CORDUROY_ANALYSIS_library.ipf

#pragma rtGlobals=2		// Use modern global access method.

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///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//	CORDUROY_ANALYSIS_library
//		Contains the code for the analysis functions
//
//		Written by Joshua Dudman, Columbia University
//		Development begun January 2005
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///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
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///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_CreateFunctionList()
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

	SetDataFolder root:Analysis:Panels:AnalysisPanel
	string/G AnalysisFunctionList = "None;STATS;EVENTPEAK;SLOPE;KINETICS;SPIKES;WCSPK;XSPIKES;DUPLICATE;EMFREQ;EVENTS"

End

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///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//	RULES FOR THE CLASS OF ANALYSIS FUNCTIONS
//		1. Take two variables as input representing the left and right point of an ROI
//		2. Are handed a wave to analyze (i.e. do not control the indexing of serial analysis).
//		3. Take a variable representing the index (in a series of sequentially analyzed waves) of the handed wave
//		4. Create a folder for the analysis function which stores associated variables
//		5. Each function has a prefix used to identify output waves
//		6. Output is a multidimensional wave of the form "Wavename_PREFIX [num_vars;num_waves]"
//		7. Follows the template strucure shown below
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///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_TEMPLATE_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// This is a template function that can be followed for users who are interested in creating their own plug-in analysis routines

	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference
	WAVE local = TraceNameToWaveRef("",wave_name)	
	
// MOVE to analysis directory?
	
// Duplicate the wave within the roi to facilitate analysis

// ANALYSIS
	variable VAR
	Make/N=1 ANALYSIS_WAVE
//END ANALYSIS

// Store the respective calculations in waves for subsequent analysis
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName = baseName + ""

// If the analysis creates a single variables per ROI, something like this would work:
	variable numanalyses

	if(index==0)
		Make/N=(numwaves,numanalyses) $newName
	endif

	string ex_string
	ex_string = newName+"[index,1]="+num2str(VAR)
		Execute ex_string

// If the analysis creates a wave of values for each analyzed wave and each ROI, use something like this:
	string newName2 = baseName+"_"+num2str(index)+"WAVE_SUFFIX"	
	Duplicate /O  ANALYSIS_WAVE, $newName2
	
	
	SetDataFolder thisDF	
End // TemplateFunc
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_EVENTPEAK_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	
	String thisDF = GetDataFolder(1)

// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local = $wave_name
	endif
	
// Create some local variables
	string prefix = "", thisWave=""
	Variable maxflag=1
	variable left0, right0
	string basenameL = "baseL"+num2str(roi_num), basenameR = "baseR"+num2str(roi_num)
	
// Guess baseline and use a panel to ask if correct
	if(index==0)
		CORD_DisplayCheckCursorPanel((roi_tstart - 0.006),(roi_tstart - 0.001))		
		variable/G $basenameL, $basenameR
		NVAR baseL = $basenameL
		NVAR baseR = $basenameR
		NVAR cursorcheckL = root:Analysis:CheckCursorDialogue:CheckCursorLeft
		NVAR cursorcheckR = root:Analysis:CheckCursorDialogue:CheckCursorRight
		baseL = cursorcheckL
		baseR = cursorcheckR
	endif
	
	NVAR baseL = $basenameL
	NVAR baseR = $basenameR
	
// Initialize all the global variables to be created by the function
	NewDataFolder/O/S PeakAnalysisGlobals
	Variable/G baseline=0
	Variable/G meanpeak=0
	Variable/G netpeak=0
	Variable/G peaktime=0
	Variable/G lefthalf=0
	Variable/G righthalf=0
	Variable/G left20=0
	Variable/G right80=0
	Variable/G slope2080=0
	Variable/G totalarea=0
	SetDataFolder thisDF
	
// Subtract baseline offset to get net peak
	baseline = mean(local,baseL,baseR)

// Find the peak of the passed wave
	if(maxflag==0)
		FindPeak/B=(50)/P/Q/R=(roi_tstart,roi_tstop) $wave_name
		peaktime = V_PeakLoc
	else
		WaveStats/Q/R=(roi_tstart,roi_tstop) local
		// Decide if it is a negative or positive peak to look for...
		if(abs(V_max-baseline)>abs(V_min-baseline))
			peaktime = V_maxloc
		else
			peaktime = V_minloc		
		endif
	endif

	meanpeak = mean(local,(peaktime-0.0001),(peaktime+0.0001))
	netpeak = meanpeak - baseline
// Get halfwidth
	FindLevel/Q/R=(peaktime,-1) $wave_name, (baseline + (netpeak/2))
	lefthalf = V_LevelX
	FindLevel/Q/R=(peaktime) $wave_name, (baseline + (netpeak/2))
	righthalf = V_LevelX
// Get 20-80 rise time
	FindLevel/Q/R=(peaktime,-1) $wave_name, (baseline+(netpeak*0.2))
	left20 = V_LevelX
	FindLevel/Q/R=(peaktime,-1) $wave_name, (baseline+(netpeak*0.8))
	right80 = V_LevelX
// Get 20-80 slope
	if((right80-left20) < 0.0001) // 0.1 ms defines the shortest possible 20 80 rise time  (prevents error is neg)
		slope2080 = 0
	else
		CurveFit/N/Q/W=0 line $wave_name (left20,right80)
		slope2080 = K1
	endif
// Get area (from 10% to 10%)
	FindLevel/Q/R=(peaktime,-1) $wave_name, (baseline+(netpeak*0.1))
	left0 = V_LevelX
	FindLevel/Q/R=(peaktime) $wave_name, (baseline+(netpeak*0.1))
	if(V_flag==0)	
		right0 = V_LevelX
	else
		right0 = roi_tstop
	endif
	variable basebox = baseline * (right0 - left0)
	variable tmparea = area($wave_name,left0,right0)
	totalarea = tmparea - basebox // otherwise have to baseline traces to get area

