loci.formats.tiff

Class TiffParser

java.lang.Object

loci.formats.tiff.TiffParser

public class TiffParser
extends Object

Parses TIFF data from an input source.

Author:

Curtis Rueden ctrueden at wisc.edu, Eric Kjellman egkjellman at wisc.edu, Melissa Linkert melissa at glencoesoftware.com, Chris Allan callan at blackcat.ca

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	bigTiff Whether or not the TIFF file contains BigTIFF data.
private byte[]	cachedTileBuffer Cached tile buffer to avoid re-allocations when reading tiles.
private CodecOptions	codecOptions Codec options to be used when decoding compressed pixel data.
private boolean	doCaching
private boolean	equalStrips
private boolean	fakeBigTiff Whether or not 64-bit offsets are used for non-BigTIFF files.
private IFD	firstIFD Cached first IFD in the current file.
private IFDList	ifdList Cached list of IFDs in the current file.
protected loci.common.RandomAccessInputStream	in Input source from which to parse TIFF data.
private static org.slf4j.Logger	LOGGER
private boolean	ycbcrCorrection

Constructor Summary

Constructors

Constructor and Description
TiffParser(loci.common.RandomAccessInputStream in) Constructs a new TIFF parser from the given input source.
TiffParser(String filename) Constructs a new TIFF parser from the given file name.

Method Summary

Modifier and Type	Method and Description
Boolean	checkHeader() Checks the TIFF header.
void	fillInIFD(IFD ifd) Fill in IFD entries that are stored at an arbitrary offset.
CodecOptions	getCodecOptions() Retrieves the current set of codec options being used to decompress pixel data.
int[]	getColorMap(IFD ifd) Retrieve the color map associated with the given IFD.
String	getComment() Convenience method for obtaining a stream's first ImageDescription.
IFDList	getExifIFDs() Returns EXIF IFDs.
IFD	getFirstIFD() Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
TiffIFDEntry	getFirstIFDEntry(int tag) Retrieve a given entry from the first IFD in the stream.
long	getFirstOffset() Gets offset to the first IFD, or -1 if stream is not TIFF.
IFD	getIFD(long offset) Gets the IFD stored at the given offset.
long[]	getIFDOffsets() Gets the offsets to every IFD in the file.
IFDList	getIFDs() Returns all IFDs in the file.
Object	getIFDValue(TiffIFDEntry entry) Retrieve the value corresponding to the given TiffIFDEntry.
(package private) long	getNextOffset(long previous) Read a file offset.
IFDList	getNonThumbnailIFDs() Returns non-thumbnail IFDs.
byte[]	getSamples(IFD ifd, byte[] buf)
byte[]	getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height)
byte[]	getSamples(IFD ifd, byte[] buf, int x, int y, long width, long height, int overlapX, int overlapY)
loci.common.RandomAccessInputStream	getStream() Gets the stream from which TIFF data is being parsed.
IFDList	getThumbnailIFDs() Returns thumbnail IFDs.
byte[]	getTile(IFD ifd, byte[] buf, int row, int col)
boolean	isBigTiff() Returns whether or not the current TIFF file contains BigTIFF data.
boolean	isValidHeader() Tests this stream to see if it represents a TIFF file.
(package private) TiffIFDEntry	readTiffIFDEntry()
void	setAssumeEqualStrips(boolean equalStrips) Sets whether or not to assume that strips are of equal size.
void	setCodecOptions(CodecOptions codecOptions) Sets the codec options to be used when decompressing pixel data.
void	setDoCaching(boolean doCaching) Sets whether or not IFD entries should be cached.
void	setUse64BitOffsets(boolean use64Bit) Sets whether or not 64-bit offsets are used for non-BigTIFF files.
void	setYCbCrCorrection(boolean correctionAllowed) Sets whether or not YCbCr color correction is allowed.
static void	unpackBytes(byte[] samples, int startIndex, byte[] bytes, IFD ifd) 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

LOGGER

private static final org.slf4j.Logger LOGGER

in

protected transient loci.common.RandomAccessInputStream in

Input source from which to parse TIFF data.

cachedTileBuffer

private byte[] cachedTileBuffer

Cached tile buffer to avoid re-allocations when reading tiles.

bigTiff

private boolean bigTiff

Whether or not the TIFF file contains BigTIFF data.

fakeBigTiff

private boolean fakeBigTiff

Whether or not 64-bit offsets are used for non-BigTIFF files.

ycbcrCorrection

private boolean ycbcrCorrection

equalStrips

private boolean equalStrips

doCaching

private boolean doCaching

ifdList

private IFDList ifdList

Cached list of IFDs in the current file.

firstIFD

private IFD firstIFD

Cached first IFD in the current file.

codecOptions

private CodecOptions codecOptions

Codec options to be used when decoding compressed pixel data.

Constructor Detail

TiffParser

public TiffParser(String filename)
           throws IOException

Constructs a new TIFF parser from the given file name.

