R/XPSDiffGUI.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSDiff
Documented in
XPSDiff
#function to differentiate XPS-Sample spectra
#' @title XPSDiff for spectra differentiation
#' @description XPSDiff function is used to compute the derivative of the XPSSpectra.
#' The user can select the degree of differentiation. Tje result of the differentiation
#' is oplotted together with the original data. It is possible to amplify the
#' differentiated spectrum to be on the scale of the original spectrum.
#' @examples
#' \dontrun{
#' XPSDiff()
#' }
#' @export
#'
XPSDiff <- function(){
Differ <- function(Object){
LL <- length(Object)
tmp <- NULL
for(ii in 2:LL){
tmp[ii] <- Object[ii] - Object[ii-1]
}
tmp[1] <- tmp[2]
return(tmp)
}
BkgSubtraction <- function(data){ #linear BKG subtraction
BackGnd <<- NULL
LL <- length(data)
rng <- floor(LL/15)
if (rng<3) {rng==3}
if (rng>30) {rng==30}
bkg1 <- mean(data[1:rng])
bkg2 <- mean(data[(LL-rng):LL])
stp <- (bkg1-bkg2)/LL
Dta_Bkg <- NULL
for (ii in 1:LL){
Dta_Bkg[ii] <- data[ii]-(bkg1-ii*stp)
BackGnd[ii] <<- bkg1-ii*stp
}
return(Dta_Bkg)
}
FindNearest <- function(){
D <- NULL
Dmin <- ((LocPos$x-Corners$x[1])^2 + (LocPos$y-Corners$y[1])^2)^0.5 #init value
for (ii in 1:4) {
D[ii] <- ((LocPos$x-Corners$x[ii])^2 + (LocPos$y-Corners$y[ii])^2)^0.5 #dist P0 P1
if(D[ii] <= Dmin){
Dmin <- D[ii]
idx=ii
}
}
if (idx==1){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
}
return(Corners)
}
FindPattern <- function(TxtVect, Pattern){
chrPos <- NULL
LL <- length(TxtVect)
for(ii in 1:LL){
Pos <- gregexpr(pattern=Pattern,TxtVect[ii]) #the result of gregexpr is a list containing the character position of D.x x=differentiation degree
if (Pos[[1]][1] > 0) {
chrPos[1] <- ii
chrPos[2] <- Pos[[1]][1]
break
}
}
return(chrPos)
}
MeasureMaxMinD <- function(){ # \U0394. = greek Delta used to indicate difference in Max-Min posiitions
RefreshPlot <- function(){
XXX <- cbind(unlist(FName[[SpectIndx]]@.Data[1])) #transform the vector in a column of data
YYY <- cbind(unlist(Differentiated[2]))
Xlim <- range(XXX)
if (FName[[SpectIndx]]@Flags[1]==TRUE) {
Xlim <- rev(Xlim) ## reverse x-axis
}
Ylim <- range(YYY)
matplot(x=XXX, y=YYY, type="l", lty="solid", col="black",
xlim=Xlim, ylim=Ylim, xlab=FName[[SpectIndx]]@units[1], ylab="Differentiated Data [cps.]")
return()
}
if(length(Differentiated[[2]]) == 0) {
gmessage(msg="NON-Differentiated data. Cannot compute MAX-MIN difference", title="WARNING", icon="warning")
return()
}
if(length(svalue(D1CoreLine)) == 0) {
gmessage(msg="Please Select the Differentiated Core-Line", title="WARNING", icon="warning")
return()
}
RefreshPlot()
txt <- "LEFT button to set the MAX/MIN positions; RIGHT to exit \n Click near markers to modify the positions"
gmessage(msg=txt , title = "WARNING", icon = "warning")
pos <- locator(n=2, type="p", pch=3, col="red", lwd=1.5) #first the two corners are drawn
rect(pos$x[1], min(pos$y), pos$x[2], max(pos$y)) #marker-Corners are ordered with ymin on Left and ymax on Right
Corners$x <<- c(pos$x[1],pos$x[1],pos$x[2],pos$x[2])
Corners$y <<- c(pos$y[1],pos$y[2],pos$y[1],pos$y[2])
points(Corners, type="p", pch=3, col="red", lwd=1.5)
LocPos <<- list(x=0, y=0)
while (length(LocPos) > 0) { #if pos1 not NULL a mouse butto was pressed
LocPos <<- locator(n=1, type="p", pch=3, col="red", lwd=2) #to modify the zoom limits
if (length(LocPos$x) > 0) { #if the right mouse button NOT pressed
FindNearest()
if (FName[[SpectIndx]]@Flags[1]) { #Binding energy set
pos$x <- sort(c(Corners$x[1],Corners$x[3]), decreasing=TRUE) #pos$x in decrescent ordered => Corners$x[1]==Corners$x[2]
} else {
pos$x <- sort(c(Corners$x[1],Corners$x[3]), decreasing=FALSE) #pos$x in ascending order
}
pos$y <- sort(c(Corners$y[1],Corners$y[2]), decreasing=FALSE)
RefreshPlot() #refresh graph
rect(pos$x[1], pos$y[1], pos$x[2], pos$y[2])
points(Corners, type="p", pch=3, col="red", lwd=1.5)
}
}
MaxMinD <<- round(abs(pos$x[1]-pos$x[2]), 2)
Info <- FName[[SpectIndx]]@Info
S3 <<- "\U0394." #delta symbol
