R/XPSMoveCompGUI.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSMoveComp
Documented in
XPSMoveComp
#' @title XPSMoveComp
#' @description XPSMoveComp function to modify component position and intensity in a fit
#' this function provides a userfriendly interface change position and intensity of each
#' individual fitting component of a selected XPSCoreline. Changes are saved
#' in the .GlobalEnv main software memory.
#' @examples
#' \dontrun{
#' XPSMoveComp()
#' }
#' @export
#'
XPSMoveComp <- function(){
GetCurPos <- function(SingClick){
coords <<- NULL
EXIT <- FALSE
enabled(FitComp) <- FALSE #prevent exiting Analysis if locatore active
enabled(MCFrame4) <- FALSE #prevent exiting Analysis if locatore active
Estep <- abs(Object@RegionToFit[[1]][1] - Object@RegionToFit[[1]][2])
cat("\n 1111")
while(EXIT == FALSE){
pos <- locator(n=1)
if (is.null(pos)) {
enabled(FitComp) <- TRUE
enabled(MCFrame4) <- TRUE
EXIT <- TRUE
} else {
if (SingClick){
enabled(FitComp) <- TRUE
enabled(MCFrame4) <- TRUE
EXIT <- TRUE
}
if (SetZoom == TRUE) { #define zoom area
xx <- pos$x
yy <- pos$y
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy_BasLin <- yy-Object@Baseline$y[Xindx] #spectral intensity at xx without Baseline
coords <<- c(xx, yy, yy_BasLin)
RBmousedown() #selection of the zoom area
} else {
xx <- pos$x
yy <- pos$y
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy_BasLin <- yy-Object@Baseline$y[Xindx] #spectral intensity at xx without Baseline
coords <<- c(xx, yy, yy_BasLin)
LBmousedown() #selection of the BaseLine Edges
}
}
}
return()
}
LBmousedown <- function() { #Left mouse button down
xx <- coords[1]
yy <- coords[2]
if (SetZoom==FALSE) { #left button works only when SET ZOOM REGION inactive
MoveComp()
## loop on spectra and retrieve Pass Energy
XPSquantify(XPSSample)
refresh <<- FALSE
}
replot()
}
RBmousedown <- function() { #Right mouse button down
xx <- coords[1]
yy <- coords[2]
if (SetZoom == TRUE) { #left button works only when SET ZOOM REGION button pressed
point.coords$x[point.index] <<- coords[1] #abscissa
point.coords$y[point.index] <<- coords[2] #ordinate
if (point.index == 1) { #First rect corner C1
point.index <<- 3
Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
# } else if (point.index == 2) { #Second rect corner C2 opposite to C1
# point.index <<- 3
# Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
# Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
} else if (point.index == 3) { #modifies corner positions
D <- vector("numeric", 4)
Dmin <- ((point.coords$x[3]-Corners$x[1])^2 + (point.coords$y[3]-Corners$y[1])^2)^0.5 #valore di inizializzazione
for (ii in 1:4) {
D[ii] <- ((point.coords$x[3]-Corners$x[ii])^2 + (point.coords$y[3]-Corners$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] <<- point.coords$x[3]
Corners$y[1] <<- Corners$y[3] <<- point.coords$y[3]
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- point.coords$x[3]
Corners$y[2] <<- Corners$y[4] <<- point.coords$y[3]
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- point.coords$x[3]
Corners$y[1] <<- Corners$y[3] <<- point.coords$y[3]
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- point.coords$x[3]
Corners$y[2] <<- Corners$y[4] <<- point.coords$y[3]
}
if (Object@Flags[1]) { #Binding energy set
point.coords$x <<- sort(c(Corners$x[1],Corners$x[3]), decreasing=TRUE) #pos$x in decreasing order
point.coords$y <<- sort(c(Corners$y[1],Corners$y[4]), decreasing=FALSE)
} else {
point.coords$x <<- sort(c(Corners$x[1],Corners$x[3]), decreasing=FALSE) #pos$x in increasing order
point.coords$y <<- sort(c(Corners$y[1],Corners$y[4]), decreasing=FALSE)
}
}
replot()
}
}
Check.PE <- function(){
PassE <- NULL
PassE <- sapply( XPSSample, function(x) {
info <- x@Info[1] #retrieve info containing PE value
sss <- strsplit(info, "Pass energy") #extract PE value
PE <- strsplit(sss[[1]][2], "Iris") #PE value
PE <- gsub(" ", "", PE[[1]][1], fixed=TRUE) #drop white spaces in string PE
PE <- as.integer(PE)
return(PE)
}
)
SpectList <- XPSSpectList(activeFName)
idx <- grep("Survey", SpectList) #recognize presence of a Survey
if (length(idx) == 0){ idx <- grep("survey", SpectList) }
if (length(idx) == 0){ return(TRUE) } #No survey spectra are present in XPSSample: continue working
PEsur <- PassE[[ idx[1] ]] #if idx is a vector, select the first element
if (length(idx) > 0){ #a survey is present
SpectList <- SpectList[-idx] #eliminate the "Survey" from list of Spectral Names
PassE <- PassE[-idx] #eliminate the PassE(survey) to compare PE of only core-lines
}
Extracted <- which(PassE == 160)
LL <- length(Extracted)
if (LL > 0){
for(ii in 1:LL){
Indx <- Extracted[ii]
Indx <- unlist(strsplit(SpectList[Indx], "\\."))
Indx <- as.integer(Indx[1]) #select "NUMber." in component name
if ( hasRegionToFit(XPSSample[[Indx]])){
txt <- paste(SpectList[Extracted], collapse=" ")
txt <- paste(" Found Core Line: ", txt, " extracted from Survey.
\nCannot perform quantification here!
