R/XPSDepthProfile.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSDepthProfile
Documented in
XPSDepthProfile
# XPSDepthProfile reconstruction of Depth Profiles
#
#' @title XPSDepthProfile reconstruction of Depth Profiles
#' @description XPSDepthProfile function is used to manipulate single or
#' multiple XPS-Samples acquired by varying the tilt angle (ARXPS) or after
#' sputter-etch cycles (sputter-depth-profiles)
#' The function loads the spectra at variopus angles or at various sputter-cycles
#' defines the Baselines and computes the element quantification.
#' Results are automatically plotted as a function of the tilt angle or
#' of the etch cycles
#' @examples
#' \dontrun{
#' XPSDepthProfile()
#' }
#' @export
#'
XPSDepthProfile <- function() {
CK.Elmts <- function(){ #extracts the name of the profiled elements
CLnames <<- names(XPSSample)
TmpNames <- CLnames
LL <- length(CLnames)
ii <- 1
jj <- 1
while (LL > 0){
Sym <- TmpNames[jj]
if(Sym == "Survey" || Sym == "survey"){
jj <- jj+1
} else {
idx1 <- which(CLnames == Sym) #extracts indexes of all corelines having name == Sym
idx2 <- which(TmpNames == Sym) #extracts indexes of all corelines having name == Sym
CoreLineList[[ii]] <<- idx1
names(CoreLineList)[ii] <<- Sym
TmpNames <- TmpNames[-idx2]
ii <- ii+1
LL <- length(TmpNames)
}
if (jj > LL) {break}
}
CLnames <<- names(XPSSample)
}
MK.Panel <- function(){ #construct the list of checkboxes describing all the XPSSample corelines
CL.Sym <<- names(CoreLineList)
N.CL <<- length(CL.Sym) #Number of profiled elements
N.Cycles <<- max(sapply(CoreLineList, function(x) length(x)))
# (<<<===) This operation transform a list in a matrix maintaining column names
# length<- introduces NA if data lacking
CoreLineList <<- sapply(CoreLineList, "length<-", N.Cycles)
#CheckBoxGroup to slect the CL to analyze
delete(T1frameCoreLines, CoreLineCK)
CoreLineCK <<- gcheckboxgroup(CL.Sym,checked=FALSE, horizontal=TRUE, container=T1frameCoreLines)
}
MK.Baseline <- function(idx, splinePoints){
if (BaseLine == "shirley"){BaseLine <- "Shirley"} #different names for old/new RXPSG packages
if (BaseLine == "2p.shirley"){BaseLine <- "2P.Shirley"} #transform to new BaseLineNames.
if (BaseLine == "3p.shirley"){BaseLine <- "3P.Shirley"} #Exact Baseline Names required to generate the Baseline see XPSClass
if (BaseLine == "lp.shirley"){BaseLine <- "LP.Shirley"}
if (BaseLine == "2p.tougaard"){BaseLine <- "2P.Tougaard"}
if (BaseLine == "3p.tougaard"){BaseLine <- "3P.Tougaard"}
if (BaseLine == "4p.tougaard"){BaseLine <- "4P.Tougaard"}
XPSSample[[idx]] <<- XPSsetRegionToFit(XPSSample[[idx]])
XPSSample[[idx]] <<- XPSbaseline(XPSSample[[idx]], BaseLine, deg=0, Wgt=0, splinePoints )
XPSSample[[idx]] <<- XPSsetRSF(XPSSample[[idx]], XPSSample[[idx]]@RSF)
}
ResetVars <- function(){
CLnames <<- NULL #named of the profiled elements
N.XS <<- NULL
N.CL <<- NULL
N.Cycles <<- NULL
CL <<- NULL
CL.Sym <<- NULL
Matched <<- NULL #CoreLines present in all the XPSSample
SelectedCL <<- NULL
SelectedXPSSamp <<- list()
XPSSample <<- NULL
CoreLineList <<- list() #define a list for the XPSSample corelines
Angles <<- NULL
BaseLine <<- NULL #by default baseline selected for BKGsubtraction
splinePoints <<- list(x=NULL, y=NULL)
BL.Ends <<- list(x=NULL, y=NULL)
QntMat <<- NULL
DPrflType <<- NULL
TkoffAngles <<- NULL
}
#--- Variables
options(warn = -1)
N.XS <- NULL
N.CL <- NULL
N.Cycles <- NULL
CL <- NULL
CL.Sym <- NULL
Matched <- NULL #CoreLines present in all the XPSSample
SelectedCL <- NULL
SelectedXPSSamp <- list()
XPSSample <- NULL
CoreLineList <- list() #define a list for the XPSSample corelines
CoreLineCK <- NULL #pointer to the profiled checkbox elements
# T1frameCoreLines <- NULL
TkoffAngles <- NULL
BaseLine <- NULL #by default baseline selected for BKGsubtraction
splinePoints <- list(x=NULL, y=NULL)
BL.Ends <- list(x=NULL, y=NULL)
QntMat <- NULL
DPrflType <- NULL
ToffAngles <- NULL
MatCol <- c("black", "red1", "limegreen","blue",
"orange4","firebrick1","chartreuse4","deepskyblue",
"yellow3","orange","palegreen","dodgerblue",
"grey78","red4","green4", "lightblue3",
"orangered","olivedrab1","deepskyblue","rosybrown3",
"lightseagreen","goldenrod1","olivedrab1","dodgerblue2",
"lightskyblue3","goldenrod4","olivedrab4","dodgerblue4",
"lightskyblue4","deeppink4","darkgreen","darkblue", "darkorchid2","gold","springgreen","darkmagenta",
"deepskyblue4","brown4","olivedrab","blueviolet", "grey40","orangered","green3","blue3",
"steelblue4","yellow","yellowgreen","turquoise3", "plum1","magenta3", "darkturquoise")
if (is.na(activeFName)==TRUE){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
FNameList <- XPSFNameList() #list of all loaded XPSSamples in .GlobalEnv
#--- GUI
DPwin <- gwindow(" XPS DEPTH PROFILE ", parent(50, 10), visible=FALSE)
maingroup <- ggroup(horizontal=TRUE, container=DPwin)
T1group1 <- ggroup(spacing=2, horizontal=FALSE, container=maingroup)
T1frameFName <- gframe(text="Select the XPS-SAMPLES TO ANALYZE", horizontal=FALSE, spacing=2, container=T1group1)
SourceFLyt <- glayout(spacing=2, container=T1frameFName)
LL <- length(FNameList)
NCol <- ceiling(LL/5) #gcheckboxgroup will be split in solumns of 5 elements
for(jj in 1:NCol){ #build the checkboxes for XPSSample selection
NN <- (jj-1)*5
FList <- FNameList[(NN+1):(NN+5)]
