#pragma rtGlobals=2		// Use modern global access method.
#pragma IgorVersion = 4.1
#include "spec", version>=2.10

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

	Variable ringPeriod = 3.68258537e-6 		// ring period, time between P0 pulses (s)

	SVAR specCommand=specCommand
	if (strsearch(specCommand,"dumpLeCroyScope",0)>=0 && exists("LeCroy"))
		Wave LeCroy=LeCroy
		SVAR specValues=specValues
		// horiz_interval	= time between each point in LeCroy
		// laser_delay	= time between laser start of LeCroy and excimer
		Variable laser_delay = NumberByKey("laser_delay",specValues)
		Variable horiz_interval = NumberByKey("horiz_interval",specValues)
		laser_delay = numtype(laser_delay) ? 271.5*ringPeriod : laser_delay
		// 271.5 = 1e-3/ringPeriod, so 271.5*ringPeriod = 1ms
		horiz_interval = numtype(horiz_interval) ? ringPeriod : horiz_interval
		horiz_interval = (horiz_interval==1) ? ringPeriod : horiz_interval
		SetScale/P x -laser_delay*horiz_interval,horiz_interval ,"s", LeCroy
	endif

	if (exists("I0")==1)							// set Io wave if it exists
		Wave wI0 = I0
	elseif (exists("Io")==1)
		Wave wI0 = Io
	elseif (exists("I0_mon")==1)
		Wave wI0 = I0_mon
	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
		if (exists("filter"))
			Wave filterWave=filter
			filterTrans = 1
		endif
		if (WaveDims(wI0)==1)
			SVAR axisName=yAxisName
			if (!SVAR_EXISTS(axisName))
				SVAR axisName=specYwave
			endif
		elseif (WaveDims(wI0)==2)
			SVAR axisName=zAxisName
		else
			DoAlert 0,"cannot yet deal with 3-d data"
			return 1
		endif
//		SVAR yAxisName=yAxisName
//		if (!SVAR_EXISTS(yAxisName))
//			SVAR yAxisName=specYwave
//		endif
		axisName = StringFromList(0,axisName)	// only support one y wave here
		Duplicate $axisName sig
		// list of names that are probably photon counting detectors (obviously I0 is not in this list)
		String photonCounter="detector;scint;NaI;oxfo;oxford;Bicr;Bicron;harmonic;Det_bot;Det_top;top_harmonic"
		WAVE seconds=seconds
		SVAR dark_Io_Name=root:Packages:spec:dark_Io_Name
		Variable darkRate = specInfo(scanNum,dark_Io_Name)
		darkRate = numtype(darkRate) ? 0 : darkRate
		if ((FindListItem(axisName, photonCounter)>=0) && (exists("sig_err")!=1) && (exists("seconds")==1))
			Wave harm=harmonic
			if (WaveExists(harm))
				sig += 2*harm[p]
			elseif (exists("deadtime")==6 && exists("seconds")==1)
				sig /= seconds
				sig = deadTime(sig)					// dead time works on counts/second only
				sig *= seconds
			endif
			Duplicate $axisName sig_err
			sig_err = sqrt(sig) / max(1,wI0-seconds*darkRate) / filterTrans
			if (WaveExists(filterWave))
				sig_err /= filterWave
			endif
			// add to wave note of sig_err, identifiying it as an err and its source
			String noteStr = note(sig_err)
			noteStr  = ReplaceStringByKey("ErrorWaveSource", noteStr, "ErrorWaveSource:sig")
			Note/K sig_err
			Note sig_err, noteStr
		endif
		if (exists("seconds")==1)
			sig = sig / max(1,wI0-seconds*darkRate) / filterTrans
		else
			sig = sig / wI0 / filterTrans
		endif
		if (WaveExists(filterWave))
			sig /= filterWave
		endif
		sig *= NumVarOrDefault("root:Packages:spec:scaleFactor",1)
		axisName = "sig"
	endif
End
//Function extraSpecReadProcess(extra)
//	Variable extra
//	if (!extra)
//		return 0
//	endif
//
//	Variable ringPeriod = 3.68258537e-6 		// ring period, time between P0 pulses (s)
//
//	SVAR specCommand=specCommand
//	if (strsearch(specCommand,"dumpLeCroyScope",0)>=0 && exists("LeCroy"))
//		Wave LeCroy=LeCroy
//		SVAR specValues=specValues
//		// horiz_interval	= time between each point in LeCroy
//		// laser_delay	= time between laser start of LeCroy and excimer
//		Variable laser_delay = NumberByKey("laser_delay",specValues)
//		Variable horiz_interval = NumberByKey("horiz_interval",specValues)
//		laser_delay = numtype(laser_delay) ? 271.5*ringPeriod : laser_delay
//		// 271.5 = 1e-3/ringPeriod, so 271.5*ringPeriod = 1ms
//		horiz_interval = numtype(horiz_interval) ? ringPeriod : horiz_interval
//		horiz_interval = (horiz_interval==1) ? ringPeriod : horiz_interval
//		SetScale/P x -laser_delay*horiz_interval,horiz_interval ,"s", LeCroy
//	endif
//
//	if (exists("I0")==1)							// set Io wave if it exists
//		Wave wI0 = I0
//	elseif (exists("Io")==1)
//		Wave wI0 = Io
//	elseif (exists("I0_mon")==1)
//		Wave wI0 = I0_mon
//	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 yAxisName=yAxisName
//		if (!SVAR_EXISTS(yAxisName))
//			SVAR yAxisName=specYwave
//		endif
//		yAxisName = StringFromList(0,yAxisName)	// only support one y wave here
//		Duplicate $yAxisName sig
//		// list of names that are probably photon counting detectors (obviously I0 is not in this list)
//		String photonCounter="detector;scint;NaI;oxfo;oxford;Bicr;Bicron;harmonic;Det_bot;Det_top;top_harmonic"
//		WAVE seconds=seconds
//		SVAR dark_Io_Name=root:Packages:spec:dark_Io_Name
//		Variable darkRate = specInfo(scanNum,dark_Io_Name)
//		darkRate = numtype(darkRate) ? 0 : darkRate
//		if ((FindListItem(yAxisName, photonCounter)>=0) && (exists("sig_err")!=1) && (exists("seconds")==1))
//			if (exists("deadtime")==6 && exists("seconds")==1)
//				sig /= seconds
//				sig = deadTime(sig)					// dead time works on counts/second only
//				sig *= seconds
//			endif
//			Duplicate $yAxisName sig_err
//			sig_err = sqrt(sig) / (wI0-seconds*darkRate) / filterTrans
//			// add to wave note of sig_err, identifiying it as an err and its source
//			String noteStr = note(sig_err)
//			noteStr  = ReplaceStringByKey("ErrorWaveSource", noteStr, "ErrorWaveSource:sig")
//			Note/K sig_err
//			Note sig_err, noteStr
//		endif
//		if (exists("seconds")==1)
//			sig = sig / (wI0-seconds*darkRate) / filterTrans
//		else
//			sig = sig / wI0 / filterTrans
//		endif
//		yAxisName = "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


