loci.formats
Class FormatReader

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

Direct Known Subclasses:

AVIReader, BaseTiffReader, BioRadReader, BMPReader, DeltavisionReader, GatanReader, ICSReader, ImageIOReader, ImageJReader, ImageReader, IPLabReader, LegacyPictReader, LegacyQTReader, LegacyZVIReader, LeicaReader, OMEXMLReader, OpenlabReader, PerkinElmerReader, PictReader, QTReader, ZeissZVIReader

public abstract class FormatReader

extends FormatHandler

Abstract superclass of all biological file format readers.

Field Summary

protected static boolean	DEBUG Debugging flag.
protected static int	DEBUG_LEVEL Debugging level.
protected Hashtable	metadata Hashtable containing metadata key/value pairs.
protected Object	ome OME root node for OME-XML metadata.

Fields inherited from class loci.formats.FormatHandler

chooser, currentId, filters, format, suffixes

Constructor Summary

FormatReader(String format, String suffix)
Constructs a format reader with the given name and default suffix.

FormatReader(String format, String[] suffixes)
Constructs a format reader with the given name and default suffixes.

Method Summary

abstract void	close() Closes the currently open file.
protected void	createFilters() Creates JFileChooser file filters for this file format.
abstract int	getImageCount(String id) Determines the number of images in the given file.
Hashtable	getMetadata(String id) Obtains the hashtable containing the metadata field/value pairs from the given file.
Object	getMetadataValue(String id, String field) Obtains the specified metadata field's value for the given file.
Object	getOMENode(String id) Obtains a loci.ome.xml.OMENode object representing the file's metadata as an OME-XML DOM structure.
protected void	initFile(String id) Initializes the given file (parsing header information, etc.).
abstract boolean	isThisType(byte[] block) Checks if the given block is a valid header for this file format.
BufferedImage[]	open(String id) Opens an existing file from the given filename.
abstract BufferedImage	open(String id, int no) Obtains the specified image from the given file.
boolean	testRead(String[] args) A utility method for test reading a file from the command line, and displaying the results in a simple display.

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

DEBUG

protected static final boolean DEBUG

Debugging flag.

See Also:

Constant Field Values

DEBUG_LEVEL

protected static final int DEBUG_LEVEL

Debugging level. 1=basic, 2=extended, 3=everything.

See Also:

Constant Field Values

metadata

protected Hashtable metadata

Hashtable containing metadata key/value pairs.

ome

protected Object ome

OME root node for OME-XML metadata.

Constructor Detail

FormatReader

public FormatReader(String format,
                    String suffix)

Constructs a format reader with the given name and default suffix.

FormatReader

public FormatReader(String format,
                    String[] suffixes)

Constructs a format reader with the given name and default suffixes.

Method Detail

isThisType

public abstract boolean isThisType(byte[] block)

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

getImageCount

public abstract int getImageCount(String id)
                           throws FormatException,
                                  IOException

Determines the number of images in the given file.

Throws:

FormatException

IOException

open

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

Obtains the specified image from the given file.

Throws:

FormatException

IOException

close

public abstract void close()
                    throws FormatException,
                           IOException

Closes the currently open file.

Throws:

FormatException

IOException

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.

Throws:

FormatException

IOException

open

public BufferedImage[] open(String id)
                     throws FormatException,
                            IOException

Opens an existing file from the given filename.

Returns:

Java Images containing pixel data

Throws:

FormatException

IOException

getOMENode

public Object getOMENode(String id)
                  throws FormatException,
                         IOException

Obtains a loci.ome.xml.OMENode object representing the file's metadata as an OME-XML DOM structure.

Returns:

null if the loci.ome.xml package is not present.

Throws:

FormatException

IOException

getMetadataValue

public Object getMetadataValue(String id,
                               String field)
                        throws FormatException,
                               IOException

Obtains the specified metadata field's value for the given file.

Parameters:

field - the name associated with the metadata field

Returns:

the value, or null if the field doesn't exist

Throws:

FormatException

IOException

getMetadata

public Hashtable getMetadata(String id)
                      throws FormatException,
                             IOException

Obtains the hashtable containing the metadata field/value pairs from the given file.

Parameters:

id - the filename

Returns:

the hashtable containing all metadata from the file

Throws:

FormatException

IOException

testRead

public boolean testRead(String[] args)
                 throws FormatException,
                        IOException

A utility method for test reading a file from the command line, and displaying the results in a simple display.

Throws:

FormatException

IOException

createFilters

protected void createFilters()

Creates JFileChooser file filters for this file format.

Overrides:

createFilters in class FormatHandler