| Title: | Miscellaneous 3D Plots |
|---|---|
| Description: | A collection of miscellaneous 3d plots, including isosurfaces. |
| Authors: | Dai Feng and Luke Tierney |
| Maintainer: | Luke Tierney <[email protected]> |
| License: | GPL |
| Version: | 0.9-1 |
| Built: | 2024-11-06 03:10:35 UTC |
| Source: | https://gitlab.com/luke-tierney/misc3d |
Computes a 3D contours or isosurface by the marching cubes algorithm.
computeContour3d(vol, maxvol = max(vol), level, x = 1:dim(vol)[1], y = 1:dim(vol)[2], z = 1:dim(vol)[3], mask)computeContour3d(vol, maxvol = max(vol), level, x = 1:dim(vol)[1], y = 1:dim(vol)[2], z = 1:dim(vol)[3], mask)
vol |
a three dimensional array. |
maxvol |
maximum of the |
level |
The level at which to construct the contour surface. |
x, y, z
|
locations of grid planes at which values in |
mask |
a function of 3 arguments returning a logical array, a
three dimensional logical array, or |
Uses the marching-cubes algorithm, with adjustments for dealing with
face and internal ambiguities, to compute an isosurface.
See references for the details. The function
contour3d provides a higher-level interface.
A matrix of three columns representing the triangles making up the contour surface. Each row represents a vertex and goups of three rows represent a triangle.
Chernyaev E. (1995) Marching Cubes 33: Construction of Topologically Correct Isosurfaces Technical Report CN/95-17, CERN
Lorensen W. and Cline H. (1987) Marching Cubes: A High Resolution 3D Surface Reconstruction Algorithm Computer Graphics vol. 21, no. 4, 163-169
Nielson G. and Hamann B. (1992) The Asymptotic Decider: Resolving the Ambiguity in Marching Cubes Proc. IEEE Visualization 92, 83-91
x <- seq(-2,2,len=50) g <- expand.grid(x = x, y = x, z = x) v <- array(g$x^4 + g$y^4 + g$z^4, rep(length(x),3)) con <- computeContour3d(v, max(v), 1) drawScene(makeTriangles(con))x <- seq(-2,2,len=50) g <- expand.grid(x = x, y = x, z = x) v <- array(g$x^4 + g$y^4 + g$z^4, rep(length(x),3)) con <- computeContour3d(v, max(v), 1) drawScene(makeTriangles(con))
Computes and renders 3D contours or isosurfaces computed by the marching cubes algorithm.
contour3d(f, level, x, y, z, mask = NULL, color = "white", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, material = "default", smooth = 0, add = FALSE, draw = TRUE, engine = "rgl", separate=FALSE, ...)contour3d(f, level, x, y, z, mask = NULL, color = "white", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, material = "default", smooth = 0, add = FALSE, draw = TRUE, engine = "rgl", separate=FALSE, ...)
f |
a function of 3 arguments or a three dimensional array. |
level |
The level or levels at which to construct contour surfaces. |
x, y, z
|
locations of grid planes at which values in |
mask |
a function of 3 arguments returning a logical array, a
three dimensional logical array, or |
color |
color to use for the contour surface. Recycled to the
length of |
color2 |
opposite face color. Recycled to the length of
|
alpha |
alpha channel level, a number between 0 and 1. Recycled to the
length of |
fill |
logical; if |
col.mesh |
color to use for the wire frame. Recycled to the
length of |
smooth |
integer or logical specifying Phong shading level for
"standard" and "grid" engines or whether or not to use shading for
the "rgl" engine. Recycled to the length of |
material |
material specification; currently only used by
"standard" and "grid" engines. Currently possible values are the
character strings "dull", "shiny", "metal", and "default". Recycled
to the length of |
add |
logical; if |
draw |
logical; if |
engine |
character; currently "rgl", "standard", "grid" or "none"; for "none" the computed triangles are returned. |
separate |
logical and one for each |
... |
additional rendering arguments, e.g. material and texture
properties for the "rgl" engine. See documentation for
|
Uses the marching-cubes algorithm, with adjustments for dealing with face and internal ambiguities, to draw isosurfaces. See references for the details.
For the "rgl" engine the returned value is NULL. For the
"standard" and "grid" engines the returned value is the viewing
transformation as returned by persp. For the engine "none", or
when draw is not true, the returned value is a structure
representing the triangles making up the contour, or a list of such
structures for multiple contours.
The "rgl" engine now uses the standard rgl coordinates instead of
negating y and swapping y and z. If you need to
reproduce the previous behavior you can use
options(old.misc3d.orientation=TRUE).
Transparency only works properly in the "rgl" engine. For standard or grid graphics on pdf or quartz devices using alpha levels less than 1 does work but the triangle borders show as a less transparent mesh.
