TiffParser.java

/*
 * #%L
 * BSD implementations of Bio-Formats readers and writers
 * %%
 * Copyright (C) 2005 - 2017 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.
 * #L%
 */

package loci.formats.tiff;

import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;

import loci.common.ByteArrayHandle;
import loci.common.Constants;
import loci.common.DataTools;
import loci.common.RandomAccessInputStream;
import loci.common.Region;
import loci.common.enumeration.EnumException;
import loci.formats.FormatException;
import loci.formats.ImageTools;
import loci.formats.codec.CodecOptions;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * Parses TIFF data from an input source.
 *
 * @author Curtis Rueden ctrueden at wisc.edu
 * @author Eric Kjellman egkjellman at wisc.edu
 * @author Melissa Linkert melissa at glencoesoftware.com
 * @author Chris Allan callan at blackcat.ca
 */
public class TiffParser implements Closeable {

  // -- Constants --

  private static final Logger LOGGER =
    LoggerFactory.getLogger(TiffParser.class);

  // -- Fields --

  /** Input source from which to parse TIFF data. */
  protected transient RandomAccessInputStream in;

  /** Cached tile buffer to avoid re-allocations when reading tiles. */
  private byte[] cachedTileBuffer;

  /** Whether or not the TIFF file contains BigTIFF data. */
  private boolean bigTiff;

  /** Whether or not 64-bit offsets are used for non-BigTIFF files. */
  private boolean fakeBigTiff = false;

  private boolean ycbcrCorrection = true;

  private boolean equalStrips = false;

  private boolean doCaching;

  /** Cached list of IFDs in the current file. */
  private IFDList ifdList;

  /** Cached first IFD in the current file. */
  private IFD firstIFD;

  /** Codec options to be used when decoding compressed pixel data. */
  private CodecOptions codecOptions = CodecOptions.getDefaultOptions();

  private boolean canClose = false;

  // -- Constructors --

  /** Constructs a new TIFF parser from the given file name. */
  public TiffParser(String filename) throws IOException {
    this(new RandomAccessInputStream(filename));
    canClose = true;
  }

  /** Constructs a new TIFF parser from the given input source. */
  public TiffParser(RandomAccessInputStream in) {
    this.in = in;
    doCaching = true;
    try {
      long fp = in.getFilePointer();
      checkHeader();
      in.seek(fp);
    }
    catch (IOException e) { }
  }

  // -- Closeable methods --

  /**
   * Close the underlying stream, if this TiffParser was constructed
   * with a file path.  Closing a stream that was pre-initialized
   * is potentially dangerous.
   */
  @Override
  public void close() throws IOException {
    if (canClose && in != null) {
      in.close();
    }
  }

  // -- TiffParser methods --

  /**
   * Sets whether or not to assume that strips are of equal size.
   * @param equalStrips Whether or not the strips are of equal size.
   */
  public void setAssumeEqualStrips(boolean equalStrips) {
    this.equalStrips = equalStrips;
  }

  /**
   * Sets the codec options to be used when decompressing pixel data.
   * @param codecOptions Codec options to use.
   */
  public void setCodecOptions(CodecOptions codecOptions) {
    this.codecOptions = codecOptions;
  }

  /**
   * Retrieves the current set of codec options being used to decompress pixel
   * data.
   * @return See above.
   */
  public CodecOptions getCodecOptions() {
    return codecOptions;
  }

  /** Sets whether or not IFD entries should be cached. */
  public void setDoCaching(boolean doCaching) {
    this.doCaching = doCaching;
  }

  /** Sets whether or not 64-bit offsets are used for non-BigTIFF files. */
  public void setUse64BitOffsets(boolean use64Bit) {
    fakeBigTiff = use64Bit;
  }

  /** Sets whether or not YCbCr color correction is allowed. */
  public void setYCbCrCorrection(boolean correctionAllowed) {
    ycbcrCorrection = correctionAllowed;
  }

  /** Gets the stream from which TIFF data is being parsed. */
  public RandomAccessInputStream getStream() {
    return in;
  }

  /** Tests this stream to see if it represents a TIFF file. */
  public boolean isValidHeader() {
    try {
      return checkHeader() != null;
    }
    catch (IOException e) {
      return false;
    }
  }

  /**
   * Checks the TIFF header.
   *
   * @return true if little-endian,
   *         false if big-endian,
   *         or null if not a TIFF.
   */
  public Boolean checkHeader() throws IOException {
    if (in.length() < 4) return null;

    // byte order must be II or MM
    in.seek(0);
    int endianOne = in.read();
    int endianTwo = in.read();
    boolean littleEndian = endianOne == TiffConstants.LITTLE &&
      endianTwo == TiffConstants.LITTLE; // II
    boolean bigEndian = endianOne == TiffConstants.BIG &&
      endianTwo == TiffConstants.BIG; // MM
    if (!littleEndian && !bigEndian) return null;

    // check magic number (42)
    in.order(littleEndian);
    short magic = in.readShort();
    bigTiff = magic == TiffConstants.BIG_TIFF_MAGIC_NUMBER;
    if (magic != TiffConstants.MAGIC_NUMBER &&
      magic != TiffConstants.BIG_TIFF_MAGIC_NUMBER)
    {
      return null;
    }

    return Boolean.valueOf(littleEndian);
  }

  /** Returns whether or not the current TIFF file contains BigTIFF data. */
  public boolean isBigTiff() {
    return bigTiff;
  }

