Added function ocp2df() in CHI.R

CHI.R

@@ -3,6 +3,7 @@
 # Taha Ahmed, Jan 2011 - Feb 2011
 
 # CONTENTS
+# >>>> ocp2df
 # >>>> chronocm2df
 # >>>> chronoamp2df
 # >>>> amperometry2df
@@ -12,6 +13,70 @@
 
 
 
+##################################################
+################### ocp2df #######################
+##################################################
+ocp2df <- function(datafilename) {
+   # Function description: for recorded amperometric i-T curves
+   # 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.
+   #
+   datafile <- file(datafilename, "r")
+   chifile <- readLines(datafile, n = -1) #read all lines of input file
+   close(datafile)
+   #
+   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(matrix(scan(zz, what = numeric(), sep = ","),
+                  ncol = 2, byrow = T)))
+      close(zz)
+   }
+   names(ff) <- c("time", "potential")
+   #
+   ### 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("^Run\\sTime\\s\\(sec\\)")
+   names.attr <- c("RunTime")
+   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
+      # attrow.idx should now contain only one matching row
+      attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
+         "\\s=\\s")[[1]][2]
+   }
+   #
+   return(ff)
+}
+
+
 
 ##################################################
 ################# chronocm2df ####################