R/XPSRead.OldScienta.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
XPSRead.Oldscienta
Documented in
XPSRead.Oldscienta
# XPSRead.Oldscienta function to read old Scienta data
#Data are saved in the following folder which must be present
# /Analysis
# /Regions
# /Results
# /Specific
#
#' @title XPSRead.Oldscienta
#' @description XPSRead.Oldscienta function is used to read XPS data
#' in the old-DOS-Scienta format
#' Data are saved in the following folder which must be present
#' /Analysis
#' /Regions
#' /Results
#' /Specific
#' Selection of the DataFile in the /Analysis folder activates reading
#' data in all the folders.
#' @param filename file name or list of file names
#' @param project comment
#' @param experiment comment
#' @param out output class type default list()
#' @return XPSRead.Oldscienta returns and object of class XPSSample
#' @examples
#' \dontrun{
#' pk1 <- read.xps("c:/R/Analysis/OldScientaFiles/Analysis/DLC.48")
#' }
#' @export
XPSRead.Oldscienta <- function(filename = NULL,
project = "",
experiment = "",
out = c("list")) {
#----------------------------------------------------------------------
# Read information in Specific folder
#----------------------------------------------------------------------
readXPS.Specific <- function(filename, debug){
tmp <- list()
tmp$Filename <- basename(filename)
fp <- file(filename, open="rb")
#on.exit(close(fp))
seek(fp, where = 459, "start")
tmp$nr_curve <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
NSpectra<<-tmp$nr_curve
# check_spc_header file format
seek(fp, where = 0, "start") # skip first byte
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong SPECIFIC file format.\n")
# read labels
seek(fp, where = 0x0D, "current") ## skip 13 bytes
label <- list()
for (idx in c(1:4)) {
npt <- readBin(fp, "integer", n=1, size=1)
if (npt != 0) {
txt <- readChar(fp, nchars=npt)
skip <- (40 - npt)
} else {
txt <- readChar(fp, nchars=40)
skip <- 0
}
if ( nchar(tmp) > 0 ) {
label[[idx]] <- txt
}
seek(fp, where = skip, "current")
}
tmp$comments <- label
seek(fp, where = 189, "start")
year <- readBin(fp, "integer", n=1, size=2)
month <- readBin(fp, "integer", n=1, size=2)
day <- readBin(fp, "integer", n=1, size=2)
hour <- readBin(fp, "integer", n=1, size=2)
min <- readBin(fp, "integer", n=1, size=2)
tmp$Date <- paste(year, "/", month, "/", day, "-", hour, ":", min, sep="")
curve <- list()
for (idx in c(1:tmp$nr_curve)) {
npt <- readBin(fp, "integer", n=1, size=1)
curve[[idx]] <- readChar(fp, nchars=npt)
SpectNames[idx]<<-curve[[idx]]
if (SpectNames[idx]=="SURVEY" || SpectNames[idx]=="SUR"){SpectNames[idx]<<-"survey"}
seek(fp, where = (12 - npt), "current")
}
tmp$curves <- curve
# now close file
close(fp)
# save information into the XPSSample
OldScientaObj@Project<<-paste("Acquisition date: ", tmp$Date, sep=" ")
OldScientaObj@Sample<<-filename
OldScientaObj@Comments<<-c(tmp$comments[[1]], tmp$comments[[2]])
OldScientaObj@User<<-"Unknown"
OldScientaObj@Filename<<-tmp$Filename
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
}
#----------------------------------------------------------------------
# Read information in Regions folder
#----------------------------------------------------------------------
readXPS.Regions <- function(filename, nr_curve){
fp <- file(filename, open="rb")
#on.exit(close(fp))
tmp <- list()
for (idx in c(1:nr_curve)) {
SpectInfo<-NULL
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong REGIONS file format.\n")
seek(fp, where = 177, "current")
