source: sans/Dev/trunk/NCNR_User_Procedures/Analysis/Alpha/Auto_Fit.ipf @ 902

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


// This was originally written 2001-2003 ish. This works very differently than SANSview, and I havne't
// mentioned that this exists, so that their ideas will be new. Still, some of this may be 
// serviceable for use within the Igor package, with some cleanup of the interface and functionality.
//
//
//
// to do - July 2010
//
// X- smeared models don't work at all (now they work)
// -- the report is good, but the parsing is not great - the format
//      could be more convenient to read back in to a table (text col, num cols (matrix that can be plotted?)
//      -- Maybe the report could be compiled as waves. Then they would be numeric. Nothing to plot them against
//                      other than file names, but with a table of values and names, one could manually enter a meaningful
//                      column of values to plot against.
// -- Make_HoldConstraintEps_Waves() is  currently disabled, both on the macros menu and the checkbox on the panel
//                      Constraints and holds are part of the matrix already, soo this would only be for epsilon
// -- Many of the items on the Macros menu are just junk.
//
// -- Comprehensive instructions (after features are finalized)
//
// -- savePath seems to be obsolete. Report saving is sent to the procedure defined in Wrapper.ipf, and uses the home path
//


Menu "Macros"
        SubMenu "Auto-Fit"
                "InitializeAutoFitPanel"
                "-"
                "Generate_Data_Checklist"
//              "Make_HoldConstraintEps_Waves"          //this is currently disabled
                "-"
                "CompileAndLoadReports"
                "LoadCompiledReports"
                "Compile_GlobalFit_Reports"
                "-"
                "PrintOpenNotebooks"
                "Close Open Notebooks"
                "-"
                "Generate_PICTS_list"
                "Layout_PICTS"
                
        End
End


//***********
//Automatic fitting routines for SANS or NSE data
//requires model functions and their associated files
//
//**************



//path to the data
// ? have this automatically do the listing?
Function PDPButton(ctrlName) : ButtonControl
        String ctrlName
        
        //set the global string to the selected pathname
        NewPath/O/M="pick the data folder" dataPath
        PathInfo/S dataPath
        Return(0)
End

Function SavePathButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //set the global string to the selected pathname
        NewPath/O/M="pick the save folder" savePath
        PathInfo/S savePath
        Return(0)
End

// 
// this re-sizes AND re-initializes the guessMatrix
// and is only done when the files are re-listed, using the list button - since the 
// new list will screw up the correspondence with the guess matrix
//
Function FileListButtonProc(ctrlName) : ButtonControl
        String ctrlName

        DoAlert 1,"This will re-initialize the file list and ALL of the entries in the guess matrix. Do you want to proceed?"
        if(V_flag!=1)           //if the answer is not yes, get out
                return(0)
        endif
        
        String fileList=""
        fileList = IndexedFile(dataPath,-1,"????")
        fileList = RemoveFromList(".DS_Store", fileList, ";",0)
        List2TextWave(Filelist,";","root:AutoFit:fileListWave")
        Wave/T lw = $"root:AutoFit:fileListWave"
        Redimension/N=(-1,2) lw
        lw[][1] = ""
        Variable num = DimSize(lw,0)
        
        Wave sw = $"root:AutoFit:fileSelWave"
        Redimension/B/N=(num,2) sw
        sw[][1] = (sw[p][1] == 0) ? 2^5 : sw[p][1]              //if the element is zero, make it 32, otherwise leave it alone
        
        // force a re-size (and re-initialization) of the guess-hold-constr-range matrices
        ToMatrixButtonProc("")
        
        return(0)
End

// 
// this re-sizes AND re-initializes the guessMatrix
// and is only done when the files are re-listed, using the list button - since the 
// new list will screw up the correspondence with the guess matrix
//
Function ToMatrixButtonProc(ctrlName) : ButtonControl
        String ctrlName
        
        SetDataFolder root:AutoFit
        WAVE sel = fileSelWave
        NVAR numPar=numPar
        Variable jj,numSelFiles=0
        
        //update the number of steps for the progress bar
        // commented out - SRK - 28MAR05
//      NVAR cur=curProgress
//      NVAR totSteps=endProgress
//      cur=0
//      totSteps=numSelFiles*3          //3 fits per file
//      ValDisplay progressValdisp,limits={0,totSteps,0}
//      ControlUpdate/W=AutoFitPanel progressValdisp
        
        //redimension the matrices and lists
        Redimension/N=(numPar,DimSize(sel,0)) guessMatrix,HoldMatrix,constrMatrix,rangeMatrix
        Redimension/N=(numPar) guessList,holdList,constrList,rangeList,guessSel,holdSel,constrSel,rangeSel
        
        //Set the matrices to zero
        WAVE/T aa = guessMatrix
        WAVE/T bb = holdMatrix
        WAVE/T cc = constrMatrix
        WAVE/T rr = rangeMatrix
        aa="1"
        bb="0"
        cc=""           //set to no constraints
        rr="0"          // zero in points 0 and 1 force a fit of all of the data (default)
        //set the Lists to "0"
        WAVE/T dd=guessList
        WAVE/T ee=holdList
        WAVE/T ff=constrList
        WAVE/T rrl=rangeList
        dd="0"
        ee="0"
        ff="0"
        rrl="0"
        //Set the sel waves to 2 (editable)
        WAVE gg=guessSel
        WAVE hh=holdSel
        WAVE ii=constrSel
        WAVE rrs=rangeSel
        gg=2
        hh=2
        ii=2
        rrs=2
        
        SetDataFolder root:
        
        DisplayGuess()
        tabProc("",0)           //force the Guess tab to top
        TabControl tabC,value=0
        
        return(0)
End


//updates the lists (text waves) to display, depending on the current highlighted file
Function DisplayGuess()
        
        //find the selected data file -[][0] is the file, not the checkbox
        Variable row
        row = FindSelectedRowInLB(0)    // send 0 to look at the column with filenames

        //update the text waves based on the values in the matrix
        WAVE/T gm = root:AutoFit:guessMatrix
        WAVE/T gl = root:AutoFit:guessList
        
        // the hold matrix
        WAVE/T hm=root:AutoFit:holdMatrix
        WAVE/T hl=root:AutoFit:holdList
        
        // the constraint matrix 
        WAVE/T cm=root:AutoFit:constrMatrix
        WAVE/T cl=root:AutoFit:constrList
        
        // the range matrix 
        WAVE/T rm=root:AutoFit:rangeMatrix
        WAVE/T rl=root:AutoFit:rangeList
        
        WAVE sel = root:AutoFit:fileSelWave
        if( (sel[row][1] & 0x10) == 16 ) //box is checked
                
                gl = gm[p][row]
                hl = hm[p][row]
                cl = cm[p][row]
                rl = rm[p][row]
        else
                //file is not checked, don't display guess
                gl = "Not checked"
                hl = "Not checked"
                cl = "Not checked"
                rl = "Not checked"
        endif
        
        return(0)
End


//column 0 is the filenames, 1 is the checkboxes
//returns the row that is selected, -1 if not found
Function  FindSelectedRowInLB(col)
        Variable col
        
        WAVE sel = root:AutoFit:fileSelWave
        Variable jj=0,row=-1
        if(col==0)
                do
                        if( (sel[jj][0] & 0x01) == 1 )                  //returns 1 (bit 0) if selected, 0 otherwise    
                                row=jj
                                //print "Row = ",jj
                                break
                        endif
                        jj+=1
                while(jj<DimSize(sel,0))
        else
                do
                        if( (sel[jj][1] & 0x01) == 1 )                  //the checkbox is selected, but not necessarily checked!
                                row=jj
                                //print "Row = ",jj
                                break
                        endif
                        jj+=1
                while(jj<DimSize(sel,0))
        endif
        
        return(row)
end


Proc InitializeAutoFitPanel()
        if (wintype("AutoFitPanel") == 0)
                InitializeAutoFit()
                AutoFitPanel()
                tabProc("",0)           //force the tab control to display correctly
        else
                DoWindow/F AutoFitPanel
        endif
//      RangeCheckProc("",1)            //check the box to use all of the data
End

Function InitializeAutoFit()
        //set up all of the globals for the lists, globals, etc...
        NewDataFolder/O/S root:AutoFit
        Make/O/T/N=(1,2) fileListWave           //list boxes need text waves
        Make/O/B/N=(1,2) fileSelWave            //for the checkboxes
        Make/O/T/N=1 guessList,holdList,ConstrList,rangeList            //list boxes need text waves
        Make/O/T/N=(1,1) guessMatrix,holdMatrix,rangeMatrix                     //guesses, etc... need real values (later)
        Make/O/T/N=(1,1) constrMatrix                                   //constraint matrix is text
        Make/O/B/N=1 guessSel,holdSel,ConstrSel,rangeSel                                                //SelWave is byte data
        Variable/G numPar=5,ptLow=0,ptHigh=0,fitTol=1e-3,curProgress=0,endProgress=10
        Variable/G startTicks=0
        
