deformGrid3d {Morpho}

visualise differences between two superimposed sets of 3D landmarks

Description

visualise differences between two superimposed sets of 3D landmarks by deforming a cubic grid based on a thin-plate spline interpolation

Usage

deformGrid3d(
  matrix,
  tarmatrix,
  ngrid = 0,
  align = FALSE,
  lwd = 1,
  showaxis = c(1, 2),
  show = c(1, 2),
  lines = TRUE,
  lcol = 1,
  add = FALSE,
  col1 = 2,
  col2 = 3,
  type = c("s", "p"),
  size = NULL,
  pcaxis = FALSE,
  ask = TRUE,
  margin = 0.2,
  createMesh = FALSE,
  slice1 = NULL,
  slice2 = NULL,
  slice3 = NULL,
  gridcol = 1,
  gridwidth = 1,
  ...
)

Arguments

matrix

reference matrix containing 3D landmark coordinates or mesh of class "mesh3d"

tarmatrix

target matrix containing 3D landmark coordinates or mesh of class "mesh3d"

ngrid

number of grid lines to be plotted; ngrid=0 suppresses grid creation.

align

logical: if TRUE, tarmatrix will be aligned rigidly to matrix

lwd

width of lines connecting landmarks.

showaxis

integer (vector): which dimensions of the grid to be plotted. Options are combinations of 1,2 and 3.

show

integer (vector): if c(1:2) both configs will be plotted, show = 1 only plots the reference and show = 2 the target

lines

logical: if TRUE, lines between landmarks will be plotted.

lcol

color of lines

add

logical: add to existing rgl window.

col1

color of "matrix"

col2

color of "tarmat"

type

"s" renders landmarks as spheres; "p" as points - much faster for very large pointclouds.

size

control size/radius of points/spheres

pcaxis

logical: align grid by shape's principal axes.

ask

logical: if TRUE for > 1000 coordinates the user will be asked to prefer points over spheres.

margin

margin around the bounding box to draw the grid

createMesh

logical: if TRUE, a triangular mesh of spheres and displacement vectors (can take some time depending on number of reference points and grid density).

slice1

integer or vector of integers: select slice(s) for the dimensions

slice2

integer or vector of integers: select slice(s) for the dimensions

slice3

integer or vector of integers: select slice(s) for the dimensions

gridcol

define color of grid

gridwidth

integer: define linewidth of grid

...

additional parameters passed to rotonto in case align=TRUE

Value

if createMesh=TRUE, a mesh containing spheres of reference and target as well as the displacement vectors is returned. Otherwise the knots of the displaced grid is returned.

Author(s)

Stefan Schlager

See Also

tps3d

Examples

if (interactive()){
data(nose)
deformGrid3d(shortnose.lm,longnose.lm,ngrid=10)

## select some slices
deformGrid3d(shortnose.lm,longnose.lm,showaxis=1:3,ngrid=10,slice1=2,slice2=5,slice3=7)
}