R/XPSProcessCoreLineGUI.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSProcessCoreLine
Documented in
XPSProcessCoreLine
#CoreLine processing: adding/deleting corelines or Baseline and Fits to exiting Corelines
#' @title XPSProcessCoreLine
#' @description XPSProcessCoreLine function adds a CoreLine (with fit if existing)
#' to an object of class XPSSample, or just a BaseLine and Fit to an existing CoreLine
#' (class XPSCoreLine) or remove a CoreLine from an object of class XPSSample
#' XPSProcessCoreLine may be used to perform some simple math operations on CoreLines
#' (class XPSCoreLine) like addition, subtraction, multiplication by a constant value
#' normalization, differentiation, combination of two CoreLines.
#' @examples
#' \dontrun{
#' XPSProcessCoreLine()
#' }
#' @export
#'
XPSProcessCoreLine <- function(){
#---
CtrlRepCL <- function(destIndx, SpectName, DestSpectList){ #CTRL for repeated CL: search for core-lines with same name
winCL <- gwindow("SELECT CORELINE", visible=FALSE)
size(winCL) <- c(100, 200)
groupCL <- ggroup(horizontal=FALSE, container=winCL)
DestFile <- svalue(DestFileName)
N.CL <- length(destIndx)
msg <- paste("Found", N.CL, SpectName, "spectra in", DestFile,"\nPlease select the coreline \nto add Baseline and Fit", sep=" ")
txt <- glabel(text=msg, container=groupCL)
font(txt) <- list(family="sans",size=12)
gseparator(horizontal=TRUE, container=groupCL)
selectCL <- gradio(DestSpectList[destIndx], selected=1, horizontal=TRUE, container=groupCL)
gbutton(" OK ", handler=function(h, ...){
CoreLine <- svalue(selectCL)
CoreLine <- unlist(strsplit(CoreLine, "\\.")) #drop "NUMBER." at beginning of coreLine name
RepCLidx <<- as.numeric(CoreLine[1])
# svalue(infoWin) <- ""
dispose(winCL)
}, container=groupCL)
visible(winCL) <- TRUE
winCL$set_modal(TRUE) #nothing can be done while running this macro
} #modal mode takes the control of the 'return' value which CANNOT be used to return variable values
RenumCL <- function(SourceFile){
CLnames <- names(SourceFile)
LL <- length(SourceFile)
for(ii in 1:LL){
SourceFile[[ii]]@Symbol <- paste(ii,".",CLnames[ii], sep="")
}
return(SourceFile)
}
updateObj <- function(SFpointer, CNTRpointer, CLpointer,...){
SelectedFName <- svalue(SFpointer)
SpectList <<- XPSSpectList(SelectedFName)
SourceFName <- get(SelectedFName,envir=.GlobalEnv) #load the source XPSSample file
delete(CNTRpointer,CLpointer)
CLpointer <- gcombobox(SpectList, selected=-1, handler=function(h, ...){
SourceCoreline <- svalue(CLpointer)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #slipt strin at character "."
indx <- as.integer(SourceCoreline[1])
plot(SourceFName[[indx]])
enabled(DestFileName) <- TRUE # disable selection of the destination file
}, editable=FALSE, container=CNTRpointer)
add(CNTRpointer,CLpointer)
plot(SourceFName)
enabled(CLpointer) <- TRUE #enable core line selection
return(CLpointer)
}
MakeBaseLine <- function(SourceFile, indx, DestFile, destIndx) {
BLinfo <- SourceFile[[indx]]@Baseline$type
BasLinType <- BLinfo[1]
splinePoints <- NULL
deg <- NULL
Wgt <- NULL
if (BasLinType == "shirley"){BasLinType <- "Shirley"} #different names for old/new RXPSG packages
if (BasLinType == "2p.shirley"){BasLinType <- "2P.Shirley"} #transform to new BaseLineNames.
if (BasLinType == "3p.shirley"){BasLinType <- "3P.Shirley"} #Exact Baseline Names required to generate the Baseline see XPSClass
if (BasLinType == "lp.shirley"){BasLinType <- "LP.Shirley"}
if (BasLinType == "2p.tougaard"){BasLinType <- "2P.Tougaard"}
if (BasLinType == "3p.tougaard"){BasLinType <- "3P.Tougaard"}
if (BasLinType == "4p.tougaard"){BasLinType <- "4P.Tougaard"}
if (BasLinType == "linear" ||
BasLinType == "Shirley" || BasLinType == "2P.Shirley" || BasLinType == "2P.Tougaard" || BasLinType == "3P.Tougaard") {
txt <- paste(BLinfo[1], " background found!\n ==> Set the Baseline Limits")
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "polynomial") {
deg <- as.numeric(BLinfo[2])
gmessage(msg="Polynomial backgound found!\n ==> Set the Baseline Limits", title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "spline") {
splinePoints <- list(x=NULL, y=NULL)
txt <- "Spline background found! \n ==> LEFT click to set spline points; RIGHT to exit"
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
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=3, cex=1.5, lwd=2, pch=1)
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)
}
}
# Now make BaseLine
decr <- FALSE #Kinetic energy set
if (DestFile[[destIndx]]@Flags[1] == TRUE) { decr <- TRUE }
idx <- order(splinePoints$x, decreasing=decr)
splinePoints$x <- splinePoints$x[idx] #splinePoints$x in ascending order
splinePoints$y <- splinePoints$y[idx] #following same order select the correspondent splinePoints$y
LL <- length(splinePoints$x)
DestFile[[destIndx]]@Boundaries$x <- c(splinePoints$x[1],splinePoints$x[LL]) #set the boundaries of the baseline
DestFile[[destIndx]]@Boundaries$y <- c(splinePoints$y[1],splinePoints$y[LL])
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "3P.Shirley" || BasLinType == "LP.Shirley" || BasLinType == "4P.Tougaard") {
Wgt <- as.numeric(BLinfo[2])
txt <- paste(BLinfo[1], " background found!\n ==> Set the Baseline Limits")
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
}
plot(DestFile[[destIndx]])
return(DestFile[[destIndx]])
}
#---
SaveSpectrum <- function(){
activeFName <- svalue(DestFileName)
assign(activeFName, DestFName, envir=.GlobalEnv) #save changes in the destinationfile
assign("activeFName", activeFName, envir=.GlobalEnv) #set the Active XPSSample == DestinationFile
assign("activeSpectName", activeSpectName,envir=.GlobalEnv) #Set the activeSpect == added coreline
assign("activeSpectIndx", activeSpectIndx,envir=.GlobalEnv) #Set the active Index == index of added coreline
plot(DestFName)
XPSSaveRetrieveBkp("save")
enabled(SaveSpect) <- FALSE #SaveSpectrum file disabled
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled
enabled(SaveAndExit) <- FALSE #Saving data blocked: ctrls on Dest file needed
}
SaveNewSpectrum <- function(){
activeFName <- svalue(SourceFile11) #name of the manipulated XPSSample (one of the math operations was performed)
LL <- length(activeFName)
if ( length(activeFName)>0 ){ #Math operations performed on SourceFile11
SourceFName <- DestFName
DestFName <- get(activeFName, envir=.GlobalEnv) #retrieve original source XPSSample which will be the destination file
SpectName <- activeSpectName
SpectIndx <- activeSpectIndx
Symbol <- paste(prefix,SpectName, sep="")
CoreLineList <- names(DestFName)
destIndx <- length(CoreLineList)+1
DestFName[[destIndx]] <- SourceFName[[SpectIndx]] #this is the manipulated core line
DestFName[[destIndx]]@Symbol <- Symbol
DestFName@names <- c(CoreLineList,Symbol)
assign(activeFName, DestFName, envir=.GlobalEnv) #Save the changes in a new coreline in the destination file
assign("activeFName", activeFName, envir=.GlobalEnv)
assign("activeSpectName", SpectName,envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx,envir=.GlobalEnv)
msg <- paste(" Coreline: ", Symbol, " saved in the XPS Sample ", DestFName@Filename, sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled if SourceFile OK
} else {
activeFName <- svalue(SourceFile1)
SourceFName <- DestFName
DestFName <- get(activeFName, envir=.GlobalEnv) #retrieve original source XPSSample which will be the destination file
SpectName <- activeSpectName
SpectIndx <- activeSpectIndx
CoreLineList <- names(DestFName)
destIndx <- length(CoreLineList)+1
DestFName[[destIndx]] <- SourceFName[[SpectIndx]] #this is the manipulated core line
DestFName[[destIndx]]@Symbol <- SpectName
DestFName@names <- c(CoreLineList,SpectName)
assign(activeFName, DestFName, envir=.GlobalEnv) #Save the changes in a new coreline in the destination file
assign("activeFName", activeFName, envir=.GlobalEnv)
assign("activeSpectName", SpectName,envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx,envir=.GlobalEnv)
msg <- paste(" Coreline: ", SpectName, " saved in the XPS Sample ", DestFName@Filename, sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
}
enabled(SaveSpect) <- FALSE #SaveSpectrum file disabled
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled
enabled(SaveAndExit) <- FALSE #Saving data blocked: ctrls on Dest file needed
}
#----- variables -----
#---load list of file ID and correspondent FileNames
FNameList <- XPSFNameList()
DestFName <- NULL
RepCLidx <- NULL
activeSpectIndx <- NULL
activeSpectName <- NULL
SampID <- ""
SpectList <- ""
CullData <- NULL #rangeX of the region to cull
prefix <- ""
gmessage(msg=" Remember to save data after each operation \n otherwise you will loss the results", title="SAVE RESULTS", icon="warning")
#####----main---
ProcessWin <- gwindow("CORELINE PROCESSING", parent=c(50, 10), visible=FALSE)
Addgroup <- ggroup(horizontal=FALSE, container=ProcessWin)
NoteBK <- gnotebook(expand=TRUE, container = Addgroup)
#--- TAB1
T1group <- ggroup(label="CORELINE PROCESSING", horizontal=TRUE, spacing=5, container=NoteBK)
layout1T1 <- glayout(homogeneous=FALSE, spacing=3, container=T1group)
layout1T1[1,1] <- AddFrame1 <- gframe("SELECT THE SOURCE XPS-SAMPLE", spacing=3, container=layout1T1)
SourceFile1 <- gcombobox(FNameList, selected=-1, editable=FALSE, expand=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
SourceCoreline1 <<- updateObj(SourceFile1,AddFrame2,SourceCoreline1)
}, container = AddFrame1)
layout1T1[2,1] <- AddFrame2 <- gframe(text=" SELECT CORELINE TO PROCESS ", spacing=3, container=layout1T1)
SourceCoreline1 <- gcombobox(SpectList, selected=-1, editable=FALSE, spacing=5, handler=function(h,...) {
enabled(DestFileName) <- TRUE # selection destination file enabled
}, container=AddFrame2)
enabled(SourceCoreline1) <- FALSE #CoreLine selection blocked
layout1T1[3,1] <- AddFrame3 <- gframe(text="SELECT THE DESTINATION FILE NAME", spacing=3, container=layout1T1)
DestFileName <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...) {
SourceFile <- svalue(SourceFile1)
DestFile <- svalue(DestFileName)
# svalue(infoWin) <- ""
SpectName <- svalue(SourceCoreline1)
SpectName <- unlist(strsplit(SpectName, "\\.")) #split the string at character "."
SpectIndx <- as.integer(SpectName[1])
SpectName <- SpectName[2]
if (SourceFile == DestFile) {
gmessage(msg="Warning: Destination File Name == Source File Name" , title = "WARNING: BAD DESTINATION FILE NAME!", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFile <- get(DestFile, envir=.GlobalEnv)
destIndx <- grep(SpectName, names(DestFile))
if (length(destIndx)==0){
txt <- paste("Warning: no ",SpectName, " core line present in the destination file. Continue?")
answ <- gconfirm(msg=txt , title = "WARNING: NO CORELINE PRESENT!", icon = "warning")
if (answ == FALSE) {
return()
}
}
LL <- length(destIndx)
for(ii in 1:LL){
if (DestFile[[destIndx[ii] ]]@Flags[1] != SourceFile[[SpectIndx]]@Flags[1]) { #acquisitions made using different energy scale
gmessage(msg="XPS-Samples have different Energy units. Operation stopped!" , title = "WARNING: BAD DESTINATION FILE!", icon = "warning")
return()
}
}
plot(DestFile)
enabled(SaveSpect) <- TRUE # enable saving data if Dest File OK
enabled(SaveAndExit) <- TRUE
}
}, container = AddFrame3)
enabled(DestFileName) <- FALSE # selection of destination file blocked
layout1T1[4,1] <- AddFrame4 <- gframe(text=" ADD WHOLE CORELINE ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton1 <- gbutton("Add New Coreline and Fit", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
# svalue(infoWin) <- ""
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage(mag="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No destination file selected
gmessage(mag="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #split string at character "."
