getXRDML() - function to load xrdml data from Panalytical diffractometers using the XOP XMLutils

Mon, 05/18/2009 - 05:11 am

The getXRDML() function makes use of the XOP XMLutils by andyfaff (http://www.igorexchange.com/project/XMLutils) to load diffracted intensties from xrdml files (Panalytical diffractomters standard xml file format).
It creates a folder for each xrdml-file read. The foldername will be the xrdml-filename in lower case letters without the fileextension. The intensities are loaded into waves called 'intensities##' stored in the folder /XMLutil/XRD/'filename'.
It can also handle mutiple (repeated) scans in one xrdml-file by assigning a number '##' to each intensities wave. It also reads the scan comments and additional information about each scan in the file like scannumber, start-,endtime, start-,endposition, measurement program and so on and stores them in a note to each intensities wave.

I am grateful to andyfaff for helping me putting his XMLutils to use with the xrdml files and for reviewing this snippet.


#pragma rtGlobals=1		// Use modern global access method.


Function getXRDML()
        variable fileID
        variable ii, llength, numscans, iii, numcommlines, start, finish, numrows
	
	  string folder="", noteStr="", noteAddStr="", noteFinStr=""
	  
        open/r/d/t="????"/M="Please select the XRDML file" fileID

        if(strlen(S_filename)>0)
                fileID = XMLopenfile(S_fileName)
                if(fileID<1)
                        print "Error, can't load file"
                        return 0
                endif
        else
                return 0
        endif
        
      //Make DataFolder according to XRDML-Filename
	llength = ItemsInList(S_fileName, ":")
	folder = StringFromList(llength-1, S_fileName, ":")
	folder = RemoveEnding(lowerstr(folder), ".xml")
	folder = RemoveEnding(lowerstr(folder), ".xrdml")
	//printf "\rfolder=%s", folder
	NewDataFolder/S/O root:XMLutils
	NewDataFolder/S/O root:XMLutils:XRD
	NewDataFolder/S/O $folder

	//find out how many scans there were.
      XMLlistXpath(fileID, "//xrdml:scan", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3")
      Wave/t M_listXPath
      numscans = dimsize(M_listXPath,0)
	  
	//get measurement info and add as note to the wave
	XMLwaveFmXPath(fileID, "/xrdml:xrdMeasurements/xrdml:comment/xrdml:entry", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
      Wave/T M_xmlContent, W_xmlContentNodes
	numcommlines=dimsize(M_xmlContent,1)
	
	for(iii=0; iii<numcommlines; iii+=1)
		noteStr=noteStr+M_xmlContent[0][iii]+"\r"
	endfor
		    
	//get measurement program comment
	XMLwaveFmXPath(fileID, "/xrdml:xrdMeasurements/xrdml:xrdMeasurement/xrdml:comment/xrdml:entry", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+"Measurement program comment:\r"+M_xmlContent[0][0]+"\r"
		    
	//get sample id
	XMLwaveFmXPath(fileID, "//xrdml:sample/xrdml:id", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+"Sample Name: "+M_xmlContent[0][0]+"\r"
	 	    
	//get generator/tube info
	XMLwaveFmXPath(fileID, "//xrdml:incidentBeamPath/xrdml:xRayTube/xrdml:anodeMaterial", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+"Tube: " + XMLstrFmXPath(fileID, "//xrdml:incidentBeamPath/xrdml:xRayTube/@name", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "") + " @ "
	XMLwaveFmXPath(fileID, "//xrdml:incidentBeamPath/xrdml:xRayTube/xrdml:tension", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+M_xmlContent[0][0]+"kV/"
	XMLwaveFmXPath(fileID, "//xrdml:incidentBeamPath/xrdml:xRayTube/xrdml:current", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+M_xmlContent[0][0]+"mA\r"
	 	    
	//get wavelength info
	XMLwaveFmXPath(fileID, "//xrdml:usedWavelength", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "\n")
	noteStr=noteStr+"Wavelengths:\rkAlpha1: "+M_xmlContent[0][0]+"\rkAlpha2: "+M_xmlContent[0][1]+"\rkBeta: "+M_xmlContent[0][2]+"\r"	    
       
        //load all the xrd intensities in.
        for(ii=1 ; ii<numscans+1 ; ii+=1)
            //load the intensities and put the scaling on the wave
            XMLwaveFmXpath(fileID, "//xrdml:scan["+num2str(ii)+"]/xrdml:dataPoints/xrdml:intensities", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "")
            Wave/T M_xmlContent, W_xmlContentNodes
            numrows = dimsize(M_xmlContent,0)
            make/o/d/n=(numrows) $"intensities"+num2istr(ii)
            Wave intensity = $"intensities"+num2istr(ii)
            intensity = str2num(M_xmlcontent)
		   
		//get scan info and add to the wave note		    
		//get start/end time of scan
            noteAddStr=noteAddStr + "--- Scan #"+num2str(ii)+"---\r"
            noteAddStr=noteAddStr+"Start time: " + XMLstrFmXPath(fileID, "//xrdml:scan["+num2str(ii)+"]/xrdml:header/xrdml:startTimeStamp", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "") +"\r"
            noteAddStr=noteAddStr+"End time: " + XMLstrFmXPath(fileID, "//xrdml:scan["+num2str(ii)+"]/xrdml:header/xrdml:endTimeStamp", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "") +"\r"
             
            //here comes the scaling
            XMLwaveFmXpath(fileID, "//xrdml:scan["+num2str(ii)+"]//xrdml:positions[@axis='2Theta']/xrdml:startPosition", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "")
            start = str2num(M_xmlcontent[0])
            noteAddStr = noteAddStr + "Start position: " + M_xmlContent[0] +"\r"
            XMLwaveFmXpath(fileID, "//xrdml:scan["+num2str(ii)+"]//xrdml:positions[@axis='2Theta']/xrdml:endPosition", "xrdml=http://www.xrdml.com/XRDMeasurement/1.3", "")
            finish = str2num(M_xmlcontent[0])
            noteAddStr = noteAddStr + "End position: " + M_xmlContent[0] +"\r"
                
            noteFinStr=noteStr+noteAddStr
		Note/NOCR intensity, noteFinStr
		noteAddStr=""
		noteFinStr=""
      	SetScale/I x, start, finish, intensity
      endfor
	
	killwaves/z      M_Xmlcontent, W_xmlcontentnodes, M_listXPath
      
      if(fileID)
      	xmlclosefile(fileID, 0)
      endif
      
      SetDataFolder root:XMLutils:XRD
      return 0
End

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getXRDML() - function to load xrdml data from Panalytical diffractometers using the XOP XMLutils

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