#pragma rtGlobals=1		// Use modern global access method.

Macro load_WKF(month,today,from,to,delta,plottype)
	String month="z:2009_02" 
	String today="2009_02_02"
	variable from=4
	variable to =43
	variable delta = 23
	variable plottype=1
	Prompt plottype, "plot type:", popup "dose (Langmuir); scan number (table)"
	
		String/G imagePathStr=root:imagePathStr
		String/G imagetypeStr=root:imageTypeStr
		String/G scanNameStr=root:scanNameStr
		String/G scanNumberStr=root:scanNumberStr
		String/G lastImage=root:lastImage
		String/G separatorStr = root:separatorStr
	
	String locImagePathStr=month+":"+today+":"
	variable i=from
	String tmpStr, traceStr
	String roiStr
	String stvStr
	String pmchStr
	
	String no=num2Str(from)+"-"+num2Str(to)
	String scannoStr =  "SCANN_"+no
	String roi = "ROI_"+no
	String pressStr = "pressure_"+no
	variable nmax
	variable deltan=12
	
	make/n=(to-from+1)/o $roi, $pressStr, $scannoStr
	SetScale/P x (from),1,"", $roi, $pressStr
	
	do
		if (i<10) 
			tmpStr="00"+num2Str(i) 	
		else
			if (i<100)
				tmpStr="0"+num2Str(i) 
			else
				tmpStr=num2Str(i)
			endif 
		endif
		
		ImagePathStr = locImagePathStr+today+"_"+tmpStr+"_WKF"
		newPath/O/Q/Z imagePath ImagePathStr
		scanNameStr=today+"_"+tmpStr+"_WKF"
		scanNumberStr=tmpStr
		roiStr = today+"_"+tmpStr+"_ROI"
		stvStr = today+"_"+tmpStr+"_STV"
		pmchStr = "PMCH_"+tmpStr
		print ImagePathStr, "  ", scanNameStr
		
		loadImageScan1("")
		nmax = numpnts($stvStr)
		shoRoiScan1("")
		
		differentiate $RoiStr
		wavestats  $RoiStr
		integrate  $RoiStr
		
		//CurveFit gauss $roiStr[V_minloc-10,V_minloc+10] /X=$stvStr /D
		CurveFit/Q Sigmoid $roiStr[0,min(V_minloc+deltan,nmax)] /X=$stvStr /D
		$roi[i-from]=W_coef[2]
		
	      duplicate/o $pmchStr pwave
	      wavestats pwave
		
		$pressStr[i-from]=V_rms
		if (V_rms > 10^-4)
			$pressStr[i-from] = V_min
		endif

		$scannoStr[i-from]=i
		
		killseries("")
		killseries("")
		 
		i+=1
	while (i<=to)
	
	$pressStr/=1.3
	$pressStr*=10^6
	$pressStr*=delta
	integrate $pressStr
	
	if (plottype == 1)
		display $roi vs $pressStr
		Label bottom "\\F'Arial'\\Z16Dose (L)"

	else if  (plottype == 2)	
		display $roi vs $scannoStr
		Label bottom "\\F'Arial'\\Z16Scan number"
		Edit $scannoStr, $roi
	endif
	
	ModifyGraph mode($roi)=3,marker($roi)=19
	Label left "\\F'Arial'\\Z16Work function (eV)";DelayUpdate
	ModifyGraph axOffset(bottom)=1
	ModifyGraph axOffset=1
	ModifyGraph width=283.465,height=283.465
	
	//String newname
	//prompt newname, "enter name for WKF wave:"
	//doPrompt "duplicate W_coef:", coefStr
	//if (V_flag == 0)
	//	rename $roi newname
	//endif
	
	rename_wave(roi)
End

function rename_wave(newname)
	String newname
	String wavestr = newname
	Prompt newname, "enter name for coef wave:"
	doPrompt "rename to:", newname
	if (V_flag == 0)
		rename $wavestr $newname
		return 0
	else
		return 1
	endif
end

