//Dec. 3, 2006.		
// ==================================================================
// ------------------------------------------------------------------------------------------------------------------------------------
//     Jae-Hie J. Cho,  Gregory S. Smith, and William A. Hamilton
//     -name: NRefleCal
//     -This program is for Low-Q nuetron reflectivity simulation and data fitting
//     -We are not responsible for any incorrections of this program.
// ------------------------------------------------------------------------------------------------------------------------------------
// ==================================================================
// ***Never remove or change the letters above.
      
#pragma version = 4.1

#pragma rtGlobals=1		




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	O,hbc(bSDfqhot\lbEZKQ=I,qhru_++((`g"kD1DJ(rsK*?IoG946[p;M%Cgg?bTs39Gr!ecPpSdC>
	*V+mhYmY13=oM+c$2T3J>bQf`dr2o\](lr#Z&.#\/NBj1)uG@i/^ec58pgdC+<"Y5o<R&7CNN+5VsP
	RZ7SjSG_PPpj[c&54LJH0JNP-!!#SZ:.26O@"J
	ASCII85End
End



Function NIST_SLD_Cal()

              String url= "http://sld-calculator.appspot.com/"
              BrowseURL url
END

Function RtoRQ4_Data_Trans_Func()


    String WavR=StrVarOrDefault ("globrq4data","")
    String WavQ=StrVarOrDefault ("globqzdata","")    
    String WavdR=StrVarOrDefault ("globdrq4data","")
    String WavdQ=StrVarOrDefault ("globdqdata","")    

	Variable cons
	
	Prompt  wavR, "Choose R wave:", popup, WaveList("*",";","")	
	Prompt  wavdR, "Choose sigR wave:", popup, WaveList("*",";","")	
	Prompt  wavQ, "Choose Q wave:", popup, WaveList("*",";","")	
	Prompt  wavdQ, "Choose sigQ wave:", popup, WaveList("*",";","")	
	
       
	DoPrompt "Data Transform; R => RQ4_Trans & sigR => sigRQ4_Trans: ",wavR,wavdR,wavQ,wavdQ
	
	if (V_Flag)
	    return -1
	endif
      String/G globrq4data, globqzdata,globdrq4data,globdqdata	
      
       Wave wavR1=$wavR,wavdR1=$wavdR,wavQ1=$wavQ,wavdQ1=$wavdQ
	Duplicate /O wavR1, RQ4_Trans
	Duplicate /O wavdR1, sigRQ4_Trans
	
	RQ4_Trans=wavR1*wavQ1^4
	sigRQ4_Trans=sqrt((wavdR1*wavQ1^4))^2//+(4*wavR1* wavdQ1^3)^2)
	 
End

Function Wave_Scaling_Func()

	String wav 
	Variable cons
	
	Prompt  wav, "Choose a wave:", popup, WaveList("*",";","")	
	Prompt  cons, "Enter the Scaling factor:"
       
	DoPrompt "Manual scaling of a wave (w_new=w_old*s_factor): ",wav,cons
	
	if (V_Flag)
	    return -1
	endif

	 Wave wy=$wav
	 
	 wy=wy*cons
	 

 End
 Function Sqrt_Wave_Func()

//	String wav 
//	Variable cons
	String wav=StrVarOrDefault ("globdqdata","")    
	
	Prompt  wav, "Choose a wave:", popup, WaveList("*",";","")	
//	Prompt  cons, "Enter the Scaling factor:"
       
	DoPrompt "Manual scaling of a wave (w_new=sqrt(w_old)): ",wav//,cons
	String /G globdqdata
	if (V_Flag)
	    return -1
	endif

	 Wave wy=$wav
	 
	 wy=sqrt(wy)
	 

 End

 Function Wave_Shift_Func()

	String wav 
	Variable cons
	
	Prompt  wav, "Choose a wave:", popup, WaveList("*",";","")	
	Prompt  cons, "Enter the shift factor:"
       
	DoPrompt "Manual Shift of the values of a wave (w_new=w_old+s_factor): ",wav,cons
	
	if (V_Flag)
	    return -1
	endif

	 Wave wy=$wav
	 
	 wy=wy+cons	 

 End
 
   Function Make_sigQ_Data()
  //     String /G globdqdata
	String wav=StrVarOrDefault ("globqzdata","")   
Variable cons=NumVarOrDefault("", 0.03)	
//	Variable cons
      String Nname=StrVarOrDefault ("name", "d"+ wav) 
	String wavename_Dup=Nname
//	Variable cons
	
	
	Prompt  wav, "Choose Qdata:", popup, WaveList("*",";","")	
	Prompt  wavename_Dup, "Name dQ:"//, popup, WaveList(" ",";","")	
       Prompt  cons, "What is the Scaling factor, dQ/Q ?(eg. 0.03 for 3 % of Q):"
	DoPrompt "Make dQ data",wav,wavename_Dup,cons
	String /G globqzdata
	if (V_Flag)
	    return -1
	endif
   //   wavename_Dup=PossiblyQuoteName(wavename_Dup)
	 Wave wy=$wav
	
	 
    Duplicate /O wy $wavename_Dup
    Wave sigQ=$wavename_Dup
       sigQ=sigQ*cons
      
 //      globdqdata=wavename_Dup
//     FitRgeneral3()  
	 
 End

 
  Function Wave_Dup_Func()

	String wav 
//	Variable cons
   //   String Nname="name"
	String wavename_Dup="name"
	
	
	Prompt  wav, "Choose the wave to be duplicated:", popup, WaveList("*",";","")	
	Prompt  wavename_Dup, "Type the name of the new wave:"
       
	DoPrompt "Duplicate",wav,wavename_Dup
	
	if (V_Flag)
	    return -1
	endif
   //   wavename_Dup=PossiblyQuoteName(wavename_Dup)
	 Wave wy=$wav
	
	 
    Duplicate /O wy $wavename_Dup
	 
 End

  Function polydensity(d0,d1,d2,d3) //assumption: solvent can not penetrate into the PVP layer
 Variable d0,d1,d2,d3
 
 SVAR yyy=globprosldz//,xxx
 //String yyy=yyy1
 Wave yy=$yyy
// Wave xx=$xxx
 Duplicate /O yy polydensy
 Duplicate /O yy solvdensy
  Duplicate /O yy psvolf_a,pvpvolf_a,solv_volf_a,polyvolf_a
// Duplicate xx polydensx
 Variable i
// print yy
 for (i=0;i<=8;i=i+1)
   polydensy[i]=yy[i]-(1-(yy[i]-d0)/(yy[9]-d0))*d0-((yy[20]-d2)/(d3-d2)*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0))*d3
   solvdensy[i]=((yy[20]-d2)/(d3-d2)*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0))*d3
   psvolf_a[i]=(1-(yy[20]-d2)/(d3-d2))*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0)
   solv_volf_a[i]=solvdensy[i]/d3
   pvpvolf_a[i]=(polydensy[i]-psvolf_a[i]*d2)/d1
 endfor
 for (i=9; i<=19;i=i+1)
  polydensy[i]=yy[i]-(yy[20]-d2)/(d3-d2)*(yy[i]-d1)/(yy[20]-d1)*d3  //ps+pvp
 solvdensy[i]=(yy[20]-d2)/(d3-d2)*(yy[i]-d1)/(yy[20]-d1)*d3
 psvolf_a[i]=(1-(yy[20]-d2)/(d3-d2))*(yy[i]-d1)/(yy[20]-d1)
 solv_volf_a[i]=solvdensy[i]/d3
  pvpvolf_a[i]=(polydensy[i]-psvolf_a[i]*d2)/d1
 endfor
 for (i=20;i<=38;i=i+1)
 polydensy[i]=(1-(yy[i]-d2)/(d3-d2))*d2  //ps
 solvdensy[i]=((yy[i]-d2)/(d3-d2))*d3
 psvolf_a[i]=(1-(yy[i]-d2)/(d3-d2))
  pvpvolf_a[i]=(polydensy[i]-psvolf_a[i]*d2)/d1
 solv_volf_a[i]=solvdensy[i]/d3
 endfor
 for (i=39; i<=49;i=i+1)  
  polydensy[i]=yy[i]-(yy[20]-d2)/(d3-d2)*(yy[i]-d1)/(yy[20]-d1)*d3  //ps+pvp
solvdensy[i]=(yy[20]-d2)/(d3-d2)*(yy[i]-d1)/(yy[20]-d1)*d3
 psvolf_a[i]=(1-(yy[20]-d2)/(d3-d2))*(yy[i]-d1)/(yy[20]-d1)
  pvpvolf_a[i]=(polydensy[i]-psvolf_a[i]*d2)/d1
 solv_volf_a[i]=solvdensy[i]/d3
endfor
 for (i=50;i<= 60;i=i+1)
   polydensy[i]=yy[i]-(1-(yy[i]-d0)/(yy[9]-d0))*d0-((yy[20]-d2)/(d3-d2)*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0))*d3
   solvdensy[i]=((yy[20]-d2)/(d3-d2)*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0))*d3
    psvolf_a[i]=(1-(yy[20]-d2)/(d3-d2))*(yy[9]-d1)/(yy[20]-d1)*(yy[i]-d0)/(yy[9]-d0)
     pvpvolf_a[i]=(polydensy[i]-psvolf_a[i]*d2)/d1
    solv_volf_a[i]=solvdensy[i]/d3
 endfor
  polyvolf_a=psvolf_a+pvpvolf_a
 
 End
 
Menu "NeutronReflectivity"//"Misc Operations"
 //   Submenu "Profile Generator"
 //        "Build HGauss Profile Smtr", EJMainS()
 //   End
//    Submenu  "Reflectivity"
//	"Cal RQ4 w\ a given Profile", ParrattMaindq( ) 
//    End
//    Submenu "ReflFit"
//	"Fit RQ4 Symetry u\hGauss", ParrattFitMaindqS( ) 
//    End
//     Submenu "ReflFit"
//	"Fit RQ4 Symetry u\Arbitrary", ParrattFitMaindqSIndeM( )
//    End

   //  Submenu "Main Analysis"
	"Start NR Analysis program ...",  FitRgeneral2( )
	help={"This is the first step for the reflectivity analysis. All other menu commands will NOT work before this is done ..."}
//    End    

    Submenu "  Utilities I"
         "Sqrt of Data", Sqrt_Wave_Func()
    End     
    Submenu "  Utilities I"
         "Make dQ", Make_sigQ_Data()
    End     
    


//        Submenu "Utilities"
//         "R2RQ4",  RtoRQ4_Data_Trans_Func()
//    End

    Submenu "  Utilities I"
         "ReScale", Wave_Scaling_Func()
    End
    Submenu "  Utilities I"
         "Shift", Wave_Shift_Func()
    End
        Submenu "  Utilities I"
         "Approx. Q_c",  crtQ_cal()
    End
        Submenu "  Utilities I"
         "Approx. Theta_c",   crt_theta_cal( )
    End

    
       Submenu "  Utilities I"
         "ReBin",   Bin_Data() 
         //accept all conditions in panel
    End        
   
        Submenu "  Utilities I"
         "SLD_Cal Web",   NIST_SLD_Cal()
    End    
      Submenu "  Utilities I"
       "Copy data as", Wave_Dup_Func()
             Submenu "Pixelize SLD"
         "cstDZ",   ConstdzSLD() 
         //accept all conditions in panel
         End 
               Submenu "Pixelize SLD"
         "cstDZX2",   Numx2SLD()
         //accept all conditions in panel
         End 

 //       "new name", Wave_Dup_Func()
 //   End
    End
        Submenu "  Utilities II"
        Submenu "Special Fittings"
          help={"     Under Construction...     Under Construction...     Under Construction...     Under Construction...     Under Construction..."}
        "SLD2Fit",   ArbitraryFitting_Button() 
         //accept all conditions in panel
     
   

//    Submenu "SLD2Fit"
//         "SLD2FitS",   ArbitraryFitting_ButtonS() 
      
//    End    
    End
    End
//  

//    help= {"Current Data Folder"}


 Submenu "  Utilities II"
       Submenu "Other R Calculation: nosmear"
       help={"  No dQ smear nor incoherent smear..."}
	"Matrix Method", EMMainS()
   End
          Submenu "Other R Calculation: nosmear"
	"Rayleigh Formula: R Only", SuperMaster()
   End
          Submenu "Tools 4 Thickness"
	"(Interface position by IFT:  R Only", InvSuperMasterMag3()"
   End
//          Submenu "Tools 4 Thickness"
//	"Interface position by IFTBack:  R Only", InvSuperMasterMag()
//  End

    Submenu "Tools 4 Thickness"
         "Kiessig thickness: Note 'place cursors first'", Kiessig_Thickness()
      End   
         Submenu "To Copy Panel Window"
         "(Use key-combination Shift+PrintScreen to copy NR panel to clipboard."
    End        
    Submenu "Special Fittings"
     "SmoothFit", CSfit()
     help={"***Caution***Do NOT use this fitting...  This may not work..."}
      "CCMassFit", CCSMfit1()
      help={"***Caution; NOT for users. This will not work; CC Sym. Geometry w/ mc; Only support numbers for constriants (Low or High boxes)..."}
      End
 End
 
  "  SetDF", DataFolderNames()
  	help={"An alternative way to change the DataFolder ..."}
 End
 
  Menu  "SetDF2Root", dynamic//DF2root()
  GetDataFolder(0)+" > root",/Q, DF2root()
 help={"To change the current DataFoder to IgorPro root..."}
//     PrintAllDFNames4Menu(StrVarOrDefault(GetindexedObjName("root:",4,0),"root")),/Q, DF2root()<<< PrintAllDFNames4Menu();Not being used
    
//    DataFolderNames()
 END

// Function root()
// SetDataFolder root: 
// End
//Function  setDFf(a)
//String a//=StringFromList(1,PrintAllDataFolderNames())
//SetDataFolder root:$a

//End
//Menu "CurrentDF", dynamic //"CurrentDF"
 //  Dmenuitem()

 //    "-"
//  "ChangeDF",DataFolderNames()
 
//  End
//End
 Function /S DF2root()
  String /G globCDF=GetDataFolder(0)
  Variable aa=0
  String selec
      Variable index
    String strfollist=""
//    String selec
    String gdf=GetDataFolder(1)
    String  objName
    String aa1
//    print gdf
index=0
    do 
        objName=GetindexedObjName("root:",4,index)
        
  //      print objName
        if (exists("root:"+objName+":globExptTitle")==2)
             aa1="root:"+objName
 //           strfollist=strfollist+";"+objName+":"
            strfollist=strfollist+";"+"SetDataFolder"+aa1
        endif
        if (strlen(objName) == 0)
        break
        endif
    index +=1
    while(1)
              if (stringmatch("root:",gdf)>0)
//          strfollist=strfollist+";"+"root"
           strfollist=strfollist+";"+"SetDataFolder root:"
          endif
  SetDataFolder root://$aa1
    return strfollist    //String aa1="root:"+selec+":"

 
//return  selec

 End
Function DataFolderNames()
 String ss=GetDataFolder(0)
// print ss

 DoWindow /K CCDFwin
  NewPanel /K=1 /N=CCDFwin /W=(550,10,900,42) as "ChangeCurrentDataFolder"
//    SetVariable tiltleIn value=ss, bodyWidth=135, title=" ",  pos={130,15},frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
 
PopupMenu ccdf  value="root;"+PrintAllDataFolderNames(),title="      Select DataFolder: ",mode=1,bodyWidth=190, title="",fstyle=1, size={79,160},labelBack=(65280,43520,0),proc=popccdf,pos={110,7}
//SetVariable aa_ccdf  title=" ",value=$ss,limits={0,1,1},pos={130,7}
// ss=PrintAllDataFolderNames()
 //SetDataFolder root:ss
// Return ss
End

Function popccdf(cntrlName,popNum,popStr) : PopupMenuControl
 String cntrlName
 Variable popNum
 String popStr
 String varStr=popStr
 Variable varNum=popNum
 
 String st=popStr
// String kk=GetDataFolder(0)
//SVAR ExptName=globExptTitle
// NewDataFolder /O root:$ExptName
//print "...",GetDataFolder(1)
 if (stringmatch("root",st)>0)
 st=GetDataFolder(0)+" : "
 SetDataFolder root:
 print "IgorPro:> root:"
 else
 st="root:"+GetDataFolder(0)+":"
  SetDataFolder root:$popStr
  print "IgorPro:> root:",popStr
 endif
 
//ModifyPanel /W=CCDFwin  framestyle=0
//SetVariable aa_ccdf value=kk
End

Function /S Dmenuitem()
Variable itn
String st
//if (itn==1)
 st=GetDataFolder(0)
 if (stringmatch("root",st)>0)
 st="! "+GetDataFolder(0)+" : "
 else
 st="! "+"root:"+GetDataFolder(0)+" : "
 endif
Return st
End
//Function KillDFolder()
//String svDef=GetDataFolder(1)

Function  Bin_Data() 
 //  String RQ4data,Qzdata,ProSLDz,Proz //defl,sepdata1,veldata1   //calF
      
      Variable i,j,k,l
       
     String savDF=GetDataFolder(1)
//      Variable /G globrswitch=0
//      FitRgeneral3()
    String RQ4data=StrVarOrDefault ("globrqdata","")
    String Qzdata=StrVarOrDefault ("globqzdata","")    
    String drq4data=StrVarOrDefault ("globdrqdata","")
    String dqdata=StrVarOrDefault ("globdqdata","")    
    Variable NoBin=NumVarOrDefault("globnobin", 2)  

//     Variable SLDn=NumVarOrDefault("globvisco", 2.07)
 //    Variable SLDi=NumVarOrDefault("globdia", 5.67)
//  DoWindow RQ4vsQCal 
 //      if (V_Flag==0)
       
	Prompt  RQ4data, "Choose R Data:", popup, WaveList("*",";","")	
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("*",";","")	
	Prompt  drq4data, "Choose sigmaR Data:", popup, WaveList("*",";","")	
	Prompt  dqdata, "Choose sigmaQ Data:", popup, WaveList("*",";","")	
	Prompt  NoBin, "Number for binning:"
//	Prompt  SLDn, "Enter SLD of Substrate (E-06):"
 //      Prompt  SLDi, "Enter SLD of Incident Medium (E-06):"   

//        Prompt yn, "Did place cursors (1(y)/0(n))?"
	DoPrompt "RQ4(Only) from Given SLD Profile",RQ4data,Qzdata,drq4data,dqdata,NoBin//,SLDn, SLDi   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n

//	Variable/G globSLDn=SLDn    //Save for next time
//	Variable/G globSLDi=SLDi
      String/G globrqdata, globqzdata,globdrqdata,globdqdata
      Variable/G  globnobin=NoBin
 
	if (V_Flag)
	    return -1
	endif

	String rdatabin,qdatabin,drdatabin,dqdatabin
          	 rdatabin=(RQ4data+"_"+Num2Str(NoBin)+"B")
	 qdatabin=(Qzdata+"_"+Num2Str(NoBin)+"B")
	 drdatabin=(drq4data+"_"+Num2Str(NoBin)+"B")
	dqdatabin=(dqdata+"_"+Num2Str(NoBin)+"B")
	
   // Duplicate/O /D $RQ4data rdatabin2
     Duplicate/O /D $RQ4data rdatabin1
     Duplicate/O /D $Qzdata qdatabin1
     Duplicate/O /D $drq4data drdatabin1
     Duplicate/O /D $dqdata dqdatabin1
//     print qdatabin1
     Variable sqs,eqs,numqbin1=numpnts(qdatabin1)
       if (qdatabin1[0]>qdatabin1[numqbin1])
         sqs=numqbin1
         eqs=0
        else
         sqs=0
         eqs=numqbin1
       endif  
  //     print "*****",eqs,sqs,numqbin1
     	KillWaves /Z $rdatabin,$qdatabin,$drdatabin,$dqdatabin
    Make /O /N=1 rdatabin2, qdatabin2, drdatabin2,dqdatabin2
    WaveStats/Q /Z $RQ4data
      i=0
      k=0
      j=0
         rdatabin2=0
         qdatabin2=0
         drdatabin2=0
         dqdatabin2=0
         
if (NoBin <1)         //<<averaging has some problems near qc
//   Variable StartQ=sqs//NumVarOrDefault("globstartq", sqs)  
   Variable interQ=NumVarOrDefault("globinterq", 0.002)  
   
//    Prompt  StartQ, "Starting Value of Q:"
    Prompt  interQ, "Qbin interval:"
    DoPrompt "Constant Q Rebin (by linear interpolation)", interQ   //,StartQ    
    Variable /G globinterq=interQ//,globstartq=StartQ
    Variable jkjk=round(abs(qdatabin1[eqs]-qdatabin1[sqs])/interQ)
  Make /O /N=(jkjk) rdatabin2, qdatabin2, drdatabin2,dqdatabin2    
  print "*****",eqs,sqs,jkjk
          for (j=0;j<(jkjk);j=j+1 )  //Constant qbin using Igorpro's linear interpolation method
             rdatabin2[j]=interp(j*interQ+qdatabin1[sqs],qdatabin1,rdatabin1)
               qdatabin2[j]=interp(j*interQ+qdatabin1[sqs],qdatabin1,qdatabin1)
               drdatabin2[j]=interp(j*interQ+qdatabin1[sqs],qdatabin1,drdatabin1)
               dqdatabin2[j]=interp(j*interQ+qdatabin1[sqs],qdatabin1,dqdatabin1)
               i=i+1
          endfor
        deletepoints  jkjk-1,jkjk,rdatabin2
        deletepoints  jkjk-1,jkjk,qdatabin2
        deletepoints  jkjk-1, jkjk,drdatabin2
        deletepoints  jkjk-1,jkjk,dqdatabin2
        
 else        
         
          for (i=0;i<V_npnts;i=i+1)

	       if (k==NoBin)
	          k=0
	          j=j+1
	        endif
	        if (i>0&& k==0)
	         Insertpoints j, 1,rdatabin2
	         Insertpoints j, 1,qdatabin2
	         Insertpoints j, 1,drdatabin2
	         Insertpoints j, 1,dqdatabin2
	         endif
               rdatabin2[j]=rdatabin2[j]+rdatabin1[i]
               qdatabin2[j]=qdatabin2[j]+qdatabin1[i]
               drdatabin2[j]=sqrt(drdatabin2[j]^2+drdatabin1[i]^2)
               dqdatabin2[j]=sqrt(dqdatabin2[j]^2+dqdatabin1[i]^2)
                k=k+1
	       if (k==NoBin||i==V_npnts-1)
	         rdatabin2[j]=rdatabin2[j]/k
               qdatabin2[j]=qdatabin2[j]/k
               drdatabin2[j]=drdatabin2[j]/k
               dqdatabin2[j]=dqdatabin2[j]/k         
	       endif
          endfor
 endif         

       Duplicate/O /D rdatabin2 $rdatabin
       Duplicate/O /D qdatabin2 $qdatabin
       Duplicate/O /D drdatabin2 $drdatabin
       Duplicate/O /D dqdatabin2 $dqdatabin
	KillWaves rdatabin1, qdatabin1, drdatabin1,dqdatabin1
	KillWaves rdatabin2, qdatabin2, drdatabin2,dqdatabin2
End

Function  ParrattMain( ) 
   String RQ4data,Qzdata,ProSLDz,Proz //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)

     Variable SLDn=NumVarOrDefault("globSLDn", 2.07)
     Variable SLDi=NumVarOrDefault("globSLDi", 5.67)
//     Variable yn=NumVarOrDefault("globyn", 1)
 
    DoWindow RQ4vsQCal 
       if (V_Flag==0)
       
	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("RQ*",";","")	
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("Q*",";","")	
//	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("*",";","")	
//       Prompt yn, "Consider dQ (1(y)/0(n))?"	
	Prompt  ProSLDz, "Choose SLD Profile:", popup, WaveList("pro*",";","")	
	Prompt  Proz, "Choose Depth z:", popup, WaveList("z*",";","")	

	Prompt  SLDn, "Enter SLD of Substrate (E-06):"
       Prompt  SLDi, "Enter SLD of Incident Medium (E-06):"   

       
	DoPrompt "RQ4 from Given SLD Profile",RQ4data,Qzdata,ProSLDz,Proz,SLDn, SLDi   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
	else
	
		Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("RQ*",";","WIN:RQ4vsQCal")	
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("Q*",";","WIN:RQ4vsQCal")	
//	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("*",";","")	
//       Prompt yn, "Consider dQ (1(y)/0(n))?"  		
	Prompt  ProSLDz, "Choose SLD Profile:", popup, WaveList("pro*",";","")	
	Prompt  Proz, "Choose Depth z:", popup, WaveList("z*",";","")	

	Prompt  SLDn, "Enter SLD of Substrate (E-06):"
       Prompt  SLDi, "Enter SLD of Incident Medium (E-06):" 

//        Prompt yn, "Did place cursors (1(y)/0(n))?"
	DoPrompt "RQ4 from Given SLD Profile",RQ4data,Qzdata,ProSLDz,Proz,SLDn, SLDi   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
	endif
	
	Variable/G globSLDn=SLDn    //Save for next time
	Variable/G globSLDi=SLDi
//	Variable/G globyn=yn
//	String/G globrq4data=RQ4data
//      String/G globqzdata=Qzdata
	String/G  globprosldz=ProSLDz,globproz=Proz
	if (V_Flag)
	    return -1
	endif
//	Variable nad
//      String ss,ss1
//       sscanf defl,"%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]%d",ss,nad //str2num(nm)
//       if (nad==0)
//       sscanf defl,"%d%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]",nad,ss //str2num(nm)
//       endif
  //  String Rq_Fitname
//     String na=num2str(nad)
//     Rq_Fitname="RQ4cal"

     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $Qzdata Qzcal
//      Duplicate/O /D $dQdata dQcal
  
	//  WaveStats $Zpos
   Variable V_npnts=numpnts($Proz)
   Variable Ntot=V_npnts

   Rq_Fit=ParrattNTRNp(Qzcal,Ntot)
//print Rq_Fit
  String wname="RQ4vsQCal"
   //  	String wnameslip="FvsSSlipCal"+na
     	DoWindow $wname
 
       if (V_Flag==0)
 //    	Display f,fd1 vs ds1  
        Display  $RQ4data Rq_Fit vs $Qzdata
     	   Label left "RQ4"
          Label bottom "Q  (\U)"
          ModifyGraph  log(left)=1, mirror=1,minor=0,standoff=0,tick=2, mode($RQ4data)=3, marker($RQ4data)=5, rgb(Rq_Fit)=(0,0,65535), rgb($RQ4data)=(65280,0,26112), grid=1,gridRGB=(65280,54528,32768)

          DoWindow/C $wname
    
//      else
//           	DoWindow/F $wname
//           	DoWindow $wname
  
//             CheckDisplayed/W=$wname Rq_Fit
     
 //               if (V_flag==0)
 //              AppendToGraph/W=$("RQ4vsQCal")   $RQ4data Rq_Fit vs $Qzdata
 //              ModifyGraph/W=$("RQ4vsQCal")  rgb(Rq_Fit)=(0,0,65535) 
            
   
  //             endif
      endif
 

     KillWaves Qzcal
End


Function ParrattNTRNp(q,nt)  //: FitFunc // 1D fit: f (below) vs. h  w/o Gaussian Averaging
Variable q,nt
//NVAR SLD1g=globSLDn, SLDig=globSLDi

Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,i,dn, lamda,SLD1,SLDi,phi1,ko  //,SLDA,SLDB
SVAR hhh=globprosldz
Wave /D hh=$hhh
SVAR zz=globproz
Wave /D pz=$zz

//NVAR yn=globyn
//Variable yy=yn
  
    lamda=4.62

    SLD1=hh[nt-1]*1e-06//SLD1g*1e-06//5.69e-06//sapphire///4.14e-06  //Quartz   ////SLD for substrate

    SLDi=hh[0]*1e-06//SLDig*1e-06   /////SLD for incident medium

    ko=2*pi/lamda
    n1=rip(lamda,SLD1,0)//cmplx(1-SLD1*lamda^2/(2*pi),0)  

    ni= rip(lamda,SLDi,0)
//    dqq=sigmaq
//     print dq
//     if (yy<0.1)
//    dqq=0
//    endif
    
//    XGn=cmplx(0,0)
//    DGn=cmplx(0,0)
//    for (j=q-3*dqq;j<=q+3*dqq;j=j+sigmaq)

    phi1=asin(lamda*q/(4*pi))  //    dz=flmthickness/nolrs
    alpha=ni*cos(phi1)

    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)
    Xnp1=cmplx(0,0)
    dz=0
    for (i=nt-1;i>=0; i=i-1)   
//    z=pz[i]
    if (i==0)
    dz=(pz[1]-pz[0])/2
    elseif  (i==(nt-1))
    dz=(pz[i]-pz[i-1])/2
    else
    dz=((pz[i]-pz[i-1])+(pz[i+1]-pz[i]))/2
    endif
 
//    if (i==nt)
//    nn=ni
 //   else     
    nn= rip(lamda,hh[i]*1e-06,0)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
//    endif    
    kn=sqrt(ko^2*(nn^2-alpha^2))       //nn*ko*sin(phin)
    an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)
    Xn=an*((rn+Xnp1)/(1+rn*Xnp1))    //    Xn=an*((rn+Xnp1*anp1)/(1+rn*Xnp1*anp1))    
    Xnp1=Xn
    knp1=kn
    endfor //for i
//     XGn=XGn+Xn*DistGauss1(j,q,sigmaq)  //Gaussian average over flm thickness+-10A w/ sigma=4); need to find sigma and j for the thickness
//    DGn=DGn+DistGauss1(j,q,sigmaq)
//    endfor //for j
//  Xn=Xn*exp(-2*kn*sqrt(ko^2*(nnp1^2-(alpha^2))) *(20)^2)
    return magsqr(Xn)*q^4
End

////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////To calculate RQ^4 w/incoherent smear and sigmaQ Gaussian averaging /////////////////////
//////////Use subloutine ParrattNTRNdq() for reflectivity calculation //////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////                                                                                                ////////////////////////

Function  ParrattMaindq( ) 
 //  String ProSLDz,Proz //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
 //    String savDF=GetDataFolder(1)

//     Variable SLDn=NumVarOrDefault("globSLDn", 2.07)
//     Variable SLDi=NumVarOrDefault("globSLDi", 5.67)
     Variable yn=NumVarOrDefault("globyn", 1)
     Variable syn=NumVarOrDefault("globsyn", 60)     
         String RQ4data=StrVarOrDefault ("globrq4data","")
    String dRQ4data=StrVarOrDefault ("globdrq4data","")    
    String Qzdata=StrVarOrDefault ("globqzdata","")    
    String dQdata=StrVarOrDefault ("globdqdata","")   
    String ProSLDz=StrVarOrDefault ("globprosldz","")  
    String Proz=StrVarOrDefault ("globproz","")  

	Prompt  RQ4data, "Choose R(Q4) Data:", popup, WaveList("*",";","")	
	Prompt  dRQ4data, "Choose dR(Q4) Data:", popup, WaveList("*",";","")		
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("*",";","")	
	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("*",";","")	

	Prompt  ProSLDz, "Choose SLD Profile:", popup, WaveList("*",";","")	
	Prompt  Proz, "Choose Depth z:", popup, WaveList("*",";","")	
       Prompt yn, "Consider dQ (1(y)/0(n))?"	
       Prompt syn, "Consider incoherent smear (#A(y)/0(n))?"		
//	Prompt  SLDn, "Enter SLD of Substrate (E-06):"
//       Prompt  SLDi, "Enter SLD of Incident Medium (E-06):"   
   
	DoPrompt "R(Q4) from Given (odd # of ) SLD Profile ",ProSLDz,Proz//,SLDn, SLDi   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n///,RQ4data,dRQ4data,Qzdata,dQdata,,yn,syn
	
//	Variable/G globSLDn=SLDn    //Save for next time
	NVAR pfyn1=globpfyn,sf=globsf
	Variable/G globyn=yn
	Variable/G globsyn=syn
	String/G globrq4data=RQ4data
	String/G globdrq4data=dRQ4data
      String/G globqzdata=Qzdata
      String/G globdqdata=dqdata      

	String/G  globprosldz=ProSLDz,globproz=Proz
	Variable pfyn=pfyn1
	if (V_Flag)
	    return -1
	endif
	NVAR rswitch=globrswitch
         SVAR ExptTitle=globExptTitle
     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $RQ4data RQdata    
     Duplicate/O /D $dRQ4data dRQdata         
     Duplicate/O /D $Qzdata Qzcal
      Duplicate/O /D $dQdata dQcal
       Duplicate/O /D dRQdata  dRQtemp

   //    dRQtemp=sf*dRQdata
	//  WaveStats $Zpos
   Variable V_npnts=numpnts($Proz)
Variable datapoints=numpnts($RQ4data)
   Variable Ntot=V_npnts
   Variable xisqr,rxisqr
       
 //      Variable npd=numpnts(dQdata)
       for (i=0;i<datapoints;i=i+1)  //almost ignore negative data by resetting dQ=0.001 for calculation
        if (rswitch>0)
         if (RQdata[i]<=0 || dRQdata[i]<=0)
            dRQtemp[i]=2*abs(dRQdata[i])//1e-04*Qzcal[i]^4
         endif
        else
         if (RQdata[i]<=0 || dRQdata[i]<=0)
            dRQtemp[i]=2*abs(dRQdata[i])//1e-04
          endif
        endif
        endfor

   Rq_Fit=ParrattNTRNdq(Qzcal, dQcal,Ntot) //dQcal
   xisqr=0

         if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
 datapoints=abs(cursorb-cursora)+1
//Cursor /S=1 /W=NR#RQPlotInPanel A $RQ4data cursora
//Cursor /S=1 /W=NR#RQPlotInPanel B $RQ4data cursorb
RemoveFromGraph /Z  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs $Qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(6528,0,65280),lsize(Rq_Fit)=2
else
cursora=0
cursorb=datapoints-1
RemoveFromGraph /Z  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs $Qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(6528,0,65280),lsize(Rq_Fit)=2
endif
   for (i=cursora;i<(cursorb+1);i+=1)
  if (dRQdata[i]>0)// if (dRQdata[i]!=0) //  if (RQdata[i]>0&&dRQdata[i]>0)
   xisqr=xisqr+(RQdata[i]-Rq_Fit[i])^2/(dRQtemp[i])^2
   else
   
    xisqr=xisqr+(RQdata[i]-Rq_Fit[i])^2/(dRQtemp[i])^2
//   datapoints=datapoints-1
   endif
 // datapoints=datapoints-1
   endfor
   rxisqr=xisqr/datapoints
   Variable /G globV_chisq=xisqr,globnpntsdata=datapoints, globV_Rchisq=xisqr/(datapoints)
 
   print " Xi^2 = ",xisqr, " Xi^2/Ndatapnt = ",rxisqr
   
//print Rq_Fit
  String wname="RQ4vsQCal"
   //  	String wnameslip="FvsSSlipCal"+na
     	DoWindow $wname
 
       if (V_Flag==0)
 //    	Display f,fd1 vs ds1  
       DoWindow $ExptTitle
       if (V_flag==0)
        Display  $RQ4data Rq_Fit vs $Qzdata
     	   Label left "RQ4"
          Label bottom "Q\Bz\M  (\U)"
          ModifyGraph  log(left)=1, mirror=1,minor=0,standoff=0,tick=2, mode($RQ4data)=3, marker($RQ4data)=5, rgb(Rq_Fit)=(0,0,65535), rgb($RQ4data)=(65280,0,26112), grid=1,gridRGB=(65280,54528,32768)

          DoWindow/C $wname
         else 
         DoWindow /F $ExptTitle
         endif
      endif
 

     KillWaves /Z dRQtemp//Qzcal,dQcal,RQdata,dRQdata
End

Function crtQ_cal( )

NVAR n_lay1=globNLay
Variable n_lay=n_lay1
Wave w_fit
Variable lamda=4.62,SLDi=w_fit[0],SLDs=w_fit[n_lay+1]
Variable /D q, angl,si,ss,ni,ns
//lamda=lamda*1e-10
si=SLDi*1e-06
ss=SLDs*1e-06
ni=real(rip(lamda,si,0))
ns=real(rip(lamda,ss,0))
//print rip(lamda,si,0)
//print si,ss
if (ns/ni<=1 )
angl=acos(ns/ni)

else
print "no critical angle!"

endif

q=4*pi*sin(angl)/(lamda)
//print "critical angle =", angl*180/pi, "degrees"
print "Qc =", q, "Å^-2"
return q

END 

Function crt_theta_cal( )

NVAR n_lay1=globNLay
Variable n_lay=n_lay1
Wave w_fit
Variable lamda,SLDi=w_fit[0],SLDs=w_fit[n_lay+1]
Variable /D q, angl,si,ss,ni,ns
Prompt lamda," What is your wave length (Å)? "
DoPrompt "To Calculate Critical angle and Qc", lamda
//lamda=lamda*1e-10
si=SLDi*1e-06
ss=SLDs*1e-06
ni=real(rip(lamda,si,0))
ns=real(rip(lamda,ss,0))
//print rip(lamda,si,0)
//print si,ss
if (ns/ni<=1 )
angl=acos(ns/ni)

else
print "no critical angle!"

endif

q=4*pi*sin(angl)/(lamda)
print "critical angle =", angl*180/pi, "degrees"
print "Qc =", q, "Å^-2"
//return 0
END 


////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////                                                                                                                               //////////////////////////////////////////
Function ParrattNTRNdq(q,sigmaq,nt)  //: FitFunc // 1D fit: f (below) vs. h  w/ incoherence Gaussian Averaging  andw/ sigmaQ blurring
Variable q,nt,sigmaq
//NVAR SLD1g=globSLDn, SLDig=globSLDi
NVAR  syn1=globsyn,rswitch=globrswitch,sf1=globsf,ntlay1=globNpoint
Variable syn=syn1,sf=sf1,ntlay=ntlay1
Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,i,dn, lamda,j,jj,dqq,SLD1,SLDi,phi1,ko,XXGn,XDGn,XGn,DGn,sdqq,incsdqq,Rcal_out_result  //,SLDA,SLDB
SVAR hhh=globprosldz
Wave /D hh=$hhh
SVAR zz=globproz
SVAR ExptTitle=globExptTitle
Wave /D pz=$zz

NVAR yn=globyn
Variable yy=yn,incmhh
incmhh=hh[0]
Variable /G globcmplxcalyn
Variable cursora=-1//=strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))

if (syn>0)
Variable csrYN=strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))
//print strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))
    if (csrYN>0)
      cursora=pcsr(A, ExptTitle+"#SLDPlotInPanel")
   endif       
endif
//      if (globcmplxcalyn>1)
//      SVAR prof_IM1=globImSLDin
      Wave /D prof_IM//=$prof_IM1
//      endif
 // sigmaq=sigmaq*2
//for (i=0;i<nt;i=i+1)
//hh[i]=hh[i]-incmhh
//endfor

    lamda=4.62
    SLD1=hh[nt-1]*1e-06//SLD1g*1e-06//5.69e-06//sapphire///4.14e-06  //Quartz   ////SLD for substrate

    SLDi=hh[0]*1e-06//SLDig*1e-06   /////SLD for incident medium

    
    ko=2*pi/lamda
    n1=rip(lamda,SLD1,prof_IM[nt-1]*1e-06)//cmplx(1-SLD1*lamda^2/(2*pi),0)  

    ni= rip(lamda,SLDi,prof_IM[0]*1e-06)
    sdqq=0
    incsdqq=1
 //   sigmaq=sigmaq*2
    if (sigmaq<0.0005*abs(q))
     sigmaq=0.0005*abs(q)
   endif
    
    dqq=sigmaq

     if (yy<0.000000001)
    dqq=0

    else
    dqq=dqq*yy
    sigmaq=sigmaq*yy
      endif
    if (syn>0)
    sdqq=syn 
    incsdqq=syn//sigma for incoherent
    endif
    
    XXGn=0
    XDGn=0
    
//  for (jj= sdqq;jj<= (5*sdqq);jj=jj+incsdqq) 
  for (jj= (-2*sdqq);jj<= (2*sdqq);jj=jj+incsdqq/2)    //jj=jj+incsdqq/2)  

    XGn=0
    DGn=0
    for (j=q-2*dqq;j<=q+2*dqq;j=j+(sigmaq/2.5))

    phi1=asin(lamda*j/(4*pi))  //    dz=flmthickness/nolrs
///***     alpha=ni*(cos(asin(sin(phi1)/ni)))  <<< more accurate but not neccessary
    alpha=ni*cos(phi1/ni)  ///////03//03/2008 ni considered for phi1 ie., phi should be phi/ni in case of medium instead of air/// but will nor differ* other fit func need to be corrected******
    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)

    Xnp1=cmplx(0,0)
    dz=0
    for (i=nt-1;i>=0; i=i-1)   

        if (i==0)
        dz=(pz[1]-pz[0])/2
        elseif  (i==(nt-1))
        dz=(pz[i]-pz[i-1])/2
        else
        dz=((pz[i]-pz[i-1])+(pz[i+1]-pz[i]))/2
        endif
//        print csrYN
     if (syn>0)
       if (csrYN>0) 
          if (i==cursora)     //(ceil((nt-1)/2)-ceil(ntlay/10)))////
             dz=dz+jj
          endif
        else
            if(i==(ntlay-ceil(ntlay/10))||i==(2*ntlay-ceil(ntlay/10))||i==(3*ntlay-ceil(ntlay/10))||i==(4*ntlay-ceil(ntlay/10))||i==(5*ntlay-ceil(ntlay/10))||i==(6*ntlay-ceil(ntlay/10))||i==(7*ntlay-ceil(ntlay/10))||i==(8*ntlay-ceil(ntlay/10)))
              dz=dz+jj
            endif
        endif  
     endif
//     if (dz<=0)
//         dz=0
//     endif
    
  //    print (ceil((nt-1)/2)-ceil(ntlay/10))
 //    if (i>=18 && i<=40)
 //      dz=dz*((pz[40]-pz[18])+jj)/(pz[40]-pz[18])
 //     endif
  //   dz=dz*(pz[nt-1]+jj)/pz[nt-1]

    nn= rip(lamda,hh[i]*1e-06,prof_IM[i]*1e-06)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
  
    kn=sqrt(ko^2*(nn^2-alpha^2))       //nn*ko*sin(phin)
    an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)

    Xn=an*((rn+Xnp1)/(1+rn*Xnp1))    //    Xn=an*((rn+Xnp1*anp1)/(1+rn*Xnp1*anp1))    
    Xnp1=Xn
    knp1=kn
    endfor //for i
         XGn=XGn+magsqr(Xn)*DistGauss1(j,q,sigmaq)//Gaussian average over flm thickness+-10A w/ sigma=4); need to find sigma and j for the thickness
    DGn=DGn+DistGauss1(j,q,sigmaq)
     endfor //for j
     XXGn=XXGn+(XGn/DGn)*DistGauss1(jj,0,incsdqq)
     XDGn=XDGn+DistGauss1(jj,0,incsdqq)

//    XXGn=XXGn+(XGn/DGn)*DistGauss1(jj,(3*sdqq),incsdqq)
//     XDGn=XDGn+DistGauss1(jj,(3*sdqq),incsdqq)
     endfor //for//jj
   if (rswitch>0)
    Rcal_out_result= sf*(XXGn/XDGn)*q^4 //
    else
   Rcal_out_result= sf*(XXGn/XDGn)
    endif
    
   if (numtype (Rcal_out_result )==1)
   Rcal_out_result=1
   elseif (numtype (Rcal_out_result )==2)
    Rcal_out_result=0
   endif

 //  for (i=0;i<nt;i=i+1)
//  hh[i]=hh[i]+incmhh
 //  endfor

   
   return Rcal_out_result

End

///////////////                                                                                                                          /////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////




 Function /D /C rip(lamda,SLD,B)
     Variable lamda,SLD,B
     
     Variable /C rfr=cmplx(0,0)
     
     rfr=cmplx(1-SLD*lamda^2/(2*pi),lamda^2/(2*pi)*B)  //therfore B =im(SLD)=-crosssection*density(nuclei)/lamda

     return rfr
End          

Function  EMMainS( ) 
 //  String RQ4data,Qzdata,ProSLDz,Proz //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)
    String RQ4data=StrVarOrDefault ("globrq4data","")
    String Qzdata=StrVarOrDefault ("globqzdata","")    
    String ProSLDz=StrVarOrDefault ("grobprosldz","")
    String Proz=StrVarOrDefault ("grobproz","")    

//     Variable SLDn=NumVarOrDefault("globvisco", 2.07)
 //    Variable SLDi=NumVarOrDefault("globdia", 5.67)
  DoWindow RQ4vsQCal 
 //      if (V_Flag==0)
       
	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("*",";","")	
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("*",";","")	
	Prompt  ProSLDz, "Choose SLD Profile:", popup, WaveList("pro*",";","")	
	Prompt  Proz, "Choose Depth z:", popup, WaveList("z*",";","")	

//	Prompt  SLDn, "Enter SLD of Substrate (E-06):"
 //      Prompt  SLDi, "Enter SLD of Incident Medium (E-06):"   

//        Prompt yn, "Did place cursors (1(y)/0(n))?"
	DoPrompt "RQ4(Only) from Given SLD Profile",RQ4data,Qzdata,ProSLDz,Proz//,SLDn, SLDi   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n

//	Variable/G globSLDn=SLDn    //Save for next time
//	Variable/G globSLDi=SLDi
      String/G globrq4data, globqzdata
 	String/G globprosldz=ProSLDz,globproz=Proz
	if (V_Flag)
	    return -1
	endif
//	Variable nad
//      String ss,ss1
//       sscanf defl,"%[abc defghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]%d",ss,nad //str2num(nm)
//       if (nad==0)
//       sscanf defl,"%d%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]",nad,ss //str2num(nm)
//       endif
  //  String Rq_Fitname
//     String na=num2str(nad)
//     Rq_Fitname="RQ4cal"
     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $Qzdata Qzcal
  
