java.lang.Object
- gov.nih.mipav.model.file.FileBase
- - gov.nih.mipav.model.file.FileXML
  - - gov.nih.mipav.model.file.FileVOI

```
public class FileVOI
extends FileXML
```
VOI reader/writer. This classes incorporates the ability to write/read VOIs in three formats (MIPAV *.voi, Nuages, and MIPAV *.xml . The first is a simple text format in which the points of the VOIs are stored in text format. The VOIs can be also stored in a second format, also a text format, termed a Nauges. Nauges is a program that forms triangles (i.e., tesselates) from contours. Therefore, if one wishes to render a surface of a VOI, first save the VOI in Nauges format and supply the VOI file to the Nauges executable. MIPAV's lastest file format is based on XML and should be used in the future.
Note: A single VOI per file. However, a VOI can be formed from multiple contours.

Version:

0.1 Feb 24, 1998

Author:

Matthew J. McAuliffe, Ph.D.

See Also:

VOI

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description
`private class`	`FileVOI.MyXMLHandler`	Handle events generated while parsing the XML file.
`private class`	`FileVOI.VOIComparator`	DOCUMENT ME!
`private class`	`FileVOI.VOISortItem`	DOCUMENT ME!
`private class`	`FileVOI.XMLAnnotationHandler`	Handle events generated while parsing the Annotation XML file.
`private class`	`FileVOI.XMLCoordHandler`	Handle events generated while parsing the XML file.

Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileXML
FileXML.XMLAttributes

Field Summary

Fields
Modifier and Type	Field	Description
`private java.lang.String`	`extension`
`protected java.io.File`	`file`	File reference, it and its components are able to be modified by extending classes.
`protected java.lang.String`	`fileDir`	File directory where the VOI is to read or written.
`protected java.lang.String`	`fileName`	File name of the VOI.
`private ModelImage`	`image`	Image used to reference properties of the image to aid reading and writing of the VOI.
`private boolean`	`isXML`	Flag indicating whether the VOI should be written in MIPAV's XML format.
`private short`	`numVOIs`	The number of VOIs in the image.
`private int`	`sliceNum`	File directory where the VOI is to read or written.
`private static java.lang.String`	`TEXT_HEADER`
`private java.lang.String`	`trimmedFileName`	File name without the extension.
`private static java.lang.String`	`VOI_HEADER`	The MIPAV XML header comment.
`private static java.lang.String`	`W3C_XML_SCHEMA`	The W3C XML schema.
`private static java.lang.String`	`XML_ENCODING`	The charset the XML file is written in.
`private static java.lang.String`	`XML_HEADER`	The XML version description header.

Fields inherited from class gov.nih.mipav.model.file.FileXML
bw, fileInfo, m_kHandler, MIPAV_HEADER, pInterface, TAB, tabLevel

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

FileVOI(java.lang.String fileName, java.lang.String fileDir, ModelImage image)
VOI reader/writer constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`decodeLine(java.lang.String str, WildMagic.LibFoundation.Mathematics.Vector2f pt)`	Converts string point (x,y) to Vector2f point.
`private boolean`	`readAnnotationXML(VOIVector voiVector)`	Reads in an annotation xml (.lbl) file and puts all VOITexts into a VOIVector (to be added to the image)
`private VOI`	`readContourVOI()`	This method read a VOI file that has been saved in the MIPAV VOI format.
`private boolean`	`readCoordXML(VOI voi, boolean isLPS)`	Reads in a VOI from a file using the new VOI schema based on Scanner coordinates rather than pixel space
`private java.lang.String`	`readLine()`	Reads a line of the file and strips comments indicated by the # symbol.
`private VOI`	`readNaugeVOI(java.lang.String firstStr)`	This method read a VOI file that has been saved in the Nauge VOI format.
`VOI[]`	`readOtherOrientationVOI()`	This method read a VOI file that has been saved in the MIPAV VOI format (MIPAV .voi, Nuages, and MIPAV .xml).
`private VOI`	`readPointVOI()`	This method read a VOI.POINT file that has been saved in the MIPAV PTS format.
`VOI[]`	`readVOI(boolean doLabel)`	This method read a VOI file that has been saved in the MIPAV VOI format (MIPAV .voi, Nuages, and MIPAV .xml).
`private boolean`	`readXML(VOI voi)`	Reads in the older VOI XML schema (using pixel coordinates)
`void`	`writeAnnotationInVoiAsXML(java.lang.String voiName, boolean writeAllContours)`	Writes VOIText(s) to a .lbl file (XML based)
`void`	`writeAnnotationXML(boolean writeAll)`	Writes VOIText(s) to a .lbl file (XML based)
`void`	`writeNaugeVOI(VOI voi)`	Writes a single VOI to a file in Nauge format.
`void`	`writePointVOI(VOI voi)`	Writes a single VOI.POINT to a file MIPAV format.
`void`	`writeVOI(VOI voi, boolean saveAllContours)`	Writes a single VOI to a file MIPAV format.
`void`	`writeXML(VOI voi, boolean saveAllContours)`
`void`	`writeXML(VOI voi, boolean saveAllContours, boolean overwriteFile)`	Writes VOI to an XML formatted file.

