R/XPSEshiftGUI.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSEshift
Documented in
XPSEshift
# XPSEshift function to apply energy shifts to spectra to correct for charging effects
#' @title XPSEShift
#' @description XPSEshift function correct the energy scale of spectra
#' affected by charging effects. Generally C1s from hydrocarbons at BE=285eV
#' or Au4f 7/2 at BE=84eV are chosen as reference peaks. Charges spectra are
#' shifted forcing the reference spectra to fall at their correct BE position.
#' @examples
#' \dontrun{
#' XPSEshift()
#' }
#' @export
#'
XPSEshift <- function(){
GetCurPos <- function(SingClick){
coords <<- NULL
enabled(Eframe3) <- FALSE #prevent exiting Analysis if locatore active
enabled(ZoomBtn) <- FALSE
enabled(Eframe5) <- FALSE
enabled(BtnGroup) <- FALSE
EXIT <- FALSE
LocPos <<- list(x=0, y=0)
Nclk <- SingClick
if (Nclk == FALSE) Nclk <- 1
while(EXIT == FALSE){ #if pos1 not NULL a mouse butto was pressed
LocPos <<- locator(n=Nclk, type="p", pch=3, cex=1.5, col="blue", lwd=2) #to modify the zoom limits
if (is.null(LocPos)) {
enabled(Eframe3) <- TRUE
enabled(ZoomBtn) <- TRUE
enabled(Eframe5) <- TRUE
enabled(BtnGroup) <- TRUE
EXIT <- TRUE
} else {
if (SingClick == 1){
enabled(Eframe3) <- TRUE
enabled(ZoomBtn) <- TRUE
enabled(Eframe5) <- TRUE
enabled(BtnGroup) <- TRUE
EXIT <- TRUE
} else if (ZOOM==TRUE) {
if (SingClick == 2) {
Corners <<- LocPos #plot the zoom area the first time
if (FName[[SpectIndx]]@Flags[1]) { #Binding energy set
Corners$x <<- sort(Corners$x, decreasing=TRUE) #pos$x in decrescent ordered => Corners$x[1]==Corners$x[2]
} else {
Corners$x <<- sort(Corners$x, decreasing=FALSE) #pos$x in ascending order
}
Corners$x <<- c(Corners$x[1], Corners$x[1], Corners$x[2], Corners$x[2])
Corners$y <<- c(sort(c(Corners$y[1], Corners$y[2]), decreasing=FALSE),
sort(c(Corners$y[1], Corners$y[2]), decreasing=FALSE))
SingClick <- FALSE
Nclk <- 1
} else { #modify the zoom area
FindNearest()
}
XYrange$x <<- c(Corners$x[1], Corners$x[3])
XYrange$y <<- c(Corners$y[1], Corners$y[2])
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
rect(Corners$x[1], Corners$y[1], Corners$x[3], Corners$y[2])
points(Corners, type="p", pch=3, cex=1.5, col="blue", lwd=2)
} else {
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
points(LocPos, type="p", pch=3, cex=1.5, lwd=2, col="red")
LocPos$x <<- round(LocPos$x, digits=2)
svalue(Eobj5) <- LocPos$x
position <<- LocPos$x
tcl("update", "idletasks") #force writing cursor position in the glabel
}
}
}
}
FindNearest <- function(){
D <- NULL
Dmin <- ((LocPos$x-Corners$x[1])^2 + (LocPos$y-Corners$y[1])^2)^0.5 #init value
for (ii in 1:4) {
D[ii] <- ((LocPos$x-Corners$x[ii])^2 + (LocPos$y-Corners$y[ii])^2)^0.5 #dist P0 P1
if(D[ii] <= Dmin){
Dmin <- D[ii]
idx=ii
}
}
if (idx==1){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
}
return()
}
#--- Variables ---
if (is.na(activeFName)){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
FName <- get(activeFName,envir=.GlobalEnv) #this is the XPS Sample
ActiveFName <- get("activeFName",envir=.GlobalEnv) #this is the name of the XPS Sample
SpectIndx <- get("activeSpectIndx",envir=.GlobalEnv)
SpectList <- XPSSpectList(ActiveFName)
FNameList <- XPSFNameList()
FNidx <- grep(ActiveFName, FNameList)
FitCompList <- ""
position <- NULL
Eshift <- NULL
XYrange <- list(x=NULL, y=NULL)
LocPos <- list(x=NULL, y=NULL)
Corners <- list(x=NULL, y=NULL)
ZOOM <- FALSE
Ewin <- gwindow("ENERGY SHIFT", visible=FALSE)
size(Ewin) <- c(200, 400)
addHandlerDestroy(Ewin, handler=function(h, ...){ #if MainWindow unproperly closed with X
EXIT <<- TRUE
XPSSettings$General[4] <<- 7 #Reset to normal graphic win dimension
assign("XPSSettings", XPSSettings, envir=.GlobalEnv)
plot(FName[[SpectIndx]]) #replot the CoreLine
})
Egroup1 <- ggroup(horizontal=FALSE, container = Ewin)
Eframe1 <- gframe(" Select the XPSSample and Coreline ", horizontal=TRUE, spacing=5, container=Egroup1)
Eobj0 <- gcombobox(FNameList, selected=FNidx, editable=FALSE, handler=function(h,...){
ActiveFName <<- svalue(Eobj0)
FName <<- get(ActiveFName,envir=.GlobalEnv)
SpectList <<- XPSSpectList(ActiveFName)
FNameList <<- XPSFNameList()
