source: sans/Dev/trunk/NCNR_User_Procedures/Reduction/SANS/ILL_DataReadWrite.ipf @ 779

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

//**************************
//
// Vers. 1.2 092101
// Vers. 5.0 29MAR07 - branched from main reduction to split out facility
//                     specific calls
//
// functions for reading raw data files from the VAX
// - RAW data files are read into the RAW folder - integer data from the detector
//   is decompressed and given the proper orientation
// - header information is placed into real,integer, or text waves in the order they appear
//   in the file header
//
// Work data (DIV File) is read into the DIV folder
//
//*****************************

//simple, main entry procedure that will load a RAW sans data file (not a work file)
//into the RAW dataFolder. It is up to the calling procedure to display the file
//
// called by MainPanel.ipf and ProtocolAsPanel.ipf
//
Function LoadRawSANSData(msgStr)
        String msgStr

        String filename=""

        //each routine is responsible for checking the current (displayed) data folder
        //selecting it, and returning to root when done
        PathInfo/S catPathName          //should set the next dialog to the proper path...
        //get the filename, then read it in
        filename = PromptForPath(msgStr)                //in SANS_Utils.ipf
        //check for cancel from dialog
        if(strlen(filename)==0)
                //user cancelled, abort
                SetDataFolder root:
                DoAlert 0, "No file selected, action aborted"
                return(1)
        Endif

        ReadHeaderAndData(filename)     //this is the full Path+file
        
        Return(0)
End


//function that does the guts of reading the binary data file
//fname is the full path:name;vers required to open the file
//
// The final root:RAW:data wave is the real
//neutron counts and can be directly operated on
//
// header information is put into three waves: integersRead, realsRead, and textRead
// logicals in the header are currently skipped, since they are no use in the 
// data reduction process.
//
// The output is the three R/T/I waves that are filled at least with minimal values
// and the detector data loaded into an array named "data"
//
// see documentation for the expected information in each element of the R/T/I waves
// and the minimum set of information. These waves can be increased in length so that
// more information can be accessed as needed (propagating changes...)
//
// called by multiple .ipfs (when the file name is known)
//
//
// THIS FUNCTION DOES NOT NEED TO BE MODIFIED. ONLY THE DATA ACCESSORS NEED TO BE CONSTRUCTED
//
Function ReadHeaderAndData(fname)
        String fname
        //this function is for reading in RAW data only, so it will always put data in RAW folder
        String curPath = "root:Packages:NIST:RAW:"
        SetDataFolder curPath           //use the full path, so it will always work
        Variable/G root:Packages:NIST:RAW:gIsLogScale = 0               //initial state is linear, keep this in RAW folder
        
        Variable refNum,integer,realval,ii
        String sansfname,textstr,v0
        
        Make/O/D/N=23 $"root:Packages:NIST:RAW:IntegersRead"
        Make/O/D/N=52 $"root:Packages:NIST:RAW:RealsRead"
        Make/O/T/N=11 $"root:Packages:NIST:RAW:TextRead"
        Make/O/N=7 $"root:Packages:NIST:RAW:LogicalsRead"
        
        Wave intw=$"root:Packages:NIST:RAW:IntegersRead"
        Wave realw=$"root:Packages:NIST:RAW:RealsRead"
        Wave/T textw=$"root:Packages:NIST:RAW:TextRead"
        Wave logw=$"root:Packages:NIST:RAW:LogicalsRead"
        
        // FILL IN 3 ARRAYS WITH HEADER INFORMATION FOR LATER USE
        // THESE ARE JUST THE MINIMALLY NECESSARY VALUES
        
        // filename as stored in the file header
        Open/R refNum as fname
        //skip first two bytes (VAX record length markers, not needed here)
//      FSetPos refNum, 2
        //read the next 21 bytes as characters (fname)
        
        
        
        for (ii=0;ii<2;ii+=1)
                FReadLine refNum,textstr
                sscanf textstr,"%s",v0
        
        endfor
        
        Close refnum
        
        textw[0]= v0
        
//      print "function read raw used"
        
        // date and time of collection
        textw[1]= getFileCreationDate(fname)
        
        // run type identifier (this is a reader for RAW data)
        textw[2]= "RAW"
        
        // user account identifier (currently used only for NCNR-specific operations)
        textw[3]= getFileInstrument(fname) 

        // sample label
        textw[6]= getSampleLabel(fname)
        
        // identifier of detector type, useful for setting detector constants
        //(currently used only for NCNR-specific operations)
        textw[9]= ""
        
        

        //total counting time in seconds
        intw[2] = getCountTime(fname)
        
        
        // total monitor count
        realw[0] = getMonitorCount(fname)
        
        // total detector count
        realw[2] = getDetCount(fname)
        
        // attenuator number (NCNR-specific, your stub returns 0)
        // may also be used to hold attenuator transmission (< 1)
        realw[3] = getAttenNumber(fname)
        
        // sample transmission
        realw[4] = getSampleTrans(fname)
        
        //sample thickness (cm)
        realw[5] = getSampleThickness(fname)
        
        // following 6 values are for non-linear spatial corrections to a detector (RC timing)
        // these values are set for a detctor that has a linear correspondence between
        // pixel number and real-space distance
        // 10 and 13 are the X and Y pixel dimensions, respectively (in mm!)
        //(11,12 and 13,14 are set to values for a linear response, as from a new Ordela detector)
        realw[10] = getDetectorPixelXSize(fname)
        realw[11] = 10000
        realw[12] = 0
        realw[13] = getDetectorPixelYSize(fname)
        realw[14] = 10000
        realw[15] = 0
        
        // beam center X,Y on the detector (in units of pixel coordinates (1,N))
        realw[16] = getBeamXPos(fname)
        realw[17] = getBeamYPos(fname)
        
        // sample to detector distance (meters)
        realw[18] = getSDD(fname)