        String/G gStatFormat="\K(65535,0,0)\f01"
        String/G gStatus=gStatFormat+"the fit engine is currently idle"
        string/g gExt="ABC"
        
        fileListWave = ""
        
        //make the second column of the file sel wave a checkbox (set bit 5)
        fileSelWave[][1] = 2^5
        
        SetDataFolder root:
End

Window AutoFitPanel()
        PauseUpdate; Silent 1           // building window...
        NewPanel /W=(685,44,1001,740) /K=1
        DoWindow/C AutoFitPanel
        SetDrawLayer UserBack
//      DrawText 11,418,"Point Range"
//      DrawText 5,167,"Suffix"
        DrawLine 8,362,287,362
        PopupMenu popup0,pos={2,2},size={175,20},title="pick a function"
        PopupMenu popup0,mode=1,value= #"User_FunctionPopupList()",proc=AF_FuncPopupProc
                
        ListBox lb pos={11,90},size={280,230},proc=FileListboxProc
        ListBox lb listWave=root:AutoFit:fileListWave,selWave=root:AutoFit:fileSelWave
        ListBox lb editStyle=1,mode=5
        ListBox lb userColumnResize=1,widths={200,80}
        
//      Button DelButton,pos={245,61},size={40,20},proc=DelButtonProc,title="Del",disable=2
        Button PathButton,pos={6,61},size={50,20},proc=PDPButton,title="Path..."
        Button FileListButton,pos={182,61},size={50,20},proc=FileListButtonProc,title="List"
        ListBox guessBox,pos={24,398},size={139,208},disable=1,proc=UpdateGuessMatrixProc
        ListBox guessBox,frame=2,listWave=root:AutoFit:guessList
        ListBox guessBox,selWave=root:AutoFit:guessSel,mode= 2,selRow= 0
        Button FillAllGuessButton,pos={196,406},size={50,20},disable=1,proc=FillAllGuessButtonProc,title="Fill All"
        Button FillAllHoldButton,pos={196,406},size={50,20},disable=1,proc=FillAllHoldButtonProc,title="Fill All"
        Button FillAllConstrButton,pos={196,406},size={50,20},proc=FillAllConstrButtonProc,title="Fill All"
        Button FillAllRangeB,pos={196,406},size={50,20},disable=1,proc=FillAllRangeButtonProc,title="Fill All"
        SetVariable NumParams,pos={7,31},size={161,15},proc=SetNumParamProc,title="Number of Parameters"
        SetVariable NumParams,limits={2,Inf,0},value= root:AutoFit:numPar
//      CheckBox typeCheck,pos={207,31},size={32,14},title="NSE Data?",value=0
//      SetVariable fitTol,pos={80,208},size={80,15},title="Fit Tol"
//      SetVariable fitTol,limits={0.0001,0.1,0},value= root:AutoFit:fitTol
        CheckBox epsilonCheck,pos={156,335},size={32,14},value=0,title="Use Epsilon Wave?"

        TabControl tabC,pos={13,371},size={273,244},proc=tabProc,tabLabel(0)="Guess"
        TabControl tabC,tabLabel(1)="Hold",tabLabel(2)="Constraint",tabLabel(3)="Range",value= 0
//      CheckBox rangeCheck,pos={92,404},size={32,14},proc=RangeCheckProc,title="All"
//      CheckBox rangeCheck,value= 1,disable=2
        SetVariable lowPt,pos={136,404},size={60,15},title="low"
        SetVariable lowPt,limits={0,Inf,0},value= root:AutoFit:ptLow,noedit=1,disable=1
        SetVariable highPt,pos={201,404},size={60,15},title=" to "
        SetVariable highPt,limits={0,Inf,0},value= root:AutoFit:ptHigh,noedit=1,disable=1
        ListBox holdBox,pos={24,398},size={139,208},disable=1,proc=UpdateHoldMatrixProc
        ListBox holdBox,frame=2,listWave=root:AutoFit:holdList
        ListBox holdBox,selWave=root:AutoFit:holdSel,mode= 2,selRow= 2
        ListBox ConstrBox,pos={24,398},size={170,208},proc=UpdateConstrMatrixProc
        ListBox ConstrBox,frame=2,listWave=root:AutoFit:ConstrList
        ListBox ConstrBox,selWave=root:AutoFit:ConstrSel,mode= 2,selRow= 2
        ListBox RangeBox,pos={24,398},size={139,208},proc=UpdateRangeMatrixProc
        ListBox RangeBox,frame=2,listWave=root:AutoFit:rangeList
        ListBox RangeBox,selWave=root:AutoFit:RangeSel,mode= 2,selRow= 2
//      Button MatrixButton,pos={12,205},size={60,20},proc=ToMatrixButtonProc,title="Matrix",disable=2
        Button DoItButton,pos={21,632},size={80,20},proc=DoTheFitsButtonProc,title="Do the fits"
        Button savePathButton,pos={82,61},size={80,20},proc=SavePathButtonProc,title="Save Path..."
        TitleBox tb1,pos={139,634},size={128,12},anchor=MC,variable=root:AutoFit:gStatus,frame=0
        Button button0,pos={14,331},size={40,20},title="Plot",proc=LoadForGuessProc
//      SetVariable extStr,pos={4,170},size={40,15},title=" ",value= root:AutoFit:gExt
        
        Button GuessCoefB,pos={198,440},size={50,20},title="Guess",proc=UseCoefAsGuess
        Button GuessHoldB,pos={198,440},size={50,20},title="Guess",disable=1,proc=UseHoldAsGuess
        Button GuessConstrB,pos={198,440},size={50,20},title="Guess",disable=1,proc=UseConstraintsAsGuess
        
        ValDisplay progressValdisp,pos={113,663},size={161,7},title="00:00"
        ValDisplay progressValdisp,limits={0,root:AutoFit:endProgress,0},barmisc={0,0},value= root:AutoFit:curProgress
EndMacro


Function AF_FuncPopupProc(pa) : PopupMenuControl
        STRUCT WMPopupAction &pa

        switch( pa.eventCode )
                case 2: // mouse up
                        Variable popNum = pa.popNum
                        String popStr = pa.popStr
                        String name=pa.ctrlName
                        Variable num=0,nc
                        
                        String coefStr = getFunctionCoef(popStr)
                        String str
                        
                        NVAR pts1 = root:AutoFit:numPar
                        SVAR suff = root:AutoFit:gExt
                        
                        Wave/Z coef=$("root:"+coefStr)
                        if(WaveExists(coef))
                                num=numpnts(coef)
                                suff = getModelSuffix(popStr)           //get the suffix from the unsmeared model function
                        else
                                //try getting rid of "Smeared" from the beginning of the function string
                                nc = strlen(popStr)
                                str = getFunctionCoef(popStr[7,nc-1])
                                Wave/Z cw = $("root:"+str)
                                if(WaveExists(cw))
                                        num=numpnts(cw)
                                endif
                                suff = getModelSuffix(popStr[7,nc-1])           //get the suffix from the unsmeared model function
                        endif
                        
                        // set the globals
                        pts1 = num
                        
                        
                        
                        // set the size of the matrix of initial guesses
                        SetNumParamProc("",num,"","")
                        
                        break
        endswitch

        return 0
End


Function tabProc(name,tab)
        String name
        Variable tab
        
        Button FillAllGuessButton disable= (tab!=0)
        Button GuessCoefB disable=(tab!=0)
        ListBox guessBox disable= (tab!=0)
        
        Button FillAllHoldButton disable= (tab!=1)
        Button GuessHoldB disable=(tab!=1)
        ListBox holdBox disable=(tab!=1)
        
        Button FillAllConstrButton disable= (tab!=2)
        Button GuessConstrB disable=(tab!=2)
        ListBox ConstrBox disable=(tab!=2)
        
        //no buttons on the range tab
        ListBox RangeBox disable=(tab!=3)
        Button FillAllRangeB disable= (tab!=3)
        
        return(0)
End


Function FillAllGuessButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //fills all of the guesses with the "current" list of guesses
        WAVE/T gl=root:AutoFit:guessList
        WAVE/T gm=root:AutoFit:guessMatrix
        gm[][] = gl[p]
        return(0)
End

Function FillAllHoldButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //fills all of the guesses with the "current" list of guesses
        WAVE/T hl=root:AutoFit:holdList
        WAVE/T hm=root:AutoFit:holdMatrix
        hm[][] = hl[p]
        return(0)
End

Function FillAllConstrButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //fills all of the guesses with the "current" list of guesses
        WAVE/T cl=root:AutoFit:constrList
        WAVE/T cm=root:AutoFit:ConstrMatrix
        cm[][] = cl[p]
        return(0)
End

Function FillAllRangeButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //fills all of the range values with the top values
        WAVE/T rl=root:AutoFit:rangeList
        WAVE/T rm=root:AutoFit:rangeMatrix
        rm[][] = rl[p]
        return(0)
End

