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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmReplaceRemovedSlices
extends AlgorithmBase
```
This algorithm is used to insert averaged slices where slices have been removed -If slices were removed at the beginning of the original movie, these slices will not be replaced. - Slices are only inserted between the first and last kept slices

Author:

Ben Link

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`	`destFlag`	DOCUMENT ME!
`private float`	`imageMin`	DOCUMENT ME!
`private boolean`	`insertBlank`	If true, insert a blank rather than a weighted average.
`private boolean`	`isDicom`	DOCUMENT ME!
`private boolean`	`isSplit`	DOCUMENT ME!
`private boolean[]`	`removedSlices`	every false value in the array corresponds to a slice within the movie passed in. true values represent removed slices
`private ModelImage`	`resultImage`	DOCUMENT ME!

Fields inherited from class gov.nih.mipav.model.algorithms.AlgorithmBase
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
`AlgorithmReplaceRemovedSlices(ModelImage srcImage, boolean[] removedSlices, boolean isSplit, boolean destFlag, boolean insertBlank)`	Constructor for algorithm.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Local cleanup.
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getResultImage()`	Retrieves the result image.
`private void`	`insertAveragedSlices(float[] buffer1, float[] buffer2, int start, int end)`	Insert weighted averaged slices between the two indices.
`private void`	`insertBlankSlices(float[] buffer1, int start, int end)`	Insert blank slices between the two indices.
`void`	`runAlgorithm()`	Function called by thread to run the algorithm.

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
  - destFlag
```
private boolean destFlag
```
    DOCUMENT ME!
  - imageMin
```
private float imageMin
```
    DOCUMENT ME!
  - insertBlank
```
private boolean insertBlank
```
    If true, insert a blank rather than a weighted average.
  - isDicom
```
private boolean isDicom
```
    DOCUMENT ME!
  - isSplit
```
private boolean isSplit
```
    DOCUMENT ME!
  - removedSlices
```
private boolean[] removedSlices
```
    every false value in the array corresponds to a slice within the movie passed in. true values represent removed slices
  - resultImage
```
private ModelImage resultImage
```
    DOCUMENT ME!
- Constructor Detail
  - AlgorithmReplaceRemovedSlices
```
public AlgorithmReplaceRemovedSlices(ModelImage srcImage,
                                     boolean[] removedSlices,
                                     boolean isSplit,
                                     boolean destFlag,
                                     boolean insertBlank)
```
    Constructor for algorithm.
    
    Parameters:
    
    srcImage - the source image
    
    removedSlices - an array showing which slices were removed
    
    isSplit - DOCUMENT ME!
    
    destFlag - DOCUMENT ME!
    
    insertBlank - If true, insert a blank rather than a weighted average
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    Local cleanup.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultImage
```
public ModelImage getResultImage()
```
    Retrieves the result image.
    
    Returns:
    
    resultImage the new image
  - runAlgorithm
```
public void runAlgorithm()
```
    Function called by thread to run the algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - insertAveragedSlices
```
private void insertAveragedSlices(float[] buffer1,
                                  float[] buffer2,
                                  int start,
                                  int end)
```
    Insert weighted averaged slices between the two indices.
    
    Parameters:
    
    buffer1 - empty buffer to hold the first slice
    
    buffer2 - empty buffer to hold the last slice
    
    start - start index
    
    end - end index
  - insertBlankSlices
```
private void insertBlankSlices(float[] buffer1,
                               int start,
                               int end)
```
    Insert blank slices between the two indices.
    
    Parameters:
    
    buffer1 - empty buffer to hold the minimum value
    
    start - start index
    
    end - end index

Class AlgorithmReplaceRemovedSlices

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

destFlag

imageMin

insertBlank

isDicom

isSplit

removedSlices

resultImage

Constructor Detail

AlgorithmReplaceRemovedSlices

Method Detail

disposeLocal

finalize

getResultImage

runAlgorithm

insertAveragedSlices

insertBlankSlices