de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation

Class RootImageSegmentationOperator

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement

de.unihalle.informatik.MiToBo.apps.minirhizotron.segmentation.RootImageSegmentationOperator

All Implemented Interfaces:

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

public abstract class RootImageSegmentationOperator
extends de.unihalle.informatik.Alida.operator.ALDOperatorCollectionElement

Abstract super class for operators segmenting roots from images.

Author:

Birgit Moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RootImageSegmentationOperator.LayerSubset
static class	RootImageSegmentationOperator.OpWorkingMode

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 HashMap<Integer,ij.ImagePlus>	inputImages Input images.
protected HashMap<Integer,Vector<MTBRootTree>>	inputTreelines Input treelines to be improved and updated.
protected HashMap<Integer,Vector<MTBRootTree>>	resultTreelines Resulting enhanced treeline annotations.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
RootImageSegmentationOperator() Default constructor.

Method Summary

Modifier and Type	Method and Description
HashMap<Integer,ij.ImagePlus>	getAllInputImages() Getter for all input images.
HashMap<Integer,Vector<MTBRootTree>>	getAllInputTreelines() Getter for the input treelines of the specified layer.
HashMap<Integer,Vector<MTBRootTree>>	getAllResultTreelines() Getter for all result treelines.
ij.ImagePlus	getInputImage(int layer) Getter for the input image of specified layer.
Vector<MTBRootTree>	getInputTreelines(int layer) Getter for the input treelines of the specified layer.
abstract EnumSet<RootImageSegmentationOperator.LayerSubset>	getLayerSubsetForInputImages() Request the set of layers from which to provide images to the operator.
abstract EnumSet<RootImageSegmentationOperator.LayerSubset>	getLayerSubsetForInputTreelines() Request the set of layers from which to provide treelines to the operator.
abstract boolean	getOnlySelectedTreelines() Ask operator if only selected or all treelines should be provided.
abstract RootImageSegmentationOperator.OpWorkingMode	getOperatorWorkingMode() Request working mode of the operator, i.e., how the operator deals with treelines.
Vector<MTBRootTree>	getResultTreelines(int layer) Getter for the result treelines of a specific layer.
void	setInputImages(HashMap<Integer,ij.ImagePlus> images) Setter for the input image.
void	setInputTreelines(HashMap<Integer,Vector<MTBRootTree>> tls) Provide treelines to be enhanced.

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

inputImages

protected HashMap<Integer,ij.ImagePlus> inputImages

Input images.

The hashmap stores for layer indices the corresponding images.

inputTreelines

protected HashMap<Integer,Vector<MTBRootTree>> inputTreelines

Input treelines to be improved and updated.

The hashmap stores for layer indices the corresponding treelines.

resultTreelines

protected HashMap<Integer,Vector<MTBRootTree>> resultTreelines

Resulting enhanced treeline annotations.

Constructor Detail

RootImageSegmentationOperator

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

Default constructor.

Throws:

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

Method Detail

getLayerSubsetForInputImages

public abstract EnumSet<RootImageSegmentationOperator.LayerSubset> getLayerSubsetForInputImages()

Request the set of layers from which to provide images to the operator.

Returns:

Subset of layers from which the operator wants to get the images.

getLayerSubsetForInputTreelines

public abstract EnumSet<RootImageSegmentationOperator.LayerSubset> getLayerSubsetForInputTreelines()

Request the set of layers from which to provide treelines to the operator.

Returns:

Subset of layers from which the operator wants to get treeline annotations.

getOnlySelectedTreelines

public abstract boolean getOnlySelectedTreelines()

Ask operator if only selected or all treelines should be provided.

Returns:

True if only selected treelines are desired, otherwise false.

getOperatorWorkingMode

public abstract RootImageSegmentationOperator.OpWorkingMode getOperatorWorkingMode()

Request working mode of the operator, i.e., how the operator deals with treelines.

Returns:

Working mode of the operator.

setInputImages

public void setInputImages(HashMap<Integer,ij.ImagePlus> images)

Setter for the input image.

Parameters:

imgs - - ImagePlus images per layer to be processed.

setInputTreelines

public void setInputTreelines(HashMap<Integer,Vector<MTBRootTree>> tls)

Provide treelines to be enhanced.

Parameters:

tls - Set of treelines per layer.

getAllInputImages

public HashMap<Integer,ij.ImagePlus> getAllInputImages()

Getter for all input images.

Returns:

The map of input images indexed with layer as key.

getInputImage

public ij.ImagePlus getInputImage(int layer)

Getter for the input image of specified layer.

Parameters:

layer - Input layer for which image is requested.

Returns:

The requested input image as an ImagePlus, null if non-existent.

getAllInputTreelines

public HashMap<Integer,Vector<MTBRootTree>> getAllInputTreelines()

Getter for the input treelines of the specified layer.

Returns:

The map of input treelines indexed with layer as key.

getInputTreelines

public Vector<MTBRootTree> getInputTreelines(int layer)

Getter for the input treelines of the specified layer.

Parameters:

layer - Input layer for which treelines are requested.

Returns:

List of input treelines of desired layer, null is non-existent.

getAllResultTreelines

public HashMap<Integer,Vector<MTBRootTree>> getAllResultTreelines()

Getter for all result treelines.

Returns:

List of updated treelines.

getResultTreelines

public Vector<MTBRootTree> getResultTreelines(int layer)

Getter for the result treelines of a specific layer.

Returns:

List of updated treelines for given layer.