MPMFFilter2D (mitobo 2.5 API)

java.lang.Object
- de.unihalle.informatik.Alida.operator.ALDOperator
- - de.unihalle.informatik.MiToBo.core.operator.MTBOperator
  - - de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener, loci.common.StatusReporter
```
@ALDAOperator(genericExecutionMode=ALL,
              level=APPLICATION)
public class MPMFFilter2D
extends MTBOperator
implements loci.common.StatusReporter
```
Multiscale Production of the Matched Filter (MPMF) implementation.
This operator applies matched filters on multiple scales. The results are then combined by pairwise multiplication followed by hysteresis thresholding of each resulting product. Finally, all binary images are combined into a single result map applying logical OR operations.
As matched filters a second order Gaussian derivative filter, i.e., a Mexican hat filter function is applied. Here we use MiToBo's implementation of such a filter which is to be found in class GaussPDxxFilter2D.
Related publication:
Q. Li, J. You, and D. Zhang, "Vessel Segmentation and Width Estimation in Retinal Images using Multiscale Production of Matched Filter Responses", Expert Systems with Applications, 39 (2012), pp. 7600-7610.
Here we assume vessels to exhibit a Gaussian profile (while in the paper a box profile is assumed). The width of the vessels is defined as two-times the standard deviation of the Gaussian kernel mask. To normalize the filter responses of different scales we follow the scheme proposed in
Sofka and Stewart, "Retinal Vessel Centerline Extraction Using Multiscale Matched Filters, Confidence and Edge Measures", IEEE TMI, vol. 25, no. 12, pp. 1531-1546, December 2006,
i.e. apply $(\sigma \cdot \sigma)^{\frac{3}{4}}$ as normalization factor at scale $\sigma$ .

Author:

Birgit Moeller

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`private class`	`MPMFFilter2D.ResponseDifference` Function to find roots during middle scale calculation.
`static class`	`MPMFFilter2D.VesselMode` Detection scenario mode.

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
`protected int`	`angleSampling` Sampling step size for orientations considered.
`private static double`	`higherThresholdRatio` Factor to choose higher threshold in hysteresis thresholding automatically.
`protected MTBImage`	`inputImg` Input image to be processed.
`protected double`	`maxWidth` Expected width of thick vessels.
`protected double`	`minWidth` Expected width of thin vessels.
`protected MPMFFilter2D.VesselMode`	`mode` Scenario for detecting vessels, i.e. relation of foreground to background.
`private MTBImageDouble`	`responseStack` Result stack with intermediate results.
`protected MTBImageByte`	`resultVesselMap` Resulting binary vessel map.
`private static double`	`scaleNormalizationFactor` Factor to normalize filter responses of different scales appropriately.
`protected Vector<loci.common.StatusListener>`	`statusListeners` Vector of installed StatusListeners.
`protected double`	`threshold` Higher threshold for binarization.

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator
completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors
Constructor and Description

MPMFFilter2D()
Default constructor.

Constructors
Constructor and Description
`MPMFFilter2D()` Default constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addStatusListener(loci.common.StatusListener statuslistener)`
`protected double`	`findMiddleScale(double minScale, double maxScale)` Numerically finds the middle scale between to given scales.
`MTBImageByte`	`getBinaryResultMap()` Returns the final binary map.
`MTBImageDouble`	`getResponseStack()` Returns stack with intermediate (non-binary) results.
`protected static double`	`normalizedFilterResponse(double vScale, double fScale)` Computes the (ideal) filter response to the Gaussian derivative kernel.
`void`	`notifyListeners(loci.common.StatusEvent e)`
`protected void`	`operate()`
`protected Object`	`readResolve()` Init function for deserialized objects.
`void`	`removeStatusListener(loci.common.StatusListener statuslistener)`
`void`	`validateCustom()`

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, 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
  - scaleNormalizationFactor
```
private static final double scaleNormalizationFactor
```
    Factor to normalize filter responses of different scales appropriately.
    See Sofka and Stewart, 2006, for details.
    
    See Also:
    
    Constant Field Values
  - higherThresholdRatio
```
private static final double higherThresholdRatio
```
    Factor to choose higher threshold in hysteresis thresholding automatically.
    The threshold is determined by multiplying this factor with the intensity maximum to be found in the image to threshold. Its value has been chosen according to some empirical experiments.
    
