de.unihalle.informatik.MiToBo.segmentation.basics

Class SegmentationInitializer

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD)
public class SegmentationInitializer
extends MTBOperator

Operator for initializing objects of type MTBSegmentationInterface.

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SegmentationInitializer.InputMode Available data sources.
static class	SegmentationInitializer.SegmentationDimension Available dimensions for segmentations.
static class	SegmentationInitializer.ShapeType Available shape types.

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 MTBImage	binaryImage
protected SegmentationInitializer.InputMode	inMode
protected MTBImage	labelImage
protected boolean	regionBinaryMode
protected MTBRegion2DSet	regionSet
protected SegmentationInitializer.SegmentationDimension	segDim
protected MTBSegmentationInterface	segObject
protected SegmentationInitializer.ShapeType	shape
protected double	shapeDimX
protected double	shapeDimY
protected double	shapeDimZ
protected int	shapeMaskSizeX
protected int	shapeMaskSizeY
protected int	shapeMaskSizeZ
protected double	shapePosX
protected double	shapePosY
protected double	shapePosZ
protected double	threshold
protected MTBImage	thresholdImage

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
SegmentationInitializer() Default constructor.

Method Summary

Modifier and Type	Method and Description
protected void	generateSegmentation() Generates segmentation objects given specified data.
protected MTBSegmentation2D	get2DInterface(MTBImage labelImg, boolean binaryMode) Generates 2D segmentation.
protected MTBSegmentation2D	get2DMask() Generates a synthetic 2D mask according to given specification.
protected MTBSegmentation3D	get3DInterface(MTBImage labelImg, boolean binaryMode) Generates 3D segmentation.
MTBSegmentation3D	get3DMask() Generates a synthetic 3D mask according to given specification.
MTBImage	getBinaryImage() Get the image for binary mode.
SegmentationInitializer.InputMode	getInputMode() Get input mode.
MTBImage	getLabelImage() Get the label image.
MTBRegion2DSet	getRegionSet() Get the region set.
SegmentationInitializer.SegmentationDimension	getSegDim() Get target dimension.
MTBSegmentationInterface	getSegmentation() Get the generated segmentation object.
SegmentationInitializer.ShapeType	getShape() Get the selected shape.
double	getShapeDimX() Get extent of shape in x dimension.
double	getShapeDimY() Get extent of shape in y dimension.
double	getShapeDimZ() Get extent of shape in z dimension.
int	getShapeMaskSizeX() Get size of shape mask in x dimension.
int	getShapeMaskSizeY() Get size of shape mask in y dimension.
int	getShapeMaskSizeZ() Get size of shape mask in z dimension.
double	getShapePosX() Get position of shape in x dimension.
double	getShapePosY() Get position of shape in y dimension.
double	getShapePosZ() Get position of shape in z dimension.
protected MTBSegmentationInterface	getSynthMask(SegmentationInitializer.SegmentationDimension sDim) Generate synthetic mask.
double	getThreshold() Get threshold to be applied to image.
MTBImage	getThresholdImage() Get image for thresholding
boolean	isRegionBinaryMode() Check for region input mode.
protected void	operate()
void	setBinaryImage(MTBImage _binaryImage) Set the binary image.
void	setInputMode(SegmentationInitializer.InputMode _mode) Set input mode.
void	setLabelImage(MTBImage _labelImage) Set the label image.
void	setRegionBinaryMode(boolean _regionBinaryMode) Specify region input mode.
void	setRegionSet(MTBRegion2DSet _regionSet) Set the region set.
void	setSegDim(SegmentationInitializer.SegmentationDimension _segDim) Set target dimension.
void	setShape(SegmentationInitializer.ShapeType _shape) Specify shape for synthetic initialization.
void	setShapeDimX(double _shapeDimX) Set extent of shape in x dimension.
void	setShapeDimY(double _shapeDimY) Set extent of shape in y dimension.
void	setShapeDimZ(double _shapeDimZ) Set extent of shape in z dimension.
void	setShapeMaskSizeX(int _shapeMaskSizeX) Set size of shape mask in x dimension.
void	setShapeMaskSizeY(int _shapeMaskSizeY) Set size of shape mask in y dimension.
void	setShapeMaskSizeZ(int _shapeMaskSizeZ) Set size of shape mask in z dimension.
void	setShapePosX(double _shapePosX) Set position of shape in x dimension.
void	setShapePosY(double _shapePosY) Set position of shape in y dimension.
void	setShapePosZ(double _shapePosZ) Set position of shape in z dimension.
void	setThreshold(double _threshold) Set threshold for threshold mode.
void	setThresholdImage(MTBImage _thresholdImage) Set image for thresholding.
void	validateCustom()

