de.unihalle.informatik.MiToBo.apps.xylem

Class XylemInitialSegmentation

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              shortDescription="Makes an initial segmentation of Xylem Cell Images")
public class XylemInitialSegmentation
extends MTBOperator

Purpose of this operator is to make an initial segmentation of Xylem Cell Images.

The input image is a grey level image of the Xylem cells. The output image is a binary image of the initial segmentation.

1. Calculate otsu threshold
2. Binarize the greyscaled image based on the otsu threshold
3. Open the bin-image
4. Remove small components
5. Erode the image
6. Remove small components
7. Remove uncompact regions

Author:

Tim Langhammer, Halle/Saale, Europe, posch

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
static int	DEFAULT_minAreaAfterOpening
static double	DEFAULT_minCompactness
static int	DEFAULT_seOpeningSize
private MTBImageByte	initSegImageByte The resulting binary image after the initial segmentation.
private int	minAreaAfterErosion The minimum size of regions after the erosion to get preserved.
private int	minAreaAfterOpening Minimal area (in pixels) of a region required after opening.
private double	minCompactness Minimal compactness of a region required after opening.
private boolean	printTiming Should time of processing be printed to stdout
private int	seErosionSize Size of the structuring element for the erosion.
private int	seOpeningSize Size of the structuring element for Opening.
private BasicMorphology.maskShape	shapeForErosion The shape of structuring element for the Erosion.
private BasicMorphology.maskShape	shapeForOpening The shape of structuring element for the opening.
private MTBImage	xylemGrayedImage The Xylem Cell microscope MTBImageByte grey level image.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
XylemInitialSegmentation() Default constructor.
XylemInitialSegmentation(MTBImageByte grayScaleXylemImage)

Method Summary

Modifier and Type	Method and Description
String	getDocumentation()
MTBImageByte	getInitSegImageByte() Return the resulting initial segmentation image.
int	getMinAreaAfterErosion()
int	getMinAreaAfterOpening()
double	getMinCompactness()
int	getSeErosionSize()
int	getSeOpeningSize()
BasicMorphology.maskShape	getShapeForErosion()
BasicMorphology.maskShape	getShapeForOpening()
MTBImage	getXylemImage() Return the input xylem image.
protected void	operate()
void	setInitSegImageByte(MTBImageByte initSegImageByte)
void	setMinAreaAfterErosion(int minAreaAfterErosion)
void	setMinAreaAfterOpening(int minAreaAfterOpening)
void	setMinCompactness(double minCompactness)
void	setSeErosionSize(int seErosionSize)
void	setSeOpeningSize(int seOpeningSize)
void	setShapeForErosion(BasicMorphology.maskShape shapeForErosion)
void	setShapeForOpening(BasicMorphology.maskShape shapeForOpening)
void	setXylemImage(MTBImage xylemImage) Set the input xylem image - this must be an 8bit image.

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, 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

DEFAULT_seOpeningSize

public static final int DEFAULT_seOpeningSize

See Also:

Constant Field Values

DEFAULT_minAreaAfterOpening

public static final int DEFAULT_minAreaAfterOpening

See Also:

Constant Field Values

DEFAULT_minCompactness

public static final double DEFAULT_minCompactness

See Also:

Constant Field Values

xylemGrayedImage

@Parameter(label="XylemCellGrayImage",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="The Xylem Cell microscope grey level image")
private transient MTBImage xylemGrayedImage

The Xylem Cell microscope MTBImageByte grey level image.

seOpeningSize

@Parameter(label="SizeStructuringElementOpening",
           required=false,
           dataIOOrder=2,
           direction=IN,
           description="The size of the structuring element for the opening",
           mode=ADVANCED)
private int seOpeningSize

Size of the structuring element for Opening.

minAreaAfterOpening

@Parameter(label="MinRegionSize",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="The minimal size of the region required after opening",
           mode=ADVANCED)
private int minAreaAfterOpening

Minimal area (in pixels) of a region required after opening.

If the size of the region is < minAreaAfterOpening the region will be removed by the ComponentPostprocess operator.

minCompactness

@Parameter(label="MinCompactness",
           required=false,
           dataIOOrder=4,
           direction=IN,
           description="The minimal compactness of the region required after opening",
           mode=ADVANCED)
private double minCompactness

Minimal compactness of a region required after opening.

If the compactness of the region is < minCompactness the region will be removed by the ComponentPostprocess operator.

printTiming

@Parameter(label="PrintTiming",
           required=false,
           dataIOOrder=4,
           direction=IN,
           description="Print timing information to standard output",
           mode=ADVANCED)
private boolean printTiming

Should time of processing be printed to stdout

initSegImageByte

@Parameter(label="InitialSegmentation",
           required=true,
           dataIOOrder=1,
           direction=OUT,
           description="The resulting initial segmentation as a binary image")
private transient MTBImageByte initSegImageByte

The resulting binary image after the initial segmentation.

seErosionSize

private int seErosionSize

Size of the structuring element for the erosion.

shapeForOpening

private BasicMorphology.maskShape shapeForOpening

The shape of structuring element for the opening.

shapeForErosion

private BasicMorphology.maskShape shapeForErosion

The shape of structuring element for the Erosion.

minAreaAfterErosion

private int minAreaAfterErosion

The minimum size of regions after the erosion to get preserved.

Constructor Detail

XylemInitialSegmentation

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

XylemInitialSegmentation

public XylemInitialSegmentation(MTBImageByte grayScaleXylemImage)
                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:

grayScaleXylemImage -

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

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

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getXylemImage

public MTBImage getXylemImage()

Return the input xylem image.

Returns:

setXylemImage

public void setXylemImage(MTBImage xylemImage)

Set the input xylem image - this must be an 8bit image.

Parameters:

xylemImage -

getInitSegImageByte

public MTBImageByte getInitSegImageByte()

Return the resulting initial segmentation image.

Returns:

setInitSegImageByte

public void setInitSegImageByte(MTBImageByte initSegImageByte)

Parameters:

initSegImageByte -

getSeOpeningSize

public int getSeOpeningSize()

setSeOpeningSize

public void setSeOpeningSize(int seOpeningSize)

getSeErosionSize

public int getSeErosionSize()

setSeErosionSize

public void setSeErosionSize(int seErosionSize)

getMinAreaAfterOpening

public int getMinAreaAfterOpening()

setMinAreaAfterOpening

public void setMinAreaAfterOpening(int minAreaAfterOpening)

getMinAreaAfterErosion

public int getMinAreaAfterErosion()

setMinAreaAfterErosion

public void setMinAreaAfterErosion(int minAreaAfterErosion)

getMinCompactness

public double getMinCompactness()

setMinCompactness

public void setMinCompactness(double minCompactness)

getShapeForOpening

public BasicMorphology.maskShape getShapeForOpening()

setShapeForOpening

public void setShapeForOpening(BasicMorphology.maskShape shapeForOpening)

getShapeForErosion

public BasicMorphology.maskShape getShapeForErosion()

setShapeForErosion

public void setShapeForErosion(BasicMorphology.maskShape shapeForErosion)

getDocumentation

public String getDocumentation()

Overrides:

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