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

All Implemented Interfaces:

java.awt.event.ActionListener, java.awt.event.WindowListener, java.lang.Runnable, java.util.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
  java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

Fields
Modifier and Type	Field	Description
`protected org.jocl.cl_context`	`cl`
`protected int`	`color`
`protected int[]`	`colorMask`	Color flags.
`protected static java.util.Vector<org.jocl.cl_context>`	`contextLibrary`
`protected int`	`depth`
`protected org.jocl.cl_device_id`	`device`
`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`
`protected static java.util.Vector<java.lang.Long>`	`openCLTypeLibrary`
`private static 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`checkError(int errcode)`	Checks the OpenCL error status.
`void`	`finalize()`	Prepare this class for destruction.
`static int`	`getInt(org.jocl.cl_device_id device, int paramName)`	Returns the value of the device info parameter with the given name
`static int[]`	`getInts(org.jocl.cl_device_id device, int paramName, int numValues)`	Returns the values of the device info parameter with the given name
`static long`	`getLong(org.jocl.cl_device_id device, int paramName)`	Returns the value of the device info parameter with the given name
`static long[]`	`getLongs(org.jocl.cl_device_id device, int paramName, int numValues)`	Returns the values of the device info parameter with the given name
`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.
`static java.lang.String`	`getString(org.jocl.cl_device_id device, int paramName)`	Returns the value of the device info parameter with the given name
`static java.lang.String`	`getString(org.jocl.cl_platform_id platform, int paramName)`	Returns the value of the platform info parameter with the given name
`protected void`	`initCL(long iType, com.jogamp.opengl.GL3 gl)`
`private static void`	`initContextProperties(org.jocl.cl_context_properties contextProperties, com.jogamp.opengl.GL gl)`	Initializes the given context properties so that they may be used to create an OpenCL context for the given GL object.
`static boolean`	`isOCLAvailable()`
`static java.lang.String`	`readKernelFile(java.lang.String fileName)`	Helper function which reads the file with the given name and returns the contents of this file as a String.
`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, 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

contextLibrary

protected static java.util.Vector<org.jocl.cl_context> contextLibrary

openCLTypeLibrary

protected static java.util.Vector<java.lang.Long> openCLTypeLibrary

cl
```
protected org.jocl.cl_context cl
```

device
```
protected org.jocl.cl_device_id device
```

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 Detail

OpenCLAlgorithmBase
```
public OpenCLAlgorithmBase()
```

OpenCLAlgorithmBase

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

Method Detail
- initCL
```
protected void initCL(long iType,
                      com.jogamp.opengl.GL3 gl)
```
- initContextProperties
```
private static void initContextProperties(org.jocl.cl_context_properties contextProperties,
                                          com.jogamp.opengl.GL gl)
```
  Initializes the given context properties so that they may be used to create an OpenCL context for the given GL object.
  
  Parameters:
  
  contextProperties - The context properties
  
  gl - The GL object
- checkError
```
protected void checkError(int errcode)
```
  Checks the OpenCL error status.
  
  Parameters:
  
  errcode -
- 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)
```
- getInt
```
public static int getInt(org.jocl.cl_device_id device,
                         int paramName)
```
  Returns the value of the device info parameter with the given name
  
  Parameters:
  
  device - The device
  
  paramName - The parameter name
  
  Returns:
  
  The value
- getInts
```
public static int[] getInts(org.jocl.cl_device_id device,
                            int paramName,
                            int numValues)
```
  Returns the values of the device info parameter with the given name
  
  Parameters:
  
  device - The device
  
  paramName - The parameter name
  
  numValues - The number of values
  
  Returns:
  
  The value
- getLong
```
public static long getLong(org.jocl.cl_device_id device,
                           int paramName)
```
  Returns the value of the device info parameter with the given name
  
  Parameters:
  
  device - The device
  
  paramName - The parameter name
  
  Returns:
  
  The value
- getLongs
```
public static long[] getLongs(org.jocl.cl_device_id device,
                              int paramName,
                              int numValues)
```
  Returns the values of the device info parameter with the given name
  
  Parameters:
  
  device - The device
  
  paramName - The parameter name
  
  numValues - The number of values
  
  Returns:
  
  The value
- getString
```
public static java.lang.String getString(org.jocl.cl_device_id device,
                                         int paramName)
```
  Returns the value of the device info parameter with the given name
  
  Parameters:
  
  device - The device
  
  paramName - The parameter name
  
  Returns:
  
  The value
- getString
```
public static java.lang.String getString(org.jocl.cl_platform_id platform,
                                         int paramName)
```
  Returns the value of the platform info parameter with the given name
  
  Parameters:
  
  platform - The platform
  
  paramName - The parameter name
  
  Returns:
  
  The value
- 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 java.lang.String readKernelFile(java.lang.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:

Class OpenCLAlgorithmBase

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

contextLibrary

openCLTypeLibrary

cl

device

isOCLAvailable

isOCL_CPU_Available

isOCL_GPU_Available

wasOCLChecked

platformIndex

width

height

depth

time

color

colorMask

m_iDeviceType

m_kGL

entireImage

Constructor Detail

OpenCLAlgorithmBase

OpenCLAlgorithmBase

Method Detail

initCL

initContextProperties

checkError

finalize

saveImage

saveImage

isOCLAvailable

roundUp

getInt

getInts

getLong

getLongs

getString

getString

setBlue

setGreen

setRed

setTime

readKernelFile

getMaxMemoryUsed