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### R code from vignette source 'laser.Rnw'
### Encoding: UTF-8
###################################################
### code chunk number 1: startup
###################################################
#system ("mkdir fig")
options(SweaveHooks=list(fig=function() {
par(mar = c (4.1, 4.1, 1, .6))
trellis.pars <- trellis.par.get ("layout.heights")
trellis.pars [grep ("padding", names (trellis.pars))] <- 0
trellis.par.set(layout.heights = trellis.pars)
trellis.pars <- trellis.par.get ("layout.widths")
trellis.pars [grep ("padding", names (trellis.pars))] <- 0
trellis.par.set(layout.widths = trellis.pars)
}))
options ("width" = 100, "digits" = 5)
library (hyperSpec)
# redefine lattice functions so that the result is printed without external print command
setMethod ("plot",
signature (x = "hyperSpec", y = "character"),
function (x, y, ...){
tmp <- hyperSpec:::.plot (x, y, ...)
if (is (tmp, "trellis"))
print (tmp)
invisible (tmp)
})
plotmap <- function (...) print (hyperSpec:::plotmap (...))
setMethod ("levelplot", signature (x = "hyperSpec", data = "missing"),
function (x, data, ...) {
l <- hyperSpec:::.levelplot (x = formula (spc ~ x * y), data = x, ...)
print (l)
}
)
setMethod ("levelplot", signature (x = "formula", data = "hyperSpec"),
function (x, data, ...) print (hyperSpec:::.levelplot (x, data, ...))
)
plotc <- function (...){
call <- match.call ()
call [[1]] <- hyperSpec:::plotc
print (eval (call))
}
ploterrormsg <- function (fn, pkg) {
plot (0, 0, type = "n", axes = FALSE, bty = "n", xlab = "", ylab = "")
text (0, 0, paste ("Function", fn, "not available:\npackage", pkg, "needed."))
}
griderrormsg <- function (fn, pkg) {
require (grid)
grid.text (label = paste ("Function", fn, "not available:\npackage", pkg, "needed."))
NA
}
texterrormsg <- function (fn, pkg) {
cat ("Function", fn, "not available:\npackage", pkg, "needed.\n")
}
nice.paste <- function (...){
fnames <- c (...)
if (length (fnames) == 2L)
fnames <- paste (fnames, collapse = " and ")
if (length (fnames) > 1L){
fnames [length (fnames)] <- paste ("and", tail (fnames, 1))
fnames <- paste (fnames, collapse = ", ")
}
fnames
}
check.req.pkg <- function (pkg = stop ("pkg needed"),
texterrors = NULL, ploterrors = NULL, griderrors = NULL,
hynstext = NULL, hynsplot = NULL, hynsgrid = NULL,
donothing = NULL, special = NULL, v = TRUE){
if (v) cat ("\\item[\\Rpackage{", pkg, "}:] ", sep = "")
dummies <- list ()
if (pkg.exists (pkg)){
if (v) cat ("available\n")
} else {
for (fn in as.character (texterrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) texterrormsg (.(fn), .(pkg))))
for (fn in as.character (ploterrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) ploterrormsg (.(fn), .(pkg))))
for (fn in as.character (griderrors))
dummies <- c (dummies, bquote (.(fn) <- function (...) griderrormsg (.(fn), .(pkg))))
for (fn in as.character (hynstext))
assignInNamespace (x = fn,
value = eval (bquote (function (...) texterrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
for (fn in as.character (hynsplot))
assignInNamespace (x = fn,
value = eval (bquote (function (...) ploterrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
for (fn in as.character (hynsgrid))
assignInNamespace (x = fn,
value = eval (bquote (function (...) griderrormsg (.(fn), .(pkg)))),
ns = "hyperSpec")
fnames <- nice.paste (texterrors, ploterrors, griderrors, hynstext, hynsplot, hynsgrid, names (special))
if (v && length (fnames) > 0L) cat (fnames, "replaced.")
for (fn in as.character (donothing))
dummies <- c (dummies, bquote (.(fn) <- function (...) invisible (NULL)))
fnames <- nice.paste (donothing)
if (v && length (fnames) > 0L) cat (fnames, "missing.")
if (v) cat ("\n")
}
invisible (dummies)
}
plotvoronoi <- function (...) print (hyperSpec:::plotvoronoi (...))
