source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/NCNR_Utils.ipf @ 857

#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=128
        Variable/G root:myGlobals:gNPixelsY=128
        
        // as of Jan2008, detector pixel sizes are read directly from the file header, so they MUST
        // be set correctly in instr.cfg
        Variable/G root:myGlobals:PixelResNG3_ILL = 1.0         //pixel resolution in cm
        Variable/G root:myGlobals:PixelResNG5_ILL = 1.0
        Variable/G root:myGlobals:PixelResNG7_ILL = 1.0
        Variable/G root:myGlobals:PixelResNG3_ORNL = 0.5
        Variable/G root:myGlobals:PixelResNG5_ORNL = 0.5
        Variable/G root:myGlobals:PixelResNG7_ORNL = 0.5
        Variable/G root:myGlobals:PixelResDefault = 0.5
        
        Variable/G root:myGlobals:DeadtimeNG3_ILL = 3.0e-6              //deadtime in seconds
        Variable/G root:myGlobals:DeadtimeNG5_ILL = 3.0e-6
        Variable/G root:myGlobals:DeadtimeNG7_ILL = 3.0e-6
        Variable/G root:myGlobals:DeadtimeNG3_ORNL_VAX = 3.4e-6         //pre - 23-JUL-2009 used VAX
        Variable/G root:myGlobals:DeadtimeNG3_ORNL_ICE = 1.5e-6         //post - 23-JUL-2009 used ICE
        Variable/G root:myGlobals:DeadtimeNG5_ORNL = 0.6e-6                     //as of 9 MAY 2002
        Variable/G root:myGlobals:DeadtimeNG7_ORNL_VAX = 3.4e-6         //pre 25-FEB-2010 used VAX
        Variable/G root:myGlobals:DeadtimeNG7_ORNL_ICE = 2.3e-6         //post 25-FEB-2010 used ICE
        Variable/G root:myGlobals:DeadtimeDefault = 3.4e-6
        
        //new 11APR07
        Variable/G root:myGlobals:BeamstopXTol = -8                     // (cm) is BS Xpos is -5 cm or less, it's a trans measurement
        // sample aperture offset is NOT stored in the VAX header, but it should be
        // - when it is, remove the global and write an accessor AND make a place for 
        // it in the RealsRead 
        Variable/G root:myGlobals:apOff = 5.0                           // (cm) distance from sample aperture to sample position

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)


// more readable method for calculating the variance in Q
// EXCEPT - this is calculated for Qo, NOT qBar
// (otherwise, they are nearly equivalent, except for close to the beam stop)
//      Variable kap,a_val,a_val_l2,m_h
//      g = 981.0                               //gravity acceleration [cm/s^2]
//      m_h     = 252.8                 // m/h [=] s/cm^2
//      
//      kap = 2*pi/lambda
//      a_val = L2*(L1+L2)*g/2*(m_h)^2
//      a_val_L2 = a_val/L2*1e-16               //convert 1/cm^2 to 1/A^2
//
//      sigmaQ = 0
//      sigmaQ = 3*(S1/L1)^2
//      
//      if(usingLenses != 0)
//              sigmaQ += 2*(S2/lp)^2*(lambdaWidth)^2   //2nd term w/ lenses
//      else    
//              sigmaQ += 2*(S2/lp)^2                                           //2nd term w/ no lenses
//      endif
//      
//      sigmaQ += (del_r/L2)^2
//      sigmaQ += 2*(r0/L2)^2*(lambdaWidth)^2
//      sigmaQ += 4*(a_val_l2)^2*lambda^4*(lambdaWidth)^2
//      
//      sigmaQ *= kap^2/12
//      sigmaQ = sqrt(sigmaQ)


        results = "success"
        Return results
End


//
//**********************
// 2D resolution function calculation - ***NOT*** in terms of X and Y
// but written in terms of Parallel and perpendicular to the Q vector at each point
//
// -- it is more naturally written this way since the 2D function is an ellipse with its major
// axis pointing in the direction of Q_parallel. Hence there is no way to properly define the 
// elliptical gaussian in terms of sigmaX and sigmaY
//
// For a full description of the gravity effect on the resolution, see:
//
//      "The effect of gravity on the resolution of small-angle neutron diffraction peaks"
//      D.F.R Mildner, J.G. Barker & S.R. Kline J. Appl. Cryst. (2011). 44, 1127-1129.
//      [ doi:10.1107/S0021889811033322 ]
//
//              2/17/12 SRK
//              NOTE: the first 2/3 of this code is the 1D code, copied here just to have the beam stop
//                              calculation here, if I decide to implement it. The real calculation is all at the 
//                              bottom and is quite compact
//
//
//
//
// - 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)
//
// passed values are read from RealsRead
// except DDet and apOff, which are set from globals before passing
//
// phi is the azimuthal angle, CCW from +x axis
// r_dist is the real-space distance from ctr of detector to QxQy pixel location
//
// MAR 2011 - removed the del_r terms, they don't apply since no bining is done to the 2D data
//
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
        
        //lots of calculation variables
        Variable a2, 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]
        Variable m_h    = 252.8                 // m/h [=] s/cm^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
        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

        Variable kap,a_val,a_val_L2,proj_DDet
        
        kap = 2*pi/lambda
        a_val = L2*(L1+L2)*g/2*(m_h)^2
        a_val_L2 = a_val/L2*1e-16               //convert 1/cm^2 to 1/A^2


        // the detector pixel is square, so correct for phi
        proj_DDet = DDet*cos(phi) + DDet*sin(phi)


