de.unihalle.informatik.MiToBo.filters.nonlinear

Class RankOperator

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              shortDescription="Applies a non-linear rank operator to the image.")
public class RankOperator
extends MTBOperator
implements loci.common.StatusReporter

Rank operator class to compute Median, Minimum or Maximum filter for hyperstack, stack and plain images. Slow but memory efficient implementation.

Author:

gress

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RankOperator.RankOpMode Defines the operation

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 MTBImage	inImg
private int	m_idx index of the minimum, median or maximum element in the sorted array
private int	m_rC Radius of the median in the corresponding dimension.
private int	m_rT Radius of the median in the corresponding dimension.
private int	m_rX Radius of the median in the corresponding dimension.
private int	m_rY Radius of the median in the corresponding dimension.
private int	m_rZ Radius of the median in the corresponding dimension.
private int	m_sizeC Size of the dimensions, size of the real stack.
private int	m_sizeT Size of the dimensions, size of the real stack.
private int	m_sizeX Size of the dimensions, size of the real stack.
private int	m_sizeY Size of the dimensions, size of the real stack.
private int	m_sizeZ Size of the dimensions, size of the real stack.
private Vector<loci.common.StatusListener>	m_statusListeners vector of installed StatusListeners
private int	maskRadiusC
private int	maskRadiusT
private int	maskRadiusX
private int	maskRadiusY
private int	maskRadiusZ
private RankOperator.RankOpMode	rankOpMode
private MTBImage	resultImg

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
RankOperator() Constructor
RankOperator(MTBImage inImg, RankOperator.RankOpMode mode, int maskRadius) Constructor
RankOperator(MTBImage inImg, RankOperator.RankOpMode mode, int maskRadiusX, int maskRadiusY, int maskRadiusZ, int maskRadiusT, int maskRadiusC) Constructor

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
String	getDocumentation()
MTBImage	getInImg() Get value of Input argument inImg.
int	getMaskRadiusC() Get value of Parameter argument maskRadiusC.
int	getMaskRadiusT() Get value of Parameter argument maskRadiusT.
int	getMaskRadiusX() Get value of Parameter argument maskRadiusX.
int	getMaskRadiusY() Get value of Parameter argument maskRadiusY.
int	getMaskRadiusZ() Get value of Parameter argument maskRadiusZ.
RankOperator.RankOpMode	getRankOpMode() Get value of Parameter argument rankOpMode.
MTBImage	getResultImg() Get value of Output argument resultImg.
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
private double	rankedValueAt(int x, int y, int z, int t, int c, MTBImage img, double[] values) Compute rank operator value for coordinate (x,y,z,t,c) Treatment at boundaries: Image values are mirrored at the border element to determine values under the mask that are outside the image.
protected MTBImage	rankOp(MTBImage img, RankOperator.RankOpMode mode, int radiusX, int radiusY, int radiusZ, int radiusT, int radiusC) Compute the rank operation of a gray-valued image, stack or hyperstack
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	setInImg(MTBImage img) Set value of Input argument inImg.
void	setMaskRadiusC(int value) Set value of Parameter argument maskRadiusC.
void	setMaskRadiusT(int value) Set value of Parameter argument maskRadiusT.
void	setMaskRadiusX(int value) Set value of Parameter argument maskRadiusX.
void	setMaskRadiusY(int value) Set value of Parameter argument maskRadiusY.
void	setMaskRadiusZ(int value) Set value of Parameter argument maskRadiusZ.
void	setRankOpMode(RankOperator.RankOpMode opMode) Set value of Parameter argument rankOpMode.
protected void	setResultImg(MTBImage img) Set value of Output argument resultImg.
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

inImg

@Parameter(label="Input image",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=1,
           description="Input image")
private MTBImage inImg

resultImg

@Parameter(label="Result image",
           required=true,
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           description="Resulting image")
private MTBImage resultImg

rankOpMode

@Parameter(label="Rank operation",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Type of the rank operation")
private RankOperator.RankOpMode rankOpMode

maskRadiusX

@Parameter(label="Mask-radius x",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=3,
           description="Radius of the mask in x-dimension in a city-block sense (rectangular mask)")
private int maskRadiusX

maskRadiusY

@Parameter(label="Mask-radius y",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=4,
           description="Radius of the mask in y-dimension in a city-block sense (rectangular mask)")
private int maskRadiusY

maskRadiusZ

@Parameter(label="Mask-radius z",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=5,
           description="Radius of the mask in z-dimension in a city-block sense (rectangular mask)")
private int maskRadiusZ

maskRadiusT

@Parameter(label="Mask-radius t",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=6,
           description="Radius of the mask in t-dimension in a city-block sense (rectangular mask)")
private int maskRadiusT

maskRadiusC

@Parameter(label="Mask-radius c",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=7,
           description="Radius of the mask in c-dimension in a city-block sense (rectangular mask)")
private int maskRadiusC

m_sizeX

private int m_sizeX

Size of the dimensions, size of the real stack. These values are set when the median(..) function is called with an ImagePlus object

m_sizeY

private int m_sizeY

Size of the dimensions, size of the real stack. These values are set when the median(..) function is called with an ImagePlus object

m_sizeZ

private int m_sizeZ

Size of the dimensions, size of the real stack. These values are set when the median(..) function is called with an ImagePlus object

m_sizeT

private int m_sizeT

Size of the dimensions, size of the real stack. These values are set when the median(..) function is called with an ImagePlus object

m_sizeC

private int m_sizeC

Size of the dimensions, size of the real stack. These values are set when the median(..) function is called with an ImagePlus object

