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114 lines
4.8 KiB
R
114 lines
4.8 KiB
R
14 years ago
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source("/home/taha/chepec/chetex/common/R/common.R")
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##################################################
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################### lsv2df #######################
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##################################################
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lsv2df <- function(datafilename, wearea = 1) {
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## Description:
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## Reads LSV datafiles from CHI 760 potentiostat
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## (potential, current, and charge)
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## and returns a dataframe with the data,
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## the data attributes (experimental conditions),
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## and calculated current density and charge density.
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## Usage:
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## lsv2df(datafilename, wearea)
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## Arguments:
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## datafilename: text string with full path to experimental file
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## wearea: (optional) area of working electrode (in square centimeter)
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## Value:
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## Dataframe with the following columns (and no extra attributes):
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## $ sampleid : chr (id)
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## $ segment : num (id)
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## $ potential : num (measure)
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## $ current : num (measure)
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## $ charge : num (measure)
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## $ currentdensity : num (measure)
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## $ chargedensity : num (measure)
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## $ InitE : num (id)
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## $ FinalE : num (id)
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## $ ScanRate : num (id)
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## $ SampleInterval : num (id)
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## $ QuietTime : num (id)
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## $ Sensitivity : num (id)
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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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lsvfile <- file(datafilename, "r")
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chifile <- readLines(lsvfile, n = -1) #read all lines of input file
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close(lsvfile)
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#
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sampleid <- ProvideSampleId(datafilename)
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#
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rgxp.number <- "^\\-?\\d\\.\\d+,"
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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 a comma.
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# Note that backslashes are escaped.
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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(stringsAsFactors = FALSE,
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sampleid, segment = s,
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matrix(scan(zz, what = numeric(), sep = ","),
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ncol = 3, byrow = T)))
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close(zz)
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}
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names(ff) <- c("sampleid", "segment", "potential", "current", "charge")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff, currentdensity = currentdensity)
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# Calculate charge density
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chargedensity <- ff$charge / wearea
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ff <- cbind(ff, chargedensity = chargedensity)
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#
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### Collect attributes of this experiment
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# InitE (volt)
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position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
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InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
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ff$InitE <- InitE
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# FinalE (volt)
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position.FinalE <- regexpr("^Final\\sE\\s\\(V\\)", chifile)
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FinalE <- as.numeric(strsplit(chifile[which(position.FinalE == 1)], "\\s=\\s")[[1]][2])
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ff$FinalE <- FinalE
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# ScanRate (volt per second)
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position.ScanRate <- regexpr("^Scan\\sRate\\s\\(V/s\\)", chifile)
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ScanRate <- as.numeric(strsplit(chifile[which(position.ScanRate == 1)], "\\s=\\s")[[1]][2])
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ff$ScanRate <- ScanRate
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# SampleInterval (volt)
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position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
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SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
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ff$SampleInterval <- SampleInterval
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# Quiet time (seconds)
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position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
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QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
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ff$QuietTime <- QuietTime
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# Sensitivity (ampere per volt)
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position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
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Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
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ff$Sensitivity <- Sensitivity
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#
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return(ff)
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}
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