Chernyaev E. (1995) Marching Cubes 33: Construction of Topologically Correct Isosurfaces Technical Report CN/95-17, CERN
Daniel Adler, Oleg Nenadic and Walter Zucchini (2003) RGL: A R-library for 3D visualization with OpenGL
Lorensen W. and Cline H. (1987) Marching Cubes: A High Resolution 3D Surface Reconstruction Algorithm Computer Graphics vol. 21, no. 4, 163-169
Nielson G. and Hamann B. (1992) The Asymptotic Decider: Resolving the Ambiguity in Marching Cubes Proc. IEEE Visualization 92, 83-91
triangles3d, material3d,
surface3d.
#Example 1: Draw a ball f <- function(x, y, z)x^2+y^2+z^2 x <- seq(-2,2,len=20) contour3d(f,4,x,x,x) contour3d(f,4,x,x,x, engine = "standard") # ball with one corner removed. contour3d(f,4,x,x,x, mask = function(x,y,z) x > 0 | y > 0 | z > 0) contour3d(f,4,x,x,x, mask = function(x,y,z) x > 0 | y > 0 | z > 0, engine="standard", screen = list(x = 290, y = -20), color = "red", color2 = "white") # ball with computed colors w <- function(x,y,z) { v <- sin(x) + cos(2 * y) * sin(5 * z) r <- range(v) n <- 100 i <- pmax(pmin(ceiling(n * (v - r[1]) / (r[2] - r[1])), n), 1) terrain.colors(n)[i] } contour3d(f,4,x,x,x, color = w) #Example 2: Nested contours of mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) g <- function(n = 40, k = 5, alo = 0.1, ahi = 0.5, cmap = heat.colors) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) al <- seq(alo, ahi, len = length(th)) x <- seq(-2, 2, len=n) contour3d(f,th,x,x,x,color=col,alpha=al) rgl::bg3d(col="white") } g(40,5) gs <- function(n = 40, k = 5, cmap = heat.colors, ...) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) x <- seq(-2, 2, len=n) m <- function(x,y,z) x > .25 | y < -.3 contour3d(f,th,x,x,x,color=col, mask = m, engine = "standard", scale = FALSE, ...) rgl::bg3d(col="white") } gs(40, 5, screen=list(z = 130, x = -80), color2 = "lightgray", cmap=rainbow) ## Not run: #Example 3: Nested contours for FMRI data. library(AnalyzeFMRI) a <- f.read.analyze.volume(system.file("example.img", package="AnalyzeFMRI")) a <- a[,,,1] contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), alpha = c(0.2, 0.5, 1), color = c("white", "red", "green")) # alternative masking out a corner m <- array(TRUE, dim(a)) m[1:30,1:30,1:10] <- FALSE contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), mask = m, color = c("white", "red", "green")) contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), color = c("white", "red", "green"), color2 = c("gray", "red", "green"), mask = m, engine="standard", scale = FALSE, screen=list(z = 60, x = -120)) ## End(Not run) #Example 4: Separate the triangles from the contours of # mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.3*dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3*dnorm(x, -2*m, s) * dnorm(y, -2*m, s) * dnorm(z, -2*m, s) + 0.4*dnorm(x, -3*m, s) * dnorm(y, -3 * m, s) * dnorm(z, -3*m, s) } f <- function(x,y,z) nmix3(x,y,z,0.5,.1) n <- 20 x <- y <- z <- seq(-2, 2, len=n) contour3dObj <- contour3d(f, 0.35, x, y, z, draw=FALSE, separate=TRUE) for(i in 1:length(contour3dObj)) contour3dObj[[i]]$color <- rainbow(length(contour3dObj))[i] drawScene.rgl(contour3dObj)#Example 1: Draw a ball f <- function(x, y, z)x^2+y^2+z^2 x <- seq(-2,2,len=20) contour3d(f,4,x,x,x) contour3d(f,4,x,x,x, engine = "standard") # ball with one corner removed. contour3d(f,4,x,x,x, mask = function(x,y,z) x > 0 | y > 0 | z > 0) contour3d(f,4,x,x,x, mask = function(x,y,z) x > 0 | y > 0 | z > 0, engine="standard", screen = list(x = 290, y = -20), color = "red", color2 = "white") # ball with computed colors w <- function(x,y,z) { v <- sin(x) + cos(2 * y) * sin(5 * z) r <- range(v) n <- 100 i <- pmax(pmin(ceiling(n * (v - r[1]) / (r[2] - r[1])), n), 1) terrain.colors(n)[i] } contour3d(f,4,x,x,x, color = w) #Example 2: Nested contours of mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) g <- function(n = 40, k = 5, alo = 0.1, ahi = 0.5, cmap = heat.colors) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) al <- seq(alo, ahi, len = length(th)) x <- seq(-2, 2, len=n) contour3d(f,th,x,x,x,color=col,alpha=al) rgl::bg3d(col="white") } g(40,5) gs <- function(n = 40, k = 5, cmap = heat.colors, ...) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) x <- seq(-2, 2, len=n) m <- function(x,y,z) x > .25 | y < -.3 contour3d(f,th,x,x,x,color=col, mask = m, engine = "standard", scale = FALSE, ...) rgl::bg3d(col="white") } gs(40, 5, screen=list(z = 130, x = -80), color2 = "lightgray", cmap=rainbow) ## Not run: #Example 3: Nested contours for FMRI data. library(AnalyzeFMRI) a <- f.read.analyze.volume(system.file("example.img", package="AnalyzeFMRI")) a <- a[,,,1] contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), alpha = c(0.2, 0.5, 1), color = c("white", "red", "green")) # alternative masking out a corner m <- array(TRUE, dim(a)) m[1:30,1:30,1:10] <- FALSE contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), mask = m, color = c("white", "red", "green")) contour3d(a, 1:64, 1:64, 1.5*(1:21), lev=c(3000, 8000, 10000), color = c("white", "red", "green"), color2 = c("gray", "red", "green"), mask = m, engine="standard", scale = FALSE, screen=list(z = 60, x = -120)) ## End(Not run) #Example 4: Separate the triangles from the contours of # mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.3*dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3*dnorm(x, -2*m, s) * dnorm(y, -2*m, s) * dnorm(z, -2*m, s) + 0.4*dnorm(x, -3*m, s) * dnorm(y, -3 * m, s) * dnorm(z, -3*m, s) } f <- function(x,y,z) nmix3(x,y,z,0.5,.1) n <- 20 x <- y <- z <- seq(-2, 2, len=n) contour3dObj <- contour3d(f, 0.35, x, y, z, draw=FALSE, separate=TRUE) for(i in 1:length(contour3dObj)) contour3dObj[[i]]$color <- rainbow(length(contour3dObj))[i] drawScene.rgl(contour3dObj)
Draw scenes consisting of one or more surfaces described by triangular mesh data structures.
drawScene(scene, light = c(0, 0, 1), screen = list(z = 40, x = -60), scale = TRUE, R.mat = diag(4), perspective = FALSE, distance = if (perspective) 0.2 else 0, fill = TRUE, xlim = NULL, ylim = NULL, zlim = NULL, aspect = c(1, 1), col.mesh = if (fill) NA else "black", polynum = 100, lighting = phongLighting, add = FALSE, engine = "standard", col.bg = "transparent", depth = 0, newpage = TRUE) drawScene.rgl(scene, add = FALSE, ...)drawScene(scene, light = c(0, 0, 1), screen = list(z = 40, x = -60), scale = TRUE, R.mat = diag(4), perspective = FALSE, distance = if (perspective) 0.2 else 0, fill = TRUE, xlim = NULL, ylim = NULL, zlim = NULL, aspect = c(1, 1), col.mesh = if (fill) NA else "black", polynum = 100, lighting = phongLighting, add = FALSE, engine = "standard", col.bg = "transparent", depth = 0, newpage = TRUE) drawScene.rgl(scene, add = FALSE, ...)
scene |
a triangle mesh object of class |
light |
numeric vector of length 3 or 4. The first three
elements represent the direction to the light in viewer coordinates;
the viewer is at |
screen |
as for |
scale |
logical. Before viewing the x, y and z coordinates of the
scene defining the surface are transformed to the interval
[-0.5,0.5]. If |
R.mat |
initial rotation matrix in homogeneous coordinates, to be
applied to the data before |
perspective |
logical, whether to render a perspective
view. Setting this to |
distance |
numeric, between 0 and 1, controls amount of
perspective. The distance of the viewing point from the origin (in
the transformed coordinate system) is |
fill |
logical; if |
xlim, ylim, zlim
|
x-, y- and z-limits. The scene is rendered so that the rectangular volume defined by these limits is visible. |
aspect |
vector of length 2. Gives the relative aspects of the y-size/x-size and z-size/x-size of the enclosing cube. |
col.mesh |
color to use for the wire frame if |
polynum |
integer. Number of triangles to pass in batches to grid primitives for the "grid" engine. The default should be adequate. |
lighting |
a lighting function. Current options are
|
add |
logical; if |
engine |
character; currently "standard" or "grid". |
col.bg |
background dolor to use in color depth cuing. |
depth |
numeric, between 0 and 1. Controls the amount of color
blending to |
newpage |
logical; if |
... |
rgl material and texture properties; see documentation for
|
drawScene renders a scene consisting of one or more triangle
mesh objects using standard or grid graphics. Object-specific
rendering features such as smoothing and material are controlled by
setting in the objects. Arguments to drawScene control global
factors such as viewer and light position.
drawScene.rgl renders the scene in an rgl window.