	//  WaveStats $Zpos
   Variable V_npnts=numpnts($Proz)
   Variable Ntot=V_npnts
 //   Variable SLDn=NumVarOrDefault("globvisco", 2.07)
 //   Variable SLDi=NumVarOrDefault("globdia", 5.67)

   Rq_Fit=cMaxRp(Qzcal, Ntot)
//print Rq_Fit
  String wname="RQ4vsQCal"
   //  	String wnameslip="FvsSSlipCal"+na
     	DoWindow $wname
 
       if (V_Flag==10000)
        Display  $RQ4data Rq_Fit vs $Qzdata
     	   Label left "RQ4"
          Label bottom "Q (\U)"
          ModifyGraph  log(left)=1, mirror=1,minor=0,standoff=0,tick=2, mode($RQ4data)=3, marker($RQ4data)=5, rgb(Rq_Fit)=(0,0,65535), rgb($RQ4data)=(65280,0,26112), grid=1,gridRGB=(65280,54528,32768)

          DoWindow/C $wname
    
      endif
 

     KillWaves Qzcal
End


Function cMaxRp(q,nt)//: FitFunc
//	wave w
	Variable q,nt

 Variable i
  NVAR rswitch=globrswitch
  Variable  lamd,angle,vz
//  Variable Bangle
  Variable  /C n1,n2,nz,ns,ctheta   //,e1,e2
  Variable dz,zzd,zz1
  Variable  /C alpha,p1p,pfp,p1s,pfs,psi
  Variable dtype,rb,ko,sldA,sldB,sldS
  SVAR hhh=globprosldz
  Wave /D hh=$hhh
  SVAR zz=globproz
  Wave /D pz=$zz
  // KillWaves bmp,bms,ms,mp,fms,fmp,cms,cmp,cfms,cfmp
  lamd=4.62  //angstrng

  sldA=hh[nt-1]*1e-06//substrate

  sldS=hh[0]*1e-06//4.14e-06   //incident phase quartz
  //* Inputs */
//    e1=cmplx((1-sldS*lamd^2/(2*pi))^2,0)//1.429*1.429,0)3*1.3,0)
    n1=cmplx((1-sldS*lamd^2/(2*pi)),0)

//    e2=cmplx((1-sldA*lamd^2/(2*pi))^2,0)
    n2=cmplx((1-sldA*lamd^2/(2*pi)),0)

//* Initial values for the calculation */

    Make /D /C /O /N=(2,2) bmp,bms,ms,mp,fms,fmp,M_product

    alpha=(cmplx(0.,0))
    ctheta=cmplx(0,0)
    ko=2*pi/lamd

   angle=pi/2-asin(q*lamd/(4*pi)) //-0.00004
///***alpha=n1*(sin(angle))  << less accurate and thus the following is tried which considered a possible situation where the fronting medium is not air/vacuum,
///** and the BC at air/fronting was considered.
  alpha=n1*(sin(acos(cos(angle)/n1)))   
//    print alpha
//    print angle*180/(pi)
 
 //* Preparing numerical integration and matrix multiplication */ 
     ms[0][0]=cmplx(1,0)
     ms[0][1]=cmplx(0,0)
     ms[1][0]=cmplx(0,0)
     ms[1][1]=cmplx(1,0)

     mp[0][0]=cmplx(1,0)
     mp[0][1]=cmplx(0,0)
     mp[1][0]=cmplx(0,0)
     mp[1][1]=cmplx(1,0)

//     zz=0      eps=e1

      i=0

 		for(i=0;i<=nt-1;i=i+1)
                   if (i==0)
                   dz=(pz[1]-pz[0])/2
                   elseif  (i==(nt-1))
                   dz=(pz[i]-pz[i-1])/2
                   else
                     dz=((pz[i]-pz[i-1])+(pz[i+1]-pz[i]))/2
                    endif
	//	       dz=(pz[i]-pz[i-1])

			ns= rip(lamd,hh[i]*1e-06,0)
			ctheta=cos(asin(alpha/ns))

		       psi=(ko*ns*dz*ctheta)
// /*  without matrix approx. */

			      bms[0][0]=cmplx(1,0)*cos(psi)
				bmp[0][0]=cmplx(1,0)*cos(psi)
				bms[1][1]=cmplx(1,0)*cos(psi)
				bmp[1][1]=cmplx(1,0)*cos(psi)

                          bms[1][0]=cmplx(0,-1)*sin(psi)*ns*ctheta				
                          bmp[1][0]=cmplx(0,-1)*sin(psi)*ctheta/ns
			       bms[0][1]=cmplx(0,-1)*sin(psi)/(ns*ctheta)
			       bmp[0][1]=cmplx(0,-1)*sin(psi)*ns/ctheta
			       
			       matrixmultiply ms,bms
			       fms=M_product
			       ms=fms
			       matrixmultiply mp,bmp
			       fmp=M_product
			       mp=fmp

		   endfor	   

		p1s=n1*cos(angle)//sqrt(e1-alpha2)
		pfs=n1*cos(asin(alpha/n2))//sqrt(e2-alpha2)
		p1p=cos(angle)/n1//sqrt(1-alpha2/e1)/sqrt(e1)
		pfp=cos(asin(alpha/n2))/n1//sqrt(1-alpha2/e2)/sqrt(e2)
  // print q
		rb=creflneutrm(p1p,p1s,pfp,pfs,fmp,fms)	

KillWaves bmp,bms,ms,mp,fms,fmp,M_product
   if (rswitch>0)
     return rb*q^4 //
    else
     return rb
    endif

//  return rb*q^4
  End
  

  Function creflneutrm(pip,pis,prp,prs,Cmatrixp,Cmatrixs)

	Wave /C Cmatrixp,Cmatrixs
	Variable /C pip,pis,prp,prs

	Variable /C aaus, aads,aas, aaup,aadp,aap
 //       Variable /C aabb,apbp,ccdd,cpdp
//	Variable A,B,C,D
	Variable RatiorpsR,RatiorpsI,Ratioo
	Variable rp1,rp2,rs2,rs1,phip,phip1,phip2,phis,phis1,phis2,rhop,rhos
	Variable rho,dphi
        Variable sn,pm
       
       aaup= Cmatrixp[0][0]*pip-Cmatrixp[1][1]*prp+Cmatrixp[0][1]*pip*prp-Cmatrixp[1][0]  
       aadp=  Cmatrixp[0][0]*pip+Cmatrixp[1][1]*prp+Cmatrixp[0][1]*pip*prp+Cmatrixp[1][0]   
       aap=aaup/aadp
        
       aaus=Cmatrixs[0][0]*pis-Cmatrixs[1][1]*prs+Cmatrixs[0][1]*pis*prs-Cmatrixs[1][0]
       aads=Cmatrixs[0][0]*pis+Cmatrixs[1][1]*prs+Cmatrixs[0][1]*pis*prs+Cmatrixs[1][0]
       aas=aaus/aads
       
      rhop=(magsqr(aap))
      rhos=(magsqr(aas))
            
      phip2=arctan1p(Real(aadp),Imag(aadp))
      phip1=arctan1p(Real(aaup),Imag(aaup))
     
      phip=phip1-phip2
      phis2=arctan1p(Real(aads),Imag(aads))
      phis1=arctan1p(Real(aaus),Imag(aaus))
      phis=phis1-phis2     
      print phip*180/pi,rhop,phis*180/pi,rhos

//        pm=0.027 //phase shift due to modul. crystal
 //       dphi=abs(phip-phis) //0.65*0.10+pm)  //phase shift due to glass cell strain (vacuum) + modul crystal

	 rho=(rhop+rhos)/2
//        rho=RatiorpsI*cos(pm)
  
	return rho
END

Function arctan1p(ar,ai)
  Variable ar, ai
  
	Variable c
      c=0.
	if (ai >=0) 
	c=atan2(ai,ar) 
	endif
	if (ai == 0 && ar < 0) 
	c=pi  
	endif
	if (ai < 0) 
	c=atan2(ai,ar)+2*pi  
	endif
	return c
End

Function DistGauss1(x1,u,s)
Variable x1,u,s

Variable z1,G1

       z1=(x1-u)/s
       G1=1/(sqrt(2*pi)*s)*exp(-(z1^2)/2)//*s  ///<<===????
 //      G1=cmplx(G1,0)
// print G     
return G1
END
 
 Function FitNTRN(w,q): FitFunc  ///Do not use this function ; need to be checked!!!!!!!!!!!!!!!!!!!!!!!
Wave w; Variable q

Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,n2,n2A,n2B//,phin,phinp1
Variable z,dz,i,dn, lamda,xi,flmthickness,nolrs,vc,M,redt,SLDA,SLDB,SLDS,SLD1,phi1,ko,j,h
    
    lamda=4.62

    SLD1=5.69e-06//sapphire///4.14e-06  //Quartz
    SLDA=1.89e-06//P2VP///1.8e-06//PVP///6.45e-06  //D2O
    SLDB=1.41e-06//PS///6.64e-06//d-PS///1.43e-06  //BPic
    SLDS=5.67e-06//d-toluene
    //SLDS=0.65e-06//toluene
   // redt=0.08/(273.15+37)//20/(273.15+37)//1.12/(273.15+37)///
   // xi=5.2/redt^(0.632)
    ko=2*pi/lamda
    n1=rip(lamda,SLD1,0)//cmplx(1-SLD1*lamda^2/(2*pi),0)  
    n2A=rip(lamda,SLDA,0)//cmplx(1-SLDA*lamda^2/(2*pi),0)  
    n2B=rip(lamda,SLDB,0)//cmplx(1-SLDB*lamda^2/(2*pi),0)  
    n2=rip(lamda,SLDS,0)//cmplx(1-SLDS*lamda^2/(2*pi),0)  
  //  n2=sqrt(vc*n2A^2+(1-vc)*n2B^2)
    
    phi1=asin(lamda*q/(4*pi))
    nolrs=80
    flmthickness=1200
    dz=flmthickness/nolrs
    alpha=n1*cos(phi1)

    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)
    Xnp1=cmplx(0,0)

    for (i=0;i<=nolrs; i=i+1)   
    z=i*dz//-dz/2    
//    if (i<=nolrs/2)
//    j=i
//    else
//    j=nolrs-i
 //   w[i]=w[j]
 //   endif

    if (i==nolrs)
    nn=n1
    else    
//    if (i>=nolrs/2)
//    h=w[nolrs-i-1]
//   else
    h=w[i]    
//    endif
//    if (i>=nolrs/2-w[nolrs] || i<=nolrs/2+w[nolrs] -1)
//    h=SLDS/1e-06
//    endif
    h=abs(h)
    w[i]=h 
    nn=rip(lamda,h*1e-06,0)//cmplx(w[i],0)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
    endif    
    kn=sqrt(ko^2*(nn^2-alpha^2))       //nn*ko*sin(phin)
    an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)
    Xn=an*((rn+Xnp1)/(1+rn*Xnp1))    //    Xn=an*((rn+Xnp1*anp1)/(1+rn*Xnp1*anp1))    
    Xnp1=Xn
    knp1=kn
    endfor
 // Xn=Xn*exp(-2*kn*sqrt(ko^2*(nnp1^2-(alpha^2))) *(20)^2)
    
    return magsqr(Xn)*q^4
End

Function ProfExp(hn,hn1,an,dsn,cas,xx)
Variable hn,hn1,an,dsn,xx,cas

Variable y

if (cas==0) //even
y=(hn-hn1)*exp(-(xx-an)^2/dsn^2)+hn1  //dsn=dsn ,hn1=h(n-1)
else
y=(hn1-hn)*exp(-(xx-an)^2/dsn^2)+hn 
endif

return y
End


///Fit function w/ profile generator
///Make waveforfit (w[i]) nl+2 for (height inc/ substrates)/nl+1 for size of each layers/nl+1 for ratio, an/sigma.
Function EProfileS(w,nl,nopntalayer)//, q)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable nopntalayer,nl
//Variable q//,sigmaq,nt

 Variable i,j,k,m,nn,n,td,ad,vertexstr//,nopntalayer=10,nl=6  //nopntalayer=#of sublayers of each component(eg,PS) 
 nn=(nl)*10
Make /O /D /N=((nl+1)*nopntalayer +1+(nl+1)) prof,zz  //+(nl+1)
Make /O /D /N=(nl+1) aa
 k=1

 m=1

 vertexstr=1
//td=w[29]
aa[0]=0//w[7]
prof[0]=w[0]
zz[0]=0
  for (i=vertexstr;i<=(nl+1);i=i+1)
      if (i>vertexstr)
        ad=1
       else
       ad=0
      endif
        
        aa[i]=ad*(w[(3*nl+3)+(i-1)])+w[(nl+1)+i]+aa[i-1]
      
      for (j=0; j<=nopntalayer-1; j=j+1)
//      for (mm=1; mm<=2;mm=mm+1)
       if ( m==0)
          zz[k]=zz[k-1]+(w[(nl+1)+i]*0.1*((nopntalayer-1)-j+1)/(5*(nopntalayer/10)^2+0.5*(nopntalayer/10)))//46.5//21
          prof[k]=ProfExp(w[i],w[i-1],aa[i],w[(nl+1)+i]/w[2*(nl+1)+i],m,zz[k])
  //        if (i>ceil((nl+1)/2)
  //         prof[k]=ProfExp(w[i],w[i-1],aa[i],w[(nl+1)+i]/w[2*(nl+1)+i],m,zz[k])
       elseif ( m==1)
    //       aa[i]=aa[i-1]-ad*w[(3*nl+3)+(i-1)]
           zz[k]=zz[k-1]+w[(nl+1)+i]*0.1*(j+1)/(5*(nopntalayer/10)^2+0.5*(nopntalayer/10))//21//(5.5)
           prof[k]=ProfExp(w[i],w[i-1],aa[(i-1)]+ad*w[(3*nl+3)+(i-1)],w[(nl+1)+i]/w[2*(nl+1)+i],m,zz[k])   
        endif
       

       if ( j==nopntalayer-1)
        k=k+1
       zz[k]=zz[k-1]+w[(3*nl+3)+i]
       prof[k]=prof[k-1]
       endif

        k=k+1
//      aa[i]=aa[i-1]+ad*w[(3*nl+3)+(i-1)] 
        endfor         
      m=m+1
      if (m==2)
      m=0
//      if (i>3&& i< 5)
//      m=m+1
//      endif    
      endif
  endfor

  return 1
  End
        
Function  EJMainS( ) 
   String ProPara//defl,sepdata1,veldata1   //calF
      
//   Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)
     Variable NoLayerwoSub=NumVarOrDefault("globNoLayerwoSub", 6)
     Variable NoPperlayer=NumVarOrDefault("globNoPperlayer", 10)

       
	Prompt  ProPara, "Choose the wave for Exp parameters:", popup, WaveList("w*",";","")	

	Prompt  NoLayerwoSub, "How many # of layers except substrates?:"
       Prompt  NoPperlayer, "How many points in a layer?"   

       
	DoPrompt "IN nl+2 Ht; nl+1size; nl+1a/sig; nl+1flat tkns: OUT prof vs. zz",ProPara,NoLayerwoSub,NoPperlayer  //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
	
	Variable/G globNoLayerwoSub=NoLayerwoSub    //Save for next time
	Variable/G globNoPperlayer=NoPperlayer

	if (V_Flag)
	    return -1
	endif

     Duplicate/O /D $ProPara PrPa

   EProfileS(PrPa,NoLayerwoSub,NoPperlayer)

     KillWaves PrPa
End

Function  B4Efit( ) 
   String Qdata
   String sigmaQdata //defl,sepdata1,veldata1   //calF
     String savDF=GetDataFolder(1)
//     Variable NoLayerwoSub=NumVarOrDefault("globNoLayerwoSub", 6)
//     Variable NoPperlayer=NumVarOrDefault("globNoPperlayer", 10)

       
	Prompt  Qdata, "Choose the Q data:", popup, WaveList("Q*",";","")	

	Prompt  sigmaQdata, "Choose the Q data:", popup, WaveList("sigmaQ*",";","")
//       Prompt  NoPperlayer, "How many points in a layer?"   

       
	DoPrompt "To Globlize Q & SigmaQ data For Fitting",Qdata, sigmaQdata  //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
	String/G globq4fit=Qdata
      String/G globdq4fit=sigmaQdata
	if (V_Flag)
	    return -1
	endif

//     Duplicate/O /D $ProPara PrPa
       End
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////       
 //Dialog function for Parratt Fit with sigmaQ and EProfile Model////Odd # of profile points +1extra (substrate)///////
Function  ParrattFitMaindqS( )  ///Works for 6layers w/symetry
   String RQ4data,dRQ4data,Qzdata,dQdata,www //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)

     Variable Nlay=NumVarOrDefault("globNlay", 6)
     Variable Npoint=NumVarOrDefault("globNpoint", 10)
//     Variable yn=NumVarOrDefault("globyn", 1)
     Variable syn=NumVarOrDefault("globsyn", 200)
          Variable nsi=NumVarOrDefault("globnsi", 2) 
          Variable ssi=NumVarOrDefault("globssi", 2) 
     
    DoWindow RQ4vsQCalFitE 
//       if (V_Flag==0)
       
	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("RQ*",";","")	
	Prompt  dRQ4data, "Choose dRQ4 Data:", popup, WaveList("sigRQ*",";","")		
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("Q*",";","")	
	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("sigmaQ*",";","")	
	Prompt  www, "Choose Adjtbl Paramters:", popup, WaveList("w*",";","")	
	 Prompt syn, "Consider incoherent smear (#(y)/0(n))?"		
//       Prompt yn, "Consider dQ (1(y)/0(n))?"	
       Prompt nsi, "How many # of symetric interface?"	     
       Prompt ssi, "Which interface starts the symetry from bottom?"	                    
	Prompt  Nlay, "How many layers except subs?"
       Prompt  Npoint, "How many points per layer?"   
 

       
	DoPrompt "Fit w/ Exp SLD profile",RQ4data,dRQ4data,Qzdata,dQdata,www,syn,nsi,ssi,Nlay,Npoint//,yn   //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
//	else
	
//	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	
//	Prompt  dRQ4data, "Choose dRQ4 Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")		
//	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	
//	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	

//	Prompt  www, "Choose Adjtbl Paramters:", popup, WaveList("*",";","")		
//       Prompt yn, "Consider dQ (1(y)/0(n))?"	     	
//       Prompt nsi, "How many # of symetric interface?"	    
//       Prompt ssi, "Which interface starts the symetry from bottom?"	           
//	Prompt  Nlay, "How many layers except subs?"
//       Prompt  Npoint, "How many points per layer?"   
  
	


//	DoPrompt "Fit w/ Exp SLD profile",RQ4data,dRQ4data,Qzdata,dQdata,www,yn,nsi,ssi,Nlay, Npoint     //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
//	endif
	
//	Variable/G globSLDn=SLDn    //Save for next time
//	Variable/G globSLDi=SLDi
	Variable/G globNlay=Nlay    //Save for next time
	Variable/G globNpoint=Npoint	
	Variable/G globsyn=syn
//	Variable/G globyn=yn
	Variable/G globnsi=nsi
	Variable/G globssi=ssi	
//	String/G globrq4data=RQ4data
//	String/G globdrq4data=dRQ4data	
      String/G globqzdata=Qzdata
      String/G globdqata=dqdata      
//	String/G  globprosldz=ProSLDz,globproz=Proz
	String/G  globwww=www
	if (V_Flag)
	    return -1
	endif
//	Variable nad
//      String ss,ss1
//       sscanf defl,"%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]%d",ss,nad //str2num(nm)
//       if (nad==0)
//       sscanf defl,"%d%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]",nad,ss //str2num(nm)
//       endif
  //  String Rq_Fitname
//     String na=num2str(nad)
//     Rq_Fitname="RQ4cal"
     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $RQ4data RQdata    
     Duplicate/O /D $dRQ4data dRQdata         
//     Duplicate/O /D $Qzdata Qzcal
//     Duplicate/O /D $dQdata dQcal
     Duplicate/O /D $www W_coef  
	//  WaveStats $Zpos
///For symtric case///////////////////////////////////////////////////////////////////////////////////////////
	Variable ii,jj,kk
Make /O /D /N=((((Nlay+2)+(Nlay+1)+(Nlay+1)+Nlay+1)-4*(nsi))) tempw  //for symetric sub-interfaces
jj=1
kk=0
tempw[0]=W_coef[0]
for (kk=0;kk<=3;kk=kk+1)
 for (ii=(kk*(Nlay+1)+1);ii<=((kk+1)*(Nlay+1));ii=ii+1)
 if (ii <((kk+1)*(Nlay+1)-(ssi-1)-(nsi-1)) || ii >((kk+1)*(Nlay+1)-(ssi-1)))
 tempw[jj]=W_coef[ii]
//print jj,tempw[jj]
 jj=jj+1
 endif
 endfor
 endfor
//tempw[((((Nlay+2)+(Nlay+1)+(Nlay+1)+Nlay+1)-4*(nsi)))]=1
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
   Variable/G globNtot=((nlay+1)*Npoint +1+(nlay+1))//Npoint+1+(Nlay+1)
 //  Variable xisqr
 Variable V_npnts=numpnts($www)
 Variable nopara=V_npnts
//   xisqr=0
//   for (i=0;i<Ntot;i+=1)
//   xisqr=xisqr+(RQdata[i]-Rq_Fit[i])^2/(dRQdata[i])^2
//   endfor
//   xisqr=xisqr/Ntot
//   print " Xi^2/Npnt = ",xisqr
   
//print Rq_Fit
  String wname="RQ4vsQCalFitE"
 
 Make/O/T/N=6 T_Constraints
T_Constraints[0] = {"K0>= 5.66", "K0<= 5.8","K3>= 0.94","K7>=3", "K8<= 2.7","K9>= 2.7"}//"K0<= 6.0", "K0>= 5.6", "K3>= 0.94"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}


 FuncFit /H="0000000000000"  EProfile4FitS tempw RQdata /W=dRQdata  /I=1 /D=Rq_Fit /E=w_fiteps /C=T_Constraints
 // FuncFit EProfile4FitS tempw RQdata /W=dRQdata  /I=1 /D=Rq_Fit /C=T_Constraints [pcsr(A),pcsr(B)] 

   KillWaves tempw,aa//,T_Constraints
     KillWaves RQdata,dRQdata//,Rq_Fit,Qzcal,dQcal
End
//To generate E profile and fit data using Ecoeff Wave. //Run B4Efit first
Function EProfile4FitS(tempw,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave tempw
Variable qq//,nopntalayer,nl
//Variable /G globyn=1
//Variable q//,sigmaq,nt
NVAR nt1=globNtot, nl1=globNlay, np1=globNpoint, syn1=globsyn,nsi1=globnsi,ssi1=globssi//, yn1=globyn
Variable nt=nt1, nl=nl1, nopntalayer=np1,syn=syn1,nsi=nsi1,ssi=ssi1//,yn=yn1
SVAR qqq=globqzdata
SVAR dddq=globdqata
Wave q4f=$qqq
Wave dq4f=$dddq
Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
//String prof1, zz1


//SVAR prof2=//Variable

 Variable i,j,k,y,m,nn11,n,td,ad//,nopntalayer=10,nl=6  //nopntalayer=#of sublayers of each component(eg,PS) 
 nn11=(nl)*10
Make /O /D /N=((nl+1)*nopntalayer +1+(nl+1)) prof,zz  //+(nl+1)
Make /O /D /N=(nl+1) aa
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Make /O /D /N=(((nl+2)+(nl+1)+(nl+1)+nl)+1) w_fit  //for semi-symetric profile temp
Variable ii,jj,kk//,ratio
jj=0
//ratio=tempw[(((nl+2)+(nl+1)+(nl+1)+nl+1)+1)]
 for (ii=0;ii<=((nl+1)-nsi);ii=ii+1)
 if (ii <((nl+1)-nsi))  //5
 w_fit[jj]=tempw[ii]
   jj=jj+1
 else
 do
  w_fit[jj]=tempw[ii-(jj-(ceil(((nl+1+1-0.1)+0)/2)-1))]  //ceil(x) smallest interger larger than x
  jj=jj+1
 while (jj<=(1*(nl+1)))
// w_fit[(nl+1)]=tempw[((nl+1)-nsi)]
//  jj=jj+1
 endif
 endfor
 
 for (kk=1;kk<=2;kk=kk+1)
 for (ii=(kk*((nl+1)-nsi)+1);ii<=((kk+1)*((nl+1)-nsi));ii=ii+1)
// if (ii <=((kk+1)*((nl+1)-nsi))) //10
 w_fit[jj]=tempw[ii]
   jj=jj+1
// else 
 endfor
  do
  w_fit[jj]=tempw[ii-(jj-(ceil(((kk+1)*(nl+1)+(kk*(nl+1))+1+0.1)/2-1)))]  //ceil(x) smallest interger larger than x
  jj=jj+1
 while  (jj<=(((kk+1)*(nl+1))))

// endif
// endfor
 endfor
 
 k=3
  for (ii=(kk*((nl+1)-nsi)+1);ii<=((kk+1)*((nl+1)-nsi));ii=ii+1)
// if (ii <((kk+1)*((nl+1)-nsi+1))) //10
  w_fit[jj]=tempw[ii]
   jj=jj+1
 //   else 
 endfor
  do
  w_fit[jj]=tempw[ii-(jj-(ceil(((kk+1)*(nl+1)+(kk*(nl+1))+1+0.1)/2)))-2] 
  jj=jj+1     //ceil(x) smallest interger larger than x/  jj=jj+1
 while  (jj<=((kk+1)*(nl+1))-1) 
 w_fit[((kk+1)*(nl+1))]=10//tempw[((kk+1)*((nl+1)-nsi+1))]
// endif
// endfor
 
// for (i=0;i<=24;i=i+1)
// print i,w_fit[i]
// endfor
// return 0
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 k=1
 
 m=1   //for symetric 5 layers+subs    0 for semismetry 6 layers eg, si/silane/pvp/ps/tol/ps/pvp/s
 w_fit=abs(w_fit)
//td=w[29]
aa[0]=0//w[7]
prof[0]=w_fit[0]
zz[0]=0
  for (i=1;i<=(nl+1);i=i+1)
      if (i>1)
        ad=1
       else
       ad=0
      endif
        
      aa[i]=ad*(w_fit[(3*nl+3)+(i-1)])+w_fit[(nl+1)+i]+aa[i-1]
      
      for (j=0; j<=nopntalayer-1; j=j+1)
//      for (mm=1; mm<=2;mm=mm+1)

       if ( m==0)
          zz[k]=zz[k-1]+((w_fit[(nl+1)+i]*0.1*((nopntalayer-1)-j+1)/(5*(nopntalayer/10)^2+0.5*(nopntalayer/10))))//46.5//21
          prof[k]=ProfExp(w_fit[i],w_fit[i-1],aa[i],w_fit[(nl+1)+i]/w_fit[2*(nl+1)+i],m,zz[k])
  //        if (i>ceil((nl+1)/2)
  //         prof[k]=ProfExp(w[i],w[i-1],aa[i],w[(nl+1)+i]/w[2*(nl+1)+i],m,zz[k])
       elseif ( m==1)
    //       aa[i]=aa[i-1]-ad*w[(3*nl+3)+(i-1)]
           zz[k]=zz[k-1]+(w_fit[(nl+1)+i]*0.1*(j+1)/(5*(nopntalayer/10)^2+0.5*(nopntalayer/10)))//21//(5.5)
           prof[k]=ProfExp(w_fit[i],w_fit[i-1],aa[(i-1)]+ad*w_fit[(3*nl+3)+(i-1)],w_fit[(nl+1)+i]/w_fit[2*(nl+1)+i],m,zz[k])   
        endif
        if (j==nopntalayer-1)
        k=k+1
       zz[k]=zz[k-1]+(w_fit[(3*nl+3)+i])
        prof[k]=prof[k-1]
       endif
        k=k+1
//      aa[i]=aa[i-1]+ad*w[(3*nl+3)+(i-1)] 
        endfor         
      m=m+1
      if (m==2)
      m=0
//      if (i>3&& i< 5)
//      m=m+1
//      endif    
      endif
  endfor
//NVAR SLD1g=globSLDn, SLDig=globSLDi

Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,dn, lamda,sdqq,dqq,SLD1,SLDi,phi1,ko,XXGn,XDGn,XGn,DGn,incsdqq  //,SLDA,SLDB
//Duplicate /O /D prof hh
//Duplicate /O /D zz pz

//print q, sigmaq, yn  
    lamda=4.62
//   print hh[3]
//    return 1
    SLD1=prof[nt-1]*1e-06//SLD1g*1e-06//5.69e-06//sapphire///4.14e-06  //Quartz   ////SLD for substrate

    SLDi=prof[0]*1e-06//SLDig*1e-06   /////SLD for incident medium

    ko=2*pi/lamda
    n1=rip(lamda,SLD1,0)//cmplx(1-SLD1*lamda^2/(2*pi),0)  

    ni= rip(lamda,SLDi,0)
    dqq=sigmaq
    sdqq=0
    incsdqq=1

//     if (yn<0.1)
//    dqq=0
//    endif
    if (syn>0)
    sdqq=syn 
    incsdqq=syn//sigma for incoherent
    endif
    
    XXGn=0
    XDGn=0
    for (jj= sdqq;jj<= (sdqq*5);jj=jj+incsdqq) 
   
    XGn=0
    DGn=0
   
    for (j=q-2*dqq;j<=q+2*dqq;j=j+sigmaq)  

    phi1=asin(lamda*j/(4*pi))  //    dz=flmthickness/nolrs
    alpha=ni*cos(phi1)

    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)
    Xnp1=cmplx(0,0)
    dz=0
    for (i=nt-1;i>=0; i=i-1)   
//    z=pz[i]
//if ( i>(ceil(nt/2)))
//       dz=zz[i]-zz[i-1]
    if (i==(ceil((nt)/2)))
    dz=((zz[i]-zz[(i-1)])+(zz[i+1]-zz[i]))/2+jj
    elseif (i==(nt-1)) 
    dz=(zz[nt-1]-zz[nt-2])/2
    elseif ( i==0)
    dz=(zz[1]-zz[0])/2
     else
    dz=((zz[i]-zz[(i-1)])+(zz[i+1]-zz[i]))/2
    endif
 
//    if (i==nt)
//    nn=ni
 //   else     
    nn= rip(lamda,prof[i]*1e-06,0)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
//    endif    
    kn=sqrt(ko^2*(nn^2-alpha^2))       //nn*ko*sin(phin)
    an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)
    Xn=an*((rn+Xnp1)/(1+rn*Xnp1))    //    Xn=an*((rn+Xnp1*anp1)/(1+rn*Xnp1*anp1))    
    Xnp1=Xn
    knp1=kn
    endfor //for i
     XGn=XGn+magsqr(Xn)*DistGauss1(j,q,sigmaq)//Gaussian average over flm thickness+-10A w/ sigma=4); need to find sigma and j for the thickness
    DGn=DGn+DistGauss1(j,q,sigmaq)
     endfor //for j
     XXGn=XXGn+(XGn/DGn)*DistGauss1(jj,(3*sdqq),incsdqq)
     XDGn=XDGn+DistGauss1(jj,(3*sdqq),incsdqq)
     endfor //for//jj
//  Xn=Xn*exp(-2*kn*sqrt(ko^2*(nnp1^2-(alpha^2))) *(20)^2)
//    XGn=magsqr(XGn
    return (XXGn/XDGn)*q^4 //
End                                                                            
//////////////                                                                                                                                                   //////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////same as ParrattFitMaindq but for model independent fitting by using sld as adjustible parameters///////////////////
//////////////////////Odd # of profile points (no z)////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////                                                                                                                                    /////////////////////////////////

 //Dialog function for Parratt Fit with sigmaQ and EProfile Model
Function  ParrattFitMaindqSIndeM( )  ///Works for 6layers w/symetry
   String RQ4data,dRQ4data,Qzdata,dQdata,www //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)

     Variable Nlay=NumVarOrDefault("globNlay", 6)
     Variable Npoint=NumVarOrDefault("globNpoint", 10)
     Variable yn=NumVarOrDefault("globyn", 1)
     Variable syn=NumVarOrDefault("globsyn", 200)
      Variable ssyn=NumVarOrDefault("globssyn", 1)
     Variable thick=NumVarOrDefault("globthick", 5)
    Variable pfyn=NumVarOrDefault("globfpyn", 0)
     
    DoWindow RQ4vsQCalFitE 
//       if (V_Flag==0)
       
	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("RQ*",";","")	
	Prompt  dRQ4data, "Choose dRQ4 Data:", popup, WaveList("sigRQ*",";","")		
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("Q*",";","")	
	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("sigmaQ*",";","")	
	Prompt  www, "Choose Adjtbl Parameters:", popup, WaveList("p*",";","")	
	 Prompt syn, "Consider incoherent smear (#(y)/0(n))?"		
       Prompt yn, "Consider dQ (1(y)/0(n))?"	
	 Prompt ssyn, "Is the interface symetric (1(y)/0(n))?"		
	  Prompt thick, "Scale for thickness (eg. 1)?"	
	  Prompt pfyn, "Did you cursor for region fitting (1(y)/0(n))?"		  

       
	DoPrompt "Fit w/ Abtr SLD profile",RQ4data,dRQ4data,Qzdata,dQdata,www,syn,yn,ssyn,thick,pfyn  //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
//	else
	
//	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	
//	Prompt  dRQ4data, "Choose dRQ4 Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")		
//	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	
//	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("*",";","WIN:RQ4vsQCalFitE")	

//	Prompt  www, "Choose Adjtbl Paramters:", popup, WaveList("*",";","")		
//       Prompt yn, "Consider dQ (1(y)/0(n))?"	     	
//       Prompt nsi, "How many # of symetric interface?"	    
//       Prompt ssi, "Which interface starts the symetry from bottom?"	           
//	Prompt  Nlay, "How many layers except subs?"
//       Prompt  Npoint, "How many points per layer?"   
  
	


//	DoPrompt "Fit w/ Exp SLD profile",RQ4data,dRQ4data,Qzdata,dQdata,www,yn,nsi,ssi,Nlay, Npoint     //sepdata1,veldata1,sl,n,dg,yn//,vel,,n
//	endif
	
//	Variable/G globSLDn=SLDn    //Save for next time
//	Variable/G globSLDi=SLDi
//	Variable/G globNlay=Nlay    //Save for next time

	Variable/G globsyn=syn
	Variable/G globyn=yn
	Variable/G globssyn=ssyn	
	Variable/G globpfyn=pfyn	

      String/G globqzdata=Qzdata
      String/G globdqata=dqdata      
//	Variable/G globnsi=nsi
//	Variable/G globssi=ssi	
//	String/G  globwww=www
	if (V_Flag)
	    return -1
	endif
//	Variable nad
//      String ss,ss1
//       sscanf defl,"%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]%d",ss,nad //str2num(nm)
//       if (nad==0)
//       sscanf defl,"%d%[abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ]",nad,ss //str2num(nm)
//       endif
  //  String Rq_Fitname
//     String na=num2str(nad)
//     Rq_Fitname="RQ4cal"
     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $RQ4data RQdata    
     Duplicate/O /D $dRQ4data dRQdata         
//     Duplicate/O /D $Qzdata Qzcal
//     Duplicate/O /D $dQdata dQcal
     Duplicate/O /D $www W_coef  
	//  WaveStats $Zpos
///For symtric case///////////////////////////////////////////////////////////////////////////////////////////

Variable/G globNpoint=(ceil(numpnts($www)/2)-1)  ///only for this case
 
 Variable nopara=globNpoint
  Make /O /D /N=(nopara+2) tempw 
	Variable ii,jj,kk
	if (ssyn>0)
	   for (i=0;i<=(nopara);i=i+1)
         tempw[i]=W_coef[i]
 //        print tempw[i]
         endfor
       endif
//           if (thick<0.1)
//           thick=1
//           endif
     tempw[(nopara+1)]=thick   // scaling factor for total thickness
 
//print Rq_Fit
  String wname="RQ4vsQCalFitE"
 
// Make/O/T/N=2 T_Constraints
//T_Constraints[0] = {"K0 >=5.66","K8 <= 5.8"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
if (pfyn==1)
 FuncFit  /H="10000000000000000000000000000000000000000000000000000000000000000"  EProfile4FitSIndeM tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=profeps  /I=1 /D=Rq_Fit ///C=T_Constraints
else
 FuncFit  /H="10000000000000000000000000000000000000000000000000000000000000000"  EProfile4FitSIndeM tempw RQdata /W=dRQdata /E=profeps  /I=1 /D=Rq_Fit ///C=T_Constraints
endif
 // FuncFit EProfile4FitS tempw RQdata /W=dRQdata  /I=1 /D=Rq_Fit /C=T_Constraints
      thick=  tempw[(nopara+1)]
	 Variable/G globthick=thick    
 //  KillWaves tempw//,aa//,T_Constraints
     KillWaves RQdata,dRQdata//,Rq_Fit,Qzcal,dQcal

End
//To generate E profile and fit data using Ecoeff Wave. //Run B4Efit first
Function EProfile4FitSIndeM(w,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable qq//,nopntalayer,nl
//Variable /G globyn=1
//Variable q//,sigmaq,nt
NVAR nt1=globNpoint, syn1=globsyn, yn1=globyn, ssyn1=globssyn
Variable nt=nt1,syn=syn1,yn=yn1,ssyn=ssyn1
SVAR qqq=globqzdata
SVAR dddq=globdqata
Wave q4f=$qqq
Wave dq4f=$dddq

Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable i,j,k,y,m,nn11,n,td,ad//,nopntalayer=10,nl=6  //nopntalayer=#of sublayers of each component(eg,PS) 
Variable ii,jj,kk
Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,dn,dp, lamda,sdqq,dqq,SLD1,SLDi,phi1,ko,XXGn,XDGn,XGn,DGn,incsdqq  //,SLDA,SLDB
    lamda=4.62
    Make /O /D /N=(2*nt+1) prof,zz,dzz//,dprof  //+(nl+1)
  //  dprof[0]=prof[0]
  //  dzz[0]=0
  
      dqq=sigmaq
    sdqq=0
    incsdqq=1
    
     if (yn<0.1)
    dqq=0
    endif
    if (syn>0)
    sdqq=syn 
    incsdqq=syn//sigma for incoherent
    endif
    
  dp=0
  zz[0]=0

//  w[0]=5.67
 if (w[0]<(5.67-0.0567))
     w[0]=5.67-0.0567
     elseif (w[0]>(5.67+0.0567))
     w[0]=5.67+0.0567
  endif
  prof[0]=w[0]

  if (ssyn==1)
    for (i=0;i<=(nt);i=i+1)
  //  if (w[i]<0.98 )
//  w[i]=abs(abs(w[i])-0.5)
  //  endif
    if (abs(w[i])>20)
     w[i]=w[i]/1000
    endif
    prof[i]=abs(w[i])
    if (i<nt/2)
    dp=10 
    else
    dp=10//abs(w[i]-w[i-1])
    endif
//       if (dp>100)
//       dp=100
//       elseif (dp<0.01)
//       dp=0.01
//       endif

     if (i==0)
     dzz[i]=abs(w[nt+1])*dp/2
     zz[i]=0
     else
      dzz[i]=abs(w[nt+1])*dp
      zz[i]=zz[i-1]+dzz[i]
     endif
      endfor
//        dzz[0]=abs(w[nt+1])*dp/2
      for (i=(nt+1);i<=(2*nt);i=i+1)
       prof[i]=prof[((2*nt)-i)]

       dzz[i]=dzz[((2*nt)-i)]
  
       if (i==(2*nt))
       zz[i]=zz[i-1]+dzz[0]*2   /// For dzz[1], the equal thickness of profile slabs are assumed.
       else
       zz[i]=zz[i-1]+dzz[i]
       endif
      endfor
  endif
 //   zz[2*nt]=zz[2*nt-1]+10
 //   prof[2*nt]=prof[(2*nt-1)]
    
    SLD1=prof[(2*nt)]*1e-06//SLD1g*1e-06//5.69e-06//sapphire///4.14e-06  //Quartz   ////SLD for substrate

    SLDi=prof[0]*1e-06//SLDig*1e-06   /////SLD for incident medium

    ko=2*pi/lamda
    n1=rip(lamda,SLD1,0)//cmplx(1-SLD1*lamda^2/(2*pi),0)  

    ni= rip(lamda,SLDi,0)

    XXGn=0
    XDGn=0
    for (jj= (sdqq);jj<= (5*sdqq);jj=jj+incsdqq) 
   
    XGn=0
    DGn=0
   
    for (j=q-2*dqq;j<=q+2*dqq;j=j+sigmaq)  

    phi1=asin(lamda*j/(4*pi))  //    dz=flmthickness/nolrs
    alpha=ni*cos(phi1)

    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)
    Xnp1=cmplx(0,0)
    dz=0
    for (i=(2*nt);i>=0; i=i-1)   
// //    z=pz[i]
        if (i==0)
        dz=(zz[1]-zz[0])/2
        elseif  (i==(2*nt))
        dz=(zz[i]-zz[i-1])/2
        else
        dz=((zz[i]-zz[i-1])+(zz[i+1]-zz[i]))/2
        endif
    
       if (i==(ceil(nt)))
        dz=dz+jj
       endif
    nn= rip(lamda,prof[i]*1e-06,0)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
//    endif    
    kn=sqrt(ko^2*(nn^2-alpha^2))       //nn*ko*sin(phin)
    an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)
    Xn=an*((rn+Xnp1)/(1+rn*Xnp1))    //    Xn=an*((rn+Xnp1*anp1)/(1+rn*Xnp1*anp1))    
    Xnp1=Xn
    knp1=kn
//    if (real(Xn)>1)
//     Xn=cmplx(1,imag(Xn))
//     elseif (real(Xn)<01)
//     Xn=cmplx(0,imag(Xn))
//     endif
    endfor //for i
  
  //Gaussian average over flm thickness+-10A w/ sigma=4); need to find sigma and j for the thickness
    DGn=DGn+DistGauss1(j,q,sigmaq)
     endfor //for j
     XXGn=XXGn+(XGn/DGn)*DistGauss1(jj,(3*sdqq),incsdqq)
     XDGn=XDGn+DistGauss1(jj,(3*sdqq),incsdqq)
     endfor //for//jj
//  Xn=Xn*exp(-2*kn*sqrt(ko^2*(nnp1^2-(alpha^2))) *(20)^2)
//    XGn=magsqr(XGn
    return (XXGn/XDGn)*q^4 //
End

////////////////////////                                                                                                                                   //////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////same as ParrattFitMaindq but for general fitting by                                                  ///////////////////
//////////////////////Odd # of profile points (no z)////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////                                                                                                                                    /////////////////////////////////

 //Dialog function for Parratt Fit with sigmaQ and EProfile Model
Function  FitRgeneral( )  ///Works for 6layers w/symetry
   String RQ4data,dRQ4data,Qzdata,dQdata,www //defl,sepdata1,veldata1   //calF
      
      Variable r,b,i,v1,z0,df0
       
     String savDF=GetDataFolder(1)

     Variable Nlay=NumVarOrDefault("globNlay", 6)
     Variable Npoint=NumVarOrDefault("globNpoint", 10)
     Variable yn=NumVarOrDefault("globyn", 1)
     Variable syn=NumVarOrDefault("globsyn", 200)
      Variable ssyn=NumVarOrDefault("globssyn", 1)
     Variable thick=NumVarOrDefault("globthick", 5)
    Variable pfyn=NumVarOrDefault("globfpyn", 0)
     
DoWindow RQ4vsQCalFitE 
//       if (V_Flag==0)
       
	Prompt  RQ4data, "Choose RQ4 Data:", popup, WaveList("RQ*",";","")	
	Prompt  dRQ4data, "Choose dRQ4 Data:", popup, WaveList("sigRQ*",";","")		
	Prompt  Qzdata, "Choose Q Data:", popup, WaveList("Q*",";","")	
	Prompt  dQdata, "Choose dQ Data:", popup, WaveList("sigmaQ*",";","")	
	Prompt  www, "Choose Adjtbl Paramters:", popup, WaveList("w*",";","")	
	 Prompt syn, "Consider incoherent smear (#(y)/0(n))?"		
       Prompt yn, "Consider dQ (1(y)/0(n))?"	
	  Prompt pfyn, "Did you cursor for region fitting (1(y)/0(n))?"		 
	 Prompt  Nlay, "How many layers except subs?" 
       Prompt  Npoint, "How many points per layer?"   


