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## =============================================================================
## 3-D visualisation of volumetric data using isosurfaces
## =============================================================================
# x, y, z vectors or arrays, colvar: array
isosurf3D <- function(x, y, z, colvar, ...,
phi = 40, theta = 40,
level = mean(colvar, na.rm = TRUE), isofunc = createisosurf,
col = NULL, border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
clab = NULL, bty = "b",
lighting = FALSE, shade = 0.5, ltheta = -135, lphi = 0,
add = FALSE, plot = TRUE) {
plist <- initplist(add)
dot <- splitdotpersp(list(...), bty, lighting,
shade = shade, ltheta = ltheta, lphi = lphi, x, y, z, plist = plist, breaks = NULL)
if (! ispresent(colvar))
stop("'colvar' has to be defined and be an array of dimension 3")
DD <- dim(colvar)
if (length(DD) != 3)
stop("'colvar' has to be an array of dimension 3")
cr <- range(colvar, na.rm = TRUE)
na <- level[level > cr[2] | level < cr[1]]
if (length(na) > 0)
stop("cannot calculate isosurfaces - change 'level': valid range ", formatC(cr[1]),
" - ", formatC(cr[2]))
nlevel <- length(level)
if (is.null(col)) {
if (nlevel == 1)
col <- "grey"
else
col <- jet.col(nlevel)
} else if (length(col) != nlevel)
stop ("number of colors in 'col' must equal number of levels")
if (! is.null(dot$alpha)) col <- setalpha(col, dot$alpha)
iscolkey <- is.colkey(colkey, col)
if (iscolkey)
colkey <- check.colkey(colkey)
if (is.null(plist)) {
do.call("perspbox", c(alist(x = range(x), y = range(y),
z = range(z, na.rm = TRUE), phi = phi, theta = theta,
plot = plot, colkey = colkey, col = col),
dot$persp))
plist <- getplist()
}
if (is.function(panel.first))
panel.first(plist$mat)
Poly <- list()
# calculate isosurface for all levels
for (i in 1:nlevel) {
Tri <- isofunc (x, y, z, colvar, level[i])
Col <- rep(col[i], length.out = nrow(Tri)/3)
lwd <- dot$points$lwd
if (is.null(lwd))
lwd <- 1
lty <- dot$points$lty
if (is.null(lty))
lty <- 1
X <- matrix(nrow = 3, data = Tri[ ,1])
Y <- matrix(nrow = 3, data = Tri[ ,2])
Z <- matrix(nrow = 3, data = Tri[ ,3])
proj <- project(colMeans(X), colMeans(Y), colMeans(Z), plist)
if (! dot$shade$type == "none")
Col <- facetcols.tri (Tri, Col, dot$shade)
Col <- createcolors(facets, border, Col)
alpha <- dot$alpha; if (is.null(alpha)) alpha <- NA
Poly <- list(
x = cbind(Poly$x, rbind(X, NA)),
y = cbind(Poly$y, rbind(Y, NA)),
z = cbind(Poly$z, rbind(Z, NA)),
col = c(Poly$col, Col$facet),
border = c(Poly$border, Col$border),
lwd = c(Poly$lwd, rep(lwd, length.out = ncol(X))),
lty = c(Poly$lty, rep(lty, length.out = ncol(X))),
isimg = c(Poly$isimg, rep(0, length.out = ncol(X))),
alpha = c(Poly$alpha, rep(alpha, length.out = ncol(X))),
img = Poly$img,
proj = c(Poly$proj, proj))
}
class(Poly) <- "poly"
if (iscolkey) {
colkey$at <- 1:nlevel
colkey$labels <- level
zlim <- c(0.5, nlevel + 0.5)
plist <- plistcolkey(plist, colkey, col, zlim, clab, FALSE,
type = "isosurf3D", breaks = NULL)
}
plist <- plot_struct_3D(plist, poly = Poly, plot = plot)
setplist(plist)
invisible(plist$mat)
}
## =============================================================================
## plotting triangles
## =============================================================================
triangle3D <- function(tri, colvar = NULL,
..., phi = 40, theta = 40,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
lighting = FALSE, shade = 0.5, ltheta = -135, lphi = 0,
clim = NULL, clab = NULL,
bty = "b", add = FALSE, plot = TRUE) {
if (add)
plist <- getplist()
else
plist <- NULL
if (! is.matrix(tri))
stop("'tri' should be a matrix with 3 columns")
if (ncol(tri) != 3)
stop("'tri' should be a matrix with 3 columns")
if (nrow(tri)%%3 != 0)
stop("'tri' should be a matrix with number of rows a multiple of 3")
# split in x, y, z
x <- matrix(nrow = 3, data = tri[, 1])
y <- matrix(nrow = 3, data = tri[, 2])
z <- matrix(nrow = 3, data = tri[, 3])
len <- ncol(x) # number of triangles
dot <- splitdotpersp(list(...), bty, lighting, x, y, z, plist = plist,
shade, lphi, ltheta, breaks = breaks)
# colors
if (ispresent(colvar)) {
if (length(colvar) != len)
stop("'colvar' should have same length as number of triangles")
if (is.null(col) & is.null(breaks))
col <- jet.col(100)
else if (is.null(col))
col <- jet.col(length(breaks)-1)
breaks <- check.breaks(breaks, col)
if (length(col) == 1)
col <- c(col, col)
if (is.null(clim))
clim <- range(colvar, na.rm = TRUE)
if (dot$clog) {
colvar <- log(colvar)
clim <- log(clim)
}
iscolkey <- is.colkey(colkey, col)
if (iscolkey)
colkey <- check.colkey(colkey)
if (! is.null(dot$alpha))
col <- setalpha(col, dot$alpha)
Col <- variablecol(colvar, col, NAcol, clim, breaks)
} else {
if (is.null(col))
col <- "grey"
if (! is.null(dot$alpha))
col <- setalpha(col, dot$alpha)
Col <- rep(col, length.out = len)
iscolkey <- FALSE
}
if (is.null(plist)) {
do.call("perspbox",
c(alist(x = range(x, na.rm = TRUE), y = range(y, na.rm = TRUE),
z = range(z, na.rm = TRUE),
phi = phi, theta = theta, plot = plot,
colkey = colkey, col = col), dot$persp))
plist <- getplist()
}
if (is.function(panel.first))
panel.first(plist$mat)
lwd <- dot$points$lwd
if (is.null(lwd))
lwd <- 1
lty <- dot$points$lty
if (is.null(lty))
lty <- 1
alpha <- dot$alpha; if (is.null(alpha)) alpha <- NA
alpha <- rep(alpha, length.out = len)
proj <- project(colMeans(x), colMeans(y), colMeans(z), plist)
if (! dot$shade$type == "none")
Col <- facetcols.tri (tri, Col, dot$shade)
Col <- createcolors(facets, border, Col)
Poly <- list(x = rbind(x, NA),
y = rbind(y, NA),
z = rbind(z, NA),
col = Col$facet,
border = Col$border,
lwd = rep(lwd , length.out = len),
lty = rep(lty , length.out = len),
isimg = rep(0, length.out = len),
img = NULL,
alpha = alpha,
proj = proj)
class(Poly) <- "poly"
if (iscolkey)
plist <- plistcolkey(plist, colkey, col, clim, clab,
dot$clog, type = "triangle3D", breaks = breaks)
plist <- plot_struct_3D(plist, poly = Poly, plot = plot)
setplist(plist)
invisible(plist$mat)
}
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