Package alphashape3d

May 23, 2014

Type Package
Title Implementation of the 3D alpha-shape for the reconstruction of 3D sets from a point cloud
Version 1.1
Date 2014-05-19
Author Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer Beatriz Pateiro-Lopez <[email protected]>
Depends geometry, rgl
Suggests alphahull
Description The package alphashape3d presents the implementation in R of the alpha-shape of a -
nite set of points in the three-dimensional space. This geometric structure generalizes the con-
vex hull and allows to recover the shape of non-convex and even non-
connected sets in 3D, given a random sample of points taken into it. Besides the computa-
tion of the alpha-shape, the package alphashape3d provides users with functions to com-
pute the volume of the alpha-shape, identify the connected components and facilitate the three-
dimensional graphical visualization of the estimated set.
License GPL-2
LazyLoad yes
NeedsCompilation yes
Repository CRAN
Date/Publication 2014-05-23 11:14:12
R topics documented:
alphashape3d-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
ashape3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
components_ashape3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
inashape3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1
2 ashape3d
plot.ashape3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
rtorus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
surfaceNormals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
volume_ashape3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Index 12
alphashape3d-package Computation of the 3D -shape
Description
The package alphashape3d presents the implementation in R of the -shape of a nite set of points
in the three-dimensional space. This geometric structure generalizes the convex hull and allows
to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of
points taken into it. Besides the computation of the -shape, the package alphashape3d provides
users with functions to compute the volume of the -shape, identify the connected components and
facilitate the three-dimensional graphical visualization of the estimated set.
Details
Package: alphashape3d
Type: Package
Version: 1.1
Date: 2014-05-19
License: GPL-2
LazyLoad: yes
Author(s)
Thomas Lafarge, Beatriz Pateiro-Lopez.
Maintainers: Beatriz Pateiro-Lopez <[email protected]>
References
Edelsbrunner, H., Mucke, E. P. (1994). Three-Dimensional Alpha Shapes. ACM Transactions on
Graphics, 13(1), pp.43-72.
ashape3d 3D -shape computation
ashape3d 3
Description
This function calculates the 3D -shape of a given sample of points in the three-dimensional space
for > 0.
Usage
ashape3d(x, alpha, pert = FALSE, eps = 1e-09)
Arguments
x A 3-column matrix with the coordinates of the input points. Alternatively, an
object of class "ashape3d" can be provided, see Details.
alpha A single value or vector of values for .
pert Logical. If the input points are not in general position and pert it set to TRUE
the observations are perturbed by adding random noise, see Details.
eps Scaling factor used for data perturbation when the input points are not in general
position, see Details.
Details
If x is an object of class "ashape3d", then ashape3d does not recompute the 3D Delaunay triangu-
lation (it reduces the computational cost).
If the input points x are not in general position and pert is set to TRUE, the function adds random
noise to the data. The noise is generated from a normal distribution with mean zero and standard
deviation eps*sd(x).
Value
An object of class "ashape3d" with the following components (see Edelsbrunner and Mucke (1994)
for notation):
tetra For each tetrahedron of the 3D Delaunay triangulation, the matrix tetra stores
the indices of the sample points dening the tetrahedron (columns 1 to 4), a value
that denes the intervals for which the tetrahedron belongs to the -complex
(column 5) and for each a value (1 or 0) indicating whether the tetrahedron
belongs to the -shape (columns 6 to last).
triang For each triangle of the 3D Delaunay triangulation, the matrix triang stores the
indices of the sample points dening the triangle (columns 1 to 3), a value (1
or 0) indicating whether the triangle is on the convex hull (column 4), a value
(1 or 0) indicating whether the triangle is attached or unattached (column 5),
values that dene the intervals for which the triangle belongs to the -complex
(columns 6 to 8) and for each a value (0, 1, 2 or 3) indicating, respectively, that
the triangle is not in the -shape or it is interior, regular or singular (columns
9 to last). As dened in Edelsbrunner and Mucke (1994), a simplex in the -
complex is interior if it does not belong to the boundary of the -shape. A
simplex in the -complex is regular if it is part of the boundary of the -shape
and bounds some higher-dimensional simplex in the -complex. A simplex in
4 components_ashape3d
the -complex is singular if it is part of the boundary of the -shape but does
not bounds any higher-dimensional simplex in the -complex.
