XylemGrower (mitobo 2.0 API)

java.lang.Object
- de.unihalle.informatik.Alida.operator.ALDOperator
- - de.unihalle.informatik.MiToBo.core.operator.MTBOperator
  - - de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener
```
@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              shortDescription="Implements region growing for xylem segmentation.")
public class XylemGrower
extends MTBOperator
```
This operators implements region growing for xylem segmentation.
Prerequisite is HS[X]-image (hue, saturation, intensity/value/brightness) as the input and some thresholds to control the growing process and an initial segmentation of xylem regions supplied as a binary image.
All three channels of the hs[x] image are assume to be a byte image and values in the range 0 - 255.
The initial regions are eroded to get seed regions, where we determine the mean-value of the hue and/or saturation and/or I/V/B-channel.
Subsequently the region are grown via region growing. We compare each pixel of the contour of those seed regions with the pixel of the background beside them, either in a 4-neighbourhood or an 8-neighbourhood.
This is repeated until the list of uninspected pixel is not empty. Afterwards we may do some post processing. E.G. calculate gradient informations on the found regions to split regions who contain more then one xylem.

Author:

Tim Langhammer, Halle/Saale, Europe , posch

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`XylemGrower.GrowingMode` The region growing modus.
`private class`	`XylemGrower.GrowingRegion2D` This class is responsible for the growing of a single MTBRegion2D which is the result of the preprocessing steps.
`static class`	`XylemGrower.Neighbourhood` The kind of neighbourhood to inspect a pixel.
`static class`	`XylemGrower.SortMode` Sort Mode for different MTBRegion2D's.

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_erodeSize` Default size of the structuring element to erode the image
`static double`	`DEFAULT_hueThresh` Default hue threshold
`static XylemGrower.GrowingMode`	`DEFAULT_linkageMode` Default linkage mode for growing
`static int`	`DEFAULT_minAreaPostProcessing` Minimum area of a region in post processing.
`static int`	`DEFAULT_minAreaSeedRegions` Default minimum area for a region to be further eroded
`static XylemGrower.Neighbourhood`	`DEFAULT_neighbourhood` Default neighborhood for growing
`static int`	`DEFAULT_openingSESize` Default size of structuring element for opening (post processing)
`static double`	`DEFAULT_satThresh` Default saturation threshold
`static double`	`DEFAULT_xThresh` Default intensity threshold
`private int`	`erodeSize` The size of the structuring element for erosion to compute seed regions.
`private MTBImageByte`	`grownRegions` Resulting regions from growing.
`private double`	`hueThresh` The hue threshold.
`private MTBImageByte`	`initialSegmentation` Initial segmentation of xylem regions.
`private XylemGrower.GrowingMode`	`linkageMode` The algorithm we use to link new pixels to the region.
`private static int`	`MIN_SE_SIZE` Minimum size of an SE.
`private int`	`minAreaPostProcessing` The minimum size of a `MTBRegion2D` to not be removed (after opening the grown regions).
`private int`	`minAreaSeedRegions` The minimum size of a `MTBRegion2D` to further erode when computing seed regions.
`private XylemGrower.Neighbourhood`	`neighbourhood` The neighbourhood mode to inspect new pixel.
`private int`	`openingSESize` The minimum size of a `MTBRegion2D` before erosion.
`private MTBTableModel`	`resultsTable` A table containing information for each region
`private MTBImageByte`	`resultXylemRegions` Final xylem regions after post processing.
`private double`	`satThresh` The saturation threshold.
`private MTBImageByte`	`seedRegions` The seed regions as a binary image after the final erosion.
`private int`	`sizeX`
`private int`	`sizeY`
`private double`	`xThresh` The Intensity/Brightness/Value threshold.
`private MTBImageByte`	`xylemHsxImage` HS(X)-Color Channel Image.

