read.r
In spectro: Spectroscopy data analysis

rm(list=ls())
library(spectro)

setwd("/Users/baptiste/Documents/Vigo/data/2010/02/01/")

d.long <- assignFiles()

d.wide <- reshape(d.long)

s <- with(d.wide, list(wavelength=testsignal$wavelength,
                       intensity=testsignal$intensity / testlamp$intensity))


quartz()
## levelplot(value~wavelength+pixel, data=d.long[[2]])
## image(s$intensity)
visualize.peaks(s$intensity, s$wavelength)

quartz()
peaks <- with(s, findPeaks(intensity, wavelength, thres=0))

quartz()
with(s, visualize.peaks(intensity, wavelength, peaks, log=TRUE))

spectra <- extract.spectra(intensity, wavelength, peaks)

all <- melt(spectra, meas="intensity")
qplot(wavelength, value, data=all[all$wavelength < 760, ],colour=L1, group=L1,  geom="path")