edge For each edge of the 3D Delaunay triangulation, the matrix edge stores the
indices of the sample points dening the edge (columns 1 and 2), a value (1
or 0) indicating whether the edge is on the convex hull (column 3), a value (1 or
0) indicating whether the edge is attached or unattached (column 4), values that
dene the intervals for which the edge belongs to the -complex (columns 5 to
7) and for each a value (0, 1, 2 or 3) indicating, respectively, that the edge is
not in the -shape or it is interior, regular or singular (columns 8 to last).
vertex For each sample point, the matrix vertex stores the index of the point (column
1), a value (1 or 0) indicating whether the point is on the convex hull (column
2), values that dene the intervals for which the point belongs to the -complex
(columns 3 and 4) and for each a value (1, 2 or 3) indicating, respectively, if
the point is interior, regular or singular (columns 5 to last).
x A 3-column matrix with the coordinates of the original sample points.
alpha A single value or vector of values of .
xpert A 3-column matrix with the coordinates of the perturbated sample points (only
when the input points are not in general position and pert is set to TRUE).
References
Edelsbrunner, H., Mucke, E. P. (1994). Three-Dimensional Alpha Shapes. ACM Transactions on
Graphics, 13(1), pp.43-72.
Examples
T1 <- rtorus(1000, 0.5, 2)
T2 <- rtorus(1000, 0.5, 2, ct = c(2, 0, 0), rotx = pi/2)
x <- rbind(T1, T2)
# Value of alpha
alpha <- 0.25
# 3D alpha-shape
ashape3d.obj <- ashape3d(x, alpha = alpha)
plot(ashape3d.obj)
# For new values of alpha, we can use ashape3d.obj as input (faster)
alpha <- c(0.15, 1)
ashape3d.obj <- ashape3d(ashape3d.obj, alpha = alpha)
plot(ashape3d.obj, indexAlpha = 2:3)
components_ashape3d Connected subsets computation
Description
This function calculates and clusters the different connected components of the -shape of a given
sample of points in the three-dimensional space.
components_ashape3d 5
Usage
components_ashape3d(as3d, indexAlpha = 1)
Arguments
as3d An object of class "ashape3d" that represents the -shape of a given sample of
points in the three-dimensional space, see ashape3d.
indexAlpha A single value or vector with the indexes of as3d$alpha that should be used for
the computation, see Details.
Details
The function components_ashape3d computes the connected components of the -shape for each
value of in as3d$alpha[indexAlpha] when indexAlpha is numeric.
If indexAlpha="all" or indexAlpha="ALL" then the function computes the connected compo-
nents of the -shape for all values of in as3d$alpha.
Value
If indexAlpha is a single value then the function returns a vector v of length equal to the sample
size. For each sample point i, v[i] represents the label of the connected component to which the
point belongs (for isolated points, v[i]=-1). The labels of the connected components are ordered
by size where the largest one (in number of vertices) gets the smallest label which is one.
Otherwise components_ashape3d returns a list of vectors describing the connected components of
the -shape for each selected value of .
See Also
ashape3d, plot.ashape3d
Examples
T1 <- rtorus(1000, 0.5, 2)
T2 <- rtorus(1000, 0.5, 2, ct = c(2, 0, 0), rotx = pi/2)
x <- rbind(T1, T2)
alpha <- c(0.25, 2)
ashape3d.obj <- ashape3d(x, alpha = alpha)
plot(ashape3d.obj, indexAlpha = "all")
# Connected components of the alpha-shape for both values of alpha
comp <- components_ashape3d(ashape3d.obj, indexAlpha = "all")
class(comp)
# Number of components and points in each component for alpha=0.25
table(comp[[1]])
# Number of components and points in each component for alpha=2
table(comp[[2]])
# Plot the connected components for alpha=0.25
plot(ashape3d.obj, byComponents = TRUE, indexAlpha = 1)
6 inashape3d
inashape3d Test of the inside of an -shape
Description
This function checks whether points are inside an -shape.
