Changeset 75

Timestamp:

Apr 6, 2007 4:20:53 PM (15 years ago)

Author:

srkline

Message:

Final set of first pass changes to reduction code. Next is to throuroughly test before heading to the second pass of non-obvious function calls and documentation of the "required" stubs for a particular file type.

Location:

sans/SANSReduction/branches/kline_29MAR07/Put in User Procedures/SANS_Reduction_v5.00

Files:

• Marquee.ipf (modified) (1 diff)
• NCNR_DataReadWrite.ipf (modified) (12 diffs)
• PatchFiles.ipf (modified) (2 diffs)
• Transmission.ipf (modified) (19 diffs)

sans/SANSReduction/branches/kline_29MAR07/Put in User Procedures/SANS_Reduction_v5.00/Marquee.ipf

@@ -147 +147 @@
         //ReWriteReal() takes care of open/close on its own
         Print counts, " counts in XY box"
-        ReWriteReal(filename,counts,494)
+        WriteBoxCountsToHeader(filename,counts)
         
 End

sans/SANSReduction/branches/kline_29MAR07/Put in User Procedures/SANS_Reduction_v5.00/NCNR_DataReadWrite.ipf

@@ -187 +187 @@
         intw[17] = integer
         
-        //1 text field
+        //1 text field - the file association for transmission are the first 4 bytes
         FSetPos refNum,404
         FReadLine/N=42 refNum,textstr
@@ -571 +571 @@
         intw[17] = integer
         
-        //1 text field
+        //1 text field - the file association for transmission are the first 4 bytes
         FSetPos refNum,404
         FReadLine/N=42 refNum,textstr
@@ -1009 +1009 @@
 //this procedure takes care of all file open/close pairs needed
 //
-Function ReWriteReal(path,value,start)
+Function WriteVAXReal(path,value,start)
         String path
         Variable value,start
@@ -1054 +1054 @@
         //Print "Wrote end of header to " + num2str(V_filePOS)
         
-        Close refnum                            //at this point, it is as the VAX would have written it. 
+        Close refnum            //at this point, it is as the VAX would have written it. 
         
         Return(0)
 End
+
+//sample transmission is a real value at byte 158
+Function WriteTransmissionToHeader(fname,trans)
+        String fname
+        Variable trans
+        
+        WriteVAXReal(fname,trans,158)           //transmission start byte is 158
+        return(0)
+End
+
+//whole transmission is a real value at byte 392
+Function WriteWholeTransToHeader(fname,trans)
+        String fname
+        Variable trans
+        
+        WriteVAXReal(fname,trans,392)           //transmission start byte is 392
+        return(0)
+End
+
+//box sum counts is a real value at byte 494
+Function WriteBoxCountsToHeader(fname,counts)
+        String fname
+        Variable counts
+        
+        WriteVAXReal(fname,counts,494)          // start byte is 494
+        return(0)
+End
+
+//beam stop X-pos is at byte 368
+Function WriteBSXPosToHeader(fname,xpos)
+        String fname
+        Variable xpos
+        
+        WriteVAXReal(fname,xpos,368)
+        return(0)
+End
+
+//sample thickness is at byte 162
+Function WriteThicknessToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,162)
+        return(0)
+End
+
+//beam center X pixel location is at byte 252
+Function WriteBeamCenterXToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,252)
+        return(0)
+End
+
+//beam center Y pixel location is at byte 256
+Function WriteBeamCenterYToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,256)
+        return(0)
+End
+
+//attenuator number (not its transmission) is at byte 51
+Function WriteAttenNumberToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,51)
+        return(0)
+End
+
+//monitor count is at byte 39
+Function WriteMonitorCountToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,39)
+        return(0)
+End
+
+//total detector count is at byte 47
+Function WriteDetectorCountToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,47)
+        return(0)
+End
+
+//transmission detector count is at byte 388
+Function WriteTransDetCountToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,388)
+        return(0)
+End
+
+//wavelength is at byte 292
+Function WriteWavelengthToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,292)
+        return(0)
+End
+
+//wavelength spread is at byte 296
+Function WriteWavelengthDistrToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,296)
+        return(0)
+End
+
+//temperature is at byte 186
+Function WriteTemperatureToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,186)
+        return(0)
+End
+
+//magnetic field is at byte 190
+Function WriteMagnFieldToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,190)
+        return(0)
+End
+
+//Source Aperture diameter is at byte 280
+Function WriteSourceApDiamToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,280)
+        return(0)
+End
+
+//Sample Aperture diameter is at byte 284
+Function WriteSampleApDiamToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,284)
+        return(0)
+End
+
+//Source to sample distance is at byte 288
+Function WriteSrcToSamDistToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,288)
+        return(0)
+End
+
+//detector offset is at byte 264
+Function WriteDetectorOffsetToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,264)
+        return(0)
+End
+
+//beam stop diameter is at byte 272
+Function WriteBeamStopDiamToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,272)
+        return(0)
+End
+
+//detector offset is at byte 260
+Function WriteSDDToHeader(fname,num)
+        String fname
+        Variable num
+        
+        WriteVAXReal(fname,num,260)
+        return(0)
+End
+
 
