//
// 	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 GE equipment.    
 
// 	Version 1.2G 
// 	Requires ImageJ v 1.43k as minimum
 
// 	Author - Lindsay Mungutroy
//		 Jarvis Breast Centre, Guildford.
//
// 	Date 29 March 2013
//



//
// 	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)" + "," + "View" + "," + "Image Time" + "," + "Image Type" + "," + "Model" + "," + "Device Serial No" + "," + "Study Date");

// 	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 getInfo 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 = getInfo("0008,0068");
          ImageType = substring(ImageType,6,8);
 
//	Blank Fields required for columns in Patient Dose software

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

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

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

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

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

          ImageTime = getInfo("0008,0033");                  
          ViewCode = getInfo("0008,103E");
          ViewProtocol = getInfo("0018,1030");
	  ViewProtocol = getInfo("0018,5101");
	  ViewLR = getInfo("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 == " LCC")
                ViewProtocol = "LCC";
             else if (ViewProtocol == " R CC")
                ViewProtocol = "RCC";
             else if (ViewProtocol == " RCC")
                ViewProtocol = "RCC";
             else if (ViewProtocol == " L MLO ")
                ViewProtocol = "LOB";
             else if (ViewProtocol == " LMLO")
                ViewProtocol = "LOB";
            else if (ViewProtocol == " R MLO ")
                ViewProtocol = "ROB";
            else if (ViewProtocol == " R MLO ")
                ViewProtocol = "ROB";
            else
                ViewProtocol = ViewProtocol;

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

//	Convert uAs to mAs

          mAsExposure = parseInt(Exposure)/1000;

          FocalSpot = getInfo("0018,1190");
          CompressionForce = getInfo("0018,11A2");
	  autoorman = getInfo("0018,7060");
          AECMode = getInfo("0018,7062");
          AECModeNum1 = indexOf(AECMode, "AOP ");
          AECModeNum1 = AECModeNum1 + 4;
          AECMode1 = substring(AECMode,AECModeNum1);
          AECModeNum2 = indexOf(AECMode1, " ");
          AECModeNum2 = AECModeNum2 + 1;
          AECMode = substring(AECMode1,0,AECModeNum2);

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

// 	Convert to Large Paddle Yes/No

	  Rowsint = parseInt(Rows);
	  if (Rowsint <= 2400)
	     LPadYesNo = "No";
          else
	     LPadYesNo = "Yes";
          
          Target = getInfo("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 = getInfo("0019,1029");
	  // not available for GE
	 

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

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

          Filter = getInfo("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 + "," + ViewCode + "," + ImageTime + "," + ImageType + "," + Model + "," +  DeviceSerialNo + "," + StudyDate);
	}
        close();
      } 
     } 
  }