org.shapelogic.imageprocessing
Class BaseParticleCounter

java.lang.Object
  org.shapelogic.imageutil.BaseImageOperation
      org.shapelogic.imageprocessing.BaseParticleCounter

All Implemented Interfaces:

java.lang.Runnable, RecursiveContext, IParticleCounter, ImageOperation

Direct Known Subclasses:

ColorParticleAnalyzer, ParticleCounter

public class BaseParticleCounter
extends BaseImageOperation
implements IParticleCounter, RecursiveContext

ParticleCounter count number of particles in a particle image.
This is using the SBSegmentation that is also used by Segmenter.
In this base implementation:
Find a color hypothesis.
Set everything in the background color into one segment.
Segment the rest into normal segments regardless of color.
If this is overridden then there can be more segments in the background color.
How do I know what is background colored?

Author:

Sami Badawi

Field Summary

protected int	_backgroundArea
protected java.lang.Integer	_backgroundColor
protected int	_backgroundCount
protected double	_boundingBoxArea
protected XOrListStream	_categorizer
protected ColorHypothesis	_colorHypothesis
protected IColorHypothesisFinder	_colorHypothesisFinder
protected java.util.Map	_context
protected boolean	_countOnly
protected boolean	_displayInternalInfo
protected boolean	_displayTable
protected java.lang.Integer	_inputColor
protected int	_iterations
protected double	_maxDistance
protected int	_maxPixelsInArea
protected int	_minPixelsInArea
protected boolean	_modifying Modifying colors
protected int	_paintBackground
protected int	_paintForground
protected RecursiveContext	_parentContext
protected java.lang.Integer	_particleCount
protected java.lang.Boolean	_particleImage
protected java.util.List<IColorAndVariance>	_particlesFiltered
protected java.util.List<IColorAndVariance>	_particlesOrig
protected java.lang.Integer	_referenceColor
protected boolean	_saveArea Create a IColorAndVariance, area for each particle.
protected SBSegmentation	_segmentation
protected boolean	_toMask
protected boolean	_useReferenceAsBackground
protected static int	ITERATIONS_DEFAULTS
protected static double	MAX_DISTANCE_DEFAULTS
protected static int	MAX_PIXELS_IN_AREA_DEFAULTS
protected static int	MIN_PIXELS_IN_AREA_DEFAULTS

Fields inherited from class org.shapelogic.imageutil.BaseImageOperation

_arg, _guiWrapper, _image, _keyValueParser, _setupReturnValue

Constructor Summary

BaseParticleCounter()

Method Summary

protected void	categorizeStreams() Analyzes particles and group them.
protected void	customColumnDefinitions() Define extra streams and also extra columns.
protected void	customStreamDefinitions() Define extra streams and also extra columns.
protected void	defaultColumnDefinitions() Setup all the stream and other needed things.
protected void	defaultStreamDefinitions() Define extra streams and also extra columns.
void	displayInternalInfo()
protected void	displayResultsTable()
protected boolean	findBackground() Count background pixels. Should be called when only background have been segmented. Not sure that this really makes sense, or I can assume that there is always 1 background.
protected void	findColorHypothesis() Everything related to setting the background color.
IColorHypothesisFinder	getColorHypothesisFinder()
java.util.Map	getContext()
double	getImageArea()
java.lang.Integer	getInputColor()
java.lang.StringBuffer	getInternalInfo()
int	getIterations()
double	getMaxDistance()
int	getMinPixelsInArea()
RecursiveContext	getParentContext()
int	getParticleCount()
java.util.List<IColorAndVariance>	getParticleFiltered()
SBSegmentation	getSegmentation()
java.lang.String	getStatus()
protected void	globalFilter()
protected void	init() Setup all the needed factory methods based on what type the image has.
boolean	isParticleImage() This is not fine tuned.
boolean	isUseReferenceAsBackground()
protected void	populateResultsTable() Populate the table with the streams.
protected boolean	populateResultsTableRow(int index) Populate one row of the result table with the default fields.
protected void	populateResultsTableRowCustom(int index) Populate one row of the result table with the extra fields.
void	run()
protected void	segment()
void	setColorHypothesisFinder(IColorHypothesisFinder colorHypothesisFinder)
void	setDisplayTable(boolean table)
void	setInputColor(java.lang.Integer color)
void	setIterations(int iterations)
void	setMaxDistance(double maxDistance)
void	setMinPixelsInArea(int minPixelsInArea)
void	setToMask(boolean toMask)
void	setUseReferenceAsBackground(boolean referenceAsBackground)
protected void	showResultDialog()

Methods inherited from class org.shapelogic.imageutil.BaseImageOperation

getGuiWrapper, getImage, getKeyValueParser, getSetupReturnValue, isImageValid, setArg, setGuiWrapper, setKeyValueParser, setSetupReturnValue, setup, showAbout, showMessage

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.shapelogic.imageutil.ImageOperation

getGuiWrapper, getImage, getKeyValueParser, getSetupReturnValue, isImageValid, setArg, setGuiWrapper, setKeyValueParser, setSetupReturnValue, setup, showAbout, showMessage

Field Detail

ITERATIONS_DEFAULTS

protected static final int ITERATIONS_DEFAULTS

See Also:

Constant Field Values

MAX_DISTANCE_DEFAULTS

protected static final double MAX_DISTANCE_DEFAULTS

See Also:

Constant Field Values

MIN_PIXELS_IN_AREA_DEFAULTS

protected static final int MIN_PIXELS_IN_AREA_DEFAULTS

See Also:

Constant Field Values

MAX_PIXELS_IN_AREA_DEFAULTS

protected static final int MAX_PIXELS_IN_AREA_DEFAULTS

See Also:

Constant Field Values

_particleImage

protected java.lang.Boolean _particleImage

_modifying

protected boolean _modifying

Modifying colors

_segmentation

protected SBSegmentation _segmentation

_saveArea

protected boolean _saveArea

Create a IColorAndVariance, area for each particle.