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, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

inMode

@Parameter(label="Input Mode",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="Source from where to read the data.")
protected SegmentationInitializer.InputMode inMode

segDim

@Parameter(label="Dimension",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Dimension of generated segmentation object.")
protected SegmentationInitializer.SegmentationDimension segDim

binaryImage

@Parameter(label="Binary Mode Image",
           required=false,
           dataIOOrder=10,
           direction=IN,
           description="Image for two-class segmentation.")
protected transient MTBImage binaryImage

labelImage

@Parameter(label="Label Mode Image",
           required=false,
           dataIOOrder=11,
           direction=IN,
           description="Label image for n-class segmentation.")
protected transient MTBImage labelImage

regionSet

@Parameter(label="Region Set",
           required=false,
           dataIOOrder=12,
           direction=IN,
           description="Region set for for two- or n-class segmentation.")
protected MTBRegion2DSet regionSet

regionBinaryMode

@Parameter(label="Region Mode",
           required=false,
           dataIOOrder=13,
           direction=IN,
           description="Assign all regions to the common foreground.")
protected boolean regionBinaryMode

thresholdImage

@Parameter(label="Threshold Image",
           required=false,
           dataIOOrder=14,
           direction=IN,
           description="Input image for thresholding.")
protected transient MTBImage thresholdImage

threshold

@Parameter(label="Threshold",
           required=false,
           dataIOOrder=15,
           direction=IN,
           description="Threshold to be applied to threshold image.")
protected double threshold

shape

@Parameter(label="Shape",
           required=false,
           dataIOOrder=16,
           direction=IN,
           description="Type of sythetic shape.")
protected SegmentationInitializer.ShapeType shape

shapeMaskSizeX

@Parameter(label="Shape Mask Size X",
           required=false,
           dataIOOrder=17,
           direction=IN,
           description="Size of mask in x dimension.")
protected int shapeMaskSizeX

shapeMaskSizeY

@Parameter(label="Shape Mask Size Y",
           required=false,
           dataIOOrder=18,
           direction=IN,
           description="Size of mask in y dimension.")
protected int shapeMaskSizeY

shapeMaskSizeZ

@Parameter(label="Shape Mask Size Z",
           required=false,
           dataIOOrder=19,
           direction=IN,
           description="Size of mask in z dimension.")
protected int shapeMaskSizeZ

shapePosX

@Parameter(label="Shape position X",
           required=false,
           dataIOOrder=20,
           direction=IN,
           description="Shape position in x dimension.")
protected double shapePosX

shapePosY

@Parameter(label="Shape position Y",
           required=false,
           dataIOOrder=21,
           direction=IN,
           description="Shape position in y dimension.")
protected double shapePosY

shapePosZ

@Parameter(label="Shape position Z",
           required=false,
           dataIOOrder=22,
           direction=IN,
           description="Shape position in z dimension.")
protected double shapePosZ

shapeDimX

@Parameter(label="Shape dimension X",
           required=false,
           dataIOOrder=23,
           direction=IN,
           description="Extent of shape in x dimension.")
protected double shapeDimX

shapeDimY

@Parameter(label="Shape dimension Y",
           required=false,
           dataIOOrder=24,
           direction=IN,
           description="Extent of shape in y dimension.")
protected double shapeDimY

shapeDimZ

@Parameter(label="Shape dimension Z",
           required=false,
           dataIOOrder=25,
           direction=IN,
           description="Extent of shape in z dimension.")
protected double shapeDimZ

segObject

@Parameter(label="Generated segmentation",
           direction=OUT,
           description="Segmentation.")
protected transient MTBSegmentationInterface segObject

Constructor Detail

SegmentationInitializer

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

Default constructor.

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

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

getSegDim

public SegmentationInitializer.SegmentationDimension getSegDim()

Get target dimension.

Returns:

Target dimension.

setSegDim

public void setSegDim(SegmentationInitializer.SegmentationDimension _segDim)

Set target dimension.

Parameters:

_segDim - Target dimension to be used.

getInputMode

public SegmentationInitializer.InputMode getInputMode()

Get input mode.

Returns:

Input mode.

setInputMode

public void setInputMode(SegmentationInitializer.InputMode _mode)

Set input mode.

Parameters:

_mode - Input mode to be used.

getBinaryImage

public MTBImage getBinaryImage()

Get the image for binary mode.

Returns:

Binary mode image.

setBinaryImage

public void setBinaryImage(MTBImage _binaryImage)

Set the binary image.

Parameters:

_binaryImage - Binary image for mask initialization.

getLabelImage

public MTBImage getLabelImage()

Get the label image.

Returns:

Label image.

setLabelImage

public void setLabelImage(MTBImage _labelImage)

Set the label image.

Parameters:

_labelImage - Label image for n-class initialization.

getRegionSet

public MTBRegion2DSet getRegionSet()

Get the region set.

Returns:

Region set.

setRegionSet

public void setRegionSet(MTBRegion2DSet _regionSet)

Set the region set.

Parameters:

_regionSet - Set for 2-/n-class initialization.

isRegionBinaryMode

public boolean isRegionBinaryMode()

Check for region input mode.

