org.shapelogic.imageprocessing
Class ColorParticleAnalyzerIJ

java.lang.Object
  extended by org.shapelogic.imageutil.BaseImageOperation
      extended by org.shapelogic.imageprocessing.BaseParticleCounter
          extended by org.shapelogic.imageprocessing.ColorParticleAnalyzer
              extended by 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  ij.measure.ResultsTable _rt
           
protected static boolean _toMaskStatic
           
 
Fields inherited from class org.shapelogic.imageprocessing.ColorParticleAnalyzer
_aspectRatioStream, _curveArchCountStream, _edgeTracer, _grayValueStream, _hardCornerCountStream, _inflectionPointCountStream, _particleStream, _polygonStream, _roundishStream, loadLetterStreams, loadParticleStreams, loadPolygonStreams
 
Fields inherited from class org.shapelogic.imageprocessing.BaseParticleCounter
_backgroundArea, _backgroundColor, _backgroundCount, _boundingBoxArea, _categorizer, _colorHypothesis, _colorHypothesisFinder, _context, _countOnly, _displayInternalInfo, _displayTable, _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
protected  void defaultColumnDefinitions()
          Setup all the stream and other needed things.
 void displayInternalInfo()
           
protected  void displayResultsTable()
           
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)
           
 int showDialog(ij.ImagePlus imp, java.lang.String command, ij.plugin.filter.PlugInFilterRunner pfr)
           
 
Methods inherited from class org.shapelogic.imageprocessing.ColorParticleAnalyzer
categorizeStreams, customStreamDefinitions, defaultStreamDefinitions, getInternalInfo, init, populateResultsTable
 
Methods inherited from class org.shapelogic.imageprocessing.BaseParticleCounter
customColumnDefinitions, findBackground, findColorHypothesis, getColorHypothesisFinder, getContext, 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
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

defaultColumnDefinitions

protected void defaultColumnDefinitions()
Description copied from class: BaseParticleCounter
Setup all the stream and other needed things.

Overrides:
defaultColumnDefinitions in class BaseParticleCounter

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


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