///////// OLD - don't use ---
//in terms of Q_parallel ("x") and Q_perp ("y") - this works, since parallel is in the direction of Q and I
// can calculate that from the QxQy (I just need the projection)
//// for test case with no gravity, set a_val = 0
//// note that gravity has no wavelength dependence. the lambda^4 cancels out.
////
////    a_val = 0
////    a_val_l2 = 0
//
//      
//      // this is really sigma_Q_parallel
//      SigmaQX = kap*kap/12 * (3*(S1/L1)^2 + 3*(S2/LP)^2 + (proj_DDet/L2)^2 + (sin(phi))^2*8*(a_val_L2)^2*lambda^4*lambdaWidth^2)
//      SigmaQX += inQ*inQ*v_lambda
//
//      //this is really sigma_Q_perpendicular
//      proj_DDet = DDet*sin(phi) + DDet*cos(phi)               //not necessary, since DDet is the same in both X and Y directions
//
//      SigmaQY = kap*kap/12 * (3*(S1/L1)^2 + 3*(S2/LP)^2 + (proj_DDet/L2)^2 + (cos(phi))^2*8*(a_val_L2)^2*lambda^4*lambdaWidth^2)
//      
//      SigmaQX = sqrt(SigmaQX)
//      SigmaQy = sqrt(SigmaQY)
//      

/////////////////////////////////////////////////
/////   
//      ////// this is all new, inclusion of gravity effect into the parallel component
//       perpendicular component is purely geometric, no gravity component
//
// the shadow factor is calculated as above -so keep the above calculations, even though
// most of them are redundant.
//
        
////    //
        Variable yg_d,acc,sdd,ssd,lambda0,DL_L,sig_l
        Variable var_qlx,var_qly,var_ql,qx,qy,sig_perp,sig_para, sig_para_new
        
        G = 981.  //!   ACCELERATION OF GRAVITY, CM/SEC^2
        acc = vz_1              //      3.956E5 //!     CONVERT WAVELENGTH TO VELOCITY CM/SEC
        SDD = L2                //1317
        SSD = L1                //1627          //cm
        lambda0 = lambda                //              15
        DL_L = lambdaWidth              //0.236
        SIG_L = DL_L/sqrt(6)
        YG_d = -0.5*G*SDD*(SSD+SDD)*(LAMBDA0/acc)^2
/////   Print "DISTANCE BEAM FALLS DUE TO GRAVITY (CM) = ",YG
//              Print "Gravity q* = ",-2*pi/lambda0*2*yg_d/sdd
        
        sig_perp = kap*kap/12 * (3*(S1/L1)^2 + 3*(S2/LP)^2 + (proj_DDet/L2)^2)
        sig_perp = sqrt(sig_perp)
        
        
        FindQxQy(inQ,phi,qx,qy)

// missing a factor of 2 here, and the form is different than the paper, so re-write    
//      VAR_QLY = SIG_L^2 * (QY+4*PI*YG_d/(2*SDD*LAMBDA0))^2
//      VAR_QLX = (SIG_L*QX)^2
//      VAR_QL = VAR_QLY + VAR_QLX  //! WAVELENGTH CONTRIBUTION TO VARIANCE
//      sig_para = (sig_perp^2 + VAR_QL)^0.5
        
        // r_dist is passed in, [=]cm
        // from the paper
        a_val = 0.5*G*SDD*(SSD+SDD)*m_h^2 * 1e-16               //units now are cm /(A^2)
        
        var_QL = 1/6*(kap/SDD)^2*(DL_L)^2*(r_dist^2 - 4*r_dist*a_val*lambda0^2*sin(phi) + 4*a_val^2*lambda0^4)
        sig_para_new = (sig_perp^2 + VAR_QL)^0.5
        
        
///// return values PBR 
        SigmaQX = sig_para_new
        SigmaQy = sig_perp
        
////    
        
        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]
// detStr is passed as TextRead[9]
//
// *** as of Jan 2008, depricated. Now detector pixel sizes are read from the file header
// rw[10] = x size (mm); rw[13] = y size (mm)
//
Function xDetectorPixelResolution(fileStr,detStr)
        String fileStr,detStr
        
        Variable DDet
        String instr=fileStr[1,3]       //filestr is "[NGnSANSn] " or "[NGnSANSnn]" (11 characters total)
        
        NVAR PixelResNG3_ILL = root:myGlobals:PixelResNG3_ILL           //pixel resolution in cm
        NVAR PixelResNG5_ILL = root:myGlobals:PixelResNG5_ILL
        NVAR PixelResNG7_ILL = root:myGlobals:PixelResNG7_ILL
        NVAR PixelResNG3_ORNL = root:myGlobals:PixelResNG3_ORNL
        NVAR PixelResNG5_ORNL = root:myGlobals:PixelResNG5_ORNL
        NVAR PixelResNG7_ORNL = root:myGlobals:PixelResNG7_ORNL
        NVAR PixelResDefault = root:myGlobals:PixelResDefault
        
        strswitch(instr)
                case "NG3":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                DDet= PixelResNG3_ILL
                        else
                                DDet = PixelResNG3_ORNL //detector is ordella-type
                        endif
                        break
                case "NG5":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                DDet= PixelResNG5_ILL
                        else
                                DDet = PixelResNG5_ORNL //detector is ordella-type
                        endif
                        break
                case "NG7":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                DDet= PixelResNG7_ILL
                        else
                                DDet = PixelResNG7_ORNL //detector is ordella-type
                        endif
                        break
                default:                                                        
                        //return error?
                        DDet = PixelResDefault  //0.5 cm, typical for new ORNL detectors
        endswitch
        
        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]
// detStr is passed as TextRead[9]
// dateAndTimeStr is passed as TextRead[1]
//      --- if no date/time string is passed, ICE values are the default
//
// Due to the switch from VAX -> ICE, there were some hardware changes that led to
// a change in the effective detector dead time. The dead time was re-measured by J. Barker
// as follows:
//      Instrument                              Date measured                           deadtime constant
//      NG3                                                     DECEMBER 2009                           1.5 microseconds
//      NG7                                                     APRIL2010                                       2.3 microseconds
//
// The day of the switch to ICE on NG7 was 25-FEB-2010 (per J. Krzywon) 
// The day of the switch to ICE on NG3 was 23-JUL-2009 (per C. Gagnon)
//
// so any data after these dates is to use the new dead time constant. The switch is made on the
// data collection date.
//
//
Function DetectorDeadtime(fileStr,detStr,[dateAndTimeStr])
        String fileStr,detStr,dateAndTimeStr
        
