de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators

Class CellCounterDetectOperator

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement

de.unihalle.informatik.MiToBo.imageJ.plugins.cellCounter.operators.CellCounterDetectOperator

All Implemented Interfaces:

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

Direct Known Subclasses:

CellCounterDetectOperatorParticlesUWT, CellCounterDetectOperatorStromules

public abstract class CellCounterDetectOperator
extends de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement
implements loci.common.StatusListener, loci.common.StatusReporter

Container base class for all detectors used in the cell counter.

This class basically serves as a place-holder and defines the interface. Detector functionality is to be implemented in related sub-classes.

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
protected Vector<CellCntrMarker>	detectResults Detection result.
protected int	detectZSlice Index of input image slice if z-stack is provided as input.
protected boolean	highQualityData Flag to enable extraction of data with highest accuracy.
protected MTBImage	inputImage Input image to process.
protected Vector<loci.common.StatusListener>	m_statusListeners Vector of installed StatusListener objects.
protected HashMap<Integer,CellCntrMarkerVector>	markerVects Set of available marker vectors.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CellCounterDetectOperator() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statListener) Method is to be called for cleaning-up the operator resources.
Vector<CellCntrMarker>	getDetectionResults() Get the detection results.
abstract String	getShortName() Get common short name of operator for GUI.
void	notifyListeners(loci.common.StatusEvent e)
void	removeStatusListener(loci.common.StatusListener statListener)
void	setHighQualityData(boolean flag) Enable or disable extraction of high quality data.
void	setInputImage(MTBImage img) Set input image.
void	setMarkerVectors(HashMap<Integer,CellCntrMarkerVector> v) Set currently available marker vectors.
void	setSliceZid(int i) Set index of slice in stack, starting with 0 for first slice.
void	statusUpdated(loci.common.StatusEvent e)

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

getUniqueClassIdentifier

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, operate, print, print, print, printInterface, printInterface, readHistory, readResolve, 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

inputImage

protected transient MTBImage inputImage

Input image to process.

detectZSlice

protected int detectZSlice

Index of input image slice if z-stack is provided as input.

markerVects

protected HashMap<Integer,CellCntrMarkerVector> markerVects

Set of available marker vectors.

These are passed to the operators in case that individual operators require access to the results of others. Note that each operator is responsible for acquiring the information which marker vector refers to the markers it needs.

detectResults

@Parameter(label="Detection Results",
           direction=OUT,
           dataIOOrder=1,
           description="Detection results.")
protected Vector<CellCntrMarker> detectResults

Detection result.

highQualityData

protected boolean highQualityData

Flag to enable extraction of data with highest accuracy.

m_statusListeners

protected Vector<loci.common.StatusListener> m_statusListeners

Vector of installed StatusListener objects.

Constructor Detail

CellCounterDetectOperator

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

Constructor.

Throws:

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

Method Detail

getShortName

public abstract String getShortName()

Get common short name of operator for GUI.

Returns:

Name of operator.

getDetectionResults

public Vector<CellCntrMarker> getDetectionResults()

Get the detection results.

Returns:

Vector of detected objects.

setHighQualityData

public void setHighQualityData(boolean flag)

Enable or disable extraction of high quality data.

Extracting high quality data is allowed to take a bit longer than normal. For example in case of region contours high quality data could refer to an extraction of ordered lists of boundary points compared to unordered lists which is much faster.

Parameters:

flag - If true, high quality data is requested.

setInputImage

public void setInputImage(MTBImage img)

Set input image.

Parameters:

img - Input image to process.

setSliceZid

public void setSliceZid(int i)

Set index of slice in stack, starting with 0 for first slice.

Parameters:

i - Index in stack.

setMarkerVectors

public void setMarkerVectors(HashMap<Integer,CellCntrMarkerVector> v)

Set currently available marker vectors.

Parameters:

v - Hashmap with marker vectors indexed by type.

addStatusListener

public void addStatusListener(loci.common.StatusListener statListener)

Method is to be called for cleaning-up the operator resources.

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 statListener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter

statusUpdated

public void statusUpdated(loci.common.StatusEvent e)

Specified by:

statusUpdated in interface loci.common.StatusListener