 //rewrite a text field back to the header
@@ -1080 +1270 @@
 end
 
+Function WriteSamLabelToHeader(fname,str)
+        String fname,str
+        
+        RewriteTextToHeader(fname,str,98)
+        return(0)
+End
+
 //rewrite an integer field back to the header
 // fname is the full path:name
@@ -1101 +1298 @@
 end
 
+Function WriteCountTimeToHeader(fname,num)
+        String fname
+        Variable num
+        
+        RewriteIntegerToHeader(fname,num,31)
+        return(0)
+End
+
 // read specific bits of information from the header
 // each of these operations MUST take care of open/close on their own
@@ -1117 +1322 @@
         return(str)
 End
+
 // file suffix (4 characters @ byte 19)
 Function/S getSuffix(fname)
@@ -1122 +1328 @@
         
         return(getStringFromHeader(fname,19,4))
+End
+
+// associated file suffix (for transmission) (4 characters @ byte 404)
+Function/S getAssociatedFileSuffix(fname)
+        String fname
+        
+        return(getStringFromHeader(fname,404,4))
 End
 
@@ -1187 +1400 @@
 end
 
+//box counts are stored at byte 494
+Function getBoxCounts(fname)
+        String fname
+        
+        return(getRealValueFromHeader(fname,494))
+end
+
+//whole detector trasmission is at byte 392
+Function getSampleTransWholeDetector(fname)
+        String fname
+        
+        return(getRealValueFromHeader(fname,392))
+end
+
 //SampleThickness is at byte 162
 Function getSampleThickness(fname)
@@ -1229 +1456 @@
 end
 
-//SDD is at byte 260
+//sample to detector distance is at byte 260
 Function getSDD(fname)
         String fname
@@ -1340 +1567 @@
 /////   TRANSMISSION RELATED FUNCTIONS    ////////
 //box coordinate are returned by reference
-Function GetXYBoxFromFile(filename,x1,x2,y1,y2)
+Function getXYBoxFromFile(filename,x1,x2,y1,y2)
         String filename
         Variable &x1,&x2,&y1,&y2
@@ -1378 +1605 @@
         return(0)
 End
+
+//associated file suffix is the first 4 characters of a text field starting
+// at byte 404
+Function WriteAssocFileSuffixToHeader(fname,suffix)
+        String fname,suffix
+        
+        Variable refnum
+        
+        Open/A/T="????TEXT" refnum as fname
+        FSetPos refnum,404
+        FBinWrite refnum, suffix
+        FStatus refnum
+        FSetPos refnum,V_logEOF
+        Close refnum
+        
+        return(0)
+end

sans/SANSReduction/branches/kline_29MAR07/Put in User Procedures/SANS_Reduction_v5.00/PatchFiles.ipf

@@ -412 +412 @@
         Wave/T textVal
         
-        Variable refnum,num,start
+        Variable refnum,num
         String textstr
         
         //change the sample label ?
         if(change[0])
-                RewriteTextToHeader(fname,textVal[0],98)
+                WriteSamLabelToHeader(fname,textVal[0])
         Endif
         
@@ -423 +423 @@
         if(change[6])
                 num =str2num(textVal[6])
-                RewriteIntegerToHeader(fname,num,31)
+                WriteCountTimeToHeader(fname,num)
         Endif
         