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- length(DestFName)+1
DestFName[[destIndx]] <<- SourceFile[[SpectIndx]]
DestFName@names <<- c(CoreLineList,SourceFile[[SpectIndx]]@Symbol)
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Coreline: ", SourceCoreline[2], "added to XPS Sample. PLEASE SAVE DATA!", DestFName@Filename)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame4)
layout1T1[6,1] <- AddFrame5 <- gframe(text=" ADD BASELINE AND FIT ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton2 <- gbutton("Add Baseline and Fit to Original Coreline", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
# svalue(infoWin) <- ""
if (length(SourceCoreline)==0) { #no coreline selected
gmessage(msg="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #no destination file selected
gmessage(msg="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The index of the coreline in the destinationFile can be different from that od sourceFile => grep()
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
if (length(destIndx) == 0) {
text <- paste(SpectName, "not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION", icon = "warning")
} else {
if (length(SourceFile[[SpectIndx]]@RegionToFit) == 0){
text <- paste("ATTENTION: NO fit found for ",SpectName, " of the Source XPS-Sample. Operation stopped!", sep="")
gmessage(msg=text , title = "BAD SOURCE CORELINE SELECTION", icon = "warning")
return()
}
if (length(DestFName[[destIndx]]@Components) > 0) { #a fit is present for the selected coreline
text <- paste("ATTENTION: constraints of ",SpectName, " fit will be kept! Continue?", sep="")
answ <- gconfirm(msg=text , title = "WARNING!", icon = "warning")
if (answ) {
DestFName[[destIndx]] <<- XPSremove(DestFName[[destIndx]],"all")
} else {
return()
}
}
DestFName[[destIndx]] <<- MakeBaseLine(SourceFile, SpectIndx, DestFName, destIndx)
DestFName[[destIndx]]@Components <<- SourceFile[[SpectIndx]]@Components
RescaleH <- max(DestFName[[destIndx]]@RegionToFit$y)/max(SourceFile[[SpectIndx]]@RegionToFit$y) #scale factor between source and destination corelines
LL=length(DestFName[[destIndx]]@Components)
tmp <- NULL
if (LL > 0) {
for(ii in 1:LL) {
varmu <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="mu")
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="mu", value=varmu)
varh <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="h")
DestFName[[destIndx]]@Components[[ii]] <<- Ycomponent(DestFName[[destIndx]]@Components[[ii]], x=DestFName[[destIndx]]@RegionToFit$x, y=DestFName[[destIndx]]@Baseline$y/RescaleH) #Rescale Baseline Y values
DestFName[[destIndx]]@Components[[ii]]@ycoor <<- RescaleH*DestFName[[destIndx]]@Components[[ii]]@ycoor #Rescale Values of Y Components respect DestFName Y data
varh$start <- max(DestFName[[destIndx]]@Components[[ii]]@ycoor-DestFName[[destIndx]]@Baseline$y) #Substract Baseline
varh$min <- 0
varh$max <- 5*varh$start
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="h", value=varh)
}
tmp <- sapply(DestFName[[destIndx]]@Components, function(z) matrix(data=z@ycoor))
DestFName[[destIndx]]@Fit$y <<- (colSums(t(tmp)) - length(DestFName[[destIndx]]@Components)*(DestFName[[destIndx]]@Baseline$y))
} #transpose of tmp
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Fit data added to ", SpectName, "PLASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <<- msg
}
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame5)
layout1T1[7,1] <- AddFrame6 <- gframe(text=" ADD FIT ONLY ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton2 <- gbutton("Add Fit", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
svalue(warning) <- ""
if (length(SourceCoreline)==0) { #No coreline has been selected in source File
gmessage(msg="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No Destination File has been selected
gmessage(msg="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #split string at char "."
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The selected CoreLine name could be in any posiiton in the Destination XPSSample => source Samp Index could be different from Dest Samp index
if (length(destIndx) == 0) {
text <- paste(SpectName, "not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION STOPPED", icon = "warning")
} else {
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
if (length(DestFName[[destIndx]]@Components) > 0) { #Core line already fitted
text <- paste("ATTENTION: fit present on ",SpectName, " New fit constaints will be kept! Continue?")
answ <- gconfirm(msg=text , title = "WARNING!", icon = "warning")
if (answ) {
DestFName[[destIndx]] <<- XPSremove(DestFName[[destIndx]],"all")
} else {
return()
}
}
if (length(DestFName[[destIndx]]@Baseline) == 0) { #baseline not present
text <- paste("Baseline not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION STOPPED", icon = "warning")
return()
}
DestFName[[destIndx]] <<- XPSsetRSF(DestFName[[destIndx]])
DestFName[[destIndx]]@Components <<- SourceFile[[SpectIndx]]@Components
RescaleH <- max(DestFName[[destIndx]]@RegionToFit$y)/max(SourceFile[[SpectIndx]]@RegionToFit$y) #fattore di scala tra source coreline e destination coreline
LL=length(DestFName[[destIndx]]@Components)
for(ii in 1:LL) {
varmu <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="mu")
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="mu", value=varmu)
varh <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="h")
DestFName[[destIndx]]@Components[[ii]] <<- Ycomponent(DestFName[[destIndx]]@Components[[ii]], x=DestFName[[destIndx]]@RegionToFit$x, y=DestFName[[destIndx]]@Baseline$y/RescaleH) #calcola la Y ed aggiunge la baseline
DestFName[[destIndx]]@Components[[ii]]@ycoor <<- RescaleH*DestFName[[destIndx]]@Components[[ii]]@ycoor
varh$start <- max(DestFName[[destIndx]]@Components[[ii]]@ycoor-DestFName[[destIndx]]@Baseline$y)
varh$min <- 0
varh$max <- 5*varh$start
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="h", value=varh)
}
tmp <- sapply(DestFName[[destIndx]]@Components, function(z) matrix(data=z@ycoor))
DestFName[[destIndx]]@Fit$y <<- (colSums(t(tmp)) - length(DestFName[[destIndx]]@Components)*(DestFName[[destIndx]]@Baseline$y))
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Fit data added to ", SpectName, "PLASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}
}, container=AddFrame6)
# layout1T1[8,1] <- warn2 <- glabel(text=" " , container=layout1T1)
layout1T1[9,1] <- AddFrame7 <- gframe(text="OVERWRITE A CORELINE ", horizontal=FALSE, spacing=3, container=layout1T1)
overbutton <- gbutton("Overwrite", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No dest File selected
gmessage("Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFName <<- get(DestFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The selected CoreLine name could be in any posiiton in the Destination XPSSample => source Samp Index could be different from Dest Samp index
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
DestFName[[destIndx]] <<- SourceFile[[SpectIndx]]
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste("Coreline ", SpectName, "overwritten. PLASE SAVE DATA!")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame7)
# layout1T1[10,1] <- warn3 <- glabel(text=" " , container=layout1T1)
layout1T1[11,1] <- AddFrame8 <- gframe(text=" REMOVE/DUPLICATE CORELINE ", horizontal=TRUE, spacing=3, container=layout1T1)
delbutton <- gbutton(" Remove ", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
SpectList <<- XPSSpectList(SourceFile)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
}
if (length(SourceFile)==0) { #No Source File selected
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
} else {
enabled(SaveSpect) <- TRUE # enabling the Save options if the destination file name is OK
enabled(SaveAndExit) <- TRUE
svalue(DestFileName) <<- SourceFile
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
plot(SourceFile[[SpectIndx]])
text <- paste("ATTENTION: are you sure to delete the",svalue(SourceCoreline1), "core line ?", sep="")
answ <- gconfirm(msg=text, title="WARNING", icon="warning")
if (answ) {
SourceFile[[SpectIndx]] <- NULL #this eliminates the coreline
# SourceFile <- RenumCL(SourceFile)
DestFName <<- SourceFile #move updated XPSSample in the destinatin file for saving
activeSpectIndx <<- 1
activeSpectName <<- names(SourceFile)[1]
msg <- paste("Coreline ", SpectName, "deleted. PLEASE SAVE DATA!")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(SourceFile)
} else {
return() #do nothing
}
SpectList <<- names(SourceFile) #update the SpectrumList
idx <- seq(1:length(SpectList)) #cannot use XPSSpectList because loads the SourceFile from the .GlobalEnv
SpectList <<- paste(idx, SpectList, sep=".")
delete(AddFrame2,SourceCoreline1)
SourceCoreline1 <<- gcombobox(SpectList, selected=-1, handler=function(h, ...){ #update the selection of corelines
SourceCoreline <- svalue(SourceCoreline1)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
plot(SourceFile[[SpectIndx]])
enabled(DestFileName) <- TRUE #enable selection of the destination file
}, editable=FALSE, container=AddFrame2)
add(AddFrame2,SourceCoreline1)
enabled(SaveSpect) <- TRUE # Enable Save Spectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame8)
duplibutton <- gbutton(" Duplicate ", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No Coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
}
if (length(DestFile)==0) { #Destination file not selected
DestFile <- SourceFile
}
if (SourceFile != DestFile) {#Source different from Destination file
DestFile <- SourceFile
}
if (length(SourceFile)==0) { #Source File not selected
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
} else {
enabled(SaveSpect) <- TRUE #Save Destination file enabled if SourceFile OK
enabled(SaveAndExit) <- TRUE
svalue(DestFileName) <<- SourceFile
DestFName <<- get(SourceFile, envir=.GlobalEnv)
#--- eliminates the initial N. and reconstruct CLname also
# in presence of compex names as 10.D.2.ST.VB
tmp <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(tmp[1])
LL1 <- nchar(tmp[1])+2 # +2: substr(x,start,stop) start includes the character at 'start'
LL2 <- nchar(SourceCoreline)
SpectName <- substr(SourceCoreline, start=LL1, stop=LL2) #In case of XPSCLname="4.D1.C1s" SpectName must be "D1.C1s"
CoreLineList <- names(DestFName)
destIndx <- length(DestFName)+1
DestFName[[destIndx]] <<- DestFName[[SpectIndx]]
DestFName[[destIndx]]@Symbol <<- SpectName
DestFName@names <<- c(CoreLineList,SpectName)
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Coreline: ", SpectName, "added to XPS Sample", DestFName@Filename, ". PLEASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame8)
#---
layout2T1 <- glayout(homogeneous=FALSE, spacing=3, container=T1group)
layout2T1[1,1] <- AddFrame9 <- gframe(text=" PICK UP DATA ", horizontal=FALSE, spacing=3, container=layout2T1)
posgroup <- ggroup(horizontal=FALSE, container=AddFrame9)
CullFrom <- gedit(initial.msg ="From?", handler=function(h, ...){
CullData[1] <<- as.numeric(svalue(CullFrom))
}, container=posgroup)
CullTo <- gedit(initial.msg ="To?", handler=function(h, ...){
CullData[2] <<- as.numeric(svalue(CullTo))
}, container=posgroup)
gbutton("MOUSE", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
DestFile <- SourceFile
svalue(CullFrom) <<- ""
svalue(CullTo) <<- ""
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
svalue(CullFrom) <- NULL
svalue(CullTo) <- NULL
CullData <- NULL
if (length(SourceFile)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
return()
}
if (length(SourceCoreline)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
return()
} else {
svalue(DestFileName) <<- SourceFile
DestFName <<- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
if (length(DestFName[[SpectIndx]]@RegionToFit)>0) { #non e' stata selezionata alcuna coreline
gmessage("Baseline or Fit present. Reset analysis before culling data!" , title = " RESET ANALYSIS ", icon = "warning")
return()
}
plot(DestFName[[SpectIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2, pch=3)
CullData[1] <<- pos$x[1]
CullData[2] <<- pos$x[2]
}
}, container=posgroup)
cullgroup <- ggroup(horizontal=TRUE, container=AddFrame9)
cullButton <- gbutton("Select Data", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
svalue(DestFileName) <<- SourceFile
DestFile <- SourceFile
if (length(SourceFile)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
return()
}
if (length(SourceCoreline)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else {
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
DestFName <<- get(SourceFile, envir=.GlobalEnv)
if (length(DestFName[[SpectIndx]]@RegionToFit)>0) { #non e' stata selezionata alcuna coreline
gmessage("Baseline or Fit present. Reset analysis before culling data!" , title = " RESET ANALYSIS ", icon = "warning")
return()
}
if (is.null(CullData[1]) || is.null(CullData[2])) {
gmessage("From/To points NOT defined!" , title = " DEFINE FROM/TO ", icon = "warning")
return()
}
from <- findXIndex(DestFName[[SpectIndx]]@.Data[[1]], CullData[1])
to <- findXIndex(DestFName[[SpectIndx]]@.Data[[1]], CullData[2])
if (from > to) {
tmp <- from
from <- to
to <- tmp
}
DestFName[[SpectIndx]]@.Data[[1]] <<- DestFName[[SpectIndx]]@.Data[[1]][from:to]
DestFName[[SpectIndx]]@.Data[[2]] <<- DestFName[[SpectIndx]]@.Data[[2]][from:to]
DestFName[[SpectIndx]]@.Data[[3]] <<- DestFName[[SpectIndx]]@.Data[[3]][from:to]
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
plot(DestFName[[SpectIndx]])
msg <- "Please SAVE Selected Data"
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame9)
resetButton <- gbutton("RESET", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
svalue(DestFileName) <<- SourceFile
svalue(CullFrom) <<- ""
svalue(CullTo) <<- ""
DestFName <<- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
plot(DestFName[[SpectIndx]])
}, container=AddFrame9)
###---TAB2
T2group <- ggroup(label="CORELINE MATH", horizontal=FALSE, spacing=3, container=NoteBK)
layoutT2 <- glayout(homogeneous=FALSE, spacing=3, container=T2group)
layoutT2[1,1] <- MathFrame1 <- gframe(text="SELECT XPS-SAMPLE 1", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup1 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame1)
SourceFile11 <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
svalue(DestFileName) <- svalue(SourceFile11)
CoreLine11 <<- updateObj(SourceFile11,MathGroup2,CoreLine11)
addHandlerChanged(CoreLine11, handler=function(h,...) {
SourceFile <- svalue(SourceFile11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
Coreline <- svalue(CoreLine11)
Coreline <- unlist(strsplit(Coreline, "\\.")) #Split string at point
SpectIndx <- as.integer(Coreline[1])
Range <- range(SourceFile[[SpectIndx]]@.Data[1])
Range <- round(Range, 1)
svalue(CLRange11) <<- paste("Range", " ", Coreline[2], " X: ", Range[1], ", ", Range[2], sep="")
enabled(DestFileName) <- TRUE # Enable the choice of the destination file
})
}, container = MathGroup1)
layoutT2[1,2] <- MathFrame11 <- gframe("SELECT XPS-SAMPLE 2", horizontal = FALSE, spacing=3,container=layoutT2)
MathGroup11 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame11)
SourceFile22 <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
if (length(svalue(CoreLine11))==0) {
gmessage(msg="Please select the CORELINE1 first", title = "WARNING: CORELINE1 NOT DEFINED ", icon = "warning")
svalue(SourceFile22) <- NULL
} else {
CoreLine22 <<- updateObj(SourceFile22,MathGroup22,CoreLine22)
addHandlerChanged(CoreLine22, handler=function(h,...) {
SourceFile <- svalue(SourceFile22)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
Coreline <- svalue(CoreLine22)
Coreline <- unlist(strsplit(Coreline, "\\."))
