de.unihalle.informatik.MiToBo.segmentation.evaluation

Class GroundtruthEvaluation

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.evaluation.GroundtruthEvaluation

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class GroundtruthEvaluation
extends MTBOperator

Implementation of segmentation evaluation measures.

The operator takes a segmentation image and a ground truth image. It evaluates both segmentations based on region and/or contour information

Both images have to be region images and have to have the same size.

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
private boolean	DE Check if you want to compute the Detection Errors
private boolean	GTC Check if you want to compute Recall and Precision
protected int[]	gtIDs Match list of set entries to original groundtruth labels.
protected MTBImageShort	gtLabelImage Preprocessed groundtruth label image with short pixel type.
protected MTBImage	gtLabelsOrig Groundtruth labeling.
private boolean	HAU Check if you want to compute the Hausdorff-Distance
protected int	height Height of label images.
private Boolean	invertGroundtrouth Flag to invert ground-truth image prior to evaluation.
private Boolean	invertInputImage Flag to invert input image.
private ArrayList<Integer>	labelListGT List of groundtruth region labels.
private ArrayList<Integer>	labelListSG List of labels found in segmentation.
protected TreeSet<Integer>	labelSetGT Set of available groundtruth labels.
protected TreeSet<Integer>	labelSetSG Set of available segmentation labels.
protected byte[][]	matchingMatrix Matching matrix.
protected int	maxRegionCount Maximum number of regions in groundtruth or segmented region set.
protected String	measureInfo Info string to structure GUI.
protected int	minRegionCount Minimum number of regions in groundtruth or segmented region set.
protected int	n For Odet's criteria only
private boolean	Odet Check if you want to compute Odet's criteria
private Boolean	omitAssignment Flag to omit region assignment.
private boolean	PRA Check if you want to compute Pratt's figure of merit
private de.unihalle.informatik.Alida.datatypes.ALDFileString	resultFile Optional file where to save the result table.
protected MTBTableModel	resultTable Table with result data.
protected double[][]	scoreMatrix Score matrix with pairwise overlaps.
protected MTBImageShort	segLabelImage Preprocessed segmentation label image with short pixel type.
protected MTBImage	segLabelsOrig Label image of segmentation result.
protected int[]	sgIDs Match list of set entries to original segmentation labels.
protected HashMap<Integer,Integer>	sizesGT Array of sizes of groundtruth regions.
protected HashMap<Integer,Integer>	sizesSG Array of sizes of segmented regions.
protected int	width Width of label images.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
GroundtruthEvaluation() Default constructor.
GroundtruthEvaluation(MTBImage _segLabels, MTBImage _gtLabels, Boolean noAssignment) Default constructor with parameters.

Method Summary

Modifier and Type	Method and Description
protected void	convertLabelImages() Converts input images to short pixel format and optionally inverts them.
protected void	createResultTable() This method prepares the result table for the solution.
protected HashMap<String,HashMap<Integer,Double>>	doEvaluation() Calculates evaluation measures.
protected void	extractLabelsSizesOverlaps() Extracts evaluation data in terms of overlaps and missed pixels.
protected void	fillResultTable(HashMap<String,HashMap<Integer,Double>> data) Method to fill the result table.
MTBTableModel	getResultTable() Get evaluation results.
protected void	operate()

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

gtLabelsOrig

@Parameter(label="Groundtruth Label Image",
           required=true,
           direction=IN,
           dataIOOrder=0,
           description="Groundtruth label image.")
protected transient MTBImage gtLabelsOrig

Groundtruth labeling.

segLabelsOrig

@Parameter(label="Segmentation Label Image",
           required=true,
           direction=IN,
           dataIOOrder=1,
           description="Segmentation result label image.")
protected transient MTBImage segLabelsOrig

Label image of segmentation result.

resultTable

@Parameter(label="Result data table",
           direction=OUT,
           supplemental=true,
           description="Result data table")
protected MTBTableModel resultTable

Table with result data.

measureInfo

@Parameter(label="Measure info string",
           required=true,
           dataIOOrder=2,
           direction=IN,
           description="Info string.",
           info=true)
protected String measureInfo

Info string to structure GUI.