	DoPrompt "Fit w/ Abtr SLD profile",RQ4data,dRQ4data,Qzdata,dQdata,www,syn,yn,pfyn,Nlay,Npoint  //sepdata1,veldata1,sl,n,dg,yn//,vel,,n


	Variable/G globsyn=syn
	Variable/G globyn=yn

	Variable/G globpfyn=pfyn	
	Variable/G globNpoint=Npoint	
	Variable/G globNlay=Nlay	
	String/G globrq4data=RQ4data
	String/G globdrq4data=dRQ4data
      String/G globqzdata=Qzdata
      String/G globdqata=dqdata      
	String/G  globwww=www

	if (V_Flag)
	    return -1
	endif

     Duplicate/O /D $RQ4data Rq_Fit
     Duplicate/O /D $RQ4data RQdata    
     Duplicate/O /D $dRQ4data dRQdata         

     Duplicate/O /D $www W_coef  
	//  WaveStats $Zpos
///For symtric case///////////////////////////////////////////////////////////////////////////////////////////

Variable/G globNpara=(numpnts($www))  ///only for this case
 
 Variable nopara=globNpara
  Make /O /D /N=(nopara) tempw,weps1
  Make /O /T /N=(nopara) namepara
  weps1=0.01
  tempw=0
	Variable ii,jj,kk
//	if (ssyn>0)
	   for (i=0;i<nopara;i=i+1)
         tempw[i]=W_coef[i]
  //       print tempw[i]
         endfor
  //     endif

  //   tempw[(nopara+1)]=thick   // scaling factor for total thickness
 
//DoWindow/T RA0,"  Reflectivity Anals              J. Cho"
//  String wname="RQ4vsQCalFitE"
  String wname="RQ4vsQCal"
     	DoWindow $wname
//Display/HOST=# $globrq4data vs $globqzdata
       if (V_Flag==0)
        Display  $RQ4data Rq_Fit vs $Qzdata
     	   Label left "RQ4"
          Label bottom "Q  (\U)"
          ModifyGraph  log(left)=1, mirror=1,minor=0,standoff=0,tick=2, mode($RQ4data)=3, marker($RQ4data)=5, rgb(Rq_Fit)=(0,0,65535), rgb($RQ4data)=(65280,0,26112), grid=1,gridRGB=(65280,54528,32768)

          DoWindow/C $wname
 
      endif
// Execute "RAWin()"  //    
if (Nlay==1)
   Make/O/T/N=4 T_Constraints
  T_Constraints[0] = {"K3 <=K5/4","K4 <= K5/4","K3 >=1","K4 >=1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
   if (pfyn==1)
   FuncFit  /H="000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
   else
   FuncFit  /H="101000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
   endif
elseif (Nlay==2)
   Make/O/T/N=7 T_Constraints
   T_Constraints[0] = {"K4<=K7/4","K5 <= K7/4","K5 <= K8/4","K6 <= K8/4","K4 >1","K5 >1","K6 >1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
  if (pfyn==1)
   FuncFit  /H="000000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
  else
   FuncFit  /H="100100000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
  endif
  elseif (Nlay==3)
   Make/O/T/N=10 T_Constraints
   T_Constraints[0] = {"K5 <=K9/4","K6 <= K9/4","K6 <= K10/4","K7 <= K10/4","K7 <= K11/4","K8 <= K11/4","K5 >1","K6 >1","K7 >1","K8 >1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
  if (pfyn==1)
   FuncFit  /H="000000000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
  else
   FuncFit  /H="100010000000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
  endif
  elseif (Nlay==4)
   Make/O/T/N=13 T_Constraints
   T_Constraints[0] = {"K6 <=K11/4","K7 <= K11/4","K7 <= K12/4","K8 <= K12/4","K8 <= K13/4","K9 <= K13/4","K9 <= K14/4","K10 <= K14/4","K6 >1","K7 >1","K8 >1","K9 >1","K10>1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
  if (pfyn==1)
   FuncFit  /H="000000000000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
  else
   FuncFit  /H="100001000000000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
  endif
  elseif (Nlay==5)
   Make/O/T/N=(16+2*7+3*2) T_Constraints
T_Constraints[0] = {"K3 >0","K4 >0","K5 >0","K3 <5","K4 < 5","K5 <5","K1 <K5","K1 > K5","K2 <K4","K2 > K4","K7 <K12","K7 > K12","K8 <K11","K8 > K11","K9 <K10","K9 > K10","K13 <K17","K13 > K17","K14 <K16","K14 > K16"}//"K8 <= K14/4","K 
T_Constraints[20] = {"K7 <=K13/4","K8 <= K13/4","K8 <= K14/4","K9 <= K14/4","K9 <= K15/4","K10 <= K15/4","K10 <= K16/4","K11 <= K16/4","K11 <= K17/4","K12 <= K17/4","K7 >1","K8 >1","K9 >1","K10 >1","K11>1","K12>1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
  if (pfyn==1)
   FuncFit  /H="000000000000000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
  else
   FuncFit  /H="100000100000000000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
  endif
    elseif (Nlay==6)
   Make/O/T/N=19 T_Constraints
   T_Constraints[0] = {"K8 <=K15/4","K9 <= K15/4","K9 <= K16/4","K10 <= K16/4","K10 <= K17/4","K11 <= K17/4","K11 <= K18/4","K12 <= K18/4","K12 <= K19/4","K13 <= K19/4","K13 <= K20/4","K14 <= K20/4","K8 >1","K9 >1","K10 >1","K11 >1","K12>1","K13>1","K14>1"}//,"K6 >= 0"}//,"K6 <= K8"}//,"K5 >= 0","K6 >= 0","K7 >= 0","K8 >= 0"}
//T_Constraints[0] = {"K2<6","K3<6","K4<6","K5<6","K6<6","K7<6","K8<6","K9<6","K10<6","K11<6","K12<6","K7 >= 3","K8 >= 3","K9 >=3"}//"K27 > 0","K23=K27","K24=K26"}

//?  /H="100000000000000000000000000000000" 
  if (pfyn==1)
   FuncFit  /H="000000000000000000000"  Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQdata /E=weps  /I=1 /D=Rq_Fit ///C=T_Constraints
  else
   FuncFit  /H="100000010000000000000"  Profile4Fit tempw RQdata /W=dRQdata /E=weps1  /I=1 /D=Rq_Fit  /C=T_Constraints
  endif
 endif

 // FuncFit EProfile4FitS tempw RQdata /W=dRQdata  /I=1 /D=Rq_Fit /C=T_Constraints
//      thick=  tempw[(nopara +1)]
//	 Variable/G globthick=thick    

//   KillWaves tempw//,aa//,T_Constraints
     KillWaves dRQdata//,RQdata,//,Rq_Fit,Qzcal,dQcal

End
//To generate E profile and fit data using Ecoeff Wave. //Run B4Efit first
Function Profile4Fit(w,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable qq//,nopntalayer,nl
 
 Variable V_chisq
//Variable /G globyn=1
//Variable q//,sigmaq,nt
NVAR  npt1=globNpoint, syn1=globsyn, yn1=globyn,npara1=globNpara,lay1=globNlay//, sf=globsf//, ssyn1=globssyn
Variable npt=npt1, npara=npara1,syn=syn1,yn=yn1,lay=lay1//,ssyn=ssyn1
SVAR qqq=globqzdata
SVAR dddq=globdqdata
//SVAR dddr=globdrq4data
SVAR fitfun1=globfitfun
String /G globprew
NVAR s2sld1=globStop2SLD
//SVAR df=globweps

 Variable /G globautoR,globautowav
 

Wave q4f=$qqq
Wave dq4f=$dddq

Wave /D fitfun=$fitfun1//, w1=tempw
//Wave /D prew=$prew1

Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable i,j,k,y,m,nn11,n,td,ad//,nopntalayer=10,nl=6  //nopntalayer=#of sublayers of each component(eg,PS) 
Variable ii,jj,kk,notp,Rq_Fitout,deltad
Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,dn,dp, lamda,sdqq,dqq,SLD1,SLDi,phi1,ko,XXGn,XDGn,XGn,DGn,incsdqq,zzorg,Erfv //,SLDA,SLDB
//    lamda=4.62
//Rq_Fitout=0
    notp=npt*(lay+1)+1 //No. of total points
    Make /O /D /N=(notp) prof,zz//,dprof  //+(nl+1)
    String/G  globprosldz="prof",globproz="zz"
   Make /O /D /N=(npara) weps1//,prew
   String/G globprew
   Make /O /D /N=(npara) $globprew
   Wave /D prew=$globprew
    	String/G  globweps="weps1"//,globprew="prew"
    	Variable Rq_Fitpre=NumVarOrDefault("globRq_Fitpre", 1)
 //   	Variable /G globStop2SLD
   // 	Make /O /N=(lay+1) $fitfun
 //   	    String/G  globfitfun="fitfun"
//    	fitfun=0 //default values (erf) for functions
//    prew=1
    Variable /G globsf
    
 //   Variable sf=sf1
    Variable sf=w[npara-1]
    
//Wave drr4f=$dddr
//Wave dRQ_temp
     //     dRQ_temp=sf*drr4f    
    
    Variable/G  cslay //massnorm=0,//=10000
//   Make /O/N=(lay+1) cslay1=10000
    Variable inn

    globsf=sf
     npara=npara-1
     
Variable /G globcmplxcalyn

Wave /D im_SLD_in//=$im_SLD_in1

Make  /O /D /N=(notp) prof_IM
 
//  for (i=(lay+1)+2;i<=(2*(lay+1));i=i+1)
//   w[i]=abs(w[i])
//   endfor

// Variable temp15=w[15]   
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////building a model profile against z /////////////////////////////////////////
   if (abs(w[npara-(2*lay+1)])<10)
     zz[0]=-abs(w[npara-(2*lay+1)])*2-10
   elseif (abs(w[npara-(2*lay+1)])>100)
    zz[0]=-abs(w[npara-(2*lay+1)])*2-100
    else
    zz[0]=-abs(w[npara-(2*lay+1)])*3
   endif
    zz[1]=-abs(w[npara-(2*lay+1)])*2 //initial point move back to 2times of sigma (of the first layer)

    ii=1
    for (i=0;i<=(lay);i=i+1)  // # of interfaces is no. of layers +1
     //  w[npara-(2*lay+1)+i]=abs(w[npara-(2*lay+1)+i])
    if (abs(w[npara-(2*lay+1)+i])<1e-04) //to elliminate a bug when a becomes 0
    w[npara-(2*lay+1)+i]=1e-04///*sign(w[npara-(2*lay+1)+i])
    endif
//  if (fitfun[ii]!=8)   
    for (j=1; j<=(npt);j=j+1)   //improved the SLD profile builder
  
        if (j==1&&i!=0)
          zz[ii]=zz[ii-1]+(zz[ii-1]-zz[ii-2])
        elseif (j<npt-1)
          if (i==0&&ii==1)
          else
          zz[ii]=zz[ii-1]+(4*w[npara-(2*lay+1)+i])/(npt-2)
          endif
        elseif(j==npt-1)
          zz[ii]=zz[i*npt+1]+4*w[npara-(2*lay+1)+i]
        else
          zz[ii]=zz[ii-1]+((w[npara-lay+i]-2*(w[npara-(2*lay+1)+i]+w[npara-(2*lay+1)+1+i])))/2
        endif
      ii=ii+1
    endfor  // j endfor
//   else //  If the interfacial function is  a slpine function...
   //    zz[notp-2]=zz[notp-3]+ abs(w[npara-(1*lay+1)])*2  // add the last point of SLD
   if (abs(w[npara-(1*lay+1)])<10)
       zz[notp-1]=zz[notp-2]+10
    elseif (abs(w[npara-(1*lay+1)])>100)
    zz[notp-1]=zz[notp-2]+100
    else
       zz[notp-1]=zz[notp-2]+ abs(w[npara-(1*lay+1)]) // add the last point of SLD
   endif 
     
     
  // endif //endif (fitfun[i]!=8)
  endfor
     ii=1
     zzorg=0
    for (i=0;i<=(lay);i=i+1)

      if (i>0)
       zzorg=zzorg+w[npara-(lay-(i-1))]
      endif

      for (j=1; j<=(npt);j=j+1)
       if (fitfun[i]==0)

          Erfv=(erf((zz[ii]-zzorg)/((w[(lay+2)+i])))/2+0.5) //modifying erf adaptable to profile

       elseif (fitfun[i]==1)
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          else
          Erfv=exp((-(((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/((w[(lay+2)+i])))^2)/2) //leftGaussian
          endif
       elseif (fitfun[i]==2)
          if ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=1-exp((-(((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/((w[(lay+2)+i])))^2)/2) //rightGaussian
          endif
       elseif (fitfun[i]==3)
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=1-((((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/(4*abs(w[(lay+2)+i])))^2) //leftParabola 
          endif
       elseif (fitfun[i]==4)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=((((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/(4*(w[(lay+2)+i])))^2) //rightParabola
          endif
      elseif (fitfun[i]==5)         
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=exp((-(abs((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/((w[(lay+2)+i])))))  //leftExp
          endif
       elseif (fitfun[i]==6)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=1-exp((-(((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/((w[(lay+2)+i]))))) //rightExp
          endif
        elseif (fitfun[i]==7)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
         Erfv=((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/(4*(w[(lay+2)+i])) //Linear
          endif  
        elseif (fitfun[i]==8)     
         if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=MyOwn(zz[ii],zzorg,(w[(lay+2)+i]))
          endif  
  //       elseif (fitfun[i]==9)     
   //      if (cslay>9999)  //figure out which interface is cspline...
   //          cslay=i
     //       endif   
   //           cslay1[i]=i //ith interface; spline on
           
//         if ((zz[ii]-zzorg)>0)//2*(w[(lay+2)+i]))    //
//          Erfv=1
//          elseif ((zz[ii]-zzorg)<0)//-2*(w[(lay+2)+i]))
 //         Erfv=0
 //         else       
  //          Erfv=0.5
           // Erfv=(erf((zz[ii]-zzorg)/((w[(lay+2)+i])))/2+0.5) //error func
 //         endif  
        endif          
  //     Erfv=abs(Erfv)
       prof[ii]=w[i]*(1-Erfv)+w[i+1]*(Erfv)
      if (globcmplxcalyn>1)
      
      prof_IM[ii]=im_SLD_in[i]*(1-Erfv)+im_SLD_in[i+1]*(Erfv)
      else
      prof_IM[ii]=0
      endif
   //    if (prof[ii]>10)   //
  //    prof[ii]=10        // <<<=== specify maximum SLD !!!!??
  //     endif                //
       ii=ii+1
      endfor
    endfor
// zz[0]=-w[npara-(2*lay+1)]*3//-w[npara-(2*lay+1)]/10
//  zz[1]=-w[npara-(2*lay+1)]*2//-w[npara-(2*lay+1)]/10
   prof[0]=w[0]
    prof_IM[0]=im_SLD_in[0]
  prof_IM[(notp-1)]=im_SLD_in[(lay+1)]

  prof[(notp-1)]=w[(lay+1)] // sld of substrate
    // w[15]  =  temp15
  
       if (cslay>0)  //Cubic Slpine Smoothing all the interface no matter which interface has this function...
        
     //    Make /O/N=(4) profcs//,zzcs
    //     Make /O/N=(npt*(lay+1)+1) proftemp,zztemp
         Duplicate/O zz zztemp
         Duplicate/O prof proftemp
   
        Interpolate2/T=2/N=(npt*(lay+1)+1)/F=1 /Y=proftemp/X=zztemp  zz,prof //[cslay*npt,(cslay+1)*npt]
             for (inn=0;inn<=(npt*(lay+1));inn=inn+1)
                 prof[inn]=proftemp[inn]   
                 zz[inn]=zztemp[inn]      
             endfor
        //     Numx2SLD()
        //      ConstdzSLD() 
       KillWaves proftemp,zztemp
  //       smooth/E=2 7,proftemp
   //     Duplicate/O proftemp prof
   //     Duplicate/O zztemp, zz
    //       prof[0]=w[0]
  //  prof_IM[0]=im_SLD_in[0]
 // prof_IM[(notp-1)]=im_SLD_in[(lay+1)]

// prof[(notp-1)]=w[(lay+1)] // sld of substrate

   //       for (inn=0;inn<=(npt*(lay+1));inn=inn+1)
    //         prof[inn]=proftemp[inn]
             
    //     endfor
    //     ConstdzSLD() 
//       prof[0]=w[0]
//       prof[(notp-1)]=w[(lay+1)] // sld of substrate

       endif
  //      Smooth/E=2 13, prof
  //      Variable ci
//        for (ci=cslay*npt+1;ci<=(cslay+1)*npt;ci=ci+1)
 //      prof[ci]=profcs[ci]
//       zz[ci]=zzcs[ci]
    //    endfor
   //     KillWaves  zzcs,profcs,zztemp,proftemp
  //    endif
 //   Variable /G globmass
 //  Integrate/METH=1 prof/X=zz/D=prof_INT
 //  globmass=(1351.16+prof_INT[60])/5.66

 if (s2sld1==1)
   s2sld1=0
 return 0
 endif
//   endif  // end if for the # of layers >=1

 /////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// String/G  globImSLDin="im_SLD_in",globImSLDout="im_SLD_out" 
String/G  globImSLDin="prof_IM"

if (globautoR>0&&globautowav>0)
// if (stringmatch(dddq,"SelectData")==1)
//  Wave dQ_Fit1=SimdQ_Pre_Cal,Qz_Fit1=SimQ_Pre_Cal
// else
  Wave dQ_Fit1=$dddq+"_Pre_Cal",Qz_Fit1=$qqq+"_Pre_Cal"
// endif
Rq_Fitout=ParrattNTRNdq(Qz_Fit1, dQ_Fit1,notp)
else
Rq_Fitout=ParrattNTRNdq(q, sigmaq,notp)
endif
//  for (i=0;i<=(lay);i=i+1)  // # of interfaces is no. of layers +1
//     w[npara-(2*lay+1)+i]=abs(w[npara-(2*lay+1)+i])
//  endfor

//print Rq_Fitout
npara=npara+1
   	Variable/G globRq_Fitpre=Rq_Fitpre

for (i=0;i<npara;i=i+1)
deltad=(w[i]-prew[i])

weps1[i]=(Rq_Fitout-Rq_Fitpre)/(deltad)//(Rq_Fitout-weps1[i])/(deltad)
//return 0
prew[i]=w[i]
 

//if (weps1[i]>1)
//weps1[i]=1
//endif
if (abs(weps1[i])<1e-06)
weps1[i]=1e-06*sign(weps1[i])
endif
if (abs(weps1[i])>1e+06)
weps1[i]=1e+06*sign(weps1[i])
endif

endfor
Rq_Fitpre=Rq_Fitout
//print V_chisq
//V_chisq=V_chisq/(sf*sf)
    return Rq_Fitout //
End
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

Function CCSMfit1() //To fit SYmetric or Asym for ccell geometry.NLay=5(sym),6(asymw/Si),7(symw/tail),8(Asymw/Si&tail)
//String cntrlName

Variable/G globpfyn,globNpara,globNlay,globNpoint,globcmplxcalyn
String/G globwww,globT_Constraints_temp,globrq4data,globdrq4data,globqzdata//, globprew
SVAR checkhold1=globcheckhold
SVAR ExptTitle=globExptTitle
NVAR  syn1=globsyn,rswitch=globrswitch
Variable /G globsf//incohenrent smearing length
Variable pfyn=globpfyn,nopara=globNpara,Nlay=globNlay,syn=syn1,Npoint_per_Lay=globNpoint//,sf=sf1
String w_fit_temp=globwww,TC_temp=globT_Constraints_temp//,weps=globweps
String rdata=globrq4data, drdata=globdrq4data, qzdata1=globqzdata
Wave checkhold=$checkhold1
Wave w_fit=$w_fit_temp,RQdata=$rdata,dRQdata=$drdata, qzdata=$qzdata1
Wave /T  T_Constraints_temp=$TC_temp
 Variable mnm=NumVarOrDefault("massnorm", 1)
 DoWindow /N AdvanceFit

  Prompt  mnm, "Intg[beta(solvent)-beta(z)] (for all z) = ?"   

       
	DoPrompt "SLDmass for mass conservation:",mnm
  
	if (V_Flag|| NLay<5 ||NLay>9)
	    return -1
	endif
Variable /G massnorm=mnm
Variable /G cslay=0
Variable i,j,k
String holdstring,holdstring1=""
print "*****", ExptTitle, "Fitting Started .....................................................................v v v v v"
 Duplicate /O T_Constraints_temp T_Constraints_temp_temp
// if (cmpstr(cntrlName,"rst1")==0)
// FitRgeneral2()
// endif
SetWindow $ExptTitle hook=$" " //kwTopWin
  Make /O/D/N=((NLay-Ceil(NLay/2))*3+4)  tempw1,checkholdc
Duplicate /O w_fit tempw
if (NLay>0)
 for (i=0;i<NLay;i=i+1)
   if (w_fit[2*NLay+3+i]<2*(w_fit[NLay+2+i]+w_fit[NLay+3+i]))
     w_fit[2*NLay+3+i]=2*(w_fit[NLay+2+i]+w_fit[NLay+3+i])
   endif
 endfor
 tempw=w_fit
endif
Duplicate /O RQdata Rq_Fit
Make /O /N=(nopara) weps1,prew
Make /O /T /N=(2*nopara+Nlay) T_Constraints
//Make /O /T /N=(2*(nopara-3*ceil(NLay/2))+(Nlay-ceil(NLay/2))) T_Constraints1
Make /O /N=(NLay) sw4incohe

String/G globprew="prew"
Make /O /N=(nopara) prew

if (syn1>0)
Variable cursorprofA
 if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
    cursorprofA=pcsr(A, ExptTitle+"#SLDPlotInPanel")
 endif
endif
Variable/G globgraphhold
Variable graphhold=globgraphhold
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rdata cursora
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rdata cursorb
RemoveFromgraph /Z  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(6528,0,65280),lsize(Rq_Fit)=2
else
RemoveFromgraph  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit vs qzdata
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
endif
//    for (i=0;i<=(Nlay);i=i+1)  // # of interfaces is no. of layers +1
 //    tempw[nopara-(2*Nlay+1)+i-1]=abs(tempw[nopara-(2*Nlay+1)+i-1])
 // endfor
 
  prew=w_fit
 weps1=1e-06//0.001//prew*0.1//
  holdstring=""
  k=0
  
  //massnorm=0           //ON/OFF is currently manual
for (i=0;i<((NLay-Ceil(NLay/2))*3+4) ;i=i+1)
 if (i<=Ceil((NLay+0.5)/2))
 tempw1[i]=tempw[i]
 checkholdc[i]=checkhold[i]
 elseif (i<=2*Ceil((NLay+0.5)/2))
 tempw1[i]=tempw[i+Ceil(NLay/2)]
 checkholdc[i]=checkhold[i+Ceil(NLay/2)]
 elseif (i<=3*Ceil((NLay+0.5)/2)-1)
 tempw1[i]=tempw[i+2*Ceil(NLay/2)]
 checkholdc[i]=checkhold[i+2*Ceil(NLay/2)]
 else
 tempw1[i]=tempw[nopara-1]
  checkholdc[i]=checkhold[nopara-1]
 endif
 holdstring1=holdstring1+num2str(checkholdc[i])
 endfor
//  if (cmpstr(cntrlName,"rst1")==0 || cmpstr(cntrlName,"rst1a")==0)
      for (i=0;i<(2*nopara+Nlay);i=i+1) //to avoid conflict by both constrainted and held
      if (i<2*nopara)
      for (j=0; j<nopara;j=j+1)   
        if ((checkhold[j])==1 && stringmatch(T_Constraints_temp[i],"*K"+num2str(j))==1&&checkhold[ceil((i-1)/2)]==0)
//        print checkhold[j],T_Constraints_temp[i],j,stringmatch(T_Constraints_temp[i],"*K"+num2str(j)),checkhold[ceil((i-1)/2)], ceil((i-1)/2)
           T_Constraints_temp[i]=num2str(w_fit[j])
           
        endif
     endfor
     else
//    print "qq", ceil((i-1)/2)
       for (j=0; j<nopara;j=j+1)   
        if ((checkhold[j])==1 && stringmatch(T_Constraints_temp[i],("K"+num2str(j)))==1)
           T_Constraints_temp[i]=num2str(w_fit[j])
        endif
     endfor
     endif
     endfor
  for (i=0;i<nopara;i=i+1)
    
   if (checkhold[i]<1)
     if (stringmatch(T_Constraints_temp[2*i], "")==1||stringmatch(T_Constraints_temp[2*i], " ")==1||stringmatch(T_Constraints_temp[2*i], "  ")==1||stringmatch(T_Constraints_temp[2*i], "   ")==1)
      T_Constraints[2*i]="0x"
       if (i>NLay+1&&i<2*NLay+3)
        T_Constraints[2*i]="K"+num2str(i)+">"+"0.001"
       endif
     else
     T_Constraints[2*i]="K"+num2str(i)+">"+T_Constraints_temp[2*i]
     endif
     if (stringmatch(T_Constraints_temp[2*i+1], "")==1||stringmatch(T_Constraints_temp[2*i+1], " ")==1||stringmatch(T_Constraints_temp[2*i+1], "  ")==1||stringmatch(T_Constraints_temp[2*i+1], "   ")==1)
     T_Constraints[2*i+1]="0x"
     else   
     T_Constraints[2*i+1]="K"+num2str(i)+"<"+T_Constraints_temp[2*i+1]
     endif
   else
   T_Constraints[2*i]="0x"//"K"+num2str(Nlay+2)+">"+"K"+num2str(Nlay+2)  //fake constraint
   T_Constraints[2*i+1]="0x"//"K"+num2str(Nlay+2)+"<"+"K"+num2str(Nlay+2)  //fake constraint
   k=k+2
   endif
   holdstring=holdstring+num2str(checkhold[i])
  endfor
//  Variable /G globmass
  
 //  Profile4Fit(w_fit,x)
 //  Integrate/METH=1 prof/X=zz/D=prof_INT
//   globmass=(1351.16+prof_INT[60])/5.66
for (j=0;j<NLay;j=j+1)
  if (syn>0)
     if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
          if (j==(ceil(cursorprofA/Npoint_per_Lay)-1))
             sw4incohe[j]=2*syn+1
          else
            sw4incohe[j]=1
          endif
      else
 //         if (j==(ntlay-ceil(ntlay/10))||i==(2*ntlay-ceil(ntlay/10))||i==(3*ntlay-ceil(ntlay/10))||i==(4*ntlay-ceil(ntlay/10))||i==(5*ntlay-ceil(ntlay/10))||i==(6*ntlay-ceil(ntlay/10))||i==(7*ntlay-ceil(ntlay/10))||i==(8*ntlay-ceil(ntlay/10)))

               sw4incohe[j]=2*syn+1
   //       else
            sw4incohe[j]=1
  //        endif
     endif      
  endif
endfor
  j=0
  for (i=2*nopara;i<(2*nopara+Nlay);i=i+1)
  if (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]<1 && checkhold[nopara-2*(Nlay+1)+j+1]<1)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*K"+num2str(nopara-2*(Nlay+1)+j)+"+2*K"+num2str(nopara-2*(Nlay+1)+j+1)+"+"+num2str(sw4incohe[j])
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]>0 && checkhold[nopara-2*(Nlay+1)+j+1]<1 )
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*"+num2str(w_fit[nopara-2*(Nlay+1)+j])+"+2*K"+num2str(nopara-2*(Nlay+1)+j+1)+"+"+num2str(sw4incohe[j])
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]<1 && checkhold[nopara-2*(Nlay+1)+j+1]>0)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*K"+num2str(nopara-2*(Nlay+1)+j)+"+2*"+num2str(w_fit[nopara-2*(Nlay+1)+j+1])+"+"+num2str(sw4incohe[j])  
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]>0 && checkhold[nopara-2*(Nlay+1)+j+1]>0)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*"+num2str(w_fit[nopara-2*(Nlay+1)+j])+"+2*"+num2str(w_fit[nopara-2*(Nlay+1)+j+1])+"+"+num2str(sw4incohe[j])    
  else
   T_Constraints[i]="0x"
   k=k+1
   endif 
  j=j+1
  endfor

Duplicate /O/T T_Constraints T_Constraints1
     //  T_Constraints[2*nopara+Nlay]="globmass-8-2*K13-2*K14 > K15"  //added for one more constraint May08
  //  T_Constraints[2*nopara+Nlay+1]="globmass-8-2*K13-2*K14 < K15"  //added for one more constraint May08
  j=0
 //constraints for sym geometry

 String conva,convb
   //??
   for (i=0;i<(2*nopara+Nlay);i=i+1) //constraints for sym geometry
     if ((i>(((NLay+1)-Ceil(NLay/2)+1)*2-1)&& (i<(NLay+2)*2))  || (i>=((2*(NLay+1)-Ceil(NLay/2)+1)*2)&& i<(2*NLay+3)*2  ) || (i>=(((3*(NLay+1))-Ceil(NLay/2))*2)&& i<(3*NLay+3)*2) || (i>=(2*nopara+Nlay)-Ceil(NLay/2)))//0)
 
      T_Constraints1[i]="0x"
      elseif  (i>=(NLay+2)*2 && i<((2*(NLay+1)-Ceil(NLay/2)+1)*2)&& Stringmatch(T_Constraints1[i],"*K"+num2Str(Ceil((i+0.5)/2)-1)+"*")==1)
    
           if (Stringmatch(T_Constraints1[i],"*>*")==1)
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-Ceil(NLay/2))+">"+StringFromList(1,T_Constraints[i],">")
           else
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-Ceil(NLay/2))+"<"+StringFromList(1,T_Constraints[i],"<")
           endif
      elseif  (i>=(2*NLay+3)*2 && i<(((3*(NLay+1))-Ceil(NLay/2))*2)&& Stringmatch(T_Constraints1[i],"*K"+num2Str(Ceil((i+0.5)/2)-1)+"*")==1)

           if (Stringmatch(T_Constraints1[i],"*>*")==1)
               
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-2*Ceil(NLay/2))+">"+StringFromList(1,T_Constraints[i],">")
           else
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-2*Ceil(NLay/2))+"<"+StringFromList(1,T_Constraints[i],"<")
           endif

 //       T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-2*Ceil(NLay/2))+StringFromList(1,T_Constraints[i],convTC)
      elseif  (i>=(3*NLay+3)*2 && i<((2*nopara))&& Stringmatch(T_Constraints1[i],"*K"+num2Str(Ceil((i+0.5)/2)-1)+"*")==1)
           if (Stringmatch(T_Constraints1[i],"*>*")==1)
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-3*Ceil(NLay/2))+">"+StringFromList(1,T_Constraints[i],">")
           else
              T_Constraints1[i]="K"+num2Str(Ceil((i+0.5)/2)-1-3*Ceil(NLay/2))+"<"+StringFromList(1,T_Constraints[i],"<")
           endif

      elseif  (i>=(2*nopara))//-Ceil(NLay/2)))//&& Stringmatch(T_Constraints1[i],"*K"+num2Str(Ceil((i+0.5)/2)-1-NLay)+"*")==1)
               conva="K"+num2Str(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2))
               convb="K"+num2Str(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2)+1)
              if (checkholdc[(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2))]>0)
              conva=num2str(tempw1[(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2))])
              endif
              if (checkholdc[(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2)+1)]>0)
                  convb=num2str(tempw1[(Ceil((i)/2)-4*Ceil(NLay/2)-Ceil((NLay+0.5)/2)+1)])
               endif
              T_Constraints1[i]="K"+num2Str(Ceil((i)/2)-4*Ceil(NLay/2))+">2*"+conva+"+1+2*"+convb
    //          print T_Constraints1[i]
              if (checkholdc[(Ceil((i)/2)-4*Ceil(NLay/2))]>0)
               T_Constraints1[i]="0x"
              endif
     endif
     
    endfor
   if (NLay==7)
   
  insertpoints i,2, T_Constraints1
//   noconstrnt=noconstrnt-1
       T_Constraints1[i]="K11>2*K7+2*K8+1" 
      T_Constraints1[i+1]="K11<2*K7+2*K8+1"
endif
Variable noconstrnt 
k=0
    for (i=0;i<(2*nopara+Nlay);i=i+1) 
        
    if (stringmatch(T_Constraints1[i],"0x")==1)
    deletepoints i,1,T_Constraints1
    i=i-1
    k=k+1
    noconstrnt=(2*nopara+Nlay)-k 
   endif 

   if (stringmatch(T_Constraints[i],"0x")==1)
    deletepoints i,1,T_Constraints
    i=i-1
   endif
//   T_Constraints[i]= T_Constraints1[j]
 //  j=j+1
  endfor



  Variable /G globV_chisq
  Variable /G globV_Rchisq
  Variable /G globnpntsdata
  Duplicate /O dRQdata dRQ_temp
// dRQ_temp=dRQ_temp^2
  Variable nodata=numpnts(dRQdata)
   for (i=0;i<(nodata);i=i+1) //
    if (rswitch>0)
       if (dRQdata[i]<=0|| RQdata[i]<=0)
          dRQ_temp[i]=5*abs(dRQdata[i])//1e-04*qzdata[i]^4
       endif
    else
      if (dRQdata[i]<=0|| RQdata[i]<=0)
          dRQ_temp[i]=5*abs(dRQdata[i])//1e-04
       endif
    endif
   endfor

// Variable w15init=w_fit[15]
if (noconstrnt==0)
   if (pfyn==1)
   FuncFit /H=holdstring1 Profile4FitCCS1 tempw1 RQdata[pcsr(A),pcsr(B)] /W=dRQ_temp   /I=1 /D=Rq_Fit // /C=T_Constraints ///M=MaskRQdata
   else
   FuncFit /H=holdstring1 Profile4FitCCS1 tempw1 RQdata /W=dRQ_temp  /D=Rq_Fit   /I=1 // /C=T_Constraints ///M=MaskRQdata// /R=Res_try
   endif
 else

   if (pfyn==1)
  // redimension/N=10 weps1
  
   FuncFit /H=holdstring1 Profile4FitCCS1 tempw1 RQdata[pcsr(A),pcsr(B)]    /I=1 /D=Rq_Fit /C=T_Constraints1 /W=dRQ_temp  ///E=weps1///M=MaskRQdata //need update T_Constraints1 
   else
   FuncFit /H=holdstring1 Profile4FitCCS1 tempw1 RQdata /W=dRQ_temp /D=Rq_Fit   /I=1  /C=T_Constraints1 ///M=MaskRQdata// /R=Res_try
   endif
 endif
//for (i=0;i<((NLay-Ceil(NLay/2))*3+4) ;i=i+1)
//   if (i<=Ceil((NLay+0.5)/2))
//    tempw[i]=tempw1[i]
//      if (i!=(NLay+1)-i)
//        tempw[(NLay+1)-i]=tempw1[i]
//      endif
//   elseif (i<=2*Ceil((NLay+0.5)/2))
//    tempw[i+Ceil(NLay/2)]=tempw1[i]
//    tempw[2*(NLay+1)-(i-Ceil((NLay+0.5)/2)-1)]=tempw1[i]
//   elseif (i<=3*Ceil((NLay+0.5)/2)-1)
//   tempw[i+2*Ceil(NLay/2)]= tempw1[i]
//      if ((i+2*Ceil(NLay/2))==3*(NLay+1)-(i-2*Ceil((NLay+0.5)/2)))
//        tempw[3*(NLay+1)-(i-2*Ceil((NLay+0.5)/2))]=(massnorm-(5.66*2*(tempw1[7]+tempw1[8])-2*(tempw1[1]*tempw1[7]+tempw1[2]*tempw1[8])-4*tempw1[5]/3*(tempw1[2]-tempw1[3])))/(5.66-tempw1[3])  
//             print "tempw[",3*(NLay+1)-(i-2*Ceil((NLay+0.5)/2)),"] = ", tempw[3*(NLay+1)-(i-2*Ceil((NLay+0.5)/2))]
//      else
 //       tempw[3*(NLay+1)-(i-2*Ceil((NLay+0.5)/2))]=tempw1[i]
//      endif
//   else
//    tempw[nopara-1]=tempw1[i] 
//   endif
// endfor


Duplicate /O T_Constraints_temp_temp $TC_temp
KillWaves /Z T_Constraints_temp_temp
 SetActiveSubWindow $ExptTitle
   if (V_chisq>0)
   globV_chisq=V_chisq
   globV_Rchisq=V_chisq/(V_npnts)
   globnpntsdata=V_npnts
   endif
     KillWaves /Z  dRQ_temp
//  endif
// massnorm=0
  SetWindow  $ExptTitle, hook=winhookproc
  print "*****", ExptTitle, "Fitting Finished .................................................................. ^ ^ ^ ^ ^"
//SetActiveSubWindow $ExptTitle
End


Function Profile4FitCCS1(w1,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w1
Variable qq//,nopntalayer,nl

 Variable V_chisq
//Variable /G globyn=1
//Variable q//,sigmaq,nt
NVAR  npt1=globNpoint, syn1=globsyn, yn1=globyn,npara1=globNpara,lay1=globNlay//, ssyn1=globssyn
Variable npt=npt1, npara=npara1,syn=syn1,yn=yn1,lay=lay1//,ssyn=ssyn1
SVAR qqq=globqzdata
SVAR dddq=globdqdata
SVAR dddr=globdrq4data
SVAR fitfun1=globfitfun
String /G globprew
NVAR s2sld1=globStop2SLD
//SVAR df=globweps

 Variable /G globautoR,globautowav
 
// Make /O/D/N=19 w
Wave w=tempw
Wave q4f=$qqq
Wave dq4f=$dddq
//Wave drq4f=$dddr
Wave /D fitfun=$fitfun1
//Wave /D prew=$prew1
Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable i,j,k,y,m,nn11,n,td,ad//,nopntalayer=10,nl=6  //nopntalayer=#of sublayers of each component(eg,PS) 
Variable ii,jj,kk,notp,Rq_Fitout,deltad
Variable /C Xn,Xnp1,fn,fnp1,rn,an,anp1,kn,knp1
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable z,dz,dn,dp, lamda,sdqq,dqq,SLD1,SLDi,phi1,ko,XXGn,XDGn,XGn,DGn,incsdqq,zzorg,Erfv //,SLDA,SLDB
//    lamda=4.62
//Rq_Fitout=0
    notp=npt*(lay+1)+1 //No. of total points
    Make /O /D /N=(notp) prof,zz//,dprof  //+(nl+1)
    String/G  globprosldz="prof",globproz="zz"
   Make /O /D /N=(npara) weps1//,prew
   String/G globprew
   Make /O /D /N=(npara) $globprew
   Wave /D prew=$globprew
    	String/G  globweps="weps1"//,globprew="prew"
    	Variable Rq_Fitpre=NumVarOrDefault("globRq_Fitpre", 1)
    Variable /G globsf
        Variable/G  massnorm,cslay
 //   Variable sf=sf1

     
Variable /G globcmplxcalyn

for (i=0;i<((lay-Ceil(lay/2))*3+4) ;i=i+1)
   if (i<=Ceil((lay+0.5)/2))
     w[i]= w1[i]
      if (i!=(lay+1)-i)
         w[(lay+1)-i]= w1[i]
      endif

   elseif (i<=2*Ceil((lay+0.5)/2))
     w[i+Ceil(lay/2)]= abs(w1[i])
     w[2*(lay+1)-(i-Ceil((lay+0.5)/2)-1)]= abs(w1[i])

   elseif (i<=3*Ceil((lay+0.5)/2)-1)
     w[i+2*Ceil(lay/2)]=  w1[i]
     w[3*(lay+1)-(i-2*Ceil((lay+0.5)/2))]=w1[i]
 //    print i
   else

    w[npara-1]=w1[i] 
   endif

 endfor
 
 if (lay<6)
 
  w[3*(lay+1)-Ceil(lay/2)]=(massnorm-(5.66*2*( w1[7]+ w1[8])-2*( w1[1]* w1[7]+w1[2]*w1[8])-4*w1[6]/3*(w1[2]-w1[3])))/(5.66-w1[3])  //w[3*(lay+1)-(i-2*Ceil((lay+0.5)/2))]=(massnorm-(5.66*2*( w1[7]+ w1[8])-2*( w1[1]* w1[7]+w1[2]*w1[8])-4*w1[6]/3*(w1[2]-w1[3])))/(5.66-w1[3])  
elseif(lay<7)
elseif(lay<8)
  w[3*(lay+1)-Ceil(lay/2)]=(massnorm-(5.66*2*( w1[9]+ w1[10]+w1[11])-2*( w1[1]* w1[9]+w1[2]*w1[10]+w1[3]*w1[11])-4*w1[7]/3*(w1[2]-w1[3])+2*(w1[3]*w1[8]-w1[4]*w1[8])))/(5.66-w1[4])  //w[3*(lay+1)-(i-2*Ceil((lay+0.5)/2))]=(massnorm-(5.66*2*( w1[7]+ w1[8])-2*( w1[1]* w1[7]+w1[2]*w1[8])-4*w1[6]/3*(w1[2]-w1[3])))/(5.66-w1[3])  
else
//  w[3*(lay+1)-Ceil(lay/2)]=(massnorm-(5.66*2*( w1[7]+ w1[8])-2*( w1[1]* w1[7]+w1[2]*w1[8])-4*w1[6]/3*(w1[2]-w1[3])))/(5.66-w1[3])  //w[3*(lay+1)-(i-2*Ceil((lay+0.5)/2))]=(massnorm-(5.66*2*( w1[7]+ w1[8])-2*( w1[1]* w1[7]+w1[2]*w1[8])-4*w1[6]/3*(w1[2]-w1[3])))/(5.66-w1[3])  
endif
   Variable sf=w[npara-1]

    globsf=sf
     npara=npara-1
 //w[0]=w1[0]
 //  w[1]=w1[1]
 //   w[5]=w1[1]
 //   w[4]=w1[2]
 //    w[2]=w1[2]
 //     w[3]=w1[3]
 //      w[6]=w1[0]
 //     w[7]=w1[4]
//      w[12]=w1[4]
//      w[8]=w1[5]
//       w[11]=w1[5]
 //      w[9]=w1[6]
  //     w[10]=w1[6]
 //     w[13]=w1[7]
 //      w[17]=w1[7]
 //     w[14]=w1[8]
//      w[16]=w1[8]

 //     w[18]=w1[9]

 // w[15]=(massnorm-(5.66*2*(w1[7]+w1[8])-2*(w1[1]*w1[7]+w1[2]*w1[8])-4*w1[5]/3*(w1[2]-w1[3])))/(5.66-w1[3])
 
  Wave drr4f=$dddr
Wave dRQ_temp
      //    dRQ_temp=sf*drr4f    


Wave /D im_SLD_in//=$im_SLD_in1

Make  /O /D /N=(notp) prof_IM

// Variable temp15=w[15]   
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////building a model profile against z /////////////////////////////////////////
   if (abs(w[npara-(2*lay+1)])<10)
     zz[0]=-abs(w[npara-(2*lay+1)])*2-10
     elseif (abs(w[npara-(2*lay+1)])>100)
     zz[0]=-abs(w[npara-(2*lay+1)])*2-100
   else
    zz[0]=-abs(w[npara-(2*lay+1)])*3
   endif
    zz[1]=-abs(w[npara-(2*lay+1)])*2 //initial point move back to 2times of sigma (of the first layer)

    ii=1
    for (i=0;i<=(lay);i=i+1)  // # of interfaces is no. of layers +1
   //   w[npara-(2*lay+1)+i]=abs(w[npara-(2*lay+1)+i])
    if (abs(w[npara-(2*lay+1)+i])<1e-04) //to elliminate a bug when a becomes 0
    w[npara-(2*lay+1)+i]=1e-04///*sign(w[npara-(2*lay+1)+i])
    endif
//  if (fitfun[ii]!=8)   
    for (j=1; j<=(npt);j=j+1)   //improved the SLD profile builder
  
        if (j==1&&i!=0)
          zz[ii]=zz[ii-1]+(zz[ii-1]-zz[ii-2])
        elseif (j<npt-1)
          if (i==0&&ii==1)
          else
          zz[ii]=zz[ii-1]+(4*w[npara-(2*lay+1)+i])/(npt-2)
          endif
        elseif(j==npt-1)
          zz[ii]=zz[i*npt+1]+4*w[npara-(2*lay+1)+i]
        else
          zz[ii]=zz[ii-1]+((w[npara-lay+i]-2*(w[npara-(2*lay+1)+i]+w[npara-(2*lay+1)+1+i])))/2
        endif
      ii=ii+1
    endfor  // j endfor
//   else //  If the interfacial function is  a slpine function...
   //    zz[notp-2]=zz[notp-3]+ abs(w[npara-(1*lay+1)])*2  // add the last point of SLD
   if (abs(w[npara-(1*lay+1)])<10)
       zz[notp-1]=zz[notp-2]+10
       elseif (abs(w[npara-(1*lay+1)])>100)
       zz[notp-1]=zz[notp-2]+100
    else
       zz[notp-1]=zz[notp-2]+ abs(w[npara-(1*lay+1)]) // add the last point of SLD
   endif 
     