SpectIndx <- as.integer(Coreline[1])
Range <- range(SourceFile[[SpectIndx]]@.Data[1])
Range <- round(Range, 1)
svalue(CLRange22) <<- paste("Range", " ", Coreline[2], " X: ", Range[1], ", ", Range[2], sep="")
})
}
}, container = MathGroup11)
layoutT2[2,1] <- MathFrame2 <- gframe(text="SELECT CORELINE 1", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup2 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame2)
CoreLine11 <- gcombobox(SpectList, selected=-1, editable=FALSE, container=MathGroup2)
CLRange11 <- glabel(text="Range CoreLine1: ", container=MathFrame2)
enabled(CoreLine11) <- FALSE
layoutT2[2,2] <- MathFrame22 <- gframe(text="SELECT CORELINE 2", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup22 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame22)
CoreLine22 <- gcombobox(SpectList, selected=-1, editable=FALSE, container=MathGroup22)
CLRange22 <- glabel(text="Range CoreLine2: ", container=MathFrame22)
enabled(CoreLine22) <- FALSE
layoutT2[3,1] <- MathGroup3 <- ggroup(horizontal=FALSE, container=layoutT2)
MathFrame3 <- gframe("ADD A CONSTANT VALUE TO CORELINE1", horizontal=TRUE,spacing=3,container=MathGroup3)
AddValue <- gedit(selected=-1, editable=TRUE, handler=function(h, ...){
# svalue(infoWin) <- ""
value <- as.numeric(svalue(AddValue))
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceCoreline <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
SourceFile[[SpectIndx]]@.Data[[2]] <- SourceFile[[SpectIndx]]@.Data[[2]]+value
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0)
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]+value
if (length(SourceFile[[SpectIndx]]@Baseline)>0)
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]+value
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL>0) {
for (jj in c(1:LL)) {
SourceFile[[SpectIndx]]@Components[[jj]]@ycoor <- SourceFile[[SpectIndx]]@Components[[jj]]@ycoor+value
}
}
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
prefix <<- "M."
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("Constant ",value, " added to CoreLine ", SpectName)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame3)
MathFrame33 <- gframe("MULTIPLY CORELINE1 BY A CONSTANT", horizontal=TRUE, spacing=3, container=MathGroup3)
MultValue <- gedit(selected=-1, editable=TRUE, handler=function(h, ...){
# svalue(infoWin) <- ""
value <- as.numeric(svalue(MultValue))
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceCoreline <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
SourceFile[[SpectIndx]]@.Data[[2]] <- SourceFile[[SpectIndx]]@.Data[[2]]*value
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0)
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]*value
if (length(SourceFile[[SpectIndx]]@Baseline)>0)
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]*value
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL > 0) {
for (jj in c(1:LL)) {
SourceFile[[SpectIndx]]@Components[[jj]]@ycoor <- SourceFile[[SpectIndx]]@Components[[jj]]@ycoor*value
}
SourceFile[[SpectIndx]]@Fit$y <- SourceFile[[SpectIndx]]@Fit$y*value
}
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("XX CoreLine ", SpectName, " multiplied by ", value)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame33)
layoutT2[3,2] <- MathFrame5 <- gframe(" COMBINE CORELINE1 and CORELINE2 \n Coreline2 added to Coreline1", horizontal=FALSE, spacing=3, container=layoutT2)
CombineButton <- gbutton("COMBINE", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx1 <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
CoreLine2 <- svalue(CoreLine22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx2 <- as.integer(CoreLine2[1])
if (length(SourceFile1[[SpectIndx1]]@RegionToFit)>0 || length(SourceFile2[[SpectIndx2]]@RegionToFit)){
txt <- paste("Combine CoreLines allowed ONLY on RAW data! RESET ANALYSIS")
gmessage(msg=txt, title = "WARNING: FIT PRESENT ", icon = "warning")
} else {
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
if (SourceFile2[[SpectIndx2]]@Flags[1] == TRUE){
SourceFile2[[SpectIndx2]]@.Data[[1]] <- rev(SourceFile2[[SpectIndx2]]@.Data[[1]])
SourceFile2[[SpectIndx2]]@.Data[[2]] <- rev(SourceFile2[[SpectIndx2]]@.Data[[2]])
}
Rng1 <- range(SourceFile1[[SpectIndx1]]@.Data[[1]])
Rng2 <- range(SourceFile2[[SpectIndx2]]@.Data[[1]])
MaxX1 <- max(Rng1)
MaxX2 <- max(Rng2)
MinX1 <- min(Rng1)
MinX2 <- min(Rng2)
LL1 <- length(SourceFile1[[SpectIndx1]]@.Data[[1]])
LL2 <- length(SourceFile2[[SpectIndx2]]@.Data[[1]])
if ( MaxX1 > MaxX2) {
if (MaxX2 < MinX1) {
gmessage("XPS-SAMPLE1 and XPS-SAMPLE2 are separated! \n
XPS-SAMPLE1 must overlap XPS-SAMPLE2 at least in ONE point", icon="warning")
return()
} else {
Idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], MinX1)
DataToCombineX <- SourceFile2[[SpectIndx2]]@.Data[[1]][1:Idx2]
DataToCombineY <- SourceFile2[[SpectIndx2]]@.Data[[2]][1:Idx2]
yy1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][1] #average intensity of second block of data in the combination point
yy2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2] #average intensity of first block of data in the combination point
Dy <- yy2-yy1 #difference of the intensities between block1, block2 od data in the combination point
SourceFile1[[SpectIndx1]]@.Data[[1]] <- c(DataToCombineX, SourceFile1[[SpectIndx1]]@.Data[[1]])
SourceFile1[[SpectIndx1]]@.Data[[2]] <- c(DataToCombineY-Dy, SourceFile1[[SpectIndx1]]@.Data[[2]])
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){ #Restore original order
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
plot(SourceFile1[[SpectIndx1]])
svalue(DestFileName) <- svalue(SourceFile11)
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
}
} else if ( MaxX2 > MaxX1) {
if (MaxX1 < MinX2) {
gmessage("XPS-SAMPLE1 and XPS-SAMPLE2 are separated! \n
XPS-SAMPLE1 must overlap XPS-SAMPLE2 at least in ONE point", icon="warning")
return()
} else {
MaxX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][LL1]
Idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], MaxX1)+1 #+1 needed to not start with the data next to MaxX1
DataToCombineX <- SourceFile2[[SpectIndx2]]@.Data[[1]][Idx2:LL2]
DataToCombineY <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2:LL2]
yy1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][LL1] #average intensity of first block of data in the combination point
yy2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2] #average intensity of second block of data in the combination point
Dy <- yy2-yy1 #difference of the intensities between block1, block2 od data in the combination point
SourceFile1[[SpectIndx1]]@.Data[[1]] <- c(SourceFile1[[SpectIndx1]]@.Data[[1]], DataToCombineX)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- c(SourceFile1[[SpectIndx1]]@.Data[[2]], DataToCombineY-Dy)
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){ #Restore original order
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
plot(SourceFile1[[SpectIndx1]])
svalue(DestFileName) <- svalue(SourceFile11)
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
}
}
}
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(svalue(CoreLine11), "-", svalue(SourceFile11)," combined with ", svalue(CoreLine22), "-", svalue(SourceFile22), " Combined")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame5)
layoutT2[4,1] <- MathFrame4 <- gframe("DIFFERENTIATE", horizontal=FALSE, spacing=3, container=layoutT2)
DiffButt <- gbutton("DIFFERENTIATE CORELINE1", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
LL <- length(SourceFile[[SpectIndx]]@.Data[[1]])
SourceFile[[SpectIndx]]@RegionToFit <- list(x=NULL, y=NULL)
SourceFile[[SpectIndx]]@Baseline <- list(x=NULL, y=NULL, type=NULL)
SourceFile[[SpectIndx]]@Baseline$x <- SourceFile[[SpectIndx]]@RegionToFit$x <- SourceFile[[SpectIndx]]@.Data[[1]]
SourceFile[[SpectIndx]]@Baseline$y <- rep(0, LL) #creo una baseline fittizia nulla
SourceFile[[SpectIndx]]@Baseline$type <- "linear"
k <- max(SourceFile[[SpectIndx]]@.Data[[2]])-min(SourceFile[[SpectIndx]]@.Data[[2]])
for (ii in 2:LL){
SourceFile[[SpectIndx]]@RegionToFit$y[ii] <- SourceFile[[SpectIndx]]@.Data[[2]][ii]-SourceFile[[SpectIndx]]@.Data[[2]][ii-1]
}
SourceFile[[SpectIndx]]@RegionToFit$y[1] <- SourceFile[[SpectIndx]]@RegionToFit$y[2]
Dmin <- min(SourceFile[[SpectIndx]]@RegionToFit$y)
Dmax <- max(SourceFile[[SpectIndx]]@RegionToFit$y)
SourceFile[[SpectIndx]]@RegionToFit$y <- k*(SourceFile[[SpectIndx]]@RegionToFit$y-Dmin)/(Dmax-Dmin)
matplot(x=matrix(c(SourceFile[[SpectIndx]]@.Data[[1]], SourceFile[[SpectIndx]]@RegionToFit$x), nrow=LL, ncol=2),
y=matrix(c(SourceFile[[SpectIndx]]@.Data[[2]], SourceFile[[SpectIndx]]@RegionToFit$y), nrow=LL, ncol=2),
type="l", lty=c(1,1), col=c("black","blue"),
xlab=SourceFile[[SpectIndx]]@units[1], ylab=SourceFile[[SpectIndx]]@units[2])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "D1."
msg <- paste(CoreLine1[2], " differentiated", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame4)
layoutT2[4,2] <- MathFrame44 <- gframe("ADD CORELINE2 TO CORELINE1", horizontal=FALSE, spacing=3, container=layoutT2)
AddButt <- gbutton("ADD SPECTRA", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #split string at point
SpectIndx1 <- as.integer(CoreLine1[1]) #keep first part
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- svalue(CoreLine22)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\."))
SpectIndx2 <- as.integer(CoreLine2[1])
if (hasBaseline(SourceFile1[[SpectIndx1]]) || hasBaseline(SourceFile2[[SpectIndx2]]) ){
answ <- gmessage(msg="ADDITION CAN BE DONE ONLY ON RAW DATA: PLEASE REMOVE ANALYSIS" , title = "WARNING!", icon = "warning")
} else {
txt=" ==> ADDITION WILL BE PERFOMED IN THE COMMON ENERGY RANGE\nSAVE AND SAVE&EXIT WILL OVERWRITE THE RESULT TO CORE LINE 1"
answ <- gconfirm(msg=txt , title = "WARNING!", icon = "warning")
if (answ) {
Range1 <- range(SourceFile1[[SpectIndx1]]@.Data[1])
Range2 <- range(SourceFile2[[SpectIndx2]]@.Data[1])
lim1 <- max(Range1[1], Range2[1]) #the greater of the lower limits
lim2 <- min(Range1[2], Range2[2]) #the smaller of the higher limits
idx1 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim2)
if (SourceFile1[[SpectIndx1]]@Flags[1]) { #Binding energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx2:idx1]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx2:idx1]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx2:idx1] #Analyzer Transf Funct.
} else { #Kinetic energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx1:idx2]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx1:idx2]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx1:idx2] #Analyzer Transf Funct.