FNidx <<- grep(ActiveFName, FNameList)
plot(FName)
svalue(Eobj2) <<- ""
delete(Eframe1, Eobj1)
Eobj1 <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h, ...){
SpectName <- svalue(Eobj1)
SpectName <- unlist(strsplit(SpectName, "\\.")) #skip the number at beginning of string
SpectIndx <<- as.numeric(SpectName[1])
plot(FName[[SpectIndx]])
tmp <- names(FName[[SpectIndx]]@Components)
FitCompList <- c(FitCompList,tmp)
delete(Eframe2,Eobj2)
Eobj2 <<- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, handler=function(h, ...){
Component <- svalue(Eobj2)
FName <- get(ActiveFName, envir=.GlobalEnv) #reload FName if a new EShift will be set
OldValue <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"] # actual value of the fit component position
OldValue <- round(as.numeric(OldValue), digits=2)
svalue(Eobj5) <- OldValue #display the actual value of the component position in GEdit
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
if (FName[[SpectIndx]]@Flags[1]) { #reverse if BE scale
XYrange$x <<- rev(XYrange$x)
}
}, container=Eframe2)
enabled(Eobj2) <- TRUE
}, container=Eframe1)
}, container=Eframe1)
Eobj1 <- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h, ...){
SpectName <- svalue(Eobj1)
SpectName <- unlist(strsplit(SpectName, "\\."))
SpectIndx <<- as.numeric(SpectName[1])
plot(FName[[SpectIndx]])
tmp <- names(FName[[SpectIndx]]@Components)
FitCompList <- c(FitCompList,tmp)
delete(Eframe2,Eobj2)
Eobj2 <<- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, handler=function(h, ...){
Component <- svalue(Eobj2)
FName <- get(ActiveFName, envir=.GlobalEnv) #reload FName if a new EShift will be set
OldValue <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"] # actual value of the fit component position
OldValue <- round(as.numeric(OldValue), digits=2)
svalue(Eobj5) <- OldValue #display the actual value of the component position in GEdit
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
if (FName[[SpectIndx]]@Flags[1]) { #reverse if BE scale
XYrange$x <<- rev(XYrange$x)
}
}, container=Eframe2)
enabled(Eobj2) <- TRUE
}, container=Eframe1)
Eframe2 <- gframe(" Select Component ", horizontal=TRUE, spacing=5, container=Egroup1)
Eobj2 <- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, container=Eframe2)
tkconfigure(Eobj2$widget, width=20)
enabled(Eobj2) <- FALSE
Eframe3 <- gframe("Apply Shift" , spacing=5, container=Egroup1)
ShiftObj <- gradio(c("All Corelines", "Selected Coreline Only"), selected=1, horizontal=TRUE, container=Eframe3)
Eframe4 <- gframe("Set Zoom Region" , horizontal=FALSE, spacing=5, container=Egroup1)
glabel("Define the Zoom Area", container=Eframe4)
ZoomBtn <- gbutton("Set the Zoom Area", handler=function(h, ...){
SpectName <- svalue(Eobj1)
if(length(SpectName)==0) {
gmessage(msg="WARNING: no coreline selected, zoom stopped", title = "WARNING",icon = "warning" )
return()
}
txt <- " LEFT Mouse Button to Set the TWO Opposite Corners of the Zoom Area\n RIGHT Mouse Button to exit \n Click Near Markers to Modify The zoom area"
gmessage(msg=txt , title = "WARNING", icon = "warning")
ZOOM <<- TRUE
GetCurPos(SingClick=2) #this to draw/modify the zooming area
ZOOM <<- FALSE
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
}, container = Eframe4)
Eframe5 <- gframe("Peak Position", horizontal=FALSE, spacing=5, container=Egroup1)
CursorBtn <- gbutton("Cursor", handler=function(h, ...){
SpectName <- svalue(Eobj1)
if(length(SpectName)==0) {
gmessage(msg="WARNING: no coreline selected", title = "WARNING",icon = "warning" )
return()
}
gmessage(msg="LEFT Mouse Button to Read Marker's Position; RIGHT Mouse Button to Exit" , title = "WARNING", icon = "warning")
GetCurPos(SingClick=FALSE) #this to draw/modify the zooming area
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
}, container=Eframe5)
glabel("Please Enter the New Energy Value:", spacing=1, container=Eframe5)
Eobj5 <- gedit(initial.msg ="E?", handler=function(h,...){
NewE <- svalue(Eobj5)
Component <- svalue(Eobj2)
if (is.null(position) && length(Component)==0){
gmessage(msg="Cursor-Peak-Position or Fit Component lacking! Please select", title="LACKING REFERENCE POSITION", icon="warning")
svalue(Eobj5) <- "E?"
