MorphologyAnalyzer2D (mitobo 2.0 API)

java.lang.Object
- de.unihalle.informatik.Alida.operator.ALDOperator
- - de.unihalle.informatik.MiToBo.core.operator.MTBOperator
  - - de.unihalle.informatik.MiToBo.features.MorphologyAnalyzer2D

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener
```
@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=false)
public class MorphologyAnalyzer2D
extends MTBOperator
```
Operator to extract shape and region features for given regions.
Note that the operator assumes squared pixels. If the pixels are not squared several feature values will not be calculated correctly.

Author:

Markus Glass, Birgit Moeller

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class MorphologyAnalyzer2D.FeatureNames
Set of region features calculated from segmented cell regions.
- 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

Nested Classes
Modifier and Type	Class and Description
`static class`	`MorphologyAnalyzer2D.FeatureNames` Set of region features calculated from segmented cell regions.

Field Summary

Fields
Modifier and Type	Field and Description
`private boolean`	`analyzeProtrusionsIndentations` Flag to turn on/off analysis of protrusions and indentations.
`private Vector<Double>`	`areas`
`private Vector<Double>`	`avgApicalIndentationLengths`
`private Vector<Double>`	`avgApicalProtrusionLengths`
`private Vector<Double>`	`avgBasalIndentationLengths`
`private Vector<Double>`	`avgBasalProtrusionLengths`
`private Vector<Double>`	`avgBaselineIndentationLengths`
`private Vector<Double>`	`avgBaselineProtrusionLengths`
`private Vector<Double>`	`avgBranchLengths`
`private Vector<Double>`	`avgConcavities`
`private Vector<Double>`	`avgEndpointDistances`
`private Vector<Double>`	`avgEquatorIndentationLengths`
`private Vector<Double>`	`avgEquatorProtrusionLengths`
`private Vector<Double>`	`avgIndentationLengths`
`private Vector<Double>`	`avgLobeDepths`
`private Vector<Double>`	`avgNeckDepths`
`private Vector<Double>`	`avgProtrusionLengths`
`private int`	`bgLabel`
`private Vector<Double>`	`branchCounts`
`private boolean`	`calcArea`
`private boolean`	`calcCircularity`
`private boolean`	`calcConcavityData` Flag to turn on/off analysis of concavities.
`private boolean`	`calcConvexHullMeasures` Flag to turn on/off analysis of convex hull.
`private boolean`	`calcEccentricity`
`private boolean`	`calcLengthWidth`
`private boolean`	`calcMarginRoughness` Flag to turn on/off calculation of margin roughness.
`private boolean`	`calcPerimeter`
`private boolean`	`calcSkeletonBranchFeatures` Flag to turn on/off calculation of skeleton branch features.
`private boolean`	`calcSolidity` Flag to turn on/off calculation of solidity.
`private Vector<Double>`	`circularities`
`private int`	`concavityMaskSize` Masksize for concavity calculations.
`private Vector<Double>`	`convexHullAreas`
`private Vector<Double>`	`convexHullConvexities`
`private Vector<Double>`	`convexHullPerimeters`
`private Vector<Double>`	`convexHullRoundnessValues`
`private boolean`	`createCurvatureInfoImage` Flag to enable drawing curvature information to info image.
`private boolean`	`createSkeletonInfoImage` Flag to enable drawing skeleton information to info image.
`private MTBImageRGB`	`curvatureInfoImg` Info image for curvature analysis.
`private Double`	`deltaXY`
`private Vector<Double>`	`eccentricities`
`private Integer`	`fracDigits`
`private double`	`gaussianSigma` Standard deviation of Gaussian kernel in curvature smoothing.
`private int`	`height` Height of currently processed image.
`private MTBImage`	`inLabelImg`
`private Vector<MorphologyAnalyzer2DInProData>`	`inProDetails` Vector with detailed result data on indentations and protrusions.
`private MTBRegion2DSet`	`inRegions`
`private MTBImage`	`labelImg`
`private Vector<Integer>`	`labels`
`private Vector<Double>`	`lengths`
`private Vector<Double>`	`longestPathLengths`
`private Vector<Double>`	`marginRoughnessValues`
`private Vector<Double>`	`maxCoreRegionWidths`
`private Vector<Double>`	`minCoreRegionWidths`
`private double`	`minimalCurvature` Threshold for minimal curvature.
`private int`	`minIndentationLength` Minimal number of pixels a valid indentation requires.
`private int`	`minProtrusionLength` Minimal number of pixels a valid protrusion requires.
`private NumberFormat`	`nf`
`private Vector<Double>`	`nonProtrusionAreas`
`private static String`	`operatorID` Identifier string for this operator class.
`private Vector<Double>`	`perimeters`
`private Vector<Integer>`	`protrusionCounts`
`private Vector<Double>`	`radiiMaxInscribedEmptyCircles`
`private MTBRegion2DSet`	`regions`
`private MTBImageRGB`	`skeletonInfoImg` Info image for skeleton analysis.
`private Vector<Double>`	`solidities`
`private Vector<Double>`	`stdDevConcavities`
`private MTBTableModel`	`table`
`private String`	`unitXY`
`private int`	`width` Width of currently processed image.
`private Vector<Double>`	`widths`

