Changeset 1202 for sans

Timestamp:

Aug 18, 2019 11:12:25 PM (3 years ago)

Author:

geishm

Message:

Completed port and checks from ANSTO IGOR 6 QUOKKA macros.

Location:

sans/Dev/branches/quokka_update

Files:

• NCNR_Igor_Procedures/NCNR_Package_Loader.ipf (modified) (1 diff)
• NCNR_User_Procedures/Common/NIST_XML_v40.ipf (modified) (2 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_DataReadWrite.ipf (modified) (14 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_Transmission.ipf (modified) (4 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_Utils.ipf (modified) (17 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_CatVSTable.ipf (modified) (13 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_Correct.ipf (modified) (8 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_DesmearingUtils.ipf (added)
• NCNR_User_Procedures/Reduction/SANS/QKK_Includes_ANSTO.ipf (modified) (3 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_LakeDesmearing_JB.ipf (added)
• NCNR_User_Procedures/Reduction/SANS/QKK_MainPanel.ipf (modified) (2 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_Menu.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/SANS/QKK_MultipleReduce.ipf (modified) (23 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_PatchFiles.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/SANS/QKK_ProDiv.ipf (modified) (3 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_ProtocolAsPanel.ipf (modified) (10 diffs)
• NCNR_User_Procedures/Reduction/SANS/QKK_WorkFileUtils.ipf (modified) (5 diffs)

sans/Dev/branches/quokka_update/NCNR_Igor_Procedures/NCNR_Package_Loader.ipf

@@ -188 +188 @@
                         Execute/P "COMPILEPROCEDURES "
                         Execute/P ("Initialize()")
+                        Execute/P ("Init_MainUSANS()")                                   
                         Execute/P ("DoIgorMenu \"Control\" \"Retrieve All Windows\"")
 

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Common/NIST_XML_v40.ipf

@@ -3 +3 @@
 #pragma IgorVersion=6.1
 
-
 //#if( exists("XmlOpenFile") && exists("NCNR_VSANS") )
-#if( exists("XmlOpenFile") && exists("NCNR_VSANS") )
+#if ( exists("XmlOpenFile") )
 
 #include "cansasXML", version >= 1.10
@@ -1105 +1104 @@
 
         Function WriteNISTXML(fileName, NISTfile)
-                String fileName, NISTfile
+                String fileName
+                Struct NISTXMLfile &NISTfile
+                
                 Abort  "XML function provided by XMLutils XOP is not available, get the XOP from : http://www.igorexchange.com/project/XMLutils (see http://www.smallangles.net/wgwiki/index.php/cansas1d_binding_IgorPro for details)"
                 RETURN(-6)
         End
-        
+
         Function WriteXMLWaves_W_Protocol(type,fullpath,dialog)
                 String type,fullpath

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_DataReadWrite.ipf

@@ -81 +81 @@
         
         Make/D/O/N=23 $"root:Packages:NIST:RAW:IntegersRead"
-        Make/D/O/N=52 $"root:Packages:NIST:RAW:RealsRead"
+        Make/D/O/N=57 $"root:Packages:NIST:RAW:RealsRead"
         Make/O/T/N=11 $"root:Packages:NIST:RAW:TextRead"
         Make/O/N=7 $"root:Packages:NIST:RAW:LogicalsRead"
@@ -103 +103 @@
         
         // user account identifier (currently used only for NCNR-specific operations)
-        textw[3]= ""
+        textw[3]= getInstrumentType(fname)
 
         // sample label
@@ -110 +110 @@
         // identifier of detector type, useful for setting detector constants
         //(currently used only for NCNR-specific operations)
-        textw[9]= ""
+        textw[9]= getDetectorType(fname)
 
         //total counting time in seconds
@@ -177 +177 @@
         realw[27] = getWavelengthSpread(fname)
         
+        // If lens configuraiton is used, put in a 1, otherwise 0
+        realw[28] = getLens(fname)
+        
         // beam stop X-position (motor reading, approximate cm from zero position)
         // currently NCNR-specific use to identify transmission measurements
         // you return 0
         realw[37] = 0
+        
+        // add the 4 stAl and stHe constants (scale and thickness by 2)
+        realw[52] = getDetectorParameter(fname, "stAlScale")
+        realw[53] = getDetectorParameter(fname, "stAlWindow")
+        realw[54] = getDetectorParameter(fname, "stHeScale")
+        realw[55] = getDetectorParameter(fname, "stHeWindow")
+        realw[56] = getDetectorParameter(fname, "deadtime")
 
 // the actual data array, dimensions are set as globals in 
@@ -437 +447 @@
         String destFolder
         Make/O/D/N=23 $("root:Packages:NIST:"+destFolder+":IntegersRead")
-        Make/O/D/N=52 $("root:Packages:NIST:"+destFolder+":RealsRead")
+        Make/O/D/N=57 $("root:Packages:NIST:"+destFolder+":RealsRead")
         Make/O/T/N=11 $("root:Packages:NIST:"+destFolder+":TextRead")
         
@@ -775 +785 @@
 
         Wave hmm_xy = $(dfName+":data:hmm_xy")
+        Wave hmm =  $(dfName+":data:hmm")
         
         //redimension /I /N = (dimsize(hmm_xy, 2), dimsize(hmm_xy, 1)), data
         //nha. Count arrays need to be floating point, since the data will be divided, normalised etc. 
-        redimension /N = (dimsize(hmm_xy, 2), dimsize(hmm_xy, 1)), data
-        data[][] = hmm_xy[0][q][p]
+
+        if (WaveExists(hmm_xy))
+                if (dimsize(hmm_xy, 2) == 0)
+                        redimension /N = (dimsize(hmm_xy, 1), dimsize(hmm_xy, 0)), data
+                        data[][] = hmm_xy[q][p]
+                else
+                        redimension /N = (dimsize(hmm_xy, 2), dimsize(hmm_xy, 1)), data
+                        data[][] = hmm_xy[0][q][p]
+                endif
+        elseif (WaveExists(hmm))
+                redimension /N = (dimsize(hmm, 3), dimsize(hmm, 2)), data
+                data[][] = hmm[0][0][q][p]
+        else
+                print "hmm or hmm_xy was not found"
+        endif
         
         //nha workaround. for wrongly dimensioned Quokka data 191x192
@@ -864 +888 @@
 End
 
+// get the detector effeciency parameters for the app. detector
+// ideally try to get it from the hdf file and use the 
+// defaults based on the detector type
+// TBD - the HDF parameter names need to be updated 
+Function getDetectorParameter(fname, pmtag)
+        String fname, pmtag
+        
+        String dfName = ""
+        hdfReadSimulated(fname, dfName)
+        
+        Variable value, scaleAl, thickAl, scaleHe, depthHe
+        Variable deadtime
+
+        String detType = getDetectorType(fname)
+        strswitch(detType)
+                case "BNL":
+                        deadtime = 24.2e-9
+                        scaleAl = 0.00967
+                        thickAl = 2.02
+                        scaleHe = 0.146
+                        depthHe = 4.0
+                        break
+                case "ORD":
+                default:
+                        deadtime = 2.14e-6
+                        scaleAl = 0.00967
+                        thickAl = 1.52
+                        scaleHe = 0.055553
+                        depthHe = 6.35
+        endswitch
+        strswitch(pmtag)
+                case "deadtime":
+                        value = getHdfParameterValue(fname, "deadtime", deadtime)
+                        break
+                case "stAlScale":
+                        value = scaleAl
+                        break
+                case "stAlWindow":
+                        value = getHdfParameterValue(fname, "al_window_thickness", thickAl)
+                        break                   
+                case "stHeScale":
+                        value = scaleHe
+                        break
+                case "stHeWindow":
+                        value = getHdfParameterValue(fname, "he_window_thickness", depthHe)
+                        break
+        endswitch
+        return (value)
+End     
+
+// instrument type 
+Function/S getInstrumentType(fpath)
+        String fpath
+        
+        // just uses the the first 3 characters of the fname
+        String fname = ParseFilePath(0, fpath, ":", 1, 0)
+        String instr = fname[0,2]
+        
+        return (instr)
+End
+
+// detector type for QKK is based on date
+// QKK switch from Ordela to BNL detector on 9-Nov-2018
+Function/S getDetectorType(fpath)
+        String fpath
+        
+        String detType = "---"
+        String instr = getInstrumentType(fpath)
+        If (cmpstr(instr, "QKK") == 0)
+                String dateStr = getFileCreationDate(fpath)
+
+                // convert string to igor date
+                Variable rDate = stringDate2Secs("2018-11-09 0:0:0")
+                Variable cDate = stringDate2Secs(dateStr)
+                if (cDate >= rDate)
+                        detType = "BNL"
+                else
+                        detType = "ORD"
+                endif
+        Endif
+        return detType
+End
+        
 // file creation date
 Function/S getFileCreationDate(fname)
@@ -903 +1010 @@
 End
 
+// expected format YYYY-MM-DD HH:MM:SS
+Function stringDate2Secs(dateStr)
+        String dateStr
+        Variable year, month, day, hours, mins, secs
+        String formatStr = "%d-%d-%d %d:%d:%d"
+        sscanf dateStr, formatStr, year, month, day, hours, mins, secs
+        Variable dt = date2Secs(year, month, day) + 3600 * hours + 60 * mins + secs
+        return dt
+End
+
+Function getHdfParameterValue(fname, pmtag, defvalue)
+        String fname, pmtag
+        Variable defvalue
+
+        String dfName = ""
+        hdfReadSimulated(fname, dfName)
+        
+        Variable value
+        Wave pmwave = $(dfName + ":" + pmtag)
+        if(WaveExists(pmwave))
+                value = pmwave[0]
+        else
+                print "Can't find parameter " + nameofwave(pmwave)
+                value = defvalue
+        endif   
+        
+        return (value)
+End
 
 //monitor count
 Function getMonitorCount(fname)
         String fname
-        Variable value
+        Variable value, bmTime, detTime
         Variable att, err
         string dfName = ""
@@ -928 +1063 @@
                 print "Can't find Monitor Count in " + fname
         endif   
+
+        //[geish]
+        //scale the monitor count to the detector acquisition time      
+        Wave wTime1 = $(dfName+":instrument:detector:time0") 
+        Wave wTime2 = $(dfName+":monitor:bm1_time") 
+        
+        if (WaveExists(wTime1) && WaveExists(wTime2))
+                detTime = wTime1[0]
+                bmTime = wTime2[0]
+                value =  round( value * detTime / bmTime )
+        else
+                print "Can't find Count Time in " + fname
+        endif
 
