R/XPSAddFitComponent.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSaddComponent
XPSaddFitComponent
Documented in
XPSaddFitComponent
## =================================================
# XPSaddFitComponent
# Impostazione delle variabili: numero componenti
# posizione, Sigma e altezza delle componenti
## =================================================
#' @title XPSaddFitComponent adds a fit component to the XPSCoreLine
#' @description XPSaddFitComponent() adds a fit component to the XPSCoreLine object.
#' This function is called after the definition of the baseline (\code{XPSbaseline}).
#' Different types of function could be added as component, see \code{\link{XPSfitAlgorithms}}
#' for a list of the implemented functions.
#' @param Object XPSCoreLine object
#' @param type name of the fitting function used. Default "Gauss"
#' @param range_h the value used to determine \code{min} and \code{max} range
#' for \code{Intensity}
#' @param range_mu the value used to determine \code{min} and \code{max} range
#' for \code{xCenter}
#' @param peakPosition a list with x,y value corresponding the center and height
#' of the new component. Default is \code{NULL} then the position is asked
#' trough the plot with the cursor
#' @param ... to add additional values such as FWHM if needed
#' @return Usually the values \code{xCenter} and \code{Amplitude} are get trough
#' a click with the mouse on the plot of the XPSCoreLine. All the parameters
#' will be added to the slot \code{Components} of the XPSCoreLine.
#' @seealso \link{XPSfitAlgorithms}, \link{XPSbaseline}, \link{findXIndex}
#' @examples
#' \dontrun{
#' XPSdata[["C1s"]] <- XPSaddFitComponent(XPSdata[["C1s"]], type="Voigt", range_h=3)
#' }
#' @export
#'
XPSaddFitComponent <- function(Object, type="Gauss", range_h=5, range_mu=1.5, peakPosition=NULL, ...)
{
Object <- XPSaddComponent(Object, type, range_h, range_mu, peakPosition, ...)
plot(Object)
return(Object)
}
#-----------
XPSaddComponent <- function(Object, type, range_h=5, range_mu=1.5, peakPosition=NULL, ...)
{
dot.args <- list(...) #retrieve arguments passed by ...
# check if Baseline is already present
if ( ! hasBaseline(Object) ) {
stop("Baseline not defined for Core Line ", slot(Object,"Symbol") )
}
#modified Giorgio 17-1-2017
fit_functions <- sapply(fitAlgorithms, slot, "funcName") #fit_functions=list of all the fitting function-names
funct <- match.arg(type, unname(fit_functions) ) #selection of the fit function
#modified Giorgio 5-2-2019
if (type=="Initialize"){ #creation of an empty component
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(0, 0, 0)) ##CoreLine intensity set in XPSAnalysis.r with mouse
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(0, 0, 0))
# set sigma: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="sigma",value = c(0, 0, 0))
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="")
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
# add the y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# now set the rsf for this component
# if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 ) {slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")}
return(Object)
}
#modified Giorgio 5-2-2019
if (type=="Generic"){ #creation of an empty component
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
names(Object@Components)[num] <- paste("C",as.character(num),sep="")
return(Object)
}
if (type=="Linear"){ #creation of an empty component of type Linear
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
m <-(peakPosition$y[2]-peakPosition$y[1])/(peakPosition$x[1]-peakPosition$x[2]) #line slope
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="m", value = c(m, -Inf, Inf)) #Intensity and position set in XPSAnalysis.r with mouse
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="c",value = c(0, -Inf, Inf))
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="") #labels of the components in the plot
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
# add the y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# now set the rsf for this component
# if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 ) {slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")}
return(Object)
}
#modified Giorgio 10-11-2018
if (type=="HillSigmoid"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord peakPosition$x[1]=A, peakPosition$x[2]=FlexPos, peakPosition$x[3]=B
X <- peakPosition$x[2] #this corresponds to the mu parameter = position of the Sigmoid flex point
RTF_x <- Object@RegionToFit$x
idx <- findXIndex(RTF_x, X)
# substract the baseline value correspondent to the X position
RTF_y <- Object@RegionToFit$y #- Object@Baseline$y
Y <- peakPosition$y[2] - Object@Baseline$y[idx]
LL <- length(RTF_x)
XXX <- seq(1, LL) #temporary positive abscissa to generate the Hill Sigmoid
newX <- XXX[idx]
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*1.5))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(newX, 0, LL))
# set Powr: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="pow",value = c(8, 1, 50))
# set A: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="A",value = c(peakPosition$y[1], 0.5*peakPosition$y[1], 1.5*peakPosition$y[1]))
# set B: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="B",value = c(peakPosition$y[3], -1, 1.5*peakPosition$y[3]))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"HS" #Label indicating Hill Sigmoid in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=XXX, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=Object@Components[[num]]@ycoor, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
if (type=="HillSigmoid.KE"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord
X <- peakPosition$x[2] #this corresponds to the mu parameter = position of the Sigmoid flex point
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y[2] - Object@Baseline$y[idx]
RTF_x <- Object@RegionToFit$x
#HillSigmoid needs positive abscissas defined from 0 to LL*dx dx=energy step
dx <- abs(RTF_x[2]-RTF_x[1])
LL <- length(RTF_x)
XXX <- NULL
for (ii in 1:LL){ #new X coords: Step and number of absissas are equal to the original ones
XXX[ii]<-dx*(ii-1)
}
newX <- XXX[idx]
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*1.5))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(newX, 0, newX+5))
# set Powr: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="pow",value = c(8, 1, 50))
# set A: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="A",value = c(peakPosition$y[1], 0.5*peakPosition$y[1], 1.5*peakPosition$y[1]))
# set B: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="B",value = c(peakPosition$y[3], -1, 1.5*peakPosition$y[3]))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"HS" #Label indicating Hill Sigmoid in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=XXX, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=NULL, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
#modified Giorgio 20-12-2020
if (type=="VBFermi"){ #creation of an empty component of type VBFermi: needed to store VBFermi Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord
X <- peakPosition$x
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y - Object@Baseline$y[idx]
RTF_x <- Object@RegionToFit$x
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, 10*Y))
# set Ef: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(X, -2, 2))
# set k: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="k",value = c(1, 0, 5))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"Ef" #Label indicating the Fermi Edge in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=RTF_x, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=NULL, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
#modified Giorgio 17-1-2017
if (type=="VBtop"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
#now call the prototype function relative to funct_name defined in XPSFitCompClass
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
#now compute the fit function and add the values for this component see XPSFitCompClass
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# Now just set the component identifier
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <-"VBtop" #Label indicating the VBtop in the plot
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # V name of the VBtop component
return(Object)
}
if (type=="Derivative"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# add the y values for this component: in this case a series of NA (see XPSFitAlgorithms.r)
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"D1" #Label indicating the Derivate in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the Derivate component
return(Object)
}
if (is.null(peakPosition)) {
## get the position from the plot
plot(Object)
peakPosition <- locator(1)
}
#---> now add the fit component to the Object
# Set the x,y coord
X <- peakPosition$x #this corresponds to the mu parameter = position of the fitting comp.
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y - Object@Baseline$y[idx]
# increase the number of components
num <- length(names(Object@Components)) + 1
# add the new component: recall the fitAlgorithm with all the preset parameters (start, min, max) values
# and fill the slots Component@param, Component@rsf, Component@ycoor, Component@link
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*range_h))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(X, X-range_mu, X+range_mu))
# needed new value of sigma passed through ... to AddFitComponent()
if("sigma" %in% names(dot.args)){
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="sigma",value = c(dot.args$sigma, 0, 10))
}
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="")
#--- Compute the conversion factor to obtain a component intensity == mouse position (add component in XPSAnalysis.r)
# NB: this operation works if all the slots of the new component are defined
Yfactor <- GetHvalue(Object, num, type, 1) #computes the intensity of the fit function selected for the new fitComponent
#--- Re-set Amplitude
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Yfactor*Y, 0, Yfactor*Y*range_h))
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
## add the fitfunction y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
## now set the rsf for this component
## if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 )
slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")
## sort the Components slot
Object <- sortComponents(Object)
return(Object)
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSaddComponent XPSaddFitComponent
Documented in XPSaddFitComponent
## =================================================
# XPSaddFitComponent
# Impostazione delle variabili: numero componenti
# posizione, Sigma e altezza delle componenti
## =================================================
#' @title XPSaddFitComponent adds a fit component to the XPSCoreLine
#' @description XPSaddFitComponent() adds a fit component to the XPSCoreLine object.
#' This function is called after the definition of the baseline (\code{XPSbaseline}).
#' Different types of function could be added as component, see \code{\link{XPSfitAlgorithms}}
#' for a list of the implemented functions.