tmp$mode <- readBin(fp, "integer", n=1, size=1)
tmp$pass_energy <- readBin(fp, "integer", n=1, size=1)
if (tmp$pass_energy==5) {tmp$pass_energy<-1000}
if (tmp$pass_energy==4) {tmp$pass_energy<-500}
if (tmp$pass_energy==3) {tmp$pass_energy<-300}
if (tmp$pass_energy==2) {tmp$pass_energy<-150}
if (tmp$pass_energy==1) {tmp$pass_energy<-75}
seek(fp, where = 54, "current") ## skip 54 bytes
tmp$mode_type <- readBin(fp, "integer", n=1, size=1)
tmp$xmin <- readBin(fp, "double", n=1, size=8)
tmp$xmax <- readBin(fp, "double", n=1, size=8)
tmp$xstep <- readBin(fp, "double", n=1, size=8)
tmp$t_acq <- readBin(fp, "double", n=1, size=8)
tmp$sweeps <- readBin(fp, "integer", n=1, size=2)
tmp$half_range <- readBin(fp, "double", n=1, size=8)
tmp$t_acq_2 <- readBin(fp, "double", n=1, size=8)
seek(fp, where = 8, "current")
# generate the XPSCoreline structure
# OldScientaObj[[idx]] <<- new("XPSCoreLine", .Data = list(x = X, y = Y, t=T))
OldScientaObj[[idx]] <<- new("XPSCoreLine")
# save information into the XPSSample Coreline
if(tmp$xmin > tmp$xmax) { #Acquisition made using BE scale
OldScientaObj[[idx]]@units <<- c("Binding Energy [eV]","Intensity [cps]")
OldScientaObj[[idx]]@Flags <<- c(TRUE, FALSE, TRUE) #BE scale, CPS, ScientaData
sgn <- -1
} else if(tmp$xmin < tmp$xmax) { #Acquisition made using KE scale
OldScientaObj[[idx]]@units <<- c("Kinetic Energy [eV]","Intensity [cps]")
OldScientaObj[[idx]]@Flags <<- c(FALSE, FALSE, TRUE)
sgn <- 1
}
OldScientaObj[[idx]]@.Data[[1]] <<- seq(from=tmp$xmin, to=tmp$xmax, by=(sgn*tmp$xstep)) #X axis has to be genrated from range and Xstep
TotTime <- tmp$t_acq*(abs(tmp$xmax-tmp$xmin)/tmp$xstep)*tmp$sweeps
SpectInfo[1] <- paste(" XPS Spectrum Lens Mode:",tmp$mode," Resolution:Pass energy ", as.character(tmp$pass_energy)," Iris(Aper):manual", sep="")
SpectInfo[2] <- paste(" Acqn. Time(s): ", as.character(TotTime)," Sweeps: ", as.character(tmp$sweeps)," Anode:Mono Al Ka=1486.6eV Step(meV): ",as.character(tmp$xstep), sep="")
SpectInfo[3] <- paste(" Dwell Time(ms):", as.character(tmp$t_acq*1000)," Charge Neutraliser :manual Acquired On :unspecified")
OldScientaObj[[idx]]@Boundaries[[1]]<<-c(tmp$xmin,tmp$xmax)
OldScientaObj[[idx]]@Info<<-SpectInfo
OldScientaObj[[idx]]@Symbol<<-SpectNames[idx]
#save acquisition info to change COUNTS in CPS
Tint[idx] <<- tmp$t_acq
Nsweeps[idx] <<- tmp$sweeps
PE[idx] <<- tmp$pass_energy
Estep[idx] <<- tmp$xstep
}
OldScientaObj@names <<- SpectNames #All regions defined, now is possible to save SpectNames
close(fp) # now close file
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
}
#----------------------------------------------------------------------
# Read information in Results folder
#----------------------------------------------------------------------
readXPS.Results <- function(filename, nr_curve){
fp <- file(filename, open="rb")
#on.exit(close(fp))
ymin <- NULL
ymax <- NULL
tmp <- list()
for (idx in c(1:nr_curve)) {
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong REGIONS file format.\n")
seek(fp, where = 180, "current")
tmp$n_182 <- readBin(fp, "double", n=1, size=8)
tmp$npt <- readBin(fp, "integer", n=1, size=2)
tmp$half_range <- readBin(fp, "double", n=1, size=8)
tmp$xrange <- readBin(fp, "double", n=1, size=8)
# cat(seek(fp, where = NA),"\n")
tmp$data <- readBin(fp, "integer", n=tmp$npt, size=4)
seek(fp, where = (128 - ((4*tmp$npt + 208)%%128)), "current")
# save information into the XPSSample Coreline
if ( Tint[idx] > 99 ) Tint[idx] <- Tint[idx]/1000 #acq time could be expressed in msec.
