loci.formats
Class ImageReader

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

public class ImageReader

extends FormatReader

ImageReader is master file format reader for all supported formats.

Field Summary

protected int	index Current form index.
protected static Class[]	readerClasses List of reader classes.
protected FormatReader[]	readers List of supported file format readers.

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

ImageReader()
Constructs a new ImageReader.

Method Summary

void	close() Closes any open files.
protected void	createFilters() Creates JFileChooser file filters for this file format.
String	getFormat(String id) Gets a string describing the file format for the given file.
int	getImageCount(String id) Determines the number of images in the given image 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.
FormatReader	getReader(Class c) Gets the file format reader instance matching the given class.
FormatReader	getReader(String id) Gets the reader used to open the given file.
protected void	initFile(String id) Initializes the given image file.
boolean	isThisType(byte[] block) Checks if the given block is a valid header for an image file.
boolean	isThisType(String name) Checks if the given string is a valid filename for any supported format.
static void	main(String[] args)
BufferedImage[]	open(String id) Opens an existing file from the given filename.
BufferedImage	open(String id, int no) Obtains the specified image from the given image 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

Methods inherited from class java.lang.Object

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

Field Detail

readerClasses

protected static Class[] readerClasses

List of reader classes.

readers

protected FormatReader[] readers

List of supported file format readers.

index

protected int index

Current form index.

Constructor Detail

ImageReader

public ImageReader()

Constructs a new ImageReader.

Method Detail

getFormat

public String getFormat(String id)
                 throws FormatException,
                        IOException

Gets a string describing the file format for the given file.

Throws:

FormatException

IOException

getReader

public FormatReader getReader(String id)
                       throws FormatException,
                              IOException

Gets the reader used to open the given file.

Throws:

FormatException

IOException

getReader

public FormatReader getReader(Class c)

Gets the file format reader instance matching the given class.

isThisType

public boolean isThisType(byte[] block)

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

Specified by:

isThisType in class FormatReader

getImageCount

public int getImageCount(String id)
                  throws FormatException,
                         IOException

Determines the number of images in the given image 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 image 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

open

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

Opens an existing file from the given filename.

Overrides:

open in class FormatReader

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.

Overrides:

getOMENode in class FormatReader

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.

Overrides:

getMetadataValue in class FormatReader

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.

Overrides:

getMetadata in class FormatReader

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.

Overrides:

testRead in class FormatReader

Throws:

FormatException

IOException

createFilters

protected void createFilters()

Creates JFileChooser file filters for this file format.

Overrides:

createFilters in class FormatReader

isThisType

public boolean isThisType(String name)

Checks if the given string is a valid filename for any supported format.

Overrides:

isThisType in class FormatHandler

initFile

protected void initFile(String id)
                 throws FormatException,
                        IOException

Initializes the given image file.

Overrides:

initFile in class FormatReader

Throws:

FormatException

IOException

main

public static void main(String[] args)
                 throws FormatException,
                        IOException

Throws:

FormatException

IOException