return()
}
if (NewE == "" ){
gmessage("New energy position NULL. Please give a correct value", title="ENERGY POSITION NULL", icon="warning")
svalue(Eobj5) <- "E?"
return()
}
if (NewE != "E?"){
NewE <- as.numeric(NewE)
Component <- svalue(Eobj2)
if (length(Component)==0){ #no fit present, no components, position read from cursor
Eshift <<- as.numeric(NewE-position)
} else {
Component <- as.numeric(substr(Component, 2,nchar(Component))) #exttract the component name
CompPos <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"]
Eshift <<- as.numeric(NewE-CompPos)
}
Escale <- FName[[SpectIndx]]@units[1]
if (svalue(ShiftObj)=="All Corelines") {
NCoreLines <- length(FName)
for (ii in 1:NCoreLines){
if (Escale == FName[[ii]]@units[1]) { #Eshift calculated on a BE scale and CoreLine[[ii]] sa same Energy Units
FName[[ii]] <<- XPSapplyshift(FName[[ii]], Eshift)
} else {
FName[[ii]] <<- XPSapplyshift(FName[[ii]], -Eshift) # Eshift calculated on a BE scale while CoreLine[[ii]] is in Kinetic (or viceversa)
}
}
plot(FName[[SpectIndx]])
} else if (svalue(ShiftObj)=="Selected Coreline Only"){ #Apply Eshift only on the selected coreline
if (Escale == FName[[SpectIndx]]@units[1]) { #Eshift calculated on a BE scale and CoreLine[[ii]] sa same Energy Units
FName[[SpectIndx]] <<- XPSapplyshift(FName[[SpectIndx]], Eshift)
} else {
FName[[SpectIndx]] <<- XPSapplyshift(FName[[SpectIndx]],-Eshift) # Eshift calculated on a BE scale while CoreLine[[ii]] is in Kinetic (or viceversa)
}
plot(FName[[SpectIndx]])
}
}
svalue(Eobj5) <- "E?"
}, container=Eframe5)
BtnGroup <- ggroup(horizontal=TRUE, container = Egroup1)
gbutton(" RESET ", container = BtnGroup, handler = function(h, ...){
FName <- XPSapplyshift(FName)
svalue(Eobj5) <- "E?"
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y)
assign(ActiveFName, FName, envir=.GlobalEnv)
})
gbutton(" SAVE ", container=BtnGroup, handler=function(...){
assign(ActiveFName, FName, envir=.GlobalEnv)
XPSSaveRetrieveBkp("save")
})
gbutton(" SAVE & EXIT ", container=BtnGroup, handler=function(...){
dispose(Ewin)
assign(ActiveFName, FName, envir=.GlobalEnv)
XPSSaveRetrieveBkp("save")
})
visible(Ewin) <- TRUE
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSEshift
Documented in XPSEshift
# XPSEshift function to apply energy shifts to spectra to correct for charging effects
#' @title XPSEShift
#' @description XPSEshift function correct the energy scale of spectra
#' affected by charging effects. Generally C1s from hydrocarbons at BE=285eV
#' or Au4f 7/2 at BE=84eV are chosen as reference peaks. Charges spectra are
#' shifted forcing the reference spectra to fall at their correct BE position.