         //ReWriteReal() takes care of open/close on its own
-        if(change[1])
+        if(change[1])           //sample transmission
                 num = str2num(textVal[1])
-                start = 158      //transmission
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[2])
+                WriteTransmissionToHeader(fname,num)
+        Endif
+        if(change[2])           //sample thickness
                 num = str2num(textVal[2])
-                start = 162      //thickness
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[3])
+                WriteThicknessToHeader(fname,num)
+        Endif
+        if(change[3])           //pixel X
                 num = str2num(textVal[3])
-                start = 252      //pixel x
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[4])
+                WriteBeamCenterXToHeader(fname,num)
+        Endif
+        if(change[4])           // pixel Y
                 num = str2num(textVal[4])
-                start = 256      //pixel y
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[5])
+                WriteBeamCenterYToHeader(fname,num)
+        Endif
+        if(change[5])           //attenuator number
                 num = str2num(textVal[5])
-                start = 51      //atten
-                ReWriteReal(fname,num,start)
+                WriteAttenNumberToHeader(fname,num)
         Endif
         //[6] was the counting time, integer written above
-        if(change[7])
-                num = str2num(textVal[7])
-                start = 39      //monitor count
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[8])
+        if(change[7])    //monitor count
+                num = str2num(textVal[7]) 
+                WriteMonitorCountToHeader(fname,num)
+        Endif
+        if(change[8])     //total detector count
                 num = str2num(textVal[8])
-                start = 47      //total detector count
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[9])
+                WriteDetectorCountToHeader(fname,num)
+        Endif
+        if(change[9])      //trans det count
                 num = str2num(textVal[9])
-                start = 388      //trans det count
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[10])
+                WriteTransDetCountToHeader(fname,num)
+        Endif
+        if(change[10])      //wavelength
                 num = str2num(textVal[10])
-                start = 292      //wavelength
-                ReWriteReal(fname,num,start)
+                WriteWavelengthToHeader(fname,num)
         Endif
         ///
-        if(change[11])
+        if(change[11])      //wavelength spread
                 num = str2num(textVal[11])
-                start = 296      //wavelength spread
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[12])
+                WriteWavelengthDistrToHeader(fname,num)
+        Endif
+        if(change[12])      //temperature
                 num = str2num(textVal[12])
-                start = 186      //temperture
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[13])
+                WriteTemperatureToHeader(fname,num)
+        Endif
+        if(change[13])      //magnetic field
                 num = str2num(textVal[13])
-                start = 190      //magnetic field
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[14])
+                WriteMagnFieldToHeader(fname,num)
+        Endif
+        if(change[14])      //source aperture
                 num = str2num(textVal[14])
-                start = 280      //source aperture
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[15])
+                WriteSourceApDiamToHeader(fname,num)
+        Endif
+        if(change[15])      //sample aperture
                 num = str2num(textVal[15])
-                start = 284      //sample aperture
-                ReWriteReal(fname,num,start)
+                WriteSampleApDiamToHeader(fname,num)
         Endif
         ///
-        if(change[16])
+        if(change[16])      //source-sam dist
                 num = str2num(textVal[16])
-                start = 288      //source-sam dist
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[17])
+                WriteSrcToSamDistToHeader(fname,num)
+        Endif
+        if(change[17])      //det offset
                 num = str2num(textVal[17])
-                start = 264      //det offset
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[18])
+                WriteDetectorOffsetToHeader(fname,num)
+        Endif
+        if(change[18])      //beamstop diam
                 num = str2num(textVal[18])
-                start = 272      //beamstop diam
-                ReWriteReal(fname,num,start)
-        Endif
-        if(change[19])
+                WriteBeamStopDiamToHeader(fname,num)
+        Endif
+        if(change[19])     //SDD
                 num = str2num(textVal[19])
-                start = 260      //SDD
-                ReWriteReal(fname,num,start)
-        Endif
-        //if ReWriteReal() was the last thing called, the file is closed already. just exit     
+                WriteSDDToHeader(fname,num)
+        Endif
         Return(0)
 End

sans/SANSReduction/branches/kline_29MAR07/Put in User Procedures/SANS_Reduction_v5.00/Transmission.ipf

@@ -252 +252 @@
         Variable isTrans, xTol= -5
 
-        String textstr,temp,labelStr,date_time,suffix,assoc
-        Variable ctime,lambda,sdd,detcnt,cntrate,refNum,trans,thick,xcenter,ycenter,numatten
-        Variable lastPoint, beamstop, Whole
+//      String textstr,temp,labelStr,date_time,suffix,assoc
+//      Variable ctime,lambda,sdd,detcnt,cntrate,refNum,trans,thick,xcenter,ycenter,numatten
+        Variable lastPoint//, beamstop, Whole
 
         isTrans = isTransFile(fname, xTol)
@@ -283 +283 @@
         lastPoint = numpnts(GLambda)
         
