Changeset 999 for sans

Timestamp:

May 20, 2016 4:28:56 PM (7 years ago)

Author:

srkline

Message:

changes to a few analysis models to make these Igor 7-ready

adding mask editing utilities

many changes to event mode for easier processing of split lists

updated event mode help file

+ lots more!

Location:

sans/Dev/trunk

Files:

• NCNR_Help_Files/EventModeData_Help_v1.0.ihf (modified) (previous)
• NCNR_User_Procedures/Analysis/Models/NewModels_2006/SchulzSpheres_v40.ipf (modified) (1 diff)
• NCNR_User_Procedures/Analysis/Models/ProlateCoreShell_Sq_v40.ipf (modified) (2 diffs)
• NCNR_User_Procedures/Analysis/Packages/ModelPicker/SANSModelPicker_v40.ipf (modified) (1 diff)
• NCNR_User_Procedures/Analysis/Packages/Wrapper_v40.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/SANS/EventModeProcessing.ipf (modified) (22 diffs)
• NCNR_User_Procedures/Reduction/SANS/Menu.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/VSANS/VC_DetectorBinning_Utils.ipf (modified) (10 diffs)
• NCNR_User_Procedures/Reduction/VSANS/VC_HDF5_VSANS_Utils.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/VSANS/VC_VCALCPanel_MockUp.ipf (modified) (3 diffs)
• NCNR_User_Procedures/Reduction/VSANS/VSANS_Includes.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/VSANS/V_DataPlotting.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/VSANS/V_DetectorCorrections.ipf (modified) (12 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_HDF5_Read.ipf (modified) (2 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_IQ_Utilities.ipf (modified) (5 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_Initialize.ipf (modified) (1 diff)
• NCNR_User_Procedures/Reduction/VSANS/V_MaskUtils.ipf (added)
• NCNR_User_Procedures/Reduction/VSANS/V_Test_RAW_Panel.ipf (modified) (5 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_Testing_Data_Procs.ipf (modified) (5 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_VSANS_Preferences.ipf (modified) (3 diffs)
• NCNR_User_Procedures/Reduction/VSANS/V_WorkFolderUtils.ipf (modified) (6 diffs)

sans/Dev/trunk/NCNR_User_Procedures/Analysis/Models/NewModels_2006/SchulzSpheres_v40.ipf

@@ -72 +72 @@
 End
         
-
+//
+Proc PlotSchulzSpheresBeta(num,qmin,qmax)
+        Variable num=128,qmin=0.001,qmax=0.7
+        Prompt num "Enter number of data points for model: "
+        Prompt qmin "Enter minimum q-value (A^-1) for model: "
+        Prompt qmax "Enter maximum q-value (A^-1) for model: "
+        
+        Make/O/D/N=(num) xwave_sch_beta,ywave_sch_beta
+        xwave_sch_beta = alog( log(qmin) + x*((log(qmax)-log(qmin))/num) )
+        Make/O/D coef_sch_beta = {0.01,60,0.2,1e-6,3e-6,0.001}
+        make/O/T parameters_sch_beta = {"Volume Fraction (scale)","mean radius (A)","polydisp (sig/avg)","SLD sphere (A-2)","SLD solvent (A-2)","bkg (cm-1 sr-1)"}
+        Edit parameters_sch_beta,coef_sch_beta
+        
+        Variable/G root:g_sch_beta
+        g_sch_beta := SchulzSpheresBeta(coef_sch_beta,ywave_sch_beta,xwave_sch_beta)
+        Display ywave_sch_beta vs xwave_sch_beta
+        ModifyGraph log=1,marker=29,msize=2,mode=4
+        Label bottom "q (A\\S-1\\M)"
+        Label left "Intensity (cm\\S-1\\M)"
+        AutoPositionWindow/M=1/R=$(WinName(0,1)) $WinName(0,2)
+        
+        AddModelToStrings("SchulzSpheresBeta","coef_sch_beta","parameters_sch_beta","sch_beta")
+End
 
 Function Schulz_Point(x,avg,zz)

sans/Dev/trunk/NCNR_User_Procedures/Analysis/Models/ProlateCoreShell_Sq_v40.ipf

@@ -108 +108 @@
 //      Killwaves/Z form_PEF_HS,struct_PEF_HS
         
-        return (yw)
+        return (0)
 End
 
@@ -528 +528 @@
 //      Killwaves/Z form_PEF_2Y,struct_PEF_2Y
         
-        return (yw)
+        return (0)
 End
 

sans/Dev/trunk/NCNR_User_Procedures/Analysis/Packages/ModelPicker/SANSModelPicker_v40.ipf

@@ -80 +80 @@
                 
                 // always turn off file checking for me
-                checkForFiles = !(stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"s*ine"))                //zero for me
-                checkForFiles = !(stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"ajj"))          //and zero for me
-                checkForFiles = !(stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"andrewjackson"))                //and zero for me
-                
+                if( stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"s*ine") )
+                        checkforfiles = 0
+                endif
+                if( stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"ajj") )
+                        checkforfiles = 0
+                endif
+                if( stringmatch(ParseFilePath(0,SpecialDirPath("Desktop",0,0,0),":",1,1),"andrewjackson") )
+                        checkforfiles = 0
+                endif
+
                 // turn off file checking if the proper alias to the NCNR procedures is there
                 PathInfo igor
                 NewPath/O/Q tmpUPPath S_Path + "User Procedures"  
                 String fileList = IndexedFile(tmpUPPath,-1,"????")
+                if(strsearch(fileList, "NCNR_User_Procedures", 0  , 2) != -1)   //ignore case
+                        checkforfiles = 0
+                        Print "found the proper procedures"
+                endif
+
+        // check the Documents:WaveMetrics:IP: UP folder (always writeable)
+        //      print SpecialDirPath("Igor Pro User Files",0,0,0)
+        //      Macintosh HD:Users:srkline:Documents:WaveMetrics:Igor Pro 7 User Files:
+        
+                NewPath/O/Q tmpUPPath  SpecialDirPath("Igor Pro User Files",0,0,0) + "User Procedures" 
+                fileList = IndexedFile(tmpUPPath,-1,"????")
                 if(strsearch(fileList, "NCNR_User_Procedures", 0  , 2) != -1)   //ignore case
                         checkforfiles = 0

sans/Dev/trunk/NCNR_User_Procedures/Analysis/Packages/Wrapper_v40.ipf

@@ -627 +627 @@
                         w[0] += 1e-6
                         w[0] -= 1e-6
-        
+
+        
+                                        
                         break
         endswitch

sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/EventModeProcessing.ipf

@@ -16 +16 @@
 //
 // -- NEW 2016
+//
+// -- see the Procedure DecodeBinaryEvents(numToPrint) for a first implementation of a "viewer"
+//    for the binary events. Prints out the decoded 32-bit binary to the command window for inspection
+//    Could be modified as needed to flag events, see what bad events really look like, etc. (May 2016)
+
 //  -- see the proc DisplayForSlicing() that may aid in setting the bins properly by plotting the 
 //     bins along with the differential collection rate
@@ -189 +194 @@
 
 // for decimation
-        Variable/G root:Packages:NIST:Event:gEventFileTooLarge = 150            // 150 MB considered too large
+        Variable/G root:Packages:NIST:Event:gEventFileTooLarge = 2500           // 2500 MB considered too large
         Variable/G root:Packages:NIST:Event:gDecimation = 100
         Variable/G root:Packages:NIST:Event:gEvent_t_longest_decimated = 0
@@ -280 +285 @@
         Button button16_1,pos={488,450},size={110,20},proc=AccumulateSlicesButton,title="Add Next Slice"
         Button button17_2,pos={620,425},size={110,20},proc=AccumulateSlicesButton,title="Display Total"
+        Button button22,pos={620,450},size={120,20},proc=Osc_LoadAdjList_BinOnFly,title="Load+Accumulate"
 
         CheckBox chkbox1_0,pos={25,34},size={69,14},title="Oscillatory",fSize=10
@@ -584 +590 @@
 // now before binning, sort the data
 
-        //this is slow - undoing the sorting and starting over, but if you don't,
+        //MakeIndex is REALLY SLOW - this is slow - to allow undoing the sorting and starting over, but if you don't,
         // you'll never be able to undo the sort
         //
+        //
+        // for a 500 MB hst, MakeIndex = 83s, everything else in this function totalled < 5s
+        //
         SetDataFolder root:Packages:NIST:Event:
 
         if(WaveExists($"root:Packages:NIST:Event:OscSortIndex") == 0 )
                 Duplicate/O rescaledTime OscSortIndex
+//              tic()
                 MakeIndex rescaledTime OscSortIndex
+//              toc()
+//              tic()
                 IndexSort OscSortIndex, yLoc,xLoc,timePt,rescaledTime   
+//              toc()
                 //SetDataFolder root:Packages:NIST:Event
+//              tic()
                 IndexForHistogram(xLoc,yLoc,binnedData)                 // index the events AFTER sorting
+//              toc()
                 //SetDataFolder root:
         Endif
@@ -600 +615 @@
         Wave index = root:Packages:NIST:Event:SavedIndex                //this is the histogram index
 
+//      tic()
         for(ii=0;ii<nslices;ii+=1)
                 if(ii==0)
@@ -634 +650 @@
         endfor
 
+//      toc()
         Duplicate/O slicedData,root:Packages:NIST:Event:dispsliceData,root:Packages:NIST:Event:logSlicedData
         Wave logSlicedData = root:Packages:NIST:Event:logSlicedData
@@ -992 +1009 @@
 