    See Also:
    
    Constant Field Values
  - statusListeners
```
protected transient Vector<loci.common.StatusListener> statusListeners
```
    Vector of installed StatusListeners.
  - inputImg
```
@Parameter(label="Input Image",
           required=true,
           dataIOOrder=-10,
           direction=IN,
           mode=STANDARD,
           description="Input image.")
protected transient MTBImage inputImg
```
    Input image to be processed.
  - mode
```
@Parameter(label="Scenario",
           required=true,
           dataIOOrder=1,
           direction=IN,
           mode=STANDARD,
           description="Relation of vessels to background.")
protected MPMFFilter2D.VesselMode mode
```
    Scenario for detecting vessels, i.e. relation of foreground to background.
  - minWidth
```
@Parameter(label="Thin Vessel Width",
           required=true,
           dataIOOrder=2,
           direction=IN,
           mode=STANDARD,
           description="Expected width of thin vessels.")
protected double minWidth
```
    Expected width of thin vessels.
  - maxWidth
```
@Parameter(label="Thick Vessel Width",
           required=true,
           dataIOOrder=3,
           direction=IN,
           mode=STANDARD,
           description="Expected width of thick vessels.")
protected double maxWidth
```
    Expected width of thick vessels.
  - angleSampling
```
@Parameter(label="Angular Sampling Steps",
           required=true,
           direction=IN,
           mode=ADVANCED,
           description="Angular sampling step size (in degrees).",
           dataIOOrder=5)
protected int angleSampling
```
    Sampling step size for orientations considered.
  - threshold
```
@Parameter(label="(Upper) Threshold",
           required=false,
           dataIOOrder=0,
           direction=IN,
           mode=ADVANCED,
           description="Binarization threshold, if set to -1 a threshold is determined automatically.")
protected double threshold
```
    Higher threshold for binarization.
  - resultVesselMap
```
@Parameter(label="Result Map",
           dataIOOrder=0,
           direction=OUT,
           description="Resulting vessel map.")
protected transient MTBImageByte resultVesselMap
```
    Resulting binary vessel map.
  - responseStack
```
@Parameter(label="Filter Response Stack",
           dataIOOrder=1,
           direction=OUT,
           description="Filter response stack.")
private transient MTBImageDouble responseStack
```
    Result stack with intermediate results.
    Only generated in verbose mode.
- Constructor Detail
  - MPMFFilter2D
```
public MPMFFilter2D()
             throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException
```
    Default constructor.
    
    Throws:
    
    de.unihalle.informatik.Alida.exceptions.ALDOperatorException
- Method Detail
  - getBinaryResultMap
```
public MTBImageByte getBinaryResultMap()
```
    Returns the final binary map.
    
    Returns:
    
    Binary result map.
  - getResponseStack
```
public MTBImageDouble getResponseStack()
```
    Returns stack with intermediate (non-binary) results.
    Note that the stack is only created if the verbose mode is activated.
    
    Returns:
    
    Stack with intermediate results.
  - 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.
  - 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,
                       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
  - findMiddleScale
```
protected double findMiddleScale(double minScale,
                                 double maxScale)
```
    Numerically finds the middle scale between to given scales.
    
    Parameters:
    
    minScale - Scale of thin vessels (given as standard deviation).
    
    maxScale - Scale of thick vessels (given as standard deviation).
    
    Returns:
    
    Standard deviation of middle scale.
  - 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
  - normalizedFilterResponse
```
protected static double normalizedFilterResponse(double vScale,
                                                 double fScale)
```
    Computes the (ideal) filter response to the Gaussian derivative kernel.
    The function returns the result of convolving a Gaussian function centered at and having a standard deviation of $%preamble{\usepackage{amssymb, amsmath}}$ (defining the model of a vessel) with a second derivative Gaussian matched filter with standard deviation $%preamble{\usepackage{amssymb, amsmath}}$ .The result is normalized as proposed in Sofka et al.
    
    Parameters:
    
    vScale - Standard deviation of the Gaussian vessel function.
    
    fScale - Standard deviation of the matched filter kernel.
    
    Returns:
    
    Normalized filter response.

Class MPMFFilter2D

Nested Class Summary

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

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

scaleNormalizationFactor

higherThresholdRatio

statusListeners

inputImg

mode

minWidth

maxWidth

angleSampling

threshold

resultVesselMap

responseStack

Constructor Detail

MPMFFilter2D

Method Detail

getBinaryResultMap

getResponseStack

readResolve

validateCustom

operate

findMiddleScale

addStatusListener

notifyListeners

removeStatusListener

normalizedFilterResponse