  // -- TiffParser methods - IFD parsing --

  /** Returns the main list of IFDs in the file.
   *
   * This does not include SUBIFDS.
   */
  public IFDList getMainIFDs() throws IOException {
    if (ifdList != null) return ifdList;

    long[] offsets = getIFDOffsets();
    IFDList ifds = new IFDList();

    for (long offset : offsets) {
      IFD ifd = getIFD(offset);
      if (ifd == null) continue;
      if (ifd.containsKey(IFD.IMAGE_WIDTH)) {
        ifds.add(ifd);
      }
    }
    if (doCaching) {
      ifdList = ifds;
    }

    return ifds;
  }

  /** Returns the SUBIFDS belonging to a given IFD. */
  public IFDList getSubIFDs(IFD ifd) throws IOException {
    IFDList list = new IFDList();
    long[] offsets = null;
    try {
      fillInIFD(ifd);
      offsets = ifd.getIFDLongArray(IFD.SUB_IFD);
    } catch (FormatException e) {
    }

    if (offsets != null) {
      for (long offset : offsets) {
        list.add(getIFD(offset));
      }
    }

    return list;
  }

  /** Returns all IFDs in the file, including SUBIFDS.
   * @deprecated Use {@link #getMainIFDs()} and {@link #getSubIFDs(IFD)} instead.
   */
  @Deprecated
  public IFDList getIFDs() throws IOException {
    if (ifdList != null) return ifdList;

    long[] offsets = getIFDOffsets();
    IFDList ifds = new IFDList();

    for (long offset : offsets) {
      IFD ifd = getIFD(offset);
      if (ifd == null) continue;
      if (ifd.containsKey(IFD.IMAGE_WIDTH)) ifds.add(ifd);
      long[] subOffsets = null;
      try {
        if (!doCaching && ifd.containsKey(IFD.SUB_IFD)) {
          fillInIFD(ifd);
        }
        subOffsets = ifd.getIFDLongArray(IFD.SUB_IFD);
      }
      catch (FormatException e) { }
      if (subOffsets != null) {
        for (long subOffset : subOffsets) {
          IFD sub = getIFD(subOffset);
          if (sub != null) {
            ifds.add(sub);
          }
        }
      }
    }
    if (doCaching) ifdList = ifds;

    return ifds;
  }

  /** Returns thumbnail IFDs. */
  public IFDList getThumbnailIFDs() throws IOException {
    IFDList ifds = getMainIFDs();
    IFDList thumbnails = new IFDList();
    for (IFD ifd : ifds) {
      Number subfile = (Number) ifd.getIFDValue(IFD.NEW_SUBFILE_TYPE);
      int subfileType = subfile == null ? 0 : subfile.intValue();
      if (subfileType == 1) {
        thumbnails.add(ifd);
      }
    }
    return thumbnails;
  }

  /** Returns non-thumbnail IFDs. */
  public IFDList getNonThumbnailIFDs() throws IOException {
    IFDList ifds = getMainIFDs();
    IFDList nonThumbs = new IFDList();
    for (IFD ifd : ifds) {
      Number subfile = (Number) ifd.getIFDValue(IFD.NEW_SUBFILE_TYPE);
      int subfileType = subfile == null ? 0 : subfile.intValue();
      if (subfileType != 1 || ifds.size() <= 1) {
        nonThumbs.add(ifd);
      }
    }
    return nonThumbs;
  }

  /** Returns EXIF IFDs. */
  public IFDList getExifIFDs() throws FormatException, IOException {
    IFDList ifds = getMainIFDs();
    IFDList exif = new IFDList();
    for (IFD ifd : ifds) {
      long offset = ifd.getIFDLongValue(IFD.EXIF, 0);
      if (offset != 0) {
        IFD exifIFD = getIFD(offset);
        if (exifIFD != null) {
          exif.add(exifIFD);
        }
      }
    }
    return exif;
  }

  /** Gets the offsets to every IFD in the file. */
  public long[] getIFDOffsets() throws IOException {
    // check TIFF header
    int bytesPerEntry = bigTiff ? TiffConstants.BIG_TIFF_BYTES_PER_ENTRY :
      TiffConstants.BYTES_PER_ENTRY;

    final List<Long> offsets = new ArrayList<Long>();
    long offset = getFirstOffset();
    while (offset > 0 && offset < in.length()) {
      in.seek(offset);
      offsets.add(offset);
      long nEntries = bigTiff ? in.readLong() : in.readUnsignedShort();
      long entryBytes = nEntries * bytesPerEntry;
      if (in.getFilePointer() + entryBytes + (bigTiff ? 8 : 4) > in.length()) {
        // this can easily happen when writing multiple planes to a file
        break;
      }
      in.skipBytes(entryBytes);
      offset = getNextOffset(offset);
    }

    long[] f = new long[offsets.size()];
    for (int i=0; i<f.length; i++) {
      f[i] = offsets.get(i).longValue();
    }

    return f;
  }

  /**
   * Gets the first IFD within the TIFF file, or null
   * if the input source is not a valid TIFF file.
   */
  public IFD getFirstIFD() throws IOException {
    if (firstIFD != null) return firstIFD;
    long offset = getFirstOffset();
    IFD ifd = getIFD(offset);
    if (doCaching) firstIFD = ifd;
    return ifd;
  }

  /**
   * Retrieve a given entry from the first IFD in the stream.
   *
   * @param tag the tag of the entry to be retrieved.
   * @return an object representing the entry's fields.
   * @throws IOException when there is an error accessing the stream.
   * @throws IllegalArgumentException when the tag number is unknown.
   */
  // TODO : Try to remove this method.  It is only being used by
  //        loci.formats.in.MetamorphReader.
  public TiffIFDEntry getFirstIFDEntry(int tag) throws IOException {
    // Get the offset of the first IFD
    long offset = getFirstOffset();
    if (offset < 0) return null;

    // The following loosely resembles the logic of getIFD()...
    in.seek(offset);
    long numEntries = bigTiff ? in.readLong() : in.readUnsignedShort();

    for (int i = 0; i < numEntries; i++) {
      in.seek(offset + // The beginning of the IFD
        (bigTiff ? 8 : 2) + // The width of the initial numEntries field
        (bigTiff ? TiffConstants.BIG_TIFF_BYTES_PER_ENTRY :
        TiffConstants.BYTES_PER_ENTRY) * i);

      TiffIFDEntry entry = readTiffIFDEntry();
      if (entry.getTag() == tag) {
        return entry;
      }
    }
    throw new IllegalArgumentException("Unknown tag: " + tag);
  }

  /**
   * Gets offset to the first IFD, or -1 if stream is not TIFF.
   */
  public long getFirstOffset() throws IOException {
    Boolean header = checkHeader();
    if (header == null) return -1;
    if (bigTiff) in.skipBytes(4);
    return getNextOffset(0);
  }

  /** Gets the IFD stored at the given offset.  */
  public IFD getIFD(long offset) throws IOException {
    if (offset < 0 || offset >= in.length()) return null;
    IFD ifd = new IFD();

