| fiber.curve {GoodFibes} | R Documentation |
Calculate the relative curvature of muscle fibers
Description
Calculates a metric for fiber curvature. This is the ratio between the total length of the curved smoothed fiber, to the straight line distance between the end points of the fiber. A straight fiber will have a curvature value of ~ 1 (small differences may be due to the calculation of fiber length across a smoothed curve), and values > 1 represent more curvature.
Optionally identified which fibers show unusual curvature (are outliers), for possible removal.
Usage
fiber.curve(fib.list, df, check = TRUE, length.out=500)
Arguments
fib.list |
A list of fibers containing $fiber.points. Produced by good.fibes or the various cleaning functions (quality check, fuse.fibers, check.overlap) |
df |
Corresponds to the df argument in splines2::nsp. Determines the shape of the smoothing spline (df = 1 represents straight muscle fibers) |
check |
Should unusually curved fibers be identified? |
length.out |
The number of straight line segments that the smoothed curve will be divided into for calculation of length |
Value
curvature |
The ratio of fiber length to end-to-end length |
problem.fibers |
Fibers with unusually high curvature. Given as the index of these fibers in the original list. |
Author(s)
J. Arbour
References
Arbour, J. In Prep. GoodFibes: an R package for the detection of muscle fibers from diceCT scans.
See Also
Examples
data(ant.final)
fcr<-fiber.curve(ant.final,df=2,check=TRUE)
#fibers reconstructed with a curve here merely to demonstrate function
#ant fibers were fairly straight
sort(fcr$curvature)
#all fibers are close to 1 even with a "curved" reconstruction