if (NN+5 > LL) FList <- FNameList[(NN+1):LL]
SourceFLyt[1, jj] <- gcheckboxgroup(FList, selected=-1, spacing=2, horizontal=FALSE, handler=function(h,...){
for(jj in 1:NCol){
SelectedXPSSamp[[jj]] <<- svalue(SourceFLyt[1, jj])
}
}, container=SourceFLyt)
}
T1frameDPType <- gframe(text="ARXPS or Sputter Depth Profile?", horizontal=TRUE, spacing=2, container=T1group1)
DepthPrflCK <- gcheckboxgroup(c("ARXPS", "Sputt. Dpth-Prf."), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
DPrflType <<- svalue(DepthPrflCK)
SelectedXPSSamp <<- unlist(SelectedXPSSamp)
if (length(SelectedXPSSamp) == 0){
svalue(DepthPrflCK, index=TRUE) <- c(0,0)
gmessage("Select the XPSSample to analyze first", title="WARNING", icon="warning")
return()
}
if (DPrflType == "ARXPS"){
winDP <- gwindow("ARXPS TILT ANGLES", visible=FALSE)
groupDP1 <- ggroup(horizontal=FALSE, container=winDP)
txt1 <- glabel("How many Take-off Angles used in ARXPS?", container=groupDP1)
font(txt1) <- list(family="sans",size=11)
groupDP2 <- ggroup(horizontal=TRUE, container=groupDP1)
glabel("Number of Take-off Angles: ", container=groupDP2)
NTkOff <- gedit(initial.msg="N. Take-off", width=10, container=groupDP2)
tkconfigure(NTkOff$widget, width=10)
addHandlerChanged(NTkOff, handler=function(h, ...){
blockHandlers(NTkOff, ...)
Nang <- svalue(NTkOff)
if (Nang == ""){
svalue(DepthPrflCK, index=TRUE) <- c(0,0)
gmessage("Set the Number of Take-off Angles first!", title="WARNING", icon="warning")
return()
}
Nang <- as.integer(Nang)
msg <- "For each of the selected XPSSample set the take-off angle"
txt2 <- glabel(text=msg, container=groupDP1)
font(txt2) <- list(family="sans",size=11)
gseparator(horizontal=TRUE, container=groupDP1)
LayoutAngles <- glayout(spacing=2, container=groupDP1)
for(ii in 1:Nang){
txt <- paste("Take-off angle ", ii, sep="")
LayoutAngles[ii,1] <- glabel(txt, container=LayoutAngles)
LayoutAngles[ii,2] <- gedit(initial.msg = "Take-off angle", container=LayoutAngles)
}
gbutton(" OK ", handler=function(h, ...){
for(ii in 1:Nang){
TkoffAngles[ii] <<- svalue(LayoutAngles[ii,2])
}
dispose(winDP)
}, container=groupDP1)
})
visible(winDP) <- TRUE
#winDP$set_modal(TRUE) #nothing can be done while running this macro
}
SelectedXPSSamp <<- unlist(SelectedXPSSamp)
N.XS <<- length(SelectedXPSSamp)
if (N.XS == 1) {
XPSSample <<- get(SelectedXPSSamp[1], envir=.GlobalEnv) #load the active XPSSample in memory
assign("activeFName", SelectedXPSSamp[1], envir=.GlobalEnv)
} else if (N.XS > 1){ #more XPSSamp are loaded as for example in ARXPS: one XPSSample for each tilt angle
Filename <- NULL
XPSSample <<- new("XPSSample")
for(ii in 1:N.XS){
tmp <- get(SelectedXPSSamp[ii], envir=.GlobalEnv)
XPSSample <<- c(XPSSample, tmp)
Filename <- paste(Filename, tmp@Filename,",", sep="")
}
XPSSample@Project <<- ""
XPSSample@Sample <<- dirname(tmp@Sample)
XPSSample@Comments <<- paste(DPrflType, Filename, spe=" ")
XPSSample@User <<- ""
# XPSSample@names <- "" #this is already set by c(X, tmp)
if (DPrflType == "ARXPS"){ #assign the filename to save the analysis in a unique datafile
XPSSample@Filename <<- "ARXPS.RData"
assign("activeFName", "ARXPS.RData", envir=.GlobalEnv)
} else if (DPrflType == "Sputt. Dpth-Prf."){
XPSSample@Filename <<- "SputtDP.RData"
assign("activeFName", "SputtDP.RData", envir=.GlobalEnv)
}
}
plot(XPSSample)
CK.Elmts()
MK.Panel()
enabled(BaseLineCK1) <- TRUE
enabled(BaseLineCK2) <- TRUE
enabled(SelectButt) <- TRUE
enabled(ConcButt) <- TRUE
}, container=T1frameDPType)
T1frameCoreLines <- gframe(text="Select the CORE LINES to analyze", horizontal=TRUE, spacing=2, container=T1group1)
CoreLineCK <- glabel(" ", container=T1frameCoreLines) #just to insert some space in T1frameCoreLines
T1frameBaseline <- gframe(text="Select the BASELINE to apply", horizontal=FALSE, spacing=2, container=T1group1)
BaseLineCK1 <- gradio(c("Linear", "Shirley", "2P.Shirley"), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
svalue(BaseLineCK2, index=TRUE) <- -1 #clear selection of gradio2
BaseLine <<- svalue(BaseLineCK1)
}, container=T1frameBaseline)
BaseLineCK2 <- gradio(c("2P.Tougaard", "3P.Tougaard", "Spline"), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
svalue(BaseLineCK1, index=TRUE) <- -1 #clear selection of gradio1
BaseLine <<- svalue(BaseLineCK2)
}, container=T1frameBaseline)
enabled(BaseLineCK1) <- FALSE
enabled(BaseLineCK2) <- FALSE
SelectButt <- gbutton(" SELECT/ADD BASELINE ", handler=function(h,...){
SelectedCL <<- svalue(CoreLineCK)
#--- Build data matrix for plotting
Matched <<- match(SelectedCL, CL.Sym) #index of the selected CL among the acquired CL
N.CL <<- length(Matched)
for(ii in Matched){
if (hasBaseline(XPSSample[[CL.Sym[ii]]])){
gmessage("BaseLine already defined!", title="WARNING", icon="warning")
} else {
answ <- "FALSE"
while(answ == "FALSE"){
#---- Graphics: generate the data matrix (spectra only) for plotting
X <- Y <- NULL
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@.Data[[1]])
Y <- cbind(Y, XPSSample[[idx]]@.Data[[2]])
}
xrange <- range(XPSSample[[idx]]@.Data[[1]])
if (XPSSample[[idx]]@Flags[1]) xrange <- sort(xrange, decreasing=TRUE)
matplot(X, Y, xlim=xrange, type="l", lty=1, col=MatCol[1:N.Cycles], main=CL.Sym[ii], cex.axis=1.25,
cex.lab=1.3, xlab=XPSSample[[idx]]@units[1], ylab=XPSSample[[idx]]@units[2])
while(length(BaseLine)==0){
