GoodFibes (version 0.1.13)

fiber.curve: 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)

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.

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

Author

J. Arbour

References

Arbour, J. In Prep. GoodFibes: an R package for the detection of muscle fibers from diceCT scans.

See Also

fiber.lengths,fiber.angle

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