// Store the respective calculations in waves for subsequent analysis
	string ChanName = ""
	if( stringmatch(wave_name,"Record*") )
		sscanf wave_name, "Record%1s", ChanName
	else
		ChanName = "X"
	endif
	
	// need a check on total string length
	string folderName
	if(strlen(GetDataFolder(0))>11)
		sscanf GetDataFolder(0), "%15s", folderName

	else
		folderName = GetDataFolder(0)
	endif
	
	string baseName = folderName + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string peakName = baseName + "peak"
	string kinName = baseName + "kinetics"	
	string assignstring
	
	WAVE outputWave = $peakName
	if(!WaveExists(outputWave))
		Make/N=(numwaves,5)/O $peakName
		Make/N=(numwaves,5)/O $kinName
	endif
	
	WAVE output1 = $peakName
	WAVE output2 = $kinName
		
	output1[index][0]=netpeak
	output1[index][1]=peaktime
	output1[index][2]=meanpeak
	output1[index][3]=totalarea
	output1[index][4]=left0

	output2[index][0]=righthalf - lefthalf
	output2[index][1]=slope2080
	output2[index][2]=right80-left20
	output2[index][3]=totalarea
	output2[index][4]=left20

	if(index==(numwaves-1))
		KillDataFolder :PeakAnalysisGlobals
		variable numoutput=4
		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_peak = {"Net depolarization (V)","Time of peak(ms)","Peak potential (V)","Area (mV.ms)","Onset"}
		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_kinetics = {"Halfwidth (ms)","20-80 Rise Slope (V/ms) ","20-80 Rise Time (V/ms) ","Area ","Onset"}

		if(roi_num==1)
			print  EVENTPEAK_outputlabels_peak
			print  EVENTPEAK_outputlabels_kinetics
		endif
	endif
	
	if(index==0) // confirm that the various analysis values are correctly calculated
		DoWindow/K OnLineDisp
		Make/O/N=2 areaPnts
		areaPnts[0] = left0
		areaPnts[1] = right0
		Make/O/N=2 areaLev = baseline+(netpeak*0.1)

		Make/O/N=2 risePnts
		risePnts[0] = left20
		risePnts[1] = right80
		Make/O/N=2 riseLev
		riseLev[0] = local(left20)
		riseLev[1] = local(right80)

		Display/W=(0,0,400,400)/K=1 local
		DoWindow/C OnLineDisp
		AppendToGraph areaLev vs areaPnts
		AppendToGraph riseLev vs risePnts
		
		ModifyGraph live=1, mode(areaLev)=4,marker(areaLev)=43,msize(areaLev)=6,mode(riseLev)=3,marker(riseLev)=43,msize(riseLev)=6,rgb(areaLev)=(0,43690,65535),rgb(riseLev)=(0,0,0)
		thisWave = wave_name
		
	elseif(index<(numwaves-1))
		RemoveFromGraph /W=OnLineDisp $thisWave
		RemoveFromGraph /W=OnLineDisp areaLev
		RemoveFromGraph /W=OnLineDisp riseLev
		areaPnts[0] = left0
		areaPnts[1] = right0
		areaLev[] = baseline+(netpeak*0.1)
		risePnts[0] = left20
		risePnts[1] = right80
		riseLev[0] = local(left20)
		riseLev[1] = local(right80)

		AppendToGraph /W=OnLineDisp local
		AppendToGraph areaLev vs areaPnts
		AppendToGraph riseLev vs risePnts

		ModifyGraph live=1, mode(areaLev)=3,marker(areaLev)=43,msize(areaLev)=6,mode(riseLev)=3,marker(riseLev)=43,msize(riseLev)=6,mode(areaLev)=4,rgb(areaLev)=(0,43690,65535),rgb(riseLev)=(0,0,0)
		thisWave = wave_name
	
	else
		DoWindow/K OnLineDisp
	
	endif

	DoUpdate /W=OnLineDisp
	
		
	SetDataFolder thisDF
End // EVENTPEAK 
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_KINETICS_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// Create all the global variables to be created by the function
	NewDataFolder/O/S PeakAnalysisGlobals
	Variable/G tau=0
	Variable/G RbError=0
	SetDataFolder thisDF

// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local = $wave_name
	endif

// ANALYSIS
	variable VAR
	CurveFit/N/Q/W=0 exp, $wave_name (roi_tstart,roi_tstop)
	WAVE W_coef
	RbError = W_coef[0]
	tau = 1 / W_coef[2]
// END ANALYSIS