     
  // endif //endif (fitfun[i]!=8)
  endfor

     ii=1
     zzorg=0
    for (i=0;i<=(lay);i=i+1)

      if (i>0)
       zzorg=zzorg+w[npara-(lay-(i-1))]
      endif

      for (j=1; j<=(npt);j=j+1)
       if (fitfun[i]==0)
          Erfv=(erf((zz[ii]-zzorg)/((w[(lay+2)+i])))/2+0.5) //modifying erf adaptable to profile
       elseif (fitfun[i]==1)
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          else
          Erfv=exp((-(((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/((w[(lay+2)+i])))^2)/2) //leftGaussian
          endif
       elseif (fitfun[i]==2)
          if ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=1-exp((-(((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/((w[(lay+2)+i])))^2)/2) //rightGaussian
          endif
       elseif (fitfun[i]==3)
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=1-((((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/(4*abs(w[(lay+2)+i])))^2) //leftParabola 
          endif
       elseif (fitfun[i]==4)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=((((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/(4*(w[(lay+2)+i])))^2) //rightParabola
          endif
      elseif (fitfun[i]==5)         
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else
          Erfv=exp((-(abs((zz[ii]-zzorg)-2*(w[(lay+2)+i]))/((w[(lay+2)+i])))))  //leftExp
          endif
       elseif (fitfun[i]==6)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=1-exp((-(((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/((w[(lay+2)+i]))))) //rightExp
          endif
        elseif (fitfun[i]==7)    
          if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
         Erfv=((zz[ii]-zzorg)+2*(w[(lay+2)+i]))/(4*(w[(lay+2)+i])) //Linear
          endif  
        elseif (fitfun[i]==8)     
         if ((zz[ii]-zzorg)>=2*(w[(lay+2)+i]))
          Erfv=1
          elseif ((zz[ii]-zzorg)<=-2*(w[(lay+2)+i]))
          Erfv=0
          else       
          Erfv=MyOwn(zz[ii],zzorg,(w[(lay+2)+i]))
          endif  
        endif          
  //     Erfv=abs(Erfv)
       prof[ii]=w[i]*(1-Erfv)+w[i+1]*(Erfv)
      if (globcmplxcalyn>1)
      
      prof_IM[ii]=im_SLD_in[i]*(1-Erfv)+im_SLD_in[i+1]*(Erfv)
      else
      prof_IM[ii]=0
      endif
   //    if (prof[ii]>10)   //
  //    prof[ii]=10        // <<<=== specify maximum SLD !!!!??
  //     endif                //
       ii=ii+1
      endfor
    endfor
// zz[0]=-w[npara-(2*lay+1)]*3//-w[npara-(2*lay+1)]/10
//  zz[1]=-w[npara-(2*lay+1)]*2//-w[npara-(2*lay+1)]/10
   prof[0]=w[0]
    prof_IM[0]=im_SLD_in[0]
  prof_IM[(notp-1)]=im_SLD_in[(lay+1)]

  prof[(notp-1)]=w[(lay+1)] // sld of substrate
    // w[15]  =  temp15
       if (cslay>0)  //Cubic Slpine Smoothing all the interface no matter which interface has this function...
         Variable inn
         Make /O/N=(npt) zzcs,profcs,zztemp,proftemp
         for (inn=0;inn<npt;inn=inn+1)
           profcs[inn]=prof[inn+cslay*npt+1]
           zzcs[inn]=zz[inn+cslay*npt+1]
        endfor

  //     duplicate/O prof, profcs
  //      duplicate/O zz, zzcs
       Interpolate2/T=2/N=(npt) /E=2 /Y=proftemp /X=zztemp zzcs, profcs //[cslay*npt,(cslay+1)*npt]
        for (inn=0;inn<npt;inn=inn+1)
           prof[inn+cslay*npt+1]=proftemp[inn]
           zz[inn+cslay*npt+1]=zztemp[inn]
        endfor
  //      Smooth/E=2 13, prof
  //      Variable ci
//        for (ci=cslay*npt+1;ci<=(cslay+1)*npt;ci=ci+1)
 //      prof[ci]=profcs[ci]
//       zz[ci]=zzcs[ci]
    //    endfor
   //     KillWaves  zzcs,profcs,zztemp,proftemp
      endif
 //   Variable /G globmass
 //  Integrate/METH=1 prof/X=zz/D=prof_INT
 //  globmass=(1351.16+prof_INT[60])/5.66

 if (s2sld1==1)
   s2sld1=0
 return 0
 endif
//   endif  // end if for the # of layers >=1

 /////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
// String/G  globImSLDin="im_SLD_in",globImSLDout="im_SLD_out" 
String/G  globImSLDin="prof_IM"

if (globautoR>0&&globautowav>0)
// if (stringmatch(dddq,"SelectData")==1)
//  Wave dQ_Fit1=SimdQ_Pre_Cal,Qz_Fit1=SimQ_Pre_Cal
// else
  Wave dQ_Fit1=$dddq+"_Pre_Cal",Qz_Fit1=$qqq+"_Pre_Cal"
// endif
Rq_Fitout=ParrattNTRNdq(Qz_Fit1, dQ_Fit1,notp)
else
Rq_Fitout=ParrattNTRNdq(q, sigmaq,notp)
endif
//  for (i=0;i<=(lay);i=i+1)  // # of interfaces is no. of layers +1
//     w[npara-(2*lay+1)+i]=abs(w[npara-(2*lay+1)+i])
//  endfor

//print Rq_Fitout
npara=npara+1
   	Variable/G globRq_Fitpre=Rq_Fitpre

for (i=0;i<npara;i=i+1)
deltad=(w[i]-prew[i])

weps1[i]=(Rq_Fitout-Rq_Fitpre)/(deltad)//(Rq_Fitout-weps1[i])/(deltad)
//return 0
prew[i]=w[i]
 

//if (weps1[i]>1)
//weps1[i]=1
//endif
if (abs(weps1[i])<1e-06)
weps1[i]=1e-06*sign(weps1[i])
endif
if (abs(weps1[i])>1e+06)
weps1[i]=1e+06*sign(weps1[i])
endif

endfor
Rq_Fitpre=Rq_Fitout
//print V_chisq
//V_chisq=V_chisq/(sf*sf)
    return Rq_Fitout //
End

///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


Function holdcheckbox(cntrlName,checked)
String cntrlName
Variable checked
SVAR checkhold1=globcheckhold
SVAR ExptTitle=globExptTitle
NVAR Nlay1=globNLay
Variable Nlay=Nlay1
Wave checkhold=$checkhold1
NVAR nopara1=globNpara
Variable nopara=nopara1,i,a
String matc,namelow,namehigh
 for (i=0;i<nopara;i=i+1)
 matc="K"+num2str(i)
 namelow="low"+num2str(i)
 namehigh="high"+num2str(i)
 a=stringmatch(cntrlName,matc)
 if (a==1)
 checkhold[i]=checked
     if (i<nopara-1)
        SetVariable $namelow win=$ExptTitle,disable=checkhold[i]
       SetVariable $namehigh win=$ExptTitle,disable=checkhold[i]
       else
       SetVariable $namelow win=$ExptTitle,disable=checkhold[i]//,format="%f"
       SetVariable $namehigh win=$ExptTitle,disable=checkhold[i]
       endif

 endif
 endfor
//print matc
//print cntrlName
 


End
Function UserGetInputPanel_ContButton(cntrlName)
String cntrlName
DoWindow /K Rcal4DataorPreCal //tmp_GetInputPanel 
End

Function UserGetGDE_ContButton(cntrlName)
String cntrlName
DoWindow /K GraphDraworEdit //tmp_GetInputPanel 
End


Function UserIn2InPanel_ContButton(cntrlName)
String cntrlName
if (cmpstr(cntrlName,"rst4i")==0||cmpstr(cntrlName,"rst4ia")==0)
Duplicate /O  w_fit, tempw 
//Profile4Fit(tempw,x)
endif
End






Function LogoButton(cntrlName) : ButtonControl 
String cntrlName
End

Function funselect(ctrlName,popNum,popStr)
String ctrlName
Variable popNum
String popStr

String sss=ctrlName
Variable j=strlen(ctrlname)-1
NVAR Nlay1=globNlay
Variable Nlay=Nlay1
Make /O /D /N=(Nlay+1) fitfun1
String /G globfitfun="fitfun1"

//Variable fitf=fitfun1[j]
fitfun1[j]=popNum-1
if (popNum==9)
DisplayProcedure "MyOwn"
endif
Variable /G globautoR,globautoS
 if (globautoR>0||globautoS>0)
  autoRup(" ",0," "," ")
  endif
End

Function R4DoPC(ctrlName,popNum,popStr): PopupMenuControl
String ctrlName
Variable popNum
String popStr

Variable modecalRDP

modecalRDP=popNum
Variable /G globmodecalRDP=modecalRDP

End
Function GED4PSD(ctrlName,popNum,popStr): PopupMenuControl
String ctrlName
Variable popNum
String popStr

Variable modeGraphdrawEdit

modeGraphdrawEdit=popNum
Variable /G globmodeGraphdrawEdit=modeGraphdrawEdit

End


////////////////////////                                                                                                                                   //////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////


Function keepscald(ctrlName,varNum,varStr,varName) : SetVariableControl
String ctrlName
Variable varNum
String varStr
String varName
  if (cmpstr(ctrlName,"tempw18")==0)
NVAR sf1=globsf
sf1=varNum
endif
End

Function  /S PrintAllDataFolderNames()
    String objName
    Variable index=0,index1=0
    String strfollist=""
    String /G globcomWin, globExptTitle
//    String helwin=" "
  
    do 
        objName=GetindexedObjName("root:",4,index)
        if (exists("root:"+objName+":globExptTitle")==2)
        
  //         if (StringMatch(globExptTitle,objName)>0)
     //         strfollist=strfollist+";"+objName 
  //        Execute "helwin=root:"+objName+":globcomWin "
   //          else
        //   helwin="Note:"+helwin
  //     if (strlen(helwin)!=0)
        strfollist=strfollist+";"+objName //+helwin//+"\\Z08\K(26112,26112,26112)"+globcomWin
  //      helwin=" "
  //          endif
        endif
        if (strlen(objName) == 0)
        break
        endif
    index +=1
    while(1)
     strfollist=SortList(strfollist)
    return strfollist
End



Function  /S PrintAllDFNames4Menu(objName)
    String objName
    Variable index
    String strfollist=""
    String selec
    String gdf=GetDataFolder(1)
//    print gdf
index=0
    do 
        objName=GetindexedObjName("root:",4,index)
  //      print objName
        if (exists("root:"+objName+":globExptTitle")==2)
          if (stringmatch(gdf,"root:"+objName+":")>0)
           strfollist=strfollist+";"+objName+"!>"//+", SetDataFolder root:"+objName
          else
            strfollist=strfollist+";"+objName//+", SetDataFolder root:"+objName
          endif
          
        endif
        if (strlen(objName) == 0)
        break
        endif
    index +=1
    while(1)
              if (stringmatch("root:",gdf)>0)
          strfollist=strfollist+";"+"root"+"!>"//+"; SetDataFolder root:"
          else
          strfollist=strfollist+";"+"root"//+"; SetDataFolder root:"
          endif

    return strfollist
End

Function LoadWaveFromFile(cntrlName) : ButtonControl 
String cntrlName

if (cmpstr(cntrlName,"LWF")==0||cmpstr(cntrlName,"LWFa")==0)
String svFD=GetDataFolder(1)
NewDataFolder /S/O root:F_L_temp
String /G globExptTitle
String /G S_fileName
Execute "LoadWave /G/D/L={4, 0, 0, 0,4}/B=\"N=Qz;N=Rn;N=dRn;N=dQz;\" "

if (strlen(S_fileName)>=0)
      if (strlen(S_fileName)>25)
          if (Stringmatch(S_fileName,"REF_L*")>0)
           globExptTitle=StringFromList(1,S_fileName,"_")+"_"+StringFromList(2,S_fileName,"_")
           else 
            globExptTitle="toolongfilename"
           endif
       else
       globExptTitle=StringFromList(0,S_fileName,".")
       endif
    If (Stringmatch(globExptTitle,"*-*")>0)
    globExptTitle=ReplaceString("-",globExptTitle,"_")
    endif
    If (Stringmatch(globExptTitle,"* *")>0)
    globExptTitle=ReplaceString(" ",globExptTitle,"_")
    endif

String wn=WinName(0,1)
   If (Stringmatch(wn,"Untitled")>0)
//    DoWindow /K $wn
    endif

else
KillDataFolder root:F_L_temp
endif
if (Strsearch(PrintAllDataFolderNames(),globExptTitle,0)<0)
RenameDataFolder root:F_L_temp $globExptTitle
else
KillDataFolder root:F_L_temp
//SetDataFolder svFD
//globExptTitle=globExptTitle+"X2"
//RenameDataFolder root:F_L_temp $globExptTitle
endif
SetDataFolder root:$globExptTitle
      Variable /G globmoderq4=2  
      Variable /G globmodedrq=3  
      Variable /G globmodeqz=1  
      Variable /G globmodedqz=4 


FitRgeneral2( )
SVAR qzdata1=globqzdata,rdata=globrq4data,drdata=globdrq4data
String /G globdqdata
String qzdata=qzdata1
 if (stringmatch(globdqdata,"SelectData")==1)
  
 Wave qdata=$qzdata, rd=$rdata,drd=$drdata
 Duplicate /O qdata SelectData
 SelectData=0.02*qdata
globdqdata="d"+qzdata1+"2p"
Rename SelectData $globdqdata
Wave dqdata=$globdqdata
Variable i
	     for (i=0;i<=20000;i=i+1)
		      if ( drd[i]==NaN && rd[i]==NaN && qdata[i]==NaN )
		      break
		      endif
		  if ( drd[i]<0 ||rd[i]<0||qdata[i]<0||drd[i]==NaN||rd[i]==NaN||qdata[i]==NaN||rd[i]==inf)
		  deletepoints i, 1, qdata,dqdata,drd,rd
//		  deleteponts i 1 dqdata
//		  deleteponts i 1 drd
//		  deleteponts i 1 rd
		     i=i-1
		   endif	
	     endfor
 Duplicate /O rd Rq_Fit
Sort $qzdata1 $rdata,$drdata,$globdqdata,$qzdata1
Variable /G globmodedqz=4 
    FitRgeneral3( )
 endif
 

//Killwaves SelectData
endif
End


//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

Function  FitRgeneral2( )  ///Random Profile fit
//     SetDataFolder root:
     String /G S_fileName
      String ExptTitle=StrVarOrDefault ("globExptTitle", "Untitled")

        NewDataFolder /S/O root:$ExptTitle

      Variable r,b,i,j,k,kk,v1,z0,df0
          String /G globExptTitle=ExptTitle
          String /G globExptTitlepre
     Variable Nlay=NumVarOrDefault("globNlay", 2)
     Variable Npoint=NumVarOrDefault("globNpoint", 10)
     Variable yn=NumVarOrDefault("globyn", 0)
     Variable syn=NumVarOrDefault("globsyn", 0)
      Variable ssyn=NumVarOrDefault("globssyn", 0)
     Variable thick=NumVarOrDefault("globthick", 6)
    Variable pfyn=NumVarOrDefault("globpfyn", 0)
     Variable nopara=NumVarOrDefault("globNpara", 2)
     Variable rswitch=NumVarOrDefault("globrswitch", 0)
     Variable sf=NumVarOrDefault("globsf", 1)
//Variable update911=NumVarOrDefault("globupdate911", 0)
   String /G globRQdata
   String /G globdRQdata
    String RQ4data=StrVarOrDefault ("globrq4data","")
    String dRQ4data=StrVarOrDefault ("globdrq4data","")    
    String Qzdata=StrVarOrDefault ("globqzdata","")    
    String dQdata=StrVarOrDefault ("globdqdata","")   
    String fitfun= StrVarOrDefault ("globfitfun","")  
      Variable moderq4= NumVarOrDefault ("globmoderq4",1)  
      Variable modedrq= NumVarOrDefault ("globmodedrq",1)  
      Variable modeqz= NumVarOrDefault ("globmodeqz",1)  
      Variable modedqz= NumVarOrDefault ("globmodedqz",1)  
      Variable cmplxcalyn=NumVarOrDefault("globcmplxcalyn",1)
 
      Variable /G globcmplxcalyn= cmplxcalyn//1
      Variable /G globNNDF=1
	Variable/G globsyn=syn
	Variable/G globyn=yn

	Variable/G globpfyn=pfyn	
	Variable/G globNpoint=Npoint	
	Variable/G globNlay=Nlay	
	Variable /G globNLay_1
	Variable/G globrswitch=rswitch
	Variable/G globsf=sf
	   String /G globcomWin//="" 
	   Variable gsw=rswitch
	    Variable /G globautoR=0
	    Variable /G globautoS=0
	   globrswitch=0
	   rswitch=0
          //  rswitch=0
//	Variable/G globwinup=winup
  Make /O  /N=3 SelectData
   for (i=0;i<2; i=i+1)
     SelectData[i]=i/100
   endfor
  SelectData[0]=0.003
  SelectData[1]=0.1
   SelectData[2]=0.3

DoWindow RQ4vsQCalFitE 
	if (V_Flag)
	    return -1
	endif
 
         nopara=(globNlay*3+3+1)  //1 for rescaling R incase of neutron coming through other superstrate  than air
  Variable/G globNpara=nopara, massnorm=0,cslay=0

//String/G globcheckhold
 Make /O /D /N=(nopara) w_fit,weps1, tempw
   //   Duplicate/O /D w_fit, tempw  
         tempw[nopara-1]=sf
         
   Make /O /T /N=(nopara) namepara
      Make /O /T /N=(2*nopara) namecnstrnt
      Make /O /T /N=(2*nopara) T_Constraints_temp//,T_Constraints
      Make /O /D /N=(globNlay+1) fitfun1
      Make /O /D /N=(nopara) checkhold
 
      fitfun="fitfun1"
 
      String/G RRQ4nPlot
      String/G dRQ4nPlot
  	String/G  globwww="w_fit"
      String/G globfitfun="fitfun1"
	String/G globT_Constraints_temp="T_Constraints_temp" 
	String /G globprosldz,globproz
	String names,namelow,namehigh,low,nametempw,nametitle,namefun,Rdata,dRdata,Qdata,dQzdata
 
          if (rswitch>0)
     	   RRQ4nPlot="RQ\\S4"
     	   dRQ4nPlot="SigRQ\\S4"
       	   else
     	   RRQ4nPlot="R"
     	   dRQ4nPlot="SigR"     	   
     	   endif
     If (strsearch(WinList(ExptTitle,";","WIN:"),ExptTitle,0)>=0)
     SetWindow  $ExptTitle hook=$" "    
       DoWindow /R/K  $ExptTitle
    endif

        Display /K=1 /N=$ExptTitle  /W=(7*72/96-5,3*72/96,1156*72/96-5,762*72/96)  as "NRfit 6:// "+ExptTitle
       DefaultGuiFont /W=$ExptTitle /Win all={"MS Sans Serif",12,0}
      SetDataFolder  root:$ExptTitle
     GroupBox topgb0 frame=1,size={1140,1},pos={5,55}//, labelBack=(55000,0,0)
      ModifyGraph /W=$ExptTitle gbRGB=(60416,59648,55296)
  TitleBox expt_title title="Title:                                   ",  pos={48,32},fsize=13,fstyle=1,frame=4,labelBack=(65280,43520,0),help={" Support no special characters... Use only letters, digits or _"}//pos={750+50,16},(60416,59648,55296)
   SetVariable tiltleIn value=globExptTitle, bodyWidth=135, title=" ", proc=ExtTitleUp1, pos={177,36},labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
   globExptTitlepre=globExptTitle
PopupMenu tiltleInPop  value=PrintAllDataFolderNames(),mode=moderq4,bodyWidth=20, title="",fstyle=1, size={79,200},labelBack=(65280,43520,0),proc=popExtTitleUp,pos={172,34},help={globcomWin}
      
              j=727 
      TitleBox title0 title="Neutron",  pos={385,14},fsize=22,fstyle=1,font="Lucida Calligraphy",frame=0, fcolor=(20000,20000,20000),help={"Nuetron and X-Ray Reflectivity Analysis ..." }//(370,9),labelBack=(55000,55000,65000)
     TitleBox title01 title="Reflectivity",  pos={585,14},fsize=22,fstyle=1,font="Lucida Calligraphy",frame=0, fcolor=(20000,20000,20000),help={"Nuetron and X-Ray Reflectivity Analysis ..." }//(370,9),labelBack=(55000,55000,65000)
     TitleBox Company title="ORNL",  pos={1055,6},fsize=14,fstyle=1,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox Author title="Neutron Scattering Sciences Division",  pos={1000,25},fsize=9,fstyle=1,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox WDate title=date(),  pos={1027,40},fsize=10,fstyle=0,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
 Button nnbutton picture=ProcGlobal#nbutton,pos={510,7},size={5,5},proc=LogoButton,title="",help={" Developed by Jae-Hie J. Cho, Gregory S. Smith, and William A. Hamilton at the Oak Ridge National Laboratory"}
 Button nnbutton2 picture=ProcGlobal#reflico,pos={1040,320},size={5,4},proc=LogoButton,title=" " ,help={"A manual will be here in the future ... : Contact; jhjcho@gmail.com "} //reflico
       GroupBox gb0 frame=1,size={1013,1},pos={5,55+50}     
     
     TitleBox Data1 title=" DATA ",  pos={49,45+10},fstyle=1,frame=3,labelBack=(65280,33520,0)//labelBack=(60416,59648,55296)////, fcolor=(65000,65000,650000)//labelBack=(60416,59648,55296)
  //    GroupBox gbdata1 frame=1,size={3,50},pos={4,56}  
//     TitleBox Data2 title=" ",  pos={4,45+25},fstyle=1,frame=3,labelBack=(65280,33520,0)//labelBack=(60416,59648,55296)
     TitleBox title1 title="GLOBAL VARIABLES",  pos={50,45+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox rticktitleR title="R",  pos={80,90+50},fsize=12,fstyle=1,frame=0//, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox rticktitleRQ4 title="RQ\\S4\\M",  pos={180,83+50},fsize=12,fstyle=1,frame=0//, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     GroupBox rbox frame=1,size={180,30},pos={50,80+50}//,title="Reflectivity calculation"
     Slider objectR, pos={110,90+50},size={50,40},fsize=10,ticks=0,limits={0,1,1},value=rswitch,userTicks={tickNumbers,tickLabels},vert=0,side=0,proc=SliderobjectR, labelback=(60416,59648,55296),help={"To choose Reflectivity to be calculated; R or RQ4?"}
       SetVariable setvar0 bodyWidth=30,title="    Number of Layers                     ",value=globNlay,limits={0,31,1},labelBack=(60416,59648,55296),proc=updatewinpan,pos={180,115+50},help={"How many layers (films) are there throughout the interface?   (Note that no more than 9 are recommended.)"}
     SetVariable setvar1 bodyWidth=41,value=globNpoint,title="    Points per Each Layer          ",limits={3,1000,5}, pos={180,135+50},labelBack=(60416,59648,55296),proc=autoRup,help={"Number of points for the each interface+film on the SLD profile? (eg., choose 10, 20, 30, etc.)"}
     SetVariable setvar2 bodyWidth=30,value=globyn,limits={0,10,1},title="    SigmaQ Smear? (y(1)/n(0))       ",pos={180,155+50},labelBack=(60416,59648,55296),proc=autoRup,help={"Would you like to consider Gaussian averging for the uncertainty of Qz?"}
     SetVariable setvar3 bodyWidth=40,title="    Incoherent Smear (Å)            ",value=globsyn,limits={0,500,5},pos={180,175+50},labelBack=(60416,59648,55296),proc=incoherentpointproc,help={"If u not know, set to 0. Or move the cursor to the point on the SLD profile graph at which the incoherent averaging takes place."}
     SetVariable setvar4 bodyWidth=30,title="    Ranged by Cursors? (y(1)/n(0))",value=globpfyn,limits={0,1,1},pos={180,195+50},labelBack=(60416,59648,55296),proc=FitRangeDraw,help={"Use the cursor on the R(Q4) Graph to choose the range for fitting; mouse (or arrow key) can be used for holding and moving it."}
    PopupMenu setvar5a  value="No;Yes",mode=globcmplxcalyn,pos={152,215+50},fstyle=0, size={80,200},bodyWidth=50,labelBack=(60416,59648,55296),proc=PopCmplxYn, title="Any Complex SLDs?          ",help={"Are any SLDs complex number? The imaginary SLD (im(SLD)=-crosssection*density/lamda) input boxes will appear on the right side."}
      TitleBox title2 title="FIT PARAMETERS",  pos={275,45+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title11a title="Layer",  pos={276,80+50},fstyle=1,frame=0//,frame=4//,labelBack=(55000,55000,65000)     
     TitleBox title11 title="No.",  pos={276,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)     
//     TitleBox title11a title="Hold?",  pos={302,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)     
     TitleBox title3 title="SLD (10\\S-6\\MÅ\\S-2\\M)",  pos={385,76+50},fstyle=1,frame=0,help={"SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, Sapphire=5.69, D2O=6.25, h-Toluene=0.94, d-Toluene=5.66, P2VP=1.87, h-PS=1.4, d-PS=6.4, H2O=-0.56"} //,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title4 title="Interfacial Roughness (Å)  &",  pos={555,80+50},fstyle=1,frame=0,help={"Note that this roughness is a quarter of the interfacial thickness. To get STD roughness, divide these values by sqrt(2)"}//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title5 title="Shape",  pos={725,80+50},fstyle=1,frame=0,help={"The function to describe the interface" }//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title6 title="Thickness (Å)",  pos={875,80+50},fstyle=1,frame=0,help={"This value equal to  (2 * top interfacial roughness+2*bottom interfacial roughness)+ extra thickness."}//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title7 title="    Low      In            Out      High",  pos={338,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title8 title="    Low      In            Out      High",  pos={545,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title9 title="Functions",  pos={720,95+50},fstyle=0,frame=0,help={"The functions to describe the interface" }//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title10 title="    Low      In            Out      High",  pos={835,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
       if (moderq4==0)
        moderq4=1
       endif
        if (modedrq==0)
         modedrq=1 
       endif
        if (modeqz==0)
        modeqz=1
        endif
        if (modedqz==0)
         modedqz=1
         endif
	PopupMenu RQ4data  value=WaveList("*",";",""),mode=moderq4,bodyWidth=150, title="R",fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
	PopupMenu dRQ4data value=WaveList("*",";",""),mode=modedrq,bodyWidth=150, title="dR",fstyle=1,size={80,200},proc=datadRInput,pos={430,70},help={"Uncertainty of Reflectivity Data"}
	PopupMenu Qzdata  value=WaveList("*",";",""),mode=modeqz,bodyWidth=150, title="Q",fstyle=1,size={80,200},proc=dataQInput,pos={650,70},help={"Qz Data"}
 //   if (globyn==0)
//	PopupMenu dQdata  value="sigQ Smear: Turned Off",mode=modedqz,bodyWidth=150, title="sigQ",fstyle=1,disable=2,size={80,200},proc=datadQInput,pos={870,70},help={"Uncertainty of Qz Data"}
//     else
  	PopupMenu dQdata  value=WaveList("*",";",""),mode=modedqz,bodyWidth=150, title="dQ",fstyle=1,disable=0,size={80,200},proc=datadQInput,pos={870,70},help={"Uncertainty of Qz Data"}
 //   endif
       Variable/G globmoderq4=moderq4,globmodedrq=modedrq,globmodeqz=modeqz,globmodedqz=modedqz
	RQ4data=WaveName("",moderq4-1, 4)
	dRQ4data=WaveName("",modedrq-1, 4)
	Qzdata=WaveName("",modeqz-1, 4)
      dQdata=WaveName("",modedqz-1, 4)	
		String/G globrq4data=RQ4data
	String/G globdrq4data=dRQ4data
      String/G globqzdata=Qzdata
      String/G globdqdata=dQdata
		String/G globrq4dataold=RQ4data
	String/G globdrq4dataold=dRQ4data
      String/G globqzdataold=Qzdata
      String/G globdqdataold=dQdata
		String/G globrqdata=RQ4data
	String/G globdrqdata=dRQ4data

//        String Rq_Fit=globdrq4data+"_Cal"
      If ((WaveExists(prof)<1 || exists (globprosldz)<1))
  //  checkhold=1
         checkhold[0]=1
        checkhold[Nlay+1]=1
        checkhold[nopara-1]=1
        checkhold[NLay+Nlay+2]=1
         
      endif

	j=0
	k=1
	kk=0
 for (i=0; i<globNpara; i=i+1)
       names="para"+num2str(i)
       namelow="low"+num2str(i)
       namehigh="high"+num2str(i)
       nametempw="tempw"+num2str(i)
       nametitle="title"+num2str(i+12)
       
       if (i<=(globNlay+1))
       if (i==0)
 //      TitleBox  super title="                                                                                                                                  Superstrate \F'Symbol'(  ¥  )    ",pos={276,115+i*20+47},fstyle=1,fsize=12,frame=5,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)

       TitleBox  super2 title="                                                  ",pos={504,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)

       TitleBox  super1 title="                                                  ",pos={297,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
//      TitleBox  super0p5 title="    ",pos={800,115+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
       TitleBox  super title="        \W545   Superstrate            ",pos={796,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,(65280,43520,0)fcolor=(65000,65000,65000),(65280,21760,0)
       TitleBox  super1p5 title="                    ",pos={709,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)

       TitleBox  $nametitle title=" S ",  pos={270,114+i*20+46},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}  //title=num2str(i)    
//       TitleBox  colorboxsuper  title="                                    ",  pos={276+68,115+i*20+47},fstyle=1,frame=5,labelBack=(65280,43520,0),help={"Superstrate"}  //title=num2str(i)    
    TitleBox  super3 title="    ",pos={702,114+i*20+50-2},fstyle=1,fsize=17,frame=0,labelBack=(65280,43520,0),help={"Incident Medium"}
//    GroupBox Mbox frame=1,size={734,25},pos={270,114+i*20+50-4}

       elseif (i==(globNlay+1))
          KillControl sub
          KillControl sub1
          KillControl sub2
         KillControl sub3
   //       KillControl sub4
          KillControl sub1p5
   //       KillControl sub0p5
          KillControl Sbox
        TitleBox  sub2 title="                                                   ",  pos={503,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)
       
       TitleBox  sub1 title="                                                  ",  pos={296,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)
 
       TitleBox  sub title="            \W545 Substrate              ",  pos={796,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)
       TitleBox  sub1p5 title="                    ",pos={709,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000),(65280,21760,0)
       TitleBox  $nametitle title=" S ",  pos={270,116+i*20+46},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}       //title=num2str(i)
       TitleBox  sub3 title="  ",pos={702,115+i*20+50-1},fstyle=1,fsize=17,frame=0,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000),(65280,21760,0)        
   //    TitleBox  subo title="               ",pos={504,115+i*20-23},fstyle=1,fsize=10 ,frame=0,labelBack=(60416,59648,55296),help={"Substrate"}//,fcolor=(65000,65000,65000),(65280,21760,0)        

//       GroupBox Sbox frame=1,size={734,25},pos={270,116+i*20+46}//,labelBack=(0,65280,23024),help={"Substrate"} 
     
       else
       TitleBox  $nametitle title=num2str(i),  pos={280,115+i*20+51.5},fstyle=1,frame=0,help={"layer number "+num2str(i)}        
       endif
       low="K"+num2str(i)
       if (i==0)
       TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=(65280,43520,0)
       elseif (i==(globNlay+1))
       TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=(0,65280,38024)
       else
       TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=0
       endif
       if (i==0)
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i],labelBack=(65280,43520,0),help={"     Hold?"} 
       SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},labelBack=(65280,43520,0),pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},labelBack=(65280,43520,0),pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],labelBack=(65280,43520,0),pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
       SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},labelBack=(65280,43520,0),pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}

       elseif (i==(globNlay+1))
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i],labelBack=(0,65280,38024),help={"     Hold?"} 
       SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},labelBack=(0,65280,38024),pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},labelBack=(0,65280,38024),pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],labelBack=(0,65280,38024),pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
       SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},labelBack=(0,65280,38024),pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
        TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0
       else
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} 
       endif
       SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
       SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}

       elseif (i<=(2*globNlay+2))
       low="K"+num2str(i)
        namefun=""
       for (kk=0;kk<=j;kk=kk+1)
        namefun=namefun+"f"
        endfor
        Killcontrol $namefun
//       String/G gPopupList="Error;LGaussian;RGaussian;LParabola;RParabola;Linear"
       PopupMenu $namefun  value="Erf;LGaussian;RGaussian;LParabola;RParabola;LExp;RExp;Linear;MyOwn",bodyWidth=65,size={70,100},mode=(fitfun1[j]+1),proc=funselect,pos={708,(102+52+(i-globNlay-1)*20)},help={"The function to describe the interface  (Note that the thickness of interfaces is 4 time of the value for roughness.)" }
       if (i==(2*globNlay+2))
       CheckBox $low,pos={510,(106+51+(i-globNlay-1)*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} //,labelBack=(0,65280,38024)
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={536,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0.001,4000,10},pos={583,(105+51+(i-globNlay-1)*20)},proc=autoRup,format="%4.1f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={620,(105+51+(i-globNlay-1)*20)},limits={0,4000,0},format="%4.2f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={656,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}

 //      PopupMenu $namefun  value="Erf;LGaussian;RGaussian;LParabola;RParabola;Linear;MyOwn",bodyWidth=65,size={70,100},mode=(fitfun1[j]+1),popColor=(0,65280,23024),proc=funselect,pos={708,(102+60+(i-globNlay-1)*20)},help={"The function to describe the interface  (Note that the thickness of interfaces is 4 time of the value for roughness.)" }
        else
       CheckBox $low,pos={510,(106+51+(i-globNlay-1)*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} 
 //      PopupMenu $namefun  value="Erf;LGaussian;RGaussian;LParabola;RParabola;Linear;MyOwn",bodyWidth=65,size={70,100},mode=(fitfun1[j]+1),proc=funselect,pos={708,(102+60+(i-globNlay-1)*20)},help={"The function to describe the interface  (Note that the thickness of interfaces is 4 time of the value for roughness.)" }
  //     PopupMenu $namefun labelBack=(0,65280,38024)
        endif
       TitleBox $low+"T" title=low,pos={532,(106+51+(i-globNlay-1)*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={536,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0.001,4000,10},pos={583,(105+51+(i-globNlay-1)*20)},proc=autoRup,format="%4.1f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={620,(105+51+(i-globNlay-1)*20)},limits={0,4000,0},format="%4.2f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={656,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
      
       j=j+1
       elseif (i<nopara-1)//(i>(2*globNlay+2)
       low="K"+num2str(i)
       CheckBox $low,pos={805,(116+50+(i-2*(globNlay+1))*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"}
       TitleBox $low+"T" title=low,pos={824,(116+50+(i-2*(globNlay+1))*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={828,(115+50+(i-2*(globNlay+1))*20)},disable=checkhold[i] ,help={"Low limit constraint (Note that this value should be larger than (2 * top interfacial roughness+2*bottom interfacial roughness).)"}
         SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={1,20000,20},pos={875,(115+50+(i-2*(globNlay+1))*20)},proc=autoRup,format="%4.1f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={912,(115+50+(i-2*(globNlay+1))*20)},limits={0,9000,0},format="%4.1f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={948,(115+50+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       
       k=k+1
       else
      low="K"+num2str(i)
      GroupBox sfbox frame=1,size={250,30},pos={534,(145+45+(i-2*(globNlay+1))*20)}
      CheckBox $low,pos={570,(153+45+(i-2*(globNlay+1))*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"}
     TitleBox titlesf title="RScale",  pos={510,(149+45+(i-2*(globNlay+1))*20)},fstyle=1,frame=4,labelBack=(60416,59648,55296),help={"To rescale the calculation values of R(Q4) in case, otherwise it should be set to 1."}   
      TitleBox $low+"T" title=low,pos={592,(153+45+(i-2*(globNlay+1))*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={599,(152+45+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}//,format="%f"
         SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0,1000,0.1},pos={646,(152+45+(i-2*(globNlay+1))*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={683,(152+45+(i-2*(globNlay+1))*20)},limits={0,1000,0},format="%5.3f",proc=keepscald,help={"Results: (This Scaling factor value will be used for all the R(Q4) calculations and stored as 'globsf' and in 'tempw'.)"}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={719,(152+45+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       endif
 endfor

k=((globNlay+1)*20+115)-200
if (k>0)
j=((globNlay+1)*20+115)+50
else
j=250
endif  
Variable jfl=j    
  Variable comcorc=0
    if (jfl>365)
    comcorc=0.1
    endif
   SetVariable /Z comWinIn bodyWidth=865, frame=0, labelback=(60416,59648,55296),title=" ",pos={90, ((jfl*(1+comcorc)+40+45+40)*72/96+372)}, proc=ComLineinWin, value=globcomWin//,labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
//     TitleBox comman title="Command (? :^ )",pos={50,(j+40+45+40)*72/96+372}, frame=0
     TitleBox comman title="Note:",pos={50,((jfl*(1+comcorc)+40+45+40)*72/96+372)}, frame=0,help={"Note ..."}//, labelback=(60416,59648,55296)

      GroupBox gb1 frame=1,size={1,(j-52)},pos={250,60+50}     
     GroupBox gb2 frame=1,size={1013,1},pos={5,j+10+50}     
     TitleBox titlegraph title="PLOTS",  pos={50, j+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     CheckBox autoR,pos={210, j+88},title="",variable=globautoR, proc=autoRupbutt,mode=0,labelBack=(60416,59648,55296),help={"     Automatically update R (R_Pre_Cal; green line w/ no xi sqr update) in the graph whenever the SLD is updated."}  
     CheckBox autoS,pos={691, j+88},title="",variable=globautoS, proc=autoSupbutt,mode=0,labelBack=(60416,59648,55296),help={"     Automatically update SLD profile by changing the fit parameter IN values."} 
     
   Button  titlegraph0,pos={230, j+40+45},size={92,20},fColor=(60416,59648,55296),fstyle=1   //pos={1027,80}
  Button  titlegraph0,proc=MakeGraph_RButton,title="Reflectivity",help={"Make a new graph : "+globrq4data+" and Rq_Fit vs. "+globqzdata}   
   Button  titlegraph1,pos={711, j+40+45},size={92,20},fColor=(60416,59648,55296),fstyle=1   //pos={1027,80}
  Button  titlegraph1,proc=MakeGraph_sldButton,title="SLD Profile",help={"Make a new graph : "+globprosldz+" vs. "+globproz}   
     globNLay_1=NLay
    If (WaveExists(prof)<1 &&WaveExists(zz)<1)//|| exists (globprosldz)<1) //No. of total points
    String /G globprew="prew"
    String prew                               
//    Make /O /D /N=(Npoint*(Nlay+1)+1) prof,zz//,dprof  //+(nl+1)
   Make /O /D /N=11 prof,zz//,dprof  //+(nl+1)
  
    String/G  globprosldz="prof",globproz="zz"
    zz=x*50-50
    prof=6.25
    //prof=(abs(7*sin(Pi*x/20))) 
    prof[0]=0
    prof[1]=0
    
    for (i=0;i<nopara;i=i+1)
     if (i<Nlay+2)    
    w_fit[i]=i
           if (i==Nlay) 
          w_fit[i]=3.16
//          checkhold[i]=1
       endif

       if (i==Nlay+1) 
          w_fit[i]=2.07
//          checkhold[i]=1
       endif
     T_Constraints_temp [2*i]=Num2Str(0.5)
     T_Constraints_temp [2*i+1]=Num2Str(w_fit[i]*2)

//    checkhold[i]=0
    elseif (i<(Nlay+2+Nlay+1))
      w_fit[i]=1   
  //    checkhold[i]=0   
     T_Constraints_temp [2*i]=Num2Str(1)
     T_Constraints_temp [2*i+1]=Num2Str(w_fit[i]*2)

    elseif (i<nopara-1)
     w_fit[i]=20 
          T_Constraints_temp [2*i]=Num2Str(w_fit[i]*0.2)
     T_Constraints_temp [2*i+1]=Num2Str(w_fit[i]*2)

//     checkhold[i]=0
     else
     w_fit[i]=1 
          T_Constraints_temp [2*i]=Num2Str(w_fit[i]*0.2)
     T_Constraints_temp [2*i+1]=Num2Str(w_fit[i]*2)

//     checkhold[i]=1
     endif
    endfor
//<<    tempw=0
     T_Constraints_temp=" "
     for (i=0;i<nopara;i=i+1)
       if (i>(NLay+1) && i<(Nlay+2+Nlay+1))
         T_Constraints_temp [2*i]=Num2Str(1)
       endif
      endfor
    
   endif
 //    Profile4Fit(w_fit,x)
 
        String/G globcheckhold="checkhold"
     If (WaveExists(Rq_Fit)<1 )
     Duplicate/O /D $RQ4data  Rq_Fit 
     elseif (gsw>0)
     wave Qzdata1=$Qzdata
//     Wave Rq_Fit
      Rq_Fit= Rq_Fit/Qzdata1^4
     endif
     Duplicate/O /D w_fit W_coef  
      
 
         Display /W=(37,(j+40+45+40)*72/96,370,(j+40+45+40)*72/96+187) /HOST=$globExptTitle  /N=RQplotInPanel $RQ4data Rq_Fit vs $Qzdata as "ReflectivityPlot4RQFitGraph"
     	    Label left "\\f01"+RRQ4nPlot
          Label bottom "\\f01Q\Bz\M  (Å\\S-1\\M)"
          ModifyGraph  framestyle=5,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280), rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1,lsize(Rq_Fit)=2, lowTrip=0.0001//,grid=1,gridRGB=(65280,54528,32768)
          ModifyGraph gbRGB=(57000,57000,57000), wbRGB=(54000,54000,54000),lblRot(left)=-90
          ErrorBars $RQ4data Y ,wave=($dRQ4data,$dRQ4data)//XY,wave=($dqdata,$dqdata)
  //       TitleBox Rnplot title=RRQ4nPlot,pos={52, j+220},fsize=12,fstyle=1, frame=0, labelBack=(53760,53760,53760),variable=RRQ4nPlot   //Left Label to vary by slider
    if (pfyn>0)
        Cursor /S=1 /W=$globExptTitle#RQPlotInPanel A $RQ4data leftx($RQ4data)
        Cursor /S=1 /W=$globExptTitle#RQPlotInPanel B $RQ4data numpnts($RQ4data)
   else
//SetActiveSubWindow NR#RQPlotInPanel
        Cursor /K /W=$globExptTitle#RQPlotInPanel A //$rq4data1
        Cursor /K /W=$globExptTitle#RQPlotInPanel B //$rq4data1
//SetAxis /W=NR#RQPlotInPanel /A bottom
  endif

 //Profile4Fit(w_fit,x)
               Display /W=(400,(j+40+45+40)*72/96,733,(j+40+45+40)*72/96+187) /HOST=$globExptTitle /N=SLDplotInPanel $globprosldz vs $globproz
     	   Label left "\\F'Arial'\\f0110\\S6\\MSLD (Å\\S-2\\M)"
          Label bottom "\\f01z  (Å)"
          ModifyGraph  framestyle=5, mirror=1,minor=0,standoff=1,tick=2,mode($globprosldz)=4,marker($globprosldz)=19,msize($globprosldz)=2,lsize($globprosldz)=1.5,opaque($globprosldz)=1,zColor($globprosldz)={$globprosldz,*,*,Rainbow},grid=1,gridRGB=(60000,60000,60000)//(65280,54528,32768)
          ModifyGraph gbRGB=(57000,57000,57000), wbRGB=(54000,54000,54000)//,useMrkStrokeRGB=1//,  mrkStrokeRGB($globprosldz)=(30464,30464,30464) 
    if (syn>0)
//    Variable cursorasld=pcsr(A,"NR#SLDPlotInPanel")
    Cursor /S=2 /C=(26368,0,52224) /W=$globExptTitle#SLDPlotInPanel A prof ceil((numpnts(prof)-1)/2)-1
    else
    Cursor /K /W=$globExptTitle#SLDPlotInPanel A //$rq4data1
    endif
 ///For symtric case///////////////////////////////////////////////////////////////////////////////////////////

   weps1=0.01
//<<  tempw=0
	Variable ii,jj

	   for (i=0;i<nopara;i=i+1)
 //        tempw[i]=W_coef[i]
         endfor
      SetActiveSubWindow $globExptTitle
 Variable /G globV_chisq
Variable /G globV_Rchisq
Variable /G globnpntsdata

    
   TitleBox chisqtitle title="\\F'symbol'c\\S2\\M\\Bn\\M =",pos={440, j+35+50},labelBack=(60416,59648,55296), frame=0
   SetVariable chisq1, title=" ", value=globV_chisq,frame=0,pos={468, j+40+50},limits={0,1000,0},size={50,20}, labelback=(60416,59648,55296),format="%8.23f",noedit=1
   SetVariable npntsdata, title="/ ",value=globnpntsdata,frame=0,pos={518, j+40+50},limits={0,1000,0}, labelback=(60416,59648,55296),size={40,20},noedit=1
   SetVariable chisq2, title="= ",value=globV_Rchisq,frame=0,pos={560, j+39+50},limits={0,1000,0}, labelback=(60416,59648,55296),size={100,20},noedit=1 //,format="%7.3f" //
 
//   SetVariable /Z comWinIn value=globcomWin,  pos={915,(j+40+45+40)*72/96+372}, bodyWidth=830, frame=0,title=" ", proc=ComLineinWin//,labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
//     TitleBox comman title="Command (? :^ )",pos={50,(j+40+45+40)*72/96+372}, frame=0

 
     if (GlobNLay>9)
      GroupBox gb3 frame=1,size={1,695+(globNLay-9)*18+25},pos={1020,60}     
      GroupBox bottomgb0 frame=1,size={1149,1},pos={0,757+(globNLay-9)*18+25}
     GroupBox rightg3 frame=1,size={1,758+(globNLay-9)*18+25},pos={1147,0}  
      else
       GroupBox gb3 frame=1,size={1,695},pos={1020,60}     
      GroupBox bottomgb0 frame=1,size={1149,1},pos={0,757}
     GroupBox rightg3 frame=1,size={1,758},pos={1147,0}  
     endif