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors
Constructor and Description

MorphologyAnalyzer2D()

MorphologyAnalyzer2D(MTBImage labelImg)
constructor

MorphologyAnalyzer2D(MTBRegion2DSet rs)

Constructors
Constructor and Description
`MorphologyAnalyzer2D()`
`MorphologyAnalyzer2D(MTBImage labelImg)` constructor
`MorphologyAnalyzer2D(MTBRegion2DSet rs)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private void`	`analyzeLocalCurvatures()` Calculates and analyses pixel-wise local curvatures.
`boolean`	`calcArea()`
`boolean`	`calcCircularity()`
`boolean`	`calcEccentricity()`
`boolean`	`calcLengthWidth()`
`boolean`	`calcPerimeter()`
`private void`	`calculateConcavityData()` Extracts average concavity and standard deviation of concavities.
`private void`	`calculateConvexHullMeasures()` Calculates convex hull convexities and roundnesses.
`private void`	`calculateConvexHulls()` Calculates convex hull areas and perimeters.
`private void`	`calculateSolidityValues()` Calculates solidity values.
`private void`	`callbackArea()` Callback function called in case of changes of parameter `calcArea`.
`private void`	`callbackConcavity()` Callback function called in case of changes of parameter `calcConcavityData`.
`private void`	`callbackCurvature()` Callback function called in case of changes of parameters `analyzeProtrusionsIndentations` or `calcMarginRoughness`.
`private void`	`callbackSolidity()` Callback function called in case of changes of parameter `calcSolidity`.
`private void`	`getCalibration()`
`MTBImageRGB`	`getCurvatureInfoImage()` Access info image about curvature analysis.
`Double`	`getDeltaXY()`
`Vector<MorphologyAnalyzer2DInProData>`	`getDetailedInProResults()` Access detailed information on indentations and protrusions.
`MTBImage`	`getLabelImage()` Get the label image.
`private void`	`getSimpleShapeFeatures()` calculate several shape features in one method
`MTBImageRGB`	`getSkeletonInfoImage()` Access info image about skeleton analysis.
`MTBTableModel`	`getTable()`
`String`	`getUnitXY()`
`private void`	`makeTable()` create result table
`protected void`	`operate()`
`void`	`setAnalyzeProtrusionsAndIndentations(boolean flag)` Turn on/off analysis of contour protrusions and indentations.
`void`	`setCalcArea(boolean calcArea)`
`void`	`setCalcCircularity(boolean flag)` Turn of/off calculation of circularity.
`void`	`setCalcConcavityData(boolean flag)` Turn on/off calculation of concavity information.
`void`	`setCalcConvexHullMeasures(boolean flag)` Turn on/off calculation of convex hull measures.
`void`	`setCalcEccentricity(boolean flag)` Turn of/off calculation of eccentricity.
`void`	`setCalcLengthWidth(boolean flag)` Turn of/off calculation of region length and width.
`void`	`setCalcMarginRoughness(boolean flag)` Turn on/off calculation of margin roughness values.
`void`	`setCalcPerimeter(boolean calcPerimeter)`
`void`	`setCalcSkeletonBranchFeatures(boolean flag)` Turn on/off calculation of skeleton branch features.
`void`	`setCalcSolidity(boolean flag)` Turn on/off calculation of solidities.
`void`	`setConcavityMaskSize(int m)` Specify size of local mask for concavity calculations.
`void`	`setDeltaXY(Double dXY)`
`void`	`setDrawCurvatureInfoImage(boolean flag)` Enable/disable display of curvature info image.
`void`	`setDrawSkeletonInfoImage(boolean flag)` Enable/disable display of skeleton info image.
`void`	`setFractionalDigits(int digits)` specify the number of fractional digits for the results table
`void`	`setGaussianSigmaCurvatureSmoothing(double s)` Set Gaussian standard deviation for smoothing curvature values.
`void`	`setLabelImage(MTBImage img)` Set input label image.
`void`	`setMinimalCurvatureThreshold(double c)` Set minimal curvature threshold.
`void`	`setMinimalLobeLength(int m)` Set minimal pixel count a lobe requires.
`void`	`setRegionSet(MTBRegion2DSet regs)` Set regions.
`void`	`setUnitXY(String unitXY)`

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
  - operatorID
```
private static final String operatorID
```
    Identifier string for this operator class.
    
    See Also:
    
    Constant Field Values
  - inLabelImg
```
@Parameter(label="Label image",
           required=false,
           direction=IN,
           supplemental=false,
           description="label image",
           dataIOOrder=0,
           callback="getCalibration",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage inLabelImg
```
  - inRegions
```
@Parameter(label="Regions",
           required=false,
           direction=IN,
           supplemental=false,
           description="input regions",
           dataIOOrder=1)
private MTBRegion2DSet inRegions
```
  - deltaXY
```
@Parameter(label="Pixel length",
           required=false,
           direction=IN,
           supplemental=false,
           description="Pixel length, note that we assume square pixels!",
           dataIOOrder=2)
private Double deltaXY
```
  - unitXY
```
@Parameter(label="Unit in x/y",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit x/y",
           dataIOOrder=4)
private String unitXY
```
  - calcArea
```
@Parameter(label="Calculate area",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s areas be calculated",
           dataIOOrder=5,
           callback="callbackArea",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean calcArea
```
  - calcPerimeter
```
@Parameter(label="Calculate perimeter",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s perimeters be calculated",
           dataIOOrder=6)
private boolean calcPerimeter
```
  - calcLengthWidth
```
@Parameter(label="Calculate length and width",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s length and width (fitting ellipse\'s major/minor axes length) be calculated",
           dataIOOrder=7)
private boolean calcLengthWidth
```
  - calcCircularity
```
@Parameter(label="Calculate circularity",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s circularities be calculated",
           dataIOOrder=8)
private boolean calcCircularity
```
  - calcEccentricity
```
@Parameter(label="Calculate eccentricity",
           required=false,
           direction=IN,
           supplemental=false,
           description="should object\'s eccentricities be calculated",
           dataIOOrder=9)
private boolean calcEccentricity
```
  - calcSolidity
```
@Parameter(label="Calculate solidity",
           required=false,
           direction=IN,
           supplemental=false,
           description="Should object\'s solidity be calculated?",
           dataIOOrder=10,
           callback="callbackSolidity",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean calcSolidity
```
    Flag to turn on/off calculation of solidity.
  - calcMarginRoughness
```
@Parameter(label="Calculate margin roughness",
           required=false,
           direction=IN,
           supplemental=false,
           description="If true margin roughness is calculated.",
           dataIOOrder=11,
           callback="callbackCurvature",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean calcMarginRoughness
```
    Flag to turn on/off calculation of margin roughness.
  - analyzeProtrusionsIndentations
```
@Parameter(label="Analyze protrusions and indentations",
           required=false,
           direction=IN,
           supplemental=false,
           description="If true protrusions/indentations are analyzed.",
           dataIOOrder=12,
           callback="callbackCurvature",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean analyzeProtrusionsIndentations
```
    Flag to turn on/off analysis of protrusions and indentations.
  - minimalCurvature
```
@Parameter(label="    - Minimal curvature",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=13,
           description="Curvature below this value are handled as noise.")
private double minimalCurvature
```
    Threshold for minimal curvature.
  - gaussianSigma
```
@Parameter(label="    - Gaussian \u03c3 in curvature analysis",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=14,
           description="If true margin roughness is calculated.")
private double gaussianSigma
```
    Standard deviation of Gaussian kernel in curvature smoothing.
  - minProtrusionLength
```
@Parameter(label="    - Minimal length of a protrusion section",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=15,
           description="Minimal pixel number a protrusion requires to be valid.")
private int minProtrusionLength
```
    Minimal number of pixels a valid protrusion requires.
  - minIndentationLength
```
@Parameter(label="    - Minimal length of an indentation section",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=16,
           description="Minimal pixel number an indentation requires to be valid.")
private int minIndentationLength
```
    Minimal number of pixels a valid indentation requires.
    Note that too short protrusions are removed first, and indentations are only checked afterwards.
  - calcSkeletonBranchFeatures
```
@Parameter(label="Calculate skeleton branch features",
           required=false,
           dataIOOrder=17,
           direction=IN,
           supplemental=false,
           description="If true skeleton branches are analyzed.")
private boolean calcSkeletonBranchFeatures
```
    Flag to turn on/off calculation of skeleton branch features.
  - calcConcavityData
```
@Parameter(label="Calculate concavity information",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=18,
           description="If true average concavity and standard deviation are calculated.",
           callback="callbackConcavity",
           paramModificationMode=MODIFIES_INTERFACE)
private boolean calcConcavityData
```
    Flag to turn on/off analysis of concavities.
  - concavityMaskSize
```
@Parameter(label="    - Concavity Masksize",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=19,
           description="Size of local mask in concavity calculations.")
private int concavityMaskSize
```
    Masksize for concavity calculations.
    Refer to operator Contour2DConcavityCalculator for details.
  - calcConvexHullMeasures
```
@Parameter(label="Calculate convex hull measures",
           required=false,
           direction=IN,
           supplemental=false,
           dataIOOrder=20,
           description="If true some measures of the convex hull are calculated.")
private boolean calcConvexHullMeasures
```
    Flag to turn on/off analysis of convex hull.
  - fracDigits
```
@Parameter(label="Fractional digits",
           required=false,
           direction=IN,
           supplemental=false,
           description="fractional digits",
           dataIOOrder=21,
           mode=ADVANCED)
private Integer fracDigits
```
  - createCurvatureInfoImage
```
@Parameter(label="Show curvature analysis info image?",
           required=false,
           direction=IN,
           supplemental=true,
           dataIOOrder=0,
           description="If selected info image with curvature data is shown.")
private boolean createCurvatureInfoImage
```
    Flag to enable drawing curvature information to info image.
  - curvatureInfoImg
```
@Parameter(label="Curvature data image",
           required=false,
           direction=OUT,
           supplemental=true,
           dataIOOrder=10,
           description="Curvature data image.")
private transient MTBImageRGB curvatureInfoImg
```
    Info image for curvature analysis.
  - createSkeletonInfoImage
```
@Parameter(label="Show skeleton analysis info image?",
           required=false,
           direction=IN,
           supplemental=true,
           dataIOOrder=0,
           description="If selected info image with skeleton data is shown.")