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	
	string ex_string
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string stepkinName = baseName + "stepkin"
	
	if(index==0)
		Make/O/N=(numwaves,2) $stepkinName
	endif
	
	ex_string = stepkinName+"["+num2str(index)+"][0]="+num2str(tau)
		Execute ex_string
	ex_string = stepkinName+"["+num2str(index)+"][1]="+num2str(RbError)
		Execute ex_string
	
	SetDataFolder thisDF	
End // KINETICS
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_SLOPE_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local = $wave_name
	endif
	
// ANALYSIS
	variable/G slope
	CurveFit/N/Q/W=0 line  $wave_name (roi_tstart,roi_tstop)
	WAVE W_coef
	slope = W_coef[1]
// END ANALYSIS

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	
	string ex_string
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName = baseName + "fslope"	
	
	if(index==0)
//		KillWaves $newName
		Make/O/N=(numwaves,1) $newName
	endif
	
	ex_string = newName+"["+num2str(index)+"][0]="+num2str(slope)
		Execute ex_string
	
	SetDataFolder thisDF	
End // SLOPE
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_STATS_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local = $wave_name
	endif
	
// ANALYSIS
	variable/G average, minval, maxval, stdev
	WaveStats /M=2 /Q/R=(roi_tstart,roi_tstop) local
	average = V_avg
	minval = V_min
	maxval = V_max
	stdev = V_sdev
// END ANALYSIS

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	
	string ex_string
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName = baseName + "stats"	
	
	if(index==0)
		Make/O/N=(numwaves,4) $newName
	endif
	
	WAVE local2 = $newName 
	
	local2[index][0]= average
	local2[index][1]= minval
	local2[index][2]= maxval
	local2[index][3]= stdev
	
	SetDataFolder thisDF	
End // STATS
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_SPIKES_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""

// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local1 = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local1 = $wave_name
	endif
	
// Get the time scaling of the wave
	variable dt = DimDelta(local1, 0)
	variable raster_bin = 0.001 // make a 1ms bin for the display of raster plots
	
	Duplicate /O/R=(roi_tstart,roi_tstop) local1, local
	Make /D/O/N=(numpnts(local1)) raster = 0 
	Make /D/O/N=(numpnts(local1)/(raster_bin/dt)) raster_disp = 0

	variable numspikes = 0
	WaveStats/Q local
	
	if(V_max>-0.02)

// ANALYSIS

// Ultimately this should be updated to allow parameterization
		Differentiate local
		WaveStats/Q local
		variable ThreshMaxAccel = V_max*0.25
		
		// loop through the entire wave finding ThreshMaxAccel crossings
		variable count=0 //, spindex=0
		variable/G spindex=0

		FindLevels/Q /EDGE=1 /M=0.002 /R=(0,) local, ThreshMaxAccel
			
		numspikes = V_LevelsFound
		Duplicate/O W_FindLevels, times
		Duplicate/O W_FindLevels, indices
		indices[] = index
		
//END ANALYSIS
	endif

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif

	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName1 = baseName+"nspikes"
	string newName2 = baseName+"delta"
	string newName3 = baseName+num2str(index)+"_t"	
	string newName4 = baseName+"r_x"
	string newName5 = baseName+"r_y"
	
	if(index==0)
		Make/O/N=(numwaves,1) $newName1 = numspikes
		Make/O/N=(numpnts(raster),numwaves) $newName2
				SetScale /P x, 0, dt, "s", $newName2
		Make/D/O/N=(0) $newName4
		Make/D/O/N=(0) $newName5
	else
		Wave local3 = $newName1
		local3[index] = numspikes
	endif

	string exstr = newName2+"[*]["+num2str(index)+"] = raster[p]"
		Execute exstr
		
	string exstr2 = ""
	variable cindex=0, pntcount=0

	Wave local4 = $newName4
	Wave local5 = $newName5
	
	if(numspikes>0)
		Concatenate "times;", local4
		Concatenate "indices;", local5
	endif

	KillWaves raster, times, raster_disp
	
	if(index==numwaves-1)
	// For raster display
		DoWindow/K RasterPlot
		Display/K=1/W=(0,0,500,300) local5 vs local4 as "RasterPlot"
		DoWindow/C RasterPlot
		ModifyGraph mode=3,marker=10,mrkThick=2,rgb=(0,0,0)
		ModifyGraph noLabel(left)=2,axRGB(left)=(65535,65535,65535)
		SetAxis /W=RasterPlot bottom, 0, (numpnts(local1)*dt) 
		SetAxis /W=RasterPlot left, 0, numwaves
		 		
	endif
	
	SetDataFolder thisDF
	
End // SPIKES
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_WCSPK_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""

// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local1 = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local1 = $wave_name
	endif
	
// Get the time scaling of the wave
	variable dt = DimDelta(local1, 0)
	variable raster_bin = 0.001 // make a 1ms bin for the display of raster plots
	
	Duplicate /O/R=(roi_tstart,roi_tstop) local1, local
	Make /D/O/N=(numpnts(local1)) raster = 0 
	Make /D/O/N=(numpnts(local1)/(raster_bin/dt)) raster_disp = 0

	variable numspikes = 0
	WaveStats/Q local
	
	if(V_max>-0.02)