Throws:

IOException

TiffParser

public TiffParser(loci.common.RandomAccessInputStream in)

Constructs a new TIFF parser from the given input source.

Method Detail

setAssumeEqualStrips

public void setAssumeEqualStrips(boolean equalStrips)

Sets whether or not to assume that strips are of equal size.

Parameters:

equalStrips - Whether or not the strips are of equal size.

setCodecOptions

public void setCodecOptions(CodecOptions codecOptions)

Sets the codec options to be used when decompressing pixel data.

Parameters:

codecOptions - Codec options to use.

getCodecOptions

public CodecOptions getCodecOptions()

Retrieves the current set of codec options being used to decompress pixel data.

Returns:

See above.

setDoCaching

public void setDoCaching(boolean doCaching)

Sets whether or not IFD entries should be cached.

setUse64BitOffsets

public void setUse64BitOffsets(boolean use64Bit)

Sets whether or not 64-bit offsets are used for non-BigTIFF files.

setYCbCrCorrection

public void setYCbCrCorrection(boolean correctionAllowed)

Sets whether or not YCbCr color correction is allowed.

getStream

public loci.common.RandomAccessInputStream getStream()

Gets the stream from which TIFF data is being parsed.

isValidHeader

public boolean isValidHeader()

Tests this stream to see if it represents a TIFF file.

checkHeader

public Boolean checkHeader()
                    throws IOException

Checks the TIFF header.

Returns:

true if little-endian, false if big-endian, or null if not a TIFF.

Throws:

IOException

isBigTiff

public boolean isBigTiff()

Returns whether or not the current TIFF file contains BigTIFF data.

getIFDs

public IFDList getIFDs()
                throws IOException

Returns all IFDs in the file.

Throws:

IOException

getThumbnailIFDs

public IFDList getThumbnailIFDs()
                         throws IOException

Returns thumbnail IFDs.

Throws:

IOException

getNonThumbnailIFDs

public IFDList getNonThumbnailIFDs()
                            throws IOException

Returns non-thumbnail IFDs.

Throws:

IOException

getExifIFDs

public IFDList getExifIFDs()
                    throws FormatException,
                           IOException

Returns EXIF IFDs.

Throws:

FormatException

IOException

getIFDOffsets

public long[] getIFDOffsets()
                     throws IOException

Gets the offsets to every IFD in the file.

Throws:

IOException

getFirstIFD

public IFD getFirstIFD()
                throws IOException

Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.

Throws:

IOException

getFirstIFDEntry

public TiffIFDEntry getFirstIFDEntry(int tag)
                              throws IOException

Retrieve a given entry from the first IFD in the stream.

Parameters:

tag - the tag of the entry to be retrieved.

Returns:

an object representing the entry's fields.

Throws:

IOException - when there is an error accessing the stream.

IllegalArgumentException - when the tag number is unknown.

getFirstOffset

public long getFirstOffset()
                    throws IOException

Gets offset to the first IFD, or -1 if stream is not TIFF.

Throws:

IOException

getIFD

public IFD getIFD(long offset)
           throws IOException

Gets the IFD stored at the given offset.

Throws:

IOException

fillInIFD

public void fillInIFD(IFD ifd)
               throws IOException

Fill in IFD entries that are stored at an arbitrary offset.

Throws:

IOException

getIFDValue

public Object getIFDValue(TiffIFDEntry entry)
                   throws IOException

Retrieve the value corresponding to the given TiffIFDEntry.

Throws:

IOException

getComment

public String getComment()
                  throws IOException

Convenience method for obtaining a stream's first ImageDescription.

Throws:

IOException

getColorMap

public int[] getColorMap(IFD ifd)
                  throws IOException

Retrieve the color map associated with the given IFD.

Throws:

IOException

getTile

public byte[] getTile(IFD ifd,
                      byte[] buf,
                      int row,
                      int col)
               throws FormatException,
                      IOException

Throws:

FormatException

IOException

getSamples

public byte[] getSamples(IFD ifd,
                         byte[] buf)
                  throws FormatException,
                         IOException

Throws:

FormatException

IOException

getSamples

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

Throws:

FormatException

IOException

getSamples

public byte[] getSamples(IFD ifd,
                         byte[] buf,
                         int x,
                         int y,
                         long width,
                         long height,
                         int overlapX,
                         int overlapY)
                  throws FormatException,
                         IOException

Throws:

FormatException

IOException

unpackBytes

public static void unpackBytes(byte[] samples,
                               int startIndex,
                               byte[] bytes,
                               IFD ifd)
                        throws FormatException

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.

Throws:

FormatException

getNextOffset

long getNextOffset(long previous)
            throws IOException

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.

Throws:

IOException

readTiffIFDEntry

TiffIFDEntry readTiffIFDEntry()
                       throws IOException

Throws:

IOException