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## =============================================================================
## 3-D visualisation of volumetric data using contour slices in x, y or z
## =============================================================================
# x, y, z vectors or arrays, colvar: array
ContourLines <- function (x = seq(0, 1, length.out = nrow(z)),
y = seq(0, 1, length.out = ncol(z)), z, nlevels = 10,
levels = pretty(range(z, na.rm = TRUE), nlevels)) {
# Check for decreasing values of x and y
if (all(diff(x) < 0)) {
x <- rev(x)
z <- z[nrow(z):1, ]
}
if (all(diff(y) < 0)) {
y <- rev(y)
z <- z[, (ncol(z):1)]
}
contourLines(x = x, y = y, z= z, nlevels = nlevels, levels = levels)
}
slicecont3D <- function(x, y, z, colvar, ...,
phi = 40, theta = 40,
xs = NULL,
ys = NULL,
zs = NULL, level = NULL,
col = NULL, NAcol = "white", breaks = NULL,
border = NA, facets = TRUE,
colkey = NULL, panel.first = NULL,
clim = NULL, clab = NULL, bty = "b",
dDepth = 0., add = FALSE, plot = TRUE) {
if (add)
plist <- getplist()
else
plist <- NULL
dot <- splitdotpersp(list(...), bty, NULL, x, y, z, plist = plist, breaks = breaks)
if (! ispresent(colvar))
stop("'colvar' has to be defined and be an array of dimension 3")
# check dimensionality
DD <- dim(colvar)
if (length(DD) != 3)
stop("'colvar' has to be an array of dimension 3")
if (DD[1] != length(x))
stop("dimension of 'colvar' not compatible with length of 'x'")
if (DD[2] != length(y))
stop("dimension of 'colvar' not compatible with length of 'y'")
if (DD[3] != length(z))
stop("dimension of 'colvar' not compatible with length of 'z'")
if (! is.null(xs))
if (! is.vector(xs))
stop("'xs' should be a vector")
if (! is.null(ys))
if (! is.vector(ys))
stop("'ys' should be a vector")
if (! is.null(zs))
if (! is.vector(zs))
stop("'zs' should be a vector")
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 (! is.null(dot$alpha))
col <- setalpha(col, dot$alpha)
iscolkey <- is.colkey(colkey, col)
if (iscolkey)
colkey <- check.colkey(colkey)
if (is.null(clim))
clim <- range(colvar, na.rm = TRUE)
if (dot$clog) {
colvar <- log(colvar)
clim <- log(clim)
}
# Colors for NA values
if (any (is.na(colvar)) & ! is.null(NAcol) ) {
CC <- checkcolors(colvar, col, NAcol, clim)
clim <- CC$lim
col <- CC$col
colvar <- CC$colvar
}
crange <- diff(clim)
N <- length(col) -1
if (is.null(breaks))
getcol <- function(v)
col[1 + trunc((v - clim[1])/crange*N)]
else
getcol <- function(v)
col[.bincode(v,breaks)]
lwd <- ifelse(is.null(dot$points$lwd), 1, dot$points$lwd)
dot$points$lwd <- NULL
lty <- ifelse(is.null(dot$points$lty), 1, dot$points$lty)
dot$points$lty <- NULL
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)
Seg <- NULL
templines <- function(clines, x = NULL, y = NULL, z = NULL) {
if (! is.null(x)){
x <- rep(x, length.out = length(clines[[2]]))
y <- clines[[2]]
z <- clines[[3]]
} else if (! is.null(y)) {
y <- rep(y, length.out = length(clines[[2]]))
x <- clines[[2]]
z <- clines[[3]]
} else if (! is.null(z)) {
z <- rep(z, length.out = length(clines[[2]]))
x <- clines[[2]]
y <- clines[[3]]
}
Col <- getcol(clines[[1]])
Seg <<- addlines(Seg, x = x, y = y, z = z, col = Col,
plist = plist, lwd = lwd, lty = lty, alpha = dot$alpha)
} # end function templines
if (is.null(level))
level <- pretty(clim, 10)
for (x.s in xs) {
ix <- max(1, FindInterval(x.s, x, all.inside = FALSE))
Data <- colvar[ix, , ]
cL <- ContourLines(y, z, Data, levels = level)
invisible(lapply(cL, templines, x = x.s))
}
for (y.s in ys) {
iy <- max(1, FindInterval(y.s, y, all.inside = FALSE))
Data <- colvar[, iy, ]
cL <- ContourLines(x, z, Data, levels = level)
invisible(lapply(cL, templines, y = y.s))
}
for (z.s in zs) {
iz <- max(1, FindInterval(z.s, z, all.inside = FALSE))
Data <- colvar[, , iz]
cL <- ContourLines(x, y, Data, levels = level)
invisible(lapply(cL, templines, z = z.s))
}
if (iscolkey)
plist <- plistcolkey(plist, colkey, col, clim, clab, dot$clog,
type = "slicecont3D", breaks = NULL)
if (ispresent(border)) {
for (x.s in xs)
Seg <- addlines(Seg, x = rep(x.s, length.out = 4),
y = c(y[1], y[1], y[length(y)], y[length(y)]),
z = c(z[1], z[length(z)], z[length(z)], z[1]),
plist = plist, col = border)
for (y.s in ys)
Seg <- addlines(Seg, z = c(z[1], z[length(z)], z[length(z)], z[1]),
x = c(x[1], x[1], x[length(x)], x[length(x)]),
y = rep(y.s, length.out = 4),
plist = plist, col = border)
for (z.s in zs)
Seg <- addlines(Seg, x = c(x[1], x[length(x)], x[length(x)], x[1]),
y = c(y[1], y[1], y[length(y)], y[length(y)]),
z = rep(z.s, length.out = 4),
plist = plist, col = border)
}
# change projection depth such that lines are on top of images
Seg$proj <- Seg$proj + dDepth*plist$persp$expand
plist <- plot_struct_3D(plist, segm = Seg, plot = plot)
setplist(plist)
invisible(plist$mat)
}
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