#' @examples
#' \dontrun{
#' XPSEshift()
#' }
#' @export
#'
XPSEshift <- function(){
GetCurPos <- function(SingClick){
coords <<- NULL
enabled(Eframe3) <- FALSE #prevent exiting Analysis if locatore active
enabled(ZoomBtn) <- FALSE
enabled(Eframe5) <- FALSE
enabled(BtnGroup) <- FALSE
EXIT <- FALSE
LocPos <<- list(x=0, y=0)
Nclk <- SingClick
if (Nclk == FALSE) Nclk <- 1
while(EXIT == FALSE){ #if pos1 not NULL a mouse butto was pressed
LocPos <<- locator(n=Nclk, type="p", pch=3, cex=1.5, col="blue", lwd=2) #to modify the zoom limits
if (is.null(LocPos)) {
enabled(Eframe3) <- TRUE
enabled(ZoomBtn) <- TRUE
enabled(Eframe5) <- TRUE
enabled(BtnGroup) <- TRUE
EXIT <- TRUE
} else {
if (SingClick == 1){
enabled(Eframe3) <- TRUE
enabled(ZoomBtn) <- TRUE
enabled(Eframe5) <- TRUE
enabled(BtnGroup) <- TRUE
EXIT <- TRUE
} else if (ZOOM==TRUE) {
if (SingClick == 2) {
Corners <<- LocPos #plot the zoom area the first time
if (FName[[SpectIndx]]@Flags[1]) { #Binding energy set
Corners$x <<- sort(Corners$x, decreasing=TRUE) #pos$x in decrescent ordered => Corners$x[1]==Corners$x[2]
} else {
Corners$x <<- sort(Corners$x, decreasing=FALSE) #pos$x in ascending order
}
Corners$x <<- c(Corners$x[1], Corners$x[1], Corners$x[2], Corners$x[2])
Corners$y <<- c(sort(c(Corners$y[1], Corners$y[2]), decreasing=FALSE),
sort(c(Corners$y[1], Corners$y[2]), decreasing=FALSE))
SingClick <- FALSE
Nclk <- 1
} else { #modify the zoom area
FindNearest()
}
XYrange$x <<- c(Corners$x[1], Corners$x[3])
XYrange$y <<- c(Corners$y[1], Corners$y[2])
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
rect(Corners$x[1], Corners$y[1], Corners$x[3], Corners$y[2])
points(Corners, type="p", pch=3, cex=1.5, col="blue", lwd=2)
} else {
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
points(LocPos, type="p", pch=3, cex=1.5, lwd=2, col="red")
LocPos$x <<- round(LocPos$x, digits=2)
svalue(Eobj5) <- LocPos$x
position <<- LocPos$x
tcl("update", "idletasks") #force writing cursor position in the glabel
}
}
}
}
FindNearest <- function(){
D <- NULL
Dmin <- ((LocPos$x-Corners$x[1])^2 + (LocPos$y-Corners$y[1])^2)^0.5 #init value
for (ii in 1:4) {
D[ii] <- ((LocPos$x-Corners$x[ii])^2 + (LocPos$y-Corners$y[ii])^2)^0.5 #dist P0 P1
if(D[ii] <= Dmin){
Dmin <- D[ii]
idx=ii
}
}
if (idx==1){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[1] <<- Corners$y[3] <<- LocPos$y
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- LocPos$x
Corners$y[2] <<- Corners$y[4] <<- LocPos$y
}
return()
}
#--- Variables ---
if (is.na(activeFName)){
gmessage("No data present: please load and XPS Sample", title="XPS SAMPLES MISSING", icon="error")
return()
}
FName <- get(activeFName,envir=.GlobalEnv) #this is the XPS Sample
ActiveFName <- get("activeFName",envir=.GlobalEnv) #this is the name of the XPS Sample
SpectIndx <- get("activeSpectIndx",envir=.GlobalEnv)
SpectList <- XPSSpectList(ActiveFName)
FNameList <- XPSFNameList()
FNidx <- grep(ActiveFName, FNameList)
FitCompList <- ""
position <- NULL
Eshift <- NULL
XYrange <- list(x=NULL, y=NULL)
LocPos <- list(x=NULL, y=NULL)
Corners <- list(x=NULL, y=NULL)
ZOOM <- FALSE
Ewin <- gwindow("ENERGY SHIFT", visible=FALSE)
size(Ewin) <- c(200, 400)
addHandlerDestroy(Ewin, handler=function(h, ...){ #if MainWindow unproperly closed with X
EXIT <<- TRUE
XPSSettings$General[4] <<- 7 #Reset to normal graphic win dimension
assign("XPSSettings", XPSSettings, envir=.GlobalEnv)
plot(FName[[SpectIndx]]) #replot the CoreLine
})
Egroup1 <- ggroup(horizontal=FALSE, container = Ewin)
Eframe1 <- gframe(" Select the XPSSample and Coreline ", horizontal=TRUE, spacing=5, container=Egroup1)
Eobj0 <- gcombobox(FNameList, selected=FNidx, editable=FALSE, handler=function(h,...){
ActiveFName <<- svalue(Eobj0)
FName <<- get(ActiveFName,envir=.GlobalEnv)
SpectList <<- XPSSpectList(ActiveFName)
FNameList <<- XPSFNameList()
FNidx <<- grep(ActiveFName, FNameList)
plot(FName)
svalue(Eobj2) <<- ""
delete(Eframe1, Eobj1)
Eobj1 <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h, ...){
SpectName <- svalue(Eobj1)
