Started work on mask analysis

Determine if a fiber is within an epithelial region
Updates for today
Added ROI processing.

Current version separates training cases better than anything I've tried
so far.

Added filters for length, curvature, and width of fibers (getFIRE.m).
Starting work on SVM analysis

Will output a big matrix and put it into an SVM for training the
classifier thresholds. Hopefully this will help justify some of the
thresholds.
SVM update

Setting up the SVM training array.
test SVM analysis
Attempt to make this function more efficient

Now only draw line through center that is 2X dist threshold long. This
is not quite exact. If the fiber is on a 45, then the line will be sqrt2
longer than if it is horizontal or vertical. Should fix this, but not
sure how much it matters. Also, this is still not fast enough in my
opinion.
Added in holes to the boundaries
Commented out plot functions

A couple other tweeks to the roiScores. Still need to optimize last
threshold for how many positive fibers per roi constitute a positive
score.
Validation Changes

Starting setup validation run, ie full feature extraction. Make sure all
important features are output! Need to do this.
Validation

write out all relevant features, need to increase this. It will be key
to have as many features as possible, so I don't have to re-run the
whole data set so many times.
Minor updates
SVM and survival analysis
Added polynomial line fit

This will produce slightly better boundary angle measures.
Changed yellow to cyan
Worked out row column order issues
Minor edits (non permanent)
Compute results for DFS and DSS
Minor updates
Fiber feature training infrastructure

Fiber feature extraction organization.