source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/HFIR_Utils.ipf @ 940

#pragma rtGlobals=1             // Use modern global access method.
#pragma version=5.0
#pragma IgorVersion=6.1

// this file contains globals and functions that are specific to a
// particular facility or data file format
// branched out 29MAR07 - SRK
//
// functions are either labeled with the procedure file that calls them,
// or noted that they are local to this file

// initializes globals that are specific to a particular facility
// - number of XY pixels
// - pixexl resolution [cm]
// - detector deadtime constant [s]
//
// called by Initialize.ipf
//
Function InitFacilityGlobals()

        //Detector -specific globals
        Variable/G root:myGlobals:gNPixelsX=192                                 // number of detector X and Y pixels
        Variable/G root:myGlobals:gNPixelsY=192
        
        // pixel dimensions are now read directly from the file header.
        Variable/G root:myGlobals:PixelResDefault = 0.51        //pixel resolution in cm
        //No dead time measured for HFIR detector but the count rate is set very low. For now, set the detector perfect.
        // This should be updated when the condition is changed.   JHC 09/02/09
        Variable/G root:myGlobals:DeadtimeDefault =  0       //3.4e-6 (NIST value)      //deadtime in seconds

        Variable/G root:myGlobals:apOff = 5.0           // (cm) distance from sample aperture to sample positio

End


//**********************
// Resolution calculation - used by the averaging routines
// to calculate the resolution function at each q-value
// - the return value is not used
//
// equivalent to John's routine on the VAX Q_SIGMA_AVE.FOR
// Incorporates eqn. 3-15 from J. Appl. Cryst. (1995) v. 28 p105-114
//
// - 21 MAR 07 uses projected BS diameter on the detector
// - APR 07 still need to add resolution with lenses. currently there is no flag in the 
//          raw data header to indicate the presence of lenses.
//
// - Aug 07 - added input to switch calculation based on lenses (==1 if in)
//
// - called by CircSectAvg.ipf and RectAnnulAvg.ipf
//
// passed values are read from RealsRead
// except DDet and apOff, which are set from globals before passing
//
//
Function/S getResolution(inQ,lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,del_r,usingLenses,SigmaQ,QBar,fSubS)
        Variable inQ, lambda, lambdaWidth, DDet, apOff, S1, S2, L1, L2, BS, del_r,usingLenses
        Variable &fSubS, &QBar, &SigmaQ         //these are the output quantities at the input Q value
        
        //lots of calculation variables
        Variable a2, q_small, lp, v_lambda, v_b, v_d, vz, yg, v_g
        Variable r0, delta, inc_gamma, fr, fv, rmd, v_r1, rm, v_r

        //Constants
        Variable vz_1 = 3.956e5         //velocity [cm/s] of 1 A neutron
        Variable g = 981.0                              //gravity acceleration [cm/s^2]

        String results
        results ="Failure"

        S1 *= 0.5*0.1                   //convert to radius and [cm]
        S2 *= 0.5*0.1

        L1 *= 100.0                     // [cm]
        L1 -= apOff                             //correct the distance

        L2 *= 100.0
        L2 += apOff
        del_r *= 0.1                            //width of annulus, convert mm to [cm]
        
        BS *= 0.5*0.1                   //nominal BS diameter passed in, convert to radius and [cm]
        // 21 MAR 07 SRK - use the projected BS diameter, based on a point sample aperture
        Variable LB
        LB = 20.1 + 1.61*BS                     //distance in cm from beamstop to anode plane (empirical)
        BS = bs + bs*lb/(l2-lb)         //adjusted diameter of shadow from parallax
        
        //Start resolution calculation
        a2 = S1*L2/L1 + S2*(L1+L2)/L1
        q_small = 2.0*Pi*(BS-a2)*(1.0-lambdaWidth)/(lambda*L2)
        lp = 1.0/( 1.0/L1 + 1.0/L2)

        v_lambda = lambdaWidth^2/6.0
        
//      if(usingLenses==1)                      //SRK 2007
        if(usingLenses != 0)                    //SRK 2008 allows for the possibility of different numbers of lenses in header
                v_b = 0.25*(S1*L2/L1)^2 +0.25*(2/3)*(lambdaWidth/lambda)^2*(S2*L2/lp)^2         //correction to 2nd term
        else
                v_b = 0.25*(S1*L2/L1)^2 +0.25*(S2*L2/lp)^2              //original form
        endif
        
        v_d = (DDet/2.3548)^2 + del_r^2/12.0
        vz = vz_1 / lambda
        yg = 0.5*g*L2*(L1+L2)/vz^2
        v_g = 2.0*(2.0*yg^2*v_lambda)                                   //factor of 2 correction, B. Hammouda, 2007

