de.unihalle.informatik.MiToBo.filters.linear
Class MeanFilter

java.lang.Object
  extended by de.unihalle.informatik.Alida.operator.ALDOperator
      extended by de.unihalle.informatik.MiToBo.core.operator.MTBOperator
          extended by de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
All Implemented Interfaces:
de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener, loci.common.StatusReporter

@ALDMetaInfo(export=ALLOWED)
@ALDAOperator(genericExecutionMode=ALL)
public class MeanFilter
extends MTBOperator
implements loci.common.StatusReporter

Multidimensional mean filter. *

Author:
posch

Nested Class Summary
 
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode
 
Field Summary
 
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider
 
Constructor Summary
MeanFilter()
          Constructor with default parameters sizeX=1, sizeY=1, sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE.
MeanFilter(MTBImage img, Integer sizeX, Integer sizeY)
          Constructor for mean filtering in x- and y-dimension.
MeanFilter(MTBImage img, Integer sizeX, Integer sizeY, Integer sizeZ)
          Constructor for mean filtering in x-, y- and z-dimension.
MeanFilter(MTBImage img, Integer sizeX, Integer sizeY, Integer sizeZ, Integer sizeT, Integer sizeC, MTBImageWindow.BoundaryPadding boundaryPadding)
          Constructor for mean filtering.
 
Method Summary
 void addStatusListener(loci.common.StatusListener statuslistener)
           
 MTBImageWindow.BoundaryPadding getBoundaryPadding()
          Get value of Parameter argument boundaryPadding.
 MTBImage getInputImg()
          Get input image.
 MTBImage getMeanKernelC()
          Get mean kernel image (non-normalized) in c-dimension for given parameters, null if size is zero in c-dimension
 MTBImage getMeanKernelT()
          Get mean kernel image (non-normalized) in t-dimension for given parameters, null if size is zero in t-dimension
 MTBImage getMeanKernelX()
          Get mean kernel image (non-normalized) in x-dimension for given parameters, null if size is zero in x-dimension
 MTBImage getMeanKernelY()
          Get mean kernel image (non-normalized) in y-dimension for given parameters, null if size is zero in y-dimension
 MTBImage getMeanKernelZ()
          Get mean kernel image (non-normalized) in z-dimension for given parameters, null if size is zero in z-dimension
 MTBImage.MTBImageType getResultImageType()
           
 MTBImage getResultImg()
          Get resulting image.
 Integer getSizeC()
          Get standard deviation (size) in c-dimension.
 Integer getSizeT()
          Get standard deviation (size) in t-dimension.
 Integer getSizeX()
          Get standard deviation (size) in x-dimension.
 Integer getSizeY()
          Get standard deviation (size) in y-dimension.
 Integer getSizeZ()
          Get standard deviation (size) in z-dimension.
protected  MTBImage meanFilter()
          compute the mean filter
 void notifyListeners(loci.common.StatusEvent e)
           
protected  void operate()
          This function calls the actual mean filtering method.
protected  Object readResolve()
          Init function for deserialized objects.
 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 setSizeC(Integer sizeC)
          Set standard deviation (size) in c-dimension.
 void setSizeT(Integer sizeT)
          Set standard deviation (size) in t-dimension.
 void setSizeX(Integer sizeX)
          Set standard deviation (size) in x-dimension.
 void setSizeY(Integer sizeY)
          Set standard deviation (size) in y-dimension.
 void setSizeZ(Integer sizeZ)
          Set standard deviation (size) in z-dimension.
 void validateCustom()
          The validation of parameters and inputs.
 
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
addOperatorExecutionProgressEventListener, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getHidingMode, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterNames, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, 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
 

Constructor Detail

MeanFilter

public MeanFilter()
           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor with default parameters sizeX=1, sizeY=1, sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE. An input image must be specified before running this operator.

Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MeanFilter

public MeanFilter(MTBImage img,
                  Integer sizeX,
                  Integer sizeY)
           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor for mean filtering in x- and y-dimension. Default for other parameters: sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE, boundaryPadding=PADDING_BORDER

Parameters:
img - input image
sizeX - standard deviation in x-dimension
sizeY - standard deviation in y-dimension
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MeanFilter

public MeanFilter(MTBImage img,
                  Integer sizeX,
                  Integer sizeY,
                  Integer sizeZ)
           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor for mean filtering in x-, y- and z-dimension. Default for other parameters: sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE boundaryPadding=PADDING_BORDER

Parameters:
img - input image
sizeX - standard deviation in x-dimension
sizeY - standard deviation in y-dimension
sizeZ - standard deviation in z-dimension
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

MeanFilter

public MeanFilter(MTBImage img,
                  Integer sizeX,
                  Integer sizeY,
                  Integer sizeZ,
                  Integer sizeT,
                  Integer sizeC,
                  MTBImageWindow.BoundaryPadding boundaryPadding)
           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Constructor for mean filtering. Set any size to 0 to prevent filtering in the corresponding dimension

Parameters:
img - input image
sizeX - standard deviation in x-dimension
sizeY - standard deviation in y-dimension
sizeZ - standard deviation in z-dimension
sizeT - standard deviation in t-dimension
sizeC - standard deviation in c-dimension
boundaryPadding - determines how pixel values outside the image domain are treated (see LinearFilter)
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail

readResolve

protected Object readResolve()
Description copied from class: MTBOperator
Init function for deserialized objects.

This function is called on an instance of this class being deserialized from file, prior to handing the instance over to the user. It takes care of a proper initialization of transient member variables as they are not initialized to the default values during deserialization.

Overrides:
readResolve in class MTBOperator
Returns:
Updated deserialized object.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
This function calls the actual mean filtering method.

Specified by:
operate in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

validateCustom

public void validateCustom()
                    throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
The validation of parameters and inputs.

Overrides:
validateCustom in class de.unihalle.informatik.Alida.operator.ALDOperator
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException

meanFilter

protected MTBImage meanFilter()
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                              de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
compute the mean filter

Returns:
resulting image
Throws:
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getInputImg

public MTBImage getInputImg()
Get input image.


setInputImg

public void setInputImg(MTBImage img)
Set input image.


getResultImg

public MTBImage getResultImg()
Get resulting image.


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

getSizeC

public Integer getSizeC()
Get standard deviation (size) in c-dimension.


setSizeC

public void setSizeC(Integer sizeC)
Set standard deviation (size) in c-dimension.


getSizeZ

public Integer getSizeZ()
Get standard deviation (size) in z-dimension.


setSizeZ

public void setSizeZ(Integer sizeZ)
Set standard deviation (size) in z-dimension.


getSizeY

public Integer getSizeY()
Get standard deviation (size) in y-dimension.


setSizeY

public void setSizeY(Integer sizeY)
Set standard deviation (size) in y-dimension.


getSizeX

public Integer getSizeX()
Get standard deviation (size) in x-dimension.


setSizeX

public void setSizeX(Integer sizeX)
Set standard deviation (size) in x-dimension.


getSizeT

public Integer getSizeT()
Get standard deviation (size) in t-dimension.


setSizeT

public void setSizeT(Integer sizeT)
Set standard deviation (size) in t-dimension.


getMeanKernelX

public MTBImage getMeanKernelX()
Get mean kernel image (non-normalized) in x-dimension for given parameters, null if size is zero in x-dimension


getMeanKernelY

public MTBImage getMeanKernelY()
Get mean kernel image (non-normalized) in y-dimension for given parameters, null if size is zero in y-dimension


getMeanKernelC

public MTBImage getMeanKernelC()
Get mean kernel image (non-normalized) in c-dimension for given parameters, null if size is zero in c-dimension


getMeanKernelT

public MTBImage getMeanKernelT()
Get mean kernel image (non-normalized) in t-dimension for given parameters, null if size is zero in t-dimension


getMeanKernelZ

public MTBImage getMeanKernelZ()
Get mean kernel image (non-normalized) in z-dimension for given parameters, null if size is zero in z-dimension


getResultImageType

public MTBImage.MTBImageType getResultImageType()
Returns:
the resultImageType

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


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