#pragma rtGlobals=3		// Use modern global access method and strict wave access.

//Usage:
//Before opening/compiling this, first open Analysis - Packages - Multipeak Fitting - Multipeak Fitting 2
//Waves need to be appropriately scaled: this does not recognize "X" waves
//Fit peaks on a single graph first using multi peak fitting
//Be sure to hold appropriate parameters and add constraints if desired
//Save a checkpoint. This makes a folder within the Packages folder for the fitting set with "CP" appended
//Then create a graph with all the spectra on the same graph
//Run this function with that graph as the top graph
//Example usage: MultiBatchFitting("root:packages:MultiPeakFit2:MPF_SetFolder_1CP")

Function MultiBatchFitting(datafoldername)
	String datafolderName
	String ywavelist = TraceNameList("", ";", 1)
	string ywave
	
	String remove1,remove2,rmv
	
	Variable nfits = ItemsInList(ywavelist)
	
	// The structure required by MPF2_DoMPFit()
	STRUCT MPFitInfoStruct MPStruct

	Variable i, err
	
	String saveDF = GetDataFolder(1)
	
	//Delete all previous "batchpeakfit" folders
	SetDataFolder saveDF
	string folderlist=DataFolderDir(1)
	variable lastspot=strsearch(folderlist,"BatchPeakFit",Inf,1)
	variable lastwave=0
	string foldertokill=""
	variable killfolder=0
	if(lastspot>-1)
		lastspot+=13
		lastwave=str2num(folderlist[lastspot,lastspot+3]) // add 0 for up to 9 folders, add 1 for up to 99 folders, add 2 for up to 999 folders
		do
			foldertokill="BatchPeakFit_"+num2str(killfolder)
			KillDataFolder $foldertokill
			killfolder+=1
		while (killfolder <= lastwave)
		Print "Killed old fit data folders."
	endif
	
	// Switch to the Multi-peak fit folder and look up some stuff
	//String saveDF = GetDataFolder(1)
	SetDataFolder datafolderName
		// Look up the function type list saved by Multi-peak Fit
		SVAR SavedFunctionTypes
		MPStruct.ListOfFunctions = SavedFunctionTypes

		// Create the list of coefficient waves and hold strings
		MPStruct.ListOfCWaveNames = ""
		MPStruct.ListOfHoldStrings = ""
		
		Wave/Z cw = 'Baseline Coefs'
		if (WaveExists(cw))
			MPStruct.ListOfCWaveNames = NameOfWave(cw)
		endif
		MPStruct.ListOfCWaveNames += ";"
		
		Variable npeaks = 0
		do
			Wave/Z cw = $("Peak "+num2istr(npeaks)+" Coefs")
			if (!WaveExists(cw))
				break
			endif
			MPStruct.ListOfCWaveNames += NameOfWave(cw)+";"
			npeaks += 1
		while (1)
		variable howmanypeaks = npeaks
		
		//Add hold strings
		Wave/T/Z hsw = 'HoldStrings'
		string holdinfo=""
		string holdstrings=""
		variable myi=0
		do
			holdinfo=hsw[myi]
			holdstrings += holdinfo +";"
			myi += 1
		while (myi <= howmanypeaks)
		MPStruct.ListOfHoldStrings = holdstrings
		
		//Get constraints
		wave/T ctw=$"constraintsTextWave"
		string constring="", cons="",newcons=""
		variable imax=0, pk=0,ia=0,totalcount=0,maxval=nan,minval=nan
		for(pk=0;pk<numpnts(ctw);pk+=1)
			constring=ctw[pk]
			imax=itemsinlist(constring)
			for(ia=0;ia<imax;ia+=1)
				cons=StringFromList(ia,constring)
				if(StringMatch(cons[0,2],"MAX"))
					maxval=str2num(cons[strsearch(cons,":",0)+1,inf])
					if(!numtype(maxval))
						newcons+="K"+num2str(floor(totalcount))+"<"+num2str(maxval)+";"
					endif
				endif
				if(StringMatch(cons[0,2],"MIN"))
					minval=str2num(cons[strsearch(cons,":",0)+1,inf])
					if(!numtype(minval))
						newcons +="K"+num2str(floor(totalcount))+">"+num2str(minval)+";"
					endif
				endif
				totalcount+=0.5
			endfor
		endfor
		if(strlen(newcons)!=0)
			Print "Applying constraints."
		endif
		