         // davidm
@@ -1254 +1402 @@
         // [davidm]
         hdfReadSimulated(fname, dfName)
-        if (exists(dfName+":sample:tc1:sensor:value") != 1)
+        
+        if(!WaveExists($(dfName+":sample:tc1:sensor:value")) && !WaveExists($(dfName+":sample:tc1:sensor:sensorValueA")) && !WaveExists($(dfName+":sample:tc1:Loop1:start_temperature")))
                 err = hdfRead(fname, dfName)
                 //err not handled here
         endif
-
-        Wave wSample_tc1_value = $(dfName+":sample:tc1:sensor:value")
-        if (WaveExists(wSample_tc1_value))
-                value = wSample_tc1_value[0]
-        else
-                print "Can't find Sample Rotation Angle in " + fname
+        
+        if (WaveExists($(dfName+":sample:tc1:sensor:value")))
+                Wave values = $(dfName+":sample:tc1:sensor:value")
+                value = values[0]
+        elseif(WaveExists($(dfName+":sample:tc1:sensor:sensorValueA")))
+                Wave values = $(dfName+":sample:tc1:sensor:sensorValueA")
+                value = values[0]
+        elseif(WaveExists($(dfName+":sample:tc1:Loop1:start_temperature")))
+                Wave values = $(dfName+":sample:tc1:Loop1:start_temperature")
+                value = values[0]
+        else
+                print "Can't find Temperature in " + fname
+        endif
+        
+        // [davidm]
+        //KillWaves wSample_tc1_value
+        
+        return(value)
+end
+
+// magnetic field strength
+Function getHtrSw(fname)
+        String fname
+        Variable value
+        
+        // your code returning value
+        variable err
+        string dfName = ""
+        
+        // [davidm]
+        hdfReadSimulated(fname, dfName)
+        
+        variable flag = 0
+        if (WaveExists($(dfName+":sample:ma1:htr_sw")))
+                flag = 1
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:htr_sw")))
+                flag = 1
+        endif
+        
+        if (flag == 0)
+                err = hdfRead(fname, dfName)
+                //err not handled here
+        endif
+        
+        if (WaveExists($(dfName+":sample:ma1:htr_sw")))
+                Wave values = $(dfName+":sample:ma1:htr_sw")
+                value = values[0]
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:htr_sw")))
+                Wave values = $(dfName+":sample:ma1:magnet:htr_sw")
+                value = values[0]
+        else
+                value = -1
+        endif
+
+        return(value)
+end
+Function getMSetpoint(fname)
+        String fname
+        Variable value
+        
+        // your code returning value
+        variable err
+        string dfName = ""
+        
+        // [davidm]
+        hdfReadSimulated(fname, dfName)
+        
+        variable flag = 0
+        if (WaveExists($(dfName+":sample:ma1:setpoint")))
+                flag = 1
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:setpoint")))
+                flag = 1
+        endif
+        
+        if (flag == 0)
+                err = hdfRead(fname, dfName)
+                //err not handled here
+        endif
+        
+        if (WaveExists($(dfName+":sample:ma1:setpoint")))
+                Wave values = $(dfName+":sample:ma1:setpoint")
+                value = values[0]
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:setpoint")))
+                Wave values = $(dfName+":sample:ma1:magnet:setpoint")
+                value = values[0]
+        else
+                print "Can't find Magnetic Field Setpoint in " + fname
+        endif
+
+        return(value)
+end
+Function getMField(fname)
+        String fname
+        Variable value
+        
+        // your code returning value
+        variable err
+        string dfName = ""
+        
+        // [davidm]
+        hdfReadSimulated(fname, dfName)
+        
+        variable flag = 0
+        if (WaveExists($(dfName+":sample:ma1:field")))
+                flag = 1
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:field")))
+                flag = 1
+        endif
+        
+        if (flag == 0)
+                err = hdfRead(fname, dfName)
+                //err not handled here
+        endif
+                
+        if (WaveExists($(dfName+":sample:ma1:field")))
+                Wave values = $(dfName+":sample:ma1:field")
+                value = values[0]
+        elseif (WaveExists($(dfName+":sample:ma1:magnet:field")))
+                Wave values = $(dfName+":sample:ma1:magnet:field")
+                value = values[0]
+        else
+                print "Can't find Magnetic Field Strength in " + fname
+        endif
+        
+        if (getHtrSw(fname) == 0)
+                value = getMSetpoint(fname)
+        endif
+        
+        // [davidm]
+        //KillWaves wSample_tc1_value
+        
+        return(value)
+end
+
+// electric field strength
+Function getEField(fname)
+        String fname
+        Variable value
+        
+        // your code returning value
+        variable err
+        string dfName = ""
+        
+        // [davidm]
+        hdfReadSimulated(fname, dfName)
+        
+        if(!WaveExists($(dfName+":sample:volts1")))
+                err = hdfRead(fname, dfName)
+                //err not handled here
+        endif
+        
+        if (WaveExists($(dfName+":sample:volts1")))
+                Wave values = $(dfName+":sample:volts1")
+                value = values[0]
+        else
+                print "Can't find Electric Field Strength in " + fname
         endif
         
@@ -1870 +2169 @@
 end
 
+
+
+
+//lens
+Function getLens(fname)
+        String fname
+        String str
+        Variable value = 0
+        // your code returning value
+        variable err
+        string dfName = ""
+        //err = hdfRead(fname, dfName)
+        //err not handled here
+
+        // [davidm]
+        hdfReadSimulated(fname, dfName)
+
+        variable flag = 0
+        if(WaveExists($(dfName+":instrument:parameters:GuideConfig")))  //canonical location
+                flag = 1
+        endif
+
+        if(flag == 0)
+                err = hdfRead(fname, dfName)
+                //err not handled here
+        endif   
+
+        if(WaveExists($(dfName+":instrument:parameters:GuideConfig")))  //canonical location
+                Wave/T guideConfig = $(dfName+":instrument:parameters:GuideConfig")
+                str = guideConfig[0]
+                value = StringMatch(str, "lens")
+        else
+                print "Can't find Guide Config in " + fname
+        endif
+        
+        KillWaves guideConfig
+        
+        return(value)
+end
+
+
 //wavelength spread (FWHM)
 Function WriteWavelengthDistrToHeader(fname,wavelengthSpread)
@@ -1948 +2288 @@
 end
 
-
-//total count time (seconds)
+//[geish]
+// getCountTime returns the total detector count time (seconds)
 Function getCountTime(fname)
         String fname
@@ -1960 +2300 @@
         
         // [davidm]
+        // [geish]
+        // 'time' is a keyword in IGOR and the HDF parameter 'time' is renamed
+        // to 'time0' after the HDF file is loaded
         hdfReadSimulated(fname, dfName)
-        if (exists(dfName+":monitor:bm1_time")!= 1)
+        if (exists(dfName+":instrument:detector:time0")!= 1)
                 err = hdfRead(fname, dfName)
                 //err not handled here
         endif
 
-        Wave wTime1 = $(dfName+":monitor:bm1_time") 
+        Wave wTime1 = $(dfName+":instrument:detector:time0") 
         
         if (WaveExists(wTime1))
@@ -2071 +2414 @@
 end
 
-// read the detector deadtime (in seconds)
-Function getDetectorDeadtime(fname)
-        String fname
-        
-        return(0)
-end
-
-// Write the detector deadtime to the file header (in seconds)
-Function WriteDeadtimeToHeader(fname,num)
-        String fname
-        Variable num
-        
-        return(0)
-End
 
 //reads the wavelength from a reduced data file (not very reliable)

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_Transmission.ipf

@@ -367 +367 @@
 
                 do
-//                      Execute  "ProgressWindow spin"
+                        //Execute  "ProgressWindow spin"
                         xpath_config = xpath_SampleEnv + "/config[" + num2str(jj) + "]" //there may be multiple config per report
 
@@ -733 +733 @@
         variable FilesAreMissing = 0
 
-//      Execute "ProgressWindow open, text=\"Loading Table...\""
+        //Execute "ProgressWindow open, text=\"Loading Table...\""
         
         ii = 0
@@ -741 +741 @@
                 emp_fname = S_path + EMP_Filenames[ii]
 
-//              Execute "ProgressWindow text=\"Loading Table...\n" + S_Filenames[ii] + "\""
+                //Execute "ProgressWindow text=\"Loading Table...\n" + S_Filenames[ii] + "\""
                 
                 InsertPoints ii,1,S_Labels
@@ -816 +816 @@
                 
                 ii+=1
-//              Execute  "ProgressWindow percent=" + Num2Str(100*ii/lastPoint)
+                //Execute  "ProgressWindow percent=" + Num2Str(100*ii/lastPoint)
                 
         while(ii<lastPoint)
         
-//      Execute "ProgressWindow close"
+        //Execute "ProgressWindow close"
         
         if (FilesAreMissing)

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_ANSTO_Utils.ipf

@@ -23 +23 @@
         Variable/G root:myGlobals:gNPixelsX=192                                 // number of 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 = 0.5                 //pixel resolution in cm
-        
-        Variable/G root:myGlobals:DeadtimeDefault = 2.14e-6 // 3.4e-6           //deadtime in seconds ???nha
 
         Variable/G root:myGlobals:apOff = 5.0           // (cm) distance from sample aperture to sample position
@@ -156 +151 @@
         
         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
-//
-Function DetectorDeadtime(fileStr,detStr)
-        String fileStr,detStr
-        
-        // [davidm]
-        nvar DeadtimeDefault = root:myGlobals:DeadtimeDefault
-
-        return DeadtimeDefault
-        
 End
 
@@ -690 +667 @@
 End
 
+Function/S CollapseRuns(lo, hi)
+        Variable lo, hi
+        
+        String seqn
+        if (lo < hi)
+                seqn = num2istr(lo) + "-" + num2istr(hi)
+        else
+                seqn = num2istr(lo)
+        endif
+        return seqn
+End
+
+// generates a comma separate sequence of runs using '-' 
+// collapse a sequential sequence of numbers    
+Function/S RunListToSequence(runs, emptyValue)
+        WAVE runs
+        Variable emptyValue
+        
+        Variable numRuns = numpnts(runs)
+        String  seqn = ""
+        if (numRuns == 0)
+                return (seqn)
+        endif
+        Variable ix, prv, lo, hi
+        prv = runs[0]
+        lo = runs[0]
+        hi = runs[0]
+        Variable nonEmpty = (hi != emptyValue)
+        for (ix = 1; ix < numRuns; ix += 1)
+                hi = runs[ix]
+                if (hi != emptyValue)
+                        nonEmpty = 1
+                endif
+                if (lo == emptyValue)   // leave blank and restart
+                        seqn += ","
+                        lo = hi
+                        prv = hi
+                elseif (hi == prv + 1)
+                        prv = hi                
+                else    
+                        seqn += CollapseRuns(lo, prv) + ","
+                        lo = hi
+                        prv = hi
+                endif
+        endfor
+        if ((lo != emptyValue) && (hi != emptyValue))
+                if (lo != hi)
+                        seqn += num2istr(lo) + "-" + num2istr(hi)
+                else
+                        seqn += num2istr(hi)
+                endif
+        endif
+        
+        if (nonEmpty)
+                return (seqn + ",")
+        else
+                return ""
+        endif   
+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***
@@ -709 +746 @@
         
         String newList="",item="",tempStr=""
-        Variable num,ii,runNum
+        Variable num,ii,runNum, checkAlerts = 1
         
         //expand number ranges, if any
@@ -725 +762 @@
                         //valid name, add to list
                         //Print "it's a file"
-                                if(strlen(newList)==0)
+                                if(ii==0)
                                         newList = tempStr
                                 else
                                         newList += "," + tempStr
                                 endif           
-                        else
+                else
                         //not a valid name
                         //is it a number?
@@ -736 +773 @@
                         //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("")
+                                //not a number -  maybe an error        
+                                if (checkAlerts)
+                                        DoAlert 1,"List item "+item+" is not a valid run number or filename. Leave items empty and continue?"
+                                        if (V_Flag == 1)
+                                                checkAlerts = 0
+                                        else
+                                                Abort "Aborting request. Fix run sequence and retry."
+                                        endif
+                                endif
+                                // comma is inserted before item so skip if first item
+                                if (ii > 0)
+                                        newList += ","
+                                endif
                         else
                                 //a run number or an error
@@ -747 +794 @@
                                         return("")
                                 else
-                                        newList += tempStr + ","
+                                        newList += "," + tempStr
                                 endif
                         endif
@@ -753 +800 @@
         endfor          //loop over all items in list
         
+        // check if the len newList matches list, if not pad with trailing commas
+        Variable n
+        For (n = itemsinlist(newList,","); n < num; n += 1)
+                newList += ","
+        EndFor
+
         return(newList)
 End
@@ -810 +863 @@
         endif
         for(ii=lo;ii<=hi;ii+=1)
-                numList += num2str(ii) + ","
+                numList += RunDigitString(ii) + ","
         endfor
         
@@ -855 +908 @@
         endif
         
-//      if( (lambda < 5) || (lambda > 5 ) )
-//              Abort "Wavelength out of calibration range (5A). You must manually enter the absolute parameters"
-//      Endif
-        
-        if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) )
-                Execute "MakeAttenTable()"
-        Endif
+        if(WaveExists($attStr))
+                KillWaves $attStr
+        endif
+        if(WaveExists($lamStr))
+                KillWaves $lamStr
+        endif
+        
+        Execute "MakeAttenTable()"
         //just in case creating the tables fails....
         if(!(WaveExists($attStr)) || !(WaveExists($lamStr)) )
@@ -867 +921 @@
         Endif
         
+        Wave att = $attStr
+        Wave lam = $lamstr
+        
+        // check range
+        Variable lamMin = WaveMin(lam)
+        Variable lamMax = WaveMax(lam)
+        if ((lambda < lamMin) || (lambda > lamMax))
+                Abort "Wavelength out of calibration range. 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 lam = $lamstr
-        //nha - commented below out until we have attenuation factors over multiple lambda values
-        //trans = interp(lambda,lam,att)
-        
-//      Print "trans = ",trans
-        //nha - delete this line when multiple lambda values
-        trans = att[0]
+        trans = interp(lambda,lam,att)
+        
+        print "lambda: ", lambda, " attenuator:", trans
         
         return trans
@@ -888 +945 @@
         //do explicitly to avoid data folder problems, redundant, but it must work without fail
 
