source: sans/Release/trunk/NCNR_User_Procedures/SANS/Reduction/FACILITY_DataReadWrite.ipf @ 338

#pragma rtGlobals=1             // Use modern global access method.
#pragma version=5.0
#pragma IgorVersion = 6.0

//**************************
//
// 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:RAW"
        SetDataFolder curPath           //use the full path, so it will always work
        Variable/G root:RAW:gIsLogScale = 0             //initial state is linear, keep this in RAW folder
        
        Variable refNum,integer,realval
        String sansfname,textstr
        
        Make/D/O/N=23 $"root:RAW:IntegersRead"
        Make/D/O/N=52 $"root:RAW:RealsRead"
        Make/O/T/N=11 $"root:RAW:TextRead"
        
        Wave intw=$"root:RAW:IntegersRead"
        Wave realw=$"root:RAW:RealsRead"
        Wave/T textw=$"root:RAW:TextRead"
        
        // FILL IN 3 ARRAYS WITH HEADER INFORMATION FOR LATER USE
        // THESE ARE JUST THE MINIMALLY NECESSARY VALUES
        
        // filename as stored in the file header
        textw[0]= fname 
        
        // 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]= ""

        // 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[3] = 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] = 1000
        realw[12] = 0
        realw[13] = getDetectorPixelYSize(fname)
        realw[14] = 1000
        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] = 65
        
        // 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)
        
        // 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
        
        Make/D/O/N=(XPix,YPix) $"root:RAW:data"
        WAVE data=$"root:RAW:data"

        // fill the data array with the detector values
        getDetectorData(fname,data)
        
        //keep a string with the filename in the RAW folder
        String/G root:RAW:fileList = textw[0]
        
        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:DIV:data"
        NewImage/F/K=1/S=2 $waveStr
        ModifyImage '' ctab= {*,*,YellowHot,0}
        
        String/G root:DIV:fileList = "WORK.DIV"
        
        SetDataFolder root:             //(redundant)
End



// 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:"+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 in 
        // InitFacilityGlobals()
        NVAR XPix = root:myGlobals:gNPixelsX
        NVAR YPix = root:myGlobals:gNPixelsX
        
        Make/O/D/N=(XPix,YPix) $(curPath + ":data")
        WAVE data = $(curPath + ":data")
        
        
        // (1)
        // fill in your reader for the header here so that intw, realw, and textW are filled in
        // ? possibly a duplication of the raw data reader
        
        
        
        //(2)
        // then fill in a reader for the data array that will DIVIDE your data
        // to get the corrected values.
        

        

        //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:"+destPath

        NVAR pixelsX = root:myGlobals:gNPixelsX
        NVAR pixelsY = root:myGlobals:gNPixelsY
        Variable refNum=0,ii,p1,p2,tot,num=pixelsX,numHdrLines=20
        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/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/N=23 $("root:"+destFolder+":IntegersRead")
        Make/O/N=52 $("root:"+destFolder+":RealsRead")
        Make/O/T/N=11 $("root:"+destFolder+":TextRead")
        
        Wave intw=$("root:"+destFolder+":IntegersRead")
        Wave realw=$("root:"+destFolder+":RealsRead")
        Wave/T textw=$("root:"+destFolder+":TextRead")
        
        //Put in appropriate "fake" values
        //parse values as needed from headerLines
        Wave/T hdr=$("root:"+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]=5                     //detector calibration constants, needed for averaging
        realw[11]=10000
        realw[12]=0
        realw[13]=5
        realw[14]=10000
        realw[15]=0
        //
        // used in the resolution calculation, ONLY here to keep the routine from crashing
        realw[20]=65            //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:"+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
        
        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
        
        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
        
        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
        
        return(0)
End

//sample thickness in cm
Function WriteThicknessToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//beam center X pixel location (detector coordinates)
Function WriteBeamCenterXToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//beam center Y pixel location (detector coordinates)
Function WriteBeamCenterYToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        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
        
        return(0)
End

// total monitor count during data collection
Function WriteMonitorCountToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//total detector count
Function WriteDetectorCountToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        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
        
        return(0)
End

//wavelength spread (FWHM)
Function WriteWavelengthDistrToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//temperature of the sample (C)
Function WriteTemperatureToHeader(fname,num)
        String fname
        Variable num
        
        //  your code here
        
        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
        
        return(0)
End

//Sample Aperture diameter (millimeters)
Function WriteSampleApDiamToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        
        return(0)
End

//Source aperture to sample aperture distance (meters)
Function WriteSrcToSamDistToHeader(fname,num)
        String fname
        Variable num
        
        //      your code here
        
        return(0)
End

//lateral detector offset (centimeters)
Function WriteDetectorOffsetToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        
        return(0)
End

//beam stop diameter (millimeters)
Function WriteBeamStopDiamToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        return(0)
End

//sample to detector distance (meters)
Function WriteSDDToHeader(fname,num)
        String fname
        Variable num
        
        //your code here
        
        return(0)
End

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

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

// sample label string
Function WriteSamLabelToHeader(fname,str)
        String fname,str
        
        // your code here

        return(0)
End

// total counting time (seconds)
Function WriteCountTimeToHeader(fname,num)
        String fname
        Variable num
        
        // your code here
        
        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
        
        return(0)
End

// file suffix (NCNR data file name specific)
// return null string
Function/S getSuffix(fname)
        String fname
        
        return("")
End

// associated file suffix (for transmission)
// NCNR Transmission calculation specific
// return null string
Function/S getAssociatedFileSuffix(fname)
        String fname
        
        return("")
End

// sample label
Function/S getSampleLabel(fname)
        String fname
        
        String str
        
        // your code, returning str
        
        return(str)
End

// file creation date
Function/S getFileCreationDate(fname)
        String fname
        
        String str
        
        // your code, returning str
        
        return(str)
End


//monitor count
Function getMonitorCount(fname)
        String fname
        
        Variable value
        
        // your code returning 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
        
        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
        
        return(value)
end

//transmission
Function getSampleTrans(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        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
        
        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
        
        return(value)
end

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

//temperature (C)
Function getTemperature(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        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
        
        return(value)
end

//center of beam Y pos in pixel coordinates
Function getBeamYPos(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//sample to detector distance (meters)
Function getSDD(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//lateral detector offset (centimeters)
Function getDetectorOffset(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//Beamstop diameter (millimeters)
Function getBSDiameter(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

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

//sample aperture diameter (millimeters)
Function getSampleApertureDiam(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//source AP to Sample AP distance (meters)
Function getSourceToSampleDist(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//wavelength (Angstroms)
Function getWavelength(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

//wavelength spread (FWHM)
Function getWavelengthSpread(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        return(value)
end

// physical x-dimension of a detector pixel, in mm
Function getDetectorPixelXSize(fname)
        String fname
        
        Variable value
        
        // your code here returning value
        
        return(value)
end

// physical y-dimension of a detector pixel, in mm
Function getDetectorPixelYSize(fname)
        String fname
        
        Variable value
        
        // your code here returning value
        
        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)
Function getCountTime(fname)
        String fname
        
        Variable value
        
        // your code returning value
        
        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
Function getXYBoxFromFile(filename,x1,x2,y1,y2)
        String filename
        Variable &x1,&x2,&y1,&y2
        
        Variable refnum
        String tmpFile = FindValidFilename(filename)
        // tmpFile is only a parital path

        // return your bounding box coordinates or default values of 0
        x1=0
        y1=0
        x2=0
        y2=0
        
        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
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
        
        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
                
        // your code to write bounding box to the header, or nothing
        
        return(0)
end