 Button rst1,pos={1040,260},size={92,20},fColor=(26368,0,52224),fstyle=1   //pos={1027,80}
  Button rst1,proc=UserRestartPanel_ContButton2,title="Do Fit",help={"To Start fitting."}   
   Button upbutton,pos={1040,110},size={92,20},fColor=(65280,21760,0),fstyle=1   //pos={1027,80}
  Button upbutton,proc=UserUpdatePanel_ContButton,title="ReNew",help={"To reload this control window; Some of features in the graph could be changed."}   
//      Button rst4i,pos={1030,140},size={92,20},fColor=(65280,43520,0),fstyle=1//pos={/{1027,110}
//  Button rst4i,proc=UserIn2InPanel_ContButton,title="IN\\F'Symbol'® \\M\\F'Arial'OUT",help={"To copy input paramters to output."}
    Button rst4,pos={1040,140},size={92,20},fColor=(65280,43520,0),fstyle=1//pos={/{1027,110}
  Button rst4,proc=UserOut2InPanel_ContButton,title="OUT\\F'Symbol'® \\M\\F'Arial'IN",help={"To copy output paramters to input."}
   Button rst2,pos={1040,170},size={92,20},fColor=(0,5000,0),fstyle=1//pos={1027,140}
  Button rst2,proc=UserPara2SLDPanel_ContButton,title="IN \\F'Symbol'® \\M\\F'Arial'SLD",help={"To calculate SLD profile from the input paramters."}
 Button rst5,pos={1040,200},size={92,20},fColor=(0,43520,65280),fstyle=1//pos={1027,170},
  Button rst5,proc=UserEditSLD_ContButton,title="SLD Draw",help={"To Edit the present SLD profile on the graph or to return the graph to the normal mode."}
  Button rst3,pos={1040,230},size={92,20},fColor=(0,15872,50000),fstyle=1//pos={1027,170},
  Button rst3,proc=UserSLD2RPanel_ContButton,title="SLD \\F'Symbol'® \\M\\F'Arial'R(Q4)",help={"To calculate reflectivity (R or RQ4; blue line) and xi sqr from the present SLD profile. "}

 Button LWF,pos={1040,80},size={92,20},fColor=(55000,0,0),fstyle=1//pos={1027,170},
  Button LWF,proc=LoadWaveFromFile,title="LoadFile",help={"Choose a text file to load your data. Use only if you want to have the title from the file name you would load."}
 //Expt_Title="ddd"
 

// print  "kk=",Expt_Title  LoadWaveFromFile
   
 Button rst1a,pos={230,10-2},size={20,20},fColor=(26368,0,52224),fstyle=1   //pos={1027,80}
  Button rst1a,proc=UserRestartPanel_ContButton2,help={"To start fitting."},title="F"
   Button upbuttona,pos={80,10-2},size={20,20},fColor=(65280,21760,0),fstyle=1   //pos={1027,80}
  Button upbuttona,proc=UserUpdatePanel_ContButton,help={"To reload this control window; Some of features in the graph will be changed."},title="N"   
//      Button rst4ia,pos={110,15},size={20,20},fColor=(65280,43520,0),fstyle=1//pos={/{1027,110}
 // Button rst4ia,proc=UserOut2InPanel_ContButton,help={"To copy input paramters to output."},title="I"
    Button rst4a,pos={110,10-2},size={20,20},fColor=(65280,43520,0),fstyle=1//pos={/{1027,110}
  Button rst4a,proc=UserOut2InPanel_ContButton,help={"To copy output paramters to input."},title="I"
   Button rst2a,pos={140,10-2},size={20,20},fColor=(0,5000,0),fstyle=1//pos={1027,140}
  Button rst2a,proc=UserPara2SLDPanel_ContButton,help={"To calculate SLD profile from the input paramters."},title="S"
 Button rst5a,pos={170,10-2},size={20,20},fColor=(0,43520,65280),fstyle=1//pos={1027,170},
  Button rst5a,proc=UserEditSLD_ContButton,help={"To Edit the present SLD profile in the graph or to return the graph to the normal mode."},title="D"
   Button rst3a,pos={200,10-2},size={20,20},fColor=(0,15872,50000),fstyle=1//pos={1027,170},
  Button rst3a,proc=UserSLD2RPanel_ContButton,help={"To calculate reflectivity (R or RQ4; blue line) and xi sqr  from the present SLD profile."},title="R"
 Button LWFa,pos={50,10-2},size={20,20},fColor=(55000,0,0),fstyle=1,fsize=14//pos={1027,170},
  Button LWFa,proc=LoadWaveFromFile,title="L",help={"Choose a text file to load your data. Use this button only one time per the same data file."}

  String namesim//, nametempwim
   Make /O /N=(globNlay+2) Im_SLD_in//,Im_SLD_out
   String /G globImSLDin="Im_SLD_in"//,globImSLDout="Im_SLD_out"  

if (globcmplxcalyn>1)
     TitleBox titleImag title="\f01   Imaginary \f00\r    SLD (10\\S-6\\MÅ\\S-2\\M)",  pos={1040,432},fstyle=1,frame=0,help={" Imaginary part of SLD; The imaginary profile is 'prof_IM' vs 'zz'."}//,help={"Some SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, D2O=6.25, h-Toluene=0.94, Cyclohexane=-0.278, P2VP=1.87, h-PS=1.4, d-PS=6.4"} //,frame=4//,labelBack=(55000,55000,65000)
 //    TitleBox titleImaginout title="Real         Imaginary",  pos={1046,447},fstyle=0,frame=0//,help={"Some SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, D2O=6.25, h-Toluene=0.94, Cyclohexane=-0.278, P2VP=1.87, h-PS=1.4, d-PS=6.4"} //,frame=4//,labelBack=(55000,55000,65000)
 //    GroupBox SLDIMbox frame=1,size={102,83+20*i},pos={1025,475}

 for (i=0; i<=globNlay+1; i=i+1)
       namesim="ImSLDin"+num2str(i)
 //      nametempw="ImSLDout"+num2str(i)
        low="K"+num2str(i)
        if (i==0)
        TitleBox  $low+"Tim" title="M               ",pos={1045,471+20*i},fstyle=1,fsize=13,frame=5,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
       elseif (i==(globNlay+1))
      KillControl SLDIMbox
       TitleBox  $low+"Tim" title="S               ",  pos={1045,471+20*i},fstyle=1,fsize=13,frame=5,labelBack=(0,65280,38024),help={"Substrate"}       //title=num2str(i)
      GroupBox SLDIMbox frame=1,size={102,83+20*i},pos={1035,425}

       else    
       TitleBox $low+"Tim" title=num2str(i),pos={1050,477+20*i},frame=0
       endif
       SetVariable $namesim bodyWidth=55,title=" ",value=$globImSLDin[i],pos={1069,475+20*i},limits={-100,100,0},proc=autoRup,help={" Imaginary part of SLD; These are fixed for fitting and stored in 'Im_SLD_in'."}//,format="%4.2f"
//       SetVariable $nametempw bodyWidth=35,title=" ",value=$globImSLDout[i],pos={1077,465+20*i},limits={-10,10,0},help={" Results; these outputs are calculated as ImSLD_input*ReSLD_out/ReSLD_in."}//,format="%5.3f"
endfor
//       Im_SLD_out=Im_SLD_in
else 

   KillControl SLDIMbox
     Im_SLD_in=0
 //    Im_SLD_out=0
endif
//  Profile4Fit( )
   SetVariable /Z comWinIn bodyWidth=865, frame=0, labelback=(60416,59648,55296),title=" ",pos={90, ((jfl*(1+comcorc)+40+45+40)*72/96+372)}, proc=ComLineinWin, value=globcomWin//,labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
//     TitleBox comman title="Command (? :^ )",pos={50,(j+40+45+40)*72/96+372}, frame=0
     TitleBox comman title="Note:",pos={50,((jfl*(1+comcorc)+40+45+40)*72/96+372)}, frame=0,help={"Note ..."}//, labelback=(60416,59648,55296)

  Variable /G globstop2sld=1
  Duplicate /O $dRQ4data dRQ_temp 
   Profile4Fit(w_fit,x)
  KillWaves dRQ_temp 
SetWindow  $globExptTitle, hook=winhookproc

// FitRgeneral3()
// print ExptTitle
End
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function winhookproc(infoStr)
String infoStr

String wn=WinName(0,1)
//String ExptTitle//=globExptTitle
if( StrSearch(infoStr,"EVENT:activate",0) >= 0)
 // SetIgorMenuMode "Graph","Append Traces to G", enableItem
//    String wn=WinName(0,1)
    SetDataFolder root:$wn   
    String /G globExptTitle
           globExptTitle=wn
                
            FitRgeneral3( )
    SetDataFolder root:$wn   
    SetIgorMenuMode "Graph", "Append Traces to Graph",DisableItem
   SetIgorMenuMode "Analysis", "Curve Fitting",DisableItem
    SetIgorMenuMode "Windows", "Control", DisableItem
//   Execute  "Menu Graph Submenu (Append traces to graph...  end  End"
elseif ( StrSearch(infoStr,"EVENT:deactivate",0) >= 0)
 SetIgorMenuMode "Graph", "Append Traces To Graph",EnableItem
 SetIgorMenuMode "Analysis", "Curve Fitting",EnableItem
 SetIgorMenuMode "Windows", "Control", EnableItem
 
//  elseif ( StrSearch(infoStr,"EVENT:deactivate",0) >= 0||StrSearch(infoStr,"EVENT:kill",0) >=2) 
 elseif ( StrSearch(infoStr,"EVENT:kill",0) >=2)

  // SetIgorMenuMode "NeutronReflectivity","Other R Calculation: nosmear", disableItem
       //  SetIgorMenuMode "Windows","Graph Macros", DisableItem
   //       DoWindow /K "Close Window"
   
		SetDataFolder root:
		if (StrSearch(infoStr,"EVENT:kill",0) >=2)
	//	       Execute "Cancel"
		      
		      Variable yeskillDF=0


 //       DoWindow /K Stop4NewDFName 
  //      NewPanel /N=Stop4NewDFName /W=(2,0,450,100)
 //       PopupMenu $wn  value="No;Yes",mode=yeskillDF, pos={110,20},fstyle=1, size={80,100},bodyWidth=250, title= "Remove '"+wn+"' permanently? (0(No)/1(Yes))"	/////////,fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
  //      Button buttonSNDFN,pos={155,65},size={92,20},fstyle=1
 //       Button buttonSNDFN,proc=Stop4NewDFName_ContButton,title="Continue"
  //      PauseForUser Stop4NewDFName


		      
		  	Prompt  yeskillDF, "Remove '"+wn+"' permanently? (0(No)/1(Yes))"		  		
             	DoPrompt "Kill DataFolder named '"+wn+"'",yeskillDF  //<< this command gives a choice for killing previous datafolder but had a problem with FitRgeneral2()<<problem solved!!
                   if (V_flag)
             	 SetDataFolder root:$wn
              	 FitRGeneral2()

                    elseif (yeskillDF!=0)
   //                 Execute "Cancel"
             	  
                      KillWindow $wn 
             	  KillDataFolder root:$wn
             //	  else
             //	 Execute "Cancel"
             	  //SetDataFolder root:$wn
             	 // FitRGeneral2()
 
             	 endif
      //      	            	    SetIgorMenuMode "Graph", "Append Traces To Graph",EnableItem
     //                 SetIgorMenuMode "Windows", "Control", EnableItem
  //                         	    SetIgorMenuMode "Graph", "Append Traces To Graph",EnableItem
 //                      SetIgorMenuMode "Windows", "Control", EnableItem
      //            endif
		endif
 endif


END
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function  FitRgeneral3( )  ///Renew Window panel
      
 
            SVAR ExptTitle=globExptTitle
      String savDF=GetDataFolder(1)
     // print  savDF
      NewDataFolder /S/O root:$ExptTitle
 
  String /G globExptTitlepre

      Variable r,b,i,j,k,kk,v1,z0,df0
       
//     String savDF=GetDataFolder(1)
     Variable Nlay=NumVarOrDefault("globNlay", 3)
     Variable Npoint=NumVarOrDefault("globNpoint", 50)
     Variable yn=NumVarOrDefault("globyn", 0)
     Variable syn=NumVarOrDefault("globsyn", 0)
      Variable ssyn=NumVarOrDefault("globssyn", 0)
     Variable thick=NumVarOrDefault("globthick", 6)
    Variable pfyn=NumVarOrDefault("globpfyn", 0)
     Variable nopara=NumVarOrDefault("globNpara", 2)
     Variable rswitch=NumVarOrDefault("globrswitch", 1)
     Variable sf=NumVarOrDefault("globsf", 1)
//Variable update911=NumVarOrDefault("globupdate911", 0)
//String ExptTitle=StrVarOrDefault ("globExptTitle", "Experiment")
    SVAR RQ4data=globrq4data
    SVAR dRQ4data=globdrq4data
    Wave RQdata1=$RQ4data, dRQdata1=$dRQ4data
    String RQdata=StrVarOrDefault ("globrqdata","")
    String dRQdata=StrVarOrDefault ("globdrqdata","")    
    String Qzdata=StrVarOrDefault ("globqzdata","")    
    String dQdata=StrVarOrDefault ("globdqdata","")   
    String fitfun= StrVarOrDefault ("globfitfun","")  
   Variable moderq4= NumVarOrDefault ("globmoderq4",1)  
   Variable modedrq= NumVarOrDefault ("globmodedrq",1)  
   Variable modeqz= NumVarOrDefault ("globmodeqz",1)  
   Variable modedqz= NumVarOrDefault ("globmodedqz",1)  
 //  Variable winup=NumVarOrDefault ("globwinup",0)
  //  String www=StrVarOrDefault ("globwww","")      
    Variable cmplxcalyn=NumVarOrDefault("globcmplxcalyn",1)
// Variable cmplxcalyn1=cmplxcalyn
Variable /G globcmplxcalyn= cmplxcalyn//1
     
	Variable/G globsyn=syn
	Variable/G globyn=yn

	Variable/G globpfyn=pfyn	
	Variable/G globNpoint=Npoint	
	Variable/G globNlay=Nlay	
	Variable /G globNLay_1

	Variable/G globrswitch=rswitch
	Variable/G globsf=sf
//	Variable/G globwinup=winup
//     Wave w_fit
   Variable /G globautoR
   Variable /G globautoS

DoWindow RQ4vsQCalFitE 
   
   
	if (V_Flag)
	    return -1
	endif
// DefaultFont "MS Sans Serif"
         nopara=(globNlay*3+3+1)  //1 for rescaling R incase of neutron coming through other superstrate  than air
   Variable fk,pt4insdel
 Variable/G globNpara=nopara
    Wave checkhold//,w_fit,tempw
  	Variable  NLay_1= globNLay_1
  	pt4insdel=0
  	      for (fk=1;fk<=NLay_1+1;fk=fk+1)
  	        if(checkhold[fk]>0)
  	        pt4insdel=fk-1
  	       // fk=NLay_1+2
  	        Break
  	        else
  	        pt4insdel=0
  	        endif
  	      endfor
       If (globNLay>globNLay_1)                      //add (delete) points from 1st layer when Nlay is changed.
       InsertPoints 1+pt4insdel,globNLay-globNLay_1,checkhold,w_fit,tempw
                         
       InsertPoints 0+pt4insdel,globNLay-globNLay_1,fitfun1
       InsertPoints 2*(1+pt4insdel),2*(globNLay-globNLay_1), T_Constraints_temp
       InsertPoints globNLay+2+pt4insdel,globNLay-globNLay_1,checkhold,w_fit,tempw
        InsertPoints 2*((globNLay+2)+pt4insdel),2*(globNLay-globNLay_1), T_Constraints_temp
       InsertPoints 2*(globNLay+1)+1+pt4insdel,globNLay-globNLay_1,checkhold,w_fit,tempw
                            
       InsertPoints 2*(( 2*(globNLay+1)+1)+pt4insdel),2*(globNLay-globNLay_1), T_Constraints_temp
         if (globcmplxcalyn>1)
         InsertPoints 1+pt4insdel,globNLay-globNLay_1,Im_SLD_in
         endif
       elseif (globNLay<globNLay_1)
       pt4insdel=pt4insdel
       DeletePoints 1+pt4insdel,abs(globNLay_1-globNLay),checkhold,w_fit,tempw
       DeletePoints 0+pt4insdel,abs(globNLay-globNLay_1),fitfun1
       DeletePoints 2*(1+pt4insdel),2*abs(globNLay-globNLay_1), T_Constraints_temp
       DeletePoints globNLay+2+pt4insdel,abs(globNLay-globNLay_1),checkhold,w_fit,tempw
       DeletePoints 2*((globNLay+2)+pt4insdel),2*abs(globNLay-globNLay_1), T_Constraints_temp
       DeletePoints 2*(globNLay+1)+1+pt4insdel,abs(globNLay-globNLay_1),checkhold,w_fit,tempw
      DeletePoints 2*(( 2*(globNLay+1)+1)+pt4insdel),2*abs(globNLay-globNLay_1), T_Constraints_temp      
         if (globcmplxcalyn>1)
         DeletePoints 1+pt4insdel,abs(globNLay_1-globNLay),Im_SLD_in
         endif

       endif
       Redimension /N=(nopara) checkhold
 //     Make /O /D /N=(nopara) checkhold

 Make /O /D /N=(nopara) w_fit,weps1
 // w_fit[1+pt4insdel]=1; w_fit[globNLay+2+pt4insdel]=1;w_fit[2*(globNLay+1)+1+pt4insdel]=4
   //   Duplicate/O /D w_fit, tempw  //<<<081706
   Wave tempw     //<<<081706
         tempw[nopara-1]=sf
         
   Make /O /T /N=(nopara) namepara
      Make /O /T /N=(2*nopara) namecnstrnt
      Make /O /T /N=(2*nopara) T_Constraints_temp//,T_Constraints
      Make /O /D /N=(globNlay+1) fitfun1
      
      
             If (globNLay>globNLay_1)   
                         for (fk=globNLay+2+pt4insdel;fk<(globNLay+2+pt4insdel+globNLay-globNLay_1);fk=fk+1)
                            w_fit[fk]=1
                            w_fit[fk+(globNLay+1)]=4
             //               tempw[fk]=1
                            T_Constraints_temp[2*fk]="1"
                           endfor
   endif

      
      fitfun="fitfun1"
            String/G globcheckhold="checkhold"
      String/G RRQ4nPlot
      String/G dRQ4nPlot
  	String/G  globwww="w_fit"
      String/G globfitfun="fitfun1"
	String/G globT_Constraints_temp="T_Constraints_temp" 
	String /G globprosldz,globproz
	String names,namelow,namehigh,low,nametempw,nametitle,namefun,Rdata,dRdata,Qdata,dQzdata
          if (rswitch>0)
     	   RRQ4nPlot="RQ\\S4"
     	   dRQ4nPlot="SigRQ\\S4"
     	   else
     	   RRQ4nPlot="R"
     	   dRQ4nPlot="SigR"     	   
     	   endif
  String /G globExptTitle=ExptTitle

      ModifyGraph /W=$globExptTitle gbRGB=(60416,59648,55296)
    KillControl tiltleIn
        SetVariable tiltleIn value=globExptTitle, bodyWidth=135, title=" ", proc=ExtTitleUp1, pos={177,36},labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
 
   String /G globExptTitlepre=globExptTitle

              j=727 
     TitleBox title0 title="Neutron",  pos={385,14},fsize=22,fstyle=1,font="Lucida Calligraphy",frame=0, fcolor=(20000,20000,20000),help={"Nuetron and X-Ray Reflectivity Analysis ..." }//(370,9),labelBack=(55000,55000,65000) //"Monotype Corsiva"
     TitleBox title01 title="Reflectivity",  pos={590,14},fsize=22,fstyle=1,font="Lucida Calligraphy",frame=0, fcolor=(20000,20000,20000),help={"Nuetron and X-Ray Reflectivity Analysis ..." }//(370,9),labelBack=(55000,55000,65000) //"Monotype Corsiva"
     TitleBox Company title="ORNL",  pos={1055,6},fsize=14,fstyle=1,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox Author title="Neutron Scattering Sciences Division",  pos={1000,25},fsize=9,fstyle=1,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox WDate title=date(),  pos={1027,40},fsize=10,fstyle=0,font="Times New Roman",frame=0, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
 Button nnbutton picture=ProcGlobal#nbutton,pos={510,7},size={5,5},proc=LogoButton,title="",help={" Developed by Jae-Hie J. Cho, Gregory S. Smith, and William A. Hamilton at the Oak Ridge National Laboratory"}
     GroupBox topgb0 frame=1,size={1140,1},pos={5,55}
//     TitleBox Inputddd title="INPUT DATA",  pos={50,45},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)     
      GroupBox gb0 frame=1,size={1013,1},pos={5,55+50}     
     TitleBox title1 title="GLOBAL VARIABLES",  pos={50,45+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox rticktitleR title="R",  pos={80,90+50},fsize=12,fstyle=1,frame=0//, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     TitleBox rticktitleRQ4 title="RQ\\S4\\M",  pos={180,83+50},fsize=12,fstyle=1,frame=0//, fcolor=(20000,20000,20000)//,labelBack=(55000,55000,65000)
     GroupBox rbox frame=1,size={180,30},pos={50,80+50}//,title="Reflectivity calculation"
     Slider objectR, pos={110,90+50},size={50,40},fsize=10,ticks=0,limits={0,1,1},value=rswitch,userTicks={tickNumbers,tickLabels},vert=0,side=0,proc=SliderobjectR, labelback=(60416,59648,55296),help={"To choose Reflectivity to be calculated; R or RQ4?"}
     SetVariable setvar0 //pos={180-142,115+50}
     SetVariable setvar1 //pos={180-142,135+50}
     SetVariable setvar2 //pos={180-142,155+50}
     SetVariable setvar3 //pos={180-142,175+50}
     SetVariable setvar4 //pos={180-142,195+50}
     TitleBox title2 title="FIT PARAMETERS",  pos={275,45+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title11a title="Layer",  pos={276,80+50},fstyle=1,frame=0//,frame=4//,labelBack=(55000,55000,65000)     
     TitleBox title11 title="No.",  pos={276,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)     
     TitleBox title3 title="SLD (10\\S-6\\MÅ\\S-2\\M)",  pos={385,76+50},fstyle=1,frame=0,help={"Some SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, D2O=6.25, h-Toluene=0.94,d-Toluene=5.66, P2VP=1.87, h-PS=1.4, d-PS=6.4, H2O=-0.56"} //,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title4 title="Interfacial Roughness (Å)  &",  pos={555,80+50},fstyle=1,frame=0,help={"Note that this roughness is a quarter of the interfacial thickness. To get STD roughness, divide these values by sqrt(2)"}//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title5 title="Shape",  pos={725,80+50},fstyle=1,frame=0,help={"The function to describe the interface" }//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title6 title="Thickness (Å)",  pos={875,80+50},fstyle=1,frame=0,help={"This value equal to  (2 * top interfacial roughness+2*bottom interfacial roughness)+ extra thickness."}//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title7 title="    Low      In            Out      High",  pos={338,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title8 title="    Low      In            Out      High",  pos={545,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title9 title="Functions",  pos={720,95+50},fstyle=0,frame=0,help={"The functions to describe the interface" }//,frame=4//,labelBack=(55000,55000,65000)
     TitleBox title10 title="    Low      In            Out      High",  pos={835,95+50},fstyle=0,frame=0//,frame=4//,labelBack=(55000,55000,65000)
       if (moderq4==0)
        moderq4=1
       endif
        if (modedrq==0)
         modedrq=1 
       endif
        if (modeqz==0)
        modeqz=1
        endif
        if (modedqz==0)
         modedqz=1
         endif

	PopupMenu RQdata value=WaveList("*",";",""),mode=moderq4,bodyWidth=150, title="R",fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
	PopupMenu dRQdata value=WaveList("*",";",""),mode=modedrq,bodyWidth=150, title="dR",fstyle=1,size={80,200},proc=datadRInput,pos={430,70},help={"Uncertainty of Reflectivity Data"}
	PopupMenu Qzdata  value=WaveList("*",";",""),mode=modeqz,bodyWidth=150, title="Q",fstyle=1,size={80,200},proc=dataQInput,pos={650,70},help={"Qz Data"}
//    if (globyn==0)
//	PopupMenu dQdata  value="sigQ Smear: Turned Off",mode=modedqz,bodyWidth=150, title="sigQ",fstyle=1,disable=2,size={80,200},proc=datadQInput,pos={870,70},help={"Uncertainty of Qz Data"}
//     else
  	PopupMenu dQdata  value=WaveList("*",";",""),mode=modedqz,bodyWidth=150, title="dQ",fstyle=1,disable=0,size={80,200},proc=datadQInput,pos={870,70},help={"Uncertainty of Qz Data"}
//    endif
	//  TitleBox Rtitle title="",pos={112,70}, frame=0,fstyle=1, variable=RRQ4nPlot   //Left Label to vary by slider
	//  TitleBox dRtitle title="",pos={313,70}, frame=0,fstyle=1, variable=dRQ4nPlot   //Left Label to vary by slider
 
      Variable/G globmoderq4=moderq4,globmodedrq=modedrq,globmodeqz=modeqz,globmodedqz=modedqz
		RQdata=WaveName("",moderq4-1, 4)
	dRQdata=WaveName("",modedrq-1, 4)


	Qzdata=WaveName("",modeqz-1, 4)
      dQdata=WaveName("",modedqz-1, 4)	
 		String/G globrqdata=RQdata
	String/G globdrqdata=dRQdata
      String/G globqzdata=Qzdata
      String/G globdqdata=dQdata
		String/G globrq4dataold=RQ4data
	String/G globdrq4dataold=dRQ4data
      String/G globqzdataold=Qzdata
      String/G globdqdataold=dQdata
      

	j=0
	k=1
	kk=0

if ( NLay!=NLay_1)
 for (i=0; i<globNpara; i=i+1)
       names="para"+num2str(i)
       namelow="low"+num2str(i)
       namehigh="high"+num2str(i)
       nametempw="tempw"+num2str(i)
       nametitle="title"+num2str(i+12)
       KillControl  $names
        KillControl  $namelow
         KillControl  $namehigh
          KillControl  $nametempw
           KillControl  $nametitle

       if (i<=(globNlay+1))
       if (i==0)
//          KillControl super
//          KillControl super1
//          KillControl super2
//          KillControl super3
 
//          KillControl super1p5
 
          KillControl Mbox
//      TitleBox  super2 title="                                                  ",pos={504,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)

//       TitleBox  super1 title="                                                  ",pos={297,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
//       TitleBox  super title="            \W545   Medium              ",pos={796,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
//       TitleBox  super1p5 title="                    ",pos={709,114+i*20+50-4},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)

       TitleBox  $nametitle title=" M ",  pos={270,114+i*20+46},fstyle=1,fsize=13,frame=4,labelBack=(65280,43520,0),help={"Incident Medium"}  //title=num2str(i)    
//       TitleBox  super3 title="    ",pos={702,114+i*20+50-2},fstyle=1,fsize=17,frame=0,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)        
//       GroupBox Mbox frame=1,size={734,25},pos={270,114+i*20+50-4}

       elseif (i==(globNlay+1))
          KillControl sub
          KillControl sub1
          KillControl sub2
          KillControl sub3
          KillControl sub1p5
          KillControl Sbox
       TitleBox  sub2 title="                                                   ",  pos={503,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)
       
       TitleBox  sub1 title="                                                  ",  pos={296,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)

       TitleBox  sub title="            \W545 Substrate              ",  pos={796,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000)
       TitleBox  sub1p5 title="                    ",pos={709,115+i*20+50-3},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000),(65280,21760,0)
       TitleBox  $nametitle title=" S ",  pos={270,116+i*20+46},fstyle=1,fsize=14,frame=4,labelBack=(0,65280,38024),help={"Substrate"}       //title=num2str(i)
       TitleBox  sub3 title="  ",pos={702,115+i*20+50-1},fstyle=1,fsize=17,frame=0,labelBack=(0,65280,38024),help={"Substrate"}//,fcolor=(65000,65000,65000),(65280,21760,0)        

 //      GroupBox Sbox frame=1,size={734,25},pos={270,116+i*20+46}//,labelBack=(0,65280,23024),help={"Substrate"} 

       else
       TitleBox  $nametitle title=num2str(i),  pos={280,115+i*20+51.5},fstyle=1,frame=0,labelBack=(60416,59648,55296),help={"layer number "+num2str(i)}        
       endif

       low="K"+num2str(i)
       KillControl $low
       KillControl $low+"T"
       if (i==0)
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i],labelBack=(65280,43520,0),help={"     Hold?"} 
       SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},labelBack=(65280,43520,0),pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},labelBack=(65280,43520,0),pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],labelBack=(65280,43520,0),pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
       SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},labelBack=(65280,43520,0),pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=(65280,43520,0)
       elseif (i==(globNlay+1))
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i],labelBack=(0,65280,38024),help={"     Hold?"} 
       SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},labelBack=(0,65280,38024),pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},labelBack=(0,65280,38024),pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],labelBack=(0,65280,38024),pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
       SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},labelBack=(0,65280,38024),pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
        TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=(0,65280,38024)
       else
       CheckBox $low,pos={305,(116+50+i*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} 
       TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0,labelBack=0
       endif

 //      TitleBox $low+"T" title=low,pos={328,(116+50+i*20)},frame=0
    //     KillControl 
              SetVariable $namelow bodyWidth=30,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={328,(115+50+i*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
          SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={-50,100,0.2},pos={375,(115+50+i*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
  //     valDisplay $namehigh bodyWidth=32,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={200,(230+20*(i+1))}
          SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={412,(115+50+i*20)},limits={-5,99,0},format="%5.3f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}
          SetVariable $namehigh bodyWidth=30,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={444,(115+50+i*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
   
       elseif (i<=(2*globNlay+2))
       nametitle="title"+num2str(i+12)
       KillControl $nametitle
       low="K"+num2str(i)
        namefun=""
       for (kk=0;kk<=j;kk=kk+1)
        namefun=namefun+"f"
        endfor
//       String/G gPopupList="Error;LGaussian;RGaussian;LParabola;RParabola;Linear"
      KillControl $namefun

     PopupMenu $namefun  value="Erf;LGaussian;RGaussian;LParabola;RParabola;LExp;RExp;Linear;MyOwn",bodyWidth=65,size={70,100},mode=(fitfun1[j]+1),proc=funselect,pos={708,(102+52+(i-globNlay-1)*20)},help={"The function to describe the interface  (Note that the thickness of interfaces is 4 time of the value for roughness.)" }
      KillControl $low
       KillControl $low+"T"
       if (i==(2*globNlay+2))
       CheckBox $low,pos={510,(106+51+(i-globNlay-1)*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} //labelBack=(0,65280,38024),
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={536,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0.001,4000,10},pos={583,(105+51+(i-globNlay-1)*20)},proc=autoRup,format="%4.1f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={620,(105+51+(i-globNlay-1)*20)},limits={0,4000,0},format="%4.2f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={656,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
          if (w_fit[i] <0.001)
            w_fit[i] =0.001
          endif
       else
       CheckBox $low,pos={510,(106+51+(i-globNlay-1)*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"} 
       endif
       TitleBox $low+"T" title=low,pos={532,(106+51+(i-globNlay-1)*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={536,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
       SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0.001,4000,10},pos={583,(105+51+(i-globNlay-1)*20)},proc=autoRup,format="%4.1f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={620,(105+51+(i-globNlay-1)*20)},limits={0,4000,0},format="%4.2f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={656,(105+51+(i-globNlay-1)*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
           if (w_fit[i] <0.001)
             w_fit[i] =0.001
           endif

       j=j+1
       elseif (i<nopara-1)//(i>(2*globNlay+2)
        nametitle="title"+num2str(i+12)
       KillControl $nametitle

       low="K"+num2str(i)
        KillControl $low
       CheckBox $low,pos={805,(116+50+(i-2*(globNlay+1))*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"}
       TitleBox $low+"T" title=low,pos={824,(116+50+(i-2*(globNlay+1))*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={828,(115+50+(i-2*(globNlay+1))*20)},disable=checkhold[i] ,help={"Low limit constraint (Note that this value should be larger than (2 * top interfacial roughness+2*bottom interfacial roughness).)"}
         SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={1,20000,20},pos={875,(115+50+(i-2*(globNlay+1))*20)},proc=autoRup,format="%4.1f",help={" Initial Guess"}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={912,(115+50+(i-2*(globNlay+1))*20)},limits={0,9000,0},format="%4.1f",help={" Results; The values are stored in a column (so called a wave) named as 'tempw'."}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={948,(115+50+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}
          if (w_fit[i] <1)
            w_fit[i] =1
          endif
       
       
       k=k+1
       else
      low="K"+num2str(i)
       KillControl $low
      GroupBox sfbox frame=1,size={250,30},pos={534,(145+45+(i-2*(globNlay+1))*20)}
      CheckBox $low,pos={570,(153+45+(i-2*(globNlay+1))*20)},title=" ",proc=holdcheckbox,value=checkhold[i], labelback=(60416,59648,55296),help={"     Hold?"}
     TitleBox titlesf title="RScale",  pos={510,(149+45+(i-2*(globNlay+1))*20)},fstyle=1,frame=4,labelBack=(60416,59648,55296),help={"To rescale the calculation values of R(Q4) in case, otherwise it should be set to 1."}   
      TitleBox $low+"T" title=low,pos={592,(153+45+(i-2*(globNlay+1))*20)},frame=0
       SetVariable $namelow bodyWidth=32,title=" ", value=T_Constraints_temp [2*i],limits={0,1,1},pos={599,(152+45+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" Low limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}//,format="%f"
         SetVariable $names bodyWidth=45,title=" ",value=w_fit[i],limits={0,100,0.1},pos={646,(152+45+(i-2*(globNlay+1))*20)},proc=autoRup,format="%4.2f",help={" Initial Guess; The values are stored in a column (so called a wave) named as 'w_fit'."}
       SetVariable $nametempw bodyWidth=35,title=" ",value=tempw[i],pos={683,(152+45+(i-2*(globNlay+1))*20)},limits={0,1000,0},format="%5.3f",proc=keepscald,help={"Results: (This Scaling factor value will be used for all the R(Q4) calculations and stored as 'globsf' and in 'tempw'.)"}//,disable=2
       SetVariable $namehigh bodyWidth=34,title=" ",value=T_Constraints_temp [2*i+1],limits={0,1,1},pos={719,(152+45+(i-2*(globNlay+1))*20)},disable=checkhold[i],help={" High limit constraint; The values are stored in a column (so called a wave) named as 'T_Constraints_temp'."}

       endif
 endfor
     namefun=""
     for (j=0;j<=Nlay;j=j+1)
     namefun=namefun+"f"
     endfor
      for (i=globNpara; i<=100; i=i+1)
      namefun=namefun+"f"
      low="K"+num2str(i)
       names="para"+num2str(i)
       namelow="low"+num2str(i)
       namehigh="high"+num2str(i)
       nametempw="tempw"+num2str(i)
       nametitle="title"+num2str(i+12)
       KillControl $namefun
        KillControl  $low
        KillControl  $low+"T"
       KillControl  $names
        KillControl  $namelow
         KillControl  $namehigh
          KillControl  $nametempw
           KillControl  $nametitle
      endfor     
 endif    
      
k=((globNlay+1)*20+115)-200
if (k>0)
j=((globNlay+1)*20+115)+50
else
j=250
endif
  
     GroupBox gb1 frame=1,size={1,(j-52)},pos={250,60+50}     
     GroupBox gb2 frame=1,size={1013,1},pos={5,j+10+50}     
     TitleBox titlegraph title="PLOTS",  pos={50, j+50},fstyle=1,frame=4,labelBack=(60416,59648,55296)//,frame=4//,labelBack=(55000,55000,65000)
     CheckBox autoR,pos={210, j+88},title="",variable=globautoR, proc=autoRupbutt, mode=0,labelBack=(60416,59648,55296),help={"     Automatically update R (R_Pre_Cal; green line w/ no xi sqr update) in the graph whenever the SLD is updated."}  
     CheckBox autoS,pos={691, j+88},title="",variable=globautoS, proc=autoSupbutt,mode=0,labelBack=(60416,59648,55296),help={"     Automatically update SLD profile by changing the fit parameter IN values."} 
     
     Button  titlegraph0,pos={230, j+40+45},size={92,20},fColor=(60416,59648,55296),fstyle=1   //pos={1027,80}
     Button  titlegraph0,proc=MakeGraph_RButton,title="Reflectivity",help={"Make a new graph : "+rq4data+" and Rq_Fit vs. "+globqzdata}   
     Button  titlegraph1,pos={711, j+40+45},size={92,20},fColor=(60416,59648,55296),fstyle=1   //pos={1027,80}
     Button  titlegraph1,proc=MakeGraph_sldButton,title="SLD Profile",help={"Make a new graph : "+globprosldz+" vs. "+globproz}   

//     Make /O/N=(globNlay+1) thickneswvx,thickneswvy 
     
 //    for (i=0;i<(globNlay+1);i=i+1)
 //      if (i==0)
 //       thickneswvx[i]=0
 //      else
 //      thickneswvx[i]=w_fit[2*globNlay+2+i-1]+w_fit[2*globNlay+2+i]
  //     endif
  //      thickneswvy[i]=interp( thickneswvx[i],zz,prof)
  //   endfor

     SetDataFolder root:$globExptTitle
     If (WaveExists(Rq_Fit)<1 )
  
     Duplicate/O /D $RQ4data Rq_Fit
     endif
     Duplicate/O /D w_fit W_coef  
     MoveSubwindow  /W=$globExptTitle#RQplotInPanel fnum=(37,(j+40+45+40)*72/96,370,(j+40+45+40)*72/96+187)//(37,j+20,370,j+227)

       Label  /W=$globExptTitle#RQplotInPanel left "\\f01"+RRQ4nPlot
    If (WaveExists(prof)<1 || exists (globprosldz)<1)
                                            //No. of total points
    Make /O /D /N=(Npoint*(Nlay+1)+1) prof,zz//,dprof  //+(nl+1)
    String/G  globprosldz="prof",globproz="zz"
    prof=1
    zz=1
    endif
//    RemoveFromGraph /Z  /W=$globExptTitle#SLDPlotInPanel  thickneswvy
//        AppendToGraph /W=$globExptTitle# SLDplotInPanel  thickneswvy vs  thickneswvx
//       ModifyGraph /W=$globExptTitle# SLDplotInPanel mode(thickneswvy)=1

  //      TitleBox Rnplot title=RRQ4nPlot,pos={52, (j+220)},fsize=12,fstyle=1, frame=0, labelback=(53760,53760,53760),variable=RRQ4nPlot   //Left Label to vary by slider
  
        MoveSubwindow  /W=$globExptTitle# SLDplotInPanel fnum=(400,(j+40+45+40)*72/96,733,(j+40+45+40)*72/96+187)//(400, j+20,733,j+227)
    if (syn>0 && strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
    Variable cursorasld=pcsr(A,globExptTitle+"#SLDPlotInPanel")
    Cursor /S=2 /C=(26368,0,52224) /W=$globExptTitle#SLDPlotInPanel A prof cursorasld
    else
    Cursor /K /W=$globExptTitle#SLDPlotInPanel A //$rq4data1
    endif
	Variable ii,jj

 if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $globExptTitle#RQPlotInPanel
//Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rq4data leftx($rq4data)
//Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rq4data numpnts($rq4data)

cursora=pcsr(A, globExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, globExptTitle+"#RQPlotInPanel")

//Cursor /S=1 /W=NR#RQPlotInPanel A $RQ4data cursora
//Cursor /S=1 /W=NR#RQPlotInPanel B $RQ4data cursorb

//SetActiveSubWindow $globExptTitle
RemoveFromGraph /Z  /W=$globExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$globExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs $Qzdata[cursora,cursorb]
 ModifyGraph /W=$globExptTitle#RQPlotInPanel rgb(Rq_Fit)=(6528,0,65280),lsize(Rq_Fit)=2
endif
 
   
//SetActiveSubWindow $globExptTitle#RQPlotInPanel

   RemoveFromGraph  /Z /W=$globExptTitle#RQplotInPanel $RQ4data
   RemoveFromGraph  /Z /W=$globExptTitle#RQplotInPanel $RQdata
   if (rswitch<1)
   String trace_wave="RQ4_Trans_"+RQdata
   RemoveFromGraph  /Z /W=$globExptTitle#RQplotInPanel $trace_wave
   endif
   AppendToGraph /W=$globExptTitle#RQplotInPanel $RQ4data vs $qzdata
  //      RemoveFromGraph  /Z /W=$globExptTitle#RQplotInPanel $RQdata
        ModifyGraph /Z /W=$globExptTitle#RQplotInPanel   framestyle=5,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars  /W=$globExptTitle#RQplotInPanel $RQ4data Y,wave=($dRQ4data,$dRQ4data)//XY,wave=($dqdata,$dqdata)
 CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data+"_Pre_Cal")
 if(V_flag==1)
 ReorderTraces /W=$globExptTitle#RQplotInPanel $RQ4data,{$(RQ4data+"_Pre_Cal")}
 endif
  CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
 if(V_flag==1)
 ReorderTraces /W=$globExptTitle#RQplotInPanel Rq_Fit,{$RQ4data}
 endif

 if (pfyn>0)
 Cursor /S=1 /W=$globExptTitle#RQPlotInPanel A $RQ4data cursora
Cursor /S=1 /W=$globExptTitle#RQPlotInPanel B $RQ4data cursorb
 endif
 //return 0
     SetActiveSubWindow $globExptTitle
Variable /G globV_chisq
Variable /G globV_Rchisq
Variable /G globnpntsdata

   
   TitleBox chisqtitle title="\\F'symbol'c\\S2\\M\\Bn\\M =",pos={440, j+35+50}, frame=0

   SetVariable chisq1, title=" ", value=globV_chisq,frame=0,pos={468, j+40+50},limits={0,1000,0},size={50,20},format="%8.2f",noedit=1
   SetVariable npntsdata, title="/ ",value=globnpntsdata,frame=0,pos={518, j+40+50},limits={0,1000,0},size={40,20},noedit=1
   SetVariable chisq2, title="= ",value=globV_Rchisq,frame=0,pos={560, j+39+50},limits={0,1000,0},size={100,20} ,noedit=1//,format="%7.3f" //
//    SetVariable /Z comWinIn pos={0,(j+40+45+40)*72/96+372}, bodyWidth=850//value=globcomWin, title="        Command:", , bodyWidth=910, title=" Command:"proc=ComLineinWin, pos={20,740}
  Variable comcorc=0
//   if (k>0)
    if (j>365)
    comcorc=0.1
    endif
   SetVariable /Z comWinIn value=globcomWin,  pos={90, (j*(1+comcorc)+40+45+40)*72/96+372}, bodyWidth=865, frame=0, labelback=(60416,59648,55296),title=" ", proc=ComLineinWin//,labelBack=(65280,43520,0),frame=1//,fstyle=0//,fColor=(55000,0,0)//,help={" Low limit "}
//     TitleBox comman title="Command (? :^ )",pos={50,(j+40+45+40)*72/96+372}, frame=0
     TitleBox comman title="Note:",pos={50,(j*(1+comcorc)+40+45+40)*72/96+372}, frame=0,help={"Note ..."}//, labelback=(60416,59648,55296)
 
     if (GlobNLay>9)
      GroupBox gb3 frame=1,size={1,695+(globNLay-9)*18+25},pos={1020,60}     
      GroupBox bottomgb0 frame=1,size={1149,1},pos={0,757+(globNLay-9)*18+25}
     GroupBox rightg3 frame=1,size={1,758+(globNLay-9)*18+25},pos={1147,0}  
      else
       GroupBox gb3 frame=1,size={1,695},pos={1020,60}     
      GroupBox bottomgb0 frame=1,size={1149,1},pos={0,757}
     GroupBox rightg3 frame=1,size={1,758},pos={1147,0}  
     endif
String namesim//, nametempwim
   Make /O /N=(globNlay+2) Im_SLD_in//,Im_SLD_out
 String /G globImSLDin="Im_SLD_in"//,globImSLDout="Im_SLD_out"
   
if (globcmplxcalyn>1)

