/*=========================================================================

  Program: GDCM (Grassroots DICOM). A DICOM library

  Copyright (c) 2006-2011 Mathieu Malaterre
  All rights reserved.
  See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/

/**
 * Simple example showing how to bind a custom Observer to the Scanner in response
 * to ProgressEvent
 * If found, icons will be extracted or else they will be generated and save as PNG
 *
 * Compilation:
 * $ CLASSPATH=gdcm.jar javac ../../gdcm/Examples/Java/ScanDirectory.java -d .
 *
 * Usage:
 * $ LD_LIBRARY_PATH=. CLASSPATH=gdcm.jar:. java ScanDirectory gdcmData
 */
import gdcm.*;
import gdcm.Reader;
import gdcm.LookupTable;
import java.io.File;
import java.io.*;
import java.awt.image.*;
import javax.imageio.ImageIO;

public class ScanDirectory
{
  public static class MyWatcher extends SimpleSubjectWatcher
    {
    public MyWatcher(Subject s) { super(s,"Override String"); }
    protected void ShowProgress(Subject caller, Event evt)
      {
      ProgressEvent pe = ProgressEvent.Cast(evt);
      System.out.println( "This is my progress: " + pe.GetProgress() );
      }
    }

  public static byte[] GetAsByte(Bitmap input)
    {
    long len = input.GetBufferLength();
    byte[] buffer = new byte[ (int)len ];
    PhotometricInterpretation pi = input.GetPhotometricInterpretation();
    if( pi.GetType() == PhotometricInterpretation.PIType.MONOCHROME1 )
      {
      ImageChangePhotometricInterpretation icpi = new ImageChangePhotometricInterpretation();
      icpi.SetInput( input );
      icpi.SetPhotometricInterpretation(
        new PhotometricInterpretation(
          PhotometricInterpretation.PIType.MONOCHROME2 ) );
      if( icpi.Change() )
        {
        Bitmap output = icpi.GetOutput();
        output.GetArray( buffer );
        }
      return buffer;
      }
    else
      {
      input.GetArray( buffer );
      return buffer;
      }
    }
  public static short[] GetAsShort(Bitmap input)
    {
    long len = input.GetBufferLength(); // length in bytes
    short[] buffer = new short[ (int)len / 2 ];
    PhotometricInterpretation pi = input.GetPhotometricInterpretation();
    if( pi.GetType() == PhotometricInterpretation.PIType.MONOCHROME1 )
      {
      ImageChangePhotometricInterpretation icpi = new ImageChangePhotometricInterpretation();
      icpi.SetInput( input );
      icpi.SetPhotometricInterpretation(
        new PhotometricInterpretation(
          PhotometricInterpretation.PIType.MONOCHROME2 ) );
      if( icpi.Change() )
        {
        Bitmap output = icpi.GetOutput();
        output.GetArray( buffer );
        }
      return buffer;
      }
    else
      {
      input.GetArray( buffer );
      return buffer;
      }
    }
  public static boolean WritePNG(Bitmap input, String outfilename )
    {
    int imageType = BufferedImage.TYPE_CUSTOM;
    PixelFormat pf = input.GetPixelFormat();
    PhotometricInterpretation pi = input.GetPhotometricInterpretation();
    // We need to handle both public and private icon
    // It could well be that we are getting an RGB Icon or 16 bits Icon:
    ColorModel colorModel = null;
    if( pf.GetSamplesPerPixel() == 1 )
      {
      if( pi.GetType() == PhotometricInterpretation.PIType.MONOCHROME1
         || pi.GetType() == PhotometricInterpretation.PIType.MONOCHROME2 )
        {
        if( pf.GetScalarType() == PixelFormat.ScalarType.UINT8 )
          {
          imageType = BufferedImage.TYPE_BYTE_GRAY;
          }
        else if( pf.GetScalarType() == PixelFormat.ScalarType.UINT12 )
          {
          imageType = BufferedImage.TYPE_USHORT_GRAY;
          }
        else if( pf.GetScalarType() == PixelFormat.ScalarType.UINT16 )
          {
          imageType = BufferedImage.TYPE_USHORT_GRAY;
          }
        }
      else if( pi.GetType() == PhotometricInterpretation.PIType.PALETTE_COLOR )
        {
        LookupTable lut = input.GetLUT();
        long rl = lut.GetLUTLength( LookupTable.LookupTableType.RED );
        byte[] rbuf = new byte[ (int)rl ];
        long rl2 = lut.GetLUT( LookupTable.LookupTableType.RED, rbuf );
        assert rl == rl2;
        long gl = lut.GetLUTLength( LookupTable.LookupTableType.GREEN );
        byte[] gbuf = new byte[ (int)gl ];
        long gl2 = lut.GetLUT( LookupTable.LookupTableType.GREEN, gbuf );
        assert gl == gl2;
        long bl = lut.GetLUTLength( LookupTable.LookupTableType.BLUE );
        byte[] bbuf = new byte[ (int)bl ];
        long bl2 = lut.GetLUT( LookupTable.LookupTableType.BLUE, bbuf );
        assert bl == bl2;
        colorModel = new IndexColorModel(8, (int)rl, rbuf, gbuf, bbuf);
        // For code below
        imageType = BufferedImage.TYPE_BYTE_GRAY;
        }
      }
    else if( pf.GetSamplesPerPixel() == 3 )
      {
      if( pf.GetScalarType() == PixelFormat.ScalarType.UINT8 )
        {
        // FIXME should be TYPE_3BYTE_RGB
        imageType = BufferedImage.TYPE_3BYTE_BGR;
        }
      }
    //System.out.println( "pf: " + pf.toString() );
    //System.out.println( "pi: " + pi.toString() );
    long width  = input.GetDimension(0);
    long height = input.GetDimension(0);
    BufferedImage bi;
    if( pi.GetType() == PhotometricInterpretation.PIType.PALETTE_COLOR )
      {
      bi = new BufferedImage(colorModel,
        colorModel.createCompatibleWritableRaster((int)width, (int)height),
        false, null);
      }
    else
      {
      bi = new BufferedImage((int)width,(int)height,imageType);
      }
    WritableRaster wr = bi.getRaster();
    //System.out.println( "imagetype: " + imageType );
    if( imageType == BufferedImage.TYPE_BYTE_GRAY
      || imageType == BufferedImage.TYPE_3BYTE_BGR )
      {
      byte[] buffer = GetAsByte( input );
      wr.setDataElements (0, 0, (int)width, (int)height, buffer);
      }
    else if( imageType == BufferedImage.TYPE_USHORT_GRAY )
      {
      short[] buffer = GetAsShort( input );
      wr.setDataElements (0, 0, (int)width, (int)height, buffer);
      }

