checkLM: Visually browse through a sample rendering its landmarks and...

In Morpho: Calculations and Visualisations Related to Geometric Morphometrics

Visually browse through a sample rendering its landmarks and corresponding surfaces.

Description

Browse through a sample rendering its landmarks and corresponding surfaces. This is handy e.g. to check if the landmark projection using placePatch was successful, and to mark specific specimen.

Usage

checkLM(
  dat.array,
  path = NULL,
  prefix = "",
  suffix = ".ply",
  col = "white",
  pt.size = NULL,
  alpha = 1,
  begin = 1,
  render = c("w", "s"),
  point = c("s", "p"),
  add = FALSE,
  meshlist = NULL,
  Rdata = FALSE,
  atlas = NULL,
  text.lm = FALSE
)

Arguments

dat.array	array or list containing landmark coordinates.
path	optional character: path to files where surface meshes are stored locally. If not specified only landmarks are displayed.
prefix	prefix to attach to the filenames extracted from dimnames(dat.array)[[3]] (in case of an array), or names(dat.array) (in case of a list)
suffix	suffix to attach to the filenames extracted from dimnames(dat.array)[[3]] (in case of an array), or names(dat.array) (in case of a list)
col	mesh color
pt.size	size of plotted points/spheres. If point="s". pt.size defines the radius of the spheres. If point="p" it sets the variable size used in point3d.
alpha	value between 0 and 1. Sets transparency of mesh 1=opaque 0= fully transparent.
begin	integer: select a specimen to start with.
render	if render="w", a wireframe will be drawn, else the meshes will be shaded.
point	how to render landmarks. "s"=spheres, "p"=points.
add	logical: add to existing rgl window.
meshlist	list holding meshes in the same order as dat.array (Overrides path).
Rdata	logical: if the meshes are previously stored as Rdata-files by calling save(), these are simply loaded and rendered. Otherwise it is assumed that the meshes are stored in standard file formats such as PLY, STL or OBJ, that are then imported with the function file2mesh.
atlas	provide object generated by createAtlas to specify coloring of surface patches, curves and landmarks
text.lm	logical: number landmarks. Only applicable when atlas=NULL.

Value

returns an invisible vector of indices of marked specimen.

See Also

placePatch, createAtlas, plotAtlas, file2mesh

Examples

data(nose)
###create mesh for longnose
longnose.mesh <- tps3d(shortnose.mesh,shortnose.lm,longnose.lm,threads=1)
### write meshes to disk
save(shortnose.mesh, file="shortnose")
save(longnose.mesh, file="longnose")

## create landmark array
data <- bindArr(shortnose.lm, longnose.lm, along=3)
dimnames(data)[[3]] <- c("shortnose", "longnose")
## Not run: 
checkLM(data, path="./",Rdata=TRUE, suffix="")

## End(Not run)

## now visualize by using an atlas:
atlas <- createAtlas(shortnose.mesh, landmarks =
           shortnose.lm[c(1:5,20:21),],
patch=shortnose.lm[-c(1:5,20:21),])
if (interactive()){
checkLM(data, path="./",Rdata=TRUE, suffix="", atlas=atlas)
}
## remove data from disk
unlink("shortnose")
unlink("longnose")

Morpho documentation built on June 22, 2024, 7:19 p.m.