java.lang.Object
- java.lang.Thread
- - gov.nih.mipav.model.algorithms.AlgorithmBase
  - - gov.nih.mipav.model.algorithms.AlgorithmPrincipalComponents

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.FocusListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmPrincipalComponents
extends AlgorithmBase
implements java.awt.event.ActionListener, java.awt.event.FocusListener
```
This algorithm operates on 3D black and white images and on 2D and 3D color images. The user can select 1 or both of 2 output images: The first image is a filtered 3D image containing only the first n principal components, where n is selected by the user after viewing images of the first 10 (or the number that exist if less than 10) principal components. The second image is a 2D image created by averaging together the images in the 3D image. Note that red, green, and blue are treated as separate 2D planes. This implementation assumes that the noise variance is equal in every slice and that the noise is uncorrelated between slices. Principal components maximizes data variance in components; it concentrates the information content of the data in as small a number of components as possible. This algorithm is based on: 1.) Digital Image Processing, Third Edition by Rafael C. Gonzalez and Richard E. Woods, Section 11.4 Use of Principal Components for Description, pp. 842 - 852, 2008 by Pearson Education, Inc. Information about using a matchImage: Eigenfaces for Recognition by Matthew Turk and Alex Pentland Vision and Modeling Group The Media Laboratory Massachusetts Institute of Technology 2.) Gabor Feature Based Classification Using the Enhanced Linear Discriminant Model for Face Recognition by Chengjun Liu and Harry Wechsler states "For the Eigenfaces method, the Mahalanobis distance measure performs better than the L1 distance measure, followed in order by the L2 distance measure and the cosine similarity measure as shown in Fig. 6. The Mahalanobis distance measure performs better than the other similarity measures because the Mahalanobis distance measure counteracts the fact that the L1 and L2 distance measures in PCA space weight preferentially for low frequencies, and this is consistent with results reported by Moghaddam and Pentland and Sung and Poggio. As the L2 measure weights more the low frequencies than L1 does, the L1 distance measure should perform better than the L2 distance measure, a conjecture validated by our experiments as shown in Figure 6. The cosine similarity measure does not compensate the low frequency preference, and it performs worst among all the measures." 3.) "The statistical properties of three noise removal procedures for multichannel remotely sensed data" by M. Berman, CSIRO Division of Mathemetics and Statistics P.O. Box 218, Lindfield, N.S.W., 2070 Consulting Report NSW/85/31/MB9 Note that this algorithm has 4 different names: Hotelling, eigenvector, principal component, and Karhunen-Loeve transform. Also note that when the noise variance is the same in all bands and the noise is uncorrelated between bands the principal component transformation is equivalent to the maximum noise fraction transformation. In the more general case, the MNF transform is equivalent to a transformation of the data to a coordinate system in which the noise covariance matrix is the identity matrix, followed by a principal components transformation. The transform in this form is the noise-adjusted principal components transform. In forward order MNF maximizes the noise content in successive components that are uncorrelated over the dataset or equivalently in reverse order MNF maximizes the signal to noise ratio of each component. Information about the signal to noise ratio improvement is found in "Information Extraction, SNR Improvement, and Data Compression in MultiSpectral Imagery", Patrick J. Ready and Paul A. Wintz, IEEE Transactions on Communications, Vol. COM-21, No. 10, October, 1973, pp. 1123-1130.

Nested Class Summary
- Nested classes/interfaces inherited from class java.lang.Thread
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`private ModelImage[]`	`destImage`	DOCUMENT ME!
`private boolean`	`displayAndAsk`	DOCUMENT ME!
`private boolean`	`doAveraging`	if true create an image averaging together the slices in the filtered version.
`private boolean`	`doFilter`	if true create a filtered version of the original image.
`private boolean`	`doMahalanobisDistance`
`private boolean`	`haveColor`	DOCUMENT ME!
`private ModelImage`	`matchImage`	If this 2D black and white image is present, it is matched to the closest slice and/or color in the source image model by looking for the closest match of the weights of the principal components.
`private int`	`nPlanes`	number of image planes present.
`private int`	`nPresent`	number of principal components displayed 10 or less than 10 if fewer exist.