GTC

@Parameter(label="Recalls, Precisions, F1-Scores and Jaccard Indices",
           required=true,
           dataIOOrder=3,
           direction=IN,
           description="Calculate recalls, precisions, F1-scores and Jaccard indices.")
private boolean GTC

Check if you want to compute Recall and Precision

PRA

@Parameter(label="Pratt\'s Figure of Merit",
           required=true,
           dataIOOrder=4,
           direction=IN,
           description="Calculate Pratt\'s figure of merit.")
private boolean PRA

Check if you want to compute Pratt's figure of merit

HAU

@Parameter(label="Hausdorff Distance",
           required=true,
           dataIOOrder=5,
           direction=IN,
           description="Calculate Hausdorff distance.")
private boolean HAU

Check if you want to compute the Hausdorff-Distance

DE

@Parameter(label="Detection Errors",
           required=true,
           dataIOOrder=6,
           direction=IN,
           description="Calculate Detection Errors.")
private boolean DE

Check if you want to compute the Detection Errors

Odet

@Parameter(label="Odet\'s criteria",
           required=true,
           dataIOOrder=7,
           direction=IN,
           description="Calculate Odet\'s criteria.")
private boolean Odet

Check if you want to compute Odet's criteria

n

@Parameter(label="Odet\'s criteria exponent",
           required=true,
           dataIOOrder=8,
           direction=IN,
           description="Exponent for calculating Odet\'s criterias.")
protected int n

For Odet's criteria only

invertGroundtrouth

@Parameter(label="Invert groundtruth image",
           required=false,
           direction=IN,
           dataIOOrder=1,
           description="Apply inversion to groundtruth image.")
private Boolean invertGroundtrouth

Flag to invert ground-truth image prior to evaluation.

invertInputImage

@Parameter(label="Invert input image",
           required=false,
           direction=IN,
           dataIOOrder=2,
           description="Apply inversion to input image.")
private Boolean invertInputImage

Flag to invert input image.

omitAssignment

@Parameter(label="Automatic region assignment off",
           required=false,
           direction=IN,
           dataIOOrder=3,
           description="No automatic region assignment.")
private Boolean omitAssignment

Flag to omit region assignment.

resultFile

@Parameter(label="(Optional) result file",
           required=false,
           direction=IN,
           dataIOOrder=4)
private de.unihalle.informatik.Alida.datatypes.ALDFileString resultFile

Optional file where to save the result table.

width

protected int width

Width of label images.

height

protected int height

Height of label images.

gtLabelImage

protected MTBImageShort gtLabelImage

Preprocessed groundtruth label image with short pixel type.

segLabelImage

protected MTBImageShort segLabelImage

Preprocessed segmentation label image with short pixel type.

labelSetGT

protected TreeSet<Integer> labelSetGT

Set of available groundtruth labels.

labelSetSG

protected TreeSet<Integer> labelSetSG

Set of available segmentation labels.

labelListGT

private ArrayList<Integer> labelListGT

List of groundtruth region labels.

labelListSG

private ArrayList<Integer> labelListSG

List of labels found in segmentation.

gtIDs

protected int[] gtIDs

Match list of set entries to original groundtruth labels.

sgIDs

protected int[] sgIDs

Match list of set entries to original segmentation labels.

sizesGT

protected HashMap<Integer,Integer> sizesGT

Array of sizes of groundtruth regions.

sizesSG

protected HashMap<Integer,Integer> sizesSG

Array of sizes of segmented regions.

minRegionCount

protected int minRegionCount

Minimum number of regions in groundtruth or segmented region set.

maxRegionCount

protected int maxRegionCount

Maximum number of regions in groundtruth or segmented region set.

scoreMatrix

protected double[][] scoreMatrix

Score matrix with pairwise overlaps.

matchingMatrix

protected byte[][] matchingMatrix

Matching matrix.

Constructor Detail

GroundtruthEvaluation

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

Default constructor.

Throws:

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

GroundtruthEvaluation

public GroundtruthEvaluation(MTBImage _segLabels,
                             MTBImage _gtLabels,
                             Boolean noAssignment)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor with parameters.

Parameters:

_segLabels - Label image of segmentation result.

_gtLabels - Label image of groundtruth segmentation.

noAssignment - Flag, set true if label images imply assignment.

Throws:

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

Method Detail

getResultTable

public MTBTableModel getResultTable()

Get evaluation results.

Returns:

Table with evaluation results.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Specified by:

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

convertLabelImages

protected void convertLabelImages()
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                  de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Converts input images to short pixel format and optionally inverts them.

Throws:

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

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

extractLabelsSizesOverlaps

protected void extractLabelsSizesOverlaps()

Extracts evaluation data in terms of overlaps and missed pixels.

doEvaluation

protected HashMap<String,HashMap<Integer,Double>> doEvaluation()
                                                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                                               de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Calculates evaluation measures.

Returns:

Evaluation measures.

Throws:

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

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

fillResultTable

protected void fillResultTable(HashMap<String,HashMap<Integer,Double>> data)

Method to fill the result table.

Parameters:

data - Evaluation data to fill into the table.

createResultTable

protected void createResultTable()

This method prepares the result table for the solution. POST: > result table of the necessary size and with a header