        Variable deadtime
        String instr=fileStr[1,3]       //filestr is "[NGnSANSn] " or "[NGnSANSnn]" (11 characters total)
        
        NVAR DeadtimeNG3_ILL = root:myGlobals:DeadtimeNG3_ILL           //pixel resolution in cm
        NVAR DeadtimeNG5_ILL = root:myGlobals:DeadtimeNG5_ILL
        NVAR DeadtimeNG7_ILL = root:myGlobals:DeadtimeNG7_ILL
        NVAR DeadtimeNG3_ORNL_VAX = root:myGlobals:DeadtimeNG3_ORNL_VAX
        NVAR DeadtimeNG3_ORNL_ICE = root:myGlobals:DeadtimeNG3_ORNL_ICE
        NVAR DeadtimeNG5_ORNL = root:myGlobals:DeadtimeNG5_ORNL
        NVAR DeadtimeNG7_ORNL_VAX = root:myGlobals:DeadtimeNG7_ORNL_VAX
        NVAR DeadtimeNG7_ORNL_ICE = root:myGlobals:DeadtimeNG7_ORNL_ICE
        NVAR DeadtimeDefault = root:myGlobals:DeadtimeDefault
        
        // if no date string is passed, default to the ICE values
        if(strlen(dateAndTimeStr)==0)
                dateAndTimeStr = "01-JAN-2011"          //dummy date to force to ICE values
        endif
        
        
        Variable NG3_to_ICE = ConvertVAXDay2secs("23-JUL-2009")
        Variable NG7_to_ICE = ConvertVAXDay2secs("25-FEB-2010")
        Variable fileTime = ConvertVAXDay2secs(dateAndTimeStr)

        
        strswitch(instr)
                case "NG3":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                deadtime= DeadtimeNG3_ILL
                        else
                                if(fileTime > NG3_to_ICE)
                                        deadtime = DeadtimeNG3_ORNL_ICE //detector is ordella-type, using ICE hardware
                                else
                                        deadtime = DeadtimeNG3_ORNL_VAX //detector is ordella-type
                                endif
                        endif
                        break
                case "NG5":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                deadtime= DeadtimeNG5_ILL
                        else
                                deadtime = DeadtimeNG5_ORNL     //detector is ordella-type
                        endif
                        break
                case "NG7":
                        if(cmpstr(detStr, "ILL   ") == 0 )
                                deadtime= DeadtimeNG7_ILL
                        else
                                if(fileTime > NG7_to_ICE)
                                        deadtime = DeadtimeNG7_ORNL_ICE //detector is ordella-type, using ICE hardware
                                else
                                        deadtime = DeadtimeNG7_ORNL_VAX //detector is ordella-type
                                endif
                        endif
                        break
                default:                                                        
                        //return error?
                        deadtime = DeadtimeDefault      //1e-6 seconds, typical for new ORNL detectors
        endswitch
        
        return(deadtime)
End

// converts ONLY DD-MON-YYYY portion of the data collection time
// to a number of seconds from midnight on 1/1/1904, as Igor likes to do
//
// dateAndTime is the full string of "dd-mon-yyyy hh:mm:ss" as returned by the function
// getFileCreationDate(file)
//
Function ConvertVAXDay2secs(dateAndTime)
        string dateAndTime
        
        Variable day,yr,mon,time_secs
        string monStr

        sscanf dateandtime,"%d-%3s-%4d",day,monStr,yr
        mon = monStr2num(monStr)
//      print yr,mon,day
        time_secs = date2secs(yr,mon,day)

        return(time_secs)
end

// dd-mon-yyyy hh:mm:ss -> seconds
// the VAX uses 24 hr time for hh
//
Function ConvertVAXDateTime2secs(dateAndTime)
        string dateAndTime
        
        Variable day,yr,mon,hh,mm,ss,time_secs
        string str,monStr
        
        str=dateandtime
        sscanf str,"%d-%3s-%4d %d:%d:%d",day,monStr,yr,hh,mm,ss
        mon = monStr2num(monStr)
//      print yr,mon,day,hh,mm,ss
        time_secs = date2secs(yr,mon,day)
        time_secs += hh*3600 + mm*60 + ss


        return(time_secs)
end

// takes a month string and returns the corresponding number
//
Function monStr2num(monStr)
        String monStr
        
        String list=";JAN;FEB;MAR;APR;MAY;JUN;JUL;AUG;SEP;OCT;NOV;DEC;"
        return(WhichListItem(monStr, list ,";"))
end


//make a three character string of the run number
//Moved to facility utils
Function/S RunDigitString(num)
        Variable num
        
        String numStr=""
        if(num<10)
                numStr = "00"+num2str(num)
        else
                if(num<100)
                        numStr = "0"+num2str(num)
                else
                        numStr = num2str(num)
                Endif
        Endif
        //Print "numstr = ",numstr
        return(numstr)
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
//
// NCNR-specifc, does not really belong here - but it's a beta procedure used for the
// Combine Files Panel
//
Function/S GetPrefixStrFromFile(item)
        String item
        String invalid = ""     //"" is not a valid run prefix, since it's text
        Variable num=-1
        
        //find the "dot"
        String runStr=""
        Variable pos = strsearch(item,".",0)
        if(pos == -1)
                //"dot" not found
                return (invalid)
        else
                //found, skip the three characters preceeding it
                if (pos <=3)
                        //not enough characters
                        return (invalid)
                else
                        runStr = item[0,pos-4]
                        return (runStr)
                Endif
        Endif
End