charPos <- FindPattern(FName[[SpectIndx]]@Info, " ::: Max.Min.\U0394. = ")[1] #charPos[1] = row index of Info where "::: Max.Min.D = " is found
if(length(charPos) > 0){ #save the Max/Min difference in FName Info
FName[[SpectIndx]]@Info[charPos] <<- paste(" ::: Max.Min.", S3, " = ", MaxMinD, sep="") #overwrite previous MAx\Min Dist value
} else {
answ <- gconfirm(msg="Save new value of Max-Min difference?", title="WARNING", icon="warning")
if (answ == TRUE){
nI <- length(FName[[SpectIndx]]@Info)+1
FName[[SpectIndx]]@Info[nI] <<- paste(" ::: Max.Min.", S3, " = ", MaxMinD, sep="")
}
}
Symbol <- paste(S3, S2, DiffDeg, S1, sep="", collapse="") #compose the CoreLine Symbol "\U0394." "D." CLname
if(hasRegionToFit(FName[[SpectIndx]])==FALSE){
setClass("baseline", representation(baseline="list"), contains="list", prototype(baseline=list()))
FName[[SpectIndx]]@RegionToFit$x <<- FName[[SpectIndx]]@.Data[[1]] #defines the RegionToFit equal to original data
FName[[SpectIndx]]@RegionToFit$y <<- FName[[SpectIndx]]@.Data[[2]] #defines the RegionToFit equal to original data
FName[[SpectIndx]]@Baseline$x <<- FName[[SpectIndx]]@.Data[[1]]
FName[[SpectIndx]]@Baseline$y <<- rep(0, length(FName[[SpectIndx]]@.Data[[1]])) #defines a zero-Baseline
FName[[SpectIndx]]@Baseline[["baseline"]] <<- new("baseline") #defines a new Baseline component of class baseline and package attribute .GlobalEnv
attr(FName[[SpectIndx]]@Baseline$baseline, "package") <<- ".GlobalEnv"
FName[[SpectIndx]]@Baseline$type <<- "linear"
FName[[SpectIndx]] <<- XPSaddComponent(FName[[SpectIndx]], type = "Derivative")
}
#Set the measured MaxMinD for the differeniated CoreLine
FName[[SpectIndx]]@Symbol <<- Symbol # '\U0394' = Delta: the MaxMin diff was measured
FName@names[SpectIndx] <<- Symbol #update/add core line name to list of names
FName[[SpectIndx]]@Components[[1]]@param["mu", "min"] <<- pos$x[1] #abscissas of Max/Min positions
FName[[SpectIndx]]@Components[[1]]@param["mu", "max"] <<- pos$x[2]
idx <- findXIndex(FName[[SpectIndx]]@.Data[[1]], pos$x[1]) #finds index corresponding to Max/min positions
FName[[SpectIndx]]@Components[[1]]@param["h", "min"] <<- FName[[SpectIndx]]@.Data[[2]][idx] #ordinate of Max/min position
idx <- findXIndex(FName[[SpectIndx]]@.Data[[1]], pos$x[2]) #finds index corresponding to Max/min positions
FName[[SpectIndx]]@Components[[1]]@param["h", "max"] <<- FName[[SpectIndx]]@.Data[[2]][idx] #ordinate of Max/min position
assign(activeFName, FName, envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx, envir=.GlobalEnv)
cat("\n ==> Data saved")
plot(FName)
svalue(DistLab) <- MaxMinD
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- TRUE
}
plotData <- function() {
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #set the activeSpectIndex to the actual CoreLine
XXX <- cbind(unlist(FName[[SpectIndx]]@.Data[1]))
LL <- length(XXX)
YYY <- cbind(unlist(FName[[SpectIndx]]@.Data[2]), unlist(Differentiated[2]), rep(0, LL))
Xlim <- range(XXX)
if (FName[[SpectIndx]]@Flags[1]==TRUE) {
Xlim <- rev(Xlim) ## reverse x-axis
}
Ylim <- range(YYY)
matplot(x=XXX, y=YYY, type="l", lty=c("solid", "solid", "dashed"),lw=c(1.75, 1, 1), col=c("black", "red3", "black"),
xlim=Xlim, ylim=Ylim, xlab=FName[[SpectIndx]]@units[1], ylab=FName[[SpectIndx]]@units[2])
return()
}
makeCombo <- function(){
activeFName <<- svalue(D1XpsSpect)
FName <<- get(activeFName,envir=.GlobalEnv) #load the XPSSample
assign("activeFName", activeFName, envir=.GlobalEnv)
SpectList <<- XPSSpectList(activeFName)
SpectIndx <<- 1
delete(D1Frame2, D1CoreLine)
D1CoreLine <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPSCLname <- svalue(D1CoreLine)
tmp <- unlist(strsplit(XPSCLname, "\\.")) #skip the ".NUMBER" at beginning CoreLine name
SpectIndx <<- as.integer(tmp[1])
LL1 <- nchar(tmp[1])+2 # +2: substr(x,start,stop) start includes the character at 'start'
LL2 <- nchar(XPSCLname)
S1 <<- substr(XPSCLname, start=LL1, stop=LL2) #In case of XPSCLname="4.D1.C1s" SpectName must be "D1.C1s"
S3 <<- S2 <<- ""
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
S1S2S3 <- unlist(strsplit(S1, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D."
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
# DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
DiffDeg <<- as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
}
}
assign("activeSpectName", S1, envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx, envir=.GlobalEnv)
plot(FName[[SpectIndx]])
enabled(DDeg) <- TRUE
CLBkp <<- FName[[SpectIndx]] #backUp original data
}, container=D1Frame2)
plot(FName)
}
SaveFName <- function(saveMode){
if(DiffDeg == 0 && length(as.numeric(svalue(DDeg)))==0){
gmessage(msg="Before saving data make differentiation please.", title="ERROR", icon="error")
return()
}
#save data in NEW CORELINE mode
if (S2 != "" && saveMode=="NewCL") { #"D." is present, one or more core-lines are differentiated
Idx <- length(FName) #number of corelines +1
Info <- FName[[Idx]]@Info
nI <- length(Info)
N.spaces <- gregexpr(" ", Info[nI]) #finds how many space characters are in info
if (length(N.spaces[[1]]) != nchar(Info[nI])){ #if == FALSE if a blank raw is found
nI <- nI +1 #then add new Info line
}
Idx <- Idx+1
FName[[Idx]] <<- new("XPSCoreLine") #Add the new Coreline using the starting core-line
if (length(svalue(DDeg)) > 0){ #working on previously differentiated data
FName[[Idx]]@.Data <<- Differentiated #update New Coreline with dufferentiated data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D."
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
Symbol <- paste(S3, S2, DiffDeg, S1, sep="")
}
} else {
Symbol <- paste(S3, S2, DiffDeg, ".", S1, sep="") #DiffDeg updated in 'Differentiation'
}
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
}
#save data in OVERWRITE mode
if (S2 != "" && saveMode=="Overwrite") { #"D." is present: working on previously differentiated data, and overwrite new data
Idx <- activeSpectIndx
FName[[Idx]]@.Data <<- Differentiated #change the original diff. data with the new differented data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #the CoreLine was pre-differentiated
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D." # %in% search if "D" is present in S1S2S3. %in% gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #add precedent diff. degree
Symbol <- paste(S3, S2, DiffDeg, S1, sep="")
}
} else {
Symbol <- paste(S3, S2, DiffDeg, ".", S1, sep="") #DiffDeg updated in 'Differentiation'
}
Info <- FName[[Idx]]@Info
chrPos <- FindPattern(Info, " ::: Differentiated ")
nI <- chrPos[1] #Overwrite previous Info
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
if (S2 == "" && saveMode=="Overwrite") { #"D." NOT present Differentiation not performed we should work on already differentiated data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D." # %in% search if "D" is present in S1S2S3. %in% gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #add precedent diff. degree
} else {
gmessage(msg="ERROR: Wrong Data Information", title="ERROR", icon="error")
return()
}
Idx <- activeSpectIndx #number of corelines
Symbol <- paste(S3, S2, DiffDeg, S1, sep="") # '\U0394.' = Delta representing the MaxMin diff
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
}
Info[nI] <- paste(" ::: Differentiated ", Symbol, ": Diff. degree: ", DiffDeg, sep="") #Update Differentiation information
FName[[Idx]]@Info <<- Info
assign(activeFName, FName,envir=.GlobalEnv) #setto lo spettro attivo eguale ell'ultimo file caricato
assign("activeSpectName", Symbol,.GlobalEnv) #set the activeSpectral name to the actual CoreLine name
assign("activeSpectIndx", Idx,.GlobalEnv) #set the activeSpectral name to the actual CoreLine name
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
makeCombo()
return(Idx)
}
#--- Variables
plot.new()
if (length(activeFName)==0){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
# activeFName <- get("activeFName", envir=.GlobalEnv) #cload the XPSSample name (string)
FName <- get(activeFName, envir=.GlobalEnv) #load the active XPSSample (data)
FNameList <- XPSFNameList() #list of loaded XPSSamples
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #load the index of the active CoreLine
SpectName <- get("activeSpectName", envir=.GlobalEnv) #namer of the active CoreLine
SpectList <- XPSSpectList(activeFName) #list of CoreLine spectra belonging to FName XPSSample
Differentiated <- NULL
DiffBkp <- NULL
CLBkp <- NULL
BackGnd <- NULL
Corners <- list(x=NULL, y=NULL)
LocPos <- list()
MaxMinD <- NULL
DiffDeg <- 0
S1 <- "" #to store the 'FName@Symbol'
S2 <- "" #to store 'D.x' if differentiation was performed
S3 <- "" #to store '/U0395' if Max/Min diff was done
#===== Main Panel
