org.shapelogic.imageprocessing
Class ColorParticleAnalyzer

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

All Implemented Interfaces:

java.lang.Runnable, RecursiveContext, IParticleCounter, ImageOperation

Direct Known Subclasses:

ColorParticleAnalyzerIJ

public class ColorParticleAnalyzer
extends BaseParticleCounter

Analyzes a particle image in gray or RGB and group the particles according to shape rules.
Find a place in the base class where there is a hook for this extended functionality.
Some of the methods can be moved to ColorParticleAnalyzer to remove dependency of ImageJ.

Author:

Sami Badawi

Field Summary

protected NumberedStream<java.lang.Integer>	_areaStream
protected NumberedStream<java.lang.Double>	_aspectRatioStream
protected NumberedStream<java.lang.Integer>	_curveArchCountStream
protected IEdgeTracer	_edgeTracer
protected NumberedStream<java.lang.Integer>	_grayValueStream
protected NumberedStream<java.lang.Integer>	_hardCornerCountStream
protected NumberedStream<java.lang.Integer>	_inflectionPointCountStream
protected java.lang.String	_neuralNetworkFile
protected WrappedListStream<IColorAndVariance>	_particleStream
protected NumberedStream<java.lang.Double>	_perimeterStream
protected ListStream<Polygon>	_polygonStream
protected java.util.List<java.lang.String>	_printListOverwrite
protected ListCalcStream1<IColorAndVariance,java.lang.Boolean>	_roundishStream
protected BaseTableBuilder	_tableBuilder
protected TableDefinition	_tableDefinition
protected boolean	_useNeuralNetwork
protected NumberedStream<java.lang.Double>	_xMaxStream
protected NumberedStream<java.lang.Double>	_xMinStream
protected NumberedStream<java.lang.Double>	_yMaxStream
protected NumberedStream<java.lang.Double>	_yMinStream
protected LoadLetterStreams	loadLetterStreams
protected LoadParticleStreams	loadParticleStreams
protected LoadPolygonStreams	loadPolygonStreams

Fields inherited from class org.shapelogic.imageprocessing.BaseParticleCounter

_backgroundArea, _backgroundColor, _backgroundCount, _boundingBoxArea, _categorizer, _colorHypothesis, _colorHypothesisFinder, _context, _countOnly, _displayInternalInfo, _displayTable, _errorMessage, _inputColor, _iterations, _maxDistance, _maxPixelsInArea, _minPixelsInArea, _modifying, _paintBackground, _paintForground, _parentContext, _particleCount, _particleImage, _particlesFiltered, _particlesOrig, _referenceColor, _saveArea, _segmentation, _toMask, _useReferenceAsBackground, ITERATIONS_DEFAULTS, MAX_DISTANCE_DEFAULTS, MAX_PIXELS_IN_AREA_DEFAULTS, MIN_PIXELS_IN_AREA_DEFAULTS

Fields inherited from class org.shapelogic.imageutil.BaseImageOperation

_arg, _guiWrapper, _image, _keyValueParser, _setupReturnValue

Constructor Summary

ColorParticleAnalyzer()

Method Summary

protected void	categorizeStreams() Analyzes particles and group them. Not sure if I should use named streams or try to avoid it to make it more thread safe.
protected void	customStreamDefinitions() Define extra streams.
protected void	defaultColumnDefinitions() Setup all the stream and other needed things.
protected void	defaultStreamDefinitions() Define extra streams and also extra columns.
protected void	defineNeuralNetwork() Method to override if you want to define your own neural network. The default network is very simple it is marking particles Dark or Light.
protected void	defineRules() Method to override if you want to define your own rule set. The default network is very simple it is marking particles Tall, Flat based on their aspect ratio.
java.lang.StringBuffer	getInternalInfo()
java.util.List	getTableBuilderOutputList() This is only for testing the result table.
void	init() Setup all the needed factory methods based on what type the image has.
protected void	makeBBoxStreams()
protected void	populateResultsTable() Populate the table with the streams.
void	setNeuralNetworkFile(java.lang.String neuralNetworkFile)
protected void	setupTableBuilder()
void	setUseNeuralNetwork(boolean useNeuralNetwork)