\nPlease exit MOVE COMPONENT and run QUANTIFY option to correct Core Line intensity")
gmessage(msg=txt, title="WARNING", icon="warning")
return(FALSE)
break
}
}
}
return(TRUE)
}
MoveComp <- function(...) {
# FComp <- svalue(FitComp)
if (length(FComp)==0) {
gmessage(msg="Select Component Please", title="WARNING", icon = "warning")
} else {
# FComp <- as.numeric(unlist(strsplit(FComp, split="C"))) #index of the selected component
# FComp <- FComp[2]
xx <- coords[1]
yy <- coords[2] #Component max value with baseline
zz <- coords[3] #Component max value without baseline
FitFunct <- Object@Components[[FComp]]@funcName
newh <- GetHvalue(Object, FComp, FitFunct, zz) #Get value computes the Component value given the fit parameters and the Ymax value
#range limits for mu
varmu <- getParam(Object@Components[[FComp]],variable="mu")
minmu <- varmu$start-varmu$min
maxmu <- varmu$max-varmu$start
newmu <- c(xx, xx-minmu, xx+maxmu)
#range limits for h
varh <- getParam(Object@Components[[FComp]],variable="h")
minh <- varh$start-varh$min
maxh <- varh$max-varh$start
if (maxh > 0) {
newh <- c(newh, 0, newh*5) # No constraints on h
}
if (maxh==0){
newh <- c(newh, newh, newh) # h is fixed
}
if (maxh < 0){
newh <- c(newh, 0, newh*5) # maxh cannot be <0: => force newH to correct values
}
if (varh$start < 0) {
newh <- c(0, 0, 1e5) #set a positive value for an hypotheic fit
}
Object@Components[[FComp]] <<- setParam(Object@Components[[FComp]], parameter=NULL, variable="mu", value=newmu)
Object@Components[[FComp]] <<- setParam(Object@Components[[FComp]], parameter=NULL, variable="h", value=newh)
#Now compute the new component Y values for the new xy position
Object@Components[[FComp]] <<- Ycomponent(Object@Components[[FComp]], x=Object@RegionToFit$x, y=Object@Baseline$y) #eomputes the Y value and add baseline
#Fit computed addind fit components with the modified ones
tmp <- sapply(Object@Components, function(z) matrix(data=z@ycoor))
Object@Fit$y <<- ( colSums(t(tmp)) - length(Object@Components)*(Object@Baseline$y))
Object <<- sortComponents(Object)
#if component order changed then re-number them
LL <- length(Object@Components) #N. fit components
for (ii in 1:LL){
if (xx == Object@Components[[ii]]@param["mu",1]) { #compare marker position with component positions
idx <- ii
break()
}
}
svalue(FitComp) <- paste("C", idx, sep="") #update component gradio
XPSSample[[Indx]] <<- Object
}
}
replot <- function(...) {
if (point.index==1 && refresh==FALSE) { #point.index==1 when moving mcomponent
plot(Object, xlim=Xlimits, ylim=Ylimits)
points(x=coords[1], y=coords[2], col=2, cex=1.2, lwd=2.5, pch=1) # if refresh==FALSE plot spectrum with component marker
} else if (SetZoom == TRUE){ #set zoom area corners
if (point.index == 1) { #normal plot
plot(Object)
points(point.coords, type="p", col=4, cex=1.2, lwd=2.5, pch=3)
} else if (point.index == 3){ #plot zoom area corners
plot(Object, xlim=Xlimits, ylim=Ylimits)
points(Corners, type="p", col=4, cex=1.2, lwd=2.5, pch=3)
rect(point.coords$x[1], point.coords$y[1], point.coords$x[2], point.coords$y[2])
}
} else {
plot(Object, xlim=Xlimits, ylim=Ylimits)
}
if (! is.null(coords)){
svalue(StatBar) <- paste("x =",round(coords[1],2), "y =",round(coords[2],2), sep=" ")
}
}
reset.plot <- function(h, ...) {
point.coords$x <<- range(Object@RegionToFit$x) #set original X range
point.coords$y <<- range(Object@RegionToFit$y) #set original Y range
Object@Boundaries <<- point.coords
Xlimits <<- point.coords$x
Ylimits <<- sort(point.coords$y, decreasing=FALSE)
Corners <- list(x=c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2]),
y=c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2]))
replot()
}
ComponentMenu <- function(){
FComp <<- 1
delete(MCFrame3,MCGroup3)
MCGroup3 <<- ggroup(spacing=3, horizontal=FALSE, container=MCFrame3)
FitComplyt <<- glayout(spacing=5, container=MCGroup3)
if (length(ComponentList) > 1){ #gradio works with at least 2 items
FitComp <<- gradio(ComponentList, selected=1, handler = function(h,...){
FComp <<- svalue(FitComp)
cat("\n selected component:", FComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit$x)
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
yy <- Object@Components[[FComp]]@param[1,1] #component height h
FuncName <- Object@Components[[FComp]]@funcName
yy <- yy/GetHvalue(Object,FComp, FuncName, 1) #provides the correct yy value for complex functions
Estep <- abs(Object@RegionToFit$x[1]-Object@RegionToFit$x[2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh <<- TRUE #cancel previous selections
replot() #plot spectrum without marker
refresh <<- FALSE #now plot also the component marker
replot() #replot spectrum and marker
if (ShowMsg==TRUE){
gmessage("Left click to enter Fit Component position. Right click to stop slection", title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
}
GetCurPos(SingClick=FALSE)
}, container = MCGroup3)
LL <- length(ComponentList)
NCol <- ceiling(LL/5) #gradio will be split in solumns of 5 elements
for(ii in 1:LL){
tkpack.forget(FitComp$widgets[[ii]]) # unparent widgets (uses library call)
}
for(kk in 1:NCol){
NN <- (kk-1)*5
for (ii in 1:5) {
if((ii+NN) > LL) {break}
FitComplyt[ii,kk] <<- FitComp$widgets[[(ii+NN)]]
}
}
}
if (length(ComponentList) == 1){ #gradio works with at least 2 items
FitComp <<- gcheckboxgroup(ComponentList, checked=TRUE, handler = function(h,...){
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected compoent
FComp <<- FComp[2]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit[[1]])
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh<<-TRUE #cancel previous component markers
replot() #plot spectrum only
refresh <<- FALSE #now plot spectrum + component marker
replot()
if (O.Sys == "linux"){ #in Linux locator is activated to read cursor positions
if (ShowMsg==TRUE){
gmessage("Left click to enter Fit Component position. Right click to stop slection", title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
}
GetCurPos(SingClick=FALSE)
}
}, container = MCGroup3)
}
txt <- paste("The selection of a Core-Line or Fit-Component always activates reading the [X,Y] cursor position.",
"\n=> Left click with the mouse to enter the cursor coordinates.",
"\n=> Right click to stop position selection and cursor position reading when not required.",
"\n",
"=> Do not show these WARNING messages again press YES, let WARNINGS active press NO", sep="")
ShowMsg <<- !gconfirm(msg=txt, title="WARNING", icon="question", width=30) #ShowMsg==FALSE if answer=YES
tcl("update", "idletasks") #closes the gmessage window
GetCurPos(SingClick=FALSE)
}
LoadCoreLine <- function(){
XPSSample <<- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <<- activeSpectIndx
Object <<- XPSSample[[Indx]]
Xlimits <<- range(Object@RegionToFit$x)
Ylimits <<- range(Object@RegionToFit$y)
Object@Boundaries$x <<- Xlimits
Object@Boundaries$y <<- Ylimits
point.coords$x <<- Xlimits #set original X range
point.coords$y <<- Ylimits #set original Y range
ComponentList <<- names(slot(Object,"Components"))
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
return()
}
xx <- Object@Components[[1]]@param[2,1] #component position mu
yy <- Object@Components[[1]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh <<- FALSE #now plot the component marker
replot() #replot spectrum and marker of selected fit component
if (UpdateCompMenu == TRUE){ ComponentMenu() }
}
editFitFrame <- function(h,...){