        // detector physical width (right now assumes square...) (in cm)
        realw[20] = 102
        
        // beam stop diameter (assumes circular) (in mm)
        realw[21] = getBSDiameter(fname)
        
        // source aperture diameter (mm)
        realw[23] = getSourceApertureDiam(fname)
        
        // sample aperture diameter (mm)
        realw[24] = getSampleApertureDiam(fname)
        
        // source aperture to sample aperture distance
        realw[25] = getSourceToSampleDist(fname)
        
        // wavelength (A)
        realw[26] = getWavelength(fname)
        
        // wavelength spread (FWHM)
        realw[27] = getWavelengthSpread(fname)
        
        realw[52] = getreactorpower(fname)
        
        // beam stop X-position (motor reading, approximate cm from zero position)
        // currently NCNR-specific use to identify transmission measurements
        // you return 0
        realw[37] = 0
        
        
// the actual data array, dimensions are set as globals in 
// InitFacilityGlobals()
        NVAR XPix = root:myGlobals:gNPixelsX
        NVAR YPix = root:myGlobals:gNPixelsX
        
        SetDataFolder curPath
        
        Make/D/O/N=(XPix,YPix) $"root:Packages:NIST:RAW:data"
        WAVE data=$"root:Packages:NIST:RAW:data"

        // fill the data array with the detector values
        getDetectorData(fname,data)
        
        Setdatafolder curpath
        
        Duplicate/O data $"root:Packages:NIST:RAW:linear_data"                  // data is "fresh" and linear scale, so copy it now
        
        //keep a string with the filename in the RAW folder
        String/G root:Packages:NIST:RAW:fileList = textw[0]
        
        Setdatafolder root:

        
        Return 0

End

//****************
//main entry procedure for reading a "WORK.DIV" file
//displays a quick image of the  file, to check that it's correct
//data is deposited in root:DIV data folder
//
// local, just for testing
//
Proc ReadWork_DIV()
        
        String fname = PromptForPath("Select detector sensitivity file")
        ReadHeaderAndWork("DIV",fname)          //puts what is read in work.div
        
        String waveStr = "root:Packages:NIST:DIV:data"
        NewImage/F/K=1/S=2 $waveStr
        ModifyImage '' ctab= {*,*,YellowHot,0}
        
        String/G root:Packages:NIST:DIV:fileList = "WORK.DIV"
        
        SetDataFolder root:             //(redundant)
End




/////////DIV file created with NIST reduction so has the VAX format.... painful
//      
// Detector sensitivity files have the same header structure as RAW SANS data
// as NCNR, just with a different data array (real, rather than integer data)
//
// So for your facility, make this reader specific to the format of whatever
// file you use for a pixel-by-pixel division of the raw detector data
// to correct for non-uniform sensitivities of the detector. This is typically a
// measurement of water, plexiglas, or another uniform scattering sample.
//
// The data must be normalized to a mean value of 1
//
// called from ProtocolAsPanel.ipf
//
// type is "DIV" on input
Function ReadHeaderAndWork(type,fname)
        String type,fname
        
        //type is the desired folder to read the workfile to
        //this data will NOT be automatically displayed
        // gDataDisplayType is unchanged

        String cur_folder = type
        String curPath = "root:Packages:NIST:"+cur_folder
        SetDataFolder curPath           //use the full path, so it will always work
        
        Variable refNum,integer,realval
        String sansfname,textstr
        Variable/G $(curPath + ":gIsLogScale") = 0              //initial state is linear, keep this in DIV folder
        
        Make/O/D/N=23 $(curPath + ":IntegersRead")
        Make/O/D/N=52 $(curPath + ":RealsRead")
        Make/O/T/N=11 $(curPath + ":TextRead")
        
        WAVE intw=$(curPath + ":IntegersRead")
        WAVE realw=$(curPath + ":RealsRead")
        WAVE/T textw=$(curPath + ":TextRead")
        
        // the actual data array, dimensions are set as globals inÊ
        // InitFacilityGlobals()
        NVAR XPix = root:myGlobals:gNPixelsX
        NVAR YPix = root:myGlobals:gNPixelsX
        
        Make/O/D/N=(XPix,YPix) $(curPath + ":data")
        WAVE data = $(curPath + ":data")
        
        Make/O/D/N=(XPix,YPix) $(curPath + ":linear_data")
        WAVE linear_data = $(curPath + ":linear_data")
        
        // (1)
        // fill in your reader for the header here so that intw, realw, and textW are filled in
        // -- these are not really needed at all, so skip them for now
        // a simple duplication of some other data may be sufficient
        if(exists("root:Packages:NIST:raw:realsread") == 1)
                Duplicate/O $("root:Packages:NIST:raw:realsread"),$(curPath+ ":realsread")
                Duplicate/O $("root:Packages:NIST:raw:integersread"),$(curPath+ ":integersread")
                Duplicate/O/T $("root:Packages:NIST:raw:Textread"),$(curPath+ ":Textread")
        endif

        //(2)
        // then fill in a reader for the data array that will DIVIDE your data
        // to get the corrected values.