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

Constructor Summary

Constructors
Constructor and Description
`XylemGrower()` Default Constructor.
`XylemGrower(MTBImageByte binaryImage, MTBImageByte hsxImage, XylemGrower.GrowingMode linkageMode)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private List<MTBRegion2D>`	`createSeedRegions(MTBImageByte imageToErode, int minimumPixelPerArea, int sizeOfStructuringElement)` Create seed regions from the intial segmentation.
`private void`	`deleteRegionFromImage(MTBImageByte prelabeledImage, MTBRegion2D regionToClear)` Set pixels of the points contained in the given region to `0(zero)`.
`(package private) static MTBImage`	`erodeImageWithCircle(MTBImage image, int sizeOfSE)` Erode an image of type `MTBImageByte`.
`String`	`getDocumentation()`
`int`	`getErodeSize()` The size of the eroding element.
`MTBImageByte`	`getGrownRegions()` Returns a `MTBImageByte` image after growing.
`double`	`getHueThresh()` Return the treshold for the hue channel.
`MTBImage`	`getInitialSegmentation()`
`XylemGrower.GrowingMode`	`getLinkageMode()`
`int`	`getminAreaSeedRegions()`
`int`	`getMinRegionArea()`
`XylemGrower.Neighbourhood`	`getNeighbourhood()`
`int`	`getOpeningSESize()`
`MTBTableModel`	`getResultsTable()`
`MTBImageByte`	`getResultXylemRegions()` Return the binary image after the post processing of the grown region image.
`double`	`getSatTresh()`
`MTBImageByte`	`getSeedRegions()`
`double`	`getXThresh()` The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
`MTBImage`	`getXylemImage()` Return the Hue/Saturation/{Intensity\|Brightness\|Value}-`MTBImage`.
`(package private) static MTBRegion2DSet`	`labelComponentsOfImage(MTBImage image)` Label a MTBImage.
`private MTBTableModel`	`makeTable(MTBRegion2DSet regionSet, MTBImage labelImg, int imgWidth, int imgHeight)` create results table
`private static MTBImage`	`openByteImageWithCircle(MTBImage image, int sizeOfSE)` Open an image of type `MTBImageByte`.
`protected void`	`operate()`
`private MTBImageByte`	`postProcessAfterGrowing(MTBImageByte grownRegionBinImage)` Here we do some morphological operations to the shape of the regions from the region growing of XylemGrower.
`static String`	`printReadabeTimeInfo(long cTime)`
`private static boolean`	`regionTouchesBoundary(MTBRegion2D region2D, int width, int height)` Test whether a region is located at, i.e. touches, the boundary of the image.
`private void`	`relabelRegion(MTBImageByte preLabeledImage, MTBRegion2D region)` Set the unique id of the given region to the pixel value found at the coordinate of the first pixel in the region on the pre labeled `MTBImageByte`.
`private static MTBImage`	`removeSmallComponents(MTBImageByte image, int minimalArea)` Remove small componentes from an image of type `MTBImageByte`.
`void`	`setErodSize(int size)` Set the size of the eroding element in pixel.
`void`	`setGrownRegions(MTBImageByte imageByte)`
`void`	`setHueThresh(double hueThresh)`
`void`	`setInitalSegmentation(MTBImageByte image)`
`void`	`setLinkageMode(XylemGrower.GrowingMode linkageMode)`
`void`	`setminAreaSeedRegions(int minAreaSeedRegions)`
`void`	`setMinRegionArea(int minAreaPostProcessing)`
`void`	`setNeighbourhood(XylemGrower.Neighbourhood nb)`
`void`	`setOpeningSESize(int size)`
`void`	`setResultsTable(MTBTableModel resultsTable)`
`void`	`setSatTresh(double satTresh)`
`void`	`setSeedImage(MTBImageByte seedRegions)`
`void`	`setXThresh(double xThresh)` Set the Intensity/Brighntness/Value-Parameter (depending on the used input image type).
`void`	`setXylemImage(MTBImageByte hsxMTBImage)` Set the Hue/Saturation/{Intensity\|Brightness\|Value}-`MTBImage`.
`void`	`setXylemResultRegions(MTBImageByte regions)` Set the binary image after the morphological processing on the grown region image.
`private static Collection<MTBRegion2D>`	`sortRegionSetBy(MTBRegion2DSet regionSet, XylemGrower.SortMode sortMode)`
`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, 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