FComp <- svalue(FitComp)
FComp <- as.integer(gsub("[^0-9]", "", FComp)) #index selected component
fitParam <<- Object@Components[[FComp]]@param #load DataFrame relative to the selected component
VarNames <- rownames(fitParam)
idx <- grep("lg", VarNames)
if(length(idx) > 0){VarNames[idx] <- "Mix.L.G"}
idx <- grep("gv", VarNames)
if(length(idx) > 0){VarNames[idx] <- "Mix.G.V"}
fitParam <<- as.matrix(fitParam) #this is needed to construct correctly the data.frame
fitParam <<- data.frame(cbind(VarNames,fitParam), stringsAsFactors=FALSE) #in the dataframe add a column with variable names
newFitParam <<- fitParam
Label=paste("C", FComp, "- COMPONENT FIT PARAMETERS")
DFwin <- gwindow(title=Label, visible=FALSE) # open a window to edit the dataframe
DFgroup <- ggroup(horizontal=FALSE, container=DFwin)
txt <- paste("Fit Function: ", Object@Components[[FComp]]@funcName, sep="")
glabel(txt, container=DFgroup)
DFrame <- gdf(items=fitParam, container=DFgroup)
size(DFrame) <- c(550, 200)
tkconfigure(DFrame$widget, width=550, height=200)
addHandlerChanged(DFrame, handler=function(h,...){ #addHandlerChanged dowload the dataFrame with modified parameters in NewFirParam (global variable)
newFitParam <<- h$obj[]
})
gbutton(" SAVE AND EXIT ", handler=function(h,...){
newFP <- lapply(newFitParam[,2:ncol(newFitParam)], function(x) {as.numeric(x)} ) #the dataframe contais strings
fitParam <<- fitParam[,-1] #remove labels introduced in the first column of the DataFrame
fitParam[, 1:ncol(fitParam)] <<- newFP #this operation preserves the class(fitParam)=data.base nneded to save parameters in the relative slot of XPSSSample
Object@Components[[FComp]]@param <<- fitParam #save parameters in the slot of XPSSample
XPSSample[[Indx]] <<- Object
NComp <- length(Object@Components)
tmp <- NULL
for(ii in 1:NComp){
Object@Components[[ii]] <<- Ycomponent(Object@Components[[ii]], x=Object@RegionToFit$x, y=Object@Baseline$y)
tmp <- cbind(tmp, Object@Components[[ii]]@ycoor) #fit is the sum of fitting components
Object@Fit$y <<- colSums(t(tmp)) - length(Object@Components)*(Object@Baseline$y) #substract NComp*Baseline
}
Object <<- sortComponents(Object)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit[[1]])
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
yy <- Object@Components[[FComp]]@param[1,1] #component height h
FuncName <- Object@Components[[FComp]]@funcName
yy <- yy/GetHvalue(Object,FComp, FuncName, 1) #provides the correct yy value for complex functions
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy + Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx #Marker coords
coords[2] <<- yy
assign(activeFName, XPSSample, envir = .GlobalEnv)
dispose(DFwin)
XPSSaveRetrieveBkp("save")
replot()
return()
}, container = DFgroup)
visible(DFwin) <- TRUE
}
reset.vars <- function(){
XPSSample <<- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <<- 1
assign("activeSpectIndx", 1, envir=.GlobalEnv)
if(activeSpectIndx > length(XPSSample)) { Indx <<- 1 }
OldXPSSample <<- XPSSample
Object <<- XPSSample[[Indx]]
SpectName <<- NULL
ComponentList <<- names(Object@Components)
FNameList <<- XPSFNameList()
SpectList <<- XPSSpectList(activeFName)
FComp <<- 1
if (is.null(FitComp) == FALSE){
delete(MCGroup3, FitComp)
}
UpdateCompMenu <<- TRUE
coords <<- c(xx=NA, yy=NA, yy_BasLin=NA)
CompCoords <<- c(xx=NA, yy=NA, yy_BasLin=NA)
refresh <<- TRUE
SetZoom <<- FALSE
NoFit <<- FALSE
ShowMsg <<- TRUE
WinSize <<- as.numeric(XPSSettings$General[4])
hscale <<- hscale <- as.numeric(WinSize)
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
Xlimits <<- range(Object@.Data[1])
Ylimits <<- range(Object@.Data[2])
NoFit <<- TRUE
return()
}
}
# --- Variable definitions ---
XPSSample <- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <- activeSpectIndx
if(activeSpectIndx > length(XPSSample)) { Indx <- 1 }
OldXPSSample <- XPSSample
Object <- XPSSample[[Indx]]
SpectName <- NULL
ComponentList <<- names(Object@Components)
FNameList <- XPSFNameList()
SpectList <- XPSSpectList(activeFName)
FComp <- 1
FitComp <- NULL
UpdateCompMenu <- TRUE
WinSize <- as.numeric(XPSSettings$General[4])
hscale <- hscale <- as.numeric(WinSize)
coords <- c(xx=NA, yy=NA, yy_BasLin=NA)
CompCoords <- c(xx=NA, yy=NA, yy_BasLin=NA)
xx <- NULL
yy <- NULL
refresh <- TRUE
SetZoom <- FALSE
NoFit <- FALSE
ShowMsg <- TRUE
#Coreline boundaries
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
point.index <- 1
point.coords <- list(x=range(Object@RegionToFit$x), #set the X window extension == x range
y=range(Object@RegionToFit$y)) #set the Y window extension == x range
Xlimits <- range(Object@.Data[1])
Ylimits <- range(Object@.Data[2])
Object@Boundaries$x <- Xlimits
Object@Boundaries$y <- Ylimits
Corners <- list(x=NULL, y=NULL)
NoFit <- TRUE
} else {
LL <- length(Object@.Data[[1]])
point.index <- 1
point.coords <- list(x=range(Object@RegionToFit$x), #set the X window extension == x range
y=range(Object@RegionToFit$y)) #set the Y window extension == x range
Corners <- list(x=c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2]),
y=c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2]))
Xlimits <- range(Object@RegionToFit$x)
Ylimits <- range(Object@RegionToFit$y)
Object@Boundaries$x <- Xlimits
Object@Boundaries$y <- Ylimits
}
plot(Object)
if (Check.PE() == FALSE) { return() }
O.Sys <- unname(tolower(Sys.info()["sysname"]))
#--- GWidget definition ---
MCWindow <- gwindow("XPS MOVE COMPONENT", parent=c(50,10), visible = FALSE)
addHandlerDestroy(MCWindow, handler=function(h, ...){ #if MainWindow unproperly closed with X
EXIT <<- TRUE
XPSSettings$General[4] <<- 7 #Reset to normal graphic win dimension
assign("XPSSettings", XPSSettings, envir=.GlobalEnv)
plot(XPSSample[[Indx]]) #replot the CoreLine
})
#--- Selection Group ---
SelectGroup <- ggroup(horizontal=FALSE, spacing = 5, container=MCWindow)
MCGroup1 <- ggroup(horizontal=TRUE, spacing = 5, container=SelectGroup)
MCFrame1 <- gframe(text = " XPS Samples ", container = MCGroup1)
XPS.Sample <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
reset.vars()
ActFName <- svalue(XPS.Sample)
assign("activeFName", ActFName, envir=.GlobalEnv)
XPSSample <<- get(ActFName, envir=.GlobalEnv)
Indx <<- activeSpectIndx
if(activeSpectIndx > length(XPSSample)) { Indx <<- 1 }
Object <<- XPSSample[[Indx]]
SpectList <- XPSSpectList(activeFName)
delete(MCFrame1, Core.Lines)
Core.Lines <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPS.CL <- svalue(Core.Lines)
XPS.CL <- unlist(strsplit(XPS.CL, "\\."))
Indx <<- as.integer(XPS.CL[1]) #select "NUMber." in component name
SpectName <<- XPS.CL[2]
Object <<- XPSSample[[Indx]]
ComponentList <<- names(Object@Components)
assign("activeSpectName", SpectName,envir=.GlobalEnv) #set activeSpectName == last selected spectrum
assign("activeSpectIndx", Indx,envir=.GlobalEnv) #set the activeIndex == last selected spectrum
point.index <<- 1
UpdateCompMenu <<- TRUE
LoadCoreLine()
}, container = MCFrame1)
refresh <<- FALSE #now plot also the component marker
Xlimits <<- range(Object@RegionToFit$x)
Ylimits <<- range(Object@RegionToFit$y)
Object@Boundaries$x <<- Xlimits
Object@Boundaries$y <<- Ylimits
plot(Object)
}, container = MCFrame1)
svalue(XPS.Sample) <- activeFName
MCFrame2 <- gframe(text = " Core-Lines ", container = MCGroup1)
Core.Lines <- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPS.CL <- svalue(Core.Lines)
XPS.CL <- unlist(strsplit(XPS.CL, "\\."))
