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@ -3,6 +3,7 @@
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# Taha Ahmed, Jan 2011 - Feb 2011
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# CONTENTS
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# >>>> ocp2df
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# >>>> chronocm2df
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# >>>> chronoamp2df
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# >>>> amperometry2df
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@ -12,6 +13,70 @@
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##################################################
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################### ocp2df #######################
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##################################################
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ocp2df <- function(datafilename) {
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# Function description: for recorded amperometric i-T curves
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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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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rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
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# regexp that matches a decimal number at the beginning of the line.
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# Matches numbers with or without a negative sign (hyphen),
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# followed by one digit before the decimal, a decimal point,
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# and an arbitrary number of digits after the decimal point,
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# immediately followed by either the letter 'e' or a comma.
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# Note that backslashes are escaped due to the way R handles strings.
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#
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numrow.idx <- regexpr(rgxp.number, chifile)
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# Save the match length attribute to another variable,
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numrow.len <- attr(numrow.idx, "match.length")
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# then scrap the attribute of the original variable.
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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 indices of data ranges
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starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
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# End indices, except for the last
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ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
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# Fix the last index of end indices
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ends <- c(ends, length(numrow.idx))
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#
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ff <- data.frame(NULL)
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for (s in 1:length(starts)) {
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zz <- textConnection(chifile[starts[s]:ends[s]], "r")
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ff <- rbind(ff,
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data.frame(matrix(scan(zz, what = numeric(), sep = ","),
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ncol = 2, byrow = T)))
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close(zz)
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}
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names(ff) <- c("time", "potential")
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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Run\\sTime\\s\\(sec\\)")
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names.attr <- c("RunTime")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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# attrow.idx should now contain only one matching row
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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################# chronocm2df ####################
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