}
LL1 <- length(CoreLineY1)
idx1 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim2)
if (SourceFile2[[SpectIndx2]]@Flags[1]) { #Binding energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx2:idx1]
} else { #Kinetic energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx1:idx2]
}
LL2 <- length(CoreLineY2)
if(LL1 > LL2){ #verify CoreLine1, CoreLine2 have same length
kk <- LL1-LL2 #if CoreLine1 is longer
CoreLineY2[LL2:(LL2+kk)] <- CoreLineY2[LL2] #add lacking values to CoreLine2
} else if (LL1 < LL2){ #if CoreLine2 longer
kk <- LL2-LL1
CoreLineY2 <- CoreLineY2[1:(LL2-kk)] #drop exceeding values
}
Nswps1 <- strsplit(SourceFile1[[SpectIndx1]]@Info[2], "Sweeps:") #split str in 2 parts: before and after "sweeps:"
Nsw1 <- as.numeric(substr(Nswps1[[1]][2], 1, 2)) #keep the first 2 characters of the second part = Nsweeps and transform in integer
Nswps2 <- strsplit(SourceFile1[[SpectIndx2]]@Info[2], "Sweeps:")
Nsw2 <- as.numeric(substr(Nswps2[[1]][2], 1, 2))
SourceFile1[[SpectIndx1]]@.Data[[1]] <- CoreLineX1
SourceFile1[[SpectIndx1]]@.Data[[2]] <- (CoreLineY1*Nsw1+CoreLineY2*Nsw2)/(Nsw1+Nsw2) #renormalize data
SourceFile1[[SpectIndx1]]@.Data[[3]] <- CoreLineSF1
Nsw <- as.character(Nsw1+Nsw2)
Nswps1 <- paste(Nswps1[[1]][1], "Sweeps: ",Nsw,substr(Nswps1[[1]][2], 3, nchar(Nswps1[[1]][2])), sep="") #compose the new second part of the string with correct number of sweeps
SourceFile1[[SpectIndx1]]@Info[2] <- Nswps1
plot(SourceFile1[[SpectIndx1]])
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(CoreLine2[2],"-", svalue(SourceFile22), " added to ", CoreLine1[2], "-", svalue(SourceFile11))
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}
}
}, container=MathFrame44)
layoutT2[5,1] <- MathFrame5 <- gframe("SELEC NORMALIZ ATION MODE", horizontal=FALSE, spacing=3, container=layoutT2)
NormButt <- gcombobox(c("Normalize to the main Peak", "Normalize to Selected Peak"), selected=-1, handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
if (length(SourceFile) == 0 || length(CoreLine1) == 0){
gmessage("Source XPSSample or Source Core-Line not defined!", title="WARNING", icon="warning")
return()
}
SourceFile <- get(SourceFile, envir=.GlobalEnv)
answ <- svalue(NormButt, index=TRUE)
if (answ == 1){
maxY <- max(SourceFile[[SpectIndx]]@.Data[[2]])
minY <- min(SourceFile[[SpectIndx]]@.Data[[2]])
} else if (answ == 2){
gmessage("Define the Reference Peak Edges", title="PEAK EDGES DEFINITION", icon="info")
pos <- locator(n=2, type="p", col="red", cex=1.5, lwd=2, pch=1)
LL <- length(SourceFile[[SpectIndx]]@.Data[[1]])
idx <- NULL
idx[1] <- findXIndex(SourceFile[[SpectIndx]]@.Data[[1]], pos$x[1])
idx[2] <- findXIndex(SourceFile[[SpectIndx]]@.Data[[1]], pos$x[2])
idx <- sort(idx, decreasing = FALSE)
maxY <- max(SourceFile[[SpectIndx]]@.Data[[2]][idx[1]:idx[2]])
minY <- min(SourceFile[[SpectIndx]]@.Data[[2]][idx[1]:idx[2]])
}
SourceFile[[SpectIndx]]@.Data[[2]] <- (SourceFile[[SpectIndx]]@.Data[[2]]-minY)/(maxY-minY)
if(length(SourceFile[[SpectIndx]]@RegionToFit) > 0){
SourceFile[[SpectIndx]]@RegionToFit$y <- (SourceFile[[SpectIndx]]@RegionToFit$y-minY)/(maxY-minY)
}
if(length(SourceFile[[SpectIndx]]@Baseline) > 0){
SourceFile[[SpectIndx]]@Baseline$y <- (SourceFile[[SpectIndx]]@Baseline$y-minY)/(maxY-minY)
}
LL <- length(SourceFile[[SpectIndx]]@Components)
if(LL > 0){
for(ii in 1:LL){
SourceFile[[SpectIndx]]@Components[[ii]]@ycoor <- (SourceFile[[SpectIndx]]@Components[[ii]]@ycoor-minY)/(maxY-minY)
}
SourceFile[[SpectIndx]]@Fit$y <- SourceFile[[SpectIndx]]@Fit$y/(maxY-minY)
}
SourceFile[[SpectIndx]]@Boundaries$y <- c(0, 1)
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- ""
msg <- paste(CoreLine1[2], " normalized", sep="")
cat("\n ==> ", msg)
svalue(NormButt, index=TRUE) <- -1
# svalue(infoWin) <- msg
}, container=MathFrame5)
layoutT2[6,1] <- MathFrame6 <- gframe("SUBTRACT THE BASELINE", horizontal=FALSE, spacing=3, container=layoutT2)
glabel(">>> WARNING: Data OUTSIDE the \n BaseLine Range will be lost!", container=MathFrame6)
SubtrBlButt <- gbutton("SUBTRACT", handler=function(h, ...){
# svalue(infoWin) <- ""
if (gconfirm(msg="ATTENTION: original data will be IRREVERSIBLY modified!" , title = "BASELINE SUBTRACTION", icon = "warning")) {
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0 && length(SourceFile[[SpectIndx]]@Baseline)>0) {
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]-SourceFile[[SpectIndx]]@Baseline[[2]]
}
SourceFile[[SpectIndx]]@.Data <- SourceFile[[SpectIndx]]@RegionToFit
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL>0) {
for (ii in 1:LL) {
SourceFile[[SpectIndx]]@Components[[ii]]@ycoor <- SourceFile[[SpectIndx]]@Components[[ii]]@ycoor - SourceFile[[SpectIndx]]@Baseline[[2]]
}
}
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]*0 #annullo la baseline
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("Baseline substracted")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}
}, container=MathFrame6)
layoutT2[5,2] <- MathFrame55 <- gframe("SUBTRACT CORELINE2 FROM CORELINE1", horizontal=FALSE, spacing=3, container=layoutT2)
SubtrSpectButt <- gbutton("SUBTRACT SPECTRA", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx1 <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- svalue(CoreLine22)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx2 <- as.integer(CoreLine2[1])
if (hasBaseline(SourceFile1[[SpectIndx1]]) || hasBaseline(SourceFile2[[SpectIndx2]]) ){
answ <- gmessage(msg="SUBTRACTION CAN BE DONE ONLY ON RAW DATA: PLEASE REMOVE ANALYSIS" , title = "WARNING!", icon = "warning")
} else {
txt=" ==> SUBTRACTION WILL BE PERFOMED IN THE COMMON ENERGY RANGE\nSAVE AND SAVE&EXIT WILL OVERWRITE SUBTRACTION TO THE ORIGINAL CORE LINE"
answ <- gconfirm(msg=txt , title = "WARNING!", icon = "warning")
if (answ) {
Range1 <- range(SourceFile1[[SpectIndx1]]@.Data[1])
Range2 <- range(SourceFile2[[SpectIndx2]]@.Data[1])
lim1 <- max(Range1[1], Range2[1]) #il piu' grande dei limiti inferiori
lim2 <- min(Range1[2], Range2[2]) #il piu' piccolo dei limiti superiori
idx1 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim2)
if (SourceFile1[[SpectIndx1]]@Flags[1]) { #Binding energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx2:idx1]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx2:idx1]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx2:idx1] #Analyzer Transf Funct.
} else { #Kinetic energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx1:idx2]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx1:idx2]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx1:idx2] #Analyzer Transf Funct.
}
LL1 <- length(CoreLineY1)
idx1 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim2)
if (SourceFile2[[SpectIndx2]]@Flags[1]) { #Binding energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx2:idx1]
} else { #Kinetic energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx1:idx2]
}
LL2 <- length(CoreLineY2)
if(LL1 > LL2){ #verify CoreLine1, CoreLine2 have same length
kk <- LL1-LL2 #if CoreLine1 is longer
CoreLineY2[LL2:(LL2+kk)] <- CoreLineY2[LL2] #add lacking values to CoreLine2
} else if (LL1 < LL2){ #if CoreLine2 longer
kk <- LL2-LL1
CoreLineY2 <- CoreLineY2[1:(LL2-kk)] #drop exceeding values
}
SourceFile1[[SpectIndx1]]@.Data[[1]] <- CoreLineX1
SourceFile1[[SpectIndx1]]@.Data[[3]] <- CoreLineSF1
Nswps1 <- strsplit(SourceFile1[[SpectIndx1]]@Info[2], "Sweeps:") #taglia la str in 2 parti: ql prima e ql dopo "Sweeps:"
Nsw1 <- as.numeric(substr(Nswps1[[1]][2], 1, 2)) #della seconda parte prendo i primi due caratteri che indicano Nswps e trasforno in intero
Nswps2 <- strsplit(SourceFile1[[SpectIndx2]]@Info[2], "Sweeps:")
Nsw2 <- as.numeric(substr(Nswps2[[1]][2], 1, 2))
if (Nsw1 >= Nsw2) {
SourceFile1[[SpectIndx1]]@.Data[[2]] <- CoreLineY1-CoreLineY2
Nsw1 <- as.character(Nsw1)
Nswps1 <- paste(Nswps1[[1]][1], "Sweeps: ",Nsw1,substr(Nswps1[[1]][2], 3, nchar(Nswps1[[1]][2])), sep="") #ricostruisco la secopnda parte della stinga
SourceFile1[[SpectIndx1]]@Info[2] <- Nswps1
plot(SourceFile1[[SpectIndx1]])
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(CoreLine2[2],"-", svalue(SourceFile22), " subtracted from ", CoreLine1[2], "-", svalue(SourceFile11))
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
} else {
answ <- gmessage(msg="Nsweeps CoreLine2 > Nsweeps CoreLine1: SUBTRACTION NOT ALLOWED" , title = "WARNING!", icon = "warning")
}
}
}
}, container=MathFrame55)
#---InfoWin
# InfoFrame <- gframe("PROCESSING INFO", horizontal=FALSE, spacing=3, container=Addgroup)
# infoWin <- glabel(text=" " , container=InfoFrame)
#---COMMON BUTTONS
ButtGroup1 <- ggroup(horizontal=TRUE, spacing=5, container=Addgroup)
SaveSpect <- gbutton(" SAVE ", handler=function(h, ...) { SaveSpectrum() }, container=ButtGroup1)
enabled(SaveSpect) <- FALSE # Saving data blocked: ctrls on Dest file needed
SaveNewSpect <- gbutton(" SAVE AS A NEW CORELINE ", handler=function(h, ...){
SaveNewSpectrum()
}, container=ButtGroup1)
enabled(SaveNewSpect) <- FALSE # Saving data blocked: ctrls on Dest file needed
SaveAndExit <- gbutton(" SAVE & EXIT ", handler=function(h, ...){
if (prefix=="D1." || length(CullData>0)){ #differentiation was performed
CullData <<- NULL
SaveNewSpectrum() #for spectral differentiation or culled data saving is forced in a new coreline
} else {
SaveSpectrum()
}
dispose(ProcessWin)
XPSSaveRetrieveBkp("save")
}, container=ButtGroup1)
enabled(SaveAndExit) <- FALSE # Saving data blocked: ctrls on Dest file needed
gbutton(" EXIT ", handler=function(h, ...) {
dispose(ProcessWin)
XPSSaveRetrieveBkp("save")
},container=ButtGroup1)
visible(ProcessWin) <- TRUE
svalue(NoteBK) <- 2
svalue(NoteBK) <- 1 #set the first page
ProcessWin$set_modal(TRUE)
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
R Package Documentation
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Defines functions XPSProcessCoreLine
Documented in XPSProcessCoreLine
#CoreLine processing: adding/deleting corelines or Baseline and Fits to exiting Corelines
#' @title XPSProcessCoreLine
#' @description XPSProcessCoreLine function adds a CoreLine (with fit if existing)
#' to an object of class XPSSample, or just a BaseLine and Fit to an existing CoreLine
#' (class XPSCoreLine) or remove a CoreLine from an object of class XPSSample
#' XPSProcessCoreLine may be used to perform some simple math operations on CoreLines
#' (class XPSCoreLine) like addition, subtraction, multiplication by a constant value
#' normalization, differentiation, combination of two CoreLines.
#' @examples
#' \dontrun{
#' XPSProcessCoreLine()
#' }
#' @export
#'
XPSProcessCoreLine <- function(){
#---
CtrlRepCL <- function(destIndx, SpectName, DestSpectList){ #CTRL for repeated CL: search for core-lines with same name
winCL <- gwindow("SELECT CORELINE", visible=FALSE)
size(winCL) <- c(100, 200)
groupCL <- ggroup(horizontal=FALSE, container=winCL)
DestFile <- svalue(DestFileName)
N.CL <- length(destIndx)
msg <- paste("Found", N.CL, SpectName, "spectra in", DestFile,"\nPlease select the coreline \nto add Baseline and Fit", sep=" ")
txt <- glabel(text=msg, container=groupCL)
font(txt) <- list(family="sans",size=12)
gseparator(horizontal=TRUE, container=groupCL)
selectCL <- gradio(DestSpectList[destIndx], selected=1, horizontal=TRUE, container=groupCL)
gbutton(" OK ", handler=function(h, ...){
CoreLine <- svalue(selectCL)
CoreLine <- unlist(strsplit(CoreLine, "\\.")) #drop "NUMBER." at beginning of coreLine name
RepCLidx <<- as.numeric(CoreLine[1])
# svalue(infoWin) <- ""
dispose(winCL)
}, container=groupCL)
visible(winCL) <- TRUE
winCL$set_modal(TRUE) #nothing can be done while running this macro
} #modal mode takes the control of the 'return' value which CANNOT be used to return variable values
RenumCL <- function(SourceFile){
CLnames <- names(SourceFile)
LL <- length(SourceFile)
for(ii in 1:LL){
SourceFile[[ii]]@Symbol <- paste(ii,".",CLnames[ii], sep="")
}
return(SourceFile)
}
updateObj <- function(SFpointer, CNTRpointer, CLpointer,...){
SelectedFName <- svalue(SFpointer)
SpectList <<- XPSSpectList(SelectedFName)
SourceFName <- get(SelectedFName,envir=.GlobalEnv) #load the source XPSSample file
delete(CNTRpointer,CLpointer)
CLpointer <- gcombobox(SpectList, selected=-1, handler=function(h, ...){
SourceCoreline <- svalue(CLpointer)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #slipt strin at character "."