Function SetNumParamProc(ctrlName,varNum,varStr,varName) : SetVariableControl
        String ctrlName
        Variable varNum
        String varStr
        String varName

        //set the number of parameters for the function
        Variable/G numPar=varNum
        
        // adjust the number of parameters in the guesses
        SetMatrixRows(varNum)
        
        return(0)
End

//expand or collapse the matrices to the number of parameters
Function SetMatrixRows(newRows)
        Variable newRows
        
        SetDataFolder root:AutoFit
        
        WAVE/T aa = guessMatrix
        WAVE/T bb = holdMatrix
        WAVE/T cc = constrMatrix
        WAVE/T rr = rangeMatrix
        
        Redimension/N=(newRows,-1) aa,bb,cc,rr
        
        //redimension the lists too
        WAVE/T dd=guessList
        WAVE/T ee=holdList
        WAVE/T ff=constrList
        WAVE/T rrl=rangeList
        Redimension/N=(newRows) dd,ee,ff,rrl
        
        WAVE gg=guessSel
        WAVE hh=holdSel
        WAVE ii=constrSel
        WAVE rrs=rangeSel
        //set the selection wave for the individual lists to 2 == editable
        Redimension/N=(newRows) gg,hh,ii,rrs
        gg=2
        hh=2
        ii=2
        rrs=2
        
        SetDataFolder root:
        
        return 0
end


Function FileListboxProc(ctrlName,row,col,event)
        String ctrlName     // name of this control
        Variable row        // row if click in interior, -1 if click in title
        Variable col        // column number
        Variable event      // event code
        
        if(event==4 && col==0)          //selection of a file, not a checkbox
                //then update the listbox display of guesses for the new file
        //      Print "file selected"
                DisplayGuess()
        Endif
        
        return 0            // other return values reserved
End

Function UpdateGuessMatrixProc(ctrlName,row,col,event)
        String ctrlName     // name of this control
        Variable row        // row if click in interior, -1 if click in title
        Variable col        // column number
        Variable event      // event code
        
        if(event==7)            //finished edit of a cell, update the matrix of guesses
                //Print "updating"
                WAVE/T gl=root:AutoFit:guessList
                WAVE/T gm=root:AutoFit:guessMatrix
                //put new value in guessMatrix
                Variable datafile
                datafile = FindSelectedRowInLB(0)               //selected row in file list
                gm[row][datafile] = gl[row]
                //print "row= ",row
        Endif
        return 0            // other return values reserved
End

Function UpdateHoldMatrixProc(ctrlName,row,col,event)
        String ctrlName     // name of this control
        Variable row        // row if click in interior, -1 if click in title
        Variable col        // column number
        Variable event      // event code
        
        if(event==7)            //finished edit of a cell, update the matrix of guesses
                //Print "updating"      
                WAVE/T hl=root:AutoFit:holdList
                WAVE/T hm=root:AutoFit:holdMatrix
                // put new value in holdMatrix
                Variable datafile
                datafile = FindSelectedRowInLB(0)
                hm[row][datafile] = hl[row]
                //print "row= ",row
        Endif
        return 0            // other return values reserved
End

Function UpdateConstrMatrixProc(ctrlName,row,col,event)
        String ctrlName     // name of this control
        Variable row        // row if click in interior, -1 if click in title
        Variable col        // column number
        Variable event      // event code
        
        if(event==7)            //finished edit of a cell, update the matrix of guesses
                //Print "updating"
                WAVE/T cl=root:AutoFit:ConstrList
                WAVE/T cm=root:AutoFit:constrMatrix
                //put new value in constrMatrix
                Variable datafile
                datafile = FindSelectedRowInLB(0)
                cm[row][datafile] = cl[row]
                //print "row= ",row
        Endif
        return 0            // other return values reserved
End

Function UpdateRangeMatrixProc(ctrlName,row,col,event)
        String ctrlName     // name of this control
        Variable row        // row if click in interior, -1 if click in title
        Variable col        // column number
        Variable event      // event code
        
        if(event==7)            //finished edit of a cell, update the matrix of guesses
                //Print "updating"
                WAVE/T cl=root:AutoFit:RangeList
                WAVE/T cm=root:AutoFit:RangeMatrix
                //put new value in constrMatrix
                Variable datafile
                datafile = FindSelectedRowInLB(0)
                cm[row][datafile] = cl[row]
                //print "row= ",row
        Endif
        return 0            // other return values reserved
End

//returns the total number of files checked
Function numChecked()
        
        WAVE sel = root:AutoFit:fileSelWave
        
        Variable ii,num=0
        for(ii=0;ii<DimSize(sel,0);ii+=1)
                if( (sel[ii][1] & 0x10) == 16 ) 
                        num += 1
                endif
        endfor
        return num
        
End


//Function RangeCheckProc(ctrlName,checked) : CheckBoxControl
//      String ctrlName
//      Variable checked
//      
//      SetVariable lowPt disable=(checked)
//      SetVariable highPt disable=(checked)
//End

Function DoTheFitsButtonProc(ctrlName) : ButtonControl
        String ctrlName

        //read the values from the panel
        ControlInfo/W=AutoFitPanel popup0
        String funcStr=S_Value
        String fileName
        NVAR numPar=root:AutoFit:numPar
        NVAR startTicks=root:AutoFit:startTicks
        NVAR curProgress=root:AutoFit:curProgress
        NVAR endProgress=root:AutoFit:endProgress
        
        WAVE/T fileWave=root:AutoFit:fileListWave
        WAVE sel = root:AutoFit:fileSelWave
        
        WAVE/T guessMatrix=root:AutoFit:guessMatrix
        WAVE/T holdMatrix=root:AutoFit:holdMatrix
        WAVE/T constrMatrix=root:AutoFit:constrMatrix
        WAVE/T rangeMatrix=root:AutoFit:rangeMatrix
                
        Variable ii=0,numFiles=DimSize(fileWave,0),t1=ticks,t2,matrixindex,count=0
        //print numFiles
        //for the timer-progress bar - timer shows time, bar shows number of fits remaining
        curProgress = 0
        endProgress = 3*numChecked()                    //3 fits per file that is fit
        ValDisplay progressValdisp,limits={0,endProgress,0}
        ControlUpdate/W=AutoFitPanel progressValdisp
        
        //print "numChecked() = ",numChecked()
        startTicks=t1                   //starting now
        for(ii=0;ii<numFiles;ii+=1)             //loop over everything in the file list, dispatching only checked items
                if( (sel[ii][1] & 0x10) == 16 )         //the box is checked, then go fit it
                        fileName = fileWave[ii][0]
                        DoOneFit(funcStr,fileName,numPar,fileWave,ii,guessMatrix,holdMatrix,constrMatrix,rangeMatrix)
                        count+=1
                endif
        endfor
        UpdateStatusString("All files processed")
        t2=ticks
        t1=(t2-t1)/60
        Printf "All %d files processed in %g seconds =(%g minutes) =(%g hours)\r",count,t1,t1/60,t1/60/60
        return(0)
End


Function DoOneFit(funcStr,fileName,numPar,fileWave,ii,guessMatrix,holdMatrix,constrMatrix,rangeMatrix)
        String funcStr,fileName
        Variable numPar
        WAVE/T fileWave //length <= ii
        Variable ii             //index in the full list
        WAVE/T guessMatrix,holdMatrix,constrMatrix,rangeMatrix
        
        String list="",fullName="",dataname="",str=""
        //be sure all is clear (no data, window... etc)
        DoWindow/K AutoGraph                            //no error is reported
        DoWindow/K AutoGraph_NSE                                
        list=WaveList("*__*",";","")            //not case sensitive?
        DoKillList(list)                                                //get rid of all of the old data
        list=WaveList("wave*",";","")           //"wave(n)" can be generated if not all NSE times are collected
        DoKillList(list)
        
        //SANS or NSE data?
        ControlInfo/W=AutoFitPanel typeCheck
        Variable isNSE=v_value
        //load in the data
        PathInfo dataPath
        fullName = S_path
        //fullName += fileWave[ii]
        fullName += fileName
        if(isNSE)
                //load, don't plot
                str = "A_LoadNSEDataWithName(\""+fullName+"\",0)"
                Execute str
//              A_LoadNSEDataWithName(fullName,0)                               //load, don't plot
        else
                //load, default name, no plot, overwrite data if needed
                str = "A_LoadOneDDataToName(\""+fullName+"\",\"\",0,1)"
                Execute str
//              A_LoadOneDDataToName(fullName,"",0,1)           //load, default name, no plot, overwrite data if needed
        endif
        dataName=GetFileNameFromPathNoSemi(fullName)
        dataname=CleanupName(dataname,0)
        
        //graph it - creates window named "AutoGraph"
        if(isNSE)
                Execute "DoGraph_NSE(\""+dataname+"\")"
        else
                Execute "DoGraph(\""+dataname+"\")"
        endif
        
        //generate the needed strings to add to the execute stmt
        // rangeStr, guessStr,constrStr,holdStr
        // and waves - the coefficient wave and paramter wave
        Variable useRes,useEps,useCursors,useConstr
        Variable val,pt1,pt2
        useEps = 0
        useConstr = 0
        useCursors = 0
        useRes = 0
        