-        Open/R refNum as fname
-        
         InsertPoints lastPoint,1,G_TRANS_Filenames
         G_TRANS_Filenames[lastPoint]=""
@@ -292 +290 @@
         
         //read the file suffix
-        FSetPos refNum,19
-        FReadLine/N=4 refNum,suffix
-        //print suffix
         InsertPoints lastPoint,1,GSuffix
-        GSuffix[lastPoint]=suffix
+        GSuffix[lastPoint]=getSuffix(fname)
 
         //read any suffix that this file is associated with
-        //FSetPos refNum,91             //wrong position
-        FSetPos refNum,404
-        FReadLine/N=4 refNum,assoc
-        //print isTrans, assoc
         InsertPoints lastPoint,1,GSuffices
-        GSuffices[lastPoint]=assoc
+        GSuffices[lastPoint]=getAssociatedFileSuffix(fname)
             
         // read the sample.label text field
-        FSetPos refNum,98               //will start reading at byte 99
-        FReadLine/N=60 refNum,labelStr
         InsertPoints lastPoint,1,GLabels
-        GLabels[lastPoint]=labelStr
-
-        Close refNum
+        GLabels[lastPoint]=getSampleLabel(fname)
             
-        //read the reals with GBLoadWave
-        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
-        String strToExecute
-        
+
         //Transmission
-        strToExecute = GBLoadStr + "/S=158/U=1" + "\"" + fname + "\""
-        Execute strToExecute
-        Wave w=$"tempGBWave0"
-        trans = w[0]
         InsertPoints lastPoint,1,GTransmission
-        GTransmission[lastPoint]=trans
-        
-        //Whole Transmission
-        strToExecute = GBLoadStr + "/S=392/U=1" + "\"" + fname + "\""
-        Execute strToExecute
-        Wave w=$"tempGBWave0"
-        Whole = w[0]
+        GTransmission[lastPoint]=getSampleTrans(fname)
+        
+        //Whole detector Transmission
         InsertPoints lastPoint,1,GWhole
-        GWhole[lastPoint]=Whole
+        GWhole[lastPoint]=getSampleTransWholeDetector(fname)
             
         //SDD
-        strToExecute = GBLoadStr + "/S=260/U=1" + "\"" + fname + "\""
-        Execute strToExecute
-        sdd = w[0]
         InsertPoints lastPoint,1,GSDD
-        GSDD[lastPoint]=sdd
+        GSDD[lastPoint]=getSDD(fname)
             
         //wavelength
-        strToExecute = GBLoadStr + "/S=292/U=1" + "\"" + fname + "\""
-        Execute strToExecute
-        lambda = w[0]
         InsertPoints lastPoint,1,GLambda
-        GLambda[lastPoint]=lambda
-        
-//      InsertPoints lastPoint,1,GWhole
-//      GWhole[lastPoint]=1
-        
-        KillWaves/Z w
-
+        GLambda[lastPoint]=getWavelength(fname)
+        
+        return(0)
 End
 
@@ -533 +499 @@
                                         suffix=T_GSuffix[jj]
                                         filename = pathname + T_GFilenames[ii]
-                                        Open/A/T="????TEXT" refnum as filename
-                                        //FSetPos refnum,91             //wrong position
-                                        FSetPos refnum,404
-                                        FBinWrite refnum, suffix
-                                        FStatus refnum
-                                        FSetPos refnum,V_logEOF
-                                        Close refnum
+                                        WriteAssocFileSuffixToHeader(filename,suffix)
                                 endif
                                 jj+=1
@@ -556 +516 @@
                                         suffix=T_GSuffix[jj]
                                         filename = pathname + S_GFilenames[ii]
-                                        Open/A/T="????TEXT" refnum as filename
-                                        //FSetPos refnum,91             //wrong position
-                                        FSetPos refnum,404
-                                        FBinWrite refnum, suffix
-                                        FStatus refnum
-                                        FSetPos refnum,V_logEOF
-                                        Close refnum
+                                        WriteAssocFileSuffixToHeader(filename,suffix)
                                 endif
                                 jj+=1
@@ -601 +555 @@
                                         suffix=T_GSuffix[jj]
                                         filename = pathname + T_GFilenames[ii]
-                                        Open/A/T="????TEXT" refnum as filename
-                                        //FSetPos refnum,91             //wrong position
-                                        FSetPos refnum,404
-                                        FBinWrite refnum, suffix
-                                        FStatus refnum
-                                        FSetPos refnum,V_logEOF
-                                        Close refnum
+                                        WriteAssocFileSuffixToHeader(filename,suffix)
                                 endif
                                 jj+=1
@@ -662 +610 @@
                         
