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51 lines
1.8 KiB
R
51 lines
1.8 KiB
R
# Renishaw.R
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# Functions to read data from the Renishaw Raman spectrometer
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# Taha Ahmed, Feb 2011
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# CONTENTS
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# >>>> Raman2df
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##################################################
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################### Raman2df #######################
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##################################################
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Raman2df <- function(datafilename) {
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# Function description: for reading Raman spectrum into dataframe
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#
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datafile <- file(datafilename, "r")
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chifile <- readLines(datafile, n = -1) #read all lines of input file
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close(datafile)
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#
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#####
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# A nice algorithm that extracts the filename from the datafilename argument
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# and uses that as a sampleid in the returned dataframe
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# THIS SHOULD PROBABLY BE CONVERTED INTO A STAND-ALONE FUNCTION
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# Also make sure it works for vectors as well as single strings
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#####
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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, datafilename, 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 <- datafilename
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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(datafilename, sampleidmtch, (sampleidmtch + attr(sampleidmtch, "match.length") - 1))
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#
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ff <- data.frame(NULL)
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zz <- textConnection(chifile, "r")
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ff <- rbind(ff, data.frame(sampleid,
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matrix(scan(zz, what = numeric(), sep = "\t"),
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ncol = 2, byrow = T)))
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close(zz)
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names(ff) <- c("sampleid", "shift", "counts")
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#
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return(ff)
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}
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