        String holdStr="",rangeStr="",cStr="",epsilonStr=""
        String DF="root:"+dataname+":"  

        
        Make/O/D/N=(numPar) myCoef              //always named "myCoef"
        Wave cw = root:myCoef

        //range string
        useCursors = ParseRangeString(ii,dataname,rangeMatrix,pt1,pt2)          //read range from the matrix, return values and set flag

        
        //params to hold
        holdStr = ParseHoldString(ii,numpar,holdMatrix)
        //initial guesses
        ParseGuessString(ii,numpar,guessMatrix,"myCoef")
        //constraints
        cStr = ParseConstraints(ii,numpar,constrMatrix,"myConstraints")
        WAVE/Z constr = $"myConstraints"
        if(strlen(cStr)!=0)
                useConstr = 1
        endif
        //epsilon wave
        epsilonStr = GetEpsilonWave()
        if(strlen(epsilonStr) > 0)
                Wave eps=$epsilonStr            //in the root folder
                useEps = 1
        endif
        
        //fit it
        //these two global variables must be created for IGOR to set them, so that
        //any errors in the fitting can be diagnosed
        Variable/G V_FitError=0                         //0=no err, 1=error,(2^1+2^0)=3=singular matrix
        Variable/G V_FitQuitReason=0            //0=ok,1=maxiter,2=user stop,3=no chisq decrease
        NVAR tol=root:AutoFit:fitTol
        Variable/G V_FitTol=tol         //default is 0.0001
        Variable/G V_fitOptions=4               //suppress the dialog during fitting (we're not waiting for OK, anyways)


        Wave yw = $(DF+dataName+"_i")
        Wave xw = $(DF+dataName+"_q")
        Wave sw = $(DF+dataName+"_s")
        
        if(stringmatch(funcStr, "Smear*"))              // if it's a smeared function, need a struct
                useRes=1
        endif
        
        Struct ResSmearAAOStruct fs
        WAVE/Z resW = $(DF+dataName+"_res")                     //these may not exist, if 3-column data is used 
        WAVE/Z fs.resW =  resW
        WAVE yw=$(DF+dataName+"_i")
        WAVE xw=$(DF+dataName+"_q")
        WAVE sw=$(DF+dataName+"_s")
        Wave fs.coefW = cw
        Wave fs.yW = yw
        Wave fs.xW = xw
        
        Duplicate/O yw $(DF+"FitYw")
        WAVE fitYw = $(DF+"FitYw")
        fitYw = NaN
        
        NVAR useGenCurveFit = root:Packages:NIST:gUseGenCurveFit
        ///// SEE FitWrapper() for more details.
        
        Variable nPass = 1
        
        do      // outer do is the loop over passes
        do      // this inner loop is abig switch to select the correct FutFunc to dispatch
                if(useGenCurveFit)
#if !(exists("GenCurveFit"))
                        // XOP not available
                        useGenCurveFit = 0
                        Abort "Genetic Optimiztion XOP not available. Reverting to normal optimization."        
#endif
                        //send everything to a function, to reduce the clutter
                        // useEps and useConstr are not needed
                        // pass the structure to get the current waves, including the trimmed USANS matrix
                        Variable chi,pt

                        chi = DoGenCurveFit(useRes,useCursors,sw,fitYw,fs,funcStr,ParseHoldString(ii,numpar,holdMatrix),val,lolim,hilim,pt1,pt2)
                        pt = val

                        break
                        
                endif
                
                
                if(useRes && useEps && useCursors && useConstr)         //do it all
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /E=eps /D=fitYw /C=constr /STRC=fs
                        break
                endif
                
                if(useRes && useEps && useCursors)              //no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /E=eps /D=fitYw /STRC=fs
                        break
                endif
                
                if(useRes && useEps && useConstr)               //no crsr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /E=eps /D=fitYw /C=constr /STRC=fs
                        break
                endif
                
                if(useRes && useCursors && useConstr)           //no eps
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /D=fitYw /C=constr /STRC=fs
                        break
                endif
                
                if(useRes && useCursors)                //no eps, no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /D=fitYw /STRC=fs
                        break
                endif
                
                if(useRes && useEps)            //no crsr, no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /E=eps /D=fitYw /STRC=fs
                        break
                endif
        
                if(useRes && useConstr)         //no crsr, no eps
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /D=fitYw /C=constr /STRC=fs
                        break
                endif
                
                if(useRes)              //just res
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /D=fitYw /STRC=fs
                        break
                endif
                
/////   same as above, but all without useRes (no /STRC flag)
                if(useEps && useCursors && useConstr)           //do it all
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /E=eps /D=fitYw /C=constr
                        break
                endif
                
                if(useEps && useCursors)                //no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /E=eps /D=fitYw
                        break
                endif
                
                if(useEps && useConstr)         //no crsr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /E=eps /D=fitYw /C=constr
                        break
                endif
                
                if(useCursors && useConstr)             //no eps
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /D=fitYw /C=constr
                        break
                endif
                
                if(useCursors)          //no eps, no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw[pt1,pt2] /X=xw /W=sw /I=1 /D=fitYw
                        break
                endif
                
                if(useEps)              //no crsr, no constr
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /E=eps /D=fitYw
                        break
                endif
        
                if(useConstr)           //no crsr, no eps
                        FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /D=fitYw /C=constr
                        break
                endif
                
                //just a plain vanilla fit
                FuncFit/H=ParseHoldString(ii,numpar,holdMatrix) /NTHR=0 $funcStr cw, yw /X=xw /W=sw /I=1 /D=fitYw
        
        while(0)                //always exit the inner do to select the FutFunc syntax. The break will exit this loop
        
                if(nPass == 1)
                        UpdateStatusString(dataname +" Fit #1")
                        Variable/G gChiSq1 = V_chisq
                endif
                
                if(nPass == 2)
                        UpdateStatusString(dataname +" Fit #2")
                        Variable/G gChiSq2 = V_chisq
                endif
                
                if(nPass == 3)
                        UpdateStatusString(dataname +" Fit #3")
                endif
                
                nPass += 1
        while(nPass < 4)

        // append the fit
        // need to manage duplicate copies
        // Don't plot the full curve if cursors were used (set fitYw to NaN on entry...)
        String traces=TraceNameList("", ";", 1 )                //"" as first parameter == look on the target graph
        if(strsearch(traces,"FitYw",0) == -1)
                if(useGenCurveFit && useCursors)
                        WAVE trimX = trimX
                        AppendtoGraph fitYw vs trimX
                else
                        AppendToGraph FitYw vs xw
                endif
        else
                RemoveFromGraph FitYw
                if(useGenCurveFit && useCursors)
                        WAVE trimX = trimX
                        AppendtoGraph fitYw vs trimX
                else
                        AppendToGraph FitYw vs xw
                endif
        endif
        ModifyGraph lsize(FitYw)=2,rgb(FitYw)=(52428,1,1)


        //do the report calling the function, not the proc
        String topGraph= WinName(0,1)   //this is the topmost graph
        SVAR suffix = root:AutoFit:gExt         //don't try to read as getModelSuffix(funcStr), since the smeared() may not be plotted
        String parStr=GetWavesDataFolder(cw,1)+ WaveList("*param*"+"_"+suffix, "", "TEXT:1," )          // this is *hopefully* one wave

        if(isNSE)
                GenerateReport_NSE(funcStr,dataname,"par","myCoef",1)
        else
                W_GenerateReport(funcStr,dataname,$parStr,$"myCoef",1,V_chisq,W_sigma,V_npnts,V_FitError,V_FitQuitReason,V_startRow,V_endRow,topGraph)

//              AutoFit_GenerateReport(funcStr,dataname,"par","myCoef",1)       
        endif
        
        return(0)
End

//// to be able to simply fill in the pt range of the yw[lo,hi]
//Function LowRange()
//      NVAR val = root:AutoFit:ptLow
//      return(val)
//End
//
//Function HighRange()
//      NVAR val = root:AutoFit:ptHigh
//      return(val)
//End

//updates the status string, forcing a redraw twice, to overcome what seems to be a bug in Igor4
//also updates the progress bar and the countdown
Function UpdateStatusString(newStr)
        String newStr
        
        SVAR gStatus=root:AutoFit:gStatus
        SVAR gStatFormat=root:AutoFit:gStatFormat
        gStatus=""
        ControlUpdate/W=AutoFitPanel tb1                //clears the line
        gStatus=gStatFormat+newStr
        ControlUpdate/W=AutoFitPanel tb1
        
        //update the progress bar and timer
        NVAR cur=root:AutoFit:curProgress
        NVAR endProgress=root:AutoFit:endProgress
        NVAR startTicks=root:AutoFit:startTicks
        cur+=1
        
