Class ParticleCounter_

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

All Implemented Interfaces:

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

public class ParticleCounter_
extends ParticleCounter
implements ij.plugin.filter.ExtendedPlugInFilter

Automatic particle counter for 24 bit RGB and 8 bit Gray.
Currently just a wrapper around segmenter. Works with rectangular ROIs

Author:

Sami Badawi

Field Summary

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

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

ParticleCounter_()

Method Summary

protected void	defaultColumnDefinitions() Setup all the stream and other needed things.
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.BaseParticleCounter

categorizeStreams, customColumnDefinitions, customStreamDefinitions, defaultStreamDefinitions, displayInternalInfo, findBackground, findColorHypothesis, getColorHypothesisFinder, getContext, getImageArea, getInputColor, getInternalInfo, getIterations, getMaxDistance, getMinPixelsInArea, getParentContext, getParticleCount, getParticleFiltered, getSegmentation, getStatus, globalFilter, init, isParticleImage, isUseReferenceAsBackground, populateResultsTable, 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.imageprocessing.IParticleCounter

getColorHypothesisFinder, getIterations, getMaxDistance, getMinPixelsInArea, getParticleCount, getSegmentation, getStatus, isParticleImage, setColorHypothesisFinder, setIterations, setMaxDistance, setMinPixelsInArea

Methods inherited from interface org.shapelogic.imageutil.ImageOperation

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

Methods inherited from interface java.lang.Runnable

run

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

Constructor Detail

ParticleCounter_

public ParticleCounter_()

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

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

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