#pragma TextEncoding = "UTF-8"
#pragma rtGlobals=3		// Use modern global access method and strict wave access.


Function Dichroism( string wave1str, string wave2str)
	Wave wave1 = $(wave1str), wave2 = $(wave2str), temp
	Variable w1x= DimSize(wave1, 0),  w1y= DimSize(wave1, 1)
	Variable w1x0= DimOffset(wave1, 0), w1y0= DimOffset(wave1, 0)
	Variable w1dx=DimDelta(wave1, 0), w1dy= DimDelta(wave1, 1)
	
	String sampleName, dud, IDnum1, IDnum2		//Set up the dichroism wave
	SplitString/E="([[:alnum:]]+)_([[:digit:]]+)_txt_([[:digit:]]+)" wave1str, sampleName, dud, IDnum1
	SplitString/E="([[:alnum:]]+)_([[:digit:]]+)_txt_([[:digit:]]+)" wave2str, sampleName, dud, IDnum2	
	String dichroWave = "DiWave_" + IDnum1 + "-" + IDnum2
	Make/O/N=(w1x, w1y) $(dichroWave)
	Wave diChro = $(dichroWave)	
	SetScale/P x, w1x0, w1dx, diChro
	SetScale/P y, w1y0, w1dy, diChro
	
	diChro = (wave1 - wave2)/(wave1 + wave2) 	//make the dichroism
	
	if(DataFolderExists("root:Dichroisms"))	// set up folders
		NewDataFolder/O/S root:Dichroisms:dichrowave
	else
		NewDataFolder/O/S root:Dichroisms
		NewDataFolder/O/S root:Dichroisms:dichrowave
	endif
	
	SetDataFolder root:Dichroisms //set up color wave in the right folder
	Make2DColorTable()	
	Wave ColorTable= RedBlackBlue2D
	Variable dimColors = DimSize(ColorTable, 1)
	SetDataFolder root:Dichroisms:dichrowave
	
	Make/O/N=(w1x, w1y, dimColors) $("Vol" + dichroWave)
	Wave VolDiChro= $("Vol" + dichroWave)
	VolDiChro= 0
	SetScale/P x, w1x0, w1dx, VolDiChro
	SetScale/P y, w1y0, w1dy, VolDiChro
	variable diMax= WaveMax(diChro), diMin= WaveMin(diChro)
	variable diDelta = (diMax-diMin)/dimColors
	
	variable i, j, k
	For(i=0; i < w1x; i+=1)
		For(j=0; i < w1y; j+=1)
		
			k= round(diChro[i][j]/diDelta) 
			VolDiChro[i][j][k]= diChro[i][j]
			
		EndFor
	EndFor
	
	Display;DelayUpdate
	For(i=0; i<dimColors; i+=1)
	
		temp= VolDiChro[p][q][i]
		AppendImage temp
		// set temp colorscale using ColorTable[][i][], based on (wave1 + wave2)/maxSrcWaves values
		// set temp values of 0 to completely transparent
		
	EndFor
	
// Code Graveyard //
	
//	Display;DelayUpdate		// Display dichroism
//	AppendImage diChro
//	ModifyImage $(dichroWave) ctab={-0.5,0.5,RedWhiteBlue,0}
End

//////////////////////////////////////
////////// Helper Functions //////////
//////////////////////////////////////

Function Make2DColorTable()
	Variable iRGB= 255 + 1 + 255 // = 511
	Make/O/N=(256, iRGB, 3) RedBlackBlue2D
	
	// Green channel easy to define
	RedBlackBlue2D[][][1]= 255 - p
	
	//Define the saturdated values first
	RedBlackBlue2D[255][0,255][0]= 255 - q
	RedBlackBlue2D[255][0,255][2]= 0
	
	RedBlackBlue2D[255][256, iRGB-1][0]= 0
	RedBlackBlue2D[255][256, iRGB-1][2]= q - 255
	
	//Fill in the rest of the wave by linearly interpolating along x
	variable i, f0
	For( i= 0; i<iRGB; i+= 1)
		f0= RedBlackBlue2D[255][i][0]
		RedBlackBlue2D[0,254][i][0] = round( (f0 - 255)*p/255 + 255 )

		f0= RedBlackBlue2D[255][i][2]
		RedBlackBlue2D[0,254][i][2] = round( (f0 - 255)*p/255 + 255 ) 
	EndFor
	// To get desired color table, take RedBlackBlue[i][][]
End