#pragma rtGlobals=2		// Use modern global access method.
#include <Image Common>
Function GetInputWave()
	// This function pops up an "Open File" dialog for a single wave.
	// In the context of this program it's used to select the IRF data file.

	// Declares some variables, slaps a title on the box.
	Variable refNum
	String message = "Select the IRF data file"
	String outputPath
	String fileFilters = "Data Files (*.txt,*.dat,*.csv):.txt,.dat,.csv;"
	fileFilters += "All Files:.*;"
 
	// This is the actual dialog box here.
	Open /D /R /F=fileFilters /M=message refNum
	outputPath = S_fileName
 
	// Checks to see if the operation was cancelled.
	// Otherwise, this uses the LoadWave function on the input file.
	// The output will be wave(# of regular waves) due to the order in which this is called.
	// In this case for example this will name the wave "wave2".
	if (strlen(outputPath) == 0)
		Print "Cancelled"
		return 0
	else
		LoadWave/G/M/D/N=waveIRF outputPath
		return 1
	endif
End

Function GetInputWaves(rWave1)
	// This function pops up an "Open File" dialog for multiple waves.
	// At this point this function is built to handle as many input files as you want.
	// The program, however, is built to deal with two waves and an IRF wave, so don't exceed that.
	// In the context of this program it's used to select the two actual data files.
 
	// Declares some variables.
	Wave/WAVE rWave1
	Variable refNum
	String message = "Select two electron scatter data files:"
	String outputPaths
	String fileFilters = "Data Files (*.txt,*.dat,*.csv):.txt,.dat,.csv;"
	fileFilters += "All Files:.*;"
	// Here's the dialog box again. The filename output is a delimted list of the chosen files.
	Open /D /R /MULT=1 /F=fileFilters /M=message refNum
	outputPaths = S_fileName
 
	// Checks to see if it was cancelled, otherwise performs a LoadWave function per file.
	// The output will be wave0, wave1, wave2, ..., wave(n-1).
	// In this case the output waves will be wave0 and wave1.
	if (strlen(outputPaths) == 0)
		Print "Cancelled"
		return 0
	else
		Variable numFilesSelected = ItemsInList(outputPaths, "\r")
		Variable i
		for(i=0; i<numFilesSelected; i+=1)
			String path = StringFromList(i, outputPaths, "\r")
			Printf "%d: %s\r", i, path
			LoadWave/G/M/D/A=fileWave path
 
			// Check that a wave was successfully loaded.
			// <----
			if (V_flag == 1)
				WAVE loadedWave = $(StringFromList(0, S_waveNames, ";"))
				rWave1[i]=loadedWave
			else
				// You might report an error here
			endif
			// <----
		endfor
	endif
 
	// Returns the number of wave files for possible use in expanding the program.
	// Could be used to make the program work with 3, 4, 5 different waves, etc.
	return numFilesSelected
End

Function multipleOffset(input0,input1)
	// This function is used to calculate the multiplier offset for waves on a graph.
	// From the looks of the commands it seems the lab tech arbitrarily picked numbers to make the graphs overlap.
	// As such, I've taken the maximum peak values of the two waves, and calculated the ratio between them.
	// This will allow the correct vertical multiplier to be applied.
	
	// Matt's input is needed here regarding this is the correct choice or whether the multipliers
	// should be arbitrary constants.
	
	// Variable declaration.
	Wave input0, input1
	
	Variable max0 = 0
	Variable max1 =0
	
	
	// WaveStats creates a bunch of new variables with the info from the input wave.
	// V_max is the vertical maximum value, and is used here.
	WaveStats/Q input0
	max0 = V_max
	
	WaveStats/Q input1
	max1 = V_max
	
	// If the maxima are equal, no multiplier is used.
	// If the maximum of wave0 is 0 (impossible but still), this returns 0 to avoid a DIV/#0 error.
	// Otherwise, this returns the ratio of max1/max0.
	if(max0 == max1)
		return 0
	elseif(max0 == 0)
		return 0
	else
		return max1/max0
	endif
End
	
Function RunThisProgram()
	// The purpose of this program is two take two electron scatter images, plot their linear
	// Profiles and Convolutions for comparison purposes, compare the data to an IRF standard,
	// and fit double exponential curve fits through the Convolutions.
	
	// This should prompt for three files. Choose the two waves first, then the IRF file.
	
	// This is the actual coded script.

	// Variable declarations.
	Make/O/Wave RefWave
	Make/O/Wave RefProfWave
	Make/O/Wave RefConvWave
	Make/O LineProfileX
	Make/O LineProfileY
	Make/O returnWave
	Make/O W_ImageProfileGraph
	Make/O waveIRF0_Prof1
	Wave RefWave, RefProfWave, RefConvWave, returnWave, LineProfileX, LineProfileY, W_ImageProfileGraph, waveIRF0_Prof1
	Variable i
	String profName, convName
	
	// Prompts user with an "Open" dialog to select n waves, returned as numWaves.
	Variable/G numWaves = GetInputWaves(RefWave)
	if (numWaves == 0)
		Printf "The operation has been cancelled."
		return 0
	endif
	
	Make/O/D/N=2 xWave,yWave
	// This displays the 3-D plots (in charts called "ElectronScatter'i'").
	for (i=0;i<numWaves;i+=1)
		Display/N=ElectronScatter
		// Here's where the problem starts. I've added a bit of code to duplicate the created 2-D profile into a wave called returnWave.
		// The documentation leads to believe that waves are global variables, however it doesn't seem to like this.
		// It also doesn't like calling AppendImage on RefWave[i], which it believes is not a wave variable.
		AppendImage RefWave[i]
		Wave newRef = $(GetWavesDataFolder(RefWave[i], 2))
		
		LineProfileY={889,889,NaN,689,689}
		LineProfileX={-INF,INF,NaN,-INF,INF}
		yWave=LineProfileY+789
		yWave-=100
		xWave={DimOffset(newRef,0),DimOffset(newRef,0)+DimDelta(newRef,0)*DimSize(newRef,0)}
		// Here's the crazy function, you can see the code in the other pastebin (not written by me).
		ImageLineProfile/SC srcWave=newRef, xWave=LineProfileX, yWave=LineProfileY, width=200
		//ImageLineProfile srcWave=RefWave[i], xWave=LineProfileX, yWave=LineProfileY, width=200
		// returnWave is set in the WMCreateImageLineProfileGraph() function, or at least it should be. This has caused problems so far.
		profName = "prof" + num2str(i)
		Duplicate/O W_ImageLineProfile, $(profName)
		Wave newProfRef = $(profName)
		RefProfWave[i] = newProfRef
	endfor
	
	// Creates a new graph for the wave Profiles and makes each wave a distinctive color (in theory).
	for (i=0;i<numWaves;i+=1)
		Display/N=Profiles
		AppendToGraph/W=Profiles RefProfWave[i]
		//ModifyGraph/W=Profiles rgb($(GetWavesDataFolder(RefProfWave[i], 2)))=(i*10,i*30,i*50)
	endfor
	
	// Calculates and applies the multiplier offset. Might not be necessary. Ignore this section of the code.
	//Variable theoffset = multipleOffset(wave0_Prof1,wave1_Prof1)
	//ModifyGraph muloffset(wave0_Prof1)={0,theoffset}
	
	// Time to select the IRF data file. This is the curve by which the others are convolved.
	Variable canc = GetInputWave()
	if (canc==0)
		Printf "The operation has been cancelled."
		return 0
	endif
	
	// Displays the scatter plot for IRF data, creates the line profile.
	// Similar issues with WMCreateImageLineProfileGraph(). Because this will be a single IRF wave,
	// a reference wave is not necessary and makes variable use easier.
	Display/N=electronIRF
	AppendImage/W=electronIRF waveIRF0
	ImageLineProfile srcWave=waveIRF0, xWave=LineProfileX, yWave=LineProfileY, width=200
	Duplicate/O W_ImageLineProfile, waveIRF0_Prof1
	// Adds the new IRF profile to the "Profiles" graph, turns it green, and adds a legend.
	AppendToGraph/W=Profiles waveIRF0_Prof1
	//ModifyGraph/W=Profiles rgb(W_ImageProfileGraph)=(0,65280,0)
	