Indx <<- as.integer(XPS.CL[1]) #select "NUMber." in component name
SpectName <<- XPS.CL[2]
Object <<- XPSSample[[Indx]]
ComponentList <<- names(slot(Object,"Components"))
assign("activeSpectName", SpectName,envir=.GlobalEnv) #set activeSpectName == last selected spectrum
assign("activeSpectIndx", Indx,envir=.GlobalEnv) #set the activeIndex == last selected spectrum
point.index <<- 1
UpdateCompMenu <<- TRUE
LoadCoreLine()
}, container = MCFrame2)
svalue(Core.Lines) <- SpectList[Indx]
MCFrame3 <- gframe(text = " COMPONENTS ", spacing=5, container = SelectGroup)
MCGroup3 <- ggroup(spacing=3, horizontal=FALSE, container=MCFrame3)
FitComplyt <- glayout(spacing=5, container=MCGroup3)
FitComplyt[1, 1] <- glabel(" ", container=FitComplyt) #just to add a space in MCFrame3
MCFrame4 <- gframe(text = " OPTIONS ", spacing=5, container = SelectGroup)
Buttlyt <- glayout(spacing=5, container=MCFrame4)
Buttlyt[1,1] <- LMFitbutton <- gbutton(" FIT Lev.Marq. ", handler=function(h,...){
svalue(FitComp) <- -1
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
Object <<- XPSFitLM(Object, plt=FALSE)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx #coords of marker of the first fit component
coords[2] <<- yy
Object <<- sortComponents(Object)
refresh <<- FALSE #now plot also the component marker
assign("Object", Object, envir = .GlobalEnv)
replot()
}, container = Buttlyt)
Buttlyt[1,2] <- MFFitbutton <- gbutton(" FIT Modfit ", handler=function(h,...){
svalue(FitComp) <- -1
if( is.na(match("FME", Pkgs)) == TRUE ){ #check if the package 'FME' is installed
txt <- "Package 'FME' not installed. \nOption 'ModFit' not available"
gmessage(msg=txt, title="WARNING", icon="error")
return()
}
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
Object <<- XPSModFit(Object, plt=FALSE)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
Object <<- sortComponents(Object)
refresh <<- FALSE #now plot also the component marker
assign("Object", Object, envir = .GlobalEnv)
replot()
}, container = Buttlyt)
Buttlyt[2,1] <- ZRbutton <- gbutton(" SET ZOOM REGION ", handler = function(h, ...){
CompCoords <<- coords #save the of position component_marker
point.coords <<- NULL #point.coords contain the X, Y data ranges
enabled(LMFitbutton) <- FALSE
enabled(MFFitbutton) <- FALSE
enabled(RSTbutton) <- FALSE
SetZoom <<- TRUE
point.coords$x <<- range(Object@RegionToFit$x)
point.coords$y <<- range(Object@RegionToFit$y)
if (Object@Flags[1]) { #Binding energy set
point.coords$x <<- sort(c(point.coords$x[1], point.coords$x[2]), decreasing=TRUE) #pos$x in decreasing order
}
Xlimits <<- point.coords$x
Ylimits <<- point.coords$y
Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
Marker <<- list(Points=Corners, col=4, cex=1.2, lwd=2.5, pch=3)
point.index <<- 3 #plot initial zoom area
replot()
if (O.Sys == "windows"){
msg <- paste("\n => Right click near corners to adjust Zoom Region Dimensions",
"\n => When Zoom Region OK, press MAKE ZOOM", sep="")
gmessage(msg, title="WARNING", icon="warning")
} else if (O.Sys == "linux"){
msg <- paste("\n => Left click near corners to adjust Zoom Region Dimensions",
"\n => When Zoom Region OK, right click and press MAKE ZOOM", sep="")
gmessage(msg, title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
GetCurPos(SingClick=FALSE)
}
}, container = Buttlyt)
Buttlyt[2,2] <- MZbutton <- gbutton(" MAKE ZOOM ", handler = function(h, ...){
if (Object@Flags[1]) { #Binding energy set
point.coords$x <- sort(point.coords$x, decreasing=TRUE) #pos$x in decreasing order
point.coords$x[1] <- point.coords$x[1]
point.coords$x[2] <- point.coords$x[2]
} else {
point.coords$x<-sort(point.coords$x, decreasing=FALSE) #pos$x in increasing order
point.coords$x[1] <- point.coords$x[1]
point.coords$x[2] <- point.coords$x[2]
}
Xlimits <<- point.coords$x
Ylimits <<- sort(point.coords$y, decreasing=FALSE)
slot(Object,"Boundaries") <<- point.coords
point.index <<- 1
coords <<- CompCoords #restore of position component_marker
refresh <<- FALSE
SetZoom <<- FALSE
assign("Object", Object, envir = .GlobalEnv)
replot()
enabled(LMFitbutton) <- TRUE
enabled(MFFitbutton) <- TRUE
enabled(RSTbutton) <- TRUE
}, container = Buttlyt)
Buttlyt[3,1] <- RSTbutton <- gbutton(" RESET PLOT ", handler = function(h, ...) {
SetZoom <<- FALSE
refresh <<- FALSE
point.index <<- 1
reset.plot()
}, container = Buttlyt)
Buttlyt[3,2] <- gbutton(" UNDO ", handler = function(h, ...) {
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
XPSSample <<- OldXPSSample
Object <<- XPSSample[[Indx]]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
replot()
}, container = Buttlyt)
Buttlyt[4,1] <- gbutton(" EDIT PARAMETERS ", handler=editFitFrame, container = Buttlyt)
Buttlyt[4,2] <- gbutton(" RE-LOAD DATA ", handler=function(h,...){
svalue(FitComp) <- -1
UpdateCompMenu <<- FALSE
LoadCoreLine()
svalue(FitComp, index=TRUE) <- 1
OldXPSSample <<- XPSSample
}, container = Buttlyt)
Buttlyt[5,1] <- gbutton(" SAVE ", handler=function(h,...){
# With button SAVE the Component parameters are updated and are now available for FiTConstraints
svalue(FitComp) <- -1
Indx <- get("activeSpectIndx", envir=.GlobalEnv)
XPSSample[[Indx]] <<- Object
OldXPSSample[[Indx]] <<- XPSSample[[Indx]]
assign("Object", XPSSample[[Indx]], envir = .GlobalEnv)
assign(activeFName, XPSSample, envir = .GlobalEnv)
replot()
XPSSaveRetrieveBkp("save")
}, container = Buttlyt)
Buttlyt[5,2] <- gbutton(" EXIT ", handler=function(h,...){
#----- stopping mouse handler
dispose(MCWindow) #Disposing MCWindow will activate GDestroyHandler which re-opens the graphic window
XPSSample <- get(activeFName, envir=.GlobalEnv) #Update XPSSample with all changes before plotting
XPSSaveRetrieveBkp("save")
plot(XPSSample[[Indx]]) #replot the CoreLine
}, container = Buttlyt)
StatBar <- gstatusbar("status", container = MCWindow)
#--- Marker-----
if (NoFit==FALSE){
coords[1] <- Object@Components[[1]]@param[2,1] #component position mu
coords[2] <- Object@Components[[1]]@param[1,1] #component1 height h
FuncName <- Object@Components[[1]]@funcName
coords[2] <- coords[2]/GetHvalue(Object,1, FuncName, 1)
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > coords[1]-Estep/2 & Object@RegionToFit[[1]] < coords[1]+Estep/2) #indice del vettore X corrispondente alla posizione della componente
coords[2] <- coords[2]+Object@Baseline$y[Xindx]
refresh <- FALSE
replot()
refresh <- TRUE
}
enabled(LMFitbutton) <- TRUE
enabled(MFFitbutton) <- TRUE
enabled(RSTbutton) <- TRUE
visible(MCWindow) <- TRUE
tkevent.generate(MCWindow$widget, "<Expose>", when="now") #forces the MCWindow to be exposed
tcl("update", "idletasks") #Complete the idle tasks
#--- Interactive mouse control ---
if (length(ComponentList) > 0) {
ComponentMenu()
}
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSMoveComp
Documented in XPSMoveComp
#' @title XPSMoveComp
#' @description XPSMoveComp function to modify component position and intensity in a fit
#' this function provides a userfriendly interface change position and intensity of each
#' individual fitting component of a selected XPSCoreline. Changes are saved
#' in the .GlobalEnv main software memory.