        r0 = L2*tan(2.0*asin(lambda*inQ/(4.0*Pi) ))
        delta = 0.5*(BS - r0)^2/v_d

        if (r0 < BS) 
                inc_gamma=exp(gammln(1.5))*(1-gammp(1.5,delta))
        else
                inc_gamma=exp(gammln(1.5))*(1+gammp(1.5,delta))
        endif

        fSubS = 0.5*(1.0+erf( (r0-BS)/sqrt(2.0*v_d) ) )
        if (fSubS <= 0.0) 
                fSubS = 1.e-10
        endif
        fr = 1.0 + sqrt(v_d)*exp(-1.0*delta) /(r0*fSubS*sqrt(2.0*Pi))
        fv = inc_gamma/(fSubS*sqrt(Pi)) - r0^2*(fr-1.0)^2/v_d

        rmd = fr*r0
        v_r1 = v_b + fv*v_d +v_g

        rm = rmd + 0.5*v_r1/rmd
        v_r = v_r1 - 0.5*(v_r1/rmd)^2
        if (v_r < 0.0) 
                v_r = 0.0
        endif
        QBar = (4.0*Pi/lambda)*sin(0.5*atan(rm/L2))
        SigmaQ = QBar*sqrt(v_r/rmd^2 +v_lambda)

        results = "success"
        Return results
End



//Utility function that returns the detector resolution (in cm)
//Global values are set in the Initialize procedure
//
// - called by CircSectAvg.ipf, RectAnnulAvg.ipf, and ProtocolAsPanel.ipf
//
// fileStr is passed as TextRead[3] and is the filename
// detStr is passed as TextRead[9] and is an identifier for the detector
//
// depricated - pixel dimensions are read directly from the file header
Function xDetectorPixelResolution(fileStr,detStr)
        String fileStr,detStr
        
        Variable DDet
        NVAR PixelResDefault = root:myGlobals:PixelResDefault
        //your code here
        DDet = PixelResDefault  //0.515 cm, typical for new ORNL detectors
        return(DDet)
End

//Utility function that returns the detector deadtime (in seconds)
//Global values are set in the Initialize procedure
//
// - called by WorkFileUtils.ipf
//
// fileStr is passed as TextRead[3] and is the filename
// detStr is passed as TextRead[9] and is an identifier for the detector
//
// [dateAndTimeStr] is optional, and could be used as a switch for 
// different historical detector configurations
Function DetectorDeadtime(fileStr,detStr,[dateAndTimeStr,dtime])
        String fileStr,detStr,dateAndTimeStr
        Variable dtime
        
        Variable deadtime
        NVAR DeadtimeDefault = root:myGlobals:DeadtimeDefault
        
        deadtime = DeadtimeDefault      //3.4e-6 seconds, typical for new ORNL detectors //???????????????????????????
        return(deadtime)
End



// item is a filename
//
// this function extracts some sort of number from the file
// presumably some sort of automatically incrementing run number set by the
// acquisition system
//
// this run number should be a unique identifier for the file
//Because HFIR data format is w/ 2X 4digit number. We add them to get a unique number => This will cause the arrow button not working.
Function GetRunNumFromFile(item)
        String item
        Variable invalid = -1   //negative numbers are invalid
        Variable num=-1
        
        //find the "dot"
        String runStr=""
        Variable pos = strsearch(item,".",0)
        if(pos == -1)
                //"dot" not found
                return (invalid)
        else
                //found, get the nine characters preceeding it
                if (pos <=8)
                        //not enough characters
                        return (invalid)
                else
                        Variable pos_bio = strsearch( LowerStr(item),"biosans",0)
                        //if  (pos_bio== -1)
                                runStr  = item[pos-9,pos-6]     //first 4 numbers
                        //else
                                runStr  += item[pos-4,pos-1]    //add last 4 numbers
                        //endif
                        //convert to a number
                        num = str2num(runStr)
                        
                        //if valid, return it
                        if (num == NaN)
                                //8 characters were not a number
                                return (invalid)
                        else
                                //run was OK
                                return (num)
                        Endif
                Endif
        Endif
        
End


// item is a filename
//
// this function extracts some sort of number from the file
// presumably some sort of automatically incrementing run number set by the
// acquisition system
//
// this run number should be a unique identifier for the file
//
// same as GetRunNumFromFile(0), just with a string return
//
// "ABC" returned as an invalid result
// XXXXSANS_expXX._scan1234_5678.xmp ==> "12345678"
// -- result is an 8-character string
//
Function/S GetRunNumStrFromFile(item)   //,numposition)
        String item
        Variable numposition
        
        String invalid = "ABC"  //"ABC" is not a valid run number, since it's text
        String retStr
        retStr=invalid

        //find the "dot"
        Variable pos = strsearch( LowerStr(item),".xml",0)
        if(pos == -1)
                //"dotxml" not found
                return (retStr)
        else
                pos = strsearch( LowerStr(item),"_scan",0)
                
                if  (pos == -1)
                        //not a raw data file
                        return (retStr)
                else
                        //Variable pos_bio = strsearch( LowerStr(item),"biosans_",0)  //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
                        //if  (numposition == 0)
                                //Take the first four: //HiResSANS
                                retStr = item[pos+5,pos+8]
                        //else  
                                //add the last four: //BioSANS
                                retStr += item[pos+10,pos+13]
                        //Endif
                        return (retStr)
                Endif
        Endif
        
End

//returns a string containing the full path to the file containing the 
//run number "num". The null string is returned if no valid file can be found.
//
//
// search in the path "catPathName" (hard-wired), will abort if this path does not exist
//the file returned will be a RAW SANS data file, other types of files are 
//filtered out.
//
// called by Buttons.ipf and Transmission.ipf, and locally by parsing routines
//
Function/S FindFileFromRunNumber(num)
        Variable num

        String fullName="",partialName="",item=""
        //get list of raw data files in folder that match "num" (add leading zeros)
        if( (num>99999999) || (num<0) )
                //Print "error in  FindFileFromRunNumber(num), file number too large or too small"
                Return ("")
        Endif
        //make a four character string of the run number
        String numStr=""
        
        if(num > 9999999 && num < 100000000)
                numStr = num2istr(num)
        endif
        if(num > 999999 && num < 10000000)
                numStr = "0"+num2istr(num)
        endif   
        if(num > 99999 && num < 1000000)
                numStr = "00"+num2istr(num)
        endif   
        if(num > 9999 && num < 100000)
                numStr = "000"+num2istr(num)
        endif
        if(num > 999 && num < 10000)
                numStr =  "0000"+num2istr(num)
        endif
        if(num > 99 && num < 1000)
                numStr = "00000"+num2istr(num)
        endif   
        if(num > 9 && num < 100)
                numStr = "000000"+num2istr(num)
        endif   
        if(num < 10 && num >0)
                numStr = "0000000"+num2iStr(num)
        endif
        if(num == 0)
                numStr = "00000000"
        endif

        //make sure that path exists
        PathInfo catPathName
        String path = S_path
        if (V_flag == 0)
                Abort "folder path does not exist - use Pick Path button"
        Endif
        String list="",newList="",testStr=""
        
        list = IndexedFile(catPathName,-1,"????")       //get all files in folder
        //find (the) one with the number in the run # location in the name
        Variable numItems,ii,runFound,isRAW
        numItems = ItemsInList(list,";")                //get the new number of items in the list

        ii=0
        do
                //parse through the list in this order:
                // 1 - does item contain run number (as a string) "NAMESANS_expNN_scan####_####.xml" : Let's check the 8  nums.
                // 2 - exclude by isRaw? (to minimize disk access)
                item = StringFromList(ii, list  ,";" )
                
                if(strlen(item) != 0)
                        //find the run number, if it exists as a 8 character string
                        testStr = GetRunNumStrFromFile(item)    //0)
                        runFound= cmpstr(numStr,testStr)        //compare the three character strings, 0 if equal
                        
                        if(runFound == 0)
                                //the run Number was found
                                //build valid filename
                                partialName = FindValidFileName(item)
                                
                                if(strlen(partialName) != 0)            //non-null return from FindValidFileName()
                                        fullName = path + partialName
                                        //check if RAW, if so,this must be the file!
                                        isRAW = CheckIfRawData(fullName)
                                        if(isRaw)
                                                //stop here
                                                return(fullname)
                                        Endif
                                Endif
                        Endif
                        
                Endif
                ii+=1
        while(ii<numItems)              //process all items in list
        print "The run number (", numStr, " +- 1 ) does not exist... (Note: The run number is defined as 12345678 if the file name is NameSANS_exp##_scan1234_5678.xml)"
        Return ("")     //null return if file not found in list 
End


//make an (N) character string of the run number
//Moved to facility utils
//
// same scheme to get 8-character string as in GetRunNumStrFromFile(item)
//
Function/S RunDigitString(num)
        Variable num

        String numStr=""

        //make 8 digit string from run number
        sprintf numStr,"%08u",num
        
        if(strlen(numStr) > 8)
                return("")
        else
                return(numstr)
        endif
        
End

//given a filename of a SANS data filename of the form
//TTTTTnnn.SAn_TTT_Txxx
//returns the prefix "TTTTT" as some number of characters
//returns "" as an invalid file prefix
//
// HFIR writes out files with a "prefix" of the following -- since there is really no "prefix" 
// like in the VAX scheme:
//                      newFileName = ReplaceString(".xml",textPath[0],"")              //removes 4 chars
//                      newFileName = ReplaceString("SANS",newFileName,"")              //removes 4 more chars = 8
//                      newFileName = ReplaceString("exp",newFileName,"")                       //removes 3 more chars = 11
//                      newFileName = ReplaceString("scan",newFileName,"")              //removes 4 more chars = 15, should be enough?
//
//
// -- so the raw data:          BioSANS_exp9_scan1828_0001.xml
// -- translates to:            Bio_9_1828_0001.AVE     
//
//
// NCNR-specifc, does not really belong here - it's a beta procedure used for the
// Combine Files Panel, and I'm not sure of how I'm really going to get this to work properly
// since the .ABS file written is not of the form that NSORT->Set3NSORTFiles(low,med,hi,pref)
// is trying to construct
//
// changed (Oct 2010) the naming for HFIR from ExecuteProtocol to:
//                      newFileName = GetPrefixStrFromFile(textPath[0])+GetRunNumStrFromFile(textPath[0])
// -- translates to:            BioSANS18280001.AVE
//
Function/S GetPrefixStrFromFile(item)
        String item
        String invalid = ""     //"" is not a valid run prefix, since it's text
        Variable num=-1
        
        //find the "dash"
        String runStr=""
        Variable pos = strsearch(item,"_",0)
        if(pos == -1)
                //"dot" not found
                return (invalid)
        else
                //found
                if (pos <=3)
                        //not enough characters
                        return (invalid)
                else
                        runStr = item[0,pos-1]
                        return (runStr)
                Endif
        Endif
End



//function to test a binary file to see if it is a RAW binary SANS file
//first checks the total bytes in the file (which for raw data is 33316 bytes)
//**note that the "DIV" file will also show up as a raw file by the run field
//should be listed in CAT/SHORT and in patch windows
//
//Function then checks the file fname (full path:file) for "RAW" run.type field
//if not found, the data is not raw data and zero is returned
//
// called by many procedures (both external and local)
//
Function CheckIfRawData(fname)
        String fname
              
        String tempheadhfir                                            
        Variable ind=0
        Variable refNum
        
        //If not have .xml extension, return 0.
        if (stringmatch(fname,"*.xml") <1)
                print fname+": Failed. Not a *.xml file."
                return 0                                //Not *.xml. Do nothing...
        endif
        //actually open the file
        refNum = XmlOpenFile(fname)     
        if (refNum < 0)
                print "==> "+ fname+ "\r  ==> Failed to load: Not a standard xml file format or broken.. Please check the file if properly written..."
                return 0                                //Not a xml file. Do nothing...
        endif
        
        // Check if  it is the SPICE version = 1.1
        Variable  item,i,ns = 0
        String thislocation
        if (refNum >0)
                ns = str2num(XMLstrFmXpath(refNum, "//SPICErack/@SPICE_version","",""))
        endif
        XmlCloseFile(refNum,0)
        if (ns <1.1)
                ns =0
        else
                ns =1
        endif
        
        return ns
End

// for HFIR data, both DIV and RAW are determined by looking for "*.xml"
Function CheckIfDIVData(fname)
        String fname
        return(CheckIfRawData(fname))
End

// function returns 1 if file is a transmission file, 0 if not
//
// called by Transmission.ipf, CatVSTable.ipf, NSORT.ipf
//
// SRK MAR 2010 - apparently from what I can see in the files, the beam stop "out"
// position is 25 mm for all four beam stop Y POSITIONS
// - if one is larger, (in the hundreds of mm) then it's in, and the run is not a transmission
// - so if all four y positions are less than (tol) 30 mm, call it a trans file
//
// there is a field for this in the header, write "True", so I don't need to guess again.
// -- but this field is often incorrect - for some sample data ALL FILES were "True"
// -- better to check the physical location every time
//
// tol changed to 401 per Gernot's experience 6/24/10
//
Function isTransFile(fName)   ///  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
        String fname
        