txt <- paste(" Select BaseLine for Core-Line ", CL.Sym[ii],"\n Then press OK to proceed.", sep="")
gmessage(msg=txt, title="SELECT BASELINE", icon="info")
}
#-----
cat("\n ==> Applying ", BaseLine, "BaseLine for background subtraction")
if (BaseLine == "Spline") {
splinePoints <<- list(x=NULL, y=NULL)
txt <- "Spline background \n ==> LEFT click to set spline points; RIGHT to exit"
gmessage(msg=txt, title="HELP INFO", icon="info")
pos <- c(1,1) # only to enter in the loop
while (length(pos) > 0) { #pos != NULL => mouse right button not pressed
pos <- locator(n=1, type="p", col="green3", cex=1.5, lwd=2, pch=16)
if (length(pos) > 0) {
splinePoints$x <<- c(splinePoints$x, pos$x) # $x and $y must be separate to add new coord to splinePoints
splinePoints$y <<- c(splinePoints$y, pos$y)
}
}
decr <- FALSE #Kinetic energy set
if (XPSSample[[idx]]@Flags[1] == TRUE) { decr <- TRUE }
kk <- order(splinePoints$x, decreasing=decr)
splinePoints$x <<- splinePoints$x[kk] #splinePoints$x in ascending order
splinePoints$y <<- splinePoints$y[kk] #following same order select the correspondent splinePoints$y
LL <- length(splinePoints$x)
BL.Ends$x <- c(splinePoints$x[1],splinePoints$x[LL]) #set the boundaries of the baseline
BL.Ends$y <- c(splinePoints$y[1],splinePoints$y[LL])
} else {
gmessage(msg="Please select the BaseLine end-Points", title="DEFINE END-POINTS", icon="info")
BL.Ends <- locator(n=2, type="p", col=2, lwd=2, pch=16)
}
cat("\n ==> Perform Background subtraction")
for(jj in 1:N.Cycles){ #given the BL.End$x limits finds the corres[pondent ordinates
idx <- CoreLineList[jj, ii]
XPSSample[[idx]]@Boundaries$x <<- BL.Ends$x
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], BL.Ends$x[1])
XPSSample[[idx]]@Boundaries$y[1] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-2):(kk+2)])
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], BL.Ends$x[2])
XPSSample[[idx]]@Boundaries$y[2] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-2):(kk+2)])
if (BaseLine == "Spline") { #given SplinePoints$X for the first spectrum find the SplinePoints$Y for the other spectra
Npti <- length(splinePoints$x)
for(ll in 1:Npti){
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], splinePoints$x[ll])
splinePoints$y[ll] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-1):(kk+1)])
}
}
MK.Baseline(idx, splinePoints, ...)
}
#---- Graphics: generate the data matrix (spectra + BKGD) for plotting
Colr <- NULL
X <- Y <- NULL
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@Baseline$x)
Y <- cbind(Y, XPSSample[[idx]]@Baseline$y)
Colr <- c(Colr, 584) #Sienna color for the Baselines
}
Colr <- c(Colr, MatCol[1:N.Cycles])
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@RegionToFit$x)
Y <- cbind(Y, XPSSample[[idx]]@RegionToFit$y)
}
xrange <- range(XPSSample[[idx]]@RegionToFit$x)
if (XPSSample[[idx]]@Flags[1]) xrange <- sort(xrange, decreasing=TRUE)
matplot(X, Y, xlim=xrange, type="l", lty=1, col=Colr, main=CL.Sym[ii], cex.axis=1.25,
cex.lab=1.3, xlab=XPSSample[[idx]]@units[1], ylab=XPSSample[[idx]]@units[2])
#-----
svalue(BaseLineCK1, index=TRUE) <- -1 #clear selection of gradio1
svalue(BaseLineCK2, index=TRUE) <- -1 #clear selection of gradio2
answ <- gconfirm(msg="BaseLine OK?", title="BASELINE CTRL", icon="info")
if(answ == "FALSE"){
txt <- paste(" Change BaseLine for Core-Line ", CL.Sym[ii],"\n Then press OK to proceed.", sep="")
gmessage(msg=txt, title="CHANGE BASELINE", icon="warning")
}
}
}
BaseLine <<- NULL #activate selection BaseLine for the next Core-Line
}
}, container=T1frameBaseline)
enabled(SelectButt) <- FALSE
T1frameProf <- gframe(text="Compute Concentration Profile", horizontal=FALSE, spacing=2, container=T1group1)
ConcButt <- gbutton("CONCENTRATION PROFILING", handler=function(h,...){
#among the elements determine the max number of acquired CL. Likely same number of CL for all elements = N Cycles etching
QntMat <- matrix(data=NA, ncol=N.CL, nrow=N.Cycles)
SelectedCL <<- svalue(CoreLineCK)
if (length(SelectedCL) == 0){
gmessage("Select Elements to Profile first!", title="WARNING", icon="warning")
return()
}
for(jj in 1:N.Cycles){
XSampTmp <- NULL
XSampTmp <- new("XPSSample") #generate a temporary XPSSample
kk <- 0
Matched <<- match(SelectedCL, CL.Sym) #index of the selected CL among the acquired CL
N.CL <<- length(Matched)
for(ii in Matched){ #for now runs only on the selected CL
idx <- CoreLineList[jj,ii]
if(!is.na(CoreLineList[jj,ii])){
kk <- kk+1
XSampTmp[[kk]] <- XPSSample[[idx]] #load the acquired coreline atetch cycle ii
}
}
#cannot load directly quantification results into QntMat because acquisition of some coreline could be stopped
#this generates a CoreLineList where some elements (corelines) are lacking and NA is inserted see ((<<<===))
tmp <- XPSquantify(XSampTmp, verbose=FALSE) #compute the quantification
TotQ <- sum(unlist(sapply(tmp, function(x) x$quant)))
kk <- 0
for(ii in Matched){
if(!is.na(CoreLineList[jj, ii])){
kk <- kk+1
QntMat[jj,kk] <- tmp[[kk]]$quant/TotQ #load quantification data into the QntMat matrix
}
}
}
Lgnd <- NULL
for(ii in Matched){
Lgnd <- c(Lgnd, CL.Sym[ii])
}
X <- seq(from=1, to=N.Cycles, by=1) #make the abscissa matrix
X <- rep(X, N.CL)
X <- matrix(X, nrow=N.Cycles, ncol=N.CL)
Xlab="Etch Cycles"
if(svalue(DepthPrflCK)=="ARXPS"){
Xlab <- "Take-off Angle (deg.)"