private boolean createSkeletonInfoImage
```
    Flag to enable drawing skeleton information to info image.
  - skeletonInfoImg
```
@Parameter(label="Skeleton data image",
           required=false,
           direction=OUT,
           supplemental=true,
           dataIOOrder=10,
           description="Skeleton data image.")
private transient MTBImageRGB skeletonInfoImg
```
    Info image for skeleton analysis.
  - 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
```
private Vector<Integer> labels
```
  - areas
```
private Vector<Double> areas
```
  - perimeters
```
private Vector<Double> perimeters
```
  - lengths
```
private Vector<Double> lengths
```
  - widths
```
private Vector<Double> widths
```
  - circularities
```
private Vector<Double> circularities
```
  - eccentricities
```
private Vector<Double> eccentricities
```
  - solidities
```
private Vector<Double> solidities
```
  - marginRoughnessValues
```
private Vector<Double> marginRoughnessValues
```
  - avgConcavities
```
private Vector<Double> avgConcavities
```
  - stdDevConcavities
```
private Vector<Double> stdDevConcavities
```
  - convexHullAreas
```
private Vector<Double> convexHullAreas
```
  - convexHullPerimeters
```
private Vector<Double> convexHullPerimeters
```
  - convexHullConvexities
```
private Vector<Double> convexHullConvexities
```
  - convexHullRoundnessValues
```
private Vector<Double> convexHullRoundnessValues
```
  - branchCounts
```
private Vector<Double> branchCounts
```
  - avgBranchLengths
```
private Vector<Double> avgBranchLengths
```
  - longestPathLengths
```
private Vector<Double> longestPathLengths
```
  - avgEndpointDistances
```
private Vector<Double> avgEndpointDistances
```
  - minCoreRegionWidths
```
private Vector<Double> minCoreRegionWidths
```
  - maxCoreRegionWidths
```
private Vector<Double> maxCoreRegionWidths
```
  - radiiMaxInscribedEmptyCircles
```
private Vector<Double> radiiMaxInscribedEmptyCircles
```
  - protrusionCounts
```
private Vector<Integer> protrusionCounts
```
  - nonProtrusionAreas
```
private Vector<Double> nonProtrusionAreas
```
  - avgProtrusionLengths
```
private Vector<Double> avgProtrusionLengths
```
  - avgApicalProtrusionLengths
```
private Vector<Double> avgApicalProtrusionLengths
```
  - avgBasalProtrusionLengths
```
private Vector<Double> avgBasalProtrusionLengths
```
  - avgBaselineProtrusionLengths
```
private Vector<Double> avgBaselineProtrusionLengths
```
  - avgEquatorProtrusionLengths
```
private Vector<Double> avgEquatorProtrusionLengths
```
  - avgIndentationLengths
```
private Vector<Double> avgIndentationLengths
```
  - avgApicalIndentationLengths
```
private Vector<Double> avgApicalIndentationLengths
```
  - avgBasalIndentationLengths
```
private Vector<Double> avgBasalIndentationLengths
```
  - avgBaselineIndentationLengths
```
private Vector<Double> avgBaselineIndentationLengths
```
  - avgEquatorIndentationLengths
```
private Vector<Double> avgEquatorIndentationLengths
```
  - inProDetails
```
private Vector<MorphologyAnalyzer2DInProData> inProDetails
```
    Vector with detailed result data on indentations and protrusions.
  - avgLobeDepths
```
private Vector<Double> avgLobeDepths
```
  - avgNeckDepths
```
private Vector<Double> avgNeckDepths
```
  - regions
```
private MTBRegion2DSet regions
```
  - labelImg
```
private MTBImage labelImg
```
  - width
```
private int width
```
    Width of currently processed image.
  - height
```
private int height
```
    Height of currently processed image.
- Constructor Detail
  - MorphologyAnalyzer2D
```
public MorphologyAnalyzer2D()
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
```
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  - MorphologyAnalyzer2D
```
public MorphologyAnalyzer2D(MTBImage labelImg)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
```
    constructor
    