    // save little-endian flag to internal LITTLE_ENDIAN tag
    ifd.put(Integer.valueOf(IFD.LITTLE_ENDIAN), Boolean.valueOf(in.isLittleEndian()));
    ifd.put(Integer.valueOf(IFD.BIG_TIFF), Boolean.valueOf(bigTiff));

    // read in directory entries for this IFD
    LOGGER.trace("getIFD: seeking IFD at {}", offset);
    in.seek(offset);
    long numEntries = bigTiff ? in.readLong() : in.readUnsignedShort();
    LOGGER.trace("getIFD: {} directory entries to read", numEntries);
    if (numEntries == 0 || numEntries == 1) return ifd;

    int bytesPerEntry = bigTiff ?
      TiffConstants.BIG_TIFF_BYTES_PER_ENTRY : TiffConstants.BYTES_PER_ENTRY;
    int baseOffset = bigTiff ? 8 : 2;

    for (int i=0; i<numEntries; i++) {
      in.seek(offset + baseOffset + bytesPerEntry * i);

      TiffIFDEntry entry = null;
      try {
        entry = readTiffIFDEntry();
      }
      catch (EnumException e) {
        LOGGER.debug("", e);
      }
      if (entry == null) break;
      int count = entry.getValueCount();
      int tag = entry.getTag();
      long pointer = entry.getValueOffset();
      int bpe = entry.getType().getBytesPerElement();

      if (count < 0 || bpe <= 0) {
        // invalid data
        in.skipBytes(bytesPerEntry - 4 - (bigTiff ? 8 : 4));
        continue;
      }
      Object value = null;

      long inputLen = in.length();
      if (count * bpe + pointer > inputLen) {
        int oldCount = count;
        count = (int) ((inputLen - pointer) / bpe);
        LOGGER.trace("getIFD: truncated {} array elements for tag {}",
          (oldCount - count), tag);
        if (count < 0) count = oldCount;
      }
      if (count < 0 || count > in.length()) break;

      if (pointer != in.getFilePointer() && !doCaching) {
        value = entry;
      }
      else value = getIFDValue(entry);

      if (value != null && !ifd.containsKey(Integer.valueOf(tag))) {
        ifd.put(Integer.valueOf(tag), value);
      }
    }

    long newOffset =offset + baseOffset + bytesPerEntry * numEntries;
    if (newOffset < in.length()) {
      in.seek(newOffset);
    }
    else {
      in.seek(in.length());
    }

    return ifd;
  }

  /** Fill in IFD entries that are stored at an arbitrary offset. */
  public void fillInIFD(IFD ifd) throws IOException {
    HashSet<TiffIFDEntry> entries = new HashSet<TiffIFDEntry>();
    for (Object key : ifd.keySet()) {
      if (ifd.get(key) instanceof TiffIFDEntry) {
        entries.add((TiffIFDEntry) ifd.get(key));
      }
    }

    for (TiffIFDEntry entry : entries) {
      if ((entry.getValueCount() < 10 * 1024 * 1024 || entry.getTag() < 32768) &&
        entry.getTag() != IFD.COLOR_MAP)
      {
        ifd.put(Integer.valueOf(entry.getTag()), getIFDValue(entry));
      }
    }
  }

  /** Retrieve the value corresponding to the given TiffIFDEntry. */
  public Object getIFDValue(TiffIFDEntry entry) throws IOException {
    IFDType type = entry.getType();
    int count = entry.getValueCount();
    long offset = entry.getValueOffset();

    LOGGER.trace("Reading entry {} from {}; type={}, count={}",
      new Object[] {entry.getTag(), offset, type, count});

    if (offset >= in.length()) {
      return null;
    }

    if (offset != in.getFilePointer()) {
      if (fakeBigTiff && offset < 0) {
        offset &= 0xffffffffL;
        offset += 0x100000000L;
      }
      if (offset >= in.length()) {
        return null;
      }
      in.seek(offset);
    }

    if (type == IFDType.BYTE) {
      // 8-bit unsigned integer
      if (count == 1) return in.readUnsignedByte();
      byte[] bytes = new byte[count];
      in.readFully(bytes);
      // bytes are unsigned, so use shorts
      short[] shorts = new short[count];
      for (int j=0; j<count; j++) shorts[j] = (short) (bytes[j] & 0xff);
      return shorts;
    }
    else if (type == IFDType.ASCII) {
      // 8-bit byte that contain a 7-bit ASCII code;
      // the last byte must be NUL (binary zero)
      byte[] ascii = new byte[count];
      in.read(ascii);

      // count number of null terminators
      int nullCount = 0;
      for (int j=0; j<count; j++) {
        if (ascii[j] == 0 || j == count - 1) nullCount++;
      }

      // convert character array to array of strings
      String[] strings = nullCount == 1 ? null : new String[nullCount];
      String s = null;
      int c = 0, ndx = -1;
      for (int j=0; j<count; j++) {
        if (ascii[j] == 0) {
          s = new String(ascii, ndx + 1, j - ndx - 1, Constants.ENCODING);
          ndx = j;
        }
        else if (j == count - 1) {
          // handle non-null-terminated strings
          s = new String(ascii, ndx + 1, j - ndx, Constants.ENCODING);
        }
        else s = null;
        if (strings != null && s != null) strings[c++] = s;
      }
      return strings == null ? (Object) s : strings;
    }
    else if (type == IFDType.SHORT) {
      // 16-bit (2-byte) unsigned integer
      if (count == 1) return Integer.valueOf(in.readUnsignedShort());
      int[] shorts = new int[count];
      for (int j=0; j<count; j++) {
        shorts[j] = in.readUnsignedShort();
      }
      return shorts;
    }
    else if (type == IFDType.LONG || type == IFDType.IFD) {
      // 32-bit (4-byte) unsigned integer
      if (count == 1) return Long.valueOf(in.readUnsignedInt());
      long[] longs = new long[count];
      for (int j=0; j<count; j++) {
        if (in.getFilePointer() + 4 <= in.length()) {
          longs[j] = in.readUnsignedInt();
        }
      }
      return longs;
    }
    else if (type == IFDType.LONG8 || type == IFDType.SLONG8
             || type == IFDType.IFD8) {
      if (count == 1) return Long.valueOf(in.readLong());
      long[] longs = null;

