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

```
public class FileZVI
extends FileBase
```
Documentation used was the ZVI Format Specification V 2.0.5 - August, 2010. The following email was sent to Zeiss support: Here are problems I spotted in ZVI Format Specification V 2.0.5 - August, 2010: 2.1.1 stream of the container image: TypeDescription is VT_EMPTY rather than VT_BSTR FileName is VT_EMPTY rather than VT_BSTR m_PluginCLSID is VT_BLOB rather than VT_CLSID The {Tags} VT_STORED_OBJECT that goes between the {Layers} and {Scaling} VT_STORED_OBJECTs is missing. 2.2.1 stream of the image item: Version is used rather than unused with minor = 1003 hex and major = 3000 hex. TypeDescription is VT_EMPTY rather than VT_BSTR. FileName is VT_EMPTY rather than VT_BSTR m_PluginCLSID is VT_BLOB rather than VT_CLSID Items after the {Others} VT_BLOB are completely different from what's listed. I find: VT_DISPATCH VT_STORED_OBJECT with a string = Tags VT_DISPATCH VT_DISPATCH VT_DISPATCH RAW pixel data 3.3 Coordinate ID for Image Dimensions: Index should be 0 1 2 3 4 5 6 7 instead of the existing 0 1 3 4 5 6 7 8. 3.4 Tag IDs ID 301 is used for both ImageBaseTimeFirst and ImageBaseTime1. I suspect the ImageBaseTimeFirst entry should be deleted. The following tags show up in .ZVI files but are not listed in your table: 2071, 20478. What is the info for these tags? 65781 has both AuroxCamRes6 and AuroxCamCFactor. Information for decoding the 64-bit VT_DATE structure is missing. Is it available somewhere? Is it possible for me to obtain sample .ZVI files so I can improve the ZVI file read in the MIPAV image processing program? Sincerely, William Gandler

Field Summary

Fields
Modifier and Type	Field	Description
`private boolean`	`add128`
`private int`	`ap`
`private int`	`backupZDim`
`private double[]`	`cameraImageAcquisitionTime`
`private int[]`	`cArray`
`private int`	`channelNumber`
`private boolean`	`endianess`
`private java.io.File`	`file`	DOCUMENT ME!
`private java.lang.String`	`fileDir`	DOCUMENT ME!
`private FileInfoZVI`	`fileInfo`	DOCUMENT ME!
`private java.lang.String`	`fileName`	DOCUMENT ME!
`private int`	`icp`
`private int`	`icp2`
`private int`	`icp3`
`private int`	`icp4`
`private int`	`icp5`
`private int`	`icp6`
`private int`	`icp7`
`private int`	`icpOriginalX`
`private int`	`icpOriginalY`
`private int`	`icpX`
`private int`	`icpY`
`private ModelImage`	`image`	DOCUMENT ME!
`private double[]`	`imageBlackValueArray`
`private int[]`	`imageC2Array`
`private int[]`	`imageC3Array`
`private int[]`	`imageC6Array`
`private int[]`	`imageC7Array`
`private int`	`imageCount`
`private int[]`	`imageExtents`	DOCUMENT ME!
`private double[]`	`imageFocusPositionArray`
`private int`	`imageHeight`
`private double[]`	`imageOriginalStagePositionXArray`
`private double[]`	`imageOriginalStagePositionYArray`
`private int[]`	`imageOriginalZXArray`
`private int[]`	`imageOriginalZYArray`
`private int`	`imagePixelFormat`
`private double[]`	`imageRelativeTime`
`private double[]`	`imageRelFocusPosition1Array`
`private double[]`	`imageRelFocusPosition2Array`
`private double[]`	`imageStagePositionXArray`
`private double[]`	`imageStagePositionYArray`
`private int[]`	`imageT2Array`
`private int[]`	`imageT3Array`
`private int[]`	`imageT6Array`
`private int[]`	`imageT7Array`
`private double[]`	`imageWhiteValueArray`
`private int`	`imageWidth`
`private int[]`	`imageZ2Array`
`private int[]`	`imageZ3Array`
`private int[]`	`imageZ4Array`
`private int[]`	`imageZ5Array`
`private int[]`	`imageZ6Array`
`private int[]`	`imageZ7Array`
`private int[]`	`imageZArray`
`private int[]`	`imageZXArray`
`private int[]`	`imageZYArray`
`private float[]`	`imgBuffer`	DOCUMENT ME!
`private float[]`	`imgResols`	DOCUMENT ME!
`private ModelLUT`	`LUT`	DOCUMENT ME!
`private int`	`maxC`
`private int`	`maxPosition`
`private int`	`maxT`
`private int`	`maxZ`
`private int`	`minC`
`private int`	`minPosition`
`private int`	`minT`
`private int`	`minZ`
`private int[]`	`offsetArray`
`private int[]`	`positionArray`
`private int`	`positionNumber`
`private int[]`	`sat`
`private int`	`sectorSize`
`private int`	`shortSectorSize`
`private int[]`	`shortSectorTable`
`private int`	`shortStreamStartSect`
`private int[]`	`startSectorArray`
`private int[]`	`tArray`
`private int`	`tDim`
`private long`	`totalShortStreamSize`
`private static short`	`VT_BLOB`
`private static short`	`VT_BOOL`
`private static short`	`VT_BSTR`
`private static short`	`VT_DATE`
`private static short`	`VT_DISPATCH`
`private static short`	`VT_EMPTY`
`private static short`	`VT_I2`
`private static short`	`VT_I4`
`private static short`	`VT_R8`
`private static short`	`VT_STORED_OBJECT`
`private int[]`	`zArray`
`private int`	`zDim`

