Morpho (version 2.1)

meshDist.matrix: calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.

Description

calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.

Usage

## S3 method for class 'matrix':
meshDist(x, mesh2 = NULL, distvec = NULL, from = NULL,
  to = NULL, steps = 20, ceiling = FALSE, uprange = 1, plot = TRUE,
  sign = TRUE, tol = NULL, type = c("s", "p"), radius = NULL,
  displace = FALSE, add = FALSE, ...)
meshDist(x, ...)
## S3 method for class 'mesh3d':
meshDist(x, mesh2 = NULL, distvec = NULL, from = NULL,
  to = NULL, steps = 20, ceiling = FALSE, file = "default",
  imagedim = "100x800", uprange = 1, ray = FALSE, raytol = 50,
  save = FALSE, plot = TRUE, sign = TRUE, tol = NULL,
  displace = FALSE, shade = TRUE, method = c("morpho", "vcglib"),
  add = FALSE, ...)

Arguments

x

reference mesh; object of class "mesh3d" or a n x 3 matrix containing 3D coordinates.

mesh2

target mesh: either object of class "mesh3d" or a character pointing to a surface mesh (ply, obj or stl file)

distvec

vector: optional, a vector containing distances for each vertex of mesh1, if distvec != NULL, x will be ignored.

from

numeric: minimum distance to be colorised; default is set to 0 mm

to

numeric: maximum distance to be colorised; default is set to the maximum distance

steps

integer: determines break points for color ramp: n steps will produce n-1 colors.

ceiling

logical: if TRUE, the next larger integer of "to" is used

uprange

numeric between 0 and 1: restricts "to" to a quantile of "to", if to is NULL.

plot

logical: visualise result as 3D-plot and distance charts

sign

logical: request signed distances. Only meaningful, if mesh2 is specified or distvec contains signed distances.

tol

numeric: threshold to color distances within this threshold green.

type

character: "s" shows coordinates as spheres, while "p" shows 3D dots.

radius

determines size of spheres; if not specified, optimal radius size will be estimated by centroid size of the configuration.

displace

logical: if TRUE, displacement vectors between original and closest points are drawn colored according to the distance.

add

logical: if TRUE, visualization will be added to the rgl window currently in focus

file

character: filename for mesh and image files produced. E.g. "mydist" will produce the files mydist.ply and mydist.png

imagedim

character of type 100x200 where 100 determines the width and 200 the height of the image.

ray

logical: if TRUE, the search is along vertex normals.

raytol

maximum distance to follow a normal.

save

logical: save a colored mesh.

shade

logical: if FALSE, the rendering of the colored surface will be supressed.

method

accepts: "vcglib" and "morpho" (and any abbreviation). vcglib uses a command line tool using vcglib headers, morpho uses fortran routines based on a kd-tree search for closest triangles.

...

additional arguments passed to shade3d. See rgl.material for details.

Value

• Returns an object of class "meshDist" if the input is a surface mesh and one of class "matrixDist" if input is a matrix containing 3D coordinates.
• colMesh
  object of mesh3d with colors added
• dists
  vector with distances
• cols
  vector with color values
• params
  list of parameters used

Details

calculates the distances from a mesh or a set of 3D coordinates to another at each vertex; either closest point or along the normals

this function needs the command line tools from the Auxiliaries section in http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries installed.

References

Detection of inside/outside uses the algorithm proposed in:

Baerentzen, Jakob Andreas. & Aanaes, H., 2002. Generating Signed Distance Fields From Triangle Meshes. Informatics and Mathematical Modelling, .

See Also

render.meshDist, , export.meshDist, shade3d

Examples

require(rgl)
data(nose)##load data
##warp a mesh onto another landmark configuration:
warpnose.long <- warp.mesh(shortnose.mesh, shortnose.lm, longnose.lm)
meshDist(warpnose.long, shortnose.mesh, method="m")
#use signed distances and
#color distances < 0.01 green:
meshDist(warpnose.long, shortnose.mesh, sign=TRUE, tol=0.01, method="m")