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R

source("/home/taha/chepec/chetex/common/R/common.R")
##################################################
################# chronoamp2df ###################
##################################################
chronoamp2df <- function(datafilename, wearea = 1) {
## Description:
## Reads current-time data (from CHI 760 potentiostat)
## and returns a dataframe with the data and the
## data attributes (experimental conditions).
## Usage:
## chronoamp2df(datafilename, wearea)
## Arguments:
## datafilename: text string with full path to experimental file
## wearea: (optional) area of working electrode (in square centimeters)
## Value:
## Dataframe with the following columns (and no extra attributes):
## $ sampleid : chr
## $ step : num
## $ time : num
## $ current : num
## $ currentdensity : num
## $ InitE : num
## $ HighE : num
## $ LowE : num
## $ InitPN : chr
## $ Step : num
## $ Pulse width : num
## $ Sample interval : num
## $ Quiet Time : num
## $ Sensitivity : num
## Note:
## The CH Instruments 760 potentiostat records all data
## using standard SI units, therefore this function
## assumes all potential values to be in volts,
## currents to be in amperes, charges in Coulombs,
## time in seconds, and so on.
#
datafile <- file(datafilename, "r")
chifile <- readLines(datafile, n = -1) #read all lines of input file
close(datafile)
#
sampleid <- ProvideSampleId(datafilename)
#
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
# regexp that matches a decimal number at the beginning of the line.
# Matches numbers with or without a negative sign (hyphen),
# followed by one digit before the decimal, a decimal point,
# and an arbitrary number of digits after the decimal point,
# immediately followed by either the letter 'e' or a comma.
# Note that backslashes are escaped.
#
numrow.idx <- regexpr(rgxp.number, chifile)
# Save the match length attribute to another variable,
numrow.len <- attr(numrow.idx, "match.length")
# then scrap the attribute of the original variable.
attr(numrow.idx, "match.length") <- NULL
#
i <- seq(1, length(numrow.idx) - 1, 1)
j <- seq(2, length(numrow.idx), 1)
# Start indices of data ranges
starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
# End indices, except for the last
ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
# Fix the last index of end indices
ends <- c(ends, length(numrow.idx))
#
ff <- data.frame(NULL)
for (s in 1:length(starts)) {
zz <- textConnection(chifile[starts[s]:ends[s]], "r")
ff <- rbind(ff,
data.frame(sampleid, step.current = s,
matrix(scan(zz, what = numeric(), sep = ","),
ncol = 2, byrow = T)))
close(zz)
}
names(ff) <- c("sampleid", "step.current", "time", "current")
# Calculate current density
currentdensity <- ff$current / wearea
ff <- cbind(ff, currentdensity = currentdensity)
#
### Collect attributes of this experiment
# InitE (volt)
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
ff$InitE <- InitE
# HighE (volt)
position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
ff$HighE <- HighE
# LowE (volt)
position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
ff$LowE <- LowE
# InitPN
position.InitPN <- regexpr("^Init\\sP/N", chifile)
InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
ff$InitPN <- InitPN
# Steps (total number of steps)
position.Steps <- regexpr("^Step\\s", chifile)
Steps <- as.numeric(strsplit(chifile[which(position.Steps == 1)], "\\s=\\s")[[1]][2])
ff$Steps <- Steps
# Pulse width (s)
position.PulseWidth <- regexpr("^Pulse\\sWidth\\s\\(sec\\)", chifile)
PulseWidth <- as.numeric(strsplit(chifile[which(position.PulseWidth == 1)], "\\s=\\s")[[1]][2])
ff$PulseWidth <- PulseWidth
# Sample interval (s)
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
ff$SampleInterval <- SampleInterval
# Quiet Time (s)
position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
ff$QuietTime <- QuietTime
# Sensitivity (A/V)
position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
ff$Sensitivity <- Sensitivity
#
return(ff)
}