de.unihalle.informatik.MiToBo.segmentation.snakes.optimize

Class SnakeOptimizerSingle

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable

de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer

de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventListener, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter, de.unihalle.informatik.Alida.operator.events.ALDControlEventListener, de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

Direct Known Subclasses:

SnakeOptimizerSingleGreedy, SnakeOptimizerSingleVarCalc

public abstract class SnakeOptimizerSingle
extends SnakeOptimizer

 Image contour segmentation using parametric snakes.
 

Author:

moeller, misiak

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SnakeOptimizerSingle.EnergyNormalizationMode Snake normalization mode.
static class	SnakeOptimizerSingle.IntensityNormalizationMode Image intensity normalization mode.

Nested classes/interfaces inherited from class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer

SnakeOptimizer.Snake_status

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatusHandle, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorExecutionStatus

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 MTBImageRGB	dispImg Image for showing/saving intermediate results.
protected Boolean	doResampling Flag to enable/disable snake resampling.
protected double	energy Current energy of the snake.
protected boolean	energyCalculationRequested Flag for invoking energy calculations.
protected SnakeOptimizerSingle.IntensityNormalizationMode	intNormMode Mode for normalizing image intensities.
protected SnakeOptimizerSingle.EnergyNormalizationMode	normMode Mode for normalizing energies.
protected double	previousEnergy Snake energy in previous iteration (for change assessment).
protected MTBSnake	previousSnake Old snake of previous iteration (for evolution assessment).
protected Double	resampleSegLength Target length of snake segments in resampling.
protected double	scaleFactor Scale factor for snake normalization.
protected MTBSnake	snake The snake on which the algorithm works.
protected UserTime	timer Timer object for time measurements.
protected MTBImage	workingImage Image on which to actually do the segmentation.

Fields inherited from class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer

counterClockwiseSnakePointOrderRequested, energyData, excludeMask, iChannels, iHeight, inImg, initialSnakes, intermediateResults, itCounter, iWidth, outIntermediateResultsStack, outIntermediateResultsStackInterval, outIntermediateResultsStackWanted, outSnakes, outSnakesImg, sampleEnergyData, saveIntermediateResults, saveIntermediateResultsPath, showIntermediateResults, snakeNum

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

configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, stepSize, stepWiseExecution

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
SnakeOptimizerSingle() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	closeWindows() Close all windows openened by this operator (for clean-up).
void	disableEnergyCalculation() Disable energy calculations completely.
Boolean	doResampleSnake() Returns true if snake should be resampled during optimization.
void	enableEnergyCalculation() Enable energy calculation in each iteration.
MTBSnake	getCurrentSnake() Returns a copy of the current snake.
MTBPolygon2DSet	getCurrentSnakes() Returns a set with current snake(!).
abstract MTBSet_ActiveContourEnergy	getEnergySet() Returns a reference to the set of energies.
double	getEnergyValue() Get current energy value for the snake.
SnakeOptimizerSingle.IntensityNormalizationMode	getIntensityNormalizationMode() Request mode for normalizing image intensities.
SnakeOptimizerSingle.EnergyNormalizationMode	getNormalizationMode() Returns energy normalization mode.
double	getPreviousEnergyValue() Get old energy value for the snake at last iteration.
MTBSnake	getPreviousSnake() Returns the previous snake.
Double	getSegmentLength() Returns desired segment length for resampling.
MTBImage	getWorkingImage() Returns working image.
protected abstract boolean	hasEnergies() Check if energies are given.
protected void	initOptimizer() Initializes the optimizer.
MTBImage	normalizeInputImage(MTBImage inimg) Normalizes image intensities according to normalization mode of operator.
void	printParams() Print current parameter settings to standard output device.
protected Object	readResolve() Function for proper initialization of deserialized objects.
protected void	resampleSnake() Resamples the snake using the specified segment length.
protected void	saveSnake() Save intermediate results.
abstract void	setEnergySet(MTBSet_ActiveContourEnergy eSet) Specify set of energies.
void	setNormalizationMode(SnakeOptimizerSingle.EnergyNormalizationMode m) Set energy normalization mode.
protected void	showSnake() Display intermediate results by overlaying the input image with the current snake result.
String	toString()
void	validateCustom()

Methods inherited from class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer

clone, disableSaveIntermediateResults, disableShowIntermediateResults, doIteration, enableSaveIntermediateResults, enableShowIntermediateResults, getExcludeMask, getInitialSnakes, getInputImage, getIterationCount, getResultSnakeImage, getResultSnakes, getSnakeNumber, getStackWithIntermediateResults, operate, setExcludeMask, setInitialSnakes, setInputImage, setIntermediateResultPath, supportsStepWiseExecution, wantStackWithIntermediateResults

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

addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getControlStatus, getControlStatusHandle, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setControlStatus, setNotifyRecursiveFlag

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

intNormMode

@Parameter(label="Image intensity normalization mode",
           direction=IN,
           required=false,
           dataIOOrder=9,
           description="Normalization mode for image intensities.")
protected SnakeOptimizerSingle.IntensityNormalizationMode intNormMode

Mode for normalizing image intensities.

normMode

@Parameter(label="Energy normalization mode",
           direction=IN,
           required=false,
           dataIOOrder=10,
           description="Normalization mode for snake/energies.")
protected SnakeOptimizerSingle.EnergyNormalizationMode normMode

Mode for normalizing energies.

resampleSegLength

@Parameter(label="Resample Segment Length",
           mode=ADVANCED,
           direction=IN,
           required=false,
           dataIOOrder=12,
           description="Desired resampling segment length.")
protected Double resampleSegLength

Target length of snake segments in resampling.

doResampling

@Parameter(label="Do Resampling",
           mode=ADVANCED,
           direction=IN,
           required=false,
           dataIOOrder=11,
           description="Flag for snake resampling.")
protected Boolean doResampling

Flag to enable/disable snake resampling.

snake

protected transient MTBSnake snake

The snake on which the algorithm works.

workingImage

protected transient MTBImage workingImage

Image on which to actually do the segmentation.