If add=TRUE in standard or grid graphics then coordinates are
not further scaled after the transformations implied by R.mat,
and distance are applied. For the grid engine drawing occurs
in the current viewport.
drawScene.rgl returns NULL. The return value of
drawScene is the viewing transformation as returned by
persp.
The "rgl" engine now uses the standard rgl coordinates instead of
negating y and swapping y and z. If you need to
reproduce the previous behavior you can use
options(old.misc3d.orientation=TRUE).
Transparency only works properly in the "rgl" engine. For standard or grid graphics on devices that support transparency using alpha levels less than 1 does work but the triangle borders show as a less transparent mesh.
vtri <- local({ z <- 2 * volcano x <- 10 * (1:nrow(z)) y <- 10 * (1:ncol(z)) surfaceTriangles(x, y, z, color="green3") }) drawScene(vtri, scale = FALSE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE, perspective = TRUE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE, perspective = TRUE, depth = 0.4)vtri <- local({ z <- 2 * volcano x <- 10 * (1:nrow(z)) y <- 10 * (1:ncol(z)) surfaceTriangles(x, y, z, color="green3") }) drawScene(vtri, scale = FALSE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE, perspective = TRUE) drawScene(vtri, screen=list(x=40, y=-40, z=-135), scale = FALSE, perspective = TRUE, depth = 0.4)
Writing out scenes consisting of one or more surfaces represented by triangular mesh data structures to textual files.
exportScene(scene, filename, format=c("OFF", "IDTF", "ASY"))exportScene(scene, filename, format=c("OFF", "IDTF", "ASY"))
scene |
a triangle mesh object of class |
filename |
the name of the exported textual file. |
format |
the format of the exported textual file. It must be one of "OFF", "IDTF", or "ASY" and can be abbreviated. The default is "OFF". |
exportScene writes out scenes to textual files,
which can be used for other purposes, for example the
generation of U3d and PRC files for interactive 3D visualization in
a PDF.
Textual files representing triangular mesh scenes.
nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) gs1 <- function(n = 40, k = 5, cmap = heat.colors, ...) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) x <- seq(-2, 2, len=n) m <- function(x,y,z) x > .25 | y < -.3 contour3d(f,th,x,x,x,color=col, mask = m, engine = "none", scale = FALSE, ...) } conts <- gs1(40, 5, screen=list(z = 130, x = -80), color2 = "lightgray", cmap=rainbow) filename <- file.path(tempdir(), "nmix") exportScene(conts, filename, "OFF")nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) gs1 <- function(n = 40, k = 5, cmap = heat.colors, ...) { th <- seq(0.05, 0.2, len = k) col <- rev(cmap(length(th))) x <- seq(-2, 2, len=n) m <- function(x,y,z) x > .25 | y < -.3 contour3d(f,th,x,x,x,color=col, mask = m, engine = "none", scale = FALSE, ...) } conts <- gs1(40, 5, screen=list(z = 130, x = -80), color2 = "lightgray", cmap=rainbow) filename <- file.path(tempdir(), "nmix") exportScene(conts, filename, "OFF")
Plots points on a three dimensional grid representing values in a three dimensional array. Assumes high values are inside and uses alpha blending to make outside points more transparent.
image3d(v, x = 1:dim(v)[1], y = 1:dim(v)[2], z = 1:dim(v)[3], vlim = quantile(v, c(.9, 1),na.rm=TRUE), col = heat.colors(256), alpha.power = 2, alpha = ((1:length(col))/ length(col))^alpha.power, breaks, sprites = TRUE, jitter = FALSE, radius = min(diff(x), diff(y), diff(z)), add = FALSE,...)image3d(v, x = 1:dim(v)[1], y = 1:dim(v)[2], z = 1:dim(v)[3], vlim = quantile(v, c(.9, 1),na.rm=TRUE), col = heat.colors(256), alpha.power = 2, alpha = ((1:length(col))/ length(col))^alpha.power, breaks, sprites = TRUE, jitter = FALSE, radius = min(diff(x), diff(y), diff(z)), add = FALSE,...)
v |
three dimensional data array. |
x, y, z
|
locations of grid planes at which values in |
vlim |
minimum and maximum |
col |
vector of colors for the points as generated by
|
alpha.power |
used to calculate the alpha values. The larger the
power, the smaller the alpha, the more transparent the point. Only
used if |
alpha |
vector of alpha values between 0 and 1. The length of
the vector should be equal to the length of |
breaks |
breakpoints for the colors; must give one more breakpoint than colors. |
sprites |
logical; if |
radius |
radius used in |
jitter |
logical; if |
add |
logical; if |
... |
material and texture properties. See |
Daniel Adler, Oleg Nenadic and Walter Zucchini (2003) RGL: A R-library for 3D visualization with OpenGL
image, sprites3d,
points3d, jitter.
