de.unihalle.informatik.MiToBo.segmentation.evaluation.measures

Class PreprocessLabelImages

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.evaluation.measures.PreprocessLabelImages

All Implemented Interfaces:

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

public class PreprocessLabelImages
extends MTBOperator

Helper class to preprocess label images for segmentation evaluation.

This class extracts the intensity values of regions in label images as well as the regions' contours.

Author:

Birgit Moeller, Felix Knispel

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
protected ArrayList<ArrayList<Point>>	gtContours List of contours of groudtruth objects.
protected MTBImage	gtImage Groundtruth labeling.
protected ArrayList<Integer>	gtLabels List of labels of groundtruth regions.
protected ArrayList<ArrayList<Point>>	segContours List of contours of segmented objects.
protected MTBImage	segImage Label image of segmentation result.
protected ArrayList<Integer>	segLabels List of labels of segmented regions.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
PreprocessLabelImages() Default constructor.
PreprocessLabelImages(MTBImage gtImg, MTBImage segImg, ArrayList<Integer> sLabels, ArrayList<Integer> gLabels) Constructor.

Method Summary

Modifier and Type	Method and Description
private boolean[][]	CollectContoursStageOne(MTBImage img, ArrayList<Integer> regions) This method collects all contour pixels for a region in a given MTBImage.
private void	CollectContoursStageTwo(MTBImage img, ArrayList<Integer> regions, ArrayList<ArrayList<Point>> contours, boolean[][] isContour) This method implements the final stage of the contour detection.
ArrayList<ArrayList<Point>>	getGtContours() Get list of groundtruth contours.
ArrayList<ArrayList<Point>>	getSegContours() Get list of segmentation contours.
protected void	operate() This method initializes all required components.
void	validateCustom()

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

readResolve

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

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

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

Field Detail

segImage

@Parameter(label="Segmentation label image",
           required=true,
           direction=IN,
           description="Segmentation result label image.")
protected transient MTBImage segImage

Label image of segmentation result.

gtImage

@Parameter(label="Groundtruth label image",
           required=true,
           direction=IN,
           description="Groundtruth label image.")
protected transient MTBImage gtImage

Groundtruth labeling.

segLabels

@Parameter(label="Segmented Region Labels",
           direction=IN,
           description="Segmented Region Labels.")
protected transient ArrayList<Integer> segLabels

List of labels of segmented regions.

gtLabels

@Parameter(label="Groundtruth Region Labels",
           direction=IN,
           description="Groundtruth Labels.")
protected transient ArrayList<Integer> gtLabels

List of labels of groundtruth regions.

segContours

@Parameter(label="Segmented contours.",
           direction=OUT,
           description="Segmented contours.")
protected ArrayList<ArrayList<Point>> segContours

List of contours of segmented objects.

gtContours

@Parameter(label="Groundtruth contours.",
           direction=OUT,
           description="Groundtruth contours.")
protected ArrayList<ArrayList<Point>> gtContours

List of contours of groudtruth objects.

Constructor Detail

PreprocessLabelImages

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

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

PreprocessLabelImages

public PreprocessLabelImages(MTBImage gtImg,
                             MTBImage segImg,
                             ArrayList<Integer> sLabels,
                             ArrayList<Integer> gLabels)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Parameters:

gtImg - Groundtruth image.

segImg - Segmentation image.

sLabels - List of labels in segmentation image.

gLabels - List of labels in groundtruth image.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - Thrown in case of failure.

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()

This method initializes all required components.

Specified by:

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

CollectContoursStageOne

private boolean[][] CollectContoursStageOne(MTBImage img,
                                            ArrayList<Integer> regions)

This method collects all contour pixels for a region in a given MTBImage. PRE: > requires the region image > requires a list of Integer, where these Integer is the color value of a region in the image POST: > outputs an boolean array where 'true' means a pixel on this coordinates is a contour pixel, and false not

Parameters:

img - Region image.

regions - Label set.

Returns:

Boolean array.

CollectContoursStageTwo

private void CollectContoursStageTwo(MTBImage img,
                                     ArrayList<Integer> regions,
                                     ArrayList<ArrayList<Point>> contours,
                                     boolean[][] isContour)

This method implements the final stage of the contour detection.

It is needed for region images with unclean borders. PRE: > requires the region image where all contours are white (255) > requires a list of Integer, where these Integer is the color value of a region in the image > requires a list, where the contours have to be stored (will be overwritten) POST: > outputs the new and final contour-list for all regions in the image

Parameters:

img - Region image with white contours.

regions - Labels of regions.

contours - Data structure for result contours.

isContour - Array where contour pixels are marked.

getSegContours

public ArrayList<ArrayList<Point>> getSegContours()

Get list of segmentation contours.

Returns:

Segmented contours.

getGtContours

public ArrayList<ArrayList<Point>> getGtContours()

Get list of groundtruth contours.

Returns:

Groundtruth contours.