/////VAX filename/Run number parsing utilities
//
// a collection of uilities for processing vax filenames
//and processing lists (especially for display in popup menus)
//
//required to correctly account for VAX supplied version numbers, which
//may or may not be removed by the ftp utility
//
// - parses lists of run numbers into real filenames
// - selects proper detector constants
//
//**************************
//
//given a filename of a SANS data filename of the form
//TTTTTnnn.SAn_TTT_Txxx
//returns the run number "nnn" as a number
//returns -1 as an invalid file number
//
// called by several ipfs
//
//
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 three characters preceeding it
                if (pos <=2)
                        //not enough characters
                        return (invalid)
                else
                        runStr = item[pos-3,pos-1]
                        //convert to a number
                        num = str2num(runStr)
                        //if valid, return it
                        if (num == NaN)
                                //3 characters were not a number
                                return (invalid)
                        else
                                //run was OK
                                return (num)
                        Endif
                Endif
        Endif
End

//given a filename of a SANS data filename of the form
//TTTTTnnn.SAn_TTT_Txxx
//returns the run number "nnn" as a STRING of THREE characters
//returns "ABC" as an invalid file number
//
// local function to aid in locating files by run number
//
Function/S GetRunNumStrFromFile(item)
        String item
        String invalid = "ABC"  //"ABC" is not a valid run number, since it's text
        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 three characters preceeding it
                if (pos <=2)
                        //not enough characters
                        return (invalid)
                else
                        runStr = item[pos-3,pos-1]
                        return (runStr)
                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
//the path "catPathName" used and is 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>999) || (num<=0) )
                //Print "error in  FindFileFromRunNumber(num), file number too large or too small"
                Return ("")
        Endif
        //make a three character string of the run number
        String numStr=""
        if(num<10)
                numStr = "00"+num2str(num)
        else
                if(num<100)
                        numStr = "0"+num2str(num)
                else
                        numStr = num2str(num)
                Endif
        Endif
        //Print "numstr = ",numstr
        
        //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) "TTTTTnnn.SAn_XXX_Tyyy"
                // 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 three character string
                        testStr = GetRunNumStrFromFile(item)
                        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
        Return ("")     //null return if file not found in list
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
        
        Variable refnum,totalBytes
        String testStr=""
        
        Open/R/T="????TEXT" refNum as fname
        if(strlen(s_filename) == 0)     //user cancel (/Z not used, so V_flag not set)
                return(0)
        endif
        
        //get the total number of bytes in the file
        FStatus refNum
        totalBytes = V_logEOF
        //Print totalBytes
        if(totalBytes < 100)
                Close refNum
                return(0)               //not a raw file
        endif
        FSetPos refNum,75
        FReadLine/N=3 refNum,testStr
        Close refNum
        
        if(totalBytes == 33316 && ( cmpstr(testStr,"RAW")==0 ||  cmpstr(testStr,"SIM")==0))
                //true, is raw data file
                Return(1)
        else
                //some other file
                Return(0)
        Endif
End

//function to test a file to see if it is a DIV file
//
// returns truth 0/1
//
// called by many procedures (both external and local)
//
Function CheckIfDIVData(fname)
        String fname
        

        Variable refnum,totalBytes
//      String testStr=""
        
        Open/R/T="????TEXT" refNum as fname
        if(strlen(s_filename) == 0)     //user cancel (/Z not used, so V_flag not set)
                return(0)
        endif
        
        //get the total number of bytes in the file
        FStatus refNum
        totalBytes = V_logEOF
        //Print totalBytes
        if(totalBytes < 100)
                Close refNum
                return(0)               //not a raw file
        endif
//      FSetPos refNum,75
//      FReadLine/N=3 refNum,testStr
        Close refNum
        
        if(totalBytes == 66116)         // && ( cmpstr(testStr,"RAW")==0 ||  cmpstr(testStr,"SIM")==0))
                //true, is raw data file
                Return(1)
        else
                //some other file
                Return(0)
        Endif

End

//function to check the header of a raw data file (full path specified by fname)
//checks the field of the x-position of the beamstop during data collection
//if the x-position is more negative (farther to the left) than xTol(input)
//the the beamstop is "out" and the file is a transmission run and not a scattering run
//xtol typically set at -5 (cm) - trans runs have bs(x) at -10 to -15 cm 
// function returns 1 if beamstop is out, 0 if beamstop is in
//
// tolerance is set as a global value "root:myGlobals:BeamstopXTol"
//
// called by Transmission.ipf, CatVSTable.ipf, NSORT.ipf
//
Function isTransFile(fName)
        String fname
        
        Variable refnum,xpos
        NVAR xTol = root:myGlobals:BeamstopXTol
        
        //pos = 369, read one real value
        
        SetDataFolder root:
        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
        String strToExecute=""
        // 1 R*4 value
        strToExecute = GBLoadStr + "/S=368/U=1" + "\"" + fname + "\""
        Execute strToExecute
        Wave w=$"root:tempGBWave0"
        xPos = w[0]
        KillWaves/Z w
        //Print "xPos = ",xpos
        
        if(xpos<=xTol)
                //xpos is farther left (more negative) than xtol (currently -5 cm)
                Return(1)
        else
                //some other file
                Return(0)
        Endif
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
//
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.
// - checks as is
// - adds ";vers" for possible VAX files
// - strips spaces
// - permutations of upper/lowercase
//
// added 11/99 - uppercase and lowercase versions of the file are tried, if necessary
// since from marquee, the filename field (textread[0]) must be used, and can be a mix of
// upper/lowercase letters, while the filename on the server (should) be all caps
// now makes repeated calls to ValidFileString()
//
// 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=""
        