X <- as.numeric(unlist(strsplit(TkoffAngles, ",")))
X <- rep(X, N.CL)
X <- matrix(X, nrow=N.Cycles, ncol=N.CL)
}
xx <- min(X)
yy <- 1.2*max(QntMat)
SymIdx <- c(19,15,17,25,18,1,0,2,6,5,4,8,7,10,9,11,12,14,13,3)
matplot(X, QntMat, ylim=c(0,yy), type="b", lty=1, lw=2, pch=SymIdx, col=MatCol,
cex=1.2, cex.axis=1.3, cex.lab=1.35, xlab=Xlab, ylab="Concentration (%)")
legend(x=xx, y=yy, xjust=0, legend=Lgnd, ncol=(N.CL+1), lty=1, pch=SymIdx,
lw=2, bty="n", col=MatCol, border=MatCol, text.col=MatCol, text.font=2)
colnames(QntMat) <- CL.Sym[Matched]
QntMat <- 100*QntMat #matrix of concentrations in percent
#--- NOW build textual table of concentrations
txt <- c("\n", paste(activeFName, " Depth Profile",sep=""), "\n")
txt <- c(txt, "\n", paste("Quantification: ", sep=""), "\n\n")
txt <- " " #space for N.Cycle or Take-off angle
for(ii in Matched){ #Column names
txt <- c(txt, format(paste(CL.Sym[ii], "%", sep=""), digits=2, justify="right", width=6))
}
txt <- c(txt, "\n")
#separator
txt <- c(txt, paste(rep("--------", (N.CL+1)), collapse=""), "\n")
#now concentration table
for(jj in 1:N.Cycles){
lbl <- paste("Etch Cycle ", jj, sep="")
if(svalue(DepthPrflCK)=="ARXPS"){
lbl <- unlist(strsplit(TkoffAngles, ","))[jj]
lbl <- paste("Take-Off ", lbl, sep="")
}
txt <- c(txt, lbl)
for(ii in 1:N.CL){
txt <- c(txt, format(QntMat[jj,ii], digits=3, justify="centre", width=6))
}
txt <- c(txt, "\n")
}
cat("\n", txt)
# svalue(Results) <- capture.output(cat("\n ", txt))
insert(Results, paste(txt, collapse=""))
}, container=T1frameProf)
enabled(ConcButt) <- FALSE
gseparator(horizontal=TRUE, container=T1group1)
Results <- gtext(" ", wrap=FALSE, container=maingroup)
size(Results) <- c(300, 300)
gbutton(" RESET ANALYSIS ", handler=function(h,...){
LL <- length(FNameList)
NCol <- ceiling(LL/5) #gcheckboxgroup will be split in solumns of 5 elements
for(jj in 1:NCol){ #build the checkboxes for XPSSample selection
svalue(SourceFLyt[1, jj]) <- -1
}
svalue(DepthPrflCK) <- -1
delete(T1frameCoreLines, CoreLineCK)
CoreLineCK <<- glabel(" ", container=T1frameCoreLines) #just to insert some space in T1frameCoreLines
delete(maingroup, Results) #erase gtext content
Results <<- gtext(" ", wrap=FALSE, container=maingroup)
size(Results) <- c(300, 300)
enabled(BaseLineCK1) <- FALSE
enabled(BaseLineCK2) <- FALSE
enabled(SelectButt) <- FALSE
enabled(ConcButt) <- FALSE
ResetVars()
}, container=T1group1)
gbutton(" SAVE & EXIT ", handler=function(h,...){
dispose(DPwin)
for(jj in 1:N.Cycles){
for(ii in Matched){
if(svalue(DepthPrflCK)=="ARXPS"){
lbl <- unlist(strsplit(TkoffAngles, ","))[jj]
Info <- paste(" ::: ARXPS Take-off Angle (deg.): ", lbl, sep="")
}
if(svalue(DepthPrflCK)=="Sputt. Dpth-Prf."){
Info <- paste(" ::: Sputter Depth-Profile Cycle N.", jj, sep="")
}
idx <- CoreLineList[jj, ii]
XPSSample[[idx]]@Info <<- Info
}
}
assign(activeFName, XPSSample, envir = .GlobalEnv)
XPSSaveRetrieveBkp("save")
options(warn = 0)
}, container=T1group1)
gbutton(" EXIT ", handler=function(h,...){
dispose(DPwin)
assign("activeFName", SelectedXPSSamp[1], envir = .GlobalEnv)
XPSSaveRetrieveBkp("save")
options(warn = 0)
}, container=T1group1)
visible(DPwin) <- TRUE
DPwin$set_modal(TRUE)
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSDepthProfile
Documented in XPSDepthProfile
# XPSDepthProfile reconstruction of Depth Profiles
#
#' @title XPSDepthProfile reconstruction of Depth Profiles
#' @description XPSDepthProfile function is used to manipulate single or
#' multiple XPS-Samples acquired by varying the tilt angle (ARXPS) or after
#' sputter-etch cycles (sputter-depth-profiles)
#' The function loads the spectra at variopus angles or at various sputter-cycles
#' defines the Baselines and computes the element quantification.