DEFAULT_erodeSize
```
public static final int DEFAULT_erodeSize
```
Default size of the structuring element to erode the image

See Also:

Constant Field Values

DEFAULT_minAreaSeedRegions
```
public static final int DEFAULT_minAreaSeedRegions
```
Default minimum area for a region to be further eroded

See Also:

Constant Field Values

DEFAULT_linkageMode

public static final XylemGrower.GrowingMode DEFAULT_linkageMode

Default linkage mode for growing

DEFAULT_hueThresh
```
public static final double DEFAULT_hueThresh
```
Default hue threshold

See Also:

Constant Field Values

DEFAULT_satThresh
```
public static final double DEFAULT_satThresh
```
Default saturation threshold

See Also:

Constant Field Values

DEFAULT_xThresh
```
public static final double DEFAULT_xThresh
```
Default intensity threshold

See Also:

Constant Field Values

DEFAULT_neighbourhood

public static final XylemGrower.Neighbourhood DEFAULT_neighbourhood

Default neighborhood for growing

DEFAULT_openingSESize
```
public static final int DEFAULT_openingSESize
```
Default size of structuring element for opening (post processing)

See Also:

Constant Field Values

DEFAULT_minAreaPostProcessing
```
public static final int DEFAULT_minAreaPostProcessing
```
Minimum area of a region in post processing.

See Also:

Constant Field Values

MIN_SE_SIZE
```
private static final int MIN_SE_SIZE
```
Minimum size of an SE.

See Also:

Constant Field Values

xylemHsxImage

@Parameter(label="XylemImageHSX",
           required=true,
           dataIOOrder=0,
           direction=IN,
           description="Xylem image as HSX-image")
private transient MTBImageByte xylemHsxImage

HS(X)-Color Channel Image.

Should be of type {

initialSegmentation

@Parameter(label="Inital segmentation",
           required=true,
           dataIOOrder=1,
           direction=IN,
           description="Initial segmentation as a binary image")
private transient MTBImageByte initialSegmentation

Initial segmentation of xylem regions.

erodeSize

@Parameter(label="SizeErosion",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="Size of structuring element for ersion to compute seed regions",
           mode=ADVANCED)
private int erodeSize

The size of the structuring element for erosion to compute seed regions. If ErodeMode is set to Dynamic, you should use a small size. Otherwise use a size >= 20.

minAreaSeedRegions

@Parameter(label="MinAreaToErode",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="Minimal size of a region for further erosion of seed regions",
           mode=ADVANCED)
private int minAreaSeedRegions

The minimum size of a MTBRegion2D to further erode when computing seed regions.

linkageMode

@Parameter(label="The growing mode",
           required=true,
           dataIOOrder=5,
           direction=IN,
           description="The method for growing the region")
private XylemGrower.GrowingMode linkageMode

The algorithm we use to link new pixels to the region.

hueThresh

@Parameter(label="HueThreshold",
           required=true,
           dataIOOrder=6,
           direction=IN,
           description="Hue channel threshold")
private double hueThresh

The hue threshold.

Indicates whether a new pixel is part of a region or not, depending on growing algorithm.

satThresh

@Parameter(label="SaturationThreshold",
           required=true,
           dataIOOrder=7,
           direction=IN,
           description="Saturation channel threshold")
private double satThresh

The saturation threshold.

Indicates whether a new pixel is part of a region or not, depending on growing algorithm.

xThresh
```
@Parameter(label="XThreshold",
           required=true,
           dataIOOrder=8,
           direction=IN,
           description="Intensity channel threshold")
private double xThresh
```
The Intensity/Brightness/Value threshold.
Indicated whether a pixel is part of a region. Since we calculate the derivation of the mean of the regions value, this can be set to arbitrary values > 0.

neighbourhood

@Parameter(label="Neighbourhood used",
           required=false,
           dataIOOrder=9,
           direction=IN,
           description="The neighbourhood for the pixel to visit",
           mode=ADVANCED)
private XylemGrower.Neighbourhood neighbourhood

The neighbourhood mode to inspect new pixel.

openingSESize

@Parameter(label="SizeOpening (post processing)",
           required=true,
           dataIOOrder=10,
           direction=IN,
           description="Size of SE for opening (post processing)")
private int openingSESize