      if (equalStrips && (entry.getTag() == IFD.STRIP_BYTE_COUNTS ||
        entry.getTag() == IFD.TILE_BYTE_COUNTS))
      {
        longs = new long[1];
        longs[0] = in.readLong();
      }
      else if (entry.getTag() == IFD.STRIP_OFFSETS ||
        entry.getTag() == IFD.TILE_OFFSETS ||
        entry.getTag() == IFD.STRIP_BYTE_COUNTS ||
        entry.getTag() == IFD.TILE_BYTE_COUNTS)
      {
        OnDemandLongArray offsets = new OnDemandLongArray(in);
        offsets.setSize(count);
        return offsets;
      }
      else {
        longs = new long[count];
        for (int j=0; j<count; j++) longs[j] = in.readLong();
      }
      return longs;
    }
    else if (type == IFDType.RATIONAL || type == IFDType.SRATIONAL) {
      // Two LONGs or SLONGs: the first represents the numerator
      // of a fraction; the second, the denominator
      if (count == 1) return new TiffRational(in.readUnsignedInt(), in.readUnsignedInt());
      TiffRational[] rationals = new TiffRational[count];
      for (int j=0; j<count; j++) {
        rationals[j] = new TiffRational(in.readUnsignedInt(), in.readUnsignedInt());
      }
      return rationals;
    }
    else if (type == IFDType.SBYTE || type == IFDType.UNDEFINED) {
      // SBYTE: An 8-bit signed (twos-complement) integer
      // UNDEFINED: An 8-bit byte that may contain anything,
      // depending on the definition of the field
      if (count == 1) return Byte.valueOf(in.readByte());
      byte[] sbytes = new byte[count];
      in.read(sbytes);
      return sbytes;
    }
    else if (type == IFDType.SSHORT) {
      // A 16-bit (2-byte) signed (twos-complement) integer
      if (count == 1) return Short.valueOf(in.readShort());
      short[] sshorts = new short[count];
      for (int j=0; j<count; j++) sshorts[j] = in.readShort();
      return sshorts;
    }
    else if (type == IFDType.SLONG) {
      // A 32-bit (4-byte) signed (twos-complement) integer
      if (count == 1) return Integer.valueOf(in.readInt());
      int[] slongs = new int[count];
      for (int j=0; j<count; j++) slongs[j] = in.readInt();
      return slongs;
    }
    else if (type == IFDType.FLOAT) {
      // Single precision (4-byte) IEEE format
      if (count == 1) return Float.valueOf(in.readFloat());
      float[] floats = new float[count];
      for (int j=0; j<count; j++) floats[j] = in.readFloat();
      return floats;
    }
    else if (type == IFDType.DOUBLE) {
      // Double precision (8-byte) IEEE format
      if (count == 1) return Double.valueOf(in.readDouble());
      double[] doubles = new double[count];
      for (int j=0; j<count; j++) {
        doubles[j] = in.readDouble();
      }
      return doubles;
    }

    return null;
  }

  /** Convenience method for obtaining a stream's first ImageDescription. */
  public String getComment() throws IOException {
    IFD firstIFD = getFirstIFD();
    if (firstIFD == null) {
      return null;
    }
    fillInIFD(firstIFD);
    return firstIFD.getComment();
  }

  /**
   * Retrieve the color map associated with the given IFD.
   */
  public int[] getColorMap(IFD ifd) throws IOException {
    Object map = ifd.get(IFD.COLOR_MAP);
    if (map == null) {
      return null;
    }
    int[] colorMap = null;
    if (map instanceof TiffIFDEntry) {
      colorMap = (int[]) getIFDValue((TiffIFDEntry) map);
    }
    else if (map instanceof int[]) {
      colorMap = (int[]) map;
    }
    return colorMap;
  }

  // -- TiffParser methods - image reading --

  public byte[] getTile(IFD ifd, byte[] buf, int row, int col)
    throws FormatException, IOException
  {
    byte[] jpegTable = (byte[]) ifd.getIFDValue(IFD.JPEG_TABLES);

    codecOptions.interleaved = true;
    codecOptions.littleEndian = ifd.isLittleEndian();

    long tileWidth = ifd.getTileWidth();
    long tileLength = ifd.getTileLength();
    int samplesPerPixel = ifd.getSamplesPerPixel();
    int planarConfig = ifd.getPlanarConfiguration();
    TiffCompression compression = ifd.getCompression();

    long numTileCols = ifd.getTilesPerRow();

    int pixel = ifd.getBytesPerSample()[0];
    int effectiveChannels = planarConfig == 2 ? 1 : samplesPerPixel;

    if (ifd.get(IFD.STRIP_BYTE_COUNTS) instanceof OnDemandLongArray) {
      OnDemandLongArray counts = (OnDemandLongArray) ifd.get(IFD.STRIP_BYTE_COUNTS);
      if (counts != null) {
        counts.setStream(in);
      }
    }
    if (ifd.get(IFD.TILE_BYTE_COUNTS) instanceof OnDemandLongArray) {
      OnDemandLongArray counts = (OnDemandLongArray) ifd.get(IFD.TILE_BYTE_COUNTS);
      if (counts != null) {
        counts.setStream(in);
      }
    }

    long[] stripByteCounts = ifd.getStripByteCounts();
    long[] rowsPerStrip = ifd.getRowsPerStrip();

    int offsetIndex = (int) (row * numTileCols + col);
    int countIndex = offsetIndex;
    if (equalStrips) {
      countIndex = 0;
    }
    if (stripByteCounts[countIndex] == (rowsPerStrip[0] * tileWidth) &&
      pixel > 1)
    {
      stripByteCounts[countIndex] *= pixel;
    }
    else if (stripByteCounts[countIndex] < 0 && countIndex > 0) {
      LOGGER.debug("byte count #{} was {}; correcting to {}", countIndex,
        stripByteCounts[countIndex], stripByteCounts[countIndex - 1]);
      stripByteCounts[countIndex] = stripByteCounts[countIndex - 1];
    }

    long stripOffset = 0;
    long nStrips = 0;

    if (ifd.getOnDemandStripOffsets() != null) {
      OnDemandLongArray stripOffsets = ifd.getOnDemandStripOffsets();
      stripOffsets.setStream(in);
      stripOffset = stripOffsets.get(offsetIndex);
      nStrips = stripOffsets.size();
    }
    else {
      long[] stripOffsets = ifd.getStripOffsets();
      stripOffset = stripOffsets[offsetIndex];
      nStrips = stripOffsets.length;
    }

    int size = (int) (tileWidth * tileLength * pixel * effectiveChannels);

    if (buf == null) buf = new byte[size];
    if (stripByteCounts[countIndex] == 0 || stripOffset >= in.length()) {
      // make sure that the buffer is cleared before returning
      // the caller may be reusing the same buffer for multiple calls to getTile
      Arrays.fill(buf, (byte) 0);
      return buf;
    }
    int tileSize = (int) stripByteCounts[countIndex];
    if (jpegTable != null) {
      tileSize += jpegTable.length - 2;
    }
    byte[] tile = new byte[tileSize];

