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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmMatchImages
extends AlgorithmBase
```
Matches two ModelImages. The output of this Algorithm is two ModelImages that have the same units of measure, the same resolutions, and the same extents. If the user chooses, the image orientations (left-to-right, anterior-to-posterior, inferior-to-superior, etc) will be matched. If the user chooses, the image origins will be matched. Either imageA, imageB or sometimes neither will be different after the algorithm completes. The result images are returned with the getImageA() and getImageB() functions.

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 boolean`	`doOrients`	flag for turning on/off using the image orientations to match the images
`private boolean`	`doOrigins`	flag for turning on/off using the image origins to match the images
`private float[]`	`padValue`	image values to use for padding the images, if necessary
`private ModelImage`	`srcImageB`	srcImageB: image to match to srcImage
`private boolean`	`useReferenceResolutions`	When true resolution matching defaults to the reference image.

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

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

Constructor Summary

Constructors
Constructor	Description
`AlgorithmMatchImages(ModelImage kImageA, ModelImage kImageB, boolean doOrigins, boolean doOrients)`	Create an AlgorithmMatchImages to match the two input images.
`AlgorithmMatchImages(ModelImage kImageA, ModelImage kImageB, boolean doOrigins, boolean doOrients, boolean useReferenceResolutions)`	Create an AlgorithmMatchImages to match the two input images.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private ModelImage`	`changeResolutions(ModelImage kImage, float[] afNewRes)`	Changes the resolutions of the input image.
`void`	`disposeLocal()`	remove local memory
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getImageA()`	Returns imageA, which may have changed during the match.
`ModelImage`	`getImageB()`	Returns imageB, which may have changed during the match.
`private boolean`	`matchOriginsExtents(ModelImage imageA, ModelImage imageB, int[] padAFront, int[] padABack, int[] padBFront, int[] padBBack)`	Matches the origins and extents of the two input images.
`private float[]`	`matchResolutions(ModelImage imageA, ModelImage imageB)`	Match the resolutions of the two images.
`private void`	`matchUnits(ModelImage imageA, ModelImage imageB)`	Matches the units of measure for the two input images.
`private ModelImage`	`padImage(ModelImage kImage, int[] padFront, int[] padBack)`	Adds or removes margins to the input image.
`void`	`runAlgorithm()`	Actually runs the algorithm.
`void`	`setPadValue(float value)`	Sets the pad value for single-channel images.
`void`	`setPadValue(float red, float green, float blue)`	Sets the pad value for color images

Methods inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
actionPerformed, 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
  - srcImageB
```
private ModelImage srcImageB
```
    srcImageB: image to match to srcImage
  - doOrigins
```
private boolean doOrigins
```
    flag for turning on/off using the image origins to match the images
  - doOrients
```
private boolean doOrients
```
    flag for turning on/off using the image orientations to match the images
  - useReferenceResolutions
```
private boolean useReferenceResolutions
```
    When true resolution matching defaults to the reference image.
  - padValue
```
private float[] padValue
```
    image values to use for padding the images, if necessary
- Constructor Detail
  - AlgorithmMatchImages
```
public AlgorithmMatchImages(ModelImage kImageA,
                            ModelImage kImageB,
                            boolean doOrigins,
                            boolean doOrients)
```
    Create an AlgorithmMatchImages to match the two input images.
    
    Parameters:
    
    kImageA - target image to match to
    
    kImageB - image that is changing to match to imageA
    
    doOrigins - flag for turning on/off using the image origins to match the images
    
    doOrients - flag for turning on/off using the image orientations to match the images
  - AlgorithmMatchImages
```
public AlgorithmMatchImages(ModelImage kImageA,
                            ModelImage kImageB,
                            boolean doOrigins,
                            boolean doOrients,
                            boolean useReferenceResolutions)
```
    Create an AlgorithmMatchImages to match the two input images.
    
    Parameters:
    
    kImageA - target image to match to
    
    kImageB - image that is changing to match to imageA
    
    doOrigins - flag for turning on/off using the image origins to match the images
    
    doOrients - flag for turning on/off using the image orientations to match the images
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    remove local memory
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getImageA
```
public ModelImage getImageA()
```
    Returns imageA, which may have changed during the match.
    
    Returns:
    
    imageA
  - getImageB
```
public ModelImage getImageB()
```
    Returns imageB, which may have changed during the match.
    
    Returns:
    
    imageB
  - setPadValue
```
public void setPadValue(float value)
```
    Sets the pad value for single-channel images.
    
    Parameters:
    
    value - value used to pad images.
  - setPadValue
```
public void setPadValue(float red,
                        float green,
                        float blue)
```
    Sets the pad value for color images
    
    Parameters:
    
    red - red pad value
    
    green - green pad value
    
    blue - blue pad value
  - runAlgorithm
```
public void runAlgorithm()
```
    Description copied from class: AlgorithmBase
    
    Actually runs the algorithm. Implemented by inheriting algorithms.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - matchUnits
```
private void matchUnits(ModelImage imageA,
                        ModelImage imageB)
```
    Matches the units of measure for the two input images.
    
    Parameters:
    
    imageA - target image to match to.
    
    imageB - image that is being changed.
  - matchResolutions
```
private float[] matchResolutions(ModelImage imageA,
                                 ModelImage imageB)
```
    Match the resolutions of the two images. Determines the lowest resolution of either image along each dimension. If useReferenceResolutions is true, the reference image (imageA) resolutions are used.
    
    Parameters:
    
    imageA -
    
    imageB -
    
    Returns:
    
    new resolutions that will be applied to both images.
  - changeResolutions
```
private ModelImage changeResolutions(ModelImage kImage,
                                     float[] afNewRes)
```
    Changes the resolutions of the input image.
    
    Parameters:
    
    kImage - input image.
    
    afNewRes - new resolutions.
    
    Returns:
    
    new ModelImage, or the input image if unchanged.
  - matchOriginsExtents
```
private boolean matchOriginsExtents(ModelImage imageA,
                                    ModelImage imageB,
                                    int[] padAFront,
                                    int[] padABack,
                                    int[] padBFront,
                                    int[] padBBack)
```
    Matches the origins and extents of the two input images. Matching origins is an option the user sets.
    
    Parameters:
    
    imageA - input image A.
    
    imageB - input image B.
    
    padAFront - output values for adding or removing voxels to the front of imageA [left,top,front,time]
    
    padABack - output values for adding or removing voxels to the back of imageA [right,bottom,back,time]
    
    padBFront - output values for adding or removing voxels to the front of imageB [left,top,front,time]
    
    padBBack - output values for adding or removing voxels to the back of imageB [right,bottom,back,time]
    
    Returns:
    
    true if either image requires changing to match the two images, false if neither image requires changing.
  - padImage
```
private ModelImage padImage(ModelImage kImage,
                            int[] padFront,
                            int[] padBack)
```
    Adds or removes margins to the input image.
    
    Parameters:
    
    kImage - input images.
    
    padFront - margins to add or remove to the front of the image [left,top,front,time]
    
    padBack - margins to add or remove to the end of the image [right,bottom,back,time]
    
    Returns:
    
    new image or the original input image if no change.

Class AlgorithmMatchImages

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

srcImageB

doOrigins

doOrients

useReferenceResolutions

padValue

Constructor Detail

AlgorithmMatchImages

AlgorithmMatchImages

Method Detail

disposeLocal

finalize

getImageA

getImageB

setPadValue

setPadValue

runAlgorithm

matchUnits

matchResolutions

changeResolutions

matchOriginsExtents

padImage