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@ -18,10 +18,36 @@ source("/home/taha/chepec/chetex/common/R/common.R")
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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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## Description:
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## Reads potential-time data (from CHI 760 potentiostat)
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## and returns a dataframe with the data and
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## the data attributes (experimental conditions).
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## Usage:
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## ocp2df(datafilename)
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## Arguments:
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## datafilename: text string with full path to experimental file
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## Value:
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## Dataframe with the following columns (and no extra attributes):
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## $ sampleid : chr
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## $ time : num
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## $ current : num
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## $ currentdensity : num
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## $ timediff : num
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## $ dIdt : num
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## $ didt : num
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## $ charge : num
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## $ chargedensity : num
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## $ InitE : num
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## $ SampleInterval : num
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## $ RunTime : num
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## $ QuietTime : num
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## $ Sensitivity : num
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## Note:
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## The CH Instruments 760 potentiostat records all data
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## using standard SI units, therefore this function
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## assumes all potential values to be in volts,
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## currents to be in amperes, charges in Coulombs,
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## time in seconds, and so on.
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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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@ -63,18 +89,10 @@ ocp2df <- function(datafilename) {
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names(ff) <- c("sampleid", "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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# RunTime (sec)
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position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
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RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
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ff$RunTime <- RunTime
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#
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return(ff)
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}
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