    LOGGER.debug("Reading tile Length {} Offset {}", tile.length, stripOffset);

    if (jpegTable != null) {
      System.arraycopy(jpegTable, 0, tile, 0, jpegTable.length - 2);
      in.seek(stripOffset + 2);
      in.read(tile, jpegTable.length - 2, tile.length - (jpegTable.length - 2));
    }
    else {
      in.seek(stripOffset);
      in.read(tile);
    }

    // reverse bits in each byte if FillOrder == 2

    if (ifd.getIFDIntValue(IFD.FILL_ORDER) == 2 &&
      (compression.getCode() <= TiffCompression.GROUP_4_FAX.getCode() ||
       compression.getCode() == TiffCompression.DEFLATE.getCode() ||
       compression.getCode() == TiffCompression.PROPRIETARY_DEFLATE.getCode()))
    {
      for (int i=0; i<tile.length; i++) {
        tile[i] = (byte) (Integer.reverse(tile[i]) >> 24);
      }
    }

    codecOptions.maxBytes = (int) Math.max(size, tile.length);
    codecOptions.ycbcr =
      ifd.getPhotometricInterpretation() == PhotoInterp.Y_CB_CR &&
      ifd.getIFDIntValue(IFD.Y_CB_CR_SUB_SAMPLING) == 1 && ycbcrCorrection;

    tile = compression.decompress(tile, codecOptions);
    TiffCompression.undifference(tile, ifd);
    unpackBytes(buf, 0, tile, ifd);

    if (planarConfig == 2 && !ifd.isTiled() && ifd.getSamplesPerPixel() > 1) {
      int channel = (int) (row % nStrips);
      if (channel < ifd.getBytesPerSample().length) {
        int realBytes = ifd.getBytesPerSample()[channel];
        if (realBytes != pixel) {
          // re-pack pixels to account for differing bits per sample

          boolean littleEndian = ifd.isLittleEndian();
          int[] samples = new int[buf.length / pixel];
          for (int i=0; i<samples.length; i++) {
            samples[i] =
              DataTools.bytesToInt(buf, i * realBytes, realBytes, littleEndian);
          }

          for (int i=0; i<samples.length; i++) {
            DataTools.unpackBytes(
              samples[i], buf, i * pixel, pixel, littleEndian);
          }
        }
      }
    }

    return buf;
  }

  public byte[] getSamples(IFD ifd, byte[] buf)
    throws FormatException, IOException
  {
    long width = ifd.getImageWidth();
    long length = ifd.getImageLength();
    return getSamples(ifd, buf, 0, 0, width, length);
  }

  public byte[] getSamples(IFD ifd, byte[] buf, int x, int y,
    long width, long height) throws FormatException, IOException
  {
    return getSamples(ifd, buf, x, y, width, height, 0, 0);
  }

  public byte[] getSamples(IFD ifd, byte[] buf, int x, int y,
    long width, long height, int overlapX, int overlapY)
    throws FormatException, IOException
  {
    LOGGER.trace("parsing IFD entries");

    // get internal non-IFD entries
    boolean littleEndian = ifd.isLittleEndian();
    in.order(littleEndian);

    // get relevant IFD entries
    int samplesPerPixel = ifd.getSamplesPerPixel();
    long tileWidth = ifd.getTileWidth();
    long tileLength = ifd.getTileLength();
    if (tileLength <= 0) {
      LOGGER.trace("Tile length is {}; setting it to {}", tileLength, height);
      tileLength = height;
    }

    long numTileRows = ifd.getTilesPerColumn();
    long numTileCols = ifd.getTilesPerRow();

    PhotoInterp photoInterp = ifd.getPhotometricInterpretation();
    int planarConfig = ifd.getPlanarConfiguration();
    int pixel = ifd.getBytesPerSample()[0];
    int effectiveChannels = planarConfig == 2 ? 1 : samplesPerPixel;

    if (LOGGER.isTraceEnabled()) {
      ifd.printIFD();
    }

    if (width * height > Integer.MAX_VALUE) {
      throw new FormatException("Sorry, ImageWidth x ImageLength > " +
        Integer.MAX_VALUE + " is not supported (" +
        width + " x " + height + ")");
    }
    if (width * height * effectiveChannels * pixel > Integer.MAX_VALUE) {
      throw new FormatException("Sorry, ImageWidth x ImageLength x " +
        "SamplesPerPixel x BitsPerSample > " + Integer.MAX_VALUE +
        " is not supported (" + width + " x " + height + " x " +
        samplesPerPixel + " x " + (pixel * 8) + ")");
    }

    // casting to int is safe because we have already determined that
    // width * height is less than Integer.MAX_VALUE
    int numSamples = (int) (width * height);

    // read in image strips
    LOGGER.trace("reading image data (samplesPerPixel={}; numSamples={})",
      samplesPerPixel, numSamples);