 // MODE_TISANE
-
+//TODO -- tisane doesn't do anything different than oscillatory. Is this really correct??
+        if(mode == MODE_TISANE)         // TISANE mode - don't adjust the times, we get periodic t0 to reset t=0
+                Duplicate/O timePt rescaledTime
+                rescaledTime *= 1e-7                    //convert to seconds and that's all
+                t_longest = waveMax(rescaledTime)               //if oscillatory, won't be the last point, so get it this way
+        
+                KillWaves/Z OscSortIndex                        //to make sure that there is no old index hanging around
+        endif
+        
 // MODE_TOF
         if(mode == MODE_TOF)            // TOF mode - don't adjust the times, we get periodic t0 to reset t=0
@@ -1275 +1300 @@
         totBytes = V_logEOF
         Print "total bytes = ", totBytes
-        
+        if(EventDataType(filePathStr) != 1)             //if not hst extension of raw data
+                Abort "Data must be raw event data with file extension .hst for this operation"
+                return(0)
+        endif   
 //toc()
 //
@@ -1768 +1796 @@
         Print "total bytes = ", totBytes
         
+        if(EventDataType(filePathStr) != 1)             //if not hst extension of raw data
+                Abort "Data must be raw event data with file extension .hst for this operation"
+                return(0)
+        endif
 //
 //      Print "scan only"
@@ -2436 +2468 @@
                         Wave xLoc = xLoc
                         Wave yLoc = yLoc
-                        Save/T xLoc,yLoc,timePt ,rescaledTime           //will ask for a name
+                        Save/T xLoc,yLoc,timePt,rescaledTime            //will ask for a name
                         
                         SetDataFolder root:
@@ -2464 +2496 @@
                         // load in the waves, saved as Igor text to preserve the data type
                         PathInfo/S catPathName          //should set the next dialog to the proper path...
-                        LoadWave/T/O/P=catPathName
-                        filePathStr = S_fileName
+                        filePathStr = PromptForPath("Pick the edited event data")
+                        if(EventDataType(filePathStr) != 2)             //if not itx extension of edited data
+                                Abort "Data must be edited data with file extension .itx for this operation"
+                                return(0)
+                        endif
+                        LoadWave/T/O/P=catPathName filePathStr
+//                      filePathStr = S_fileName
+
                         if(strlen(S_fileName) == 0)
                                 //user cancelled
@@ -3047 +3085 @@
         
         for(ii=0;ii<numSplit;ii+=1)
-                outStr = (thePath+baseStr+num2str(ii))
+                outStr = (thePath+baseStr+num2str(ii)+".hst")
 //              Print "outStr = ",outStr
                 Open outRef as outStr
@@ -3057 +3095 @@
 
                 Close outRef
-//              listStr += outStr+";"
-                listStr += baseStr+num2str(ii)+";"
+//              listStr += outStr+";"           //no, this is the FULL path
+                listStr += baseStr+num2str(ii)+".hst"+";"
         endfor
 
         Make/O/B/U/N=(frac) leftover
         // ii was already incremented past the loop
-        outStr = (thePath+baseStr+num2str(ii))
+        outStr = (thePath+baseStr+num2str(ii)+".hst")
         Open outRef as outStr
         for(jj=0;jj<num;jj+=1)
@@ -3074 +3112 @@
         Close outRef
 //      listStr += outStr+";"
-        listStr += baseStr+num2str(ii)+";"
+        listStr += baseStr+num2str(ii)+".hst"+";"
 
         FSetPos refNum,V_logEOF
@@ -3127 +3165 @@
 End
 
-Function AccumulateSlices(mode)
-        Variable mode
-        
+// added an extra (optional) parameter for silent operation - to be used when a list of
+// files are processed - so the user can walk away as it works. Using the buttons from the
+// panel will still present the alerts
+//
+Function AccumulateSlices(mode,[skipAlert])
+        Variable mode,skipAlert
+        
+        if(ParamIsDefault(skipAlert))
+                skipAlert = 0
+        endif
         SetDataFolder root:Packages:NIST:Event:
 
         switch(mode)    
                 case 0:
-                        DoAlert 0,"The current data has been copied to the accumulated set. You are now ready to add more data."
+                        if(!skipAlert)
+                                DoAlert 0,"The current data has been copied to the accumulated set. You are now ready to add more data."
+                        endif
                         KillWaves/Z accumulatedData
-                        Duplicate/O slicedData accumulatedData          
+                        Duplicate/O slicedData accumulatedData  
+                        KillWaves/Z accum_BinCount              // the accumulated BinCount
+                        Duplicate/O binCount accum_binCount     
                         break
                 case 1:
-                        DoAlert 0,"The current data has been added to the accumulated data. You can add more data."
+                        if(!skipAlert)
+                                DoAlert 0,"The current data has been added to the accumulated data. You can add more data."
+                        endif
                         Wave acc=accumulatedData
                         Wave cur=slicedData
                         acc += cur
+                        Wave binCount = binCount
+                        Wave accum_binCount = accum_BinCount
+                        accum_BinCount += binCount
+                        binCount = accum_binCount                       // !! NOTE - the bin count wave is now the total
+//                      AccumulateSlices(2,skipAlert=skipAlert)                                         // and a recursive call to show the total!
                         break
                 case 2:
-                        DoAlert 0,"The accumulated data is now the display data and is ready for display or export."
+                        if(!skipAlert)
+                                DoAlert 0,"The accumulated data is now the display data and is ready for display or export."
+                        endif
                         Duplicate/O accumulatedData slicedData
                         // do something to "touch" the display to force it to update
@@ -3413 +3471 @@
         
         Variable fileref
-
+        Variable num,ii
+        
         SVAR filename = root:Packages:NIST:Event:gEvent_logfile
         NVAR t_longest = root:Packages:NIST:Event:gEvent_t_longest
@@ -3444 +3503 @@
 
         //loop through everything in the list
-        Variable num,ii
         num = ItemsInList(listStr)
+        if(num == 0)
+                DoAlert 0,"Enter the file names in the table, then click 'Load From List' again."
+                return (0)
+        endif
         
         for(ii=0;ii<num;ii+=1)
@@ -3451 +3513 @@
 // (1) load the file, prepending the path               
                 filename = pathStr + StringFromList(ii, listStr  ,";")
-                
+                if(EventDataType(filename) != 1)                //if not hst extension of raw data
+                        Abort "Data must be raw event data with file extension .hst for this operation"
+                        return(0)
+                endif           
 
 #if (exists("EventLoadWave")==4)
@@ -3555 +3620 @@
         num = ItemsInList(listStr)
         
+        if(num == 0)
+                DoAlert 0,"Enter the file names in the table, then click 'Load From List' again."
+                return(0)
+        endif
+        
         for(ii=0;ii<num;ii+=1)
 
 // (1) load the file, prepending the path               
                 filename = pathStr + StringFromList(ii, listStr  ,";")
-                
+                if(EventDataType(filename) != 2)                //if not itx extension of edited data
+                        Abort "Data must be edited data with file extension .itx for this operation"
+                        return(0)
+                endif           
                 SetDataFolder root:Packages:NIST:Event:
                 LoadWave/T/O fileName
@@ -3635 +3708 @@
         Variable num,ii,jj
         num = ItemsInList(listStr)
-
-
+        if(num == 0)
+                DoAlert 0,"Enter the file names in the table, then click 'Load From List' again."
+                return(0)
+        endif
+        
 ////////////////
 // declarations for the binning
@@ -3679 +3755 @@
 // (1) load the file, prepending the path               
                 filename = pathStr + StringFromList(jj, listStr  ,";")
-                
+                if(EventDataType(filename) != 2)                //if not itx extension of edited data
+                        Abort "Data must be edited data with file extension .itx for this operation"
+                        return(0)
+                endif           
                 SetDataFolder root:Packages:NIST:Event:
                 LoadWave/T/O fileName
@@ -3825 +3904 @@
 end
 /////////////////////////////
+
+Proc GetListofITXorSplitFiles(searchStr)
+        String searchStr = ".itx"
+        ShowList_ToLoad("")
+        GetListofITXHST(searchStr)
+end
+
+// needs SANS_Utilites.ipf
+Function GetListofITXHST(searchStr)
+        String searchStr
+        
+        String fullList = IndexedFile(catpathName, -1, "????" )
+        
+        // list is currently everything -- trim it
+        searchStr = "*" + searchStr + "*"
+        String list = ListMatch(fullList, searchStr )
+        
+        Print "searchString = ",searchStr
+        //
+        Wave/T tw = root:Packages:NIST:Event:SplitFileWave
+        List2TextWave(list,tw)
+        Sort/A tw,tw                    //alphanumeric sort
+        Edit tw
+        return(0)
+End
+
+//
+// loads a list of files that have been adjusted and saved
+// -- MUST run one through first manually to set the bin sapcing, then this
+//    won't touch that, just process all of the files
+// -- bins as they are loaded
+//
+Function Osc_LoadAdjList_BinOnFly(ctrlName)
+        String ctrlName
+        
+        Variable fileref
+
+        SVAR filename = root:Packages:NIST:Event:gEvent_logfile
+        SVAR listStr = root:Packages:NIST:Event:gSplitFileList
+
+        String pathStr,fileStr,tmpStr
+        PathInfo catPathName
+        pathStr = S_Path
+
+// if "Osc" mode is not checked - abort
+        NVAR gEventModeRadioVal= root:Packages:NIST:Event:gEvent_mode
+        if(gEventModeRadioVal != MODE_OSCILL)
+                Abort "The mode must be 'Oscillatory' to use this function"
+                return(0)
+        endif
+
+// if the list has been edited, turn it into a list
+        WAVE/T/Z tw = root:Packages:NIST:Event:SplitFileWave
+        if(WaveExists(tw))
+                listStr = TextWave2SemiList(tw)
+        else
+                ShowSplitFileTable()
+                DoAlert 0,"Enter the file names in the table, then click 'Load From List' again."
+                return(0)
+        endif
+        
+
+        //loop through everything in the list
+        Variable num,ii,jj
+        num = ItemsInList(listStr)
+
+//handle the first file differently
+//(1) load (import edited)
+        jj=0
+        filename = pathStr + StringFromList(jj, listStr  ,";")
+        if(EventDataType(filename) != 2)                //if not itx extension of edited data
+                Abort "Data must be edited data with file extension .itx for this operation"
+                return(0)
+        endif
+        
+        SetDataFolder root:Packages:NIST:Event:
+        LoadWave/T/O fileName
+        SetDataFolder root:Packages:NIST:Event:                 //LoadEvents sets back to root: ??
+
+        // clear out the old sort index, if present, since new data is being loaded
+        KillWaves/Z OscSortIndex        
+        SVAR dispStr = root:Packages:NIST:Event:gEventDisplayString
+        sprintf tmpStr, "%s: a user-modified event file\r",StringFromList(jj, listStr  ,";")
+        dispStr = tmpStr        
+        
+//(2) bin
+        Osc_ProcessEventLog("")
+        
+//(3) display bin details
+        Execute "ShowBinTable()"
+        Execute "BinEventBarGraph()"
+        
+//(4) add first
+        AccumulateSlices(0,skipAlert=1)         //bypass the dialog
+
+        // with remaining files
+        // load
+        // bin
+        // add next
+
+// start w/file 1, since "0th" file was already processed
+        for(jj=1;jj<num;jj+=1)
+        
+        //(1) load (import edited)
+                filename = pathStr + StringFromList(jj, listStr  ,";")
+                if(EventDataType(filename) != 2)                //if not itx extension of edited data
+                        Abort "Data must be edited data with file extension .itx for this operation"
+                        return(0)
+                endif
+                SetDataFolder root:Packages:NIST:Event:
+                LoadWave/T/O fileName
+                SetDataFolder root:Packages:NIST:Event:                 //LoadEvents sets back to root: ??
+        
+                // clear out the old sort index, if present, since new data is being loaded
+                KillWaves/Z OscSortIndex        
+                SVAR dispStr = root:Packages:NIST:Event:gEventDisplayString
+                sprintf tmpStr, "%s: a user-modified event file\r",StringFromList(jj, listStr  ,";")
+                dispStr = tmpStr        
+                
+        //(2) bin
+                Osc_ProcessEventLog("")
+                
+        //(3) display bin details
+                Execute "ShowBinTable()"
+                Execute "BinEventBarGraph()"
+                
+        //(4) add next
+                AccumulateSlices(1,skipAlert=1)
+        
+        endfor  //end loop over the file list
+
+        
+        //display total
+        AccumulateSlices(2,skipAlert=1)
+
+        // let user know we're done
+        DoAlert 0,"The list has been processed and is ready for export"
+        SetDataFolder root:
+
+        return(0)
+End
+
+
+//returns 0 for unknown data
+// 1 for raw hst files
+// 2 for edited ITX files
+//
+//  TODO
+//  -- currently, this blindly assumes an .hst extension for raw HST data, and .itx for edited data
+//
+Function EventDataType(filename)
+        string filename
+        
+        Variable type
+        Variable offset = strsearch(filename,".",Inf,1)         //work backwards
+        String extension = filename[offset+1,strlen(filename)-1]
+        //Print extension
+        type = 0
+        if(cmpstr(extension,"hst") == 0)
+                type = 1
+        endif
+        if(cmpstr(extension,"itx") == 0)
+                type = 2
+        endif
+        return(type)
+end
+
+////////////
+// this could be jazzed up quite a bit, but it is a first pass at
+// figuring out what is going on with the events
+//
+Proc DecodeBinaryEvents(numToPrint)
+        Variable numToPrint=10
+        
+        DecodeEvents(numToPrint)
+end
+
+//      sscanf %x takes hex input and gives a real value output
+// printf %d val gives the integer representation of the sscanf output
+// printf %b val gives the binary representation.
+Function DecodeEvents(numToPrint)
+        Variable numToPrint
+
+        String filePathStr,buffer
+        Variable fileRef,type,dataval,num0,num1,num2,num3
+        Variable numT0,numPP,numZero,numXYevents,bit29
+        Variable ii
+
+        ii=0
+        Open/R fileref
+        tic()
+        do
+                do
+                        FReadLine fileref, buffer                       //skip the "blank" lines that have one character
+                while(strlen(buffer) == 1)              
+
+                if (strlen(buffer) == 0)
+                        break
+                endif
+                
+                sscanf buffer,"%x",dataval
+                if(ii<numToPrint)
+                        printf "%s  %0.32b  ",buffer[0,7],dataval
+                endif
+                
+                // two most sig bits (31-30)
+                type = (dataval & 0xC0000000)/1073741824                //right shift by 2^30
+
+                if(ii<numToPrint)
+                        printf "%0.2b  ",type
+                endif
+                                                
+                if(type == 0)
+                        num0 += 1
+                        numXYevents += 1
+                endif
+                if(type == 2)
+                        num2 += 1
+                        numXYevents += 1
+                endif
+                if(type == 1)
+                        num1 += 1
+                endif
+                if(type == 3)
+                        num3 += 1
+                endif   
+                
+                bit29 = (dataval & 0x20000000)/536870912                //bit 29 only , shift by 2^29
+                if(ii<numToPrint)
+                        printf "%0.1b  ",bit29
+                endif
+                                
+                if(type==0 || type==2)
+                        numPP += round(bit29)
+                endif
+                
+                if(type==1 || type==3)
+                        numT0 += round(bit29)
+                endif
+                
+                if(dataval == 0)
+                        numZero += 1
+                endif
+                
+                if(ii<numToPrint)
+                        printf "\r"
+                        ii += 1
+                endif
+                
+        while(1)
+        Close fileref
+toc()
+
+        Print "(Igor) numT0 = ",numT0   
+        Print "num0 = ",num0    
+        Print "num1 = ",num1    
+        Print "num2 = ",num2    
+        Print "num3 = rollover = ",num3
+        Print "numXY = ",numXYevents
+        Print "numZero = ",numZero
+        Print "numPP = ",numPP
+        
+        return(0)
+
+End

sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/Menu.ipf

@@ -50 +50 @@
                 "-"
                 "Split Large File",SplitBigFile()
+                "Get List of ITX or Split Files",GetListofITXorSplitFiles()
                 "Accumulate First Slice",AccumulateSlices(0)
                 "Add Current Slice",AccumulateSlices(1)

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/VC_DetectorBinning_Utils.ipf

@@ -238 +238 @@
                         newX = data_realDistX[xCtr][0]
                         newY = data_realDistY[0][yCtr]
+                        //newX = xCtr
+                        //newY = yCtr
                 endif           
                                 
@@ -668 +670 @@
 //    a blanket correction (matrix multiply) for an entire panel?
 //
+//
+//
 // folderStr = WORK folder, type = the binning type (may include multiple detectors)
 Function VC_fDoBinning_QxQy2D(folderStr,type)
@@ -690 +694 @@
 //
 
+// TODO:
+// -- Solid_Angle -- waves will be present for WORK data other than RAW, but not for RAW
+//
 // assume that the mask files are missing unless we can find them. If VCALC data, 
 //  then the Mask is missing by definition
@@ -986 +993 @@
 
 //TODO: properly define the errors here - I'll have this if I do the simulation
+// -- need to propagate the errors up to this point
+//
         if(WaveExists(iErr)==0  && WaveExists(inten) != 0)
                 Duplicate/O inten,iErr
@@ -1055 +1064 @@
 //
 // this needs to be a double loop now...
+// TODO:
+// -- the iErr wave and accumulation of error is NOT CALCULATED CORRECTLY YET
+// -- the solid angle per pixel is not yet implemented.
+//    it will be present for WORK data other than RAW, but not for RAW
 
 // if any of the masks don't exist, display the error, and proceed with the averaging, using all data
@@ -1074 +1087 @@
                                 val = inten[ii][jj]
                                 
-                                if(isVCALC || maskMissing)              // mask_val == 1 == keep
-                                        mask_val = 1
+                                if(isVCALC || maskMissing)              // mask_val == 0 == keep, mask_val == 1 = YES, mask out the point
+                                        mask_val = 0
                                 else
                                         mask_val = mask[ii][jj]
                                 endif
-                                if (numType(val)==0 && mask_val == 1)           //count only the good points, ignore Nan or Inf
+                                if (numType(val)==0 && mask_val == 0)           //count only the good points, ignore Nan or Inf
                                         iBin_qxqy[binIndex] += val
                                         iBin2_qxqy[binIndex] += val*val
@@ -1103 +1116 @@
                                 
                                 if(isVCALC || maskMissing)
-                                        mask_val = 1
+                                        mask_val = 0
                                 else
                                         mask_val = mask2[ii][jj]
                                 endif
-                                if (numType(val)==0 && mask_val == 1)           //count only the good points, ignore Nan or Inf
+                                if (numType(val)==0 && mask_val == 0)           //count only the good points, ignore Nan or Inf
                                         iBin_qxqy[binIndex] += val
                                         iBin2_qxqy[binIndex] += val*val
@@ -1131 +1144 @@
                                 
                                 if(isVCALC || maskMissing)
-                                        mask_val = 1
+                                        mask_val = 0
                                 else
                                         mask_val = mask3[ii][jj]
                                 endif
-                                if (numType(val)==0 && mask_val == 1)           //count only the good points, ignore Nan or Inf
+                                if (numType(val)==0 && mask_val == 0)           //count only the good points, ignore Nan or Inf
                                         iBin_qxqy[binIndex] += val
                                         iBin2_qxqy[binIndex] += val*val
@@ -1156 +1169 @@
                                 
                                 if(isVCALC || maskMissing)
-                                        mask_val = 1
+                                        mask_val = 0
                                 else
                                         mask_val = mask4[ii][jj]
                                 endif
-                                if (numType(val)==0 && mask_val == 1)           //count only the good points, ignore Nan or Inf
+                                if (numType(val)==0 && mask_val == 0)           //count only the good points, ignore Nan or Inf
                                         iBin_qxqy[binIndex] += val
                                         iBin2_qxqy[binIndex] += val*val
@@ -1174 +1187 @@
 // after looping through all of the data on the panels, calculate errors on I(q),
 // just like in CircSectAve.ipf
+// TODO:
+// -- Errors were NOT properly acculumated above, so this loop of calculations is NOT MEANINGFUL (yet)
         for(ii=0;ii<nq;ii+=1)
                 if(nBin_qxqy[ii] == 0)

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/VC_HDF5_VSANS_Utils.ipf

@@ -302 +302 @@
 
 
-////////////////////// MASK FILE
-
-
-// TODO
-// currently, there are no dummy fill values or attributes for the fake MASK file
-//
-Proc Setup_VSANS_MASK_Struct()
-
-        // lays out the tree and fills with dummy values
-        H_Setup_VSANS_MASK_Structure()
-        
-        // writes in the attributes
-//      H_Fill_VSANS_Attributes()
-        
-        // fill in with VCALC simulation bits
-//      H_Fill_VSANS_wSim()
-        
-End
-
-Proc Save_VSANS_MASK_Nexus(fileName)
-        String fileName="Test_VSANS_MASK_file"
-
-        // save as HDF5 (no attributes saved yet)
-        Save_VSANS_file("root:VSANS_MASK_file", fileName+".h5")
-        
-        // read in a data file using the gateway-- reads from the home path
-        H_HDF5Gate_Read_Raw(fileName+".h5")
-        
-        // after reading in a "partial" file using the gateway (to generate the xref)
-        // Save the xref to disk (for later use)
-        Save_HDF5___xref("root:"+fileName,"HDF5___xref")
-        
-        // after you've generated the HDF5___xref, load it in and copy it
-        // to the necessary folder location.
-        Copy_HDF5___xref("root:VSANS_MASK_file", "HDF5___xref")
-        
-        // writes out the contents of a data folder using the gateway
-        H_HDF5Gate_Write_Raw("root:VSANS_MASK_file", fileName+".h5")
-
-        // re-load the data file using the gateway-- reads from the home path
-        // now with attributes
-        H_HDF5Gate_Read_Raw(fileName+".h5")
-        
-End
-
-////////////// fake MASK file tests
-//
-//
-//      Make/O/T/N=1    file_name       = "VSANS_MASK_test.h5"
-//
-// simple generation of a fake MASK file. for sans, nothing other than the creation date was written to the 
-// file header. nothing more is needed (possibly)
-//
-//
-// TODO -- make the number of pixels GLOBAL
-// TODO -- there will be lots of work to do to develop the procedures necessary to actually generate the 
-//      9 data sets to become the MASK file contents. More complexity here than for the simple SANS case.
-//
-// TODO -- this is currently random 0|1 values, need to write an editor
-//
-// currently set up to use 0 = exclude and 1 = keep 
-//
-Proc H_Setup_VSANS_MASK_Structure()
-        
-        NewDataFolder/O/S root:VSANS_MASK_file          
-
-        NewDataFolder/O/S root:VSANS_MASK_file:entry    
-                Make/O/T/N=1    title   = "This is a fake MASK file for VSANS"
-                Make/O/T/N=1    start_date      = "2015-02-28T08:15:30-5:00"
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument         
-                        Make/O/T/N=1    name    = "NG3_VSANS"
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_B      
-                        Make/O/I/N=(150,150)    data    = 1
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_MR             
-                        Make/O/I/N=(48,128)     data    = 1
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_ML             
-                        Make/O/I/N=(48,128)     data    = 1
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_MT             
-                        Make/O/I/N=(128,48)     data    = 1
-                        data[0,49][] = 0
-                        data[78,127][] = 0
-                        data[50,77][] = 1
-                        
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_MB             
-                        Make/O/I/N=(128,48)     data    = 1
-                        data[0,49][] = 0
-                        data[78,127][] = 0
-                        data[50,77][] = 1
-                        
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_FR             
-                        Make/O/I/N=(48,128)     data    = 1
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_FL             
-                        Make/O/I/N=(48,128)     data    = 1
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_FT             
-                        Make/O/I/N=(128,48)     data    = 1
-                        data[0,49][] = 0
-                        data[78,127][] = 0
-                        data[50,77][] = 1
-
-                NewDataFolder/O/S root:VSANS_MASK_file:entry:instrument:detector_FB             
-                        Make/O/I/N=(128,48)     data    = 1
-                        data[0,49][] = 0
-                        data[78,127][] = 0
-                        data[50,77][] = 1
-                        
-        SetDataFolder root:
-
-End
+
+
 
 

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/VC_VCALCPanel_MockUp.ipf

@@ -647 +647 @@
         NewDataFolder/O root:Packages:NIST:VSANS
         NewDataFolder/O root:Packages:NIST:VSANS:VCALC
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_B
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MB
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MT
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_ML
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MR
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FB
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FT
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FL
-                NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FR
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_B
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MB
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MT
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_ML
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_MR
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FB
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FT
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FL
+        NewDataFolder/O root:Packages:NIST:VSANS:VCALC:entry:instrument:detector_FR
 
 //      NewDataFolder/O root:Packages:NIST:VSANS:VCALC:Front
@@ -808 +808 @@
         Variable/G gBack_h = 150
         
-        Make/O/D/N=1 :entry:instrument:detector_B:x_pixel_size = 0.1            // 1mm resolution (units of cm here)
+        Make/O/D/N=1 :entry:instrument:detector_B:x_pixel_size = 0.1            // 1 mm resolution (units of cm here)
         Make/O/D/N=1 :entry:instrument:detector_B:y_pixel_size = 0.1            
 //      Variable/G gBack_pixelX = 0.1           
@@ -873 +873 @@
         Make/O/D/N=(pixel_num_x[0],pixel_num_y[0]) det_B
         Duplicate/O det_B qTot_B,qx_B,qy_B,qz_B
-
-
 
 

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/VSANS_Includes.ipf

@@ -59 +59 @@
 #include "V_Testing_Data_Procs"
 
+// mask files
+#include "V_MaskUtils"
+
+

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_DataPlotting.ipf

@@ -59 +59 @@
 End
 
-
-
-//
-// see the VCALC BinAllMiddlePanels() for an example of this
-//
-// TODO 
-// x- detector "B" is currently skipped since the calibration waves are not faked
-//    when the raw data is loaded. Then the qxqyqz waves are not generated.
-//
-// -- REDO the logic here. It's a mess, and will get the calculation wrong 
-//
-// -- figure out the binning type (where is it set?)
-// -- binning type is HARD-WIRED
-// -- figure out when this is to be called to re-calculate the I vs Q
-//
-Function V_QBinAllPanels(folderStr)
-        String folderStr
-
-        // do the back, middle, and front separately
-        
-//      figure out the binning type (where is it set?)
-        Variable binType,ii,delQ
-        String detStr
-        binType = 1
-        
-        
-
-//// TODO:
-// x- currently the "B" detector is skipped - it was skipped in 
-//       previous functions where q values are calculated       
-//      
-        delQ = SetDeltaQ(folderStr,"B")
-        
-        // dispatch based on binning type
-        if(binType == 1)
-                VC_fDoBinning_QxQy2D(folderStr, "B")            //normal binning, nothing to combine
-        endif
-
-// TODO -- this is only a temporary fix for slit mode   
-        if(binType == 4)
-                /// this is for a tall, narrow slit mode        
-                VC_fBinDetector_byRows(folderStr,"B")
-        endif   
-
-// these are the binning types where detectors are not combined
-// other combined binning is below the loop
-        for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
-                detStr = StringFromList(ii, ksDetectorListNoB, ";")
-                
-                // set delta Q for binning
-                delQ = SetDeltaQ(folderStr,detStr)
-                
-                // dispatch based on binning type
-                if(binType==1)
-                        VC_fDoBinning_QxQy2D(folderStr,detStr)
-                endif
-                
-                // TODO -- this is only a temporary fix for slit mode   
-                if(binType == 4)
-                        /// this is for a tall, narrow slit mode        
-                        VC_fBinDetector_byRows(folderStr,detStr)
-                endif   
-                
-        endfor
-        
-        // bin in pairs
-        if(binType == 2)
-                VC_fDoBinning_QxQy2D(folderStr,"MLR")
-                VC_fDoBinning_QxQy2D(folderStr,"MTB")
-                VC_fDoBinning_QxQy2D(folderStr,"FLR")
-                VC_fDoBinning_QxQy2D(folderStr,"FTB")   
-        endif
-        
-        // bin everything on front or middle together
-        if(binType == 3)
-                VC_fDoBinning_QxQy2D(folderStr,"MLRTB")
-                VC_fDoBinning_QxQy2D(folderStr,"FLRTB")
-        endif
-
-        return(0)
-End
 
 

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_DetectorCorrections.ipf

@@ -370 +370 @@
                 if(cmpstr(orientation,"vertical")==0)
                 //      this is vertical tube data dimensioned as (Ntubes,Npix)
-                        pixSize = 8                     //V_getDet_y_pixel_size(fname,detStr)
+                        pixSize = 8.4           //V_getDet_y_pixel_size(fname,detStr)
                         
                 elseif(cmpstr(orientation,"horizontal")==0)
@@ -396 +396 @@
 
 //
+// TODO:
+// -- MUST VERIFY the definition of SDD and how (if) setback is written to the data files
+// -- currently I'm assuming that the SDD is the "nominal" value which is correct for the 
+//    L/R panels, but is not correct for the T/B panels (must add in the setback)
+//
+//
+//
 // data_realDistX, Y must be previously generated from running NonLinearCorrection()
 //
@@ -411 +418 @@
 // get all of the geometry information  
         orientation = V_getDet_tubeOrientation(fname,detStr)
-        sdd = V_getDet_distance(fname,detStr)
+//      sdd = V_getDet_distance(fname,detStr)           //[cm]
+//      sdd += V_getDet_TBSetback(fname,detStr)/10              // written in [mm], convert to [cm], returns 0 for L/R/B panels
+
+        sdd = V_getDet_ActualDistance(fname,detStr)             //sdd derived, including setback [cm]
         sdd/=100                // sdd reported in cm, pass in m
         // this is the ctr in pixels
@@ -552 +562 @@
 //    to each pixel
 //
-// not actually used for anything, but here for completeness if anyone asks
+// not actually used for any calculations, but here for completeness if anyone asks, or for 2D data export
 //
 // this properly accounts for qz
@@ -579 +589 @@
 End
 
