meshDist: calculates and visualises distances between surface meshes or...

In zarquon42b/Morpho: Calculations and Visualisations Related to Geometric Morphometrics

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 class '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 class '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",
  ...
)

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.

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

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

Author(s)

Stefan Schlager

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)
## Not run: 
mD <- meshDist(longnose.mesh, shortnose.mesh)
##now change the color ramp
render(mD,rampcolors = c("white","red"))

## End(Not run)
#use unsigned distances and a ramp from blue to red
#color distances < 0.01 green:
## Not run: 
meshDist(longnose.mesh, shortnose.mesh, rampcolors = c("blue", "red"),sign=FALSE, tol=0.5)

## End(Not run)

zarquon42b/Morpho documentation built on Jan. 28, 2024, 2:11 p.m.