Surface fitting

Annoying dependencies

Currently depends on 2 (temporarily) private repositories:

• https://github.com/JaneliaSciComp/SurfaceFit (graph cut)
• https://github.com/kephale/sema-cost (cost function implementation)

and 2 hot-knife branches:

• https://github.com/saalfeldlab/hot-knife/tree/surface-fitting (many people contributed to this branch)
• https://github.com/saalfeldlab/hot-knife/tree/surface-fitting-loadmask (a branch by just @kephale at the moment which also includes a spark job for computing the cost function) Note: this branch originates from surface-fitting, and might be best merged into surface-fitting prior to merging surface-fitting into master

Pipeline usage:

1. run SparkComputeCost from surface-fitting-loadmask branch
   pre: a N5 volume of aligned 3D data
   post: a N5 volume with a s1-scale based on the specified cost steps
   command: sh run-cost-sec25-kyletest.sh
2. run the python scripts for creating the scale pyramid
   pre: a N5 volume with s1-scale of the cost function
   post: N5 volumes for scales s2-s8
   command: sh run-fit-scales-cost-sec25-kyletest.sh
3. run the graphcut for solving the actual surface
   pre: N5 volumes of a cost function with a scale pyramid of s1-s8
   post: two N5 heightfields for the min and max surface of the volume
   command: run-fit-surfaces-sec25-kyletest.sh

Visualization

See ViewFlattened, PaintHeightField, and @kephale's BigWarp fork (for nailing)