                         // write in zeros for the box coordinates
-                        Open/A/T="????TEXT" refnum as filename
-                        FSetPos refnum,478
-                        FBinWrite/F=3/B=3 refNum, zero
-                        FBinWrite/F=3/B=3 refNum, zero
-                        FBinWrite/F=3/B=3 refNum, zero
-                        FBinWrite/F=3/B=3 refNum, zero
-                        FStatus refnum                                  //move to the end of the file before closing
-                        FSetPos refnum,V_logEOF
-                        Close refnum
-        
+                        WriteXYBoxToHeader(filename,0,0,0,0)
+                        
                         // write in a null suffix
-                        Open/A/T="????TEXT" refnum as filename
-                        FSetPos refnum,404                      //suffix start byte is 404
-                        FBinWrite refnum, suffix
-                        FStatus refnum
-                        FSetPos refnum,V_logEOF
-                        Close refnum
+                        WriteAssocFileSuffixToHeader(filename,suffix)
                         
-                        //write a trans==1 to the file header of the raw data (open/close done in function)
-                        ReWriteReal(filename,1,158)             //transmission start byte is 158
-                        ReWriteReal(filename,1,392)             //WholeTrans start byte is 392
+                        //write a trans==1 to the file header of the raw data
+                        WriteTransmissionToHeader(filename,1)           //sample trans
+                        
+                        WriteWholeTransToHeader(filename,1)             //WholeTrans start byte is 392
                         
                         //then update the table that is displayed
@@ -693 +629 @@
         endif
         
-//      // Write suffix of empty beam file into transmission files
-//      ii= 0
-//      do
-//              if (cmpstr(T_EMP_Filenames[ii],"")!=0)
-//                      jj=0
-//                      do
-//                              if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
-//                                      suffix=T_GSuffix[jj]
-//                                      filename = pathname + T_GFilenames[ii]
-//                                      Open/A/T="????TEXT" refnum as filename
-//                                      //FSetPos refnum,91             //wrong position
-//                                      FSetPos refnum,404
-//                                      FBinWrite refnum, suffix
-//                                      FStatus refnum
-//                                      FSetPos refnum,V_logEOF
-//                                      Close refnum
-//                              endif
-//                              jj+=1
-//                      while(jj<num_t_files)
-//              endif
-//      ii+=1
-//      while(ii<num_t_files)
  
         if(target == 1)
@@ -721 +635 @@
                 do
                         filename = pathname + S_GFilenames[ii]
-                        Open/A/T="????TEXT" refnum as filename
-                        //FSetPos refnum,91             //wrong position
-                        FSetPos refnum,404
-                        FBinWrite refnum, suffix
-                        FStatus refnum
-                        FSetPos refnum,V_logEOF
-                        Close refnum
+                        // write in a null suffix
+                        WriteAssocFileSuffixToHeader(filename,suffix)
                         
                         //write a trans==1 to the file header of the raw data (open/close done in function)
-                        ReWriteReal(filename,1,158)             //transmission start byte is 158
+                        WriteTransmissionToHeader(filename,1)           //sample trans
                         