		SetDataFolder saveDF
	
	// fill in more members of the structure
	MPStruct.NPeaks = npeaks
	MPStruct.XPointRangeBegin = 0
	// this function always fits the entire data set
	MPStruct.FitCurvePoints = 1000
	MPStruct.fitOptions = 4	// you might want to change this to 4
	
	// loop through each of the data sets, calling MPF2_DoMPFit
	// on each one. After each call, the results are checked and acted
	// on appropriately.
	variable wasalert=0
	for (i = 0; i < nfits; i += 1)
		// We make a copy of the Multi-peak fit folder for
		// each data set. That also duplicates all the coefficient waves
		// so that we preserve the results for each fit. The duplicated data folder
		// is created inside the current data folder.
		String BatchDFName = "BatchPeakFit_"+num2str(i)
		DuplicateDataFolder $datafolderName, $BatchDFName
		
		// Most of the contents of the structure don't need to change.
		// Naturally, we have to put in a wave reference to the
		// data set being fit this time through the loop
		ywave = StringFromList(i,ywavelist)
		//ywave = ywave[1,(strlen(ywave)-2)] //uncomment this line if single quotes needed
		
		//Wave MPStruct.yWave = $StringFromList(i, ywavelist) // works if no quotes around wave
		Wave MPStruct.yWave = $ywave
		
		//apply constraints if any were found
		if(strlen(newcons)!=0)
			//Print newcons
			Make/N=1/O/T fittingconstraints
			fittingconstraints=newcons
			Wave/T MPStruct.Constraints = fittingconstraints
		endif
	
		//print which point is which wave from the top graph
		string messag="Point " + num2str((i)) + " wave " + ywave
		rmv=ywave
		ywave="'"+ywave+"'"
		Print messag

		// just in case the new wave has a different number of points
		MPStruct.XPointRangeEnd = numpnts(MPStruct.yWave)-1
		
		err = MPF2_DoMPFit(MPStruct, saveDF+BatchDFName+":")
		if (err)
			// error return from MPF2_DoMPFit generally indicates
			// a programmer error
			DoAlert 0, "Error calling MPF2_DoMPFit: "+num2str(err)
			return err
		endif
		if (MPStruct.fitQuitReason == 2)
			// if the user aborts a fit, we assume that the whole process
			// should be aborted
			DoAlert 0, "User aborted batch fit"
			return -1
		endif
		if (MPStruct.fitError)
			// Something went wrong with the current fit, and it
			// failed to converge. We note this fact to the user via
			// an alert, then move on to the next one. You may wish
			// to do something more sophisticated than this.
			
			// Avoid a long line by concatenating the message
			// in small pieces
			String alertMsg = "Error doing fit to "
			alertMsg += StringFromList(i, ywavelist)+": "
			alertMsg += num2str(MPStruct.fitError)+ " | "
			alertMsg += MPStruct.fitErrorMsg
			alertMsg += "; continuing with next fit."
			Print alertMsg
			wasalert=1
			//DoAlert 0, alertMsg
		endif
		remove1 = "fit_"+rmv
		remove2 = "Res_"+rmv
		RemoveFromGraph $remove1,$remove2
	endfor
	if(wasalert==1)
			alertMsg="Error detected, check history window."
			DoAlert 0,alertMsg
	endif
	
	/////////////////////////////////////////////////
	//Everything below this point is custom code to display whatever parameters you want to extract
	
	SetDataFolder saveDF
	Make/O/N=(nfits) spanov5bws
	Make/O/N=(nfits) spanov5gws
	Make/O/N=(nfits) spanov5amps
	variable peak0bw,peak0gw,peak0amp
	for (i = 0; i < nfits; i += 1)
		
		// Get desired peak data by looping through folders
		BatchDFName = saveDF+"BatchPeakFit_"+num2str(i)
		SetDataFolder BatchDFName
		wave peak0vars='Peak 0 Coefs'

		peak0bw=peak0vars[0]
		peak0gw=peak0vars[2]
		peak0amp=peak0vars[4]
		
		SetDataFolder saveDF
		spanov5bws[i]=peak0bw
		spanov5gws[i]=peak0gw
		spanov5amps[i]=peak0amp
	endfor
	
	Display spanov5bws
	Display spanov5gws
	Display spanov5amps
end