gt:     catch (ReflectException exc) {
context: /*
   * #%L
   * OME Bio-Formats package for BSD-licensed readers and writers.
   * %%
   * Copyright (C) 2005 - 2013 Open Microscopy Environment:
   *   - Board of Regents of the University of Wisconsin-Madison
   *   - Glencoe Software, Inc.
   *   - University of Dundee
   * %%
   * Redistribution and use in source and binary forms, with or without
   * modification, are permitted provided that the following conditions are met:
   * 
   * 1. Redistributions of source code must retain the above copyright notice,
   *    this list of conditions and the following disclaimer.
   * 2. Redistributions in binary form must reproduce the above copyright notice,
   *    this list of conditions and the following disclaimer in the documentation
   *    and/or other materials provided with the distribution.
   * 
   * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
   * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
   * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
   * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
   * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
   * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
   * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
   * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
   * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
   * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
   * POSSIBILITY OF SUCH DAMAGE.
   * 
   * The views and conclusions contained in the software and documentation are
   * those of the authors and should not be interpreted as representing official
   * policies, either expressed or implied, of any organization.
   * #L%
   */
  
  package loci.formats.in;
  
  import java.awt.image.BufferedImage;
  import java.awt.image.RenderedImage;
  import java.io.File;
  import java.io.FileNotFoundException;
  import java.io.IOException;
  
  import loci.common.FileHandle;
  import loci.common.IRandomAccess;
  import loci.common.Location;
  import loci.common.ReflectException;
  import loci.common.ReflectedUniverse;
  import loci.formats.CoreMetadata;
  import loci.formats.FormatException;
  import loci.formats.FormatTools;
  import loci.formats.MetadataTools;
  import loci.formats.MissingLibraryException;
  import loci.formats.gui.AWTImageTools;
  import loci.formats.meta.MetadataStore;
  
  /**
   * TiffJAIReader is a file format reader for TIFF images. It uses the
   * Java Advanced Imaging library (javax.media.jai) to read the data.
   *
   * Much of this code was adapted from
   * <a href="http://java.sun.com/products/java-media/jai/forDevelopers/samples/MultiPageRead.java">this example</a>.
   *
   * <dl><dt><b>Source code:</b></dt>
   * <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/TiffJAIReader.java">Trac</a>,
   * <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/TiffJAIReader.java;hb=HEAD">Gitweb</a></dd></dl>
   *
   * @author Curtis Rueden ctrueden at wisc.edu
   */
  public class TiffJAIReader extends BIFormatReader {
  
    // -- Constants --
  
    private static final String NO_JAI_MSG =
      "Java Advanced Imaging (JAI) is required to read some TIFF files. " +
      "Please install JAI from https://jai.dev.java.net/";
  
    // -- Fields --
  
    /** Reflection tool for JAI calls. */
    protected ReflectedUniverse r;
  
    // -- Constructor --
  
    /** Constructs a new TIFF reader that uses Java Image I/O. */
    public TiffJAIReader() {
      super("Tagged Image File Format", TiffReader.TIFF_SUFFIXES);
      domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
    }
  
    // -- IFormatReader API methods --
  
    /* @see loci.formats.IFormatReader#openPlane(int, int, int, int, int int) */
    public Object openPlane(int no, int x, int y, int w, int h)
      throws FormatException, IOException
    {
      FormatTools.checkPlaneParameters(this, no, -1, x, y, w, h);
      BufferedImage img = openBufferedImage(no);
      return AWTImageTools.getSubimage(img, isLittleEndian(), x, y, w, h);
    }
  
    // -- Internal FormatReader API methods --
  
    /* @see loci.formats.FormatReader#initFile(String) */
    protected void initFile(String id) throws FormatException, IOException {
      LOGGER.info("Checking for JAI");
      try {
        r = new ReflectedUniverse();
        r.exec("import javax.media.jai.NullOpImage");
        r.exec("import javax.media.jai.OpImage");
        r.exec("import com.sun.media.jai.codec.FileSeekableStream");
        r.exec("import com.sun.media.jai.codec.ImageDecoder");
        r.exec("import com.sun.media.jai.codec.ImageCodec");
      }
      catch (ReflectException exc) {
        throw new MissingLibraryException(NO_JAI_MSG, exc);
      }
  
      super.initFile(id);
  
      LOGGER.info("Reading movie dimensions");
  
      // map Location to File or RandomAccessFile, if possible
      IRandomAccess ira = Location.getMappedFile(id);
      if (ira != null) {
        if (ira instanceof FileHandle) {
          FileHandle fh = (FileHandle) ira;
          r.setVar("file", fh.getRandomAccessFile());
        }
        else {
          throw new FormatException(
            "Unsupported handle type" + ira.getClass().getName());
        }
      }
      else {
        String mapId = Location.getMappedId(id);
        File file = new File(mapId);
        if (file.exists()) {
          r.setVar("file", file);
        }
        else throw new FileNotFoundException(id);
      }
      r.setVar("tiff", "tiff");
      r.setVar("param", null);
  
      // create TIFF decoder
      int numPages;
      try {
        r.exec("s = new FileSeekableStream(file)");
        r.exec("dec = ImageCodec.createImageDecoder(tiff, s, param)");
        numPages = ((Integer) r.exec("dec.getNumPages()")).intValue();
      }
      catch (ReflectException exc) {
        throw new FormatException(exc);
      }
      if (numPages < 0) {
        throw new FormatException("Invalid page count: " + numPages);
      }
  
      // decode first image plane
      BufferedImage img = openBufferedImage(0);
      if (img == null) throw new FormatException("Invalid image stream");
  
      LOGGER.info("Populating metadata");
  
      CoreMetadata m = core.get(0);
  
      m.imageCount = numPages;
  
      m.sizeX = img.getWidth();
      m.sizeY = img.getHeight();
      m.sizeZ = 1;
      m.sizeC = img.getSampleModel().getNumBands();
      m.sizeT = numPages;
  
      m.rgb = m.sizeC > 1;
  
      m.dimensionOrder = "XYCZT";
      m.pixelType = AWTImageTools.getPixelType(img);
      m.interleaved = true;
      m.littleEndian = false;
      m.metadataComplete = true;
      m.indexed = false;
      m.falseColor = false;
  
      // populate the metadata store
      MetadataStore store = makeFilterMetadata();
      MetadataTools.populatePixels(store, this);
    }
  
    /** Obtains a BufferedImage from the given data source using JAI. */
    protected BufferedImage openBufferedImage(int no) throws FormatException {
      r.setVar("no", no);
      RenderedImage img;
      try {
        r.exec("img = dec.decodeAsRenderedImage(no)");
        img = (RenderedImage)
          r.exec("new NullOpImage(img, null, OpImage.OP_IO_BOUND, null)");
      }
  