SpectName <- unlist(strsplit(SpectName, "\\.")) #skip the number at beginning of string
SpectIndx <<- as.numeric(SpectName[1])
plot(FName[[SpectIndx]])
tmp <- names(FName[[SpectIndx]]@Components)
FitCompList <- c(FitCompList,tmp)
delete(Eframe2,Eobj2)
Eobj2 <<- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, handler=function(h, ...){
Component <- svalue(Eobj2)
FName <- get(ActiveFName, envir=.GlobalEnv) #reload FName if a new EShift will be set
OldValue <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"] # actual value of the fit component position
OldValue <- round(as.numeric(OldValue), digits=2)
svalue(Eobj5) <- OldValue #display the actual value of the component position in GEdit
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
if (FName[[SpectIndx]]@Flags[1]) { #reverse if BE scale
XYrange$x <<- rev(XYrange$x)
}
}, container=Eframe2)
enabled(Eobj2) <- TRUE
}, container=Eframe1)
}, container=Eframe1)
Eobj1 <- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h, ...){
SpectName <- svalue(Eobj1)
SpectName <- unlist(strsplit(SpectName, "\\."))
SpectIndx <<- as.numeric(SpectName[1])
plot(FName[[SpectIndx]])
tmp <- names(FName[[SpectIndx]]@Components)
FitCompList <- c(FitCompList,tmp)
delete(Eframe2,Eobj2)
Eobj2 <<- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, handler=function(h, ...){
Component <- svalue(Eobj2)
FName <- get(ActiveFName, envir=.GlobalEnv) #reload FName if a new EShift will be set
OldValue <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"] # actual value of the fit component position
OldValue <- round(as.numeric(OldValue), digits=2)
svalue(Eobj5) <- OldValue #display the actual value of the component position in GEdit
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
if (FName[[SpectIndx]]@Flags[1]) { #reverse if BE scale
XYrange$x <<- rev(XYrange$x)
}
}, container=Eframe2)
enabled(Eobj2) <- TRUE
}, container=Eframe1)
Eframe2 <- gframe(" Select Component ", horizontal=TRUE, spacing=5, container=Egroup1)
Eobj2 <- gcombobox(FitCompList, selected=-1, editable=FALSE, index=TRUE, container=Eframe2)
tkconfigure(Eobj2$widget, width=20)
enabled(Eobj2) <- FALSE
Eframe3 <- gframe("Apply Shift" , spacing=5, container=Egroup1)
ShiftObj <- gradio(c("All Corelines", "Selected Coreline Only"), selected=1, horizontal=TRUE, container=Eframe3)
Eframe4 <- gframe("Set Zoom Region" , horizontal=FALSE, spacing=5, container=Egroup1)
glabel("Define the Zoom Area", container=Eframe4)
ZoomBtn <- gbutton("Set the Zoom Area", handler=function(h, ...){
SpectName <- svalue(Eobj1)
if(length(SpectName)==0) {
gmessage(msg="WARNING: no coreline selected, zoom stopped", title = "WARNING",icon = "warning" )
return()
}
txt <- " LEFT Mouse Button to Set the TWO Opposite Corners of the Zoom Area\n RIGHT Mouse Button to exit \n Click Near Markers to Modify The zoom area"
gmessage(msg=txt , title = "WARNING", icon = "warning")
ZOOM <<- TRUE
GetCurPos(SingClick=2) #this to draw/modify the zooming area
ZOOM <<- FALSE
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
}, container = Eframe4)
Eframe5 <- gframe("Peak Position", horizontal=FALSE, spacing=5, container=Egroup1)
CursorBtn <- gbutton("Cursor", handler=function(h, ...){
SpectName <- svalue(Eobj1)
if(length(SpectName)==0) {
gmessage(msg="WARNING: no coreline selected", title = "WARNING",icon = "warning" )
return()
}
gmessage(msg="LEFT Mouse Button to Read Marker's Position; RIGHT Mouse Button to Exit" , title = "WARNING", icon = "warning")
GetCurPos(SingClick=FALSE) #this to draw/modify the zooming area
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y) #refresh graph
}, container=Eframe5)
glabel("Please Enter the New Energy Value:", spacing=1, container=Eframe5)
Eobj5 <- gedit(initial.msg ="E?", handler=function(h,...){
NewE <- svalue(Eobj5)
Component <- svalue(Eobj2)
if (is.null(position) && length(Component)==0){
gmessage(msg="Cursor-Peak-Position or Fit Component lacking! Please select", title="LACKING REFERENCE POSITION", icon="warning")
svalue(Eobj5) <- "E?"