//      Print "****"
//      Print "cur = ",cur
        
        Variable t2=ticks,projTot,projRemain
        String titleStr=""
        
        projTot = (t2-startTicks)/(cur-1)*endProgress
        projRemain = projTot - (t2-startTicks)
        projRemain /= 60.15             //to seconds
        DoWindow/F AutoFitPanel
        ValDisplay progressValdisp,title=Secs2time(projRemain,5)
        ControlUpdate/W=AutoFitPanel progressValdisp
        
//      Print "End Progress = ",endProgress
//      Print "ProjTot = ",projTot/60.15
//      Print "ProjRemain = ",projRemain
        
        return(0)
End

// returns a string with the name of the epsilon wave, or null if it doesn't exist
Function/S GetEpsilonWave()
        
        String retStr="",testStr
        SVAR extStr = root:AutoFit:gExt
        //do you want to use epsilon wave?
        ControlInfo/W=AutoFitPanel epsilonCheck
        if(V_Value == 0)                //not checked
                return(retStr)
        endif
        
        testStr = "Epsilon_"+extStr
        if(waveexists($testStr) != 0)
//              return(" /E="+testStr)
                return(testStr)
        endif
        return(retStr)
End

//returns the y data to fit - "_i" suffix, and range if selected
// enter the range as the first element[0] as low point, second element[1] as high point
// leave the other elements blank
//
// if either point value is not entered, the whole data set is used
//
// -- if both of the elements are between 0 and 1, assume they are q-values (check for fractional part)
// and find the appropriate points...
//
Function ParseRangeString(set,dataStr,rMat,lo,hi)
        Variable set
        String dataStr
        WAVE/T rMat
        Variable &lo,&hi
        
        Variable useCursors
                        
        lo = str2num(rMat[0][set])
        hi = str2num(rMat[1][set])
        
        if(lo == 0 && hi == 0)
                return(0)
        endif
        
        if(numtype(lo) != 0 || numtype(hi) != 0)                //not a normal number
                return(0)               //don't use cursor values, use all of the dataset
        endif
        
        
        if(lo>=hi) //error in specification, or all data desired (both zero or undefined)
                return(0)               //use all of the dataset
        endif
        
        
        if(trunc(lo) != lo || trunc(hi) != hi)          //values have fractional parts
                WAVE xW = $("root:"+dataStr+":"+dataStr + "_q")
                FindLevel/P/Q xW, lo
                lo = trunc(V_levelX)            //find the corresponding point values
                FindLevel/P/Q xW, hi
                hi = trunc(V_levelX)
        endif
        
        Variable/G root:AutoFit:ptLow = lo
        Variable/G root:AutoFit:ptHigh = hi

        return(1)
End

//returns the holdStr, i.e. "1010101"
Function/S ParseHoldString(set,npar,hMat)
        Variable set,npar
        WAVE/T hMat
        
        Variable ii
        String retStr=""
        
        for(ii=0;ii<npar;ii+=1)
                if(strlen(hMat[ii][set]) == 0)
                        retStr += "0"
                else
                        retStr += hMat[ii][set]
                endif
        endfor

//      Print retStr
        
        return(retStr)
End

//returns only error - wave must already exist
Function ParseGuessString(set,npar,gMat,outWStr)
        Variable set,npar
        WAVE/T gMat
        String outWStr
        
        Variable ii
        String retStr=outWStr
        
        WAVE outWave=$outWStr
        for(ii=0;ii<npar;ii+=1)
                outWave[ii] = str2num(gMat[ii][set])
        endfor
        return(0)
End

//the constraint wave is created here
Function/S ParseConstraints(set,npar,cMat,outWStr)
        Variable set,npar
        WAVE/T cMat
        String outWStr
        
        String retStr="",loStr="",hiStr=""
        Variable ii=0,jj=0      
        Make/O/T/N=0 $outWStr
        WAVE/T cw = $outWStr    
        //return "/C="+outWStr if parsed ok, or null if not

        String listStr=""
        for(ii=0;ii<npar;ii+=1)
                listStr=cMat[ii][set]
                loStr=StringFromList(0, listStr ,";")
                hiStr=StringFromList(1, listStr ,";")
                if(cmpstr(loStr,"")!=0) //something there...
                        InsertPoints jj,1,cw            //insert before element jj
                        cw[jj] = "K"+num2Str(ii)+">"+loStr
                        jj+=1
                endif
                if(cmpstr(hiStr,"")!=0) //something there...
                        InsertPoints jj,1,cw            //insert before element jj
                        cw[jj] = "K"+num2Str(ii)+"<"+hiStr
                        jj+=1
                endif
        endfor
        if(numpnts(cw) > 0 )
                retStr = "/C=" + outWStr
        Endif
//      print "strlen, conStr= ",strlen(retStr),retstr

        return(retStr)  //null string will be returned if no constraints
End


//*************************
Proc DoGraph(dataname)
        String dataname
        
        SetDataFolder $dataname

        PauseUpdate; Silent 1           // building window...
        Display /W=(5,42,301,313)/K=1 $(dataname+"_i") vs $(dataname+"_q")
        DoWindow/C AutoGraph
        ModifyGraph mode($(dataname+"_i"))=3
        ModifyGraph marker($(dataname+"_i"))=19
        ModifyGraph rgb($(dataname+"_i"))=(1,4,52428)
        ModifyGraph msize($(dataname+"_i"))=2
        ModifyGraph grid=1
        ModifyGraph log=1
        ModifyGraph tickUnit=1
        //
        ModifyGraph mirror=2
        //
        ErrorBars $(dataname+"_i") Y,wave=($(dataname+"_s"),$(dataname+"_s"))
//      Legend/A=LB
//      Legend/A=LB/X=0.00/Y=-32                //defaults to the top right
        Legend/A=MT/E           // /X=-16.16/Y=5.17/E
        
        SetDataFolder root:
        
EndMacro

Proc DoGraph_NSE(dataname)
        String dataname
        
        SetDataFolder $dataname

        PauseUpdate; Silent 1           // building window...
        Display /W=(5,42,301,313)/K=1 $(dataname+"_i") vs $(dataname+"_q")
        DoWindow/C AutoGraph_NSE
        ModifyGraph mode($(dataname+"_i"))=3
        ModifyGraph marker($(dataname+"_i"))=19
        ModifyGraph rgb($(dataname+"_i"))=(1,4,52428)
        ModifyGraph msize($(dataname+"_i"))=3
        ModifyGraph zColor($(dataname+"_i"))={$(dataname+"__Q"),$(dataname+"__Q")[0]*0.99,*,Rainbow}
        ModifyGraph grid=1
        ModifyGraph mirror=2
        ModifyGraph log(left)=1
        ErrorBars $(dataname+"_i") Y,wave=($(dataname+"_s"),$(dataname+"_s"))
        Legend/A=MB
        SetAxis/A/E=1 bottom
        ModifyGraph standoff=0
        SetAxis left 0.1,1
        //ModifyGraph tickUnit(left)=1
EndMacro

