de.unihalle.informatik.MiToBo.segmentation.basics

Class CalcSegmentationStatistics

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL)
public class CalcSegmentationStatistics
extends MTBOperator

Operator for doing statistical calculations on segmentations of images.

The segmentations and input images processed by this operator can have either 2 or 3 dimensions. In addition, multiple channels are supported. In case of time series images being handed over to this operator only the image for the first point in time is processed.

Note: It is assumed that the given segmentation covers at least the domain of the input image. There are no checks performed if this is really true!

Author:

moeller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CalcSegmentationStatistics.CalcTargets Statistical numbers provided by this class.

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 int	iChannels Number of channels of working image.
private int	iDepth Depth of working image.
private int	iHeight Height of working image.
private MTBImage	image Input image.
private int	iWidth Width of working image.
private double[][]	regionMeans List of calculated region average values.
private int[]	regionSizes List of calculated region sizes.
private double[][]	regionVars List of calculated region variance values.
private MTBSegmentationInterface	segmentation Segmentation object.
private Vector<CalcSegmentationStatistics.CalcTargets>	targetList List of targets to calculate.

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
CalcSegmentationStatistics() Default constructor without arguments.
CalcSegmentationStatistics(MTBImage im) Default constructor.
CalcSegmentationStatistics(MTBImage im, MTBSegmentationInterface seg) Default constructor.
CalcSegmentationStatistics(MTBImage im, MTBSegmentationInterface seg, Vector<CalcSegmentationStatistics.CalcTargets> targets) Default constructor.

Method Summary

Modifier and Type	Method and Description
double[]	getRegionMeans() Get average intensity array indexed with class labels for first channel.
double[][]	getRegionMeansAllChannels() Get average intensity array indexed with class labels for all channels.
int[]	getRegionSizes() Get array of region areas indexed with class labels for first channel.
double[]	getRegionVars() Get intensity variance array indexed with class labels for first channel.
double[][]	getRegionVarsAllChannels() Get intensity variance array indexed with class labels for all channels.
protected void	operate()
void	setInputImage(MTBImage img) Set the input image.
void	setSegmentation(MTBSegmentationInterface seg) Specifiy image segmentation.
void	setTargets(Vector<CalcSegmentationStatistics.CalcTargets> targets) Specify targets to calculate.

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

image

@Parameter(label="Input Image",
           direction=IN,
           required=true,
           description="Input image to work on.")
private MTBImage image

Input image.

segmentation

@Parameter(label="Segmentation",
           direction=IN,
           required=true,
           description="Segmentation of image.")
private MTBSegmentationInterface segmentation

Segmentation object.

targetList

@Parameter(label="Calculation Targets",
           direction=IN,
           required=true,
           description="List of targets to calculate.")
private Vector<CalcSegmentationStatistics.CalcTargets> targetList

List of targets to calculate.

regionSizes

@Parameter(label="Region Sizes",
           direction=OUT,
           description="Calculated region sizes.")
private int[] regionSizes

List of calculated region sizes.

regionMeans

@Parameter(label="Region Means",
           direction=OUT,
           description="Calculated region averages.")
private double[][] regionMeans

List of calculated region average values.

The first dimension of the array covers the channel.

regionVars

@Parameter(label="Region Variances",
           direction=OUT,
           description="Calculated region variances.")
private double[][] regionVars

List of calculated region variance values.

The first dimension of the array covers the channel.

iWidth

private int iWidth

Width of working image.

iHeight

private int iHeight

Height of working image.

iDepth

private int iDepth

Depth of working image.

iChannels

private int iChannels

Number of channels of working image.

Constructor Detail

CalcSegmentationStatistics

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

Default constructor without arguments.

Note, there are parameters that need to be set prior to executing the operator. Don't call runOp() before doing that!

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CalcSegmentationStatistics

public CalcSegmentationStatistics(MTBImage im)
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

im - Image to work on.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CalcSegmentationStatistics

public CalcSegmentationStatistics(MTBImage im,
                                  MTBSegmentationInterface seg)
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

im - Image to work on.

seg - Segmentation.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

CalcSegmentationStatistics

public CalcSegmentationStatistics(MTBImage im,
                                  MTBSegmentationInterface seg,
                                  Vector<CalcSegmentationStatistics.CalcTargets> targets)
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Parameters:

im - Image to work on.

seg - Image segmentation.

targets - List of statistical numbers to calculate per region.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setInputImage

public void setInputImage(MTBImage img)

Set the input image.

Parameters:

img - Image to process.

setSegmentation

public void setSegmentation(MTBSegmentationInterface seg)

Specifiy image segmentation.

setTargets

public void setTargets(Vector<CalcSegmentationStatistics.CalcTargets> targets)

Specify targets to calculate.

getRegionSizes

public int[] getRegionSizes()

Get array of region areas indexed with class labels for first channel.

getRegionMeans

public double[] getRegionMeans()

Get average intensity array indexed with class labels for first channel.

getRegionMeansAllChannels

public double[][] getRegionMeansAllChannels()

Get average intensity array indexed with class labels for all channels.

The first dimension of the array covers the channel.

getRegionVars

public double[] getRegionVars()

Get intensity variance array indexed with class labels for first channel.

The first dimension of the array covers the channel.

getRegionVarsAllChannels

public double[][] getRegionVarsAllChannels()

Get intensity variance array indexed with class labels for all channels.

The first dimension of the array covers the channel.

operate

protected void operate()

Specified by:

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