        //here you load in your file, you're already in the DIV folder
        LoadWave/O fname                //since fname is the full path
                
        String loadedStr = StringFromList(0,S_waveNames,";")            //then name of the wave loaded
        
//      data loaded should be named "linear_data" (this is set in the DIV writer)
        Duplicate/O linear_data,data                    // folder is in linear scale in its as-loaded state, so both are linear

        //keep a string with the filename in the DIV folder
        String/G $(curPath + ":fileList") = textw[0]
        
        //return the data folder to root
        SetDataFolder root:
        
        Return(0)
End


/////   ASC FORMAT READER  //////
/////   FOR WORKFILE MATH PANEL //////
//
//function to read in the ASC output of SANS reduction
// currently the file has 20 header lines, followed by a single column
// of 16384 values, Data is written by row, starting with Y=1 and X=(1->128)
//
//returns 0 if read was ok
//returns 1 if there was an error
//
// called by WorkFileUtils.ipf
//
//
// If the ASC data was generated by the NCNR data writer, then 
// NOTHING NEEDS TO BE CHANGED HERE
//
Function ReadASCData(fname,destPath)
        String fname, destPath
        //this function is for reading in ASCII data so put data in user-specified folder
        SetDataFolder "root:Packages:NIST:"+destPath

        NVAR pixelsX = root:myGlobals:gNPixelsX
        NVAR pixelsY = root:myGlobals:gNPixelsY
        Variable refNum=0,ii,p1,p2,tot,num=pixelsX,numHdrLines=220   ///waas 20 for NIST
        String str=""
        //data is initially linear scale
        Variable/G :gIsLogScale=0
        Make/O/T/N=(numHdrLines) hdrLines
        Make/O/D/N=(pixelsX*pixelsY) data                       //,linear_data
        
        //full filename and path is now passed in...
        //actually open the file
//      SetDataFolder destPath
        Open/R/Z refNum as fname                // /Z flag means I must handle open errors
        if(refnum==0)           //FNF error, get out
                DoAlert 0,"Could not find file: "+fname
                Close/A
                SetDataFolder root:
                return(1)
        endif
        if(V_flag!=0)
                DoAlert 0,"File open error: V_flag="+num2Str(V_Flag)
                Close/A
                SetDataFolder root:
                return(1)
        Endif
        // 
        for(ii=0;ii<numHdrLines;ii+=1)          //read (or skip) 18 header lines
                FReadLine refnum,str
                hdrLines[ii]=str
        endfor
        //      
        Close refnum
        
//      SetDataFolder destPath

//loadwave  /A=tempGBwave/L={0, start, numrow, 0, numcol}/N/G/D/O/E=1/K=1


        LoadWave/Q/G/D/N=temp fName 
        Wave/Z temp0=temp0
        data=temp0
        Redimension/N=(pixelsX,pixelsY) data            //,linear_data
        
        //linear_data = data
        
        KillWaves/Z temp0 
        
        //return the data folder to root
        SetDataFolder root:
        
        Return(0)
End

// fills the "default" fake header so that the SANS Reduction machinery does not have to be altered
// pay attention to what is/not to be trusted due to "fake" information.
// uses what it can from the header lines from the ASC file (hdrLines wave)
//
// destFolder is of the form "myGlobals:WorkMath:AAA"
//
//
// called by WorkFileUtils.ipf
//
// If the ASC data was generated by the NCNR data writer, then 
// NOTHING NEEDS TO BE CHANGED HERE
//
Function FillFakeHeader_ASC(destFolder)
        String destFolder
        Make/O/D/N=23 $("root:Packages:NIST:"+destFolder+":IntegersRead")
        Make/O/D/N=52 $("root:Packages:NIST:"+destFolder+":RealsRead")
        Make/O/T/N=11 $("root:Packages:NIST:"+destFolder+":TextRead")
        
        Wave intw=$("root:Packages:NIST:"+destFolder+":IntegersRead")
        Wave realw=$("root:Packages:NIST:"+destFolder+":RealsRead")
        Wave/T textw=$("root:Packages:NIST:"+destFolder+":TextRead")
        
        //Put in appropriate "fake" values
        //parse values as needed from headerLines
        Wave/T hdr=$("root:Packages:NIST:"+destFolder+":hdrLines")
        Variable monCt,lam,offset,sdd,trans,thick
        Variable xCtr,yCtr,a1,a2,a1a2Dist,dlam,bsDiam
        String detTyp=""
        String tempStr="",formatStr="",junkStr=""
        formatStr = "%g %g %g %g %g %g"
        tempStr=hdr[3]
        sscanf tempStr, formatStr, monCt,lam,offset,sdd,trans,thick
//      Print monCt,lam,offset,sdd,trans,thick,avStr,step
        formatStr = "%g %g %g %g %g %g %g %s"
        tempStr=hdr[5]
        sscanf tempStr,formatStr,xCtr,yCtr,a1,a2,a1a2Dist,dlam,bsDiam,detTyp
//      Print xCtr,yCtr,a1,a2,a1a2Dist,dlam,bsDiam,detTyp
        
        realw[16]=xCtr          //xCtr(pixels)
        realw[17]=yCtr  //yCtr (pixels)
        realw[18]=sdd           //SDD (m)
        realw[26]=lam           //wavelength (A)
        //
        // necessary values
        realw[10]=8                     //detector calibration constants, needed for averaging
        realw[11]=10000
        realw[12]=0
        realw[13]=8
        realw[14]=10000
        realw[15]=0
        //
        // used in the resolution calculation, ONLY here to keep the routine from crashing
        realw[20]=102           //det size
        realw[27]=dlam  //delta lambda
        realw[21]=bsDiam        //BS size
        realw[23]=a1            //A1
        realw[24]=a2    //A2
        realw[25]=a1a2Dist      //A1A2 distance
        realw[4]=trans          //trans
        realw[3]=0              //atten
        realw[5]=thick          //thick
        //
        //
        realw[0]=monCt          //def mon cts

        // fake values to get valid deadtime and detector constants
        //
        textw[9]=detTyp+"  "            //6 characters 4+2 spaces
        textw[3]="[NGxSANS00]"  //11 chars, NGx will return default values for atten trans, deadtime... 
        