//*************************


//**************************
// Generate the report
//**************************

////must have AutoGraph as the name of the graph window (any size)
//// func is the name of the function (for print only)
////par and coef are the exact names of the waves
////yesSave==1 will save the file(name=func+time)
////
////
//// general report function from the wrapper is used instead
////    W_GenerateReport(funcStr,folderStr,$parStr,cw,yesSave,V_chisq,W_sigma,V_npnts,V_FitError,V_FitQuitReason,V_startRow,V_endRow,topGraph)
////
//Function AutoFit_GenerateReport(func,dataname,par,myCoef,yesSave)
//      String func,dataname,par,myCoef
//      Variable yesSave
//      
//      String str,pictStr="P_"
//      Wave sigWave=$"W_sigma"
//      Wave ans=$myCoef
////    Wave/T param=$par
//      SVAR ext=root:AutoFit:gExt
//      Wave/T param=$"parameters_"+ext
//      
//      NVAR V_chisq = V_chisq
//      NVAR V_npnts = V_npnts
//      NVAR V_FitError = V_FitError
//      NVAR V_FitQuitReason = V_FitQuitReason
//      NVAR chi1=gChiSq1
//      NVAR chi2=gChiSq2
//      NVAR V_startRow = V_startRow
//      NVAR V_endRow = V_endRow
//      
//      // bring report up
//      DoWindow/F Report
//      if (V_flag == 0)                // Report notebook doesn't exist ?
//              NewNotebook/W=(10,45,550,620)/F=1/N=Report as "Report"
//      endif
//      
//      // delete old stuff
//      Notebook Report selection={startOfFile, endOfFile}, text="\r", selection={startOfFile, startOfFile}
//      
//      // insert title
//      Notebook Report newRuler=Title, justification=1, rulerDefaults={"Times", 16, 1, (0, 0, 0)}
//      sprintf str, "Fit to %s, %s, %s\r\r", func,Secs2Date(datetime, 0), time()
//      Notebook Report ruler=Title, text=str
//      
//      // insert fit results
//      Variable num=numpnts(ans),ii=0
//      Notebook Report ruler=Normal; Notebook Report  margins={18,18,504}, tabs={63 + 3*8192}
//      str = "Data file: " + dataname + "\r\r"
//      Notebook Report text=str
//      do
//              sprintf str, "%s = %g±%g\r", param[ii],ans[ii],sigwave[ii]
//              Notebook Report text=str
//              ii+=1
//      while(ii<num)
//      
//      //
//      Wave dataXw = $(dataname+"_q")
//      Variable nData=numpnts(dataXw)
//      
//      //
//      sprintf str,"chisq = %g , %g , %g\r",chi1,chi2,V_chisq
//      Notebook Report textRGB=(65000,0,0),fstyle=1,text=str
//      sprintf str,"Npnts = %g, sqrt(X^2/N) = %g\r",V_npnts,sqrt(V_chisq/V_npnts)
//      Notebook Report textRGB=(0,0,0),fstyle=0, text=str
//      sprintf str "Fitted range = [%d,%d] = %g < Q < %g\r",V_startRow,V_endRow,dataXw(V_startRow),dataXw(V_endRow)
//      Notebook Report textRGB=(0,0,0),fstyle=0, text=str
//      sprintf str,"V_FitError = %g\t\tV_FitQuitReason = %g\r",V_FitError,V_FitQuitReason
//      Notebook Report textRGB=(65000,0,0),fstyle=1,text=str
//      Notebook Report ruler=Normal
//      
//      // insert graphs
//      Notebook Report picture={AutoGraph(0, 0, 400, 300), 0, 1}, text="\r"
//      
//
//      //Notebook Report picture={Table1, 0, 0}, text="\r"
//      
//      // show the top of the report
//      Notebook Report  selection= {startOfFile, startOfFile},  findText={"", 1}
//      
//      //save the notebook
//      if(yesSave)
//              String nameStr=CleanupName(func,0)
//              nameStr = nameStr[0,8]  //shorten the name
//              nameStr += "_"+dataname
//              //make sure the name is no more than 31 characters
//              namestr = namestr[0,30]         //if shorter than 31, this will NOT pad to 31 characters
//              Print "file saved as ",nameStr
//              SaveNotebook /O/P=savePath/S=2 Report as nameStr
//              //save the graph separately as a PICT file, 2x screen
//              pictStr += nameStr
//              pictStr = pictStr[0,28]         //need a shorter name - why?
//              DoWindow/F AutoGraph
//              // E=-5 is png @screen resolution
//              // E=2 is PICT @2x screen resolution
//              SavePICT /E=2/O/I/P=savePath /W=(0,0,3,3) as pictStr
//      Endif
//      
//      // ???maybe print the notebook too?
//End



//
//Proc DoGenerateReport(fname,dataname,param,coef,yesno)
//      String fname,dataname="",param,coef,yesno="No"
//      Prompt fname,"function name",popup,FunctionList("!Sme*",";","KIND:15,")
//      Prompt dataname,"name of the dataset"
//      Prompt param,"parameter names",popup,WaveList("par*",";","")
//      Prompt coef,"coefficient wave",popup,WaveList("coe*",";","")
//      Prompt yesno,"Save the report?",popup,"Yes;No;"
//      
//      //Print "fname = ",fname
//      //Print "param = ",param
//      //Print "coef = ",coef
//      //Print "yesno = ",yesno
//      
//      Variable doSave=0
//      if(cmpstr(yesno,"Yes")==0)
//              doSave=1
//      Endif
//      GenerateReport(fname,dataname,param,coef,dosave)
//      
//End



//must have AutoGraph_NSE as the name of the graph window (any size)
// func is the name of the function (for print only)
//par and coef are the exact names of the waves
//yesSave==1 will save the file(name=func+time)
//
Function GenerateReport_NSE(func,dataname,par,coef,yesSave)
        String func,dataname,par,coef
        Variable yesSave
        
        String str
        Wave sigWave=$"W_sigma"
        Wave ans=$coef
        Wave/T param=$par
        
        NVAR V_chisq = V_chisq
        NVAR V_npnts = V_npnts
        NVAR V_FitError = V_FitError
        NVAR V_FitQuitReason = V_FitQuitReason
        
        // bring report up
        DoWindow/F Report
        if (V_flag == 0)                // Report notebook doesn't exist ?
                NewNotebook/W=(10,45,550,620)/F=1/N=Report as "Report"
        endif
        
        // delete old stuff
        Notebook Report selection={startOfFile, endOfFile}, text="\r", selection={startOfFile, startOfFile}
        
        // insert title
        Notebook Report newRuler=Title, justification=1, rulerDefaults={"Times", 16, 1, (0, 0, 0)}
        sprintf str, "Fit to %s, %s, %s\r\r", func,Secs2Date(datetime, 0), time()
        Notebook Report ruler=Title, text=str
        
        // insert fit results
        Variable num=numpnts(ans),ii=0
        Notebook Report ruler=Normal; Notebook Report  margins={18,18,504}, tabs={63 + 3*8192}
        str = "Data file: " + dataname + "\r\r"
        Notebook Report text=str
        do
                sprintf str, "%s = %g±%g\r", param[ii],ans[ii],sigwave[ii]
                Notebook Report text=str
                ii+=1
        while(ii<num)
                
        sprintf str,"chisq = %g\r",V_chisq
        Notebook Report textRGB=(65000,0,0),fstyle=1,text=str
        sprintf str,"Npnts = %g\r",V_npnts
        Notebook Report textRGB=(0,0,0),fstyle=0, text=str
        sprintf str,"V_FitError = %g\rV_FitQuitReason = %g\r",V_FitError,V_FitQuitReason
        Notebook Report textRGB=(65000,0,0),fstyle=1,text=str
        Notebook Report ruler=Normal
        
        // insert graphs
        Notebook Report picture={AutoGraph_NSE(0, 0, 400, 300), 0, 1}, text="\r"
        //Notebook Report picture={Table1, 0, 0}, text="\r"
        
        // show the top of the report
        Notebook Report  selection= {startOfFile, startOfFile},  findText={"", 1}
        
        //save the notebook
        if(yesSave)
                String nameStr=CleanupName(func,0)
                nameStr = nameStr[0,8]  //shorten the name
                nameStr += "_"+dataname
                //make sure the name is no more than 31 characters
                namestr = namestr[0,30]         //if shorter than 31, this will NOT pad to 31 characters
                Print "file saved as ",nameStr
                SaveNotebook /O/P=savePath/S=2 Report as nameStr
        Endif

        //save a pict file, just of the graph
        namestr = "PICT_" + namestr
        namestr = namestr[0,28]         //PICT names in IGOR must be shorter, to allow auto-naming?
        DoWindow/F AutoGraph_NSE
        SavePICT /E=2/O/I/P=savePath /W=(0,0,3,3) as nameStr
End


//*********************
//
//*********************
// List utilities
//*********************
//
// List2TextWave is also in SANS_Utilities.ipf, but to keep from having big lists of dependencies,
// have definitions here that are local and Static

//
Static Function List2TextWave(list,sep,waveStr)
        String list,sep,waveStr
        
        Variable n= ItemsInList(list,sep)
        Make/O/T/N=(n) $waveStr= StringFromList(p,list,sep)
End

Function List2NumWave(list,sep,waveStr)
        String list,sep,waveStr
        
        Variable n= ItemsInList(list,sep)
        Make/O/D/N=(n) $waveStr= str2num( StringFromList(p,list,sep) )
End

Function/S TextWave2List(w,sep)
        Wave/T w
        String sep
        
        String newList=""
        Variable n=numpnts(w),ii=0
        do
                newList += w[ii] + sep
                ii+=1
        while(ii<n)
        return(newList)
End

//for single precision numerical waves
Function/S NumWave2List(w,sep)
        Wave w
        String sep
        
        String newList="",temp=""
        Variable n=numpnts(w),ii=0,val
        do
                val=w[ii]
                temp=""
                sprintf temp,"%g",val
                newList += temp
                newList += sep
                ii+=1
        while(ii<n)
        return(newList)
End

Function DoKillList(list)
        String list
        
        String item=""
        do
                item = StringFromList(0, list ,";" )
                KillWaves/Z $item
                list = RemoveFromList(item, list, ";")
        while(ItemsInList(list, ";")>0)
End

//*********************



//*******************
//Notebook Utils
//*******************

Proc PrintOpenNotebooks()

        String list=WinList("*", ";", "WIN:16")
        String item = ""
        do
                item=StringFromList(0,list,";")
                Print item
                PrintNotebook $item
                list = RemoveFromList(item, list, ";")
        while(ItemsInList(list, ";")>0)
End

Proc CloseOpenNotebooks()

        String list=WinList("*", ";", "WIN:16")
        String item = ""
        do
                item=StringFromList(0,list,";")
                DoWindow/K $item
                list = RemoveFromList(item, list, ";")
        while(ItemsInList(list, ";")>0)
End

Proc Generate_PICTS_list()
        fGenerate_PICTS_list()
End

//spits up a list of PICTS
Function fGenerate_PICTS_list()

