de.unihalle.informatik.MiToBo.apps.plantCells.plastids

Class PlastidNucleiDistanceAnalyzer2D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.plantCells.plastids.PlastidNucleiDistanceAnalyzer2D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class PlastidNucleiDistanceAnalyzer2D
extends MTBOperator
implements loci.common.StatusReporter

Operator to measure distances between plastids and nuclei per cell and to evaluate stromules orientation with regard to cell nucleus.

Author:

Birgit Moeller

Nested Class Summary

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	cellBoundaryChannel Channel with boundary information.
private de.unihalle.informatik.Alida.datatypes.ALDFileString	inFileSegData File with segmentation data.
private MTBImage	inStack Input image stack.
protected Vector<loci.common.StatusListener>	m_statusListeners Vector of installed StatusListener objects.
private int	markerTypeNuclei Type of cell nuclei.
private int	markerTypePlastid Type of plastids without stromules.
private int	markerTypePlastidWithStromuli Type of plastids with stromules.
private int	markerTypeStromuliOrientation Type of stromuli orientation markers.
private static String	opIdentifier Identifier for outputs in verbose mode.
private MTBTableModel	resultDistanceTable Result table with plastid-to-nuclei distances.
private MTBImageRGB	resultImage Debug image to visualize measurements.
private MTBTableModel	resultStromulesOrientationTable Result table with stromule orientation data.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
PlastidNucleiDistanceAnalyzer2D() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
void	removeStatusListener(loci.common.StatusListener statuslistener)

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

Field Detail

opIdentifier

private static final String opIdentifier

Identifier for outputs in verbose mode.

See Also:

Constant Field Values

inFileSegData

@Parameter(label="Segmentation Data",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="Segmentation data.")
private de.unihalle.informatik.Alida.datatypes.ALDFileString inFileSegData

File with segmentation data.

inStack

@Parameter(label="Input Image Stack",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Input image.")
private transient MTBImage inStack

Input image stack.

cellBoundaryChannel

@Parameter(label="Boundary Channel",
           required=true,
           dataIOOrder=2,
           direction=IN,
           description="Boundary channel, starting with 1.")
private int cellBoundaryChannel

Channel with boundary information.

markerTypeNuclei

@Parameter(label="Type of Nuclei Markers",
           required=true,
           dataIOOrder=3,
           direction=IN,
           description="Nuclei marker type.")
private int markerTypeNuclei

Type of cell nuclei.

markerTypePlastid

@Parameter(label="Type of Plastid Markers",
           required=true,
           dataIOOrder=4,
           direction=IN,
           description="Plastid marker type.")
private int markerTypePlastid

Type of plastids without stromules.

markerTypePlastidWithStromuli

@Parameter(label="Type of Stromuli Markers",
           required=true,
           dataIOOrder=5,
           direction=IN,
           description="Stromuli marker type.")
private int markerTypePlastidWithStromuli

Type of plastids with stromules.

markerTypeStromuliOrientation

@Parameter(label="Type of Stromuli Orientation Markers",
           required=true,
           dataIOOrder=6,
           direction=IN,
           description="Stromuli orientation marker type.")
private int markerTypeStromuliOrientation

Type of stromuli orientation markers.

resultDistanceTable

@Parameter(label="Result Table Distances",
           dataIOOrder=0,
           direction=OUT,
           description="Result table with plastid distance statistics.")
private MTBTableModel resultDistanceTable

Result table with plastid-to-nuclei distances.

resultStromulesOrientationTable

@Parameter(label="Result Table Stromule Orientations",
           dataIOOrder=1,
           direction=OUT,
           description="Result table with stromule orientations.")
private MTBTableModel resultStromulesOrientationTable

Result table with stromule orientation data.

resultImage

@Parameter(label="Result Image",
           dataIOOrder=2,
           required=true,
           direction=OUT,
           description="Output image.")
private MTBImageRGB resultImage

Debug image to visualize measurements.

m_statusListeners

protected Vector<loci.common.StatusListener> m_statusListeners

Vector of installed StatusListener objects.

Constructor Detail

PlastidNucleiDistanceAnalyzer2D

public PlastidNucleiDistanceAnalyzer2D()
                                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

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

Method Detail

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

addStatusListener

public void addStatusListener(loci.common.StatusListener statuslistener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener statuslistener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter