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

All Methods Static Methods Instance Methods Concrete Methods
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.

Class FileSpar

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

hdrEXTENSIONS

imgEXTENSIONS

fileDir

fileName

image

outInfo

imageAInfo

imageA

fileInfo

Constructor Detail

FileSpar

FileSpar

Method Detail

parseDouble

parseInt

readHeader

setLowerExtents

setUpperExtents

readImage

getFileInfo

updateTransformMatrix

getCompleteFileNameList

getHeaderFile

isHeaderFile

isImageFile