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source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
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##################################################
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################### ocp2df #######################
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##################################################
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ocp2df <- function(datafilename) {
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## Description:
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## Reads time vs potential 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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close(datafile)
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#
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sampleid <- ProvideSampleId(datafilename)
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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(stringsAsFactors = FALSE,
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sampleid, 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("sampleid", "time", "potential")
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#
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### Collect attributes of this experiment
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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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