Package gov.nih.mipav.model.file

Class FileMetaImage

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

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!