MainWin <- gwindow("DATA DIFFERENTIATION", parent=c(30, 30), visible=FALSE)
size(MainWin) <- c(320, 200)
mainFrame <- gframe(text="Differentiate", horizontal=FALSE, spacing=5, container=MainWin)
Maingroup <- ggroup(spacing=5, horizontal=FALSE, container=mainFrame)
# --- Line 1 ---
D1Group1 <- ggroup(spacing=5, horizontal=TRUE, container=Maingroup)
D1frame1 <- gframe(" Select XPS Sample ", spacing=5, container=D1Group1)
D1XpsSpect <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
makeCombo()
svalue(DistLab) <- "Max Min Dist: "
}, container=D1frame1)
D1Frame2 <- gframe(" Select Coreline ", spacing=5, container=D1Group1)
D1CoreLine <- gcombobox(" ", selected=-1, editable=FALSE, container = D1Frame2)
D1Frame3 <- gframe(" Update XPSSample/Coreline Lists ", spacing=5, container=D1Group1)
UpdateButt <- gbutton(" UPDATE ", handler=function(h,...){
DiffBkp <<- NULL
BackGnd <<- NULL
Differentiated <<- NULL
DiffDeg <<- 0
S1 <<- S2 <<- S3 <<- ""
svalue(DDeg) <- ""
svalue(AmpliDeg) <- ""
svalue(D1XpsSpect) <- ""
svalue(D1CoreLine) <- ""
enabled(DiffButt) <- FALSE
enabled(ResButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = D1Frame3)
# --- Line 2 ---
D2frame1 <- gframe(" Select Differentiation Degree ", spacing=5, container=Maingroup)
DDeg <- gcombobox(c(1,2,3,4,5), selected=-1, editable=FALSE, handler=function(h,...){
enabled(DiffButt) <- TRUE
enabled(ResButt) <- TRUE
}, container = D2frame1)
tkconfigure(DDeg$widget, width=10)
Negative <- gcheckbox(text="Negative", checked = FALSE, container=D2frame1)
DiffButt <- gbutton(" Differentiate ", handler=function(h,...){
Ndiff <- as.numeric(svalue(DDeg))
if (length(Ndiff) == 0){
gmessage("Please Select the Differentiation Degree", title="Warning", icon="warning")
return()
}
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #set the activeSpectIndex to the actual CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
Object <- FName[[SpectIndx]]@.Data[[2]]
for(ii in 1:Ndiff){
Object <- Differ(Object)
}
if (svalue(Negative) == TRUE) { Object <- -Object }
Differentiated[[2]] <<- Object
S2 <<- "D."
DiffDeg <<- Ndiff
DiffBkp <<- Differentiated
# BkgSubtraction(FName[[SpectIndx]]@.Data[[2]]) #plotData needs the backgrnd to be defined
plotData()
enabled(SaveNewButt) <- TRUE
enabled(OverWButt) <- TRUE
}, container = D2frame1)
ResButt <- gbutton(" RESET ", handler=function(h,...){
DiffBkp <<- NULL
BackGnd <<- NULL
Differentiated <<- NULL
DiffDeg <<- 0
S1 <<- S2 <<- S3 <<- ""
svalue(DDeg) <- ""
svalue(AmpliDeg) <- ""
svalue(D1XpsSpect) <- ""
svalue(D1CoreLine) <- ""
SpectIndx <<- grep(S1, names(FName)) #restore
FName[[SpectIndx]] <<- CLBkp
plot(FName[[SpectIndx]])
enabled(DiffButt) <- FALSE
enabled(ResButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = D2frame1)
# --- Line 2 ---
D2frame2 <- gframe(" Amplify Diff. Data ", horizontal=TRUE, spacing=5, container=Maingroup)
AmpliDeg <- gedit(initial.msg="10,50, 100...", handler=function(h,...){
AA <- as.integer(svalue(AmpliDeg))
Differentiated[[2]] <<- AA*DiffBkp[[2]]
plotData()
}, container = D2frame2)
space <- glabel(" ", spacing = 5, container= D2frame2)
gbutton("Measure Max-Min Dist.", handler=function(h,...){
MeasureMaxMinD()
}, container = D2frame2)
DistLab <- glabel("Max Min Dist: ", spacing = 5, container= D2frame2)
#--- Common buttons
DButtgroup <- ggroup(horizontal=TRUE, container=mainFrame)
SaveNewButt <- gbutton("SAVE AS A NEW CORE LINE", handler=function(h,...){ #Filtered data saved in a new coreline
SaveFName("NewCL")
BackGnd <<- NULL
svalue(DDeg) <- ""
XPSSaveRetrieveBkp("save")
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = DButtgroup)
OverWButt <- gbutton("OVERWRITE PREVIOUS DIFFERENTIATION", handler=function(h,...){ #Filtered data saved in a new coreline
SaveFName("Overwrite")
BackGnd <<- NULL
svalue(DDeg) <- ""
XPSSaveRetrieveBkp("save")
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = DButtgroup)
gbutton("EXIT", handler=function(h,...){
dispose(MainWin)
XPSSaveRetrieveBkp("save")
}, container = DButtgroup)
enabled(DDeg) <- FALSE
enabled(DiffButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
visible(MainWin) <- TRUE
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSDiff
Documented in XPSDiff
#function to differentiate XPS-Sample spectra
#' @title XPSDiff for spectra differentiation
#' @description XPSDiff function is used to compute the derivative of the XPSSpectra.
#' The user can select the degree of differentiation. Tje result of the differentiation
#' is oplotted together with the original data. It is possible to amplify the
#' differentiated spectrum to be on the scale of the original spectrum.