#' @examples
#' \dontrun{
#' XPSMoveComp()
#' }
#' @export
#'
XPSMoveComp <- function(){
GetCurPos <- function(SingClick){
coords <<- NULL
EXIT <- FALSE
enabled(FitComp) <- FALSE #prevent exiting Analysis if locatore active
enabled(MCFrame4) <- FALSE #prevent exiting Analysis if locatore active
Estep <- abs(Object@RegionToFit[[1]][1] - Object@RegionToFit[[1]][2])
cat("\n 1111")
while(EXIT == FALSE){
pos <- locator(n=1)
if (is.null(pos)) {
enabled(FitComp) <- TRUE
enabled(MCFrame4) <- TRUE
EXIT <- TRUE
} else {
if (SingClick){
enabled(FitComp) <- TRUE
enabled(MCFrame4) <- TRUE
EXIT <- TRUE
}
if (SetZoom == TRUE) { #define zoom area
xx <- pos$x
yy <- pos$y
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy_BasLin <- yy-Object@Baseline$y[Xindx] #spectral intensity at xx without Baseline
coords <<- c(xx, yy, yy_BasLin)
RBmousedown() #selection of the zoom area
} else {
xx <- pos$x
yy <- pos$y
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy_BasLin <- yy-Object@Baseline$y[Xindx] #spectral intensity at xx without Baseline
coords <<- c(xx, yy, yy_BasLin)
LBmousedown() #selection of the BaseLine Edges
}
}
}
return()
}
LBmousedown <- function() { #Left mouse button down
xx <- coords[1]
yy <- coords[2]
if (SetZoom==FALSE) { #left button works only when SET ZOOM REGION inactive
MoveComp()
## loop on spectra and retrieve Pass Energy
XPSquantify(XPSSample)
refresh <<- FALSE
}
replot()
}
RBmousedown <- function() { #Right mouse button down
xx <- coords[1]
yy <- coords[2]
if (SetZoom == TRUE) { #left button works only when SET ZOOM REGION button pressed
point.coords$x[point.index] <<- coords[1] #abscissa
point.coords$y[point.index] <<- coords[2] #ordinate
if (point.index == 1) { #First rect corner C1
point.index <<- 3
Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
# } else if (point.index == 2) { #Second rect corner C2 opposite to C1
# point.index <<- 3
# Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
# Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
} else if (point.index == 3) { #modifies corner positions
D <- vector("numeric", 4)
Dmin <- ((point.coords$x[3]-Corners$x[1])^2 + (point.coords$y[3]-Corners$y[1])^2)^0.5 #valore di inizializzazione
for (ii in 1:4) {
D[ii] <- ((point.coords$x[3]-Corners$x[ii])^2 + (point.coords$y[3]-Corners$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] <<- point.coords$x[3]
Corners$y[1] <<- Corners$y[3] <<- point.coords$y[3]
} else if (idx==2){
Corners$x[1] <<- Corners$x[2] <<- point.coords$x[3]
Corners$y[2] <<- Corners$y[4] <<- point.coords$y[3]
} else if (idx==3){
Corners$x[3] <<- Corners$x[4] <<- point.coords$x[3]
Corners$y[1] <<- Corners$y[3] <<- point.coords$y[3]
} else if (idx==4){
Corners$x[3] <<- Corners$x[4] <<- point.coords$x[3]
Corners$y[2] <<- Corners$y[4] <<- point.coords$y[3]
}
if (Object@Flags[1]) { #Binding energy set
point.coords$x <<- sort(c(Corners$x[1],Corners$x[3]), decreasing=TRUE) #pos$x in decreasing order
point.coords$y <<- sort(c(Corners$y[1],Corners$y[4]), decreasing=FALSE)
} else {
point.coords$x <<- sort(c(Corners$x[1],Corners$x[3]), decreasing=FALSE) #pos$x in increasing order
point.coords$y <<- sort(c(Corners$y[1],Corners$y[4]), decreasing=FALSE)
}
}
replot()
}
}
Check.PE <- function(){
PassE <- NULL
PassE <- sapply( XPSSample, function(x) {
info <- x@Info[1] #retrieve info containing PE value
sss <- strsplit(info, "Pass energy") #extract PE value
PE <- strsplit(sss[[1]][2], "Iris") #PE value
PE <- gsub(" ", "", PE[[1]][1], fixed=TRUE) #drop white spaces in string PE
PE <- as.integer(PE)
return(PE)
}
)
SpectList <- XPSSpectList(activeFName)
idx <- grep("Survey", SpectList) #recognize presence of a Survey
if (length(idx) == 0){ idx <- grep("survey", SpectList) }
if (length(idx) == 0){ return(TRUE) } #No survey spectra are present in XPSSample: continue working
PEsur <- PassE[[ idx[1] ]] #if idx is a vector, select the first element
if (length(idx) > 0){ #a survey is present
SpectList <- SpectList[-idx] #eliminate the "Survey" from list of Spectral Names
PassE <- PassE[-idx] #eliminate the PassE(survey) to compare PE of only core-lines
}
Extracted <- which(PassE == 160)
LL <- length(Extracted)
if (LL > 0){
for(ii in 1:LL){
Indx <- Extracted[ii]
Indx <- unlist(strsplit(SpectList[Indx], "\\."))
Indx <- as.integer(Indx[1]) #select "NUMber." in component name
if ( hasRegionToFit(XPSSample[[Indx]])){
txt <- paste(SpectList[Extracted], collapse=" ")
txt <- paste(" Found Core Line: ", txt, " extracted from Survey.
\nCannot perform quantification here!
\nPlease exit MOVE COMPONENT and run QUANTIFY option to correct Core Line intensity")
gmessage(msg=txt, title="WARNING", icon="warning")
return(FALSE)
break
}
}
}
return(TRUE)
}
MoveComp <- function(...) {
# FComp <- svalue(FitComp)
if (length(FComp)==0) {
gmessage(msg="Select Component Please", title="WARNING", icon = "warning")
} else {
# FComp <- as.numeric(unlist(strsplit(FComp, split="C"))) #index of the selected component
# FComp <- FComp[2]
xx <- coords[1]
yy <- coords[2] #Component max value with baseline
zz <- coords[3] #Component max value without baseline
FitFunct <- Object@Components[[FComp]]@funcName
newh <- GetHvalue(Object, FComp, FitFunct, zz) #Get value computes the Component value given the fit parameters and the Ymax value
#range limits for mu
varmu <- getParam(Object@Components[[FComp]],variable="mu")
minmu <- varmu$start-varmu$min
maxmu <- varmu$max-varmu$start
newmu <- c(xx, xx-minmu, xx+maxmu)
#range limits for h
varh <- getParam(Object@Components[[FComp]],variable="h")
minh <- varh$start-varh$min
maxh <- varh$max-varh$start
if (maxh > 0) {
newh <- c(newh, 0, newh*5) # No constraints on h
}
if (maxh==0){
newh <- c(newh, newh, newh) # h is fixed
}
if (maxh < 0){
newh <- c(newh, 0, newh*5) # maxh cannot be <0: => force newH to correct values
}
if (varh$start < 0) {
newh <- c(0, 0, 1e5) #set a positive value for an hypotheic fit
}
Object@Components[[FComp]] <<- setParam(Object@Components[[FComp]], parameter=NULL, variable="mu", value=newmu)
Object@Components[[FComp]] <<- setParam(Object@Components[[FComp]], parameter=NULL, variable="h", value=newh)
#Now compute the new component Y values for the new xy position
Object@Components[[FComp]] <<- Ycomponent(Object@Components[[FComp]], x=Object@RegionToFit$x, y=Object@Baseline$y) #eomputes the Y value and add baseline
#Fit computed addind fit components with the modified ones
tmp <- sapply(Object@Components, function(z) matrix(data=z@ycoor))
Object@Fit$y <<- ( colSums(t(tmp)) - length(Object@Components)*(Object@Baseline$y))