#' @param Object XPSCoreLine object
#' @param type name of the fitting function used. Default "Gauss"
#' @param range_h the value used to determine \code{min} and \code{max} range
#' for \code{Intensity}
#' @param range_mu the value used to determine \code{min} and \code{max} range
#' for \code{xCenter}
#' @param peakPosition a list with x,y value corresponding the center and height
#' of the new component. Default is \code{NULL} then the position is asked
#' trough the plot with the cursor
#' @param ... to add additional values such as FWHM if needed
#' @return Usually the values \code{xCenter} and \code{Amplitude} are get trough
#' a click with the mouse on the plot of the XPSCoreLine. All the parameters
#' will be added to the slot \code{Components} of the XPSCoreLine.
#' @seealso \link{XPSfitAlgorithms}, \link{XPSbaseline}, \link{findXIndex}
#' @examples
#' \dontrun{
#' XPSdata[["C1s"]] <- XPSaddFitComponent(XPSdata[["C1s"]], type="Voigt", range_h=3)
#' }
#' @export
#'
XPSaddFitComponent <- function(Object, type="Gauss", range_h=5, range_mu=1.5, peakPosition=NULL, ...)
{
Object <- XPSaddComponent(Object, type, range_h, range_mu, peakPosition, ...)
plot(Object)
return(Object)
}
#-----------
XPSaddComponent <- function(Object, type, range_h=5, range_mu=1.5, peakPosition=NULL, ...)
{
dot.args <- list(...) #retrieve arguments passed by ...
# check if Baseline is already present
if ( ! hasBaseline(Object) ) {
stop("Baseline not defined for Core Line ", slot(Object,"Symbol") )
}
#modified Giorgio 17-1-2017
fit_functions <- sapply(fitAlgorithms, slot, "funcName") #fit_functions=list of all the fitting function-names
funct <- match.arg(type, unname(fit_functions) ) #selection of the fit function
#modified Giorgio 5-2-2019
if (type=="Initialize"){ #creation of an empty component
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(0, 0, 0)) ##CoreLine intensity set in XPSAnalysis.r with mouse
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(0, 0, 0))
# set sigma: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="sigma",value = c(0, 0, 0))
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="")
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
# add the y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# now set the rsf for this component
# if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 ) {slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")}
return(Object)
}
#modified Giorgio 5-2-2019
if (type=="Generic"){ #creation of an empty component
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
names(Object@Components)[num] <- paste("C",as.character(num),sep="")
return(Object)
}
if (type=="Linear"){ #creation of an empty component of type Linear
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
m <-(peakPosition$y[2]-peakPosition$y[1])/(peakPosition$x[1]-peakPosition$x[2]) #line slope
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="m", value = c(m, -Inf, Inf)) #Intensity and position set in XPSAnalysis.r with mouse
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="c",value = c(0, -Inf, Inf))
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="") #labels of the components in the plot
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
# add the y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# now set the rsf for this component
# if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 ) {slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")}
return(Object)
}
#modified Giorgio 10-11-2018
if (type=="HillSigmoid"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord peakPosition$x[1]=A, peakPosition$x[2]=FlexPos, peakPosition$x[3]=B
X <- peakPosition$x[2] #this corresponds to the mu parameter = position of the Sigmoid flex point
RTF_x <- Object@RegionToFit$x
idx <- findXIndex(RTF_x, X)
# substract the baseline value correspondent to the X position
RTF_y <- Object@RegionToFit$y #- Object@Baseline$y
Y <- peakPosition$y[2] - Object@Baseline$y[idx]
LL <- length(RTF_x)
XXX <- seq(1, LL) #temporary positive abscissa to generate the Hill Sigmoid
newX <- XXX[idx]
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*1.5))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(newX, 0, LL))
# set Powr: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="pow",value = c(8, 1, 50))
# set A: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="A",value = c(peakPosition$y[1], 0.5*peakPosition$y[1], 1.5*peakPosition$y[1]))
# set B: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="B",value = c(peakPosition$y[3], -1, 1.5*peakPosition$y[3]))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"HS" #Label indicating Hill Sigmoid in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=XXX, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=Object@Components[[num]]@ycoor, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
if (type=="HillSigmoid.KE"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord
X <- peakPosition$x[2] #this corresponds to the mu parameter = position of the Sigmoid flex point
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y[2] - Object@Baseline$y[idx]
RTF_x <- Object@RegionToFit$x
#HillSigmoid needs positive abscissas defined from 0 to LL*dx dx=energy step
dx <- abs(RTF_x[2]-RTF_x[1])
LL <- length(RTF_x)
XXX <- NULL
for (ii in 1:LL){ #new X coords: Step and number of absissas are equal to the original ones