Usage
inashape3d(as3d, indexAlpha = 1, points)
Arguments
as3d An object of class "ashape3d" that represents the -shape of a given sample of
points in the three-dimensional space, see ashape3d.
indexAlpha A single value or vector with the indexes of as3d$alpha that should be used for
the computation, see Details.
points A 3-column matrix with the coordinates of the input points.
Details
The function inashape3d checks whether each point in points is inside the -shape for each value
of in as3d$alpha[indexAlpha].
If indexAlpha="all" or indexAlpha="ALL" then the function checks whether each point in points
is inside the -shape for all values of in as3d$alpha.
Value
If indexAlpha is a single value then the function returns a vector of boolean of length the number
of input points. The element at position i is TRUE if the point in points[i,] is inside the -shape.
Otherwise inashape3d returns a list of vectors of boolean values (each object in the list as described
above).
See Also
ashape3d
Examples
T1 <- rtorus(2000, 0.5, 2)
T2 <- rtorus(2000, 0.5, 2, ct = c(2, 0, 0), rotx = pi/2)
x <- rbind(T1, T2)
ashape3d.obj <- ashape3d(x, alpha = 0.4)
# Random sample of points in a plane
points <- matrix(c(5*runif(10000) - 2.5, rep(0.01, 5000)), nc = 3)
in3d <- inashape3d(ashape3d.obj, points = points)
plot(ashape3d.obj, transparency = 0.2)
plot.ashape3d 7
colors <- ifelse(in3d, "blue", "green")
rgl.points(points, col = colors)
plot.ashape3d Plot the -shape in 3D
Description
This function plots the -shape in 3D using the package rgl.
Usage
## S3 method for class ashape3d
plot(x, clear = TRUE, col = c(2, 2, 2), byComponents = FALSE,
indexAlpha = 1, transparency = 1, walpha = FALSE, ...)
Arguments
x An object of class "ashape3d" that represents the -shape of a given sample of
points in the three-dimensional space, see ashape3d.
clear Logical, specifying whether the current rgl device should be cleared.
col A vector of length three specifying the colors of the triangles, edges and vertices
composing the -shape, respectively.
byComponents Logical, if TRUE the connected components of the -shape are represented in
different colors, see components_ashape3d.
indexAlpha A single value or vector with the indexes of x$alpha that should be used for the
computation, see Details.
transparency The coefcient of transparency, from 0 (transparent) to 1 (opaque), used to plot
the -shape.
walpha Logical, if TRUE the value of is displayed in the rgl device.
... Material properties. See rgl.material for details.
Details
The function plot.ashape3d opens a rgl device for each value of in x$alpha[indexAlpha].
Device information is displayed in the console.
If indexAlpha="all" or indexAlpha="ALL" then the function represents the -shape for all values
of in as3d$alpha.
See Also
ashape3d, components_ashape3d
8 rtorus
Examples
T1 <- rtorus(1000, 0.5, 2)
T2 <- rtorus(1000, 0.5, 2, ct = c(2, 0, 0), rotx = pi/2)
x <- rbind(T1, T2)
alpha <- c(0.15, 0.25, 1)
ashape3d.obj <- ashape3d(x, alpha = alpha)
# Plot the alpha-shape for all values of alpha
plot(ashape3d.obj, indexAlpha = "all")
# Plot the connected components of the alpha-shape for alpha=0.25
plot(ashape3d.obj, byComponents = TRUE, indexAlpha = 2)
rtorus Generate points in the torus
Description
This function generates n random points within the torus whose minor radius is r, major radius is
R and center is ct.
Usage
rtorus(n, r, R, ct = c(0, 0, 0), rotx = NULL)
Arguments
n Number of observations.
r Minor radius (radius of the tube).
R Major radius (distance from the center of the tube to the center of the torus).
ct A vector with the coordinates of the center of the torus.
rotx If not NULL, a rotation through an angle rotx (in radians) about the x-axis is
performed.