#' Results are automatically plotted as a function of the tilt angle or
#' of the etch cycles
#' @examples
#' \dontrun{
#' XPSDepthProfile()
#' }
#' @export
#'
XPSDepthProfile <- function() {
CK.Elmts <- function(){ #extracts the name of the profiled elements
CLnames <<- names(XPSSample)
TmpNames <- CLnames
LL <- length(CLnames)
ii <- 1
jj <- 1
while (LL > 0){
Sym <- TmpNames[jj]
if(Sym == "Survey" || Sym == "survey"){
jj <- jj+1
} else {
idx1 <- which(CLnames == Sym) #extracts indexes of all corelines having name == Sym
idx2 <- which(TmpNames == Sym) #extracts indexes of all corelines having name == Sym
CoreLineList[[ii]] <<- idx1
names(CoreLineList)[ii] <<- Sym
TmpNames <- TmpNames[-idx2]
ii <- ii+1
LL <- length(TmpNames)
}
if (jj > LL) {break}
}
CLnames <<- names(XPSSample)
}
MK.Panel <- function(){ #construct the list of checkboxes describing all the XPSSample corelines
CL.Sym <<- names(CoreLineList)
N.CL <<- length(CL.Sym) #Number of profiled elements
N.Cycles <<- max(sapply(CoreLineList, function(x) length(x)))
# (<<<===) This operation transform a list in a matrix maintaining column names
# length<- introduces NA if data lacking
CoreLineList <<- sapply(CoreLineList, "length<-", N.Cycles)
#CheckBoxGroup to slect the CL to analyze
delete(T1frameCoreLines, CoreLineCK)
CoreLineCK <<- gcheckboxgroup(CL.Sym,checked=FALSE, horizontal=TRUE, container=T1frameCoreLines)
}
MK.Baseline <- function(idx, splinePoints){
if (BaseLine == "shirley"){BaseLine <- "Shirley"} #different names for old/new RXPSG packages
if (BaseLine == "2p.shirley"){BaseLine <- "2P.Shirley"} #transform to new BaseLineNames.
if (BaseLine == "3p.shirley"){BaseLine <- "3P.Shirley"} #Exact Baseline Names required to generate the Baseline see XPSClass
if (BaseLine == "lp.shirley"){BaseLine <- "LP.Shirley"}
if (BaseLine == "2p.tougaard"){BaseLine <- "2P.Tougaard"}
if (BaseLine == "3p.tougaard"){BaseLine <- "3P.Tougaard"}
if (BaseLine == "4p.tougaard"){BaseLine <- "4P.Tougaard"}
XPSSample[[idx]] <<- XPSsetRegionToFit(XPSSample[[idx]])
XPSSample[[idx]] <<- XPSbaseline(XPSSample[[idx]], BaseLine, deg=0, Wgt=0, splinePoints )
XPSSample[[idx]] <<- XPSsetRSF(XPSSample[[idx]], XPSSample[[idx]]@RSF)
}
ResetVars <- function(){
CLnames <<- NULL #named of the profiled elements
N.XS <<- NULL
N.CL <<- NULL
N.Cycles <<- NULL
CL <<- NULL
CL.Sym <<- NULL
Matched <<- NULL #CoreLines present in all the XPSSample
SelectedCL <<- NULL
SelectedXPSSamp <<- list()
XPSSample <<- NULL
CoreLineList <<- list() #define a list for the XPSSample corelines
Angles <<- NULL
BaseLine <<- NULL #by default baseline selected for BKGsubtraction
splinePoints <<- list(x=NULL, y=NULL)
BL.Ends <<- list(x=NULL, y=NULL)
QntMat <<- NULL
DPrflType <<- NULL
TkoffAngles <<- NULL
}
#--- Variables
options(warn = -1)
N.XS <- NULL
N.CL <- NULL
N.Cycles <- NULL
CL <- NULL
CL.Sym <- NULL
Matched <- NULL #CoreLines present in all the XPSSample
SelectedCL <- NULL
SelectedXPSSamp <- list()
XPSSample <- NULL
CoreLineList <- list() #define a list for the XPSSample corelines
CoreLineCK <- NULL #pointer to the profiled checkbox elements
# T1frameCoreLines <- NULL
TkoffAngles <- NULL
BaseLine <- NULL #by default baseline selected for BKGsubtraction
splinePoints <- list(x=NULL, y=NULL)
BL.Ends <- list(x=NULL, y=NULL)
QntMat <- NULL
DPrflType <- NULL
ToffAngles <- NULL
MatCol <- c("black", "red1", "limegreen","blue",
"orange4","firebrick1","chartreuse4","deepskyblue",
"yellow3","orange","palegreen","dodgerblue",
"grey78","red4","green4", "lightblue3",
"orangered","olivedrab1","deepskyblue","rosybrown3",
"lightseagreen","goldenrod1","olivedrab1","dodgerblue2",
"lightskyblue3","goldenrod4","olivedrab4","dodgerblue4",
"lightskyblue4","deeppink4","darkgreen","darkblue", "darkorchid2","gold","springgreen","darkmagenta",
"deepskyblue4","brown4","olivedrab","blueviolet", "grey40","orangered","green3","blue3",
"steelblue4","yellow","yellowgreen","turquoise3", "plum1","magenta3", "darkturquoise")
if (is.na(activeFName)==TRUE){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
FNameList <- XPSFNameList() #list of all loaded XPSSamples in .GlobalEnv
#--- GUI
DPwin <- gwindow(" XPS DEPTH PROFILE ", parent(50, 10), visible=FALSE)
maingroup <- ggroup(horizontal=TRUE, container=DPwin)
T1group1 <- ggroup(spacing=2, horizontal=FALSE, container=maingroup)
T1frameFName <- gframe(text="Select the XPS-SAMPLES TO ANALYZE", horizontal=FALSE, spacing=2, container=T1group1)
SourceFLyt <- glayout(spacing=2, container=T1frameFName)
LL <- length(FNameList)
NCol <- ceiling(LL/5) #gcheckboxgroup will be split in solumns of 5 elements
for(jj in 1:NCol){ #build the checkboxes for XPSSample selection
NN <- (jj-1)*5
FList <- FNameList[(NN+1):(NN+5)]
if (NN+5 > LL) FList <- FNameList[(NN+1):LL]
SourceFLyt[1, jj] <- gcheckboxgroup(FList, selected=-1, spacing=2, horizontal=FALSE, handler=function(h,...){
for(jj in 1:NCol){
SelectedXPSSamp[[jj]] <<- svalue(SourceFLyt[1, jj])
}
}, container=SourceFLyt)
}
T1frameDPType <- gframe(text="ARXPS or Sputter Depth Profile?", horizontal=TRUE, spacing=2, container=T1group1)
