//
// 	Image J Macro to extract DICOM header tags required for NHSBSP Patient Dose software  
//	into a csv file (MS Excel compatible).
// 	This version is specific for images produced by Philips/Sectra X-ray equipment.    
 
// 	Version 1.2P beta version only
// 	Requires ImageJ v 1.43k as minimum
 
// 	Author - Lindsay Mungutroy
//		 Jarvis Breast Centre, Guildford.
//
// 	Date 20 May 2014
//



//
// 	locate folder where images are

dir = getDirectory("Browse to select folder where images are");

//	set up file for data output - not in the same folder as images (as explained in manual)

  f = File.open("");

// 	set up header information for output file.  The headers are the same as used in the Patient Dose software 
  
print(f, "Survey Number" + "," + "Patient Number" + "," + "View code" + ","+ "kV" + "," + "Anode" + "," + "Filter"+ ","  + "Thickness (mm)" + "," + "mAs" + "," + "large cassette used" + "," + "auto/man" + "," + "Automatic mode" + "," + "AEC density set" + "," + "Age" + "," + "Comment" + "," + "Error" + "," + "AEC Density Mode" + "," + "Force" + ","  + "Focal Spot(mm)"  + "," + "Image Time" + "," + "Image Type" + "," + "Model" + "," + "Device Serial No" + "," + "Study Date" + "," + "View");

// 	use batch mode to reduce on-screen processing (does not dsplay images)

setBatchMode(true);

// extract dose info from individual image in folder

     list = getFileList(dir);
     for (i=0; i<list.length; i++) { 
        if (endsWith(list[i], "/"))
           getDoseInfo(""+dir+list[i]);
     } 

//   close data output file and return to normal mode
   
File.close(f)
setBatchMode(false);

//
// 	Function to extract dose information by looking in folder and sub-folders recursively
// 	Uses the getTag plugin to get DICOM headers  
//
 
function getDoseInfo(dir) { 
   list = getFileList(dir);  
   for (i=0; i<list.length; i++) { 
       if (endsWith(list[i], "/"))
          getDoseInfo(""+dir+list[i]);        
       else {
          path = dir+list[i];
          open(path);

// Check for Image Type first
 
          ImageType = getTag("0008,0068");
          ImageType = substring(ImageType,6,8);

//	Blank Fields required for columns in Patient Dose software

	  SurveyNo = " ";
	  comment = " ";
	  error = " "; 

          StudyDate = getTag("0008,0020");
          Model = getTag("0008,1090");
          DeviceSerialNo = getTag("0018,1000");

          PatientID = getTag("0010,0020"); 
          PatientAge = getTag("0010,1010");

//  	Extract 2-digit age for patient's age if available or leave as blank

          if (PatientAge == "")
	     PatientAge = PatientAge;
          else if (PatientAge == " ")
             PatientAge = PatientAge;
	  else
 	     PatientAge = substring(PatientAge,2,4);

          ImageTime = getTag("0008,0033");                  
          ViewCode = getTag("0008,103E");
          ViewProtocol = getTag("0018,1030");
	  ViewProtocol = getTag("0018,5101");
	  ViewLR = getTag("0020,0062");
	  ViewLR = substring(ViewLR,0,2);
	  ViewProtocol = ViewLR + ViewProtocol;

//	Convert View Protocol to required format for Patient Dose software
 
             if (ViewProtocol == " L CC")
                ViewProtocol = "LCC";
             else if (ViewProtocol == " R CC")
                ViewProtocol = "RCC";
             else if (ViewProtocol == " L MLO ")
                ViewProtocol = "LOB";
             else if (ViewProtocol == " R MLO ")
                ViewProtocol = "ROB";
             else
                ViewProtocol = ViewProtocol;

          Thickness = getTag("0018,11A0");
          kVp = getTag("0018,0060");       
          Exposure = getTag("0018,1153");

//	Convert uAs to mAs

          mAsExposure = parseInt(Exposure)/1000;

          FocalSpot = getTag("0018,1190");
          CompressionForce = getTag("0018,11A2");
	  //autoorman = getTag("0018,7060");
	  autoorman = getTag("0019,1047");
	  AECMode = getTag("0019,1052");
          //AECMode = getTag("0018,7062");
          

//     Get No of pixels by row and columns to interpolate paddle size
 
	  Rows = getTag("0028,0010");
	  Columns = getTag("0028,0011");

// 	Convert to Large Paddle Yes/No

	  Rowsint = parseInt(Rows);
	  if (Rowsint <= 2400)
	     LPadYesNo = "No";
	  //else if (Rowsint > 2400)
          else
	     LPadYesNo = "Yes";
	  //else
	     //LPadYesNo = Rows;
          
          Target = getTag("0018,1191");

// 	Convert the target to required format

          if (Target == " TUNGSTEN")
             Target = "W";
          else if (Target == " MOLYBDENUM")
	     Target = "Mo";
	  else if (Target == " RHODIUM")
             Target = "Rh";
	  else if (Target == " RHODIUM ")
             Target = "Rh";
	  else 
	     Target = Target;
 
          //AECDensitySetting = getTag("0019,1029");
	 

//	Convert the AEC Density Setting to required format
	
	  //AECDsetNum = indexOf(AECDensitySetting,"g");
	  //AECDsetNum = AECDsetNum + 1;
	  //AECDset = substring(AECDensitySetting,AECDsetNum);
          AECDset = " ";

          AECDensityMode = getTag("0019,1025");
	  AECDensityMode = " ";

          Filter = getTag("0018,7050");

// 	Convert the filter to required format

          if (Filter == " ALUMINUM")
             Filter = "Al";
          else if (Filter == " ALUMINIUM")
             Filter = "Al";
          else if (Filter == " SILVER")
             Filter = "Ag";        
          else if (Filter == " RHODIUM")
             Filter = "Rh";
	  else if (Filter == " RHODIUM ")
             Filter = "Rh";
          else if (Filter == " MOLYBDENUM")
             Filter = "Mo";
	  else if (Filter == " COPPER")
	     Filter = "Cu";
          else 
             Filter = Filter;

//	print output to file for each image

        if (ImageType == "RE") {
	     //close();
        print(f, SurveyNo + "," + PatientID + "," + ViewProtocol + ","+ kVp + "," + Target + "," + Filter + "," + Thickness + "," + mAsExposure + "," + LPadYesNo + "," + autoorman + "," + AECMode + "," + AECDset + "," + PatientAge + "," + comment + "," + error + "," + AECDensityMode + "," + CompressionForce + ","  + FocalSpot + "," + ImageTime + "," + ImageType + "," + Model + "," +  DeviceSerialNo + "," + StudyDate + "," + ViewCode);
	}
        close();
      } 
     } 
  } 


// This function returns the numeric value of the 
// specified tag (e.g., "0018,0050"). Returns NaN 
// (not-a-number) if the tag is not found or it 
// does not have a numeric value.

  function getNumericTag(tag) {
    value = getTag(tag);
    if (value=="") return NaN;
    index3 = indexOf(value, "\\");
    if (index3>0)
      value = substring(value, 0, index3);
    value = 0 + value; // convert to number
    return value;
  }

// This function returns the value of the specified 
// tag  (e.g., "0010,0010") as a string. Returns "" 
// if the tag is not found.

  function getTag(tag) {
      info = getImageInfo();
      index1 = indexOf(info, tag);
      if (index1==-1) return "";
      index1 = indexOf(info, ":", index1);
      if (index1==-1) return "";
      index2 = indexOf(info, "\n", index1);
      value = substring(info, index1+1, index2);
      return value;
  }