# view density of mixture of tri-variate normals nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) x<-seq(-2,2,len=50) g <- expand.grid(x = x, y = x, z = x) v <- array(f(g$x, g$y, g$z), c(length(x), length(x), length(x))) image3d(v) image3d(v, jitter = TRUE)# view density of mixture of tri-variate normals nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } f <- function(x,y,z) nmix3(x,y,z,.5,.5) x<-seq(-2,2,len=50) g <- expand.grid(x = x, y = x, z = x) v <- array(f(g$x, g$y, g$z), c(length(x), length(x), length(x))) image3d(v) image3d(v, jitter = TRUE)
Evaluates a three dimensional kernel density estimate using a Gaussian kernel with diagonal covariance matrix on a regular grid.
kde3d(x, y, z, h, n = 20, lims = c(range(x), range(y), range(z)))kde3d(x, y, z, h, n = 20, lims = c(range(x), range(y), range(z)))
x, y, z
|
|
h |
vector of three bandwidths for the density estimate;
recycled if length is less than three; default is based on the
normal reference bandwidth (see |
n |
numbers of grid points to use for each dimension; recycled if length is less than three. |
lims |
lower and upper limits on the region for which the density
estimate is to be computed, provides as a vector of length 6,
corresponding to low and high values of |
A list of four components, x, y, z, and
d. x, y, and z are the coordinates of the
grid points at which the density estimate has been evaluated, and
d is a three dimensional array of the estimated density values.
Based on the function kde2d in package
MASS.
with(quakes, { d <- kde3d(long, lat, -depth, n = 40) contour3d(d$d, exp(-12), d$x/22, d$y/28, d$z/640, color = "green", color2 = "gray", scale=FALSE, engine = "standard") })with(quakes, { d <- kde3d(long, lat, -depth, n = 40) contour3d(d$d, exp(-12), d$x/22, d$y/28, d$z/640, color = "green", color2 = "gray", scale=FALSE, engine = "standard") })
Functions to compute colors modified for lighting effects.
phongLighting(normals, view, light, color, color2, alpha, material = "default") perspLighting(normals, view, light, color, color2, alpha, material = "default")phongLighting(normals, view, light, color, color2, alpha, material = "default") perspLighting(normals, view, light, color, color2, alpha, material = "default")
normals |
numeric matrix with three columns representing surface normal vectors. |
view |
numeric vector of length 3 representing the direction to the viewer. |
light |
numeric vector of length 3 or 4. The first three elements represent the direction to the light. The fourth element, if present, represents light intensity; the default is 1. |
color |
colors to use for faces in the direction of the normal vectors. |
color2 |
opposite face color. |
alpha |
alpha channel level, a number between 0 and 1. |
material |
material specification. Currently possible values are the character strings "dull", "shiny", "metal", and "default". |
phongLighting uses the Phong lighting model to compute colors
modified for view direction, light direction, and material properties.
perspLighting implements approximately the same lighting model
as the persp function.
Vector of color specifications.
Creates a scene consisting of lines made up of small tetrahedra centered at points along them.
linesTetrahedra(x, y, z, delta=c(min(x[,2]-x[,1])/10, min(y[,2]-y[,1])/10, min(z[,2]-z[,1])/10), lwd = 0.01, color = "black", ...)linesTetrahedra(x, y, z, delta=c(min(x[,2]-x[,1])/10, min(y[,2]-y[,1])/10, min(z[,2]-z[,1])/10), lwd = 0.01, color = "black", ...)
x, y, z
|
numeric vectors of length two or matrices with two columns representing coordinates of starting and ending points of line(s). |
delta |
numeric; increase in each dimension used to locate points along the lines; recycled to length 3. |
lwd |
numeric; used for the size of the tetrahedron in each dimension; recycled to length 3. |
color |
color to use for the tetrahedra. |
... |
additional arguments to be passed on to
|
The function uses the Bresenham's line algorithm to locate points along lines and then creates a triangle mesh scene representing tetrahedra centered at those points.