# set standardized color palettes
seq.palette <- colorRampPalette (c ("white", "dark green"), space = "Lab")
YG.palette <- function (n = 20) rgb (colorRamp (c("#F7FCF5", "#E5F5E0", "#C7E9C0", "#A1D99B", "#74C476",
"#41AB5D", "#238B45", "#006D2C", "#00441B"), space = "Lab")
# was: brewer.pal (9, "Greens")
(seq (1/3, 1, length.out = n)^2), maxColorValue = 255)
div.palette <- colorRampPalette (c("#00008B", "#351C96", "#5235A2", "#6A4CAE", "#8164BA", "#967CC5",
"#AC95D1", "#C1AFDC", "#D5C9E8", "#E0E3E3", "#F8F8B0", "#F7E6C2",
"#EFCFC6", "#E6B7AB", "#DCA091", "#D08977", "#C4725E", "#B75B46",
"#A9432F", "#9A2919", "#8B0000"), space = "Lab")
pkgSuggests <- function (...)
strsplit (packageDescription (..., fields="Suggests"), ",\\s*")[[1]]
pkg.exists <- function (pkg = stop ("package name needed"), lib.loc = NULL){
dir <- sapply (pkg, function (p) system.file (package = p, lib.loc = lib.loc))
nzchar (dir) > 0L
}
is.basepkg <- function (pkg){
pkg.exists (pkg) && grepl ("^base$", packageDescription (pkg, fields = "Priority"))
}
pkg.or.base <- function (pkg){
pkg [sapply (pkg, is.basepkg)] <- "base"
pkg
}
citation.or.file <- function (pkg, svd.cit = sprintf ("%s.CITATION", pkg)){
if (pkg.exists (pkg))
citation (pkg)
else if (file.exists (svd.cit))
readCitationFile (file = svd.cit)
else
NULL
}
make.cite.keys <- function (pkg, entries){
pkg <- pkg.or.base (pkg)
if (! pkg.exists (pkg))
return (pkg)
if (missing (entries))
entries <- citation.or.file (pkg)
keys <- sapply (unclass (entries), attr, "key")
noname <- which (sapply (keys, is.null))
if (length (keys) == 1L && noname == 1L) {
keys <- pkg
} else {
for (i in noname)
keys [[i]] <- paste (pkg, i, sep = ".")
}
keys <- make.unique (unlist (keys))
keys
}
citation.with.key <- function (pkg = "base"){
pkg <- pkg.or.base (pkg)
tmp <- citation.or.file (pkg)
keys <- make.cite.keys (pkg, tmp)
for (entry in seq_along (tmp))
tmp [entry]$"key" <- keys [[entry]]
tmp
}
cite.pkg <- function (p, entries, citefun = "cite"){
paste ("\\\\", citefun, "{", paste (make.cite.keys (p, entries), collapse = ", "), "}", sep = "")
}
make.bib <- function (..., file = NULL) {
pkg <- c (...)
if (length (pkg) == 0L) {
pkg <- loadedNamespaces()
pkg <- unique (pkg.or.base (pkg))
}
l <- lapply (pkg, citation.with.key)
l <- do.call ("c", l [! sapply (l, is.null)])
if (!is.null (file))
if (is.null (l))
cat (NULL, file = file) # touches file
else
cat (toBibtex (l), file = file, sep = "\n")
invisible (l)
}
###################################################
### code chunk number 2: mailme
###################################################
cat ("\\newcommand{\\mailme}{\\href{mailto:",
packageDescription ("hyperSpec")$Maintainer,
"}{\\texttt{",
packageDescription ("hyperSpec")$Maintainer,
"}}}\n",
sep = "")
###################################################
### code chunk number 3: listfunctions
###################################################
texListFun <- function (pattern){
funs <- ls (envir = getNamespace ("hyperSpec"), pattern = pattern)
funs <- paste ("\\\\Rfunction{", funs, "}", sep ="")
nice.paste (funs)
}
###################################################
### code chunk number 4: cleanup (eval = FALSE)
###################################################
## sessionInfo ()
## rm (list = ls ())
## library (tools)
###################################################
### code chunk number 5: check-required
###################################################
check.req.pkg ("rgl", donothing = "")
###################################################
### code chunk number 6: rawspc
###################################################
getOption("SweaveHooks")[["fig"]]()
laser <- scan.txt.Renishaw ("rawdata/laser.txt.gz", data = "ts")
plot (laser, "spcprctl5")
###################################################
### code chunk number 7: cut
###################################################
getOption("SweaveHooks")[["fig"]]()
laser <- laser [,,-75~0]
plot (laser, "spcprctl5")
###################################################
### code chunk number 8: wlspc1
###################################################
wl (laser) <- wl (laser) + 50
###################################################
### code chunk number 9: wlcalc
###################################################
wl (laser) <- list (
wl = 1e7 / (1/405e-7 - wl (laser)),
label = expression (lambda / nm)
)
###################################################
### code chunk number 10: wlspc
###################################################