                         //then update the table that is displayed
@@ -742 +651 @@
         return(0)
 End
-
-
-// assigns both the empty file to the trans file
-// and the trans file to the scattering file
-// - writes out 4 characters to the file headers @ byte 404
-//
-// assignments are only permanently made when the transmissions
-// are actually calculated
-//
-// NOT USED - AssignSelTransFilestoData(first,last) has been generalized to take a range
-// 3/31/04 SRK
-//Function AssignTransFilesToData()
-//
-//      Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
-//      Wave/T T_GSuffices = $"root:myGlobals:TransHeaderInfo:T_Suffices"
-//      Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
-//      Wave/T T_GSuffix = $"root:myGlobals:TransHeaderInfo:T_Suffix"
-//      
-//      Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
-//      Wave/T S_GSuffices = $"root:myGlobals:TransHeaderInfo:S_Suffices"
-//      Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
-//      Wave/T S_GSuffix = $"root:myGlobals:TransHeaderInfo:S_Suffix"
-//      
-//      Variable num_s_files, num_t_files, ii, jj
-//      Variable refnum
-//      num_t_files = numpnts(T_GFilenames)
-//      num_s_files = numpnts(S_GFilenames)
-//      String suffix = ""
-//      PathInfo catPathName
-//      String pathname = S_path
-//      String filename
-//
-//      // Write suffix of empty beam file into transmission files
-//      ii= 0
-//      do
-//              if (cmpstr(T_EMP_Filenames[ii],"")!=0)
-//                      jj=0
-//                      do
-//                              if (cmpstr(T_EMP_Filenames[ii],T_GFilenames[jj])==0)
-//                                      suffix=T_GSuffix[jj]
-//                                      filename = pathname + T_GFilenames[ii]
-//                                      Open/A/T="????TEXT" refnum as filename
-//                                      //FSetPos refnum,91             //wrong position
-//                                      FSetPos refnum,404
-//                                      FBinWrite refnum, suffix
-//                                      FStatus refnum
-//                                      FSetPos refnum,V_logEOF
-//                                      Close refnum
-//                              endif
-//                      jj+=1
-//                      while(jj<num_t_files)
-//              endif
-//              ii+=1
-//      while(ii<num_t_files)
-// 
-//      // Write suffix of transmission files into scattering files
-//      ii= 0
-//      do
-//              if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
-//                      jj=0
-//                      do
-//                              if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
-//                                      suffix=T_GSuffix[jj]
-//                                      filename = pathname + S_GFilenames[ii]
-//                                      Open/A/T="????TEXT" refnum as filename
-//                                      //FSetPos refnum,91             //wrong position
-//                                      FSetPos refnum,404
-//                                      FBinWrite refnum, suffix
-//                                      FStatus refnum
-//                                      FSetPos refnum,V_logEOF
-//                                      Close refnum
-//                              endif
-//                              jj+=1
-//                      while(jj<num_t_files)
-//              endif
-//              ii+=1
-//      while(ii<num_s_files)
-//
-//      return(0)
-//End
-
-
-
-// NOT USED --- CalcSelTransFromHeader(first,last) has been generalized to accept a selection
-// and modified to account for different attenuation factors. 3/31/04 SRK
-//
-//Function CalcTransFromHeader()
-//      String filename
-//      Wave/T T_EMP_Filenames = $"root:myGlobals:TransHeaderInfo:T_EMP_Filenames"
-//      Wave/T T_GFilenames = $"root:myGlobals:TransHeaderInfo:T_Filenames"
-//      
-//      Wave/T S_TRANS_Filenames = $"root:myGlobals:TransHeaderInfo:S_TRANS_Filenames"
-//      Wave/T S_GFilenames = $"root:myGlobals:TransHeaderInfo:S_Filenames"
-//      Wave S_GTransmission =  $"root:myGlobals:TransHeaderInfo:S_Transmission"
-//      
-//      Variable num_s_files, num_t_files, ii, jj
-//      Variable refnum, transCts, emptyCts
-//      num_t_files = numpnts(T_GFilenames)
-//      num_s_files = numpnts(S_GFilenames)
-//      String suffix = ""
-//      PathInfo catPathName
-//      String pathname = S_path
-//      String textStr="",abortStr=""
-//      String emptyFile, transFile
-//      
-//      ii= 0
-//      do
-//              if (cmpstr(S_TRANS_Filenames[ii],"")!=0)
-//                      jj=0
-//                      do
-//                              if (cmpstr(S_TRANS_Filenames[ii],T_GFilenames[jj])==0)
-//                              //Look for an empty beam for the transmission then
-//                                      if (cmpstr(T_EMP_Filenames[jj],"")!=0)//Do the transmission calculation
-//                                              textStr = ""
-//                                              filename=pathname+S_GFilenames[ii]
-//                                              emptyFile = pathname+T_EMP_Filenames[jj]
-//                                              transFile = pathname+T_GFilenames[jj]
-//                                              //////////
-//                                              // check the empty beam file for previously selected coordinates
-//                                              //if they exist, set the xy string , save the normalized counts somewhere
-//                                              //the value was written to an unused r*4 header analysis.factor (@b494)
-//                                              Variable x1,x2,y1,y2,err
-//                                              Open/R refnum as emptyFile
-//                                              FSetPos refnum,478
-//                                              FBinRead/F=3/B=3 refnum, x1
-//                                              FBinRead/F=3/B=3 refnum, x2
-//                                              FBinRead/F=3/B=3 refnum, y1
-//                                              FBinRead/F=3/B=3 refnum, y2
-//                                              Close refnum
-//                                              //read the real count value
-//                                              String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
-//                                              String strToExecute
-//                                              strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
-//                                              Execute strToExecute
-//                                              Wave w=$"tempGBWave0"
-//                                              Variable/G root:myGlobals:Patch:gTransCts = w[0]
-//                                              emptyCts = w[0]
-//                      
-//                                              //
-//                                              if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
-//                                                      //no region selected    
-//                                                      //prompt user to select box w/marquee
-//                                                      DoWindow/F TransFileTable
-//                                                      Abort "Use \"Set BCENT File\", then \"SetXYBox\" to select XY range in empty beam file "+T_EMP_Filenames[jj]
-//                                                      //from here the Marquee menu selection must handle the task of setting the box
-//                                                      //and updating the information in the file header
-//                                              Endif
-//              
-//                                              //read in trans file to add to SAM
-//                                              ReadHeaderAndData(transFile)
-//                                              //adds to SAM
-//                                              err = Raw_to_work("SAM")
-//                                              //sum region in SAM
-//                                              transCts =  SumCountsInBox(x1,x2,y1,y2,"SAM")
-//                                              
-//                                              //calculate trans based on empty beam value
-//                                              Variable trans= transCts/emptyCts
-//                                              
-//                                              //write out counts and transmission
-//                                              textstr += "  Trans counts = "+num2str(transCts) + "   Trans = "+num2str(trans)
-//                                              Print S_GFilenames[ii], textstr
-//                                              //Print ii,jj
-//                                              //Print  "Empty counts = ",emptycts, "Trans counts = "+num2str(transCts) + "   Trans = "+num2str(trans)
-//                                              
-//                                              //write the trans to the file header of the raw data (open/close done in function)
-//                                              Variable start = 158            //transmission start byte
-//                                              ReWriteReal(filename,trans,start)
-//                                              
-//                                              //then update the global that is displayed
-//                                              S_GTransmission[ii] = trans
-//      
-//                                      else  // There is no empty assigned
-//                                               abortStr = "Empty beam file not assigned properly for " + T_GFilenames[jj]
-//                                               Print abortStr
-//                                               //Abort abortStr
-//                                               return(1)
-//                                      endif
-//                              endif
-//                              jj+=1
-//                      while(jj<num_t_files)
-//              else //no transmission file
-//                      abortStr = "Transmission beam file not assigned properly for " + S_GFilenames[ii]
-//                      Print abortStr
-//              endif
-//              ii+=1
-//      while(ii<num_s_files)
-//      print "done"
-//      return(0)
-//End
-
-
 