+
+//
+// TODO -- VERIFY calculations
+// -- This is the actual solid angle per pixel, not a ratio vs. some "unit SA" 
+//    Do I just correct for the different area vs. the "nominal" central area?
+// -- decide how to implement - either directly change the data values (as was done in the past)
+//    or use this as a weighting for when the data is binned to I(q). In the second method, 2D data
+//    would need this to be applied before exporting
+// -- do I keep a wave note indicating that this correction has been applied to the data
+//    so that it can be "un-applied"?
+// -- do I calculate theta from geometry directly, or get it from Q (Assuming it's present?)
+//    (probably just from geometry, since I need SDD and dx and dy values...)
+//
+//
+Function SolidAngleCorrection(w,w_err,fname,detStr,destPath)
+        Wave w,w_err
+        String fname,detStr,destPath
+
+        Variable sdd,xCtr,yCtr,lambda
+
+// get all of the geometry information  
+//      orientation = V_getDet_tubeOrientation(fname,detStr)
+        sdd = V_getDet_ActualDistance(fname,detStr)
+        sdd/=100                // sdd in cm, pass in m
+
+        // this is ctr in mm
+        xCtr = V_getDet_beam_center_x_mm(fname,detStr)
+        yCtr = V_getDet_beam_center_y_mm(fname,detStr)
+        lambda = V_getWavelength(fname)
+        
+        SetDataFolder $(destPath + ":entry:instrument:detector_"+detStr)
+        
+        Wave data_realDistX = data_realDistX
+        Wave data_realDistY = data_realDistY
+
+        Duplicate/O w solid_angle,tmp_theta,tmp_dist            //in the current df
+
+//// calculate the scattering angle
+//      dx = (distX - xctr)             //delta x in mm
+//      dy = (distY - yctr)             //delta y in mm
+        tmp_dist = sqrt((data_realDistX - xctr)^2 + (data_realDistY - yctr)^2)
+        
+        tmp_dist /= 10  // convert mm to cm
+        sdd *=100               //convert to cm
+
+        tmp_theta = atan(tmp_dist/sdd)          //this is two_theta, the scattering angle
+
+        Variable ii,jj,numx,numy,dx,dy
+        numx = DimSize(tmp_theta,0)
+        numy = DimSize(tmp_theta,1)
+        
+        for(ii=0        ;ii<numx;ii+=1)
+                for(jj=0;jj<numy;jj+=1)
+                        
+                        if(ii==0)               //do a forward difference if ii==0
+                                dx = (data_realDistX[ii+1][jj] - data_realDistX[ii][jj])        //delta x for the pixel
+                        else
+                                dx = (data_realDistX[ii][jj] - data_realDistX[ii-1][jj])        //delta x for the pixel
+                        endif
+                        
+                        
+                        if(jj==0)
+                                dy = (data_realDistY[ii][jj+1] - data_realDistY[ii][jj])        //delta y for the pixel
+                        else
+                                dy = (data_realDistY[ii][jj] - data_realDistY[ii][jj-1])        //delta y for the pixel
+                        endif
+        
+                        dx /= 10
+                        dy /= 10                // convert mm to cm (since sdd is in cm)
+                        solid_angle[ii][jj] = dx*dy             //this is in cm^2
+                endfor
+        endfor
+        
+        // to cover up any issues w/negative dx or dy
+        solid_angle = abs(solid_angle)
+        
+        // solid_angle correction
+        // == dx*dy*cos^3/sdd^2
+        solid_angle *= (cos(tmp_theta))^3
+        solid_angle /= sdd^2
+        
+        // Here it is! Apply the correction to the intensity (I divide -- to get the counts per solid angle!!)
+        w /= solid_angle
+        
+        
+        // TODO:
+        // correctly apply the correction to the error wave (assume a perfect value?)
+        // w_err /= solid_angle         //is this correct??
+
+// TODO -- clean up after I'm satisfied computations are correct                
+//      KillWaves/Z tmp_theta,tmp_dist
+        
+        return(0)
+end
 
 
@@ -668 +772 @@
                         // so divide here to get the correct answer (5/22/08 SRK)
                         if(doEfficiency)
-                                data[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)
-                                data_err[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)
+//                              data[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)
+//                              data_err[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)
 //                              solidAngle[ii][jj] /= DetEffCorr(lambda,dtdist,xd,yd)           //testing only
                         endif
@@ -718 +822 @@
 
 
-//distances passed in are in mm
-// dtdist is SDD
-// xd and yd are distances from the beam center to the current pixel
-//
-// TODO:
-//   --         DoAlert 0,"This has not yet been updated for VSANS"
-//
-Function DetEffCorr(lambda,dtdist,xd,yd)
-        Variable lambda,dtdist,xd,yd
-
-        DoAlert 0,"This has not yet been updated for VSANS"
-        
-        Variable theta,cosT,ff,stAl,stHe
-        
-        theta = atan( (sqrt(xd^2 + yd^2))/dtdist )
-        cosT = cos(theta)
-        
-        stAl = 0.00967*lambda*0.8               //dimensionless, constants from JGB memo
-        stHe = 0.146*lambda*2.5
-        
-        ff = exp(-stAl/cosT)*(1-exp(-stHe/cosT)) / ( exp(-stAl)*(1-exp(-stHe)) )
-                
-        return(ff)
-End
 
 // DIVIDE the intensity by this correction to get the right answer
@@ -1031 +1111 @@
         
         Variable err
-        err = DIVCorrection(type)               //returns err = 1 if data doesn't exist in specified folders
+        err = V_DIVCorrection(type)             //returns err = 1 if data doesn't exist in specified folders
         
         if(err)
-                Abort "error in DIVCorrection()"
+                Abort "error in V_DIVCorrection()"
         endif
         
@@ -1056 +1136 @@
 // TODO:
 //   --         DoAlert 0,"This has not yet been updated for VSANS"
-//  -- how is the error propagation  handled?
+//   -- how is the error propagation handled?
 //
 //function will divide the contents of "workType" folder with the contents of 
@@ -1062 +1142 @@
 // all data is linear scale for the calculation
 //
-Function DIVCorrection(data,data_err,detStr,workType)
+Function V_DIVCorrection(data,data_err,detStr,workType)
         Wave data,data_err
         String detStr,workType
@@ -1071 +1151 @@
 
         if(WaveExists(data) == 0)
-                Print "The data wave does not exist in DIVCorrection()"
+                Print "The data wave does not exist in V_DIVCorrection()"
                 Return(1)               //error condition
         Endif
@@ -1080 +1160 @@
         WAVE/Z div_data = $("root:Packages:NIST:VSANS:DIV:entry:instrument:detector_"+detStr+":data")
         if(WaveExists(div_data) == 0)
-                Print "The DIV wave does not exist in DIVCorrection()"
+                Print "The DIV wave does not exist in V_DIVCorrection()"
                 Return(1)               //error condition
         Endif

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_HDF5_Read.ipf

@@ -1385 +1385 @@
 End
 
-Function V_getDet_distance(fname,detStr)
+Function V_getDet_NominalDistance(fname,detStr)
         String fname,detStr
 
         String path = "entry:instrument:detector_"+detStr+":distance"
         return(V_getRealValueFromHDF5(fname,path))
+End
+
+//this is a DERIVED distance, since the nominal sdd is for the carriage (=LR panels)
+Function V_getDet_ActualDistance(fname,detStr)
+        String fname,detStr
+
+        Variable sdd
+        sdd = V_getDet_NominalDistance(fname,detStr)            //[cm]
+        sdd += V_getDet_TBSetback(fname,detStr)/10              // written in [mm], convert to [cm], returns 0 for L/R/B panels
+                
+        return(sdd)
 End
 
@@ -1426 +1437 @@
 End
 
-// TODO - be sure this is defined correctly
+// TODO - be sure this is defined correctly (with correct units!)
 // -- only returns for T/B detectors
 Function V_getDet_TBSetback(fname,detStr)

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_IQ_Utilities.ipf

@@ -10 +10 @@
 // -- fill in all of the details...
 //
+
+
+//
+// see the VCALC BinAllMiddlePanels() for an example of this
+// see the binning routines in VC_DetectorBinning_Utils.ipf for the details
+//
+// TODO 
+// x- detector "B" is currently skipped since the calibration waves are not faked
+//    when the raw data is loaded. Then the qxqyqz waves are not generated.
+//
+// -- REDO the logic here. It's a mess, and will get the calculation wrong 
+//
+// -- figure out the binning type (where is it set for VSANS?)
+// -- don't know, so currently VSANS binning type is HARD-WIRED
+// -- figure out when this needs to be called to (force) re-calculate I vs Q
+//
+Function V_QBinAllPanels(folderStr)
+        String folderStr
+
+        // do the back, middle, and front separately
+        
+//      figure out the binning type (where is it set?)
+        Variable binType,ii,delQ
+        String detStr
+        binType = 1
+        
+        
+
+//// TODO:
+// x- currently the "B" detector is skipped - it was skipped in 
+//       previous functions where q values are calculated       
+//      
+        delQ = SetDeltaQ(folderStr,"B")
+        
+        // dispatch based on binning type
+        if(binType == 1)
+                VC_fDoBinning_QxQy2D(folderStr, "B")            //normal binning, nothing to combine
+        endif
+
+// TODO -- this is only a temporary fix for slit mode   
+        if(binType == 4)
+                /// this is for a tall, narrow slit mode        
+                VC_fBinDetector_byRows(folderStr,"B")
+        endif   
+
+
+
+// these are the binning types where detectors are not combined
+// other combined binning is below the loop
+        for(ii=0;ii<ItemsInList(ksDetectorListNoB);ii+=1)
+                detStr = StringFromList(ii, ksDetectorListNoB, ";")
+                
+                // set delta Q for binning
+                delQ = SetDeltaQ(folderStr,detStr)
+                
+                // dispatch based on binning type
+                if(binType==1)
+                        VC_fDoBinning_QxQy2D(folderStr,detStr)
+                endif
+                
+                // TODO -- this is only a temporary fix for slit mode   
+                if(binType == 4)
+                        /// this is for a tall, narrow slit mode        
+                        VC_fBinDetector_byRows(folderStr,detStr)
+                endif   
+                
+        endfor
+        
+        // bin in pairs
+        if(binType == 2)
+                VC_fDoBinning_QxQy2D(folderStr,"MLR")
+                VC_fDoBinning_QxQy2D(folderStr,"MTB")
+                VC_fDoBinning_QxQy2D(folderStr,"FLR")
+                VC_fDoBinning_QxQy2D(folderStr,"FTB")   
+        endif
+        
+        // bin everything on front or middle together
+        if(binType == 3)
+                VC_fDoBinning_QxQy2D(folderStr,"MLRTB")
+                VC_fDoBinning_QxQy2D(folderStr,"FLRTB")
+        endif
+
+        return(0)
+End
+
+
+
+
+
 Macro V_Combine1DData()
 
@@ -26 +115 @@
         
 // write out the data set to a file
-
-
-End
-
-
-
+        String/G saveName=""
+        V_GetNameForSave("")
+        V_Write1DData(type,saveName)
+
+End
+
+Proc V_GetNameForSave(str)
+        String str
+        String/G saveName=str
+End
 
 
@@ -122 +215 @@
 
 // TODO:
+// -- resolution waves are ignored
+// -- only a sort is done, no rescaling of data sets
+//    (it's too late now anyways, since the data was concatenated
+//
 // see Auto_Sort() in the SANS Automation ipf for the rest of the details of
-// how to combine the resolution waves (they also need to be concatenated, which is currently not done.
-//
+// how to combine the resolution waves (they also need to be concatenated, which is currently not done)
+// 
 Function V_TmpSort1D(folderStr)
         String folderStr
@@ -197 +294 @@
 
 
+
 // TODO:
 // -- this is a temporary solution before a real writer is created
 // -- resolution is not handled here (and it shouldn't be) since resolution is not known yet.
 //
-//
 // this will bypass save dialogs
 // -- AND WILL OVERWITE DATA WITH THE SAME NAME
 //
-Function V_Write1DData(folderStr,delim,term)
-        String folderStr,delim,term
+Function V_Write1DData(folderStr,saveName)
+        String folderStr,saveName
         
         String formatStr="",fullpath=""
         Variable refnum,dialog=1
+
+        SetDataFolder $("root:Packages:NIST:VSANS:"+folderStr)
+
+        Wave qw = tmp_q
+        Wave iw = tmp_i
+        Wave sw = tmp_s
         
         String dataSetFolderParent,basestr
         
-        //Abuse ParseFilePath to get path without folder name
-        dataSetFolderParent = ParseFilePath(1,folderStr,":",1,0)
-        //Abuse ParseFilePath to get basestr
-        basestr = ParseFilePath(0,folderStr,":",1,0)
+        // ParseFilePath to get path without folder name
+//      dataSetFolderParent = ParseFilePath(1,folderStr,":",1,0)
+        // ParseFilePath to get basestr
+//      basestr = ParseFilePath(0,folderStr,":",1,0)
         
         //make sure the waves exist
-        SetDataFolder $(dataSetFolderParent+basestr)
-        WAVE/Z qw = $(baseStr+"_q")
-        WAVE/Z iw = $(baseStr+"_i")
-        WAVE/Z sw = $(baseStr+"_s")
-        WAVE/Z resw = $(baseStr+"_res")
         
         if(WaveExists(qw) == 0)
@@ -234 +332 @@
                 Abort "s is missing"
         endif
-        if(WaveExists(resw) == 0)
-                Abort "Resolution information is missing."
-        endif
-        
-        Duplicate/O qw qbar,sigQ,fs
-        if(dimsize(resW,1) > 4)
-                //it's USANS put -dQv back in the last 3 columns
-                NVAR/Z dQv = USANS_dQv
-                if(NVAR_Exists(dQv) == 0)
-                        SetDataFolder root:
-                        Abort "It's USANS data, and I don't know what the slit height is."
-                endif
-                sigQ = -dQv
-                qbar = -dQv
-                fs = -dQv
-        else
-                //it's SANS
-                sigQ = resw[p][0]
-                qbar = resw[p][1]
-                fs = resw[p][2]
-        endif
-        
+//      if(WaveExists(resw) == 0)
+//              Abort "Resolution information is missing."
+//      endif
+        
+//      Duplicate/O qw qbar,sigQ,fs
+//      if(dimsize(resW,1) > 4)
+//              //it's USANS put -dQv back in the last 3 columns
+//              NVAR/Z dQv = USANS_dQv
+//              if(NVAR_Exists(dQv) == 0)
+//                      SetDataFolder root:
+//                      Abort "It's USANS data, and I don't know what the slit height is."
+//              endif
+//              sigQ = -dQv
+//              qbar = -dQv
+//              fs = -dQv
+//      else
+//              //it's SANS
+//              sigQ = resw[p][0]
+//              qbar = resw[p][1]
+//              fs = resw[p][2]
+//      endif
+//      
+
         PathInfo catPathName
-        fullPath = S_Path + folderStr
+        fullPath = S_Path + saveName
 
         Open refnum as fullpath
 
         fprintf refnum,"Combined data written from folder %s on %s\r\n",folderStr,(date()+" "+time())
-        formatStr = "%15.4g %15.4g %15.4g %15.4g %15.4g %15.4g\r\n"     
-        fprintf refnum, "The 6 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. I(Q) (1/cm) | sigmaQ | meanQ | ShadowFactor|\r\n"        
-
-        wfprintf refnum,formatStr,qw,iw,sw,sigQ,qbar,fs
+
+// TODO -- make this work for 6-columns
+//      formatStr = "%15.4g %15.4g %15.4g %15.4g %15.4g %15.4g\r\n"     
+//      fprintf refnum, "The 6 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. I(Q) (1/cm) | sigmaQ | meanQ | ShadowFactor|\r\n"        
+//      wfprintf refnum,formatStr,qw,iw,sw,sigQ,qbar,fs
+
+        //currently, only three columns
+        formatStr = "%15.4g %15.4g %15.4g\r\n"  
+        fprintf refnum, "The 3 columns are | Q (1/A) | I(Q) (1/cm) | std. dev. I(Q) (1/cm)\r\n" 
+
+        wfprintf refnum,formatStr,qw,iw,sw
         Close refnum
         
-        KillWaves/Z sigQ,qbar,fs
+//      KillWaves/Z sigQ,qbar,fs
         
         SetDataFolder root:

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_Initialize.ipf

@@ -156 +156 @@
         // Analysis is not mine. So for VSANS, there is a new, separate file: V_VSANS_Preferences.ipf
 
+        //this is critical to initialize now - as it has the y/n flags for the detector correction steps
         Execute "Initialize_VSANSPreferences()" 
 

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_Test_RAW_Panel.ipf

@@ -141 +141 @@
         
         Button button_tagFile,pos={603,412},size={70,20},proc=TagFileButtonProc,title="Tag File"
+        Button button_saveIQ,pos={720,412},size={70,20},proc=SaveIQ_ButtonProc,title="Save I(Q)"
         Button button_BeamCtr,pos={603,450},size={70,20},proc=BeamCtrButtonProc,title="Beam Ctr"
         Button button_SpreadPanels,pos={603,488},size={100,20},proc=SpreadPanelButtonProc,title="Spread Panels"
         Button button_RestorePanels,pos={603,526},size={100,20},proc=RestorePanelButtonProc,title="Restore Panels"
+
 
 // on the tabs, always visible
@@ -350 +352 @@
                                         yctr = V_getDet_beam_center_y_mm(gCurDispType,detStr)   
                                         
-                                        sdd = V_getDet_distance(gCurDispType,detStr)    / 100   //written in cm, pass in meters
+                                        sdd = V_getDet_ActualDistance(gCurDispType,detStr)      / 100   //written in cm, pass in meters
                                         lam = V_getVSWavelength(gCurDispType)           //A
 //                                      pixSizeX = V_getDet_x_pixel_size(gCurDispType,detStr)           // written mm? need mm
@@ -697 +699 @@
 // ? controls here to select how the data is processed/grouped/saved, etc.
 //
+// -- currently just the graph, no controls
+// -- this re-bins the data every time by calling V_QBinAllPanels(folderStr)
 Function IvsQPanelButtonProc(ba) : ButtonControl
         STRUCT WMButtonAction &ba
@@ -737 +741 @@
                         str += "Wavelength is "+num2str(V_getWavelength(type)) + " A \r"
                         if(curTab == 2)
-                                str += "SDD B = "+num2str(V_getDet_distance(type,"B")) + " cm \r"               //V_getDet_distance(fname,detStr)
+                                str += "SDD B = "+num2str(V_getDet_ActualDistance(type,"B")) + " cm \r"         //V_getDet_distance(fname,detStr)
                         endif
                         if(curTab == 1)
-                                str += "SDD ML = "+num2str(V_getDet_distance(type,"ML")) + " cm \r"
-                                str += "SDD MR = "+num2str(V_getDet_distance(type,"MR")) + " cm \r"
-                                str += "SDD MT = "+num2str(V_getDet_distance(type,"MT")) + " cm \r"
-                                str += "SDD MB = "+num2str(V_getDet_distance(type,"MB")) + " cm \r"
+                                str += "SDD ML = "+num2str(V_getDet_ActualDistance(type,"ML")) + " cm \r"
+                                str += "SDD MR = "+num2str(V_getDet_ActualDistance(type,"MR")) + " cm \r"
+                                str += "SDD MT = "+num2str(V_getDet_ActualDistance(type,"MT")) + " cm \r"
+                                str += "SDD MB = "+num2str(V_getDet_ActualDistance(type,"MB")) + " cm \r"
                         endif
                         if(curTab == 0)
-                                str += "SDD FL = "+num2str(V_getDet_distance(type,"FL")) + " cm \r"
-                                str += "SDD FR = "+num2str(V_getDet_distance(type,"FR")) + " cm \r"
-                                str += "SDD FT = "+num2str(V_getDet_distance(type,"FT")) + " cm \r"
-                                str += "SDD FB = "+num2str(V_getDet_distance(type,"FB")) + " cm \r"
+                                str += "SDD FL = "+num2str(V_getDet_ActualDistance(type,"FL")) + " cm \r"
+                                str += "SDD FR = "+num2str(V_getDet_ActualDistance(type,"FR")) + " cm \r"
+                                str += "SDD FT = "+num2str(V_getDet_ActualDistance(type,"FT")) + " cm \r"
+                                str += "SDD FB = "+num2str(V_getDet_ActualDistance(type,"FB")) + " cm \r"
                         endif
                         