`private javax.swing.JButton`	`OKButton`	DOCUMENT ME!
`private int`	`pNumber`	number of principal components to be retained.
`private javax.swing.JDialog`	`pNumberDialog`	DOCUMENT ME!
`private boolean`	`pressedOK`	DOCUMENT ME!
`private ModelImage`	`srcImage`	DOCUMENT ME!
`private javax.swing.JTextField`	`textNumber`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
destFlag, image25D, mask, maxProgressValue, minProgressValue, multiThreadingEnabled, nthreads, progress, progressModulus, progressStep, runningInSeparateThread, separable, threadStopped

Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors
Constructor	Description
`AlgorithmPrincipalComponents(ModelImage[] destImg, ModelImage srcImg, boolean doFilter, boolean doAveraging, boolean displayAndAsk, int pNumber)`	Creates a new AlgorithmPrincipalComponents object.
`AlgorithmPrincipalComponents(ModelImage[] destImg, ModelImage srcImg, ModelImage matchImage, boolean doFilter, boolean doAveraging, boolean displayAndAsk, int pNumber, boolean doMahalanobisDistance)`	Creates a new AlgorithmPrincipalComponents object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`actionPerformed(java.awt.event.ActionEvent event)`	Calls various methods depending on the action.
`private void`	`createPNumberDialog(java.awt.event.ActionListener al)`	DOCUMENT ME!
`void`	`finalize()`	Prepares this class for destruction.
`void`	`focusGained(java.awt.event.FocusEvent event)`	Do nothing.
`void`	`focusLost(java.awt.event.FocusEvent event)`	Do nothing.
`private void`	`pComponent()`	DOCUMENT ME!
`void`	`runAlgorithm()`	Start algorithm.
`void`	`updateFileInfo(ModelImage image, ModelImage resultImage)`	Copy important file information to resultant image structure.

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
addListener, addProgressChangeListener, calculateImageSize, calculatePrincipleAxis, computeElapsedTime, computeElapsedTime, convertIntoFloat, delinkProgressToAlgorithm, delinkProgressToAlgorithmMulti, displayError, errorCleanUp, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, fireProgressStateChanged, generateProgressValues, getDestImage, getElapsedTime, getMask, getMaxProgressValue, getMinProgressValue, getNumberOfThreads, getProgress, getProgressChangeListener, getProgressChangeListeners, getProgressModulus, getProgressStep, getProgressValues, getSrcImage, isCompleted, isImage25D, isMultiThreadingEnabled, isRunningInSeparateThread, isThreadStopped, linkProgressToAlgorithm, linkProgressToAlgorithm, makeProgress, notifyListeners, removeListener, removeProgressChangeListener, run, setCompleted, setImage25D, setMask, setMaxProgressValue, setMinProgressValue, setMultiThreadingEnabled, setNumberOfThreads, setProgress, setProgressModulus, setProgressStep, setProgressValues, setProgressValues, setRunningInSeparateThread, setSrcImage, setStartTime, setThreadStopped, startMethod, windowActivated, windowClosed, windowClosing, windowDeactivated, windowDeiconified, windowIconified, windowOpened

Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, toString, yield

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

- Field Detail
  - destImage
```
private ModelImage[] destImage
```
    DOCUMENT ME!
  - displayAndAsk
```
private boolean displayAndAsk
```
    DOCUMENT ME!
  - doAveraging
```
private boolean doAveraging
```
    if true create an image averaging together the slices in the filtered version.
  - doFilter
```
private boolean doFilter
```
    if true create a filtered version of the original image.
  - haveColor
```
private boolean haveColor
```
    DOCUMENT ME!
  - nPlanes
```
private int nPlanes
```
    number of image planes present.
  - nPresent
```
private int nPresent
```
    number of principal components displayed 10 or less than 10 if fewer exist.
  - OKButton
```
private javax.swing.JButton OKButton
```
    DOCUMENT ME!
  - pNumber
```
private int pNumber
```
    number of principal components to be retained.
  - pNumberDialog
```
private javax.swing.JDialog pNumberDialog
```
    DOCUMENT ME!
  - pressedOK
```
private boolean pressedOK
```
    DOCUMENT ME!