indx <- as.integer(SourceCoreline[1])
plot(SourceFName[[indx]])
enabled(DestFileName) <- TRUE # disable selection of the destination file
}, editable=FALSE, container=CNTRpointer)
add(CNTRpointer,CLpointer)
plot(SourceFName)
enabled(CLpointer) <- TRUE #enable core line selection
return(CLpointer)
}
MakeBaseLine <- function(SourceFile, indx, DestFile, destIndx) {
BLinfo <- SourceFile[[indx]]@Baseline$type
BasLinType <- BLinfo[1]
splinePoints <- NULL
deg <- NULL
Wgt <- NULL
if (BasLinType == "shirley"){BasLinType <- "Shirley"} #different names for old/new RXPSG packages
if (BasLinType == "2p.shirley"){BasLinType <- "2P.Shirley"} #transform to new BaseLineNames.
if (BasLinType == "3p.shirley"){BasLinType <- "3P.Shirley"} #Exact Baseline Names required to generate the Baseline see XPSClass
if (BasLinType == "lp.shirley"){BasLinType <- "LP.Shirley"}
if (BasLinType == "2p.tougaard"){BasLinType <- "2P.Tougaard"}
if (BasLinType == "3p.tougaard"){BasLinType <- "3P.Tougaard"}
if (BasLinType == "4p.tougaard"){BasLinType <- "4P.Tougaard"}
if (BasLinType == "linear" ||
BasLinType == "Shirley" || BasLinType == "2P.Shirley" || BasLinType == "2P.Tougaard" || BasLinType == "3P.Tougaard") {
txt <- paste(BLinfo[1], " background found!\n ==> Set the Baseline Limits")
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "polynomial") {
deg <- as.numeric(BLinfo[2])
gmessage(msg="Polynomial backgound found!\n ==> Set the Baseline Limits", title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "spline") {
splinePoints <- list(x=NULL, y=NULL)
txt <- "Spline background found! \n ==> LEFT click to set spline points; RIGHT to exit"
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- c(1,1) # only to enter in the loop
while (length(pos) > 0) { #pos != NULL => mouse right button not pressed
pos <- locator(n=1, type="p", col=3, cex=1.5, lwd=2, pch=1)
if (length(pos) > 0) {
splinePoints$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)
}
}
# Now make BaseLine
decr <- FALSE #Kinetic energy set
if (DestFile[[destIndx]]@Flags[1] == TRUE) { decr <- TRUE }
idx <- order(splinePoints$x, decreasing=decr)
splinePoints$x <- splinePoints$x[idx] #splinePoints$x in ascending order
splinePoints$y <- splinePoints$y[idx] #following same order select the correspondent splinePoints$y
LL <- length(splinePoints$x)
DestFile[[destIndx]]@Boundaries$x <- c(splinePoints$x[1],splinePoints$x[LL]) #set the boundaries of the baseline
DestFile[[destIndx]]@Boundaries$y <- c(splinePoints$y[1],splinePoints$y[LL])
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
} else if (BasLinType == "3P.Shirley" || BasLinType == "LP.Shirley" || BasLinType == "4P.Tougaard") {
Wgt <- as.numeric(BLinfo[2])
txt <- paste(BLinfo[1], " background found!\n ==> Set the Baseline Limits")
gmessage(msg=txt, title="HELP INFO", icon="info")
plot(DestFile[[destIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2)
DestFile[[destIndx]]@Boundaries$x <- pos$x
DestFile[[destIndx]]@Boundaries$y <- pos$y
DestFile[[destIndx]] <- XPSsetRegionToFit(DestFile[[destIndx]])
DestFile[[destIndx]] <- XPSbaseline(DestFile[[destIndx]], BasLinType, deg, Wgt, splinePoints )
DestFile[[destIndx]]@RSF <- SourceFile[[indx]]@RSF
}
plot(DestFile[[destIndx]])
return(DestFile[[destIndx]])
}
#---
SaveSpectrum <- function(){
activeFName <- svalue(DestFileName)
assign(activeFName, DestFName, envir=.GlobalEnv) #save changes in the destinationfile
assign("activeFName", activeFName, envir=.GlobalEnv) #set the Active XPSSample == DestinationFile
assign("activeSpectName", activeSpectName,envir=.GlobalEnv) #Set the activeSpect == added coreline
assign("activeSpectIndx", activeSpectIndx,envir=.GlobalEnv) #Set the active Index == index of added coreline
plot(DestFName)
XPSSaveRetrieveBkp("save")
enabled(SaveSpect) <- FALSE #SaveSpectrum file disabled
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled
enabled(SaveAndExit) <- FALSE #Saving data blocked: ctrls on Dest file needed
}
SaveNewSpectrum <- function(){
activeFName <- svalue(SourceFile11) #name of the manipulated XPSSample (one of the math operations was performed)
LL <- length(activeFName)
if ( length(activeFName)>0 ){ #Math operations performed on SourceFile11
SourceFName <- DestFName
DestFName <- get(activeFName, envir=.GlobalEnv) #retrieve original source XPSSample which will be the destination file
SpectName <- activeSpectName
SpectIndx <- activeSpectIndx
Symbol <- paste(prefix,SpectName, sep="")
CoreLineList <- names(DestFName)
destIndx <- length(CoreLineList)+1
DestFName[[destIndx]] <- SourceFName[[SpectIndx]] #this is the manipulated core line
DestFName[[destIndx]]@Symbol <- Symbol
DestFName@names <- c(CoreLineList,Symbol)
assign(activeFName, DestFName, envir=.GlobalEnv) #Save the changes in a new coreline in the destination file
assign("activeFName", activeFName, envir=.GlobalEnv)
assign("activeSpectName", SpectName,envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx,envir=.GlobalEnv)
msg <- paste(" Coreline: ", Symbol, " saved in the XPS Sample ", DestFName@Filename, sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled if SourceFile OK
} else {
activeFName <- svalue(SourceFile1)
SourceFName <- DestFName
DestFName <- get(activeFName, envir=.GlobalEnv) #retrieve original source XPSSample which will be the destination file
SpectName <- activeSpectName
SpectIndx <- activeSpectIndx
CoreLineList <- names(DestFName)
destIndx <- length(CoreLineList)+1
DestFName[[destIndx]] <- SourceFName[[SpectIndx]] #this is the manipulated core line
DestFName[[destIndx]]@Symbol <- SpectName
DestFName@names <- c(CoreLineList,SpectName)
assign(activeFName, DestFName, envir=.GlobalEnv) #Save the changes in a new coreline in the destination file
assign("activeFName", activeFName, envir=.GlobalEnv)
assign("activeSpectName", SpectName,envir=.GlobalEnv)
assign("activeSpectIndx", SpectIndx,envir=.GlobalEnv)
msg <- paste(" Coreline: ", SpectName, " saved in the XPS Sample ", DestFName@Filename, sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
}
enabled(SaveSpect) <- FALSE #SaveSpectrum file disabled
enabled(SaveNewSpect) <- FALSE #Save Destination file disabled
enabled(SaveAndExit) <- FALSE #Saving data blocked: ctrls on Dest file needed
}
#----- variables -----
#---load list of file ID and correspondent FileNames
FNameList <- XPSFNameList()
DestFName <- NULL
RepCLidx <- NULL
activeSpectIndx <- NULL
activeSpectName <- NULL
SampID <- ""
SpectList <- ""
CullData <- NULL #rangeX of the region to cull
prefix <- ""
gmessage(msg=" Remember to save data after each operation \n otherwise you will loss the results", title="SAVE RESULTS", icon="warning")
#####----main---
ProcessWin <- gwindow("CORELINE PROCESSING", parent=c(50, 10), visible=FALSE)
Addgroup <- ggroup(horizontal=FALSE, container=ProcessWin)
NoteBK <- gnotebook(expand=TRUE, container = Addgroup)
#--- TAB1
T1group <- ggroup(label="CORELINE PROCESSING", horizontal=TRUE, spacing=5, container=NoteBK)
layout1T1 <- glayout(homogeneous=FALSE, spacing=3, container=T1group)
layout1T1[1,1] <- AddFrame1 <- gframe("SELECT THE SOURCE XPS-SAMPLE", spacing=3, container=layout1T1)
SourceFile1 <- gcombobox(FNameList, selected=-1, editable=FALSE, expand=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
SourceCoreline1 <<- updateObj(SourceFile1,AddFrame2,SourceCoreline1)
}, container = AddFrame1)
layout1T1[2,1] <- AddFrame2 <- gframe(text=" SELECT CORELINE TO PROCESS ", spacing=3, container=layout1T1)
SourceCoreline1 <- gcombobox(SpectList, selected=-1, editable=FALSE, spacing=5, handler=function(h,...) {
enabled(DestFileName) <- TRUE # selection destination file enabled
}, container=AddFrame2)
enabled(SourceCoreline1) <- FALSE #CoreLine selection blocked
layout1T1[3,1] <- AddFrame3 <- gframe(text="SELECT THE DESTINATION FILE NAME", spacing=3, container=layout1T1)
DestFileName <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...) {
SourceFile <- svalue(SourceFile1)
DestFile <- svalue(DestFileName)
# svalue(infoWin) <- ""
SpectName <- svalue(SourceCoreline1)
SpectName <- unlist(strsplit(SpectName, "\\.")) #split the string at character "."
SpectIndx <- as.integer(SpectName[1])
SpectName <- SpectName[2]
if (SourceFile == DestFile) {
gmessage(msg="Warning: Destination File Name == Source File Name" , title = "WARNING: BAD DESTINATION FILE NAME!", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFile <- get(DestFile, envir=.GlobalEnv)
destIndx <- grep(SpectName, names(DestFile))
if (length(destIndx)==0){
txt <- paste("Warning: no ",SpectName, " core line present in the destination file. Continue?")
answ <- gconfirm(msg=txt , title = "WARNING: NO CORELINE PRESENT!", icon = "warning")
if (answ == FALSE) {
return()
}
}
LL <- length(destIndx)
for(ii in 1:LL){
if (DestFile[[destIndx[ii] ]]@Flags[1] != SourceFile[[SpectIndx]]@Flags[1]) { #acquisitions made using different energy scale
gmessage(msg="XPS-Samples have different Energy units. Operation stopped!" , title = "WARNING: BAD DESTINATION FILE!", icon = "warning")
return()
}
}
plot(DestFile)
enabled(SaveSpect) <- TRUE # enable saving data if Dest File OK
enabled(SaveAndExit) <- TRUE
}
}, container = AddFrame3)
enabled(DestFileName) <- FALSE # selection of destination file blocked
layout1T1[4,1] <- AddFrame4 <- gframe(text=" ADD WHOLE CORELINE ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton1 <- gbutton("Add New Coreline and Fit", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
# svalue(infoWin) <- ""
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage(mag="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No destination file selected
gmessage(mag="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #split string at character "."
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- length(DestFName)+1
DestFName[[destIndx]] <<- SourceFile[[SpectIndx]]
DestFName@names <<- c(CoreLineList,SourceFile[[SpectIndx]]@Symbol)
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Coreline: ", SourceCoreline[2], "added to XPS Sample. PLEASE SAVE DATA!", DestFName@Filename)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame4)
layout1T1[6,1] <- AddFrame5 <- gframe(text=" ADD BASELINE AND FIT ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton2 <- gbutton("Add Baseline and Fit to Original Coreline", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
# svalue(infoWin) <- ""
if (length(SourceCoreline)==0) { #no coreline selected
gmessage(msg="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #no destination file selected
gmessage(msg="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The index of the coreline in the destinationFile can be different from that od sourceFile => grep()
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
if (length(destIndx) == 0) {
text <- paste(SpectName, "not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION", icon = "warning")
} else {
if (length(SourceFile[[SpectIndx]]@RegionToFit) == 0){
text <- paste("ATTENTION: NO fit found for ",SpectName, " of the Source XPS-Sample. Operation stopped!", sep="")
gmessage(msg=text , title = "BAD SOURCE CORELINE SELECTION", icon = "warning")
return()
}
if (length(DestFName[[destIndx]]@Components) > 0) { #a fit is present for the selected coreline
text <- paste("ATTENTION: constraints of ",SpectName, " fit will be kept! Continue?", sep="")
answ <- gconfirm(msg=text , title = "WARNING!", icon = "warning")
if (answ) {
DestFName[[destIndx]] <<- XPSremove(DestFName[[destIndx]],"all")
} else {
return()
}
}
DestFName[[destIndx]] <<- MakeBaseLine(SourceFile, SpectIndx, DestFName, destIndx)
DestFName[[destIndx]]@Components <<- SourceFile[[SpectIndx]]@Components
RescaleH <- max(DestFName[[destIndx]]@RegionToFit$y)/max(SourceFile[[SpectIndx]]@RegionToFit$y) #scale factor between source and destination corelines
LL=length(DestFName[[destIndx]]@Components)
tmp <- NULL
if (LL > 0) {
for(ii in 1:LL) {
varmu <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="mu")
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="mu", value=varmu)
varh <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="h")
DestFName[[destIndx]]@Components[[ii]] <<- Ycomponent(DestFName[[destIndx]]@Components[[ii]], x=DestFName[[destIndx]]@RegionToFit$x, y=DestFName[[destIndx]]@Baseline$y/RescaleH) #Rescale Baseline Y values
DestFName[[destIndx]]@Components[[ii]]@ycoor <<- RescaleH*DestFName[[destIndx]]@Components[[ii]]@ycoor #Rescale Values of Y Components respect DestFName Y data
varh$start <- max(DestFName[[destIndx]]@Components[[ii]]@ycoor-DestFName[[destIndx]]@Baseline$y) #Substract Baseline
varh$min <- 0
varh$max <- 5*varh$start
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="h", value=varh)
}
tmp <- sapply(DestFName[[destIndx]]@Components, function(z) matrix(data=z@ycoor))
DestFName[[destIndx]]@Fit$y <<- (colSums(t(tmp)) - length(DestFName[[destIndx]]@Components)*(DestFName[[destIndx]]@Baseline$y))
} #transpose of tmp
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Fit data added to ", SpectName, "PLASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <<- msg
}
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame5)
layout1T1[7,1] <- AddFrame6 <- gframe(text=" ADD FIT ONLY ", horizontal=FALSE, spacing=3, container=layout1T1)
Addbutton2 <- gbutton("Add Fit", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
svalue(warning) <- ""
if (length(SourceCoreline)==0) { #No coreline has been selected in source File
gmessage(msg="Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No Destination File has been selected
gmessage(msg="Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
DestFName <<- get(DestFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #split string at char "."
