Added functions for converting to/from wavelength and wavenumbers.

ConvertRefPot.R

@@ -1,6 +1,6 @@
-source("/home/taha/chepec/chetex/common/R/common/SHE2AVS.R")
+source(HomeByHost("/home/taha/chepec/chetex/common/R/common/SHE2AVS.R"))
-source("/home/taha/chepec/chetex/common/R/common/AVS2SHE.R")
+source(HomeByHost("/home/taha/chepec/chetex/common/R/common/AVS2SHE.R"))
-source("/home/taha/chepec/chetex/common/R/common/ConvertRefPotEC.R")
+source(HomeByHost("/home/taha/chepec/chetex/common/R/common/ConvertRefPotEC.R"))
 
 ##################################################
 ################# ConvertRefPot ##################

CountRods.R

@@ -0,0 +1,26 @@
+##################################################
+################## CountRods #####################
+##################################################
+CountRods <- function() {
+   ## Description:
+   ##   
+   ## Usage:
+   ##   
+   ## Arguments:
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ##   
+   ## Return value:
+   ##  
+   #
+   
+   return()
+}

SubfigureGenerator.R

@@ -47,7 +47,7 @@ SubfigureGenerator <- function(images,
       if (landscape == TRUE) {
          cat("\\begin{sidewaysfigure}\\centering\n", file = zz)
       } else {
-         cat("\\begin{figure}[tb]\\centering\n", file = zz)
+         cat("\\begin{figure}[hb]\\centering\n", file = zz)
       }
       
       # display images in a X-by-Y grid

SubstrateHistory.R

@@ -1,4 +1,4 @@
-source("/home/taha/chepec/chetex/common/R/common/LoadRData2Variable.R")
+source(HomeByHost("/home/taha/chepec/chetex/common/R/common/LoadRData2Variable.R"))
 
 ##################################################
 ############## SubstrateHistory ##################

eV2nm.R

@@ -1,13 +1,16 @@
 ##################################################
 #################### eV2nm #######################
 ##################################################
+source(HomeByHost("/home/taha/chepec/chetex/common/R/sunlight/solarconstants.R"))
+
 eV2nm <- function(eV) {
    # Converts energy in eV to wavelength in nm
    #
-   # Define some constants needed for the calculations
+   sun.constants <- solar.constants()
-   Plancks.constant <- 4.135667516E-15 # \electron\volt\per\second
+   
-   speed.of.light   <- 299792458       # \meter\per\second
+   nm <- 
+      sun.constants["h.eV", "value"] * 
+      1E9 * sun.constants["c", "value"] / eV
    
-   nm <- Plancks.constant * 1E9 * speed.of.light / eV
    return(nm)
 }

nm2eV.R

@@ -1,13 +1,16 @@
 ##################################################
 #################### nm2eV #######################
 ##################################################
+source(HomeByHost("/home/taha/chepec/chetex/common/R/sunlight/solarconstants.R"))
+
 nm2eV <- function(nm) {
    # Converts wavelength in nm to energy in eV
    #
-   # Define some constants needed for the calculations
+   sun.constants <- solar.constants()
-   Plancks.constant <- 4.135667516E-15 # \electron\volt\per\second
+   
-   speed.of.light   <- 299792458       # \meter\per\second
+   eV <- 
+      sun.constants["h.eV", "value"] * 
+      1E9 * sun.constants["c", "value"] / nm
    
-   eV <- Plancks.constant * 1E9 * speed.of.light / nm
    return(eV)
 }

siunitx-exp-uncert.R

@@ -0,0 +1,81 @@
+# Writing number with exponent (such as scientific notation) with uncertainty using siunitx
+
+# Origin of problem, this kind of code:
+# \SI[separate-uncertainty=true]{\Sexpr{formatC(cd.flux, format = "e", digits = 2)} \pm \Sexpr{formatC(cd.flux.error, format = "e", digits = 2)}}{\milli\coulomb\per\square\cm\per\second}
+# makes siunitx throw the error:  
+# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+# !
+# ! siunitx error: "misplaced-sign-token"
+# ! 
+# ! Misplaced sign token '\pm '.
+# ! 
+# ! See the siunitx documentation for further information.
+# ! 
+# ! For immediate help type H <return>.
+# !...............................................  
+
+
+# This is status-by-design according to Joseph Wright.
+# http://tex.stackexchange.com/questions/123771/exponent-notation-in-siunitx
+
+# But if the two numbers (number and uncertainty) have the same exponent, that is ok.
+# So here we try to write a function that accepts two numbers, 
+# and returns them written in a common exponent (as strings).
+
+siunitx.uncertainty <- function(quantity, uncertainty, digits = 6) {
+   # both arguments should be numeric
+   
+   # how to find common exponent for two numbers?
+   
+   # find exponent of quantity (tiopotensen for kvantiteten)
+   quantity.exponent <- floor(log(abs(quantity), 10))
+   
+   # find coefficient of quantity
+   # warning, numeric-to-string-to-numeric conversion ...
+   quantity.coefficient <- 
+      as.numeric(strsplit(formatC(quantity, format="e", digits=digits), "[Ee]-")[[1]][1])
+   
+   # construct return quantity string
+   rquantity.string <- 
+      paste0(formatC(quantity.coefficient, format="f", digits=digits), "e", quantity.exponent)
+   
+   
+      
+   # find exponent of uncertainty (tiopotensen for the uncertainty)
+   uncertainty.exponent <- floor(log(abs(uncertainty), 10))
+   
+   # find coefficient of uncertainty
+   # warning, numeric-to-string-to-numeric conversion ...
+   uncertainty.coefficient <- 
+      as.numeric(strsplit(formatC(uncertainty, format="e", digits=digits), "[Ee]-")[[1]][1])
+   
+   # adjust uncertainty to the same exponent as the quantity
+   # express uncertainty with the same exponent as quantity 
+   # (adjust number of uncertainty accordingly)
+   runcertainty.exponent <- quantity.exponent
+   runcertainty.coefficient <- uncertainty.coefficient * 10^(uncertainty.exponent - quantity.exponent)
+   
+   runcertainty.string <- 
+      paste0(formatC(runcertainty.coefficient, format="f", digits=digits), "e", runcertainty.exponent)
+      
+
+   # create a string directly suitable for the siunitx \num{} command
+   siunitx.string <- paste(quantity.coefficient, "\\pm", runcertainty.string)
+
+   return(c(quantity = rquantity.string, 
+            uncertainty = runcertainty.string,
+            siunitx = siunitx.string))
+}
+   
+   
+   
+   
+   
+   
+   
+   
+   
+   
+   
+   
+   

thth2d.R

@@ -33,6 +33,6 @@ thth2d <- function(thth, wavelength = 1.540562) {
    #    Zn-Kb1 wavelength=1.295250
    # Usage:
    # thth       : vector with thth values in degrees
-   # wavelength : radiation wavelength in Ångström
+   # wavelength : radiation wavelength in Angstrom
    return (wavelength / (2 * sin(as.radians(thth))))
 }

wavelength2num.R

@@ -0,0 +1,13 @@
+##################################################
+################ wavelength2num ##################
+##################################################
+
+wavelength2num <- function(wavelength) {
+   # Converts wavelength (nm) to wavenumber (cm-1)
+   # Only valid for absolute wavelengths, 
+   # NOT delta wavelengths (ranges)
+   # http://www.powerstream.com/inverse-cm.htm
+	wavenumber <-
+		10E6 / wavelength
+   return(wavenumber)
+}

wavenum2length.R

@@ -0,0 +1,13 @@
+##################################################
+################ wavenum2length ##################
+##################################################
+
+wavenum2length <- function(wavenumber) {
+   # Converts wavenumber (cm-1) to wavelength (nm)
+   # Only valid for absolute wavenumbers,
+   # NOT delta wavenumbers (ranges)
+   # http://www.powerstream.com/inverse-cm.htm
+	 wavelength <-
+	    10E6 / wavenumber
+   return(wavelength)
+}