-        //Quokka specific nha.
-        Variable num=12         
+        //Quokka specific
+        Variable num=9
         
         Make/O/N=(num) root:myGlobals:Attenuators:att0
@@ -903 +960 @@
         Make/O/N=(num) root:myGlobals:Attenuators:att10
         Make/O/N=(num) root:myGlobals:Attenuators:att11
-        
+
         // epg
         // note 5A only at this stage but other wavelengths as measured
         // these values have to be re-determined as were measured on time and not monitor counts
-        //Make/O/N=(num) root:myGlobals:Attenuators:lambda={5}
-        Make/O/N=(num) root:myGlobals:Attenuators:lambda={4.94} 
+        //Make/O/N=(num) root:myGlobals:Attenuators:lambda={4.94}       
+        //Make/O/N=(num) root:myGlobals:Attenuators:lambda={5, 6, 7, 8, 9}
+        Make/O/N=(num) root:myGlobals:Attenuators:lambda={2.55, 3.5, 4.501, 5, 6, 7, 8, 9, 10, 11, 12}
 
         //Quokka attenuator factors. 19/1/09 nha
@@ -929 +987 @@
         
         // [davidm] 19/12/2011 new attenuators
-        root:myGlobals:Attenuators:att0 = {1}
-        root:myGlobals:Attenuators:att1 = {0.493851474862975}
-        root:myGlobals:Attenuators:att2 = {0.172954232066555}
-        root:myGlobals:Attenuators:att3 = {0.0730333204657658}
-        root:myGlobals:Attenuators:att4 = {0.0338860321760628}
-        root:myGlobals:Attenuators:att5 = {0.0123806637881081}
-        root:myGlobals:Attenuators:att6 = {0.00547518298963546}
-        root:myGlobals:Attenuators:att7 = {0.00243389583698184}
-        root:myGlobals:Attenuators:att8 = {0.000833797438995085}
-        root:myGlobals:Attenuators:att9 = {0.000314495412044638}
-        root:myGlobals:Attenuators:att10 = {6.18092704241135e-05}
-        root:myGlobals:Attenuators:att11 = {1.1150347032482e-06}
+//      root:myGlobals:Attenuators:att0 = {1}
+//      root:myGlobals:Attenuators:att1 = {0.493851474862975}
+//      root:myGlobals:Attenuators:att2 = {0.172954232066555}
+//      root:myGlobals:Attenuators:att3 = {0.0730333204657658}
+//      root:myGlobals:Attenuators:att4 = {0.0338860321760628}
+//      root:myGlobals:Attenuators:att5 = {0.0123806637881081}
+//      root:myGlobals:Attenuators:att6 = {0.00547518298963546}
+//      root:myGlobals:Attenuators:att7 = {0.00243389583698184}
+//      root:myGlobals:Attenuators:att8 = {0.000833797438995085}
+//      root:myGlobals:Attenuators:att9 = {0.000314495412044638}
+//      root:myGlobals:Attenuators:att10 = {6.18092704241135e-05}
+//      root:myGlobals:Attenuators:att11 = {1.1150347032482e-06}
+        
+        // [davidm] 07/06/2013 new attenuators
+//      root:myGlobals:Attenuators:att0 = {1, 1, 1, 1, 1}
+//      root:myGlobals:Attenuators:att1 = {0.4851907714365690, 0.4690588000946720, 0.4476524578618430, 0.4242186524985810, 0.4064643249758360}
+//      root:myGlobals:Attenuators:att2 = {0.1749832052428250, 0.1533207360856960, 0.1334775844094730, 0.1193958669543340, 0.1076837185558930}
+//      root:myGlobals:Attenuators:att3 = {0.0740102935513494, 0.0607995713605108, 0.0502589403877112, 0.0423552403243808, 0.0367911673784652}
+//      root:myGlobals:Attenuators:att4 = {0.0338662640088968, 0.0263695325927806, 0.0206752375996348, 0.0163968351793478, 0.0136583575078807}
+//      root:myGlobals:Attenuators:att5 = {0.0129316048762597, 0.0092424708747183, 0.0068177214056475, 0.0050849439569495, 0.0040301873995815}
+//      root:myGlobals:Attenuators:att6 = {0.0057659775936329, 0.0038824010252366, 0.0027324743768650, 0.0019309536935497, 0.0014790015704855}
+//      root:myGlobals:Attenuators:att7 = {0.0025701666721922, 0.0016193521455181, 0.0010771127904439, 0.0007309304781609, 0.0005396690171419}
+//      root:myGlobals:Attenuators:att8 = {0.0008805002197972, 0.0005182454618666, 0.0003263459159077, 0.0002160554020075, 0.0001648875531385}
+//      root:myGlobals:Attenuators:att9 = {0.0003360142267874, 0.0001881638518150, 0.0001174132554013, 0.0000835561000000, 0.0000673555000000}
+//      root:myGlobals:Attenuators:att10 = {0.0000724312302049, 0.0000424158975402, 0.0000320186000000, 0.0000281932718010, 0.0000260300000000}
+//      root:myGlobals:Attenuators:att11 = {0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032}
+
+        // [davidm] 06/09/2013 new attenuators
+//      root:myGlobals:Attenuators:att0 = {1, 1, 1, 1, 1, 1, 1, 1, 1}
+//      root:myGlobals:Attenuators:att1 = {0.5015120154857073, 0.4851907391153646, 0.4690588000946720, 0.4476524578618430, 0.4242186524985810, 0.4064643249758360, 0.3915825187818079, 0.383155417316738, 0.3691476334100751}
+//      root:myGlobals:Attenuators:att2 = {0.1879599996486973, 0.1749831534458974, 0.1533207360856960, 0.1334775844094730, 0.1193958669543340, 0.1076837185558930, 0.146780838516843, 0.09070379140896381, 0.08469695381015514}
+//      root:myGlobals:Attenuators:att3 = {0.0830522756360301, 0.07401023541505114, 0.0607995713605108, 0.0502589403877112, 0.0423552403243808, 0.0367911673784652, 0.09732611681072782, 0.02850777154582489, 0.02512618567498705}
+//      root:myGlobals:Attenuators:att4 = {0.04126295911722724, 0.03386620335224088, 0.0263695325927806, 0.0206752375996348, 0.0163968351793478, 0.0136583575078807, 0.07443250666451248, 0.009988519969243473, 0.008641262326618814}
+//      root:myGlobals:Attenuators:att5 = {0.01585079879042115, 0.01293154290526562, 0.0092424708747183, 0.0068177214056475, 0.0050849439569495, 0.0040301873995815, 0.02056800794367422, 0.00272693052867672, 0.002208661232545322}
+//      root:myGlobals:Attenuators:att6 = {0.007385904293214549, 0.005754264308460257, 0.0038824010252366, 0.0027324743768650, 0.0019309536935497, 0.0014790015704855, 0.007278118324039542, 0.0009569347878502309, 0.0007197877270150088}
+//      root:myGlobals:Attenuators:att7 = {0.003442395510483513, 0.002583673513066073, 0.0016193521455181, 0.0010771127904439, 0.0007309304781609, 0.0005396690171419, 0.002711562994361441, 0.0003282078764354223, 0.0002481189736315548}
+//      root:myGlobals:Attenuators:att8 = {0.001252411237481238, 0.0008803260406144675, 0.0005182454618666, 0.0003263459159077, 0.0002160554020075, 0.0001648875531385, 0.0007746800906738829, 9.65128643341844e-05, 6.892342768233427e-05}
+//      root:myGlobals:Attenuators:att9 = {0.0004894124083498131, 0.0003406723119465761, 0.0001881638518150, 0.0001174132554013, 0.0000835561000000, 0.0000673555000000, 0.0003052956213536012, 4.18080108490353e-05, 3.065566944060116e-05}
+//      root:myGlobals:Attenuators:att10 = {0.0001094104254873829, 7.344149189383619e-05, 0.0000424158975402, 0.0000320186000000, 0.0000281932718010, 0.0000260300000000, 0.000127680099859085, 2.112291309365988e-05, 1.57968144929931e-05}
+//      root:myGlobals:Attenuators:att11 = {9.569103942045486e-06, 1.66985e-06, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 6.459382963805258e-05, 1.168373206643029e-05, 9.114523175100284e-06}
+
+        // [davidm] 17/04/2015 new attenuators
+        root:myGlobals:Attenuators:att0 = {1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1}
+        root:myGlobals:Attenuators:att1 = {0.5833466663785198, 0.5445353434014982, 0.5015120154857073, 0.4851907391153646, 0.4690588000946720, 0.4476524578618430, 0.4242186524985810, 0.4064643249758360, 0.3915864257771861, 0.383155417316738, 0.3691476334100751}
+        root:myGlobals:Attenuators:att2 = {0.2639110962334992, 0.2212212220703998, 0.1879599996486973, 0.1749831534458974, 0.1533207360856960, 0.1334775844094730, 0.1193958669543340, 0.1076837185558930, 0.0978267819972345, 0.09070379140896381, 0.08469695381015514}
+        root:myGlobals:Attenuators:att3 = {0.1372597677635557, 0.1076917120035716, 0.0830522756360301, 0.07401023541505114, 0.0607995713605108, 0.0502589403877112, 0.0423552403243808, 0.0367911673784652, 0.0324241778063643, 0.02850777154582489, 0.02512618567498705}
+        root:myGlobals:Attenuators:att4 = {0.07647885821139964, 0.05518044441708623, 0.04126295911722724, 0.03386620335224088, 0.0263695325927806, 0.0206752375996348, 0.0163968351793478, 0.0136583575078807, 0.01239678492410995, 0.009988519969243473, 0.008641262326618814}
+        root:myGlobals:Attenuators:att5 = {0.03658821871096959, 0.02408611980401762, 0.01585079879042115, 0.01293154290526562, 0.0092424708747183, 0.0068177214056475, 0.0050849439569495, 0.0040301873995815, 0.003425615799080442, 0.00272693052867672, 0.002208661232545322}
+        root:myGlobals:Attenuators:att6 = {0.02005392374000794, 0.0120842415105319, 0.007385904293214549, 0.005754264308460257, 0.0038824010252366, 0.0027324743768650, 0.0019309536935497, 0.0014790015704855, 0.001212175587771235, 0.0009569347878502309, 0.0007197877270150088}
+        root:myGlobals:Attenuators:att7 = {0.0108062446668512, 0.006010377629875024, 0.003442395510483513, 0.002583673513066073, 0.0016193521455181, 0.0010771127904439, 0.0007309304781609, 0.0005396690171419, 0.0004516126724145509, 0.0003282078764354223, 0.0002481189736315548}
+        root:myGlobals:Attenuators:att8 = {0.004805949253881572, 0.002382365795428234, 0.001252411237481238, 0.0008803260406144675, 0.0005182454618666, 0.0003263459159077, 0.0002160554020075, 0.0001648875531385, 0.0001290234992670594, 9.65128643341844e-05, 6.892342768233427e-05}
+        root:myGlobals:Attenuators:att9 = {0.002296371755067186, 0.001040815202883871, 0.0004894124083498131, 0.0003406723119465761, 0.0001881638518150, 0.0001174132554013, 0.0000835561000000, 0.0000673555000000, 5.084719467062561e-05, 4.18080108490353e-05, 3.065566944060116e-05}
+        root:myGlobals:Attenuators:att10 = {0.0006618554731030182, 0.0002589844830011295, 0.0001094104254873829, 7.344149189383619e-05, 0.0000424158975402, 0.0000320186000000, 0.0000281932718010, 0.0000260300000000, 2.126520801155025e-05, 2.112291309365988e-05, 1.57968144929931e-05}
+        root:myGlobals:Attenuators:att11 = {4.646119982685115e-05, 1.701737969038749e-05, 9.569103942045486e-06, 1.66985e-06, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 0.0000011150347032, 1.075814653208927e-05, 1.168373206643029e-05, 9.114523175100284e-06}
 