DepthPrflCK <- gcheckboxgroup(c("ARXPS", "Sputt. Dpth-Prf."), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
DPrflType <<- svalue(DepthPrflCK)
SelectedXPSSamp <<- unlist(SelectedXPSSamp)
if (length(SelectedXPSSamp) == 0){
svalue(DepthPrflCK, index=TRUE) <- c(0,0)
gmessage("Select the XPSSample to analyze first", title="WARNING", icon="warning")
return()
}
if (DPrflType == "ARXPS"){
winDP <- gwindow("ARXPS TILT ANGLES", visible=FALSE)
groupDP1 <- ggroup(horizontal=FALSE, container=winDP)
txt1 <- glabel("How many Take-off Angles used in ARXPS?", container=groupDP1)
font(txt1) <- list(family="sans",size=11)
groupDP2 <- ggroup(horizontal=TRUE, container=groupDP1)
glabel("Number of Take-off Angles: ", container=groupDP2)
NTkOff <- gedit(initial.msg="N. Take-off", width=10, container=groupDP2)
tkconfigure(NTkOff$widget, width=10)
addHandlerChanged(NTkOff, handler=function(h, ...){
blockHandlers(NTkOff, ...)
Nang <- svalue(NTkOff)
if (Nang == ""){
svalue(DepthPrflCK, index=TRUE) <- c(0,0)
gmessage("Set the Number of Take-off Angles first!", title="WARNING", icon="warning")
return()
}
Nang <- as.integer(Nang)
msg <- "For each of the selected XPSSample set the take-off angle"
txt2 <- glabel(text=msg, container=groupDP1)
font(txt2) <- list(family="sans",size=11)
gseparator(horizontal=TRUE, container=groupDP1)
LayoutAngles <- glayout(spacing=2, container=groupDP1)
for(ii in 1:Nang){
txt <- paste("Take-off angle ", ii, sep="")
LayoutAngles[ii,1] <- glabel(txt, container=LayoutAngles)
LayoutAngles[ii,2] <- gedit(initial.msg = "Take-off angle", container=LayoutAngles)
}
gbutton(" OK ", handler=function(h, ...){
for(ii in 1:Nang){
TkoffAngles[ii] <<- svalue(LayoutAngles[ii,2])
}
dispose(winDP)
}, container=groupDP1)
})
visible(winDP) <- TRUE
#winDP$set_modal(TRUE) #nothing can be done while running this macro
}
SelectedXPSSamp <<- unlist(SelectedXPSSamp)
N.XS <<- length(SelectedXPSSamp)
if (N.XS == 1) {
XPSSample <<- get(SelectedXPSSamp[1], envir=.GlobalEnv) #load the active XPSSample in memory
assign("activeFName", SelectedXPSSamp[1], envir=.GlobalEnv)
} else if (N.XS > 1){ #more XPSSamp are loaded as for example in ARXPS: one XPSSample for each tilt angle
Filename <- NULL
XPSSample <<- new("XPSSample")
for(ii in 1:N.XS){
tmp <- get(SelectedXPSSamp[ii], envir=.GlobalEnv)
XPSSample <<- c(XPSSample, tmp)
Filename <- paste(Filename, tmp@Filename,",", sep="")
}
XPSSample@Project <<- ""
XPSSample@Sample <<- dirname(tmp@Sample)
XPSSample@Comments <<- paste(DPrflType, Filename, spe=" ")
XPSSample@User <<- ""
# XPSSample@names <- "" #this is already set by c(X, tmp)
if (DPrflType == "ARXPS"){ #assign the filename to save the analysis in a unique datafile
XPSSample@Filename <<- "ARXPS.RData"
assign("activeFName", "ARXPS.RData", envir=.GlobalEnv)
} else if (DPrflType == "Sputt. Dpth-Prf."){
XPSSample@Filename <<- "SputtDP.RData"
assign("activeFName", "SputtDP.RData", envir=.GlobalEnv)
}
}
plot(XPSSample)
CK.Elmts()
MK.Panel()
enabled(BaseLineCK1) <- TRUE
enabled(BaseLineCK2) <- TRUE
enabled(SelectButt) <- TRUE
enabled(ConcButt) <- TRUE
}, container=T1frameDPType)
T1frameCoreLines <- gframe(text="Select the CORE LINES to analyze", horizontal=TRUE, spacing=2, container=T1group1)
CoreLineCK <- glabel(" ", container=T1frameCoreLines) #just to insert some space in T1frameCoreLines
T1frameBaseline <- gframe(text="Select the BASELINE to apply", horizontal=FALSE, spacing=2, container=T1group1)
BaseLineCK1 <- gradio(c("Linear", "Shirley", "2P.Shirley"), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
svalue(BaseLineCK2, index=TRUE) <- -1 #clear selection of gradio2
BaseLine <<- svalue(BaseLineCK1)
}, container=T1frameBaseline)
BaseLineCK2 <- gradio(c("2P.Tougaard", "3P.Tougaard", "Spline"), spacing=2, selected=-1, horizontal=TRUE, handler = function(h, ...){
svalue(BaseLineCK1, index=TRUE) <- -1 #clear selection of gradio1
BaseLine <<- svalue(BaseLineCK2)
}, container=T1frameBaseline)
enabled(BaseLineCK1) <- FALSE
enabled(BaseLineCK2) <- FALSE
SelectButt <- gbutton(" SELECT/ADD BASELINE ", handler=function(h,...){
SelectedCL <<- svalue(CoreLineCK)
#--- Build data matrix for plotting
Matched <<- match(SelectedCL, CL.Sym) #index of the selected CL among the acquired CL
N.CL <<- length(Matched)
for(ii in Matched){
if (hasBaseline(XPSSample[[CL.Sym[ii]]])){
gmessage("BaseLine already defined!", title="WARNING", icon="warning")
} else {
answ <- "FALSE"
while(answ == "FALSE"){
#---- Graphics: generate the data matrix (spectra only) for plotting
X <- Y <- NULL
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@.Data[[1]])
Y <- cbind(Y, XPSSample[[idx]]@.Data[[2]])
}
xrange <- range(XPSSample[[idx]]@.Data[[1]])
if (XPSSample[[idx]]@Flags[1]) xrange <- sort(xrange, decreasing=TRUE)
matplot(X, Y, xlim=xrange, type="l", lty=1, col=MatCol[1:N.Cycles], main=CL.Sym[ii], cex.axis=1.25,
cex.lab=1.3, xlab=XPSSample[[idx]]@units[1], ylab=XPSSample[[idx]]@units[2])
while(length(BaseLine)==0){
txt <- paste(" Select BaseLine for Core-Line ", CL.Sym[ii],"\n Then press OK to proceed.", sep="")
gmessage(msg=txt, title="SELECT BASELINE", icon="info")
}
#-----
