Package gov.nih.mipav.model.file

Class FileVOI

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 String	extension
protected File	file	File reference, it and its components are able to be modified by extending classes.
protected String	fileDir	File directory where the VOI is to read or written.
protected String	fileName	File name of the VOI.
private final 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 final short	numVOIs	The number of VOIs in the image.
private int	sliceNum	File directory where the VOI is to read or written.
private static final String	TEXT_HEADER
private String	trimmedFileName	File name without the extension.
private static final String	VOI_HEADER	The MIPAV XML header comment.
private static final String	W3C_XML_SCHEMA	The W3C XML schema.
private static final String	XML_ENCODING	The charset the XML file is written in.
private static final 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(String fileName, String fileDir, ModelImage image)	VOI reader/writer constructor.

Method Summary

Modifier and Type	Method	Description
private void	decodeLine(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 String	readLine()	Reads a line of the file and strips comments indicated by the # symbol.
private VOI	readNaugeVOI(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(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 Details

W3C_XML_SCHEMA

private static final String W3C_XML_SCHEMA

The W3C XML schema.

See Also:

• Constant Field Values

XML_ENCODING

private static final String XML_ENCODING

The charset the XML file is written in.

See Also:

• Constant Field Values

XML_HEADER

private static final String XML_HEADER

The XML version description header.

See Also:

• Constant Field Values

VOI_HEADER

private static final String VOI_HEADER

The MIPAV XML header comment.

See Also:

• Constant Field Values

TEXT_HEADER

private static final String TEXT_HEADER

See Also:

• Constant Field Values

file

protected File file

File reference, it and its components are able to be modified by extending classes.

fileDir

protected String fileDir

File directory where the VOI is to read or written.

fileName

protected 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 String trimmedFileName

File name without the extension.

extension

private String extension

Constructor Details

FileVOI

public FileVOI(String fileName,
 String fileDir,
 ModelImage image)
        throws 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:

IOException - if there is an error making the files

Method Details

readVOI

public VOI[] readVOI(boolean doLabel)
              throws 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:

IOException - if there is an error reading the file

readOtherOrientationVOI

public VOI[] readOtherOrientationVOI()
                              throws 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:

IOException - if there is an error reading the file

writeAnnotationXML

public void writeAnnotationXML(boolean writeAll)
                        throws 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:

IOException - exception thrown if there is an error writing the file

writeAnnotationInVoiAsXML

public void writeAnnotationInVoiAsXML(String voiName,
 boolean writeAllContours)
                               throws 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:

IOException - exception thrown if there is an error writing the file

writeNaugeVOI

public void writeNaugeVOI(VOI voi)
                   throws IOException

Writes a single VOI to a file in Nauge format.

Parameters:

voi - VOI to write

Throws:

IOException - if there is an error writing the file

writePointVOI

public void writePointVOI(VOI voi)
                   throws IOException

Writes a single VOI.POINT to a file MIPAV format.

Parameters:

voi - VOI.POINT to write

Throws:

IOException - if there is an error writing the file

writeVOI

public void writeVOI(VOI voi,
 boolean saveAllContours)
              throws 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:

IOException - if there is an error writing the file

writeXML

public void writeXML(VOI voi,
 boolean saveAllContours)
              throws IOException

Throws:

IOException

writeXML

public void writeXML(VOI voi,
 boolean saveAllContours,
 boolean overwriteFile)
              throws 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:

IOException - exception thrown if there is an error writing the file

decodeLine

private void decodeLine(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 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:

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 String readLine()
                 throws IOException

Reads a line of the file and strips comments indicated by the # symbol.

Returns:

the line read in

Throws:

IOException - if there is an error reading the file

readNaugeVOI

private VOI readNaugeVOI(String firstStr)
                  throws 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:

IOException - if there is an error reading the file

readPointVOI

private VOI readPointVOI()
                  throws 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:

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