de.unihalle.informatik.MiToBo.filters.linear

Class LinearFilter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

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

de.unihalle.informatik.MiToBo.filters.linear.LinearFilter

All Implemented Interfaces:

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

@ALDAOperator(genericExecutionMode=ALL,
              shortDescription="Convolves an image with a user-specified kernel.")
public class LinearFilter
extends MTBOperator
implements loci.common.StatusReporter

Generic linear filter operation class

Author:

gress

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 MTBImageWindow.BoundaryPadding	boundaryPadding
private MTBImage	inputImg
private MTBImage	kernelImg
private MTBBooleanData	kernelNormalization
private int[]	kernelOrigin
private Vector<loci.common.StatusListener>	m_statusListeners vector of installed StatusListeners
private MTBImage.MTBImageType	resultImageType
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
LinearFilter() Empty constructor
LinearFilter(MTBImage inImg, MTBImage kernelImg) Constructor
LinearFilter(MTBImage inImg, MTBImage kernelImg, int[] kernelOrigin, boolean kernelNormalization, MTBImageWindow.BoundaryPadding boundaryPadding) Constructor

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
protected MTBImage	convolve(MTBImage img, MTBImage kernel, int[] kernelAnchor, boolean normalize, MTBImageWindow.BoundaryPadding boundaryPadding) Convolve an image with a specified kernel.
MTBImageWindow.BoundaryPadding	getBoundaryPadding() Get value of Parameter argument boundaryPadding.
String	getDocumentation()
MTBImage	getInputImg() Get input image.
MTBImage	getKernelImg() Get convolution kernel (image).
boolean	getKernelNormalization() Get value of Parameter argument kernelNormalization.
int[]	getKernelOrigin() Get value of Parameter argument kernelOrigin.
MTBImage.MTBImageType	getResultImageType()
MTBImage	getResultImg() Get resulting image.
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	setBoundaryPadding(MTBImageWindow.BoundaryPadding boundaryPadding) Set value of Parameter argument boundaryPadding.
void	setInputImg(MTBImage img) Set input image.
void	setKernelImg(MTBImage kernelImg) Set convolution kernel (image).
void	setKernelNormalization(boolean kernelNormalization) Set value of Parameter argument kernelNormalization.
void	setKernelNormalization(MTBBooleanData kn) Enable or disable kernel normalization.
void	setKernelOrigin(int[] kernelOrigin) Set value of Parameter argument kernelOrigin.
void	setResultImageType(MTBImage.MTBImageType resultImageType)
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

m_statusListeners

private Vector<loci.common.StatusListener> m_statusListeners

vector of installed StatusListeners

inputImg

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

kernelImg

@Parameter(label="Kernel image",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Convolution kernel (image)")
private MTBImage kernelImg

kernelOrigin

@Parameter(label="Kernel origin",
           required=false,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=3,
           description="Coordinate of the kernel\'s origin in the kernel image. If not specified (null) it defaults to the center of the kernel image rounded down.")
private int[] kernelOrigin

kernelNormalization

@Parameter(label="Kernel normalization",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=4,
           description="If true, kernel values are normalized to sum to 1 (Default)")
private MTBBooleanData kernelNormalization

boundaryPadding

@Parameter(label="Boundary padding",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=5,
           description="Image is padded by the specified method (Default: 0s are assumed outside the image)")
private MTBImageWindow.BoundaryPadding boundaryPadding

resultImageType

@Parameter(label="Type of result image",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=6,
           description="Type of result image (Default: MTB_DOUBLE)")
private MTBImage.MTBImageType resultImageType

resultImg

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

Constructor Detail

LinearFilter

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

Empty constructor

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

LinearFilter

public LinearFilter(MTBImage inImg,
                    MTBImage kernelImg)
             throws IllegalArgumentException,
                    de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor

Throws:

IllegalArgumentException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

LinearFilter

public LinearFilter(MTBImage inImg,
                    MTBImage kernelImg,
                    int[] kernelOrigin,
                    boolean kernelNormalization,
                    MTBImageWindow.BoundaryPadding boundaryPadding)
             throws IllegalArgumentException,
                    de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor

Throws:

IllegalArgumentException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

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()
                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

convolve

protected MTBImage convolve(MTBImage img,
                            MTBImage kernel,
                            int[] kernelAnchor,
                            boolean normalize,
                            MTBImageWindow.BoundaryPadding boundaryPadding)

Convolve an image with a specified kernel.

Parameters:

img - input image

kernel - kernel image

kernelAnchor - array of length 5 to specify the kernel element, under which the result value is stored ([0]=x-position, [1]=y-pos, [2]=z-pos, [3]=t-pos, [4]=c-pos)

normalize - flag for kernel normalization (kernel weights sum to 1)

boundaryPadding - set the padding method outside the boundaries of the underlying image (see static final fields)

getKernelOrigin

public int[] getKernelOrigin()

Get value of Parameter argument kernelOrigin.

Returns:

int array with five elements specifying the image coordinate [x,y,z,t,c] considered as the origin (0,0,0,0,0) of the kernel

setKernelOrigin

public void setKernelOrigin(int[] kernelOrigin)

Set value of Parameter argument kernelOrigin.

Parameters:

int - array with five elements specifying the image coordinate [x,y,z,t,c] considered as the origin (0,0,0,0,0) of the kernel

getBoundaryPadding

public MTBImageWindow.BoundaryPadding getBoundaryPadding()

Get value of Parameter argument boundaryPadding.

Returns:

value of boundaryPadding

setBoundaryPadding

public void setBoundaryPadding(MTBImageWindow.BoundaryPadding boundaryPadding)

Set value of Parameter argument boundaryPadding.

Parameters:

value - of boundaryPadding

getKernelNormalization

public boolean getKernelNormalization()

Get value of Parameter argument kernelNormalization.

Returns:

value of kernelNormalization

setKernelNormalization

public void setKernelNormalization(boolean kernelNormalization)

Set value of Parameter argument kernelNormalization.

Parameters:

value - of kernelNormalization

setKernelNormalization

public void setKernelNormalization(MTBBooleanData kn)

Enable or disable kernel normalization.

Using this method with MiToBo wrapper datatypes instead of passing over directly a boolean preserves consistency in the processing history.

Parameters:

kn - Value for the kernel normalization flag.

getInputImg

public MTBImage getInputImg()

Get input image.

setInputImg

public void setInputImg(MTBImage img)

Set input image.

getKernelImg

public MTBImage getKernelImg()

Get convolution kernel (image).

Returns:

value of kernelImg

setKernelImg

public void setKernelImg(MTBImage kernelImg)

Set convolution kernel (image).

getResultImageType

public MTBImage.MTBImageType getResultImageType()

Returns:

the resultImageType

setResultImageType

public void setResultImageType(MTBImage.MTBImageType resultImageType)

Parameters:

resultImageType - the resultImageType to set

getResultImg

public MTBImage getResultImg()

Get resulting image.

addStatusListener

public void addStatusListener(loci.common.StatusListener statuslistener)

Specified by:

addStatusListener in interface loci.common.StatusReporter

notifyListeners

public void notifyListeners(loci.common.StatusEvent e)

Specified by:

notifyListeners in interface loci.common.StatusReporter

removeStatusListener

public void removeStatusListener(loci.common.StatusListener statuslistener)

Specified by:

removeStatusListener in interface loci.common.StatusReporter

getDocumentation

public String getDocumentation()

Overrides:

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