// ANALYSIS

// Ultimately this should be updated to allow parameterization
		Differentiate local
		WaveStats/Q local
		variable ThreshMaxAccel = V_max*0.25
		
		// loop through the entire wave finding ThreshMaxAccel crossings
		variable count=0 //, spindex=0
		variable/G spindex=0

		FindLevels/Q /EDGE=1 /M=0.002 /R=(0,) local, ThreshMaxAccel
			
		numspikes = V_LevelsFound
		Duplicate/O W_FindLevels, times
		Duplicate/O W_FindLevels, indices
		indices[] = index
		
//END ANALYSIS
	endif

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif

	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName1 = baseName+"nspikes"
	string newName2 = baseName+"delta"
	string newName3 = baseName+num2str(index)+"_t"	
	string newName4 = baseName+"r_x"
	string newName5 = baseName+"r_y"
	
	if(index==0)
		Make/O/N=(numwaves,1) $newName1 = numspikes
		Make/O/N=(numpnts(raster),numwaves) $newName2
				SetScale /P x, 0, dt, "s", $newName2
		Make/D/O/N=(0) $newName4
		Make/D/O/N=(0) $newName5
	else
		Wave local3 = $newName1
		local3[index] = numspikes
	endif

	string exstr = newName2+"[*]["+num2str(index)+"] = raster[p]"
		Execute exstr
		
	string exstr2 = ""
	variable cindex=0, pntcount=0

	Wave local4 = $newName4
	Wave local5 = $newName5
	
	if(numspikes>0)
		Concatenate "times;", local4
		Concatenate "indices;", local5
	endif

	KillWaves raster, times, raster_disp
	
	if(index==numwaves-1)
	// For raster display
		DoWindow/K RasterPlot
		Display/K=1/W=(0,0,500,300) local5 vs local4 as "RasterPlot"
		DoWindow/C RasterPlot
		ModifyGraph mode=3,marker=10,mrkThick=2,rgb=(0,0,0)
		ModifyGraph noLabel(left)=2,axRGB(left)=(65535,65535,65535)
		SetAxis /W=RasterPlot bottom, 0, (numpnts(local1)*dt) 
		SetAxis /W=RasterPlot left, 0, numwaves
		 		
	endif
	
	SetDataFolder thisDF
	
End // WCSPK
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_XSPIKES_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""

// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local1 = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local1 = $wave_name
	endif
	
	// Get the time scaling of the wave
	variable dt = DimDelta(local1, 0)
	variable raster_bin = 0.001 // make a 1ms bin for the display of raster plots
	
	Duplicate /O/R=(roi_tstart,roi_tstop) local1, local
	Make /I/O/N=(0) times
	Make /I/O/N=(1) tmp
	Make /D/O/N=(numpnts(local1)) raster = 0 
	Make /D/O/N=(numpnts(local1)/(raster_bin/dt)) raster_disp = 0

	variable numspikes = 0
	WaveStats/Q local
	
// ANALYSIS
		Differentiate local
		WaveStats/Q local
		variable ThreshMaxAccel = ((V_min-V_avg)/2)+V_avg
		print ThreshMaxAccel
		// loop through the entire wave finding ThreshMaxAccel crossings
		variable count=0, spindex=0
			
		FindLevels/Q /EDGE=2 /M=0.003 /P /R=[0,numpnts(local)] local, ThreshMaxAccel 
		numspikes = V_LevelsFound	
		Duplicate/O W_FindLevels, raster
		WAVE pnt_levels = W_FindLevels	
		Duplicate/O W_FindLevels, time_levels
		time_levels *= dt

// END ANALYSIS

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif

	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName1 = baseName+"nspikes"
	string newName2 = baseName+"delta"
	string newName3 = baseName+num2str(index)+"_t"	
	string newName4 = baseName+"r_x"
	string newName5 = baseName+"r_y"
	
	if(index==0)
		Make/O/N=(numwaves,1) $newName1 = numspikes
		Make/O/N=(numpnts(local)/(0.001/dt),numwaves) $newName2
		Make/D/O/N=(0) $newName4
		Make/D/O/N=(0) $newName5
	else
		Wave local3 = $newName1
		local3[index] = numspikes
	endif
	
	string exstr=""
	variable jindex=0, curr_pnt = 0
	WAVE local_delta = $newName2
	local_delta = 0
	for(jindex=0;jindex<numpnts(pnt_levels);jindex+=1)
		curr_pnt = round(time_levels[jindex]*1000)
		local_delta[curr_pnt][index] = 1
	endfor
	
	SetScale /P x, x, 1e-3 , "s", local_delta
		
	string exstr2 = ""
	variable cindex=0, pntcount=0

	Wave local4 = $newName4
	Wave local5 = $newName5
	
	if(numspikes>0)
		for(cindex=0;cindex<numspikes;cindex+=1)
				pntcount = numpnts(local4)
			exstr2 = newName4+"["+num2str(pntcount)+"] = {"+num2str(time_levels[cindex])+"}"
				Execute exstr2
			exstr2 = newName5+"["+num2str(pntcount)+"] = {"+num2str(index)+"}"
				Execute exstr2
		endfor
	endif
	
