de.unihalle.informatik.MiToBo.transforms

Class UndecimatedWaveletTransform

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable

de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventListener, de.unihalle.informatik.Alida.operator.events.ALDConfigurationEventReporter, de.unihalle.informatik.Alida.operator.events.ALDControlEventListener, de.unihalle.informatik.Alida.operator.events.ALDControlEventReporter, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener, loci.common.StatusReporter

@ALDAOperator(genericExecutionMode=NONE)
public class UndecimatedWaveletTransform
extends MTBOperatorControllable
implements loci.common.StatusReporter

Undecimated wavelet transform (UWT) operator.

Author:

gress

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	UndecimatedWaveletTransform.TransformationMode

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatusHandle, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorExecutionStatus

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 Boolean	denoise
private MTBImage	excludeMask
private MTBImage	img
private Integer	Jmax
private MTBImage[]	kernels
private double[]	m_sigmaScales noise sigma scale factors for different wavelet scales
private Vector<loci.common.StatusListener>	m_statusListeners vector of installed StatusListeners
private static String	opIdentifier Identifier for outputs in verbose mode.
private UndecimatedWaveletTransform.TransformationMode	transform
private MTBImageSet	uwtImages

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

configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, stepSize, stepWiseExecution

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

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
UndecimatedWaveletTransform() Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z, no image and denoise set to false.
UndecimatedWaveletTransform(MTBImage _img, int _Jmax, boolean _denoise) Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present).
UndecimatedWaveletTransform(MTBImage _img, int _Jmax, boolean _denoise, boolean sigmaEqualsOne) Constructor with default Gaussian kernel for sd = 1 [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present) or sd=0.5 [0.0002638651, 0.1064507720, 0.7865707259, 0.1064507720, 0.0002638651] if sigmaEqualsOne is false
UndecimatedWaveletTransform(MTBImage _img, int _Jmax, boolean _denoise, MTBImage[] _kernels) Constructor.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
protected MTBImage[]	aTrousDWT(MTBImage _img, int _Jmax, MTBImage[] _kernels) A trous DWT
protected double[]	computeSigmaScales() Compute scaling factors of noise sigma for wavelet scales (these scaling factors are estimated using a gaussian noise image with sigma=1 to measure noise in the wavelet scales)
protected MTBImage	conv(MTBImage img, MTBImage[] scaleOneKernels, int j) Convolve input image with an 'a trous' kernel (zeros inserted) given the original kernel and scale j
protected MTBImage	createGaussianNoiseImage(double mean, double sigma, double clippingFactor, int bins, int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC) Create an image with Gaussian noise
protected void	denoise(MTBImage img, double sigma) Denoise wavelet coefficients using Jeffrey's noninformative prior for a given sigma of noise
protected void	denoiseDWTJeffreys(MTBImage[] dwt, double scaleOneSigma, double[] sigmaScales) Denoise wavelet coefficients using Jeffrey's noninformative prior [..]
protected double	get3SigClippedStdDev(MTBImage img) Get the standard deviation (sigma) of an image only using values clipped by 3*sigma from a first estimate of sigma
boolean	getDenoise() Get the denoising flag. true if denoising is activated.
MTBImage	getExcludeMask()
MTBImage	getImg() Get reference to the (input) image.
int	getJmax() Get Jmax (maximum scale 2^Jmax - 1)
protected MTBImage[]	getKernels() Get smoothing kernels
protected double	getSample(double[] cdf) Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
protected double	getStdDev(MTBImage img) Get standard deviation of the image
MTBImageSet	getUWT() Get the UWT coefficient images.
protected MTBImage	inverseATrousDWT(MTBImage[] dwt) Inverse a trous DWT
boolean	isForwardTransform() Test if parameter object is set to (forward) transform (image to wavelet)
boolean	isInverseTransform() Test if parameter object is set to Inverse Transform (wavelet to image)
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
void	removeStatusListener(loci.common.StatusListener statuslistener)
protected void	setDenoise(boolean denoise) Set the denoising flag. true to activate denoising.
void	setExcludeMask(MTBImage excludeMask)
void	setForwardTransform() Toggle computation of the (forward) transform (image to wavelet)
void	setImg(MTBImage img) Set the image domain image
void	setInverseTransform() Set computation of the inverse transform (wavelet to image)
protected void	setJmax(int Jmax) Set Jmax (maximum scale 2^Jmax - 1)
protected void	setKernels(MTBImage[] kernels) Set smoothing kernels
void	setUWT(MTBImageSet uwtImages) Set UWT coefficient images
boolean	supportsStepWiseExecution()

