You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
97 lines
3.4 KiB
R
97 lines
3.4 KiB
R
14 years ago
|
# AUTOLAB.R
|
||
|
|
# Functions to read and manipulate data from AUTOLAB potentiostats/galvanostats
|
||
|
|
# Taha Ahmed, June 2011
|
||
|
|
|
||
|
|
# CONTENTS
|
||
|
|
source("/home/taha/chepec/chetex/common/R/common.R")
|
||
|
|
# >>>> chronoamp2df
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
##################################################
|
||
|
|
################# chronoamp2df ###################
|
||
|
|
##################################################
|
||
|
|
chronoamp2df <- function(datafilename, wearea = 1) {
|
||
|
|
## Description:
|
||
|
|
## Reads current-time data (from AUTOLAB potentiostat)
|
||
|
|
## and returns a dataframe with the data and some
|
||
|
|
## calculated quantities based on the data.
|
||
|
|
## 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:
|
||
|
|
## $ sampleid : chr
|
||
|
|
## $ time : num
|
||
|
|
## $ current : num
|
||
|
|
## $ currentdensity : num
|
||
|
|
## $ timediff : num
|
||
|
|
## $ dIdt : num
|
||
|
|
## $ didt : num
|
||
|
|
## $ charge : num
|
||
|
|
## $ chargedensity : num
|
||
|
|
#
|
||
|
|
datafile <- file(datafilename, "r")
|
||
|
|
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||
|
|
close(datafile)
|
||
|
|
#
|
||
|
|
sampleid <- ProvideSampleId(datafilename)
|
||
|
|
#
|
||
|
|
rgxp.number <- "^\\d+\\.\\d+"
|
||
|
|
# regexp that matches a decimal number at the beginning of the line.
|
||
|
|
# Matches numbers _without_ a negative sign (hyphen),
|
||
|
|
# followed by one or more digits before the decimal, a decimal point,
|
||
|
|
# and an one or more digits after the decimal point.
|
||
|
|
# 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,
|
||
|
|
matrix(scan(zz, what = numeric(), sep = ""),
|
||
|
|
ncol = 2, byrow = T)))
|
||
|
|
close(zz)
|
||
|
|
}
|
||
|
|
names(ff) <- c("sampleid", "time", "current")
|
||
|
|
# Calculate current density
|
||
|
|
currentdensity <- ff$current / wearea
|
||
|
|
ff <- cbind(ff, currentdensity = currentdensity)
|
||
|
|
# Calculate time diff and current diff
|
||
|
|
timediff <- c(ff$time[1], diff(ff$time))
|
||
|
|
currentdiff <- c(ff$current[1], diff(ff$current))
|
||
|
|
currentdensitydiff <- c(ff$currentdensity[1], diff(ff$currentdensity))
|
||
|
|
# Calculate differential of current and current density
|
||
|
|
dIdt <- currentdiff / timediff
|
||
|
|
didt <- currentdensitydiff / timediff
|
||
|
|
# Calculate charge and charge density
|
||
|
|
charge <- cumsum(ff$current)
|
||
|
|
chargedensity <- cumsum(ff$currentdensity)
|
||
|
|
# Update ff dataframe
|
||
|
|
ff <- cbind(ff,
|
||
|
|
timediff = timediff,
|
||
|
|
dIdt = dIdt,
|
||
|
|
didt = didt,
|
||
|
|
charge = charge,
|
||
|
|
chargedensity = chargedensity)
|
||
|
|
#
|
||
|
|
return(ff)
|
||
|
|
}
|