loci.formats.tiff

Class TiffSaver

java.lang.Object

loci.formats.tiff.TiffSaver

public class TiffSaver
extends java.lang.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 to write BigTIFF data.
protected loci.common.ByteArrayHandle	bytes Output bytes.
protected java.lang.String	filename Output filename.
private static org.slf4j.Logger	LOGGER
private CodecOptions	options The codec options if set.
protected loci.common.RandomAccessOutputStream	out Output stream to use when saving TIFF data.
private java.lang.Long	sequentialTileFilePointer
private java.util.List<java.lang.Long>	sequentialTileOffsets Store tile offsets and original file pointer when writing sequentially.
private boolean	sequentialWrite

Constructor Summary

Constructors

Constructor and Description
TiffSaver(loci.common.RandomAccessOutputStream out, loci.common.ByteArrayHandle bytes) Constructs a new TIFF saver from the given output source.
TiffSaver(loci.common.RandomAccessOutputStream out, java.lang.String filename) Constructs a new TIFF saver from the given output source.
TiffSaver(java.lang.String filename) Constructs a new TIFF saver from the given filename.

Method Summary

Modifier and Type	Method and Description
void	close() Closes the output stream if not null.
loci.common.RandomAccessOutputStream	getStream() Gets the stream from which TIFF data is being saved.
boolean	isBigTiff() Returns whether or not we are writing BigTIFF data.
boolean	isLittleEndian() Returns whether or not we are writing little-endian data.
private void	makeValidIFD(IFD ifd, int pixelType, int nChannels) Makes a valid IFD.
void	overwriteComment(loci.common.RandomAccessInputStream in, java.lang.Object value) Convenience method for overwriting a file's first ImageDescription.
void	overwriteIFDOffset(loci.common.RandomAccessInputStream raf, long offset, long nextPointer)
void	overwriteIFDValue(loci.common.RandomAccessInputStream raf, int ifd, int tag, java.lang.Object value) Surgically overwrites an existing IFD value with the given one.
void	overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, java.lang.Object value) Surgically overwrites an existing IFD value with the given one.
void	overwriteIFDValue(loci.common.RandomAccessInputStream raf, long ifdOffset, int tag, java.lang.Object value, boolean skipHeaderCheck) Surgically overwrites an existing IFD value with the given one.
void	overwriteLastIFDOffset(loci.common.RandomAccessInputStream raf)
void	setBigTiff(boolean bigTiff) Sets whether or not BigTIFF data should be written.
void	setCodecOptions(CodecOptions options) Sets the codec options.
void	setLittleEndian(boolean littleEndian) Sets whether or not little-endian data should be written.
void	setWritingSequentially(boolean sequential) Sets whether or not we know that the planes will be written sequentially.
private long[]	toPrimitiveArray(java.util.List<java.lang.Long> l) Coverts a list to a primitive array.
void	writeHeader() Writes the TIFF file header.
void	writeIFD(IFD ifd, long nextOffset)
private void	writeIFDStrips(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y, long defaultByteCount)
void	writeIFDValue(loci.common.RandomAccessOutputStream extraOut, long offset, int tag, java.lang.Object value) Writes the given IFD value to the given output object.
void	writeImage(byte[][] buf, IFDList ifds, int pixelType)
void	writeImage(byte[] buf, IFD ifd, int no, int pixelType, boolean last)
void	writeImage(byte[] buf, IFD ifd, int no, int pixelType, int x, int y, int w, int h, boolean last) Writes to any rectangle from the passed block.
void	writeImage(byte[] buf, IFD ifd, int no, int pixelType, int x, int y, int w, int h, boolean last, java.lang.Integer nChannels, boolean copyDirectly)
private void	writeImageIFD(IFD ifd, int no, byte[][] strips, int nChannels, boolean last, int x, int y) Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.
private void	writeIntValue(loci.common.RandomAccessOutputStream out, long offset) Write the given value to the given RandomAccessOutputStream.

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

out

protected loci.common.RandomAccessOutputStream out

Output stream to use when saving TIFF data.

filename

protected java.lang.String filename

Output filename.

bytes

protected loci.common.ByteArrayHandle bytes

Output bytes.

bigTiff

private boolean bigTiff

Whether or not to write BigTIFF data.

sequentialWrite

private boolean sequentialWrite

sequentialTileOffsets

private java.util.List<java.lang.Long> sequentialTileOffsets

Store tile offsets and original file pointer when writing sequentially.

sequentialTileFilePointer

private java.lang.Long sequentialTileFilePointer

options

private CodecOptions options

The codec options if set.