     TitleBox titleImag title="\f01   Imaginary \f00\r    SLD (10\\S-6\\MÅ\\S-2\\M)",  pos={1040,432},fstyle=1,frame=0,help={" Imaginary part of SLD; The imaginary profile is 'prof_IM' vs 'zz'."}//,help={"Some SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, D2O=6.25, h-Toluene=0.94, Cyclohexane=-0.278, P2VP=1.87, h-PS=1.4, d-PS=6.4"} //,frame=4//,labelBack=(55000,55000,65000)
 //    TitleBox titleImaginout title="Real         Imaginary",  pos={1046,447},fstyle=0,frame=0//,help={"Some SLDs; Si=2.07, SiO2=3.16, Quartz=4.2, D2O=6.25, h-Toluene=0.94, Cyclohexane=-0.278, P2VP=1.87, h-PS=1.4, d-PS=6.4"} //,frame=4//,labelBack=(55000,55000,65000)
      for (i=0; i<=globNlay+9; i=i+1)
           namesim="ImSLDin"+num2str(i)
           low="K"+num2str(i)
           KillControl  $low+"Tim" 
           KillControl $namesim 
//       SetVariable $nametempw bodyWidth=35,title=" ",value=$globImSLDout[i],pos={1077,465+20*i},limits={-10,10,0},help={" Results; these outputs are calculated as ImSLD_input*ReSLD_out/ReSLD_in."}//,format="%5.3f"
    endfor
 for (i=0; i<=globNlay+1; i=i+1)
       namesim="ImSLDin"+num2str(i)
 //      nametempw="ImSLDout"+num2str(i)
        low="K"+num2str(i)
        if (i==0)
        TitleBox  $low+"Tim" title="M               ",pos={1045,471+20*i},fstyle=1,fsize=13,frame=5,labelBack=(65280,43520,0),help={"Incident Medium"}//,fcolor=(65000,65000,65000),(65280,21760,0)
       elseif (i==(globNlay+1))
       KillControl SLDIMbox
       TitleBox  $low+"Tim" title="S               ",  pos={1045,471+20*i},fstyle=1,fsize=13,frame=5,labelBack=(0,65280,38024),help={"Substrate"}       //title=num2str(i)
      GroupBox SLDIMbox frame=1,size={102,83+20*i},pos={1035,425}

       else    
       TitleBox $low+"Tim" title=num2str(i),pos={1050,477+20*i},frame=0
       endif
       SetVariable $namesim bodyWidth=55,title=" ",value=$globImSLDin[i],pos={1069,475+20*i},limits={-100,100,0},proc=autoRup,help={" Imaginary part of SLD; These are fixed for fitting and stored in 'Im_SLD_in'."}//,format="%4.2f"
//       SetVariable $nametempw bodyWidth=35,title=" ",value=$globImSLDout[i],pos={1077,465+20*i},limits={-10,10,0},help={" Results; these outputs are calculated as ImSLD_input*ReSLD_out/ReSLD_in."}//,format="%5.3f"
endfor
//       Im_SLD_out=Im_SLD_in
else 
   KillControl SLDIMbox
    KillControl titleImag
     for (i=0; i<=globNlay+9; i=i+1)
           namesim="ImSLDin"+num2str(i)
           low="K"+num2str(i)
           KillControl  $low+"Tim" 
           KillControl $namesim 
//       SetVariable $nametempw bodyWidth=35,title=" ",value=$globImSLDout[i],pos={1077,465+20*i},limits={-10,10,0},help={" Results; these outputs are calculated as ImSLD_input*ReSLD_out/ReSLD_in."}//,format="%5.3f"
    endfor
     Im_SLD_in=0
 //    Im_SLD_out=0

endif
   globNLay_1=globNLay
End
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Function autoRup(ctrlName,varNum,varStr,varName)//: SetVariableControl
  String ctrlName
  Variable varNum
    String varStr
    String varName
    Variable /G globautoS
    Variable /G globautoR
    Variable /G globNlay
 if (globautoS<1)
     globautoR=0
    if (stringmatch(ctrlName,"setvar2")==1)
       FitRgeneral3()
     endif
  else
   SVAR rq4data1=globrq4data,drq4data1=globdrq4data,qzdata1=globqzdata,dqdata1=globdqdata
  Variable i 
   String  rq4data2=rq4data1,drq4data2=drq4data1,qzdata2=qzdata1,dqdata2=dqdata1
   Wave rq4data=$rq4data2,drq4data=$drq4data2, qzdata=$qzdata2,dqdata=$dqdata2
  // Wave Rq_Fit
   Duplicate /O drq4data dRQ_temp
//   String Rq_Fit1=rq4data2+"_Pre_Cal"
   Wave w_fit
   if (globNlay>0)
    for (i=globNlay+2;i<(3*globNlay+3);i=i+1)
    if (stringmatch(ctrlName,"para"+num2str(i))==1)
       if (i==globNlay+2&&w_fit[i]>(w_fit[i+globNlay+1]/2-w_fit[i+1]))
           w_fit[i+globNlay+1]=2*(w_fit[i]+w_fit[i+1])
       elseif (i==2*globNlay+2&&w_fit[i]>(w_fit[i+globNlay]/2-w_fit[i-1]))
           w_fit[i+globNlay]=2*(w_fit[i]+w_fit[i-1])
       elseif (i>globNlay+2&&i<2*globNlay+2)
            if (w_fit[i]>(w_fit[i+globNlay+1]/2-w_fit[i+1]))
               w_fit[i+globNlay+1]=2*(w_fit[i]+w_fit[i+1])
             endif
            if (w_fit[i]>(w_fit[i+globNlay]/2-w_fit[i-1]))
               w_fit[i+globNlay]=2*(w_fit[i]+w_fit[i-1])
            endif
        elseif ( i>2*globNlay+2)
            if  (w_fit[i]<2*(w_fit[i-globNlay-1]+w_fit[i-globNlay]))
               w_fit[i]=2*(w_fit[i-globNlay-1]+w_fit[i-globNlay])
            endif
       endif
       break
     endif
    endfor    
    endif
 //   Variable idq
 //  for (idq=0;idq<numpnts(dqdata);idq=idq+1)     ///////////////////////
 //    if  (dqdata[idq]<0.0005*abs(qzdata[idq]))       /////////////////////
 //       dqdata[idq]=0.0005*abs(qzdata[idq])       ///////////newchange Nov. 16. 2007////////
 //     endif                                                          //////////////////////
//   endfor                                                           //////////////////
   Variable npt,int=0.001
      npt=round(abs(qzdata[0]-qzdata[numpnts(qzdata)])/int)
//   if (stringmatch(rq4data2,"SelectData")==1)
//   Make /O/N=(npt+1) SimR_Pre_Cal

//  Make /O/N=(npt+1) SimQ_Pre_Cal
//   Make /O/N=(npt+1) SimdQ_Pre_Cal
 //  Wave Rq_Fit1=SimR_Pre_Cal,dQ_Fit1=SimdQ_Pre_Cal,Qz_Fit1=SimQ_Pre_Cal
//  else
     Make /O/N=(npt+1) $rq4data2+"_Pre_Cal"

   Make /O/N=(npt+1) $qzdata2+"_Pre_Cal"
   Make /O/N=(npt+1) $dqdata2+"_Pre_Cal"
   Wave Rq_Fit1=$rq4data2+"_Pre_Cal",dQ_Fit1=$dqdata2+"_Pre_Cal",Qz_Fit1=$qzdata2+"_Pre_Cal"
// endif
   Wave prof//,Rq_Fit
   Variable /G globautoR,globautowav
   globautowav=0
     Variable notp=numpnts(prof)
//   print rq4data
// print  w_fit,x
Variable/G globgraphhold
Variable graphhold=globgraphhold
SVAR ExptTitle=globExptTitle
Qz_Fit1=min(qzdata[0],qzdata[numpnts(qzdata)])+int*x//-int/2
dQ_Fit1=interp(Qz_Fit1,qzdata,dqdata)
// SetWindow $ExptTitle hook=$" " //kwTopWin 
If(stringmatch(ctrlName,"editt")!=1)

  if (stringmatch(ctrlName,"setvar1")==1||stringmatch(ctrlName,"setvar2")==1)
    FitRgeneral3()
  endif
    if (graphhold>0)

     ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
endif
Variable /G globmodecalRDP=1



      
        if (npt>2)
          if (stringmatch(ctrlName,"editt")==1)
            Rq_Fit1= ParrattNTRNdq(Qz_Fit1, dQ_Fit1,notp)
           else
           globautowav=1
           Rq_Fit1= Profile4Fit(w_fit,x)
           globautowav=0
          endif
         CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit1
         if (V_flag!=1)       
           AppendToGraph/C=(0,39168,0) /W=$ExptTitle#RQplotInPanel  Rq_Fit1  vs Qz_Fit1 
         
  //         SetWindow $ExptTitle#RQplotInPanel kwTopWin 
     //         if (stringmatch(rq4data2,"SelectData")==1)
      
      //         ModifyGraph  /Z /W=$ExptTitle#RQplotInPanel lsize(SimR_Pre_Cal)=1.5//,rgb(Rq_Fit1)=(0,39168,0)
   //            else
              ModifyGraph  /Z /W=$ExptTitle#RQplotInPanel lsize($rq4data2+"_Pre_Cal")=1.5//,rgb(Rq_Fit1)=(0,39168,0)
   //           endif
         endif 
        else
       
             Variable/G globstop2sld=1
           Profile4Fit(w_fit,x)
        endif  
 //         if (stringmatch(rq4data2,"SelectData")==1)
 //         CheckDisplayed /W= $ExptTitle#RQplotInPanel SimR_Pre_Cal         
 //       else
          CheckDisplayed /W= $ExptTitle#RQplotInPanel $rq4data2+"_Pre_Cal"
 //        endif
//          print V_flag
            if (globautoR<1&&V_flag>0)
  //             if (stringmatch(rq4data2,"SelectData")==1)
 //              RemoveFromGraph /W=$ExptTitle#RQplotInPanel  SimR_Pre_Cal
   //            else
               RemoveFromGraph /W=$ExptTitle#RQplotInPanel  $rq4data2+"_Pre_Cal"
   //           endif
          endif
   killwaves /Z dRQ_temp
 
 //  CheckDisplayed /W=$ExptTitle#RQPlotInPanel Rq_Fit
// if (V_flag>0)
//ReorderTraces /W=$ExptTitle#RQPlotInPanel Rq_Fit, {$rq4data2}
//endif

// if (globautoR>0)
// Variable ss=V_flag
//CheckDisplayed /W=$ExptTitle#RQPlotInPanel $rq4data2+"_Pre_Cal"
// if (V_flag>0 && ss>0)
// ReorderTraces /W=$ExptTitle#RQPlotInPanel  $rq4data2+"_Pre_Cal", {$rq4data2,Rq_Fit}
// endif

// endif
  endif
 End

Function autoRupbutt(ctrlName,checked): CheckBoxControl
  String ctrlName
  Variable checked
     Variable /G globautoR, globautoS
  
   if (checked>0)
    globautoS=1
    autoRup("",0,"","")

    endif
//   globautoR=checked
  autoRup("editt",0," ", " ")
End
Function autoSupbutt(ctrlName,checked): CheckBoxControl
  String ctrlName
  Variable checked
   Variable /G globautoR,globautoS
  
   if (checked<1)
    globautoR=0
    globautoS=1
    autoRupbutt("",0)
    globautoS=0
     endif
  autoRup(" ",0," ", " ")
End


Function AbtrProfile4FitS(w,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable qq//,nopntalayer,nl
 
//Variable /G globyn=1
//Variable q//,sigmaq,nt
NVAR  npt1=globNpoint, syn1=globsyn, yn1=globyn,npara1=globNpara,lay1=globNlay//, ssyn1=globssyn
Variable npt=npt1, npara=npara1,syn=syn1,yn=yn1,lay=lay1//,ssyn=ssyn1
SVAR qqq=globqzdata
SVAR dddq=globdqdata
NVAR s2sld1=globStop2SLD

Wave q4f=$qqq
Wave dq4f=$dddq
Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable i,j,k,ad,s_thick
Variable notp,Rq_Fitout,deltad
Variable z,zzorg,ceilnotp//,sf,sf1
//NVAR sf=globsf
//Variable s_thick_1=NumVarOrDefault("globs_thick_1", 1)
//Variable sf1=sf
   notp=numpnts(prof)
  
 //   notp=npt*(lay+1)+1 //No. of total points
    Make /O /D /N=(notp) prof,zz//,abtr_zz_temp
    String/G  globprosldz="prof",globproz="zz"

    ceilnotp=ceil(notp-1)/2  //30

   s_thick=abs(w[(ceilnotp)])
  for (i=0;i<notp;i=i+1)  // # of interfaces is no. of layers +1
     if (i<ceilnotp)
     prof[i]=w[i]
     zz[i]=zz[i]
 //    zz[i]=s_thick*zz[i]/s_thick_1
     elseif (i<(notp-3))
     zz[i]=2*(zz[ceilnotp-1]-zz[0])-zz[((notp-i-1)-2)]+2*zz[0]
     prof[i]=prof[((notp-i-1)-2)]
//     print zz[ceilnotp-1]-zz[0],zz[((notp-ceilnotp-1)-2)],2*(zz[ceilnotp-1]-zz[0]),2*(zz[ceilnotp-1]-zz[0])-zz[((notp-ceilnotp-1)-2)]
//     return 0
     else
     zz[i]=2*(zz[ceilnotp-1]-zz[0])-(zz[1]-zz[0])/3+2*zz[0]
     prof[i]=prof[((notp-i-1)/3)]
     endif
     
//     zz[i]=s_thick*zz[i]/s_thick_1

  endfor
//  s_thick_1=s_thick

//Variable /G globs_thick_1=s_thick_1
 
 Rq_Fitout=ParrattNTRNdq(q, sigmaq,notp)


    return Rq_Fitout
End

Function ArbtrProfile4Fit(w,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable qq//,nopntalayer,nl

 
 Variable alpha=1e-06
 

 Variable /G globzz_sfpre
NVAR  npt1=globNpoint,lay1=globNlay//, ssyn1=globssyn
Variable npt=npt1,lay=lay1//,ssyn=ssyn1

SVAR qqq=globqzdata
SVAR dddq=globdqdata
 
Wave q4f=$qqq
Wave dq4f=$dddq
//Wave zz

Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable zz_sf
Variable notp,Rq_Fitout,deltad,i
Variable /G globpre_wnotp, globsf
 Wave prof
 Wave zz  
    notp=numpnts(prof)// npt*(lay+1)+1 //No. of total points
//   zz_sf=w[notp]   
     globsf=w[notp]
     zz_sf=w[notp+1]
     zz=zz/globzz_sfpre*zz_sf
     duplicate /O w prof
 Redimension /N=(notp) prof
       Make /O /D /N=(notp+2) abtr_weps1,abtr_prew
    	String/G  globabtr_weps="abtr_weps1",globprew="abtr_prew"
    	Variable Rq_Fitpre=NumVarOrDefault("globRq_Fitpre", 1)
   abtr_prew=1
Duplicate /O prof profext
Duplicate /O zz zzext
Interpolate2/T=2/N=(notp*3)  /E=2 /Y=prof/X=zz zzext, profext
Rq_Fitout=ParrattNTRNdq(q, sigmaq,notp*3)
Duplicate /O prof profcspix
Duplicate /O zz zzcspix
 
Duplicate /O profext prof
Duplicate /O zzext zz
globzz_sfpre=zz_sf
  globpre_wnotp=w[notp]
       wave tempw
       tempw[3*lay+3]=globsf
     	Variable/G globRq_Fitpre=Rq_Fitpre

for (i=0;i<notp+2;i=i+1)
deltad=(w[i]-abtr_prew[i])

abtr_weps1[i]=(Rq_Fitout-Rq_Fitpre)/(deltad)//(Rq_Fitout-weps1[i])/(deltad)
abtr_prew[i]=w[i]
 


if (abs(abtr_weps1[i])< alpha)
abtr_weps1[i]= alpha*sign(abtr_weps1[i])
endif
if (abs(abtr_weps1[i])> alpha)
abtr_weps1[i]= alpha*sign(abtr_weps1[i])
endif
////abtr_weps1[i]=0.1 //need to be removed when others are enabled
endfor
Rq_Fitpre=Rq_Fitout
    return Rq_Fitout //
End
Function ArbtrProfile4FitZ(w,qq): FitFunc//,nl, nopntalayer)//: FitFunc//q,sigmaq,nt,nl) : FitFunc  //nl = # of total layers, nt=# of total q points
//Variable w
Wave w
Variable qq//,nopntalayer,nl

 
 Variable alpha=1e-06//0.0001
NVAR  npt1=globNpoint,lay1=globNlay//, ssyn1=globssyn
Variable npt=npt1,lay=lay1//,ssyn=ssyn1

SVAR qqq=globqzdata
SVAR dddq=globdqdata

 
Wave q4f=$qqq
Wave dq4f=$dddq


Variable q=q4f[qq]
Variable sigmaq=dq4f[qq]
Variable zz_sf
Variable notp,Rq_Fitout,deltad,i
Variable /G globpre_wnotp
String/G globproz
Wave zz
    notp=numpnts(prof)// npt*(lay+1)+1 //No. of total points
//   zz_sf=w[notp]   
       Duplicate /O zz zzd
 
       Make /O /D /N=(notp+1) abtr_weps1,abtr_prew
    	String/G  globabtr_weps="abtr_weps1",globprew="abtr_prew"
    	Variable Rq_Fitpre=NumVarOrDefault("globRq_Fitpre", 1)
   abtr_prew=1

  for (i=1;i<notp;i=i+1)
   
//  if ((abs(w[i+1]-w[i])-abs(w[i-1]-w[i]))>0 || (abs(w[i+1]-w[i])-abs(w[i-1]-w[i]))<0)
//    zzd[i]= (zz[i+1]-zz[i-1])/2//+(abs(w[i+1]-w[i])-abs(w[i-1]-w[i]))/(abs(w[i]))
//   else
   if (i==notp-1)
     zzd[i]=0
   else
   zzd[i]=(zz[i+1]-zz[i-1])/2
   endif
//   endif

  endfor
  
  for (i=1;i<notp;i=i+1)
     zz[i]= zz[i-1]+ zzd[i]
  endfor

Rq_Fitout=ParrattNTRNdq(q, sigmaq,notp)
  globpre_wnotp=w[notp]
     	Variable/G globRq_Fitpre=Rq_Fitpre
   
for (i=0;i<notp;i=i+1)
deltad=(w[i]-abtr_prew[i])

abtr_weps1[i]=(Rq_Fitout-Rq_Fitpre)/(deltad)//(Rq_Fitout-weps1[i])/(deltad)
abtr_prew[i]=w[i]
 


if (abs(abtr_weps1[i])< alpha)
abtr_weps1[i]= alpha*sign(abtr_weps1[i])
endif
if (abs(abtr_weps1[i])> alpha)
abtr_weps1[i]= alpha*sign(abtr_weps1[i])
endif
////abtr_weps1[i]=0.1 //need to be removed when others are enabled
endfor
Rq_Fitpre=Rq_Fitout
    return Rq_Fitout //
End

Function ConstdzSLD()
SVAR prof1=globprosldz,zz1=globproz
//NVAR npoint1=globNpoint, Nlay1=globNlay
Wave /D prof=$prof1,zz=$zz1
Variable intp//,npoint=npoint1,Nlay=Nlay1
Duplicate /O prof, prof_temp
Duplicate /O zz, zz_temp

Variable npnts_prof=numpnts(prof)
for (intp=1;intp<(npnts_prof-1);intp=intp+1)
 prof_temp[intp]=interp(zz[0]+intp*(zz[npnts_prof-1]-zz[0])/(npnts_prof-1),zz,prof)
 zz_temp[intp]=zz[0]+intp*(zz[npnts_prof-1]-zz[0])/(npnts_prof-1)
 endfor
 prof_temp[0]=prof[0]
 zz_temp[0]=zz[0]
 prof_temp[npnts_prof-1]=prof[npnts_prof-1]
 zz_temp[npnts_prof-1]=zz[npnts_prof-1]

 prof=prof_temp
 zz=zz_temp
 Killwaves prof_temp,zz_temp
 Variable /G globautoR
     if (globautoR>0)
    autoRup("editt",0," "," ")
    endif

 End
 
Function Numx2SLD()
SVAR prof1=globprosldz,zz1=globproz
//NVAR npoint1=globNpoint, Nlay1=globNlay
Wave /D prof=$prof1,zz=$zz1
Variable intp//,npoint=npoint1,Nlay=Nlay1
Duplicate /O prof, prof_temp
Duplicate /O zz, zz_temp

Variable npnts_prof=numpnts(prof)
ReDimension /N=(2*npnts_prof-1) prof_temp, zz_temp
for (intp=1;intp<(2*npnts_prof-1);intp=intp+1)
 prof_temp[intp]=interp(zz[0]+intp/2*(zz[npnts_prof-1]-zz[0])/(npnts_prof-1),zz,prof)
 zz_temp[intp]=zz[0]+intp/2*(zz[npnts_prof-1]-zz[0])/(npnts_prof-1)
 endfor
 prof_temp[0]=prof[0]
 zz_temp[0]=zz[0]
 prof_temp[2*npnts_prof-2]=prof[npnts_prof-1]
 zz_temp[2*npnts_prof-2]=zz[npnts_prof-1]
ReDimension /N=(2*npnts_prof-1) prof, zz
  prof=prof_temp
  zz=zz_temp
 Killwaves prof_temp,zz_temp
  Variable /G globautoR
     if (globautoR>0)
    autoRup("editt",0," "," ")
    endif

 End
 
Function ArbitraryFitting_Button()//cntrlName)//: ButtonControl //To fit,use 10point-per-layer profile//Only for symetric geometric case
//String cntrlName

Variable/G globpfyn,globsyn
Variable /G globpre_wnotp=1

 Variable /G globzz_sfpre=1

Variable alpha=1e-06//0.0001
NVAR  npt1=globNpoint,lay1=globNlay
Variable npt=npt1,lay=lay1
Variable pfyn=globpfyn,syn=globsyn
SVAR rdata=globrq4data, drdata=globdrq4data, qzdata1=globqzdata
//Variable s_thick_1=NumVarOrDefault("globs_thick_1", 1)
SVAR prof1=globprosldz,zz1=globproz
SVAR ExptTitle=globExptTitle
NVAR gaS= globautoS
Wave /D prof=$prof1,zz=$zz1
Wave /D RQdata=$rdata,dRQdata=$drdata,qzdata=$qzdata1
Wave checkhold
Wave /D w_fit
Variable npnts_prof=numpnts(prof)//npt*(lay+1)+1
SetWindow  $ExptTitle hook=$" "

Duplicate /O prof, pro_In_org
Make /O /N=(npnts_prof+2) abtr_weps1//=1
InsertPoints npnts_prof,2, pro_In_org
 
//Make /O /T  /N=(2*(npnts_prof)) abtr_T_Constraints_temp//="1" ////abtr_T_Constraints_temp needs to make active when constraint are needed.
Variable/G globgraphhold
Variable graphhold=globgraphhold
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif

if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rdata cursora
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rdata cursorb
RemoveFromgraph /Z /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
else
RemoveFromgraph  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit vs qzdata
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
endif
Variable i,j
  Variable /G globV_chisq
  Variable /G globV_Rchisq
  Variable /G globnpntsdata


  //Initialize the values of parameters///////////////////////////////////////////////
  Duplicate /O RQdata Rq_Fit
   Duplicate /O dRQdata dRQ_temp
   Variable nodata=numpnts(dRQdata)
      for (i=0;i<(nodata);i=i+1) //masking points
   if (dRQdata[i]<=0)
    //  dRQ_temp[i]=abs(RQdata[i])
    endif
//    MaskRQdata[i]=0
//   else
//     MaskRQdata[i]=1
//   endif 
   endfor

  
  String holdstring
   holdstring=""


 if (gaS<1)
 Make /T /O /N=2 abtr_T_Constraints_temp
abtr_T_Constraints_temp[0]="K"+num2str((npnts_prof)+1)+">"+"0.1"
abtr_T_Constraints_temp[1]="K"+num2str((npnts_prof)+1)+"<"+"10"
endif
  for (i=0;i<(npnts_prof+2);i=i+1) 
//     abtr_T_Constraints_temp[2*i]="K"+num2str(i)+">"+num2str(pro_In_org[i]-0.5*abs(pro_In_org[i]))
//   abtr_T_Constraints_temp[2*i+1]="K"+num2str(i)+"<"+num2str(pro_In_org[i]+0.5*abs(pro_In_org[i]))    

   if (i==0)
       if (i==0)
         holdstring=holdstring+"1"
       endif
   abtr_weps1[i]= alpha//
   elseif (i==(npnts_prof)-1)
         holdstring=holdstring+"1"
         abtr_weps1[i]= alpha
   elseif (i==(npnts_prof))
            holdstring=holdstring+num2str(checkhold(numpnts(checkhold)-1))   
            pro_In_org[i]=w_fit[3*lay+3]
            abtr_weps1[i]= alpha
    elseif (i==(npnts_prof)+1)
           holdstring=holdstring+num2str(gaS)
           pro_In_org[i]=1
           abtr_weps1[i]= alpha
   else
   
   holdstring=holdstring+"0" 
   abtr_weps1[i]= alpha/(zz[i]-zz[i-1])
   endif

  endfor

//       deletepoints 0,1,abtr_T_Constraints_temp
////       deletepoints 0,1,abtr_T_Constraints_temp
//       deletepoints (2*npnts_prof-2-2),1,abtr_T_Constraints_temp  //<<?? need changed since no. of point of prof_In and _temp are changed
//       deletepoints (2*npnts_prof-2-2),1,abtr_T_Constraints_temp   //<<??

  if (gaS<1)
   if (pfyn==1)
   FuncFit/H=holdstring  ArbtrProfile4Fit pro_In_org  RQdata[pcsr(A),pcsr(B)] /W=dRQ_temp  /I=1 /D=Rq_Fit  /E=abtr_weps1 /C=abtr_T_Constraints_temp 
   else
   FuncFit/H=holdstring  ArbtrProfile4Fit pro_In_org RQdata /W=dRQ_temp  /I=1 /D=Rq_Fit  /E=abtr_weps1 /C=abtr_T_Constraints_temp // 

   endif
  else
    if (pfyn==1)
   FuncFit/H=holdstring  ArbtrProfile4Fit pro_In_org  RQdata[pcsr(A),pcsr(B)] /W=dRQ_temp  /I=1 /D=Rq_Fit  /E=abtr_weps1 //C=abtr_T_Constraints_temp 
   else
   FuncFit/H=holdstring  ArbtrProfile4Fit pro_In_org RQdata /W=dRQ_temp  /I=1 /D=Rq_Fit  /E=abtr_weps1 //C=abtr_T_Constraints_temp // 

   endif
 endif
 SetActiveSubWindow $ExptTitle

   if (V_chisq>0)
   globV_chisq=V_chisq
   globV_Rchisq=V_chisq/(V_npnts-npnts_prof-1)
   globnpntsdata=V_npnts-npnts_prof-1
   endif
 SetWindow  $ExptTitle, hook=winhookproc
 KillVariables /Z globpre_wnotp
 Killwaves /Z  dRQ_temp, abtr_T_Constraints_temp,profext,zzext,prof_In_org
//  endif
//  Variable /G globs_thick_1=s_thick_1

End





Function UserUpdatePanel_ContButton(cntrlName) : ButtonControl //To restart in NR window
String cntrlName
if (cmpstr(cntrlName,"upbutton")==0||cmpstr(cntrlName,"upbuttona")==0)
Variable/G globgraphhold
Variable graphhold=globgraphhold
//SVAR ExptTitlepre=globExptTitlepre
String wn=WinName(0,1)


String /G globExptTitlepre
    if (graphhold>0)
    GraphNormal /W=$wn#SLDplotinPanel
    globgraphhold=0
    endif

SetDataFolder root:$wn
String /G globExptTitle=wn
// SetWindow  $globExptTitle hook=$" "    
FitRgeneral2()
endif
End








Function ArbitraryFitting_ButtonS()//cntrlName) : ButtonControl //To fit,use 10point-per-layer profile//Only for symetric geometric case
//String cntrlName

Variable/G globpfyn
String/G globrq4data,globdrq4data,globqzdata
SVAR abtr_prof=globprosldz
String ab_prof=abtr_prof
Wave /D abtemp_prof=$ab_prof
NVAR  npt1=globNpoint,lay1=globNlay
Variable npt=npt1,lay=lay1
Variable pfyn=globpfyn
SVAR ExptTitle=globExptTitle
String rdata=globrq4data, drdata=globdrq4data,qzdata1=globqzdata
//Variable s_thick_1=NumVarOrDefault("globs_thick_1", 1)
 SetWindow  kwTopWin, hook=$" "
Wave /D RQdata=$rdata,dRQdata=$drdata,qzdata=$qzdata1

Variable npnts_prof=npt*(lay+1)+1

Variable/G globgraphhold
Variable graphhold=globgraphhold
    if (graphhold>0)
     ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif

if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rdata cursora
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rdata cursorb
RemoveFromgraph  /Z /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
else
RemoveFromgraph  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit vs qzdata
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
endif
Make /O /N=(ceil(npnts_prof-1)/2+0) prof_In_temp=1,abtr_weps1//=1
//Make /O /N=(npnts_prof) prof_In
Make /O /T  /N=(2*(ceil(npnts_prof-1)/2-1-8*npt/10)+2) abtr_T_Constraints_temp//="1"
Variable i,j
  Variable /G globV_chisq
  Variable /G globV_Rchisq
  Variable /G globnpntsdata


Duplicate /O RQdata Rq_Fit
   Duplicate /O dRQdata dRQ_temp
   Variable nodata=numpnts(dRQdata)
      for (i=0;i<(nodata);i=i+1) //masking points
   if (dRQdata[i]<=0)
     // dRQ_temp[i]=abs(RQdata[i])
    endif

   endfor


  //Initialize the values of parameters///////////////////////////////////////////////
   abtr_weps1=0.001
     Duplicate /O abtemp_prof pro_In_org

  for (i=0;i<(ceil(npnts_prof-1)/2+0);i=i+1) 
   if (i<8*npt/10)
   prof_In_temp[i]=pro_In_org[i]  //half-profile as input paramters
//   abtr_T_Constraints_temp[2*i]="K"+num2str(i)+">"+num2str( prof_In_temp[i])
 //  abtr_T_Constraints_temp[2*i+1]="K"+num2str(i)+"<"+num2str( prof_In_temp[i])      
   else //(i<ceil(npnts_prof-1)/2)
   prof_In_temp[i]=pro_In_org[i]  //half-profile as input paramters
   abtr_T_Constraints_temp[2*(i-8*npt/10)]="K"+num2str(i)+">"+num2str( prof_In_temp[i]-0.1)
   abtr_T_Constraints_temp[2*(i-8*npt/10)+1]="K"+num2str(i)+"<"+num2str( prof_In_temp[i]+0.1)      
//    else
                                                      //   prof_In_temp[30]= 0.552614//s_thick_1  //thickness and Rscale parameters
 //  prof_In_temp[i]= 1//s_thick_1  //thickness and Rscale parameters   
//   abtr_T_Constraints_temp[2*i]="K"+num2str(i)+">"+num2str(prof_In_temp[i]-0.5)
//   abtr_T_Constraints_temp[2*i+1]="K"+num2str(i)+"<"+num2str(prof_In_temp[i]+0.5)   
   endif
  endfor
 Variable V_FitError=0
//Variable V_FitQuitReason
   if (pfyn==1)
   FuncFit/H="11111111"  AbtrProfile4FitS prof_In_temp RQdata[pcsr(A),pcsr(B)] /W=dRQ_temp  /I=1 /D=Rq_Fit  /E=abtr_weps1 /C=abtr_T_Constraints_temp 
   else
   FuncFit/H="11111111" AbtrProfile4FitS prof_In_temp RQdata /W=dRQ_temp  /I=1 /D=Rq_Fit /E=abtr_weps1 /C=abtr_T_Constraints_temp // 
   //  print V_FitQuitReason
   endif
   SetActiveSubWindow $ExptTitle
   if (V_chisq>0)
   globV_chisq=V_chisq
   globV_Rchisq=V_chisq/(V_npnts)
   globnpntsdata=V_npnts
   endif
   Killwaves /Z  dRQ_temp
 SetWindow  $ExptTitle, hook=winhookproc
//  endif
//  Variable /G globs_thick_1=s_thick_1

End



Function UserOut2InPanel_ContButton(cntrlName)
String cntrlName
NVAR autoR1=globautoR
Variable autoR=autoR1
if (cmpstr(cntrlName,"rst4")==0||cmpstr(cntrlName,"rst4a")==0)
Variable/G globgraphhold
Variable graphhold=globgraphhold
SVAR ExptTitle=globExptTitle
    if (graphhold>0)
     ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
Duplicate /O tempw, w_fit 
//Profile4Fit(tempw,x)
if (autoR>0)
autoRup(" ",0," ", " ")
endif
endif

End


Function CSFit()
Variable /G cslay=2
UserRestartPanel_ContButton2("rst1")
cslay=0
End

Function UserRestartPanel_ContButton2(cntrlName) : ButtonControl //To fit
String cntrlName

Variable/G globpfyn,globNpara,globNlay,globNpoint,globcmplxcalyn,cslay
String/G globwww,globT_Constraints_temp,globrq4data,globdrq4data,globqzdata//, globprew
SVAR checkhold1=globcheckhold
SVAR ExptTitle=globExptTitle
NVAR  syn1=globsyn, rswitch=globrswitch
Variable /G globsf//incohenrent smearing length
Variable pfyn=globpfyn,nopara=globNpara,Nlay=globNlay,syn=syn1,Npoint_per_Lay=globNpoint//,sf=sf1
String w_fit_temp=globwww,TC_temp=globT_Constraints_temp//,weps=globweps
String rdata=globrq4data, drdata=globdrq4data, qzdata1=globqzdata
Wave checkhold=$checkhold1
Wave w_fit=$w_fit_temp,RQdata=$rdata,dRQdata=$drdata, qzdata=$qzdata1
Wave /T  T_Constraints_temp=$TC_temp
Variable i,j,k
String holdstring
print "*****", ExptTitle, "Fitting Started .....................................................................v v v v v"
 Duplicate /O T_Constraints_temp T_Constraints_temp_temp
// if (cmpstr(cntrlName,"rst1")==0)
// FitRgeneral2()
// endif
SetWindow $ExptTitle hook=$" " //kwTopWin
Duplicate /O w_fit tempw
if (NLay>0)
 for (i=0;i<NLay;i=i+1)
   if (w_fit[2*NLay+3+i]<2*(w_fit[NLay+2+i]+w_fit[NLay+3+i]))
     w_fit[2*NLay+3+i]=2*(w_fit[NLay+2+i]+w_fit[NLay+3+i])
   endif
 endfor
 tempw=w_fit
endif
Duplicate /O RQdata Rq_Fit
Make /O /N=(nopara) weps1,prew
Make /O /T /N=(2*nopara+Nlay) T_Constraints
Make /O /N=(NLay) sw4incohe

String/G globprew="prew"
Make /O /N=(nopara) prew

if (syn1>0)
Variable cursorprofA
 if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
    cursorprofA=pcsr(A, ExptTitle+"#SLDPlotInPanel")
 endif
endif
Variable/G globgraphhold
Variable graphhold=globgraphhold
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
if (pfyn==1)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
k=numpnts(Rq_Fit)
 
   for (i=0;i<k;i=i+1)
     
      if ((cursora<cursorb)&&(i<cursora||i>cursorb))
        Rq_Fit[i]=-inf
      elseif ((cursora>cursorb)&&(i>cursora||i<cursorb))
       Rq_Fit[i]=-inf
       endif
   endfor
     
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rdata cursora
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rdata cursorb
RemoveFromgraph /Z  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit[cursora,cursorb] vs qzdata[cursora,cursorb]
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(6528,0,65280),lsize(Rq_Fit)=2
else
RemoveFromgraph  /W=$ExptTitle#RQPlotInPanel Rq_Fit
AppendToGraph /W=$ExptTitle#RQPlotInPanel Rq_Fit vs qzdata
 ModifyGraph /W=$ExptTitle#RQPlotInPanel rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2
endif
//    for (i=0;i<=(Nlay);i=i+1)  // # of interfaces is no. of layers +1
 //    tempw[nopara-(2*Nlay+1)+i-1]=abs(tempw[nopara-(2*Nlay+1)+i-1])
 // endfor
 
  prew=w_fit
 weps1=1e-06//0.001//prew*0.1//
  holdstring=""
  k=0

  if (cmpstr(cntrlName,"rst1")==0 || cmpstr(cntrlName,"rst1a")==0)
      for (i=0;i<(2*nopara+Nlay);i=i+1) //to avoid conflict by both constrainted and held
      if (i<2*nopara)
      for (j=0; j<nopara;j=j+1)   
        if ((checkhold[j])==1 && stringmatch(T_Constraints_temp[i],"*K"+num2str(j))==1&&checkhold[ceil((i-1)/2)]==0)
//        print checkhold[j],T_Constraints_temp[i],j,stringmatch(T_Constraints_temp[i],"*K"+num2str(j)),checkhold[ceil((i-1)/2)], ceil((i-1)/2)
           T_Constraints_temp[i]=num2str(w_fit[j])
        endif
     endfor
     else
//    print "qq", ceil((i-1)/2)
       for (j=0; j<nopara;j=j+1)   
        if ((checkhold[j])==1 && stringmatch(T_Constraints_temp[i],("K"+num2str(j)))==1)
           T_Constraints_temp[i]=num2str(w_fit[j])
        endif
     endfor
     endif
     endfor
  for (i=0;i<nopara;i=i+1)
   if (checkhold[i]<1)
     if (stringmatch(T_Constraints_temp[2*i], "")==1||stringmatch(T_Constraints_temp[2*i], " ")==1||stringmatch(T_Constraints_temp[2*i], "  ")==1||stringmatch(T_Constraints_temp[2*i], "   ")==1)
      T_Constraints[2*i]="0x"
       if (i>NLay+1&&i<2*NLay+3)
        T_Constraints[2*i]="K"+num2str(i)+">"+"0.001"
       endif
     else
     T_Constraints[2*i]="K"+num2str(i)+">"+T_Constraints_temp[2*i]
     endif
     if (stringmatch(T_Constraints_temp[2*i+1], "")==1||stringmatch(T_Constraints_temp[2*i+1], " ")==1||stringmatch(T_Constraints_temp[2*i+1], "  ")==1||stringmatch(T_Constraints_temp[2*i+1], "   ")==1)
     T_Constraints[2*i+1]="0x"
     else   
     T_Constraints[2*i+1]="K"+num2str(i)+"<"+T_Constraints_temp[2*i+1]
     endif
   else
   T_Constraints[2*i]="0x"//"K"+num2str(Nlay+2)+">"+"K"+num2str(Nlay+2)  //fake constraint
   T_Constraints[2*i+1]="0x"//"K"+num2str(Nlay+2)+"<"+"K"+num2str(Nlay+2)  //fake constraint
   k=k+2
   endif
   holdstring=holdstring+num2str(checkhold[i])
  endfor
//  Variable /G globmass
  
 //  Profile4Fit(w_fit,x)
 //  Integrate/METH=1 prof/X=zz/D=prof_INT
//   globmass=(1351.16+prof_INT[60])/5.66
for (j=0;j<NLay;j=j+1)
  if (syn>0)
     if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
          if (j==(ceil(cursorprofA/Npoint_per_Lay)-1))
             sw4incohe[j]=2*syn+1
            
          else
            sw4incohe[j]=1
          
          endif
    else
 //         if (j==(ntlay-ceil(ntlay/10))||i==(2*ntlay-ceil(ntlay/10))||i==(3*ntlay-ceil(ntlay/10))||i==(4*ntlay-ceil(ntlay/10))||i==(5*ntlay-ceil(ntlay/10))||i==(6*ntlay-ceil(ntlay/10))||i==(7*ntlay-ceil(ntlay/10))||i==(8*ntlay-ceil(ntlay/10)))

             sw4incohe[j]=2*syn+1
     endif  
   else
            sw4incohe[j]=1//3
  //        endif
   
    
  endif
  
endfor
  j=0
  for (i=2*nopara;i<(2*nopara+Nlay);i=i+1)
  if (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]<1 && checkhold[nopara-2*(Nlay+1)+j+1]<1)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*K"+num2str(nopara-2*(Nlay+1)+j)+"+2*K"+num2str(nopara-2*(Nlay+1)+j+1)+"+"+num2str(sw4incohe[j])
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]>0 && checkhold[nopara-2*(Nlay+1)+j+1]<1 )
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*"+num2str(w_fit[nopara-2*(Nlay+1)+j])+"+2*K"+num2str(nopara-2*(Nlay+1)+j+1)+"+"+num2str(sw4incohe[j])
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]<1 && checkhold[nopara-2*(Nlay+1)+j+1]>0)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*K"+num2str(nopara-2*(Nlay+1)+j)+"+2*"+num2str(w_fit[nopara-2*(Nlay+1)+j+1])+"+"+num2str(sw4incohe[j])  
  elseif (checkhold[nopara-Nlay-1+j]<1 && checkhold[nopara-2*(Nlay+1)+j]>0 && checkhold[nopara-2*(Nlay+1)+j+1]>0)
  T_Constraints[i]="K"+num2str(nopara-Nlay-1+j)+">"+"2*"+num2str(w_fit[nopara-2*(Nlay+1)+j])+"+2*"+num2str(w_fit[nopara-2*(Nlay+1)+j+1])+"+"+num2str(sw4incohe[j])    
  else
   T_Constraints[i]="0x"
   k=k+1
   endif 
  
  j=j+1
  endfor
  
  
     //  T_Constraints[2*nopara+Nlay]="globmass-8-2*K13-2*K14 > K15"  //added for one more constraint May08
  //  T_Constraints[2*nopara+Nlay+1]="globmass-8-2*K13-2*K14 < K15"  //added for one more constraint May08



//print k, noconstrnt
  j=0
  k=0
  for (i=0;i<(2*nopara+Nlay);i=i+1) // to remove held parameters from being constrainted
   if (stringmatch(T_Constraints[i],"0x")==1)
    deletepoints i,1,T_Constraints
    i=i-1
    k=k+1
   endif
//   T_Constraints[i]= T_Constraints1[j]
 //  j=j+1
  endfor
     Variable noconstrnt=(2*nopara+Nlay)-k
 //  deletepoints i,1, T_Constraints
//   noconstrnt=noconstrnt-1
 // print noconstrnt,k
  Variable /G globV_chisq
  Variable /G globV_Rchisq
  Variable /G globnpntsdata
  Duplicate /O dRQdata dRQ_temp
// dRQ_temp=dRQ_temp^2
  Variable nodata=numpnts(dRQdata)
   for (i=0;i<(nodata);i=i+1) //
    if (rswitch>0)
       if (dRQdata[i]<=0|| RQdata[i]<=0)
          dRQ_temp[i]=5*abs(dRQdata[i])//1e-04*qzdata[i]^4
       endif
    else
      if (dRQdata[i]<=0|| RQdata[i]<=0)
         dRQ_temp[i]=5*abs(dRQdata[i])//1e-04
       endif
    endif
   endfor
   Variable/G massnorm   //mass norm procedure ON(>0)/OFF(0)
 if (massnorm>0)      
 massnorm =w_fit[15]       //mass norm procedure ON(>0)/OFF(0)
  tempw[15]=massnorm    //mass norm procedure ON(>0)/OFF(0)
  //massnorm=0           //ON/OFF is currently manual
  endif                      //mass norm procedure ON(>0)/OFF(0)

// Variable w15init=w_fit[15]
Duplicate /O tempw tempwfit
if (noconstrnt==0)
   if (pfyn==1)
   FuncFit /H=holdstring Profile4Fit tempw RQdata[pcsr(A),pcsr(B)] /W=dRQ_temp  /I=1 /D=Rq_Fit /E=weps1 //M=MaskRQdata// /C=T_Constraints ///M=MaskRQdata
   else
   FuncFit /H=holdstring Profile4Fit tempw RQdata /W=dRQ_temp  /D=Rq_Fit   /I=1  /E=weps1 //M=MaskRQdata// /C=T_Constraints ///M=MaskRQdata// /R=Res_try
   endif
 else

   if (pfyn==1)
   FuncFit /H=holdstring Profile4Fit tempw  RQdata[pcsr(A),pcsr(B)]  /I=1 /D=Rq_Fit /C=T_Constraints /W=dRQ_temp /E=weps1 //M=MaskRQdata  ///M=MaskRQdata
   else
   FuncFit /H=holdstring Profile4Fit tempw  RQdata /W=dRQ_temp  /D=Rq_Fit   /I=1  /C=T_Constraints  /E=weps1 //M=MaskRQdata//M=MaskRQdata// /R=Res_try
   endif
 endif
// weps1=prew*0.1
//  for (i=0;i<=(Nlay);i=i+1)  // # of interfaces is no. of layers +1
//    tempw[nopara-(2*Nlay+1)+i-1]=abs(tempw[nopara-(2*Nlay+1)+i-1])
// endfor
Variable/G massnorm   //mass norm procedure ON(>0)/OFF(0)
 if (massnorm>0)             //mass norm procedure ON(>0)/OFF(0)
  tempw[15]=massnorm    //mass norm procedure ON(>0)/OFF(0)
  //massnorm=0           //ON/OFF is currently manual
  endif                      //mass norm procedure ON(>0)/OFF(0)
//  w_fit[15]= w15init
 cslay=0
Duplicate /O T_Constraints_temp_temp $TC_temp
KillWaves /Z T_Constraints_temp_temp,tempwfit
 SetActiveSubWindow $ExptTitle
   if (V_chisq>0)
   globV_chisq=V_chisq
   globV_Rchisq=V_chisq/(V_npnts)
   globnpntsdata=V_npnts
   endif
     KillWaves /Z  dRQ_temp//, dRQmod
  endif
  SetWindow  $ExptTitle, hook=winhookproc
  print "*****", ExptTitle, "Fitting Finished .................................................................. ^ ^ ^ ^ ^"
//SetActiveSubWindow $ExptTitle
End


Function FitRangeDraw(ctrlName,varNum,varStr,varName)
String ctrlName,varStr,varName
Variable varNum
SVAR rq4data1=globrq4data
SVAR qzdata1=globqzdata
SVAR ExptTitle=globExptTitle
NVAR autoR=globautoR

Variable/G globgraphhold
Variable graphhold=globgraphhold
//SetWindow  $ExptTitle hook=$" "
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
 if (varNum>0)
//SetActiveSubWindow NR#RQPlotInPanel
//RemoveFromgraph /Z /W=NR#RQPlotInPanel Rq_Fit
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $rq4data1 leftx($rq4data1)
Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $rq4data1 numpnts($rq4data1)
if (autoR>0)
 CheckDisplayed /W=$ExptTitle#RQPlotInPanel $rq4data1+"_Pre_Cal"
 if (V_flag>0)
ReorderTraces /W=$ExptTitle#RQPlotInPanel $rq4data1,{$rq4data1+"_Pre_Cal"}
endif
endif
 CheckDisplayed /W=$ExptTitle#RQPlotInPanel Rq_Fit
 if (V_flag>0)
ReorderTraces /W=$ExptTitle#RQPlotInPanel $rq4data1,{Rq_Fit}
endif


//cursora=pcsr(A,"NR#RQPlotInPanel")
//cursorb=pcsr(B,"NR#RQPlotInPanel")
//SetAxis /W=NR#RQPlotInPanel /A bottom //qzdata[cursora],qzdata[cursorb]
else
//SetActiveSubWindow NR#RQPlotInPanel
Cursor /K /W=$ExptTitle#RQPlotInPanel A //$rq4data1
Cursor /K /W=$ExptTitle#RQPlotInPanel B //$rq4data1
//SetAxis /W=NR#RQPlotInPanel /A bottom