	// Prompt for eV values. Then creates a Legend for the graph.
	for (i=0;i<numWaves;i+=1)
		Variable eValue
		String legendString = ""
		Prompt eValue, "eV Value "+num2str(i+1)
		DoPrompt "Choose the eV value: ",eValue
		legendString = legendString + "\\s($(GetWavesDataFolder(RefProfWave[i], 2))) " + num2str(eValue) + " eV\r"
	endfor
	legendString = legendString + "\\s(waveIRF0_Prof1) IRF"
	Legend/W=Profiles/C/N=profLegend/J legendString
	
	// Adds a multiplier offset to the IRF data to fit it to the regular data curves.
	// Ignore this for now.
	//Variable irfoffset = multipleOffset(waveIRF0_Prof1,waveIRF0_Prof1)
	//ModifyGraph/W=Profiles muloffset(waveIRF0_Prof1)={0,irfoffset}
	
	// Autoscales the axis, displays an info box below the graph.
	SetAxis/W=Profiles/A
	ShowInfo/W=Profiles
	
	// Gives the option to truncate data, eliminating some noise in the convolutions.
	Variable LeftTrunc,RightTrunc
	Prompt LeftTrunc, "Left Truncation Value: "
	Prompt RightTrunc, "Right Truncation Value: "
	DoPrompt "Choose the Left & Right Truncation Values: ",LeftTrunc,RightTrunc
	
	DeletePoints LeftTrunc,RightTrunc,waveIRF0_Prof1
	
	// Displays linear convolutions of the waves.
	// Other types of convolutions (circular and linear acasual) can be added easily.
	// Simply call Convolve/C or Convolve/A instead respectively.
	Display/N=Convolutions
	
	for (i=0;i<numWaves;i+=1)
		convName = "conv" + num2str(i)
		Duplicate/O $(GetWavesDataFolder(RefProfWave[i], 2)),$(convName)
		Wave newConvRef = $(convName)
		Convolve waveIRF0_Prof1, newConvRef
		AppendToGraph/W=Convolutions newConvRef
		RefConvWave[i] = newConvRef
		//ModifyGraph/W=Convolutions rgb($(GetWavesDataFolder(RefConvWave[i], 2)))=(i*5,i*10,i*20)
	endfor
	
	// Adds a multiplier offset for the Convolutions.
	//Variable convoffset = multipleOffset(wave0_Prof1_conv,wave1_Prof1_conv)
	//ModifyGraph muloffset(wave0_Prof1_conv)={0,convoffset}
	
	
	// Once again, could prompt for eV values. In the final code this'll just be taken from the first legend prompts.
	for (i=0;i<numWaves;i+=1)
		Variable eValueC
		String legendStringC = ""
		Prompt eValueC, "eV Value "+num2str(i+1)
		DoPrompt "Choose the eV value: ",eValueC
		legendStringC = legendStringC + "\\s($(GetWavesDataFolder(RefConvWave[i], 2))) " + num2str(eValueC) + " eV\r"
	endfor
	Legend/W=Convolutions/C/N=convLegend/J/F=0/A=MC legendStringC

	// Changes the y-axis to a log scale, displays the info box below the graph.
	ModifyGraph/W=Convolutions log(left)=1
	ShowInfo/W=Convolutions
	
	// Only examine the topmost part of the peak.
	Variable j = 0
	for (i=0;i<numWaves;i+=1)
		WaveStats/Q $(GetWavesDataFolder(RefConvWave[i], 2))
		if (V_Max > j)
			j = V_Max
		endif
	endfor
		
	SetAxis/W=Convolutions left (j/100),(j+10)
	
	// Convolution curve fits.
	
	for (i=0;i<numWaves;i+=1)
		String fitName = "fit_"
		CurveFit/NTHR=0/TBOX=984 dblexp_XOffset $(GetWavesDataFolder(RefProfWave[i], 2))[327,800] /D  
		//fitName = fitName + $(GetWavesDataFolder(RefProfWave[i], 2))
		//ModifyGraph/W=Convolutions rgb($fitName)=(i*50,i*30,i*10)
	endfor

	// End of program.
	return 0
End