java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileMetaImage

public class FileMetaImage
extends FileBase

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`asciiFormat`
`private java.lang.String`	`baseName`
`private java.lang.String`	`category`
`private boolean`	`compressedData`
`private int`	`compressedDataSize`
`private long`	`currentLocation`
`private java.io.File`	`defaultFileData`
`private boolean`	`defaultFileDataExists`
`private java.lang.String`	`defaultFileDataName`
`private int[]`	`extents`
`private java.lang.String`	`fieldSeparator`	DOCUMENT ME!
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private java.io.File`	`fileHeader`
`private FileInfoMetaImage`	`fileInfo`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private long`	`headerSize`
`private ModelImage`	`image`	DOCUMENT ME!
`private TransMatrix`	`matrix`
`private int`	`nDims`
`private int`	`numValues`
`private boolean`	`oneFile`	If true, header and data both stored in .mha file.
`private float[]`	`origin`	DOCUMENT ME!
`private float[]`	`resolutions`
`private boolean`	`sepFound`
`private java.lang.String[]`	`values`
`private java.util.zip.Inflater`	`zlibDecompresser`

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

FileMetaImage(java.lang.String fName, java.lang.String fDir)
Constructs new file object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`ModelImage`	`readImage(boolean one)`	reads the MetaImatge file header and data.
`private void`	`readLine()`	readLine() - reads a line of the file header separate into category, subcategory, and values.
`private void`	`updateorigins(FileInfoBase[] fileInfo)`	Updates the start locations.
`boolean`	`writeHeader(ModelImage image, int nImagesSaved, int nTimeSaved, java.lang.String fileName, java.lang.String fileDir, boolean oneFile, int headerIndex, long[] finalHeaderPosition)`	Writes a MetaImage header to a separate file.
`private void`	`writeHeader3DTo2D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options, boolean oneFile, long[] finalHeaderPosition)`	This method is used when saving a 3D image in an array of 2D files.
`private void`	`writeHeader4DTo3D(ModelImage image, java.lang.String fileName, java.lang.String fileDir, FileWriteOptions options, boolean oneFile, long[] finalHeaderPosition)`	This method is used when saving a 4D image in an array of 3D files.
`void`	`writeImage(ModelImage image, FileWriteOptions options)`	Writes an MetaImage format type 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

fileDir
```
private java.lang.String fileDir
```
DOCUMENT ME!

fileInfo
```
private FileInfoMetaImage fileInfo
```
DOCUMENT ME!

fileName
```
private java.lang.String fileName
```
DOCUMENT ME!

headerSize
```
private long headerSize
```

currentLocation
```
private long currentLocation
```

file
```
private java.io.File file
```
DOCUMENT ME!

image
```
private ModelImage image
```
DOCUMENT ME!

origin
```
private float[] origin
```
DOCUMENT ME!

resolutions
```
private float[] resolutions
```

numValues
```
private int numValues
```

fieldSeparator

private java.lang.String fieldSeparator

DOCUMENT ME!

category
```
private java.lang.String category
```

baseName
```
private java.lang.String baseName
```

values
```
private java.lang.String[] values
```

nDims
```
private int nDims
```

defaultFileDataName

private java.lang.String defaultFileDataName

defaultFileData
```
private java.io.File defaultFileData
```

defaultFileDataExists
```
private boolean defaultFileDataExists
```

asciiFormat
```
private boolean asciiFormat
```

compressedData
```
private boolean compressedData
```

extents
```
private int[] extents
```

matrix
```
private TransMatrix matrix
```

compressedDataSize
```
private int compressedDataSize
```

sepFound
```
private boolean sepFound
```

zlibDecompresser

private java.util.zip.Inflater zlibDecompresser

oneFile
```
private boolean oneFile
```
If true, header and data both stored in .mha file. If false, header stored in filename.mhd and data stored in filename.raw.

fileHeader
```
private java.io.File fileHeader
```

Constructor Detail
- FileMetaImage
```
public FileMetaImage(java.lang.String fName,
                     java.lang.String fDir)
```
  Constructs new file object.
  
  Parameters:
  
  fName - File name.
  
  fDir - File directory.

Method Detail
- readImage
```
public ModelImage readImage(boolean one)
                     throws java.io.IOException
```
  reads the MetaImatge file header and data.
  
  Parameters:
  
  one - DOCUMENT ME!
  
  Returns:
  
  DOCUMENT ME!
  
  Throws:
  
  java.io.IOException - if there is an error reading the file
- updateorigins
```
private void updateorigins(FileInfoBase[] fileInfo)
```
  Updates the start locations. Each image has a fileinfo where the start locations are stored. Note that the start location for the Z (3rd) dimension change with the change is the slice. The origin is in the upper left corner and we are using the right hand rule. + x -> left to right; + y -> top to bottom and + z -> into screen.
  
  Parameters:
  
  fileInfo - DOCUMENT ME!
- readLine
```
private void readLine()
               throws java.io.IOException
```
  readLine() - reads a line of the file header separate into category, subcategory, and values.
  
  Throws:
  
  java.io.IOException - if there is an error reading the file
- writeImage
```
public void writeImage(ModelImage image,
                       FileWriteOptions options)
                throws java.io.IOException
```
  Writes an MetaImage format type image.
  
  Parameters:
  
  image - Image model of data to write.
  
  Throws:
  
  java.io.IOException - if there is an error writing the file
  
  See Also:
  
  FileInfoMeta, FileRaw
- writeHeader
```
public boolean writeHeader(ModelImage image,
                           int nImagesSaved,
                           int nTimeSaved,
                           java.lang.String fileName,
                           java.lang.String fileDir,
                           boolean oneFile,
                           int headerIndex,
                           long[] finalHeaderPosition)
                    throws java.io.IOException
```
  Writes a MetaImage header to a separate file.
  
  Parameters:
  
  image - Image model of data to write.
  
  fileName - File name.
  
  fileDir - File directory.
  
  Returns:
  
  Flag to confirm a successful read.
  
  Throws:
  
  java.io.IOException - if there is an error
  
  See Also:
  
  FileInfoMetaImage
- writeHeader3DTo2D
```
private void writeHeader3DTo2D(ModelImage image,
                               java.lang.String fileName,
                               java.lang.String fileDir,
                               FileWriteOptions options,
                               boolean oneFile,
                               long[] finalHeaderPosition)
                        throws java.io.IOException
```
  This method is used when saving a 3D image in an array of 2D files. The file name has numbers appended to correctly order the images.
  
  Parameters:
  
  image - the image dataset to be saved
  
  fileName - the file name
  
  fileDir - the file directory
  
  options - file options indicate how to save the image
  
  Throws:
  
  java.io.IOException - DOCUMENT ME!
- writeHeader4DTo3D
```
private void writeHeader4DTo3D(ModelImage image,
                               java.lang.String fileName,
                               java.lang.String fileDir,
                               FileWriteOptions options,
                               boolean oneFile,
                               long[] finalHeaderPosition)
                        throws java.io.IOException
```
  This method is used when saving a 4D image in an array of 3D files. The file name has numbers appended to correctly order the images.
  
  Parameters:
  
  image - the image dataset to be saved
  
  fileName - the file name
  
  fileDir - the file directory
  
  options - file options indicate how to save the image
  
  Throws:
  
  java.io.IOException - DOCUMENT ME!

Class FileMetaImage

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

fileDir

fileInfo

fileName

headerSize

currentLocation

file

image

origin

resolutions

numValues

fieldSeparator

category

baseName

values

nDims

defaultFileDataName

defaultFileData

defaultFileDataExists

asciiFormat

compressedData

extents

matrix

compressedDataSize

sepFound

zlibDecompresser

oneFile

fileHeader

Constructor Detail

FileMetaImage

Method Detail

readImage

updateorigins

readLine

writeImage

writeHeader

writeHeader3DTo2D

writeHeader4DTo3D