        Variable beamtrap_1y=0,beamtrap_2y=0,beamtrap_3y=0,beamtrap_4y=0,tol=401
        //Check by key "transsmission"
//      if (stringmatch( getIsTrans(fName),"True")>0)
//              return (1)
//      else
                //Check from beam stop motor position
        //      if(your test here)
                beamtrap_1y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_101mm","mm")
                beamtrap_2y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_25mm","mm")
                beamtrap_3y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_50mm","mm")
                beamtrap_4y=getRealValueFromHeader(fname,"//Motor_Positions/trap_y_76mm","mm")

                if (beamtrap_1y < tol && beamtrap_2y < tol && beamtrap_3y < tol && beamtrap_4y < tol)   
                        //Write the flag ON
                        Write_isTransmissionToHeader(fName,"True")
                        return (1)
                else
                        //some other file
                        Write_isTransmissionToHeader(fName,"False")
                        return (0)
                endif
                
//      endif

        return (0)
End



//function to remove all spaces from names when searching for filenames
//the filename (as saved) will never have interior spaces (TTTTTnnn_AB _Bnnn)
//but the text field in the header WILL, if less than 3 characters were used for the 
//user's initials, and can have leading spaces if prefix was less than 5 characters
//
//returns a string identical to the original string, except with the interior spaces removed
//
// local function for file name manipulation
//
// NO CHANGE NEEDED
//
Function/S RemoveAllSpaces(str)
        String str
        
        String tempstr = str
        Variable ii,spc,len             //should never be more than 2 or 3 trailing spaces in a filename
        ii=0
        do
                len = strlen(tempStr)
                spc = strsearch(tempStr," ",0)          //is the last character a space?
                if (spc == -1)
                        break           //no more spaces found, get out
                endif
                str = tempstr
                tempStr = str[0,(spc-1)] + str[(spc+1),(len-1)] //remove the space from the string
        While(1)        //should never be more than 2 or 3
        
        If(strlen(tempStr) < 1)
                tempStr = ""            //be sure to return a null string if problem found
        Endif
        
        //Print strlen(tempstr)
        
        Return(tempStr)
                
End



//Function attempts to find valid filename from partial name by checking for
// the existence of the file on disk
//
// returns a valid filename (No path prepended) or a null string
//
// called by any functions, both external and local
//
Function/S FindValidFilename(partialName)
        String PartialName
        
        String retStr=partialName

        //your code here
        //try name with no changes - to allow for ABS files that have spaces in the names 12APR04
        retStr = ValidFileString(partialName)
        if(cmpstr(retStr,"") !=0)
                return(retStr)
        endif
        
        //if the partial name is derived from the file header, there can be spaces at the beginning
        //or in the middle of the filename - depending on the prefix and initials used
        //
        //remove any leading spaces from the name before starting
        partialName = RemoveAllSpaces(partialName)
        
        //try name with no spaces
        retStr = ValidFileString(partialName)
        if(cmpstr(retStr,"") !=0)
                //non-null return
                return(retStr)
        endif
        
        //try all UPPERCASE
        partialName = UpperStr(partialName)
        retStr = ValidFileString(partialName)
        if(cmpstr(retStr,"") !=0)
                //non-null return
                return(retStr)
        endif
        
        //try all lowercase (ret null if failure)
        partialName = LowerStr(partialName)
        retStr = ValidFileString(partialName)
        if(cmpstr(retStr,"") !=0)
                //non-null return
                return(retStr)
        else
                return(retStr)
        endif
End

// Function checks for the existence of a file

// *** the PATH is hard-wired to catPathName (which is assumed to exist)
// version numers up to ;10 are tried
// only the "name;vers" is returned if successful. The path is not prepended
//
// local function
//
Function/S ValidFileString(partialName)
        String partialName
        
        String tempName = "",msg=""
        Variable ii,refnum

        ii=0
        do
                if(ii==0)
                        //first pass, try the partialName
                        tempName = partialName
                        Open/Z/R/T="????TEXT"/P=catPathName refnum tempName     //Does open file (/Z flag)
                        if(V_flag == 0)
                                //file exists
                                Close refnum            //YES needed, 
                                break
                        endif
                else
                        tempName = partialName + ";" + num2str(ii)
                        Open/Z/R/T="????TEXT"/P=catPathName refnum tempName
                        if(V_flag == 0)
                                //file exists
                                Close refnum
                                break
                        endif
                Endif
                ii+=1

        while(ii<11)
        //go get the selected bits of information, using tempName, which exists
        if(ii>=11)
                //msg = partialName + " not found. is version number > 11?"
                //DoAlert 0, msg
                //PathInfo catPathName
                //Print S_Path
                Return ("")             //use null string as error condition
        Endif
                
        Return (tempName)
End


//returns a string containing filename (WITHOUT the ;vers)
//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
//with the folders separated by colons
//
// called by MaskUtils.ipf, ProtocolAsPanel.ipf, WriteQIS.ipf
//
// NO CHANGE NEEDED
//