 CheckDisplayed /W=$ExptTitle#RQPlotInPanel Rq_Fit
 if (V_flag>0)
ReorderTraces /W=$ExptTitle#RQPlotInPanel Rq_Fit, {$rq4data1}
endif

 if (autoR>0)
 Variable ss=V_flag
CheckDisplayed /W=$ExptTitle#RQPlotInPanel $rq4data1+"_Pre_Cal"
 if (V_flag>0 && ss>0)
 ReorderTraces /W=$ExptTitle#RQPlotInPanel  $rq4data1+"_Pre_Cal", {$rq4data1,Rq_Fit}
 endif

 endif
endif
//DrawRect  /W=NR#RQPlotInPanel 0.01,7e-08,0.06,0
 //SetWindow  $ExptTitle, hook=winhookproc
End

Function PopCmplxYn(ctrlName,popNum,popStr): PopupMenuControl
String ctrlName
Variable popNum
String popStr

Variable cmplxcalyn

cmplxcalyn=popNum
Variable /G globcmplxcalyn=cmplxcalyn
Variable/G globgraphhold
Variable graphhold=globgraphhold
SVAR ExptTitle=globExptTitle
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
FitRgeneral3( )

End
Function popAddD(cntrlName,popNum,popStr) : PopupMenuControl
 String cntrlName
 Variable popNum
 String popStr
 String varStr=popStr
 Variable varNum=popNum

 AddDCUp("D",varNum,varStr,"")
End

Function popAddC(cntrlName,popNum,popStr) : PopupMenuControl
 String cntrlName
 Variable popNum
 String popStr
 String varStr=popStr
 Variable varNum=popNum

 AddDCUp("C",varNum,varStr,"")
End
Function AddDCUp(cntrlName,varNum,varStr,varName) //: SetVariableControl
String cntrlName
Variable varNum
String varStr
String varName
String get_temp
// NewDataFolder /O root:$varStr
String /G globExptTitle//=varStr
String svDF=GetDataFolder(1)
Variable /G globrswitch

String wn=WinName(0,1)

SetDataFolder  root:$varStr

SVAR rdata1=globRQ4data
SVAR drdata1=globdRQ4data
SVAR qdata1=globqzdata
String rfit="Rq_Fit"//_Dup"
String rname, drname,qname,rfitname

rname="r"+varStr
drname="dr"+varStr
qname="q"+varStr
rfitname="rfit"+varStr

Wave Rq_Fit
Duplicate /O $rdata1 $rname
Duplicate /O $drdata1 $drname
Duplicate /O $qdata1 $qname
Duplicate /O Rq_Fit $rfitname
Variable i
///To find max unumber of dataplots
    String objName
    Variable index=0
    do 
        objName=GetindexedObjName("root:",4,index)
        if (strlen(objName) == 0)
        break
        endif
    index +=1
    while(1)
//    print Tracenamelist(" ",";",1)  
    ///the max number stored in index
 Variable j=0

 String texstr
  texstr="\\s("+rname+") "+varStr+" "

if (stringmatch(cntrlName,"D")>0)
CheckDisplayed  $rname
if (V_flag>0)
 RemoveFromGraph $rname
 else
        AppendText /N=texgra   texstr

endif
if (varNum<index/3)
AppendToGraph /C=(65535, 65535-65535*(3*varNum/index),65535*(3*varNum/index) ) $rname vs $qname
elseif (varNum<2*index/3)
AppendToGraph /C=(65535-65535*3/2*varNum/(index), 65535 ,65535*3/2*(varNum/index)) $rname vs $qname
else
AppendToGraph /C=(65535*(varNum/index), 65535*(varNum/index) ,65535-65535*varNum/(index)) $rname vs $qname
endif
       ErrorBars  $rname Y,wave=($drname,$drname)//XY,wave=($dqdata,$dqdata)

        for (i=1;i<2*index*10;i=i+1)
     
        if (stringmatch(WaveName("",i,1),"rfit*")<1)
        
         ModifyGraph /Z   mode[i]=3,marker[i]=19,msize[i]=2,opaque[i]=1,useMrkStrokeRGB[i]=1//,grid=1,gridRGB=(65280,54528,32768)
                   
  //      TextBox /C/N=texgra texstr

        endif
        endfor
       

elseif (stringmatch(cntrlName,"C")>0)
 CheckDisplayed  $rfitname
if (V_flag>0)
RemoveFromGraph $rfitname
endif
//Duplicate /O $rfit Rq_Fit_Dup
AppendToGraph /C=(65535*varNum/(index),0,65535-65535*varNum/(index)) $rfitname vs $qname 
   //     print stringmatch(WaveName("",i,1),"Rq_Fit*")
        for (i=1;i<2*index*10;i=i+1)
       if (stringmatch(WaveName("",i,1),"rfit*")>0)

           ModifyGraph /Z lsize[i]=1.5
      endif
       endfor

endif

SetDataFolder svDF

End

Function popExtTitleUp(cntrlName,popNum,popStr) : PopupMenuControl
 String cntrlName
 Variable popNum
 String popStr
 String varStr=popStr
 Variable varNum=popNum

 ExtTitleUp("",varNum,varStr,"")
End

Function ExtTitleUp(cntrlName,varNum,varStr,varName) : SetVariableControl
String cntrlName
Variable varNum
String varStr
String varName
String get_temp
// NewDataFolder /O root:$varStr
String /G globExptTitle//=varStr
String svDF=GetDataFolder(1)

    If (Stringmatch(globExptTitle,"*-*")>0)
    globExptTitle=ReplaceString("-",globExptTitle,"_")
    endif

String wn=WinName(0,1)

NewDataFolder /O root:$globExptTitle

globExptTitle=varStr
 If (strsearch(WinList(globExptTitle,";","WIN:"),globExptTitle,0)>=0)
   DoWindow /F $globExptTitle//
 else
     if (Strsearch(PrintAllDataFolderNames(),globExptTitle,0)<0||Strsearch(varStr,wn,0)<1)
      FitRgeneral2()
     else
      FitRgeneral3()

     endif
 endif
SetDataFolder svDF
globExptTitle= wn
SetDataFolder root:$varStr

End

Function ComLineinWin(cntrlName,varNum,varStr,varName) : SetVariableControl
String cntrlName
Variable varNum
String varStr
String varName
String comIn=" "
String commanLine=varStr
String /G globcomWin 
 
sprintf globcomWin,"%s", commanLine
 
//print globcomWin    //Redoing these 3lines activates the commend line excution.
//Execute globcomWin
//globcomWin=""
//globcomWin=commanLine
End 

Function ChoiceNewDFName(ctrlName,popNum,popStr): PopupMenuControl
String ctrlName
Variable popNum
String popStr
SetDataFolder root:
SetDataFolder root:$ctrlName
Variable /G globNNDF
globNNDF=popNum
//print globNNDF,GetDataFolder(1)

End


Function ExtTitleUp1(cntrlName,varNum,varStr,varName) : SetVariableControl //does not work yet!!!
String cntrlName
Variable varNum
String varStr
String varName
String get_temp
// NewDataFolder /O root:$varStr
String /G globExptTitle//=varStr
String svDF=GetDataFolder(1)
Variable  modeDF=1//=NumVarOrDefault("globNNDF",1)
    If (Stringmatch(globExptTitle,"*-*")>0)
    globExptTitle=ReplaceString("-",globExptTitle,"_")
//    globExptTitle=ReplaceString("-",globExptTitle,"_")
//    globExptTitle=ReplaceString("-",globExptTitle,"_")
    endif

String wn=WinName(0,1)
//Variable /G root:globExptTitleroot=varStr
NewDataFolder /O root:$globExptTitle

Variable /G globNNDF=modeDF

//String svDF1=GetDataFolder(1)
//print svDF1,globExptTitle,wn,varStr

globExptTitle=varStr
 If (strsearch(WinList(globExptTitle,";","WIN:"),globExptTitle,0)>=0)
   DoWindow /F $globExptTitle//
 else
     if (Strsearch(PrintAllDataFolderNames(),globExptTitle,0)<0||Strsearch(varStr,wn,0)<1)     
       
       if (Strsearch(PrintAllDataFolderNames(),globExptTitle,0)<0)     
        DoWindow /K Stop4NewDFName 
        NewPanel /N=Stop4NewDFName /W=(2,0,450,100)
        PopupMenu $wn  value="Yes;No",mode=modeDF,proc=ChoiceNewDFName, pos={110,20},fstyle=1, size={80,100},bodyWidth=150, title=" Would you like to copy the current data too?"/////////,fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
        Button buttonSNDFN,pos={155,65},size={92,20},fstyle=1
        Button buttonSNDFN,proc=Stop4NewDFName_ContButton,title="Continue"
        PauseForUser Stop4NewDFName
       SetDataFolder root:$wn
        Variable /G globNNDF
        
//            print globNNDF,GetDataFolder(1),varStr,wn,globExptTitle
        if (globNNDF!=2) 
             KillDataFolder /Z root:$varStr
             DuplicateDataFolder root:$wn, root:$varStr
        endif     
      
      endif
//      SetDataFolder svDF
//      Variable /G globNNDF=1
//     SetDataFolder root:$varStr
     globExptTitle=varStr
      FitRgeneral2()
     else
      FitRgeneral3()
//print globExptTitle
//Execute "SetActiveSubWindow $globExptTitle"
     endif
 endif
SetDataFolder svDF
globExptTitle= wn
SetDataFolder root:$varStr
//KillVariables /Z root:globNNDF
End

Function Stop4NewDFName_ContButton(cntrlName)
String cntrlName
DoWindow /K Stop4NewDFName //tmp_GetInputPanel 
End


Function MakeGraph_sldButton(cntrlName) : ButtonControl //To restart in NR window
String cntrlName
SVAR ExptTitle=globExptTitle
SVAR prosldz=globprosldz,proz=globproz//RQ4data=globrq4data, Qzdata=globqzdata,RRQ4nPlot=RRQ4nPlot,dqdata=globdqdata,dRQ4data=globdRQ4data
String name, namet
   name="SLD_"+ExptTitle
 namet="SLD"+ExptTitle
if (cmpstr(cntrlName,"titlegraph1")==0)
      SetDataFolder root:$ExptTitle
       If (strsearch(WinList(namet,";","WIN:2"),namet,0)<0)
      
           Edit /N=$namet  /W=(5,10,400,650) $prosldz, $proz
      
         else
         DoWindow /F $namet

        endif

      If (strsearch(WinList(name,";","WIN:1"),name,0)>=0)

       DoWindow /F $name
    //  SetDataFolder root:$ExptTitle
      else

         SetDataFolder root:$ExptTitle

        Display /N=$name $prosldz vs $proz as name///N=name
        Label left "\\F'Arial'\\f0110\\S6\\MSLD (Å\\S2\\M)"
        Label bottom "\\f01z  (Å)"
        ModifyGraph  framestyle=0, mirror=1,minor=0,standoff=1,tick=2,mode($prosldz)=4,marker($prosldz)=19,msize($prosldz)=2,lsize($prosldz)=1.5,opaque($prosldz)=1,zColor($prosldz)={$prosldz,*,*,Rainbow}//,grid=1,gridRGB=(60000,60000,60000)//(65280,54528,32768)
        ModifyGraph gbRGB=(61000,61000,61000), wbRGB=(65535,65535,65535) //,useMrkStrokeRGB($prosldz)=2//,mrkStrokeRGB($prosldz)=(30464,30464,30464)
 
     endif
        SetDataFolder root:
endif
  
End



Function UserEditSLD_ContButton(cntrlName)
String cntrlName
 Variable graphhold=NumVarOrDefault("globgraphhold", 0)
 Variable modeGraphdrawEdit=NumVarOrDefault("globmodeGraphdrawEdit",1)
 Variable modeGraphdrawEdit1=modeGraphdrawEdit
SVAR ExptTitle=globExptTitle
Variable /G globautoR
if ((cmpstr(cntrlName,"rst5")==0|| cmpstr(cntrlName,"rst5a")==0))
   if (graphhold==0)
   DoWindow /K GraphDraworEdit
NewPanel /N=GraphDraworEdit /W=(2,0,450,120)
PopupMenu GraphDE  value="Edit;Draw",mode=modeGraphdrawEdit1,pos={310,20},fstyle=1,proc=GED4PSD, size={80,100},bodyWidth=50, title="Do you like to EDIT or DRAW the SLD profile?   "//,fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
 TitleBox note4GDEl title="    Use mouse click to edit and double click to finish.",   pos={45,45}, frame=0
 TitleBox note4GDE title="*Note that Choosing 'Draw' will remove the current SLD profile.", pos={48,65}, frame=0
 Button buttonGDE,pos={155,90},size={92,20},fstyle=1
 Button buttonGDE,proc=UserGetGDE_ContButton,title="Continue"
Variable /G globmodeGraphdrawEdit=modeGraphdrawEdit1
 PauseForUser GraphDraworEdit
       if (globmodeGraphdrawEdit<2)
       GraphWaveEdit/M /W=$ExptTitle#SLDplotinPanel prof
      else
         if (WaveExists(prof_back)==1)
  //          RemoveFromGraph /W=##/Z prof_back
           RemoveFromGraph  /W=$ExptTitle#SLDplotinPanel/Z prof_back, zz_back     
//            Rename prof prof_back, zz_back //prof_GraphDraw, zz_GraphDraw
         endif

         Duplicate /O prof, prof_back
         Duplicate /O zz, zz_back
         AppendToGraph /W=$ExptTitle#SLDplotinPanel prof_back vs zz_back
        ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof_back)=0,marker(prof_back)=19,msize(prof_back)=1,lsize(prof_back)=3,opaque(prof_back)=1, rgb(prof_back)=(32768,65280,32768),zColor(prof_back)=0//,zColor(prof_back)={prof_back,*,*,Grays}
        ReorderTraces  /W=$ExptTitle#SLDplotinPanel prof, {prof_back}
 //          ModifyGraph /W=$ExptTitle#SLDplotinPanel mode(prof)=4,marker(prof)=19,msize(prof)=2,lsize(prof)=1.5,opaque(prof)=1,zColor(prof)={prof,*,*,Rainbow},grid=1,gridRGB=(60000,60000,60000)//(65280,54528,32768)

        
         GraphWaveDraw /M /O /W=$ExptTitle#SLDplotinPanel prof, zz
   
      endif
   graphhold=1
   else
 ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
//      ModifyGraph /W=$ExptTitle#SLDplotinPanel mode(prof)=4,marker(prof)=19,msize(prof)=2,lsize(prof)=1.5,opaque(prof)=1,zColor(prof)={prof,*,*,Rainbow},grid=1,gridRGB=(60000,60000,60000)//(65280,54528,32768)

   GraphNormal /W=$ExptTitle#SLDplotinPanel
   graphhold=0

 endif
    if (globautoR>0)
    autoRup("editt",0," "," ")
    endif
 //   FitRGeneral3()
//     ModifyGraph /W=$ExptTitle#SLDplotinPanel mode(prof)=4,marker(prof)=19,msize(prof)=2,lsize(prof)=1.5,opaque(prof)=1,zColor(prof)={prof,*,*,Rainbow},grid=1,gridRGB=(60000,60000,60000)

endif
 globmodeGraphdrawEdit=1
Variable /G globgraphhold=graphhold
End


Function UserPara2SLDPanel_ContButton(cntrlName): ButtonControl
String cntrlName
if (cmpstr(cntrlName,"rst2")==0||cmpstr(cntrlName,"rst2a")==0)
Variable/G globgraphhold,globautoS
Variable graphhold=globgraphhold
SVAR ExptTitle=globExptTitle
    if (graphhold>0)
     ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
//Variable /G globstop2sld=1
if (globautoS<1)
Profile4Fit(w_fit,x)
endif
//f (cmpstr(cntrlName,"up")==0)
autoRup(" ",0," "," ")
endif
End

Function Kiessig_Thickness()

SVAR qzdata1=globqzdata
//Variable s_thick_1=NumVarOrDefault("globs_thick_1", 1)

Wave /D qzdata=$qzdata1

SVAR ExptTitle=globExptTitle
Variable/G globpfyn
Variable pfyn=globpfyn
    if (pfyn>0)
Variable cursora,cursorb
SetActiveSubWindow $ExptTitle#RQPlotInPanel
Variable apprxtoltalthick
 apprxtoltalthick=abs(2*Pi/(qzdata[pcsr(B)]-qzdata[pcsr(A)]))
 print "Q[B]-Q[A] =", (qzdata[pcsr(B)]-qzdata[pcsr(A)])
 print "Total film thickness from Kiessig-fringes, d =", apprxtoltalthick,"Å"
else
print "****Please set 'Ranged by Cursor' to 1, and place cursors on the reflectivity graph first. Then, look at 'Command Window' which can be brought by 'Ctrl+J'. ************"
endif
//SetActiveSubWindow dennissingleair
End


Function incoherentpointproc(ctrlName,varNum,varStr,varName)
String ctrlName,varStr,varName
Variable varNum
SVAR prosldz1=globprosldz
SVAR proz1=globproz, ExptTitle=globExptTitle

Variable/G globsyn
Variable syn=globsyn
Variable center_point4_inc,notp
     notp=numpnts(prof)
     center_point4_inc=ceil((notp-1)/2)

 if (varNum>0)
//SetActiveSubWindow NR#RQPlotInPanel
//RemoveFromgraph /Z /W=NR#RQPlotInPanel Rq_Fit
 if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))<=0)
Cursor /S=2 /L=0 /C=(26368,0,52224) /W=$ExptTitle#SLDPlotInPanel A $prosldz1 center_point4_inc
endif

else //if (strlen(CsrInfo(A, ExptTitle+"#SLDPlotInPanel"))>0)
//SetActiveSubWindow NR#RQPlotInPanel
Cursor /K /W=$ExptTitle#SLDPlotInPanel A //$rq4data1
endif

End

Function updatewinpan(ctrlName,varNum,varStr,varName)
String ctrlName,varStr,varName
Variable varNum

Variable/G globgraphhold
Variable graphhold=globgraphhold
SVAR ExptTitle=globExptTitle
    if (graphhold>0)
    ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
    FitRgeneral3()
autoRup(" ",0," "," ")
//

End

//Master formula calculation of R
Function SuperMaster() // v: q values for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
Variable /C rsin,rcos
Variable rho,i,j,RSM,lamda=5.46//e-10
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz,q1=globqzdata, ExptTitle=globExptTitle
Wave q=$q1,prof=$prof1,zz=$zz1
Duplicate /O prof dprof
Duplicate /O zz dzz
Variable nptnsprof=numpnts(prof)
Differentiate prof /X=zz /D=dprof
///METH=1 /X=zz
Differentiate zz/D=dzz ///METH=1
Make /O /N=(numpnts(q)) R1_FT

rho=0
for (i=0;i<nptnsprof;i=i+1)
dprof[i]=dprof[i]*1e-06
 rho=rho+dprof[i]*dzz[i]
endfor

for (j=0;j<numpnts(q);j=j+1)

rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0

for (i=0;i<nptnsprof;i=i+1)
 rsin=rsin+dzz[i]*dprof[i]*exp(cmplx(0,-1)*sqrt(q[j]^2-1.0*(sqrt(2*rho*lamda^2/(2*Pi))*4*Pi/lamda)^2)*zz[i])//(sqrt(v^2-abs(prof[nptnsprof-1]-prof[0])*1e-06*(4*Pi))*zz[i]) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*
endfor

RSM=(magsqr(rsin))*((sqrt((q[j]-sqrt(q[j]^2-(sqrt(2*rho*lamda^2/(2*Pi))*4*Pi/lamda)^2))/(q[j]+sqrt(q[j]^2-(sqrt(2*rho*lamda^2/(2*Pi))*4*Pi/lamda)^2))))^2/(rho))^2//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/
R1_FT[j]=RSM
if (R1_FT[j]>1)
R1_FT[j]=1
endif
endfor

CheckDisplayed /W=$ExptTitle#RQPlotInPanel R1_FT//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#RQPlotInPanel R1_FT vs $q1
ModifyGraph lsize(R1_FT)=2
endif
//endif
return 0//RSM//*2e+9//*1e+02
End 

Function InvSuperMasterReal()//,xx)//: FitFunc // v: xvalues for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
//Variable xx
Variable /C rsin,rcos,RSM
Variable i,j,lamda=5.46//,rho//e-10
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz, rq1=globrq4data,q1=globqzdata, ExptTitle=globExptTitle
Wave rq2=$rq1,q=$q1,prof=$prof1,zz=$zz1
//Duplicate /O rq rqtrans
//Variable z=zz[xx]
Duplicate /O rq2 rq
Duplicate /O q dq
Variable nptnsprof=numpnts(prof)
Variable nptnsrq=numpnts(rq)
Make /O /C /D /N=(2*nptnsrq) rqtrans//,drqtrans
Make /O /D /N=(2*nptnsrq) q_f,dq_f,rq_f
Make /O /N=1200 prof1_IFT,prof1_IFT1,prof1_IFT2, zz1_IFT
zz1_IFT=x-100
Variable qc
Variable rho=(prof[nptnsprof-1]-prof[0])
for (j=0;j<numpnts(zz1_IFT);j=j+1)
rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0
qc=0.00001
for (i=0;i<1*nptnsrq;i=i+1)
if (rq[i]<1e-09)
rq[i]=1e-09
endif

if ((rq[i]>0.8 && rq[i+1]<0.8)||(rq[i+1]<0.8 && rq[i]>0.8))
qc=(q[i]+q[i+1])/2
endif
endfor
for (i=0;i<nptnsrq;i=i+1)
if (i==0)
dq[i]=abs(q[i+1]-q[i])/2
elseif (i==nptnsrq-1)
dq[i]=abs(q[i]-q[i-1])/2
else
dq[i]=abs(q[i]-q[i-1])/2+abs(q[i+1]-q[i])/2
endif

dq_f[i+nptnsrq]=dq[i]
q_f[i+nptnsrq]=q[i]
rq_f[i+nptnsrq]=rq[i]
rqtrans[i+nptnsrq]=(rq_f[i+nptnsrq]/((((q_f[i+nptnsrq]-sqrt(q_f[i+nptnsrq]^2-qc^2))/(q_f[i+nptnsrq]+sqrt(q_f[i+nptnsrq]^2-qc^2)))^2)/(rho*1e-06)^2))//((qc)^2/(16*Pi))^2))
endfor
for (i=0;i<nptnsrq;i=i+1)
dq_f[i]=dq[nptnsrq-i-1]
q_f[i]=-q[nptnsrq-i-1]
if(abs(q_f[i])<qc)
rq_f[i]=rq[nptnsrq-i-1]*(exp(-(abs(3*q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
elseif(abs(q_f[i])<3*qc) 
rq_f[i]=rq[nptnsrq-i-1]*(1-exp(-(abs(q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
else
rq_f[i]=rq[nptnsrq-i-1]
endif
rqtrans[i]=(rq_f[i]/((((q_f[i]-sqrt(q_f[i]^2-qc^2))/(q_f[i]+sqrt(q_f[i]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))
endfor

for (i=0;i<2*nptnsrq;i=i+1)
 rsin=rsin+dq_f[i]*sqrt(rqtrans[i])*exp(cmplx(0,1)*(sqrt(q_f[i]^2-1.0*qc^2)*zz1_IFT[j]))//cmplx(0,(q[i]))*z) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*
endfor

RSM=1/(2*Pi)*((rsin))//rcos//+magsqr(rcos)))//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/
//prof1_IFT1[j]=sqrt(magsqr(RSM))*1e+06*50 //((abs(zz1_IFT[j]))^(1/3))*10//-
prof1_IFT1[j]=((Real(RSM)*1e+06*50)/(exp(-abs(zz1_IFT[j])/500)+1))*3 //((abs(zz1_IFT[j]))^(1/3))*10//-
//prof1_IFT[j]=(prof1_IFT1[j]-1*prof1_IFT2[j])
endfor

InsertPoints nptnsprof, 1, zz1_IFT
  zz1_IFT[nptnsprof]=zz1_IFT[nptnsprof-1]+1
//Execute "integrate prof1_IFT1 /X=zz1_IFT /D=prof1_IFT1"
Execute "InvSuperMasterImag()"
DeletePoints 0, 1, zz1_IFT
prof1_IFT=(prof1_IFT1-1.0*prof1_IFT2)//*sign(rho)
DeletePoints 0, 20, zz1_IFT,prof1_IFT,prof1_IFT1,prof1_IFT2
//zz1_IFT=zz1_IFT-20
//DSPDetrend /F=sigmoid prof1_IFT1
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFT//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFT vs zz1_IFT//, prof1_IFT1
//ModifyGraph /W=NR#SLDPlotInPanel rgb(prof1_IFT)=(0,0,65280)
endif//endif
//IFFT /R /DEST=prof1_IFT rq_f
KillWaves rq,rqtrans,q_f,dq_f,rq_f,dq,prof1_IFT1,prof1_IFT2//,prof1_IFT1
return 0//(Real(RSM))*1e+06*100//*6.1128e+11//*1e+02
End 

Function InvSuperMasterImag()//,xx)//: FitFunc // v: xvalues for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
//Variable xx
Variable /C rsin,rcos,RSM
Variable i,j,lamda=5.46//,rho//e-10
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz, rq1=globrq4data,q1=globqzdata
Wave rq2=$rq1,q=$q1,prof=$prof1,zz=$zz1
//Duplicate /O rq rqtrans
//Variable z=zz[xx]
Duplicate /O rq2 rq
Duplicate /O q dq
Variable nptnsprof=numpnts(prof)
Variable nptnsrq=numpnts(rq)
Make /O /C /D /N=(2*nptnsrq) rqtrans
Make /O /D /N=(2*nptnsrq) q_f,dq_f,rq_f
Make /O /N=1200  zz1_IFT,prof1_IFT2
zz1_IFT=x-100

Variable qc
Variable rho=(prof[nptnsprof-1]-prof[0])
for (j=0;j<numpnts(zz1_IFT);j=j+1)
rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0
qc=0.00001
for (i=0;i<1*nptnsrq;i=i+1)
if (rq[i]<1e-09)
rq[i]=1e-09
endif
if ((rq[i]>0.8 && rq[i+1]<0.8)||(rq[i+1]<0.8 && rq[i]>0.8))
qc=(q[i]+q[i+1])/2
endif
endfor
for (i=0;i<nptnsrq;i=i+1)
if (i==0)
dq[i]=abs(q[i+1]-q[i])/2
elseif (i==nptnsrq-1)
dq[i]=abs(q[i]-q[i-1])
else
dq[i]=abs(q[i]-q[i-1])/2+abs(q[i+1]-q[i])/2
endif
dq_f[i+nptnsrq]=dq[i]
q_f[i+nptnsrq]=q[i]
rq_f[i+nptnsrq]=rq[i]
rqtrans[i+nptnsrq]=(rq_f[i+nptnsrq]/((((q_f[i+nptnsrq]-sqrt(q_f[i+nptnsrq]^2-qc^2))/(q_f[i+nptnsrq]+sqrt(q_f[i+nptnsrq]^2-qc^2)))^2)/(rho*1e-06)^2))//((qc)^2/(16*Pi))^2))
endfor
for (i=0;i<nptnsrq;i=i+1)
dq_f[i]=dq[nptnsrq-i-1]
q_f[i]=-q[nptnsrq-i-1]
if(abs(q_f[i])<qc)
rq_f[i]=rq[nptnsrq-i-1]*(exp(-(abs(3*q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
elseif(abs(q_f[i])<3*qc) 
rq_f[i]=rq[nptnsrq-i-1]*(1-exp(-(abs(q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
else
rq_f[i]=rq[nptnsrq-i-1]
endif
rqtrans[i]=(rq_f[i]/((((q_f[i]-sqrt(q_f[i]^2-qc^2))/(q_f[i]+sqrt(q_f[i]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))
endfor

for (i=0;i<2*nptnsrq;i=i+1)
 rsin=rsin+dq_f[i]*sqrt(rqtrans[i])*exp(cmplx(0,1)*(sqrt(q_f[i]^2-1.0*qc^2)*zz1_IFT[j]))//cmplx(0,(q[i]))*z) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*
endfor

RSM=1/(2*Pi)*((rsin))//rcos//+magsqr(rcos)))//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/
prof1_IFT2[j]=-((Imag(RSM)*1e+06*50)/(exp(-abs(zz1_IFT[j])/100)+1))*200//((abs(zz1_IFT[j]))^(1/3))*10//-
endfor
InsertPoints nptnsprof, 1, zz1_IFT
  zz1_IFT[nptnsprof]=zz1_IFT[nptnsprof-1]+1
//Execute "integrate prof1_IFT2 /X=zz1_IFT /D=prof1_IFT2"
Execute "Differentiate prof1_IFT2 /X=zz1_IFT /D=prof1_IFT2"
Execute "Differentiate prof1_IFT2 /X=zz1_IFT /D=prof1_IFT2"
Execute "Differentiate prof1_IFT2 /X=zz1_IFT /D=prof1_IFT2"


KillWaves rq,rqtrans,q_f,dq_f,rq_f,dq
return 0//(Real(RSM))*1e+06*100//*6.1128e+11//*1e+02
End 

Function InvSuperMasterMag1()//,xx)//: FitFunc // v: xvalues for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
//Variable xx
Variable /C rsin,rcos,RSM
Variable i,j,lamda=5.46//,rho//e-10
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz, rq1=globrq4data,q1=globqzdata, ExptTitle=globExptTitle
Wave rq2=$rq1,q=$q1,prof=$prof1,zz=$zz1
//Duplicate /O rq rqtrans
//Variable z=zz[xx]
Duplicate /O rq2 rq
Duplicate /O q dq
Variable nptnsprof=numpnts(prof)
Variable nptnsrq=numpnts(rq)
Make /O /C /D /N=(2*nptnsrq) rqtrans
Make /O /D /N=(2*nptnsrq) q_f,dq_f,rq_f
Make /O /N=1200 prof1_IFT,prof1_IFT2,prof1_IFTMag, zz1_IFT
zz1_IFT=x-100
Variable qc
Variable rho=(prof[nptnsprof-1]-prof[0])
for (j=0;j<numpnts(zz1_IFT);j=j+1)
rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0
qc=0.00001
for (i=0;i<1*nptnsrq;i=i+1)
if (rq[i]<1e-09)
rq[i]=1e-09
endif
if ((rq[i]>0.8 && rq[i+1]<0.8)||(rq[i+1]<0.8 && rq[i]>0.8))
qc=(q[i]+q[i+1])/2
endif
endfor
for (i=0;i<nptnsrq;i=i+1)
if (i==0)
dq[i]=abs(q[i+1]-q[i])/2
elseif (i==nptnsrq-1)
dq[i]=abs(q[i]-q[i-1])
else
dq[i]=abs(q[i]-q[i-1])/2+abs(q[i+1]-q[i])/2
endif
dq_f[i+nptnsrq]=dq[i]
q_f[i+nptnsrq]=q[i]
rq_f[i+nptnsrq]=rq[i]
rqtrans[i+nptnsrq]=(rq_f[i+nptnsrq]/((((q_f[i+nptnsrq]-sqrt(q_f[i+nptnsrq]^2-qc^2))/(q_f[i+nptnsrq]+sqrt(q_f[i+nptnsrq]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))//(rho*1e-06)^2))//((qc)^2/(16*Pi))^2))
endfor
for (i=0;i<nptnsrq;i=i+1)
dq_f[i]=dq[nptnsrq-i-1]
q_f[i]=-q[nptnsrq-i-1]
if(abs(q_f[i])<qc)
rq_f[i]=rq[nptnsrq-i-1]*(exp(-(abs(3*q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
elseif(abs(q_f[i])<3*qc) 
rq_f[i]=rq[nptnsrq-i-1]*(1-exp(-(abs(q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
else
rq_f[i]=rq[nptnsrq-i-1]
endif
rqtrans[i]=(rq_f[i]/((((q_f[i]-sqrt(q_f[i]^2-qc^2))/(q_f[i]+sqrt(q_f[i]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))
endfor

for (i=0;i<2*nptnsrq;i=i+1)
 rsin=rsin+dq_f[i]*sqrt(rqtrans[i])*exp(cmplx(0,1)*(sqrt(q_f[i]^2-1.0*qc^2)*zz1_IFT[j]))//cmplx(0,(q[i]))*z) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*
endfor

RSM=1/(2*Pi)*((rsin))//rcos//+magsqr(rcos)))//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/
//prof1_IFTMag[j]=Real(RSM)*1e+06*100
prof1_IFTMag[j]=(((Real(RSM))*(1e+06*50))/(exp(-abs(zz1_IFT[j])/100)+1))*(abs(zz1_IFT[j]+800))/600//*5
endfor
WaveStats /Q /Z prof1_IFTMag
for (j=0;j<numpnts(zz1_IFT);j=j+1)
if (abs(prof1_IFTMag[j])<3*V_adev)//abs(prof1_IFTMag[100]))
prof1_IFTMag[j]=0
else
prof1_IFTMag[j]=prof1_IFTMag[j]
endif
endfor
prof1_IFTMag[100]=prof1_IFTMag[100]*2
InsertPoints nptnsprof, 1, zz1_IFT
  zz1_IFT[nptnsprof]=zz1_IFT[nptnsprof-1]+1
//Execute "integrate prof1_IFT1 /X=zz1_IFT /D=prof1_IFT1"
Execute "InvSuperMasterImag()"
DeletePoints 0, 1, zz1_IFT
//prof1_IFTMag=(prof1_IFTMag-1.0*prof1_IFT2)
DeletePoints 0, 20, zz1_IFT,prof1_IFTMag,prof1_IFT2
//zz1_IFT=zz1_IFT-20
//DSPDetrend /F=sigmoid prof1_IFT1
smooth 9,prof1_IFTMag
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFTMag//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFTMag vs zz1_IFT//, prof1_IFT1
ModifyGraph /W=$ExptTitle#SLDPlotInPanel rgb(prof1_IFTMag)=(0,0,65280)
endif//endif
KillWaves rq,rqtrans,q_f,dq_f,rq_f,dq,prof1_IFT2//,prof1_IFT1
return 0//(Real(RSM))*1e+06*100//*6.1128e+11//*1e+02
End 


Function MakeGraph_RButton(cntrlName) : ButtonControl 
String cntrlName
//String  svDF=GetDataFolder(1)
SVAR ExptTitle=globExptTitle
// SetDataFolder root:$ExptTitle
SVAR RQ4data=globrq4data, Qzdata=globqzdata,RRQ4nPlot=RRQ4nPlot,dqdata=globdqdata,dRQ4data=globdRQ4data

String name1,name1t
NVAR brswitch1=globrswitch
Variable rswitch=brswitch1

   name1="RvsQ_"+ExptTitle
   name1t="Table_"+ExptTitle

if (cmpstr(cntrlName,"titlegraph0")==0)
         SetDataFolder root:$ExptTitle
          If (strsearch(WinList(name1t,";","WIN:2"),name1t,0)>=0)
          DoWindow /F $name1t
          else
          Edit   /N=$name1t /W=(5,10,500,650) $RQ4data,$dRQ4data,$Qzdata,$dqdata,Rq_Fit
          endif
  //         DoWindow /K $name1
            SetDataFolder root:$ExptTitle
           If (strsearch(WinList(name1,";","WIN:"),name1,0)>=0&& strsearch(TraceNameList(name1,";",0),RQ4data,0)>=0)
     
               DoWindow /F $name1           
            
          else
     //       DoWindow /K $name1
              String rname="r"+ExptTitle
              String drname="dr"+ExptTitle
              String qname="q"+ExptTitle
              String rfitname="rfit"+ExptTitle


              Duplicate /O $RQ4data $rname
              Duplicate /O $dRQ4data $drname
              Duplicate /O $Qzdata $qname
              Duplicate /O Rq_Fit $rfitname
             DoWindow $name1
             if (V_flag>0)
          //  Duplicate /O Rq_Fit Rq_Fit_Dup
            Display /N=$name1 $rname $rfitname vs $qname
            ModifyGraph height=200
            ControlBar  40
            TitleBox but1, pos={0,0},size={130,40},labelBack=(65280,49152,16384),frame=4,title="\\f01\\Z12Scenic View"
            ModifyGraph height=0
            PopupMenu adddata  value=PrintAllDataFolderNames(),mode=1,bodyWidth=20, title="Append Data",fstyle=1, size={79,200},labelBack=(65280,43520,0),proc=popaddD,pos={170,12}, help={"   This is a copy of your data... Make sure that the modes (R or RQ4) for data sets are consistent with each other..."}
            PopupMenu addcal  value=PrintAllDataFolderNames(),mode=1,bodyWidth=20, title="Append Fit",fstyle=1, size={79,200},labelBack=(65280,43520,0),proc=popaddC,pos={340,12}, help={"   This is a copy of your data fit and will not be auto-updated..."}

            else
            Display /N=$name1 $RQ4data Rq_Fit vs $Qzdata 
            endif
            
            SetDataFolder root:$ExptTitle
    
     	  Label left "\\f01"+RRQ4nPlot
          Label bottom "\\f01Q\Bz\M  (Å\\S-1\\M)"
          if (V_flag>0)
          ModifyGraph  framestyle=0,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($rname)=3, msize($rname)=2,marker($rname)=19,opaque($rname)=1, rgb($rfitname)=(0,0,65280),lsize($rfitname)=2, rgb($rname)=(65280,21760,0),useMrkStrokeRGB($rname)=1, lowTrip=0.0001//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars $rname, Y wave=($drname,$drname)
          String texstr="\\s("+rname+") "+ExptTitle+" "
         TextBox /C/N=texgra texstr
           else
          ModifyGraph  framestyle=0,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, lowTrip=0.0001//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars $RQ4data, Y wave=($dRQ4data,$dRQ4data)
        
           endif
          ModifyGraph gbRGB=(61000,61000,61000), wbRGB=(65535,65535,65535),lblRot(left)=-90
         //, X,wave=($dqdata)
       //  ErrorBars $RQ4data  XY wave=($dRQ4data,$dqdata) 
          If (rswitch<1)
              CheckDisplayed /W= $ExptTitle#RQplotInPanel R_cal
               if (V_flag==1)
               
    //          AppendToGraph /W=$name1 R_cal vs Q_cal
              ModifyGraph  /W=$name1  rgb(R_cal)=(65280,0,0),lsize=2
              endif
          else
           CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_cal
             if (V_flag==1)
            AppendToGraph /W=$name1 RQ4_cal vs Q_cal
            ModifyGraph  /W=$name1  rgb(RQ4_cal)=(65280,0,0),lsize=2
            endif
         endif
        endif
endif
//SetDataFolder root:
End





Function InvSuperMasterMag()//,xx)//: FitFunc // v: xvalues for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
//Variable xx
Variable /C rsin,rcos,RSM
Variable i,j,lamda=5.46//,rho//e-10
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz, rq1=globrq4data,q1=globqzdata, ExptTitle=globExptTitle
Wave rq2=$rq1,q=$q1,prof=$prof1,zz=$zz1
//Duplicate /O rq rqtrans
//Variable z=zz[xx]
Duplicate /O rq2 rq
Duplicate /O q dq
Variable nptnsprof=numpnts(prof)
Variable nptnsrq=numpnts(rq)
Make /O /C /D /N=(2*nptnsrq) rqtrans
Make /O /D /N=(2*nptnsrq) q_f,dq_f,rq_f
Make /O /N=1200 prof1_IFT0,prof1_IFT00,prof1_IFTMag, zz1_IFT0
zz1_IFT0=x-100

Variable qc
Variable rho
rho=(prof[nptnsprof-1]-prof[0])
//print sign(rho)
for (j=0;j<numpnts(zz1_IFT0);j=j+1)
rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0
qc=0.00001
for (i=0;i<1*nptnsrq;i=i+1)
if (rq[i]<1e-09)
rq[i]=1e-09
endif
if ((rq[i]>0.8 && rq[i+1]<0.8)||(rq[i+1]<0.8 && rq[i]>0.8))
qc=(q[i]+q[i+1])/2
endif
endfor
for (i=0;i<nptnsrq;i=i+1)
if (i==0)
dq[i]=abs(q[i+1]-q[i])/2
elseif (i==nptnsrq-1)
dq[i]=abs(q[i]-q[i-1])
else
dq[i]=abs(q[i]-q[i-1])/2+abs(q[i+1]-q[i])/2
endif
dq_f[i+nptnsrq]=dq[i]
q_f[i+nptnsrq]=q[i]
rq_f[i+nptnsrq]=rq[i]
rqtrans[i+nptnsrq]=(rq_f[i+nptnsrq]/((((q_f[i+nptnsrq]-sqrt(q_f[i+nptnsrq]^2-qc^2))/(q_f[i+nptnsrq]+sqrt(q_f[i+nptnsrq]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))//(rho*1e-06)^2))//((qc)^2/(16*Pi))^2))
endfor
for (i=0;i<nptnsrq;i=i+1)
dq_f[i]=dq[nptnsrq-i-1]
q_f[i]=-q[nptnsrq-i-1]
if(abs(q_f[i])<qc)
rq_f[i]=rq[nptnsrq-i-1]*(exp(-(abs(3*q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
elseif(abs(q_f[i])<3*qc) 
rq_f[i]=rq[nptnsrq-i-1]*(1-exp(-(abs(q_f[i]/(qc)))))//*sin(abs(-q_f[nptnsrq-i])+qc)
else
rq_f[i]=rq[nptnsrq-i-1]
endif
rqtrans[i]=(rq_f[i]/((((q_f[i]-sqrt(q_f[i]^2-qc^2))/(q_f[i]+sqrt(q_f[i]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))
endfor

for (i=0;i<2*nptnsrq;i=i+1)
 rsin=rsin+dq_f[i]*sqrt(rqtrans[i])*exp(cmplx(0,1)*(sqrt(q_f[i]^2-1.0*qc^2)*zz1_IFT0[j]))//cmplx(0,(q[i]))*z) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*
endfor

RSM=1/(2*Pi)*((rsin))//rcos//+magsqr(rcos)))//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/
//prof1_IFTMag[j]=Real(RSM)*1e+06*100
prof1_IFTMag[j]=(Imag(RSM*exp(cmplx(0,1)*Pi/2)))*(1e+06)*10
endfor
for (j=0;j<numpnts(zz1_IFT0);j=j+1)
prof1_IFTMag[j]=prof1_IFTMag[j]/prof1_IFTMag[100]*3/exp(-zz1_IFT0[j]/500)*sign(rho)
endfor
WaveStats /Q /Z prof1_IFTMag

InsertPoints nptnsprof, 1, zz1_IFT0
  zz1_IFT0[nptnsprof]=zz1_IFT0[nptnsprof-1]+1
//Execute "InvSuperMasterImag()"
DeletePoints 0, 1, zz1_IFT0
//prof1_IFTMag=(prof1_IFTMag-1.0*prof1_IFT2)
DeletePoints 0, 20, zz1_IFT0//,prof1_IFTMag,prof1_IFT2
//zz1_IFT=zz1_IFT-20
//DSPDetrend /F=sigmoid prof1_IFT1
smooth 9,prof1_IFTMag
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFTMag//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFTMag vs zz1_IFT0//, prof1_IFT1
ModifyGraph /W=$ExptTitle#SLDPlotInPanel rgb(prof1_IFTMag)=(0,0,65280)
endif//endif
KillWaves rq,rqtrans,q_f,dq_f,rq_f,dq,prof1_IFT00,prof1_IFT0
print sign(rho)
return 0//(Real(RSM))*1e+06*100//*6.1128e+11//*1e+02
End 


Function InvSuperMasterMag3()//,xx)//: FitFunc // v: xvalues for the R calculation; ex, make /N=? RSM > RSM=SuperMaster(Qcal)
//Variable xx
Variable /C rsin,rcos,RSM
Variable i,j,lamda=4.62//5.46//,rho//e-10
NVAR Nlay1=globNlay
Variable Nlay=Nlay1
//Variable /C epnt
SVAR prof1=globprosldz, zz1=globproz, rq1=globrqdata,q1=globqzdata, ExptTitle=globExptTitle
Wave rq2=$rq1,q=$q1,prof=$prof1,zz=$zz1

Wave w_fit
Variable sld_in=w_fit[0]
Variable sld_sub=w_fit[NLay+1]
Wave ph
//Duplicate /O rq rqtrans
//Variable z=zz[xx]
Duplicate /O rq2 rq
Duplicate /O q dq
Variable nptnsprof=numpnts(prof)
Variable nptnsrq=numpnts(rq)
Make /O /C /D /N=(nptnsrq) rqtrans
Make /O /D /N=(nptnsrq) q_f,dq_f,rq_f
Make /O /N=1200 prof1_IFT,prof1_IFT2,prof1_IFTMaga, zz1_IFT
zz1_IFT=(x-100)*0.5

Variable qc
Variable rho
//rho=(prof[nptnsprof-1]-prof[0])

Variable /C kn,knp1,rn
Variable /C alpha,nn,nnp1,n1,ni//,n2//,n2A,n2B//,phin,phinp1
Variable SLD1,SLDi,phi1,ko//,rf


//      if (globcmplxcalyn>1)
      SVAR prof_IM1=globImSLDin
     
     Wave prof_IM=$prof_IM1

 
    SLD1=w_fit[NLay+1]*1e-06//SLD1g*1e-06//5.69e-06//sapphire///4.14e-06  //Quartz   ////SLD for substrate

    SLDi=w_fit[0]*1e-06//SLDig*1e-06   /////SLD for incident medium
   rho=SLD1-SLDi
    
    ko=2*pi/lamda
    n1=rip(lamda,SLD1,prof_IM[NLay+1]*1e-06)//cmplx(1-SLD1*lamda^2/(2*pi),0)  

    ni= rip(lamda,SLDi,prof_IM[0]*1e-06)

   
    qc=crtQ_cal( )

//print sign(rho)
for (j=0;j<numpnts(zz1_IFT);j=j+1)
rsin=cmplx(0,0)
rcos=cmplx(0,0)
RSM=0