If image normalization is applied to the given input image, i.e. if the input image is normalized to intensities in range [0,1], this working image contains the normalized image.

previousSnake

protected transient MTBSnake previousSnake

Old snake of previous iteration (for evolution assessment).

energyCalculationRequested

protected transient boolean energyCalculationRequested

Flag for invoking energy calculations. TODO really needed?

energy

protected transient double energy

Current energy of the snake.

previousEnergy

protected transient double previousEnergy

Snake energy in previous iteration (for change assessment).

scaleFactor

protected transient double scaleFactor

Scale factor for snake normalization.

timer

protected transient UserTime timer

Timer object for time measurements.

dispImg

protected transient MTBImageRGB dispImg

Image for showing/saving intermediate results.

Constructor Detail

SnakeOptimizerSingle

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

readResolve

protected Object readResolve()

Function for proper initialization of deserialized objects.

This function is called on an instance of this class being deserialized from file, prior to handing the instance over to the user. It takes care of a proper initialization of transient member variables as they are not initialized to the default values during deserialization.

Overrides:

readResolve in class SnakeOptimizer

Returns:

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Overrides:

validateCustom in class SnakeOptimizer

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

initOptimizer

protected void initOptimizer()
                      throws MTBSnakeException

Description copied from class: SnakeOptimizer

Initializes the optimizer.

Needs to be implemented by any derived class. This routine is automatically called on invoking the local operate routine.

Specified by:

initOptimizer in class SnakeOptimizer

Throws:

MTBSnakeException

showSnake

protected void showSnake()

Display intermediate results by overlaying the input image with the current snake result.

Specified by:

showSnake in class SnakeOptimizer

closeWindows

protected void closeWindows()

Description copied from class: SnakeOptimizer

Close all windows openened by this operator (for clean-up).

Specified by:

closeWindows in class SnakeOptimizer

saveSnake

protected void saveSnake()

Save intermediate results.

Specified by:

saveSnake in class SnakeOptimizer

hasEnergies

protected abstract boolean hasEnergies()

Check if energies are given.

Returns:

True, if energies are available.

printParams

public void printParams()

Description copied from class: SnakeOptimizer

Print current parameter settings to standard output device.

Specified by:

printParams in class SnakeOptimizer

toString

public String toString()

Overrides:

toString in class SnakeOptimizer

getEnergySet

public abstract MTBSet_ActiveContourEnergy getEnergySet()

Returns a reference to the set of energies.

Returns:

Set of energies.

setEnergySet

public abstract void setEnergySet(MTBSet_ActiveContourEnergy eSet)

Specify set of energies.

Parameters:

eSet - Set of energies.

getWorkingImage

public MTBImage getWorkingImage()

Description copied from class: SnakeOptimizer

Returns working image.

Usually this will be the input image, however, e.g. in case of image normalization being applied the normalized image will be returned.

Specified by:

getWorkingImage in class SnakeOptimizer

Returns:

Image on which the operator works.

getCurrentSnakes

public MTBPolygon2DSet getCurrentSnakes()

Returns a set with current snake(!).

In case of the SnakeOptimizerSingle class this set will always have exactly one element.

Specified by:

getCurrentSnakes in class SnakeOptimizer

Returns:

Current set of snake contours.

enableEnergyCalculation

public void enableEnergyCalculation()

Enable energy calculation in each iteration. TODO really needed?

disableEnergyCalculation

public void disableEnergyCalculation()

Disable energy calculations completely. TODO really needed?

setNormalizationMode

public void setNormalizationMode(SnakeOptimizerSingle.EnergyNormalizationMode m)

Set energy normalization mode.

getNormalizationMode

public SnakeOptimizerSingle.EnergyNormalizationMode getNormalizationMode()

Returns energy normalization mode.

getIntensityNormalizationMode

public SnakeOptimizerSingle.IntensityNormalizationMode getIntensityNormalizationMode()

Request mode for normalizing image intensities.

Returns:

Mode of image intensity normalization.

getCurrentSnake

public MTBSnake getCurrentSnake()

Returns a copy of the current snake.

Returns:

Current snake.

getPreviousSnake

public MTBSnake getPreviousSnake()

Returns the previous snake.

Returns:

Snake contour of previous iteration.

getEnergyValue

public double getEnergyValue()

Get current energy value for the snake.

Returns:

Energy value of the snake.

getPreviousEnergyValue

public double getPreviousEnergyValue()

Get old energy value for the snake at last iteration.

Returns:

Old snake energy value of the previous iteration.

getSegmentLength

public Double getSegmentLength()

Returns desired segment length for resampling.

Returns:

Desired snake segment length.

doResampleSnake

public Boolean doResampleSnake()

Returns true if snake should be resampled during optimization.

Returns:

True, if snake is to be resampled.

normalizeInputImage

public MTBImage normalizeInputImage(MTBImage inimg)

Normalizes image intensities according to normalization mode of operator.

Parameters:

inimg - Image to be normalized.

Returns:

Result image with normalized intensities.

resampleSnake

protected void resampleSnake()

Resamples the snake using the specified segment length.

Note: if snake is normalized, segment length will also be normalized! Normalization of segment length is done by resampling!