 End
@@ -977 +1077 @@
                 item = StringFromList(ii, list  ,";")
                 //simply remove all that are not raw data files (SA1 SA2 SA3)
-                if( !stringmatch(item,"*.SA1*") && !stringmatch(item,"*.SA2*") && !stringmatch(item,"*.SA3*") )
-                        if( !stringmatch(item,".*") && !stringmatch(item,"*.pxp") && !stringmatch(item,"*.DIV"))                //eliminate mac "hidden" files, pxp, and div files
-                                newlist += item + ";"
+                // hdf and other file removed on 18th May 2017 by David and Jitendra
+                if( !stringmatch(item,"*.HDF") && !stringmatch(item,"*.XML") && !stringmatch(item,"*.CSV") && !stringmatch(item,"*.PDF") && !stringmatch(item,"*.BMP") && !stringmatch(item,"*.MAS") && !stringmatch(item,"*.DB"))
+                        if( !stringmatch(item,"*.SA1*") && !stringmatch(item,"*.SA2*") && !stringmatch(item,"*.SA3*") )
+                                if( !stringmatch(item,".*") && !stringmatch(item,"*.pxp") && !stringmatch(item,"*.DIV"))                //eliminate mac "hidden" files, pxp, and div files
+                                        newlist += item + ";"
+                                endif
                         endif
                 endif
@@ -1184 +1287 @@
         //For ANSTO
         Wave GSSD = $"root:myGlobals:CatVSHeaderInfo:SSD"
-        Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
+        //Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
         Wave/T GHDF = $"root:myGlobals:CatVSHeaderInfo:HDF"
         
@@ -1201 +1304 @@
         
                 case "SortFilenamesButton":
-                        Sort GFilenames, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GFilenames, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortLabelsButton":
-                        Sort GLabels, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GLabels, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortDateAndTimeButton":
-                        Sort GDateTime, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GDateTime, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortSSDButton":
-                        Sort GSSD, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GSSD, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortSDDButton":
-                        Sort GSDD, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GSDD, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortLambdaButton":
-                        Sort GLambda, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GLambda, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortCountTimButton":
-                        Sort GCntTime, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GCntTime, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortTotalCountsButton":
-                        Sort GTotCnts, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GTotCnts, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortCountRateButton":
-                        Sort GCntRate, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GCntRate, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortMonitorCountsButton":
-                        Sort GMonCnts, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GMonCnts, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortTransmissionButton":
-                        Sort GTransmission, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GTransmission, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
                         
                 case "SortThicknessButton":
-                        Sort GThickness, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GSICS, GHDF
+                        Sort GThickness, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens, GRunNumber, GIsTrans, GRot, GTemp, GField, GMCR, GHDF
                         break
         

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_CatVSTable.ipf

@@ -21 +21 @@
 //parsing the filenames in the list and (dispatching) to write out the 
 //appropriate information to the notebook window
-Function BuildCatVeryShortTable()
+Function BuildCatVeryShortTable(ctrlName)
+        String ctrlName
         
         Variable err
         Variable t1 = ticks
+        Variable reload = (cmpstr(ctrlName,"FileCatalogButton")==0)
         
         PathInfo catPathName
@@ -36 +38 @@
         DoWindow/F CatVSTable
         
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Filenames"
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Suffix"
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Labels"
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:DateAndTime"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:SDD"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Lambda"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:CntTime"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:TotCnts"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:CntRate"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:MonCnts"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Transmission"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Thickness"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:XCenter"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:YCenter"
-        Make/O/B/N=0 $"root:myGlobals:CatVSHeaderInfo:nGuides"
-        Make/O/B/N=0 $"root:myGlobals:CatVSHeaderInfo:NumAttens"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:RunNumber"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:IsTrans"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:RotAngle"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Temperature"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Field"
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:MCR"              //added Mar 2008
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Pos"              //added Mar 2010
-        //For ANSTO
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:SSD" // [davidm] for Quokka
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:SICS"     
-        Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:HDF"
-        
-        Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Reactorpower"       //only used for for ILL, June 2008,
+        If(V_Flag==0)
+                Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Filenames"
+                Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Suffix"
+                Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:Labels"
+                Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:DateAndTime"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:SDD"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Lambda"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:CntTime"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:TotCnts"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:CntRate"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:MonCnts"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Transmission"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Thickness"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:XCenter"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:YCenter"
+                Make/O/B/N=0 $"root:myGlobals:CatVSHeaderInfo:nGuides"
+                Make/O/B/N=0 $"root:myGlobals:CatVSHeaderInfo:NumAttens"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:RunNumber"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:IsTrans"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:RotAngle"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Temperature"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Field"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:MCR"              //added Mar 2008
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Pos"              //added Mar 2010
+                //For ANSTO
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:SSD" // [davidm] for Quokka
+                //Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:SICS"   
+                Make/O/T/N=0 $"root:myGlobals:CatVSHeaderInfo:HDF"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:M_Field"
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:E_Field"
+                
+                Make/O/D/N=0 $"root:myGlobals:CatVSHeaderInfo:Reactorpower"       //only used for for ILL, June 2008,
+        Endif
+        
         WAVE ReactorPower = $"root:myGlobals:CatVSHeaderInfo:Reactorpower"
 
@@ -92 +99 @@
         //For ANSTO
         WAVE SSD = $"root:myGlobals:CatVSHeaderInfo:SSD" // [davidm]
-        WAVE SICS = $"root:myGlobals:CatVSHeaderInfo:SICS"      
+        //WAVE SICS = $"root:myGlobals:CatVSHeaderInfo:SICS"    
         WAVE HDF = $"root:myGlobals:CatVSHeaderInfo:HDF"
+        WAVE M_Field = $"root:myGlobals:CatVSHeaderInfo:M_Field"
+        WAVE E_Field = $"root:myGlobals:CatVSHeaderInfo:E_Field"
+        
+        If (reload)
+                Variable rows = numpnts(Filenames) 
+                DeletePoints 0, rows, Filenames,Suffix,Labels,DateAndTime,SDD,Lambda,CntTime,TotCnts,CntRate,MonCnts,Transmission
+                DeletePoints 0, rows, Thickness,XCenter,YCenter,nGuides,NumAttens,RunNumber,IsTrans,RotAngle,Temperature,Field,MCR,Pos
+                DeletePoints 0, rows, SSD,HDF,M_Field,E_Field
+        Endif
         
         If(V_Flag==0)
@@ -109 +125 @@
                 ModifyTable width(:myGlobals:CatVSHeaderInfo:NumAttens)=30
                 ModifyTable width(:myGlobals:CatVSHeaderInfo:RotAngle)=50
-                ModifyTable width(:myGlobals:CatVSHeaderInfo:Field)=50
+                ModifyTable width(:myGlobals:CatVSHeaderInfo:Temperature)=70
+                //ModifyTable width(:myGlobals:CatVSHeaderInfo:Field)=50
                 ModifyTable width(:myGlobals:CatVSHeaderInfo:MCR)=50
 #if (exists("QUOKKA")==6)
                 //ANSTO
                 ModifyTable width(:myGlobals:CatVSHeaderInfo:SSD)=40 // [davidm]
-                ModifyTable width(:myGlobals:CatVSHeaderInfo:SICS)=80
-                ModifyTable width(:myGlobals:CatVSHeaderInfo:HDF)=40
+                //ModifyTable width(:myGlobals:CatVSHeaderInfo:SICS)=80
+                //ModifyTable width(:myGlobals:CatVSHeaderInfo:HDF)=40
+                ModifyTable width(:myGlobals:CatVSHeaderInfo:M_Field)=50
+                ModifyTable width(:myGlobals:CatVSHeaderInfo:E_Field)=50
 #endif          
                 
@@ -142 +161 @@
         //***version numbers have been removed***
         String str,fullName
-        Variable lastPoint
+        Variable lastPoint, loadFile
         ii=0
         
-//      Execute "ProgressWindow open, text=\"Loading Table...\""
+        //Execute "ProgressWindow open, text=\"Loading Table...\""
         
         Make/T/O/N=0 notRAWlist
+        
+        // If it is updating the file list then remove the non-RAW files otherwise the column lengths are not
+        // equal when the sort is invoked
+        Variable fileCount = numpnts(Filenames)
+        Variable rawCount = numpnts(Labels)
+        Variable notRAWcount = fileCount - rawCount
+        if (notRAWcount > 0)
+                InsertPoints 0,notRAWcount,notRAWlist
+                notRAWlist[0, notRAWcount-1] = Filenames[p+rawCount]
+                DeletePoints rawCount, notRAWcount, Filenames
+        endif   
+        
         do
         
@@ -165 +196 @@
                         Endif
                 else
-//                      Execute "ProgressWindow text=\"Loading Table...\n" + tempName + "\""
-                
                         //prepend path to tempName for read routine 
                         PathInfo catPathName
                         FullName = S_path + tempName
-                        //make sure the file is really a RAW data file
-                        ok = (numtype(str2num(partialName[0])) != 0) && CheckIfRawData(fullName) // first character needs to be a letter                
-                        if (!ok)
-                                //write to notebook that file was not a RAW SANS file
-                                lastPoint = numpnts(notRAWlist)
-                                InsertPoints lastPoint,1,notRAWlist
-                                notRAWlist[lastPoint]=tempname
+                        
+                        if (!reload) 
+                                FindValue/TEXT=tempName Filenames
+                                loadFile = (V_Value == -1)
                         else
-                                //go write the header information to the Notebook
-                                GetHeaderInfoToWave(fullName,tempName)
+                                loadFile = 1
+                        Endif
+                        if (loadFile)
+                                //Execute "ProgressWindow text=\"Loading Table...\n" + tempName + "\""
+                                                        
+                                //make sure the file is really a RAW data file
+                                ok = (numtype(str2num(partialName[0])) != 0) && CheckIfRawData(fullName) // first character needs to be a letter                
+                                if (!ok)
+                                        //write to notebook that file was not a RAW SANS file
+                                        lastPoint = numpnts(notRAWlist)
+                                        InsertPoints lastPoint,1,notRAWlist
+                                        notRAWlist[lastPoint]=tempname
+                                else
+                                        //go write the header information to the Notebook
+                                        GetHeaderInfoToWave(fullName,tempName)
+                                Endif
                         Endif
                 Endif
                 
                 ii+=1
-//              Execute  "ProgressWindow percent=" + Num2Str(100*ii/numitems)
+                //Execute  "ProgressWindow percent=" + Num2Str(100*ii/numitems)
                 
         while(ii<numitems)
@@ -192 +232 @@
         AppendNotRAWFiles(notRAWlist)   
         KillWaves/Z notRAWlist
-//      Execute "ProgressWindow close"
+        //Execute "ProgressWindow close"
 //
 //      Print "Total time (s) = ",(ticks - t1)/60.15
@@ -242 +282 @@
         //For ANSTO
         Wave GSSD = $"root:myGlobals:CatVSHeaderInfo:SSD"
-        Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
+        //Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
         Wave/T GHDF = $"root:myGlobals:CatVSHeaderInfo:HDF"
+        Wave GM_Field = $"root:myGlobals:CatVSHeaderInfo:M_Field"
+        Wave GE_Field = $"root:myGlobals:CatVSHeaderInfo:E_Field"
 
 #if (exists("ILL_D22")==6)
@@ -251 +293 @@
 #elif (exists("QUOKKA")==6)
     //ANSTO
-        Sort GFilenames, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens,GRunNumber,GIsTrans,GRot,GTemp,GField,GMCR, GSICS, GHDF
+        Sort GFilenames, GSuffix, GFilenames, GLabels, GDateTime, GSSD, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens,GRunNumber,GIsTrans,GRot,GTemp,GField,GMCR, GHDF, GM_Field, GE_Field // , GSICS
 #else
         Sort GSuffix, GSuffix, GFilenames, GLabels, GDateTime, GSDD, GLambda, GCntTime, GTotCnts, GCntRate, GMonCnts, GTransmission, GThickness, GXCenter, GYCenter, GNumAttens,GRunNumber,GIsTrans,GRot,GTemp,GField,GMCR
 #endif
-
 
         return(0)
@@ -285 +326 @@
         Wave Pos = $"root:myGlobals:CatVSHeaderInfo:Pos"
         Wave/Z ReactorPower = $"root:myGlobals:CatVSHeaderInfo:reactorpower"       //activate for ILL, June 08 (+ edit line)
-        Wave/Z SICS = $"root:myGlobals:CatVSHeaderInfo:SICS" // For ANSTO June 2010
+        //Wave/Z SICS = $"root:myGlobals:CatVSHeaderInfo:SICS" // For ANSTO June 2010
         Wave/Z HDF = $"root:myGlobals:CatVSHeaderInfo:HDF" // For ANSTO June 2010
+        Wave M_Field = $"root:myGlobals:CatVSHeaderInfo:M_Field" // For ANSTO June 2016
+        Wave E_Field = $"root:myGlobals:CatVSHeaderInfo:E_Field" // For ANSTO June 2016
         