Methods inherited from class gov.nih.mipav.model.file.FileXML
closedTag, closedTag, closedTag, finalize, openTag, readHeader, setPBar

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
  - W3C_XML_SCHEMA
```
private static final java.lang.String W3C_XML_SCHEMA
```
    The W3C XML schema.
    
    See Also:
    
    Constant Field Values
  - XML_ENCODING
```
private static final java.lang.String XML_ENCODING
```
    The charset the XML file is written in.
    
    See Also:
    
    Constant Field Values
  - XML_HEADER
```
private static final java.lang.String XML_HEADER
```
    The XML version description header.
    
    See Also:
    
    Constant Field Values
  - VOI_HEADER
```
private static final java.lang.String VOI_HEADER
```
    The MIPAV XML header comment.
    
    See Also:
    
    Constant Field Values
  - TEXT_HEADER
```
private static final java.lang.String TEXT_HEADER
```
    See Also:
    
    Constant Field Values
  - file
```
protected java.io.File file
```
    File reference, it and its components are able to be modified by extending classes.
  - fileDir
```
protected java.lang.String fileDir
```
    File directory where the VOI is to read or written.
  - fileName
```
protected java.lang.String fileName
```
    File name of the VOI.
  - image
```
private final ModelImage image
```
    Image used to reference properties of the image to aid reading and writing of the VOI.
  - isXML
```
private boolean isXML
```
    Flag indicating whether the VOI should be written in MIPAV's XML format.
  - numVOIs
```
private final short numVOIs
```
    The number of VOIs in the image.
  - sliceNum
```
private int sliceNum
```
    File directory where the VOI is to read or written.
  - trimmedFileName
```
private java.lang.String trimmedFileName
```
    File name without the extension.
  - extension
```
private java.lang.String extension
```
- Constructor Detail
  - FileVOI
```
public FileVOI(java.lang.String fileName,
               java.lang.String fileDir,
               ModelImage image)
        throws java.io.IOException
```
    VOI reader/writer constructor.
    
    Parameters:
    
    fileName - file name
    
    fileDir - file directory
    
    image - image model: needed during the read process to ensure the VOI "fits" in the image space.
    
    Throws:
    
    java.io.IOException - if there is an error making the files
- Method Detail
  - readVOI
```
public VOI[] readVOI(boolean doLabel)
              throws java.io.IOException
```
    This method read a VOI file that has been saved in the MIPAV VOI format (MIPAV *.voi, Nuages, and MIPAV *.xml).
    
    Parameters:
    
    doLabel - boolean telling to read the files as VOITexts (labels)
    
    Returns:
    
    the VOI read off the disk
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readOtherOrientationVOI
```
public VOI[] readOtherOrientationVOI()
                              throws java.io.IOException
```
    This method read a VOI file that has been saved in the MIPAV VOI format (MIPAV *.voi, Nuages, and MIPAV *.xml).
    
    Returns:
    
    the VOI read off the disk
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - writeAnnotationXML
```
public void writeAnnotationXML(boolean writeAll)
                        throws java.io.IOException
```
    Writes VOIText(s) to a .lbl file (XML based)
    
    Parameters:
    
    writeAll - whether or not to write all VOITexts into the same file, or only the selected VOIText
    
    Throws:
    
    java.io.IOException - exception thrown if there is an error writing the file
  - writeAnnotationInVoiAsXML
```
public void writeAnnotationInVoiAsXML(java.lang.String voiName,
                                      boolean writeAllContours)
                               throws java.io.IOException
```
    Writes VOIText(s) to a .lbl file (XML based)
    
    Parameters:
    
    String - voiName Name of VOIText to write out
    
    boolean - writeAllContours Whether to write all contours or only selected contours
    
    Throws:
    
    java.io.IOException - exception thrown if there is an error writing the file
  - writeNaugeVOI
```
public void writeNaugeVOI(VOI voi)
                   throws java.io.IOException
```
    Writes a single VOI to a file in Nauge format.
    