Examples
T1 <- rtorus(2000, 0.5, 2.5)
rgl.bbox()
rgl.points(T1, col = 4)
T2 <- rtorus(2000, 0.5, 2.5, ct = c(2, 0, 0.5), rotx = pi/2)
rgl.points(T2, col = 2)
surfaceNormals 9
surfaceNormals Normal vectors computation
Description
This function calculates the normal vectors of all the triangles which belong to the boundary of the
-shape.
Usage
surfaceNormals(x, indexAlpha = 1, display = FALSE, col = 3, scale = 1, ...)
Arguments
x An object of class "ashape3d" that represents the -shape of a given sample of
points in the three-dimensional space, see ashape3d.
indexAlpha A single value or vector with the indexes of as3d$alpha that should be used for
the computation, see Details.
display Logical, if TRUE, surfaceNormals open a new rgl device and display the re-
lated -shape and its normals vectors.
col Color of the normal vectors.
scale Scale parameter to control the length of the surface normals, only affect display.
... Material properties. See rgl.material for details.
Details
The function surfaceNormals computes the normal vectors of all the triangles which belong to the
boundary of the -shape for each value of in x$alpha[indexAlpha]. The magnitude of each
vector is equal to the area of its associated triangle.
If indexAlpha="all" or indexAlpha="ALL" then the function computes the normal vectors for all
values of in as3d$alpha.
Value
If indexAlpha is a single value then the function returns an object of class "normals" with the
following components:
normals Three-column matrix with the euclidean coordinates of the normal vectors.
centers Three-column matrix with the euclidean coordinates of the centers of the trian-
gles that form the -shape.
Otherwise surfaceNormals returns a list of class "normals-List" (each object in the list as de-
scribed above).
See Also
ashape3d
10 volume_ashape3d
Examples
x <- rtorus(1000, 0.5, 1)
alpha <- 0.25
ashape3d.obj <- ashape3d(x, alpha = alpha)
surfaceNormals(ashape3d.obj, display = TRUE)
volume_ashape3d Volume computation
Description
This function calculates the volume of the -shape of a given sample of points in the three-dimensional
space.
Usage
volume_ashape3d(as3d, byComponents = FALSE, indexAlpha = 1)
Arguments
as3d An object of class "ashape3d" that represents the -shape of a given sample of
points in the three-dimensional space, see ashape3d.
byComponents Logical, if FALSE (default) volume_ashape3d computes the volume of the
whole -shape. If TRUE, volume_ashape3d computes the volume of each con-
nected component of the -shape separately.
indexAlpha A single value or vector with the indexes of as3d$alpha that should be used for
the computation, see Details.
Details
The function volume_ashape3d computes the volume of the -shape for each value of in as3d$alpha[indexAlpha]
when indexAlpha is numeric.
If indexAlpha="all" or indexAlpha="ALL" then the function computes the volume of the -shape
for all values of in as3d$alpha.
Value
If indexAlpha is a single value then the function returns the volume of the -shape (if the argument
byComponents is set to FALSE) or a vector with the volumes of each connected component of the
-shape (if the argument byComponents is set to TRUE).
Otherwise volume_ashape3d returns a list (each object in the list as described above).
See Also
ashape3d, components_ashape3d
volume_ashape3d 11
Examples
C1 <- matrix(runif(6000), nc = 3)
C2 <- matrix(runif(6000), nc = 3) + 2
x <- rbind(C1, C2)
ashape3d.obj <- ashape3d(x, alpha = 0.75)
plot(ashape3d.obj, byComponents = TRUE)
# Compute the volume of the alpha-shape
volume_ashape3d(ashape3d.obj)
# Compute the volumes of the connected components of the alpha-shape
volume_ashape3d(ashape3d.obj, byComponents = TRUE)
Index
Topic package
alphashape3d-package, 2
ashape3d, 2
components_ashape3d, 4
inashape3d, 6
plot.ashape3d, 7
surfaceNormals, 9
volume_ashape3d, 10
alphashape3d-package, 2
ashape3d, 2, 57, 9, 10
components_ashape3d, 4, 7, 10
inashape3d, 6
plot.ashape3d, 5, 7
rgl, 7
rgl.material, 7, 9
rtorus, 8
surfaceNormals, 9
volume_ashape3d, 10
12