cat("\n ==> Applying ", BaseLine, "BaseLine for background subtraction")
if (BaseLine == "Spline") {
splinePoints <<- list(x=NULL, y=NULL)
txt <- "Spline background \n ==> LEFT click to set spline points; RIGHT to exit"
gmessage(msg=txt, title="HELP INFO", icon="info")
pos <- c(1,1) # only to enter in the loop
while (length(pos) > 0) { #pos != NULL => mouse right button not pressed
pos <- locator(n=1, type="p", col="green3", cex=1.5, lwd=2, pch=16)
if (length(pos) > 0) {
splinePoints$x <<- c(splinePoints$x, pos$x) # $x and $y must be separate to add new coord to splinePoints
splinePoints$y <<- c(splinePoints$y, pos$y)
}
}
decr <- FALSE #Kinetic energy set
if (XPSSample[[idx]]@Flags[1] == TRUE) { decr <- TRUE }
kk <- order(splinePoints$x, decreasing=decr)
splinePoints$x <<- splinePoints$x[kk] #splinePoints$x in ascending order
splinePoints$y <<- splinePoints$y[kk] #following same order select the correspondent splinePoints$y
LL <- length(splinePoints$x)
BL.Ends$x <- c(splinePoints$x[1],splinePoints$x[LL]) #set the boundaries of the baseline
BL.Ends$y <- c(splinePoints$y[1],splinePoints$y[LL])
} else {
gmessage(msg="Please select the BaseLine end-Points", title="DEFINE END-POINTS", icon="info")
BL.Ends <- locator(n=2, type="p", col=2, lwd=2, pch=16)
}
cat("\n ==> Perform Background subtraction")
for(jj in 1:N.Cycles){ #given the BL.End$x limits finds the corres[pondent ordinates
idx <- CoreLineList[jj, ii]
XPSSample[[idx]]@Boundaries$x <<- BL.Ends$x
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], BL.Ends$x[1])
XPSSample[[idx]]@Boundaries$y[1] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-2):(kk+2)])
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], BL.Ends$x[2])
XPSSample[[idx]]@Boundaries$y[2] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-2):(kk+2)])
if (BaseLine == "Spline") { #given SplinePoints$X for the first spectrum find the SplinePoints$Y for the other spectra
Npti <- length(splinePoints$x)
for(ll in 1:Npti){
kk <- findXIndex(XPSSample[[idx]]@.Data[[1]], splinePoints$x[ll])
splinePoints$y[ll] <<- mean(XPSSample[[idx]]@.Data[[2]][(kk-1):(kk+1)])
}
}
MK.Baseline(idx, splinePoints, ...)
}
#---- Graphics: generate the data matrix (spectra + BKGD) for plotting
Colr <- NULL
X <- Y <- NULL
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@Baseline$x)
Y <- cbind(Y, XPSSample[[idx]]@Baseline$y)
Colr <- c(Colr, 584) #Sienna color for the Baselines
}
Colr <- c(Colr, MatCol[1:N.Cycles])
for(jj in 1:N.Cycles){
idx <- CoreLineList[jj, ii]
X <- cbind(X, XPSSample[[idx]]@RegionToFit$x)
Y <- cbind(Y, XPSSample[[idx]]@RegionToFit$y)
}
xrange <- range(XPSSample[[idx]]@RegionToFit$x)
if (XPSSample[[idx]]@Flags[1]) xrange <- sort(xrange, decreasing=TRUE)
matplot(X, Y, xlim=xrange, type="l", lty=1, col=Colr, main=CL.Sym[ii], cex.axis=1.25,
cex.lab=1.3, xlab=XPSSample[[idx]]@units[1], ylab=XPSSample[[idx]]@units[2])
#-----
svalue(BaseLineCK1, index=TRUE) <- -1 #clear selection of gradio1
svalue(BaseLineCK2, index=TRUE) <- -1 #clear selection of gradio2
answ <- gconfirm(msg="BaseLine OK?", title="BASELINE CTRL", icon="info")
if(answ == "FALSE"){
txt <- paste(" Change BaseLine for Core-Line ", CL.Sym[ii],"\n Then press OK to proceed.", sep="")
gmessage(msg=txt, title="CHANGE BASELINE", icon="warning")
}
}
}
BaseLine <<- NULL #activate selection BaseLine for the next Core-Line
}
}, container=T1frameBaseline)
enabled(SelectButt) <- FALSE
T1frameProf <- gframe(text="Compute Concentration Profile", horizontal=FALSE, spacing=2, container=T1group1)
ConcButt <- gbutton("CONCENTRATION PROFILING", handler=function(h,...){
#among the elements determine the max number of acquired CL. Likely same number of CL for all elements = N Cycles etching
QntMat <- matrix(data=NA, ncol=N.CL, nrow=N.Cycles)
SelectedCL <<- svalue(CoreLineCK)
if (length(SelectedCL) == 0){
gmessage("Select Elements to Profile first!", title="WARNING", icon="warning")
return()
}
for(jj in 1:N.Cycles){
XSampTmp <- NULL
XSampTmp <- new("XPSSample") #generate a temporary XPSSample
kk <- 0
Matched <<- match(SelectedCL, CL.Sym) #index of the selected CL among the acquired CL
N.CL <<- length(Matched)
for(ii in Matched){ #for now runs only on the selected CL
idx <- CoreLineList[jj,ii]
if(!is.na(CoreLineList[jj,ii])){
kk <- kk+1
XSampTmp[[kk]] <- XPSSample[[idx]] #load the acquired coreline atetch cycle ii
}
}
#cannot load directly quantification results into QntMat because acquisition of some coreline could be stopped
#this generates a CoreLineList where some elements (corelines) are lacking and NA is inserted see ((<<<===))
tmp <- XPSquantify(XSampTmp, verbose=FALSE) #compute the quantification
TotQ <- sum(unlist(sapply(tmp, function(x) x$quant)))
kk <- 0
for(ii in Matched){
if(!is.na(CoreLineList[jj, ii])){
kk <- kk+1
QntMat[jj,kk] <- tmp[[kk]]$quant/TotQ #load quantification data into the QntMat matrix
}
}
}
Lgnd <- NULL
for(ii in Matched){
Lgnd <- c(Lgnd, CL.Sym[ii])
}
X <- seq(from=1, to=N.Cycles, by=1) #make the abscissa matrix
X <- rep(X, N.CL)
X <- matrix(X, nrow=N.Cycles, ncol=N.CL)
Xlab="Etch Cycles"
if(svalue(DepthPrflCK)=="ARXPS"){
Xlab <- "Take-off Angle (deg.)"
