de.unihalle.informatik.MiToBo.features

Class MorphologyAnalyzer3D

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer3D

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=STANDARD,
              allowBatchMode=true)
public class MorphologyAnalyzer3D
extends MTBOperator

Author:

glass

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 int	bgLabel
private boolean	calcCompactness
private boolean	calcSurfArea
private boolean	calcVolume
(package private) Vector<Double>	compactnesses
private Double	deltaX
private Double	deltaY
private Double	deltaZ
private Integer	fracDigits
private MTBImage	labelImg
(package private) Vector<Integer>	labels
private NumberFormat	nf
private MTBRegion3DSet	regions
(package private) Vector<Double>	surfaceAreas
private MTBSurface3DSet	surfaces
private MTBTableModel	table
private String	unitXYZ
(package private) Vector<Double>	volumes

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
MorphologyAnalyzer3D()
MorphologyAnalyzer3D(MTBImage labelImg)
MorphologyAnalyzer3D(MTBRegion3DSet regions, MTBSurface3DSet surfaces)

Method Summary

Modifier and Type	Method and Description
boolean	calcCompactness()
boolean	calcSurfArea()
boolean	calcVolume()
private void	getCalibration()
Double	getDeltaX()
Double	getDeltaY()
Double	getDeltaZ()
MTBImage	getLabelImg()
private void	getShapeFeatures()
MTBTableModel	getTable()
String	getUnitXYZ()
private void	makeTable() create result table
protected void	operate()
void	setCalcCompactness(boolean calcCompactness)
void	setCalcSurfArea(boolean calcSurfArea)
void	setCalcVolume(boolean calcVolume)
void	setDeltaX(Double deltaX)
void	setDeltaY(Double deltaY)
void	setDeltaZ(Double deltaZ)
void	setFractionalDigits(int digits) specify the number of fractional digits for the results table
void	setLabelImg(MTBImage labelImg)
void	setUnitXYZ(String unitXYZ)

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

labelImg

@Parameter(label="3D-label image",
           required=false,
           direction=IN,
           supplemental=false,
           description="3D-label image",
           dataIOOrder=0,
           callback="getCalibration",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage labelImg

regions

private MTBRegion3DSet regions

surfaces

private MTBSurface3DSet surfaces

deltaX

@Parameter(label="pixel length, x-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=3)
private Double deltaX

deltaY

@Parameter(label="pixel length, y-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=4)
private Double deltaY

deltaZ

@Parameter(label="pixel length, z-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in z-direction",
           dataIOOrder=5)
private Double deltaZ

unitXYZ

@Parameter(label="unit x/y/z",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit of spatial dimensions",
           dataIOOrder=6)
private String unitXYZ

calcVolume

@Parameter(label="calculate volume",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s areas be calculated",
           dataIOOrder=7)
private boolean calcVolume

calcCompactness

@Parameter(label="calculate compactness",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s areas be calculated",
           dataIOOrder=8)
private boolean calcCompactness

calcSurfArea

@Parameter(label="calculate surface area",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s areas be calculated",
           dataIOOrder=9)
private boolean calcSurfArea

fracDigits

@Parameter(label="fractional digits",
           required=false,
           direction=IN,
           supplemental=false,
           description="fractional digits",
           dataIOOrder=10,
           mode=ADVANCED)
private Integer fracDigits

table

@Parameter(label="results table",
           required=true,
           direction=OUT,
           supplemental=false,
           description="results table",
           dataIOOrder=0)
private MTBTableModel table

nf

private NumberFormat nf

bgLabel

private int bgLabel

labels

Vector<Integer> labels

volumes

Vector<Double> volumes

compactnesses

Vector<Double> compactnesses

surfaceAreas

Vector<Double> surfaceAreas

Constructor Detail

MorphologyAnalyzer3D

public MorphologyAnalyzer3D()
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MorphologyAnalyzer3D

public MorphologyAnalyzer3D(MTBImage labelImg)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MorphologyAnalyzer3D

public MorphologyAnalyzer3D(MTBRegion3DSet regions,
                            MTBSurface3DSet surfaces)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

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

getShapeFeatures

private void getShapeFeatures()

makeTable

private void makeTable()

create result table

getLabelImg

public MTBImage getLabelImg()

Returns:

the labelImg

setLabelImg

public void setLabelImg(MTBImage labelImg)

Parameters:

labelImg - the labelImg to set

getDeltaX

public Double getDeltaX()

Returns:

the deltaX

setDeltaX

public void setDeltaX(Double deltaX)

Parameters:

deltaX - the deltaX to set

getDeltaY

public Double getDeltaY()

Returns:

the deltaY

setDeltaY

public void setDeltaY(Double deltaY)

Parameters:

deltaY - the deltaY to set

getDeltaZ

public Double getDeltaZ()

Returns:

the deltaZ

setDeltaZ

public void setDeltaZ(Double deltaZ)

Parameters:

deltaZ - the deltaZ to set

getUnitXYZ

public String getUnitXYZ()

Returns:

the unitXYZ

setUnitXYZ

public void setUnitXYZ(String unitXYZ)

Parameters:

unitXYZ - the unitXYZ to set

calcVolume

public boolean calcVolume()

Returns:

are volumes to be calculated

setCalcVolume

public void setCalcVolume(boolean calcVolume)

Parameters:

calcVolume - should volumes be calculated

calcCompactness

public boolean calcCompactness()

Returns:

are compactnesses to be calculated

setCalcCompactness

public void setCalcCompactness(boolean calcCompactness)

Parameters:

calcCompactness - should compactnesses be calculated

calcSurfArea

public boolean calcSurfArea()

Returns:

are surface areas to be calculated

setCalcSurfArea

public void setCalcSurfArea(boolean calcSurfArea)

Parameters:

calcSurfArea - should surface areas be calculated

setFractionalDigits

public void setFractionalDigits(int digits)

specify the number of fractional digits for the results table

Parameters:

digits -

getTable

public MTBTableModel getTable()

Returns:

the table

getCalibration

private void getCalibration()