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

FileZVI(java.lang.String fileName, java.lang.String fileDir)
ZVI reader constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private java.lang.String`	`calculateRelativeTime(double relativeTime)`
`(package private) java.lang.String`	`calculateTimeStampString(long timeStamp)`
`private java.lang.String`	`calculateVTDateTimeString(double dateTime)`
`private void`	`displayPixelFormat(int pixelFormat)`
`void`	`finalize()`	Prepares this class for cleanup.
`FileInfoBase`	`getFileInfo()`	Accessor that returns the file info.
`float[]`	`getImageBuffer()`	Accessor that returns the image buffer.
`ModelLUT`	`getModelLUT()`	Rreturns LUT if defined.
`boolean`	`readHeader()`
`ModelImage`	`readImage(boolean multiFile, boolean one)`	Reads the LIFF header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD.
`private int`	`zviToMipavMeasurementUnits(int zviScalingUnit)`

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

VT_EMPTY
```
private static final short VT_EMPTY
```
See Also:

Constant Field Values

VT_BOOL
```
private static final short VT_BOOL
```
See Also:

Constant Field Values

VT_I2
```
private static final short VT_I2
```
See Also:

Constant Field Values

VT_I4
```
private static final short VT_I4
```
See Also:

Constant Field Values

VT_R8
```
private static final short VT_R8
```
See Also:

Constant Field Values

VT_BSTR
```
private static final short VT_BSTR
```
See Also:

Constant Field Values

VT_STORED_OBJECT
```
private static final short VT_STORED_OBJECT
```
See Also:

Constant Field Values

VT_DATE
```
private static final short VT_DATE
```
See Also:

Constant Field Values

VT_DISPATCH
```
private static final short VT_DISPATCH
```
See Also:

Constant Field Values

VT_BLOB
```
private static final short VT_BLOB
```
See Also:

