library(Hmisc)

# Rutherford Overlay
plot(count~channel,data=data2,type='l',xlim=c(50,205))
lines(c(0,1023),c(7600,7600),col="blue")
lines(count~channel,data=data3,col='red')
lines(c(0,1023),c(18500,18500),col="purple")
minor.tick(nx=5,ny=2)
dev.print(pdf,"../report/rutherford.pdf",width=6,height=3)

# calibration close-up

plot(count~channel,data=data2,type='l',xlim=c(185,205))
lines(c(0,1023),c(7600,7600),col="blue")
abline(h = 1520,col="blue",lwd=1)
abline(v = 189.12,col="blue",lwd=1)
axis(1,at=189.12,padj=1.5,"189.12±0.6")
axis(3,at=189.12,"1.706±0.05 MeV")
lines(count~channel,data=data3,col='red')
lines(c(0,1023),c(18500,18500),col="purple")
abline(h = 3700,col="purple",lwd=1)
abline(v = 203.63,col="purple",lwd=1)
axis(1,at=203.63,padj=1.5,"203.63±0.6")
axis(3,at=203.63,"1.838±0.05 MeV")
minor.tick(nx=5,ny=2)
dev.print(pdf,"../report/calibration.pdf",width=6,height=3)

# nuclear reactions
plot(count~energy,data=data1,type='l',xlim=c(7.0,8.0),ylim=c(0,100),xlab="energy (MeV)")
abline(v = 7.949,col="blue")
abline(v = 7.175,col="purple")
axis(3,at=7.175,"7.175")
abline(v = 7.583,col="purple")
axis(3,at=7.583,"7.583")
axis(3,at=7.949,"7.949")
abline(v = 7.688,col="blue")
axis(3,at=7.688,"7.688")
minor.tick(nx=8,ny=2)
dev.print(pdf,"../report/nuclear.pdf",width=6,height=3)


#
plot(count~energy,data=data1,type='l',xlim=c(0.5,2.5),ylim=c(0,25000),xlab="energy (MeV)")
minor.tick(nx=8,ny=2)
dev.print(pdf,"../report/thickness.pdf",width=6,height=3)



axis(2,at=20000)


lines(c(0,1023),c(3520,3520),col="blue")



lines(c(0,1023),c(4000,4000),col="purple")



Alpha Activity
plot(data_4_2,xlab="Energy [MeV]",ylab="Count [Alpha Particles]",pch=".")
minor.tick(nx=5,ny=2)
abline(v = 5.631,col=2,lwd=1)
axis(3,at=5.631,"5.6")
abline(v = 5.323,col=2,lwd=1)
axis(3,at=5.323,"5.3")
dev.print(pdf,"../report/activity.pdf")