Package gov.nih.mipav.model.algorithms.utilities

Class AlgorithmAddMargins

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.utilities.AlgorithmAddMargins

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.EventListener

public class AlgorithmAddMargins
extends AlgorithmBase

Algorithm to add or remove margins around the image. Margins are defined in the screen-space coordinates. marginX is screen-space left,right. marginY is screen-space top,bottom. marginZ is screen-space front,back. Margins may be positive to add to the image, or negative to crop the image.

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[]	marginColor
private int[]	marginT	marginT indicating the number of slices to be padded in time at the start and end of T dimension
private int[]	marginX	marginX indicating the number of pixels to be padded on left and the right of X dimension
private int[]	marginY	marginY indicating the number of pixels to be padded on top and the bottom of Y dimension
private int[]	marginZ	marginZ indicating the number of slices to be padded in front and the back of Z dimension

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
AlgorithmAddMargins(ModelImage srcImage, int[] x, int[] y, int[] z)	Add or remove margins from the srcImage.
AlgorithmAddMargins(ModelImage srcImage, ModelImage destImage, int[] x, int[] y, int[] z)	Add or remove margins from the srcImage and store the results in the destImage.

Method Summary

Modifier and Type	Method	Description
private void	calcStoreInDest()	Adds image margins and stores result in destImage.
private void	calcStoreInPlace()	Adds image margins and stores result in srcImage Must use getSrcImage after running this routine.
private float[]	calculateNewOrigin(ModelImage srcImg, int[] margin)	Calculates the origin values for the modified image, based on the current origin values and the added margins.
void	finalize()	Prepares this class for destruction.
ModelImage	getSrcImage()	Returns the source image.
void	runAlgorithm()	Runs the add image margins algorithm.
void	setPadValue(float[] value)	Sets the value for the added margins, for either grayscale or color images.
void	setTMargins(int[] tMargin)	Adds or removes margins in the 4th dimensions.
private void	updateFileInfo(ModelImage kRead, ModelImage kWrite)	Updates the fileInfo values for the kWrite image, uses the fileInfo values from kRead.

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

marginX

private int[] marginX

marginX indicating the number of pixels to be padded on left and the right of X dimension

marginY

private int[] marginY

marginY indicating the number of pixels to be padded on top and the bottom of Y dimension

marginZ

private int[] marginZ

marginZ indicating the number of slices to be padded in front and the back of Z dimension

marginT

private int[] marginT

marginT indicating the number of slices to be padded in time at the start and end of T dimension

marginColor

private double[] marginColor

Constructor Detail

AlgorithmAddMargins

public AlgorithmAddMargins(ModelImage srcImage,
                           ModelImage destImage,
                           int[] x,
                           int[] y,
                           int[] z)

Add or remove margins from the srcImage and store the results in the destImage.

Parameters:

srcImage - original image

destImage - output modified image

x - margin in the screen-space x-direction to add or remove [left,right]

y - margin in the screen-space y-direction to add or remove [top,bottom]

z - margin in the screen-space z-direction to add or remove [front,back]

AlgorithmAddMargins

public AlgorithmAddMargins(ModelImage srcImage,
                           int[] x,
                           int[] y,
                           int[] z)

Add or remove margins from the srcImage.

Parameters:

srcImage - original image modified by this algorithm.

x - margin in the screen-space x-direction to add or remove [left,right]

y - margin in the screen-space y-direction to add or remove [top,bottom]

z - margin in the screen-space z-direction to add or remove [front,back]

Method Detail

finalize

public void finalize()

Prepares this class for destruction.

Overrides:

finalize in class AlgorithmBase

getSrcImage

public ModelImage getSrcImage()

Returns the source image.

Overrides:

getSrcImage in class AlgorithmBase

Returns:

source image, may be modified.

runAlgorithm

public void runAlgorithm()

Runs the add image margins algorithm.

Specified by:

runAlgorithm in class AlgorithmBase

setPadValue

public void setPadValue(float[] value)

Sets the value for the added margins, for either grayscale or color images.

Parameters:

value - the image values to fill in the added margins.

setTMargins

public void setTMargins(int[] tMargin)

Adds or removes margins in the 4th dimensions.

Parameters:

tMargin - margins in time to add or remove from the image.

calcStoreInDest

private void calcStoreInDest()

Adds image margins and stores result in destImage.

calcStoreInPlace

private void calcStoreInPlace()

Adds image margins and stores result in srcImage Must use getSrcImage after running this routine.

updateFileInfo

private void updateFileInfo(ModelImage kRead,
                            ModelImage kWrite)

Updates the fileInfo values for the kWrite image, uses the fileInfo values from kRead.

Parameters:

kRead - image to read fileInfo values from

kWrite - image to write fileInfo values to.

calculateNewOrigin

private float[] calculateNewOrigin(ModelImage srcImg,
                                   int[] margin)

Calculates the origin values for the modified image, based on the current origin values and the added margins.

Parameters:

srcImg - original image

margin - margins added or removed from the image

Returns:

new origins.