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64 lines
2.4 KiB
R
64 lines
2.4 KiB
R
14 years ago
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##################################################
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#################### uxd2df ######################
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##################################################
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uxd2df <- function(uxdfile) {
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# Function for reading UXD files # Assumptions: data in two columns
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# Args: uxdfile (filename with extension)
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# Returns: dataframe with three columns
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cchar <- "[;_]" #regexpr matching the comment characters used in Bruker's UXD
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cdata <- "[0-9]" #regexpr matching one character of any digit
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# A new file (datafile) containing only data will be created,
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# extension ".data" appended to uxdfile
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#datafile <- paste(uxdfile,".data",sep="")
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ufile <- file(uxdfile, "r")
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f <- readLines(ufile, n=-1) #read _all_ lines from UXD file
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close(ufile)
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# This way we identify data rows by looking for numeric characters.
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#wh <- regexpr("[0-9]", f)
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# This way we identify header rows
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# We assume that all other rows are data
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wh <- regexpr(cchar, f)
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mh <- wh[1:length(wh)] # this gives you the corresponding index vector
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# the value of each element corresponds to the position of the regexp match.
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# value = 1 means the first character of the row is cchar (row is header)
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# value =-1 means no cchar occur on the row (row is data)
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i <- seq(1, length(mh) - 1, 1)
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j <- seq(2, length(mh), 1)
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starts <- which(mh[i] == 1 & mh[j] != 1) + 1
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ends <- length(mh)
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f <- f[starts:ends]
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rgxp.sampleid <- "[^/]*(?=\\.\\w*)" ## THIS REQUIRES perl=TRUE
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# Regular expression that extracts the filename out of a full path.
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# Matches and extracts everything from the last forward slash (assuming Unix slashes)
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# up until a dot folllowed by an arbitrary number of alphanumeric characters.
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sampleidmtch <- regexpr(rgxp.sampleid, uxdfile, perl=TRUE)
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# Check that there was a match
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if (sampleidmtch < 0) {
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# -1 means no match
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sampleid <- uxdfile
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# If match was unsuccessful we use the argument as passed to this function as sampleid
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}
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sampleid <- substr(uxdfile, sampleidmtch, (sampleidmtch + attr(sampleidmtch, "match.length") - 1))
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zz <- textConnection(f, "r")
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ff <- data.frame(sampleid, matrix(scan(zz,
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what = numeric()), ncol=2, byrow=T))
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names(ff) <- c("sampleid", "angle", "intensity")
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close(zz)
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#zz <- file(datafile, "w") #open connection to datafile
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#write.table(ff, file=datafile, row.names=F, sep=",")
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#close(zz)
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# Return dataframe
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ff
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}
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