#' @examples
#' \dontrun{
#' XPSDiff()
#' }
#' @export
#'
XPSDiff <- function(){
Differ <- function(Object){
LL <- length(Object)
tmp <- NULL
for(ii in 2:LL){
tmp[ii] <- Object[ii] - Object[ii-1]
}
tmp[1] <- tmp[2]
return(tmp)
}
BkgSubtraction <- function(data){ #linear BKG subtraction
BackGnd <<- NULL
LL <- length(data)
rng <- floor(LL/15)
if (rng<3) {rng==3}
if (rng>30) {rng==30}
bkg1 <- mean(data[1:rng])
bkg2 <- mean(data[(LL-rng):LL])
stp <- (bkg1-bkg2)/LL
Dta_Bkg <- NULL
for (ii in 1:LL){
Dta_Bkg[ii] <- data[ii]-(bkg1-ii*stp)
BackGnd[ii] <<- bkg1-ii*stp
}
return(Dta_Bkg)
}
FindNearest <- function(){
D <- NULL
Dmin <- ((LocPos$x-Corners$x[1])^2 + (LocPos$y-Corners$y[1])^2)^0.5 #init value
for (ii in 1:4) {
D[ii] <- ((LocPos$x-Corners$x[ii])^2 + (LocPos$y-Corners$y[ii])^2)^0.5 #dist P0 P1
if(D[ii] <= Dmin){
Dmin <- D[ii]
idx=ii
}
}
if (idx==1){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
}
return(Corners)
}
FindPattern <- function(TxtVect, Pattern){
chrPos <- NULL
LL <- length(TxtVect)
for(ii in 1:LL){
Pos <- gregexpr(pattern=Pattern,TxtVect[ii]) #the result of gregexpr is a list containing the character position of D.x x=differentiation degree
if (Pos[[1]][1] > 0) {
chrPos[1] <- ii
chrPos[2] <- Pos[[1]][1]
break
}
}
return(chrPos)
}
MeasureMaxMinD <- function(){ # \U0394. = greek Delta used to indicate difference in Max-Min posiitions
RefreshPlot <- function(){
XXX <- cbind(unlist(FName[[SpectIndx]]@.Data[1])) #transform the vector in a column of data
YYY <- cbind(unlist(Differentiated[2]))
Xlim <- range(XXX)
if (FName[[SpectIndx]]@Flags[1]==TRUE) {
Xlim <- rev(Xlim) ## reverse x-axis
}
Ylim <- range(YYY)
matplot(x=XXX, y=YYY, type="l", lty="solid", col="black",
xlim=Xlim, ylim=Ylim, xlab=FName[[SpectIndx]]@units[1], ylab="Differentiated Data [cps.]")
return()
}
if(length(Differentiated[[2]]) == 0) {
gmessage(msg="NON-Differentiated data. Cannot compute MAX-MIN difference", title="WARNING", icon="warning")
return()
}
if(length(svalue(D1CoreLine)) == 0) {
gmessage(msg="Please Select the Differentiated Core-Line", title="WARNING", icon="warning")
return()
}
RefreshPlot()
txt <- "LEFT button to set the MAX/MIN positions; RIGHT to exit \n Click near markers to modify the positions"
gmessage(msg=txt , title = "WARNING", icon = "warning")
pos <- locator(n=2, type="p", pch=3, col="red", lwd=1.5) #first the two corners are drawn
rect(pos$x[1], min(pos$y), pos$x[2], max(pos$y)) #marker-Corners are ordered with ymin on Left and ymax on Right
Corners$x <<- c(pos$x[1],pos$x[1],pos$x[2],pos$x[2])
Corners$y <<- c(pos$y[1],pos$y[2],pos$y[1],pos$y[2])
points(Corners, type="p", pch=3, col="red", lwd=1.5)
LocPos <<- list(x=0, y=0)
while (length(LocPos) > 0) { #if pos1 not NULL a mouse butto was pressed
LocPos <<- locator(n=1, type="p", pch=3, col="red", lwd=2) #to modify the zoom limits
if (length(LocPos$x) > 0) { #if the right mouse button NOT pressed
FindNearest()
if (FName[[SpectIndx]]@Flags[1]) { #Binding energy set
pos$x <- sort(c(Corners$x[1],Corners$x[3]), decreasing=TRUE) #pos$x in decrescent ordered => Corners$x[1]==Corners$x[2]
} else {
pos$x <- sort(c(Corners$x[1],Corners$x[3]), decreasing=FALSE) #pos$x in ascending order
}
pos$y <- sort(c(Corners$y[1],Corners$y[2]), decreasing=FALSE)
RefreshPlot() #refresh graph
rect(pos$x[1], pos$y[1], pos$x[2], pos$y[2])
points(Corners, type="p", pch=3, col="red", lwd=1.5)
}
}
MaxMinD <<- round(abs(pos$x[1]-pos$x[2]), 2)
Info <- FName[[SpectIndx]]@Info
S3 <<- "\U0394." #delta symbol
charPos <- FindPattern(FName[[SpectIndx]]@Info, " ::: Max.Min.\U0394. = ")[1] #charPos[1] = row index of Info where "::: Max.Min.D = " is found
if(length(charPos) > 0){ #save the Max/Min difference in FName Info
FName[[SpectIndx]]@Info[charPos] <<- paste(" ::: Max.Min.", S3, " = ", MaxMinD, sep="") #overwrite previous MAx\Min Dist value
} else {
answ <- gconfirm(msg="Save new value of Max-Min difference?", title="WARNING", icon="warning")
if (answ == TRUE){
nI <- length(FName[[SpectIndx]]@Info)+1
FName[[SpectIndx]]@Info[nI] <<- paste(" ::: Max.Min.", S3, " = ", MaxMinD, sep="")
}
}
Symbol <- paste(S3, S2, DiffDeg, S1, sep="", collapse="") #compose the CoreLine Symbol "\U0394." "D." CLname
if(hasRegionToFit(FName[[SpectIndx]])==FALSE){
setClass("baseline", representation(baseline="list"), contains="list", prototype(baseline=list()))
FName[[SpectIndx]]@RegionToFit$x <<- FName[[SpectIndx]]@.Data[[1]] #defines the RegionToFit equal to original data
FName[[SpectIndx]]@RegionToFit$y <<- FName[[SpectIndx]]@.Data[[2]] #defines the RegionToFit equal to original data
FName[[SpectIndx]]@Baseline$x <<- FName[[SpectIndx]]@.Data[[1]]
FName[[SpectIndx]]@Baseline$y <<- rep(0, length(FName[[SpectIndx]]@.Data[[1]])) #defines a zero-Baseline
FName[[SpectIndx]]@Baseline[["baseline"]] <<- new("baseline") #defines a new Baseline component of class baseline and package attribute .GlobalEnv
attr(FName[[SpectIndx]]@Baseline$baseline, "package") <<- ".GlobalEnv"
FName[[SpectIndx]]@Baseline$type <<- "linear"
FName[[SpectIndx]] <<- XPSaddComponent(FName[[SpectIndx]], type = "Derivative")
}
#Set the measured MaxMinD for the differeniated CoreLine
FName[[SpectIndx]]@Symbol <<- Symbol # '\U0394' = Delta: the MaxMin diff was measured
FName@names[SpectIndx] <<- Symbol #update/add core line name to list of names
FName[[SpectIndx]]@Components[[1]]@param["mu", "min"] <<- pos$x[1] #abscissas of Max/Min positions
FName[[SpectIndx]]@Components[[1]]@param["mu", "max"] <<- pos$x[2]
idx <- findXIndex(FName[[SpectIndx]]@.Data[[1]], pos$x[1]) #finds index corresponding to Max/min positions
FName[[SpectIndx]]@Components[[1]]@param["h", "min"] <<- FName[[SpectIndx]]@.Data[[2]][idx] #ordinate of Max/min position
idx <- findXIndex(FName[[SpectIndx]]@.Data[[1]], pos$x[2]) #finds index corresponding to Max/min positions
FName[[SpectIndx]]@Components[[1]]@param["h", "max"] <<- FName[[SpectIndx]]@.Data[[2]][idx] #ordinate of Max/min position
assign(activeFName, FName, envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx, envir=.GlobalEnv)
cat("\n ==> Data saved")
plot(FName)
svalue(DistLab) <- MaxMinD
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- TRUE
}
plotData <- function() {
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #set the activeSpectIndex to the actual CoreLine
XXX <- cbind(unlist(FName[[SpectIndx]]@.Data[1]))
LL <- length(XXX)
YYY <- cbind(unlist(FName[[SpectIndx]]@.Data[2]), unlist(Differentiated[2]), rep(0, LL))
Xlim <- range(XXX)
if (FName[[SpectIndx]]@Flags[1]==TRUE) {
Xlim <- rev(Xlim) ## reverse x-axis
}
Ylim <- range(YYY)
matplot(x=XXX, y=YYY, type="l", lty=c("solid", "solid", "dashed"),lw=c(1.75, 1, 1), col=c("black", "red3", "black"),
xlim=Xlim, ylim=Ylim, xlab=FName[[SpectIndx]]@units[1], ylab=FName[[SpectIndx]]@units[2])
return()
}
makeCombo <- function(){
activeFName <<- svalue(D1XpsSpect)
FName <<- get(activeFName,envir=.GlobalEnv) #load the XPSSample
assign("activeFName", activeFName, envir=.GlobalEnv)
SpectList <<- XPSSpectList(activeFName)
SpectIndx <<- 1
delete(D1Frame2, D1CoreLine)
D1CoreLine <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPSCLname <- svalue(D1CoreLine)
tmp <- unlist(strsplit(XPSCLname, "\\.")) #skip the ".NUMBER" at beginning CoreLine name
SpectIndx <<- as.integer(tmp[1])
LL1 <- nchar(tmp[1])+2 # +2: substr(x,start,stop) start includes the character at 'start'
LL2 <- nchar(XPSCLname)
S1 <<- substr(XPSCLname, start=LL1, stop=LL2) #In case of XPSCLname="4.D1.C1s" SpectName must be "D1.C1s"
S3 <<- S2 <<- ""
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
S1S2S3 <- unlist(strsplit(S1, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D."