    File outputfile = new File( outfilename );
    try {
      ImageIO.write(bi, "png", outputfile);
    } catch (IOException e) {
      return false;
    }
    return true;
    }

  public static void main(String[] args) throws Exception
    {
    String directory = args[0];

    Directory d = new Directory();
    long nfiles = d.Load( directory, true );
    if(nfiles == 0)
      {
      throw new Exception("No files found");
      }
//    System.out.println( "Files:\n" + d.toString() );
    FilenamesType fns = d.GetFilenames();

    //Scanner s = new Scanner();
    SmartPtrScan sscan = Scanner.New();
    Scanner s = sscan.__ref__();
    //SimpleSubjectWatcher watcher = new SimpleSubjectWatcher(s, "MySimple");
    MyWatcher watcher = new MyWatcher(s);
    Tag[] tagarray = {
      new Tag(0x0010, 0x0010),    // PatientName
      new Tag(0x0010, 0x0020),    // PatientID
      new Tag(0x0010, 0x0030),    // PatientBirthDate
      new Tag(0x0010, 0x0040),    // PatientSex
      new Tag(0x0010, 0x1010),    // PatientAge
      new Tag(0x0020, 0x000d),    // StudyInstanceUID
      new Tag(0x0020, 0x0010),    // StudyID
      new Tag(0x0008, 0x0020),    // StudyDate
      new Tag(0x0008, 0x1030),    // StudyDescription
      new Tag(0x0020, 0x000e),    // SeriesInstanceUID
      new Tag(0x0020, 0x0011),    // SeriesNumber
      new Tag(0x0008, 0x0021),    // SeriesDate
      new Tag(0x0008, 0x103e),    // SeriesDescription
      new Tag(0x0008, 0x0090),    // ReferringPhysicianName
      new Tag(0x0008, 0x0060),    // Modality
      new Tag(0x0054, 0x0400),    // ImageID ?? Should be Instance number ??
      new Tag(0x0008, 0x0018),    // SOPInstanceUID
      new Tag(0x0008, 0x0032),    // AcquisitionTime
      new Tag(0x0008, 0x0033),    // ContentTime
      new Tag(0x0020, 0x0013),    // InstanceNumber
      new Tag(0x0020, 0x1041),    // SliceLocation
      new Tag(0x0018, 0x0050),    // SliceThickness ?? Eg. Enhanced MR Image Storage
      new Tag(0x0008, 0x0080),    // InstitutionName
      new Tag(0x0028, 0x1050),    // WindowCenter
      new Tag(0x0028, 0x1051),    // WindowWidth
    };
    for( Tag t : tagarray ) {
      //System.out.println( "Tag: " + t.toString() );
      s.AddTag( t );
    }
    boolean b = s.Scan( fns );
    if(!b)
      {
      throw new Exception("Could not scan");
      }

    for( long idx = 0; idx < fns.size(); ++idx )
      {
      Reader r = new Reader();
      String fn = fns.get( (int)idx );
      String outfn = fn + ".png";
      r.SetFileName( fn );
      TagSetType tst = new TagSetType();
      tst.insert( new Tag(0x7fe0,0x10) );
      b = r.ReadUpToTag( new Tag(0x88,0x200), tst );
      UIntArrayType dims = ImageHelper.GetDimensionsValue( r.GetFile() );
      if( b )
        {
        IconImageFilter iif = new IconImageFilter();
        System.out.println( "Processing: " + fn );

        iif.SetFile( r.GetFile() );
        b = iif.Extract();
        if( b )
          {
          Bitmap icon = iif.GetIconImage(0);
          WritePNG(icon, outfn);
          }
        else
          {
          ImageReader ir = new ImageReader();
          ir.SetFileName( fn );
          if( ir.Read() )
            {
            Image img = ir.GetImage();
            StringFilter sf = new StringFilter();
            sf.SetFile( r.GetFile() );
            String strval = sf.ToString( new Tag(0x0028,0x0120) );
            IconImageGenerator iig = new IconImageGenerator();
            iig.SetPixmap( img );
            iig.AutoPixelMinMax( true );
            try {
              double val = Double.parseDouble( strval );
              iig.SetOutsideValuePixel( val );
            }
            catch ( NumberFormatException e) {
              }
            iig.ConvertRGBToPaletteColor( false );
            long idims[] = { 128, 128};
            iig.SetOutputDimensions( idims );
            iig.Generate();
            Bitmap icon = iig.GetIconImage();
            WritePNG(icon, outfn);
            }
          }
        }
      }

    System.out.println( "Scan:\n" + s.toString() );

    System.out.println( "success" );
    }
}