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The selected CoreLine name could be in any posiiton in the Destination XPSSample => source Samp Index could be different from Dest Samp index
if (length(destIndx) == 0) {
text <- paste(SpectName, "not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION STOPPED", icon = "warning")
} else {
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
if (length(DestFName[[destIndx]]@Components) > 0) { #Core line already fitted
text <- paste("ATTENTION: fit present on ",SpectName, " New fit constaints will be kept! Continue?")
answ <- gconfirm(msg=text , title = "WARNING!", icon = "warning")
if (answ) {
DestFName[[destIndx]] <<- XPSremove(DestFName[[destIndx]],"all")
} else {
return()
}
}
if (length(DestFName[[destIndx]]@Baseline) == 0) { #baseline not present
text <- paste("Baseline not present in the Destination File: Fit copy stopped")
gmessage(msg=text , title = "FIT COPY TO DESTINATION STOPPED", icon = "warning")
return()
}
DestFName[[destIndx]] <<- XPSsetRSF(DestFName[[destIndx]])
DestFName[[destIndx]]@Components <<- SourceFile[[SpectIndx]]@Components
RescaleH <- max(DestFName[[destIndx]]@RegionToFit$y)/max(SourceFile[[SpectIndx]]@RegionToFit$y) #fattore di scala tra source coreline e destination coreline
LL=length(DestFName[[destIndx]]@Components)
for(ii in 1:LL) {
varmu <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="mu")
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="mu", value=varmu)
varh <- getParam(DestFName[[destIndx]]@Components[[ii]],variable="h")
DestFName[[destIndx]]@Components[[ii]] <<- Ycomponent(DestFName[[destIndx]]@Components[[ii]], x=DestFName[[destIndx]]@RegionToFit$x, y=DestFName[[destIndx]]@Baseline$y/RescaleH) #calcola la Y ed aggiunge la baseline
DestFName[[destIndx]]@Components[[ii]]@ycoor <<- RescaleH*DestFName[[destIndx]]@Components[[ii]]@ycoor
varh$start <- max(DestFName[[destIndx]]@Components[[ii]]@ycoor-DestFName[[destIndx]]@Baseline$y)
varh$min <- 0
varh$max <- 5*varh$start
DestFName[[destIndx]]@Components[[ii]] <<- setParam(DestFName[[destIndx]]@Components[[ii]], parameter=NULL, variable="h", value=varh)
}
tmp <- sapply(DestFName[[destIndx]]@Components, function(z) matrix(data=z@ycoor))
DestFName[[destIndx]]@Fit$y <<- (colSums(t(tmp)) - length(DestFName[[destIndx]]@Components)*(DestFName[[destIndx]]@Baseline$y))
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Fit data added to ", SpectName, "PLASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}
}, container=AddFrame6)
# layout1T1[8,1] <- warn2 <- glabel(text=" " , container=layout1T1)
layout1T1[9,1] <- AddFrame7 <- gframe(text="OVERWRITE A CORELINE ", horizontal=FALSE, spacing=3, container=layout1T1)
overbutton <- gbutton("Overwrite", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else if (length(DestFile)==0) { #No dest File selected
gmessage("Please select the destination file please!" , title = "DESTINATION FILE SELECTION", icon = "warning")
} else {
SourceFile <- get(SourceFile, envir=.GlobalEnv)
DestFName <<- get(DestFile, envir=.GlobalEnv)
DestSpectList <- XPSSpectList(DestFile)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectName <- SourceCoreline[2]
SpectIndx <- as.integer(SourceCoreline[1])
CoreLineList <- names(DestFName)
destIndx <- grep(SpectName, CoreLineList) #The selected CoreLine name could be in any posiiton in the Destination XPSSample => source Samp Index could be different from Dest Samp index
if (length(destIndx) > 1){ #The same coreline can be present more than one time
CtrlRepCL(destIndx, SpectName, DestSpectList)
destIndx <- RepCLidx
}
DestFName[[destIndx]] <<- SourceFile[[SpectIndx]]
plot(DestFName[[destIndx]])
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste("Coreline ", SpectName, "overwritten. PLASE SAVE DATA!")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame7)
# layout1T1[10,1] <- warn3 <- glabel(text=" " , container=layout1T1)
layout1T1[11,1] <- AddFrame8 <- gframe(text=" REMOVE/DUPLICATE CORELINE ", horizontal=TRUE, spacing=3, container=layout1T1)
delbutton <- gbutton(" Remove ", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
SpectList <<- XPSSpectList(SourceFile)
if (length(SourceCoreline)==0) { #No coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
}
if (length(SourceFile)==0) { #No Source File selected
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
} else {
enabled(SaveSpect) <- TRUE # enabling the Save options if the destination file name is OK
enabled(SaveAndExit) <- TRUE
svalue(DestFileName) <<- SourceFile
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
plot(SourceFile[[SpectIndx]])
text <- paste("ATTENTION: are you sure to delete the",svalue(SourceCoreline1), "core line ?", sep="")
answ <- gconfirm(msg=text, title="WARNING", icon="warning")
if (answ) {
SourceFile[[SpectIndx]] <- NULL #this eliminates the coreline
# SourceFile <- RenumCL(SourceFile)
DestFName <<- SourceFile #move updated XPSSample in the destinatin file for saving
activeSpectIndx <<- 1
activeSpectName <<- names(SourceFile)[1]
msg <- paste("Coreline ", SpectName, "deleted. PLEASE SAVE DATA!")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(SourceFile)
} else {
return() #do nothing
}
SpectList <<- names(SourceFile) #update the SpectrumList
idx <- seq(1:length(SpectList)) #cannot use XPSSpectList because loads the SourceFile from the .GlobalEnv
SpectList <<- paste(idx, SpectList, sep=".")
delete(AddFrame2,SourceCoreline1)
SourceCoreline1 <<- gcombobox(SpectList, selected=-1, handler=function(h, ...){ #update the selection of corelines
SourceCoreline <- svalue(SourceCoreline1)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
plot(SourceFile[[SpectIndx]])
enabled(DestFileName) <- TRUE #enable selection of the destination file
}, editable=FALSE, container=AddFrame2)
add(AddFrame2,SourceCoreline1)
enabled(SaveSpect) <- TRUE # Enable Save Spectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame8)
duplibutton <- gbutton(" Duplicate ", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
if (length(SourceCoreline)==0) { #No Coreline selected
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
}
if (length(DestFile)==0) { #Destination file not selected
DestFile <- SourceFile
}
if (SourceFile != DestFile) {#Source different from Destination file
DestFile <- SourceFile
}
if (length(SourceFile)==0) { #Source File not selected
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
} else {
enabled(SaveSpect) <- TRUE #Save Destination file enabled if SourceFile OK
enabled(SaveAndExit) <- TRUE
svalue(DestFileName) <<- SourceFile
DestFName <<- get(SourceFile, envir=.GlobalEnv)
#--- eliminates the initial N. and reconstruct CLname also
# in presence of compex names as 10.D.2.ST.VB
tmp <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(tmp[1])
LL1 <- nchar(tmp[1])+2 # +2: substr(x,start,stop) start includes the character at 'start'
LL2 <- nchar(SourceCoreline)
SpectName <- substr(SourceCoreline, start=LL1, stop=LL2) #In case of XPSCLname="4.D1.C1s" SpectName must be "D1.C1s"
CoreLineList <- names(DestFName)
destIndx <- length(DestFName)+1
DestFName[[destIndx]] <<- DestFName[[SpectIndx]]
DestFName[[destIndx]]@Symbol <<- SpectName
DestFName@names <<- c(CoreLineList,SpectName)
activeSpectIndx <<- destIndx
activeSpectName <<- SpectName
msg <- paste(" Coreline: ", SpectName, "added to XPS Sample", DestFName@Filename, ". PLEASE SAVE DATA!", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
plot(DestFName)
enabled(SaveSpect) <- TRUE #Enable SaveSpectrum
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame8)
#---
layout2T1 <- glayout(homogeneous=FALSE, spacing=3, container=T1group)
layout2T1[1,1] <- AddFrame9 <- gframe(text=" PICK UP DATA ", horizontal=FALSE, spacing=3, container=layout2T1)
posgroup <- ggroup(horizontal=FALSE, container=AddFrame9)
CullFrom <- gedit(initial.msg ="From?", handler=function(h, ...){
CullData[1] <<- as.numeric(svalue(CullFrom))
}, container=posgroup)
CullTo <- gedit(initial.msg ="To?", handler=function(h, ...){
CullData[2] <<- as.numeric(svalue(CullTo))
}, container=posgroup)
gbutton("MOUSE", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
DestFile <- svalue(DestFileName)
DestFile <- SourceFile
svalue(CullFrom) <<- ""
svalue(CullTo) <<- ""
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
svalue(CullFrom) <- NULL
svalue(CullTo) <- NULL
CullData <- NULL
if (length(SourceFile)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
return()
}
if (length(SourceCoreline)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
return()
} else {
svalue(DestFileName) <<- SourceFile
DestFName <<- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
if (length(DestFName[[SpectIndx]]@RegionToFit)>0) { #non e' stata selezionata alcuna coreline
gmessage("Baseline or Fit present. Reset analysis before culling data!" , title = " RESET ANALYSIS ", icon = "warning")
return()
}
plot(DestFName[[SpectIndx]])
pos <- locator(n=2, type="p", col="red", lwd=2, pch=3)
CullData[1] <<- pos$x[1]
CullData[2] <<- pos$x[2]
}
}, container=posgroup)
cullgroup <- ggroup(horizontal=TRUE, container=AddFrame9)
cullButton <- gbutton("Select Data", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
svalue(DestFileName) <<- SourceFile
DestFile <- SourceFile
if (length(SourceFile)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the Source File please!" , title = "SOURCE FILE SELECTION", icon = "warning")
return()
}
if (length(SourceCoreline)==0) { #non e' stata selezionata alcuna coreline
gmessage("Please select the source coreline please!" , title = "SOURCE CORELINE SELECTION", icon = "warning")
} else {
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
DestFName <<- get(SourceFile, envir=.GlobalEnv)
if (length(DestFName[[SpectIndx]]@RegionToFit)>0) { #non e' stata selezionata alcuna coreline
gmessage("Baseline or Fit present. Reset analysis before culling data!" , title = " RESET ANALYSIS ", icon = "warning")
return()
}
if (is.null(CullData[1]) || is.null(CullData[2])) {
gmessage("From/To points NOT defined!" , title = " DEFINE FROM/TO ", icon = "warning")
return()
}
from <- findXIndex(DestFName[[SpectIndx]]@.Data[[1]], CullData[1])
to <- findXIndex(DestFName[[SpectIndx]]@.Data[[1]], CullData[2])
if (from > to) {
tmp <- from
from <- to
to <- tmp
}
DestFName[[SpectIndx]]@.Data[[1]] <<- DestFName[[SpectIndx]]@.Data[[1]][from:to]
DestFName[[SpectIndx]]@.Data[[2]] <<- DestFName[[SpectIndx]]@.Data[[2]][from:to]
DestFName[[SpectIndx]]@.Data[[3]] <<- DestFName[[SpectIndx]]@.Data[[3]][from:to]
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
plot(DestFName[[SpectIndx]])
msg <- "Please SAVE Selected Data"
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
}
}, container=AddFrame9)
resetButton <- gbutton("RESET", handler=function(h, ...){
SourceFile <- svalue(SourceFile1)
SourceCoreline <- svalue(SourceCoreline1)
svalue(DestFileName) <<- SourceFile
svalue(CullFrom) <<- ""
svalue(CullTo) <<- ""
DestFName <<- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\."))
SpectIndx <- as.integer(SourceCoreline[1])
plot(DestFName[[SpectIndx]])
}, container=AddFrame9)
###---TAB2
T2group <- ggroup(label="CORELINE MATH", horizontal=FALSE, spacing=3, container=NoteBK)
layoutT2 <- glayout(homogeneous=FALSE, spacing=3, container=T2group)
layoutT2[1,1] <- MathFrame1 <- gframe(text="SELECT XPS-SAMPLE 1", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup1 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame1)
SourceFile11 <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
svalue(DestFileName) <- svalue(SourceFile11)
CoreLine11 <<- updateObj(SourceFile11,MathGroup2,CoreLine11)
addHandlerChanged(CoreLine11, handler=function(h,...) {
SourceFile <- svalue(SourceFile11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
Coreline <- svalue(CoreLine11)
Coreline <- unlist(strsplit(Coreline, "\\.")) #Split string at point
SpectIndx <- as.integer(Coreline[1])
Range <- range(SourceFile[[SpectIndx]]@.Data[1])
Range <- round(Range, 1)
svalue(CLRange11) <<- paste("Range", " ", Coreline[2], " X: ", Range[1], ", ", Range[2], sep="")
enabled(DestFileName) <- TRUE # Enable the choice of the destination file
})
}, container = MathGroup1)
layoutT2[1,2] <- MathFrame11 <- gframe("SELECT XPS-SAMPLE 2", horizontal = FALSE, spacing=3,container=layoutT2)
MathGroup11 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame11)
SourceFile22 <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
# svalue(infoWin) <- ""
if (length(svalue(CoreLine11))==0) {
gmessage(msg="Please select the CORELINE1 first", title = "WARNING: CORELINE1 NOT DEFINED ", icon = "warning")
svalue(SourceFile22) <- NULL
} else {
CoreLine22 <<- updateObj(SourceFile22,MathGroup22,CoreLine22)
addHandlerChanged(CoreLine22, handler=function(h,...) {
SourceFile <- svalue(SourceFile22)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
Coreline <- svalue(CoreLine22)
Coreline <- unlist(strsplit(Coreline, "\\."))