 #if (exists("ILL_D22")==6)
@@ -299 +342 @@
 #elif (exists("QUOKKA")==6)
         //ANSTO
-        Edit/K=1 Filenames, Labels, DateAndTime, SSD, SDD, Lambda, CntTime, TotCnts, CntRate, MonCnts, Transmission, Thickness, XCenter, YCenter, NumAttens, RotAngle, Temperature, Field, MCR,SICS, HDF as "Data File Catalog"
+        Edit/K=1 Filenames, Labels, DateAndTime, SSD, SDD, Lambda, CntTime, TotCnts, CntRate, MonCnts, Transmission, Thickness, XCenter, YCenter, NumAttens, RotAngle, M_Field, E_Field, Temperature, MCR as "Data File Catalog"
 #else
         // HFIR or anything else
@@ -328 +371 @@
         //ANSTO
         Wave GSSD = $"root:myGlobals:CatVSHeaderInfo:SSD" // [davidm]
-        Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
+        //Wave/T GSICS = $"root:myGlobals:CatVSHeaderInfo:SICS"
         Wave/T GHDF = $"root:myGlobals:CatVSHeaderInfo:HDF"
+        Wave GM_Field = $"root:myGlobals:CatVSHeaderInfo:M_Field"
+        Wave GE_Field = $"root:myGlobals:CatVSHeaderInfo:E_Field"
         //END ANSTO
         Wave GSDD = $"root:myGlobals:CatVSHeaderInfo:SDD"
@@ -376 +421 @@
         
         #if (exists("QUOKKA")==6)
-                InsertPoints lastPoint,1,GSICS
-                GSICS[lastPoint]=getSICSVersion(fname)
+                //InsertPoints lastPoint,1,GSICS
+                //GSICS[lastPoint]=getSICSVersion(fname)
                         
                 //read the HDF version
                 InsertPoints lastPoint,1,GHDF
                 GHDF[lastPoint]=getHDFVersion(fname)
+                
+                // M_Field
+                InsertPoints lastPoint,1,GM_Field
+                GM_Field[lastPoint]=getMField(fname)
+                
+                // E_Field
+                InsertPoints lastPoint,1,GE_Field
+                GE_Field[lastPoint]=getEField(fname)
         #endif
                 

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_Correct.ipf

@@ -251 +251 @@
         WAVE cor_data=$"root:Packages:NIST:COR:data"
         WAVE/T cor_text=$"root:Packages:NIST:COR:textread"
+        NVAR emp_scale=$"root:Packages:NIST:EMP:scale"
         
         //get sam and bgd attenuation factors
@@ -315 +316 @@
         //do the subtraction
         fsam=1
+
         femp = tmonsam/tmonemp          //this should be ==1 since normalized files
+        femp *= emp_scale                       //user scale of the empty data
         fbgd = tmonsam/tmonbgd  //this should be ==1 since normalized files
         cor1 = fsam*sam_data/sam_attenFactor - fbgd*bgd_temp/bgd_attenFactor
@@ -424 +427 @@
         WAVE cor_data=$"root:Packages:NIST:COR:data"
         WAVE/T cor_text=$"root:Packages:NIST:COR:textread"
+        NVAR emp_scale=$"root:Packages:NIST:EMP:scale"
         
         //get sam and bgd attenuation factors
@@ -474 +478 @@
         fsam = 1
         femp = tmonsam/tmonemp          //this should be ==1 since normalized files
+        femp *= emp_scale                       // user defined scale factor
         
         cor1 = fsam*sam_data/sam_AttenFactor - femp*(tsam/temp)*emp_temp/emp_AttenFactor
@@ -549 +554 @@
         WAVE cor_data=$"root:Packages:NIST:COR:data"
         WAVE/T cor_text=$"root:Packages:NIST:COR:textread"
+        NVAR emp_scale=$"root:Packages:NIST:EMP:scale"
         
         //get sam and bgd attenuation factors
@@ -621 +627 @@
         fsam=1
         femp = tmonsam/tmonemp          //this should be ==1 since normalized files
+        femp *= emp_scale                       //user defined scale factor             
         fbgd = tmonsam/tmonbgd  //this should be ==1 since normalized files
         cor1 = fsam*sam_data/sam_attenFactor
@@ -743 +750 @@
         WAVE cor_data=$"root:Packages:NIST:COR:data"
         WAVE/T cor_text=$"root:Packages:NIST:COR:textread"
+        NVAR emp_scale=$"root:Packages:NIST:EMP:scale"
         
         //get sam and bgd attenuation factors (DRK irrelevant)
@@ -800 +808 @@
         fsam = 1
         femp = tmonsam/tmonemp          //this should be ==1 since normalized files
+        femp *= emp_scale                       //user defined scale factor
         
         cor1 = fsam*sam_data/sam_AttenFactor - femp*(tsam/temp)*emp_temp/emp_AttenFactor

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_Includes_ANSTO.ipf

@@ -20 +20 @@
 End
 
-
-
 #include "QKK_AvgGraphics"                      version>=5.0
 #include "QKK_Buttons"                          version>=5.0
@@ -39 +37 @@
 //#include "PlotUtils"                  version>=5.0
 //AJJ October 2008 - switch to shared file loader
+
 #include "PlotUtilsMacro_v40"
 #include "NIST_XML_v40"
@@ -83 +82 @@
 #include "WriteModelData_v40"
 
+// Added Desmearing functionality 
+#include "QKK_DesmearingUtils"
+#include "QKK_LakeDesmearing_JB"                                                  
 
 // a simple list of items to add to the Beta menu

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_MainPanel.ipf

@@ -155 +155 @@
 
         //BuildCatVeryShortNotebook()
-        BuildCatVeryShortTable()
+        BuildCatVeryShortTable(ctrlName)
 End
 
@@ -286 +286 @@
 Window Main_Panel()
         PauseUpdate; Silent 1           // building window...
-        NewPanel /W=(500,60,924,320) /K=2 as "SANS Reduction Controls"
+        NewPanel /W=(500,60,1015,320) /K=2 as "SANS Reduction Controls"
         ModifyPanel cbRGB=(65535,58981,27524)
         ModifyPanel fixedSize=1
 //////
 //on main portion of panel
-        Button MainButtonA,pos={9,8},size={74,20},title="Pick Path",proc=PickPath_MainButtonProc
+        Button MainButtonA,pos={5,8},size={80,20},title="Pick Path",proc=PickPath_MainButtonProc
         Button MainButtonA,help={"Pick the local data folder that contains the SANS data"}
-        Button MainButtonB,pos={92,8},size={74,20},proc=CatVShort_MainButtonProc,title="File Catalog"
-        Button MainButtonB,help={"This will generate a condensed CATalog table of all files in a specified local folder"}
+        Button FileCatalogButton,pos={90,8},size={80,20},proc=CatVShort_MainButtonProc,title="File Catalog"
+        Button FileCatalogButton,help={"This will generate a condensed CATalog table of all files in the specified local folder"}
+        Button MainButtonU,pos={175,8},size={80,20},proc=CatVShort_MainButtonProc,title="Refresh"
+        Button MainButtonU,help={"This will add any new files to the CATalog table."}
         // [davidm] create sort Button
-        Button MainButtonS,pos={175,8},size={74,20},proc=CatVShort_SortButtonProc,title="Sort Catalog"
+        Button MainButtonS,pos={260,8},size={80,20},proc=CatVShort_SortButtonProc,title="Sort Catalog"
         Button MainButtonS,help={"This will display a dialog to sort the CATalog"}
         
-        Button MainButtonC,pos={258,8},size={74,20},proc=HelpMainButtonProc,title="Help"
+        Button MainButtonC,pos={345,8},size={80,20},proc=HelpMainButtonProc,title="Help"
         Button MainButtonC,help={"Display the help file"}
-        Button MainButtonD,pos={341,8},size={74,20},proc=SR_OpenTracTicketPage,title="Feedback"
+        Button MainButtonD,pos={430,8},size={80,20},proc=SR_OpenTracTicketPage,title="Feedback"
         Button MainButtonD,help={"Submit bug reports or feature requests"}
         
-        TabControl MainTab,pos={7,49},size={410,202},tabLabel(0)="Raw Data",proc=MainTabProc
+        TabControl MainTab,pos={7,49},size={501,202},tabLabel(0)="Raw Data",proc=MainTabProc
         TabControl MainTab,tabLabel(1)="Reduction",tabLabel(2)="1-D Ops",tabLabel(3)="2-D Ops",tabLabel(4)="Misc Ops"
         TabControl MainTab,value=0

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_Menu.ipf

@@ -54 +54 @@
 End
 
+Menu "USANS"
+        "Desmear USANS Data",Desmear()
+End
 Function SANSHelp()
         DisplayHelpTopic/Z/K=1 "SANS Data Reduction Tutorial"