m_rX

private int m_rX

Radius of the median in the corresponding dimension. These values are set when the rankOp(..) function is called with an ImagePlus object

m_rY

private int m_rY

Radius of the median in the corresponding dimension. These values are set when the rankOp(..) function is called with an ImagePlus object

m_rZ

private int m_rZ

Radius of the median in the corresponding dimension. These values are set when the rankOp(..) function is called with an ImagePlus object

m_rT

private int m_rT

Radius of the median in the corresponding dimension. These values are set when the rankOp(..) function is called with an ImagePlus object

m_rC

private int m_rC

Radius of the median in the corresponding dimension. These values are set when the rankOp(..) function is called with an ImagePlus object

m_statusListeners

private Vector<loci.common.StatusListener> m_statusListeners

vector of installed StatusListeners

m_idx

private int m_idx

index of the minimum, median or maximum element in the sorted array

Constructor Detail

RankOperator

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

Constructor

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

RankOperator

public RankOperator(MTBImage inImg,
                    RankOperator.RankOpMode mode,
                    int maskRadius)
             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor

Parameters:

inImg - input image

mode - rank operation

maskRadius - mask radius in a city-block sense for cubic mask of size (2*maskRadius + 1) in x-, y-dimension and z-dimension if available

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - if given parameters are not valid

RankOperator

public RankOperator(MTBImage inImg,
                    RankOperator.RankOpMode mode,
                    int maskRadiusX,
                    int maskRadiusY,
                    int maskRadiusZ,
                    int maskRadiusT,
                    int maskRadiusC)
             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor

Parameters:

inImg - input image

mode - rank operation

maskRadiusX - mask radius in x-dimension in a city-block sense (rectangular mask)

maskRadiusY - mask radius in y-dimension in a city-block sense (rectangular mask)

maskRadiusZ - mask radius in z-dimension in a city-block sense (rectangular mask)

maskRadiusT - mask radius in t-dimension in a city-block sense (rectangular mask)

maskRadiusC - mask radius in c-dimension in a city-block sense (rectangular mask)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException - if given parameters are not valid

Method Detail

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

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

rankOp

protected MTBImage rankOp(MTBImage img,
                          RankOperator.RankOpMode mode,
                          int radiusX,
                          int radiusY,
                          int radiusZ,
                          int radiusT,
                          int radiusC)

Compute the rank operation of a gray-valued image, stack or hyperstack

Parameters:

img - input MTBImage

radius - radius of the median mask

mode - rank operator mode

Returns:

median image

rankedValueAt

private double rankedValueAt(int x,
                             int y,
                             int z,
                             int t,
                             int c,
                             MTBImage img,
                             double[] values)

Compute rank operator value for coordinate (x,y,z,t,c) Treatment at boundaries: Image values are mirrored at the border element to determine values under the mask that are outside the image. For example I(-1,-1)=I(1,1)

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

t - t-coordinate

c - c-coordinate

img - Image to compute the ranked value from

Returns:

ranked value

addStatusListener

public void addStatusListener(loci.common.StatusListener statuslistener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener statuslistener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

getMaskRadiusX

public int getMaskRadiusX()

Get value of Parameter argument maskRadiusX.

Returns:

value of maskRadiusX

setMaskRadiusX

public void setMaskRadiusX(int value)

Set value of Parameter argument maskRadiusX.

Parameters:

value - New value for maskRadiusX

getMaskRadiusT

public int getMaskRadiusT()

Get value of Parameter argument maskRadiusT.

Returns:

value of maskRadiusT

setMaskRadiusT

public void setMaskRadiusT(int value)

Set value of Parameter argument maskRadiusT.

Parameters:

value - New value for maskRadiusT

getRankOpMode

public RankOperator.RankOpMode getRankOpMode()

Get value of Parameter argument rankOpMode.

Returns:

value of rankOpMode

setRankOpMode

public void setRankOpMode(RankOperator.RankOpMode opMode)

Set value of Parameter argument rankOpMode.

Parameters:

value - New value for rankOpMode

getMaskRadiusZ

public int getMaskRadiusZ()
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Get value of Parameter argument maskRadiusZ.

Returns:

value of maskRadiusZ

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setMaskRadiusZ

public void setMaskRadiusZ(int value)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set value of Parameter argument maskRadiusZ.

Parameters:

value - New value for maskRadiusZ

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getMaskRadiusC

public int getMaskRadiusC()
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Get value of Parameter argument maskRadiusC.

Returns:

value of maskRadiusC

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setMaskRadiusC

public void setMaskRadiusC(int value)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set value of Parameter argument maskRadiusC.

Parameters:

value - New value for maskRadiusC

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getMaskRadiusY

public int getMaskRadiusY()
                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Get value of Parameter argument maskRadiusY.

Returns:

value of maskRadiusY

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setMaskRadiusY

public void setMaskRadiusY(int value)
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set value of Parameter argument maskRadiusY.

Parameters:

value - New value for maskRadiusY

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getInImg

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

Get value of Input argument inImg.

Returns:

value of inImg

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setInImg

public void setInImg(MTBImage img)
              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set value of Input argument inImg.

Parameters:

value - New value for inImg

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getResultImg

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

Get value of Output argument resultImg.

Returns:

value of resultImg

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setResultImg

protected void setResultImg(MTBImage img)
                     throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set value of Output argument resultImg.

Parameters:

value - New value for resultImg

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getDocumentation

public String getDocumentation()

Overrides:

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