#$ targen -d2 test
#$ printtarg test
#$ chartread -D5 -H test
## calibration, 60sec pause, then 10sec measurement on calibration tile
## output saved as chartread-D5_on_whiteref.txt
## raw data of dark calibration saved as darkcal106.dump
## raw data of strip reading    saved as 1890readings.dump
#$ xxd -r -p   darkcal106.dump   darkcal106.bin
#$ xxd -r -p 1890readings.dump 1890readings.bin

rawfile <-file("/Users/klaus/Documents/Farbe/argyll/i1_IR-calibration/darkcal106.bin","rb")
r1<-readBin(rawfile,integer(),128,size=2, endian="big", signed=FALSE)
r1<-ifelse(r1 >= 64000, r1-65536, r1)
darkcal <- data.frame(t(r1))
for (i in 2:106) {
	r1<-readBin(rawfile,integer(),128,size=2, endian="big", signed=FALSE)
	r1<-ifelse(r1 >= 64000, r1-65536, r1)
	darkcal <- rbind(darkcal, data.frame(t(r1)))
}
close(rawfile)
rm(r1)


rawfile <-file("/Users/klaus/Documents/Farbe/argyll/i1_IR-calibration/1890readings.bin","rb")
r1<-readBin(rawfile,integer(),128,size=2, endian="big", signed=FALSE)
r1<-ifelse(r1 >= 64000, r1-65536, r1)
readings <- data.frame(t(r1))
for (i in 2:1890) {
	r1<-readBin(rawfile,integer(),128,size=2, endian="big", signed=FALSE)
	r1<-ifelse(r1 >= 64000, r1-65536, r1)
	readings <- rbind(readings, data.frame(t(r1)))
}
close(rawfile)
rm(r1)

plot(c(0,1890),c(min(min(readings)),max(max(readings))), type="n")
lines(1:1890, readings[1:1890,70], col="black")
lines(1:1890, readings[1:1890,77], col="red")
lines(1:1890, readings[1:1890,97], col="green")
lines(1:1890, readings[1:1890,107], col="blue")
# saved as some_bands

offset1<-apply(darkcal,2,median)
offset2<-apply(readings[213:233,],2,median)

plot(offset2[-128], col="red", xlab="band", ylab="median of dark current")
points(offset1[-128], pch="x", col="black")
legend("topright",legend=c("initial calibration", "strip calibration"), pch=c("x","o"), col=c("black","red"))
# saved as offsets

boxplot(darkcal[-128], main="initial dark calibration")
# saved as boxplot_initial_dark_cal

boxplot(readings[213:233,-128])
# saved as boxplot_strip_dark_cal

summary(readings[213:233,1:20])
summary(darkcal[1:20])
# saved as summary_offset.txt

readings2 <- readings[234:1890,1:127]

plot(c(1,nrow(readings2)), c(min(min(readings2)), max(max(readings2))), type="n")
bands<-round(seq(from=1, to=127, length.out=10))
for(i in bands)
	lines(1:nrow(readings2), readings2[,i], col=rainbow(ncol(readings2), end=0.7)[i])
legend("topright",legend=paste("band", bands), lwd=2, col=rainbow(ncol(readings2), end=0.7)[bands], cex=0.65)
# saved as 10_bands