Returns:

True if binary mode is selected.

setRegionBinaryMode

public void setRegionBinaryMode(boolean _regionBinaryMode)

Specify region input mode.

Parameters:

_regionBinaryMode - Flag for region input mode.

getThresholdImage

public MTBImage getThresholdImage()

Get image for thresholding

Returns:

Image to threshold.

setThresholdImage

public void setThresholdImage(MTBImage _thresholdImage)

Set image for thresholding.

Parameters:

_thresholdImage - Image for thresholding.

getThreshold

public double getThreshold()

Get threshold to be applied to image.

Returns:

Threshold.

setThreshold

public void setThreshold(double _threshold)

Set threshold for threshold mode.

Parameters:

_threshold - Threshold to be applied to threshold image.

getShape

public SegmentationInitializer.ShapeType getShape()

Get the selected shape.

Returns:

Selected shape.

setShape

public void setShape(SegmentationInitializer.ShapeType _shape)

Specify shape for synthetic initialization.

Parameters:

_shape - Shape type to be used.

getShapeMaskSizeX

public int getShapeMaskSizeX()

Get size of shape mask in x dimension.

Returns:

Size of shape mask in x.

setShapeMaskSizeX

public void setShapeMaskSizeX(int _shapeMaskSizeX)

Set size of shape mask in x dimension.

Parameters:

_shapeMaskSizeX - Size to be used.

getShapeMaskSizeY

public int getShapeMaskSizeY()

Get size of shape mask in y dimension.

Returns:

Size of shape mask in y.

setShapeMaskSizeY

public void setShapeMaskSizeY(int _shapeMaskSizeY)

Set size of shape mask in y dimension.

Parameters:

_shapeMaskSizeY - Size to be used.

getShapeMaskSizeZ

public int getShapeMaskSizeZ()

Get size of shape mask in z dimension.

Returns:

Size of shape mask in z.

setShapeMaskSizeZ

public void setShapeMaskSizeZ(int _shapeMaskSizeZ)

Set size of shape mask in z dimension.

Parameters:

_shapeMaskSizeZ - Size to be used.

getShapePosX

public double getShapePosX()

Get position of shape in x dimension.

Returns:

Position in x.

setShapePosX

public void setShapePosX(double _shapePosX)

Set position of shape in x dimension.

Parameters:

_shapePosX - Position in x.

getShapePosY

public double getShapePosY()

Get position of shape in y dimension.

Returns:

Position in y.

setShapePosY

public void setShapePosY(double _shapePosY)

Set position of shape in y dimension.

Parameters:

_shapePosY - Position in y.

getShapePosZ

public double getShapePosZ()

Get position of shape in z dimension.

Returns:

Position in z.

setShapePosZ

public void setShapePosZ(double _shapePosZ)

Set position of shape in z dimension.

Parameters:

_shapePosZ - Position in z.

getShapeDimX

public double getShapeDimX()

Get extent of shape in x dimension.

Returns:

Extent in x.

setShapeDimX

public void setShapeDimX(double _shapeDimX)

Set extent of shape in x dimension.

Parameters:

_shapeDimX - Extent to be used.

getShapeDimY

public double getShapeDimY()

Get extent of shape in y dimension.

Returns:

Extent in y.

setShapeDimY

public void setShapeDimY(double _shapeDimY)

Set extent of shape in y dimension.

Parameters:

_shapeDimY - Extent to be used.

getShapeDimZ

public double getShapeDimZ()

Get extent of shape in z dimension.

Returns:

Extent in z.

setShapeDimZ

public void setShapeDimZ(double _shapeDimZ)

Set extent of shape in z dimension.

Parameters:

_shapeDimZ - Extent to be used.

getSegmentation

public MTBSegmentationInterface getSegmentation()

Get the generated segmentation object.

Returns:

Segmentation.

generateSegmentation

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

Generates segmentation objects given specified data.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

get2DInterface

protected MTBSegmentation2D get2DInterface(MTBImage labelImg,
                                           boolean binaryMode)

Generates 2D segmentation.

Parameters:

labelImg - Label image to process.

binaryMode - If true, two-class segmentation is generated.

Returns:

Generated 2D segmentation object.

get3DInterface

protected MTBSegmentation3D get3DInterface(MTBImage labelImg,
                                           boolean binaryMode)

Generates 3D segmentation.

Parameters:

labelImg - Label image to process.

binaryMode - If true, two-class segmentation is generated.

Returns:

Generated 3D segmentation object.

getSynthMask

protected MTBSegmentationInterface getSynthMask(SegmentationInitializer.SegmentationDimension sDim)

Generate synthetic mask.

Returns:

Generated segmentation mask.

get2DMask

protected MTBSegmentation2D get2DMask()

Generates a synthetic 2D mask according to given specification.

Returns:

2D segmentation mask.

get3DMask

public MTBSegmentation3D get3DMask()

Generates a synthetic 3D mask according to given specification.

Returns:

3D segmentation mask.