//for (i=0;i<1*nptnsrq;i=i+1)
//if (rq[i]<1e-09)
//rq[i]=1e-09
//endif
//if ((rq[i]>0.8 && rq[i+1]<0.8)||(rq[i+1]<0.8 && rq[i]>0.8))
//qc=(q[i]+q[i+1])/2
//endif
//endfor
for (i=0;i<nptnsrq;i=i+1)
if (i==0)
dq[i]=abs(q[i+1]-q[i])/2
elseif (i==nptnsrq-1)
dq[i]=abs(q[i]-q[i-1])
else
dq[i]=abs(q[i]-q[i-1])/2+abs(q[i+1]-q[i])/2
endif
dq_f[i]=dq[i]
q_f[i]=q[i]
    phi1=asin(lamda*q_f[i]/(4*pi))  //    dz=flmthickness/nolrs
///***     alpha=ni*(cos(asin(sin(phi1)/ni)))  <<< more accurate but not neccessary
    alpha=ni*cos(phi1)
    nnp1=n1
    knp1=sqrt(ko^2*(nnp1^2-(alpha^2)))  //nnp1*ko*sin(phinp1)

//    nn= rip(lamda,hh[i]*1e-06,prof_IM[i]*1e-06)//SLDprof(z,SLD1,SLDA,SLDB,SLDS,lamda)   
  
    kn=sqrt(ko^2*(ni^2-alpha^2))       //nn*ko*sin(phin)
 //   an=exp(cmplx(0,-2)*kn*dz)       //    anp1=exp(cmplx(0,2)*knp1*(z))
    rn=(kn-knp1)/(kn+knp1)

rq_f[i]=rq[i]/magsqr(rn)*(abs(rho))^2//(exp(-q_f[i]^4))^4
rqtrans[i]=rq_f[i]//(rq_f[i]/((((q_f[i]-sqrt(q_f[i]^2-qc^2))/(q_f[i]+sqrt(q_f[i]^2-qc^2)))^2)/((qc)^2/(16*Pi))^2))//(rho*1e-06)^2))//((qc)^2/(16*Pi))^2))
endfor

for (i=0;i<nptnsrq;i=i+1)
 rsin=rsin+dq_f[i]*sqrt(rqtrans[i]*exp(cmplx(0,1)*ph[i]*Pi/180))*exp(cmplx(0,1)*q_f[i]*zz1_IFT[j])//(sqrt(q_f[i]^2-1.0*qc^2)*zz1_IFT[j])/cmplx(0,(q[i]))*z) //sqrt(2*(prof[nptnsprof-1]-prof[0])*1e-06*lamda^2/(2*Pi))*4*Pi/lamda    dzz[i]*////sqrt(rqtrans[i])*exp(cmplx(0,1)*q_f[i]*zz1_IFT[j])//
 rcos=rcos+dq_f[i]//*exp(cmplx(0,1)*q_f[i]*zz1_IFT[j])
endfor

RSM=1/(2*Pi)*(rsin)//rcos//+magsqr(rcos)))//((sqrt(rho*lamda^2/(2*Pi))*4*Pi/lamda))^2 //  /(abs(rho))^2/


prof1_IFT[j]=(Real(RSM))//*exp(cmplx(0,1)*Pi/2)
prof1_IFT2[j]=(Imag(RSM))//*exp(cmplx(0,1)*Pi/2)
prof1_IFTMaga[j]=sqrt(magsqr(RSM))//*exp(cmplx(0,1)*Pi/2)
endfor
for (j=0;j<numpnts(zz1_IFT);j=j+1)
prof1_IFTMaga[j]=prof1_IFTMaga[j]*1e+06//(prof1_IFTMaga[0])///prof1_IFTMag[100]*3/exp(-zz1_IFT[j]/500)*sign(rho)
prof1_IFT[j]=prof1_IFT[j]*1e+06
prof1_IFT2[j]=prof1_IFT2[j]*1e+06
endfor
WaveStats /Q /Z prof1_IFTMaga

InsertPoints nptnsprof, 1, zz1_IFT
 zz1_IFT[nptnsprof]=zz1_IFT[nptnsprof-1]+1
Execute "integrate prof1_IFTMaga/X=zz1_IFT"
DeletePoints 0, 1, zz1_IFT

//DeletePoints 0, 20, zz1_IFT,prof1_IFTMaga,prof1_IFT2

//smooth 9,prof1_IFTMag
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFTMaga//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFTMaga vs zz1_IFT//, prof1_IFT1
ModifyGraph /W=$ExptTitle#SLDPlotInPanel rgb(prof1_IFTMaga)=(0,0,65280)
endif//endif
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFT//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFT vs zz1_IFT//, prof1_IFT1
ModifyGraph /W=$ExptTitle#SLDPlotInPanel rgb(prof1_IFT)=(65280,0,0)
endif//endif
CheckDisplayed /W=$ExptTitle#SLDPlotInPanel prof1_IFT2//NR#SLDPlotInPanel prof1_IFT
if (V_flag<1)
AppendToGraph /W=$ExptTitle#SLDPlotInPanel prof1_IFT2 vs zz1_IFT//, prof1_IFT1
ModifyGraph /W=$ExptTitle#SLDPlotInPanel rgb(prof1_IFT2)=(0,65280,0)
endif//endif

KillWaves rq,rqtrans,q_f,dq_f,rq_f,dq//,prof1_IFT2//,prof1_IFT1
//print sign(rho)
return 0//(Real(RSM))*1e+06*100//*6.1128e+11//*1e+02
End 









Function SliderobjectR(name,value,event)
String name
Variable value
Variable event
NVAR rswitch=globrswitch
SVAR ExptTitle1=globExptTitle//,  RRQ4nPlot=RRQ4nPlot
String ExptTitle=ExptTitle1
String/G RRQ4nPlot
String/G dRQ4nPlot
String/G globrq4data
//String/G globrqdata
SVAR rqdata1=globrqdata//,drqdata1=globdrqdata
String/G globdrq4data
SVAR drqdata1=globdrqdata
String /G globQzdata
String Qzdata1=globQzdata
Variable /G globmodecalRDP
Wave rqdata=$rqdata1,Qzdata=$Qzdata1,drqdata=$drqdata1
Wave Rq_Fit
   String erq="RvsQ_"+ExptTitle
//Wave R_cal
 String Rq_Fit1
 String Qz_Fit1
// String dQ_Fit1
if (event >4)
rswitch=value 

   
        if (rswitch>0)
        globrq4data="RQ4_Trans_"+rqdata1
        globdrq4data="sig_RQ4_Trans_"+drqdata1
       if ( waveExists($globrq4data) || waveExists($globdrq4data))
         Make /O/N=(numpnts(rqdata))  $globrq4data
         Make /O/N=(numpnts(drqdata))  $globdrq4data
       endif
        Duplicate /O rqdata $globrq4data
        Duplicate /O drqdata $globdrq4data
              
         Wave RQ4data=$globRQ4data
         Wave dRQ4data=$globdRQ4data
        
     	   RRQ4nPlot="RQ\\S4"
     	   dRQ4nPlot="SigRQ\\S4"     	   
     	   RQ4data=RQ4data*(Qzdata)^4
     	   dRQ4data=dRQ4data*(Qzdata)^4
     	    Rq_Fit=Rq_Fit*(Qzdata)^4
     	    Rq_Fit1=rqdata1+"_Pre_Cal"
//     	    dQ_Fit1=dqdata1+"_Pre_Cal"
     	    Qz_Fit1=qzdata1+"_Pre_Cal"
     	              GetAxis  /W= $ExptTitle#RQplotInPanel /Q left
         SetAxis  /W= $ExptTitle#RQplotInPanel /Z/A // left V_min*(Qzdata)^4, V_max*(Qzdata)^4
          GetAxis  /W= $ExptTitle#RQplotInPanel /Q bottom
           SetAxis  /W= $ExptTitle#RQplotInPanel /Z   bottom V_min, V_max

     	    
    	     CheckDisplayed /W= $ExptTitle#RQplotInPanel $Rq_Fit1

     	    if (V_flag==1)
     	    Wave rqprecal=$Rq_Fit1,qzprecal=$Qz_Fit1
     	   
     	    rqprecal=rqprecal*(qzprecal)^4
     	     RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel $Rq_Fit1
     	    Rq_Fit1=globrq4data+"_Pre_Cal"
     	    Qz_Fit1=globQzdata+"_Pre_Cal"
     	    Duplicate /O rqprecal, $Rq_Fit1
 //    	    Duplicate /O qzprecal, $Qz_Fit1
   	     AppendToGraph /C=(0,39168,0)  /W= $ExptTitle#RQplotInPanel $Rq_Fit1 vs $Qz_Fit1
   	     ModifyGraph  /W= $ExptTitle#RQplotInPanel  lsize($Rq_Fit1)=1.5
    	    endif
    	     CheckDisplayed /W= $ExptTitle#RQplotInPanel R_Cal
     	    if (V_flag==1)
            if (stringmatch(rqdata1,"R_Cal")<1)
     	     RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel R_Cal
   	     AppendToGraph /C=(65280,0,0)  /W= $ExptTitle#RQplotInPanel RQ4_Cal vs Q_Cal
   	     ModifyGraph  /W= $ExptTitle#RQplotInPanel  lsize(RQ4_Cal)=3
    	     endif
    	    endif
        DoWindow $erq
//         print V_flag
         if (V_flag>0)
           RemoveFromGraph /Z/W= $erq $rqdata1
          AppendToGraph /W= $erq  /C=(65280,0,0)  RQ4data vs Qzdata
                    ModifyGraph /W= $erq framestyle=0,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($globRQ4data)=3, marker($globRQ4data)=19,opaque($globRQ4data)=1, rgb($globRQ4data)=(65280,21760,0),useMrkStrokeRGB($globRQ4data)=1, lowTrip=0.0001//,grid=1,gridRGB=(65280,54528,32768)
   //       ModifyGraph /W= $erq gbRGB=(61000,61000,61000), wbRGB=(64000,64000,64000),lblRot(left)=-90
          ErrorBars/W= $erq $globRQ4data Y,wave=($globdRQ4data,$globdRQ4data)//XY,wave=($dqdata,$dqdata) 
           CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
            if(V_flag>0)
              CheckDisplayed /W= $ExptTitle#RQplotInPanel $globRQ4data
              if (V_flag>0)
   	       ReorderTraces /W=$erq Rq_Fit,{$globRQ4data}
   	       endif
   	     endif

//   	    SetAxis  /W= $erq  /Z /A left
   	
         endif
         
//          SetAxis  /W= $ExptTitle#RQplotInPanel /Z /A left
//           SetAxis  /W= $ExptTitle#RQplotInPanel /Z /A  bottom
     	   else
     	   
     	 DoWindow $erq
//         print V_flag
         if (V_flag>0)
          RemoveFromGraph /Z/W= $erq $globRQ4data
          AppendToGraph /W= $erq  /C=(65280,0,0)  rqdata vs Qzdata
                   ModifyGraph /W= $erq framestyle=0,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($rqdata1)=3, marker($rqdata1)=19,opaque($rqdata1)=1, rgb($rqdata1)=(65280,21760,0),useMrkStrokeRGB($rqdata1)=1, lowTrip=0.0001//,grid=1,gridRGB=(65280,54528,32768)
   //       ModifyGraph /W= $erq gbRGB=(61000,61000,61000), wbRGB=(64000,64000,64000),lblRot(left)=-90
          ErrorBars/W= $erq $rqdata1 Y,wave=($drqdata1,$drqdata1)//XY,wave=($dqdata,$dqdata) 
           CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
             if(V_flag>0)
              CheckDisplayed /W= $ExptTitle#RQplotInPanel$rqdata1
              if (V_flag>0)
   	               ReorderTraces /W=$erq Rq_Fit,{$rqdata1}
   	       endif
   	     endif


     //     CheckDisplayed /W= $erq RQ_Fit
     //        if (V_flag>0)
     //         ModifyGraph /W= $erq lsize(RQ_Fit)=2
     //         endif
          endif
           
    	    Rq_Fit1=globrq4data+"_Pre_Cal"
     	    Qz_Fit1=globQzdata+"_Pre_Cal"
    	    
     	   globrq4data=rqdata1
         globdrq4data=drqdata1

     	   RRQ4nPlot="R"
     	   dRQ4nPlot="SigR"   
     	   Rq_Fit=Rq_Fit/(Qzdata)^4  
     	   
     	              GetAxis  /W= $ExptTitle#RQplotInPanel /Q left
         SetAxis  /W= $ExptTitle#RQplotInPanel /Z/A // left V_min/(Qzdata)^4, V_max/(Qzdata)^4
          GetAxis  /W= $ExptTitle#RQplotInPanel /Q bottom
           SetAxis  /W= $ExptTitle#RQplotInPanel /Z   bottom V_min, V_max
     //	   if (globmodecalRDP<2)
 //        	     CheckDisplayed /W= $ExptTitle#RQplotInPanel $Rq_Fit1	   
  //        	     endif
     	     CheckDisplayed /W= $ExptTitle#RQplotInPanel $Rq_Fit1

     	    if (V_flag==1)
     	    Wave rqprecal=$Rq_Fit1
     	     Wave qzprecal=$Qz_Fit1
     	    rqprecal=rqprecal/(qzprecal)^4
     	    RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel $Rq_Fit1
     	    Rq_Fit1=rqdata1+"_Pre_Cal"
       	    Duplicate /O rqprecal, $Rq_Fit1
   	     AppendToGraph /C=(0,39168,0) /W= $ExptTitle#RQplotInPanel $Rq_Fit1 vs $Qz_Fit1
   	      ModifyGraph  /W= $ExptTitle#RQplotInPanel  lsize($Rq_Fit1)=1.5
    	    endif
    	    
    	    CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_Cal

     	    if (V_flag==1&&stringmatch(rqdata1,"R_Cal")<1)

     	     RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel RQ4_Cal
   	     AppendToGraph /C=(65280,0,0)  /W= $ExptTitle#RQplotInPanel R_Cal vs Q_Cal
   	     ModifyGraph  /W= $ExptTitle#RQplotInPanel  lsize(R_Cal)=2
   	     
    	    endif
     	   endif
     DoWindow $erq
         if (V_flag>0)
           Label /W=$erq /Z left "\\f01"+RRQ4nPlot
         endif
 //        CheckDisplayed /W= $ExptTitle#RQplotInPanel SimR_Pre_Cal
 //    	    if (V_flag==1)
 //   	    RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel SimR_Pre_Cal
  //   	    endif
   //      CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_Trans_SelectData_Pre_Cal
  //   	    if (V_flag==1)
  //   	    RemoveFromGraph /Z/W= $ExptTitle#RQplotInPanel RQ4_Trans_SelectData_Pre_Cal
  //   	    endif
     	    
FitRgeneral3()
//DoWindow /R ReflectivityPlot4RQFitPanel
endif
return 0
End




Function UserSLD2RPanel_ContButton(cntrlName): ButtonControl
String cntrlName
 Variable modecalRDP=NumVarOrDefault("globmodecalRDP",1)
 Variable modecalRDP1=modecalRDP
Variable /G globmodecalRDP=modecalRDP1
Variable /G globrswitch
SVAR rq4data1=globRQ4data
String rq4data=rq4data1
SVAR rqdata1=globRQdata
String rqdata=rqdata1

Variable rswitch=globrswitch
Variable i,nptproz
SVAR Proz1=globproz
SVAR ExptTitle=globExptTitle

Wave Proz=$Proz1
NVAR cmplxcalyn1=globcmplxcalyn
Variable cmplxcalyn=cmplxcalyn1
//   if (cmplxcalyn>1)
//   Profile4Fit(w_fit,x)
//   endif
//Wavestats Proz
nptproz=numpnts(Proz)
//print nptproz
if (cmpstr(cntrlName,"rst3")==0|| cmpstr(cntrlName,"rst3a")==0)
Variable/G globgraphhold
Variable graphhold=globgraphhold
    if (graphhold>0)
     ModifyGraph  /W=$ExptTitle#SLDplotinPanel mode(prof)=4,msize(prof)=2,lsize(prof)=1.5
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    
    globgraphhold=0
    endif
DoWindow /K Rcal4DataorPreCal
//print stringmatch(rq4data,"SelectData")
if (stringmatch(rqdata,"SelectData")==1||stringmatch(rq4data,"SelectData")==1||stringmatch(rq4data,"RQ4_Trans_SelectData")==1)
  if (stringmatch(rq4data,"RQ4_Trans_SelectData")==1)
     globrswitch=0
     rswitch=0
     fitRgeneral3()
   endif
   modecalRDP1=2
  else 
  modecalRDP1=1
endif
//globmodecalRDP=modecalRDP1
//modecalRDP1=1
if (modecalRDP1>1)
NewPanel /N=Rcal4DataorPreCal /W=(2,0,450,120)
PopupMenu RQ4data  value="Yes;No",mode=modecalRDP1,pos={310,20},fstyle=1, size={80,100},bodyWidth=50,proc=R4DoPC, title="Do you have Q data for this R (or RQ4) calculation?   "//,fstyle=1, size={80,200},proc=dataRInput,pos={210,70},help={"Reflectivity Data"}//WaveList("*",";","")
TitleBox note4rcal title="*Note that Choosing 'no' will generate 6 columns of data named; ",  pos={40,45}, frame=0
 TitleBox note4rcalb title="R_cal, RQ4_cal, Q_cal, sigmaR_cal, sigmaRQ4_cal, sigmaQ_cal.",  pos={43,65}, frame=0
 Button button0,pos={155,90},size={92,20},fstyle=1
Button button0,proc=UserGetInputPanel_ContButton,title="Continue"

 PauseForUser Rcal4DataorPreCal
endif
  Variable/G globmodecalRDP=modecalRDP1
 SetWindow $ExptTitle hook=$" " //kwTopWin 
  
   if (globmodecalRDP<2)
   
   ParrattMaindq( )
//   DoWindow /K RQ4vsQCal
    CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data1+"_Pre_Cal")
//    if(V_flag==1)  //<<==This is OK but w/ precal on, Fit_cal hides under precal. Need more trials. 081507
//     ReorderTraces /W=$ExptTitle#RQplotInPanel $(RQ4data1+"_Pre_Cal"),{Rq_Fit}
//    endif

   else
   Make /O /N=(256) R_cal,Q_cal, sigmaR_cal, sigmaQ_cal, RQ4_cal,sigmaRQ4_cal
     sigmaQ_cal=0.001
     Q_cal=0
      for (i=0;i<256;i=i+1)
      Q_cal[i]=(0.3-0.003)/255*i+0.003
       sigmaQ_cal[i]=Q_cal[i]*0.02
     endfor
     if (rswitch <1)
      
      
      R_cal=ParrattNTRNdq(Q_cal,sigmaQ_cal,nptproz)
    RQ4_cal=R_cal*Q_cal^4
      sigmaR_cal=R_cal*0.01
    sigmaRQ4_cal=RQ4_cal*0.01 
      CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_cal
     if (V_flag==1)
      RemoveFromGraph /W=$ExptTitle#RQplotInPanel RQ4_cal
      endif
      
          CheckDisplayed /W= $ExptTitle#RQplotInPanel R_cal
             if (V_flag==1)
          RemoveFromGraph /W=$ExptTitle#RQplotInPanel R_cal
          endif
          AppendToGraph /W=$ExptTitle#RQplotInPanel R_cal vs Q_cal
          ModifyGraph  /W=$ExptTitle#RQplotInPanel  rgb(R_cal)=(65280,0,0),lsize=2//,grid=1,gridRGB=(65280,54528,32768)
  //   endif   
      else
    
      RQ4_cal=ParrattNTRNdq(Q_cal,sigmaQ_cal,nptproz)
      R_cal=RQ4_cal/Q_cal^4
      sigmaR_cal=R_cal*0.01
      sigmaRQ4_cal=RQ4_cal*0.01  
     CheckDisplayed /W= $ExptTitle#RQplotInPanel R_cal
          if (V_flag==1)
          RemoveFromGraph /W=$ExptTitle#RQplotInPanel R_cal
         endif
         CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_cal
         if (V_flag==1)
         RemoveFromGraph /W=$ExptTitle#RQplotInPanel RQ4_cal
         endif          
     AppendToGraph /W=$ExptTitle#RQplotInPanel RQ4_cal vs Q_cal
      ModifyGraph  /W=$ExptTitle#RQplotInPanel  rgb(RQ4_cal)=(65280,0,0),lsize=2//,grid=1,gridRGB=(65280,54528,32768)
      endif
     endif
//endif
//SetActiveSubWindow $ExptTitle
  
 SetWindow  $ExptTitle, hook=winhookproc
 endif
//print globmodecalRDP
End


Function CSRPos4PCX(a)
Variable a //dummy
NVAR  syn1=globsyn
SVAR ExptTitle=globExptTitle
Variable syn=syn1
Variable cursora
if (syn>0)
cursora=pcsr(A, ExptTitle+"#SLDPlotInPanel")
endif
return cursora
END



Function dataRInput(ctrlName,popNum,popStr)
String ctrlName
Variable popNum
String popStr
String/G globrq4data=popStr
Variable/G globmoderq4=popNum
Variable /G globpfyn
Variable pfyn=globpfyn
String/G globrqdata=popStr
Variable/G globrswitch//=0
Variable rswitch=globrswitch
SVAR RQ4data=globRQ4data,Qzdata=globQzdata,dRQ4data=globdRQ4data,dqdata=globdqdata
SVAR RQ4data1old1=globRQ4dataold,Qzdata1old=globQzdataold,dRQ4data1old=globdRQ4dataold,dqdata1old=globdqdataold
SVAR ExptTitle=globExptTitle
Variable /G globautoR=0
Variable rswitchpre=rswitch
Variable/G globgraphhold
Variable graphhold=globgraphhold
String RQ4data1old=RQ4data1old1

//globrswitch=0
 if (rswitch>0)
 
 SliderobjectR(" ",0,5)
 SliderobjectR(" ",1,5)
 endif
    if (graphhold>0)
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
   if (pfyn==1)
   Variable cursora,cursorb
    //SetActiveSubWindow NR#RQPlotInPanel
    cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
    cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
//    Cursor /S=1 /W=NR#RQPlotInPanel A $RQ4data cursora
//    Cursor /S=1 /W=NR#RQPlotInPanel B $RQ4data cursorb
   endif
   
 CheckDisplayed /W= $ExptTitle#RQplotInPanel RQ4_Cal
 Variable a= V_flag
 CheckDisplayed /W= $ExptTitle#RQplotInPanel R_Cal
  a= a+V_flag
  CheckDisplayed /W= $ExptTitle#RQplotInPanel Selectdata
   a= a+V_flag
   if (a>1)
   if(rswitch>0&&(stringmatch(RQ4data,"R_Cal")==1||stringmatch(RQ4data,"RQ4_Cal")==1))
   RemoveFromGraph /W=$ExptTitle#RQplotInPanel  RQ4_Cal
   else
   RemoveFromGraph /W=$ExptTitle#RQplotInPanel  R_Cal
   endif
   endif
   
   CheckDisplayed /W= $ExptTitle#RQplotInPanel $RQ4data

 if (stringmatch(RQ4data,RQ4data1old)==1 && V_flag==1 )

 RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit
  
 endif
//if (rswitchpre>0)
//Wave Rq_Fit, qz=$Qzdata
//Rq_Fit=Rq_Fit/(qz)^4
//endif
AppendToGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit vs $Qzdata
//endif
         ModifyGraph  /W=$ExptTitle#RQplotInPanel   framestyle=5,log(left)=1, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars  /W=$ExptTitle#RQplotInPanel $RQ4data XY,wave=($dqdata,$dqdata),wave=($dRQ4data,$dRQ4data)
           Label  /W=$ExptTitle#RQplotInPanel bottom "\\f01Q\\Bz\\M  (Å\\S-1\\M)"
 CheckDisplayed /W= $ExptTitle#RQplotInPanel $RQ4data1old
//  Variable bb=V_flag
//print  RQ4data1old, V_flag, RQ4data
 if (stringmatch(RQ4data,RQ4data1old)==0  &&V_flag==1)

RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data1old Rq_Fit#1 //vs $Qzdata1old
 if (globrswitch==1)
 RemoveFromGraph /Z /W=$ExptTitle#RQplotInPanel $RQ4data
 endif
//elseif ( V_flag==1)
//RemoveFromGraph /W=NR#RQplotInPanel $RQ4data1old

endif
ReorderTraces  /W=$ExptTitle#RQplotInPanel Rq_Fit, {$RQ4data}
  if (pfyn==1)
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $RQ4data cursora
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $RQ4data cursorb
  endif
   CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")//vs $Qzdata1old
endif
//   CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
// if ( V_flag==1)
// RemoveFromGraph /W=$ExptTitle#RQplotInPanel Rq_Fit
// KillWaves Rq_Fit
//endif

//print rswitchpre//RQ4data1old,RQ4data,V_flag,(RQ4data1old+"_Pre_Cal")
// CheckDisplayed /W= NR#RQplotInPanel $RQ4data#1
RQ4data1old=RQ4data
dRQ4data1old=dRQ4data
Qzdata1old=Qzdata
dqdata1old=dqdata
FitRgeneral3( )
End

Function datadRInput(ctrlName,popNum,popStr)
String ctrlName
Variable popNum
String popStr
String/G globdrq4data=popStr
String/G globdrqdata=popStr
Variable/G globmodedrq=popNum
//String/G globrqdata=popStr
Variable/G globrswitch
Variable rswitch=globrswitch
SVAR RQ4data=globRQ4data,Qzdata=globQzdata,dRQ4data=globdRQ4data,dqdata=globdqdata
SVAR RQ4data1old1=globRQ4dataold,Qzdata1old=globQzdataold,dRQ4data1old=globdRQ4dataold,dqdata1old=globdqdataold
SVAR ExptTitle=globExptTitle
Variable /G globpfyn
Variable pfyn=globpfyn
Variable /G globautoR=0
Variable rswitchpre=rswitch
Variable/G globgraphhold
Variable graphhold=globgraphhold
String RQ4data1old=RQ4data1old1
//globrswitch=0
 if (rswitch>0)
 
 SliderobjectR(" ",0,5)
 SliderobjectR(" ",1,5)
 endif

    if (graphhold>0)
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
   if (pfyn==1)
   Variable cursora,cursorb
    //SetActiveSubWindow NR#RQPlotInPanel
    cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
    cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")

   endif
 if (stringmatch(RQ4data,RQ4data1old)==1  )
 RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit
 endif
AppendToGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit vs $Qzdata
//endif
         ModifyGraph  /W=$ExptTitle#RQplotInPanel   framestyle=5,log(left)=1,lblRot(left)=-90, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars  /W=$ExptTitle#RQplotInPanel $RQ4data XY,wave=($dqdata,$dqdata),wave=($dRQ4data,$dRQ4data)
    //           	    Label left "\\f01"+RRQ4nPlot
           Label  /W=$ExptTitle#RQplotInPanel bottom "\\f01Q\\Bz\\M  (Å\\S-1\\M)"
 CheckDisplayed /W= $ExptTitle#RQplotInPanel $RQ4data1old
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data1old Rq_Fit//#0 //vs $Qzdata1old
  if (globrswitch==1)
  RemoveFromGraph /Z /W=$ExptTitle#RQplotInPanel $RQ4data
  endif

endif
//if (rswitchpre>0)
//Wave Rq_Fit, qz=$Qzdata
//Rq_Fit=Rq_Fit/(qz)^4
//endif
ReorderTraces  /W=$ExptTitle#RQplotInPanel Rq_Fit, {$RQ4data}
  if (pfyn==1)
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $RQ4data cursora
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $RQ4data cursorb
  endif
     CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")//vs $Qzdata1old
endif
//   CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
// if ( V_flag==1)
// RemoveFromGraph /W=$ExptTitle#RQplotInPanel Rq_Fit
// KillWaves Rq_Fit
//endif

RQ4data1old=RQ4data
dRQ4data1old=dRQ4data
Qzdata1old=Qzdata
dqdata1old=dqdata
FitRgeneral3( )
End

Function dataQInput(ctrlName,popNum,popStr)
String ctrlName
Variable popNum
String popStr
String/G globqzdata=popStr
Variable/G globmodeqz=popNum
NVAR rswitch=globrswitch
SVAR RQ4data=globRQ4data,Qzdata=globQzdata,dRQ4data=globdRQ4data,dqdata=globdqdata
SVAR RQ4data1old1=globRQ4dataold,Qzdata1old=globQzdataold,dRQ4data1old=globdRQ4dataold,dqdata1old=globdqdataold
SVAR ExptTitle=globExptTitle
Variable /G globpfyn
Variable pfyn=globpfyn
Variable /G globautoR=0
Variable/G globgraphhold
Variable graphhold=globgraphhold
String RQ4data1old=RQ4data1old1
 if (rswitch>0)
 
 SliderobjectR(" ",0,5)
 SliderobjectR(" ",1,5)
 endif

 SliderobjectR(" ",1,1)
    if (graphhold>0)
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
   if (pfyn==1)
   Variable cursora,cursorb
    //SetActiveSubWindow NR#RQPlotInPanel
    cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
    cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
//    Cursor /S=1 /W=NR#RQPlotInPanel A $RQ4data cursora
//    Cursor /S=1 /W=NR#RQPlotInPanel B $RQ4data cursorb
   endif
 if (stringmatch(RQ4data,RQ4data1old)==1)// || stringmatch(RQ4data,RQ4data1old)==1)
 RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit
 endif
AppendToGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit vs $Qzdata
//endif
         ModifyGraph  /W=$ExptTitle#RQplotInPanel   framestyle=5,log(left)=1,lblRot(left)=-90, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars  /W=$ExptTitle#RQplotInPanel $RQ4data XY,wave=($dqdata,$dqdata),wave=($dRQ4data,$dRQ4data)
           Label  /W=$ExptTitle#RQplotInPanel bottom "\\f01Q\\Bz\\M  (Å\\S-1\\M)"
 CheckDisplayed /W= $ExptTitle#RQplotInPanel $RQ4data1old
if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data1old Rq_Fit//#0 //vs $Qzdata1old
 if (rswitch==1)
 RemoveFromGraph /Z /W=$ExptTitle#RQplotInPanel $RQ4data
 endif

endif
ReorderTraces  /W=$ExptTitle#RQplotInPanel Rq_Fit, {$RQ4data}
  if (pfyn==1)
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $RQ4data cursora
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $RQ4data cursorb
  endif
     CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")//vs $Qzdata1old
endif
//   CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
// if ( V_flag==1)
// RemoveFromGraph /W=$ExptTitle#RQplotInPanel Rq_Fit
// KillWaves Rq_Fit
//endif

RQ4data1old=RQ4data
dRQ4data1old=dRQ4data
Qzdata1old=Qzdata
dqdata1old=dqdata

FitRgeneral3( )
End

Function datadQInput(ctrlName,popNum,popStr)
String ctrlName
Variable popNum
String popStr
String/G globdqdata=popStr
Variable/G globmodedqz=popNum
NVAR rswitch=globrswitch
SVAR RQ4data=globRQ4data,Qzdata=globQzdata,dRQ4data=globdRQ4data,dqdata=globdqdata
SVAR RQ4data1old1=globRQ4dataold,Qzdata1old=globQzdataold,dRQ4data1old=globdRQ4dataold,dqdata1old=globdqdataold, ExptTitle=globExptTitle
Variable /G globpfyn
Variable pfyn=globpfyn
Variable /G globautoR=0
Variable/G globgraphhold
Variable graphhold=globgraphhold
String  RQ4data1old= RQ4data1old1
  if (rswitch>0)
 
 SliderobjectR(" ",0,5)
 SliderobjectR(" ",1,5)
 endif

    if (graphhold>0)
    GraphNormal /W=$ExptTitle#SLDplotinPanel
    globgraphhold=0
    endif
   if (pfyn==1)
   Variable cursora,cursorb
    //SetActiveSubWindow NR#RQPlotInPanel
    cursora=pcsr(A, ExptTitle+"#RQPlotInPanel")
    cursorb=pcsr(B, ExptTitle+"#RQPlotInPanel")
   endif
 if (stringmatch(RQ4data,RQ4data1old)==1  )
 RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit
 endif
AppendToGraph /W=$ExptTitle#RQplotInPanel $RQ4data Rq_Fit vs $Qzdata
//endif
         ModifyGraph  /W=$ExptTitle#RQplotInPanel   framestyle=5,log(left)=1,lblRot(left)=-90, mirror=1,minor=0,standoff=1,tick=2, mode($RQ4data)=3, marker($RQ4data)=19,opaque($RQ4data)=1, rgb($RQ4data)=(65280,21760,0),useMrkStrokeRGB($RQ4data)=1, rgb(Rq_Fit)=(0,0,65280),lsize(Rq_Fit)=2//,grid=1,gridRGB=(65280,54528,32768)
          ErrorBars  /W=$ExptTitle#RQplotInPanel $RQ4data XY,wave=($dqdata,$dqdata),wave=($dRQ4data,$dRQ4data)
           Label  /W=$ExptTitle#RQplotInPanel bottom "\\f01Q  (Å\\S-1\\M)"
 CheckDisplayed /W= $ExptTitle#RQplotInPanel $RQ4data1old
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $RQ4data1old Rq_Fit//#0 //vs $Qzdata1old
endif
ReorderTraces  /W=$ExptTitle#RQplotInPanel Rq_Fit, {$RQ4data}
  if (pfyn==1)
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel A $RQ4data cursora
   Cursor /S=1 /W=$ExptTitle#RQPlotInPanel B $RQ4data cursorb
  endif
     CheckDisplayed /W= $ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")
 if (stringmatch(RQ4data,RQ4data1old)==0 && V_flag==1)
RemoveFromGraph /W=$ExptTitle#RQplotInPanel $(RQ4data1old+"_Pre_Cal")//vs $Qzdata1old
 if (rswitch==1)
 RemoveFromGraph /Z /W=$ExptTitle#RQplotInPanel $RQ4data
 endif

endif
//   CheckDisplayed /W= $ExptTitle#RQplotInPanel Rq_Fit
// if ( V_flag==1)
// RemoveFromGraph /W=$ExptTitle#RQplotInPanel Rq_Fit
// KillWaves Rq_Fit
//endif

RQ4data1old=RQ4data
dRQ4data1old=dRQ4data
Qzdata1old=Qzdata
dqdata1old=dqdata
FitRgeneral3( )
End


Function CSplinefunc(zz,zzorg,roughthick)    //<<< Do not change.
Variable zz,zzorg,roughthick                 

Variable Fun_out

// example: sin
Fun_out=(sin(190*Pi/2*(zz-zzorg+2*roughthick)/(4*roughthick)))^2/(sin(1*Pi/2))^2   // <<<<<<<<<<< CHANGE THIS LINE ONLY.  You also can add variables.

//    Another example
//   Fun_out=((zz-zzorg)+2*roughthick)/(4*roughthick)   ///Linear function

return Fun_out
End


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End








///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////                               Write Your Own Function         here             //////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
/////////////////////////////////       Note: 1. Do NOT change the NAME of the function                                            ///////////////////////////////////////
/////////////////////////////////                2. Only ONE function is currently allowed                                               ///////////////////////////////////////
/////////////////////////////////                3. Rescale your function so that Fun_out=0 at zz=zzorg-2*roughthick       ///////////////////////////////////////
/////////////////////////////////                                                         and Fun_out=1 at zz=zzorg+2*roughthick.    ////////////////////////////////////////
/////////////////////////////////                4. This function enters as a volume fraction.                                           ////////////////////////////////////////
/////////////////////////////////                5. "zzorg" is the center of the interface.                                                 ////////////////////////////////////////
/////////////////////////////////                6. "roughthick" is sqrt(2) times of roughness.                                         ////////////////////////////////////////
/////////////////////////////////                7. Changes in the func are important (Not the values)                              ///////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

Function MyOwn(zz,zzorg,roughthick)    //<<< Do not change.
Variable zz,zzorg,roughthick                 

Variable Fun_out

// example: sin
Fun_out=(sin(190*Pi/2*(zz-zzorg+2*roughthick)/(4*roughthick)))^2/(sin(1*Pi/2))^2   // <<<<<<<<<<< CHANGE THIS LINE ONLY.  You also can add variables.

//    Another example
//   Fun_out=((zz-zzorg)+2*roughthick)/(4*roughthick)   ///Linear function

return Fun_out
End
///////// >>>>After done, click on "save precedure" in the file menu bar, then "compile" button below,  click on X mark on the upper-right corner, 
////////                                    and then "hide" button (NOT the "kill" button)                                                                                                ////
///////// >>>>If you did not change anything,  just click on X mark on the upper-right corner, and then "hide" button (NOT the "kill" button)        ////

/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////  Example of a function    ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//                      
//                    |                             *  *                                                                 |
//                    |                        *           *                                                             |
//                    |                   *  *                 *  *                                                     |
//               1  -|-               *                              *    *                                       1   -|-                                       * * * * * * *
//                    |            *                                                                                     |                              * * * * 
//                    |         *                                                                                        |                    * * * *
//               0  -|-      *                                                                                    0   -|-       * * * * *
//                    |___________________________________                                     |___________________________________  
//                            |                      |                       |                                                   |                      |                       |                          
//                zzorg-2*roughthick     zzorg           zzorg+2*roughthick                  zzorg-2*roughthick     zzorg           zzorg+2*roughthick
//
//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////













/////The following functions are for extracting volf distribution from the SLD profiles; the last one = the recent func for CC system
function solvolf20(btol,bps,bpvp)
  Variable btol,bps,bpvp
   SVAR yyy=globprosldz//,xxx
//   NVAR gNL=globNlay, gNp=globNpoint
 //String yyy=yyy1
 Wave yy=$yyy
// Wave xx=$xxx
Variable i
 //Duplicate /O yy polydensy
// Duplicate /O yy solvdensy
 Duplicate /O yy psvolf_a,pvpvolf_a,solv_volf_a,polyvolf_a
 Variable vpvpmax=1,alpha,gamm,alpra
   for (i=80;i>=40;i=i-1)
     psvolf_a[i]=1-(yy[i]-bps)/(btol-bps)
     solv_volf_a[i]=1- psvolf_a[i]
     pvpvolf_a[i]=0
   endfor
     alpha=(solv_volf_a[40]-(1-vpvpmax))/psvolf_a[40]
     gamm=(1-vpvpmax)
    for (i=39;i>=1;i=i-1)
     polyvolf_a[i]=((1+alpha)*(yy[i]-gamm*btol)-(1-gamm)*(bps+alpha*btol))/(bpvp*(1+alpha)-bps-alpha*btol) //<<==PVP volf  
   endfor
   for (i=39;i>=20;i=i-1)
     psvolf_a[i]= ((1-gamm)-polyvolf_a[i])/(1+alpha)
     solv_volf_a[i]= alpha*psvolf_a[i]+gamm
    pvpvolf_a[i]=polyvolf_a[i]//1-(psvolf_a[i]+ solv_volf_a[i])
   endfor
    alpra= solv_volf_a[20]/ pvpvolf_a[20]
   for (i=20;i>=0;i=i-1)
      psvolf_a[i]=0
      pvpvolf_a[i]=(1-(((1+alpra)*yy[i]-(bpvp+alpra*btol))/(4.22*(1+alpra)-bpvp-alpra*btol)))/(1+alpra)
      solv_volf_a[i]=alpra*pvpvolf_a[i]
   endfor
  End
  
  function CCvolf(bpvp,bps,btol)  //20 points
  Variable btol,bps,bpvp
   SVAR yyy=globprosldz,zzz=globproz//,xxx
   NVAR gNL1=globNlay, gNp1=globNpoint
   Variable gnl=gNL1, gnp=gNp1
 //String yyy=yyy1
 Wave yy=$yyy, zz=$zzz, w_fit
// Wave xx=$xxx
Variable i
 //Duplicate /O yy polydensy
 Duplicate /O zz zzvolf
 Duplicate /O yy psvolf_a,pvpvolf_a,solv_volf_a,polyvolf_a
 Variable vpvpmax=1,alpha,gamm,alpra, tail=1  //tail 1: for 5 layer CCell. tail 2: for 6 layer CCell.
 if (gnl>5)
   tail=2
 endif
   for (i=((gnl+1)*gnp);i>=((gnl+1)*gnp)/2-tail*gnp+1;i=i-1) //3rd interface ....assumed 5layer symetric geo.
      if (i<= ((gnl+1)*gnp)/2)
     psvolf_a[i]=1-(yy[i]-bps)/(btol-bps)
     solv_volf_a[i]=1- psvolf_a[i]
     else
          psvolf_a[i]=0
     solv_volf_a[i]=0
     endif
         pvpvolf_a[i]=0
   endfor
     alpha=(solv_volf_a[((gnl+1)*gnp)/2-tail*gnp+1]-(1-vpvpmax))/psvolf_a[((gnl+1)*gnp)/2-tail*gnp+1]
     gamm=(1-vpvpmax)
    for (i=((gnl+1)*gnp)/2-tail*gnp;i>=1;i=i-1) //1st and 2nd interface
     polyvolf_a[i]=((1+alpha)*(yy[i]-gamm*btol)-(1-gamm)*(bps+alpha*btol))/(bpvp*(1+alpha)-bps-alpha*btol) //<<==PVP volf  
   endfor
   for (i=((gnl+1)*gnp)/2-tail*gnp;i>=((gnl+1)*gnp)/2-(tail+1)*gnp;i=i-1) //2nd interface
     psvolf_a[i]= ((1-gamm)-polyvolf_a[i])/(1+alpha)
     solv_volf_a[i]= alpha*psvolf_a[i]+gamm
    pvpvolf_a[i]=polyvolf_a[i]//1-(psvolf_a[i]+ solv_volf_a[i])
   endfor
    alpra= solv_volf_a[gnp]/ pvpvolf_a[gnp]
   for (i=gnp;i>=0;i=i-1)  //1st interface
      psvolf_a[i]=0
      pvpvolf_a[i]=(1-(((1+alpra)*yy[i]-(bpvp+alpra*btol))/(w_fit[0]*(1+alpra)-bpvp-alpra*btol)))/(1+alpra)
      solv_volf_a[i]=alpra*pvpvolf_a[i]
   endfor
   for (i=0;i<((gnl+1)*gnp)/2;i=i+1)//Symetrize the other side of profile...
    psvolf_a[(gnl+1)*gnp-i]=psvolf_a[i]
    pvpvolf_a[(gnl+1)*gnp-i]=pvpvolf_a[i]
    polyvolf_a[(gnl+1)*gnp-i]=polyvolf_a[i]
    solv_volf_a[(gnl+1)*gnp-i]=solv_volf_a[i]
    endfor
  End
  
  Function Airvolf()  //2-layer model
//  Variable bps,bpvp
   SVAR yyy=globprosldz//,xxx
   NVAR  npt1=globNpoint,npara1=globNpara,lay1=globNlay//, ssyn1=globssyn
   Variable npt=npt1,npara=npara1,lay=lay1
 //String yyy=yyy1
 Wave yy=$yyy, w_fit
// Wave xx=$xxx
Variable i,j
 //Duplicate /O yy polydensy
// Duplicate /O yy solvdensy
 Duplicate /O yy psvolf_b,pvpvolf_b//,solv_volf_a,polyvolf_a
for (j=0;j<=lay;j=j+1)
    for (i=j*npt+1;i<=(j+1)*npt;i=i+1)
      if (j<lay-1)
         if (j<1)
        psvolf_b[i]=yy[i]/w_fit[1]
         pvpvolf_b[i]=0
         else
         psvolf_b[i]=(yy[i]-w_fit[2])/(w_fit[1]-w_fit[2])
         pvpvolf_b[i]=1-psvolf_b[i]
         endif
       elseif(j<lay)
        pvpvolf_b[i]=(yy[i]-w_fit[3])/(w_fit[2]-w_fit[3])
        psvolf_b[i]=0
       else
          psvolf_b[i]=0
        pvpvolf_b[i]=0
 
        endif
     endfor

   endfor
   //     psvolf_b[npt*(lay)+1]=0
 //    pvpvolf_b[npt*(lay)+1]=0

   End




  Function proAirvolf(bps,bpvp) 
  Variable bps,bpvp
   SVAR yyy=globprosldz//,xxx
   NVAR  npt1=globNpoint,npara1=globNpara,lay1=globNlay//, ssyn1=globssyn
   Variable npt=npt1,npara=npara1,lay=lay1
 //String yyy=yyy1
 Wave yy=$yyy, w_fit
// Wave xx=$xxx
Variable i,j
 //Duplicate /O yy polydensy
// Duplicate /O yy solvdensy
 Duplicate /O yy psvolf_b,pvpvolf_b//,solv_volf_a,polyvolf_a
for (j=0;j<=lay;j=j+1)
    for (i=j*npt+1;i<=(j+1)*npt;i=i+1)
      if (j<lay-1)
         if (j<1)
        psvolf_b[i]=yy[i]/w_fit[1]*(bpvp-w_fit[1])/(bpvp-bps)
         pvpvolf_b[i]=1-psvolf_b[i]
         else
         psvolf_b[i]=(yy[i]-w_fit[2])/(w_fit[1]-w_fit[2])*(bpvp-w_fit[1])/(bpvp-bps)
         pvpvolf_b[i]=1-psvolf_b[i]
         endif
       elseif(j<lay)
        pvpvolf_b[i]=(yy[i]-w_fit[3])/(w_fit[2]-w_fit[3])*(bpvp-w_fit[1])/(bpvp-bps)
        psvolf_b[i]=0
       else
          psvolf_b[i]=0
        pvpvolf_b[i]=0
 
        endif
     endfor

   endfor
        psvolf_b[npt*(lay)+1]=0
     pvpvolf_b[npt*(lay)+1]=0

   End