muscle.plot: Plot a single muscle fiber

In GoodFibes: Detection and Reconstruction of Muscle Fibers from diceCT Image Data

Plot a single muscle fiber

Description

Used to compare the muscle fiber path to the smoothed muscle fiber. Plots a single set of $fiber.points from and the smoothed fibers.

Usage

muscle.plot(fiber.dat, images, df = 4, mirror.axis = FALSE, outline = 50, size = 2)

Arguments

fiber.dat	Any set of $fiber.points produced by good.fibes
images	A character vector with image names representing the image stack, can be produced using list.files.
df	The df to be used in smoothing fiber paths in the calculation of fiber length
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
outline	The number of wireframe "outlines" to draw the muscle boundaries
size	point size for $fiber.points in plot

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.stl

Examples

olddir<-getwd()

#### this downloads the ant dataset image stack
#### if you have it already downloaded you can navigate to that folder
setwd(tempdir())
download.file(url=
"https://github.com/jessica-arbour/Ant-Muscle-Image-Stack/raw/main/Ant_data.zip",
destfile="antdata.zip")

unzip("antdata.zip")
setwd(paste0(getwd(),"/Ant data"))
####

images<-list.files(pattern=".png")

data(ant.final)
muscle.plot(ant.final[[100]]$fiber.points,images,df=1, outline=30, mirror.axis=TRUE)
setwd(olddir)

GoodFibes documentation built on Aug. 19, 2023, 1:06 a.m.