de.unihalle.informatik.MiToBo.apps.xylem

Class XylemDetector

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              shortDescription="Implements xylem detection in RGB or HSX images.")
public class XylemDetector
extends MTBOperator

This operator implements xylem detection in RGB or HSX images.

Author:

posch

Nested Class Summary

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

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
private Boolean	createContourOverlay
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	initialSegmentationOut Initial segmentation of xylem regions computed of supplied
private XylemGrower.GrowingMode	linkageMode The algorithm we use to link new pixels to the region.
private int	minAreaAfterOpeningInitSeg Minimal area (in pixels) of a region required after opening.
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 double	minCompactnessInitSeg Minimal compactness of a region required after opening.
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 postprocessing.
private double	satThresh The saturation threshold.
private MTBImageByte	seedRegions The seed regions as a binary image after the final erosion.
private int	seOpeningSizeInitSeg Size of the structuring element for Opening.
private Double	timing Consumed time in seconds where TimingMode states if this reflect user or real time.
private String	timingMode Timing mode, may be user time or real time.
private double	xThresh The Intensity/Brightness/Value threshold.
private MTBImageByte	xylemHsxImage HS(X)-Color Channel Image.
private MTBImage	xylemRegionsOverlay Resulting regions from growing.
private MTBImageRGB	xylemRGBImage RGB-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
XylemDetector() Default Constructor.

Method Summary

Modifier and Type	Method and Description
private MTBImage	createOverlay()
String	getDocumentation()
protected void	operate()
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

xylemRGBImage

@Parameter(label="XylemImageRGB",
           required=false,
           dataIOOrder=0,
           direction=IN,
           description="Xylem image as RGB-image")
private transient MTBImageRGB xylemRGBImage

RGB-Color Channel Image.

xylemHsxImage

@Parameter(label="XylemImageHSX",
           required=false,
           dataIOOrder=1,
           direction=IN,
           description="Xylem image as HSX-image")
private transient MTBImageByte xylemHsxImage

HS(X)-Color Channel Image.

Should be of type {

createContourOverlay

@Parameter(label="XylemcreateContourOverlayImageHSX",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="Create overlay image with xylem contours on initial image")
private Boolean createContourOverlay

seOpeningSizeInitSeg

@Parameter(label="SizeOpening (InitSeg)",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="The size of the structuring element for the opening (initial segmentation)",
           mode=ADVANCED)
private int seOpeningSizeInitSeg

Size of the structuring element for Opening.

minAreaAfterOpeningInitSeg

@Parameter(label="MinRegionSize (InitSeg)",
           required=false,
           dataIOOrder=4,
           direction=IN,
           description="The minimal size of the region required after opening (initial segmentation)",
           mode=ADVANCED)
private int minAreaAfterOpeningInitSeg

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

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

minCompactnessInitSeg

@Parameter(label="MinCompactness (InitSeg)",
           required=false,
           dataIOOrder=5,
           direction=IN,
           description="The minimal compactness of the region required after opening (initial segmentation)",
           mode=ADVANCED)
private double minCompactnessInitSeg

Minimal compactness of a region required after opening.

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

erodeSize

@Parameter(label="SizeErosion (growing)",
           required=false,
           dataIOOrder=6,
           direction=IN,
           description="Size of structuring element for ersion to compute seed regions (Growing)",
           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 (growing)",
           required=false,
           dataIOOrder=7,
           direction=IN,
           description="Minimal size of a region for further erosion of seed regions (Growing)",
           mode=ADVANCED)
private int minAreaSeedRegions

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

linkageMode

@Parameter(label="GrowingMode",
           required=true,
           dataIOOrder=8,
           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=9,
           direction=IN,
           description="Intensity 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=10,
           direction=IN,
           description="Intensity 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=11,
           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 (growing)",
           required=false,
           dataIOOrder=12,
           direction=IN,
           description="The neighbourhood for the pixel to visit (Growing)",
           mode=ADVANCED)
private XylemGrower.Neighbourhood neighbourhood

The neighbourhood mode to inspect new pixel.

openingSESize

@Parameter(label="SizeOpening (postprocessing growing)",
           required=true,
           dataIOOrder=13,
           direction=IN,
           description="Size of SE for opening (post processing of growing)")
private int openingSESize

The minimum size of a MTBRegion2D before erosion.

minAreaPostProcessing

@Parameter(label="MinArea (postprocessing growing)",
           required=true,
           dataIOOrder=14,
           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="XylemRegions",
           dataIOOrder=1,
           direction=OUT,
           description="Final xylem regions after postprocessing")
private transient MTBImageByte resultXylemRegions

Final xylem regions after postprocessing.

resultsTable

@Parameter(label="ResultTable",
           required=true,
           direction=OUT,
           dataIOOrder=2,
           supplemental=false,
           description="Table containing the features for each xylem")
private MTBTableModel resultsTable

A table containing information for each region

initialSegmentationOut

@Parameter(label="InitalSegmentation",
           dataIOOrder=3,
           direction=OUT,
           description="Initial segmentation as a binary image")
private transient MTBImageByte initialSegmentationOut

Initial segmentation of xylem regions computed of supplied

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 ).

xylemRegionsOverlay

@Parameter(label="XylemRegionOverlay",
           required=false,
           dataIOOrder=6,
           supplemental=true,
           direction=OUT,
           description="Xylem contours overlay in original image to segment")
private transient MTBImage xylemRegionsOverlay

Resulting regions from growing.

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

timing

@Parameter(label="Timing",
           dataIOOrder=10,
           supplemental=true,
           direction=OUT,
           description="Consumed time in seconds")
private Double timing

Consumed time in seconds where TimingMode states if this reflect user or real time.

timingMode

@Parameter(label="TimingMode",
           dataIOOrder=11,
           supplemental=true,
           direction=OUT,
           description="Timing Mode of timing")
private String timingMode

Timing mode, may be user time or real time.

Constructor Detail

XylemDetector

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

Default Constructor.

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

createOverlay

private MTBImage createOverlay()
                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                               de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getDocumentation

public String getDocumentation()

Overrides:

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