Package gov.nih.mipav.model.file

Class FileSpar

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileSpar

public class FileSpar
extends FileBase

Reads a spar/sdat file. MIPAV only uses the spar information since the sdat is spectroscopy data.

Author:

senseneyj

Field Summary

Fields

Modifier and Type	Field	Description
private java.lang.String	fileDir	File directory of the image.
private FileInfoSPAR	fileInfo	Reference fileinfo
private java.lang.String	fileName	File name of the image.
static java.lang.String[]	hdrEXTENSIONS	The extensions of ANALYZE file.
private ModelImage	image	The image read in from the file.
private ModelImage	imageA
private FileInfoBase	imageAInfo	imageA file info
static java.lang.String[]	imgEXTENSIONS
private FileInfoSPAR	outInfo	file info

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
FileSpar(ModelImage imageA, FileInfoBase imageAInfo, java.lang.String fileName, java.lang.String fileDir)
FileSpar(java.lang.String fileName, java.lang.String fileDir)

Method Summary

Modifier and Type	Method	Description
static java.lang.String[]	getCompleteFileNameList(java.lang.String absolutePath)	Returns the complete list of file names according to given file name.
FileInfoSPAR	getFileInfo()
static java.lang.String	getHeaderFile(java.lang.String[] fileNames)	======= Returns the header file.
static boolean	isHeaderFile(java.lang.String absolutePath)	Return true if the file specified by absolutePath is header file of ANALYZE.
static boolean	isImageFile(java.lang.String absolutePath)	Return true if the file specified by absolutePath is image file of ANALYZE.
private static double	parseDouble(java.lang.String nextLine)
private static int	parseInt(java.lang.String nextLine)
boolean	readHeader(java.lang.String imageFileName, java.lang.String fileDir)	Reads the spar header and stores the information in fileInfo.
ModelImage	readImage(boolean one)	Constructs a SPAR image mask based on the parameters defined in FileInfoSPAR
private int	setLowerExtents(int index)
private int	setUpperExtents(int index)
private ModelImage	updateTransformMatrix(ModelImage image)

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

hdrEXTENSIONS

public static final java.lang.String[] hdrEXTENSIONS

The extensions of ANALYZE file.

imgEXTENSIONS

public static final java.lang.String[] imgEXTENSIONS

fileDir

private java.lang.String fileDir

File directory of the image.

fileName

private java.lang.String fileName

File name of the image.

image

private ModelImage image

The image read in from the file.

outInfo

private FileInfoSPAR outInfo

file info

imageAInfo

private FileInfoBase imageAInfo

imageA file info

imageA

private ModelImage imageA

fileInfo

private FileInfoSPAR fileInfo

Reference fileinfo

Constructor Detail

FileSpar

public FileSpar(java.lang.String fileName,
                java.lang.String fileDir)

FileSpar

public FileSpar(ModelImage imageA,
                FileInfoBase imageAInfo,
                java.lang.String fileName,
                java.lang.String fileDir)

Method Detail

parseDouble

private static double parseDouble(java.lang.String nextLine)

parseInt

private static int parseInt(java.lang.String nextLine)

readHeader

public boolean readHeader(java.lang.String imageFileName,
                          java.lang.String fileDir)
                   throws java.io.IOException

Reads the spar header and stores the information in fileInfo.

Parameters:

imageFileName - File name of image (is also the spar file).

fileDir - Directory.

Returns:

Flag to confirm a successful read.

Throws:

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

See Also:

FileInfoAnalyze

setLowerExtents

private int setLowerExtents(int index)

setUpperExtents

private int setUpperExtents(int index)

readImage

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

Constructs a SPAR image mask based on the parameters defined in FileInfoSPAR

Parameters:

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

Returns:

The image.

Throws:

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

java.lang.OutOfMemoryError

See Also:

FileRaw

getFileInfo

public FileInfoSPAR getFileInfo()

updateTransformMatrix

private ModelImage updateTransformMatrix(ModelImage image)

getCompleteFileNameList

public static java.lang.String[] getCompleteFileNameList(java.lang.String absolutePath)

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

Parameters:

absolutePath - one file name of PARREC.

Returns:

the complete list of file names.

getHeaderFile

public static java.lang.String getHeaderFile(java.lang.String[] fileNames)

======= Returns the header file.

Parameters:

fileNames - DOCUMENT ME!

Returns:

DOCUMENT ME!

isHeaderFile

public static boolean isHeaderFile(java.lang.String absolutePath)

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

Parameters:

absolutePath - the file name including path information.

Returns:

true if the specified file is header file.

isImageFile

public static boolean isImageFile(java.lang.String absolutePath)

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

Parameters:

absolutePath - the file name including path information.

Returns:

true if the specified file is image file.