        //set the string values
        formatStr="FILE: %s CREATED: %s"
        sscanf hdr[0],formatStr,tempStr,junkStr
//      Print tempStr
//      Print junkStr
        String/G $("root:Packages:NIST:"+destFolder+":fileList") = tempStr
        textw[0] = tempStr              //filename
        textw[1] = junkStr              //run date-time
        
        //file label = hdr[1]
        tempStr = hdr[1]
        tempStr = tempStr[0,strlen(tempStr)-2]          //clean off the last LF
//      Print tempStr
        textW[6] = tempStr      //sample label
        
        return(0)
End


///////// ACCESSORS FOR WRITING DATA TO HEADER  /////////
/////

// Write* routines all must:
// (1) open file "fname". fname is a full file path and name to the file on disk
// (2) write the specified value to the header at the correct location in the file
// (3) close the file

//sample transmission (0<T<=1)
Function WriteTransmissionToHeader(fname,trans)
        String fname
        Variable trans
        
        // your writer here
        
        WriteReal(fname,trans,5589)     //I will define at position 10 lines position 1  by myself
        
        // 16 bites between numbers and 81 per line
        
        return(0)
End

//whole transmission is NCNR-specific right now
// leave this stub empty
Function WriteWholeTransToHeader(fname,trans)
        String fname
        Variable trans
        
        // do nothing for now
        WriteReal(fname,trans,6885)   /// //I will define at position last  lines  position 1  by myself
        
        return(0)
End

//box sum counts is a real value
// used for transmission calculation module
Function WriteBoxCountsToHeader(fname,counts)
        String fname
        Variable counts
        
        // do nothing if not using NCNR Transmission module
        
        WriteReal(fname,counts,6868)
        
        ////I will define at position 2   lines before the end and  last position   by myself
        
        
        return(0)
End

//beam stop X-position
// used for transmission module to manually tag transmission files
Function WriteBSXPosToHeader(fname,xpos)
        String fname
        Variable xpos
        
        // do nothing if not using NCNR Transmission module
        
        WriteReal(fname,xpos,5119)    ////should do it for ypos for ILL ....NEED TO REMEMBER HERE
        /// line 4 column 2    
        
        return(0)
End

//sample thickness in cm
Function WriteThicknessToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        WriteReal(fname,num,5508)  //define at 9 lines  column 1 just above transmission by myself
        
        return(0)
End

//beam center X pixel location (detector coordinates)
Function WriteBeamCenterXToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        // pos (1) on line 71 => 70 lines x 81 char
        WriteReal(fname,num*10,5670) 
        
        ///   line 11 column 1
        
        return(0)
End

//beam center Y pixel location (detector coordinates)
Function WriteBeamCenterYToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        WriteReal(fname,num*10,5686)
        
        ///   line 11 column 2
        
        return(0)
End

//attenuator number (not its transmission)
// if your beam attenuation is indexed in some way, use that number here
// if not, write a 1 to the file here as a default
//
Function WriteAttenNumberToHeader(fname,num)
        String fname
        Variable num
        
        // your code here, default of 1
        WriteReal(fname,num,5799)
        
        ///   line 12 column 4
        
        return(0)
End


Function WritereactorpowerToHeader(fname,num)
        String fname
        Variable num
        
        // your code here, default of 1
        WriteReal(fname,num,6204)
        
        ///   line 12 column 4
        
        return(0)
End








// total monitor count during data collection
Function WriteMonitorCountToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        WriteReal(fname,num,4924)
        
        ///   line 1 column 5
        
        return(0)
End

//total detector count
Function WriteDetectorCountToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        WriteReal(fname,num,4908)
        
        ///   line 1 column 4
        
        return(0)
End

//transmission detector count
// (currently unused in data reduction)
Function WriteTransDetCountToHeader(fname,num)
        String fname
        Variable num
        
        // do nothing for now
        
        return(0)
End

//wavelength (Angstroms)
Function WriteWavelengthToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        WriteReal(fname,num,5703)
        
        //   line 11 column 3
        
        return(0)
End

//wavelength spread (FWHM)
Function WriteWavelengthDistrToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        WriteReal(fname,num,5719)
        
        //   line 11 column 4
        
        return(0)
End

//temperature of the sample (C)
Function WriteTemperatureToHeader(fname,num)
        String fname
        Variable num
        
        //  your code here
        
        WriteReal(fname,num,5347)
        
        //   line 7 column 1
        
        return(0)
End

//magnetic field (Oe)
Function WriteMagnFieldToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//Source Aperture diameter (millimeters)
Function WriteSourceApDiamToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
//      WriteReal(fname,num,5348)
      WriteReal(fname,num,6027)    ///4*81 = 324
      
      // line 15 colum 3
        
        return(0)
End

//Sample Aperture diameter (millimeters)
Function WriteSampleApDiamToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        WriteReal(fname,num,6043)
        
            // line 15 colum 4
        
        return(0)
End

//Source aperture to sample aperture distance (meters)
Function WriteSrcToSamDistToHeader(fname,num)
        String fname
        Variable num
        
        //      your code here
        WriteReal(fname,num,5784)  //it is collimation at ILL
        
        
        return(0)
End

//lateral detector offset (centimeters)
Function WriteDetectorOffsetToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        
        WriteReal(fname,10*num,5849)
        
        
        
        // line 13 column 2
        
        return(0)
End

//beam stop diameter (millimeters)
Function WriteBeamStopDiamToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        WriteReal(fname,num,6059)
        
        //line 15 column 5
        
        return(0)
End

//sample to detector distance (meters)
Function WriteSDDToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        //WriteReal(fname,num,5152)
        
        
        WriteReal(fname,num,5265)
        
        // line 4 column 4
        
        // real calculated distance line 6 colunm1
        
        return(0)
End

// physical dimension of detector x-pixel (mm)
Function WriteDetPixelXToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        WriteReal(fname,num,5735)
        
        //  line 11 column 5   
        
        return(0)
end

// physical dimension of detector y-pixel (mm)
Function WriteDetPixelYToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        WriteReal(fname,num,5752)
        
        return(0)
end

// sample label string
Function WriteSamLabelToHeader(fname,str)
        String fname,str
        
        // your code here
//              WriteText(fname,"                              ",2075)  // need to write in 30 bites no more....