        //try name with no changes - to allow for ABS files that have spaces in the names 12APR04
        retStr = ValidFileString(partialName)
        if(cmpstr(retStr,"") !=0)
                //non-null return
                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
// partialName;vers (to account for VAX filenaming conventions)
// The partial name is tried first with no version number
//
// *** 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
                //print "ii=",ii
        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
//
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
//
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
//
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 VAX filename, pull off the first 8 characters to make a valid
//file string that can be used for naming averaged 1-d files
//
// called by ProtocolAsPanel.ipf and Tile_2D.ipf
//
Function/S GetNameFromHeader(fullName)
        String fullName
        String temp, newName = ""
        Variable spc,ii=0
        
        //filename is 20 characters NNNNNxxx.SAn_NNN_NNN
        //want the first 8 characters, NNNNNxxx, then strip off any spaces at the beginning
        //NNNNN was entered as less than 5 characters
        //returns a null string if no name can be found
        do
                temp = fullname[ii,7]           //characters ii,7 of the name
                spc = strsearch(temp," ",0)
                if (spc == -1)
                        break           //no more spaces found
                endif
                ii+=1
        While(ii<8)
        
        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 
//
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
//
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)
                        //print runnum
                        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
//
Function/S ExpandNumRanges(list)
        String list
        
        String newList="",dash="-",item,str
        Variable num,ii,hasDash
        
        num=itemsinlist(list,",")
//      print num
        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
//
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


////////Transmission
//******************
//lookup tables for attenuator transmissions
//NG3 and NG7 attenuators are physically different, so the transmissions are slightly different
//NG1 - (8m SANS) is not supported
//
// new calibration done June 2007, John Barker
//
Proc MakeNG3AttenTable()

        NewDataFolder/O root:myGlobals:Attenuators
        //do explicitly to avoid data folder problems, redundant, but it must work without fail
        Variable num=10         //10 needed for tables after June 2007

        Make/O/N=(num) root:myGlobals:Attenuators:ng3att0
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att1
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att2
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att3
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att4
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att5
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att6
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att7
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att8
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att9
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att10
        
        // and a wave for the errors at each attenuation factor
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att0_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att1_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att2_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att3_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att4_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att5_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att6_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att7_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att8_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att9_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng3att10_err
        
        
        //each wave has 10 elements, the transmission of att# at the wavelengths 
        //lambda = 4,5,6,7,8,10,12,14,17,20 (4 A and 20 A are extrapolated values)
        Make/O/N=(num) root:myGlobals:Attenuators:ng3lambda={4,5,6,7,8,10,12,14,17,20}
        
        // new calibration done June 2007, John Barker
        root:myGlobals:Attenuators:ng3att0 = {1, 1, 1, 1, 1, 1, 1, 1, 1, 1 }
        root:myGlobals:Attenuators:ng3att1 = {0.444784,0.419,0.3935,0.3682,0.3492,0.3132,0.2936,0.2767,0.2477,0.22404}
        root:myGlobals:Attenuators:ng3att2 = {0.207506,0.1848,0.1629,0.1447,0.1292,0.1056,0.09263,0.08171,0.06656,0.0546552}
        root:myGlobals:Attenuators:ng3att3 = {0.092412,0.07746,0.06422,0.05379,0.04512,0.03321,0.02707,0.02237,0.01643,0.0121969}
        root:myGlobals:Attenuators:ng3att4 = {0.0417722,0.03302,0.02567,0.02036,0.01604,0.01067,0.00812,0.006316,0.00419,0.00282411}
        root:myGlobals:Attenuators:ng3att5 = {0.0187129,0.01397,0.01017,0.007591,0.005668,0.003377,0.002423,0.001771,0.001064,0.000651257}
        root:myGlobals:Attenuators:ng3att6 = {0.00851048,0.005984,0.004104,0.002888,0.002029,0.001098,0.0007419,0.0005141,0.000272833,0.000150624}
        root:myGlobals:Attenuators:ng3att7 = {0.00170757,0.001084,0.0006469,0.0004142,0.0002607,0.0001201,7.664e-05,4.06624e-05,1.77379e-05,7.30624e-06}
        root:myGlobals:Attenuators:ng3att8 = {0.000320057,0.0001918,0.0001025,6.085e-05,3.681e-05,1.835e-05,6.74002e-06,3.25288e-06,1.15321e-06,3.98173e-07}
        root:myGlobals:Attenuators:ng3att9 = {6.27682e-05,3.69e-05,1.908e-05,1.196e-05,8.738e-06,6.996e-06,6.2901e-07,2.60221e-07,7.49748e-08,2.08029e-08}
        root:myGlobals:Attenuators:ng3att10 = {1.40323e-05,8.51e-06,5.161e-06,4.4e-06,4.273e-06,1.88799e-07,5.87021e-08,2.08169e-08,4.8744e-09,1.08687e-09}
  
  // percent errors as measured, May 2007 values
  // zero error for zero attenuators, appropriate average values put in for unknown values
        root:myGlobals:Attenuators:ng3att0_err = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
        root:myGlobals:Attenuators:ng3att1_err = {0.15,0.142,0.154,0.183,0.221,0.328,0.136,0.13,0.163,0.15}
        root:myGlobals:Attenuators:ng3att2_err = {0.25,0.257,0.285,0.223,0.271,0.405,0.212,0.223,0.227,0.25}
        root:myGlobals:Attenuators:ng3att3_err = {0.3,0.295,0.329,0.263,0.323,0.495,0.307,0.28,0.277,0.3}
        root:myGlobals:Attenuators:ng3att4_err = {0.35,0.331,0.374,0.303,0.379,0.598,0.367,0.322,0.33,0.35}
        root:myGlobals:Attenuators:ng3att5_err = {0.4,0.365,0.418,0.355,0.454,0.745,0.411,0.367,0.485,0.4}
        root:myGlobals:Attenuators:ng3att6_err = {0.45,0.406,0.473,0.385,0.498,0.838,0.454,0.49,0.5,0.5}
        root:myGlobals:Attenuators:ng3att7_err = {0.6,0.554,0.692,0.425,0.562,0.991,0.715,0.8,0.8,0.8}
        root:myGlobals:Attenuators:ng3att8_err = {0.7,0.705,0.927,0.503,0.691,1.27,1,1,1,1}
        root:myGlobals:Attenuators:ng3att9_err = {1,0.862,1.172,0.799,1.104,1.891,1.5,1.5,1.5,1.5}
        root:myGlobals:Attenuators:ng3att10_err = {1.5,1.054,1.435,1.354,1.742,2,2,2,2,2}
  
