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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmSubtractVOI
extends AlgorithmBase
```
Algorithm that subtracts the mean or median value of a VOI from the image. If only 1 contour is present, that contour is used whether or not it is selected. If multiple contours are present, at least 1 contour must be selected, and only selected contours are used. Note that under MIPAV all selected contours must belong to the same VOI. If the new image exceeds the range that can be stored in an image of that type the data is either clipped and stored in the original image. Or a new image of a type (int, float...) that can store the range of new data is generated. For color the dialog currently disables promotion for color because MIPAV cannot handle negative color values.

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 double`	`average`	DOCUMENT ME!
`private float`	`averageB`	DOCUMENT ME!
`private float`	`averageG`	DOCUMENT ME!
`private int`	`averageMode`	DOCUMENT ME!
`private float`	`averageR`	DOCUMENT ME!
`static int`	`CLIP`	DOCUMENT ME!
`private double`	`clipMax`	Maximum clipping modes if data result value exceeds the capacity of image's data type.
`private float`	`clipMaxC`	DOCUMENT ME!
`private double`	`clipMin`	Minimum clipping modes if data result value exceeds the capacity of image's data type.
`private float`	`clipMinC`	DOCUMENT ME!
`private int`	`clipMode`	Clipping mode.
`private double`	`max`	Used to store the image maximum.
`static int`	`MEAN`	DOCUMENT ME!
`static int`	`MEDIAN`	DOCUMENT ME!
`private double`	`min`	Used to store the image minimum.
`private double`	`minB`	DOCUMENT ME!
`private double`	`minG`	DOCUMENT ME!
`private double`	`minR`	DOCUMENT ME!
`static int`	`PROMOTE`	DOCUMENT ME!

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
`AlgorithmSubtractVOI(ModelImage srcImg, int _averageMode, int _clipMode)`	Creates a new AlgorithmSubtractVOI object.
`AlgorithmSubtractVOI(ModelImage destImg, ModelImage srcImg, int _averageMode, int _clipMode)`	Creates a new AlgorithmSubtractVOI object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcInPlace()`	Generates the new data and places in the source image.
`private void`	`calcInPlaceColor()`	Generates the new data and places in the source image.
`private void`	`calcStoreInDest()`	Generates the new data and places in a new (destination) image.
`private void`	`calcStoreInDestColor()`	Generates the new data and places in a new (destination) image.
`void`	`finalize()`	Prepares this class for destruction.
`private int`	`findType(int stType)`	Find the type able to contain the full range of the data.
`private void`	`getAverage()`	DOCUMENT ME!
`private int`	`promoteType(int presentType)`	DOCUMENT ME!
`void`	`runAlgorithm()`	Starts the program.
`private void`	`setClipValues()`	Sets clipMin and clipMax.
`private boolean`	`testType(int type, double minVal, double maxVal)`	Determine if the min and max values are in the image types range.

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
  - MEAN
```
public static final int MEAN
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - MEDIAN
```
public static final int MEDIAN
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - CLIP
```
public static final int CLIP
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - PROMOTE
```
public static final int PROMOTE
```
    DOCUMENT ME!
    
    See Also:
    
    Constant Field Values
  - average
```
private double average
```
    DOCUMENT ME!
  - averageB
```
private float averageB
```
    DOCUMENT ME!
  - averageG
```
private float averageG
```
    DOCUMENT ME!
  - averageMode
```
private int averageMode
```
    DOCUMENT ME!
  - averageR
```
private float averageR
```
    DOCUMENT ME!
  - clipMax
```
private double clipMax
```
    Maximum clipping modes if data result value exceeds the capacity of image's data type.
  - clipMaxC
```
private float clipMaxC
```
    DOCUMENT ME!
  - clipMin
```
private double clipMin
```
    Minimum clipping modes if data result value exceeds the capacity of image's data type.
  - clipMinC
```
private float clipMinC
```
    DOCUMENT ME!
  - clipMode
```
private int clipMode
```
    Clipping mode.
    CLIP = 0; clamp result data to the bounds of the input image type PROMOTE = 1; promote image type so that the range of the result fits into the new image type. ( ie. byte to short).
  - max
```
private double max
```
    Used to store the image maximum.
  - min
```
private double min
```
    Used to store the image minimum.
  - minR
```
private double minR
```
    DOCUMENT ME!
  - minG
```
private double minG
```
    DOCUMENT ME!
  - minB
```
private double minB
```
    DOCUMENT ME!
- Constructor Detail
  - AlgorithmSubtractVOI
```
public AlgorithmSubtractVOI(ModelImage srcImg,
                            int _averageMode,
                            int _clipMode)
```
    Creates a new AlgorithmSubtractVOI object.
    
    Parameters:
    
    srcImg - source image model
    
    _averageMode - mean or median of VOI
    
    _clipMode - clamp data to image type range or promote image type to hold new data range.
  - AlgorithmSubtractVOI
```
public AlgorithmSubtractVOI(ModelImage destImg,
                            ModelImage srcImg,
                            int _averageMode,
                            int _clipMode)
```
    Creates a new AlgorithmSubtractVOI object.
    
    Parameters:
    
    destImg - image model where result image is to stored
    
    srcImg - source image model
    
    _averageMode - mean or median of VOI
    
    _clipMode - clamp data to image type range or promote image type to hold new data range.
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calcInPlace
```
private void calcInPlace()
```
    Generates the new data and places in the source image.
    note that if this method is canceled part-way through a multi-sliced image, it will almost certainly be partially adjusted. This is because to save memory buffer-space, it returns an adjusted slice back to the source image after processing it; it then takes out the next slice to alter it. Canceling a job causes the current slice will not be affected, but all previous slices will be.
  - calcInPlaceColor
```
private void calcInPlaceColor()
```
    Generates the new data and places in the source image.
    note that if this method is canceled part-way through a multi-sliced image, it will almost certainly be partially adjusted. This is because to save memory buffer-space, it returns an adjusted slice back to the source image after processing it; it then takes out the next slice to alter it. Canceling a job causes the current slice will not be affected, but all previous slices will be.
  - calcStoreInDest
```
private void calcStoreInDest()
```
    Generates the new data and places in a new (destination) image.
    This method checks for thread halting actions more infrequently than the in-place method.
  - calcStoreInDestColor
```
private void calcStoreInDestColor()
```
    Generates the new data and places in a new (destination) image.
    This method checks for thread halting actions more infrequently than the in-place method.
  - findType
```
private int findType(int stType)
```
    Find the type able to contain the full range of the data.
    
    Parameters:
    
    stType - starting type of image. Image will be promoted above this type if needed.
    
    Returns:
    
    type capable of storing full range of data. See ModelStorageBase for image types.
  - getAverage
```
private void getAverage()
```
    DOCUMENT ME!
  - promoteType
```
private int promoteType(int presentType)
```
    DOCUMENT ME!
    
    Parameters:
    
    presentType - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - setClipValues
```
private void setClipValues()
```
    Sets clipMin and clipMax.
  - testType
```
private boolean testType(int type,
                         double minVal,
                         double maxVal)
```
    Determine if the min and max values are in the image types range.
    
    Parameters:
    
    type - image type
    
    minVal - min value of the image
    
    maxVal - max value of the image
    
    Returns:
    
    true if min and max are within the image type specified

Class AlgorithmSubtractVOI

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

MEAN

MEDIAN

CLIP

PROMOTE

average

averageB

averageG

averageMode

averageR

clipMax

clipMaxC

clipMin

clipMinC

clipMode

max

min

minR

minG

minB

Constructor Detail

AlgorithmSubtractVOI

AlgorithmSubtractVOI

Method Detail

finalize

runAlgorithm

calcInPlace

calcInPlaceColor

calcStoreInDest

calcStoreInDestColor

findType

getAverage

promoteType

setClipValues

testType