Returns a triangle mesh scene representing the lines.
p <- pointsTetrahedra(x=c(100,100, 257, 257), y=c(100,100, 257, 257), z=c(100,257, 257, 100), size=1) l <- linesTetrahedra(x=matrix(c(100,257, 100,257), nrow=2, byrow=TRUE), y=matrix(c(100,257, 100,257), nrow=2, byrow=TRUE), z=matrix(c(100,257, 257,100), nrow=2, byrow=TRUE), lwd=0.4, col="red") drawScene.rgl(list(p, l))p <- pointsTetrahedra(x=c(100,100, 257, 257), y=c(100,100, 257, 257), z=c(100,257, 257, 100), size=1) l <- linesTetrahedra(x=matrix(c(100,257, 100,257), nrow=2, byrow=TRUE), y=matrix(c(100,257, 100,257), nrow=2, byrow=TRUE), z=matrix(c(100,257, 257,100), nrow=2, byrow=TRUE), lwd=0.4, col="red") drawScene.rgl(list(p, l))
Plot a two-parameter surface in three dimensions.
parametric3d(fx, fy, fz, u, v, umin, umax, vmin, vmax, n = 100, color = "white", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default", add = FALSE, draw = TRUE, engine = "rgl", ...)parametric3d(fx, fy, fz, u, v, umin, umax, vmin, vmax, n = 100, color = "white", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default", add = FALSE, draw = TRUE, engine = "rgl", ...)
fx, fy, fz
|
vectorized functions of u and v to compute the
|
u |
numeric vector of u values. |
v |
numeric vector of v values. |
umin |
numeric; the minimum value of u. Ignored if |
umax |
numeric; the maximum value of u. Ignored if |
vmin |
numeric; the minimum value of v. Ignored if |
vmax |
numeric; the maximum value of v. Ignored if |
n |
the number of equally spaced |
color |
color to use for the surface. Can also be a function of three arguments. This is called with three arguments, the coordinates of the midpoints of the triangles making up the surface. The function should return a vector of colors to use for the triangles. |
color2 |
opposite face color. |
alpha |
alpha channel level, a number between 0 and 1.. |
fill |
logical; if |
col.mesh |
color to use for the wire frame. |
smooth |
integer or logical specifying Phong shading level for "standard" and "grid" engines or whether or not to use shading for the "rgl" engine. |
material |
material specification; currently only used by "standard" and "grid" engines. Currently possible values are the character strings "dull", "shiny", "metal", and "default". |
add |
logical; if |
draw |
logical; if |
engine |
character; currently "rgl", "standard", "grid" or "none"; for "none" the computed triangles are returned. |
... |
additional rendering arguments, e.g. material and texture
properties for the "rgl" engine. See documentation for
|
Analogous to Mathematica's Param3D. Evaluates the
functions fx, fy, and fz specifying the
coordinates of the surface at a grid of values for the
parameters u and v.
For the "rgl" engine the returned value is NULL. For the
"standard" and "grid" engines the returned value is the viewing
transformation as returned by persp. For the engine "none", or
when draw is not true, the returned value is a structure
representing the triangles making up the surface.
The "rgl" engine now uses the standard rgl coordinates instead of
negating y and swapping y and z. If you need to
reproduce the previous behavior you can use
options(old.misc3d.orientation=TRUE).
Transparency only works properly in the "rgl" engine. For standard or grid graphics on pdf or quartz devices using alpha levels less than 1 does work but the triangle borders show as a less transparent mesh.
Daniel Adler, Oleg Nenadic and Walter Zucchini (2003) RGL: A R-library for 3D visualization with OpenGL
surface3d,
material3d,scatterplot3d.
#Example 1: Ratio-of-Uniform sampling region of bivariate normal parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), umin = -20, umax = 20, vmin = -20, vmax = 20, n = 100) parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101)) parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), engine = "standard", scale = FALSE, screen = list(x=-90, y=20)) #Example 2: Ratio-of-Uniform sampling region of Bivariate t parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), umin = -20, umax = 20, vmin = -20, vmax = 20, n = 100, color = "green") parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), color = "green") parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), color = "green", engine = "standard", scale = FALSE) #Example 3: Surface of revolution parametric3d(fx = function(u,v) u, fy = function(u,v) sin(v)*(u^3+2*u^2-2*u+2)/5, fz = function(u,v) cos(v)*(u^3+2*u^2-2*u+2)/5, umin = -2.3, umax = 1.3, vmin = 0, vmax = 2*pi) parametric3d(fx = function(u,v) u, fy = function(u,v) sin(v)*(u^3+2*u^2-2*u+2)/5, fz = function(u,v) cos(v)*(u^3+2*u^2-2*u+2)/5, umin = -2.3, umax = 1.3, vmin = 0, vmax = 2*pi, engine = "standard", scale = FALSE, color = "red", color2 = "blue", material = "shiny")#Example 1: Ratio-of-Uniform sampling region of bivariate normal parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), umin = -20, umax = 20, vmin = -20, vmax = 20, n = 100) parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101)) parametric3d(fx = function(u, v) u * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fy = function(u, v) v * exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), fz = function(u, v) exp(-0.5 * (u^2 + v^2 - 2 * 0.75 * u * v)/sqrt(1-.75^2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), engine = "standard", scale = FALSE, screen = list(x=-90, y=20)) #Example 2: Ratio-of-Uniform sampling region of Bivariate t parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), umin = -20, umax = 20, vmin = -20, vmax = 20, n = 100, color = "green") parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), color = "green") parametric3d(fx = function(u,v) u*(dt(u,2) * dt(v,2))^(1/3), fy = function(u,v) v*(dt(u,2) * dt(v,2))^(1/3), fz = function(u,v) (dt(u,2) * dt(v,2))^(1/3), u = qcauchy((1:100)/101), v = qcauchy((1:100)/101), color = "green", engine = "standard", scale = FALSE) #Example 3: Surface of revolution parametric3d(fx = function(u,v) u, fy = function(u,v) sin(v)*(u^3+2*u^2-2*u+2)/5, fz = function(u,v) cos(v)*(u^3+2*u^2-2*u+2)/5, umin = -2.3, umax = 1.3, vmin = 0, vmax = 2*pi) parametric3d(fx = function(u,v) u, fy = function(u,v) sin(v)*(u^3+2*u^2-2*u+2)/5, fz = function(u,v) cos(v)*(u^3+2*u^2-2*u+2)/5, umin = -2.3, umax = 1.3, vmin = 0, vmax = 2*pi, engine = "standard", scale = FALSE, color = "red", color2 = "blue", material = "shiny")
Creates a scene consisting of small tetrahedra centered at specified data points in three dimensions.
pointsTetrahedra(x, y, z, size = 0.01, color = "black", ...)pointsTetrahedra(x, y, z, size = 0.01, color = "black", ...)
x, y, z
|
numeric vectors representing point coordinates. |
size |
numeric; multiple of data range to use for the size of the tetrahedron in each dimension; recycled to length 3. |
color |
color to use for the tetrahedra. |
... |
additional arguments to be passed on to
|
This function is useful, for example, for incorporating raw data along
with a density estimate surface in a scene rendered using standard or
grid graphics. For rgl rendering points3d is
an alternative.
Returns a triangle mesh scene representing the tetrahedra.
with(quakes, { d <- kde3d(long, lat, -depth, n = 40) v <- contour3d(d$d, exp(-12),d$x/22, d$y/28, d$z/640, color="green", color2="gray", draw=FALSE) p <- pointsTetrahedra(long/22, lat/28, -depth/640, size = 0.005) drawScene(list(v, p)) })with(quakes, { d <- kde3d(long, lat, -depth, n = 40) v <- contour3d(d$d, exp(-12),d$x/22, d$y/28, d$z/640, color="green", color2="gray", draw=FALSE) p <- pointsTetrahedra(long/22, lat/28, -depth/640, size = 0.005) drawScene(list(v, p)) })
Uses tkrplot to create an interactive slice view of three or four dimensional volume data.
slices3d(vol1, vol2=NULL, rlim1, rlim2, col1, col2, main, scale = 0.8, alpha=1, cross = TRUE, layout=c("counterclockwise", "clockwise"))slices3d(vol1, vol2=NULL, rlim1, rlim2, col1, col2, main, scale = 0.8, alpha=1, cross = TRUE, layout=c("counterclockwise", "clockwise"))
vol1 |
a three or four dimensional real array. If two images are overlaid, then this is the one at bottom. |
vol2 |
a three or four dimensional real array. If two images are
overlaid, then this is the one on top. The default value is
|
rlim1 |
the minimum and maximum |
rlim2 |
the minimum and maximum |
col1 |
a list of colors for |
col2 |
a list of colors for |
main |
a character vector; main title for the plot. |
scale |
real value for scaling embedded plot size. |
alpha |
real value for transparency level, if two images are overlaid. The default value is 1. |
cross |
logical; if |
layout |
a character string specifying the layout. It must be
either "counterclockwise" or "clockwise", and may be abbreviated.
The default is "counterclockwise". Images corresponding to
the x-y planes are always displayed in the third quadrant.
If |
Shows slices of 3D array along the axes as produced by image,
along with sliders for controlling which slices are shown. For 4D
data an additional slider selects the value of the fourth index.
Two images can be overlaid. This is useful for viewing medical imaging
data (e.g. PET scans and fMRI data).
#Example 1: View of a mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } x<-seq(-2, 2, len=40) g<-expand.grid(x = x, y = x, z = x) v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40)) slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256)) ## Not run: #Example 2: Put a z-map from fMRI data on top of a structure # image. The threshold value of the z-map is 2. library(AnalyzeFMRI) temp<-f.read.analyze.volume("standard.img") z<-f.read.analyze.volume("z-map.img") slices3d(vol1=temp, vol2=z[,,,1], rlim2=c(2,Inf),col2=heat.colors(20), main="Regions above threshold values.") ## End(Not run)#Example 1: View of a mixture of three tri-variate normal densities nmix3 <- function(x, y, z, m, s) { 0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) + 0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) + 0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s) } x<-seq(-2, 2, len=40) g<-expand.grid(x = x, y = x, z = x) v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40)) slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256)) ## Not run: #Example 2: Put a z-map from fMRI data on top of a structure # image. The threshold value of the z-map is 2. library(AnalyzeFMRI) temp<-f.read.analyze.volume("standard.img") z<-f.read.analyze.volume("z-map.img") slices3d(vol1=temp, vol2=z[,,,1], rlim2=c(2,Inf),col2=heat.colors(20), main="Regions above threshold values.") ## End(Not run)
Creates a triangle mesh object representing a surface over a rectangular grid.
surfaceTriangles(x, y, f, color = "red", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default")surfaceTriangles(x, y, f, color = "red", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default")
x, y
|
numeric vectors. |
f |
numeric matrix of dimension |
color |
color to use for the surface. Can also be a function of three arguments. This is called with three arguments, the coordinates of the midpoints of the triangles making up the surface. The function should return a vector of colors to use for the triangles. |
color2 |
opposite face color. |
alpha |
alpha channel level, a number between 0 and 1.. |
fill |
logical; if |
col.mesh |
color to use for the wire frame. |
smooth |
integer or logical specifying Phong shading level for "standard" and "grid" engines or whether or not to use shading for the "rgl" engine. |
material |
material specification; currently only used by "standard" and "grid" engines. Currently possible values are the character strings "dull", "shiny", "metal", and "default". |
Returns a triangle mesh object representing the surface.
persp, rgl.surface,
surface3d.
drawScene(surfaceTriangles(seq(-1,1,len=30), seq(-1,1,len=30), function(x, y) (x^2 + y^2), color2 = "green")) drawScene.rgl(surfaceTriangles(seq(-1,1,len=30), seq(-1,1,len=30), function(x, y) (x^2 + y^2), color2 = "green"))drawScene(surfaceTriangles(seq(-1,1,len=30), seq(-1,1,len=30), function(x, y) (x^2 + y^2), color2 = "green")) drawScene.rgl(surfaceTriangles(seq(-1,1,len=30), seq(-1,1,len=30), function(x, y) (x^2 + y^2), color2 = "green"))
The Utah teapot is a classic computer graphics example. This data set contains a representation in terms of triangles.
data(teapot)data(teapot)
A list with components vertices and
edges. vertices is a 3 by 1976 numeric matrix of the
coordinates of the vertices. edges is a 3 by 3751 integer matrix
of the indices of the triangles.
Converted from the netCDF file that was at one time made available by Dave Forrest at
http://www.maplepark.com/~drf5n/extras/teapot.nc.
Functions to create and modify triangle mesh objects representing 3D surfaces..
makeTriangles(v1, v2, v3, color = "red", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default") updateTriangles(triangles, color, color2, alpha, fill, col.mesh, material, smooth) translateTriangles(triangles, x = 0, y = 0, z = 0) scaleTriangles(triangles, x = 1, y = x, z = x) transformTriangles(triangles, R)makeTriangles(v1, v2, v3, color = "red", color2 = NA, alpha = 1, fill = TRUE, col.mesh = if (fill) NA else color, smooth = 0, material = "default") updateTriangles(triangles, color, color2, alpha, fill, col.mesh, material, smooth) translateTriangles(triangles, x = 0, y = 0, z = 0) scaleTriangles(triangles, x = 1, y = x, z = x) transformTriangles(triangles, R)
v1, v2, v3
|
specification of triangle coordinates. If all three
are provided then they should be matrices with three columns
representing coordinates of the first, second, and third vertices of
the triangles. If only |
triangles |
triangle mesh object. |
x, y, z
|
numeric of length one. Amounts by which to translate or scale corresponding coordinates. |
color |
color to use for the surface. Can also be a function of three arguments. This is called with three arguments, the coordinates of the midpoints of the triangles making up the surface. The function should return a vector of colors to use for the triangles. |
color2 |
opposite face color. |
alpha |
alpha channel level, a number between 0 and 1. |
fill |
logical; if |
col.mesh |
color to use for the wire frame. |
smooth |
integer or logical specifying Phong shading level for "standard" and "grid" engines or whether or not to use shading for the "rgl" engine. |
material |
material specification; currently only used by "standard" and "grid" engines. Currently possible values are the character strings "dull", "shiny", "metal", and "default". |
R |
4 by 4 homogeneous coordinate transformation matrix to apply. |
makeTriangles creates a triangle mesh object.
updateTriangles modifies fields of such an object. Both may
perform some consistency checks.
translateTriangles and scaleTriangles translate or scale
the vertex locations of triangle mesh objects by specified amounts.
transformTriangles applies a transformation specified by a 4 by
4 homogeneous transformation matrix.
A triangle mesh object of class Triangles3D.