_colorHypothesisFinder

protected IColorHypothesisFinder _colorHypothesisFinder

_colorHypothesis

protected ColorHypothesis _colorHypothesis

_backgroundArea

protected int _backgroundArea

_backgroundCount

protected int _backgroundCount

_particleCount

protected java.lang.Integer _particleCount

_boundingBoxArea

protected double _boundingBoxArea

_iterations

protected int _iterations

_maxDistance

protected double _maxDistance

_minPixelsInArea

protected int _minPixelsInArea

_maxPixelsInArea

protected int _maxPixelsInArea

_displayTable

protected boolean _displayTable

_countOnly

protected boolean _countOnly

_toMask

protected boolean _toMask

_displayInternalInfo

protected boolean _displayInternalInfo

_particlesOrig

protected java.util.List<IColorAndVariance> _particlesOrig

_particlesFiltered

protected java.util.List<IColorAndVariance> _particlesFiltered

_categorizer

protected XOrListStream _categorizer

_inputColor

protected java.lang.Integer _inputColor

_backgroundColor

protected java.lang.Integer _backgroundColor

_referenceColor

protected java.lang.Integer _referenceColor

_useReferenceAsBackground

protected boolean _useReferenceAsBackground

_context

protected java.util.Map _context

_parentContext

protected RecursiveContext _parentContext

_paintForground

protected int _paintForground

_paintBackground

protected int _paintBackground

Constructor Detail

BaseParticleCounter

public BaseParticleCounter()

Method Detail

run

public void run()

Specified by:

run in interface java.lang.Runnable

findColorHypothesis

protected void findColorHypothesis()

Everything related to setting the background color. TODO move all the set color stuff from segment() up her.

segment

protected void segment()

globalFilter

protected void globalFilter()

defaultStreamDefinitions

protected void defaultStreamDefinitions()

Define extra streams and also extra columns.

customStreamDefinitions

protected void customStreamDefinitions()

Define extra streams and also extra columns.

categorizeStreams

protected void categorizeStreams()

Analyzes particles and group them.

defaultColumnDefinitions

protected void defaultColumnDefinitions()

Setup all the stream and other needed things.

customColumnDefinitions

protected void customColumnDefinitions()

Define extra streams and also extra columns.

populateResultsTable

protected void populateResultsTable()

Populate the table with the streams.

populateResultsTableRow

protected boolean populateResultsTableRow(int index)

Populate one row of the result table with the default fields.

populateResultsTableRowCustom

protected void populateResultsTableRowCustom(int index)

Populate one row of the result table with the extra fields.

displayResultsTable

protected void displayResultsTable()

showResultDialog

protected void showResultDialog()

displayInternalInfo

public void displayInternalInfo()

getInternalInfo

public java.lang.StringBuffer getInternalInfo()

init

protected void init()
             throws java.lang.Exception

Setup all the needed factory methods based on what type the image has.

Throws:

java.lang.Exception

getStatus

public java.lang.String getStatus()

Specified by:

getStatus in interface IParticleCounter

getSegmentation

public SBSegmentation getSegmentation()

Specified by:

getSegmentation in interface IParticleCounter

isParticleImage

public boolean isParticleImage()

This is not fine tuned.

Specified by:

isParticleImage in interface IParticleCounter

findBackground

protected boolean findBackground()

Count background pixels.
Should be called when only background have been segmented.
Not sure that this really makes sense, or I can assume that there is always 1 background.

getImageArea

public double getImageArea()

getParticleCount

public int getParticleCount()

Specified by:

getParticleCount in interface IParticleCounter

getParticleFiltered

public java.util.List<IColorAndVariance> getParticleFiltered()

getColorHypothesisFinder

public IColorHypothesisFinder getColorHypothesisFinder()

Specified by:

getColorHypothesisFinder in interface IParticleCounter

setColorHypothesisFinder

public void setColorHypothesisFinder(IColorHypothesisFinder colorHypothesisFinder)

Specified by:

setColorHypothesisFinder in interface IParticleCounter

getMaxDistance

public double getMaxDistance()

Specified by:

getMaxDistance in interface IParticleCounter

setMaxDistance

public void setMaxDistance(double maxDistance)

Specified by:

setMaxDistance in interface IParticleCounter

getMinPixelsInArea

public int getMinPixelsInArea()

Specified by:

getMinPixelsInArea in interface IParticleCounter

setMinPixelsInArea

public void setMinPixelsInArea(int minPixelsInArea)

Specified by:

setMinPixelsInArea in interface IParticleCounter

getIterations

public int getIterations()

Specified by:

getIterations in interface IParticleCounter

setIterations

public void setIterations(int iterations)

Specified by:

setIterations in interface IParticleCounter

setDisplayTable

public void setDisplayTable(boolean table)

getInputColor

public java.lang.Integer getInputColor()

setInputColor

public void setInputColor(java.lang.Integer color)

isUseReferenceAsBackground

public boolean isUseReferenceAsBackground()

setUseReferenceAsBackground

public void setUseReferenceAsBackground(boolean referenceAsBackground)

getContext

public java.util.Map getContext()

Specified by:

getContext in interface RecursiveContext

getParentContext

public RecursiveContext getParentContext()

Specified by:

getParentContext in interface RecursiveContext

setToMask

public void setToMask(boolean toMask)