XXX[ii]<-dx*(ii-1)
}
newX <- XXX[idx]
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*1.5))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(newX, 0, newX+5))
# set Powr: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="pow",value = c(8, 1, 50))
# set A: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="A",value = c(peakPosition$y[1], 0.5*peakPosition$y[1], 1.5*peakPosition$y[1]))
# set B: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="B",value = c(peakPosition$y[3], -1, 1.5*peakPosition$y[3]))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"HS" #Label indicating Hill Sigmoid in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=XXX, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=NULL, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
#modified Giorgio 20-12-2020
if (type=="VBFermi"){ #creation of an empty component of type VBFermi: needed to store VBFermi Position
num <- length(names(Object@Components)) + 1
# Set the x,y coord
X <- peakPosition$x
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y - Object@Baseline$y[idx]
RTF_x <- Object@RegionToFit$x
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, 10*Y))
# set Ef: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(X, -2, 2))
# set k: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="k",value = c(1, 0, 5))
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"Ef" #Label indicating the Fermi Edge in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the HillSigmoid component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=RTF_x, y=Object@Baseline$y) #Ycomponent saves the fitting component but does not modify the RegionToFit$x
Object@Fit <- list(x=XXX, y=NULL, idx=idx) #save new absissas and index of flexpoint
return(Object)
}
#modified Giorgio 17-1-2017
if (type=="VBtop"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
#now call the prototype function relative to funct_name defined in XPSFitCompClass
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
#now compute the fit function and add the values for this component see XPSFitCompClass
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# Now just set the component identifier
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <-"VBtop" #Label indicating the VBtop in the plot
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # V name of the VBtop component
return(Object)
}
if (type=="Derivative"){ #creation of an empty component of type VBtop: needed to store VBtop Position
num <- length(names(Object@Components)) + 1
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# add the y values for this component: in this case a series of NA (see XPSFitAlgorithms.r)
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
# Now just set the component identifier
# label (used in the plot)
slot(Object@Components[[num]],"label") <-"D1" #Label indicating the Derivate in the plot
# name of this component
names(Object@Components)[num] <- "C1" # The name of the Derivate component
return(Object)
}
if (is.null(peakPosition)) {
## get the position from the plot
plot(Object)
peakPosition <- locator(1)
}
#---> now add the fit component to the Object
# Set the x,y coord
X <- peakPosition$x #this corresponds to the mu parameter = position of the fitting comp.
# substract the baseline value correspondent to the X position
idx <- findXIndex(Object@Baseline$x, X)
Y <- peakPosition$y - Object@Baseline$y[idx]
# increase the number of components
num <- length(names(Object@Components)) + 1
# add the new component: recall the fitAlgorithm with all the preset parameters (start, min, max) values
# and fill the slots Component@param, Component@rsf, Component@ycoor, Component@link
slot(Object,"Components")[[num]] <- fitAlgorithms[[funct]]
# Now set h, mu for first call
# set Amplitude:start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Y, 0, Y*range_h))
# set xCenter: start,min,max
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="mu",value = c(X, X-range_mu, X+range_mu))
# needed new value of sigma passed through ... to AddFitComponent()
if("sigma" %in% names(dot.args)){
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="sigma",value = c(dot.args$sigma, 0, 10))
}
# label (used in the plot) # #1, #2, ...
slot(Object@Components[[num]],"label") <- paste("#", as.character(num),sep="")
#--- Compute the conversion factor to obtain a component intensity == mouse position (add component in XPSAnalysis.r)
# NB: this operation works if all the slots of the new component are defined
Yfactor <- GetHvalue(Object, num, type, 1) #computes the intensity of the fit function selected for the new fitComponent
#--- Re-set Amplitude
slot(Object,"Components")[[num]] <- setParam(Object@Components[[num]],variable="h", value = c(Yfactor*Y, 0, Yfactor*Y*range_h))
# name of this component
names(Object@Components)[num] <- paste("C",as.character(num),sep="") # C1, C2, ...
## add the fitfunction y values for this component
Object@Components[[num]] <- Ycomponent(Object@Components[[num]], x=Object@RegionToFit$x, y=Object@Baseline$y)
## now set the rsf for this component
## if Object@RSF is not set then call XPSsetRSF
if ( slot(Object,"RSF") != 0 )
slot(Object@Components[[num]],"rsf") <- slot(Object,"RSF")
## sort the Components slot
Object <- sortComponents(Object)
return(Object)
}
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