Function/S GetFileNameFromPathNoSemi(fullPath)
        String fullPath
        
        Variable offset1,offset2
        String filename=""
        //String PartialPath
        offset1 = 0
        do
                offset2 = StrSearch(fullPath, ":", offset1)
                if (offset2 == -1)                              // no more colons ?
                        fileName = FullPath[offset1,strlen(FullPath) ]
                        //PartialPath = FullPath[0, offset1-1]
                        break
                endif
                offset1 = offset2+1
        while (1)
        
        //remove version number from name, if it's there - format should be: filename;N
        filename =  StringFromList(0,filename,";")              //returns null if error
        
        Return filename
End

//returns a string containing filename (INCLUDING the ;vers)
//the input string is a full path to the file (Mac-style, still works on Win in IGOR)
//with the folders separated by colons
//
// local, currently unused
//
// NO CHANGE NEEDED
//

Function/S GetFileNameFromPathKeepSemi(fullPath)
        String fullPath
        
        Variable offset1,offset2
        String filename
        //String PartialPath
        offset1 = 0
        do
                offset2 = StrSearch(fullPath, ":", offset1)
                if (offset2 == -1)                              // no more colons ?
                        fileName = FullPath[offset1,strlen(FullPath) ]
                        //PartialPath = FullPath[0, offset1-1]
                        break
                endif
                offset1 = offset2+1
        while (1)
        
        //keep version number from name, if it's there - format should be: filename;N
        
        Return filename
End

//given the full path and filename (fullPath), strips the data path
//(Mac-style, separated by colons) and returns this path
//this partial path is the same string that would be returned from PathInfo, for example
//
// - allows the user to save to a different path than catPathName
//
// called by WriteQIS.ipf
//
// NO CHANGE NEEDED
//

Function/S GetPathStrFromfullName(fullPath)
        String fullPath
        
        Variable offset1,offset2
        //String filename
        String PartialPath
        offset1 = 0
        do
                offset2 = StrSearch(fullPath, ":", offset1)
                if (offset2 == -1)                              // no more colons ?
                        //fileName = FullPath[offset1,strlen(FullPath) ]
                        PartialPath = FullPath[0, offset1-1]
                        break
                endif
                offset1 = offset2+1
        while (1)
        
        Return PartialPath
End

//given the filename trim or modify the filename to get a new
//file string that can be used for naming averaged 1-d files
//
// called by ProtocolAsPanel.ipf and Tile_2D.ipf
//
Function/S GetNameFromHeader(fName)
        String fName
        String temp, newName = ""
        Variable spc,ii=0
        
        //filename is 31-33 characters INSTRNAMESANS_exp##_scan####_####.xml (where # : numbers)
        //returns a null string if no name can be found
        Variable iimax =  strlen(fName)
        do
                temp = fname[ii,iimax-1-4]              //characters ii,all of the name
                spc = strsearch(temp," ",0)
                if (spc == -1)
                        break           //no more spaces found
                endif
                ii+=1
        While(ii<iimax)
        
        If(strlen(temp) < 1)
                newName = ""            //be sure to return a null string if problem found
        else
                newName = temp
        Endif
        
        Return(newName)
End

//list (input) is a list, typically returned from IndexedFile()
//which is semicolon-delimited, and may contain filenames from the VAX
//that contain version numbers, where the version number appears as a separate list item
//(and also as a non-existent file)
//these numbers must be purged from the list, especially for display in a popup
//or list processing of filenames
//the function returns the list, cleaned of version numbers (up to 11)
//raw data files will typically never have a version number other than 1.
//
// if there are no version numbers in the list, the input list is returned
//
// called by CatVSTable.ipf, NSORT.ipf, Transmission.ipf, WorkFileUtils.ipf 
//
// NO CHANGE NEEDED
//

Function/S RemoveVersNumsFromList(list)
        String list
        
        //get rid of version numbers first (up to 11)
        Variable ii,num
        String item 
        num = ItemsInList(list,";")
        ii=1
        do
                item = num2str(ii)
                list = RemoveFromList(item, list ,";" )
                ii+=1
        while(ii<12)
        
        return (list)
End

//input is a list of run numbers, and output is a list of filenames (not the full path)
//*** input list must be COMMA delimited***
//output is equivalent to selecting from the CAT table
//if some or all of the list items are valid filenames, keep them...
//if an error is encountered, notify of the offending element and return a null list
//
//output is COMMA delimited
//
// this routine is expecting that the "ask", "none" special cases are handled elsewhere
//and not passed here
//
// called by Marquee.ipf, MultipleReduce.ipf, ProtocolAsPanel.ipf
//
// NO CHANGE NEEDED
//

