de.unihalle.informatik.MiToBo.apps.particles2D

Class ParticleDetectorUWT2D

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.apps.particles2D.ParticleDetector

de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D

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=ALL,
              level=STANDARD,
              allowBatchMode=false,
              shortDescription="Detects spotlike structures in 2D based on the undecimated wavelet transform.")
 @ALDDerivedClass
public class ParticleDetectorUWT2D
extends ParticleDetector
implements loci.common.StatusReporter

Detector for spotlike structures (bright on dark background) in 2D based on the undecimated wavelet transform.

The undecimated wavelet transform produces wavelet coefficient images that correspond to the results of filtering the original image with a bank of filters. There is one lowpass-filtered image, one highpass-filtered image and several bandpass filtered images, depending on the parameter Jmax. The different bands/filtered images are referenced by the 'scale'. The parameters Jmin and Jmax determine the lower and upper scale limit and, thus, control the range of wavelet images that are taken into account for particle detection. Scale 1 corresponds to the highpass filtered image and increasing scales correspond to decreasing frequency bands. The scaleIntervalSize parameter determines, how many wavelet images of adjacent scales are used to compute a wavelet correlation image, which is the multiplication of wavelet coefficients over adjacent scales at each pixel.

A short example: Jmin=2, Jmax=4, scaleIntervalSize=2
This means that the bandpass filtered images of scale 2 and 3 are multiplied for one correlation image, and the bandpass filtered images of scale 3 and 4 for another.

Correlation images are then thresholded by corrThreshold to yield hypotheses of particle detections. Because multiple hypotheses can exist at the same location due to multiple correlation images, a kind of hypothesis testing is used to determine the more likely detection at a certain location.

The resulting set of particle detections can be extracted from the particle detector as a set of regions. In addition, in verbose mode the sets of computed original and binary correlation images are also available as image stacks.

The input image may be transformed if it contains Poisson noise to simulate Gaussian noise using the parameter poisson2gauss.

For further details refer to:

• O. Gress, B. Möller, N. Stöhr, S. Hüttelmaier, S. Posch, "Scale-adaptive wavelet-based particle detection in microscopy images" .
  In Proc. Bildverarbeitung für die Medizin (BVM 2010), pages 266-270, March 2010, Springer.

Author:

Oliver Gress

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	ParticleDetectorUWT2D.UWTRunner Thread class to run UWT wavelet transformation threaded.

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	additionalResultsWanted Flag to activate calculation of additional result images.
private MTBImageByte	binaryCorrelationImages Stack of binarized correlation images.
private MTBImage	correlationImages Stack of correlation images for different scale combinations.
private Double	corrThreshold Threshold for correlation images.
private MTBImageByte	excludeMask Optional mask to exclude particles in certain regions.
private boolean	initialSigmaOneHalve Flag to use initial sigma = 0.5 for the wavelet transform
private MTBImage	inputImage Input image to process.
private Integer	Jmax Maximum scale to consider.
private Integer	Jmin Minimal scale to consider.
protected Vector<loci.common.StatusListener>	m_statusListeners Vector of installed StatusListener objects.
private int	minRegionSize Minimal size of valid regions.
private static String	opIdentifier Identifier for outputs in verbose mode.
private boolean	poisson2gauss Flag to activate Poisson-to-Gaussian noise transform.
private MTBRegion2DSet	resultingRegions Set of detected particle regions.
private MTBImageByte	resultMaskBinary Binary mask of detected regions.
private MTBImage	resultOverlay Detected regions plotted into input image.
private int	resultRegionCount Number of detected regions.
private Integer	scaleIntervalSize Size of scale interval for calculating wavelet correlation images.

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
ParticleDetectorUWT2D() Constructor.
ParticleDetectorUWT2D(MTBImage img, int _Jmin, int _Jmax, double _corrThreshold, int _scaleIntervalSize, int _minRegionSize) Constructor that sets the poisson2gauss flag to true
ParticleDetectorUWT2D(MTBImage img, int _Jmin, int _Jmax, double _corrThreshold, int _scaleIntervalSize, int _minRegionSize, boolean _poisson2gauss) Constructor with non-default parameters.