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_MultipleReduce.ipf

@@ -40 +40 @@
                 //no, create the folder and the globals
                 NewDataFolder/O root:myGlobals:MRED
-//              String/G root:myGlobals:MRED:gMRedMatchStr = "*"
                 PathInfo catPathName
                 If(V_flag==1)
@@ -48 +47 @@
                         String/G root:myGlobals:MRED:gCatPathStr = "no path selected"
                 endif
-                String/G root:myGlobals:MRED:gMRedList = "none"
+                String/G root:myGlobals:MRED:gMRedSampleList = "none"
+                String/G root:myGlobals:MRED:gMRedEmptyList = "none"
                 String/G root:myGlobals:MRED:gMRProtoList = "none"
-                String/G root:myGlobals:MRED:gFileNumList=""
-//              String/G root:myGlobals:MRED:gMRS1 = "no file selected"
-//              String/G root:myGlobals:MRED:gMRS2 = "no file selected"
-//              String/G root:myGlobals:MRED:gMRS3 = "no box selected"
-//              Variable/G root:myGlobals:MRED:gMRV1 =0
-//              Variable/G root:myGlobals:MRED:gMRV2 = 999
+                String/G root:myGlobals:MRED:gSampleRuns = ""
+                String/G root:myGlobals:MRED:gEmptyRuns = ""
+                String/G root:myGlobals:MRED:actSampleRuns = ""
+                String/G root:myGlobals:MRED:actEmptyRuns = ""
+                String/G root:myGLobals:MRED:gScaleEMP = ""
+                String/G root:myGlobals:MRED:actScaleEMP = ""
         Endif 
 End
@@ -62 +62 @@
 //
 Window Multiple_Reduce_Panel()
+
+        // Layout 
+        //
+        // [Pick Path] Path [      path selected      ] [?]
+        // ------------------------------------------------
+        // Sample Runs   [      sample runs ]
+        // Empty Runs    [      empty runs  ]
+        // ------------------------------------------------
+        // [Runs to Table] [SDD List] [Table to Runs]
+        // [Protocol]                   [Reduce All] [Done]
+        
         PauseUpdate; Silent 1           // building window...
-        NewPanel /W=(535,72,951,228) /K=1 as "Multiple File Reduction"
+        NewPanel /W=(535,72,955,237) /K=1 as "Multiple File Reduction"
         ModifyPanel cbRGB=(65535,49151,29490)
         ModifyPanel fixedSize=1
-        SetDrawLayer UserBack
-        DrawLine 7,30,422,30
+
         SetVariable PathDisplay,pos={77,7},size={300,13},title="Path"
         SetVariable PathDisplay,help={"This is the path to the folder that will be used to find the SANS data while reducing. If no files appear in the popup, make sure that this folder is set correctly"}
@@ -75 +85 @@
         Button helpButton,pos={385,3},size={25,20},proc=ShowMRHelp,title="?"
         Button helpButton,help={"Show the help file for reducing multiple files using the same protocol"}
-        PopupMenu MRFilesPopup,pos={3,72},size={167,19},proc=MRedPopMenuProc,title="File(s) to Reduce"
-        PopupMenu MRFilesPopup,help={"The displayed file is the one that will be reduced. The entire list will be reduced if \"Reduce All..\" is selected. \r If no items, or the wrong items appear, click on the popup to refresh."}
-        PopupMenu MRFilesPopup,mode=1,popvalue="none",value= #"root:myGlobals:MRED:gMRedList"
-        SetVariable MRList,pos={3,48},size={350,13},proc=FileNumberListProc,title="File number list: "
-        SetVariable MRList,help={"Enter a comma delimited list of file numbers to reduce. Ranges can be entered using a dash."}
-        SetVariable MRList,limits={-Inf,Inf,1},value= root:myGlobals:MRED:gFileNumList
-        Button ReduceAllButton,pos={3,128},size={180,20},proc=ReduceAllPopupFiles,title="Reduce All Files in Popup"
+
+        SetDrawLayer UserBack
+        DrawLine 4,30,416,30
+        
+        SetVariable MRSampleList,pos={10,48},size={350,13},proc=FileNumberListProc,title = "Sample Runs:"
+        SetVariable MRSampleList,help={"Enter a comma delimited list of file numbers to reduce. Ranges can be entered using a dash."}
+        SetVariable MRSampleList,limits={-Inf,Inf,1},value= root:myGlobals:MRED:gSampleRuns
+
+        SetVariable MREmptyList,pos={10,74},size={300,13},proc=FileNumberListProc,title = "Empty Runs:"
+        SetVariable MREmptyList,help={"Enter a comma delimited list of file numbers to reduce. Ranges can be entered using a dash."}
+        SetVariable MREmptyList,limits={-Inf,Inf,1},value= root:myGlobals:MRED:gEmptyRuns
+
+        SetVariable MRScaleEMP,pos={320,74},size={80,13},proc=FileNumberListProc,title = "Scale:"
+        SetVariable MRScaleEMP,help={"Scale to be applied to the empty runs."}
+        SetVariable MRScaleEMP,limits={-Inf,Inf,0},value= root:myGlobals:MRED:gScaleEMP
+        
+        SetDrawLayer UserBack
+        DrawLine 4,105,416,105
+        
+        PopupMenu MRProto_pop,pos={4,112},size={120,19},proc=MRProtoPopMenuProc,title="Protocol "
+        PopupMenu MRProto_pop,help={"All of the data files in the popup will be reduced using this protocol"}
+        PopupMenu MRProto_pop,mode=1,popvalue="none",value= #"root:myGlobals:MRED:gMRProtoList"         
+        Button ReductionTableBtn,pos={127,112},size={100,20},proc=ShowMRReductionTable,title="Runs to Table"
+        Button ReductionTableBtn,help={"Generates a table that shows the reduction files per row."}
+        Button sddList,pos={232,112},size={90,20},proc=ScatteringAtSDDTableButton,title="Files at SDD"
+        Button sddList,help={"Use this button to generate a table of scattering files at a given ample to detector distance."}
+        Button mapToRuns,pos={327,112},size={90,20},proc=MapTableToRuns,title="Table to Runs"
+        Button mapToRuns,help={"Accept the list of files to reduce."}   
+
+        //SetDrawLayer UserBack
+        //DrawLine 4,135,416,135
+        
+        Button ReduceAllButton,pos={232,140},size={120,20},proc=ReduceAllSampleFiles,title="Reduce All"
         Button ReduceAllButton,help={"This will reduce ALL of the files in the popup list, not just the top file."}
-        Button DoneButton,pos={280,128},size={110,20},proc=MRDoneButtonProc,title="Done Reducing"
+        Button DoneButton,pos={357,140},size={60,20},proc=MRDoneButtonProc,title="Done"
         Button DoneButton,help={"When done reducing files, this will close this control panel."}
-//      Button cat_short,pos={310,72},size={90,20},proc=DoCatShort,title="File Catalog"
-//      Button cat_short,help={"Use this button to generate a table with file header information. Very useful for identifying files."}
-//      Button show_cat_short,pos={280,98},size={120,20},proc=ShowCatShort_MRED,title="Show File Catalog"
-//      Button show_cat_short,help={"Use this button to bring the File Catalog window to the front."}
-        Button sddList,pos={280,72},size={120,20},proc=ScatteringAtSDDTableButton,title="Files at SDD List"
-        Button sddList,help={"Use this button to generate a table of scattering files at a given ample to detector distance."}
-        Button acceptList,pos={280,98},size={120,20},proc=AcceptMREDList,title="Accept List"
-        Button acceptList,help={"Accept the list of files to reduce."}
-        PopupMenu MRProto_pop,pos={3,98},size={119,19},proc=MRProtoPopMenuProc,title="Protocol "
-        PopupMenu MRProto_pop,help={"All of the data files in the popup will be reduced using this protocol"}
-        PopupMenu MRProto_pop,mode=1,popvalue="none",value= #"root:myGlobals:MRED:gMRProtoList"
+        
+
+
 EndMacro
 
@@ -109 +137 @@
 End
 
+Function/S RunToQuokkaFile(num)
+        Variable num
+        
+        String fname
+        sprintf fname, "QKK%07u.nx.hdf", num
+        return (fname)
+End
 
 //function takes a list of filenames (just the name, no path , no extension)
@@ -255 +290 @@
         String list = GetValidMRedPopupList()
 //      
-        String/G root:myGlobals:MRED:gMredList = list
+        String/G root:myGlobals:MRED:gMRedSampleList = list
         ControlUpdate MRFilesPopup
 
@@ -270 +305 @@
 
         String commaList="",semiList=""
-        SVAR numList=root:myGLobals:MRED:gFileNumList
+        SVAR numList=root:myGLobals:MRED:gSampleRuns
         
         commaList = ParseRunNumberList(numList)
@@ -321 +356 @@
         DoWindow/K Multiple_Reduce_Panel
         
-        DoWindow/K SDDTable     
+        DoWindow/K CatMRTable   
         KillDataFolder root:myGlobals:MRED
+End
+
+Function CreateMRTable()
+
+        Make/O/D/N=0 $"root:myGlobals:MRED:SampleRuns"
+        Make/O/T/N=0 $"root:myGlobals:MRED:EmptyRuns"
+        Make/O/T/N=0 $"root:myGlobals:MRED:Suffix"
+        Make/O/T/N=0 $"root:myGlobals:MRED:Labels"
+        Make/O/D/N=0 $"root:myGlobals:MRED:SDD"
+        Make/O/D/N=0 $"root:myGlobals:MRED:IsTrans"
+        Make/O/T/N=0 $"root:myGlobals:MRED:Scale"
+
+        SetDataFolder root:myGlobals:MRED
+        Edit SampleRuns, EmptyRuns, Scale, SDD, Labels as "Multiple Reduction Sequence"
+        DoWindow/C $"CatMRTable"
+        
+        ModifyTable format(SampleRuns)=1                //so that HFIR 8-digit numbers are interpreted correctly as integers
+        ModifyTable format(EmptyRuns)=1         //so that HFIR 8-digit numbers are interpreted correctly as integers
+        ModifyTable width(Scale)=40
+        ModifyTable width(SDD)=40
+        ModifyTable width(Labels)=180
+
+        ModifyTable width(Point)=0              //JUN04, remove point numbers - confuses users since point != run
+End
+
+Function ClearMRTable()
+
+        WAVE SampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        WAVE/T EmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        WAVE/T Suffix = $"root:myGlobals:MRED:Suffix"
+        WAVE/T Labels = $"root:myGlobals:MRED:Labels"
+        WAVE SDD = $"root:myGlobals:MRED:SDD"
+        WAVE IsTrans = $"root:myGlobals:MRED:IsTrans"
+        WAVE/T ScaleEMP = $"root:myGlobals:MRED:Scale"
+        
+        DeletePoints 0, numpnts(SampleRuns), SampleRuns
+        DeletePoints 0, numpnts(EmptyRuns), EmptyRuns   
+        DeletePoints 0, numpnts(ScaleEMP), ScaleEMP
+        DeletePoints 0, numpnts(Suffix), Suffix
+        DeletePoints 0, numpnts(Labels), Labels 
+        DeletePoints 0, numpnts(SDD), SDD
+        DeletePoints 0, numpnts(IsTrans), IsTrans       
+End
+
+Function ShowMRReductionTable(ctrlName) : ButtonControl
+        String ctrlName
+
+        // Builds a table that lists the reduction steps to be performed but 
+        // it needs the path to the data
+        Variable err
+        PathInfo catPathName
+        if(v_flag==0)
+                err = PickPath()                //sets the local path to the data (catPathName)
+                if(err)
+                        Abort "No path to data was selected, no catalog can be made - use PickPath button"
+                Endif
+        Endif
+        
+        DoWindow/F CatMRTable
+        
+        If(V_Flag==0)
+                CreateMRTable()
+        Else
+                ClearMRTable()
+        Endif
+        
+        // Get a list of the sample and empty files from the runs
+        String sampleCSV="",emptyCSV=""
+        SVAR sampleRuns=root:myGLobals:MRED:gSampleRuns
+        SVAR emptyRuns=root:myGLobals:MRED:gEmptyRuns
+        SVAR scaleEmpty=root:myGLobals:MRED:gScaleEMP
+        
+        // reset the act runs to test need for update
+        String/G root:myGlobals:MRED:actSampleRuns = sampleRuns
+        String/G root:myGlobals:MRED:actEmptyRuns = emptyRuns
+        String/G root:myGLobals:MRED:actScaleEMP = scaleEmpty
+        
+        sampleCSV = ParseRunNumberList(sampleRuns)
+        emptyCSV = ParseRunNumberList(emptyRuns)
+        
+        // If the runs are not empty and not equal raise a warning.
+        Variable numSamples = ItemsInList(sampleCSV,",")
+        Variable numEmpty = ItemsInList(emptyCSV,",")
+        if (numSamples == 0)
+                DoAlert 0,"Specify a valid set of samples runs to run this function"
+                Return(1)
+        Endif
+        Variable fillEmpty = 0
+        if (numEmpty > 0 && numEmpty != numSamples)
+                DoAlert 1,"No 1-1 mapping to the sample runs - fill empty runs with trailing value?"
+                fillEmpty = (V_Flag == 1)
+        Endif
+        
+        Variable ix
+        String sfile, efile, spath, erun
+        String elast = ""
+        for (ix = 0; ix < numSamples; ix += 1)
+        
+                sfile = StringFromList(ix,sampleCSV,",")
+                efile = StringFromList(ix,emptyCSV,",")
+                If (ix < numEmpty)
+                        elast = efile
+                Else
+                        If (fillEmpty)
+                                efile = elast
+                        Endif
+                Endif
+                If (cmpstr(sfile,"") == 0)
+                        DoAlert 0, "Empty sample run included in the list, do you wish to continue?"
+                        If (V_Flag == 1)
+                                continue
+                        Else
+                                return (1)
+                        EndIf
+                Endif
+                PathInfo catPathName
+                spath = S_path + sfile
+
+                GetHeaderInfoToSDDWave(spath,sfile,efile,scaleEmpty)
+                
+        EndFor
+        
 End
 
@@ -331 +488 @@
 // also sets the current protocol to a global accessible to the list processing routine
 //
-Function ReduceAllPopupFiles(ctrlName) : ButtonControl
+Function ReduceAllSampleFiles(ctrlName) : ButtonControl
         String ctrlName
         
-        //popup (and global list) is a semicolon separated list of files, WITHOUT extensions
-        //transform this list into a COMMA delimited list of FULL filenames, and then they can be processed
-        
-        SVAR semiList = root:myGlobals:MRED:gMredList
-        
-        //process each item in the list, and generate commaList
-        Variable num = ItemsInList(semiList,";" )
-        Variable ii=0
-        String commaList = "",item = ""
-        do
-                item = StringFromList(ii, semiList  ,";" )
-
-                // commaList += RunNumberListToFilenameList(item) + ","
-                commaList += item + ","
+        // Firstly confirm that there is a list of files to be processed
+        DoWindow/F CatMRTable
+        If(V_Flag==0)
+                ShowMRReductionTable(ctrlName)
+        Else
+                // check if the runs sequence or scale has changed since the table was built
+                SVAR sampleRunsStr = root:myGlobals:MRED:gSampleRuns
+                SVAR emptyRunsStr = root:myGlobals:MRED:gEmptyRuns
+                SVAR scaleEMPStr = root:myGlobals:MRED:gScaleEMP
+                SVAR sampleTblStr = root:myGlobals:MRED:actSampleRuns
+                SVAR emptyTblStr = root:myGlobals:MRED:actEmptyRuns
+                SVAR scaleTableStr = root:myGlobals:MRED:actScaleEMP
                 
-                ii+=1
-        while(ii<num)
-        //080601 - send only the comma list of filenames, not full path:name    
-        //commaList = FullNameListFromFileList(commaList)               //gets the full file names (including extension) for each item in list
-
-        //get the selected protocol, and pass as a global
+                If (cmpstr(sampleRunsStr, sampleTblStr) != 0 || cmpstr(emptyRunsStr, emptyTblStr) != 0 || cmpstr(scaleEMPStr, scaleTableStr) != 0)
+                        ShowMRReductionTable(ctrlName)
+                Endif
+        Endif
+        
+        // Define a copy of the protocol after recovering the protocol from the popup.
+        // The protocol is just a text wave array. The copy just replaces the empty filename.
+        SetDataFolder root:myGlobals:Protocols
         ControlInfo MRProto_pop
         String protocolNameStr = S_Value
-        String/G root:myGlobals:Protocols:gMredProtoStr = "root:myGlobals:Protocols:"+protocolNameStr
-        
-        //also set this as the current protocol, for the function that writes the averaged waves
-        String/G root:myGlobals:Protocols:gProtoStr = protocolNameStr
-        
-        //reduce all the files in the list here, using the global protocol(the full reference)
-        //DoReduceList is found in MultipleReduce.ipf
-        DoReduceList(commaList)
-        
-        Return 0
+        String/G root:myGlobals:Protocols:gMRedProtoStr = "root:myGlobals:Protocols:" + protocolNameStr
+        SVAR baseProtocol = root:myGlobals:Protocols:gMRedProtoStr
+        
+        WAVE/T prot = $baseProtocol
+        Duplicate/O prot copyMRedProto
+        String/G root:myGlobals:Protocols:gProtoStr = NameOfWave(copyMRedProto)
+        String actProtStr = "root:myGlobals:Protocols:" + NameOfWave(copyMRedProto)
+        WAVE/T actProt = $actProtStr
+        
+        // Set up the list of files from the table
+        WAVE SampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        WAVE/T EmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        WAVE/T ScaleEMP = $"root:myGlobals:MRED:Scale"
+        
+        // Run through the list of sample files
+        Variable ix
+        Variable numScale = numpnts(ScaleEMP)
+        Variable numSample = numpnts(SampleRuns)
+        for (ix = 0; ix < numSample; ix += 1)
+        
+                String sfile = RunToQuokkaFile(SampleRuns[ix])
+                String efile = ""
+                String erun = EmptyRuns[ix]     
+                Variable scale = 1.0
+                
+                // check if an empty file is required by the protocol
+                // replace file name if "ask" or "", skip if "none"
+                if (cmpstr(prot[1],"ask") == 0 || cmpstr(prot[1],"") == 0)
+                        If (cmpstr(erun, "") != 0)
+                                efile = RunToQuokkaFile(str2num(erun))
+                        Endif
+                        if (cmpstr(efile,"") != 0)
+                                actProt[1] = efile
+                        else
+                                actProt[1] = prot[1]
+                        Endif
+                Else
+                        actProt[1] = prot[1]
+                Endif
+                // 
+                If (ix < numScale && cmpstr(ScaleEMP[ix],"") != 0)
+                        scale = str2num(ScaleEMP[ix])
+                        If (scale == NaN)
+                                DoAlert 0, "Invalid empty scale value in the list, continue with scale = 1?"
+                                If (V_Flag == 1)
+                                        scale = 1
+                                        continue
+                                Else
+                                        return (1)
+                                EndIf
+                        Endif
+                        actProt[7] = num2str(scale)
+                Else
+                        actProt[7] = prot[7]
+                Endif           
+                ExecuteProtocol(actProtStr, sfile)
+        EndFor
+        
+        return(0)
+        
 End
 
@@ -529 +736 @@
 Function ScatteringAtSDDTableButton(ctrlName)
         String ctrlName
+
+        Variable err
+        PathInfo catPathName
+        if(v_flag==0)
+                err = PickPath()                //sets the local path to the data (catPathName)
+                if(err)
+                        Abort "No path to data was selected, no catalog can be made - use PickPath button"
+                Endif
+        Endif
         
         Execute "CreateScatteringAtSDDTable()"
@@ -534 +750 @@
 End
 
-Function AcceptMREDList(ctrlName)
+Function MapTableToRuns(ctrlName)
         String ctrlName
         
-        SVAR/Z list = root:myGlobals:MRED:gFileNumList
-        if(SVAR_Exists(list)==0)                //check for myself
+        // maps the sample and empty in the table to the runs
+        SVAR/Z slist = root:myGlobals:MRED:gSampleRuns
+        SVAR/Z elist = root:myGLobals:MRED:gEmptyRuns
+        if(SVAR_Exists(slist)==0 || SVAR_Exists(elist) == 0)            //check for myself
                 DoAlert 0,"The Multiple Reduce Panel must be open for you to use this function"
                 Return(1)
         endif
         
-        // convert the wave to a comma-delimited List
-        wave/Z numW = $"root:myGlobals:MRED:RunNumber"
-        if(waveExists(numW)==0 || numpnts(numW)==0)
-                DoAlert 0, "Generate a list of files at a specific detector distance using the Files at SDD List button"
-                return(0)
-        Endif
-        
-        list = NumWave2IntegerCommaList(numW)
-        
-        //force an update If the SVAR exists, then the panel does too - MRED cleans up after itself when done
-        DoWindow/F Multiple_Reduce_Panel                        //bring to front
-        MRedPopMenuProc("MRFilesPopup",0,"")            //parse the list, pop the menu
-        
+        // convert the sample runs
+        Wave/Z sruns = $"root:myGlobals:MRED:SampleRuns"
+        slist = RunListToSequence(sruns, 0)
+        
+        // the empty runs is a string list so convert to a list of numbers and use 
+        // 0 as the empty value
+        Wave/T/Z eruns = $"root:myGlobals:MRED:EmptyRuns"
+        Variable ix, num = numpnts(eruns)
+        MAKE/U/O/N=(num) temp 
+        for (ix = 0; ix < num; ix += 1)
+                String run = eruns[ix]
+                if (cmpstr(run,"") != 0)
+                        temp[ix] = str2num(run)
+                else
+                        temp[ix] = 0
+                endif
+        endfor
+        elist = RunListToSequence(temp, 0)
+        
+        // copy the act run list to the table
+        String/G root:myGlobals:MRED:actSampleRuns = slist
+        String/G root:myGlobals:MRED:actEmptyRuns = elist
         
         return(0)
@@ -565 +792 @@
         
         NewDataFolder/O root:myGlobals:MRED
-        DoWindow/F SDDTable
-        
-        Make/O/T/N=0 $"root:myGlobals:MRED:Filenames"
-        Make/O/T/N=0 $"root:myGlobals:MRED:Suffix"
-        Make/O/T/N=0 $"root:myGlobals:MRED:Labels"
-        Make/O/D/N=0 $"root:myGlobals:MRED:SDD"
-        Make/O/D/N=0 $"root:myGlobals:MRED:RunNumber"
-        Make/O/D/N=0 $"root:myGlobals:MRED:IsTrans"
-
+        DoWindow/F CatMRTable
         If(V_Flag==0)
-                SetDataFolder root:myGlobals:MRED
-                Edit Labels, SDD, runNumber as "Scattering at SDD"
-                DoWindow/C $"SDDTable"
-                
-                ModifyTable width(SDD)=40
-                ModifyTable width(Labels)=180
-                ModifyTable format(RunNumber)=1         //so that HFIR 8-digit numbers are interpreted correctly as integers
-                
-                ModifyTable width(Point)=0              //JUN04, remove point numbers - confuses users since point != run
+                CreateMRTable()
                 SetDataFolder root:
+        Else
+                ClearMRTable()
         Endif
 
@@ -629 +842 @@
                         else
                                 //go write the header information to the Notebook
-                                GetHeaderInfoToSDDWave(fullName,tempName)
+                                GetHeaderInfoToSDDWave(fullName,tempName,"","")
+                                // add the scale factor
                         Endif
                 Endif
@@ -657 +871 @@
 Function RemoveLabeledFromSDDList(findThisStr)
         String findThisStr
-        Wave/T filenames = $"root:myGlobals:MRED:Filenames"
-        Wave/T suffix = $"root:myGlobals:MRED:Suffix"
-        Wave/T labels = $"root:myGlobals:MRED:Labels"
-        Wave sdd = $"root:myGlobals:MRED:SDD"
-        Wave runnum = $"root:myGlobals:MRED:RunNumber"
-        Wave isTrans = $"root:myGlobals:MRED:IsTrans"
+        WAVE SampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        WAVE/T EmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        WAVE/T Suffix = $"root:myGlobals:MRED:Suffix"
+        WAVE/T Labels = $"root:myGlobals:MRED:Labels"
+        WAVE SDD = $"root:myGlobals:MRED:SDD"
+        WAVE IsTrans = $"root:myGlobals:MRED:IsTrans"
         
         Variable num=numpnts(Labels),ii,loc
@@ -670 +884 @@
                 if(loc != -1)
                         Print "Remove w[ii] = ",num,"  ",labels[ii]
-                        DeletePoints ii, 1, filenames,suffix,labels,sdd,runnum,isTrans
+                        DeletePoints ii, 1, SampleRuns,EmptyRuns,Suffix,Labels,SDD,IsTrans
                 endif
                 ii-=1
@@ -682 +896 @@
         Variable tSDD
         
-        Wave/T filenames = $"root:myGlobals:MRED:Filenames"
-        Wave/T suffix = $"root:myGlobals:MRED:Suffix"
-        Wave/T labels = $"root:myGlobals:MRED:Labels"
-        Wave sdd = $"root:myGlobals:MRED:SDD"
-        Wave runnum = $"root:myGlobals:MRED:RunNumber"
-        Wave isTrans = $"root:myGlobals:MRED:IsTrans"
+        WAVE SampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        WAVE/T EmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        WAVE/T Suffix = $"root:myGlobals:MRED:Suffix"
+        WAVE/T Labels = $"root:myGlobals:MRED:Labels"
+        WAVE SDD = $"root:myGlobals:MRED:SDD"
+        WAVE IsTrans = $"root:myGlobals:MRED:IsTrans"
         
         Variable num=numpnts(sdd),ii,tol = 0.1
@@ -693 +907 @@
         do
 //              if(abs(sdd[ii] - tSDD) > tol)           //if numerically more than 0.001 m different, they're not the same
-//                      DeletePoints ii, 1, filenames,suffix,labels,sdd,runnum,isTrans
+//                      DeletePoints ii, 1, SampleRuns,EmptyRuns,Suffix,Labels,SDD,IsTrans
 //              endif
                 if(trunc(abs(sdd[ii] - tSDD)) > tol)            //just get the integer portion of the difference - very coarse comparison
-                        DeletePoints ii, 1, filenames,suffix,labels,sdd,runnum,isTrans
+                        DeletePoints ii, 1, SampleRuns,EmptyRuns,Suffix,Labels,SDD,IsTrans
                 endif
                 ii-=1
@@ -702 +916 @@
         
         // now sort
-        Sort RunNum,    filenames,suffix,labels,sdd,runnum,isTrans
+        Sort SampleRuns, SampleRuns,EmptyRuns,Suffix,Labels,SDD,IsTrans
         return(0)
 End
@@ -708 +922 @@
 
 Function RemoveTransFilesFromSDDList()
-        Wave/T filenames = $"root:myGlobals:MRED:Filenames"
-        Wave/T suffix = $"root:myGlobals:MRED:Suffix"
-        Wave/T labels = $"root:myGlobals:MRED:Labels"
-        Wave sdd = $"root:myGlobals:MRED:SDD"
-        Wave runnum = $"root:myGlobals:MRED:RunNumber"
-        Wave isTrans = $"root:myGlobals:MRED:IsTrans"
+        WAVE SampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        WAVE/T EmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        WAVE/T Suffix = $"root:myGlobals:MRED:Suffix"
+        WAVE/T Labels = $"root:myGlobals:MRED:Labels"
+        WAVE SDD = $"root:myGlobals:MRED:SDD"
+        WAVE IsTrans = $"root:myGlobals:MRED:IsTrans"
         
         Variable num=numpnts(isTrans),ii
@@ -719 +933 @@
         do
                 if(isTrans[ii] != 0)
-                        DeletePoints ii, 1, filenames,suffix,labels,sdd,runnum,isTrans
+                        DeletePoints ii, 1, SampleRuns,EmptyRuns,Suffix,Labels,SDD,IsTrans
                 endif
                 ii-=1
@@ -730 +944 @@
 //which alreay was found to exist. sname is the file;vers to be written out,
 //avoiding the need to re-extract it from fname.
-Function GetHeaderInfoToSDDWave(fname,sname)
-        String fname,sname
+Function GetHeaderInfoToSDDWave(fname,sname,ename, empscale)
+        String fname,sname,ename,empscale
         
         String textstr,temp,lbl,date_time,suffix
@@ -737 +951 @@
         Variable lastPoint, beamstop
 
