//
// OMETiffWriter.java
//

/*
LOCI Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
Eric Kjellman and Brian Loranger.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Library General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Library General Public License for more details.

You should have received a copy of the GNU Library General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

package loci.formats.out;

import java.io.IOException;
import loci.formats.*;

/**
 * OMETiffWriter is the file format writer for OME-TIFF files.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/OMETiffWriter.java">Trac</a>,
 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/OMETiffWriter.java">SVN</a></dd></dl>
 */
public class OMETiffWriter extends TiffWriter {

  // -- Constructor --

  public OMETiffWriter() {
    super("OME-TIFF", new String[] {"ome.tif", "ome.tiff"});
  }

  // -- IFormatHandler API methods --

  /* @see loci.formats.IFormatHandler#close() */
  public void close() throws IOException {
    if (out != null) out.close();
    out = null;
    if (currentId != null) {
      // extract OME-XML string from metadata object
      MetadataRetrieve retrieve = getMetadataRetrieve();
      String xml = MetadataTools.getOMEXML(retrieve);

      // insert TiffData element
      int pix = xml.indexOf("<Pixels ");
      int end = xml.indexOf("/>", pix);
      xml = xml.substring(0, end) + "><TiffData/></Pixels>" +
        xml.substring(end + 2);

      // write OME-XML to the first IFD's comment
      try {
        TiffTools.overwriteComment(currentId, xml);
      }
      catch (FormatException exc) { LogTools.trace(exc); }
      catch (IOException exc) { LogTools.trace(exc); }
    }
    super.close();
  }

}

//
// OMETiffWriter.java
//

/*
LOCI Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
Eric Kjellman and Brian Loranger.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU Library General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Library General Public License for more details.

You should have received a copy of the GNU Library General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

package loci.formats.out;

import java.io.IOException;
import loci.formats.*;

/**
 * OMETiffWriter is the file format writer for OME-TIFF files.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/loci/formats/out/OMETiffWriter.java">Trac</a>,
 * <a href="https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/formats/out/OMETiffWriter.java">SVN</a></dd></dl>
 */
public class OMETiffWriter extends TiffWriter {

  // -- Constructor --

  public OMETiffWriter() {
    super("OME-TIFF", new String[] {"ome.tif", "ome.tiff"});
  }

  // -- IFormatHandler API methods --

  /* @see loci.formats.IFormatHandler#close() */
  public void close() throws IOException {
    if (out != null) out.close();
    out = null;
    if (currentId != null) {
      // extract OME-XML string from metadata object
      MetadataRetrieve retrieve = getMetadataRetrieve();
      String xml = MetadataTools.getOMEXML(retrieve);

      // insert TiffData element
      int pix = xml.indexOf("<Pixels ");
      int end = xml.indexOf("/>", pix);
      xml = xml.substring(0, end) + "><TiffData/></Pixels>" +
        xml.substring(end + 2);

      // write OME-XML to the first IFD's comment
      try {
        TiffTools.overwriteComment(currentId, xml);
      }
      catch (FormatException exc) {
        IOException io =
          new IOException("Unable to append OME-XML comment");
        io.initCause(exc);
        throw io;
      }
    }
    super.close();
  }

}

Deal with exceptions from TiffTools.overwriteComment.