@@ -849 +853 @@
                 case 2: // mouse up
                         // click code here
-                        DoAlert 0, "TagFileButtonProc(ba) unfinished"
-                        
+                        DoAlert 0, "TagFileButtonProc(ba) unfinished - thes may be used to 'tag' a file as scatter, trans, emp, bkg, etc."
+                        
+                                
+                        break
+                case -1: // control being killed
+                        break
+        endswitch
+
+        return 0
+End
+
+// TODO
+// -- fill in more functionality
+// -- currently a straight concatentation of all data, no options
+// -- maybe allow save of single panels?
+// -- any other options?
+Function SaveIQ_ButtonProc(ba) : ButtonControl
+        STRUCT WMButtonAction &ba
+
+        switch( ba.eventCode )
+                case 2: // mouse up
+                        // click code here
+
+                        Execute "V_Combine1DData()"                     
                                 
                         break

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_Testing_Data_Procs.ipf

@@ -75 +75 @@
 
         endfor
-        
+
+        
+// writes out "perfect" detector calibration constants for all 8 tube banks
+        V_WritePerfectSpatialCalib(filename)
+// writes out "perfect" dead time constants for all 8 tube banks + back detector
+        V_WritePerfectDeadTime(filename)
         
 //? other detector geometry - lateral separation?
@@ -106 +111 @@
 
 
-// writes out "perfect" detector calibration constants for all 8 tube banks
-Function V_WritePerfectCalibration()
-
+// writes out "perfect" detector calibration constants for all 8 tube banks + back detector
+Function V_WritePerfectSpatialCalib(filename)
+        String filename
+        
+//      String fileName = V_DoSaveFileDialog("pick the file to write to")
+        
         Make/O/D/N=(3,48) tmpCalib
         // for the "tall" L/R banks
@@ -115 +123 @@
         tmpCalib[2][] = 0
         
-        V_writeDetTube_spatialCalib("","FR",tmpCalib)
-        V_writeDetTube_spatialCalib("","FL",tmpCalib)
-        V_writeDetTube_spatialCalib("","MR",tmpCalib)
-        V_writeDetTube_spatialCalib("","ML",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"FR",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"FL",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"MR",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"ML",tmpCalib)
 
         // for the "short" T/B banks
@@ -125 +133 @@
         tmpCalib[2][] = 0
         
-        V_writeDetTube_spatialCalib("","FT",tmpCalib)
-        V_writeDetTube_spatialCalib("","FB",tmpCalib)
-        V_writeDetTube_spatialCalib("","MT",tmpCalib)
-        V_writeDetTube_spatialCalib("","MB",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"FT",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"FB",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"MT",tmpCalib)
+        V_writeDetTube_spatialCalib(filename,"MB",tmpCalib)
         
         KillWaves tmpCalib
+        
+        // and for the back detector "B"
+        Make/O/D/N=3 tmpCalib
+        tmpCalib[0] = 1
+        tmpCalib[1] = 1
+        tmpcalib[2] = 10000
+        V_writeDet_cal_x(filename,"B",tmpCalib)
+        V_writeDet_cal_y(filename,"B",tmpCalib)
+
+        KillWaves tmpCalib
+
         return(0)
 end
@@ -138 +157 @@
 //V_writeDetector_deadtime(fname,detStr,inW)
 //V_writeDetector_deadtime_B(fname,detStr,val)
+// simulated count rate per tube can be Å 10^8, so I need dt >> 10^-15 to completely cancel this out
+// (partly due to fake I(q), fake count time in file...)
+
+// writes out "perfect" dead time constants for all 8 tube banks + back detector
+Function V_WritePerfectDeadTime(filename)
+        String filename
+                
+        Make/O/D/N=(48) tmpDT
+        tmpDT = 1e-18
+        V_writeDetector_deadtime(filename,"FT",tmpDT)
+        V_writeDetector_deadtime(filename,"FB",tmpDT)
+        V_writeDetector_deadtime(filename,"FL",tmpDT)
+        V_writeDetector_deadtime(filename,"FR",tmpDT)
+        V_writeDetector_deadtime(filename,"MT",tmpDT)
+        V_writeDetector_deadtime(filename,"MB",tmpDT)
+        V_writeDetector_deadtime(filename,"ML",tmpDT)
+        V_writeDetector_deadtime(filename,"MR",tmpDT)
+
+
+        // and for the back detector "B", a single value, not a wave
+        V_writeDetector_deadtime_B(filename,"B",1e-20)
+
+        KillWaves tmpDT
+
+        return(0)
+end
 
 

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_VSANS_Preferences.ipf

@@ -87 +87 @@
         Variable/G root:Packages:NIST:VSANS:Globals:gDoTubeShadowCor = 1
         
-
+        val = NumVarOrDefault("root:Packages:NIST:VSANS:Globals:gDoMonitorNormalizaton", 1 )
+        Variable/G root:Packages:NIST:VSANS:Globals:gDoMonitorNormalizaton = 1
+        
 
 // flag to allow adding raw data files with different attenuation (normally not done)   
@@ -197 +199 @@
         gVal = checked
 End
+
+Function V_DoMonitorNormPref(ctrlName,checked) : CheckBoxControl
+        String ctrlName
+        Variable checked
+        
+        NVAR gVal = root:Packages:NIST:VSANS:Globals:gDoMonitorNormalizaton
+        gVal = checked
+End
+
 
 Function V_PrefDoneButtonProc(ctrlName) : ButtonControl
@@ -243 +254 @@
         SetVariable PrefCtrl_1e,pos={21,195},size={200,15},title="# Phi Steps (annular avg)"
         SetVariable PrefCtrl_1e,limits={1,360,1},value= root:Packages:NIST:VSANS:Globals:gNPhiSteps
+        
         CheckBox PrefCtrl_1f title="Do Transmssion Correction?",size={140,14},value=root:Packages:NIST:VSANS:Globals:gDoTransmissionCor,proc=V_DoTransCorrPref
-        CheckBox PrefCtrl_1f pos={255,100},help={"TURN OFF ONLY FOR DEBUGGING. This corrects the data for angle dependent transmssion."}
+        CheckBox PrefCtrl_1f pos={255,80},help={"TURN OFF ONLY FOR DEBUGGING. This corrects the data for angle dependent transmssion."}
         CheckBox PrefCtrl_1g title="Do Efficiency Correction?",size={140,14},proc=V_DoEfficiencyCorrPref
-        CheckBox PrefCtrl_1g value=root:Packages:NIST:VSANS:Globals:gDoDetectorEffCor,pos={255,120},help={"TURN OFF ONLY FOR DEBUGGING. This corrects the data for angle dependent detector efficiency."}
+        CheckBox PrefCtrl_1g value=root:Packages:NIST:VSANS:Globals:gDoDetectorEffCor,pos={255,100},help={"TURN OFF ONLY FOR DEBUGGING. This corrects the data for angle dependent detector efficiency."}
 //      CheckBox PrefCtrl_1h title="Adjust RAW attenuation?",size={140,14},proc=V_DoRawAttenAdjPref
 //      CheckBox PrefCtrl_1h value=root:Packages:NIST:VSANS:Globals:gDoAdjustRAW_Atten,pos={255,140},help={"This is normally not done"}
 
