Inter-bone Joint Space Area Calculations

This stage of the pipeline computes the shortest distance between surface points on the bones.

Technical notes

(Liz Marai and Leor's notes for this process are at $G/src/jspBin/README.txt and $G/src/jspBin/trail_contact_areas.txt)

Follow these steps to compute the distance maps:

1. Get required data files into the data root directory
   1. get the bone Geomagic meshes in OpenInventor format (e.g., <bone_tag>.iv)
   2. get the "animation file" for each bone, (e.g., <bone_tag>_anim.RT)
   3. get anatomical coordinate system for each bone (e.g., <bone_tag>_coord.dat)
2. Prepare scripts
   1. copy the "joints_one_linux" and "joints_linux" from $G/bin/jspBin/ to your data's top-level directory
   2. replace "set data_directory" lines in both with the path to your directory
   3. replace bone tags with the ones of interest (e.g., bone_tag_1=sca15L and bone_tag_2=lun15L)