Macro load_ROIs(month,today,from,to,delta,plottype)
	String month="z:2009_01" 
	String today="2009_01_30"
	variable from=1
	variable to =23
	variable delta =1
	variable plottype=1
	Prompt plottype, "plot type:", popup "dose (Langmuir); scan number (table)"
	
		String/G imagePathStr=root:imagePathStr
		String/G imagetypeStr=root:imageTypeStr
		String/G scanNameStr=root:scanNameStr
		String/G scanNumberStr=root:scanNumberStr
		String/G lastImage=root:lastImage
		String/G separatorStr = root:separatorStr
	
	String locImagePathStr=month+":"+today+":"
	variable i=from
	String tmpStr, traceStr
	String roi1Str,roi2Str,roi3Str,roi4Str,pmchStr
	String stvStr
	variable nmax
	variable deltan=12
	
	String no=num2Str(from)+"-"+num2Str(to)
	
	String scannoStr =  "SCANN_"+no
	String roi1 = "ROI1_"+no
	String roi2 = "ROI2_"+no
	String roi3 = "ROI3_"+no
	String roi4 = "ROI4_"+no
	String pressStr = "pressure_"+no
	make/n=(to-from+1)/o $roi1,  $roi2,  $roi3, $roi4, $pressStr, $scannoStr
	SetScale/P x (from),1,"", $roi1,  $roi2,  $roi3, $roi4, 
	
	do
		if (i<10) 
			tmpStr="00"+num2Str(i) 	
		else
			if (i<100)
				tmpStr="0"+num2Str(i) 
			else
				tmpStr=num2Str(i)
			endif 
		endif
		
		ImagePathStr = locImagePathStr+today+"_"+tmpStr+"_WKF"
		newPath/O/Q/Z imagePath ImagePathStr
		scanNameStr=today+"_"+tmpStr+"_WKF"
		scanNumberStr=tmpStr
		
		traceStr=today+"_"+tmpStr+"_trace.txt"
		print "load auxiliary waves from file: ", traceStr
		Loadwave/A/D/G/K=1/O/Q/P=ImagePath/W traceStr

		roi1Str="ROI1_"+tmpStr
		roi2Str="ROI2_"+tmpStr
		roi3Str="ROI3_"+tmpStr
		roi4Str="ROI4_"+tmpStr
		stvStr = "STV_"+tmpStr
		pmchStr = "PMCH_"+tmpStr
		
		nmax = numpnts($stvStr)
		
		display
		appendToGraph $roi1Str,$roi2Str,$roi3Str,$roi4Str vs $stvStr
		
		differentiate $Roi1Str
		wavestats  $Roi1Str
		integrate  $Roi1Str
			
		CurveFit Sigmoid $roi1Str[0,min(V_minloc+deltan,nmax)] /X=$stvStr /D
		$roi1[i-from]=W_coef[2]
		
		differentiate $Roi2Str
		wavestats  $Roi2Str
		integrate  $Roi2Str
		
		CurveFit Sigmoid $roi2Str[0,min(V_minloc+deltan,nmax)] /X=$stvStr /D
		$roi2[i-from]=W_coef[2]
		
		differentiate $Roi3Str
		wavestats  $Roi3Str
		integrate  $Roi3Str
		
		CurveFit Sigmoid $roi3Str[0,min(V_minloc+deltan,nmax)] /X=$stvStr /D
		$roi3[i-from]=W_coef[2]
		
		differentiate $Roi4Str
		wavestats  $Roi4Str
		integrate  $Roi4Str
		
		CurveFit Sigmoid $roi4Str[0,min(V_minloc+deltan,nmax)] /X=$stvStr /D
		$roi4[i-from]=W_coef[2]
	
	      //duplicate/o $pmchStr pwave
	      //wavestats pwave
		
		$pressStr[i-from]=V_rms
		if (V_rms > 10^-4)
			$pressStr[i-from] = V_min
		endif

		$scannoStr[i-from]=i
		
		killseries("")
		 
		i+=1
	while (i<=to)
	
	$pressStr/=1.3
	$pressStr*=10^6
	$pressStr*=delta
	integrate $pressStr
	
	if (plottype == 1)
		display $roi1, $roi2, $roi3, $roi4 vs $pressStr
		Label bottom "\\F'Arial'\\Z16Dose (L)"
	else if  (plottype == 2)	
		display $roi1, $roi2, $roi3, $roi4 vs $scannoStr
		Label bottom "\\F'Arial'\\Z16Scan number"
		Edit $scannoStr, $roi1, $roi2, $roi3, $roi4
	endif
	
	ModifyGraph mode($roi1)=3,marker($roi1)=19,mode($roi2)=3,marker($roi2)=16;DelayUpdate
	ModifyGraph rgb($roi2)=(0,39168,0),mode($roi3)=3,marker($roi3)=17;DelayUpdate
	ModifyGraph rgb($roi3)=(0,12800,52224)
	ModifyGraph rgb($roi4)=(0,0,0)
	Label left "\\F'Arial'\\Z16Work function difference (eV)";DelayUpdate
	ModifyGraph axOffset(bottom)=1
	ModifyGraph axOffset=1
	ModifyGraph width=283.465,height=283.465
End

Function loadImageScan1(ctrlname): buttoncontrol	 //160203
	string ctrlname
	string tmpStr,newName
	variable j=0
	SVAR imagePathStr=root:imagePathStr
	SVAR imagetypeStr=root:imageTypeStr
	SVAR scanNameStr=root:scanNameStr
	SVAR scanNumberStr=root:scanNumberStr
	SVAR lastImage=root:lastImage
	SVAR separatorStr = root:separatorStr
	NVAR scanFrom=root:scanFrom
	NVAR scanTo=root:scanTo
	NVAR energy=root:energy
	NVAR layer=root:layer
	// load all waves in trace.txt
	// load info ImageNum STV     MOBJ Mesh BeamCurrent Box1 Box2 Box3 (kin energy scan)
	//             ImageNum Energy --------- Mesh BeamCurrent Box1 Box2 Box3 (photon energy scan)
	variable lastindex = strsearch(scanNameStr,"_",Inf,1)
	String nameStr=scanNameStr[0,lastindex-1]
	string scanType = scanNameStr[lastindex+1,strlen(scanNameStr)]
	print "scan type = ",scanType
	// find rootname
	print "file root name = ",nameStr
	string scaninfoStr=nameStr+"_trace.txt"
	print "load auxiliary waves from file: ", scaninfoStr
	Loadwave/A/D/G/O/Q/P=imagePath/W scaninfoStr
	lastindex = strsearch(nameStr,"_",Inf,1)
	scanNumberStr=nameStr[lastIndex+1,strlen(nameStr)]
	tmpStr = "ImageNum"+nameStr[lastIndex,strlen(nameStr)]
	print tmpStr,nameStr,scanNumberStr
	variable scanNpnts=numpnts($tmpStr)
	// rename waves
	if (exists(tmpStr)==1)
		newName = nameStr + "_NUM" 
		duplicate/o $tmpStr  $newName
		killwaves $tmpStr
	endif
	tmpStr = "STV_"+scanNumberStr
	if ( exists(tmpStr)==1 && (stringmatch(scanType,"XPS")==1) || (stringmatch(scanType,"IV")==1) || (stringmatch(scanType,"WKF")==1))
		//print "XPS scan type"
		newName =nameStr + "_STV" 
		duplicate/o $tmpStr  $newName
		scanFrom=returnWaveElement($newname,0)
		scanTo=returnWaveElement($newname,scanNpnts-1)
		killwaves $tmpStr
	endif
	tmpStr = "Energy_"+scanNumberStr
	if (exists(tmpStr)==1 && stringmatch(scanType,"XAS")==1)
		newName = NameStr + "_NRG" 
		duplicate/o $tmpStr  $newName
		scanFrom=returnWaveElement($newname,0)
		scanTo=returnWaveElement($newname,scanNpnts-1)
		killwaves $tmpStr