    Parameters:
    
    labelImg - input label image
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  - MorphologyAnalyzer2D
```
public MorphologyAnalyzer2D(MTBRegion2DSet rs)
                     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
  - getSimpleShapeFeatures
```
private void getSimpleShapeFeatures()
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
    calculate several shape features in one method
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  - makeTable
```
private void makeTable()
```
    create result table
  - setLabelImage
```
public void setLabelImage(MTBImage img)
```
    Set input label image.
    
    Parameters:
    
    img - Label image to process.
  - getLabelImage
```
public MTBImage getLabelImage()
```
    Get the label image.
    If a label image is provided this method returns the input image, otherwise the internally generated label image is returned.
    
    Returns:
    
    Image with region labels.
  - setRegionSet
```
public void setRegionSet(MTBRegion2DSet regs)
```
    Set regions.
    
    Parameters:
    
    regs - Set of regions to process.
  - getDeltaXY
```
public Double getDeltaXY()
```
    Returns:
    
    Physical pixel length.
  - setDeltaXY
```
public void setDeltaXY(Double dXY)
```
    Parameters:
    
    dXY - physical pixel length in x-direction
  - getUnitXY
```
public String getUnitXY()
```
    Returns:
    
    physical space unit
  - setUnitXY
```
public void setUnitXY(String unitXY)
```
    Parameters:
    
    unitXY - tphysical space unit
  - calcArea
```
public boolean calcArea()
```
    Returns:
    
    are areas to be calculated
  - setCalcArea
```
public void setCalcArea(boolean calcArea)
```
    Parameters:
    
    calcAreas - should areas be calculated
  - calcPerimeter
```
public boolean calcPerimeter()
```
    Returns:
    
    are perimeters to be calculated
  - setCalcPerimeter
```
public void setCalcPerimeter(boolean calcPerimeter)
```
    Parameters:
    
    calcPerimeters - should perimeters be calculated
  - calcLengthWidth
```
public boolean calcLengthWidth()
```
    Returns:
    
    are lengths to be calculated
  - setCalcLengthWidth
```
public void setCalcLengthWidth(boolean flag)
```
    Turn of/off calculation of region length and width.
    The region length and width are defined as the lengths of the major and minor axes of the ellipse best fitting.
    The method is based on using moments of the region:
    \begin{eqnarray*} b(R) &=& 2 \cdot \sqrt{ \frac{2 \cdot (\mu_{2,0} + \mu_{0,2} \pm \sqrt{ (\mu_{2,0} - \mu_{0,2})^2 + 4 \cdot \mu_{1,1}^2 })} {\mu_{0,0}}} \end{eqnarray*}
    
    Parameters:
    
    flag - If true lengths of minor and major axis are calculated.
    
    See Also:
    
    MTBRegion2D
  - calcCircularity
```
public boolean calcCircularity()
```
    Returns:
    
    are circularities to be calculated
  - setCalcCircularity
```
public void setCalcCircularity(boolean flag)
```
    Turn of/off calculation of circularity.
    The circularity is calculated according to the following equation:
    \begin{eqnarray*} c(R) &=& \frac{4 \cdot \pi \cdot A(R)}{U(R) \cdot U(R)} \\ A(R) &:=& \text{area of the region}\\ U(R) &:=& \text{perimeter of the region} \end{eqnarray*}
    
    Parameters:
    
    flag - If true, circularity is calculated.
    
    See Also:
    
    MTBRegion2D
  - calcEccentricity
```
public boolean calcEccentricity()
```
    Returns:
    
    are eccentricities to be calculated
  - setCalcEccentricity
```
public void setCalcEccentricity(boolean flag)
```
    Turn of/off calculation of eccentricity.
    The eccentricity is calculated according to the following equation:
    \begin{eqnarray*} e(R) &=& \frac{(\mu_{2,0} - \mu_{0,2})^2 + 4 \cdot \mu_{1,1}^2} {(\mu_{2,0} + \mu_{0,2})^2} \end{eqnarray*}
    
    Parameters:
    
    flag - If true eccentricities are calculated.
    
    See Also:
    
    MTBRegion2D
  - setCalcSolidity
```
public void setCalcSolidity(boolean flag)
```
    Turn on/off calculation of solidities.
    The solidity is calculated according to the following equation:
    \begin{eqnarray*} s(R) &=& \frac{A(R)}{A_C(R)} \\ A(R) &:=& \text{area of the region}\\ A_C(R) &:=& \text{area of convex hull of the region} \end{eqnarray*}
    
    Parameters:
    
    flag - If true, solidities are calculated.
  - setCalcMarginRoughness
```
public void setCalcMarginRoughness(boolean flag)
```
    Turn on/off calculation of margin roughness values.
    
    Parameters:
    
    flag - If true, margin roughness values are calculated.
  - setAnalyzeProtrusionsAndIndentations
```
public void setAnalyzeProtrusionsAndIndentations(boolean flag)
```
    Turn on/off analysis of contour protrusions and indentations.
    The analysis of protrusions and indentations subsumes the overall count of protrusions, their average lengths and some more measures.
    
    Parameters:
    
    flag - If true, protrusion/indentation measures are extracted.
  - setMinimalCurvatureThreshold
```
public void setMinimalCurvatureThreshold(double c)
```
    Set minimal curvature threshold.
    
    Parameters:
    
    c - Minimal curvature.
  - setGaussianSigmaCurvatureSmoothing
```
public void setGaussianSigmaCurvatureSmoothing(double s)
```
    Set Gaussian standard deviation for smoothing curvature values.
    The smoothing affects the calculation of margin roughness and the analysis of lobes and necks.
    
    Parameters:
    
    s - Gaussian standard deviation to apply.
  - setMinimalLobeLength
```
public void setMinimalLobeLength(int m)
```
    Set minimal pixel count a lobe requires.
    Lobes with fewer pixels will be eliminated.
    
    Parameters:
    
    m - Minimal pixel count to apply.
  - setCalcSkeletonBranchFeatures
```
public void setCalcSkeletonBranchFeatures(boolean flag)
```
    Turn on/off calculation of skeleton branch features.
    The skeleton branch features subsume the total number of skeleton branches, their average length as well as the average radius of the lobes (approximated as the distance of branch endpoints from the background).
    
    Parameters:
    
    flag - If true, skeleton branch features are extracted.
  - setCalcConcavityData
```
public void setCalcConcavityData(boolean flag)
```
    Turn on/off calculation of concavity information.
    The method calculates the average concavity of all pixels on the region boundary as well as the standard deviation of concavities. For more information on the estimation of local contour concavity refer to the operator Contour2DConcavityCalculator.
    
    Parameters:
    
    flag - If true, concavity data is calculated.
  - setConcavityMaskSize
```
public void setConcavityMaskSize(int m)
```
    Specify size of local mask for concavity calculations.
    Refer to operator Contour2DConcavityCalculator for details.
    
    Parameters:
    
    m - Size of mask to apply.
  - setCalcConvexHullMeasures
```
public void setCalcConvexHullMeasures(boolean flag)
```
    Turn on/off calculation of convex hull measures.
    
    Parameters:
    
    flag - If true, convex hull measures are calculated.
  - setFractionalDigits
```
public void setFractionalDigits(int digits)
```
    specify the number of fractional digits for the results table
    
    Parameters:
    
    digits -
  - setDrawCurvatureInfoImage
```
public void setDrawCurvatureInfoImage(boolean flag)
```
    Enable/disable display of curvature info image.
    
    Parameters:
    
    flag - If true image is drawn and shown, otherwise not.
  - setDrawSkeletonInfoImage
```
public void setDrawSkeletonInfoImage(boolean flag)
```
    Enable/disable display of skeleton info image.
    
    Parameters:
    
    flag - If true image is drawn and shown, otherwise not.
  - getTable
```
public MTBTableModel getTable()
```
    Returns:
    
    result table
  - getDetailedInProResults
```
public Vector<MorphologyAnalyzer2DInProData> getDetailedInProResults()
```
    Access detailed information on indentations and protrusions.
    These data is only available if analyzeProtrusionsIndentations has been set to true.
    
    Returns:
    
    Vector of cell-wise indentation/protrusion information.
  - getCurvatureInfoImage
```
public MTBImageRGB getCurvatureInfoImage()
```
    Access info image about curvature analysis.
    
    Returns:
    
    Info image, only non-null if construction was enabled.
  - getSkeletonInfoImage
```
public MTBImageRGB getSkeletonInfoImage()
```
    Access info image about skeleton analysis.
    
    Returns:
    
