitHub organization.

Following notation is used to group parts of the workflow:

A	Auxiliary programs and modules
I	Image (pre) processing
M	Mechanical computations
P	Post processing

Example: M-DTC-Direct-Tensor-Computation

The subgroups themselves are not ordered. While the steps of the mechanical analyzation enforce a specific procedure of computations, the image pre-processing and the auxiliary resositories often can be viewed as stand-alone programs.

Nomenclature of the data

All programs of my doctoral project rely on a data driven workflow.

General layout:

Image_Origin_Purpose_Application_Features.Suffix

Image

• Type of bone
• Consecutive number of the bones
• Consecutive number of its scan
  Examples:

FH01-1	Femoral Head 1, scan 1
PT02-1	Proximal Tibia 2, scan 1
TC00-0	Test Case

Origin

• 'cl' - clinical computed tomography scan
• 'mu' - Microfocus computed tomography scan
• 'tc' - Test case

Purpose

• 'Dev' - (Development) Data set for general research
• 'Pro' - (Production) Data set for use in publications

App

• Application that last modified the data set.

Features [Optional]

• Space for entering parameters in case of smaller studies with different parameterizations.

Suffix

• '*.raw' to mark the binary blob
• '*.meta' to mark the meta data file
• ALWAYS both of them are required as they are inherently separated

Examples of the Nomenclature

FH01s1_mu_Dev_Filters_G3S31Sig20.meta & *.raw

1. FH01-1 Femoral Head 1, Scan 1
2. mu - Microfocus computed tomogrpahy scan
3. Dev - Dataset used for research
4. Filters - Dataset used to gather information of filtering images
5. G3S31Sig20 - Specific parameters (3D Gauss, Kernel size 31, Sigma = 2.0)

FH01s3_cl_Pro_Downscaling_SF15.meta & *.raw

1. FH01-3 Femoral Head 1, Scan 3
2. mu - Clinical computed tomography scan
3. Pro - Dataset used for research
4. Downscaling - Dataset used to prove validity compare to a high resolution scan
5. SF15 - Specific parameters (Scale factor = 15)

Centralized Sources

All the repositories of this doctoral project rely on a couple of centralized sources to prevent diverging standard routines.

Add them as a subtree as follows:

cd <repository root>
git subtree add --prefix central_src [email protected]:biomechanics-hlrs-gebert/A-GLI-Geberts-Library.git  main --squash

Biomechanics @ HLRS

All of this research is conducted at the High-Performance Computing Center Stuttgart (HLRS) in the department of Numerical Methods and Libraries.

Install Scripts

For installing Open-MPI, PETSc, Metis and Lapack, simple install scripts are provided in ./install_scripts.