Package gov.nih.mipav.model.file

Class FileSiemensText

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileSiemensText

public class FileSiemensText
extends FileBase

Version:

0.1 May 27, 2009

Author:

Andrew Morse

See Also:

• FileIO

Field Summary

Fields

Modifier and Type	Field	Description
static final short	DT_2FLOAT	SiemensText file format define use to indicate 2-byte float - Intel style.
static final short	DT_2INTEGERI	SiemensText file format define use to indicate 2-byte integer - Intel style.
static final short	DT_2INTEGERS	SiemensText file format define use to indicate 2-byte integer - Sun style.
static final short	DT_4FLOAT	SiemensText file format define use to indicate 4-byte float - Sun style.
static final short	DT_4INTEGERI	SiemensText file format define use to indicate 4-byte integer - Intel style.
static final short	DT_4INTEGERS	SiemensText file format define use to indicate 4-byte integer - Sun style.
static final short	DT_BYTE	SiemensText file format define use to indicate Byte (8-bits) data type
static final short	DT_UNKNOWN	SiemensText file format define use to indicate undefined image data type.
static final String[]	EXTENSIONS	The extensions of SiemensText file.
private String	fileDir	File directory of the image.
private File	fileHeader	Reference to the header file (*.hdr).
private FileInfoSiemensText	fileInfo	Reference to the file info. for an SiemensText header
private String	fileName	File name of the image.
private ModelImage	image	The image read in from the file.
(package private) Hashtable<String,String>	storage

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
FileSiemensText(String fName, String fDir)	Constructs new file object.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
static String[]	getCompleteFileNameList(String absolutePath)	Returns the complete list of file names according to given file name.
FileInfoSiemensText	getFileInfo()	Returns the FileInfoSiemensText read from the file.
String	getHeaderFile()	Returns the header file.
static String	getHeaderFile(String[] fileNames)	Returns the header file (ends in .hdr) as a string.
String[]	getImageFiles()	Returns the image file list.
static String[]	getImageFiles(String[] fileNames)	Returns the image file list.
static boolean	isHeaderFile(String absolutePath)	Return true if the file specified by absolutePath is header file of SiemensText.
static boolean	isImageFile(String absolutePath)	Return true if the file specified by absolutePath is image file of SiemensText.
static boolean	isSiemensText(String absolutePath)
boolean	readHeader(String imageFileName, String fileDir)	Reads the SiemensText header and stores the information in fileInfo.
ModelImage	readImage(boolean one)	Reads an SiemensText image file by reading the header then making a FileRaw to read the image for all filenames in the file list.
void	readImage(float[] buffer)	Reads an SiemensText image file by reading the header then making a FileRaw to read the file.

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

addProgressChangeListener, bytesToDouble, bytesToFloat, bytesToInt, bytesToShort, doubleToBytes, 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 Details

EXTENSIONS

public static final String[] EXTENSIONS

The extensions of SiemensText file.

DT_UNKNOWN

public static final short DT_UNKNOWN

SiemensText file format define use to indicate undefined image data type.

See Also:

• Constant Field Values

DT_BYTE

public static final short DT_BYTE

SiemensText file format define use to indicate Byte (8-bits) data type

See Also:

• Constant Field Values

DT_2INTEGERI

public static final short DT_2INTEGERI

SiemensText file format define use to indicate 2-byte integer - Intel style.

See Also:

• Constant Field Values

DT_4INTEGERI

public static final short DT_4INTEGERI

SiemensText file format define use to indicate 4-byte integer - Intel style.

See Also:

• Constant Field Values

DT_2FLOAT

public static final short DT_2FLOAT

SiemensText file format define use to indicate 2-byte float - Intel style.

See Also:

• Constant Field Values

DT_4FLOAT

public static final short DT_4FLOAT

SiemensText file format define use to indicate 4-byte float - Sun style.

See Also:

• Constant Field Values

DT_2INTEGERS

public static final short DT_2INTEGERS

SiemensText file format define use to indicate 2-byte integer - Sun style.

See Also:

• Constant Field Values

DT_4INTEGERS

public static final short DT_4INTEGERS

SiemensText file format define use to indicate 4-byte integer - Sun style.

See Also:

• Constant Field Values

storage

Hashtable<String,String> storage

fileDir

private String fileDir

File directory of the image.

fileHeader

private File fileHeader

Reference to the header file (*.hdr).

fileName

private String fileName

File name of the image.

fileInfo

private FileInfoSiemensText fileInfo

Reference to the file info. for an SiemensText header

image

private ModelImage image

The image read in from the file.

Constructor Details

FileSiemensText

public FileSiemensText(String fName,
 String fDir)

Constructs new file object.

Parameters:

fName - File name.

fDir - File directory.

Method Details

finalize

public void finalize()

Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.

Overrides:

finalize in class FileBase

getCompleteFileNameList

public static String[] getCompleteFileNameList(String absolutePath)

Returns the complete list of file names according to given file name.

Parameters:

absolutePath - one file name of SiemensText.

Returns:

the complete list of file names.

getHeaderFile

public static String getHeaderFile(String[] fileNames)

Returns the header file (ends in .hdr) as a string.

Parameters:

fileNames - DOCUMENT ME!

Returns:

The header file (ends in .hdr)

getImageFiles

public static String[] getImageFiles(String[] fileNames)

Returns the image file list.

Parameters:

fileNames - DOCUMENT ME!

Returns:

the image file list.

isHeaderFile

public static boolean isHeaderFile(String absolutePath)

Return true if the file specified by absolutePath is header file of SiemensText.

Parameters:

absolutePath - the file name including path information.

Returns:

true if the specified file is header file.

isImageFile

public static boolean isImageFile(String absolutePath)

Return true if the file specified by absolutePath is image file of SiemensText.

Parameters:

absolutePath - the file name including path information.

Returns:

true if the specified file is image file.

isSiemensText

public static boolean isSiemensText(String absolutePath)

getFileInfo

public FileInfoSiemensText getFileInfo()

Returns the FileInfoSiemensText read from the file.

Returns:

File info read from file, or null if it has not been read.

getHeaderFile

public String getHeaderFile()

Returns the header file.

Returns:

DOCUMENT ME!

getImageFiles

public String[] getImageFiles()

Returns the image file list.

Returns:

the image file list.

readHeader

public boolean readHeader(String imageFileName,
 String fileDir)
                   throws IOException

Reads the SiemensText header and stores the information in fileInfo.

Parameters:

imageFileName - File name of image.

fileDir - Directory.

Returns:

Flag to confirm a successful read.

Throws:

IOException - if there is an error reading the header

See Also:

• FileInfoSiemensText

readImage

public ModelImage readImage(boolean one)
                     throws IOException,
OutOfMemoryError

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

Parameters:

one - flag indicating one image of a 3D dataset should be read in.

Returns:

The image.

Throws:

IOException - if there is an error reading the file

OutOfMemoryError

See Also:

• FileRaw

readImage

public void readImage(float[] buffer)
               throws IOException,
OutOfMemoryError

Reads an SiemensText image file by reading the header then making a FileRaw to read the file. Image data is left in buffer. If the fileInfo cannot be found, the header will be located and read first. Image is not 'flipped', and neither units of measure nor orientation are set.

Parameters:

buffer - Image buffer to store image data into.

Throws:

IOException - if there is an error reading the file

OutOfMemoryError

See Also:

• FileRaw