Morpho (version 2.12)

meshDist: 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

meshDist(x, ...)
# S3 method for mesh3d
meshDist(
  x,
  mesh2 = NULL,
  distvec = NULL,
  from = NULL,
  to = NULL,
  steps = 20,
  ceiling = FALSE,
  rampcolors = colorRamps::blue2green2red(steps - 1),
  NAcol = "white",
  file = "default",
  imagedim = "100x800",
  uprange = 1,
  ray = FALSE,
  raytol = 50,
  raystrict = FALSE,
  save = FALSE,
  plot = TRUE,
  sign = TRUE,
  tol = NULL,
  tolcol = "green",
  displace = FALSE,
  shade = TRUE,
  method = c("vcglib", "morpho"),
  add = FALSE,
  scaleramp = TRUE,
  threads = 1,
  titleplot = "Distance in mm",
  ...
)
# S3 method for matrix
meshDist(
  x,
  mesh2 = NULL,
  distvec = NULL,
  from = NULL,
  to = NULL,
  steps = 20,
  ceiling = FALSE,
  rampcolors = colorRamps::blue2green2red(steps - 1),
  NAcol = "white",
  uprange = 1,
  plot = TRUE,
  sign = TRUE,
  tol = NULL,
  tolcol = "green",
  type = c("s", "p"),
  radius = NULL,
  displace = FALSE,
  add = FALSE,
  scaleramp = FALSE,
  titleplot = "Distance in mm",
  ...
)

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

Arguments

x

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

...

additional arguments passed to shade3d. See material3d for details.

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/coordinate of x, if distvec != NULL, mesh2 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

rampcolors

character vector: specify the colors which are used to create a colorramp.

NAcol

character: specify color for values outside the range defined by from and to.

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.

uprange

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

ray

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

raytol

maximum distance to follow a normal.

raystrict

logical: if TRUE, only outward along normals will be sought for closest points.

save

logical: save a colored mesh.

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.

tolcol

a custom color to color vertices below a threshold defined by tol. Default is green.

displace

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

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.

add

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

scaleramp

logical: if TRUE, the colorramp will be symmetrical for signed distances: spanning from -max(from,to) to max(from,to).

threads

integer: number of threads to use. 0 = let system decide.

titleplot

character: axis description of heatmap.

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.

Author

Stefan Schlager

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

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

data(nose)##load data
##warp a mesh onto another landmark configuration:
longnose.mesh <- tps3d(shortnose.mesh, shortnose.lm, longnose.lm,threads=1)
if (FALSE) {
mD <- meshDist(longnose.mesh, shortnose.mesh)
##now change the color ramp
render(mD,rampcolors = c("white","red"))
}
#use unsigned distances and a ramp from blue to red
#color distances < 0.01 green:
if (FALSE) {
meshDist(longnose.mesh, shortnose.mesh, rampcolors = c("blue", "red"),sign=FALSE, tol=0.5)
}