SpectIndx <- as.integer(Coreline[1])
Range <- range(SourceFile[[SpectIndx]]@.Data[1])
Range <- round(Range, 1)
svalue(CLRange22) <<- paste("Range", " ", Coreline[2], " X: ", Range[1], ", ", Range[2], sep="")
})
}
}, container = MathGroup11)
layoutT2[2,1] <- MathFrame2 <- gframe(text="SELECT CORELINE 1", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup2 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame2)
CoreLine11 <- gcombobox(SpectList, selected=-1, editable=FALSE, container=MathGroup2)
CLRange11 <- glabel(text="Range CoreLine1: ", container=MathFrame2)
enabled(CoreLine11) <- FALSE
layoutT2[2,2] <- MathFrame22 <- gframe(text="SELECT CORELINE 2", horizontal = FALSE, spacing=3, container=layoutT2)
MathGroup22 <- ggroup(horizontal=FALSE, spacing=3, container=MathFrame22)
CoreLine22 <- gcombobox(SpectList, selected=-1, editable=FALSE, container=MathGroup22)
CLRange22 <- glabel(text="Range CoreLine2: ", container=MathFrame22)
enabled(CoreLine22) <- FALSE
layoutT2[3,1] <- MathGroup3 <- ggroup(horizontal=FALSE, container=layoutT2)
MathFrame3 <- gframe("ADD A CONSTANT VALUE TO CORELINE1", horizontal=TRUE,spacing=3,container=MathGroup3)
AddValue <- gedit(selected=-1, editable=TRUE, handler=function(h, ...){
# svalue(infoWin) <- ""
value <- as.numeric(svalue(AddValue))
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceCoreline <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
SourceFile[[SpectIndx]]@.Data[[2]] <- SourceFile[[SpectIndx]]@.Data[[2]]+value
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0)
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]+value
if (length(SourceFile[[SpectIndx]]@Baseline)>0)
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]+value
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL>0) {
for (jj in c(1:LL)) {
SourceFile[[SpectIndx]]@Components[[jj]]@ycoor <- SourceFile[[SpectIndx]]@Components[[jj]]@ycoor+value
}
}
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
prefix <<- "M."
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("Constant ",value, " added to CoreLine ", SpectName)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame3)
MathFrame33 <- gframe("MULTIPLY CORELINE1 BY A CONSTANT", horizontal=TRUE, spacing=3, container=MathGroup3)
MultValue <- gedit(selected=-1, editable=TRUE, handler=function(h, ...){
# svalue(infoWin) <- ""
value <- as.numeric(svalue(MultValue))
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceCoreline <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
SourceCoreline <- unlist(strsplit(SourceCoreline, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(SourceCoreline[1])
SpectName <- SourceCoreline[2]
SourceFile[[SpectIndx]]@.Data[[2]] <- SourceFile[[SpectIndx]]@.Data[[2]]*value
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0)
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]*value
if (length(SourceFile[[SpectIndx]]@Baseline)>0)
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]*value
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL > 0) {
for (jj in c(1:LL)) {
SourceFile[[SpectIndx]]@Components[[jj]]@ycoor <- SourceFile[[SpectIndx]]@Components[[jj]]@ycoor*value
}
SourceFile[[SpectIndx]]@Fit$y <- SourceFile[[SpectIndx]]@Fit$y*value
}
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("XX CoreLine ", SpectName, " multiplied by ", value)
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame33)
layoutT2[3,2] <- MathFrame5 <- gframe(" COMBINE CORELINE1 and CORELINE2 \n Coreline2 added to Coreline1", horizontal=FALSE, spacing=3, container=layoutT2)
CombineButton <- gbutton("COMBINE", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx1 <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
CoreLine2 <- svalue(CoreLine22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx2 <- as.integer(CoreLine2[1])
if (length(SourceFile1[[SpectIndx1]]@RegionToFit)>0 || length(SourceFile2[[SpectIndx2]]@RegionToFit)){
txt <- paste("Combine CoreLines allowed ONLY on RAW data! RESET ANALYSIS")
gmessage(msg=txt, title = "WARNING: FIT PRESENT ", icon = "warning")
} else {
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
if (SourceFile2[[SpectIndx2]]@Flags[1] == TRUE){
SourceFile2[[SpectIndx2]]@.Data[[1]] <- rev(SourceFile2[[SpectIndx2]]@.Data[[1]])
SourceFile2[[SpectIndx2]]@.Data[[2]] <- rev(SourceFile2[[SpectIndx2]]@.Data[[2]])
}
Rng1 <- range(SourceFile1[[SpectIndx1]]@.Data[[1]])
Rng2 <- range(SourceFile2[[SpectIndx2]]@.Data[[1]])
MaxX1 <- max(Rng1)
MaxX2 <- max(Rng2)
MinX1 <- min(Rng1)
MinX2 <- min(Rng2)
LL1 <- length(SourceFile1[[SpectIndx1]]@.Data[[1]])
LL2 <- length(SourceFile2[[SpectIndx2]]@.Data[[1]])
if ( MaxX1 > MaxX2) {
if (MaxX2 < MinX1) {
gmessage("XPS-SAMPLE1 and XPS-SAMPLE2 are separated! \n
XPS-SAMPLE1 must overlap XPS-SAMPLE2 at least in ONE point", icon="warning")
return()
} else {
Idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], MinX1)
DataToCombineX <- SourceFile2[[SpectIndx2]]@.Data[[1]][1:Idx2]
DataToCombineY <- SourceFile2[[SpectIndx2]]@.Data[[2]][1:Idx2]
yy1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][1] #average intensity of second block of data in the combination point
yy2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2] #average intensity of first block of data in the combination point
Dy <- yy2-yy1 #difference of the intensities between block1, block2 od data in the combination point
SourceFile1[[SpectIndx1]]@.Data[[1]] <- c(DataToCombineX, SourceFile1[[SpectIndx1]]@.Data[[1]])
SourceFile1[[SpectIndx1]]@.Data[[2]] <- c(DataToCombineY-Dy, SourceFile1[[SpectIndx1]]@.Data[[2]])
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){ #Restore original order
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
plot(SourceFile1[[SpectIndx1]])
svalue(DestFileName) <- svalue(SourceFile11)
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
}
} else if ( MaxX2 > MaxX1) {
if (MaxX1 < MinX2) {
gmessage("XPS-SAMPLE1 and XPS-SAMPLE2 are separated! \n
XPS-SAMPLE1 must overlap XPS-SAMPLE2 at least in ONE point", icon="warning")
return()
} else {
MaxX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][LL1]
Idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], MaxX1)+1 #+1 needed to not start with the data next to MaxX1
DataToCombineX <- SourceFile2[[SpectIndx2]]@.Data[[1]][Idx2:LL2]
DataToCombineY <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2:LL2]
yy1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][LL1] #average intensity of first block of data in the combination point
yy2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][Idx2] #average intensity of second block of data in the combination point
Dy <- yy2-yy1 #difference of the intensities between block1, block2 od data in the combination point
SourceFile1[[SpectIndx1]]@.Data[[1]] <- c(SourceFile1[[SpectIndx1]]@.Data[[1]], DataToCombineX)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- c(SourceFile1[[SpectIndx1]]@.Data[[2]], DataToCombineY-Dy)
if (SourceFile1[[SpectIndx1]]@Flags[1] == TRUE){ #Restore original order
SourceFile1[[SpectIndx1]]@.Data[[1]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[1]])#scale in ascending order (KE)
SourceFile1[[SpectIndx1]]@.Data[[2]] <- rev(SourceFile1[[SpectIndx1]]@.Data[[2]])#order also Y data
}
plot(SourceFile1[[SpectIndx1]])
svalue(DestFileName) <- svalue(SourceFile11)
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
}
}
}
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(svalue(CoreLine11), "-", svalue(SourceFile11)," combined with ", svalue(CoreLine22), "-", svalue(SourceFile22), " Combined")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame5)
layoutT2[4,1] <- MathFrame4 <- gframe("DIFFERENTIATE", horizontal=FALSE, spacing=3, container=layoutT2)
DiffButt <- gbutton("DIFFERENTIATE CORELINE1", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
LL <- length(SourceFile[[SpectIndx]]@.Data[[1]])
SourceFile[[SpectIndx]]@RegionToFit <- list(x=NULL, y=NULL)
SourceFile[[SpectIndx]]@Baseline <- list(x=NULL, y=NULL, type=NULL)
SourceFile[[SpectIndx]]@Baseline$x <- SourceFile[[SpectIndx]]@RegionToFit$x <- SourceFile[[SpectIndx]]@.Data[[1]]
SourceFile[[SpectIndx]]@Baseline$y <- rep(0, LL) #creo una baseline fittizia nulla
SourceFile[[SpectIndx]]@Baseline$type <- "linear"
k <- max(SourceFile[[SpectIndx]]@.Data[[2]])-min(SourceFile[[SpectIndx]]@.Data[[2]])
for (ii in 2:LL){
SourceFile[[SpectIndx]]@RegionToFit$y[ii] <- SourceFile[[SpectIndx]]@.Data[[2]][ii]-SourceFile[[SpectIndx]]@.Data[[2]][ii-1]
}
SourceFile[[SpectIndx]]@RegionToFit$y[1] <- SourceFile[[SpectIndx]]@RegionToFit$y[2]
Dmin <- min(SourceFile[[SpectIndx]]@RegionToFit$y)
Dmax <- max(SourceFile[[SpectIndx]]@RegionToFit$y)
SourceFile[[SpectIndx]]@RegionToFit$y <- k*(SourceFile[[SpectIndx]]@RegionToFit$y-Dmin)/(Dmax-Dmin)
matplot(x=matrix(c(SourceFile[[SpectIndx]]@.Data[[1]], SourceFile[[SpectIndx]]@RegionToFit$x), nrow=LL, ncol=2),
y=matrix(c(SourceFile[[SpectIndx]]@.Data[[2]], SourceFile[[SpectIndx]]@RegionToFit$y), nrow=LL, ncol=2),
type="l", lty=c(1,1), col=c("black","blue"),
xlab=SourceFile[[SpectIndx]]@units[1], ylab=SourceFile[[SpectIndx]]@units[2])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "D1."
msg <- paste(CoreLine1[2], " differentiated", sep="")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}, container=MathFrame4)
layoutT2[4,2] <- MathFrame44 <- gframe("ADD CORELINE2 TO CORELINE1", horizontal=FALSE, spacing=3, container=layoutT2)
AddButt <- gbutton("ADD SPECTRA", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #split string at point
SpectIndx1 <- as.integer(CoreLine1[1]) #keep first part
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- svalue(CoreLine22)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\."))
SpectIndx2 <- as.integer(CoreLine2[1])
if (hasBaseline(SourceFile1[[SpectIndx1]]) || hasBaseline(SourceFile2[[SpectIndx2]]) ){
answ <- gmessage(msg="ADDITION CAN BE DONE ONLY ON RAW DATA: PLEASE REMOVE ANALYSIS" , title = "WARNING!", icon = "warning")
} else {
txt=" ==> ADDITION WILL BE PERFOMED IN THE COMMON ENERGY RANGE\nSAVE AND SAVE&EXIT WILL OVERWRITE THE RESULT TO CORE LINE 1"
answ <- gconfirm(msg=txt , title = "WARNING!", icon = "warning")
if (answ) {
Range1 <- range(SourceFile1[[SpectIndx1]]@.Data[1])
Range2 <- range(SourceFile2[[SpectIndx2]]@.Data[1])
lim1 <- max(Range1[1], Range2[1]) #the greater of the lower limits
lim2 <- min(Range1[2], Range2[2]) #the smaller of the higher limits
idx1 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim2)
if (SourceFile1[[SpectIndx1]]@Flags[1]) { #Binding energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx2:idx1]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx2:idx1]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx2:idx1] #Analyzer Transf Funct.
} else { #Kinetic energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx1:idx2]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx1:idx2]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx1:idx2] #Analyzer Transf Funct.
