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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmSwapSlicesVolume
extends AlgorithmBase
```
Title: AlgorithmSwapSlicesVolume

Description: Allows user to re-slice/re-volume and associates fileInfo. This allows for slice/volume duplication, deletion, or insertion.

Version:

0.9

Author:

Justin Senseney

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 int`	`extentDest`	Internal sorting variables for sorting slices on images of greater than 3 dimensions
`private int`	`extentSrc`	Internal sorting variables for sorting slices on images of greater than 3 dimensions
`private JDialogSwapSlicesVolumes.SwapMode`	`mode`	Swap mode, either 3D or 4D.
`private int`	`nSlices`	Number of slices in mode.
`private int[][]`	`sliceRenum`	Reordering of slices/volumes.
`private int`	`sliceSize`	Number of pixels used by a slice/volume, includes colorFactor.
`private boolean[]`	`sliceTouched`	Slices that have been examined in recursive structure for swapping slices.
`private int[]`	`srcExtents`	Original extents array
`private FileInfoBase[]`	`srcFileInfos`	Original FileInfoBase array.

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
`AlgorithmSwapSlicesVolume(ModelImage destImage, JDialogSwapSlicesVolumes.SwapMode mode, int[][] sliceRenum, ModelImage srcImage)`	Import source and destination images into the class.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private boolean`	`allSlicesTouched()`
`private FileInfoBase[]`	`collectFileInfos(int in, int tDim)`	Gets the fileInfos from the specified position.
`void`	`finalize()`	Prepares this class for destruction.
`protected int`	`getColorFactor()`	Calculates and returns the color factor based on the srcImage.
`ModelImage`	`getSwappedVolume()`	Return the images extracted from the source image.
`private void`	`importFileInfos(ModelImage destImage, FileInfoBase[] fileIn, int in, int tDim)`	Inserts the fileInfos into the specified position.
`private void`	`reallocate(ModelImage image)`	Reallocate destImage so that fileInfo and buffer equal required length
`void`	`runAlgorithm()`	Calculates the final output.
`private void`	`swapSlices()`	Calculates the final output and stores it in the source image.
`private boolean`	`transferIn(int in)`	Starts method of file/image transferring
`private boolean`	`transferIn(FileInfoBase[] fileIn, java.lang.Number[] bufferIn, int in, int tDim)`	Transfers the given buffer into the given location.

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
  - mode
```
private JDialogSwapSlicesVolumes.SwapMode mode
```
    Swap mode, either 3D or 4D.
  - nSlices
```
private int nSlices
```
    Number of slices in mode.
  - sliceRenum
```
private int[][] sliceRenum
```
    Reordering of slices/volumes.
  - sliceSize
```
private int sliceSize
```
    Number of pixels used by a slice/volume, includes colorFactor.
  - sliceTouched
```
private boolean[] sliceTouched
```
    Slices that have been examined in recursive structure for swapping slices.
  - extentSrc
```
private int extentSrc
```
    Internal sorting variables for sorting slices on images of greater than 3 dimensions
  - extentDest
```
private int extentDest
```
    Internal sorting variables for sorting slices on images of greater than 3 dimensions
  - srcFileInfos
```
private FileInfoBase[] srcFileInfos
```
    Original FileInfoBase array.
  - srcExtents
```
private int[] srcExtents
```
    Original extents array
- Constructor Detail
  - AlgorithmSwapSlicesVolume
```
public AlgorithmSwapSlicesVolume(ModelImage destImage,
                                 JDialogSwapSlicesVolumes.SwapMode mode,
                                 int[][] sliceRenum,
                                 ModelImage srcImage)
```
    Import source and destination images into the class.
    
    Parameters:
    
    destImage - destination image
    
    srcImage - source image (image to extract from)
    
    sliceRenum - list of locations for slices that should be extracted/moved
    
    mode - type of swapping operation
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getSwappedVolume
```
public ModelImage getSwappedVolume()
```
    Return the images extracted from the source image.
    
    Returns:
    
    The extracted images.
  - runAlgorithm
```
public void runAlgorithm()
```
    Calculates the final output.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - getColorFactor
```
protected int getColorFactor()
```
    Calculates and returns the color factor based on the srcImage.
    
    Returns:
    
    DOCUMENT ME!
  - allSlicesTouched
```
private boolean allSlicesTouched()
```
  - collectFileInfos
```
private FileInfoBase[] collectFileInfos(int in,
                                        int tDim)
```
    Gets the fileInfos from the specified position.
  - importFileInfos
```
private void importFileInfos(ModelImage destImage,
                             FileInfoBase[] fileIn,
                             int in,
                             int tDim)
```
    Inserts the fileInfos into the specified position.
  - reallocate
```
private void reallocate(ModelImage image)
```
    Reallocate destImage so that fileInfo and buffer equal required length
    
    Parameters:
    
    image - ModelImage
  - swapSlices
```
private void swapSlices()
```
    Calculates the final output and stores it in the source image.
  - transferIn
```
private boolean transferIn(int in)
```
    Starts method of file/image transferring
    
    Parameters:
    
    in - location to import data
    
    Returns:
    
    whether import was successful
  - transferIn
```
private boolean transferIn(FileInfoBase[] fileIn,
                           java.lang.Number[] bufferIn,
                           int in,
                           int tDim)
```
    Transfers the given buffer into the given location. Also recursively transfers all the old data to the location(s) where the old data is used.
    
    Parameters:
    
    bufferIn - relieves the symptoms of arthritis
    
    in - location to import data
    
    Returns:
    
    whether import was successful

Class AlgorithmSwapSlicesVolume

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

mode

nSlices

sliceRenum

sliceSize

sliceTouched

extentSrc

extentDest

srcFileInfos

srcExtents

Constructor Detail

AlgorithmSwapSlicesVolume

Method Detail

finalize

getSwappedVolume

runAlgorithm

getColorFactor

allSlicesTouched

collectFileInfos

importFileInfos

reallocate

swapSlices

transferIn

transferIn