    Parameters:
    
    voi - VOI to write
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writePointVOI
```
public void writePointVOI(VOI voi)
                   throws java.io.IOException
```
    Writes a single VOI.POINT to a file MIPAV format.
    
    Parameters:
    
    voi - VOI.POINT to write
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeVOI
```
public void writeVOI(VOI voi,
                     boolean saveAllContours)
              throws java.io.IOException
```
    Writes a single VOI to a file MIPAV format.
    
    Parameters:
    
    voi - VOI to write
    
    saveAllContours - if true save all contours, not just the active ones
    
    Throws:
    
    java.io.IOException - if there is an error writing the file
  - writeXML
```
public void writeXML(VOI voi,
                     boolean saveAllContours)
              throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - writeXML
```
public void writeXML(VOI voi,
                     boolean saveAllContours,
                     boolean overwriteFile)
              throws java.io.IOException
```
    Writes VOI to an XML formatted file.
    
    Parameters:
    
    voi - VOI to be saved
    
    saveAllContours - if true save all contours, not just the active ones
    
    Throws:
    
    java.io.IOException - exception thrown if there is an error writing the file
  - decodeLine
```
private void decodeLine(java.lang.String str,
                        WildMagic.LibFoundation.Mathematics.Vector2f pt)
```
    Converts string point (x,y) to Vector2f point.
    
    Parameters:
    
    str - string to convert
    
    pt - point to return
  - readAnnotationXML
```
private boolean readAnnotationXML(VOIVector voiVector)
```
    Reads in an annotation xml (.lbl) file and puts all VOITexts into a VOIVector (to be added to the image)
    
    Parameters:
    
    voiVector - a VOIVector for holding the VOIs before they are transferred to the image
    
    Returns:
    
    boolean
  - readContourVOI
```
private VOI readContourVOI()
                    throws java.io.IOException
```
    This method read a VOI file that has been saved in the MIPAV VOI format.
    
    Returns:
    
    the new VOI read from the file
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readCoordXML
```
private boolean readCoordXML(VOI voi,
                             boolean isLPS)
```
    Reads in a VOI from a file using the new VOI schema based on Scanner coordinates rather than pixel space
    
    Parameters:
    
    voi - VOI to be read in
    
    Returns:
    
    boolean whether or not the VOI read in successfully
  - readLine
```
private java.lang.String readLine()
                           throws java.io.IOException
```
    Reads a line of the file and strips comments indicated by the # symbol.
    
    Returns:
    
    the line read in
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readNaugeVOI
```
private VOI readNaugeVOI(java.lang.String firstStr)
                  throws java.io.IOException
```
    This method read a VOI file that has been saved in the Nauge VOI format.
    
    Parameters:
    
    firstStr - first line of the Nauge VOI file
    
    Returns:
    
    the VOI
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readPointVOI
```
private VOI readPointVOI()
                  throws java.io.IOException
```
    This method read a VOI.POINT file that has been saved in the MIPAV PTS format.
    
    Returns:
    
    the new VOI read from the file
    
    Throws:
    
    java.io.IOException - if there is an error reading the file
  - readXML
```
private boolean readXML(VOI voi)
```
    Reads in the older VOI XML schema (using pixel coordinates)
    
    Parameters:
    
    voi - VOI
    
    Returns:
    
    boolean

Class FileVOI

Nested Class Summary

Nested classes/interfaces inherited from class gov.nih.mipav.model.file.FileXML

Field Summary

Fields inherited from class gov.nih.mipav.model.file.FileXML

Fields inherited from class gov.nih.mipav.model.file.FileBase

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.file.FileXML

Methods inherited from class gov.nih.mipav.model.file.FileBase

Methods inherited from class java.lang.Object

Field Detail

W3C_XML_SCHEMA

XML_ENCODING

XML_HEADER

VOI_HEADER

TEXT_HEADER

file

fileDir

fileName

image

isXML

numVOIs

sliceNum

trimmedFileName

extension

Constructor Detail

FileVOI

Method Detail

readVOI

readOtherOrientationVOI

writeAnnotationXML

writeAnnotationInVoiAsXML

writeNaugeVOI

writePointVOI

writeVOI

writeXML

writeXML

decodeLine

readAnnotationXML

readContourVOI

readCoordXML

readLine

readNaugeVOI

readPointVOI

readXML