  
  //old tables, pre-June 2007
//      Make/O/N=9 root:myGlobals:Attenuators:ng3lambda={5,6,7,8,10,12,14,17,20}
//      root:myGlobals:Attenuators:ng3att0 = {1, 1, 1, 1, 1, 1, 1, 1,1 }
//      root:myGlobals:Attenuators:ng3att1 = {0.421, 0.394, 0.371, 0.349, 0.316, 0.293, 0.274, 0.245,0.220}
//      root:myGlobals:Attenuators:ng3att2 = {0.187, 0.164, 0.145, 0.130, 0.106, 0.0916, 0.0808, 0.0651,0.0531}
//      root:myGlobals:Attenuators:ng3att3 = {0.0777, 0.0636, 0.0534, 0.0446, 0.0330, 0.0262, 0.0217, 0.0157 ,0.0116}
//      root:myGlobals:Attenuators:ng3att4 = {0.0328, 0.0252, 0.0195, 0.0156, 0.0104, 7.68e-3, 5.98e-3, 3.91e-3,0.00262}
//      root:myGlobals:Attenuators:ng3att5 = {0.0139, 9.94e-3, 7.34e-3, 5.44e-3, 3.29e-3, 2.25e-3, 1.66e-3, 9.95e-4, 6.12e-4}
//      root:myGlobals:Attenuators:ng3att6 = {5.95e-3, 3.97e-3, 2.77e-3, 1.95e-3, 1.06e-3, 6.81e-4, 4.71e-4, 2.59e-4 , 1.45e-4}
//      root:myGlobals:Attenuators:ng3att7 = {1.07e-3, 6.24e-4, 3.90e-4, 2.44e-4, 1.14e-4, 6.55e-5, 4.10e-5, 1.64e-5 , 7.26e-6}
//      root:myGlobals:Attenuators:ng3att8 = {1.90e-4, 9.84e-5, 5.60e-5, 3.25e-5, 1.55e-5, 6.60e-6, 3.42e-6, 1.04e-6 , 3.48e-7}
//      root:myGlobals:Attenuators:ng3att9 = {3.61e-5, 1.74e-5, 9.90e-6, 6.45e-6, 2.35e-6, 6.35e-7, 2.86e-7, 6.61e-8 , 1.73e-8}
//      root:myGlobals:Attenuators:ng3att10 = {7.60e-6, 3.99e-6, 2.96e-6, 2.03e-6, 3.34e-7, 6.11e-8, 2.39e-8, 4.19e-9 , 8.60e-10}

End

// new calibration done June 2007, John Barker
Proc MakeNG7AttenTable()

        NewDataFolder/O root:myGlobals:Attenuators
        
        Variable num=10         //10 needed for tables after June 2007
        
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att0
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att1
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att2
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att3
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att4
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att5
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att6
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att7
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att8
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att9
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att10
        
        // and a wave for the errors at each attenuation factor
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att0_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att1_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att2_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att3_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att4_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att5_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att6_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att7_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att8_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att9_err
        Make/O/N=(num) root:myGlobals:Attenuators:ng7att10_err  
        
        //NG7 wave has 10 elements, the transmission of att# at the wavelengths 
        //lambda =4, 5,6,7,8,10,12,14,17,20
        // note that some of the higher attenuations and ALL of the 4 A and 20A data is interpolated
        // none of these values are expected to be used in reality since the flux would be too low in practice
        Make/O/N=(num) root:myGlobals:Attenuators:ng7lambda={4,5,6,7,8,10,12,14,17,20}

// New calibration, June 2007, John Barker
        root:myGlobals:Attenuators:ng7att0 = {1, 1, 1, 1, 1, 1, 1, 1 ,1,1}      
        root:myGlobals:Attenuators:ng7att1 = {0.448656,0.4192,0.3925,0.3661,0.3458,0.3098,0.2922,0.2738,0.2544,0.251352}
        root:myGlobals:Attenuators:ng7att2 = {0.217193,0.1898,0.1682,0.148,0.1321,0.1076,0.0957,0.08485,0.07479,0.0735965}
        root:myGlobals:Attenuators:ng7att3 = {0.098019,0.07877,0.06611,0.05429,0.04548,0.03318,0.02798,0.0234,0.02004,0.0202492}
        root:myGlobals:Attenuators:ng7att4 = {0.0426904,0.03302,0.02617,0.02026,0.0158,0.01052,0.008327,0.006665,0.005745,0.00524807}
        root:myGlobals:Attenuators:ng7att5 = {0.0194353,0.01398,0.01037,0.0075496,0.005542,0.003339,0.002505,0.001936,0.001765,0.00165959}
        root:myGlobals:Attenuators:ng7att6 = {0.00971666,0.005979,0.004136,0.002848,0.001946,0.001079,0.0007717,0.000588,0.000487337,0.000447713}
        root:myGlobals:Attenuators:ng7att7 = {0.00207332,0.001054,0.0006462,0.0003957,0.0002368,0.0001111,7.642e-05,4.83076e-05,3.99401e-05,3.54814e-05}
        root:myGlobals:Attenuators:ng7att8 = {0.000397173,0.0001911,0.0001044,5.844e-05,3.236e-05,1.471e-05,6.88523e-06,4.06541e-06,3.27333e-06,2.81838e-06}
        root:myGlobals:Attenuators:ng7att9 = {9.43625e-05,3.557e-05,1.833e-05,1.014e-05,6.153e-06,1.64816e-06,6.42353e-07,3.42132e-07,2.68269e-07,2.2182e-07}
        root:myGlobals:Attenuators:ng7att10 = {2.1607e-05,7.521e-06,2.91221e-06,1.45252e-06,7.93451e-07,1.92309e-07,5.99279e-08,2.87928e-08,2.19862e-08,1.7559e-08}