	KillWaves raster, times, raster_disp
	
	if(index==numwaves-1)
	// For raster display
		DoWindow/K RasterPlot
		Display/K=1/W=(0,0,500,300) local5 vs local4 as "RasterPlot"
		DoWindow/C RasterPlot
		ModifyGraph mode=3,marker=10,mrkThick=2,rgb=(0,0,0)
		ModifyGraph noLabel(left)=2,axRGB(left)=(65535,65535,65535)
		SetAxis /W=RasterPlot bottom, 0, (numpnts(local1)*dt) 
		SetAxis /W=RasterPlot left, 0, numwaves
		 		
	endif
	
	SetDataFolder thisDF
	
End // XSPIKES
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_DUPLICATE_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference
	WAVE local = TraceNameToWaveRef("",wave_name) 	

// Store the respective calculations in waves for subsequent analysis
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
	string newName = baseName + "DPL"

// ANALYSIS
	Duplicate /O/R=(roi_tstart,roi_tstop) $wave_name, $newName
	variable OldDelta = DimDelta($wave_name, 0)
	SetScale /P x, 0, OldDelta, $newName
//END ANALYSIS
	
	SetDataFolder thisDF
	
End // duplicate
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_EMFREQ_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local1 = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local1 = $wave_name
	endif
	
// ANALYSIS
	Duplicate /O/R=(roi_tstart,roi_tstop) local1, local
	variable/G average
	WaveStats /M=2 /Q/R=(roi_tstart,roi_tstop) local
	average = V_avg
	local = local - average
	
	variable padd_init=numpnts(local), pad_final
	
	FFT /Z /MAGS /DEST=W_FFT local	
// END ANALYSIS

// STORE ANALYSIS RESULTS
	string ChanName = "A"
	if( stringmatch(wave_name,"RecordB*") )
		ChanName = "B"
	elseif( !(stringmatch(wave_name,"Record*")) )
		ChanName = "X"
	endif
	
	string name_string
	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"

	name_string = baseName+"fft"+num2str(index)
	Rename W_FFT, $name_string

	SetDataFolder thisDF
End // EMFREQ
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//
/// USE THESE FUNCTIONS IN YOUR EXECUTABLE FILES IN ORDER TO PROMPT FOR SETTINGS OR DISPLAY SOME OUTPUT
//
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////



///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_SETTINGS_execute(value1,name1,value2,name2,value3,name3,value4,name4,analysisfunction)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// The purpose of this function will be to create a default panel that allows the user to make settings that are used by the current analysis function
// 		Each analysis function will have a dedicated folder that holds default settings.
	variable value1
	string name1
	variable value2
	string name2
	variable value3
	string name3
	variable value4
	string name4
	string analysisfunction
	String thisDF = GetDataFolder(1)
	
	NewDataFolder/O/S root:Analysis
	string/G CurrentFunc = analysisfunction
	
	string tmp_name = "root:Analysis:"+analysisfunction
	NewDataFolder/O/S $tmp_name
	
	variable/G parameter1=value1
	variable/G parameter2=value2
	variable/G parameter3=value3
	variable/G parameter4=value4
	NVAR default_set=default_set
	if(!NVAR_exists(default_set))
		variable/G default_set=0
	endif
	
	DoWindow/F ParameterPanel
	if (V_Flag!=0)
		DoWindow/K ParameterPanel
	endif
	
	string ex_str = "CORD_ParameterPanel(\""+name1+"\",\""+name2+"\",\""+name3+"\",\""+name4+"\",\""+analysisfunction+"\")" 
		print ex_str
		Execute ex_str
	Execute "ModifyPanel cbRGB = (32125,33410,39321)"


	SetDataFolder thisDF
End
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Window CORD_ParameterPanel(name1,name2,name3,name4,analysisfunction) : Panel
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string name1,name2,name3,name4,analysisfunction
	PauseUpdate; Silent 1

	NewPanel/W=(40,500,350,700)/K=1 as "ParameterPanel"
	DoWindow/C ParameterPanel
	SetVariable var1  size={250,20}, disable=0, font="Verdana", fsize=10, pos=  {20,40}, value=$("root:Analysis:"+analysisfunction+":parameter1"), title=name1
	SetVariable var2  size={250,20}, disable=0, font="Verdana", fsize=10, pos=  {20,70}, value=$("root:Analysis:"+analysisfunction+":parameter2"), title=name2
	SetVariable var3  size={250,20}, disable=0, font="Verdana", fsize=10, pos={20,100}, value=$("root:Analysis:"+analysisfunction+":parameter3"), title=name3
	SetVariable var4  size={250,20}, disable=0, font="Verdana", fsize=10, pos={20,130}, value=$("root:Analysis:"+analysisfunction+":parameter4"), title=name4
	PopupMenu def1 size={250,20}, bodywidth=100, disable=0, font="Verdana", fsize=10, mode=1, pos={20,160},proc=CORD_SetDefaultParameterPanel, title="Make setting default? ", value="No;Yes"

