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 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 int`	`Bgr24`	8 bit triples, representing the color channels blue, green, and red
`private static int`	`Bgr48`	16 bit triples, representing the color channels blue, green, and red
`private static int`	`Bgr96Float`	Triple of 4 byte IEEE float, representing the color channels blue, green, and red
`private static int`	`Bgra32`	8 bit triples followed by an alpha (transparency) channel
`private boolean`	`endianess`
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoCZI`	`fileInfo`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private static int`	`Gray16`	16 bit unsigned
`private static int`	`Gray32`	32 bit integer [planned]
`private static int`	`Gray32Float`	32 bit IEEE float
`private static int`	`Gray64`	Double precision floating point [planned]
`private static int`	`Gray64ComplexFloat`	2 x 4 byte IEEE float, representing the real and imaginary part of a complex number
`private static 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 int`	`JpegXrFile`
`private static int`	`JpgFile`
`private static int`	`LZW`
`private static 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(java.lang.String fileName, java.lang.String fileDir)
LIFF reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
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 java.lang.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 Detail
  - 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 java.io.File file
```
    DOCUMENT ME!
  - fileDir
```
private java.lang.String fileDir
```
    DOCUMENT ME!
  - fileInfo
```
private FileInfoCZI fileInfo
```
    DOCUMENT ME!
  - fileName
```
private java.lang.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 Detail
  - FileCZI
```
public FileCZI(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException
```
    LIFF reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    Throws:
    
    java.io.IOException - if there is an error making the file
- Method Detail
  - 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 java.io.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:
    
    java.io.IOException - if there is an error reading the file
  - readCString
```
private java.lang.String readCString()
                              throws java.io.IOException
```
    Throws:
    
    java.io.IOException

Class FileCZI

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

Gray8

Gray16

Gray32Float

Bgr24

Bgr48

Bgr96Float

Bgra32

Gray64ComplexFloat

Bgr192ComplexFloat

Gray32

Gray64

Uncompressed

LZW

JpgFile

JpegXrFile

file

fileDir

fileInfo

fileName

image

imageExtents

imgBuffer

imgResols

endianess

Constructor Detail

FileCZI

Method Detail

finalize

getFileInfo

getImageBuffer

readImage

readCString