Package gov.nih.mipav.model.file

Class FileCZI

java.lang.Object

gov.nih.mipav.model.file.FileBase

gov.nih.mipav.model.file.FileCZI

public class FileCZI
extends FileBase

File written using Zeiss Release Version 1.1 for ZEN 2012

Field Summary

Fields

Modifier and Type	Field	Description
private static final int	Bgr192ComplexFloat	A triple of 2 x 4 byte IEE float, representing real and imaginary part of a complex number, for the color channels blue, green, and red
private static final int	Bgr24	8 bit triples, representing the color channels blue, green, and red
private static final int	Bgr48	16 bit triples, representing the color channels blue, green, and red
private static final int	Bgr96Float	Triple of 4 byte IEEE float, representing the color channels blue, green, and red
private static final int	Bgra32	8 bit triples followed by an alpha (transparency) channel
private final boolean	endianess
private File	file	DOCUMENT ME!
private String	fileDir	DOCUMENT ME!
private FileInfoCZI	fileInfo	DOCUMENT ME!
private String	fileName	DOCUMENT ME!
private static final int	Gray16	16 bit unsigned
private static final int	Gray32	32 bit integer [planned]
private static final int	Gray32Float	32 bit IEEE float
private static final int	Gray64	Double precision floating point [planned]
private static final int	Gray64ComplexFloat	2 x 4 byte IEEE float, representing the real and imaginary part of a complex number
private static final int	Gray8	8 bit unsigned
private ModelImage	image	DOCUMENT ME!
private int[]	imageExtents	DOCUMENT ME!
private float[]	imgBuffer	DOCUMENT ME!
private float[]	imgResols	DOCUMENT ME!
private static final int	JpegXrFile
private static final int	JpgFile
private static final int	LZW
private static final int	Uncompressed

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
FileCZI(String fileName, String fileDir)	LIFF reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
void	finalize()	Prepares this class for cleanup.
FileInfoBase	getFileInfo()	Accessor that returns the file info.
float[]	getImageBuffer()	Accessor that returns the image buffer.
private String	readCString()
ModelImage	readImage(boolean multiFile, boolean one)	Reads the CZI header.

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

Gray8

private static final int Gray8

8 bit unsigned

See Also:

• Constant Field Values

Gray16

private static final int Gray16

16 bit unsigned

See Also:

• Constant Field Values

Gray32Float

private static final int Gray32Float

32 bit IEEE float

See Also:

• Constant Field Values

Bgr24

private static final int Bgr24

8 bit triples, representing the color channels blue, green, and red

See Also:

• Constant Field Values

Bgr48

private static final int Bgr48

16 bit triples, representing the color channels blue, green, and red

See Also:

• Constant Field Values

Bgr96Float

private static final int Bgr96Float

Triple of 4 byte IEEE float, representing the color channels blue, green, and red

See Also:

• Constant Field Values

Bgra32

private static final int Bgra32

8 bit triples followed by an alpha (transparency) channel

See Also:

• Constant Field Values

Gray64ComplexFloat

private static final int Gray64ComplexFloat

2 x 4 byte IEEE float, representing the real and imaginary part of a complex number

See Also:

• Constant Field Values

Bgr192ComplexFloat

private static final int Bgr192ComplexFloat

A triple of 2 x 4 byte IEE float, representing real and imaginary part of a complex number, for the color channels blue, green, and red

See Also:

• Constant Field Values

Gray32

private static final int Gray32

32 bit integer [planned]

See Also:

• Constant Field Values

Gray64

private static final int Gray64

Double precision floating point [planned]

See Also:

• Constant Field Values

Uncompressed

private static final int Uncompressed

See Also:

• Constant Field Values

LZW

private static final int LZW

See Also:

• Constant Field Values

JpgFile

private static final int JpgFile

See Also:

• Constant Field Values

JpegXrFile

private static final int JpegXrFile

See Also:

• Constant Field Values

file

private File file

DOCUMENT ME!

fileDir

private String fileDir

DOCUMENT ME!

fileInfo

private FileInfoCZI fileInfo

DOCUMENT ME!

fileName

private String fileName

DOCUMENT ME!

image

private ModelImage image

DOCUMENT ME!

imageExtents

private int[] imageExtents

DOCUMENT ME!

imgBuffer

private float[] imgBuffer

DOCUMENT ME!

imgResols

private float[] imgResols

DOCUMENT ME!

endianess

private final boolean endianess

Constructor Details

FileCZI

public FileCZI(String fileName,
 String fileDir)
        throws IOException

LIFF reader/writer constructor.

Parameters:

fileName - file name

fileDir - file directory

Throws:

IOException - if there is an error making the file

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

getFileInfo

public FileInfoBase getFileInfo()

Accessor that returns the file info.

Returns:

FileInfoBase containing the file info

getImageBuffer

public float[] getImageBuffer()

Accessor that returns the image buffer.

Returns:

buffer of image.

readImage

public ModelImage readImage(boolean multiFile,
 boolean one)
                     throws IOException

Reads the CZI header. This method then opens a Model of an image.

Parameters:

multiFile - true if a set of files each containing a separate 2D image is present false if one file with either a 2D image or a stack of 2D images

one - true if only want to read in one image of the 3D set

Returns:

returns the image

Throws:

IOException - if there is an error reading the file

readCString

private String readCString()
                    throws IOException

Throws:

IOException