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getControlStatus, getControlStatusHandle, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setControlStatus, setNotifyRecursiveFlag

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, readResolve, 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

opIdentifier

private static final String opIdentifier

Identifier for outputs in verbose mode.

See Also:

Constant Field Values

kernels

@Parameter(label="Kernels",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=1,
           description="A set of lowpass kernels interpreted as parts of a separable kernel")
private MTBImage[] kernels

transform

@Parameter(label="Type of transform",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=4,
           description="Specifies if forward or backward transform is computed")
private UndecimatedWaveletTransform.TransformationMode transform

denoise

@Parameter(label="Denoise",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=3,
           description="Specifies whether the wavelet coefficients will be denoised using Jeffrey\'s noninformative prior")
private Boolean denoise

Jmax

@Parameter(label="Jmax",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Maximum scale index (decimal > 0)")
private Integer Jmax

img

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

excludeMask

@Parameter(label="mask image",
           required=false,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=5,
           description="mask image used for denoising: a value of zero INCLUDES a pixel")
private MTBImage excludeMask

uwtImages

@Parameter(label="UWT coefficient images",
           required=true,
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           description="Images with UWT coefficients of the different scales")
private MTBImageSet uwtImages

m_statusListeners

private Vector<loci.common.StatusListener> m_statusListeners

vector of installed StatusListeners

m_sigmaScales

private final double[] m_sigmaScales

noise sigma scale factors for different wavelet scales

Constructor Detail

UndecimatedWaveletTransform

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

Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z, no image and denoise set to false.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

UndecimatedWaveletTransform

public UndecimatedWaveletTransform(MTBImage _img,
                                   int _Jmax,
                                   boolean _denoise,
                                   MTBImage[] _kernels)
                            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor. Separable lowpass kernels are expected (i.e. Gaussian).

Parameters:

_img - input image

_Jmax - maximum scale (2^Jmax - 1)

_denoise - reduction of gaussian noise

_kernels - an array of kernels, which are inflated for each scale and used to convolve the image consecutively, because a separable filter is expected to be specified by this array

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

UndecimatedWaveletTransform

public UndecimatedWaveletTransform(MTBImage _img,
                                   int _Jmax,
                                   boolean _denoise)
                            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present).

Parameters:

img - input image

Jmax - maximum scale (2^Jmax - 1)

denoise - reduction of gaussian noise

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

UndecimatedWaveletTransform

public UndecimatedWaveletTransform(MTBImage _img,
                                   int _Jmax,
                                   boolean _denoise,
                                   boolean sigmaEqualsOne)
                            throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor with default Gaussian kernel for sd = 1 [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present) or sd=0.5 [0.0002638651, 0.1064507720, 0.7865707259, 0.1064507720, 0.0002638651] if sigmaEqualsOne is false

Parameters:

img - input image

Jmax - maximum scale (2^Jmax - 1)

denoise - reduction of gaussian noise

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

supportsStepWiseExecution

public boolean supportsStepWiseExecution()

Specified by:

supportsStepWiseExecution in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable

operate

protected 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

inverseATrousDWT

protected MTBImage inverseATrousDWT(MTBImage[] dwt)
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Inverse a trous DWT

Parameters:

dwt - DWT-coefficient images

Returns:

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

aTrousDWT

protected MTBImage[] aTrousDWT(MTBImage _img,
                               int _Jmax,
                               MTBImage[] _kernels)
                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                               de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

A trous DWT

Returns:

DWT-coefficient images ([0] lowpass coeffs, [1] highpass coeffs, [2] highest bandpass coeffs, ..., [Jmax] lowest bandpass coeffs)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

conv

protected MTBImage conv(MTBImage img,
                        MTBImage[] scaleOneKernels,
                        int j)
                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                        de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Convolve input image with an 'a trous' kernel (zeros inserted) given the original kernel and scale j

Parameters:

img - input image

scaleOneKernels - original kernel (without inserted zeros)

j - scale parameter

Returns:

filtered image

Throws:

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

denoiseDWTJeffreys

protected void denoiseDWTJeffreys(MTBImage[] dwt,
                                  double scaleOneSigma,
                                  double[] sigmaScales)

Denoise wavelet coefficients using Jeffrey's noninformative prior [..]

Parameters:

dwt -

scaleOneSigma -

sigmaScales -

denoise

protected void denoise(MTBImage img,
                       double sigma)

Denoise wavelet coefficients using Jeffrey's noninformative prior for a given sigma of noise

Parameters:

img - input image

sigma - sigma of noise

computeSigmaScales

protected double[] computeSigmaScales()
                               throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                      de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Compute scaling factors of noise sigma for wavelet scales (these scaling factors are estimated using a gaussian noise image with sigma=1 to measure noise in the wavelet scales)

Parameters:

p - DWT configuration (only Jmax is important here)

Returns:

scaling factor of noise sigma for wavelet scale 1 to Jmax

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

get3SigClippedStdDev

protected double get3SigClippedStdDev(MTBImage img)

Get the standard deviation (sigma) of an image only using values clipped by 3*sigma from a first estimate of sigma

Parameters:

img - input image

Returns:

3*sigma clipped std dev

getStdDev

protected double getStdDev(MTBImage img)

Get standard deviation of the image

Parameters:

img - input image

Returns:

sigma

createGaussianNoiseImage

protected MTBImage createGaussianNoiseImage(double mean,
                                            double sigma,
                                            double clippingFactor,
                                            int bins,
                                            int sizeX,
                                            int sizeY,
                                            int sizeZ,
                                            int sizeT,
                                            int sizeC)

Create an image with Gaussian noise

Parameters:

mean -

sigma -

clippingFactor -

bins -

sizeX -

sizeY -

sizeZ -

sizeT -

sizeC -

Returns:

getSample

protected double getSample(double[] cdf)

Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf

Parameters:

cdf - cumulative distribution array

Returns:

getDenoise

public boolean getDenoise()

Get the denoising flag. true if denoising is activated.

setDenoise

protected void setDenoise(boolean denoise)

Set the denoising flag. true to activate denoising.

getImg

public MTBImage getImg()

Get reference to the (input) image.

Returns:

Image domain image

setImg

public void setImg(MTBImage img)

Set the image domain image

getExcludeMask

public MTBImage getExcludeMask()

Returns:

the excludeMask

setExcludeMask

public void setExcludeMask(MTBImage excludeMask)

Parameters:

excludeMask - the excludeMask to set

getJmax

public int getJmax()

Get Jmax (maximum scale 2^Jmax - 1)

setJmax

protected void setJmax(int Jmax)

Set Jmax (maximum scale 2^Jmax - 1)

Parameters:

Jmax -

getKernels

protected MTBImage[] getKernels()

Get smoothing kernels

setKernels

protected void setKernels(MTBImage[] kernels)

Set smoothing kernels

isForwardTransform

public boolean isForwardTransform()

Test if parameter object is set to (forward) transform (image to wavelet)

Returns:

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setForwardTransform

public void setForwardTransform()

Toggle computation of the (forward) transform (image to wavelet)

isInverseTransform

public boolean isInverseTransform()
                           throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Test if parameter object is set to Inverse Transform (wavelet to image)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

setInverseTransform

public void setInverseTransform()
                         throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Set computation of the inverse transform (wavelet to image)

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getUWT

public MTBImageSet getUWT()

Get the UWT coefficient images. At index 0, the lowpass image stored. Indices j = 1,...,Jmax correspond to the UWT coefficients at scales 2^j - 1, meaning highpass at j=1, highest bandpass at j=2 and lowest bandpass at j=Jmax

Returns:

Reference to UWT images

setUWT

public void setUWT(MTBImageSet uwtImages)

Set UWT coefficient images

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