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