  // percent errors as measured, May 2007 values
  // zero error for zero attenuators, appropriate average values put in for unknown values
        root:myGlobals:Attenuators:ng7att0_err = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0 }
        root:myGlobals:Attenuators:ng7att1_err = {0.2,0.169,0.1932,0.253,0.298,0.4871,0.238,0.245,0.332,0.3}
        root:myGlobals:Attenuators:ng7att2_err = {0.3,0.305,0.3551,0.306,0.37,0.6113,0.368,0.413,0.45,0.4}
        root:myGlobals:Attenuators:ng7att3_err = {0.4,0.355,0.4158,0.36,0.4461,0.7643,0.532,0.514,0.535,0.5}
        root:myGlobals:Attenuators:ng7att4_err = {0.45,0.402,0.4767,0.415,0.5292,0.9304,0.635,0.588,0.623,0.6}
        root:myGlobals:Attenuators:ng7att5_err = {0.5,0.447,0.5376,0.487,0.6391,1.169,0.708,0.665,0.851,0.8}
        root:myGlobals:Attenuators:ng7att6_err = {0.6,0.501,0.6136,0.528,0.8796,1.708,0.782,0.874,1,1}
        root:myGlobals:Attenuators:ng7att7_err = {0.8,0.697,0.9149,0.583,1.173,2.427,1.242,2,2,2}
        root:myGlobals:Attenuators:ng7att8_err = {1,0.898,1.24,0.696,1.577,3.412,3,3,3,3}
        root:myGlobals:Attenuators:ng7att9_err = {1.5,1.113,1.599,1.154,2.324,4.721,5,5,5,5}
        root:myGlobals:Attenuators:ng7att10_err = {1.5,1.493,5,5,5,5,5,5,5,5}  
  

// Pre-June 2007 calibration values - do not use these anymore  
////    root:myGlobals:Attenuators:ng7att0 = {1, 1, 1, 1, 1, 1, 1, 1 ,1}
////    root:myGlobals:Attenuators:ng7att1 = {0.418, 0.393, 0.369, 0.347, 0.313, 0.291, 0.271, 0.244, 0.219 }
////    root:myGlobals:Attenuators:ng7att2 = {0.189, 0.167, 0.148, 0.132, 0.109, 0.0945, 0.0830, 0.0681, 0.0560}
////    root:myGlobals:Attenuators:ng7att3 = {0.0784, 0.0651, 0.0541, 0.0456, 0.0340, 0.0273, 0.0223, 0.0164 , 0.0121}
////    root:myGlobals:Attenuators:ng7att4 = {0.0328, 0.0256, 0.0200, 0.0159, 0.0107, 7.98e-3, 6.14e-3, 4.09e-3 , 0.00274}
////    root:myGlobals:Attenuators:ng7att5 = {0.0139, 0.0101, 7.43e-3, 5.58e-3, 3.42e-3, 2.36e-3, 1.70e-3, 1.03e-3 , 6.27e-4}
////    root:myGlobals:Attenuators:ng7att6 = {5.90e-3, 4.07e-3, 2.79e-3, 1.99e-3, 1.11e-3, 7.13e-4, 4.91e-4, 2.59e-4 , 1.42e-4}
////    root:myGlobals:Attenuators:ng7att7 = {1.04e-3, 6.37e-4, 3.85e-4, 2.46e-4, 1.16e-4, 6.86e-5, 4.10e-5, 1.64e-5 ,7.02e-6}
////    root:myGlobals:Attenuators:ng7att8 = {1.90e-4, 1.03e-4, 5.71e-5, 3.44e-5, 1.65e-5, 6.60e-6, 3.42e-6, 1.04e-6 , 3.48e-7}
////    root:myGlobals:Attenuators:ng7att9 = {3.58e-5, 1.87e-5, 1.05e-5, 7.00e-6, 2.35e-6, 6.35e-7, 2.86e-7, 6.61e-8 , 1.73e-8}
////    root:myGlobals:Attenuators:ng7att10 = {7.76e-6, 4.56e-6, 3.25e-6, 2.03e-6, 3.34e-7, 6.11e-8, 2.39e-8, 4.19e-9, 8.60e-10}
End

//returns the transmission of the attenuator (at NG3) given the attenuator number
//which must be an integer(to select the wave) and given the wavelength.
//the wavelength may be any value between 4 and 20 (A), and is interpolated
//between calibrated wavelengths for a given attenuator
//
// Mar 2010 - abs() added to attStr to account for ICE reporting -0.0001 as an attenuator position, which truncates to "-0"
Function LookupAttenNG3(lambda,attenNo,atten_err)
        Variable lambda, attenNo, &atten_err
        
        Variable trans
        String attStr="root:myGlobals:Attenuators:ng3att"+num2str(trunc(abs(attenNo)))
        String attErrWStr="root:myGlobals:Attenuators:ng3att"+num2str(trunc(abs(attenNo)))+"_err"
        String lamStr = "root:myGlobals:Attenuators:ng3lambda"
        
        if(attenNo == 0)
                return (1)              //no attenuation, return trans == 1
        endif
        
        if( (lambda < 4) || (lambda > 20 ) )
                Abort "Wavelength out of calibration range (4,20). You must manually enter the absolute parameters"
        Endif
        
        if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) || !(WaveExists($attErrWStr)))
                Execute "MakeNG3AttenTable()"
        Endif
        //just in case creating the tables fails....
        if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) )
                Abort "Attenuator lookup waves could not be found. You must manually enter the absolute parameters"
        Endif
        
