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R

## This function should be renamed to EMSA2df(). The file it reads is a so-called EMSA spectral data file.
# /TA, 111110
eds2df <- function(edstxtfile) {
## Description:
## Reads EDS textfile from INCA EDS.
## Stores data in data frame.
## Usage:
## eds2df(edstxtfile)
## Arguments:
## edstxtfile: character string, the full filename
## (with path) to one txt file.
## Value:
## A dataframe
#
incatxt <- file(edstxtfile, "r")
edsfile <- readLines(incatxt, n = -1) #read all lines of input file
close(incatxt)
#
sampleid <- ProvideSampleId(edstxtfile)
#
rgxp.comment <- "^\\#"
#
numrow.idx <- regexpr(rgxp.comment, edsfile)
# scrap the match.length attribute
attr(numrow.idx, "match.length") <- NULL
#
i <- seq(1, length(numrow.idx) - 1, 1)
j <- seq(2, length(numrow.idx), 1)
# Start index of data range
start.idx <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1) + 1
# End index of the data range
end.idx <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1)
#
zz <- textConnection(edsfile[start.idx:end.idx], "r")
#
ff <- data.frame()
ff <- data.frame(stringsAsFactors = FALSE,
sampleid = sampleid,
matrix(scan(zz, what = numeric(), sep = ","), ncol = 2, byrow = T))
close(zz)
names(ff) <- c("sampleid", "energy", "counts")
#
### Collect attributes of this experiment
# XUnit
position.XUnit <- regexpr("^\\#XUNITS", edsfile)
XUnit <- as.character(strsplit(edsfile[which(position.XUnit == 1)], ":\\s")[[1]][2])
ff$XUnit <- XUnit
# YUnit
position.YUnit <- regexpr("^\\#YUNITS", edsfile)
YUnit <- as.character(strsplit(edsfile[which(position.YUnit == 1)], ":\\s")[[1]][2])
ff$YUnit <- YUnit
# Date
position.Date <- regexpr("^\\#DATE", edsfile)
Date <- strsplit(edsfile[which(position.Date == 1)], ":\\s")[[1]][2]
ff$Date <- Date
# Time
position.Time <- regexpr("^\\#TIME", edsfile)
Time <- strsplit(edsfile[which(position.Time == 1)], ":\\s")[[1]][2]
ff$Time <- Time
# XPerChannel
position.XPerChannel <- regexpr("^\\#XPERCHAN", edsfile)
XPerChannel <- as.numeric(strsplit(edsfile[which(position.XPerChannel == 1)], ":\\s")[[1]][2])
ff$XPerChannel <- XPerChannel
# Offset
position.Offset <- regexpr("^\\#OFFSET", edsfile)
Offset <- as.numeric(strsplit(edsfile[which(position.Offset == 1)], ":\\s")[[1]][2])
ff$Offset <- Offset
# ChOffset
position.ChOffset <- regexpr("^\\#CHOFFSET", edsfile)
ChOffset <- as.numeric(strsplit(edsfile[which(position.ChOffset == 1)], ":\\s")[[1]][2])
ff$ChOffset <- ChOffset
# LiveTime
position.LiveTime <- regexpr("^\\#LIVETIME", edsfile)
LiveTime <- as.numeric(strsplit(edsfile[which(position.LiveTime == 1)], ":\\s")[[1]][2])
ff$LiveTime <- LiveTime
# DeadTime is calculated from: REALTIME - LIVETIME
position.RealTime <- regexpr("^\\#REALTIME", edsfile)
RealTime <- as.numeric(strsplit(edsfile[which(position.RealTime == 1)], ":\\s")[[1]][2])
DeadTime <- RealTime - LiveTime
ff$DeadTime <- DeadTime
# BeamEnergy
position.BeamEnergy <- regexpr("^\\#BEAMKV", edsfile)
BeamEnergy <- as.numeric(strsplit(edsfile[which(position.BeamEnergy == 1)], ":\\s")[[1]][2])
ff$BeamEnergy <- BeamEnergy
#
return(ff)
}