de.unihalle.informatik.MiToBo.apps.cytoskeleton

Class CytoskeletonFeatureExtractorHaralickMeasures

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor

de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles

de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorHaralickMeasures

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=SWING,
              level=STANDARD,
              allowBatchMode=false,
              shortDescription="Extracts Haralick texture measures from co-occurrence matrices as features for the ActinAnalyzer2D.")
 @ALDDerivedClass
public class CytoskeletonFeatureExtractorHaralickMeasures
extends CytoskeletonFeatureExtractorTiles

Operator for extracting Haralick texture measures from co-occurrence matrices as features for the ActinAnalyzer2D.

Author:

moeller

See Also:

FeatureCalculatorHaralickMeasures

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor

CytoskeletonFeatureExtractor.CellMaskFormat

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private static Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>	defaultDirections Default directions for Haralick features.
protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>	directions Directions for calculating cooccurrence matrices.
protected int	distance Distance.
protected boolean	isotropicCalcs Flag for isotropic calculations.

Fields inherited from class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor

imageDir, imageHeight, imageWidth, iRead, maskDir, maskFormat, operatorID, outDir, tileShiftX, tileShiftY, tileSizeX, tileSizeY

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CytoskeletonFeatureExtractorHaralickMeasures() Default constructor.

Method Summary

Modifier and Type	Method and Description
String	getDocumentation()
protected Vector<FeatureCalculator>	getFeatureOps() Method to request operators for feature extraction to be applied.
void	setDistance(int d) Specify distance for calculating cooccurrence matrices.
void	setFlagIsotropicCalculations(boolean flag) Enable/disable isotropic calculations.
void	setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> dirs) Set directions for which to calculate cooccurence matrices.

Methods inherited from class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractorTiles

calculateFeatures

Methods inherited from class de.unihalle.informatik.MiToBo.apps.cytoskeleton.CytoskeletonFeatureExtractor

operate, readInputImageMaxProjectChannel, readMaskImage, setCytoskeletonChannel, setImageDir, setMaskDir, setMaskFormat, setOutputDir, setTileShiftX, setTileShiftY, setTileSizeX, setTileSizeY

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

defaultDirections

private static Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> defaultDirections

Default directions for Haralick features.

distance

@Parameter(label="Haralick distance",
           required=true,
           direction=IN,
           dataIOOrder=1,
           mode=STANDARD,
           description="Desired distance.")
protected int distance

Distance.

directions

@Parameter(label="Haralick directions",
           required=true,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Directions for matrices.")
protected Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> directions

Directions for calculating cooccurrence matrices.

isotropicCalcs

@Parameter(label="Isotropic calculations",
           required=true,
           direction=IN,
           dataIOOrder=3,
           description="Flag to enable isotropic calculations.",
           mode=ADVANCED)
protected boolean isotropicCalcs

Flag for isotropic calculations.

If flag is true the average of each feature for the four directions EAST, NORTH_EAST, NORTH and NORTH_WEST is taken as result. But, note that this causes the computation time to be increased by a factor of four as well.

Constructor Detail

CytoskeletonFeatureExtractorHaralickMeasures

public CytoskeletonFeatureExtractorHaralickMeasures()
                                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

Method Detail

setDistance

public void setDistance(int d)

Specify distance for calculating cooccurrence matrices.

Parameters:

d - Pixel distance to apply.

setHaralickDirections

public void setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection> dirs)

Set directions for which to calculate cooccurence matrices.

Parameters:

dirs - List of directions.

setFlagIsotropicCalculations

public void setFlagIsotropicCalculations(boolean flag)

Enable/disable isotropic calculations.

Parameters:

flag - If true, isotropic calculations are enabled.

getFeatureOps

protected Vector<FeatureCalculator> getFeatureOps()
                                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Description copied from class: CytoskeletonFeatureExtractorTiles

Method to request operators for feature extraction to be applied.

Specified by:

getFeatureOps in class CytoskeletonFeatureExtractorTiles

Returns:

List of operators to apply.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

getDocumentation

public String getDocumentation()

Overrides:

getDocumentation in class de.unihalle.informatik.Alida.operator.ALDOperator