X <- as.numeric(unlist(strsplit(TkoffAngles, ",")))
X <- rep(X, N.CL)
X <- matrix(X, nrow=N.Cycles, ncol=N.CL)
}
xx <- min(X)
yy <- 1.2*max(QntMat)
SymIdx <- c(19,15,17,25,18,1,0,2,6,5,4,8,7,10,9,11,12,14,13,3)
matplot(X, QntMat, ylim=c(0,yy), type="b", lty=1, lw=2, pch=SymIdx, col=MatCol,
cex=1.2, cex.axis=1.3, cex.lab=1.35, xlab=Xlab, ylab="Concentration (%)")
legend(x=xx, y=yy, xjust=0, legend=Lgnd, ncol=(N.CL+1), lty=1, pch=SymIdx,
lw=2, bty="n", col=MatCol, border=MatCol, text.col=MatCol, text.font=2)
colnames(QntMat) <- CL.Sym[Matched]
QntMat <- 100*QntMat #matrix of concentrations in percent
#--- NOW build textual table of concentrations
txt <- c("\n", paste(activeFName, " Depth Profile",sep=""), "\n")
txt <- c(txt, "\n", paste("Quantification: ", sep=""), "\n\n")
txt <- " " #space for N.Cycle or Take-off angle
for(ii in Matched){ #Column names
txt <- c(txt, format(paste(CL.Sym[ii], "%", sep=""), digits=2, justify="right", width=6))
}
txt <- c(txt, "\n")
#separator
txt <- c(txt, paste(rep("--------", (N.CL+1)), collapse=""), "\n")
#now concentration table
for(jj in 1:N.Cycles){
lbl <- paste("Etch Cycle ", jj, sep="")
if(svalue(DepthPrflCK)=="ARXPS"){
lbl <- unlist(strsplit(TkoffAngles, ","))[jj]
lbl <- paste("Take-Off ", lbl, sep="")
}
txt <- c(txt, lbl)
for(ii in 1:N.CL){
txt <- c(txt, format(QntMat[jj,ii], digits=3, justify="centre", width=6))
}
txt <- c(txt, "\n")
}
cat("\n", txt)
# svalue(Results) <- capture.output(cat("\n ", txt))
insert(Results, paste(txt, collapse=""))
}, container=T1frameProf)
enabled(ConcButt) <- FALSE
gseparator(horizontal=TRUE, container=T1group1)
Results <- gtext(" ", wrap=FALSE, container=maingroup)
size(Results) <- c(300, 300)
gbutton(" RESET ANALYSIS ", handler=function(h,...){
LL <- length(FNameList)
NCol <- ceiling(LL/5) #gcheckboxgroup will be split in solumns of 5 elements
for(jj in 1:NCol){ #build the checkboxes for XPSSample selection
svalue(SourceFLyt[1, jj]) <- -1
}
svalue(DepthPrflCK) <- -1
delete(T1frameCoreLines, CoreLineCK)
CoreLineCK <<- glabel(" ", container=T1frameCoreLines) #just to insert some space in T1frameCoreLines
delete(maingroup, Results) #erase gtext content
Results <<- gtext(" ", wrap=FALSE, container=maingroup)
size(Results) <- c(300, 300)
enabled(BaseLineCK1) <- FALSE
enabled(BaseLineCK2) <- FALSE
enabled(SelectButt) <- FALSE
enabled(ConcButt) <- FALSE
ResetVars()
}, container=T1group1)
gbutton(" SAVE & EXIT ", handler=function(h,...){
dispose(DPwin)
for(jj in 1:N.Cycles){
for(ii in Matched){
if(svalue(DepthPrflCK)=="ARXPS"){
lbl <- unlist(strsplit(TkoffAngles, ","))[jj]
Info <- paste(" ::: ARXPS Take-off Angle (deg.): ", lbl, sep="")
}
if(svalue(DepthPrflCK)=="Sputt. Dpth-Prf."){
Info <- paste(" ::: Sputter Depth-Profile Cycle N.", jj, sep="")
}
idx <- CoreLineList[jj, ii]
XPSSample[[idx]]@Info <<- Info
}
}
assign(activeFName, XPSSample, envir = .GlobalEnv)
XPSSaveRetrieveBkp("save")
options(warn = 0)
}, container=T1group1)
gbutton(" EXIT ", handler=function(h,...){
dispose(DPwin)
assign("activeFName", SelectedXPSSamp[1], envir = .GlobalEnv)
XPSSaveRetrieveBkp("save")
options(warn = 0)
}, container=T1group1)
visible(DPwin) <- TRUE
DPwin$set_modal(TRUE)
}
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