-        Wave/T GFilenames = $"root:myGlobals:MRED:Filenames"
         Wave/T GSuffix = $"root:myGlobals:MRED:Suffix"
         Wave/T GLabels = $"root:myGlobals:MRED:Labels"
         Wave GSDD = $"root:myGlobals:MRED:SDD"
-        Wave GRunNumber = $"root:myGlobals:MRED:RunNumber"
+        Wave GSampleRuns = $"root:myGlobals:MRED:SampleRuns"
+        Wave/T GEmptyRuns = $"root:myGlobals:MRED:EmptyRuns"
+        Wave/T GScaleEMP = $"root:myGlobals:MRED:Scale"
         Wave GIsTrans = $"root:myGlobals:MRED:IsTrans"
         
-        lastPoint = numpnts(GLambda)
+        lastPoint = numpnts(GSampleRuns)
                 
-        InsertPoints lastPoint,1,GFilenames
-        GFilenames[lastPoint]=sname
+        //the run number
+        InsertPoints lastPoint,1,GSampleRuns
+        GSampleRuns[lastPoint] = GetRunNumFromFile(sname)
+
+        //the empty runs are left as text as they may be empty
+        InsertPoints lastPoint,1,GEmptyRuns
+        If (cmpstr(ename,"")!= 0) 
+                GEmptyRuns[lastPoint] = num2istr(GetRunNumFromFile(ename))
+        Else
+                GEmptyRuns[lastPoint] = ""
+        EndIf
+        
+        // add the scale factor 
+        InsertPoints lastPoint,1,GScaleEMP
+        GScaleEMP[lastPoint] = empscale
         
         //read the file suffix
@@ -760 +988 @@
         InsertPoints lastPoint,1,GSDD
         GSDD[lastPoint]= getSDD(fname)
-
-        //the run number (not displayed in the table, but carried along)
-        InsertPoints lastPoint,1,GRunNumber
-        GRunNumber[lastPoint] = GetRunNumFromFile(sname)
-
+                
         // 0 if the file is a scattering  file, 1 (truth) if the file is a transmission file
         InsertPoints lastPoint,1,GIsTrans

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_PatchFiles.ipf

@@ -204 +204 @@
                         //make a three character string of the run number
                         if(val<10)
-                                numStr = "00"+num2str(val)
+                                numStr = "00"+item
                         else
                                 if(val<100)
-                                        numStr = "0"+num2str(val)
+                                        numStr = "0"+item
                                 else
-                                        numStr = num2str(val)
+                                        numStr = item
                                 Endif
                         Endif

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_ProDiv.ipf

@@ -393 +393 @@
                                 proto[1] = fileStr
 #if (exists("QUOKKA")==6)
-                                err = CheckDIVBeamCenter(fileStr,39,96)
+                                err = CheckDIVBeamCenter(fileStr,34,96)
 #else
                                 err = CheckDIVBeamCenter(str,105,65)
@@ -407 +407 @@
                         if(strlen(str) > 0)
 #if (exists("QUOKKA")==6)
-                                err = CheckDIVBeamCenter(fileStr,39,96)
+                                err = CheckDIVBeamCenter(fileStr,34,96)
 #else
                                 err = CheckDIVBeamCenter(str,105,65)
@@ -673 +673 @@
         Variable xc,yc
         
-        Variable err,ii,num,tmpX,tmpY,badCtr,tol=5
+        Variable err,ii,num,tmpX,tmpY,badCtr,tol=10
         String fileStr,pathStr
         

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_ProtocolAsPanel.ipf

@@ -90 +90 @@
         String/G root:myGlobals:Protocols:gAVE="AVTYPE=Circular;SAVE=Yes;NAME=Auto;PLOT=Yes;"
         String/G root:myGlobals:Protocols:gDRK="DRK=none,DRKMODE=0,"
+        Variable/G root:myGlobals:Protocols:gScaleEMP = 1.0
         
         SetDataFolder root:
@@ -185 +186 @@
         Wave/T w=$("root:myGlobals:Protocols:" + nameStr)
         
-        String fullPath="",comma=",",list="",nameList="",PathStr="",item=""
+        String fullPath="",comma=",",list="",nameList="",PathStr="",item="",strValue=""
         Variable ii=0,numItems,checked,specialProtocol
         
@@ -215 +216 @@
         String/G root:myGlobals:Protocols:gEMP = nameList
         CheckBox prot_check_1 win=ProtocolPanel,value=checked
+        
+        //empty scale 
+        Variable scaleFactor = str2num(w[7])
+        If (scaleFactor == NaN)
+                scaleFactor = 1.0
+        Endif
+        Variable/G root:myGlobals:Protocols:gScaleEMP = scaleFactor
         
         //DIV file
@@ -496 +504 @@
         w[6] = drkStr
         
-        //w[7]
-        //currently unused
-        w[7] = ""
+        //w[7] = empty scale factor
+        NVAR scale = root:myGlobals:Protocols:gScaleEMP
+        w[7] = num2str(scale)
         
         return(0)
@@ -827 +835 @@
         CheckBox prot_check,help={"If checked, the specified background file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
         CheckBox prot_check,value= 1
-        Button pick_bgd,pos={114,75},size={100,20},proc=PickBGDButton,title="set BGD file"
+        Button pick_bgd,pos={105,75},size={100,20},proc=PickBGDButton,title="set BGD file"
         Button pick_bgd,help={"This button will set the file selected in the File Catalog table to be the background file."}
         Button recallProt,pos={7,406},size={107,20},proc=RecallProtocolButton,title="Recall Protocol"
@@ -846 +854 @@
         CheckBox prot_check_3,help={"If checked, the specified mask file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
         CheckBox prot_check_3,value= 1
-        Button pick_emp,pos={113,125},size={100,20},proc=PickEMPButton,title="set EMP file"
+        Button pick_emp,pos={105,125},size={100,20},proc=PickEMPButton,title="set EMP file"
         Button pick_emp,help={"This button will set the file selected in the File Catalog table to be the empty cell file."}
-        Button pick_DIV,pos={114,173},size={100,20},proc=PickDIVButton,title="set DIV file"
+        Button pick_DIV,pos={105,173},size={100,20},proc=PickDIVButton,title="set DIV file"
         Button pick_DIV,help={"This button will set the file selected in the File Catalog table to be the sensitivity file."}
-        Button pick_MASK,pos={119,266},size={100,20},proc=PickMASKButton,title="set MASK file"
+        Button pick_MASK,pos={105,266},size={100,20},proc=PickMASKButton,title="set MASK file"
         Button pick_MASK,help={"This button will set the file selected in the File Catalog table to be the mask file."}
         SetVariable bgdStr,pos={7,98},size={250,15},title="file:"
@@ -858 +866 @@
         SetVariable empStr,help={"Filename of the empty cell file(s) to be used in the data reduction"}
         SetVariable empStr,limits={-Inf,Inf,0},value= root:myGlobals:Protocols:gEMP
+        SetVariable empScale,pos={210,125},size={80,15},title="scale:"
+        SetVariable empScale,help={"Scale the empty cell file(s) to be used in the reduction"}
+        SetVariable empScale,limits={-Inf,Inf,0},value=root:myGlobals:Protocols:gScaleEMP
         SetVariable divStr,pos={9,197},size={250,15},title="file:"
         SetVariable divStr,help={"Filename of the detector sensitivity file to be used in the data reduction"}
@@ -869 +880 @@
         CheckBox prot_check_4,help={"If checked, the specified sample file will be included in the data reduction. If the file name is \"ask\", then the user will be prompted for the file"}
         CheckBox prot_check_4,value= 1
-        Button pick_sam,pos={115,28},size={100,20},proc=PickSAMButton,title="set SAM file"
+        Button pick_sam,pos={105,28},size={100,20},proc=PickSAMButton,title="set SAM file"
         Button pick_sam,help={"This button will set the file selected in the File Catalog table to be the sample file"}
         SetVariable samStr,pos={6,50},size={250,15},title="file:"
         SetVariable samStr,help={"Filename of the sample file(s) to be used in the data reduction"}
         SetVariable samStr,limits={-Inf,Inf,0},value= root:myGlobals:Protocols:gSAM
-        Button pick_ABS,pos={115,220},size={110,20},proc=SetABSParamsButton,title="set ABS params"
+        Button pick_ABS,pos={100,220},size={110,20},proc=SetABSParamsButton,title="set ABS params"
         Button pick_ABS,help={"This button will prompt the user for absolute scaling parameters"}
         CheckBox prot_check_9,pos={7,222},size={59,14},title="Absolute"
@@ -887 +898 @@
         CheckBox prot_check_5,help={"If checked, the specified averaging will be performed at the end of the data reduction."}
         CheckBox prot_check_5,value= 1
-        Button pick_AVE,pos={108,313},size={150,20},proc=SetAverageParamsButtonProc,title="set AVERAGE params"
+        Button pick_AVE,pos={80,313},size={150,20},proc=SetAverageParamsButtonProc,title="set AVERAGE params"
         Button pick_AVE,help={"Prompts the user for the type of 1-D averaging to perform, as well as saving options"}
         SetVariable aveStr,pos={9,336},size={250,15},title="parameters:"
@@ -1597 +1608 @@
         activeType = "EMP"
         do
+                // Update the empty scale factor
+                Variable scale = 1
+                if(cmpstr(prot[7],"") != 0)
+                        scale = str2num(prot[7])
+                        if (scale == NaN)
+                                scale = 1
+                        endif
+                endif
+                Add_scale_to_work(activeType, scale)
+                
                 if(cmpstr(prot[1],"ask") == 0)
                         err = LoadRawSANSData(msgStr)           //will prompt for file

sans/Dev/branches/quokka_update/NCNR_User_Procedures/Reduction/SANS/QKK_WorkFileUtils.ipf

@@ -20 +20 @@
 //***************************
 
-
+Function Add_scale_to_work(newType, scale)
+        String newType
+        Variable scale
+        
+        String dest = "root:Packages:NIST:"+newType+":scale"
+        NVAR/Z factor = $(dest)
+        If (NVAR_Exists(factor))
+                factor = scale
+        Else
+                Variable/G $(dest) = scale
+        Endif
+End
+        
 //testing procedure, not called anymore
 Proc Add_to_Workfile(type, add)
@@ -135 +147 @@
         endif
         
-        //deadtime corrections to raw data
-        deadTime = DetectorDeadtime(raw_text[3],raw_text[9])            //pick the correct detector deadtime
+        //deadtime is added to the reals read when file is loaded
+        deadTime = raw_reals[56]
         itim = raw_ints[2]
         cntrate = sum(raw_data,-inf,inf)/itim           //080802 use data sum, rather than scaler value
@@ -305 +317 @@
         endif
         
-        //deadtime corrections
+        //deadtime is added to the reals read when file is loaded
         itim = integersread[2]
         cntrate = sum(data,-inf,inf)/itim               //use sum of detector counts rather than scaler value
-        deadtime = DetectorDeadtime(textread[3],textread[9])    //pick the correct deadtime
+        deadtime = realsread[56]
         dscale = 1/(1-deadTime*cntrate)
         
@@ -509 +521 @@
                   solidAngle[ii][jj] = DetEffCorrILL(lambda,dtdist,xd)
 #else
-                                data[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)
-//                              solidAngle[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)           //testing only
+                                data[ii][jj] /= DetEffCorr(realsread,lambda,dtdist,xd,yd)
+//                              solidAngle[ii][jj] /= DetEffCorr(realsread,lambda,dtdist,xd,yd)         //testing only
 #endif
                         endif
@@ -588 +600 @@
 // xd and yd are distances from the beam center to the current pixel
 //
-Function DetEffCorr(lambda,dtdist,xd,yd)
+Function DetEffCorr(realsread,lambda,dtdist,xd,yd)
+        Wave realsread
         Variable lambda,dtdist,xd,yd
         
         Variable theta,cosT,ff,stAl,stHe
+        Variable alScl = realsread[52]
+        Variable alWnd = realsRead[53]
+        Variable heScl = realsread[54]
+        Variable heWnd = realsread[55]
         
         theta = atan( (sqrt(xd^2 + yd^2))/dtdist )
         cosT = cos(theta)
         
-        stAl = 0.00967    * lambda * 1.52 //dimensionless, constants provided by epg
-        stHe = 0.055553 * lambda * 3.81
+        stAl = alScl * lambda * alWnd //dimensionless, constants provided by epg
+        stHe = heScl * lambda * heWnd
         
         ff = exp(-stAl/cosT)*(1-exp(-stHe/cosT)) / ( exp(-stAl)*(1-exp(-stHe)) )