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
# DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
DiffDeg <<- as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
}
}
assign("activeSpectName", S1, envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx, envir=.GlobalEnv)
plot(FName[[SpectIndx]])
enabled(DDeg) <- TRUE
CLBkp <<- FName[[SpectIndx]] #backUp original data
}, container=D1Frame2)
plot(FName)
}
SaveFName <- function(saveMode){
if(DiffDeg == 0 && length(as.numeric(svalue(DDeg)))==0){
gmessage(msg="Before saving data make differentiation please.", title="ERROR", icon="error")
return()
}
#save data in NEW CORELINE mode
if (S2 != "" && saveMode=="NewCL") { #"D." is present, one or more core-lines are differentiated
Idx <- length(FName) #number of corelines +1
Info <- FName[[Idx]]@Info
nI <- length(Info)
N.spaces <- gregexpr(" ", Info[nI]) #finds how many space characters are in info
if (length(N.spaces[[1]]) != nchar(Info[nI])){ #if == FALSE if a blank raw is found
nI <- nI +1 #then add new Info line
}
Idx <- Idx+1
FName[[Idx]] <<- new("XPSCoreLine") #Add the new Coreline using the starting core-line
if (length(svalue(DDeg)) > 0){ #working on previously differentiated data
FName[[Idx]]@.Data <<- Differentiated #update New Coreline with dufferentiated data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D."
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #DiffDeg set in 'Differentiation'
Symbol <- paste(S3, S2, DiffDeg, S1, sep="")
}
} else {
Symbol <- paste(S3, S2, DiffDeg, ".", S1, sep="") #DiffDeg updated in 'Differentiation'
}
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
}
#save data in OVERWRITE mode
if (S2 != "" && saveMode=="Overwrite") { #"D." is present: working on previously differentiated data, and overwrite new data
Idx <- activeSpectIndx
FName[[Idx]]@.Data <<- Differentiated #change the original diff. data with the new differented data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #the CoreLine was pre-differentiated
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D." # %in% search if "D" is present in S1S2S3. %in% gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #add precedent diff. degree
Symbol <- paste(S3, S2, DiffDeg, S1, sep="")
}
} else {
Symbol <- paste(S3, S2, DiffDeg, ".", S1, sep="") #DiffDeg updated in 'Differentiation'
}
Info <- FName[[Idx]]@Info
chrPos <- FindPattern(Info, " ::: Differentiated ")
nI <- chrPos[1] #Overwrite previous Info
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
if (S2 == "" && saveMode=="Overwrite") { #"D." NOT present Differentiation not performed we should work on already differentiated data
#--- Cntrl if we are differentiating an already differentiated spectrum
Info <- FName[[SpectIndx]]@Info
chrPos <- FindPattern(Info, "Diff. degree: ")
if (length(chrPos[2]) > 0) { #it is possible to start with a pre-differentiated CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
CLname <- FName[[SpectIndx]]@Symbol
#now set the correct S1, S2, S3 and DiffDeg values
S1S2S3 <- unlist(strsplit(CLname, ".", fixed=TRUE))
if("\U0394." %in% S1S2S3) { S3 <<- "\U0394." }
jj <- which(S1S2S3 == "D") # which search if "D" is present in S1S2S3. which gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
if(length(jj) > 0){
S2 <<- "D." # %in% search if "D" is present in S1S2S3. %in% gives FALSE when compares "D" with "DD", "DyMNN", "CdMNN"
LL <- length(S1S2S3)
S1 <<- paste(".", S1S2S3[(jj+2):LL], sep="", collapse="")
DiffDeg <<- DiffDeg + as.integer(S1S2S3[(jj+1)]) #add precedent diff. degree
} else {
gmessage(msg="ERROR: Wrong Data Information", title="ERROR", icon="error")
return()
}
Idx <- activeSpectIndx #number of corelines
Symbol <- paste(S3, S2, DiffDeg, S1, sep="") # '\U0394.' = Delta representing the MaxMin diff
FName[[Idx]]@Symbol <<- Symbol
FName@names[Idx] <<- Symbol
}
}
Info[nI] <- paste(" ::: Differentiated ", Symbol, ": Diff. degree: ", DiffDeg, sep="") #Update Differentiation information
FName[[Idx]]@Info <<- Info
assign(activeFName, FName,envir=.GlobalEnv) #setto lo spettro attivo eguale ell'ultimo file caricato
assign("activeSpectName", Symbol,.GlobalEnv) #set the activeSpectral name to the actual CoreLine name
assign("activeSpectIndx", Idx,.GlobalEnv) #set the activeSpectral name to the actual CoreLine name
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
makeCombo()
return(Idx)
}
#--- Variables
plot.new()
if (length(activeFName)==0){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
# activeFName <- get("activeFName", envir=.GlobalEnv) #cload the XPSSample name (string)
FName <- get(activeFName, envir=.GlobalEnv) #load the active XPSSample (data)
FNameList <- XPSFNameList() #list of loaded XPSSamples