        String List=IndexedFile(savePath, -1, "PICT")
        List2TextWave(List,";","PICT_files")
        WAVE/T picts=$"PICT_files"
        Edit/K=1 picts
End

Proc Layout_PICTS(pStr)
        String pStr=""
        Prompt pStr,"wave of PICTs to use",popup,WaveList("PICT_f*", ";", "")
                
        String List=TextWave2List($pStr,";")
        String item = ""
        //kill old picts
        KillPicts/A/Z
        //make a new layout
        Layout/C=1 as "PICT_Layout"
        DoWindow/C PICTLayout
        do
                item=StringFromList(0,List,";")
                //load each PICT, and append it to the layout
                Print "load item = ",item
                LoadPICT /O/Q/P=savePath item
                DoWindow/F PICTLayout           //be sure layout is on top
                AppendLayoutObject /F=1/W=PICTLayout picture  $item
                //AppendToLayout $item
                //Print item
                List = RemoveFromList(item, List, ";")
        while(ItemsInList(List, ";")>0)
        //tile the PICTs in the layout
        Tile/O=8
End

//spit up a list of everything in the folder that is a text file
Proc Generate_Data_Checklist()
        fGenerate_Data_list()
End
Function fGenerate_Data_list()

        String List=IndexedFile(dataPath, -1, "TEXT")
        List2TextWave(List,";","data_files")
        WAVE/T files=$"data_files"
        Duplicate/O/T files ModelToUse,Done
        ModelToUse = ""
        Done = ""
        Edit/K=1 files,ModelToUse,Done
End

//***************

// with all of the notebooks open for a given model (with N parameters)
// this will comile the reports, save the text notebook, then load it back in
// and put it in a table for easy printing
//
Proc CompileAndLoadReports()
        Compile_Reports()
        SaveNotebook /O/P=savePath/S=2 Compilation
//      Print "Saved as:  ",S_Path
        DoWindow/K Compilation
        LoadCompiledReports(S_Path)
End

Proc LoadCompiledReports(str)
        String str
        LoadWave/J/D/W/E=1/K=0/V={"\t"," $",0,0} str
End

Proc Compile_Reports(Number_of_Parameters)
        Variable Number_of_Parameters=7
        fCompile_Reports(Number_of_Parameters)
        fCompile_ReportsTable(Number_of_Parameters)
End

Proc Compile_GlobalFit_Reports(WhichParameter,FileStr,ParamStr,ParamErrStr)
        Variable WhichParameter=7
        String FileStr="FileName_",ParamStr="par_",ParamErrStr="parErr_"
        fCompile_GlobalFit_Reports(WhichParameter,FileStr,ParamStr,ParamErrStr)
End

////
Function fCompile_Reports(nPar)
        Variable nPar
        
        String list=WinList("*", ";", "WIN:16")
        String item = "",textStr="",newStr=""
        Variable sstop,dum,chi
        
        Variable ii
        NewNotebook/F=0 /N=Compilation as "Compilation"
        Notebook Compilation text="Variable Name \tValues\tErrors\r"
        do
                item=StringFromList(0,list,";")
                DoWindow/F $item
                
                Notebook $item selection={(2,0), (3,0)}         //paragraph 3 (starts from 0) = filename
                GetSelection notebook,$item,2
                textStr=S_Selection
                textStr=textStr[0,strlen(textStr)-2]            //remove CR
                textStr=textStr[10,strlen(textStr)-1]           //remove "DATA FILE: 
                Notebook Compilation text="File:\t"+textStr+"\t"
                Notebook Compilation text=textStr+"_err\r"
                
//              printf "%s %s\r",textStr,textStr+"_err"
//
// results are written as:  "%s = \t%g\t±\t%g\r"
//
                for(ii=0;ii<nPar;ii+=1)         //gather the parameters
                
                        Notebook $item selection={(ii+4,0), (ii+5,0)}           //paragraph 5           = parameter 0
                        GetSelection notebook,$item,2
                        textStr=S_Selection
                        textStr=textStr[0,strlen(textStr)-2]
                        //textStr=textStr[13,strlen(textStr)-1]         // remove "parameter"
                        textStr = ReplaceString("=",textStr,"")
                        textStr = ReplaceString("±\t",textStr,"")
                        Notebook Compilation text=textStr+"\r"
                        //printf "%s\r",textStr
                        //Print strlen(textStr)
                endfor
                //get the chi-squared/N value
                ii+=1
                Notebook $item selection={(ii+4,0), (ii+5,0)}           //
                GetSelection notebook,$item,2
                textStr=S_Selection
                Print textStr
                
                sscanf textStr,"Npnts = %g\t\tSqrt(X^2/N) = %g\r",dum,chi
                sprintf textStr,"Sqrt(X^2/N)\t%s\t\r",num2str(chi)
                Notebook Compilation text=textStr
                
                Notebook Compilation text="\r"          //separate items
                
                list = RemoveFromList(item, list, ";")
        while(ItemsInList(list, ";")>0)
        
        DoWindow/F Compilation
        Notebook Compilation selection={startOfFile,startOfFile}
End

////
// compiles the results into a table.
Function fCompile_ReportsTable(nPar)
        Variable nPar
        
        String list=WinList("*", ";", "WIN:16")
        String item = "",textStr="",newStr="",str
        Variable sstop,dum,chi
        
        Variable ii,numRep,jj,val1,val2,pt
        numRep=ItemsInList(list,";")
        
        Make/O/T/N=(numRep) fittedFiles
        Make/O/D/N=(numRep) chiSQ
        Edit fittedFiles,chiSQ
        
        for(ii=0;ii<nPar;ii+=1)         //waves for the parameters
                Make/O/D/N=(numRep) $("par"+num2str(ii)),$("par"+num2str(ii)+"_err")
                AppendToTable $("par"+num2str(ii)),$("par"+num2str(ii)+"_err")
        endfor
        
        for(jj=0;jj<numRep;jj+=1)

                item=StringFromList(jj,list,";")
                DoWindow/F $item
                Notebook $item selection={(2,0), (3,0)}         //paragraph 3 (starts from 0) = filename
                GetSelection notebook,$item,2
                textStr=S_Selection
                textStr=textStr[0,strlen(textStr)-2]            //remove CR
                textStr=textStr[10,strlen(textStr)-1]           //remove "DATA FILE:
                
                fittedFiles[jj] = textStr
//
// results are written as:  "%s = \t%g\t±\t%g\r"
//
                for(ii=0;ii<nPar;ii+=1)         //gather the parameters
                        Notebook $item selection={(ii+4,0), (ii+5,0)}           //paragraph 5           = parameter 0
                        GetSelection notebook,$item,2
                        textStr=S_Selection
                        textStr=textStr[0,strlen(textStr)-2]
                        // find the "="
                        pt = strsearch(textStr,"=",0,0)
                        textStr = textStr[pt,strlen(textStr)-1]
                        sscanf textStr,"= \t%g\t ± \t%g\r",val1,val2
                        
                        Print textStr
                                                
                        Wave w1 = $("par"+num2str(ii))
                        Wave w2 = $("par"+num2str(ii)+"_err")
                        
                        w1[jj] = val1
                        w2[jj] = val2
                        
                        //textStr = ReplaceString("=",textStr,"")
                        //textStr = ReplaceString("±\t",textStr,"")
                        //Notebook Compilation text=textStr+"\r"
                        //printf "%s\r",textStr
                        //Print strlen(textStr)
                endfor
                //get the chi-squared/N value
                ii += 1 
                Notebook $item selection={(ii+4,0), (ii+5,0)}           //
                GetSelection notebook,$item,2
                textStr=S_Selection
                Print textStr
                
                sscanf textStr,"Npnts = %g\t\tSqrt(X^2/N) = %g\r",dum,chi
                
                chiSQ[jj] = chi 
        endfor
        
        return(0)
End


////
Function fCompile_GlobalFit_Reports(nPar,Files,Param,Param_err)
        Variable nPar
        String Files,Param,Param_Err
        
        String list=SortList(WinList("*", ";", "WIN:16"))
        String item = "",textStr="",fileStr,funcStr,dumStr
        Variable sstop,dum,chi,nFiles,val1,val2
        
        Variable ii,jj

        nFiles = ItemsInList(list)
        Make/O/D/N=(nFiles) $Param,$Param_err
        Make/O/T/N=(nFiles) $Files
        WAVE pw = $Param
        WAVE pw_err = $Param_err
        WAVE/T fw = $Files
        
        for(jj=0;jj<nFiles;jj+=1)
        
                item=StringFromList(jj,list,";")
                DoWindow/F $item
                
                Notebook $item selection={(6,0), (7,0)}         //paragraph 7 (starts from 0) = filename
                GetSelection notebook,$item,2
                textStr=S_Selection
                sscanf textStr,"Data Set:%s ; Function:%s\r",fileStr,funcStr
                fw[jj] = fileStr
//              Notebook Compilation text=fileStr+"\r"
//              Notebook Compilation text=funcStr+"\r"
                
