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

// in case you find this procedure useful for your research
// and of help to any specific publication, please cite:
// “Microstructure of Titanium Cement Lithium Disilicate Interface 
// in CAD CAM Dental Implant Crowns: A Three Dimensional Profilometric Analysis“, 
// S. Cresti et al., Clin Implant Dent Relat Res. (2013), DOI 10.1111/cid.12133

Menu "Macros"
   "Convert profilometer data...", ConvertProfilometerData()
End

Function ConvertProfilometerData()

   // here the variables and strings useful for loading profilometer data are defined:
   Variable numlines=100
   Variable numpoints=6118
   Variable length=1
   Variable step=5
   String textdatapath="C:WORK:RESEARCH:DENTAL MATs:TESI IMPIANTI:margine corone:"
   String filenamebase="profil"
   // here the data input and the respective legends are prepared:
   Prompt numlines, "Number of scan lines: " 
   Prompt numpoints, "Number of points per line: "
   Prompt step, "step between profiles (um): "
   Prompt length, "length of profile (mm): "
   Prompt textdatapath, "Profilometer files folder: "
   Prompt filenamebase, "Filename base:"
   // here the actual input window is started:
   DoPrompt "Enter profilometer data parameters", numlines, numpoints, step, length, textdatapath, filenamebase
   // the following is a control check:
   //print filenamebase
   if (V_Flag)
      return -1 // User canceled
   endif
   Variable widthinm=numlines*step/1000000
   Variable lengthinm=length/1000 
   
   // here the folder of the input data files folder is set:
   NewPath /o textdatapath textdatapath

   // here all the .dat profilometer files from 001 to numlines are to loaded into one wave each:
   variable k
   for (k=1; k<numlines+1; k+=1)
      // for each index the file name is reconstructed first: 
      // first, the number part comes:
      string filenamenumber
      if (k<10) 
         filenamenumber="00"+num2str(k)
      endif
      if ((k>9) & (k<100))
         filenamenumber="0"+num2str(k)
      endif 
      if ((k>99) & (k<1000))
         filenamenumber=num2str(k)
      endif
      // the following is a control check:
      //print "filenamenumber: "+filenamenumber  
      // second, the whole file name comes, from base + number + extension:
      String filename
      filename=filenamebase+"_"+filenamenumber+".dat"
      // the following is a control check:
      //print filename
      // finally, the file is loaded into a wave:
      LoadWave/J/D/O/L={0, 6, numpoints, 1, 1} /A=$filename /P=textdatapath filename 
   endfor

   string wave2DName=filenamebase+"2Dmap"
   // the following is a control check:   
   //print wave2Dname
   make/O wave2Dmap//$wave2Dname
   redimension /n=(numpoints,numlines) wave2Dmap //$wave2Dname

   Variable j, i
   String wavename, wavenumberprefix
      for (j=1; j<numlines+1; j+=1)
         if (j<10) 
            wavenumberprefix="00"
         endif
         if ((j>9) & (j<100))
            wavenumberprefix="0"
         endif 
         if ((j>99) & (j<1000))
            wavenumberprefix=""
         endif

         wavename=filenamebase+"_"+wavenumberprefix+num2str(j)+".dat0"
         wave w=$wavename
         for (i=0; i<numpoints; i+= 1)
            WAVE wave2Dmap
            wave2Dmap[i][j-1]=w[i]
         endfor
      endfor
      rename wave2Dmap $wave2Dname
      duplicate $wave2Dname :Images:$wave2Dname
      duplicate /O $wave2Dname :images:dummy
      //dummy=$wave2Dname
      killwaves/Z $wave2Dname
            
      // here it does the appropriate modifications of AFM image dummy:
      redimension /n=(numpoints,numlines,1) :images:dummy
      setscale /i x,0,lengthinm, "m", :images:dummy
      setscale /i y,0,widthinm, "m", :images:dummy
      //modifyimage dummy interpolate=0
      //extractlayer()
      duplicate /o $wave2Dname dummy
      //dummy=$wave2Dname
      //insertlayer()
      //doppio click sul plot dell'immagine nella finestra del sw AFM
      //settare width mode: auto, height mode: aspect= valoreRatioh/w x w
      
      Variable wanttoclear
      Prompt wanttoclear, "Want to clear data browser root?"
      // here the input window is started:
      DoPrompt "Enter wanttoclear", wanttoclear
      if (wanttoclear==1)
         KillWaves/A/Z; KillVariables/A/Z; Killstrings/A/Z
      endif
      if (V_Flag)
         return -1 // User canceled
      endif

modifyimage dummy interpolate=0

end