Created the chronoamp function for AUTOLAB.

Small changes in the chronoamp2df() for CHI.

AUTOLAB.R

@@ -0,0 +1,97 @@
+# 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)
+}

CHI.R

@@ -4,6 +4,7 @@
 
 # CONTENTS
 source("/home/taha/chepec/chetex/common/R/common.R")
+# >>>> mps2df
 # >>>> ocp2df
 # >>>> chronocm2df
 # >>>> chronoamp2df
@@ -13,13 +14,137 @@ source("/home/taha/chepec/chetex/common/R/common.R")
 
 
 
+##################################################
+################### mps2df #######################
+##################################################
+mps2df <- function(datafilename, wearea = 1) {
+   ## Description:
+   ##   Reads time vs current data (from CHI 760 potentiostat)
+   ##   and returns a dataframe with the data and 
+   ##   the data attributes (experimental conditions).
+   ## Usage:
+   ##   mps2df(datafilename, wearea)
+   ## Arguments:
+   ##   datafilename: text string with full path to experimental file
+   ##         wearea: working electrode area in square centimeters (optional)
+   ## Value:
+   ##   Dataframe with the following columns (and no extra attributes):
+   ##   $ sampleid        : chr
+   ##   $ time            : num
+   ##   $ current         : num
+   ##   $ currentdensity  : num
+   ##   $ timediff        : num
+   ##   $ dIdt            : num
+   ##   $ didt            : num
+   ##   $ charge          : num
+   ##   $ chargedensity   : num
+   ##   $ Cycle           : num
+   ##   $ SampleInterval  : num
+   ##   $ QuietTime       : 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 due to the way R handles strings.
+   #
+   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(stringsAsFactors = FALSE,
+               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$currentdensity)
+   # Update ff dataframe
+   ff <- cbind(ff, 
+      timediff = timediff, 
+      dIdt = dIdt, 
+      didt = didt,
+      charge = charge, 
+      chargedensity = chargedensity)
+   #
+   ### Collect attributes of this experiment
+   # Potential steps  #### THIS NEEDS FIXING
+   positions.PotentialSteps <- regexpr("^E\\d+\\s\\(V\\)", chifile)
+   #PotentialSteps <- as.numeric(strsplit(chifile[which(positions.PotentialSteps == 1)], "\\s=\\s")[[1]][2])
+   #ff$PotentialSteps <- PotentialSteps
+   # Time steps  #### THIS NEEDS FIXING
+   positions.Time <- regexpr("^T\\d+\\s\\(s\\)", chifile)
+   # Cycle
+   position.Cycle <- regexpr("^Cycle", chifile)
+   Cycle <- as.numeric(strsplit(chifile[which(position.Cycle == 1)], "\\s=\\s")[[1]][2])
+   ff$Cycle <- Cycle
+   # Sample interval (s)
+   position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
+   SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
+   ff$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)
+}
+
+
+
 
 ##################################################
 ################### ocp2df #######################
 ##################################################
 ocp2df <- function(datafilename) {
    ## Description:
-   ##   Reads potential-time data (from CHI 760 potentiostat)
+   ##   Reads time vs potential data (from CHI 760 potentiostat)
    ##   and returns a dataframe with the data and 
    ##   the data attributes (experimental conditions).
    ## Usage: