loci.formats
Class BaseTiffReader

java.lang.Object
  loci.formats.FormatHandler
      loci.formats.FormatReader
          loci.formats.BaseTiffReader

Direct Known Subclasses:

AndorReader, FluoviewReader, IPWReader, MetamorphReader, SEQReader, TiffReader, ZeissLSMReader

public abstract class BaseTiffReader

extends FormatReader

BaseTiffReader is the superclass for file format readers compatible with or derived from the TIFF 6.0 file format.

Field Summary

protected Hashtable[]	ifds List of IFDs for the current TIFF.
protected RandomAccessFile	in Random access file for the current TIFF.
protected int	numImages Number of images in the current TIFF stack.

Fields inherited from class loci.formats.FormatReader

DEBUG, DEBUG_LEVEL, metadata, ome

Fields inherited from class loci.formats.FormatHandler

chooser, currentId, filters, format, suffixes

Constructor Summary

BaseTiffReader(String name, String suffix)
Constructs a new BaseTiffReader.

BaseTiffReader(String name, String[] suffixes)
Constructs a new BaseTiffReader.

Method Summary

void	close() Closes any open files.
int	getImageCount(String id) Determines the number of images in the given TIFF file.
int[]	getTiffDimensions(String id) Gets the dimensions of the given (possibly multi-page) TIFF file.
protected void	initFile(String id) Initializes the given TIFF file.
protected void	initMetadata() Populates the metadata hashtable and OME root node.
protected void	initOMEMetadata() Parses OME-XML metadata.
protected void	initStandardMetadata() Parses standard metadata.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for a TIFF file.
BufferedImage	open(String id, int no) Obtains the specified image from the given TIFF file.
protected void	put(String key, boolean value)
protected void	put(String key, byte value)
protected void	put(String key, char value)
protected void	put(String key, double value)
protected void	put(String key, float value)
protected void	put(String key, Hashtable ifd, int tag)
protected void	put(String key, int value)
protected void	put(String key, long value)
protected void	put(String key, Object value)
protected void	put(String key, short value)
protected void	putInt(String key, Hashtable ifd, int tag)

Methods inherited from class loci.formats.FormatReader

createFilters, getMetadata, getMetadataValue, getOMENode, open, testRead

Methods inherited from class loci.formats.FormatHandler

getFileChooser, getFileFilters, getFormat, getSuffixes, isThisType

Methods inherited from class java.lang.Object

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

Field Detail

in

protected RandomAccessFile in

Random access file for the current TIFF.

ifds

protected Hashtable[] ifds

List of IFDs for the current TIFF.

numImages

protected int numImages

Number of images in the current TIFF stack.

Constructor Detail

BaseTiffReader

public BaseTiffReader(String name,
                      String suffix)

Constructs a new BaseTiffReader.

BaseTiffReader

public BaseTiffReader(String name,
                      String[] suffixes)

Constructs a new BaseTiffReader.

Method Detail

getTiffDimensions

public int[] getTiffDimensions(String id)
                        throws FormatException,
                               IOException

Gets the dimensions of the given (possibly multi-page) TIFF file.

Throws:

FormatException

IOException

initMetadata

protected void initMetadata()

Populates the metadata hashtable and OME root node.

initStandardMetadata

protected void initStandardMetadata()

Parses standard metadata.

initOMEMetadata

protected void initOMEMetadata()

Parses OME-XML metadata.

isThisType

public boolean isThisType(byte[] block)

Checks if the given block is a valid header for a TIFF file.

Specified by:

isThisType in class FormatReader

getImageCount

public int getImageCount(String id)
                  throws FormatException,
                         IOException

Determines the number of images in the given TIFF file.

Specified by:

getImageCount in class FormatReader

Throws:

FormatException

IOException

open

public BufferedImage open(String id,
                          int no)
                   throws FormatException,
                          IOException

Obtains the specified image from the given TIFF file.

Specified by:

open in class FormatReader

Throws:

FormatException

IOException

close

public void close()
           throws FormatException,
                  IOException

Closes any open files.

Specified by:

close in class FormatReader

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Initializes the given TIFF file.

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

put

protected void put(String key,
                   Object value)

put

protected void put(String key,
                   int value)

put

protected void put(String key,
                   boolean value)

put

protected void put(String key,
                   byte value)

put

protected void put(String key,
                   char value)

put

protected void put(String key,
                   double value)

put

protected void put(String key,
                   float value)

put

protected void put(String key,
                   long value)

put

protected void put(String key,
                   short value)

put

protected void put(String key,
                   Hashtable ifd,
                   int tag)

putInt

protected void putInt(String key,
                      Hashtable ifd,
                      int tag)