#pragma rtGlobals=2		// Use modern global access method.
#pragma IgorVersion = 4.0
#include "spec"

Function deadTime(det)
	Variable det
	Variable W0 = 559897.975452345
	Variable W1 = -563471.687494516
	Variable W2 = 1.89519906301593e-06
	Variable corrected = -ln((det-W0)/W1)/W2
	if (numtype(corrected) || corrected<det)
		return det
	else
		return corrected
	endif
End

Function extraSpecReadProcess(extra)
	Variable extra
	if (!extra)
		return 0
	endif

	if (exists("I0")==1)						// set Io wave if it exists
		Wave wI0 = I0
	endif
	if (exists("Io")==1)
		Wave wI0 = Io
	endif

	if ((exists("sig")!=1) && WaveExists(wI0))	// make a normalized wave
		String fldr= GetDataFolder(0)
		Variable scanNum = str2num(fldr[4,inf])
		Variable filterTrans=specInfo(scanNum,"filterTrans")
		filterTrans = numtype(filterTrans) ? 1 : filterTrans
		SVAR specYwave=specYwave
		Duplicate $specYwave sig
		String photonCounter="detector;scint;NaI;scint;oxfo;oxford;Bicr;Bicron;harmonic;Det_bot;Det_top"
		if ((FindListItem(specYwave, photonCounter)>=0) && (exists("sig_err")!=1))
			if (exists("deadtime")==6 && exists("seconds")==1)
				WAVE seconds=seconds
				sig /= seconds
				sig = deadTime(sig)			// dead time works on counts/second only
				sig *= seconds
			endif
			Duplicate $specYwave sig_err
			sig_err = sqrt(sig) / wI0 / filterTrans
		endif
		sig = sig / wI0 / filterTrans
		specYwave = "sig"
	endif
End

Proc extraSpecReadProcessOLD(extra)
	Variable extra
	Silent 1
	if (!extra)
		return
	endif

	string wI0=""								// find name of Io wave if it exists
	if (exists("I0")==1)
		wI0 = "I0"
	endif
	if (exists("Io")==1)
		wI0 = "Io"
	endif

	if ((exists("sig")!=1) && strlen(wI0))		// make a normalized wave
		String fldr= GetDataFolder(0)
		Variable scanNum = str2num(fldr[4,inf])
		Variable filterTrans=specInfo(scanNum,"filterTrans")
		filterTrans = numtype(filterTrans) ? 1 : filterTrans
		Duplicate $specYwave sig
		String photonCounter="detector;scint;NaI;scint;oxfo;oxford;Bicr;Bicron;harmonic;Det_bot;Det_top"
		if ((FindListItem( :specYwave, photonCounter)>=0) && (exists("sig_err")!=1))
			if (exists("deadtime")==6 && exists("seconds")==1)
				sig /= seconds
				sig = deadTime(sig)			// dead time works on counts/second only
				sig *= seconds
			endif
			Duplicate $specYwave sig_err
			sig_err = sqrt(sig) / $wI0 / filterTrans
		endif
		sig = sig / $wI0 / filterTrans
		specYwave = "sig"
	endif
End


Proc extraSpecReadProcessOLDer(extra)
	Variable extra
	Silent 1
	if (!extra)
		return
	endif

	string wI0=""								// find name of Io wave if it exists
	if (exists("I0")==1)
		wI0 = "I0"
	endif
	if (exists("Io")==1)
		wI0 = "Io"
	endif

	if ((exists("sig")!=1) && strlen(wI0))		// make a normalized wave
		String fldr= GetDataFolder(0)
		Variable scanNum = str2num(fldr[4,inf])
		Variable filterTrans=specInfo(scanNum,"filterTrans")
		filterTrans = numtype(filterTrans) ? 1 : filterTrans
		String photonCounter="detector;scint;NaI;scint;oxfo;oxford;Bicr;Bicron;harmonic;Det_bot;Det_top"
		if ((FindListItem( :specYwave, photonCounter)>=0) && (exists("sig_err")!=1))
			Duplicate $specYwave sig_err
			sig_err = sqrt($specYwave) / $wI0 / filterTrans
		endif
		Duplicate $specYwave sig
		sig = sig / $wI0 / filterTrans
		specYwave = "sig"
	endif
End



Proc extraSpecRead(fileVar)
	Variable fileVar			// file ref number
	Silent 1

	String line1,line2				// line of input from file
	Variable i

	FStatus fileVar							// this section special for reading #BL and #B lines
	Variable FilePos = V_filePos			// this should be the start of the scan

	line1 = FindDataLineType(fileVar,"#I ",1)
	if (strlen(line1)>2)
		line1 = line1[3,inf]
		SetBValues("filter",line1)
	endif

	line1 = FindDataLineType(fileVar,"#B0 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		line2 = FindDataLineType(fileVar,"#B1 ",1)
		line2=line2[4,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#B2 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		line2 = FindDataLineType(fileVar,"#B3 ",1)
		line2=line2[4,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#B4 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		line2 = FindDataLineType(fileVar,"#B5 ",1)
		line2=line2[4,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#B6 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		line2 = FindDataLineType(fileVar,"#B7 ",1)
		line2=line2[4,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#B8 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		line2 = FindDataLineType(fileVar,"#B9 ",1)
		line2=line2[4,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#B10 ",1)
	if (strlen(line1)>2)
		line1 = line1[5,inf]
		line2 = FindDataLineType(fileVar,"#B11 ",1)
		line2=line2[5,inf]
		SetBValues(line1,line2)
	endif

	line1 = FindDataLineType(fileVar,"#R1 ",0)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		String r1Names="--  peakXmax  peakmax  peakFWHM  peakCWHM  peakCOM  peakSUM"
		SetBValues(r1Names,line1)
	endif

	line1 = FindDataLineType(fileVar,"#R2 ",0)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		String r2Names="--  osaX  osaY  zpX  zpY  zpZ  wireY"
		SetBValues(r2Names,line1)
	endif

	FSetPos fileVar, FilePos					// reset file position to start of scan
End






//Function/T RemoveOneListFromAnotherXX(mainList,toRemove)
//	String mainList
//	String toRemove
//	String str
//	Variable ii
//	Variable i = 0
//	do
//		str = StringFromList(i, mainList )
//		ii = WhichListItem(str , mainList )
//		mainList = RemoveListItem(ii, mainList)
//		i += 1
//	while (strlen(str)>0)
//	return mainList
//End