Method Summary

Modifier and Type	Method and Description
void	addStatusListener(loci.common.StatusListener statuslistener)
protected MTBImage	fillHoles(MTBImage img)
protected static MTBImage	gauss2poisson(MTBImage img) Transforms image with gaussian noise to image with poisson noise J.
protected MTBImage[]	getCorrelationImages() Compute the correlation images as specified by the parameters.
Double	getCorrelationThreshold() Get threshold for thresholding wavelet correlation images
String	getDocumentation()
MTBImage	getInputImage() Get input image
Integer	getJmax() Get Jmax
Integer	getJmin() Get Jmin
protected Integer	getLabelMostInRegion(MTBRegion2D reg, MTBImage img)
protected Vector<Integer>	getLabelsInRegion(MTBRegion2D reg, MTBImage img)
protected MTBImage	getMaskFromNuclei(MTBImage nucleiImg)
int	getMinRegionSize() Get the minimum size of detected regions.
protected MTBImageHistogram	getNormalizedCumulativeHistogram(MTBImage img, int bins) Create a normalized cumulative histogram from an image
boolean	getPoisson2Gauss() Get flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
protected MTBTree	getRegionsTree(MTBImage[] binaryImages) Build a tree of regions from binarized images.
MTBImage	getResultBinaryCorrelationStack() Get resulting binarized correlation image stack.
MTBImage	getResultCorrelationStack() Get resulting correlation image stack.
MTBRegion2DSet	getResults() Get resulting regions (each detetection corresponds to a region)
protected double	getSample(double[] cdf) Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
Integer	getScaleIntervalSize() Get the size of the scale interval for correlation images
protected MTBImage	inverseATrousDWT(MTBImage[] dwt)
protected MTBImage	labelImage(MTBImage img, MTBRegion2DSet regs)
protected double	logPofRegion(MTBRegion2D reg, MTBImage img, MTBImageHistogram cumHist)
protected Vector<MTBTreeNode>	meaningfulNodes(MTBTreeNode treeNode, MTBImage[] corrImgs, MTBImageHistogram[] hists, int mode) Get the most meaningful regions from a (sub)tree.
protected double	meanOfRegion(MTBRegion2D reg, MTBImage img)
void	notifyListeners(loci.common.StatusEvent e)
protected void	operate()
static MTBImage	poisson2gauss(MTBImage img) Transforms image with poisson noise to image with gaussian noise J.
protected MTBImage	processedRegionsToBinImage(MTBImage img, MTBRegion2DSet regs, int _minRegionSize) Create a binary image from given regions.
protected MTBImage	regionsToBinImage(MTBImage img, MTBImage mask, Vector<MTBRegion2D> regs) Create binary image from a set of regions.
void	removeStatusListener(loci.common.StatusListener statuslistener)
void	setCorrelationThreshold(double corrThresh) Set threshold for thresholding wavelet correlation images
void	setExcludeMask(MTBImageByte mask) Specify exclude mask.
void	setInputImage(MTBImage img) Set input image
void	setJmax(int _Jmax) Set Jmax
void	setJmin(int _Jmin) Set Jmin
void	setMinRegionSize(int _minRegionSize) Set the minimum size of detected regions.
void	setPoisson2Gauss(boolean _poisson2gauss) Set flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
protected void	setResults(MTBRegion2DSet detectedRegions) Set detected regions
void	setScaleIntervalSize(int _scaleIntervalSize) Set the size of the scale interval for correlation images
boolean	supportsStepWiseExecution()
protected void	threshDWTCoeffs(MTBImage img, double sigma)
protected void	threshDWTJeffreys(MTBImage[] dwt, double scaleOneSigma, double[] sigmaScales)
protected MTBImage	threshImage(MTBImage img, double thresh)
protected MTBImage	threshImgNiblack(MTBImage img, double k, int winsize)
void	validateCustom()

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, 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, 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

inputImage

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

Input image to process.