Function extraSpecRead(fileVar)
	Variable fileVar							// file ref number

	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,"##",1)
	FReadLine fileVar, line2	
	if (strlen(line1)>2 && strlen(line2)>2)
		// line1 = line1[4,inf]
		Variable vertical_offset,vertical_gain,horiz_interval, laser_delay,laser_width
		sscanf line1,"##vertical_offset=%g  vertical_gain=%g  horiz_interval=%g", vertical_offset,vertical_gain,horiz_interval
		if (V_flag==3)
			String/G specValues
			SVAR dest=specValues
			dest = ReplaceNumberByKey("vertical_offset", dest, vertical_offset)
			dest = ReplaceNumberByKey("vertical_gain", dest, vertical_gain)
			// horiz_interval	= time between each point in LeCroy
			dest = ReplaceNumberByKey("horiz_interval", dest, horiz_interval)
		endif
		sscanf line2,"##laser_delay=%g  laser_width=%g", laser_delay,laser_width
		if (V_flag==2)
			String/G specValues
			SVAR dest=specValues
			// laser_delay	= time between laser start of LeCroy and excimer
			// laser_width	= width of laser pulse
			dest = ReplaceNumberByKey("laser_delay", dest, laser_delay)
			dest = ReplaceNumberByKey("laser_width", dest, laser_width)
		endif
	endif

	line1 = FindDataLineType(fileVar,"#G4 ",1)
	if (strlen(line1)>2)
		line1 = line1[4,inf]
		SetValuesIntoList("--;--;--;wavelength",line1,"specValues")
	endif

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

	FSetPos fileVar, FilePos					// reset file position to start of scan
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,"##",1)
//		FReadLine fileVar, line2	
//		if (strlen(line1)>2 && strlen(line2)>2)
//			// line1 = line1[4,inf]
//			Variable vertical_offset,vertical_gain,horiz_interval, laser_delay,laser_width
//			sscanf line1,"##vertical_offset=%g  vertical_gain=%g  horiz_interval=%g", vertical_offset,vertical_gain,horiz_interval
//			if (V_flag==3)
//				String/G specValues
//				SVAR dest=specValues
//				dest = ReplaceNumberByKey("vertical_offset", dest, vertical_offset)
//				dest = ReplaceNumberByKey("vertical_gain", dest, vertical_gain)
//				dest = ReplaceNumberByKey("horiz_interval", dest, horiz_interval)
//			endif
//			sscanf line2,"##laser_delay=%g  laser_width=%g", laser_delay,laser_width
//			if (V_flag==2)
//				String/G specValues
//				SVAR dest=specValues
//				dest = ReplaceNumberByKey("laser_delay", dest, laser_delay)
//				dest = ReplaceNumberByKey("laser_width", dest, laser_width)
//			endif
//		endif
//	
//		FSetPos fileVar, FilePos					// reset file position to start of scan
//		line1 = FindDataLineType(fileVar,"#G4 ",1)
//		if (strlen(line1)>2)
//			line1 = line1[4,inf]
//			SetValuesIntoList("--;--;--;wavelength",line1,"specValues")
//		endif
//	
//		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 specMoreInit()
	if (exists("root:Packages:spec:dark_Io_Name")!=2)
		// name of value from specInfo with the dark current in Io
		String /G root:Packages:spec:dark_Io_Name=""
	endif
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