Morpho (version 2.12)

createAtlas: Create an atlas needed in placePatch

Description

Create an atlas needed in placePatch

Usage

createAtlas(
  mesh,
  landmarks,
  patch,
  corrCurves = NULL,
  patchCurves = NULL,
  keep.fix = NULL
)

Value

Returns a list of class "atlas". Its content is corresponding to argument names.

Arguments

mesh

triangular mesh representing the atlas' surface

landmarks

matrix containing landmarks defined on the atlas, as well as on each specimen in the corresponding sample.

patch

matrix containing semi-landmarks to be projected onto each specimen in the corresponding sample.

corrCurves

a vector or a list containing vectors specifiyng the rowindices of landmarks to be curves that are defined on the atlas AND each specimen. e.g. if landmarks 2:4 and 5:10 are two distinct curves, one would specifiy corrCurves = list(c(2:4), c(5:10)).

patchCurves

a vector or a list containing vectors specifiyng the rowindices of landmarks to be curves that are defined ONLY on the atlas. E.g. if coordinates 5:10 and 20:40 on the patch are two distinct curves, one would specifiy patchCurves = list(c(5:10),c(20:40)).

keep.fix

in case corrCurves are set, specify explicitly which landmarks are not allowed to slide during projection (with placePatch)

See Also

placePatch, plotAtlas

Examples

data(nose)
atlas <- createAtlas(shortnose.mesh, landmarks =
            shortnose.lm[c(1:5,20:21),], patch=shortnose.lm[-c(1:5,20:21),])