The minimum size of a MTBRegion2D before erosion.

minAreaPostProcessing

@Parameter(label="MinArea (post processing)",
           required=true,
           dataIOOrder=11,
           direction=IN,
           description="Minimal area of a region (post processing of growing)")
private int minAreaPostProcessing

The minimum size of a MTBRegion2D to not be removed (after opening the grown regions).

resultXylemRegions

@Parameter(label="Resulting Xylem Regions",
           dataIOOrder=1,
           direction=OUT,
           description="Final xylem regions after post processing")
private transient MTBImageByte resultXylemRegions

Final xylem regions after post processing.

resultsTable

@Parameter(label="results table",
           required=true,
           direction=OUT,
           dataIOOrder=2,
           supplemental=false,
           description="table containing the resulting values")
private MTBTableModel resultsTable

A table containing information for each region

seedRegions

@Parameter(label="Seed Regions",
           required=true,
           supplemental=true,
           direction=OUT,
           dataIOOrder=4,
           description="Seed regions from erosion")
private MTBImageByte seedRegions

The seed regions as a binary image after the final erosion.

grownRegions

@Parameter(label="GrownRegions",
           required=true,
           dataIOOrder=5,
           supplemental=true,
           direction=OUT,
           description="regions from growing")
private transient MTBImageByte grownRegions

Resulting regions from growing.

Each region is identified by its own id ( possible not unique ).

sizeX
```
private int sizeX
```

sizeY
```
private int sizeY
```

Constructor Detail

XylemGrower

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

Default Constructor.

Throws:: de.unihalle.informatik.Alida.exceptions.ALDOperatorException

XylemGrower

public XylemGrower(MTBImageByte binaryImage,
                   MTBImageByte hsxImage,
                   XylemGrower.GrowingMode linkageMode)
            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:: binaryImage -; hsxImage -; linkageMode -
Throws:: de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail
- 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
- 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
- makeTable
```
private MTBTableModel makeTable(MTBRegion2DSet regionSet,
                                MTBImage labelImg,
                                int imgWidth,
                                int imgHeight)
```
  create results table
  
  Parameters:
  
  labelImg -
  
  sizeY2 -
  
  sizeX2 -
  
  ppRSet -
  
  Returns:
  
  table containing the results
- postProcessAfterGrowing
```
private MTBImageByte postProcessAfterGrowing(MTBImageByte grownRegionBinImage)
                                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Here we do some morphological operations to the shape of the regions from the region growing of XylemGrower.
  
  Parameters:
  
  grownRegionBinImage -
  
  Returns:
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- deleteRegionFromImage
```
private void deleteRegionFromImage(MTBImageByte prelabeledImage,
                                   MTBRegion2D regionToClear)
```
  Set pixels of the points contained in the given region to 0(zero).
  
  Parameters:
  
  prelabeledImage - The MTBImageByte image with prelabeled regions in it.
  
  regionToClear - The MTBRegion2D region do delete from the prelabeledImage.
- createSeedRegions
```
private List<MTBRegion2D> createSeedRegions(MTBImageByte imageToErode,
                                            int minimumPixelPerArea,
                                            int sizeOfStructuringElement)
                                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                            de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Create seed regions from the intial segmentation.
  The workflow:
  i) we label our raw input image, to get the initial regions we want to erode.
  ii) we set a unique id for each region
  { until there are regions to erode left ( area > minAreaSize )
  iii) we erode the image and relabel the result.
  iv) we put for each pixel of all eroded regions the id of the regions before erosion, to preserve the
  id's even if regions are splitted.
  - optional :
  v) if there are erased regions - we put the region before erasure to the list of regions to grow ( if set )
  } - optional :
  vi) we join splitted regions ( if set )
  Step iii-v in detail:
  After we erode the image and label it we look at first for erased region! We can't put the code for removing small regions in the same loop, because those removed regions( by us ) are handled as erased regions( by the morpho op ) in the next step!
  So don't change this order!
  
  Parameters:
  
  regionsBeforeErodeSet - The regions after the opening.
  
  regionsAfterErodeSet - The regions after the following erosion.
  