    TiffCompression compression = ifd.getCompression();

    if (compression == TiffCompression.JPEG_2000 ||
      compression == TiffCompression.JPEG_2000_LOSSY)
    {
      codecOptions = compression.getCompressionCodecOptions(ifd, codecOptions);
    }
    else codecOptions = compression.getCompressionCodecOptions(ifd);
    codecOptions.interleaved = true;
    codecOptions.littleEndian = ifd.isLittleEndian();
    long imageWidth = ifd.getImageWidth();
    long imageLength = ifd.getImageLength();

    long[] stripOffsets = null;

    if (ifd.getOnDemandStripOffsets() != null) {
      OnDemandLongArray offsets = ifd.getOnDemandStripOffsets();
      offsets.setStream(in);
      stripOffsets = offsets.toArray();
    }
    else {
      stripOffsets = ifd.getStripOffsets();
    }

    if (ifd.get(IFD.STRIP_BYTE_COUNTS) instanceof OnDemandLongArray) {
      OnDemandLongArray counts = (OnDemandLongArray) ifd.get(IFD.STRIP_BYTE_COUNTS);
      if (counts != null) {
        counts.setStream(in);
      }
    }
    if (ifd.get(IFD.TILE_BYTE_COUNTS) instanceof OnDemandLongArray) {
      OnDemandLongArray counts = (OnDemandLongArray) ifd.get(IFD.TILE_BYTE_COUNTS);
      if (counts != null) {
        counts.setStream(in);
      }
    }

    long[] stripByteCounts = ifd.getStripByteCounts();

    // if the image is stored as strips (not tiles) and
    // the strips are stored in order with no gaps then we can
    // treat them as a single strip for faster reading
    boolean contiguousTiles = tileWidth == imageWidth && planarConfig == 1;
    if (contiguousTiles) {
      for (int i=1; i<stripOffsets.length; i++) {
        if (stripOffsets[i] != stripOffsets[i - 1] + stripByteCounts[i - 1] ||
          stripOffsets[i] + stripByteCounts[i] > in.length())
        {
          contiguousTiles = false;
          break;
        }
      }
    }

    // special case: if we only need one tile, and that tile doesn't need
    // any special handling, then we can just read it directly and return
    if ((effectiveChannels == 1 || planarConfig == 1) && (ifd.getBitsPerSample()[0] % 8) == 0 &&
      photoInterp != PhotoInterp.WHITE_IS_ZERO &&
      photoInterp != PhotoInterp.CMYK && photoInterp != PhotoInterp.Y_CB_CR &&
      compression == TiffCompression.UNCOMPRESSED &&
      ifd.getIFDIntValue(IFD.FILL_ORDER) != 2 &&
      stripOffsets != null && stripByteCounts != null &&
      in.length() >= stripOffsets[0] + stripByteCounts[0] &&
      (numTileRows * numTileCols == 1 || contiguousTiles))
    {
      if (contiguousTiles) {
        stripByteCounts = new long[] {stripByteCounts[0] * stripByteCounts.length};
        stripOffsets = new long[] {stripOffsets[0]};
        tileLength = imageLength;
      }

      long column = x / tileWidth;
      int firstTile = (int) ((y / tileLength) * numTileCols + column);
      int lastTile =
        (int) (((y + height) / tileLength) * numTileCols + column);
      lastTile = (int) Math.min(lastTile, stripOffsets.length - 1);
      if (planarConfig == 2) {
        lastTile = stripOffsets.length - 1;
      }
      int bytes = ifd.getBitsPerSample()[0] / 8;

      int offset = 0;
      for (int tile=firstTile; tile<=lastTile; tile++) {
        long byteCount =
          equalStrips ? stripByteCounts[0] : stripByteCounts[tile];
        if (byteCount == numSamples && pixel > 1) {
          byteCount *= pixel;
        }

        if (stripOffsets[tile] < in.length()) {
          in.seek(stripOffsets[tile]);
        }
        else {
          continue;
        }

        if (width == tileWidth && height == imageLength) {
          // we want to entire tile, so just read the whole thing directly
          int len = (int) Math.min(buf.length - offset, byteCount);
          in.read(buf, offset, len);
          offset += len;
        }
        else {
          // we only want a piece of the tile, so read each row separately
          // this is especially necessary for large single-tile images
          int bpp = bytes * effectiveChannels;
          // the number of bytes to skip may be greater than Integer.MAX_VALUE if the tile is large
          in.skipBytes(y * bpp * tileWidth);
          for (int row=0; row<height; row++) {
            in.skipBytes(x * bpp);
            int len = (int) Math.min(buf.length - offset, width * bpp);
            if (len > 0) {
              in.read(buf, offset, len);
              offset += len;
              int skip = (int) (bpp * (tileWidth - x - width));
              if (skip + in.getFilePointer() < in.length()) {
                in.skipBytes(skip);
              }
            }
            else {
              break;
            }
          }
        }
      }
      if (effectiveChannels > 1) {
        byte[][] split = new byte[effectiveChannels][buf.length / effectiveChannels];
        for (int c=0; c<split.length; c++) {
          split[c] = ImageTools.splitChannels(buf, c, effectiveChannels, bytes, false, true);
        }
        for (int c=0; c<split.length; c++) {
          System.arraycopy(split[c], 0, buf, c * split[c].length, split[c].length);
        }
      }
      return buf;
    }

    long nrows = numTileRows;
    if (planarConfig == 2) numTileRows *= samplesPerPixel;

    Region imageBounds = new Region(x, y, (int) width, (int) height);

    int endX = (int) width + x;
    int endY = (int) height + y;

    long w = tileWidth;
    long h = tileLength;
    int rowLen = pixel * (int) w;//tileWidth;
    int tileSize = (int) (rowLen * h);//tileLength);

    int planeSize = (int) (width * height * pixel);
    int outputRowLen = (int) (pixel * width);

    int bufferSizeSamplesPerPixel = samplesPerPixel;
    if (ifd.getPlanarConfiguration() == 2) bufferSizeSamplesPerPixel = 1;
    int bpp = ifd.getBytesPerSample()[0];
    int bufferSize = (int) tileWidth * (int) tileLength *
      bufferSizeSamplesPerPixel * bpp;

    cachedTileBuffer = new byte[bufferSize];

    Region tileBounds = new Region(0, 0, (int) tileWidth, (int) tileLength);

    for (int row=0; row<numTileRows; row++) {
      // make the first row shorter to account for row overlap
      if (row == 0) {
        tileBounds.height = (int) (tileLength - overlapY);
      }

      for (int col=0; col<numTileCols; col++) {
        // make the first column narrower to account for column overlap
        if (col == 0) {
          tileBounds.width = (int) (tileWidth - overlapX);
        }

        tileBounds.x = col * (int) (tileWidth - overlapX);
        tileBounds.y = row * (int) (tileLength - overlapY);

        if (planarConfig == 2) {
          tileBounds.y = (int) ((row % nrows) * (tileLength - overlapY));
        }