                
//              printf "%s %s\r",textStr,textStr+"_err"

                for(ii=nPar;ii<=nPar;ii+=1)             //gather the parameters
                
                        Notebook $item selection={(ii+7,0), (ii+8,0)}           //paragraph 8           = parameter 0
                        GetSelection notebook,$item,2
                        textStr=S_Selection
//                      Print textStr
                        sscanf textStr,"%s %g +- %g\r",dumStr,val1,val2
                        pw[jj] = val1
                        pw_err[jj] = val2
                endfor
                
        endfor

End



//DOES NOT graph the data, does not create a weighting wave
//NSE data assumed to be 4-column 
//q (all the same) - t(ns) - I(q,t) - dI(q,t)
Static Function LoadNSEDataWithName(fileStr)
        String fileStr
        //Load the waves, using default waveX names
        //if no path or file is specified for LoadWave, the default Mac open dialog will appear
        LoadWave/G/D/A/Q fileStr
        String fileName = S_fileName
        
        
        String w0,w1,w2,n0,n1,n2,wt,w3,n3
        Variable rr,gg,bb
        
        // put the names of the four loaded waves into local names
        n0 = StringFromList(0, S_waveNames ,";" )
        n1 = StringFromList(1, S_waveNames ,";" )
        n2 = StringFromList(2, S_waveNames ,";" )
        n3 = StringFromList(3, S_waveNames ,";" )
        
        
        //remove the semicolon AND period from files from the VAX
        w0 = CleanupName((S_fileName+"__Q"),0)
        w1 = CleanupName((S_fileName+"__X"),0)
        w2 = CleanupName((S_fileName+"__Y"),0)
        w3 = CleanupName((S_fileName+"__S"),0)
        
        if(exists(w0) !=0)
                //waves already exist
                KillWaves $n0,$n1,$n2,$n3               // kill the default waveX that were loaded
                return(0)
        endif
        
        // Rename to give nice names
        Rename $n0, $w0
        Rename $n1, $w1
        Rename $n2, $w2
        Rename $n3, $w3

End

/////
//wStr is the coef_ wave with the initial guess
Function FillCoefGuess(wStr)
        String wStr
        
        Wave w=$wStr
        if (! WaveExists(w) )
                DoAlert 0, "The coefficient wave "+wStr+" does not exist. Either create the wave or enter the correct suffix"
                return(0)
        endif
        Wave/T guess=root:AutoFit:guessMatrix
        Variable ii=0,num=numpnts(w)
        Variable tmp
        
        Variable selRow,matrixRow
        selRow = FindSelectedRowInLB(0) // send 0 to look at the column with filenames

        do
                tmp=w[ii]
                guess[ii][selRow] = num2str(tmp)
                ii+=1
        while(ii<num)
End

/////
//wStr is the hold_ wave with the initial guess
Function FillHoldGuess(wStr)
        String wStr
        
        Wave w=$wStr
        if (! WaveExists(w) )
                DoAlert 0, "The hold wave "+wStr+" does not exist. Either create the wave or enter the correct suffix"
                return(0)
        endif
        Wave/T hold=root:AutoFit:holdMatrix
        Variable ii=0,num=numpnts(w)
        Variable tmp
        
        Variable selRow,matrixRow
        selRow = FindSelectedRowInLB(0) // send 0 to look at the column with filenames
        
        do
                tmp=w[ii]
                hold[ii][selRow] = num2str(tmp)
                ii+=1
        while(ii<num)
End

/////
//wStr is the Constr_ wave with the initial guess
// --- this is a Text wave
Function FillConstrGuess(wStr)
        String wStr
        
        Wave/T w=$wStr
        if (! WaveExists(w) )
                DoAlert 0, "The Constraint wave "+wStr+" does not exist. Either create the (TEXT) wave or enter the correct suffix"
                return(0)
        endif
        Wave/T constr=root:AutoFit:constrMatrix
        Variable ii=0,num=numpnts(w)
        String tmp
        
        Variable selRow,matrixRow
        selRow = FindSelectedRowInLB(0) // send 0 to look at the column with filenames

        do
                tmp=w[ii]
                constr[ii][selRow] = tmp
                ii+=1
        while(ii<num)
End

////
//need the extension of the model wave to append
//
// it will plot the UN-smeared model for generating the initial guesses
// -- fitting will use Smeared or unsmeared, depending on the popup selection
//
//
Function fLoadSelected(extStr)
        string extStr

        Variable datafile,ii
        String fullName,dataName,str
        
        WAVE/T fileWave=root:AutoFit:fileListWave
        Wave sel = root:AutoFit:fileSelWave
        ii=0
        do
                if((sel[ii][0] & 0x01) == 1)    // the file is selected in the list box
                        datafile = ii
                        break
                endif
                ii+=1
        while(ii<numpnts(sel))
        
        //load in the data
        PathInfo dataPath
        fullName = S_path
        fullName += fileWave[datafile][0]

        str = "A_LoadOneDDataToName(\""+fullName+"\",\"\",0,1)"         //don't plot, force overwrite
        Execute str             
        
        dataName=GetFileNameFromPathNoSemi(fullName)
        dataname=CleanupName(dataname,0)
        
        //graph it - creates window named "AutoGraph"
        DoWindow/K tmpGraph
        Execute "DoGraph(\""+dataname+"\")"
        DoWindow/C tmpGraph
//      Wave/Z yw = $("ywave_"+extStr)
//      Wave/Z xw = $("xwave_"+extStr)

        if(exists("ywave_"+extStr) && exists("xwave_"+extStr))
                AppendtoGraph $("ywave_"+extStr) vs $("xwave_"+extStr)
        else
                DoAlert 0,"Model data with the suffix \""+extStr+"\" does not exist. Either plot the model or enter the correct suffix"
        endif

//      ControlInfo/W=AutoFitPanel popup0
//      if(cmpstr(S_Value[0,4], "Smear" ) == 0 )
//              SetDataFolder $dataname
//              if(exists("smeared_"+extStr) && exists("smeared_qvals"))
//                      
//                      AppendtoGraph $("smeared_"+extStr) vs $("smeared_qvals")
//              else
//                      SetDataFolder root:
//                      DoAlert 0,"Smeared Model data with the suffix \""+extStr+"\" does not exist. Either plot the model or enter the correct suffix"
//              endif
//              
//      else
//              if(exists("ywave_"+extStr) && exists("xwave_"+extStr))
//                      AppendtoGraph $("ywave_"+extStr) vs $("xwave_"+extStr)
//              else
//                      DoAlert 0,"Model data with the suffix \""+extStr+"\" does not exist. Either plot the model or enter the correct suffix"
//              endif
//      endif


        SetDataFolder root:
        return(0)
End

//loads the selected file in a temporary graph
Function LoadForGuessProc(ctrlName) : ButtonControl
        String ctrlName
        
        SVAR ext=root:AutoFit:gExt
        fLoadSelected(ext)
        return(0)
End

//makes the holdWave and Constraint wave that are needed to set the values in the list boxes (and the matrix)
// these are not generated when plotting a model.
Function Make_HoldConstraintEps_Waves()
        
        SVAR  ext=root:AutoFit:gExt
        Variable num=numpnts($("coef_"+ext))
        if(WaveExists($("coef_"+ext)) == 0 )
                DoAlert 0,"coef_"+ext+" does not exist. You must set the prefix correctly and plot the model first"
        else
                Make/O/D/N=(num) $("Hold_"+ext)
                Make/O/T/N=(num) $("Constr_"+ext)
                Make/O/D/N=(num) $("Epsilon_"+ext)=0.0003
        
                String str=WinList("*", ";","WIN:2"),sel
                Prompt sel, "Select Table to Append Waves", popup str
                DoPrompt "asdf",sel
                if (V_Flag)
                        return 0        // user canceled
                endif
                DoWindow/F $sel
                AppendToTable $("Hold_"+ext), $("Constr_"+ext), $("Epsilon_"+ext)
        endif
End
//needs the name (as a string) of the coefficient wave
//it assumes "coef_" plus an extension
//
Function UseCoefAsGuess(ctrlName) : ButtonControl
        String ctrlName
        
        String wStr = "coef_"
        SVAR ext=root:AutoFit:gExt
        FillCoefGuess(wStr+ext)
        DisplayGuess()
        return(0)
End

//needs the name (as a string) of the hold string wave
//it assumes "hold_" plus an extension
//
Function UseHoldAsGuess(ctrlName) : ButtonControl
        String ctrlName
        
//      String wStr = "hold_"
//      SVAR ext=root:AutoFit:gExt
//      FillHoldGuess(wStr+ext)
//      DisplayGuess()
        return(0)
End

//needs the name (as a string) of the coefficient wave
//it assumes "constr" plus an extension
//
Function UseConstraintsAsGuess(ctrlName) : ButtonControl
        String ctrlName
        
//      String wStr = "Constr_"
//      SVAR ext=root:AutoFit:gExt
//      FillConstrGuess(wStr+ext)
//      DisplayGuess()
        return(0)
End