Methods inherited from class org.shapelogic.imageprocessing.BaseParticleCounter

displayInternalInfo, displayResultsTable, findBackground, findColorHypothesis, getColorHypothesisFinder, getContext, getErrorMessage, getImageArea, getInputColor, getIterations, getMaxDistance, getMinPixelsInArea, getParentContext, getParticleCount, getParticleFiltered, getSegmentation, getStatus, globalFilter, isParticleImage, isUseReferenceAsBackground, populateResultsTableRow, populateResultsTableRowCustom, run, segment, setColorHypothesisFinder, setDisplayTable, setInputColor, setIterations, setMaxDistance, setMinPixelsInArea, setToMask, setUseReferenceAsBackground, 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

_particleStream

protected WrappedListStream<IColorAndVariance> _particleStream

_polygonStream

protected ListStream<Polygon> _polygonStream

_edgeTracer

protected IEdgeTracer _edgeTracer

_aspectRatioStream

protected NumberedStream<java.lang.Double> _aspectRatioStream

_grayValueStream

protected NumberedStream<java.lang.Integer> _grayValueStream

_hardCornerCountStream

protected NumberedStream<java.lang.Integer> _hardCornerCountStream

_roundishStream

protected ListCalcStream1<IColorAndVariance,java.lang.Boolean> _roundishStream

_inflectionPointCountStream

protected NumberedStream<java.lang.Integer> _inflectionPointCountStream

_curveArchCountStream

protected NumberedStream<java.lang.Integer> _curveArchCountStream

loadPolygonStreams

protected LoadPolygonStreams loadPolygonStreams

loadParticleStreams

protected LoadParticleStreams loadParticleStreams

loadLetterStreams

protected LoadLetterStreams loadLetterStreams

_xMinStream

protected NumberedStream<java.lang.Double> _xMinStream

_yMinStream

protected NumberedStream<java.lang.Double> _yMinStream

_xMaxStream

protected NumberedStream<java.lang.Double> _xMaxStream

_yMaxStream

protected NumberedStream<java.lang.Double> _yMaxStream

_perimeterStream

protected NumberedStream<java.lang.Double> _perimeterStream

_areaStream

protected NumberedStream<java.lang.Integer> _areaStream

_tableDefinition

protected TableDefinition _tableDefinition

_tableBuilder

protected BaseTableBuilder _tableBuilder

_useNeuralNetwork

protected boolean _useNeuralNetwork

_neuralNetworkFile

protected java.lang.String _neuralNetworkFile

_printListOverwrite

protected java.util.List<java.lang.String> _printListOverwrite

Constructor Detail

ColorParticleAnalyzer

public ColorParticleAnalyzer()

Method Detail

init

public void init()
          throws java.lang.Exception

Description copied from class: BaseParticleCounter

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

Overrides:

init in class BaseParticleCounter

Throws:

java.lang.Exception

defaultStreamDefinitions

protected void defaultStreamDefinitions()

Description copied from class: BaseParticleCounter

Define extra streams and also extra columns.

Overrides:

defaultStreamDefinitions in class BaseParticleCounter

makeBBoxStreams

protected void makeBBoxStreams()

categorizeStreams

protected void categorizeStreams()

Analyzes particles and group them.
Not sure if I should use named streams or try to avoid it to make it more thread safe.

Overrides:

categorizeStreams in class BaseParticleCounter

defineRules

protected void defineRules()

Method to override if you want to define your own rule set.
The default network is very simple it is marking particles Tall, Flat based on their aspect ratio.

defineNeuralNetwork

protected void defineNeuralNetwork()

Method to override if you want to define your own neural network.
The default network is very simple it is marking particles Dark or Light.

customStreamDefinitions

protected void customStreamDefinitions()

Define extra streams.

Overrides:

customStreamDefinitions in class BaseParticleCounter

defaultColumnDefinitions

protected void defaultColumnDefinitions()

Description copied from class: BaseParticleCounter

Setup all the stream and other needed things.

Overrides:

defaultColumnDefinitions in class BaseParticleCounter

populateResultsTable

protected void populateResultsTable()

Description copied from class: BaseParticleCounter

Populate the table with the streams.

Overrides:

populateResultsTable in class BaseParticleCounter

setupTableBuilder

protected void setupTableBuilder()

Overrides:

setupTableBuilder in class BaseParticleCounter

getInternalInfo

public java.lang.StringBuffer getInternalInfo()

Overrides:

getInternalInfo in class BaseParticleCounter

setNeuralNetworkFile

public void setNeuralNetworkFile(java.lang.String neuralNetworkFile)

setUseNeuralNetwork

public void setUseNeuralNetwork(boolean useNeuralNetwork)

getTableBuilderOutputList

public java.util.List getTableBuilderOutputList()

This is only for testing the result table.
This is empty when running from ColorParticleAnalyzerIJ.