IqmOpFracPyramid (IQM 3.5 API)

java.lang.Object
- at.mug.iqm.api.operator.AbstractOperator
- - at.mug.iqm.img.bundle.op.IqmOpFracPyramid

All Implemented Interfaces:

IProgressEmitter, ICancelable, IOperator
```
public class IqmOpFracPyramid
extends AbstractOperator
```
2010 03 added grey value image support, Surface is calculated according to Chinga etal. J Microsc. 227 2007 not sure if it works properly!!!
2011 01 bug fix for binary images. Condition for filteredsubsample : resizing previously resized image
2011 01 added 16 bit support
2011 02 added regression data to table
2011 02 removing ModelListener extremely speeds up model configuration (adding columns, writing data,...)
2011 03 created separate method for estimation of surface area (Gradient method according to Chinga)
2011 03 added Blanket method for estimation of surface area (Blanket method according to Tang, Tao, Lam PattRec 2002, 35 1071-1081)
2011 05 added Allometric scaling (variance in dependence on the mean) according to B. West
2015 03 updated Gradient Method (Chinga) for FD estimation of grey value surfaces, coefficients of kernels have to include scale
2016 01 updated PGM (Pyramidal Gradient Method) + added PDM, both for FD estimation of grey value surfaces
2016 01 added Kolmogorov Complexity

Since:: 2009 07
Author:: Helmut Ahammer, Philipp Kainz, Michael Mayrhofer-R.

Field Summary

Fields
Modifier and Type Field and Description

private static org.apache.log4j.Logger logger
Logging variable.

private File logicalDepthDir
- Fields inherited from class at.mug.iqm.api.operator.AbstractOperator
  isCancelable, name, parentTask, pcs, type

Fields
Modifier and Type	Field and Description
`private static org.apache.log4j.Logger`	`logger` Logging variable.
`private File`	`logicalDepthDir`

Constructor Summary

Constructors
Constructor and Description

IqmOpFracPyramid()

Constructors
Constructor and Description
`IqmOpFracPyramid()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`private double[]`	`calculateKC(javax.media.jai.PlanarImage pi)` This method estimates the Kolmogorov Complexity by lossless compression
`private double[]`	`calculatePDM(javax.media.jai.PlanarImage pi)` This method calculates the sum of differences according to the PDM (see Mayrhofer-R., PhD thesis, Med.
`private double[]`	`calculateTotalsBlanketMethod(javax.media.jai.PlanarImage pi)` This method calculates the area of a grey value surface one step of Blanket Method (Minkowski dilation for surface) according to Tang, Tao, Lam.
`private double[]`	`calculateTotalsEntropyMethod(javax.media.jai.PlanarImage pi)` This method calculates the entropy of a grey value surface
`private double[]`	`calculateTotalsGradientMethod(javax.media.jai.PlanarImage pi, float[] scale)` PGM - Pyramidal Gradients Method (Sobel kernel) This method calculates the area of a grey value surface based on the PGM method developed by Michael Mayrhofer-R.
`private void`	`deleteTempFile(String fileName)` This method is used by the KC method This method looks for the file (image) and deletes it
`String`	`getName()` Gets the unique name of the `IOperator` by returning the "GlobalName" element from the `resources[][]` of the associated `IOperatorDescriptor`.
`OperatorType`	`getType()` Gets the type of the operator listed in an enumeration.
`IResult`	`run(IWorkPackage wp)` This method contains the entire logic (algorithm) of the operator.

Methods inherited from class at.mug.iqm.api.operator.AbstractOperator
addProgressListener, fireProgressChanged, getParentTask, getPcs, getProgressListeners, initializeOperator, isCancelable, isCancelled, setCancelable, setParentTask

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - logger
```
private static final org.apache.log4j.Logger logger
```
    Logging variable.
  - logicalDepthDir
```
private File logicalDepthDir
```
- Constructor Detail
  - IqmOpFracPyramid
```
public IqmOpFracPyramid()
```
- Method Detail
  - deleteTempFile
```
private void deleteTempFile(String fileName)
```
    This method is used by the KC method This method looks for the file (image) and deletes it
    
    Parameters:
    
    string -
  - calculateTotalsGradientMethod
```
private double[] calculateTotalsGradientMethod(javax.media.jai.PlanarImage pi,
                                               float[] scale)
```
    PGM - Pyramidal Gradients Method (Sobel kernel) This method calculates the area of a grey value surface based on the PGM method developed by Michael Mayrhofer-R. (see Mayrhofer-R., PhD thesis, Med. Univ. Graz, 2015) using area calculations with gradients (according to Chinga etal. J Microsc. 227 2007)
    
    Parameters:
    
    PlanarImage - pi;
  - calculatePDM
```
private double[] calculatePDM(javax.media.jai.PlanarImage pi)
```
    This method calculates the sum of differences according to the PDM (see Mayrhofer-R., PhD thesis, Med. Univ. Graz, 2015)
    
    Parameters:
    
    PlanarImage - pi;
  - calculateKC
```
private double[] calculateKC(javax.media.jai.PlanarImage pi)
```
    This method estimates the Kolmogorov Complexity by lossless compression
    
    Parameters:
    
    PlanarImage - pi;
  - calculateTotalsBlanketMethod
```
private double[] calculateTotalsBlanketMethod(javax.media.jai.PlanarImage pi)
```
    This method calculates the area of a grey value surface one step of Blanket Method (Minkowski dilation for surface) according to Tang, Tao, Lam. Patt Rec. 2002, 35,1071-1081
    
    Parameters:
    
    PlanarImage - pi2;
  - calculateTotalsEntropyMethod
```
private double[] calculateTotalsEntropyMethod(javax.media.jai.PlanarImage pi)
```
    This method calculates the entropy of a grey value surface
    
    Parameters:
    
    PlanarImage - pi2;
  - run
```
public IResult run(IWorkPackage wp)
```
    Description copied from interface: IOperator
    
    This method contains the entire logic (algorithm) of the operator. An IOperator does not declare any class members, since the execution of this code must be thread-safe.
    
    Specified by:
    
    run in interface IOperator
    
    Specified by:
    
    run in class AbstractOperator
    
    Parameters:
    
    wp - the parameters and sources
    
    Returns:
    
    a IResult containing all processed data
  - getName
```
public String getName()
```
    Description copied from interface: IOperator
    
    Gets the unique name of the IOperator by returning the "GlobalName" element from the resources[][] of the associated IOperatorDescriptor.
    
    Specified by:
    
    getName in interface IOperator
    
    Specified by:
    
    getName in class AbstractOperator
    
    Returns:
    
    the unique name of the operator
  - getType
```
public OperatorType getType()
```
    Description copied from interface: IOperator
    
    Gets the type of the operator listed in an enumeration.
    
    Specified by:
    
    getType in interface IOperator
    
    Specified by:
    
    getType in class AbstractOperator
    
    Returns:
    
    the OperatorType

Class IqmOpFracPyramid

Field Summary

Fields inherited from class at.mug.iqm.api.operator.AbstractOperator

Constructor Summary

Method Summary

Methods inherited from class at.mug.iqm.api.operator.AbstractOperator

Methods inherited from class java.lang.Object

Field Detail

logger

logicalDepthDir

Constructor Detail

IqmOpFracPyramid

Method Detail

deleteTempFile

calculateTotalsGradientMethod

calculatePDM

calculateKC

calculateTotalsBlanketMethod

calculateTotalsEntropyMethod

run

getName

getType