getOption("SweaveHooks")[["fig"]]()
plot (laser, "spcprctl5")
###################################################
### code chunk number 11: save
###################################################
save (laser, file = "laser.rda")
laser
###################################################
### code chunk number 12: locator (eval = FALSE)
###################################################
## wls <- locator()$x
###################################################
### code chunk number 13: laser.Rnw:119-120
###################################################
wls <- c(405.0063, 405.1121, 405.2885, 405.3591)
###################################################
### code chunk number 14: markspc
###################################################
getOption("SweaveHooks")[["fig"]]()
plot (laser, "spcmeansd")
cols <- c("black", "blue", "red", "darkgreen")
abline (v = wls, col = cols )
###################################################
### code chunk number 15: ts
###################################################
getOption("SweaveHooks")[["fig"]]()
plotc (laser [,, wls], spc ~ t, groups = .wavelength, type = "b", cex = 0.3, col = cols)
###################################################
### code chunk number 16: tsextra
###################################################
getOption("SweaveHooks")[["fig"]]()
plotc (laser [,, wls], spc ~ t | .wavelength, type = "b", cex = 0.3, col = "black")
###################################################
### code chunk number 17: plotmatr
###################################################
getOption("SweaveHooks")[["fig"]]()
plot (laser, "mat", contour = TRUE, col = "#00000060")
###################################################
### code chunk number 18: plotmatt
###################################################
getOption("SweaveHooks")[["fig"]]()
levelplot (spc ~ .wavelength * t, laser, contour = TRUE, col ="#00000080")
###################################################
### code chunk number 19: libraryrgl
###################################################
require (rgl)
###################################################
### code chunk number 20: rgl-plot (eval = FALSE)
###################################################
## laser <- laser [,,404.8 ~ 405.6] / 10000
## laser$t <- laser$t / 3600
## cols <- rep (matlab.palette (nrow (laser)), nwl (laser))
##
## surface3d(y = wl(laser), x = laser$t, z = laser$spc, col = cols)
## surface3d(y = wl(laser), x = laser$t, z = laser$spc + .1 * min (laser),
## col = "black", alpha = .2,front = "lines", line_antialias = TRUE)
##
## aspect3d (c(1, 1, 0.25))
##
## axes3d (c ('x+-', 'y--', 'z--'))
## axes3d ('y--', nticks = 25, labels= FALSE)
## mtext3d ("t / h", 'x+-', line = 2.5)
## mtext3d ("lambda / nm", 'y--', line = 2.5)
## mtext3d ("I / a.u.", 'z--', line = 2.5)
###################################################
### code chunk number 21: rgl-do
###################################################
if (exists (".rgl") && .rgl){ # use extra argument to turn on rgl only on local machine as it doesn't work on r-forge.
if (require (rgl)){
open3d (windowRect=c(20,20,600, 350)) # this is needed only for automatically
# producing the snapshot
laser <- laser [,,404.8 ~ 405.6] / 10000
laser$t <- laser$t / 3600
cols <- rep (matlab.palette (nrow (laser)), nwl (laser))
surface3d(y = wl(laser), x = laser$t, z = laser$spc, col = cols)
surface3d(y = wl(laser), x = laser$t, z = laser$spc + .1 * min (laser),
col = "black", alpha = .2,front = "lines", line_antialias = TRUE)
aspect3d (c(1, 1, 0.25))
axes3d (c ('x+-', 'y--', 'z--'))
axes3d ('y--', nticks = 25, labels= FALSE)
mtext3d ("t / h", 'x+-', line = 2.5)
mtext3d ("lambda / nm", 'y--', line = 2.5)
mtext3d ("I / a.u.", 'z--', line = 2.5)
par3d (userMatrix = matrix (c (-0.52, 0.4, -0.75, 0,
-0.85, -0.28, 0.44, 0,
-0.04, 0.87, 0.49, 0,
-0.75, 0.75, 0, 1), ncol = 4L),
scale = c (2.75, 5, 0.175),
windowRect = c(20L, 50L, 520L, 330L),
zoom = 0.75)
rgl.snapshot ("fig-3D.png", fmt="png", top=TRUE )
rgl.quit ()
} else {
png ("fig-3D.png")
ploterrormsg ("", "rgl")
dev.off ()
}
}
###################################################
### code chunk number 22: makebib
###################################################
make.bib (file = "laser-pkg.bib")
###################################################
### code chunk number 23: laser.Rnw:241-243
###################################################
make.bib (file = "laser-pkg.bib")
sessionInfo ()
rm (list = ls ())
library (tools)
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