  - srcImage
```
private ModelImage srcImage
```
    DOCUMENT ME!
  - textNumber
```
private javax.swing.JTextField textNumber
```
    DOCUMENT ME!
  - matchImage
```
private ModelImage matchImage
```
    If this 2D black and white image is present, it is matched to the closest slice and/or color in the source image model by looking for the closest match of the weights of the principal components.
  - doMahalanobisDistance
```
private boolean doMahalanobisDistance
```
- Constructor Detail
  - AlgorithmPrincipalComponents
```
public AlgorithmPrincipalComponents(ModelImage[] destImg,
                                    ModelImage srcImg,
                                    ModelImage matchImage,
                                    boolean doFilter,
                                    boolean doAveraging,
                                    boolean displayAndAsk,
                                    int pNumber,
                                    boolean doMahalanobisDistance)
```
    Creates a new AlgorithmPrincipalComponents object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    matchImage - match image match this image to the closest slice and/or color in the source image
    
    doFilter - if true create a filtered version of the original image
    
    doAveraging - if true create an image averaging together the slices in the filtered version
    
    displayAndAsk - if true display principal component images and ask how many to retain
    
    pNumber - if displayAndAsk if false pNumber is the number of principal component images to retain
    
    doMahalanobisDistance - Select Euclidean or Mahalanobis distance for matching
  - AlgorithmPrincipalComponents
```
public AlgorithmPrincipalComponents(ModelImage[] destImg,
                                    ModelImage srcImg,
                                    boolean doFilter,
                                    boolean doAveraging,
                                    boolean displayAndAsk,
                                    int pNumber)
```
    Creates a new AlgorithmPrincipalComponents object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    doFilter - if true create a filtered version of the original image
    
    doAveraging - if true create an image averaging together the slices in the filtered version
    
    displayAndAsk - if true display principal component images and ask how many to retain
    
    pNumber - if displayAndAsk if false pNumber is the number of principal component images to retain
- Method Detail
  - actionPerformed
```
public void actionPerformed(java.awt.event.ActionEvent event)
```
    Calls various methods depending on the action.
    
    Specified by:
    
    actionPerformed in interface java.awt.event.ActionListener
    
    Overrides:
    
    actionPerformed in class AlgorithmBase
    
    Parameters:
    
    event - event that triggered function
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - focusGained
```
public void focusGained(java.awt.event.FocusEvent event)
```
    Do nothing.
    
    Specified by:
    
    focusGained in interface java.awt.event.FocusListener
    
    Parameters:
    
    event - Focus event
  - focusLost
```
public void focusLost(java.awt.event.FocusEvent event)
```
    Do nothing.
    
    Specified by:
    
    focusLost in interface java.awt.event.FocusListener
    
    Parameters:
    
    event - Focus event
  - runAlgorithm
```
public void runAlgorithm()
```
    Start algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - updateFileInfo
```
public void updateFileInfo(ModelImage image,
                           ModelImage resultImage)
```
    Copy important file information to resultant image structure.
    
    Parameters:
    
    image - Source image.
    
    resultImage - Resultant image.
  - createPNumberDialog
```
private void createPNumberDialog(java.awt.event.ActionListener al)
```
    DOCUMENT ME!
    
    Parameters:
    
    al - DOCUMENT ME!
  - pComponent
```
private void pComponent()
```
    DOCUMENT ME!

Class AlgorithmPrincipalComponents

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Field Summary

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Fields inherited from class java.lang.Thread

Constructor Summary

Method Summary

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase

Methods inherited from class java.lang.Thread

Methods inherited from class java.lang.Object

Field Detail

destImage

displayAndAsk

doAveraging

doFilter

haveColor

nPlanes

nPresent

OKButton

pNumber

pNumberDialog

pressedOK

srcImage

textNumber

matchImage

doMahalanobisDistance

Constructor Detail

AlgorithmPrincipalComponents

AlgorithmPrincipalComponents

Method Detail

actionPerformed

finalize

focusGained

focusLost

runAlgorithm

updateFileInfo

createPNumberDialog

pComponent