From 64774c079e014519ad6f9f9b6c24c42e9b44316e Mon Sep 17 00:00:00 2001
From: Taha Ahmed <taha@mkem150>
Date: Thu, 24 Feb 2011 16:24:34 +0100
Subject: [PATCH] Added the function Raman2df().

Note: There should be a possibility to supply (as an argument to
Raman2df()) a custom sampleid which should then override the regexp-
based algorithm (only if that argument was supplied).
---
 Renishaw.R | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 Renishaw.R

diff --git a/Renishaw.R b/Renishaw.R
new file mode 100644
index 0000000..5f9526b
--- /dev/null
+++ b/Renishaw.R
@@ -0,0 +1,48 @@
+# Renishaw.R
+# Functions to read data from the Renishaw Raman spectrometer
+# Taha Ahmed, Feb 2011
+
+# CONTENTS
+# >>>> Raman2df
+
+
+
+
+
+##################################################
+################### Raman2df #######################
+##################################################
+Raman2df <- function(datafilename) {
+   # Function description: for reading Raman spectrum into dataframe
+   #
+   datafile <- file(datafilename, "r")
+   chifile <- readLines(datafile, n = -1) #read all lines of input file
+   close(datafile)
+   #
+   #####
+   # A nice algorithm that extracts the filename from the datafilename argument
+   # and uses that as a sampleid in the returned dataframe
+   #####
+   rgxp.sampleid <- "[^/]*(?=\\.\\w*)" ## THIS REQUIRES perl=TRUE
+   # Regular expression that extracts the filename out of a full path.
+   # Matches and extracts everything from the last forward slash (assuming Unix slashes)
+   # up until a dot folllowed by an arbitrary number of alphanumeric characters.
+   sampleidmtch <- regexpr(rgxp.sampleid, datafilename, perl=TRUE)
+   # Check that there was a match
+   if (sampleidmtch < 0) {
+      # -1 means no match
+      sampleid <- datafilename
+      # If match was unsuccessful we use the argument as passed to this function as sampleid
+   }
+   sampleid <- substr(datafilename, sampleidmtch, (sampleidmtch + attr(sampleidmtch, "match.length") - 1))
+   #
+   ff <- data.frame(NULL)
+   zz <- textConnection(chifile, "r")
+   ff <- rbind(ff, data.frame(sampleid,
+            matrix(scan(zz, what = numeric(), sep = "\t"),
+            ncol = 2, byrow = T)))
+   close(zz)
+   names(ff) <- c("sampleid", "shift", "counts")
+   #
+   return(ff)
+}