Constant Field Values

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

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

fileInfo
```
private FileInfoZVI 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!

LUT
```
private ModelLUT LUT
```
DOCUMENT ME!

endianess
```
private boolean endianess
```

sectorSize
```
private int sectorSize
```

shortSectorSize
```
private int shortSectorSize
```

shortSectorTable
```
private int[] shortSectorTable
```

shortStreamStartSect
```
private int shortStreamStartSect
```

totalShortStreamSize
```
private long totalShortStreamSize
```

imageWidth
```
private int imageWidth
```

imageHeight
```
private int imageHeight
```

imageCount
```
private int imageCount
```

imagePixelFormat
```
private int imagePixelFormat
```

zDim
```
private int zDim
```

backupZDim
```
private int backupZDim
```

tDim
```
private int tDim
```

channelNumber
```
private int channelNumber
```

positionNumber
```
private int positionNumber
```

zArray
```
private int[] zArray
```

cArray
```
private int[] cArray
```

tArray
```
private int[] tArray
```

positionArray
```
private int[] positionArray
```

startSectorArray
```
private int[] startSectorArray
```

offsetArray
```
private int[] offsetArray
```

ap
```
private int ap
```

imageFocusPositionArray

private double[] imageFocusPositionArray

imageStagePositionXArray

private double[] imageStagePositionXArray

imageZXArray
```
private int[] imageZXArray
```

imageZYArray
```
private int[] imageZYArray
```

imageStagePositionYArray

private double[] imageStagePositionYArray

imageOriginalStagePositionXArray

private double[] imageOriginalStagePositionXArray

imageOriginalZXArray
```
private int[] imageOriginalZXArray
```

imageOriginalZYArray
```
private int[] imageOriginalZYArray
```

imageOriginalStagePositionYArray

private double[] imageOriginalStagePositionYArray

imageZArray
```
private int[] imageZArray
```

imageZ2Array
```
private int[] imageZ2Array
```

imageC2Array
```
private int[] imageC2Array
```

imageT2Array
```
private int[] imageT2Array
```

imageBlackValueArray
```
private double[] imageBlackValueArray
```

imageZ3Array
```
private int[] imageZ3Array
```

imageC3Array
```
private int[] imageC3Array
```

imageT3Array
```
private int[] imageT3Array
```

imageWhiteValueArray
```
private double[] imageWhiteValueArray
```

imageRelFocusPosition1Array

private double[] imageRelFocusPosition1Array

imageZ4Array
```
private int[] imageZ4Array
```

imageRelFocusPosition2Array

private double[] imageRelFocusPosition2Array

imageZ5Array
```
private int[] imageZ5Array
```

cameraImageAcquisitionTime

private double[] cameraImageAcquisitionTime

imageZ6Array
```
private int[] imageZ6Array
```

imageC6Array
```
private int[] imageC6Array
```

imageT6Array
```
private int[] imageT6Array
```

imageRelativeTime
```
private double[] imageRelativeTime
```

imageZ7Array
```
private int[] imageZ7Array
```

imageC7Array
```
private int[] imageC7Array
```

imageT7Array
```
private int[] imageT7Array
```

icp
```
private int icp
```

icp2
```
private int icp2
```

icp3
```
private int icp3
```

icp4
```
private int icp4
```

icp5
```
private int icp5
```

icp6
```
private int icp6
```

icp7
```
private int icp7
```

icpX
```
private int icpX
```

icpY
```
private int icpY
```

icpOriginalX
```
private int icpOriginalX
```

icpOriginalY
```
private int icpOriginalY
```

sat
```
private int[] sat
```

add128
```
private boolean add128
```

minC
```
private int minC
```

maxC
```
private int maxC
```

minZ
```
private int minZ
```

maxZ
```
private int maxZ
```

minT
```
private int minT
```

maxT
```
private int maxT
```

minPosition
```
private int minPosition
```

maxPosition
```
private int maxPosition
```

Constructor Detail
- FileZVI
```
public FileZVI(java.lang.String fileName,
               java.lang.String fileDir)
        throws java.io.IOException
```
  ZVI reader 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.
- getModelLUT
```
public ModelLUT getModelLUT()
```
  Rreturns LUT if defined.
  
  Returns:
  
  the LUT if defined else it is null
- readImage
```
public ModelImage readImage(boolean multiFile,
                            boolean one)
                     throws java.io.IOException
```
  Reads the LIFF header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD. It then reads all the IFDs. This method then opens a Model of an image and imports the the images one slice at a time. Image slices are separated by an IFD.
  
  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
- readHeader
```
public boolean readHeader()
                   throws java.io.IOException
```
  Throws:
  
  java.io.IOException
- zviToMipavMeasurementUnits
```
private int zviToMipavMeasurementUnits(int zviScalingUnit)
```
- displayPixelFormat
```
private void displayPixelFormat(int pixelFormat)
```
- calculateTimeStampString
```
java.lang.String calculateTimeStampString(long timeStamp)
```
- calculateVTDateTimeString
```
private java.lang.String calculateVTDateTimeString(double dateTime)
```
- calculateRelativeTime
```
private java.lang.String calculateRelativeTime(double relativeTime)
```

Class FileZVI

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

VT_EMPTY

VT_BOOL

VT_I2

VT_I4

VT_R8

VT_BSTR

VT_STORED_OBJECT

VT_DATE

VT_DISPATCH

VT_BLOB

file

fileDir

fileInfo

fileName

image

imageExtents

imgBuffer

imgResols

LUT

endianess

sectorSize

shortSectorSize

shortSectorTable

shortStreamStartSect

totalShortStreamSize

imageWidth

imageHeight

imageCount

imagePixelFormat

zDim

backupZDim

tDim

channelNumber

positionNumber

zArray

cArray

tArray

positionArray

startSectorArray

offsetArray

ap

imageFocusPositionArray

imageStagePositionXArray

imageZXArray

imageZYArray

imageStagePositionYArray

imageOriginalStagePositionXArray

imageOriginalZXArray

imageOriginalZYArray

imageOriginalStagePositionYArray

imageZArray

imageZ2Array

imageC2Array

imageT2Array

imageBlackValueArray

imageZ3Array

imageC3Array

imageT3Array

imageWhiteValueArray

imageRelFocusPosition1Array

imageZ4Array

imageRelFocusPosition2Array

imageZ5Array

cameraImageAcquisitionTime

imageZ6Array

imageC6Array

imageT6Array

imageRelativeTime

imageZ7Array

imageC7Array

imageT7Array

icp