de.unihalle.informatik.MiToBo.apps.cytoskeleton

Class CytoskeletonFeatureExtractorTiles

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

All Implemented Interfaces:

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

Direct Known Subclasses:

CytoskeletonFeatureExtractorHaralickMeasures, CytoskeletonFeatureExtractorLBPs, CytoskeletonFeatureExtractorLBPsRIU

public abstract class CytoskeletonFeatureExtractorTiles
extends CytoskeletonFeatureExtractor

Operator for extracting features for the ActinAnalyzer2D.

The features which are to be extracted by operators extending this class should be specifically dedicated to filament like structures, e.g., actin fiberes or microtubuli. Compared to CytoskeletonFeatureExtractor operators sub-classing this class are expected to work tile-wise on the input image.

Author:

moeller

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 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
CytoskeletonFeatureExtractorTiles() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	calculateFeatures() Performs the feature calculation.
protected abstract Vector<FeatureCalculator>	getFeatureOps() Method to request operators for feature extraction to be applied.

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, getDocumentation, 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

Constructor Detail

CytoskeletonFeatureExtractorTiles

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

Default constructor.

Throws:

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

Method Detail

getFeatureOps

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

Method to request operators for feature extraction to be applied.

Returns:

List of operators to apply.

Throws:

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

calculateFeatures

protected void calculateFeatures()
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Description copied from class: CytoskeletonFeatureExtractor

Performs the feature calculation.

The features are saved to files in the given feature directory. If the directory is null, the output directory is to be used. Note that both directories can be the same.
For each image four files are to be saved:

• *-features.tif: stack with visualizations of individual features
• *-features.ald: history file corresponding to feature stack
• *-features.txt: features, each row refers to a specific tile, each column to an individual feature
• *-features-config.ald: history/configuration of the feature calculator

Specified by:

calculateFeatures in class CytoskeletonFeatureExtractor

Throws:

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

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