de.unihalle.informatik.MiToBo.tools.interactive

Class LabelImageEditor

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.tools.interactive.LabelImageEditor

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class LabelImageEditor
extends MTBOperator
implements MouseListener, MouseMotionListener, ActionListener

A small interactive tool for editing label images by mouse-clicks.

The editor supports removing regions by one-click operations. Images can be relabeled and open contour branches be removed. Also holes within regions, i.e., background sections and small regions completely surrounded by another region, can be eliminated.
Short gaps in boundaries can be closed by drawing free-hand lines by mouse.
To enhance the display of an image the contrast of region labels can be improved by shifting dark labels into a higher interval of gray-scale values increasing the difference (contrast) to the black background.

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
private MTBImageShort	activeImage Image currently under processing.
private ij.ImagePlus	activePlus Reference to currently active image.
private ij.process.ImageProcessor	activeProcessor Reference to processor of currently active image activePlus.
private JRadioButton	buttonBlack Button to select black pen color in drawing.
private JRadioButton	buttonWhite Button to select white pen color in drawing.
private boolean	calledFirstTime Flag to ensure that callback only works once the operator has been called.
private static String	classID Class identifier.
private String	currentFile Full path name of currently active image file.
private static int	defaultDrawLineWidth Default width of freehand border lines.
private static int	defaultMaxBorderWidth Maximal border width default value.
private boolean	finished Flag to indicate if operations are finished.
private ij.gui.ImageCanvas	ic Image canvas for displaying image and interacting.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	inputDir Image directory to process.
private String	inputRegExp Optional file filter.
private String	internalOutputDir Internal variable of output dir (to avoid modifying parameter).
private int	lastLabel Stores the last clicked label for transfer in memory mode.
private Point2D.Double	lastPathPoint Local helper variable in drawing new boundaries, stores last point of current path.
private ij.process.ImageProcessor	lastProcessor Reference to last processor before last action.
private JFrame	mainFrame Main window frame.
private boolean	memoryMode In memory mode labels can be transferred from one region to another.
private JTextField	optionsBorderMaxWidth Text field with current maximal border width.
private JTextField	optionsDrawLineWidth Text field with current width of lines when drawing boundaries.
private JFrame	optionsFrame Window for setting some options and configuration parameters.
private MTBImage	originalImage Original image currently under processing.
private String	outFileEnding Optional output file suffix.
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString	outputDir Optional output directory.
private boolean	scanPath Local flag to indicate if we are currently tracing a path for a new piece of boundary.
private boolean	stillActive Flag to indicate if process is still active.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
LabelImageEditor() Default constructor.

Method Summary

Modifier and Type	Method and Description
void	actionPerformed(ActionEvent e)
private void	callbackInputDir() Callback function called in case of changes of parameter inputDir.
private void	initMainFrame() Initialize the main window on opening the first image.
private void	initOptionsFrame() Initialize the options window.
private static void	labelNeighbors(ij.process.ImageProcessor ip, int px, int py, int label) Recursively label neighbors until approaching next region.
void	mouseClicked(MouseEvent e)
void	mouseDragged(MouseEvent e)
void	mouseEntered(MouseEvent e)
void	mouseExited(MouseEvent e)
void	mouseMoved(MouseEvent e)
void	mousePressed(MouseEvent e)
void	mouseReleased(MouseEvent e)
protected void	operate()
private void	optimizeContrast(ij.process.ImageProcessor ip) Optimize visibility by shifting labels into upper part of gray-scale range.
private void	saveFile() Saves the current processing result.

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

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, 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

classID

private static final String classID

Class identifier.

See Also:

Constant Field Values

defaultMaxBorderWidth

private static final int defaultMaxBorderWidth

Maximal border width default value.

See Also:

Constant Field Values

defaultDrawLineWidth

private static final int defaultDrawLineWidth

Default width of freehand border lines.

See Also:

Constant Field Values

inputDir

@Parameter(label="Input Directory",
           required=true,
           direction=IN,
           description="Input directory.",
           dataIOOrder=0,
           callback="callbackInputDir",
           paramModificationMode=MODIFIES_VALUES_ONLY)
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString inputDir

Image directory to process.

inputRegExp

@Parameter(label="File Filter",
           required=false,
           direction=IN,
           description="Regular expression to filter input files.",
           dataIOOrder=0)
private String inputRegExp

Optional file filter.

outputDir

@Parameter(label="Output Directory",
           required=false,
           direction=IN,
           description="Output directory.",
           dataIOOrder=1)
private de.unihalle.informatik.Alida.datatypes.ALDDirectoryString outputDir

Optional output directory.