  Returns:
  
  A MTBRegion2DSet of the possible erased regions.
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
  
  See Also:
  
  labelComponentsOfImage(de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage), #erodeImage(de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage, int), relabelRegion(de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte, de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D)
- erodeImageWithCircle
```
static MTBImage erodeImageWithCircle(MTBImage image,
                                     int sizeOfSE)
                              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                     de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Erode an image of type MTBImageByte.
  
  Parameters:
  
  image - The MTBImage to erode.
  
  sizeOfSE - The size of the structuring element ( >= 1 )
  
  Returns:
  
  The eroded MTBImage image.
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- openByteImageWithCircle
```
private static MTBImage openByteImageWithCircle(MTBImage image,
                                                int sizeOfSE)
                                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Open an image of type MTBImageByte.
  
  Parameters:
  
  image -
  
  sizeOfSE -
  
  Returns:
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- removeSmallComponents
```
private static MTBImage removeSmallComponents(MTBImageByte image,
                                              int minimalArea)
                                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Remove small componentes from an image of type MTBImageByte.
  
  Parameters:
  
  image -
  
  minimalArea -
  
  Returns:
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
- regionTouchesBoundary
```
private static boolean regionTouchesBoundary(MTBRegion2D region2D,
                                             int width,
                                             int height)
```
  Test whether a region is located at, i.e. touches, the boundary of the image.
  
  Parameters:
  
  region2D -
  
  width -
  
  height -
  
  Returns:
  
  true if region touches the boundary
- labelComponentsOfImage
```
static MTBRegion2DSet labelComponentsOfImage(MTBImage image)
                                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
```
  Label a MTBImage.
  
  Parameters:
  
  image - The MTBImage to label.
  
  Returns:
  
  The resulting MTBRegion2DSet.
  
  Throws:
  
  de.unihalle.informatik.Alida.exceptions.ALDOperatorException
  
  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
  
  See Also:
  
  LabelComponentsSequential
- relabelRegion
```
private void relabelRegion(MTBImageByte preLabeledImage,
                           MTBRegion2D region)
```
  Set the unique id of the given region to the pixel value found at the coordinate of the first pixel in the region on the pre labeled MTBImageByte.
  
  Parameters:
  
  preLabeledImage - The MTBImageByte image we fetch the wished id from.
  
  region - The MTBRegion2D region to set the found id to.
- sortRegionSetBy
```
private static Collection<MTBRegion2D> sortRegionSetBy(MTBRegion2DSet regionSet,
                                                       XylemGrower.SortMode sortMode)
```
  Parameters:
  
  regionSet -
  
  sortMode -
  
  Returns:
- printReadabeTimeInfo
```
public static String printReadabeTimeInfo(long cTime)
```
- getInitialSegmentation
```
public MTBImage getInitialSegmentation()
```
  Returns:
- setInitalSegmentation
```
public void setInitalSegmentation(MTBImageByte image)
```
  Parameters:
  
  image -
- setErodSize
```
public void setErodSize(int size)
```
  Set the size of the eroding element in pixel.
  
  Parameters:
  
  size - The site of the structuring element used for erosion in pixel.
- getErodeSize
```
public int getErodeSize()
```
  The size of the eroding element.
  
  Returns:
  
  The size of the eroding element in pixel.
- getXylemImage
```
public MTBImage getXylemImage()
```
  Return the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
  
  Returns:
- setXylemImage
```
public void setXylemImage(MTBImageByte hsxMTBImage)
```
