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

All Implemented Interfaces:: java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmCorrectSpacing
extends AlgorithmBase

Algorithm to adjust image volume for cases when the slice spacing is not equal to the slice thickness. When spacing > thickness: repeat images from original image set insert blank images (so that in the final image volume, all images will have the same slice thickness and the image volume will be to proper scale. When spacing

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`	`colorFactor`
`private int`	`DIM`	The number of dimensions in the image.
`private int`	`newTimeStepVolume`	Volume for each time step.
`private int`	`newZdim`	New Z dimension.
`private int`	`numBlanks`	Number of blank images, to make up gap.
`private int`	`numRepIm`	Number of repeated images, to compensate for gap.
`private int`	`oldTimeStepVolume`	Volume for each time step.
`private int`	`oldZdim`	Original Z dimension of the image.
`private ModelImage`	`resultImage`	Result Image.
`private int`	`sliceArea`	Area of a slice (Xdim * Ydim).
`private int`	`Tdim`	Time dimension of the image.
`private int`	`Xdim`	X dimension of the image.
`private int`	`Ydim`	Y dimension of the 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
`AlgorithmCorrectSpacing(ModelImage srcImage, ModelImage resultImage, int numRepIm, int numBlanks)`	Import source image into the class.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`disposeLocal()`	Dispose of local variables that may be taking up lots of room.
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getResultImage()`	Returns corrected image.
`void`	`runAlgorithm()`	Runs 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
  - DIM
```
private int DIM
```
    The number of dimensions in the image.
  - newZdim
```
private int newZdim
```
    New Z dimension.
  - numBlanks
```
private int numBlanks
```
    Number of blank images, to make up gap.
  - numRepIm
```
private int numRepIm
```
    Number of repeated images, to compensate for gap.
  - oldTimeStepVolume
```
private int oldTimeStepVolume
```
    Volume for each time step.
  - newTimeStepVolume
```
private int newTimeStepVolume
```
    Volume for each time step.
  - oldZdim
```
private int oldZdim
```
    Original Z dimension of the image.
  - resultImage
```
private ModelImage resultImage
```
    Result Image.
  - sliceArea
```
private int sliceArea
```
    Area of a slice (Xdim * Ydim).
  - Tdim
```
private int Tdim
```
    Time dimension of the image.
  - Xdim
```
private int Xdim
```
    X dimension of the image.
  - Ydim
```
private int Ydim
```
    Y dimension of the image.
  - colorFactor
```
private int colorFactor
```
- Constructor Detail
  - AlgorithmCorrectSpacing
```
public AlgorithmCorrectSpacing(ModelImage srcImage,
                               ModelImage resultImage,
                               int numRepIm,
                               int numBlanks)
```
    Import source image into the class.
    
    Parameters:
    
    srcImage - source image (image to clip from)
    
    resultImage - corrected image
    
    numRepIm - number of times to repeat each of original images
    
    numBlanks - number of blank images to insert
- Method Detail
  - disposeLocal
```
public void disposeLocal()
```
    Dispose of local variables that may be taking up lots of room.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getResultImage
```
public ModelImage getResultImage()
```
    Returns corrected image.
    
    Returns:
    
    resultImage
  - runAlgorithm
```
public void runAlgorithm()
```
    Runs algorithm.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase

Class AlgorithmCorrectSpacing

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

DIM

newZdim

numBlanks

numRepIm

oldTimeStepVolume

newTimeStepVolume

oldZdim

resultImage

sliceArea

Tdim

Xdim

Ydim

colorFactor

Constructor Detail

AlgorithmCorrectSpacing

Method Detail

disposeLocal

finalize

getResultImage

runAlgorithm