If left unset results are saved to input directory.

outFileEnding

@Parameter(label="Output file ending",
           required=false,
           direction=IN,
           description="Output file ending.",
           dataIOOrder=2)
private String outFileEnding

Optional output file suffix.

mainFrame

private JFrame mainFrame

Main window frame.

ic

private ij.gui.ImageCanvas ic

Image canvas for displaying image and interacting.

originalImage

private MTBImage originalImage

Original image currently under processing.

activeImage

private MTBImageShort activeImage

Image currently under processing.

activePlus

private ij.ImagePlus activePlus

Reference to currently active image.

activeProcessor

private ij.process.ImageProcessor activeProcessor

Reference to processor of currently active image activePlus.

lastProcessor

private ij.process.ImageProcessor lastProcessor

Reference to last processor before last action. activePlus.

stillActive

private boolean stillActive

Flag to indicate if process is still active.

currentFile

private String currentFile

Full path name of currently active image file.

finished

private boolean finished

Flag to indicate if operations are finished.

internalOutputDir

private String internalOutputDir

Internal variable of output dir (to avoid modifying parameter).

calledFirstTime

private boolean calledFirstTime

Flag to ensure that callback only works once the operator has been called.

memoryMode

private boolean memoryMode

In memory mode labels can be transferred from one region to another.

lastLabel

private int lastLabel

Stores the last clicked label for transfer in memory mode.

scanPath

private boolean scanPath

Local flag to indicate if we are currently tracing a path for a new piece of boundary.

lastPathPoint

private Point2D.Double lastPathPoint

Local helper variable in drawing new boundaries, stores last point of current path.

optionsFrame

private JFrame optionsFrame

Window for setting some options and configuration parameters.

optionsBorderMaxWidth

private JTextField optionsBorderMaxWidth

Text field with current maximal border width.

optionsDrawLineWidth

private JTextField optionsDrawLineWidth

Text field with current width of lines when drawing boundaries.

buttonBlack

private JRadioButton buttonBlack

Button to select black pen color in drawing.

buttonWhite

private JRadioButton buttonWhite

Button to select white pen color in drawing.

Constructor Detail

LabelImageEditor

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown if construction fails.

Method Detail

operate

protected 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

mouseClicked

public void mouseClicked(MouseEvent e)

Specified by:

mouseClicked in interface MouseListener

labelNeighbors

private static void labelNeighbors(ij.process.ImageProcessor ip,
                                   int px,
                                   int py,
                                   int label)

Recursively label neighbors until approaching next region.

Parameters:

ip - Image processor to modify.

px - Position in x where to start.

py - Position in y where to start.

label - Label to assign to new region.

mousePressed

public void mousePressed(MouseEvent e)

Specified by:

mousePressed in interface MouseListener

mouseReleased

public void mouseReleased(MouseEvent e)

Specified by:

mouseReleased in interface MouseListener

mouseEntered

public void mouseEntered(MouseEvent e)

Specified by:

mouseEntered in interface MouseListener

mouseExited

public void mouseExited(MouseEvent e)

Specified by:

mouseExited in interface MouseListener

mouseDragged

public void mouseDragged(MouseEvent e)

Specified by:

mouseDragged in interface MouseMotionListener

mouseMoved

public void mouseMoved(MouseEvent e)

Specified by:

mouseMoved in interface MouseMotionListener

actionPerformed

public void actionPerformed(ActionEvent e)

Specified by:

actionPerformed in interface ActionListener

initMainFrame

private void initMainFrame()

Initialize the main window on opening the first image.

initOptionsFrame

private void initOptionsFrame()

Initialize the options window.

optimizeContrast

private void optimizeContrast(ij.process.ImageProcessor ip)

Optimize visibility by shifting labels into upper part of gray-scale range.

Parameters:

ip - Image processor to process.

saveFile

private void saveFile()

Saves the current processing result.

callbackInputDir

private void callbackInputDir()

Callback function called in case of changes of parameter inputDir.

If the parameter outputDir is null on changes of inputDir it will get the same value.