muscle.plot.stl {GoodFibes}

Plot and export muscle fibers to stl

Description

Plot a series of muscle fibers produced by good.fibes. Fibers are smoothed using splines before plotting. Optionally export an STL file in the correct size scale.

Usage

muscle.plot.stl(fiber.list, res = 1, df = 2, radius = 1, cols = NULL,
save.plot = FALSE, file.name = "muscle.fibers.stl", mirror.axis = FALSE)

Arguments

fiber.list

A list of fibers with $fiber points. Generated by good.fibes or processed cleaned by other functions

res

The isometric resolution of the original scan (i.e., the distance between images). Provided as a linear measure (um, mm, etc.)

df

The degrees of freedom to pass to splines2::nsp for smoothing fiber paths. df = 1 gives a straight path, while >1 gives increasingly curved paths

radius

The radius of the lines plotted for muscle fibers

cols

An optional vector of colors, the same order and length of fiber.list

save.plot

When TRUE, plot is saved as an .stl object in the current working directory. Provide file in file.name argument.

file.name

Character data giving the file.name and ending in .stl

mirror.axis

Depending on the way the image stack was exported, fibers may be reflected from their original original. mirror.axis = TRUE will reflect the fibers before plotting to correct this

Value

Returns a 3D plot

Author(s)

J. Arbour

References

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

See Also

muscle.plot.multi,muscle.plot,good.fibes

Examples

data(ant.final)

muscle.plot.stl(ant.final, res = 0.000673107, df=1, radius = 1, 
mirror.axis = TRUE, save.plot = FALSE)