Object <<- sortComponents(Object)
#if component order changed then re-number them
LL <- length(Object@Components) #N. fit components
for (ii in 1:LL){
if (xx == Object@Components[[ii]]@param["mu",1]) { #compare marker position with component positions
idx <- ii
break()
}
}
svalue(FitComp) <- paste("C", idx, sep="") #update component gradio
XPSSample[[Indx]] <<- Object
}
}
replot <- function(...) {
if (point.index==1 && refresh==FALSE) { #point.index==1 when moving mcomponent
plot(Object, xlim=Xlimits, ylim=Ylimits)
points(x=coords[1], y=coords[2], col=2, cex=1.2, lwd=2.5, pch=1) # if refresh==FALSE plot spectrum with component marker
} else if (SetZoom == TRUE){ #set zoom area corners
if (point.index == 1) { #normal plot
plot(Object)
points(point.coords, type="p", col=4, cex=1.2, lwd=2.5, pch=3)
} else if (point.index == 3){ #plot zoom area corners
plot(Object, xlim=Xlimits, ylim=Ylimits)
points(Corners, type="p", col=4, cex=1.2, lwd=2.5, pch=3)
rect(point.coords$x[1], point.coords$y[1], point.coords$x[2], point.coords$y[2])
}
} else {
plot(Object, xlim=Xlimits, ylim=Ylimits)
}
if (! is.null(coords)){
svalue(StatBar) <- paste("x =",round(coords[1],2), "y =",round(coords[2],2), sep=" ")
}
}
reset.plot <- function(h, ...) {
point.coords$x <<- range(Object@RegionToFit$x) #set original X range
point.coords$y <<- range(Object@RegionToFit$y) #set original Y range
Object@Boundaries <<- point.coords
Xlimits <<- point.coords$x
Ylimits <<- sort(point.coords$y, decreasing=FALSE)
Corners <- list(x=c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2]),
y=c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2]))
replot()
}
ComponentMenu <- function(){
FComp <<- 1
delete(MCFrame3,MCGroup3)
MCGroup3 <<- ggroup(spacing=3, horizontal=FALSE, container=MCFrame3)
FitComplyt <<- glayout(spacing=5, container=MCGroup3)
if (length(ComponentList) > 1){ #gradio works with at least 2 items
FitComp <<- gradio(ComponentList, selected=1, handler = function(h,...){
FComp <<- svalue(FitComp)
cat("\n selected component:", FComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit$x)
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
yy <- Object@Components[[FComp]]@param[1,1] #component height h
FuncName <- Object@Components[[FComp]]@funcName
yy <- yy/GetHvalue(Object,FComp, FuncName, 1) #provides the correct yy value for complex functions
Estep <- abs(Object@RegionToFit$x[1]-Object@RegionToFit$x[2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh <<- TRUE #cancel previous selections
replot() #plot spectrum without marker
refresh <<- FALSE #now plot also the component marker
replot() #replot spectrum and marker
if (ShowMsg==TRUE){
gmessage("Left click to enter Fit Component position. Right click to stop slection", title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
}
GetCurPos(SingClick=FALSE)
}, container = MCGroup3)
LL <- length(ComponentList)
NCol <- ceiling(LL/5) #gradio will be split in solumns of 5 elements
for(ii in 1:LL){
tkpack.forget(FitComp$widgets[[ii]]) # unparent widgets (uses library call)
}
for(kk in 1:NCol){
NN <- (kk-1)*5
for (ii in 1:5) {
if((ii+NN) > LL) {break}
FitComplyt[ii,kk] <<- FitComp$widgets[[(ii+NN)]]
}
}
}
if (length(ComponentList) == 1){ #gradio works with at least 2 items
FitComp <<- gcheckboxgroup(ComponentList, checked=TRUE, handler = function(h,...){
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected compoent
FComp <<- FComp[2]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit[[1]])
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh<<-TRUE #cancel previous component markers
replot() #plot spectrum only
refresh <<- FALSE #now plot spectrum + component marker
replot()
if (O.Sys == "linux"){ #in Linux locator is activated to read cursor positions
if (ShowMsg==TRUE){
gmessage("Left click to enter Fit Component position. Right click to stop slection", title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
}
GetCurPos(SingClick=FALSE)
}
}, container = MCGroup3)
}
txt <- paste("The selection of a Core-Line or Fit-Component always activates reading the [X,Y] cursor position.",
"\n=> Left click with the mouse to enter the cursor coordinates.",
"\n=> Right click to stop position selection and cursor position reading when not required.",
"\n",
"=> Do not show these WARNING messages again press YES, let WARNINGS active press NO", sep="")
ShowMsg <<- !gconfirm(msg=txt, title="WARNING", icon="question", width=30) #ShowMsg==FALSE if answer=YES
tcl("update", "idletasks") #closes the gmessage window
GetCurPos(SingClick=FALSE)
}
LoadCoreLine <- function(){
XPSSample <<- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <<- activeSpectIndx
Object <<- XPSSample[[Indx]]
Xlimits <<- range(Object@RegionToFit$x)
Ylimits <<- range(Object@RegionToFit$y)
Object@Boundaries$x <<- Xlimits
Object@Boundaries$y <<- Ylimits
point.coords$x <<- Xlimits #set original X range
point.coords$y <<- Ylimits #set original Y range
ComponentList <<- names(slot(Object,"Components"))
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
return()
}
xx <- Object@Components[[1]]@param[2,1] #component position mu
yy <- Object@Components[[1]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
refresh <<- FALSE #now plot the component marker
replot() #replot spectrum and marker of selected fit component
if (UpdateCompMenu == TRUE){ ComponentMenu() }
}
editFitFrame <- function(h,...){
FComp <- svalue(FitComp)
FComp <- as.integer(gsub("[^0-9]", "", FComp)) #index selected component
fitParam <<- Object@Components[[FComp]]@param #load DataFrame relative to the selected component
VarNames <- rownames(fitParam)
idx <- grep("lg", VarNames)
if(length(idx) > 0){VarNames[idx] <- "Mix.L.G"}
idx <- grep("gv", VarNames)
if(length(idx) > 0){VarNames[idx] <- "Mix.G.V"}
fitParam <<- as.matrix(fitParam) #this is needed to construct correctly the data.frame
fitParam <<- data.frame(cbind(VarNames,fitParam), stringsAsFactors=FALSE) #in the dataframe add a column with variable names
newFitParam <<- fitParam
Label=paste("C", FComp, "- COMPONENT FIT PARAMETERS")
DFwin <- gwindow(title=Label, visible=FALSE) # open a window to edit the dataframe
DFgroup <- ggroup(horizontal=FALSE, container=DFwin)
txt <- paste("Fit Function: ", Object@Components[[FComp]]@funcName, sep="")
glabel(txt, container=DFgroup)
DFrame <- gdf(items=fitParam, container=DFgroup)
size(DFrame) <- c(550, 200)
tkconfigure(DFrame$widget, width=550, height=200)