    Info image, only non-null if construction was enabled.
  - analyzeLocalCurvatures
```
private void analyzeLocalCurvatures()
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
    Calculates and analyses pixel-wise local curvatures.
    The method extracts the following features:
    - Number of protrusions and indentations:
      The sum of all protrusions and indentations is equal to the number of inflection points found along the contour, and the number of protrusions and indentations, respectively, is each half of the total count of inflection points.
    - Protrusion and indentation measures:
      For each protrusion and indentation, respectively, various measures are extracted. The baseline of a protrusion or indentation is defined to be the line connecting the medial points of the neighboring protrusions in case of an indentation and of the neighboring indentations in case of a protrusion. If this line intersects with the background its endpoints are shifted along the region contour until a minimal number of backgroud pixels is touched while the shifts are kept as small as possible.
      In addition to the baseline also the equator of protrusions and indentations is extracted by drawing a line between the two inflection points defining the protrusion or indentation, respectively. The total length of a protrusion or indentation, and the apical and basal lengths are calculated by calculating the largest distance of any point of the baseline to the region contour. Then the intersection point of this distance line with the equator is found which splits the distance line. The length of the upper part of this line is denoted the apical length of the protrusion/indentation and the length of the lower part is denoted the basal length of the protrusion/indentation.
    - Margin roughness:
      The implementation of margin roughness is derived from the following paper T. McLellan, J. Endler, The Relative Success of Some Methods for Measuring and Describing the Shape of Complex Objects, Systematic Biology, Vol. 47, No. 2, pp. 264-281, June 1998.
      
      The margin roughness analyzes local curvature in terms of the differences in orientation of tangents at neighboring pixels on the contour. It first calculates pairwise orientation differences and the average of all differences along the contour. This average value is then compared to the average angular difference to be expected for tangents located on a perfect circle being sampled with the same number of points as the given contour. Thus, the margin roughness yields a measure for the deviation of the contour curvature from an optimal circle.
      The margin roughness MR for a contour C is here defined as follows:
      
      \begin{eqnarray*} MR(C) &=& \left( \frac{1}{N} \sum_{i=1}^{N} |A_i| \right) - \frac{360}{N}\\ N &:=& \text{Number of points on the contour} \\ A_i &:=& \text{Difference in tangent orientations between point $i$ and its neighbors} \end{eqnarray*}
      
      Note that the calculation of the tangent orientations is not the same as in the original paper.
      Here we use an algorithm of Freeman, see Contour2DCurvatureCalculator for details.
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.
    
    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with the processing history.
  - calculateConcavityData
```
private void calculateConcavityData()
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
    Extracts average concavity and standard deviation of concavities.
    For details about concavity calculation refer to Contour2DConcavityCalculator.
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.
    
    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with processing history.
  - calculateConvexHulls
```
private void calculateConvexHulls()
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
    Calculates convex hull areas and perimeters.
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.
    
    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException - Thrown in case of problems with processing history.
  - calculateSolidityValues
```
private void calculateSolidityValues()
```
    Calculates solidity values.
  - calculateConvexHullMeasures
```
private void calculateConvexHullMeasures()
```
    Calculates convex hull convexities and roundnesses.
  - getCalibration
```
private void getCalibration()
```
  - callbackCurvature
```
private void callbackCurvature()
```
    Callback function called in case of changes of parameters analyzeProtrusionsIndentations or calcMarginRoughness.
  - callbackArea
```
private void callbackArea()
```
    Callback function called in case of changes of parameter calcArea.
  - callbackSolidity
```
private void callbackSolidity()
```
    Callback function called in case of changes of parameter calcSolidity.
  - callbackConcavity
```
private void callbackConcavity()
```
    Callback function called in case of changes of parameter calcConcavityData.

Class MorphologyAnalyzer2D

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

Field Summary

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

Field Detail

operatorID

inLabelImg

inRegions

deltaXY

unitXY

calcArea

calcPerimeter

calcLengthWidth

calcCircularity

calcEccentricity

calcSolidity

calcMarginRoughness

analyzeProtrusionsIndentations

minimalCurvature

gaussianSigma

minProtrusionLength

minIndentationLength

calcSkeletonBranchFeatures

calcConcavityData

concavityMaskSize

calcConvexHullMeasures

fracDigits

createCurvatureInfoImage

curvatureInfoImg

createSkeletonInfoImage

skeletonInfoImg

table

nf

bgLabel

labels

areas

perimeters

lengths

widths

circularities

eccentricities

solidities

marginRoughnessValues

avgConcavities

stdDevConcavities

convexHullAreas

convexHullPerimeters

convexHullConvexities

convexHullRoundnessValues

branchCounts

avgBranchLengths

longestPathLengths

avgEndpointDistances

minCoreRegionWidths

maxCoreRegionWidths

radiiMaxInscribedEmptyCircles

protrusionCounts

nonProtrusionAreas

avgProtrusionLengths

avgApicalProtrusionLengths

avgBasalProtrusionLengths

avgBaselineProtrusionLengths

avgEquatorProtrusionLengths

avgIndentationLengths

avgApicalIndentationLengths

avgBasalIndentationLengths

avgBaselineIndentationLengths

avgEquatorIndentationLengths

inProDetails

avgLobeDepths

avgNeckDepths

regions

labelImg

width