Package com.xinapse.multisliceimage.roi

Class ROIStreamTokenizer

java.lang.Object

java.io.StreamTokenizer

com.xinapse.multisliceimage.roi.ROIStreamTokenizer

public class ROIStreamTokenizer
extends StreamTokenizer

An ROIStreamTokenizer used to parse ROIs from an input stream. The ROIs can either be Xinapse-type ROIs, or dispim-type ROIs. Xinapse-style ROIs can be read using this Tokenizer in two modes:

• Normal mode.
• Clinical trials mode.

Clinical trials mode is enabled by setting the System Property "Platform.GCP". In clinical trials mode, the ROIStreamTokenizer expects to encounter a checksum at the end of the input stream. If a checksum is not found before the end of the file is reached, or if the checksum is invalid, then an IOException is thrown. A checksum looks like:

   Begin Checksum
   NNNNNNNN
   End Checksum
   

where NNNNNNNN is the value of the checksum.

In normal mode, the checksum, if found, is ignored.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	ANNOTATIONTOKEN	The token written to show the ROI annotation.
static final String	AREATOKEN	The token written to show the ROI area.
static final String	COLOURTOKEN	The token written to show the ROI colour.
static final String	DEVTOKEN	The token written to show the ROI intensity "deviation" in "standard deviation".
static final String	LENGTHTOKEN	The token written to show the ROI length (for linear ROIs).
static final String	MAXTOKEN	The token written to show the ROI maximum intensity.
static final String	MEANTOKEN	The token written to show the ROI mean intensity.
static final String	MEDIANTOKEN	The token written to show the ROI intensity median.
static final String	MINTOKEN	The token written to show the ROI minimum intensity.
static final String	SLICETOKEN	The token written to show the image slice.
static final String	STDTOKEN	The token written to show the ROI intensity "standard" in "standard deviation".

Fields inherited from class java.io.StreamTokenizer

nval, sval, TT_EOF, TT_EOL, TT_NUMBER, TT_WORD, ttype

Method Summary

Modifier and Type	Method	Description
static void	main(String[] args)	Runs the self-test for the ROIStreamTokenizer class.

Methods inherited from class java.io.StreamTokenizer

commentChar, eolIsSignificant, lineno, lowerCaseMode, nextToken, ordinaryChar, ordinaryChars, parseNumbers, pushBack, quoteChar, resetSyntax, slashSlashComments, slashStarComments, toString, whitespaceChars, wordChars

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

SLICETOKEN

public static final String SLICETOKEN

The token written to show the image slice.

See Also:

• Constant Field Values

ANNOTATIONTOKEN

public static final String ANNOTATIONTOKEN

The token written to show the ROI annotation.

See Also:

• Constant Field Values

COLOURTOKEN

public static final String COLOURTOKEN

The token written to show the ROI colour.

See Also:

• Constant Field Values

AREATOKEN

public static final String AREATOKEN

The token written to show the ROI area.

See Also:

• Constant Field Values

MEANTOKEN

public static final String MEANTOKEN

The token written to show the ROI mean intensity.

See Also:

• Constant Field Values

STDTOKEN

public static final String STDTOKEN

The token written to show the ROI intensity "standard" in "standard deviation".

See Also:

• Constant Field Values

DEVTOKEN

public static final String DEVTOKEN

The token written to show the ROI intensity "deviation" in "standard deviation".

See Also:

• Constant Field Values

MEDIANTOKEN

public static final String MEDIANTOKEN

The token written to show the ROI intensity median.

See Also:

• Constant Field Values

MINTOKEN

public static final String MINTOKEN

The token written to show the ROI minimum intensity.

See Also:

• Constant Field Values

MAXTOKEN

public static final String MAXTOKEN

The token written to show the ROI maximum intensity.

See Also:

• Constant Field Values

LENGTHTOKEN

public static final String LENGTHTOKEN

The token written to show the ROI length (for linear ROIs).

See Also:

• Constant Field Values

Method Details

main

public static void main(String[] args)

Runs the self-test for the ROIStreamTokenizer class.

Parameters:

args - are ignored.