TiffParser (Bio-Formats API)

java.lang.Object
- loci.formats.tiff.TiffParser

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable
```
public class TiffParser
extends java.lang.Object
implements java.io.Closeable
```
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 boolean`	`canClose`
`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(java.lang.String filename)` Constructs a new TIFF parser from the given file name.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`java.lang.Boolean`	`checkHeader()` Checks the TIFF header.
`void`	`close()` Close the underlying stream, if this TiffParser was constructed with a file path.
`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.
`java.lang.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()` Deprecated. Use `getMainIFDs()` and `getSubIFDs(IFD)` instead.
`java.lang.Object`	`getIFDValue(TiffIFDEntry entry)` Retrieve the value corresponding to the given TiffIFDEntry.
`IFDList`	`getMainIFDs()` Returns the main list of IFDs in the file.
`(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`	`getSubIFDs(IFD ifd)` Returns the SUBIFDS belonging to a given IFD.
`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.
  - canClose
```
private boolean canClose
```
- Constructor Detail
  - TiffParser
```
public TiffParser(java.lang.String filename)
           throws java.io.IOException
```
    Constructs a new TIFF parser from the given file name.
    
    Throws:
    
    java.io.IOException
  - TiffParser
```
public TiffParser(loci.common.RandomAccessInputStream in)
```
    Constructs a new TIFF parser from the given input source.
- Method Detail
  - close
```
public void close()
           throws java.io.IOException
```
    Close the underlying stream, if this TiffParser was constructed with a file path. Closing a stream that was pre-initialized is potentially dangerous.
    
    Specified by:
    
    close in interface java.io.Closeable
    
    Specified by:
    
    close in interface java.lang.AutoCloseable
    
    Throws:
    
    java.io.IOException
  - 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 java.lang.Boolean checkHeader()
                              throws java.io.IOException
```
    Checks the TIFF header.
    
    Returns:
    
    true if little-endian, false if big-endian, or null if not a TIFF.
    
    Throws:
    
    java.io.IOException
  - isBigTiff
```
public boolean isBigTiff()
```
    Returns whether or not the current TIFF file contains BigTIFF data.
  - getMainIFDs
```
public IFDList getMainIFDs()
                    throws java.io.IOException
```
    Returns the main list of IFDs in the file. This does not include SUBIFDS.
    
    Throws:
    
    java.io.IOException
  - getSubIFDs
```
public IFDList getSubIFDs(IFD ifd)
                   throws java.io.IOException
```
    Returns the SUBIFDS belonging to a given IFD.
    
    Throws:
    
    java.io.IOException
  - getIFDs
```
@Deprecated
public IFDList getIFDs()
                            throws java.io.IOException
```
    Deprecated. Use getMainIFDs() and getSubIFDs(IFD) instead.
    
    Returns all IFDs in the file, including SUBIFDS.
    
    Throws:
    
    java.io.IOException
  - getThumbnailIFDs
```
public IFDList getThumbnailIFDs()
                         throws java.io.IOException
```
    Returns thumbnail IFDs.
    
    Throws:
    
    java.io.IOException
  - getNonThumbnailIFDs
```
public IFDList getNonThumbnailIFDs()
                            throws java.io.IOException
```
    Returns non-thumbnail IFDs.
    
    Throws:
    
    java.io.IOException
  - getExifIFDs
```
public IFDList getExifIFDs()
                    throws FormatException,
                           java.io.IOException
```
    Returns EXIF IFDs.
    
    Throws:
    
    FormatException
    
    java.io.IOException
  - getIFDOffsets
```
public long[] getIFDOffsets()
                     throws java.io.IOException
```
    Gets the offsets to every IFD in the file.
    
    Throws:
    
    java.io.IOException
  - getFirstIFD
```
public IFD getFirstIFD()
                throws java.io.IOException
```
    Gets the first IFD within the TIFF file, or null if the input source is not a valid TIFF file.
    
    Throws:
    
    java.io.IOException
  - getFirstIFDEntry
```
public TiffIFDEntry getFirstIFDEntry(int tag)
                              throws java.io.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:
    
    java.io.IOException - when there is an error accessing the stream.
    
    java.lang.IllegalArgumentException - when the tag number is unknown.
  - getFirstOffset
```
public long getFirstOffset()
                    throws java.io.IOException
```
    Gets offset to the first IFD, or -1 if stream is not TIFF.
    
    Throws:
    
    java.io.IOException
  - getIFD
```
public IFD getIFD(long offset)
           throws java.io.IOException
```
    Gets the IFD stored at the given offset.
    
    Throws:
    
    java.io.IOException
  - fillInIFD
```
public void fillInIFD(IFD ifd)
               throws java.io.IOException
```
    Fill in IFD entries that are stored at an arbitrary offset.
    
    Throws:
    
    java.io.IOException
  - getIFDValue
```
public java.lang.Object getIFDValue(TiffIFDEntry entry)
                             throws java.io.IOException
```
    Retrieve the value corresponding to the given TiffIFDEntry.
    
    Throws:
    
    java.io.IOException
  - getComment
```
public java.lang.String getComment()
                            throws java.io.IOException
```
    Convenience method for obtaining a stream's first ImageDescription.
    
    Throws:
    
    java.io.IOException
  - getColorMap
```
public int[] getColorMap(IFD ifd)
                  throws java.io.IOException
```
    Retrieve the color map associated with the given IFD.
    
    Throws:
    
    java.io.IOException
  - getTile
```
public byte[] getTile(IFD ifd,
                      byte[] buf,
                      int row,
                      int col)
               throws FormatException,
                      java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - getSamples
```
public byte[] getSamples(IFD ifd,
                         byte[] buf)
                  throws FormatException,
                         java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - getSamples
```
public byte[] getSamples(IFD ifd,
                         byte[] buf,
                         int x,
                         int y,
                         long width,
                         long height)
                  throws FormatException,
                         java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.IOException
  - getSamples
```
public byte[] getSamples(IFD ifd,
                         byte[] buf,
                         int x,
                         int y,
                         long width,
                         long height,
                         int overlapX,
                         int overlapY)
                  throws FormatException,
                         java.io.IOException
```
    Throws:
    
    FormatException
    
    java.io.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 java.io.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:
    
    java.io.IOException
  - readTiffIFDEntry
```
TiffIFDEntry readTiffIFDEntry()
                       throws java.io.IOException
```
    Throws:
    
    java.io.IOException

Class TiffParser

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOGGER

in

cachedTileBuffer

bigTiff

fakeBigTiff

ycbcrCorrection

equalStrips

doCaching

ifdList

firstIFD

codecOptions

canClose

Constructor Detail

TiffParser

TiffParser

Method Detail

close

setAssumeEqualStrips

setCodecOptions

getCodecOptions

setDoCaching

setUse64BitOffsets

setYCbCrCorrection

getStream

isValidHeader

checkHeader

isBigTiff

getMainIFDs

getSubIFDs

getIFDs

getThumbnailIFDs

getNonThumbnailIFDs

getExifIFDs

getIFDOffsets

getFirstIFD

getFirstIFDEntry

getFirstOffset

getIFD

fillInIFD

getIFDValue

getComment

getColorMap

getTile

getSamples

getSamples

getSamples

unpackBytes

getNextOffset

readTiffIFDEntry