Removed R and T calculations to their own functions to ensure consist…

…ancy between different scans

R/RTCalc.R

@@ -0,0 +1,16 @@
+ReflectionCalc <-function(r){
+  return(r*Conj(r))
+}
+
+TransmissionCalc <-function(t,angle,theta2, incident_medium.index,exit_medium.index,polarisation){
+
+  #remember t*conj(t) does NOT in general equal T.
+  #correct phase conditions accounted for in scan files, and 
+  #found originally at https://github.com/sbyrnes321/tmm
+
+  if(polarisation=="s"){
+    return(t*Conj(t)*(exit_medium.index*cos(theta2)/(incident_medium.index*cos(angle))))
+  } else if(polarisation=="p"){
+    return(t*Conj(t)*(exit_medium.index*Conj(cos(theta2))/(incident_medium.index*Conj(cos(angle)))))
+  } 
+}

R/angle_scan.R

@@ -35,16 +35,16 @@ angle_scan<-function(angle_range=seq(0,pi/2,,500),wavelength=633e-9, polarisatio
     M<-mtx.exp(M,layers$repetitions)
 
     r<-rFromTMatrix(M=M,gamma0=gamma0,gamma2=gamma2)
-    Reflection[counting_variable]<-r*Conj(r)
-    
+    Reflection[counting_variable]<-ReflectionCalc(r)
+
     t<-tFromTMatrix(M=M,gamma0=gamma0,gamma2=gamma2)
-    if(polarisation=="s"){
-      Transmission[counting_variable]<- t*Conj(t)*(exit_medium.index*cos(L$theta2)/(incident_medium.index*cos(angle)))
-    } else if(polarisation=="p"){
-      Transmission[counting_variable]<- t*Conj(t)*(exit_medium.index*Conj(cos(L$theta2))/(incident_medium.index*Conj(cos(angle))))
-    } 
-  }
-  return(data.frame(angle=angle_range,Reflection=Re(Reflection),Transmission=Re(Transmission)))
+    Transmission[counting_variable]<-TransmissionCalc(t,angle,L$theta2,incident_medium.index,exit_medium.index,polarisation)
+
+}
+  return(data.frame(angle=angle_range,
+                    Reflection=Re(Reflection),
+                    Transmission=Re(Transmission),
+                    Absorption=1-Re(Transmission)-Re(Reflection)))
 }
 
 

R/dispersion_scan.R

@@ -62,6 +62,10 @@ dispersion_scan<-function(angle_range=seq(0,pi/2,,100),wavelength_range=seq(350e
 
     }
   }
-  return(data.frame(angle=cum_angle,wavelength=cum_wavelength,Reflection=Re(Reflection),Transmission=Re(Transmission)))
+  return(data.frame(angle=cum_angle,
+                    wavelength=cum_wavelength,
+                    Reflection=Re(Reflection),
+                    Transmission=Re(Transmission),
+                    Absorption=1-Re(Transmission)-Re(Reflection)))
 }
 

R/rtFromTMatrix.R

@@ -6,9 +6,6 @@ rFromTMatrix<- function(M,gamma0,gamma2){
 }
 
 tFromTMatrix<- function(M,gamma0,gamma2){
-  #remember t*conj(t) does NOT in general equal T.
-  #correct phase conditions accounted for in scan files, and 
-  #found originally at https://github.com/sbyrnes321/tmm
 
   t<-(2*gamma0)/((gamma0*M[1,1])+(gamma0*gamma2*M[1,2])+(M[2,1])+(gamma2*M[2,2]))
   return(t)

R/wavelength_scan.R

@@ -38,19 +38,18 @@ wavelength_scan<-function(wavelength_range=seq(350e-9,850e-9,,500),angle=0, pola
     M<-mtx.exp(M,layers$repetitions)
 
     r<-rFromTMatrix(M=M,gamma0=gamma0,gamma2=gamma2)
-    Reflection[counting_variable]<-r*Conj(r)
+    Reflection[counting_variable]<-ReflectionCalc(r)
 
     t<-tFromTMatrix(M=M,gamma0=gamma0,gamma2=gamma2)
+    Transmission[counting_variable]<-TransmissionCalc(t,angle,L$theta2,incident_medium.index,exit_medium.index,polarisation)
 
-    if(polarisation=="s"){
-      Transmission[counting_variable]<- t*Conj(t)*(exit_medium.index*cos(L$theta2)/(incident_medium.index*cos(angle)))
-    } else if(polarisation=="p"){
-      Transmission[counting_variable]<- t*Conj(t)*(exit_medium.index*Conj(cos(L$theta2))/(incident_medium.index*Conj(cos(angle))))
-    }
 
   }
 
-  return(data.frame(wavelength=wavelength_range,Reflection=Re(Reflection),Transmission=Re(Transmission)))
+  return(data.frame(wavelength=wavelength_range,
+                    Reflection=Re(Reflection),
+                    Transmission=Re(Transmission),
+                    Absorption=1-Re(Transmission)-Re(Reflection)))
 }