From 52adff796b66e905789873c9102d2775ea3466e7 Mon Sep 17 00:00:00 2001
From: Taha Ahmed <taha@asks2>
Date: Wed, 29 Jun 2011 22:23:08 +0200
Subject: [PATCH] Added ocp2df() function to AUTOLAB.R.

ocp2df() is a straight-forward, no-frills function.
---
 AUTOLAB.R | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)

diff --git a/AUTOLAB.R b/AUTOLAB.R
index 912060c..6da256b 100644
--- a/AUTOLAB.R
+++ b/AUTOLAB.R
@@ -5,6 +5,7 @@
 # CONTENTS
 source("/home/taha/chepec/chetex/common/R/common.R")
 # >>>> amp2df
+# >>>> ocp2df
 
 
 
@@ -95,4 +96,67 @@ amp2df <- function(datafilename, wearea = 1) {
       chargedensity = chargedensity)
    #
    return(ff)
+}
+
+
+
+
+##################################################
+#################### ocp2df ######################
+##################################################
+ocp2df <- function(datafilename) {
+   ## Description:
+   ##   Reads voltage-time data (from AUTOLAB potentiostat)
+   ##   and returns a dataframe with the data.
+   ## Usage:
+   ##   ocp2df(datafilename)
+   ## Arguments:
+   ##   datafilename: text string with full path to experimental file
+   ## Value:
+   ##   Dataframe with the following columns:
+   ##   $ sampleid        : chr
+   ##   $ time            : num
+   ##   $ potential       : 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,
+                  stringsAsFactors = FALSE,                  
+                  matrix(scan(zz, what = numeric(), sep = ""),
+                     ncol = 2, byrow = T)))
+      close(zz)
+   }
+   names(ff) <- c("sampleid", "time", "potential")
+   #
+   return(ff)
 }
\ No newline at end of file