End


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_SetDefaultParameterPanel(cntrlName,popNum,popStr) : PopupMenuControl
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	String cntrlName
	Variable popNum	// which item is currently selected (1-based)
	String popStr		// contents of current popup item as string

	SVAR CurrentFunc = root:Analysis:CurrentFunc
	SetDataFolder $("root:Analysis:"+CurrentFunc)
	NVAR default_set = default_set

	if( stringmatch(popStr, "Yes") )
		default_set = 1
	endif
	
End


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_PANELDISP_execute(value1,name1,value2,name2,value3,name3,value4,name4,analysisfunction)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// The purpose of this function will be to create a default panel that allows the user to make settings that are used by the current analysis function
// 		Each analysis function will have a dedicated folder that holds default settings.
	variable value1
	string name1
	variable value2
	string name2
	variable value3
	string name3
	variable value4
	string name4
	string analysisfunction
	String thisDF = GetDataFolder(1)
	
	string tmp_name = "root:Analysis:"+analysisfunction
	NewDataFolder/O/S root:Analysis
	
	variable/G output1=value1
	variable/G output2=value2
	variable/G output3=value3
	variable/G output4=value4
	
	DoWindow/F OutputPanel
	if (V_Flag!=0)
		DoWindow/K OutputPanel
	endif
	
	string ex_str = "CORD_OutputPanel(\""+name1+"\",\""+name2+"\",\""+name3+"\",\""+name4+"\",\""+analysisfunction+"\")"  
		Execute ex_str
	Execute "ModifyPanel cbRGB = (32125,33410,39321)"


	SetDataFolder thisDF
	
End
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Window CORD_OutputPanel(name1,name2,name3,name4,analysisfunction) : Panel
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string name1,name2,name3,name4,analysisfunction
	PauseUpdate; Silent 1
	
	NewPanel/W=(40,500,350,700)/K=1 as "OutputPanel"
	DoWindow/C OutputPanel
	ValDisplay/Z var1  size={250,20}, barmisc={0, 350}, disable=0, font="Verdana", frame=0, fsize=10, pos=  {20,40}, value=root:Analysis:output1, title=name1
	ValDisplay/Z var2  size={250,20}, barmisc={0, 350}, disable=0, font="Verdana", frame=0, fsize=10, pos=  {20,70}, value=root:Analysis:output2, title=name2
	ValDisplay/Z var3  size={250,20}, barmisc={0, 350}, disable=0, font="Verdana", frame=0, fsize=10, pos={20,100}, value=root:Analysis:output3, title=name3
	ValDisplay/Z var4  size={250,20}, barmisc={0, 350}, disable=0, font="Verdana", frame=0, fsize=10, pos={20,130}, value=root:Analysis:output4, title=name4

End

/// IN DEVELOPMENT BELOW HERE ---------------

///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function CORD_EVENTS_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
	string wave_name
	variable roi_tstart,roi_tstop,index,numwaves,roi_num
	String thisDF = GetDataFolder(1)
	string prefix = ""
	
// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
	if( stringmatch(wave_name,"RecordA*") )
		WAVE local = TraceNameToWaveRef("",wave_name)	
	else
		WAVE local = $wave_name
	endif
	
// ANALYSIS

// Duplicate the wave region
	Duplicate /O/R=(roi_tstart,roi_tstop) local, MT_Heuristic

// FInd the template
	WAVE template = template
	if(!WaveExists(template))
		Abort "Please create a wave named 'template' before re-running..."
	endif

// Run the Template Matching algorithm
	if(RunningWindows())
		Execute /Z "MatchTemplate /C Template, MT_Heuristic"
//	else
//		MatchTemplate /C Template, MT_Heuristic		
	endif

// Threshold the results
	Duplicate /O MT_Heuristic, MT_Threshold
	variable detectthresh=25 // If you want to change threshold to that suggested by Clements And Bekkers (i.e. 4) do so here
	MT_Threshold = (MT_Threshold(x)>detectthresh) ? MT_Threshold(x) : 0  

// Find the event times
	variable HowLong = numpnts(MT_Threshold)
	variable jindex=0, count=0
	string wavebase = ""
	
	do

		if(MT_Threshold[jindex]>0)
			
			FindPeak/B=4/M=(detectthresh)/Q/R=(pnt2x(MT_Threshold, jindex), ) MT_Threshold
			if((V_PeakLoc+pnt2x(local,numpnts(template)))<roi_tstop)
				wavebase = wave_name+"_e"+num2str(count)
				Duplicate /O/R=(V_PeakLoc,(V_PeakLoc+pnt2x(local,numpnts(template)))) local, $wavebase 
				SetScale/P x 0,5e-05,"s", $wavebase
			endif
			count+=1
			jindex+=numpnts(template)

		else

			jindex+=1

		endif

	while (jindex<HowLong)

// END ANALYSIS

// STORE ANALYSIS RESULTS
//	string ChanName = "A"
//	if( stringmatch(wave_name,"RecordB*") )
//		ChanName = "B"
//	elseif( !(stringmatch(wave_name,"Record*")) )
//		ChanName = "X"
//	endif
//
//	if(index==0)
//
//	endif	
	
