createAtlas {Morpho}

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
)

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)

Value

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

Note

This is a helper function of 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),])