 //given a selection of scattering files, calculates the transmission
@@ -997 +715 @@
                                                 //if they exist, set the xy string , save the normalized counts somewhere
                                                 //the value was written to an unused r*4 header analysis.factor (@b494)
-                                                Open/R refnum as emptyFile
-                                                FSetPos refnum,478
-                                                FBinRead/F=3/B=3 refnum, x1
-                                                FBinRead/F=3/B=3 refnum, x2
-                                                FBinRead/F=3/B=3 refnum, y1
-                                                FBinRead/F=3/B=3 refnum, y2
-                                                Close refnum
+                                                GetXYBoxFromFile(emptyFile,x1,x2,y1,y2)
+                                                
                                                 //read the real count value
-                                                strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                Wave w=$"tempGBWave0"
-                                        //      Variable/G root:myGlobals:Patch:gTransCts = w[0]
-                                                emptyCts = w[0]
+                                                emptyCts = getBoxCounts(emptyFile)
                                                 // read the attenuator number of the empty beam file
-                                                strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                attenEmp = w[3]
+                                                attenEmp = getAttenNumber(emptyFile)
                                                 //
                                                 if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
@@ -1046 +753 @@
                                                 endif
                                                 //write the trans to the file header of the raw data (open/close done in function)
-                                                ReWriteReal(filename,trans,158)         //transmission start byte is 158
+                                                WriteTransmissionToHeader(filename,trans)
                                                 
