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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener
```
public class AlgorithmCrop
extends AlgorithmBase
```
Crops 2D and 3D images using a supplied VOI. Crops 4D images.

Version:

1.0 June 11, 1999

Author:

Matthew J. McAuliffe, Ph.D.

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`	`cushion`	Extra space around VOI in x and y dimensions.
`private boolean`	`RGBImage`	Flag for color or noncolor image.
`private int[]`	`x`	Storage for VOI.
`private int[]`	`y`	Storage for VOI.
`private int[]`	`z`	Storage for VOI.

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
`AlgorithmCrop(ModelImage destImg, ModelImage srcImg, int _cushion, int[] _x, int[] _y, int[] _z)`	Creates new algorithms to crop image by specified bounds.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private void`	`calcStoreInDest2D()`	This function produces a new image that has been cropped!
`private void`	`calcStoreInDest3D()`	This function produces a new image that has been cropped.
`private void`	`calcStoreInDest4D()`	This function produces a new image that has been cropped.
`private void`	`calcStoreInPlace2D()`	This function crops srcImage Must use getSrcImage after running.
`private void`	`calcStoreInPlace3D()`	This function crops srcImage Must use getSrcImage after running.
`private void`	`calcStoreInPlace4D()`	This function crops srcImage Must use getSrcImage after running.
`void`	`finalize()`	Prepares this class for destruction.
`ModelImage`	`getSrcImage()`	DOCUMENT ME!
`private float[]`	`originImg2LPS(float[] origImg, ModelImage img)`	Switch origin order from image order to LPS order.
`private float[]`	`originLPS2Img(float[] origLPS, ModelImage img)`	Switch origin order from LPS order to Img order.
`void`	`runAlgorithm()`	Starts the program.
`private void`	`updateDICOM()`	Update special case DICOM format tags.
`private void`	`updateFileInfoData()`	Updates important image attributes (start locations, orientation ) for the new cropped file by modifing the fileinfo fo the new ( destination ) image.

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, 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
  - cushion
```
private int cushion
```
    Extra space around VOI in x and y dimensions.
  - RGBImage
```
private boolean RGBImage
```
    Flag for color or noncolor image.
  - x
```
private int[] x
```
    Storage for VOI.
  - y
```
private int[] y
```
    Storage for VOI.
  - z
```
private int[] z
```
    Storage for VOI.
- Constructor Detail
  - AlgorithmCrop
```
public AlgorithmCrop(ModelImage destImg,
                     ModelImage srcImg,
                     int _cushion,
                     int[] _x,
                     int[] _y,
                     int[] _z)
```
    Creates new algorithms to crop image by specified bounds. Stores in destImg.
    
    Parameters:
    
    destImg - image model where result image is to stored, use null to do in-place calculation
    
    srcImg - source image model
    
    _cushion - extra space around VOI in x and y dimensions.
    
    _x - VOI xBounds: x[0] = min. bound and x[1] = max. bound
    
    _y - VOI yBounds: y[0] = min. bound and y[1] = max. bound
    
    _z - VOI zBounds: z[0] = min. bound and z[1] = max. bound
- Method Detail
  - finalize
```
public void finalize()
```
    Prepares this class for destruction.
    
    Overrides:
    
    finalize in class AlgorithmBase
  - getSrcImage
```
public ModelImage getSrcImage()
```
    DOCUMENT ME!
    
    Overrides:
    
    getSrcImage in class AlgorithmBase
    
    Returns:
    
    ModelImage
  - runAlgorithm
```
public void runAlgorithm()
```
    Starts the program.
    
    Specified by:
    
    runAlgorithm in class AlgorithmBase
  - calcStoreInDest2D
```
private void calcStoreInDest2D()
```
    This function produces a new image that has been cropped!
  - calcStoreInDest3D
```
private void calcStoreInDest3D()
```
    This function produces a new image that has been cropped.
  - calcStoreInDest4D
```
private void calcStoreInDest4D()
```
    This function produces a new image that has been cropped.
  - calcStoreInPlace2D
```
private void calcStoreInPlace2D()
```
    This function crops srcImage Must use getSrcImage after running.
  - calcStoreInPlace3D
```
private void calcStoreInPlace3D()
```
    This function crops srcImage Must use getSrcImage after running.
  - calcStoreInPlace4D
```
private void calcStoreInPlace4D()
```
    This function crops srcImage Must use getSrcImage after running.
  - originImg2LPS
```
private float[] originImg2LPS(float[] origImg,
                              ModelImage img)
```
    Switch origin order from image order to LPS order.
    
    Parameters:
    
    origImg - DOCUMENT ME!
    
    img - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - originLPS2Img
```
private float[] originLPS2Img(float[] origLPS,
                              ModelImage img)
```
    Switch origin order from LPS order to Img order.
    
    Parameters:
    
    origLPS - DOCUMENT ME!
    
    img - DOCUMENT ME!
    
    Returns:
    
    DOCUMENT ME!
  - updateDICOM
```
private void updateDICOM()
```
    Update special case DICOM format tags.
  - updateFileInfoData
```
private void updateFileInfoData()
```
    Updates important image attributes (start locations, orientation ) for the new cropped file by modifing the fileinfo fo the new ( destination ) image.

Class AlgorithmCrop

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

cushion

RGBImage

x

y

z

Constructor Detail

AlgorithmCrop

Method Detail

finalize

getSrcImage

runAlgorithm

calcStoreInDest2D

calcStoreInDest3D

calcStoreInDest4D

calcStoreInPlace2D

calcStoreInPlace3D

calcStoreInPlace4D

originImg2LPS

originLPS2Img

updateDICOM

updateFileInfoData