         CheckBox PrefCtrl_1i title="Do DIV Correction?",size={140,14},proc=V_DoDIVCorPref
-        CheckBox PrefCtrl_1i value=root:Packages:NIST:VSANS:Globals:gDoDIVCor,pos={255,140},help={"TURN OFF ONLY FOR DEBUGGING."}
+        CheckBox PrefCtrl_1i value=root:Packages:NIST:VSANS:Globals:gDoDIVCor,pos={255,120},help={"TURN OFF ONLY FOR DEBUGGING."}
         CheckBox PrefCtrl_1j title="Do DeadTime Correction?",size={140,14},proc=V_DoDeadTimeCorPref
-        CheckBox PrefCtrl_1j value=root:Packages:NIST:VSANS:Globals:gDoDeadTimeCor,pos={255,160},help={"TURN OFF ONLY FOR DEBUGGING."}  
+        CheckBox PrefCtrl_1j value=root:Packages:NIST:VSANS:Globals:gDoDeadTimeCor,pos={255,140},help={"TURN OFF ONLY FOR DEBUGGING."}  
         CheckBox PrefCtrl_1k title="Do Solid Angle Correction?",size={140,14},proc=V_DoSolidAngleCorPref
-        CheckBox PrefCtrl_1k value=root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor,pos={255,180},help={"TURN OFF ONLY FOR DEBUGGING."}
+        CheckBox PrefCtrl_1k value=root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor,pos={255,160},help={"TURN OFF ONLY FOR DEBUGGING."}
         CheckBox PrefCtrl_1l title="Do Non-linear Correction?",size={140,14},proc=V_DoNonLinearCorPref
-        CheckBox PrefCtrl_1l value=root:Packages:NIST:VSANS:Globals:gDoNonLinearCor,pos={255,200},help={"TURN OFF ONLY FOR DEBUGGING."}
+        CheckBox PrefCtrl_1l value=root:Packages:NIST:VSANS:Globals:gDoNonLinearCor,pos={255,180},help={"TURN OFF ONLY FOR DEBUGGING."}
         CheckBox PrefCtrl_1m title="Do Tube Shadow Correction?",size={140,14},proc=V_DoTubeShadowCorPref
-        CheckBox PrefCtrl_1m value=root:Packages:NIST:VSANS:Globals:gDoTubeShadowCor,pos={255,220},help={"TURN OFF ONLY FOR DEBUGGING."}
+        CheckBox PrefCtrl_1m value=root:Packages:NIST:VSANS:Globals:gDoTubeShadowCor,pos={255,200},help={"TURN OFF ONLY FOR DEBUGGING."}
+        CheckBox PrefCtrl_1n title="Do Tube Shadow Correction?",size={140,14},proc=V_DoMonitorNormPref
+        CheckBox PrefCtrl_1n value=root:Packages:NIST:VSANS:Globals:gDoMonitorNormalizaton,pos={255,220},help={"TURN OFF ONLY FOR DEBUGGING."}
+                
         
 //      CheckBox PrefCtrl_1a,disable=1

sans/Dev/trunk/NCNR_User_Procedures/Reduction/VSANS/V_WorkFolderUtils.ipf

@@ -408 +408 @@
                         Wave w_err = V_getDetectorDataErrW(fname,detStr)
                         
-                        DIVCorrection(w,w_err,detStr,newType)
+                        V_DIVCorrection(w,w_err,detStr,newType)
                 endfor
         else
-                Print "DIV correction not done"         // not an error since correction was unchecked
+                Print "DIV correction NOT DONE"         // not an error since correction was unchecked
         endif
         
         // (2) non-linear correction    
         // TODO:
-        // x- currently, the "B" detector is skipped
+        // x-  the "B" detector is calculated in its own routines
         // -- document what is generated here:
         //    **in each detector folder: data_realDistX and data_realDistY (2D waves of the mm? position of the pixel)
-        // -- still not sure whether to duplicate these calculations as the RAW data is loaded. It would allow the RAW
-        //    data to be properly displayed, but without all of the (complete) set of corrections
+        // x- these spatial calculations ARE DONE as the RAW data is loaded. It allows the RAW
+        //    data to be properly displayed, but without all of the (complete) set of detector corrections
         // * the corrected distances are calculated into arrays, but nothing is done with them yet
-        // * there is enough information now to calculate the q-arrays
-        // -other corrections modify the data, this does NOT
+        // * there is enough information now to calculate the q-arrays, so it is done now
+        // - other corrections may modify the data, this calculation does NOT modify the data
         NVAR gDoNonLinearCor = root:Packages:NIST:VSANS:Globals:gDoNonLinearCor
         // generate a distance matrix for each of the detectors
@@ -461 +461 @@
                 
         else
-                Print "Non-linear correction not done"
+                Print "Non-linear correction NOT DONE"
         endif
 
         // (3) solid angle correction
+        // TODO -- this currently calculates the correction factor AND applys it to the data
+        //  -- as a result, the data values are very large since they are divided by a very small
+        //     solid angle per pixel. But all of the count values are now on the basis of 
+        //    counts/(solid angle) --- meaning that they can all be binned together for I(q)
+        //    -and- TODO - this will need to be taken into account for absolute scaling (this part is already done)
+        //
+        // the solid angle correction is calculated for ALL detector panels.
         NVAR gDoSolidAngleCor = root:Packages:NIST:VSANS:Globals:gDoSolidAngleCor
         if (gDoSolidAngleCor == 1)
@@ -473 +480 @@
                         Wave w_err = V_getDetectorDataErrW(fname,detStr)
                         // any other dimensions to pass in?
-//                      SolidAngleCorrection(fill this in)
+                        SolidAngleCorrection(w,w_err,fname,detStr,destPath)
                         
                 endfor
         else
-                Print "Solid Angle correction not done"
+                Print "Solid Angle correction NOT DONE"
         endif   
         
         // (4) dead time correction
-        // TODO: -- remove the hard-wired test
+        // TODO:
+        // x- remove the hard-wired test - done
         // -- test for correct operation
-        // -- loop over all of the detectors
-        // -- B detector is a special case (do separately, then loop over NoB)
+        // x- loop over all of the detectors
+        // x- B detector is a special case (do separately, then loop over NoB)
         // -- this DOES alter the data
-        // -- verify the error propagation
+        // -- verify the error propagation (not done yet)
         //
         Variable countRate
@@ -515 +523 @@
                 
         else
-                Print "Dead Time correction not done"
+                Print "Dead Time correction NOT DONE"
         endif   
         
         
         // (5) angle-dependent tube shadowing
+        // TODO:
+        // -- not sure about this correction yet...
+        //
         NVAR gDoTubeShadowCor = root:Packages:NIST:VSANS:Globals:gDoTubeShadowCor
         if (gDoTubeShadowCor == 1)
-        
-        else
-                Print "Tube shadowing correction not done"
+                Print "(stub)Tube Shadow correction"
+        else
+                Print "Tube shadowing correction NOT DONE"
         endif   
                 
         // (6) angle dependent transmission correction
+        // TODO:
+        // -- this still needs to be filled in
+        // -- still some debate of when/where in the corrections that this is best applied
+        //    - do it here, and it's done whether the output is 1D or 2D
+        //    - do it later (where SAMPLE information is used) since this section is ONLY instrument-specific
         NVAR gDoTrans = root:Packages:NIST:VSANS:Globals:gDoTransmissionCor
         if (gDoTrans == 1)
-                Print "Doing Large-angle transmission correction"// for "+ detStr
+                Print "(stub)Doing Large-angle transmission correction"// for "+ detStr
                 for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
                         detStr = StringFromList(ii, ksDetectorListAll, ";")
@@ -539 +555 @@
                 endfor
         else
-                Print "Sample Transmission correction not done"
+                Print "Sample Transmission correction NOT DONE"
         endif   
         
@@ -546 +562 @@
         // TODO -- but there are TWO monitors - so how to switch?
         // TODO -- what do I really need to save?
-        Print "Doing monitor normalization"// for "+ detStr
-
-        defmon=1e8                      //default monitor counts
-        for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
-                detStr = StringFromList(ii, ksDetectorListAll, ";")
-                Wave w = V_getDetectorDataW(fname,detStr)
-                Wave w_err = V_getDetectorDataErrW(fname,detStr)
-                Variable monCt = V_getBeamMonNormData(fname)
-//                      MonitorNormalization(fill this in)
-        //scale the data to the default montor counts
-        
-        // TODO -- un-comment these three lines once monitor counts are reasonable - currently monCt = 9!!!
-//              scale = defmon/monCt
-//              w *= scale
-//              w_err *= scale          //assumes total monitor count is so large there is essentially no error
-
-// TODO
-// -- to write back to the local value, get the wave reference rather than the value, then I can 
-//    re-assign the value directly, rather than this method (which is not terrible)     
-                // V_getBeamMonNormSaved_count()
-                // save the true monitor counts? save the scaling factor?
-                String path = "entry:instrument:beam_monitor_norm:saved_count"
-                Wave/Z savW = $("root:Packages:NIST:VSANS:"+fname+":"+path)
-                savW[0] = scale
-        endfor
-        
+        
+        NVAR gDoMonitorNormalizaton = root:Packages:NIST:VSANS:Globals:gDoMonitorNormalizaton
+        if (gDoMonitorNormalizaton == 1)
+                Print "(stub)Doing monitor normalization"// for "+ detStr
+                
+                defmon=1e8                      //default monitor counts
+                for(ii=0;ii<ItemsInList(ksDetectorListAll);ii+=1)
+                        detStr = StringFromList(ii, ksDetectorListAll, ";")
+                        Wave w = V_getDetectorDataW(fname,detStr)
+                        Wave w_err = V_getDetectorDataErrW(fname,detStr)
+                        Variable monCt = V_getBeamMonNormData(fname)
+        //                      MonitorNormalization(fill this in)
+                //scale the data to the default montor counts
+                
+                // TODO -- un-comment these three lines once monitor counts are reasonable - currently monCt = 9!!!
+        //              scale = defmon/monCt
+        //              w *= scale
+        //              w_err *= scale          //assumes total monitor count is so large there is essentially no error
+        
+        // TODO
+        // -- to write back to the local value, get the wave reference rather than the value, then I can 
+        //    re-assign the value directly, rather than this method (which is not terrible)     
+                        // V_getBeamMonNormSaved_count()
+                        // save the true monitor counts? save the scaling factor?
+                        String path = "entry:instrument:beam_monitor_norm:saved_count"
+                        Wave/Z savW = $("root:Packages:NIST:VSANS:"+fname+":"+path)
+                        savW[0] = scale
+                endfor
+        else
+                Print "Monitor Normalization correction NOT DONE"
+        endif
         
         // (not done) angle dependent efficiency correction
         NVAR doEfficiency = root:Packages:NIST:VSANS:Globals:gDoDetectorEffCor
 
-        
-// this function, in the past did the non-linear, solid angle, transmission, and efficiency corrections all at once
-//      DetCorr(data,data_err,realsread,doEfficiency,doTrans)           //the parameters are waves, and will be changed by the function
-
-
-        
-        //update totals to put in the work header (at the end of the function)
+//update totals to put in the work header (at the end of the function)
 //      total_mon += realsread[0]
 //