  Set the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
  
  Parameters:
  
  hsxMTBImage -
- getResultXylemRegions
```
public MTBImageByte getResultXylemRegions()
```
  Return the binary image after the post processing of the grown region image.
  
  Returns:
- setXylemResultRegions
```
public void setXylemResultRegions(MTBImageByte regions)
```
  Set the binary image after the morphological processing on the grown region image.
  
  Parameters:
  
  regions -
- getResultsTable
```
public MTBTableModel getResultsTable()
```
  Returns:
  
  the resultsTable
- setResultsTable
```
public void setResultsTable(MTBTableModel resultsTable)
```
  Parameters:
  
  resultsTable - the resultsTable to set
- getHueThresh
```
public double getHueThresh()
```
  Return the treshold for the hue channel.
  
  Returns:
- setHueThresh
```
public void setHueThresh(double hueThresh)
```
  Parameters:
  
  hueThresh -
- getLinkageMode
```
public XylemGrower.GrowingMode getLinkageMode()
```
  Returns:
- setLinkageMode
```
public void setLinkageMode(XylemGrower.GrowingMode linkageMode)
```
  Parameters:
  
  linkageMode -
- getminAreaSeedRegions
```
public int getminAreaSeedRegions()
```
  Returns:
- setminAreaSeedRegions
```
public void setminAreaSeedRegions(int minAreaSeedRegions)
```
  Parameters:
  
  minAreaSeedRegions -
- getNeighbourhood
```
public XylemGrower.Neighbourhood getNeighbourhood()
```
  Returns:
- setNeighbourhood
```
public void setNeighbourhood(XylemGrower.Neighbourhood nb)
```
  Parameters:
  
  nb -
- getGrownRegions
```
public MTBImageByte getGrownRegions()
```
  Returns a MTBImageByte image after growing.
  
  Returns:
- setGrownRegions
```
public void setGrownRegions(MTBImageByte imageByte)
```
  Parameters:
  
  imageByte -
- getSatTresh
```
public double getSatTresh()
```
  Returns:
- setSatTresh
```
public void setSatTresh(double satTresh)
```
  Parameters:
  
  satTresh -
- getSeedRegions
```
public MTBImageByte getSeedRegions()
```
  Returns:
- setSeedImage
```
public void setSeedImage(MTBImageByte seedRegions)
```
  Parameters:
  
  seedRegions -
- getXThresh
```
public double getXThresh()
```
  The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
  
  Returns:
  
  The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
- setXThresh
```
public void setXThresh(double xThresh)
```
  Set the Intensity/Brighntness/Value-Parameter (depending on the used input image type).
  
  Parameters:
  
  xThresh - The threshold for the intensity/brightness/value.
- getOpeningSESize
```
public int getOpeningSESize()
```
  Returns:
- setOpeningSESize
```
public void setOpeningSESize(int size)
```
  Parameters:
  
  size -
- getMinRegionArea
```
public int getMinRegionArea()
```
- setMinRegionArea
```
public void setMinRegionArea(int minAreaPostProcessing)
```
- getDocumentation
```
public String getDocumentation()
```
  Overrides:
  
  getDocumentation in class de.unihalle.informatik.Alida.operator.ALDOperator

Class XylemGrower

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

DEFAULT_erodeSize

DEFAULT_minAreaSeedRegions

DEFAULT_linkageMode

DEFAULT_hueThresh

DEFAULT_satThresh

DEFAULT_xThresh

DEFAULT_neighbourhood

DEFAULT_openingSESize

DEFAULT_minAreaPostProcessing

MIN_SE_SIZE

xylemHsxImage

initialSegmentation

erodeSize

minAreaSeedRegions

linkageMode

hueThresh

satThresh

xThresh

neighbourhood

openingSESize

minAreaPostProcessing

resultXylemRegions

resultsTable

seedRegions

grownRegions

sizeX

sizeY

Constructor Detail

XylemGrower

XylemGrower

Method Detail

validateCustom

operate

makeTable

postProcessAfterGrowing

deleteRegionFromImage

createSeedRegions

erodeImageWithCircle

openByteImageWithCircle

removeSmallComponents

regionTouchesBoundary

labelComponentsOfImage

relabelRegion

sortRegionSetBy

printReadabeTimeInfo

getInitialSegmentation

setInitalSegmentation

setErodSize

getErodeSize

getXylemImage

setXylemImage

getResultXylemRegions

setXylemResultRegions

getResultsTable

setResultsTable

getHueThresh

setHueThresh

getLinkageMode

setLinkageMode

getminAreaSeedRegions

setminAreaSeedRegions

getNeighbourhood

setNeighbourhood

getGrownRegions

setGrownRegions

getSatTresh

setSatTresh

getSeedRegions

setSeedImage