        Variable numChars=30
        String blankStr=""
        blankStr = PadString(blankStr, numChars, 0x20)
        WriteText(fname,blankStr,2075)
        
        if(strlen(str)>numChars)
                str = str[0,numchars-1]
        endif
        
        WriteText(fname,str,2075)   //// need to change that in order to erase the title and write a new one

        return(0)
End

// total counting time (stored here as seconds/10??)
Function WriteCountTimeToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
//      WriteReal(fname,num,4894)
        WriteReal(fname,10*num,4892)
        
        
        
        return(0)
End



//////// ACCESSORS FOR READING DATA FROM THE HEADER  //////////////
//
// read specific bits of information from the header
// each of these operations MUST take care of open/close on their own
//
// fname is the full path and filname to the file on disk
// return values are either strings or real values as appropriate
//
//////


// function that reads in the 2D detector data and fills the array
// data[nx][ny] with the data values
// fname is the full name and path to the data file for opening and closing
//
//
Function getDetectorData(fname,data)
        String fname
        Wave data
        
        
        // your reader here
        
//      value = getRealValueFromHeader_2(fname,60,28,5,1,3)  // data start at 60+58 lines 
        ReadILLData2(fname,data)
        
        return (0)
End

// file suffix (NCNR data file name specific)
// return null string
Function/S getSuffix(fname)
        String fname
        
        String suffix = getStringFromHeader(fname,9341,6)
        
        // replace the leading space w/ "0"
        suffix = ReplaceString(" ",suffix,"0")
        
        return(suffix)   //// file suffix (6 characters @ byte 9341)
End

// associated file suffix (for transmission)
// NCNR Transmission calculation specific
// return null string
Function/S getAssociatedFileSuffix(fname)
        String fname
        
        string str
        
        str= getStringFromHeader(fname,9350,6)
        
        // replace leading space(s) w/zero
        str = ReplaceString(" ", str, "0" )
//      print  str
        
        return(str)  //  6 characters @ byte 9350
End

// sample label
Function/S getSampleLabel(fname)
        String fname
        
        String str
        
        // your code, returning str
        str = (getStringFromHeader(fname,2075,30))  /// 25*81  +  50////+51 30 lines before the end
        
        
        return(str)
End

// file creation date
Function/S getFileCreationDate(fname)
        String fname
        
        String str
        
        // your code, returning str
        
        str = (getStringFromHeader(fname,2106,50))   //324 +12
        
        return(str)
End


Function/S getFileInstrument(fname)
        String fname
        
        String str
        
        // your code, returning str
        
        str = (getStringFromHeader(fname,324,3))   //324 +12
        
        return(str)
End


//reactor power
Function getReactorpower(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,1,5)  //
        
        value = getRealValueFromHeader(fname,83)
        
//      print value
        
        return(value)
end





//monitor count
Function getMonitorCount(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,1,5)  //
        
        value = getRealValueFromHeader(fname,4)
        
//      print value
        
        return(value)
end

//saved monitor count
// NCNR specific for pre-processed data, never used
// return 0
Function getSavMon(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(0)
end

//total detector count
Function getDetCount(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,1,4) 
        
        value = getRealValueFromHeader(fname,3)
        
        return(value)
end

//Attenuator number, return 1 if your attenuators are not
// indexed by number
Function getAttenNumber(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,56,4) 
        
        value = getRealValueFromHeader(fname,58)
        
        return(value)
end

//transmission
Function getSampleTrans(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        value = getRealValueFromHeader(fname,45)
        
        return(value)
end

//box counts from stored transmission calculation
// return 0 if not using NCNR transmission module
Function getBoxCounts(fname)
        String fname
        
        Variable value
        
        // your code returning value
        value = getRealValueFromHeader(fname,124)
        
        return(value)
end

//whole detector trasmission
// return 0 if not using NCNR transmission module
Function getSampleTransWholeDetector(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//SampleThickness in centimeters
Function getSampleThickness(fname)
        String fname
        
        Variable value
        
        // your code returning value
        value = getRealValueFromHeader(fname,40)  //mm
        
        return(value)
end

//Sample Rotation Angle (degrees)
Function getSampleRotationAngle(fname)
        String fname
        
        Variable value
        
        // your code returning value
        value = getRealValueFromHeader(fname,64)
        
        return(value)
end

//temperature (C)
Function getTemperature(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,7,1) 
        
        value = getRealValueFromHeader(fname,30)
        
        return(value)
end

//field strength (Oe)
Function getFieldStrength(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//center of beam xPos in pixel coordinates
Function getBeamXPos(fname)
        String fname
        
        Variable value
        
        // your code returning value    
//      value = getRealValueFromHeader(fname,14)                //Lionel
        value = getRealValueFromHeader(fname,50)/10             //SRK
        
        return(value)
end

//center of beam Y pos in pixel coordinates
Function getBeamYPos(fname)
        String fname
        
        Variable value
        
        // your code returning value
//      value = getRealValueFromHeader(fname,15)                //Lionel
        value = getRealValueFromHeader(fname,51)/10             //SRK
        
        return(value)
end

//sample to detector distance (meters)
Function getSDD(fname)
        String fname
        
        Variable value
        
        // your code returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,4,4) 
//      value = getRealValueFromHeader(fname,18)  detector distance but need to add the offset due to the table
        
        value = getRealValueFromHeader(fname,25)
        
        
        return(value)
end

//lateral detector offset (centimeters)
Function getDetectorOffset(fname)
        String fname
        