	SetDataFolder thisDF	
End // EVENTS
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//Function CORD_EVENTPEAKB_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//// This function is essentially a batch version of eventpeak that uses the first 10ms of the trace as a baseline to avoid the cursor dialogue
//
//	string wave_name
//	variable roi_tstart,roi_tstop,index,numwaves,roi_num
//	
//	String thisDF = GetDataFolder(1)
//
//// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
//	if( stringmatch(wave_name,"RecordA*") )
//		WAVE local = TraceNameToWaveRef("",wave_name)	
//	else
//		WAVE local = $wave_name
//	endif
//	
//// Create some local variables
//	string prefix = ""
//	variable maxflag=1
//	variable left0, right0
//	string basenameL = "baseL"+num2str(roi_num), basenameR = "baseR"+num2str(roi_num)
//	
//// Initialize all the global variables to be created by the function
//	NewDataFolder/O/S PeakAnalysisGlobals
//	Variable/G baseline=0
//	Variable/G meanpeak=0
//	Variable/G netpeak=0
//	Variable/G peaktime=0
//	Variable/G lefthalf=0
//	Variable/G righthalf=0
//	Variable/G left20=0
//	Variable/G right80=0
//	Variable/G slope2080=0
//	Variable/G totalarea=0
//	SetDataFolder thisDF
//	
//// Assume first 10 ms of trace is the baseline to use
//	baseline = mean(local,0.0001,0.0101)
//	
//// Find the peak of the passed wave
//	if(maxflag==0)
//		FindPeak/B=(50)/P/Q/R=(roi_tstart,roi_tstop) $wave_name
//		peaktime = round(V_PeakLoc)
//	else
//		WaveStats/Q/R=(roi_tstart,roi_tstop) local
//		peaktime = V_maxloc
//	endif
//
//// Subtract baseline offset to get net peak
//	meanpeak = mean(local,(peaktime-0.001),(peaktime+0.001))
//	print peaktime
//	print meanpeak
//	print baseline
//	netpeak = meanpeak - baseline
//// Get halfwidth
//	FindLevel/Q/R=(peaktime,0) $wave_name, (baseline + (netpeak/2))
//	lefthalf = V_LevelX
//	FindLevel/Q/R=(peaktime) $wave_name, (baseline + (netpeak/2))
//	righthalf = V_LevelX
//// Get 20-80 rise time
//	FindLevel/Q/R=(peaktime,0) $wave_name, (baseline+(netpeak*0.2))
//	left20 = V_LevelX
//	FindLevel/Q/R=(peaktime,0) $wave_name, (baseline+(netpeak*0.8))
//	right80 = V_LevelX
//// Get 20-80 slope
//	if((right80-left20) < 0.0005) // 0.5 ms defines about the shortest possible 20 80 rise time observed (prevents error if neg)
//		slope2080 = 0
//	else
//		CurveFit/N/Q/W=0 line $wave_name (left20,right80)
//		slope2080 = K1
//	endif
//// Get area (from 10% to 10%)
//	FindLevel/Q/R=(peaktime,0) $wave_name, (baseline+(netpeak*0.1))
//	left0 = V_LevelX
//	FindLevel/Q/R=(peaktime) $wave_name, (baseline+(netpeak*0.1))
//	right0 = V_LevelX
//	variable basebox = baseline * (right0 - left0)
//	variable tmparea = area($wave_name,left0,right0)
//	totalarea = tmparea - basebox // otherwise have to baseline traces to get area
//
//// Store the respective calculations in waves for subsequent analysis
//	string ChanName = "A"
//	if( stringmatch(wave_name,"RecordB*") )
//		ChanName = "B"
//	elseif( !(stringmatch(wave_name,"Record*")) )
//		ChanName = "X"
//	endif
//	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
//	string peakName = baseName + "peak"
//	string kinName = baseName + "kinetics"	
//	string assignstring
//	
//	if(index==0)
//		Make/N=(numwaves,4)/O $peakName
//		Make/N=(numwaves,4)/O $kinName
//	endif
//	
//	assignstring = peakName+"["+num2str(index)+"][0]="+num2str(netpeak)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][1]="+num2str(peaktime)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][2]="+num2str(meanpeak)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][3]="+num2str(baseline)
//		Execute assignstring
//				
//	assignstring = kinName+"["+num2str(index)+"][0]="+num2str((righthalf - lefthalf))
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][1]="+num2str(slope2080)
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][2]="+num2str((right80-left20))
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][3]="+num2str(totalarea)
//		Execute assignstring
//
//	if(index==(numwaves-1))
//		KillDataFolder :PeakAnalysisGlobals
//		variable numoutput=4
//		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_peak = {"Net depolarization (V)","Time of peak(ms)","Peak potential (V)","Baseline potential (V)"}
//		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_kinetics = {"Halfwidth (ms)","20-80 Rise Slope (V/ms) ","20-80 Rise Time (V/ms) ","Area "}
//
//		if(roi_num==1)
//			print  EVENTPEAK_outputlabels_peak
//			print  EVENTPEAK_outputlabels_kinetics
//		endif
//	endif
//	
//	SetDataFolder thisDF
//End // EVENTPEAKB
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