addHandlerChanged(DFrame, handler=function(h,...){ #addHandlerChanged dowload the dataFrame with modified parameters in NewFirParam (global variable)
newFitParam <<- h$obj[]
})
gbutton(" SAVE AND EXIT ", handler=function(h,...){
newFP <- lapply(newFitParam[,2:ncol(newFitParam)], function(x) {as.numeric(x)} ) #the dataframe contais strings
fitParam <<- fitParam[,-1] #remove labels introduced in the first column of the DataFrame
fitParam[, 1:ncol(fitParam)] <<- newFP #this operation preserves the class(fitParam)=data.base nneded to save parameters in the relative slot of XPSSSample
Object@Components[[FComp]]@param <<- fitParam #save parameters in the slot of XPSSample
XPSSample[[Indx]] <<- Object
NComp <- length(Object@Components)
tmp <- NULL
for(ii in 1:NComp){
Object@Components[[ii]] <<- Ycomponent(Object@Components[[ii]], x=Object@RegionToFit$x, y=Object@Baseline$y)
tmp <- cbind(tmp, Object@Components[[ii]]@ycoor) #fit is the sum of fitting components
Object@Fit$y <<- colSums(t(tmp)) - length(Object@Components)*(Object@Baseline$y) #substract NComp*Baseline
}
Object <<- sortComponents(Object)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
Rng <- range(Object@RegionToFit[[1]])
if (xx < Rng[1]) {xx <- Rng[1]}
if (xx > Rng[2]) {xx <- Rng[2]}
yy <- Object@Components[[FComp]]@param[1,1] #component height h
FuncName <- Object@Components[[FComp]]@funcName
yy <- yy/GetHvalue(Object,FComp, FuncName, 1) #provides the correct yy value for complex functions
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy + Object@Baseline$y[Xindx] #spectral intensity + baseline at point xx
coords[1] <<- xx #Marker coords
coords[2] <<- yy
assign(activeFName, XPSSample, envir = .GlobalEnv)
dispose(DFwin)
XPSSaveRetrieveBkp("save")
replot()
return()
}, container = DFgroup)
visible(DFwin) <- TRUE
}
reset.vars <- function(){
XPSSample <<- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <<- 1
assign("activeSpectIndx", 1, envir=.GlobalEnv)
if(activeSpectIndx > length(XPSSample)) { Indx <<- 1 }
OldXPSSample <<- XPSSample
Object <<- XPSSample[[Indx]]
SpectName <<- NULL
ComponentList <<- names(Object@Components)
FNameList <<- XPSFNameList()
SpectList <<- XPSSpectList(activeFName)
FComp <<- 1
if (is.null(FitComp) == FALSE){
delete(MCGroup3, FitComp)
}
UpdateCompMenu <<- TRUE
coords <<- c(xx=NA, yy=NA, yy_BasLin=NA)
CompCoords <<- c(xx=NA, yy=NA, yy_BasLin=NA)
refresh <<- TRUE
SetZoom <<- FALSE
NoFit <<- FALSE
ShowMsg <<- TRUE
WinSize <<- as.numeric(XPSSettings$General[4])
hscale <<- hscale <- as.numeric(WinSize)
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
Xlimits <<- range(Object@.Data[1])
Ylimits <<- range(Object@.Data[2])
NoFit <<- TRUE
return()
}
}
# --- Variable definitions ---
XPSSample <- get(activeFName, envir=.GlobalEnv) #load XPSdata values from main memory
Indx <- activeSpectIndx
if(activeSpectIndx > length(XPSSample)) { Indx <- 1 }
OldXPSSample <- XPSSample
Object <- XPSSample[[Indx]]
SpectName <- NULL
ComponentList <<- names(Object@Components)
FNameList <- XPSFNameList()
SpectList <- XPSSpectList(activeFName)
FComp <- 1
FitComp <- NULL
UpdateCompMenu <- TRUE
WinSize <- as.numeric(XPSSettings$General[4])
hscale <- hscale <- as.numeric(WinSize)
coords <- c(xx=NA, yy=NA, yy_BasLin=NA)
CompCoords <- c(xx=NA, yy=NA, yy_BasLin=NA)
xx <- NULL
yy <- NULL
refresh <- TRUE
SetZoom <- FALSE
NoFit <- FALSE
ShowMsg <- TRUE
#Coreline boundaries
if (length(ComponentList)==0) {
gmessage("ATTENTION NO FIT FOUND: change coreline please!" , title = "WARNING", icon = "warning")
point.index <- 1
point.coords <- list(x=range(Object@RegionToFit$x), #set the X window extension == x range
y=range(Object@RegionToFit$y)) #set the Y window extension == x range
Xlimits <- range(Object@.Data[1])
Ylimits <- range(Object@.Data[2])
Object@Boundaries$x <- Xlimits
Object@Boundaries$y <- Ylimits
Corners <- list(x=NULL, y=NULL)
NoFit <- TRUE
} else {
LL <- length(Object@.Data[[1]])
point.index <- 1
point.coords <- list(x=range(Object@RegionToFit$x), #set the X window extension == x range
y=range(Object@RegionToFit$y)) #set the Y window extension == x range
Corners <- list(x=c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2]),
y=c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2]))
Xlimits <- range(Object@RegionToFit$x)
Ylimits <- range(Object@RegionToFit$y)
Object@Boundaries$x <- Xlimits
Object@Boundaries$y <- Ylimits
}
plot(Object)
if (Check.PE() == FALSE) { return() }
O.Sys <- unname(tolower(Sys.info()["sysname"]))
#--- GWidget definition ---
MCWindow <- gwindow("XPS MOVE COMPONENT", parent=c(50,10), visible = FALSE)
addHandlerDestroy(MCWindow, handler=function(h, ...){ #if MainWindow unproperly closed with X
EXIT <<- TRUE
XPSSettings$General[4] <<- 7 #Reset to normal graphic win dimension
assign("XPSSettings", XPSSettings, envir=.GlobalEnv)
plot(XPSSample[[Indx]]) #replot the CoreLine
})
#--- Selection Group ---
SelectGroup <- ggroup(horizontal=FALSE, spacing = 5, container=MCWindow)
MCGroup1 <- ggroup(horizontal=TRUE, spacing = 5, container=SelectGroup)
MCFrame1 <- gframe(text = " XPS Samples ", container = MCGroup1)
XPS.Sample <- gcombobox(FNameList, selected=-1, editable=FALSE, handler=function(h,...){
reset.vars()
ActFName <- svalue(XPS.Sample)
assign("activeFName", ActFName, envir=.GlobalEnv)
XPSSample <<- get(ActFName, envir=.GlobalEnv)
Indx <<- activeSpectIndx
if(activeSpectIndx > length(XPSSample)) { Indx <<- 1 }
Object <<- XPSSample[[Indx]]
SpectList <- XPSSpectList(activeFName)
delete(MCFrame1, Core.Lines)
Core.Lines <<- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPS.CL <- svalue(Core.Lines)
XPS.CL <- unlist(strsplit(XPS.CL, "\\."))
Indx <<- as.integer(XPS.CL[1]) #select "NUMber." in component name
SpectName <<- XPS.CL[2]
Object <<- XPSSample[[Indx]]
ComponentList <<- names(Object@Components)
assign("activeSpectName", SpectName,envir=.GlobalEnv) #set activeSpectName == last selected spectrum
assign("activeSpectIndx", Indx,envir=.GlobalEnv) #set the activeIndex == last selected spectrum
point.index <<- 1
UpdateCompMenu <<- TRUE
LoadCoreLine()
}, container = MCFrame1)
refresh <<- FALSE #now plot also the component marker
Xlimits <<- range(Object@RegionToFit$x)
Ylimits <<- range(Object@RegionToFit$y)
Object@Boundaries$x <<- Xlimits
Object@Boundaries$y <<- Ylimits
plot(Object)
}, container = MCFrame1)
svalue(XPS.Sample) <- activeFName
MCFrame2 <- gframe(text = " Core-Lines ", container = MCGroup1)
Core.Lines <- gcombobox(SpectList, selected=-1, editable=FALSE, handler=function(h,...){
XPS.CL <- svalue(Core.Lines)
XPS.CL <- unlist(strsplit(XPS.CL, "\\."))