return()
}
if (NewE == "" ){
gmessage("New energy position NULL. Please give a correct value", title="ENERGY POSITION NULL", icon="warning")
svalue(Eobj5) <- "E?"
return()
}
if (NewE != "E?"){
NewE <- as.numeric(NewE)
Component <- svalue(Eobj2)
if (length(Component)==0){ #no fit present, no components, position read from cursor
Eshift <<- as.numeric(NewE-position)
} else {
Component <- as.numeric(substr(Component, 2,nchar(Component))) #exttract the component name
CompPos <- FName[[SpectIndx]]@Components[[Component]]@param["mu","start"]
Eshift <<- as.numeric(NewE-CompPos)
}
Escale <- FName[[SpectIndx]]@units[1]
if (svalue(ShiftObj)=="All Corelines") {
NCoreLines <- length(FName)
for (ii in 1:NCoreLines){
if (Escale == FName[[ii]]@units[1]) { #Eshift calculated on a BE scale and CoreLine[[ii]] sa same Energy Units
FName[[ii]] <<- XPSapplyshift(FName[[ii]], Eshift)
} else {
FName[[ii]] <<- XPSapplyshift(FName[[ii]], -Eshift) # Eshift calculated on a BE scale while CoreLine[[ii]] is in Kinetic (or viceversa)
}
}
plot(FName[[SpectIndx]])
} else if (svalue(ShiftObj)=="Selected Coreline Only"){ #Apply Eshift only on the selected coreline
if (Escale == FName[[SpectIndx]]@units[1]) { #Eshift calculated on a BE scale and CoreLine[[ii]] sa same Energy Units
FName[[SpectIndx]] <<- XPSapplyshift(FName[[SpectIndx]], Eshift)
} else {
FName[[SpectIndx]] <<- XPSapplyshift(FName[[SpectIndx]],-Eshift) # Eshift calculated on a BE scale while CoreLine[[ii]] is in Kinetic (or viceversa)
}
plot(FName[[SpectIndx]])
}
}
svalue(Eobj5) <- "E?"
}, container=Eframe5)
BtnGroup <- ggroup(horizontal=TRUE, container = Egroup1)
gbutton(" RESET ", container = BtnGroup, handler = function(h, ...){
FName <- XPSapplyshift(FName)
svalue(Eobj5) <- "E?"
if (length(FName[[SpectIndx]]@RegionToFit$x) > 0){
XYrange$x <<- range(FName[[SpectIndx]]@RegionToFit$x)
XYrange$y <<- range(FName[[SpectIndx]]@RegionToFit$y)
} else {
XYrange$x <<- range(FName[[SpectIndx]]@.Data[[1]])
XYrange$y <<- range(FName[[SpectIndx]]@.Data[[2]])
}
plot(FName[[SpectIndx]], xlim=XYrange$x, ylim=XYrange$y)
assign(ActiveFName, FName, envir=.GlobalEnv)
})
gbutton(" SAVE ", container=BtnGroup, handler=function(...){
assign(ActiveFName, FName, envir=.GlobalEnv)
XPSSaveRetrieveBkp("save")
})
gbutton(" SAVE & EXIT ", container=BtnGroup, handler=function(...){
dispose(Ewin)
assign(ActiveFName, FName, envir=.GlobalEnv)
XPSSaveRetrieveBkp("save")
})
visible(Ewin) <- TRUE
}
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