        Variable value
        
        // your code returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,13,2)
        value = getRealValueFromHeader(fname,61) 
        
        return(value/10)  // need in cm ILL write in mm
end

//Beamstop diameter (millimeters)
Function getBSDiameter(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,15,5) 
        value = getRealValueFromHeader(fname,74)
        
        return(value)
end

//source aperture diameter (millimeters)
Function getSourceApertureDiam(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        value  = 52
        
        return(value)
end

//sample aperture diameter (millimeters)
Function getSampleApertureDiam(fname)
        String fname
        
        Variable value
        
        // your code returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,15,3) 
        value = getRealValueFromHeader(fname,73)
        
        if(value == 0)          //in case no aperture size was written to raw data file
                value = 10
        endif
        
        return(value)
end

//source AP to Sample AP distance (meters)
Function getSourceToSampleDist(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,12,3) 
        
        value = getRealValueFromHeader(fname,57)
        
        return(value)
end

//wavelength (Angstroms)
Function getWavelength(fname)
        String fname
        
        Variable value
        
        // your code returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,11,3) 
        value = getRealValueFromHeader(fname,52)
        
        return(value)
end

//wavelength spread (FWHM)
Function getWavelengthSpread(fname)
        String fname
        
        Variable value
        
        // your code returning value
        value = getRealValueFromHeader(fname,53)

        
        return(value)
end

// physical x-dimension of a detector pixel, in mm
Function getDetectorPixelXSize(fname)
        String fname
        
        Variable value
        
        // your code here returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,11,5) 
        value = getRealValueFromHeader(fname,54)
        
        return(value)
end

// physical y-dimension of a detector pixel, in mm
Function getDetectorPixelYSize(fname)
        String fname
        
        Variable value
        
        // your code here returning value
//      value = getRealValueFromHeader_2(fname,60,28,5,12,1) 
        value = getRealValueFromHeader(fname,55)
        
        return(value)
end

//transmission detector count (unused, return 0)
//
Function getTransDetectorCounts(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(0)
end


//total count time (seconds)
// stored here as (s/10), so multiply by 10 ?
Function getCountTime(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
//      value = getRealValueFromHeader_2(fname,60,28,5,1,3)  ///  line 1 col 3
        
        value = getRealValueFromHeader(fname,2)/10
        
        return(value)
end


//reads the wavelength from a reduced data file (not very reliable)
// - does not work with NSORTed files
// - only used in FIT/RPA (which itself is almost NEVER used...)
//
// DOES NOT NEED TO BE CHANGED IF USING NCNR DATA WRITER
Function GetLambdaFromReducedData(tempName)
        String tempName
        
        String junkString
        Variable lambdaFromFile, fileVar
        lambdaFromFile = 6.0
        Open/R/P=catPathName fileVar as tempName
        FReadLine fileVar, junkString
        FReadLine fileVar, junkString
        FReadLine fileVar, junkString
        if(strsearch(LowerStr(junkString),"lambda",0) != -1)
                FReadLine/N=11 fileVar, junkString
                FReadLine/N=10 fileVar, junkString
                lambdaFromFile = str2num(junkString)
        endif
        Close fileVar
        
        return(lambdaFromFile)
End

/////   TRANSMISSION RELATED FUNCTIONS    ////////
//box coordinate are returned by reference
//
// box to sum over is bounded (x1,y1) to (x2,y2)
//
// this function returns the bounding coordinates as stored in
// the header
//
// if not using the NCNR Transmission module, this function default to 
// returning 0000, and no changes needed
//
// filename is the full path:name to the file
Function getXYBoxFromFile(filename,x1,x2,y1,y2)
        String filename
        Variable &x1,&x2,&y1,&y2

        // return your bounding box coordinates or default values of 0
        x1=getRealValueFromHeader(filename,120)
        x2=getRealValueFromHeader(filename,121)
        y1=getRealValueFromHeader(filename,122)
        y2=getRealValueFromHeader(filename,123)
        
//      print "in get", x1,x2,y1,y2
        
        return(0)
End

// Writes the coordinates of the box to the header after user input
//
// box to sum over bounded (x1,y1) to (x2,y2)
//
// if not using the NCNR Transmission module, this function is null
//
// filename as passed in is a full path:filename
//
Function WriteXYBoxToHeader(filename,x1,x2,y1,y2)
        String filename
        Variable x1,x2,y1,y2
        
        // your code to write bounding box to the header, or nothing
        
        WriteReal(filename,x1,6804)
        WriteReal(filename,x2,6820)
        WriteReal(filename,y1,6836)
        WriteReal(filename,y2,6852)
        
        // use the last full line and the 4 first numbers
        
//      print "in write",x1,x2,y1,y2
        
        //  should start at 120  for read and  line 25
        
        /// 84 *81
        
        return(0)
End

// for transmission calculation, writes an NCNR-specific alphanumeric identifier
// (suffix of the data file)
//
// if not using the NCNR Transmission module, this function is null
Function WriteAssocFileSuffixToHeader(fname,suffix)
        String fname,suffix
                
        // replace leading space(s) w/zero
        suffix = ReplaceString(" ", suffix, "0" )
                
        suffix = suffix[0,5]            //limit to 6 characters
        
        WriteText(fname,suffix,9350)
        
        
        return(0)
end

Function/S getStringFromHeader(fname,start,num)
        String fname                            //full path:name
        Variable start,num              //starting byte and number of characters to read
        
        String str
        Variable refnum
        Open/R refNum as fname
        FSetPos refNum,start
        FReadLine/N=(num) refNum,str
        Close refnum
        
        return(str)
End

Function getRealValueFromHeader(fname,start)
        String fname
        Variable start
        Variable numLinesLoaded = 0,firstchar,countTime
        variable refnum
        Variable v1,v2,v3,v4,v5,v6,v7,v8,v9,v0,ii,valuesread,result
        String buffer 
        Make/O/D/N=128 TemporaryHeader
//      Make/O/D/N=(128) data

