org.shapelogic.imageprocessing
Class ColorParticleAnalyzerIJ

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

All Implemented Interfaces:

ij.plugin.filter.ExtendedPlugInFilter, ij.plugin.filter.PlugInFilter, java.lang.Runnable, RecursiveContext, IParticleCounter, ImageOperation

Direct Known Subclasses:

ColorParticleAnalyzer_, RGBColorParticleAnalyzerIJ

public class ColorParticleAnalyzerIJ
extends ColorParticleAnalyzer
implements ij.plugin.filter.ExtendedPlugInFilter

Automatic particle counter for 24 bit RGB and 8 bit Gray.
Works with rectangular ROIs

Author:

Sami Badawi

Field Summary

protected static boolean	_countOnlyStatic
protected static boolean	_displayInternalInfoStatic
protected ij.gui.GenericDialog	_gd
protected static int	_iterationsStatic
protected static double	_maxDistanceStatic
protected static int	_maxPixelsInAreaStatic
protected static int	_minPixelsInAreaStatic
protected static java.lang.String	_neuralNetworkFileStatic
protected ij.measure.ResultsTable	_rt
protected static boolean	_toMaskStatic
protected static boolean	_useNeuralNetworkStatic

Fields inherited from class org.shapelogic.imageprocessing.ColorParticleAnalyzer

_areaStream, _aspectRatioStream, _curveArchCountStream, _edgeTracer, _grayValueStream, _hardCornerCountStream, _inflectionPointCountStream, _neuralNetworkFile, _particleStream, _perimeterStream, _polygonStream, _printListOverwrite, _roundishStream, _tableBuilder, _tableDefinition, _useNeuralNetwork, _xMaxStream, _xMinStream, _yMaxStream, _yMinStream, loadLetterStreams, loadParticleStreams, 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

Fields inherited from interface ij.plugin.filter.ExtendedPlugInFilter

KEEP_PREVIEW

Fields inherited from interface ij.plugin.filter.PlugInFilter

CONVERT_TO_FLOAT, DOES_16, DOES_32, DOES_8C, DOES_8G, DOES_ALL, DOES_RGB, DOES_STACKS, DONE, FINAL_PROCESSING, NO_CHANGES, NO_IMAGE_REQUIRED, NO_UNDO, PARALLELIZE_STACKS, ROI_REQUIRED, SNAPSHOT, STACK_REQUIRED, SUPPORTS_MASKING

Constructor Summary

ColorParticleAnalyzerIJ()

Method Summary

void	displayInternalInfo()
protected void	displayResultsTable()
static java.lang.String	getFilePath(ij.io.OpenDialog od)
protected boolean	populateResultsTableRow(int index) Populate one row of the result table with the default fields.
void	run(ij.process.ImageProcessor ip)
void	setNPasses(int passes)
int	setup(java.lang.String arg, ij.ImagePlus imp)
protected void	setupTableBuilder()
int	showDialog(ij.ImagePlus imp, java.lang.String command, ij.plugin.filter.PlugInFilterRunner pfr)

Methods inherited from class org.shapelogic.imageprocessing.ColorParticleAnalyzer

categorizeStreams, customStreamDefinitions, defaultColumnDefinitions, defaultStreamDefinitions, defineNeuralNetwork, defineRules, getInternalInfo, getTableBuilderOutputList, init, makeBBoxStreams, populateResultsTable, setNeuralNetworkFile, setUseNeuralNetwork

Methods inherited from class org.shapelogic.imageprocessing.BaseParticleCounter

findBackground, findColorHypothesis, getColorHypothesisFinder, getContext, getErrorMessage, getImageArea, getInputColor, getIterations, getMaxDistance, getMinPixelsInArea, getParentContext, getParticleCount, getParticleFiltered, getSegmentation, getStatus, globalFilter, isParticleImage, isUseReferenceAsBackground, 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

_rt

protected ij.measure.ResultsTable _rt

_gd

protected ij.gui.GenericDialog _gd

_iterationsStatic

protected static int _iterationsStatic

_maxDistanceStatic

protected static double _maxDistanceStatic

_minPixelsInAreaStatic

protected static int _minPixelsInAreaStatic

_maxPixelsInAreaStatic

protected static int _maxPixelsInAreaStatic

_countOnlyStatic

protected static boolean _countOnlyStatic

_toMaskStatic

protected static boolean _toMaskStatic

_displayInternalInfoStatic

protected static boolean _displayInternalInfoStatic

_useNeuralNetworkStatic

protected static boolean _useNeuralNetworkStatic

_neuralNetworkFileStatic

protected static java.lang.String _neuralNetworkFileStatic

Constructor Detail

ColorParticleAnalyzerIJ

public ColorParticleAnalyzerIJ()

Method Detail

run

public void run(ij.process.ImageProcessor ip)

Specified by:

run in interface ij.plugin.filter.PlugInFilter

setup

public int setup(java.lang.String arg,
                 ij.ImagePlus imp)

Specified by:

setup in interface ij.plugin.filter.PlugInFilter

displayResultsTable

protected void displayResultsTable()

Overrides:

displayResultsTable in class BaseParticleCounter

setNPasses

public void setNPasses(int passes)

Specified by:

setNPasses in interface ij.plugin.filter.ExtendedPlugInFilter

showDialog

public int showDialog(ij.ImagePlus imp,
                      java.lang.String command,
                      ij.plugin.filter.PlugInFilterRunner pfr)

Specified by:

showDialog in interface ij.plugin.filter.ExtendedPlugInFilter

getFilePath

public static java.lang.String getFilePath(ij.io.OpenDialog od)

setupTableBuilder

protected void setupTableBuilder()

Overrides:

setupTableBuilder in class ColorParticleAnalyzer

populateResultsTableRow

protected boolean populateResultsTableRow(int index)

Description copied from class: BaseParticleCounter

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

Overrides:

populateResultsTableRow in class BaseParticleCounter

displayInternalInfo

public void displayInternalInfo()

Overrides:

displayInternalInfo in class BaseParticleCounter