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

All Implemented Interfaces:

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

Description: Extracts individual slices from 3D or 4D images and opens each slice in its own Frame

Version:

1.0

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 boolean[]`	`extract`	List of slices to remove from source image.
`private java.util.Vector<ModelImage>`	`extractedImages`	DOCUMENT ME!
`(package private) FileInfoDicom[]`	`fileInfoDicom`
`private int`	`oldZdim`	Original Z dimension of the image.
`private int`	`sliceArea`	Area of a slice (Xdim * Ydim).
`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
`AlgorithmExtractSlicesVolumes(ModelImage srcImage, boolean[] removeSlices)`	Import source and destination images into the class.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`extractSlices()`	Calculates the final output and stores it in the source image.
`void`	`finalize()`	Prepares this class for destruction.
`protected int`	`getColorFactor()`	Calculates and returns the color factor based on the srcImage.
`ModelImage[]`	`getExtractedImages()`	Return the images extracted from the source image.
`private int`	`getOffset(ModelImage img, int colorFactor, int t)`	Calculate and return the offset for the given image and time slice.
`void`	`runAlgorithm()`	Calculates the final output.
`void`	`updateFileInfo(ModelImage image, ModelImage resultImage, int slice)`	Copy important file information to resultant image structure.

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
  - extract
```
private boolean[] extract
```
    List of slices to remove from source image.
  - extractedImages
```
private java.util.Vector<ModelImage> extractedImages
```
    DOCUMENT ME!
  - oldZdim
```
private int oldZdim
```
    Original Z dimension of the image.
  - sliceArea
```
private int sliceArea
```
    Area of a slice (Xdim * Ydim).
  - Xdim
```
private int Xdim
```
    X dimension of the image.
  - Ydim
```
private int Ydim
```
    Y dimension of the image.
  - fileInfoDicom
```
FileInfoDicom[] fileInfoDicom
```
- Constructor Detail
  - AlgorithmExtractSlicesVolumes
```
public AlgorithmExtractSlicesVolumes(ModelImage srcImage,
                                     boolean[] removeSlices)
```
    Import source and destination images into the class.
    
    Parameters:
    
    srcImage - source image (image to extract from)
    
    removeSlices - list of booleans for slices that should be extracted
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getExtractedImages
```
public ModelImage[] getExtractedImages()
```
    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
  - updateFileInfo
```
public void updateFileInfo(ModelImage image,
                           ModelImage resultImage,
                           int slice)
```
    Copy important file information to resultant image structure.
    
    Parameters:
    
    image - Source image.
    
    resultImage - Resultant image.
    
    slice - DOCUMENT ME!
  - getColorFactor
```
protected int getColorFactor()
```
    Calculates and returns the color factor based on the srcImage.
    
    Returns:
    
    DOCUMENT ME!
  - extractSlices
```
private void extractSlices()
```
    Calculates the final output and stores it in the source image.
  - getOffset
```
private int getOffset(ModelImage img,
                      int colorFactor,
                      int t)
```
    Calculate and return the offset for the given image and time slice.
    
    Parameters:
    
    img - -- ModelImage whose offset is being computed
    
    colorFactor - -- the image's colorFactor
    
    t - -- current time slice
    
    Returns:
    
    -- the computed offset into the data buffer

Class AlgorithmExtractSlicesVolumes

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

extract

extractedImages

oldZdim

sliceArea

Xdim

Ydim

fileInfoDicom

Constructor Detail

AlgorithmExtractSlicesVolumes

Method Detail

finalize

getExtractedImages

runAlgorithm

updateFileInfo

getColorFactor

extractSlices

getOffset