Jmin

@Parameter(label="Jmin",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=2,
           description="Minimum scale index.")
private Integer Jmin

Minimal scale to consider.

Jmax

@Parameter(label="Jmax",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=3,
           description="Maximum scale index.")
private Integer Jmax

Maximum scale to consider.

scaleIntervalSize

@Parameter(label="Scale-interval size",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=4,
           description="Size of scale interval for correlation images.")
private Integer scaleIntervalSize

Size of scale interval for calculating wavelet correlation images.

corrThreshold

@Parameter(label="Correlation threshold",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=5,
           description="Threshold for wavelet correlation images.")
private Double corrThreshold

Threshold for correlation images.

minRegionSize

@Parameter(label="Minimum region size",
           required=true,
           direction=IN,
           mode=STANDARD,
           dataIOOrder=6,
           description="Minimum area of detected regions.")
private int minRegionSize

Minimal size of valid regions.

poisson2gauss

@Parameter(label="Apply Poisson-to-Gaussian noise transform",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=7,
           description="Transform input image with poisson noise to image with Gaussian noise (J.-L. Starck et al).")
private boolean poisson2gauss

Flag to activate Poisson-to-Gaussian noise transform.

initialSigmaOneHalve

@Parameter(label="use initial sigma = 0.5 for the wavelet transform",
           required=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=8,
           description="use initial sigma = 0.5 for the wavelet transform")
private boolean initialSigmaOneHalve

Flag to use initial sigma = 0.5 for the wavelet transform

excludeMask

@Parameter(label="Exclude mask",
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=9,
           required=false,
           description="Exclude mask.")
private transient MTBImageByte excludeMask

Optional mask to exclude particles in certain regions.

Particles in masked regions are ignored if mask is non-null.

additionalResultsWanted

@Parameter(label="Provide (binarized) correlation images",
           supplemental=true,
           direction=IN,
           mode=ADVANCED,
           dataIOOrder=10,
           description="If enabled additional intermediate results are provided.")
private boolean additionalResultsWanted

Flag to activate calculation of additional result images.

resultRegionCount

@Parameter(label="#Regions",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           description="Number of detected regions.")
private transient int resultRegionCount

Number of detected regions.

resultingRegions

@Parameter(label="Resulting particle regions",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=2,
           description="Detected particle regions.")
private transient MTBRegion2DSet resultingRegions

Set of detected particle regions.

resultOverlay

@Parameter(label="Resulting particle regions",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=3,
           description="Overlay of regions onto input image.")
private transient MTBImage resultOverlay

Detected regions plotted into input image.

resultMaskBinary

@Parameter(label="Binary particle region mask",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=4,
           description="Binary particle region mask.")
private transient MTBImageByte resultMaskBinary

Binary mask of detected regions.

correlationImages

@Parameter(label="Correlation images",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=1,
           supplemental=true,
           description="Correlation images for different scale intervals.")
private transient MTBImage correlationImages

Stack of correlation images for different scale combinations.

This stack is only generated if additionalResultsWanted is selected.

binaryCorrelationImages

@Parameter(label="Binarized correlation images",
           direction=OUT,
           mode=STANDARD,
           dataIOOrder=2,
           supplemental=true,
           description="Binarized correlation images.")
private transient MTBImageByte binaryCorrelationImages

Stack of binarized correlation images.

This stack is only generated if additionalResultsWanted is selected.

m_statusListeners

protected Vector<loci.common.StatusListener> m_statusListeners

Vector of installed StatusListener objects.

Constructor Detail

ParticleDetectorUWT2D

public ParticleDetectorUWT2D()
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ParticleDetectorUWT2D

public ParticleDetectorUWT2D(MTBImage img,
                             int _Jmin,
                             int _Jmax,
                             double _corrThreshold,
                             int _scaleIntervalSize,
                             int _minRegionSize,
                             boolean _poisson2gauss)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor with non-default parameters.