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #load the index of the active CoreLine
SpectName <- get("activeSpectName", envir=.GlobalEnv) #namer of the active CoreLine
SpectList <- XPSSpectList(activeFName) #list of CoreLine spectra belonging to FName XPSSample
Differentiated <- NULL
DiffBkp <- NULL
CLBkp <- NULL
BackGnd <- NULL
Corners <- list(x=NULL, y=NULL)
LocPos <- list()
MaxMinD <- NULL
DiffDeg <- 0
S1 <- "" #to store the 'FName@Symbol'
S2 <- "" #to store 'D.x' if differentiation was performed
S3 <- "" #to store '/U0395' if Max/Min diff was done
#===== Main Panel
MainWin <- gwindow("DATA DIFFERENTIATION", parent=c(30, 30), visible=FALSE)
size(MainWin) <- c(320, 200)
mainFrame <- gframe(text="Differentiate", horizontal=FALSE, spacing=5, container=MainWin)
Maingroup <- ggroup(spacing=5, horizontal=FALSE, container=mainFrame)
# --- Line 1 ---
D1Group1 <- ggroup(spacing=5, horizontal=TRUE, container=Maingroup)
D1frame1 <- gframe(" Select XPS Sample ", spacing=5, container=D1Group1)
D1XpsSpect <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
makeCombo()
svalue(DistLab) <- "Max Min Dist: "
}, container=D1frame1)
D1Frame2 <- gframe(" Select Coreline ", spacing=5, container=D1Group1)
D1CoreLine <- gcombobox(" ", selected=-1, editable=FALSE, container = D1Frame2)
D1Frame3 <- gframe(" Update XPSSample/Coreline Lists ", spacing=5, container=D1Group1)
UpdateButt <- gbutton(" UPDATE ", handler=function(h,...){
DiffBkp <<- NULL
BackGnd <<- NULL
Differentiated <<- NULL
DiffDeg <<- 0
S1 <<- S2 <<- S3 <<- ""
svalue(DDeg) <- ""
svalue(AmpliDeg) <- ""
svalue(D1XpsSpect) <- ""
svalue(D1CoreLine) <- ""
enabled(DiffButt) <- FALSE
enabled(ResButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = D1Frame3)
# --- Line 2 ---
D2frame1 <- gframe(" Select Differentiation Degree ", spacing=5, container=Maingroup)
DDeg <- gcombobox(c(1,2,3,4,5), selected=-1, editable=FALSE, handler=function(h,...){
enabled(DiffButt) <- TRUE
enabled(ResButt) <- TRUE
}, container = D2frame1)
tkconfigure(DDeg$widget, width=10)
Negative <- gcheckbox(text="Negative", checked = FALSE, container=D2frame1)
DiffButt <- gbutton(" Differentiate ", handler=function(h,...){
Ndiff <- as.numeric(svalue(DDeg))
if (length(Ndiff) == 0){
gmessage("Please Select the Differentiation Degree", title="Warning", icon="warning")
return()
}
SpectIndx <- get("activeSpectIndx", envir=.GlobalEnv) #set the activeSpectIndex to the actual CoreLine
Differentiated <<- FName[[SpectIndx]]@.Data
Object <- FName[[SpectIndx]]@.Data[[2]]
for(ii in 1:Ndiff){
Object <- Differ(Object)
}
if (svalue(Negative) == TRUE) { Object <- -Object }
Differentiated[[2]] <<- Object
S2 <<- "D."
DiffDeg <<- Ndiff
DiffBkp <<- Differentiated
# BkgSubtraction(FName[[SpectIndx]]@.Data[[2]]) #plotData needs the backgrnd to be defined
plotData()
enabled(SaveNewButt) <- TRUE
enabled(OverWButt) <- TRUE
}, container = D2frame1)
ResButt <- gbutton(" RESET ", handler=function(h,...){
DiffBkp <<- NULL
BackGnd <<- NULL
Differentiated <<- NULL
DiffDeg <<- 0
S1 <<- S2 <<- S3 <<- ""
svalue(DDeg) <- ""
svalue(AmpliDeg) <- ""
svalue(D1XpsSpect) <- ""
svalue(D1CoreLine) <- ""
SpectIndx <<- grep(S1, names(FName)) #restore
FName[[SpectIndx]] <<- CLBkp
plot(FName[[SpectIndx]])
enabled(DiffButt) <- FALSE
enabled(ResButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = D2frame1)
# --- Line 2 ---
D2frame2 <- gframe(" Amplify Diff. Data ", horizontal=TRUE, spacing=5, container=Maingroup)
AmpliDeg <- gedit(initial.msg="10,50, 100...", handler=function(h,...){
AA <- as.integer(svalue(AmpliDeg))
Differentiated[[2]] <<- AA*DiffBkp[[2]]
plotData()
}, container = D2frame2)
space <- glabel(" ", spacing = 5, container= D2frame2)
gbutton("Measure Max-Min Dist.", handler=function(h,...){
MeasureMaxMinD()
}, container = D2frame2)
DistLab <- glabel("Max Min Dist: ", spacing = 5, container= D2frame2)
#--- Common buttons
DButtgroup <- ggroup(horizontal=TRUE, container=mainFrame)
SaveNewButt <- gbutton("SAVE AS A NEW CORE LINE", handler=function(h,...){ #Filtered data saved in a new coreline
SaveFName("NewCL")
BackGnd <<- NULL
svalue(DDeg) <- ""
XPSSaveRetrieveBkp("save")
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = DButtgroup)
OverWButt <- gbutton("OVERWRITE PREVIOUS DIFFERENTIATION", handler=function(h,...){ #Filtered data saved in a new coreline
SaveFName("Overwrite")
BackGnd <<- NULL
svalue(DDeg) <- ""
XPSSaveRetrieveBkp("save")
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
}, container = DButtgroup)
gbutton("EXIT", handler=function(h,...){
dispose(MainWin)
XPSSaveRetrieveBkp("save")
}, container = DButtgroup)
enabled(DDeg) <- FALSE
enabled(DiffButt) <- FALSE
enabled(SaveNewButt) <- FALSE
enabled(OverWButt) <- FALSE
visible(MainWin) <- TRUE
}
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