Constructor Detail

TiffSaver

public TiffSaver(java.lang.String filename)
          throws java.io.IOException

Constructs a new TIFF saver from the given filename.

Parameters:

filename - Filename of the output stream that we may use to create extra input or output streams as required.

Throws:

java.io.IOException

TiffSaver

public TiffSaver(loci.common.RandomAccessOutputStream out,
                 java.lang.String filename)

Constructs a new TIFF saver from the given output source.

Parameters:

out - Output stream to save TIFF data to.

filename - Filename of the output stream that we may use to create extra input or output streams as required.

TiffSaver

public TiffSaver(loci.common.RandomAccessOutputStream out,
                 loci.common.ByteArrayHandle bytes)

Constructs a new TIFF saver from the given output source.

Parameters:

out - Output stream to save TIFF data to.

bytes - In memory byte array handle that we may use to create extra input or output streams as required.

Method Detail

close

public void close()
           throws java.io.IOException

Closes the output stream if not null.

Throws:

java.io.IOException - Thrown if an error occurred while closing.

setWritingSequentially

public void setWritingSequentially(boolean sequential)

Sets whether or not we know that the planes will be written sequentially. If we are writing planes sequentially and set this flag, then performance is slightly improved.

getStream

public loci.common.RandomAccessOutputStream getStream()

Gets the stream from which TIFF data is being saved.

setLittleEndian

public void setLittleEndian(boolean littleEndian)

Sets whether or not little-endian data should be written.

setBigTiff

public void setBigTiff(boolean bigTiff)

Sets whether or not BigTIFF data should be written.

isLittleEndian

public boolean isLittleEndian()

Returns whether or not we are writing little-endian data.

isBigTiff

public boolean isBigTiff()

Returns whether or not we are writing BigTIFF data.

setCodecOptions

public void setCodecOptions(CodecOptions options)

Sets the codec options.

Parameters:

options - The value to set.

writeHeader

public void writeHeader()
                 throws java.io.IOException

Writes the TIFF file header.

Throws:

java.io.IOException

writeImage

public void writeImage(byte[][] buf,
                       IFDList ifds,
                       int pixelType)
                throws FormatException,
                       java.io.IOException

Throws:

FormatException

java.io.IOException

writeImage

public void writeImage(byte[] buf,
                       IFD ifd,
                       int no,
                       int pixelType,
                       boolean last)
                throws FormatException,
                       java.io.IOException

Throws:

FormatException

java.io.IOException

writeImage

public void writeImage(byte[] buf,
                       IFD ifd,
                       int no,
                       int pixelType,
                       int x,
                       int y,
                       int w,
                       int h,
                       boolean last)
                throws FormatException,
                       java.io.IOException

Writes to any rectangle from the passed block.

Parameters:

buf - The block that is to be written.

ifd - The Image File Directories. Mustn't be null.

no - The image index within the current file, starting from 0.

pixelType - The type of pixels.

x - The X-coordinate of the top-left corner.

y - The Y-coordinate of the top-left corner.

w - The width of the rectangle.

h - The height of the rectangle.

last - Pass true if it is the last image, false otherwise.

Throws:

FormatException

java.io.IOException

writeImage

public void writeImage(byte[] buf,
                       IFD ifd,
                       int no,
                       int pixelType,
                       int x,
                       int y,
                       int w,
                       int h,
                       boolean last,
                       java.lang.Integer nChannels,
                       boolean copyDirectly)
                throws FormatException,
                       java.io.IOException

Throws:

FormatException

java.io.IOException

writeImageIFD

private void writeImageIFD(IFD ifd,
                           int no,
                           byte[][] strips,
                           int nChannels,
                           boolean last,
                           int x,
                           int y)
                    throws FormatException,
                           java.io.IOException

Performs the actual work of dealing with IFD data and writing it to the TIFF for a given image or sub-image.

Parameters:

ifd - The Image File Directories. Mustn't be null.

no - The image index within the current file, starting from 0.

strips - The strips to write to the file.

last - Pass true if it is the last image, false otherwise.

x - The initial X offset of the strips/tiles to write.

y - The initial Y offset of the strips/tiles to write.

Throws:

FormatException

java.io.IOException

writeIFD

public void writeIFD(IFD ifd,
                     long nextOffset)
              throws FormatException,
                     java.io.IOException

Throws:

FormatException

java.io.IOException

writeIFDValue

public void writeIFDValue(loci.common.RandomAccessOutputStream extraOut,
                          long offset,
                          int tag,
                          java.lang.Object value)
                   throws FormatException,
                          java.io.IOException

Writes the given IFD value to the given output object.

Parameters:

extraOut - buffer to which "extra" IFD information should be written

offset - global offset to use for IFD offset values

tag - IFD tag to write

value - IFD value to write

Throws:

FormatException

java.io.IOException

overwriteLastIFDOffset

public void overwriteLastIFDOffset(loci.common.RandomAccessInputStream raf)
                            throws FormatException,
                                   java.io.IOException

Throws:

FormatException

java.io.IOException

overwriteIFDOffset

public void overwriteIFDOffset(loci.common.RandomAccessInputStream raf,
                               long offset,
                               long nextPointer)
                        throws FormatException,
                               java.io.IOException

Throws:

FormatException

java.io.IOException

overwriteIFDValue

public void overwriteIFDValue(loci.common.RandomAccessInputStream raf,
                              int ifd,
                              int tag,
                              java.lang.Object value)
                       throws FormatException,
                              java.io.IOException

Surgically overwrites an existing IFD value with the given one. This method requires that the IFD directory entry already exist. It intelligently updates the count field of the entry to match the new length. If the new length is longer than the old length, it appends the new data to the end of the file and updates the offset field; if not, or if the old data is already at the end of the file, it overwrites the old data in place.

Parameters:

raf - the input stream representing the file to be edited

ifd - the index into the list of IFDs TiffParser.getIFDOffsets()

tag - the tag code

value - the new value for the tag

Throws:

FormatException

java.io.IOException

overwriteIFDValue

public void overwriteIFDValue(loci.common.RandomAccessInputStream raf,
                              long ifdOffset,
                              int tag,
                              java.lang.Object value)
                       throws FormatException,
                              java.io.IOException

Surgically overwrites an existing IFD value with the given one. This method requires that the IFD directory entry already exist. It intelligently updates the count field of the entry to match the new length. If the new length is longer than the old length, it appends the new data to the end of the file and updates the offset field; if not, or if the old data is already at the end of the file, it overwrites the old data in place.

Parameters:

raf - the input stream representing the file to be edited

ifdOffset - the offset to the IFD

tag - the tag code

value - the new value for the tag

Throws:

FormatException

java.io.IOException

overwriteIFDValue

public void overwriteIFDValue(loci.common.RandomAccessInputStream raf,
                              long ifdOffset,
                              int tag,
                              java.lang.Object value,
                              boolean skipHeaderCheck)
                       throws FormatException,
                              java.io.IOException

Surgically overwrites an existing IFD value with the given one. This method requires that the IFD directory entry already exist. It intelligently updates the count field of the entry to match the new length. If the new length is longer than the old length, it appends the new data to the end of the file and updates the offset field; if not, or if the old data is already at the end of the file, it overwrites the old data in place.

Parameters:

raf - the input stream representing the file to be edited

ifdOffset - the offset to the IFD

tag - the tag code

value - the new value for the tag

skipHeaderCheck - true if the TIFF header does not need to be checked

Throws:

FormatException

java.io.IOException

overwriteComment

public void overwriteComment(loci.common.RandomAccessInputStream in,
                             java.lang.Object value)
                      throws FormatException,
                             java.io.IOException

Convenience method for overwriting a file's first ImageDescription.

Throws:

FormatException

java.io.IOException

toPrimitiveArray

private long[] toPrimitiveArray(java.util.List<java.lang.Long> l)

Coverts a list to a primitive array.

Parameters:

l - The list of Long to convert.

Returns:

A primitive array of type long[] with the values from l.

writeIntValue

private void writeIntValue(loci.common.RandomAccessOutputStream out,
                           long offset)
                    throws java.io.IOException

Write the given value to the given RandomAccessOutputStream. If the 'bigTiff' flag is set, then the value will be written as an 8 byte long; otherwise, it will be written as a 4 byte integer.

Throws:

java.io.IOException

makeValidIFD

private void makeValidIFD(IFD ifd,
                          int pixelType,
                          int nChannels)

Makes a valid IFD.

Parameters:

ifd - The IFD to handle.

pixelType - The pixel type.

nChannels - The number of channels.

writeIFDStrips

private void writeIFDStrips(IFD ifd,
                            int no,
                            byte[][] strips,
                            int nChannels,
                            boolean last,
                            int x,
                            int y,
                            long defaultByteCount)
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException