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

Class SnakeOptimizer

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

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:

SnakeOptimizerCoupled, SnakeOptimizerSingle

public abstract class SnakeOptimizer
extends MTBOperatorControllable

Image contour segmentation using parametric snakes.

This class defines a generic interface for segmenting contours in an image based on parametric active contour models, i.e. snakes. It supports thread-based optimization and interaction with a graphical user interface.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SnakeOptimizer.Snake_status Indicates the current (internal) state of the snake calculations.

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	counterClockwiseSnakePointOrderRequested Flag to indicate if snakes are required to be sorted counter-clockwise.
protected MTBTableModel	energyData
protected boolean[][]	excludeMask Mask to exclude image pixels from calculations.
protected int	iChannels Image channels.
protected int	iHeight Image height.
protected MTBImage	inImg Input image to be segmented.
protected MTBPolygon2DSet	initialSnakes Set of initial snake contours.
protected Vector<MTBPolygon2DSet>	intermediateResults Set of intermediate segmentation results, required for stack generation.
protected int	itCounter Iteration counter.
protected int	iWidth Image width.
protected MTBImageRGB	outIntermediateResultsStack Image stack with intermediate result images.
protected int	outIntermediateResultsStackInterval Interval for saving intermediate results in stack.
protected Boolean	outIntermediateResultsStackWanted Flag to request a stack of intermediate result images.
protected MTBPolygon2DSet	outSnakes Result contours.
protected MTBImageRGB	outSnakesImg Image with final snake contours overlayed.
protected Boolean	sampleEnergyData
protected Boolean	saveIntermediateResults Flag to enable/disable saving of intermediate results.
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	saveIntermediateResultsPath Path to where intermediate results should be stored.
protected Boolean	showIntermediateResults Flag to enable/disable showing of intermediate results.
protected int	snakeNum Number of snakes currently managed.

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
SnakeOptimizer() Default constructor

Method Summary

Modifier and Type	Method and Description
abstract SnakeOptimizer	clone()
protected abstract void	closeWindows() Close all windows openened by this operator (for clean-up).
void	disableSaveIntermediateResults() Deactivates writing of intermediate results.
void	disableShowIntermediateResults() Deactivates display of intermediate results.
protected abstract SnakeOptimizer.Snake_status	doIteration() Here the main work should be done.
void	enableSaveIntermediateResults() Activates writing of intermediate results to disc.
void	enableShowIntermediateResults() Activates display of intermediate results.
private void	generateStackWithIntermediateResults() Generates a stack with intermediate results.
abstract MTBPolygon2DSet	getCurrentSnakes() Returns a copy of the current snake(s).
boolean[][]	getExcludeMask() Returns the current exclude mask.
MTBPolygon2DSet	getInitialSnakes() Returns initial snake.
MTBImage	getInputImage() Returns input image.
int	getIterationCount() Returns the current iteration count.
MTBImageRGB	getResultSnakeImage() Returns image with snakes contours.
MTBPolygon2DSet	getResultSnakes() Returns the set of result snakes.
int	getSnakeNumber() Returns the number of snakes currently managed.
MTBImageRGB	getStackWithIntermediateResults() Returns a stack with intermediate segmentation results.
abstract MTBImage	getWorkingImage() Returns working image.
protected abstract void	initOptimizer() Initializes the optimizer.
protected void	operate()
private void	plotSnakesToImage() Returns overlay of output snakes onto current input image.
private static MTBImageRGB	plotSnakesToImage(MTBPolygon2DSet polyset, MTBImage image, int[] colors) Returns overlay of given snakes onto given image.
abstract void	printParams() Print current parameter settings to standard output device.
protected Object	readResolve() Init function for deserialized objects.
protected abstract void	saveSnake() Save intermediate results.
void	setExcludeMask(boolean[][] mask) Set exclude mask.
void	setInitialSnakes(MTBPolygon2DSet inS) Specify initial snakes.
void	setInputImage(MTBImage img) Specify an input image for the segmentation.
void	setIntermediateResultPath(String path) Set path for intermediate results.
protected abstract void	showSnake() Display current result contour by overlaying the current snake result onto the input image.
boolean	supportsStepWiseExecution()
String	toString()
void	validateCustom()
void	wantStackWithIntermediateResults(boolean flag) Flag for turning on/off generation of stack with intermediate results.