Indx <<- as.integer(XPS.CL[1]) #select "NUMber." in component name
SpectName <<- XPS.CL[2]
Object <<- XPSSample[[Indx]]
ComponentList <<- names(slot(Object,"Components"))
assign("activeSpectName", SpectName,envir=.GlobalEnv) #set activeSpectName == last selected spectrum
assign("activeSpectIndx", Indx,envir=.GlobalEnv) #set the activeIndex == last selected spectrum
point.index <<- 1
UpdateCompMenu <<- TRUE
LoadCoreLine()
}, container = MCFrame2)
svalue(Core.Lines) <- SpectList[Indx]
MCFrame3 <- gframe(text = " COMPONENTS ", spacing=5, container = SelectGroup)
MCGroup3 <- ggroup(spacing=3, horizontal=FALSE, container=MCFrame3)
FitComplyt <- glayout(spacing=5, container=MCGroup3)
FitComplyt[1, 1] <- glabel(" ", container=FitComplyt) #just to add a space in MCFrame3
MCFrame4 <- gframe(text = " OPTIONS ", spacing=5, container = SelectGroup)
Buttlyt <- glayout(spacing=5, container=MCFrame4)
Buttlyt[1,1] <- LMFitbutton <- gbutton(" FIT Lev.Marq. ", handler=function(h,...){
svalue(FitComp) <- -1
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
Object <<- XPSFitLM(Object, plt=FALSE)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx #coords of marker of the first fit component
coords[2] <<- yy
Object <<- sortComponents(Object)
refresh <<- FALSE #now plot also the component marker
assign("Object", Object, envir = .GlobalEnv)
replot()
}, container = Buttlyt)
Buttlyt[1,2] <- MFFitbutton <- gbutton(" FIT Modfit ", handler=function(h,...){
svalue(FitComp) <- -1
if( is.na(match("FME", Pkgs)) == TRUE ){ #check if the package 'FME' is installed
txt <- "Package 'FME' not installed. \nOption 'ModFit' not available"
gmessage(msg=txt, title="WARNING", icon="error")
return()
}
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
Object <<- XPSModFit(Object, plt=FALSE)
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
Object <<- sortComponents(Object)
refresh <<- FALSE #now plot also the component marker
assign("Object", Object, envir = .GlobalEnv)
replot()
}, container = Buttlyt)
Buttlyt[2,1] <- ZRbutton <- gbutton(" SET ZOOM REGION ", handler = function(h, ...){
CompCoords <<- coords #save the of position component_marker
point.coords <<- NULL #point.coords contain the X, Y data ranges
enabled(LMFitbutton) <- FALSE
enabled(MFFitbutton) <- FALSE
enabled(RSTbutton) <- FALSE
SetZoom <<- TRUE
point.coords$x <<- range(Object@RegionToFit$x)
point.coords$y <<- range(Object@RegionToFit$y)
if (Object@Flags[1]) { #Binding energy set
point.coords$x <<- sort(c(point.coords$x[1], point.coords$x[2]), decreasing=TRUE) #pos$x in decreasing order
}
Xlimits <<- point.coords$x
Ylimits <<- point.coords$y
Corners$x <<- c(point.coords$x[1],point.coords$x[1],point.coords$x[2],point.coords$x[2])
Corners$y <<- c(point.coords$y[1],point.coords$y[2],point.coords$y[1],point.coords$y[2])
Marker <<- list(Points=Corners, col=4, cex=1.2, lwd=2.5, pch=3)
point.index <<- 3 #plot initial zoom area
replot()
if (O.Sys == "windows"){
msg <- paste("\n => Right click near corners to adjust Zoom Region Dimensions",
"\n => When Zoom Region OK, press MAKE ZOOM", sep="")
gmessage(msg, title="WARNING", icon="warning")
} else if (O.Sys == "linux"){
msg <- paste("\n => Left click near corners to adjust Zoom Region Dimensions",
"\n => When Zoom Region OK, right click and press MAKE ZOOM", sep="")
gmessage(msg, title="WARNING", icon="warning")
tcl("update", "idletasks") #closes the gmessage window
GetCurPos(SingClick=FALSE)
}
}, container = Buttlyt)
Buttlyt[2,2] <- MZbutton <- gbutton(" MAKE ZOOM ", handler = function(h, ...){
if (Object@Flags[1]) { #Binding energy set
point.coords$x <- sort(point.coords$x, decreasing=TRUE) #pos$x in decreasing order
point.coords$x[1] <- point.coords$x[1]
point.coords$x[2] <- point.coords$x[2]
} else {
point.coords$x<-sort(point.coords$x, decreasing=FALSE) #pos$x in increasing order
point.coords$x[1] <- point.coords$x[1]
point.coords$x[2] <- point.coords$x[2]
}
Xlimits <<- point.coords$x
Ylimits <<- sort(point.coords$y, decreasing=FALSE)
slot(Object,"Boundaries") <<- point.coords
point.index <<- 1
coords <<- CompCoords #restore of position component_marker
refresh <<- FALSE
SetZoom <<- FALSE
assign("Object", Object, envir = .GlobalEnv)
replot()
enabled(LMFitbutton) <- TRUE
enabled(MFFitbutton) <- TRUE
enabled(RSTbutton) <- TRUE
}, container = Buttlyt)
Buttlyt[3,1] <- RSTbutton <- gbutton(" RESET PLOT ", handler = function(h, ...) {
SetZoom <<- FALSE
refresh <<- FALSE
point.index <<- 1
reset.plot()
}, container = Buttlyt)
Buttlyt[3,2] <- gbutton(" UNDO ", handler = function(h, ...) {
FComp <<- svalue(FitComp)
FComp <<- as.numeric(unlist(strsplit(FComp, split="C"))) #index selected component
FComp <<- FComp[2]
XPSSample <<- OldXPSSample
Object <<- XPSSample[[Indx]]
xx <- Object@Components[[FComp]]@param[2,1] #component position mu
yy <- Object@Components[[FComp]]@param[1,1] #component height h
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > xx-Estep/2 & Object@RegionToFit[[1]] < xx+Estep/2)
yy <- yy+Object@Baseline$y[Xindx] #spectral intensity + Baseline at point xx
coords[1] <<- xx
coords[2] <<- yy
replot()
}, container = Buttlyt)
Buttlyt[4,1] <- gbutton(" EDIT PARAMETERS ", handler=editFitFrame, container = Buttlyt)
Buttlyt[4,2] <- gbutton(" RE-LOAD DATA ", handler=function(h,...){
svalue(FitComp) <- -1
UpdateCompMenu <<- FALSE
LoadCoreLine()
svalue(FitComp, index=TRUE) <- 1
OldXPSSample <<- XPSSample
}, container = Buttlyt)
Buttlyt[5,1] <- gbutton(" SAVE ", handler=function(h,...){
# With button SAVE the Component parameters are updated and are now available for FiTConstraints
svalue(FitComp) <- -1
Indx <- get("activeSpectIndx", envir=.GlobalEnv)
XPSSample[[Indx]] <<- Object
OldXPSSample[[Indx]] <<- XPSSample[[Indx]]
assign("Object", XPSSample[[Indx]], envir = .GlobalEnv)
assign(activeFName, XPSSample, envir = .GlobalEnv)
replot()
XPSSaveRetrieveBkp("save")
}, container = Buttlyt)
Buttlyt[5,2] <- gbutton(" EXIT ", handler=function(h,...){
#----- stopping mouse handler
dispose(MCWindow) #Disposing MCWindow will activate GDestroyHandler which re-opens the graphic window
XPSSample <- get(activeFName, envir=.GlobalEnv) #Update XPSSample with all changes before plotting
XPSSaveRetrieveBkp("save")
plot(XPSSample[[Indx]]) #replot the CoreLine
}, container = Buttlyt)
StatBar <- gstatusbar("status", container = MCWindow)
#--- Marker-----
if (NoFit==FALSE){
coords[1] <- Object@Components[[1]]@param[2,1] #component position mu
coords[2] <- Object@Components[[1]]@param[1,1] #component1 height h
FuncName <- Object@Components[[1]]@funcName
coords[2] <- coords[2]/GetHvalue(Object,1, FuncName, 1)
Estep <- abs(Object@RegionToFit[[1]][1]-Object@RegionToFit[[1]][2])
Xindx <- which(Object@RegionToFit[[1]] > coords[1]-Estep/2 & Object@RegionToFit[[1]] < coords[1]+Estep/2) #indice del vettore X corrispondente alla posizione della componente
coords[2] <- coords[2]+Object@Baseline$y[Xindx]
refresh <- FALSE
replot()
refresh <- TRUE
}
enabled(LMFitbutton) <- TRUE
enabled(MFFitbutton) <- TRUE
enabled(RSTbutton) <- TRUE
visible(MCWindow) <- TRUE
tkevent.generate(MCWindow$widget, "<Expose>", when="now") #forces the MCWindow to be exposed
tcl("update", "idletasks") #Complete the idle tasks
#--- Interactive mouse control ---
if (length(ComponentList) > 0) {
ComponentMenu()
}
}
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