de.unihalle.informatik.MiToBo.apps.cytoskeleton

Class CytoskeletonFeatureExtractorEigenStructures

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.CytoskeletonFeatureExtractorEigenStructures

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 Eigen structures as features for the ActinAnalyzer2D.")
 @ALDDerivedClass
public class CytoskeletonFeatureExtractorEigenStructures
extends CytoskeletonFeatureExtractor

Operator for extracting Eigen structures as features for the ActinAnalyzer2D.

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

Modifier and Type	Field and Description
private int	tileNumX Number of tiles in x-dimension.
private int	tileNumY Number of tiles in y-dimension.

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
CytoskeletonFeatureExtractorEigenStructures() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	calculateFeatures() Performs the feature calculation.
String	getDocumentation()

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

tileNumX

private transient int tileNumX

Number of tiles in x-dimension.

tileNumY

private transient int tileNumY

Number of tiles in y-dimension.

Constructor Detail

CytoskeletonFeatureExtractorEigenStructures

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

Default constructor.

Throws:

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

Method Detail

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.

getDocumentation

public String getDocumentation()

Overrides:

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