        //lookup the value by interpolating the wavelength
        //the attenuator must always be an integer
        Wave att = $attStr
        Wave attErrW = $attErrWStr
        Wave lam = $lamstr
        trans = interp(lambda,lam,att)
        atten_err = interp(lambda,lam,attErrW)

// the error in the tables is % error. return the standard deviation instead
        atten_err = trans*atten_err/100
                
//      Print "trans = ",trans
//      Print "trans err = ",atten_err
        
        return trans
End

//returns the transmission of the attenuator (at NG7) given the attenuator number
//which must be an integer(to select the wave) and given the wavelength.
//the wavelength may be any value between 4 and 20 (A), and is interpolated
//between calibrated wavelengths for a given attenuator
//
// this set of tables is also used for NG5 (NG1) SANS instrument - as the attenuator has never been calibrated
//
// local function
//
// Mar 2010 - abs() added to attStr to account for ICE reporting -0.0001 as an attenuator position, which truncates to "-0"
Function LookupAttenNG7(lambda,attenNo,atten_err)
        Variable lambda, attenNo, &atten_err
        
        Variable trans
        String attStr="root:myGlobals:Attenuators:ng7att"+num2str(trunc(abs(attenNo)))
        String attErrWStr="root:myGlobals:Attenuators:ng7att"+num2str(trunc(abs(attenNo)))+"_err"
        String lamStr = "root:myGlobals:Attenuators:ng7lambda"
        
        if(attenNo == 0)
                return (1)              //no attenuation, return trans == 1
        endif
        
        if( (lambda < 4) || (lambda > 20 ) )
                Abort "Wavelength out of calibration range (4,20). You must manually enter the absolute parameters"
        Endif
        
        if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) || !(WaveExists($attErrWStr)))
                Execute "MakeNG7AttenTable()"
        Endif
        //just in case creating the tables fails....
        if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) )
                Abort "Attenuator lookup waves could not be found. You must manually enter the absolute parameters"
        Endif
        
        //lookup the value by interpolating the wavelength
        //the attenuator must always be an integer
        Wave att = $attStr
        Wave attErrW = $attErrWStr
        Wave lam = $lamstr
        trans = interp(lambda,lam,att)
        atten_err = interp(lambda,lam,attErrW)

// the error in the tables is % error. return the standard deviation instead
        atten_err = trans*atten_err/100
        
//      Print "trans = ",trans
//      Print "trans err = ",atten_err
        
        return trans

End

// a utility function so that I can get the values from the command line
// since the atten_err is PBR
//
Function PrintAttenuation(instr,lam,attenNo)
        String instr
        Variable lam,attenNo
        
        Variable atten_err, attenFactor
        
        strswitch(instr)
                case "NG3":
                        attenFactor = LookupAttenNG3(lam,attenNo,atten_err)
                        break
                case "NG5":
                        //using NG7 lookup Table
                        attenFactor = LookupAttenNG7(lam,attenNo,atten_err)
                        break
                case "NG7":
                        attenFactor = LookupAttenNG7(lam,attenNo,atten_err)
                        break
                default:                                                        
                        //return error?
                        attenFactor=1
        endswitch

        Print "atten, err = ", attenFactor, atten_err
        
        return(0)
End



//returns the proper attenuation factor based on the instrument (NG3, NG5, or NG7)
//NG5 values are taken from the NG7 tables (there is very little difference in the
//values, and NG5 attenuators have not been calibrated (as of 8/01)
//
// filestr is passed from TextRead[3] = the default directory
// lam is passed from RealsRead[26]
// AttenNo is passed from ReaslRead[3]
//
// Attenuation factor as defined here is <= 1
//
// ORNL 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
//
//
// as of March 2011, returns the error (one standard deviation) in the attenuation factor as the last parameter, by reference
Function AttenuationFactor(fileStr,lam,attenNo,atten_err)
        String fileStr
        Variable lam,attenNo, &atten_err
        
        Variable attenFactor=1,loc
        String instr=fileStr[1,3]       //filestr is "[NGnSANSn] " or "[NGnSANSnn]" (11 characters total)
        
        strswitch(instr)
                case "NG3":
                        attenFactor = LookupAttenNG3(lam,attenNo,atten_err)
                        break
                case "NG5":
                        //using NG7 lookup Table
                        attenFactor = LookupAttenNG7(lam,attenNo,atten_err)
                        break
                case "NG7":
                        attenFactor = LookupAttenNG7(lam,attenNo,atten_err)
                        break
                default:                                                        
                        //return error?
                        attenFactor=1
        endswitch
//      print "instr, lambda, attenNo,attenFactor = ",instr,lam,attenNo,attenFactor
        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,"????")
        
        list = RemoveFromList(ListMatch(list,"*.SA1*",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.SA2*",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.SA3*",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,".*",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.pxp",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.DIV",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.GSP",";"), list, ";", 0)
        list = RemoveFromList(ListMatch(list,"*.MASK",";"), list, ";", 0)

        //remove VAX version numbers
        list = RemoveVersNumsFromList(List)
        //sort
        newList = SortList(List,";",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,"*.sa1*") )
                        newlist += item + ";"
                endif
                if( stringmatch(item,"*.sa2*") )
                        newlist += item + ";"
                endif
                if( stringmatch(item,"*.sa3*") )
                        newlist += item + ";"
                endif
                //print "ii=",ii
        endfor
        newList = SortList(newList,";",0)
        return(newList)
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 = FindFileFromRunNumber(num+prevnext)

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

//      print "in FU "+filename

        Return filename
End