tmp$data<-tmp$data/abs( Nsweeps[idx] * Tint[idx] * PE[idx] / Estep[idx] / 10.33) #counts to CPS conversion and normalization for different PE
ymin<-min(tmp$data)
ymax<-max(tmp$data)
OldScientaObj[[idx]]@Boundaries[[2]]<<-c(ymin,ymax)
OldScientaObj[[idx]]@.Data[[2]]<<-tmp$data
LL <- length(OldScientaObj[[idx]]@.Data[[2]])
OldScientaObj[[idx]]@.Data[[3]]<<-rep(1, LL) #data for the analyzer transfer function == unity for the Scienta Analyzers
}
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
close(fp) # now close file
}
#----------------------------------------------------------------------
# Main Variables
#----------------------------------------------------------------------
NSpectra<-NULL
SpectNames<-NULL
Tint<-NULL
Nsweeps<-NULL
PE<-NULL
Estep<-NULL
OldScientaObj <- new("XPSSample") #, Project="", Sample="", Comments="", User="", Filename="")
#---
if ( is.null(filename) ) stop("No Filename null?\n")
FName <- basename(filename)
rootdir <- dirname(dirname(filename))
cat("\n DIR:", rootdir)
cat("\n FILE:", FName)
# read Specific
cat("\n Read Specific")
readXPS.Specific(paste(rootdir, "SPECIFIC", FName, sep="/"))
# read Regions
cat("\n Read Regions")
readXPS.Regions(paste(rootdir, "REGIONS", FName, sep="/"), NSpectra)
# read Results
cat("\n Read Results")
res <- readXPS.Results(paste(rootdir, "RESULTS", FName, sep="/"), NSpectra)
cat("\n ==> ",OldScientaObj@Sample, OldScientaObj@Project)
cat("\n Sample: ",OldScientaObj@Comments)
txt<-c("Element", "Xmin", "Xmax", "Ymin", "Ymax", "N. sweeps", "t int.")
txt<-format(txt, digits=2, justify="right", width=10)
cat("\n", txt)
for (idx in 1:NSpectra) {
xmin<-min(OldScientaObj[[idx]]@Boundaries[[1]])
xmax<-max(OldScientaObj[[idx]]@Boundaries[[1]])
OldScientaObj[[idx]]@Boundaries[[2]]<-round(OldScientaObj[[idx]]@Boundaries[[2]], 2)
txt<-c(OldScientaObj[[idx]]@Symbol, xmin, xmax, OldScientaObj[[idx]]@Boundaries[[2]], Nsweeps[idx], Tint[idx])
txt<-format(txt, justify="right", width=10)
cat("\n", txt)
}
return(OldScientaObj)
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions XPSRead.Oldscienta
Documented in XPSRead.Oldscienta
# XPSRead.Oldscienta function to read old Scienta data
#Data are saved in the following folder which must be present
# /Analysis
# /Regions
# /Results
# /Specific
#
#' @title XPSRead.Oldscienta
#' @description XPSRead.Oldscienta function is used to read XPS data
#' in the old-DOS-Scienta format
#' Data are saved in the following folder which must be present
#' /Analysis
#' /Regions
#' /Results
#' /Specific
#' Selection of the DataFile in the /Analysis folder activates reading
#' data in all the folders.
#' @param filename file name or list of file names
#' @param project comment
#' @param experiment comment
#' @param out output class type default list()
#' @return XPSRead.Oldscienta returns and object of class XPSSample
#' @examples
#' \dontrun{
#' pk1 <- read.xps("c:/R/Analysis/OldScientaFiles/Analysis/DLC.48")
#' }
#' @export
XPSRead.Oldscienta <- function(filename = NULL,
project = "",
experiment = "",
out = c("list")) {
#----------------------------------------------------------------------
# Read information in Specific folder
#----------------------------------------------------------------------
readXPS.Specific <- function(filename, debug){
tmp <- list()
tmp$Filename <- basename(filename)
fp <- file(filename, open="rb")
#on.exit(close(fp))
seek(fp, where = 459, "start")
tmp$nr_curve <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
NSpectra<<-tmp$nr_curve
# check_spc_header file format
seek(fp, where = 0, "start") # skip first byte
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong SPECIFIC file format.\n")
# read labels
seek(fp, where = 0x0D, "current") ## skip 13 bytes
label <- list()
for (idx in c(1:4)) {
npt <- readBin(fp, "integer", n=1, size=1)
if (npt != 0) {
txt <- readChar(fp, nchars=npt)
skip <- (40 - npt)
} else {
txt <- readChar(fp, nchars=40)
skip <- 0
}
if ( nchar(tmp) > 0 ) {
label[[idx]] <- txt
}
seek(fp, where = skip, "current")
}
tmp$comments <- label
seek(fp, where = 189, "start")
year <- readBin(fp, "integer", n=1, size=2)
month <- readBin(fp, "integer", n=1, size=2)
day <- readBin(fp, "integer", n=1, size=2)
hour <- readBin(fp, "integer", n=1, size=2)
min <- readBin(fp, "integer", n=1, size=2)
tmp$Date <- paste(year, "/", month, "/", day, "-", hour, ":", min, sep="")
curve <- list()
for (idx in c(1:tmp$nr_curve)) {
npt <- readBin(fp, "integer", n=1, size=1)
curve[[idx]] <- readChar(fp, nchars=npt)
SpectNames[idx]<<-curve[[idx]]
if (SpectNames[idx]=="SURVEY" || SpectNames[idx]=="SUR"){SpectNames[idx]<<-"survey"}
seek(fp, where = (12 - npt), "current")
}
tmp$curves <- curve
# now close file
close(fp)
# save information into the XPSSample
OldScientaObj@Project<<-paste("Acquisition date: ", tmp$Date, sep=" ")
OldScientaObj@Sample<<-filename
OldScientaObj@Comments<<-c(tmp$comments[[1]], tmp$comments[[2]])
OldScientaObj@User<<-"Unknown"
OldScientaObj@Filename<<-tmp$Filename
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
}
#----------------------------------------------------------------------
# Read information in Regions folder
#----------------------------------------------------------------------
readXPS.Regions <- function(filename, nr_curve){
fp <- file(filename, open="rb")
#on.exit(close(fp))
tmp <- list()
for (idx in c(1:nr_curve)) {
SpectInfo<-NULL
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong REGIONS file format.\n")
seek(fp, where = 177, "current")
tmp$mode <- readBin(fp, "integer", n=1, size=1)
tmp$pass_energy <- readBin(fp, "integer", n=1, size=1)
if (tmp$pass_energy==5) {tmp$pass_energy<-1000}
if (tmp$pass_energy==4) {tmp$pass_energy<-500}
if (tmp$pass_energy==3) {tmp$pass_energy<-300}
if (tmp$pass_energy==2) {tmp$pass_energy<-150}
if (tmp$pass_energy==1) {tmp$pass_energy<-75}
seek(fp, where = 54, "current") ## skip 54 bytes
tmp$mode_type <- readBin(fp, "integer", n=1, size=1)
tmp$xmin <- readBin(fp, "double", n=1, size=8)
tmp$xmax <- readBin(fp, "double", n=1, size=8)
tmp$xstep <- readBin(fp, "double", n=1, size=8)
tmp$t_acq <- readBin(fp, "double", n=1, size=8)
tmp$sweeps <- readBin(fp, "integer", n=1, size=2)
tmp$half_range <- readBin(fp, "double", n=1, size=8)
tmp$t_acq_2 <- readBin(fp, "double", n=1, size=8)
seek(fp, where = 8, "current")
# generate the XPSCoreline structure
# OldScientaObj[[idx]] <<- new("XPSCoreLine", .Data = list(x = X, y = Y, t=T))
OldScientaObj[[idx]] <<- new("XPSCoreLine")
# save information into the XPSSample Coreline
if(tmp$xmin > tmp$xmax) { #Acquisition made using BE scale
OldScientaObj[[idx]]@units <<- c("Binding Energy [eV]","Intensity [cps]")
OldScientaObj[[idx]]@Flags <<- c(TRUE, FALSE, TRUE) #BE scale, CPS, ScientaData
sgn <- -1
} else if(tmp$xmin < tmp$xmax) { #Acquisition made using KE scale
OldScientaObj[[idx]]@units <<- c("Kinetic Energy [eV]","Intensity [cps]")
OldScientaObj[[idx]]@Flags <<- c(FALSE, FALSE, TRUE)
sgn <- 1
}
OldScientaObj[[idx]]@.Data[[1]] <<- seq(from=tmp$xmin, to=tmp$xmax, by=(sgn*tmp$xstep)) #X axis has to be genrated from range and Xstep
TotTime <- tmp$t_acq*(abs(tmp$xmax-tmp$xmin)/tmp$xstep)*tmp$sweeps
SpectInfo[1] <- paste(" XPS Spectrum Lens Mode:",tmp$mode," Resolution:Pass energy ", as.character(tmp$pass_energy)," Iris(Aper):manual", sep="")
SpectInfo[2] <- paste(" Acqn. Time(s): ", as.character(TotTime)," Sweeps: ", as.character(tmp$sweeps)," Anode:Mono Al Ka=1486.6eV Step(meV): ",as.character(tmp$xstep), sep="")
SpectInfo[3] <- paste(" Dwell Time(ms):", as.character(tmp$t_acq*1000)," Charge Neutraliser :manual Acquired On :unspecified")
OldScientaObj[[idx]]@Boundaries[[1]]<<-c(tmp$xmin,tmp$xmax)
OldScientaObj[[idx]]@Info<<-SpectInfo
OldScientaObj[[idx]]@Symbol<<-SpectNames[idx]
#save acquisition info to change COUNTS in CPS
Tint[idx] <<- tmp$t_acq
Nsweeps[idx] <<- tmp$sweeps
PE[idx] <<- tmp$pass_energy
Estep[idx] <<- tmp$xstep
}
OldScientaObj@names <<- SpectNames #All regions defined, now is possible to save SpectNames
close(fp) # now close file
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
}
#----------------------------------------------------------------------
# Read information in Results folder
#----------------------------------------------------------------------
readXPS.Results <- function(filename, nr_curve){
fp <- file(filename, open="rb")
#on.exit(close(fp))
ymin <- NULL
ymax <- NULL
tmp <- list()
for (idx in c(1:nr_curve)) {
buffer <- readBin(fp, "integer", n=1, size=2, signed = FALSE)
if (buffer != 256) warning("Wrong REGIONS file format.\n")
seek(fp, where = 180, "current")
tmp$n_182 <- readBin(fp, "double", n=1, size=8)
tmp$npt <- readBin(fp, "integer", n=1, size=2)
tmp$half_range <- readBin(fp, "double", n=1, size=8)
tmp$xrange <- readBin(fp, "double", n=1, size=8)
# cat(seek(fp, where = NA),"\n")
tmp$data <- readBin(fp, "integer", n=tmp$npt, size=4)
seek(fp, where = (128 - ((4*tmp$npt + 208)%%128)), "current")
# save information into the XPSSample Coreline
if ( Tint[idx] > 99 ) Tint[idx] <- Tint[idx]/1000 #acq time could be expressed in msec.
tmp$data<-tmp$data/abs( Nsweeps[idx] * Tint[idx] * PE[idx] / Estep[idx] / 10.33) #counts to CPS conversion and normalization for different PE
ymin<-min(tmp$data)
ymax<-max(tmp$data)
OldScientaObj[[idx]]@Boundaries[[2]]<<-c(ymin,ymax)
OldScientaObj[[idx]]@.Data[[2]]<<-tmp$data
LL <- length(OldScientaObj[[idx]]@.Data[[2]])
OldScientaObj[[idx]]@.Data[[3]]<<-rep(1, LL) #data for the analyzer transfer function == unity for the Scienta Analyzers
}
#cat(str(tmp)) ## DEBUG
#cat("\n ******\n", str(OldScientaObj)) ## DEBUG
#scan(n=1, quiet=TRUE)
close(fp) # now close file
}
#----------------------------------------------------------------------
# Main Variables
#----------------------------------------------------------------------
NSpectra<-NULL
SpectNames<-NULL
Tint<-NULL
Nsweeps<-NULL
PE<-NULL
Estep<-NULL
OldScientaObj <- new("XPSSample") #, Project="", Sample="", Comments="", User="", Filename="")
#---
if ( is.null(filename) ) stop("No Filename null?\n")
FName <- basename(filename)
rootdir <- dirname(dirname(filename))
cat("\n DIR:", rootdir)
cat("\n FILE:", FName)
# read Specific
cat("\n Read Specific")
readXPS.Specific(paste(rootdir, "SPECIFIC", FName, sep="/"))
# read Regions
cat("\n Read Regions")
readXPS.Regions(paste(rootdir, "REGIONS", FName, sep="/"), NSpectra)
# read Results
cat("\n Read Results")
res <- readXPS.Results(paste(rootdir, "RESULTS", FName, sep="/"), NSpectra)
cat("\n ==> ",OldScientaObj@Sample, OldScientaObj@Project)
cat("\n Sample: ",OldScientaObj@Comments)
txt<-c("Element", "Xmin", "Xmax", "Ymin", "Ymax", "N. sweeps", "t int.")
txt<-format(txt, digits=2, justify="right", width=10)
cat("\n", txt)
for (idx in 1:NSpectra) {
xmin<-min(OldScientaObj[[idx]]@Boundaries[[1]])
xmax<-max(OldScientaObj[[idx]]@Boundaries[[1]])
OldScientaObj[[idx]]@Boundaries[[2]]<-round(OldScientaObj[[idx]]@Boundaries[[2]], 2)
txt<-c(OldScientaObj[[idx]]@Symbol, xmin, xmax, OldScientaObj[[idx]]@Boundaries[[2]], Nsweeps[idx], Tint[idx])
txt<-format(txt, justify="right", width=10)
cat("\n", txt)
}
return(OldScientaObj)
}
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