}
LL1 <- length(CoreLineY1)
idx1 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim2)
if (SourceFile2[[SpectIndx2]]@Flags[1]) { #Binding energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx2:idx1]
} else { #Kinetic energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx1:idx2]
}
LL2 <- length(CoreLineY2)
if(LL1 > LL2){ #verify CoreLine1, CoreLine2 have same length
kk <- LL1-LL2 #if CoreLine1 is longer
CoreLineY2[LL2:(LL2+kk)] <- CoreLineY2[LL2] #add lacking values to CoreLine2
} else if (LL1 < LL2){ #if CoreLine2 longer
kk <- LL2-LL1
CoreLineY2 <- CoreLineY2[1:(LL2-kk)] #drop exceeding values
}
Nswps1 <- strsplit(SourceFile1[[SpectIndx1]]@Info[2], "Sweeps:") #split str in 2 parts: before and after "sweeps:"
Nsw1 <- as.numeric(substr(Nswps1[[1]][2], 1, 2)) #keep the first 2 characters of the second part = Nsweeps and transform in integer
Nswps2 <- strsplit(SourceFile1[[SpectIndx2]]@Info[2], "Sweeps:")
Nsw2 <- as.numeric(substr(Nswps2[[1]][2], 1, 2))
SourceFile1[[SpectIndx1]]@.Data[[1]] <- CoreLineX1
SourceFile1[[SpectIndx1]]@.Data[[2]] <- (CoreLineY1*Nsw1+CoreLineY2*Nsw2)/(Nsw1+Nsw2) #renormalize data
SourceFile1[[SpectIndx1]]@.Data[[3]] <- CoreLineSF1
Nsw <- as.character(Nsw1+Nsw2)
Nswps1 <- paste(Nswps1[[1]][1], "Sweeps: ",Nsw,substr(Nswps1[[1]][2], 3, nchar(Nswps1[[1]][2])), sep="") #compose the new second part of the string with correct number of sweeps
SourceFile1[[SpectIndx1]]@Info[2] <- Nswps1
plot(SourceFile1[[SpectIndx1]])
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(CoreLine2[2],"-", svalue(SourceFile22), " added to ", CoreLine1[2], "-", svalue(SourceFile11))
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}
}
}, container=MathFrame44)
layoutT2[5,1] <- MathFrame5 <- gframe("SELEC NORMALIZ ATION MODE", horizontal=FALSE, spacing=3, container=layoutT2)
NormButt <- gcombobox(c("Normalize to the main Peak", "Normalize to Selected Peak"), selected=-1, handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
if (length(SourceFile) == 0 || length(CoreLine1) == 0){
gmessage("Source XPSSample or Source Core-Line not defined!", title="WARNING", icon="warning")
return()
}
SourceFile <- get(SourceFile, envir=.GlobalEnv)
answ <- svalue(NormButt, index=TRUE)
if (answ == 1){
maxY <- max(SourceFile[[SpectIndx]]@.Data[[2]])
minY <- min(SourceFile[[SpectIndx]]@.Data[[2]])
} else if (answ == 2){
gmessage("Define the Reference Peak Edges", title="PEAK EDGES DEFINITION", icon="info")
pos <- locator(n=2, type="p", col="red", cex=1.5, lwd=2, pch=1)
LL <- length(SourceFile[[SpectIndx]]@.Data[[1]])
idx <- NULL
idx[1] <- findXIndex(SourceFile[[SpectIndx]]@.Data[[1]], pos$x[1])
idx[2] <- findXIndex(SourceFile[[SpectIndx]]@.Data[[1]], pos$x[2])
idx <- sort(idx, decreasing = FALSE)
maxY <- max(SourceFile[[SpectIndx]]@.Data[[2]][idx[1]:idx[2]])
minY <- min(SourceFile[[SpectIndx]]@.Data[[2]][idx[1]:idx[2]])
}
SourceFile[[SpectIndx]]@.Data[[2]] <- (SourceFile[[SpectIndx]]@.Data[[2]]-minY)/(maxY-minY)
if(length(SourceFile[[SpectIndx]]@RegionToFit) > 0){
SourceFile[[SpectIndx]]@RegionToFit$y <- (SourceFile[[SpectIndx]]@RegionToFit$y-minY)/(maxY-minY)
}
if(length(SourceFile[[SpectIndx]]@Baseline) > 0){
SourceFile[[SpectIndx]]@Baseline$y <- (SourceFile[[SpectIndx]]@Baseline$y-minY)/(maxY-minY)
}
LL <- length(SourceFile[[SpectIndx]]@Components)
if(LL > 0){
for(ii in 1:LL){
SourceFile[[SpectIndx]]@Components[[ii]]@ycoor <- (SourceFile[[SpectIndx]]@Components[[ii]]@ycoor-minY)/(maxY-minY)
}
SourceFile[[SpectIndx]]@Fit$y <- SourceFile[[SpectIndx]]@Fit$y/(maxY-minY)
}
SourceFile[[SpectIndx]]@Boundaries$y <- c(0, 1)
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- ""
msg <- paste(CoreLine1[2], " normalized", sep="")
cat("\n ==> ", msg)
svalue(NormButt, index=TRUE) <- -1
# svalue(infoWin) <- msg
}, container=MathFrame5)
layoutT2[6,1] <- MathFrame6 <- gframe("SUBTRACT THE BASELINE", horizontal=FALSE, spacing=3, container=layoutT2)
glabel(">>> WARNING: Data OUTSIDE the \n BaseLine Range will be lost!", container=MathFrame6)
SubtrBlButt <- gbutton("SUBTRACT", handler=function(h, ...){
# svalue(infoWin) <- ""
if (gconfirm(msg="ATTENTION: original data will be IRREVERSIBLY modified!" , title = "BASELINE SUBTRACTION", icon = "warning")) {
SourceFile <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile <- get(SourceFile, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
if (length(SourceFile[[SpectIndx]]@RegionToFit)>0 && length(SourceFile[[SpectIndx]]@Baseline)>0) {
SourceFile[[SpectIndx]]@RegionToFit[[2]] <- SourceFile[[SpectIndx]]@RegionToFit[[2]]-SourceFile[[SpectIndx]]@Baseline[[2]]
}
SourceFile[[SpectIndx]]@.Data <- SourceFile[[SpectIndx]]@RegionToFit
LL <- length(SourceFile[[SpectIndx]]@Components)
if (LL>0) {
for (ii in 1:LL) {
SourceFile[[SpectIndx]]@Components[[ii]]@ycoor <- SourceFile[[SpectIndx]]@Components[[ii]]@ycoor - SourceFile[[SpectIndx]]@Baseline[[2]]
}
}
SourceFile[[SpectIndx]]@Baseline[[2]] <- SourceFile[[SpectIndx]]@Baseline[[2]]*0 #annullo la baseline
plot(SourceFile[[SpectIndx]])
DestFName <<- SourceFile
activeSpectIndx <<- SpectIndx
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
msg <- paste("Baseline substracted")
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
}
}, container=MathFrame6)
layoutT2[5,2] <- MathFrame55 <- gframe("SUBTRACT CORELINE2 FROM CORELINE1", horizontal=FALSE, spacing=3, container=layoutT2)
SubtrSpectButt <- gbutton("SUBTRACT SPECTRA", handler=function(h, ...){
# svalue(infoWin) <- ""
SourceFile1 <- svalue(DestFileName) <- svalue(SourceFile11)
SourceFile1 <- get(SourceFile1, envir=.GlobalEnv)
CoreLine1 <- svalue(CoreLine11)
CoreLine1 <- unlist(strsplit(CoreLine1, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx1 <- as.integer(CoreLine1[1])
SpectName <- CoreLine1[2]
SourceFile2 <- svalue(SourceFile22)
SourceFile2 <- get(SourceFile2, envir=.GlobalEnv)
CoreLine2 <- svalue(CoreLine22)
CoreLine2 <- unlist(strsplit(CoreLine2, "\\.")) #tolgo il "NUMERO." all'inizio del nome coreline
SpectIndx2 <- as.integer(CoreLine2[1])
if (hasBaseline(SourceFile1[[SpectIndx1]]) || hasBaseline(SourceFile2[[SpectIndx2]]) ){
answ <- gmessage(msg="SUBTRACTION CAN BE DONE ONLY ON RAW DATA: PLEASE REMOVE ANALYSIS" , title = "WARNING!", icon = "warning")
} else {
txt=" ==> SUBTRACTION WILL BE PERFOMED IN THE COMMON ENERGY RANGE\nSAVE AND SAVE&EXIT WILL OVERWRITE SUBTRACTION TO THE ORIGINAL CORE LINE"
answ <- gconfirm(msg=txt , title = "WARNING!", icon = "warning")
if (answ) {
Range1 <- range(SourceFile1[[SpectIndx1]]@.Data[1])
Range2 <- range(SourceFile2[[SpectIndx2]]@.Data[1])
lim1 <- max(Range1[1], Range2[1]) #il piu' grande dei limiti inferiori
lim2 <- min(Range1[2], Range2[2]) #il piu' piccolo dei limiti superiori
idx1 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile1[[SpectIndx1]]@.Data[[1]], lim2)
if (SourceFile1[[SpectIndx1]]@Flags[1]) { #Binding energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx2:idx1]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx2:idx1]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx2:idx1] #Analyzer Transf Funct.
} else { #Kinetic energy scale
CoreLineX1 <- SourceFile1[[SpectIndx1]]@.Data[[1]][idx1:idx2]
CoreLineY1 <- SourceFile1[[SpectIndx1]]@.Data[[2]][idx1:idx2]
CoreLineSF1 <- SourceFile1[[SpectIndx1]]@.Data[[3]][idx1:idx2] #Analyzer Transf Funct.
}
LL1 <- length(CoreLineY1)
idx1 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim1)
idx2 <- findXIndex(SourceFile2[[SpectIndx2]]@.Data[[1]], lim2)
if (SourceFile2[[SpectIndx2]]@Flags[1]) { #Binding energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx2:idx1]
} else { #Kinetic energy scale
CoreLineY2 <- SourceFile2[[SpectIndx2]]@.Data[[2]][idx1:idx2]
}
LL2 <- length(CoreLineY2)
if(LL1 > LL2){ #verify CoreLine1, CoreLine2 have same length
kk <- LL1-LL2 #if CoreLine1 is longer
CoreLineY2[LL2:(LL2+kk)] <- CoreLineY2[LL2] #add lacking values to CoreLine2
} else if (LL1 < LL2){ #if CoreLine2 longer
kk <- LL2-LL1
CoreLineY2 <- CoreLineY2[1:(LL2-kk)] #drop exceeding values
}
SourceFile1[[SpectIndx1]]@.Data[[1]] <- CoreLineX1
SourceFile1[[SpectIndx1]]@.Data[[3]] <- CoreLineSF1
Nswps1 <- strsplit(SourceFile1[[SpectIndx1]]@Info[2], "Sweeps:") #taglia la str in 2 parti: ql prima e ql dopo "Sweeps:"
Nsw1 <- as.numeric(substr(Nswps1[[1]][2], 1, 2)) #della seconda parte prendo i primi due caratteri che indicano Nswps e trasforno in intero
Nswps2 <- strsplit(SourceFile1[[SpectIndx2]]@Info[2], "Sweeps:")
Nsw2 <- as.numeric(substr(Nswps2[[1]][2], 1, 2))
if (Nsw1 >= Nsw2) {
SourceFile1[[SpectIndx1]]@.Data[[2]] <- CoreLineY1-CoreLineY2
Nsw1 <- as.character(Nsw1)
Nswps1 <- paste(Nswps1[[1]][1], "Sweeps: ",Nsw1,substr(Nswps1[[1]][2], 3, nchar(Nswps1[[1]][2])), sep="") #ricostruisco la secopnda parte della stinga
SourceFile1[[SpectIndx1]]@Info[2] <- Nswps1
plot(SourceFile1[[SpectIndx1]])
DestFName <<- SourceFile1
activeSpectIndx <<- SpectIndx1
activeSpectName <<- SpectName
enabled(SaveSpect) <- TRUE
enabled(SaveNewSpect) <- TRUE
enabled(SaveAndExit) <- TRUE
prefix <<- "M."
msg <- paste(CoreLine2[2],"-", svalue(SourceFile22), " subtracted from ", CoreLine1[2], "-", svalue(SourceFile11))
cat("\n ==> ", msg)
# svalue(infoWin) <- msg
} else {
answ <- gmessage(msg="Nsweeps CoreLine2 > Nsweeps CoreLine1: SUBTRACTION NOT ALLOWED" , title = "WARNING!", icon = "warning")
}
}
}
}, container=MathFrame55)
#---InfoWin
# InfoFrame <- gframe("PROCESSING INFO", horizontal=FALSE, spacing=3, container=Addgroup)
# infoWin <- glabel(text=" " , container=InfoFrame)
#---COMMON BUTTONS
ButtGroup1 <- ggroup(horizontal=TRUE, spacing=5, container=Addgroup)
SaveSpect <- gbutton(" SAVE ", handler=function(h, ...) { SaveSpectrum() }, container=ButtGroup1)
enabled(SaveSpect) <- FALSE # Saving data blocked: ctrls on Dest file needed
SaveNewSpect <- gbutton(" SAVE AS A NEW CORELINE ", handler=function(h, ...){
SaveNewSpectrum()
}, container=ButtGroup1)
enabled(SaveNewSpect) <- FALSE # Saving data blocked: ctrls on Dest file needed
SaveAndExit <- gbutton(" SAVE & EXIT ", handler=function(h, ...){
if (prefix=="D1." || length(CullData>0)){ #differentiation was performed
CullData <<- NULL
SaveNewSpectrum() #for spectral differentiation or culled data saving is forced in a new coreline
} else {
SaveSpectrum()
}
dispose(ProcessWin)
XPSSaveRetrieveBkp("save")
}, container=ButtGroup1)
enabled(SaveAndExit) <- FALSE # Saving data blocked: ctrls on Dest file needed
gbutton(" EXIT ", handler=function(h, ...) {
dispose(ProcessWin)
XPSSaveRetrieveBkp("save")
},container=ButtGroup1)
visible(ProcessWin) <- TRUE
svalue(NoteBK) <- 2
svalue(NoteBK) <- 1 #set the first page
ProcessWin$set_modal(TRUE)
}
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