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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmRemoveSlices
extends AlgorithmBase
```
Algorithm verifies the z-th slice should be in included in the destination image, as defined in the list, remove. It copies the slice from the srcImage img to a buffer, and then from the buffer into the destination img. Copies the srcImage file info to a buffer and makes it conform to the new img, then copies it into the destImage file.
Note that an image is a set of slices; each slice is XxY, with Z slices.**(as of 1 Nov, does not yet process the more complicated DICOM images Completely)

Version:

v0.11 1 Nov 1999 (processes most images)

Author:

David Parsons (parsonsd@cbel.cit.nih.gov) (with vast help from M.McAuliffe)

See Also:

JDialogRemoveSlices

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`	`oldZdim`	Original Z dimension of the image.
`private boolean[]`	`remove`	List of slices to remove from source 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
`AlgorithmRemoveSlices(ModelImage srcImage, ModelImage destImage, boolean[] removeSlices)`	Import source and destination images into the class.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calcInPlace()`	Calculates the final output and stores it in the source image.
`void`	`calcStoreInDest()`	Calculates the final output and puts it in a destination image.
`private int[]`	`computeNewExtents()`	Calculates and returns the new extents based on the source image and the list of slices to be removed.
`void`	`finalize()`	Prepares this class for destruction.
`protected int`	`getAxisOfChange()`	Calculates and returns the axis of change based on the srcImage.
`protected int`	`getColorFactor()`	Calculates and returns the color factor based on the srcImage.
`private int`	`getNumRemoved()`	computes and returns the number of slices to remove.
`private int`	`getOffset(int ndims, int[] extents, int colorFactor, int t)`	Calculate and return the offset for the given image and time slice.
`private int`	`getOffset(ModelImage img, int colorFactor, int t)`	Calculate and return the offset for the given image and time slice.
`private FileInfoBase`	`getSliceFileInfo(int srcSlice, int destSlice, int t, int[] newExtents)`	Build and return the fileInfo for the current slice based on the source slice, the destination slice and time slice.
`void`	`runAlgorithm()`	Calculates the final output.
`static void`	`updateFileInfo(ModelImage image, ModelImage resultImage)`	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
  - oldZdim
```
private int oldZdim
```
    Original Z dimension of the image.
  - remove
```
private boolean[] remove
```
    List of slices to remove from source 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.
- Constructor Detail
  - AlgorithmRemoveSlices
```
public AlgorithmRemoveSlices(ModelImage srcImage,
                             ModelImage destImage,
                             boolean[] removeSlices)
```
    Import source and destination images into the class.
    
    Parameters:
    
    srcImage - source image (image to clip from)
    
    destImage - destination image (image to paste to)
    
    removeSlices - list of boolean indicating which slices in source should *not* be in the destination
- Method Detail
  - updateFileInfo
```
public static void updateFileInfo(ModelImage image,
                                  ModelImage resultImage)
```
    Copy important file information to resultant image structure.
    
    Parameters:
    
    image - Source image.
    
    resultImage - Resultant image.
  - calcInPlace
```
public void calcInPlace()
```
    Calculates the final output and stores it in the source image.
  - calcStoreInDest
```
public void calcStoreInDest()
```
    Calculates the final output and puts it in a destination image.
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    Calculates the final output.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - getAxisOfChange
```
protected int getAxisOfChange()
                       throws java.lang.Exception
```
    Calculates and returns the axis of change based on the srcImage. The default (for most images) is 2. DICOM images need to be checked.
    
    Returns:
    
    DOCUMENT ME!
    
    Throws:
    
    java.lang.Exception - DOCUMENT ME!
  - getColorFactor
```
protected int getColorFactor()
```
    Calculates and returns the color factor based on the srcImage.
    
    Returns:
    
    DOCUMENT ME!
  - computeNewExtents
```
private int[] computeNewExtents()
```
    Calculates and returns the new extents based on the source image and the list of slices to be removed.
    
    Returns:
    
    DOCUMENT ME!
  - getNumRemoved
```
private int getNumRemoved()
```
    computes and returns the number of slices to remove.
    
    Returns:
    
    DOCUMENT ME!
  - 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
  - getOffset
```
private int getOffset(int ndims,
                      int[] extents,
                      int colorFactor,
                      int t)
```
    Calculate and return the offset for the given image and time slice.
    
    Parameters:
    
    ndims - -- number of dimensions
    
    extents - -- the extents for the image offset
    
    colorFactor - -- the image's colorFactor
    
    t - -- current time slice
    
    Returns:
    
    -- the computed offset into the data buffer
  - getSliceFileInfo
```
private FileInfoBase getSliceFileInfo(int srcSlice,
                                      int destSlice,
                                      int t,
                                      int[] newExtents)
```
    Build and return the fileInfo for the current slice based on the source slice, the destination slice and time slice.
    
    Parameters:
    
    srcSlice - the current slice index for the src image
    
    destSlice - the current slice index for the result (dest) image
    
    t - current time slice
    
    newExtents - the extents for the result (dest) image
    
    Returns:
    
    the fileInfo for destSlice

Class AlgorithmRemoveSlices

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

oldZdim

remove

sliceArea

Xdim

Ydim

Constructor Detail

AlgorithmRemoveSlices

Method Detail

updateFileInfo

calcInPlace

calcStoreInDest

finalize

runAlgorithm

getAxisOfChange

getColorFactor

computeNewExtents

getNumRemoved

getOffset

getOffset

getSliceFileInfo