        Open/R refNum as fname          //if fname is "", a dialog will be presented
        if(refnum==0)
                return(1)               //user cancelled
        endif

//skip the next 10 lines
        For(ii=0;ii<60;ii+=1)
                FReadLine refnum,buffer
        EndFor

// read in the whole header
        For (ii=60;ii<188;ii+=1)

                numlinesloaded = ii-60
                FReadLine refNum,buffer //assume a 2nd line is there, w/16 values
                sscanf buffer,"%g %g %g %g %g ",v0,v1,v2,v3,v4
                valuesRead = V_flag
//              print valuesRead
                
//              print buffer
                
                //valuesRead = V_flag
//              print ii,refnum,v0,v1,v2,v3,v4,v5,v6,v7,v8,v9
//              print buffer
                
                TemporaryHeader[5*numlinesloaded] = v0
                TemporaryHeader[5*numlinesloaded+1] = v1                //monitor
                TemporaryHeader[5*numlinesloaded+2] = v2
                TemporaryHeader[5*numlinesloaded+3] = v3
                TemporaryHeader[5*numlinesloaded+4] = v4
        Endfor
                                                
        Close refNum            
        result= TemporaryHeader[start]
//      KillWaves/Z TemporaryHeader
        
        return (result)
End

//Function getRealValueFromHeader_1(fname,start)
//      String fname
//      Variable start
//
//      String GBLoadStr="GBLoadWave/O/N=tempGBwave/T={2,2}/J=1/W=1/Q"
//      
//      GBLoadStr += "/S="+num2str(start)+"/U=10" + "\"" + fname + "\""
//      Execute GBLoadStr
//      Wave w=$"tempGBWave0"
//      
//      return(w[0])
//End

//Function getRealValueFromHeader_2(fname,start,numrow,numcol,rowbit,colbit)
//      String fname
//      Variable start,numcol,numrow,colbit,rowbit
//      variable result
//      make /O/D/N=(numrow) w0,w1,w2,w3,w4
//      Make/O/D/N=(numrow,numcol) dataread
//      
//              
//      loadwave  /A=tempGBwave/L={0, start, numrow, 0, numcol}/N/G/D/O/K=1 fname
//      
//      Wave/Z tempGBwave0=tempGBwave0
//      Wave/Z tempGBwave1=tempGBwave1
//      Wave/Z tempGBwave2=tempGBwave2
//      Wave/Z tempGBwave3=tempGBwave3
//      Wave/Z tempGBwave4=tempGBwave4
//      
//      
//      w0=tempGBWave0
//       w1=tempGBWave1
//       w2=tempGBWave2
//       w3=tempGBWave3
//       w4=tempGBWave4
//      
/////                   redimension could use that to redimension dataread in only one colunm... but will see later..
//
//
//
//      KillWaves/Z tempGBwave0,tempGBwave1,tempGBwave3,tempGBwave2,tempGBwave4
//      ///        Make/O/D/N=(numrow,numcol),wres
//      
//      dataread[][0] = w0[p]
//      dataread[][1] = w1[p]
//      dataread[][2] = w2[p]
//      dataread[][3] = w3[p]
//      dataread[][4] = w4[p]
//
//KillWaves/Z w0,w1,w2,w3,w4
//      
////    wave wres = $"tempGBwave"  +num2str(linebit-1)
//      result  = dataread[rowbit-1][colbit-1]
//      
//      return(result)
//End


//Function ReadILLData(fname)
//      String fname
//      
//      NVAR pixelsX = root:myGlobals:gNPixelsX
//      NVAR pixelsY = root:myGlobals:gNPixelsY
//      Variable refNum=0,ii,p1,p2,tot,num=pixelsX,numHdrLines=118   ///waas 20 for NIST
//      String str=""
//      //data is initially linear scale
//      Variable/G :gIsLogScale=0
//      Make/O/T/N=(numHdrLines) hdrLines
//      Make/O/D/N=(pixelsX*pixelsY) data       
//      Make/O/D/N=(1638,10)    datahelp        //,linear_data
//      
//      //full filename and path is now passed in...
//      //actually open the file
////    SetDataFolder destPath
//      Open/R/Z refNum as fname                // /Z flag means I must handle open errors
//      if(refnum==0)           //FNF error, get out
//              DoAlert 0,"Could not find file: "+fname
//              Close/A
//              SetDataFolder root:
//              return(1)
//      endif
//      if(V_flag!=0)
//              DoAlert 0,"File open error: V_flag="+num2Str(V_Flag)
//              Close/A
//              SetDataFolder root:
//              return(1)
//      Endif
//      // 
//      for(ii=0;ii<numHdrLines;ii+=1)          //read (or skip) 18 header lines
//              FReadLine refnum,str
//              hdrLines[ii]=str
//      endfor
//      //      
//      Close refnum
//      
////    SetDataFolder destPath
//
//// loadwave  /A=tempt/L={0, 118, 1638, 1, 10}/N/J/D/O/E=1/K=1 fname
//
//loadwave  /A=tempt/L={0, 0, 1638, 0, 10}/N/G/D/O/E=1/K=1 fname
//
//Wave/Z tempt0=tempt0
//      Wave/Z tempt1=tempt1
//      Wave/Z tempt2=tempt2
//      Wave/Z tempt3=tempt3
//      Wave/Z tempt4=tempt4
//      Wave/Z tempt5=tempt5
//      Wave/Z tempt6=tempt6
//      Wave/Z tempt7=tempt7
//      Wave/Z tempt8=tempt8
//      Wave/Z tempt9=tempt9
//      
//      
//      
//      
//      datahelp[][0]=tempt0[p]
//      datahelp[][1]=tempt1[p]
//      datahelp[][2]=tempt2[p]
//      datahelp[][3]=tempt3[p]
//      datahelp[][4]=tempt4[p]
//      datahelp[][5]=tempt5[p]
//      datahelp[][6]=tempt6[p]
//      datahelp[][7]=tempt7[p]
//      datahelp[][8]=tempt8[p]
//      datahelp[][9]=tempt9[p]
//      
//      Killwaves/Z tempt1,tempt2,tempt3,tempt4,tempt0,tempt5,tempt6,tempt7,tempt8,tempt9
//
/////////////Wave/Z tempt0=tempt0
/////data=tempt
//      
//      
//      Redimension/N=(pixelsX,pixelsY) datahelp
//
//
////    LoadWave/Q/J/D/E=1/V={" " ,"non",1,1}/N=temp fName 
////    Wave/Z temp0=temp0
////    data=temp0
////    Redimension/N=(pixelsX,pixelsY) data            //,linear_data
//      
//      //linear_data = data
//      
//      KillWaves/Z temp0 
//      
//      //return the data folder to root
//      SetDataFolder root:
//      
//      Return(0)
//End