        // this tile is completely to the right of the requested image
        // all subsequent tile columns will also be to the right of the image,
        // so don't bother checking them
        if (tileBounds.x > imageBounds.x + imageBounds.width) {
          break;
        }

        if (!imageBounds.intersects(tileBounds)) continue;

        getTile(ifd, cachedTileBuffer, row, col);

        // adjust tile bounds, if necessary

        int tileX = (int) Math.max(tileBounds.x, x);
        int tileY = (int) Math.max(tileBounds.y, y);
        int realX = tileX % (int) (tileWidth - overlapX);
        int realY = tileY % (int) (tileLength - overlapY);

        int twidth = (int) Math.min(endX - tileX, tileWidth - realX);
        if (twidth <= 0) {
          twidth = (int) Math.max(endX - tileX, tileWidth - realX);
        }
        int theight = (int) Math.min(endY - tileY, tileLength - realY);
        if (theight <= 0) {
          theight = (int) Math.max(endY - tileY, tileLength - realY);
        }

        // copy appropriate portion of the tile to the output buffer

        int copy = pixel * twidth;

        realX *= pixel;
        realY *= rowLen;

        for (int q=0; q<effectiveChannels; q++) {
          int src = (int) (q * tileSize) + realX + realY;
          int dest = (int) (q * planeSize) + pixel * (tileX - x) +
            outputRowLen * (tileY - y);
          if (planarConfig == 2) dest += (planeSize * (row / nrows));

          // copying the tile directly will only work if there is no overlap
          // and only one tile needs to be read
          // otherwise, we may be overwriting a previous tile
          // (or the current tile may be overwritten by a subsequent tile)
          if (rowLen == outputRowLen && overlapX == 0 && overlapY == 0 &&
            rowLen == pixel * imageBounds.intersection(tileBounds).width)
          {
            System.arraycopy(cachedTileBuffer, src, buf, dest, copy * theight);
          }
          else {
            for (int tileRow=0; tileRow<theight; tileRow++) {
              System.arraycopy(cachedTileBuffer, src, buf, dest, copy);
              src += rowLen;
              dest += outputRowLen;
            }
          }
        }
      }
    }

    return buf;
  }

  // -- Utility methods - byte stream decoding --

  /**
   * Extracts pixel information from the given byte array according to the
   * bits per sample, photometric interpretation and color map IFD directory
   * entry values, and the specified byte ordering.
   * No error checking is performed.
   */
  public static void unpackBytes(byte[] samples, int startIndex, byte[] bytes,
    IFD ifd) throws FormatException
  {
    boolean planar = ifd.getPlanarConfiguration() == 2;

    TiffCompression compression = ifd.getCompression();
    PhotoInterp photoInterp = ifd.getPhotometricInterpretation();
    if (compression == TiffCompression.JPEG ||
      compression == TiffCompression.JPEGXR)
    {
      photoInterp = PhotoInterp.RGB;
    }

    int[] bitsPerSample = ifd.getBitsPerSample();
    int nChannels = bitsPerSample.length;

    int sampleCount = (int) (((long) 8 * bytes.length) / bitsPerSample[0]);
    if (photoInterp == PhotoInterp.Y_CB_CR) sampleCount *= 3;
    if (planar) {
      nChannels = 1;
    }
    else {
      sampleCount /= nChannels;
    }

    if (LOGGER.isTraceEnabled()) {
      LOGGER.trace(
        "unpacking {} samples (startIndex={}; totalBits={}; numBytes={})",
        new Object[] {sampleCount, startIndex, nChannels * bitsPerSample[0],
        bytes.length});
    }

    int bps0 = bitsPerSample[0];

    boolean bps8 = bps0 == 8;
    boolean bps16 = bps0 == 16;

    // Hyper optimisation that takes any 8-bit or 16-bit data, where there is
    // only one channel, the source byte buffer's size is less than or equal to
    // that of the destination buffer and for which no special unpacking is
    // required and performs a simple array copy. Over the course of reading
    // semi-large datasets this can save **billions** of method calls.
    // Wed Aug  5 19:04:59 BST 2009
    // Chris Allan <callan@glencoesoftware.com>
    if ((bps8 || bps16) && bytes.length <= samples.length && nChannels == 1
        && photoInterp != PhotoInterp.WHITE_IS_ZERO
        && photoInterp != PhotoInterp.CMYK
        && photoInterp != PhotoInterp.Y_CB_CR) {
      System.arraycopy(bytes, 0, samples, 0, bytes.length);
      return;
    }

    long imageWidth = ifd.getImageWidth();
    long imageHeight = ifd.getImageLength();

    int numBytes = ifd.getBytesPerSample()[0];
    int nSamples = samples.length / (nChannels * numBytes);

    boolean noDiv8 = bps0 % 8 != 0;
    boolean littleEndian = ifd.isLittleEndian();

    long maxValue = (long) Math.pow(2, bps0) - 1;
    if (photoInterp == PhotoInterp.CMYK) maxValue = Integer.MAX_VALUE;

    int skipBits = (int) (8 - ((imageWidth * bps0 * nChannels) % 8));
    if (skipBits == 8 ||
      (bytes.length * 8 < bps0 * (nChannels * imageWidth + imageHeight)))
    {
      skipBits = 0;
    }

