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

Class SnakeOptimizerCoupled

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.SnakeOptimizerCoupled

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

@ALDDerivedClass
 @ALDAOperator(genericExecutionMode=ALL)
public class SnakeOptimizerCoupled
extends SnakeOptimizer

Image contour segmentation using multiple parametric snakes.

This class provides methods to segment multiple contours in an image based on parametric active contour models, i.e. snakes. Multiple snakes may be coupled in the sense that overlap will be penalized by a common energy term in the functional.

Author:

Birgit Möller

Nested Class Summary

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 boolean[]	activityArray Array of active snakes, suitable for masking snakes in optimization.
protected int[]	colorArray Array containing pseudo-colors for snake visualization.
protected MTBImageRGB	dispImg Image for displaying intermediate/final results.
protected int[]	iterationsPerSnake Number of iterations done for each snake.
protected int[][]	overlapMask Mask to indicate overlap regions between snakes.
protected boolean	overlapMaskRequested Flag to indicate if overlap mask is required by at least one energy.
protected SnakeOptimizerSingle[]	snakeOpters Array of individual snake optimizers.
protected SnakeOptimizerSingle	snakeOptimizer Optimizer object for a single snake.

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
SnakeOptimizerCoupled() Default constructor.
SnakeOptimizerCoupled(MTBImage img, MTBPolygon2DSet initSnakes, SnakeOptimizerSingle sopt, boolean[] activeArray) Default constructor.

Method Summary

Modifier and Type	Method and Description
SnakeOptimizerCoupled	clone()
protected void	closeWindows() Close all windows openened by this operator (for clean-up).
protected SnakeOptimizer.Snake_status	doIteration() Here the main work should be done.
boolean[]	getActivityArray() Returns current activity array.
int[][]	getCurrentOverlapMask() Get the current overlap mask.
MTBPolygon2DSet	getCurrentSnakes() Returns a copy of the set of current snakes.
int[]	getIterationsPerSnake() Returns the total number of iterations per snake.
MTBImage	getWorkingImage() Returns working image.
protected void	initOptimizer() Initializes the optimizer.
protected void	plotImageToBackground() Copies the input image as background into the output frame.
protected void	plotSnakeToImage(MTBImageRGB img)
void	printParams() Print current parameter settings to standard output device.
protected void	saveSnake() Save intermediate results.
void	setActivityArray(boolean[] array) Specify set of active snakes.
void	setColorArray(int[] array) Specify pseudo-colors for snake visualization.
protected void	showSnake() Display input image with current snake overlayed.
String	toString()
void	updateOverlapMask() Update current overlap mask for all snakes.
void	validateCustom()

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

disableSaveIntermediateResults, disableShowIntermediateResults, enableSaveIntermediateResults, enableShowIntermediateResults, getExcludeMask, getInitialSnakes, getInputImage, getIterationCount, getResultSnakeImage, getResultSnakes, getSnakeNumber, getStackWithIntermediateResults, operate, readResolve, 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

snakeOptimizer

@Parameter(label="Snake Optimizer",
           direction=IN,
           required=true,
           dataIOOrder=3,
           description="Snake optimizer for single snake segmentation.")
protected SnakeOptimizerSingle snakeOptimizer

Optimizer object for a single snake.

activityArray

@Parameter(label="Activity array",
           direction=IN,
           required=false,
           description="Array of active snakes.")
protected boolean[] activityArray

Array of active snakes, suitable for masking snakes in optimization.

Note, per default all snakes are active. The size of the array on init is just randomly chosen, but a certain size is required since otherwise the GUI will initialize the array with false values.

iterationsPerSnake

@Parameter(label="Number of iterations per snake",
           direction=OUT,
           description="Iterations per snake.")
protected transient int[] iterationsPerSnake

Number of iterations done for each snake.

snakeOpters

protected transient SnakeOptimizerSingle[] snakeOpters

Array of individual snake optimizers.

colorArray

protected transient int[] colorArray

Array containing pseudo-colors for snake visualization.

overlapMaskRequested

protected transient boolean overlapMaskRequested

Flag to indicate if overlap mask is required by at least one energy.

overlapMask

protected transient int[][] overlapMask

Mask to indicate overlap regions between snakes.

dispImg

protected transient MTBImageRGB dispImg

Image for displaying intermediate/final results.

Constructor Detail

SnakeOptimizerCoupled

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

SnakeOptimizerCoupled

public SnakeOptimizerCoupled(MTBImage img,
                             MTBPolygon2DSet initSnakes,
                             SnakeOptimizerSingle sopt,
                             boolean[] activeArray)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

img - Image to work on.

initSnakes - Set of initial snakes.

sopt - Snake optimizer.

activeArray - Array indicating active snakes.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

validateCustom

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

Overrides:

validateCustom in class SnakeOptimizer

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

clone

public SnakeOptimizerCoupled clone()

Specified by:

clone in class SnakeOptimizer

setActivityArray

public void setActivityArray(boolean[] array)

Specify set of active snakes.

Parameters:

array - Boolean array to indicate active snakes.

getActivityArray

public boolean[] getActivityArray()

Returns current activity array.

setColorArray

public void setColorArray(int[] array)

Specify pseudo-colors for snake visualization.

initOptimizer

protected void initOptimizer()
                      throws MTBSnakeException

Initializes the optimizer.

Here internal member variables are initialized according to the given parameters, and memory for intermediate results and debug data is allocated.

Specified by:

initOptimizer in class SnakeOptimizer

Throws:

MTBSnakeException

doIteration

protected SnakeOptimizer.Snake_status doIteration()
                                           throws MTBException

Description copied from class: SnakeOptimizer

Here the main work should be done.

Specified by:

doIteration in class SnakeOptimizer

Returns:

Indicates if the iteration was successful.

Throws:

MTBException

showSnake

protected void showSnake()

Display input image with current snake overlayed.

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()

Description copied from class: SnakeOptimizer

Save intermediate results.

Specified by:

saveSnake in class SnakeOptimizer

updateOverlapMask

public void updateOverlapMask()

Update current overlap mask for all snakes.

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 copy of the set of current snakes.

Specified by:

getCurrentSnakes in class SnakeOptimizer

Returns:

Current set of snake contours.

getCurrentOverlapMask

public int[][] getCurrentOverlapMask()

Get the current overlap mask.

Returns:

Overlap mask of current snake configuration.

getIterationsPerSnake

public int[] getIterationsPerSnake()

Returns the total number of iterations per snake.

Returns:

Array of iteration counts.

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

plotImageToBackground

protected void plotImageToBackground()

Copies the input image as background into the output frame.

plotSnakeToImage

protected void plotSnakeToImage(MTBImageRGB img)