Parameters:

img - input image with bright granules on dark background

_Jmin - lowest scale index to be used for correlation image computations (scale is reciprocal to frequency properties)

_Jmax - highest scale index to be used for correlation image computations (scale is reciprocal to frequency properties)

_corrThreshold - threshold for wavelet correlation images to obtain detected region hypotheses

_scaleIntervalSize - size of the interval of scales that are used to compute wavelet correlation images

_minRegionSize - minimum size of a region to be chosen as detection

_poisson2gauss - flag if image with poisson noise is transformed to simulate gaussian noise

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

ParticleDetectorUWT2D

public ParticleDetectorUWT2D(MTBImage img,
                             int _Jmin,
                             int _Jmax,
                             double _corrThreshold,
                             int _scaleIntervalSize,
                             int _minRegionSize)
                      throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Constructor that sets the poisson2gauss flag to true

Parameters:

img - input image with bright granules on dark background

Jmin - lowest scale index to be used for correlation image computations (scale is reciprocal to frequency properties)

Jmax - highest scale index to be used for correlation image computations (scale is reciprocal to frequency properties)

corrThreshold - threshold for wavelet correlation images to obtain detected region hypotheses

scaleIntervalSize - size of the interval of scales that are used to compute wavelet correlation images

minRegionSize - minimum size of a region to be chosen as detection

Throws:

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

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 ParticleDetector

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

meaningfulNodes

protected Vector<MTBTreeNode> meaningfulNodes(MTBTreeNode treeNode,
                                              MTBImage[] corrImgs,
                                              MTBImageHistogram[] hists,
                                              int mode)

Get the most meaningful regions from a (sub)tree. The tree of regions is assumed to contain different detections from different scales in the same image location. Detections are the regions which "explain" best this image part, the most meaningful regions.

Parameters:

treeNode - root of the (sub) tree

corrImgs - correlation images

hists - cumulative histograms

mode - 0: weighted mean, 1: unweighted mean, 2: min, 3 or else: max

Returns:

getRegionsTree

protected MTBTree getRegionsTree(MTBImage[] binaryImages)
                          throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                 de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Build a tree of regions from binarized images. The binary images represent regions from different scales, fine scales have low indices in the array

Parameters:

binaryImages -

Returns:

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getCorrelationImages

protected MTBImage[] getCorrelationImages()
                                   throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                          de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Compute the correlation images as specified by the parameters.

Returns:

Array of correlation images starting with lowest scale interval which corresponds to the highest frequency interval.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

poisson2gauss

public static MTBImage poisson2gauss(MTBImage img)
                              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Transforms image with poisson noise to image with gaussian noise J.-L. Starck et al., Multiresolution Support Applied to Image Filtering and Restoration

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

gauss2poisson

protected static MTBImage gauss2poisson(MTBImage img)
                                 throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Transforms image with gaussian noise to image with poisson noise J.-L. Starck et al., Multiresolution Support Applied to Image Filtering and Restoration

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

getNormalizedCumulativeHistogram

protected MTBImageHistogram getNormalizedCumulativeHistogram(MTBImage img,
                                                             int bins)

Create a normalized cumulative histogram from an image

Parameters:

img - input image

bins - number of histogram bins

Returns:

normalized cumulative histogram

fillHoles

protected MTBImage fillHoles(MTBImage img)
                      throws IllegalArgumentException,
                             de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                             de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Throws:

IllegalArgumentException

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

threshImgNiblack

protected MTBImage threshImgNiblack(MTBImage img,
                                    double k,
                                    int winsize)
                             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                    de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getMaskFromNuclei

protected MTBImage getMaskFromNuclei(MTBImage nucleiImg)
                              throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                     de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

getLabelMostInRegion

protected Integer getLabelMostInRegion(MTBRegion2D reg,
                                       MTBImage img)

getLabelsInRegion

protected Vector<Integer> getLabelsInRegion(MTBRegion2D reg,
                                            MTBImage img)

meanOfRegion

protected double meanOfRegion(MTBRegion2D reg,
                              MTBImage img)

logPofRegion

protected double logPofRegion(MTBRegion2D reg,
                              MTBImage img,
                              MTBImageHistogram cumHist)

threshImage

protected MTBImage threshImage(MTBImage img,
                               double thresh)
                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                               de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

labelImage

protected MTBImage labelImage(MTBImage img,
                              MTBRegion2DSet regs)

regionsToBinImage

protected MTBImage regionsToBinImage(MTBImage img,
                                     MTBImage mask,
                                     Vector<MTBRegion2D> regs)

Create binary image from a set of regions. If mask != null, pixels where mask is 0 are not considered.

Parameters:

img - only used to determine the result image size

mask -

regs -

Returns:

processedRegionsToBinImage

protected MTBImage processedRegionsToBinImage(MTBImage img,
                                              MTBRegion2DSet regs,
                                              int _minRegionSize)

Create a binary image from given regions.

Regions smaller than _minRegionSize are rejected.

Parameters:

img - Input image.

regs - Region set.

_minRegionSize - Minimal size of regions considered.

Returns:

Binary image with regions.

threshDWTJeffreys

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

inverseATrousDWT

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

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

threshDWTCoeffs

protected void threshDWTCoeffs(MTBImage img,
                               double sigma)

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:

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

getInputImage

public MTBImage getInputImage()

Get input image

setInputImage

public void setInputImage(MTBImage img)

Set input image

getJmin

public Integer getJmin()

Get Jmin

setJmin

public void setJmin(int _Jmin)

Set Jmin

getJmax

public Integer getJmax()

Get Jmax

setJmax

public void setJmax(int _Jmax)

Set Jmax

getCorrelationThreshold

public Double getCorrelationThreshold()

Get threshold for thresholding wavelet correlation images

setCorrelationThreshold

public void setCorrelationThreshold(double corrThresh)

Set threshold for thresholding wavelet correlation images

getScaleIntervalSize

public Integer getScaleIntervalSize()

Get the size of the scale interval for correlation images

setScaleIntervalSize

public void setScaleIntervalSize(int _scaleIntervalSize)

Set the size of the scale interval for correlation images

getMinRegionSize

public int getMinRegionSize()

Get the minimum size of detected regions. All regions smaller than this size are rejected

setMinRegionSize

public void setMinRegionSize(int _minRegionSize)

Set the minimum size of detected regions. All regions smaller than this size are rejected

getPoisson2Gauss

public boolean getPoisson2Gauss()

Get flag if input image with poisson noise is to be transformed to image with gaussian noise following J.-L. Starck et al., Multiresolution Support Applied to Image Filtering and Restoration

setPoisson2Gauss

public void setPoisson2Gauss(boolean _poisson2gauss)

Set flag if input image with poisson noise is to be transformed to image with gaussian noise following J.-L. Starck et al., Multiresolution Support Applied to Image Filtering and Restoration

setExcludeMask

public void setExcludeMask(MTBImageByte mask)

Specify exclude mask.

getResults

public MTBRegion2DSet getResults()

Get resulting regions (each detetection corresponds to a region)

setResults

protected void setResults(MTBRegion2DSet detectedRegions)

Set detected regions

getResultCorrelationStack

public MTBImage getResultCorrelationStack()

Get resulting correlation image stack.

Note that additionalResultsWanted needs to be selected to get a non-null result here.

Returns:

Stack of correlation images.

getResultBinaryCorrelationStack

public MTBImage getResultBinaryCorrelationStack()

Get resulting binarized correlation image stack.

Note that additionalResultsWanted needs to be selected to get a non-null result here.

Returns:

Stack of binarized correlation images.

getDocumentation

public String getDocumentation()

Overrides:

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