	endif
	tmpStr = "BeamCurrent_"+scanNumberStr
	if (exists(tmpStr)==1)
		newName = nameStr + "_BCR" 
		duplicate/o $tmpStr  $newName
		killwaves $tmpStr
	endif
	tmpStr = "Mesh_"+scanNumberStr
	if (exists(tmpStr)==1)
		newName = nameStr + "_MSH" 
		duplicate/o $tmpStr  $newName
		killwaves $tmpStr
	endif
	tmpStr = "MOBJ_"+scanNumberStr
	if (exists(tmpStr)==1 && stringmatch(scanType,"FOCUS")==1)
		newName = nameStr + "_OBJ" 
		duplicate/o $tmpStr  $newName
		killwaves $tmpStr
	endif
	// darkfield
    	//variable darkfield=2
       //	prompt darkfield, "subtact darkfield", popup, "no;yes"
       //	doPrompt "open image", darkfield	
        //if ((V_flag ==0 )&& (darkfield == 2))
	//	darkfield=1
	//else
	variable darkfield=1
	//endif
	//load first image in order to dimension the array
	print "number of images: ",scanNpnts,"start energy: ",scanFrom,"end energy: ",scanTo
	tmpStr = nameStr +"_"+num2ScanNumberStr(j)+"."+imageTypeStr 
	tmpStr = OpenImage(tmpStr,darkfield)
	if  (stringMatch(tmpStr,"")!=1)
    	// initialise the stack
   	variable np=DimSize($tmpStr,0)
   	variable nq=DimSize($tmpStr,1)      
      	make/n=(np,nq,scanNpnts)/O/W $nameStr
  	imageToStack($nameStr,$tmpStr,0)
    	j+=1
      // load the rest		
      do
       	tmpStr=nameStr +"_"+num2ScanNumberStr(j)+"."+imageTypeStr //scanNameStr +"_"+num2ScanNumberStr(j)+"."+imageTypeStr 
       	tmpStr = OpenImage(tmpStr,darkfield)
       	imageToStack($nameStr,$tmpStr,j)
       	killwaves $tmpStr
       	j+=1
       while (j<scanNpnts && (stringMatch(tmpStr,"")!=1) )
	// show
	if (stringMatch(tmpStr,"")!=1)
		NewImage/S=2 $nameStr
		ModifyImage $nameStr plane=0
		PauseUpdate
		showinfo
		ControlBar 81
		ModifyGraph width=250*np/nq,height=250
		//add controls
		String commandStr="addScanControls()"
		if ((stringMatch(num2Str(np),"NaN")!=1)&&(stringMatch(num2Str(nq),"NaN")!=1)) 
			Execute commandStr
			layer=0
       			energy=scanFrom
		endif
	endif
	endif
End

Function shoRoiScan1(ctrlnameroi): buttoncontrol	//160203
	String ctrlnameroi
	Silent 1; PauseUpdate
	variable i=0
	String tmpStr=returnListFirstElement(imageNameList("",""),";")
	tmpStr= removeQuotes(tmpStr)
	variable p=dimsize($tmpStr,0)
	variable q=dimsize($tmpStr,1)
	variable r=dimsize($tmpStr,2)
	if (r==0)
		r=1
		redimension/N=(p,q,r) $tmpStr 
	endif
	String roiStr=tmpStr+"_ROI"
	//roiStr = giveRoiName(roiStr)
	make/N=(r)/O/U $roiStr
	make/n=(p,q)/o myLayer
	Silent, 1
	PauseUpdate
	do
		extract2DWaveFromStack($tmpStr,i,myLayer)
		redimension/D mylayer
		ImageStats/R=M_RoiMask myLayer
		entryToWave($roiStr,V_avg,i)
		i+=1
	while(i<=r)
	killwaves myLayer
	//normalisation
	//normaliseScan(tmpStr,roiStr)
	String graphNameStr="SCAN_"+tmpStr
	stackToFrontAndDisplay(graphNameStr,tmpStr,roiStr)
	Execute "addROIScanControls()"
End