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source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R")
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##################################################
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#################### cv2df #######################
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##################################################
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cv2df <- function(datafilename, wearea = 1) {
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# Function description:
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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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cvfile <- file(datafilename, "r")
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chifile <- readLines(cvfile, n = -1) #read all lines of input file
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close(cvfile)
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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(sampleid, cycle = as.integer(ceiling(s/2)), 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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# Column names after initial assignment
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names(ff) <- c("sampleid", "cycle", "segment", "potential", "current", "charge")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
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## Collect attributes of this experiment
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# InitE (volt)
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position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
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InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
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ff$InitE <- InitE
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# HighE (volt)
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position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
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HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
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ff$HighE <- HighE
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# LowE (volt)
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position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
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LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
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ff$LowE <- LowE
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# InitPN (positive or negative)
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position.InitPN <- regexpr("^Init\\sP/N", chifile)
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InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
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ff$InitPN <- InitPN
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# ScanRate (volt per second)
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position.ScanRate <- regexpr("^Scan\\sRate\\s\\(V/s\\)", chifile)
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ScanRate <- as.numeric(strsplit(chifile[which(position.ScanRate == 1)], "\\s=\\s")[[1]][2])
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ff$ScanRate <- ScanRate
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# Segments, number of
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position.Segments <- regexpr("^Segment\\s=", chifile)
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Segments <- as.numeric(strsplit(chifile[which(position.Segments == 1)], "\\s=\\s")[[1]][2])
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ff$Segments <- Segments
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# SampleInterval (volt)
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position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
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SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
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ff$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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