Function ReadILLData2(fname,data)
        String fname
        wave data

        Variable numLinesLoaded = 0,firstchar,countTime
        variable refnum
        Variable v1,v2,v3,v4,v5,v6,v7,v8,v9,v0,ii,valuesread
        String buffer 
        Make/O/D/N=16384 Dataline               //temporary storage

        Open/R refNum as fname          //if fname is "", a dialog will be presented
        if(refnum==0)
                return(1)               //user cancelled
        endif

//skip the next 10 lines
        For(ii=0;ii<118;ii+=1)
                FReadLine refnum,buffer
        EndFor

        For (ii=118;ii<1757;ii+=1)
                numlinesloaded = ii-118
                FReadLine refNum,buffer //assume a 2nd line is there, w/16 values
                sscanf buffer,"%g %g %g %g %g %g %g %g %g %g",v0,v1,v2,v3,v4,v5,v6,v7,v8,v9
                valuesRead = V_flag
//              print valuesRead                
//               buffer         
                //valuesRead = V_flag
//              print ii,refnum,v0,v1,v2,v3,v4,v5,v6,v7,v8,v9
//              print buffer
                
                if(ii == 1756)
                        dataline[10*numlinesloaded] = v0                                //last line has only four values
                        dataline[10*numlinesloaded+1] = v1
                        dataline[10*numlinesloaded+2] = v2
                        dataline[10*numlinesloaded+3] = v3
                else
                        dataline[10*numlinesloaded] = v0                //reading in 10 values per line
                        dataline[10*numlinesloaded+1] = v1
                        dataline[10*numlinesloaded+2] = v2
                        dataline[10*numlinesloaded+3] = v3
                        dataline[10*numlinesloaded+4] = v4
                        dataline[10*numlinesloaded+5] = v5
                        dataline[10*numlinesloaded+6] = v6
                        dataline[10*numlinesloaded+7] = v7
                        dataline[10*numlinesloaded+8] = v8
                        dataline[10*numlinesloaded+9] = v9
                endif
        Endfor
                                                
        Close refNum    
        
        data = dataline
        redimension /N=(128,128) data
        
//      Killwaves/Z dataline
        
        return (0)

end

// Write* routines all must:
// (1) open file "fname". fname is a full file path and name to the file on disk
// (2) write the specified value to the header at the correct location in the file
// (3) close the file

//
// ILL header values are 16 characters: one space followed by 15 bytes of the value, in scientific notation (pos 2 is the sign, last 4 are "e(+-)XX" )
// SRK - May 2008
Function WriteReal(path,value,start)
        string path
        variable value,start

        variable refnum
        
        String valStr
        sprintf valStr, "  %14e",value
//      print valstr, strlen(valStr)
        
        Open/A/T= "????" refnum as path
        
        FStatus refnum
        FSetPos refnum, start   
        FBinWrite refNum, valStr        
        FSetpos refnum,V_logEOF         // correct length is 142317 total bytes
        
        Close refnum
        
        return (0)

end


Function/S PromptForPathtest(msgStr)
        String msgStr
        String fullPath
        Variable refnum
        
        //this just asks for the filename, doesn't open the file
        Open/D/R/T="????"/M=(msgStr) refNum
        fullPath = S_FileName           //fname is the full path
        //      Print refnum,fullPath
        
        //null string is returned in S_FileName if user cancelled, and is passed back to calling  function
        Return(fullPath)
End


/// !!!! Make sure the text string is the correct LENGTH before sending it here!!!
// SRK - May 2008
Function WriteText(path,str,start)
        string path,str
        variable start
        
        variable refnum
        
        Open/A/T= "????TEXT" refnum as path
        
        FStatus refnum
        FSetPos refnum, start
        FBinWrite/F=0 refnum, str      //native object format (character)
        FSetPos refnum,V_logEOF
        
        Close refnum
        
        return (0)

end
////// OCT 2009, facility specific bits from ProDiv()
//"type" is the data folder that has the corrected, patched, and normalized DIV data array
//
// the header of this file is rather unimportant. Filling in a title at least would be helpful/
//
Function Write_DIV_File(type)
        String type
        
        // should have the linear display.....
        ConvertFolderToLogScale(type)

        // Your file writing function here. Don't try to duplicate the VAX binary format...
        
        SetDataFolder $("root:Packages:NIST:"+type)
        Save/C linear_data as "plex.DIV"
        
        SetDataFolder root:
        return(0)
End

////// OCT 2009, facility specific bits from MonteCarlo functions()
//"type" is the data folder that has the data array that is to be (re)written as a full
// data file, as if it was a raw data file
//
// not really necessary
//
Function/S Write_RawData_File(type,fullpath,dialog)
        String type,fullpath
        Variable dialog         //=1 will present dialog for name
        
        // Your file writing function here. Don't try to duplicate the VAX binary format...
        Print "Write_RawData_File stub"
        
        return(fullPath)
End