Package gov.nih.mipav.model.algorithms

Class OpenCLAlgorithmBase

java.lang.Object

java.lang.Thread

gov.nih.mipav.model.algorithms.AlgorithmBase

gov.nih.mipav.model.algorithms.OpenCLAlgorithmBase

All Implemented Interfaces:

ActionListener, WindowListener, Runnable, EventListener

Direct Known Subclasses:

OpenCLAlgorithmDeconvolution, OpenCLAlgorithmFFT, OpenCLAlgorithmGaussianBlur, OpenCLAlgorithmGradientMagnitude, OpenCLAlgorithmLaplacian, OpenCLAlgorithmMarchingCubes, OpenCLAlgorithmVolumeCrop, OpenCLAlgorithmVolumeNormals

public abstract class OpenCLAlgorithmBase
extends AlgorithmBase

Abstract base class for implementing Algorithms in OpenCL. Extends AlgorithmBase.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
protected int	color
protected int[]	colorMask	Color flags.
protected int	depth
protected boolean	entireImage	Flag, if true, indicates that the whole image should be processed.
protected int	height
private static boolean	isOCL_CPU_Available
private static boolean	isOCL_GPU_Available
private static boolean	isOCLAvailable
protected long	m_iDeviceType
protected com.jogamp.opengl.GL3	m_kGL
private static final int	platformIndex
protected int	time
private static boolean	wasOCLChecked
protected int	width

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
OpenCLAlgorithmBase()
OpenCLAlgorithmBase(ModelImage destImg, ModelImage srcImg, boolean entireImage, long type)

Method Summary

Modifier and Type	Method	Description
static void	fillBuffer(FloatBuffer buffer, float[] img)
static void	fillBuffer(FloatBuffer buffer, ModelImage img)
static void	fillBuffer(FloatBuffer buffer, ModelImage img, int offset)
static void	fillBuffer(IntBuffer buffer, int[] img)
void	finalize()	Prepare this class for destruction.
protected long	getMaxMemoryUsed(int nBuffers, int elementCount, float[] sigmas)	Determines the amount of memory used for the OpenCL buffers required for the gaussian kernels for the given sigmas.
protected void	initCL(long iType, com.jogamp.opengl.GL3 gl)
static boolean	isOCLAvailable()
static void	readBuffer(FloatBuffer buffer, ModelImage img)
static void	readBuffer(FloatBuffer buffer, ModelImage img, int offset)
static String	readKernelFile(String fileName)	Helper function which reads the file with the given name and returns the contents of this file as a String.
static int	roundUp(int groupSize, int globalSize)
protected static long	roundUp(long groupSize, long globalSize)
void	saveImage(float[] data, int time, boolean calcMinMax)
void	saveImage(float[] data, int time, int zSlice, boolean calcMinMax)
void	setBlue(boolean flag)	Sets the flag for the blue channel.
void	setGreen(boolean flag)	Sets the flag for the green channel.
void	setRed(boolean flag)	Sets the flag for the red channel.
void	setTime(int timeSlice)

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, runAlgorithm, 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, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

isOCLAvailable

private static boolean isOCLAvailable

isOCL_CPU_Available

private static boolean isOCL_CPU_Available

isOCL_GPU_Available

private static boolean isOCL_GPU_Available

wasOCLChecked

private static boolean wasOCLChecked

platformIndex

private static final int platformIndex

See Also:

• Constant Field Values

width

protected int width

height

protected int height

depth

protected int depth

time

protected int time

color

protected int color

colorMask

protected int[] colorMask

Color flags.

m_iDeviceType

protected long m_iDeviceType

m_kGL

protected com.jogamp.opengl.GL3 m_kGL

entireImage

protected boolean entireImage

Flag, if true, indicates that the whole image should be processed. If false only process the image over the mask areas.

Constructor Details

OpenCLAlgorithmBase

public OpenCLAlgorithmBase()

OpenCLAlgorithmBase

public OpenCLAlgorithmBase(ModelImage destImg,
 ModelImage srcImg,
 boolean entireImage,
 long type)

Method Details

initCL

protected void initCL(long iType,
 com.jogamp.opengl.GL3 gl)

finalize

public void finalize()

Prepare this class for destruction.

Overrides:

finalize in class AlgorithmBase

saveImage

public void saveImage(float[] data,
 int time,
 int zSlice,
 boolean calcMinMax)

saveImage

public void saveImage(float[] data,
 int time,
 boolean calcMinMax)

isOCLAvailable

public static boolean isOCLAvailable()

roundUp

protected static long roundUp(long groupSize,
 long globalSize)

setBlue

public void setBlue(boolean flag)

Sets the flag for the blue channel.

Parameters:

flag - if set to true then the blue channel is processed.

setGreen

public void setGreen(boolean flag)

Sets the flag for the green channel.

Parameters:

flag - if set to true then the green channel is processed.

setRed

public void setRed(boolean flag)

Sets the flag for the red channel.

Parameters:

flag - if set to true then the red channel is processed.

setTime

public void setTime(int timeSlice)

readKernelFile

public static String readKernelFile(String fileName)

Helper function which reads the file with the given name and returns the contents of this file as a String. Will exit the application if the file can not be read.

Parameters:

fileName - The name of the file to read.

Returns:

The contents of the file

getMaxMemoryUsed

protected long getMaxMemoryUsed(int nBuffers,
 int elementCount,
 float[] sigmas)

Determines the amount of memory used for the OpenCL buffers required for the gaussian kernels for the given sigmas. Plus the memory used for the nBuffers OpenCL buffers, each elementCount in size.

Parameters:

nBuffers - number of buffers

elementCount - buffer size

sigmas -

Returns:

fillBuffer

public static void fillBuffer(FloatBuffer buffer,
 ModelImage img)

fillBuffer

public static void fillBuffer(IntBuffer buffer,
 int[] img)

fillBuffer

public static void fillBuffer(FloatBuffer buffer,
 ModelImage img,
 int offset)

fillBuffer

public static void fillBuffer(FloatBuffer buffer,
 float[] img)

readBuffer

public static void readBuffer(FloatBuffer buffer,
 ModelImage img)

readBuffer

public static void readBuffer(FloatBuffer buffer,
 ModelImage img,
 int offset)

roundUp

public static int roundUp(int groupSize,
 int globalSize)