//
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//Function CORD_EVENTPEAKD_execute(wave_name,roi_tstart,roi_tstop,index,numwaves,roi_num)
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//// This function is essentially a batch version of eventpeak that uses the first 10ms of the trace as a baseline to avoid the cursor dialogue
//
//	string wave_name
//	variable roi_tstart,roi_tstop,index,numwaves,roi_num
//	
//	String thisDF = GetDataFolder(1)
//
//// String needs to be converted to a wave reference, but is either a trace reference or a name reference depending on channel
//	if( stringmatch(wave_name,"RecordA*") )
//		WAVE local = TraceNameToWaveRef("",wave_name)	
//	else
//		WAVE local = $wave_name
//	endif
//	
//// Create some local variables
//	string prefix = ""
//	variable maxflag=1
//	variable left0, right0
//	string basenameL = "baseL"+num2str(roi_num), basenameR = "baseR"+num2str(roi_num)
//	
//// Initialize all the global variables to be created by the function
//	NewDataFolder/O/S PeakAnalysisGlobals
//	Variable/G baseline=0
//	Variable/G meanpeak=0
//	Variable/G netpeak=0
//	Variable/G peaktime=0
//	Variable/G righthalf=0
//	Variable/G right20=0
//	Variable/G right80=0
//	Variable/G slope2080=0
//	Variable/G totalarea=0
//	SetDataFolder thisDF
//	
//// Assume first 10 ms of trace is the baseline to use
//	baseline = mean(local,0.0001,0.0101)
//	
//// Find the peak of the passed wave
//	if(maxflag==0)
//		FindPeak/B=(50)/P/Q/R=(roi_tstart,roi_tstop) $wave_name
//		peaktime = round(V_PeakLoc)
//	else
//		WaveStats/Q/R=(roi_tstart,roi_tstop) local
//		peaktime = V_maxloc
//	endif
//
//// Subtract baseline offset to get net peak
//	meanpeak = mean(local,(peaktime-0.001),(peaktime+0.001))
//	print peaktime
//	print meanpeak
//	print baseline
//	netpeak = meanpeak - baseline
//// Get halfdecay
//	FindLevel/Q/R=(peaktime) $wave_name, (baseline + (netpeak/2))
//	righthalf = V_LevelX
//// Get 20-80 decay
//	FindLevel/Q/R=(peaktime) $wave_name, (baseline+(netpeak*0.2))
//	right20 = V_LevelX
//	FindLevel/Q/R=(peaktime) $wave_name, (baseline+(netpeak*0.8))
//	right80 = V_LevelX
//// Get 20-80 slope
//	if((right20-right80) < 0.0005) // 0.5 ms defines about the shortest possible 20 80 rise time observed (prevents error if neg)
//		slope2080 = 0
//	else
//		CurveFit/N/Q/W=0 line $wave_name (right80,right20)
//		slope2080 = K1
//	endif
//// Get area (from 80% to 20%)
//	variable basebox = baseline * (right20 - right80)
//	variable tmparea = area($wave_name,right80,right20)
//	totalarea = tmparea - basebox // otherwise have to baseline traces to get area
//
//// Store the respective calculations in waves for subsequent analysis
//	string ChanName = "A"
//	if( stringmatch(wave_name,"RecordB*") )
//		ChanName = "B"
//	elseif( !(stringmatch(wave_name,"Record*")) )
//		ChanName = "X"
//	endif
//	string baseName = GetDataFolder(0) + "_roi" + num2str(roi_num) +"_"+ChanName+"_"
//	string peakName = baseName + "peak"
//	string kinName = baseName + "kinetics"	
//	string assignstring
//	
//	if(index==0)
//		Make/N=(numwaves,4)/O $peakName
//		Make/N=(numwaves,4)/O $kinName
//	endif
//	
//	assignstring = peakName+"["+num2str(index)+"][0]="+num2str(netpeak)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][1]="+num2str(peaktime)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][2]="+num2str(meanpeak)
//		Execute assignstring
//	assignstring = peakName+"["+num2str(index)+"][3]="+num2str(baseline)
//		Execute assignstring
//				
//	assignstring = kinName+"["+num2str(index)+"][0]="+num2str((righthalf - peaktime))
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][1]="+num2str(slope2080)
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][2]="+num2str((right20-right80))
//		Execute assignstring
//	assignstring = kinName+"["+num2str(index)+"][3]="+num2str(totalarea)
//		Execute assignstring
//
//	if(index==(numwaves-1))
//		KillDataFolder :PeakAnalysisGlobals
//		variable numoutput=4
//		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_peak = {"Net depolarization (V)","Time of peak(ms)","Peak potential (V)","Baseline potential (V)"}
//		Make/T/N=(numoutput)/O EVENTPEAK_outputlabels_kinetics = {"Half decay time (s)","20-80 Decay Slope (mV/s) ","20-80 Decay Time (mV/s) ","Area "}
//
//		if(roi_num==1)
//			print  EVENTPEAK_outputlabels_peak
//			print  EVENTPEAK_outputlabels_kinetics
//		endif
//	endif
//	
//	SetDataFolder thisDF
//End // EVENTPEAKD
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////