Package gov.nih.mipav.model.file

Class FileOME

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileOME

public class FileOME
extends FileBase

DOCUMENT ME!

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
private class	FileOME.MyXMLHandler	Private class used by the parser to parse the XML file.

Field Summary

Fields

Modifier and Type	Field	Description
private java.lang.String	fileDir	The directory where the xml header and raw image data file are located.
private FileInfoOME	fileInfo	The info for the image file.
private java.lang.String	fileName	The name of the xml image header file.
private ModelImage	image	The image to read or write.
private java.lang.String	imageFileName	The name of the raw image data file.
private ModelLUT	LUT	The image's lut.
private boolean	showProgress	Whether to show a progress bar while processing the file.
private boolean	usesLUT	Whether the image has a lut already.
private static java.lang.String	W3C_XML_SCHEMA	The W3C XML schema.

Fields inherited from class gov.nih.mipav.model.file.FileBase

BIG_ENDIAN, bitsPerPixel, fileNames, LITTLE_ENDIAN, pBarVisible, raFile, READ, READ_WRITE

Constructor Summary

Constructors

Constructor	Description
FileOME(java.lang.String fName, java.lang.String fDir, boolean show)	Constructs new file object.

Method Summary

Modifier and Type	Method	Description
boolean	readHeader(java.lang.String headerFileName, java.lang.String headerFileDir)	Read the image XML header.
ModelImage	readImage()	Reads an XML image file by reading the XML header then making a FileRaw to read the image for all filenames in the file list.

Methods inherited from class gov.nih.mipav.model.file.FileBase

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, finalize, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, floatToBytes, getBufferDouble, getBufferFloat, getBufferInt, getBufferLong, getBufferShort, getBufferUShort, getDataType, getDouble, getFloat, getInt, getLong, getProgressChangeListeners, getRaFile, getSignedShort, getString, getUInt, getUnsignedByte, getUnsignedShort, intToBytes, isBigEndian, isProgressBarVisible, linkProgress, longToBytes, readDouble, readFloat, readInt, readLong, readShort, readString, readUnsignedShort, removeProgressChangeListener, setBigEndian, setBufferFloat, setBufferInt, setBufferLong, setBufferShort, setBufferString, setDataType, setEndianess, shortToBytes, writeBytes, writeDouble, writeFloat, writeInt, writeLong, writeShort

Methods inherited from class java.lang.Object

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

Field Detail

W3C_XML_SCHEMA

private static final java.lang.String W3C_XML_SCHEMA

The W3C XML schema.

See Also:

Constant Field Values

fileDir

private java.lang.String fileDir

The directory where the xml header and raw image data file are located.

fileInfo

private FileInfoOME fileInfo

The info for the image file.

fileName

private java.lang.String fileName

The name of the xml image header file.

image

private ModelImage image

The image to read or write.

imageFileName

private java.lang.String imageFileName

The name of the raw image data file.

LUT

private ModelLUT LUT

The image's lut.

showProgress

private boolean showProgress

Whether to show a progress bar while processing the file.

usesLUT

private boolean usesLUT

Whether the image has a lut already. One is generated if this variable is false.

Constructor Detail

FileOME

public FileOME(java.lang.String fName,
               java.lang.String fDir,
               boolean show)

Constructs new file object.

Parameters:

fName - File name.

fDir - File directory.

show - Flag for showing the progress bar.

Method Detail

readHeader

public boolean readHeader(java.lang.String headerFileName,
                          java.lang.String headerFileDir)
                   throws java.io.IOException

Read the image XML header.

Parameters:

headerFileName - the header file name

headerFileDir - the directory the header file is in

Returns:

true if successful, false otherwise

Throws:

java.io.IOException - if there is an error reading the header file from disk

readImage

public ModelImage readImage()
                     throws java.io.IOException,
                            java.lang.OutOfMemoryError

Reads an XML image file by reading the XML header then making a FileRaw to read the image for all filenames in the file list. Only the one file directory (currently) supported.

Returns:

The image.

Throws:

java.io.IOException - if there is an error reading the file

java.lang.OutOfMemoryError - if there is not enough memory available to read in the image

See Also:

FileRaw