Function/S ParseRunNumberList(list)
        String list
        
        String newList="",item="",tempStr=""
        Variable num,ii,runNum
        
        //expand number ranges, if any
        list = ExpandNumRanges(list)
        
        num=itemsinlist(list,",")
        
        for(ii=0;ii<num;ii+=1)
                //get the item
                item = StringFromList(ii,list,",")
                //is it already a valid filename?
                
                tempStr=FindValidFilename(item) //returns filename if good, null if error
                if(strlen(tempstr)!=0)
                        //valid name, add to list
                        //Print "it's a file"
                        newList += tempStr + ","
                else
                        //not a valid name
                        //is it a number?
                        runNum=str2num(item)

                        if(numtype(runNum) != 0)
                                //not a number -  maybe an error                        
                                DoAlert 0,"List item "+item+" is not a valid run number or filename. Please enter a valid number or filename."
                                return("")
                        else
                                //a run number or an error
                                tempStr = GetFileNameFromPathNoSemi( FindFileFromRunNumber(runNum) )
                                if(strlen(tempstr)==0)
                                        //file not found, error
                                        DoAlert 0,"List item "+item+" is not a valid run number. Please enter a valid number."
                                        return("")
                                else
                                        newList += tempStr + ","
                                endif
                        endif
                endif
        endfor          //loop over all items in list

        return(newList)
End

//takes a comma delimited list that MAY contain number range, and
//expands any range of run numbers into a comma-delimited list...
//and returns the new list - if not a range, return unchanged
//
// local function
//
// NO CHANGE NEEDED
//

Function/S ExpandNumRanges(list)
        String list
        
        String newList="",dash="-",item,str
        Variable num,ii,hasDash
        
        num=itemsinlist(list,",")

        for(ii=0;ii<num;ii+=1)
                //get the item
                item = StringFromList(ii,list,",")
                //does it contain a dash?
                hasDash = strsearch(item,dash,0)                //-1 if no dash found
                if(hasDash == -1)
                        //not a range, keep it in the list
                        newList += item + ","
                else
                        //has a dash (so it's a range), expand (or add null)
                        newList += ListFromDash(item)           
                endif
        endfor
        
        return newList
End

//be sure to add a trailing comma to the return string...
//
// local function
//
// NO CHANGE NEEDED
//
Function/S ListFromDash(item)
        String item
        
        String numList="",loStr="",hiStr=""
        Variable lo,hi,ii
        
        loStr=StringFromList(0,item,"-")        //treat the range as a list
        hiStr=StringFromList(1,item,"-")
        lo=str2num(loStr)
        hi=str2num(hiStr)
        if( (numtype(lo) != 0) || (numtype(hi) !=0 ) || (lo > hi) )
                numList=""
                return numList
        endif
        for(ii=lo;ii<=hi;ii+=1)
                numList += num2str(ii) + ","
        endfor
        
        Return numList
End


//returns the proper attenuation factor based on the instrument
//
// filestr is passed from TextRead[3] = the default directory, used to identify the instrument
// lam is passed from RealsRead[26]
// AttenNo is passed from ReaslRead[3]
//
// Attenuation factor as defined here is <= 1
//
// Facilities can pass ("",1,attenuationFactor) and have this function simply
// spit back the attenuationFactor (that was read into rw[3])
//
// called by Correct.ipf, ProtocolAsPanel.ipf, Transmission.ipf
//
// atten_err is one std. deviation, passed back by reference
Function AttenuationFactor(fileStr,lam,attenuation, atten_err)
        String fileStr
        Variable lam,attenuation, &atten_err  //    0 =< attenuation <= 100 (%) : where no attenuator stands for 0.
        
        Variable attenFactor=1
        
        // your code here
        attenFactor = 1- attenuation*0.01  //???Attenuate transmission

        // Change April 2011 - now returns error in atten trans
        atten_err = 0
        
        return(attenFactor)
End

//function called by the popups to get a file list of data that can be sorted
// this procedure simply removes the raw data files from the string - there
//can be lots of other junk present, but this is very fast...
//
// could also use the alternate procedure of keeping only file with the proper extension
//
// another possibility is to get a listing of the text files, but is unreliable on 
// Windows, where the data file must be .txt (and possibly OSX)
//
// called by FIT_Ops.ipf, NSORT.ipf, PlotUtils.ipf
//
Function/S ReducedDataFileList(ctrlName)
        String ctrlName

        String list="",newList="",item=""
        Variable num,ii
        
        //check for the path
        PathInfo catPathName
        if(V_Flag==0)
                DoAlert 0, "Data path does not exist - pick the data path from the button on the main panel"
                Return("")
        Endif
        
        list = IndexedFile(catpathName,-1,"????")
        num=ItemsInList(list,";")

        for(ii=(num-1);ii>=0;ii-=1)
                item = StringFromList(ii, list  ,";")
                //simply remove all that are not raw data files (SA1 SA2 SA3)
                //if( !stringmatch(item,"*HiResSANS*.xml") && !stringmatch(item,"*BioSANS*.xml"))
                        if( !stringmatch(item,".*") && !stringmatch(item,"*.pxp") && !stringmatch(item,"*.DIV"))                //eliminate mac "hidden" files, pxp, and div files
                                newlist += (item) + ";"    
                        endif
                //endif
        endfor
        //remove VAX version numbers
        newList = RemoveVersNumsFromList(newList)
        //sort
        newList = SortList(newList,";",0)

        return newlist
End

// returns a list of raw data files in the catPathName directory on disk
// - list is SEMICOLON-delimited
//
// does it the "cheap" way, simply finding the ".SAn" in the file name
// = does not check for proper byte length.
//
// called by PatchFiles.ipf, Tile_2D.ipf
//
Function/S GetRawDataFileList()
        
        //make sure that path exists
        PathInfo catPathName
        if (V_flag == 0)
                Abort "Folder path does not exist - use Pick Path button on Main Panel"
        Endif
        
        String list=IndexedFile(catPathName,-1,"????")
        String newList="",item=""
        Variable num=ItemsInList(list,";"),ii
        for(ii=0;ii<num;ii+=1)
                item = StringFromList(ii, list  ,";")
                if( stringmatch(item,"*.xml") )
                        if (CheckIfRawData(S_path+item) >0)
                                newlist += item + ";"
                        endif
                endif
                // if condition is in here twice, not sure why since they are both "*.xml"
//              if( stringmatch(item,"*.xml") )
//                      if (CheckIfRawData(S_path+item) >0)
//                              newlist += item + ";"
//                      endif
//              endif
        endfor
        newList = SortList(newList,";",0)
        return(newList)
End

//**********************
// 2D resolution function calculation - in terms of X and Y
//
// based on notes from David Mildner, 2008
//
// the final NCNR version is located in NCNR_Utils.ipf
//
Function/S get2DResolution(inQ,phi,lambda,lambdaWidth,DDet,apOff,S1,S2,L1,L2,BS,del_r,usingLenses,r_dist,SigmaQX,SigmaQY,fSubS)
        Variable inQ, phi,lambda, lambdaWidth, DDet, apOff, S1, S2, L1, L2, BS, del_r,usingLenses,r_dist
        Variable &SigmaQX,&SigmaQY,&fSubS               //these are the output quantities at the input Q value
        
        return("Function Empty")
End




// Return the filename that represents the previous or next file.
// Input is current filename and increment. 
// Increment should be -1 or 1
// -1 => previous file
// 1 => next file
Function/S GetPrevNextRawFile(curfilename, prevnext)
        String curfilename
        Variable prevnext

        String filename
        
        //get the run number
        Variable num = GetRunNumFromFile(curfilename)
                
        //find the next specified file by number
        fileName = FindPrevNextRawFile(curfilename, prevnext)

        if(cmpstr(fileName,"")==0)
                //null return, do nothing
                fileName = FindFileFromRunNumber(num)
        Endif

        //print "in FU "+filename

        Return filename
End

// Find next or previous file name w/ current file name given.
// Sort the list of files and get the next/previous file name.
Function/S FindPrevNextRawFile(curfilename, prevnext)
        String curfilename
        Variable prevnext
        
        String fullName="",partialName="",item="", list=""
        Variable numItems,isRAW
                        
        //make sure that path exists
        PathInfo catPathName
        String path = S_path
        
        if (V_flag == 0)
                Abort "folder path does not exist - use Pick Path button"
        Endif

        
        list = SortList(IndexedFile(catPathName,-1,"????"),";") //get all files in folder and make sure it is sorted.
        
        //find (the) one with the number in the run # location in the name

        numItems = ItemsInList(list,";")                //get the new number of items in the list
        //index of curfilename
        Variable index = WhichListItem(curfilename,list,";",0,0)
        //get the prenextitem in the list
        item = StringFromList(index+prevnext, list  ,";")
        partialName = FindValidFileName(item)
        
        if(strlen(partialName) != 0)            //non-null return from FindValidFileName()
                fullName = path + partialName
                //check if RAW, if so,this must be the file!
                isRAW = CheckIfRawData(fullName)
                if(isRaw)
                        //stop here
                        return(fullname)
                Endif
        Endif

        print "Please type 'scan number(s)' from your file name..."
        Return ("")     //null return if file not found in list 
End