Updated chronoamp2df() to the new attributes system. Also improved docs.

master
Taha Ahmed 14 years ago
parent b687e77eb5
commit e3a7e20ff8

99
CHI.R

@ -183,10 +183,37 @@ chronocm2df <- function(datafilename) {
################# chronoamp2df ###################
##################################################
chronoamp2df <- function(datafilename, wearea = 1) {
# Function description: chronoamperometry data
# CH Instruments potentiostat records all data using standard SI units,
# so all potential values are in volts, currents are in amperes,
# charges in Coulombs, time in seconds, etc.
## 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 : num
## $ 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
@ -231,34 +258,44 @@ chronoamp2df <- function(datafilename, wearea = 1) {
currentdensity <- ff$current / wearea
ff <- cbind(ff, currentdensity = currentdensity)
#
### Collect attributes of this experiment
# These attributes are specific for each kind of experiment,
# be careful when adapting to other electrochemical data
rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
"^High\\sE\\s\\(V\\)",
"^Low\\sE\\s\\(V\\)",
"^Init\\sP/N",
"^Step\\s",
"^Pulse\\sWidth\\s\\(sec\\)",
"^Sample\\sInterval\\s\\(s\\)",
"^Quiet\\sTime\\s\\(sec\\)",
"^Sensitivity\\s\\(A/V\\)")
names.attr <- c("InitE",
"HighE",
"LowE",
"InitPN",
"Steps",
"PulseWidth",
"SamplingInterval",
"QuietTime",
"Sensitivity")
for (n in 1:length(rgxp.attr)) {
attrow.idx <- regexpr(rgxp.attr[n], chifile)
attrow.len <- attr(attrow.idx, "match.length")
attr(attrow.idx, "match.length") <- NULL
attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
"\\s=\\s")[[1]][2]
}
# InitE (volt)
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
ff$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 <- as.numeric(strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2])
ff$InitPN <- InitPN
# Step
position.Step <- regexpr("^Step\\s", chifile)
Step <- as.numeric(strsplit(chifile[which(position.Step == 1)], "\\s=\\s")[[1]][2])
ff$Step <- Step
# 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)
}

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