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java.lang.Objectde.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.operator.ALDOperatorControllable
de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable
de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
@ALDAOperator(genericExecutionMode=NONE) public class UndecimatedWaveletTransform
Undecimated wavelet transform (UWT) operator.
Nested Class Summary | |
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protected static class |
UndecimatedWaveletTransform.TransformationMode
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Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable |
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de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorControlStatus, de.unihalle.informatik.Alida.operator.ALDOperatorControllable.OperatorExecutionStatus |
Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode |
Field Summary |
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Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable |
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configurationEventlistenerList, controlEventlistenerList, notifyListenersRecursively, operatorExecStatus, operatorStatus, stepSize, stepWiseExecution |
Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider |
Constructor Summary | |
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UndecimatedWaveletTransform()
Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z. |
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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). |
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UndecimatedWaveletTransform(MTBImage _img,
int _Jmax,
boolean _denoise,
MTBImage[] _kernels)
Constructor. |
Method Summary | |
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void |
addStatusListener(loci.common.StatusListener statuslistener)
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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 |
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)
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protected void |
operate()
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void |
removeStatusListener(loci.common.StatusListener statuslistener)
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protected void |
setDenoise(boolean denoise)
Set the denoising flag. true to activate denoising. |
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()
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Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperatorControllable |
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addALDConfigurationEventListener, addALDControlEventListener, fireALDConfigurationEvent, fireALDControlEvent, getExecutionStatus, handleALDConfigurationEvent, handleALDControlEvent, removeALDConfigurationEventListener, removeALDControlEventListener, setNotifyRecursiveFlag |
Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator |
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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, readResolve, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, runOp, runOp, runOp, setConstructionMode, setHidingMode, setName, setParameter, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public UndecimatedWaveletTransform() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public UndecimatedWaveletTransform(MTBImage _img, int _Jmax, boolean _denoise, MTBImage[] _kernels) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
_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
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public UndecimatedWaveletTransform(MTBImage _img, int _Jmax, boolean _denoise) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
img
- input imageJmax
- maximum scale (2^Jmax - 1)denoise
- reduction of gaussian noise
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
Method Detail |
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public boolean supportsStepWiseExecution()
supportsStepWiseExecution
in class de.unihalle.informatik.Alida.operator.ALDOperatorControllable
protected void operate() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
operate
in class de.unihalle.informatik.Alida.operator.ALDOperator
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImage inverseATrousDWT(MTBImage[] dwt) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
dwt
- DWT-coefficient images
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
protected MTBImage[] aTrousDWT(MTBImage _img, int _Jmax, MTBImage[] _kernels) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected MTBImage conv(MTBImage img, MTBImage[] scaleOneKernels, int j) throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
img
- input imagescaleOneKernels
- original kernel (without inserted zeros)j
- scale parameter
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
protected void denoiseDWTJeffreys(MTBImage[] dwt, double scaleOneSigma, double[] sigmaScales)
dwt
- scaleOneSigma
- sigmaScales
- protected void denoise(MTBImage img, double sigma)
img
- input imagesigma
- sigma of noiseprotected double[] computeSigmaScales() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException, de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
p
- DWT configuration (only Jmax is important here)
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException
protected double get3SigClippedStdDev(MTBImage img)
img
- input image
protected double getStdDev(MTBImage img)
img
- input image
protected MTBImage createGaussianNoiseImage(double mean, double sigma, double clippingFactor, int bins, int sizeX, int sizeY, int sizeZ, int sizeT, int sizeC)
mean
- sigma
- clippingFactor
- bins
- sizeX
- sizeY
- sizeZ
- sizeT
- sizeC
-
protected double getSample(double[] cdf)
cdf
- cumulative distribution array
public boolean getDenoise()
protected void setDenoise(boolean denoise)
public MTBImage getImg()
public void setImg(MTBImage img)
public int getJmax()
protected void setJmax(int Jmax)
Jmax
- protected MTBImage[] getKernels()
protected void setKernels(MTBImage[] kernels)
public boolean isForwardTransform()
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public void setForwardTransform()
public boolean isInverseTransform() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public void setInverseTransform() throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
de.unihalle.informatik.Alida.exceptions.ALDOperatorException
public MTBImageSet getUWT()
public void setUWT(MTBImageSet uwtImages)
public void addStatusListener(loci.common.StatusListener statuslistener)
addStatusListener
in interface loci.common.StatusReporter
public void removeStatusListener(loci.common.StatusListener statuslistener)
removeStatusListener
in interface loci.common.StatusReporter
public void notifyListeners(loci.common.StatusEvent e)
notifyListeners
in interface loci.common.StatusReporter
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