    // set up YCbCr-specific values
    float lumaRed = PhotoInterp.LUMA_RED;
    float lumaGreen = PhotoInterp.LUMA_GREEN;
    float lumaBlue = PhotoInterp.LUMA_BLUE;
    int[] reference = {0, 0, 0, 0, 0, 0};
    try {
      int[] value = ifd.getIFDIntArray(IFD.REFERENCE_BLACK_WHITE);
      // TODO: Run extra validation on the value
      if (value != null) {
        reference = value;
      }
    } catch (FormatException e) {
      float[] value = (float[]) ifd.getIFDValue(IFD.REFERENCE_BLACK_WHITE);
      if (value != null && value.length == 6) {
        LOGGER.debug("ReferenceBlackWhite tag stored as float array.");
        for (int i = 0 ; i < 5; i++) {
          reference[i] = (int) value[i];
        }
      }
    }

    int[] subsampling = ifd.getIFDIntArray(IFD.Y_CB_CR_SUB_SAMPLING);
    TiffRational[] coefficients = (TiffRational[])
      ifd.getIFDValue(IFD.Y_CB_CR_COEFFICIENTS);
    if (coefficients != null) {
      lumaRed = coefficients[0].floatValue();
      lumaGreen = coefficients[1].floatValue();
      lumaBlue = coefficients[2].floatValue();
    }
    int subX = subsampling == null ? 2 : subsampling[0];
    int subY = subsampling == null ? 2 : subsampling[1];
    int block = subX * subY;
    int nTiles = (int) (imageWidth / subX);


    RandomAccessInputStream bb = null;
    try {
      if (noDiv8) {
        bb = new RandomAccessInputStream(new ByteArrayHandle(bytes));
      }
      // unpack pixels
      for (int sample=0; sample<sampleCount; sample++) {
        int ndx = startIndex + sample;
        if (ndx >= nSamples) break;

        for (int channel=0; channel<nChannels; channel++) {
          int index = numBytes * (sample * nChannels + channel);
          int outputIndex = (channel * nSamples + ndx) * numBytes;

          // unpack non-YCbCr samples
          if (photoInterp != PhotoInterp.Y_CB_CR) {
            long value = 0;

            if (noDiv8) {
              // bits per sample is not a multiple of 8

              if ((channel == 0 && photoInterp == PhotoInterp.RGB_PALETTE) ||
                (photoInterp != PhotoInterp.CFA_ARRAY &&
                photoInterp != PhotoInterp.RGB_PALETTE))
              {
                try {
                  value = bb.readBits(bps0) & 0xffff;
                }
                catch (ArrayIndexOutOfBoundsException e) {
                  // leave the value at 0 if there aren't enough bytes
                  // to cover the total number of samples
                }
                if ((ndx % imageWidth) == imageWidth - 1) {
                  bb.skipBits(skipBits);
                }
              }
            }
            else {
              // DataTools.bytesToLong can handle the numBytes == 1 case,
              // but direct assignment is faster than potentially thousands of method calls
              if (numBytes == 1){
                value = bytes[index] & 0xff;
              }
              else {
                value = DataTools.bytesToLong(bytes, index, numBytes, littleEndian);
              }
            }

            if (photoInterp == PhotoInterp.WHITE_IS_ZERO ||
              photoInterp == PhotoInterp.CMYK)
            {
              value = maxValue - value;
            }

            if (outputIndex + numBytes <= samples.length) {
              // DataTools.unpackBytes can handle the numBytes == 1 case,
              // but direct assignment is faster than potentially thousands of method calls
              if (numBytes == 1) {
                samples[outputIndex] = (byte) value;
              }
              else {
                DataTools.unpackBytes(value, samples, outputIndex, numBytes,
                  littleEndian);
              }
            }
          }
          else {
            // unpack YCbCr samples; these need special handling, as each of
            // the RGB components depends upon two or more of the YCbCr components
            if (channel == nChannels - 1) {
              int lumaIndex = sample + (2 * (sample / block));
              int chromaIndex = (sample / block) * (block + 2) + block;

              if (chromaIndex + 1 >= bytes.length) break;

              int tile = ndx / block;
              int pixel = ndx % block;
              long r = subY * (tile / nTiles) + (pixel / subX);
              long c = subX * (tile % nTiles) + (pixel % subX);

              int idx = (int) (r * imageWidth + c);

              if (idx < nSamples) {
                int y = (bytes[lumaIndex] & 0xff) - reference[0];
                int cb = (bytes[chromaIndex] & 0xff) - reference[2];
                int cr = (bytes[chromaIndex + 1] & 0xff) - reference[4];

                int red = (int) (cr * (2 - 2 * lumaRed) + y);
                int blue = (int) (cb * (2 - 2 * lumaBlue) + y);
                int green = (int)
                  ((y - lumaBlue * blue - lumaRed * red) / lumaGreen);

                samples[idx] = (byte) (red & 0xff);
                samples[nSamples + idx] = (byte) (green & 0xff);
                samples[2*nSamples + idx] = (byte) (blue & 0xff);
              }
            }
          }
        }
      }
    }
    catch (IOException e) {
      throw new FormatException(e);
    }
    finally {
      if (bb != null) {
        try {
          bb.close();
        }
        catch (IOException e) {
          throw new FormatException(e);
        }
      }
    }
  }

  /**
   * Read a file offset.
   * For bigTiff, a 64-bit number is read.  For other Tiffs, a 32-bit number
   * is read and possibly adjusted for a possible carry-over from the previous
   * offset.
   */
  long getNextOffset(long previous) throws IOException {
    if (bigTiff || fakeBigTiff) {
      return in.readLong();
    }
    long offset = (previous & ~0xffffffffL) | (in.readUnsignedInt());

    // Only adjust the offset if we know that the file is too large for 32-bit
    // offsets to be accurate; otherwise, we're making the incorrect assumption
    // that IFDs are stored sequentially.
    if (offset < previous && offset != 0 && in.length() >= Math.pow(2, 32)) {
      offset += 0x100000000L;
    }
    return offset;
  }

  TiffIFDEntry readTiffIFDEntry() throws IOException {
    int entryTag = in.readUnsignedShort();

    // Parse the entry's "Type"
    IFDType entryType;
    try {
       entryType = IFDType.get(in.readUnsignedShort());
    }
    catch (EnumException e) {
      LOGGER.error("Error reading IFD type at: {}", in.getFilePointer());
      throw e;
    }

    // Parse the entry's "ValueCount"
    int valueCount = bigTiff ? (int) in.readLong() : in.readInt();
    if (valueCount < 0) {
      throw new RuntimeException("Count of '" + valueCount + "' unexpected.");
    }

    int nValueBytes = valueCount * entryType.getBytesPerElement();
    int threshhold = bigTiff ? 8 : 4;
    long offset = nValueBytes > threshhold ?
      getNextOffset(0) : in.getFilePointer();

    return new TiffIFDEntry(entryTag, entryType, valueCount, offset);
  }
}