de.unihalle.informatik.MiToBo.apps.scratchAssay

Class ScratchAssayAnalyzer

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION,
              allowBatchMode=true,
              shortDescription="Analyzes the scratch areas in a scratch assay/ gap closure/ wound closure assays.")
public class ScratchAssayAnalyzer
extends MTBOperator

class for analyzing the scratch areas in a scratch assay/ gap closure/ wound closure assay

Author:

glass

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ScratchAssayAnalyzer.AbsenceDetectionMethod
static class	ScratchAssayAnalyzer.ScratchOrientation

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 ScratchAssayAnalyzer.AbsenceDetectionMethod	checkMethod
private Double	deltaX
private Double	deltaY
private Integer	detectionChannel
private Integer	entropyFilterSize
private MTBImage	inImg
private Boolean	isHorizontal
private double	maxIncreaseFraction
private Integer	maxIter
private Vector<Integer>	numIterations
private ScratchAssayAnalyzer.ScratchOrientation	orientation
private int	refIndex
private MTBImage	result
private MTBTableModel	resultsTable
private Vector<Long>	runtimes
private Vector<Double>	scratchAreas
private Vector<String>	scratchFiles
private Integer	sigma
private de.unihalle.informatik.Alida.datatypes.ALDFileString	svmFile
private Vector<Double>	totalAreas
private String	unitXY

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
ScratchAssayAnalyzer()
ScratchAssayAnalyzer(MTBImage inImg, int sigma, int entropyFilterSize, ScratchAssayAnalyzer.ScratchOrientation orientation, boolean check)

Method Summary

Modifier and Type	Method and Description
private void	checkForIncrease()
private void	getCalibration()
String	getDocumentation()
private MTBTableModel	makeTable() create results table
void	operate()
private MTBImage	segment(MTBImage img, String path)
void	setDetectionChannel(int channel)
void	setMaxIterations(int maxIter) set maximum number of iterations for level set segmentation
private void	showParametersForChecking()

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, 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

inImg

@Parameter(label="input image",
           required=true,
           direction=IN,
           supplemental=false,
           description="input image",
           mode=STANDARD,
           dataIOOrder=1,
           callback="getCalibration",
           paramModificationMode=MODIFIES_INTERFACE)
private transient MTBImage inImg

detectionChannel

@Parameter(label="detection channel",
           required=true,
           direction=IN,
           supplemental=false,
           description="detection channel",
           dataIOOrder=2)
private Integer detectionChannel

orientation

@Parameter(label="scratch orientation",
           required=true,
           direction=IN,
           supplemental=false,
           description="is scratch horizontally or vertically oriented",
           mode=STANDARD,
           dataIOOrder=3)
private ScratchAssayAnalyzer.ScratchOrientation orientation

sigma

@Parameter(label="\u03c3",
           required=true,
           direction=IN,
           supplemental=false,
           description="standard deviation of gauss filter",
           mode=STANDARD,
           dataIOOrder=4)
private Integer sigma

entropyFilterSize

@Parameter(label="entropy filter size",
           required=true,
           direction=IN,
           supplemental=false,
           description="size of entropy filter mask",
           mode=STANDARD,
           dataIOOrder=5)
private Integer entropyFilterSize

maxIter

@Parameter(label="maximum iterations",
           required=false,
           direction=IN,
           supplemental=false,
           description="maximum number of iterations for level set segmentation",
           mode=ADVANCED,
           dataIOOrder=6)
private Integer maxIter

checkMethod

@Parameter(label="method for checking for scratch absence",
           required=false,
           direction=IN,
           supplemental=false,
           description="which method should be used to check if scratch is present in the images",
           mode=STANDARD,
           dataIOOrder=8,
           callback="showParametersForChecking",
           paramModificationMode=MODIFIES_INTERFACE)
private ScratchAssayAnalyzer.AbsenceDetectionMethod checkMethod

maxIncreaseFraction

@Parameter(label="maximum area increase",
           required=false,
           direction=IN,
           supplemental=false,
           description="if detected scratch area between two consecutive frames increases more than this fraction the scratch will be considered as closed for all following frames",
           mode=STANDARD,
           dataIOOrder=9)
private double maxIncreaseFraction

svmFile

@Parameter(label="path to svm file",
           required=false,
           direction=IN,
           supplemental=false,
           description="absolute path to external svm model file",
           mode=STANDARD,
           dataIOOrder=11)
private de.unihalle.informatik.Alida.datatypes.ALDFileString svmFile

deltaX

@Parameter(label="pixel length, x-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in x-direction",
           dataIOOrder=12)
private Double deltaX

deltaY

@Parameter(label="pixel length, y-direction",
           required=false,
           direction=IN,
           supplemental=false,
           description="pixel length in y-direction",
           dataIOOrder=13)
private Double deltaY

unitXY

@Parameter(label="unit space",
           required=false,
           direction=IN,
           supplemental=false,
           description="unit x/y",
           dataIOOrder=14)
private String unitXY

resultsTable

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

result

@Parameter(label="segmentation results",
           required=true,
           direction=OUT,
           supplemental=false,
           description="resulting image(s)")
private transient MTBImage result

isHorizontal

private Boolean isHorizontal

scratchFiles

private Vector<String> scratchFiles

scratchAreas

private Vector<Double> scratchAreas

totalAreas

private Vector<Double> totalAreas

refIndex

private int refIndex

numIterations

private Vector<Integer> numIterations

runtimes

private Vector<Long> runtimes

Constructor Detail

ScratchAssayAnalyzer

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ScratchAssayAnalyzer

public ScratchAssayAnalyzer(MTBImage inImg,
                            int sigma,
                            int entropyFilterSize,
                            ScratchAssayAnalyzer.ScratchOrientation orientation,
                            boolean check)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Parameters:

inImg -

sigma -

entropyFilterSize -

orientation -

noCheck -

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

operate

public 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

segment

private MTBImage segment(MTBImage img,
                         String path)
                  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

makeTable

private MTBTableModel makeTable()

create results table

Returns:

table containing the results

checkForIncrease

private void checkForIncrease()

setDetectionChannel

public void setDetectionChannel(int channel)

Parameters:

channel - channel used for detection

setMaxIterations

public void setMaxIterations(int maxIter)

set maximum number of iterations for level set segmentation

Parameters:

maxIter -

getCalibration

private void getCalibration()

showParametersForChecking

private void showParametersForChecking()

getDocumentation

public String getDocumentation()

Overrides:

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