                                                 //then update the global that is displayed
@@ -1117 +824 @@
                                                 //if they exist, set the xy string , save the normalized counts somewhere
                                                 //the value was written to an unused r*4 header analysis.factor (@b494)
-                                                Open/R refnum as emptyFile
-                                                FSetPos refnum,478
-                                                FBinRead/F=3/B=3 refnum, x1
-                                                FBinRead/F=3/B=3 refnum, x2
-                                                FBinRead/F=3/B=3 refnum, y1
-                                                FBinRead/F=3/B=3 refnum, y2
-                                                Close refnum
+                                                getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
+                                                
                                                 //read the real count value
-                                                strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                Wave w=$"tempGBWave0"
-                                        //      Variable/G root:myGlobals:Patch:gTransCts = w[0]
-                                                emptyCts = w[0]
+                                                emptyCts = getBoxCounts(emptyFile)
                                                 // read the attenuator number of the empty beam file
-                                                strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                attenEmp = w[3]
+                                                attenEmp = getAttenNumber(emptyFile)
                                                 //
                                                 if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
@@ -1168 +864 @@
                                                 endif
                                                 //write the trans to the file header of the raw data (open/close done in function)
-                                                ReWriteReal(filename,trans,158)         //transmission start byte is 158
+                                                WriteTransmissionToHeader(filename,trans)               //transmission start byte is 158
                                                 
                                                 //then update the global that is displayed
@@ -1242 +938 @@
                                                 //if they exist, set the xy string , save the normalized counts somewhere
                                                 //the value was written to an unused r*4 header analysis.factor (@b494)
-                                                Open/R refnum as emptyFile
-                                                FSetPos refnum,478
-                                                FBinRead/F=3/B=3 refnum, x1
-                                                FBinRead/F=3/B=3 refnum, x2
-                                                FBinRead/F=3/B=3 refnum, y1
-                                                FBinRead/F=3/B=3 refnum, y2
-                                                Close refnum
+                                                
+                                                getXYBoxFromFile(emptyFile,x1,x2,y1,y2)
                                                 //read the real count value
-                                                strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                Wave w=$"tempGBWave0"
-                                        //      Variable/G root:myGlobals:Patch:gTransCts = w[0]
-                                                emptyCts = w[0]
+                                                emptyCts = getBoxCounts(emptyFile)
                                                 // read the attenuator number of the empty beam file
-                                                strToExecute = GBLoadStr + "/S=39/U=4" + "\"" + emptyFile + "\""
-                                                Execute strToExecute
-                                                attenEmp = w[3]
+                                                attenEmp = getAttenNumber(emptyFile)
                                                 //
                                                 if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
@@ -1298 +983 @@
                                                 endif
                                                 //write the trans to the file header of the raw data (open/close done in function)
-                                                ReWriteReal(filename,trans,392)         //WholeTrans start byte is 392
+                                                WriteWholeTransToHeader(filename,trans)
                                                 
                                                 //then update the global that is displayed
@@ -1483 +1168 @@
         //the value was written to an unused r*4 header analysis.factor (@b494)
         Variable refnum,x1,x2,y1,y2,err
-        Open/R refnum as filename
-        FSetPos refnum,478
-        FBinRead/F=3/B=3 refnum, x1
-        FBinRead/F=3/B=3 refnum, x2
-        FBinRead/F=3/B=3 refnum, y1
-        FBinRead/F=3/B=3 refnum, y2
-        Close refnum
-        //read the real count value
-        String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=2/W=1/Q"
-        String strToExecute
-        strToExecute = GBLoadStr + "/S=494/U=1" + "\"" + filename + "\""
-        Execute strToExecute
-        Wave w=$"tempGBWave0"
-        Variable/G root:myGlobals:gTransCts = w[0]                      //***NOTE this is NOT in the Trans sub-folder
+        getXYBoxFromFile(filename,x1,x2,y1,y2)
+        
+        //read the real count value, assign to a global
+        Variable/G root:myGlobals:gTransCts = getBoxCounts(filename)                    //***NOTE this is NOT in the Trans sub-folder
         //
         if( ((x1-x2)==0) || ((y1-y2)==0) )              //zero width marquee in either direction
@@ -1547 +1222 @@
         
         UpdateBoxCoordinates()
-        KillWaves/Z w
         Return (0)
 End
@@ -1795 +1469 @@
         
         Variable start
-        //x-position starts after byte 368
-        //ReWriteReal() takes care of open/close on its own
-        start = 368      //BS x-position
-        ReWriteReal(fname,xpos,start)
+        //x-position starts after byte 368 in VAX files
+        WriteBSXPosToHeader(fname,xpos)
         return(0)
 End