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

inImg

@Parameter(label="Input Image",
           mode=STANDARD,
           direction=IN,
           required=true,
           description="Input Image.",
           dataIOOrder=0)
protected transient MTBImage inImg

Input image to be segmented.

initialSnakes

@Parameter(label="Initial Snake(s)",
           mode=STANDARD,
           direction=IN,
           required=true,
           description="Initial snakes.",
           dataIOOrder=1)
protected MTBPolygon2DSet initialSnakes

Set of initial snake contours.

outSnakes

@Parameter(label="outSnakes",
           direction=OUT,
           description="Final snake(s).")
protected transient MTBPolygon2DSet outSnakes

Result contours.

outSnakesImg

@Parameter(label="Snake Plot",
           direction=OUT,
           description="Overlay with final snake(s).")
protected transient MTBImageRGB outSnakesImg

Image with final snake contours overlayed.

showIntermediateResults

@Parameter(label="Show Intermediate Results",
           mode=STANDARD,
           direction=IN,
           dataIOOrder=1,
           supplemental=true,
           description="Show intermediate results to user.")
protected Boolean showIntermediateResults

Flag to enable/disable showing of intermediate results.

saveIntermediateResults

@Parameter(label="Save Intermediate Results",
           mode=ADVANCED,
           direction=IN,
           dataIOOrder=2,
           supplemental=true,
           description="Save intermediate results to disc.")
protected Boolean saveIntermediateResults

Flag to enable/disable saving of intermediate results.

saveIntermediateResultsPath

@Parameter(label="Save Intermediate Results To...",
           mode=ADVANCED,
           supplemental=true,
           direction=IN,
           dataIOOrder=3,
           description="Path for saving intermediate results.")
protected de.unihalle.informatik.Alida.datatypes.ALDDirectoryString saveIntermediateResultsPath

Path to where intermediate results should be stored.

outIntermediateResultsStackWanted

@Parameter(label="Show Intermediate Snakes Stack",
           mode=ADVANCED,
           direction=IN,
           dataIOOrder=4,
           supplemental=true,
           description="Flag to show stack with intermediate segmentations.")
protected Boolean outIntermediateResultsStackWanted

Flag to request a stack of intermediate result images.

outIntermediateResultsStackInterval

@Parameter(label="Saving Interval for Stack",
           mode=ADVANCED,
           direction=IN,
           dataIOOrder=5,
           supplemental=true,
           description="Interval for saving results to stack.")
protected int outIntermediateResultsStackInterval

Interval for saving intermediate results in stack.

Note that memory issues might occur if number of iterations is high and the interval small...

outIntermediateResultsStack

@Parameter(label="Stack with Intermediate Results",
           direction=OUT,
           supplemental=true,
           description="Optional stack of intermediate segmentation results.")
protected transient MTBImageRGB outIntermediateResultsStack

Image stack with intermediate result images.

sampleEnergyData

@Parameter(label="Collect energy data",
           supplemental=true,
           direction=IN,
           required=false,
           dataIOOrder=15,
           description="Flag for collecting energy data in each iteration.")
protected Boolean sampleEnergyData

energyData

@Parameter(label="Energy data",
           direction=OUT,
           required=false,
           dataIOOrder=10,
           description="Table of iteration-wise energies.")
protected transient MTBTableModel energyData

snakeNum

protected transient int snakeNum

Number of snakes currently managed.

itCounter

protected transient int itCounter

Iteration counter.

iWidth

protected transient int iWidth

Image width.

iHeight

protected transient int iHeight

Image height.

iChannels

protected transient int iChannels

Image channels.

excludeMask

protected transient boolean[][] excludeMask

Mask to exclude image pixels from calculations.

counterClockwiseSnakePointOrderRequested

protected transient boolean counterClockwiseSnakePointOrderRequested

Flag to indicate if snakes are required to be sorted counter-clockwise.

intermediateResults

protected transient Vector<MTBPolygon2DSet> intermediateResults

Set of intermediate segmentation results, required for stack generation.

Constructor Detail

SnakeOptimizer

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

Default constructor

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

clone

public abstract SnakeOptimizer clone()

Overrides:

clone in class Object

validateCustom

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

Overrides:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

supportsStepWiseExecution

public boolean supportsStepWiseExecution()

Specified by:

supportsStepWiseExecution in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

readResolve

protected Object readResolve()

Init function for 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 de.unihalle.informatik.Alida.operator.ALDOperator

Returns:

initOptimizer

protected abstract void initOptimizer()
                               throws MTBSnakeException

Initializes the optimizer.

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

Throws:

MTBSnakeException

doIteration

protected abstract SnakeOptimizer.Snake_status doIteration()
                                                    throws MTBException

Here the main work should be done.

Returns:

Indicates if the iteration was successful.

Throws:

MTBException

showSnake

protected abstract void showSnake()

Display current result contour by overlaying the current snake result onto the input image.

closeWindows

protected abstract void closeWindows()

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

saveSnake

protected abstract void saveSnake()

Save intermediate results.

getCurrentSnakes

public abstract MTBPolygon2DSet getCurrentSnakes()

Returns a copy of the current snake(s).

If the optimizer deals with a single snake, the set contains only a single snake polygon.

Returns:

Current set of snake contours.

printParams

public abstract void printParams()

Print current parameter settings to standard output device.

getIterationCount

public final int getIterationCount()

Returns the current iteration count.

setInputImage

public final void setInputImage(MTBImage img)

Specify an input image for the segmentation.

Parameters:

img - Input image.

setInitialSnakes

public final void setInitialSnakes(MTBPolygon2DSet inS)

Specify initial snakes.

Parameters:

inS - Initial snakes.

getInputImage

public final MTBImage getInputImage()

Returns input image.

Returns:

Input image of operator.

getWorkingImage

public abstract MTBImage getWorkingImage()

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.

Returns:

Image on which the operator works.

getInitialSnakes

public final MTBPolygon2DSet getInitialSnakes()

Returns initial snake.

Returns:

Set of initial snakes.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getResultSnakeImage

public MTBImageRGB getResultSnakeImage()

Returns image with snakes contours.

Returns:

Image with colored result snake contour overlay.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getSnakeNumber

public final int getSnakeNumber()

Returns the number of snakes currently managed.

Returns:

Number of snakes currently handled by the optimizer.

getResultSnakes

public final MTBPolygon2DSet getResultSnakes()

Returns the set of result snakes.

Returns:

Set of snakes, object may be null!

enableShowIntermediateResults

public final void enableShowIntermediateResults()

Activates display of intermediate results.

disableShowIntermediateResults

public final void disableShowIntermediateResults()

Deactivates display of intermediate results.

enableSaveIntermediateResults

public final void enableSaveIntermediateResults()

Activates writing of intermediate results to disc.

disableSaveIntermediateResults

public final void disableSaveIntermediateResults()

Deactivates writing of intermediate results.

setIntermediateResultPath

public final void setIntermediateResultPath(String path)

Set path for intermediate results.

wantStackWithIntermediateResults

public final void wantStackWithIntermediateResults(boolean flag)

Flag for turning on/off generation of stack with intermediate results.

getStackWithIntermediateResults

public final MTBImageRGB getStackWithIntermediateResults()

Returns a stack with intermediate segmentation results.

Returns:

Stack of intermediate segmentation results.

getExcludeMask

public final boolean[][] getExcludeMask()

Returns the current exclude mask.

Returns:

Mask array, indicating which image pixels to exclude from calcs.

setExcludeMask

public final void setExcludeMask(boolean[][] mask)

Set exclude mask.

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

plotSnakesToImage

private void plotSnakesToImage()

Returns overlay of output snakes onto current input image.

plotSnakesToImage

private static MTBImageRGB plotSnakesToImage(MTBPolygon2DSet polyset,
                                             MTBImage image,
                                             int[] colors)

Returns overlay of given snakes onto given image.

Parameters:

polyset - Set of snakes.

image - Input image where to plot the snakes.

Returns:

Color image overlayed with snakes.

generateStackWithIntermediateResults

private void generateStackWithIntermediateResults()

Generates a stack with intermediate results.

toString

public String toString()

Overrides:

toString in class Object